Lipidomics studies on NIDDK / NIST human plasma samples
STUDY_TYPE
MS analysis on human plasma
STUDY_SUMMARY
The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) in with the National Institute of Standards (NIST) recently produced a human standard reference material (SRM 1950) for metabolite analysis. The SRM was by obtaining plasma samples from 100 individuals between 40 and 50 years of whose ethnicity was representative of the US population and that included an number of men and women. The intent of the NIDDK/NIST project was to provide a material that would be publically available to researchers and that could be by the clinical chemistry community to identify plasma metabolites for purposes. Signature metabolites could then be further probed for their as disease biomarkers. The LIPID MAPS Consortium has undertaken the task to this SRM by systematically identifying and quantifying the lipid molecular in the six main categories of mammalian lipids. The quantitative levels of over different lipids present in this reference human plasma sample are presented
Timecourse on RAW 264.7 cells treated with Kdo2-Lipid A and compactin
STUDY_TYPE
Timecourse experiment
STUDY_SUMMARY
Lipidomics studies on macrophages - RAW 264.7 cells treated with Kdo2-Lipid A compactin. Experiments were conducted with RAW264.7 cells fed 10% fetal calf 8-timepoint study: Measurements were taken at 0, 0.5,1,2,4,8, 12, and 24hrs (i) compactin, (ii) Kdo2-Lipid A, (iii) compactin + Kdo2-Lipid A. and (iv)
In this study, seventeen white wines including Chardonnays, Viogniers, Pinot gris, Rieslings and Sauvignon blancs (which were part of a M.S. study in the Viticulture & Enology Department on white wine mouthfeel properties), were analyzed by GC-TOF. Additionally, chemical data obtained will be mined with the sensory data collected to further investigate the chemical basis for mouthfeel properties in wine.
INSTITUTE
University of California, Davis
DEPARTMENT
Davis Genome Center
LABORATORY
Fiehn
LAST_NAME
Kind
FIRST_NAME
Tobias
ADDRESS
451 E. Health Sci. Drive, Davis, California 95616, USA
Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), rise to devastating crop losses in rice. Disease resistant rice cultivars are most economical way to combat the disease. The TP309 cultivar is susceptible to by Xoo strain PXO99. A transgenic variety, TP309_Xa21, expresses the pattern receptor Xa21, and is resistant. PXO99?raxST, a strain lacking the raxST gene, able to overcome Xa21-mediated immunity. We used a single extraction solvent to comprehensive metabolomics and transcriptomics profiling under sample limited and analyze the molecular responses of two rice lines challenged with either or PXO99?raxST. LCTOF raw data file filtering resulted in better within group of replicate samples for statistical analyses. Accurate mass match compound with molecular formula generation (MFG) ranking of 355 masses was achieved with METLIN database. GCTOF analysis yielded an additional 441 compounds after database processing, of which 154 were structurally identified by retention library matching. Multivariate statistics revealed that the susceptible and genotypes possess distinct profiles. Although few mRNA and metabolite were detected in PXO99 challenged TP309 compared to mock, many differential occurred in the Xa21-mediated response to PXO99 and PXO99?raxST. Acetophenone, fatty acids, alkaloids, glutathione, carbohydrate and lipid biosynthetic were affected. Significant transcriptional induction of several pathogenesis genes in Xa21 challenged strains, as well as differential changes to GAD, PAL, and Glutathione-S-transferase transcripts indicated limited correlation with changes under single time point global profiling conditions.
INSTITUTE
University of California, Davis
DEPARTMENT
Davis Genome Center
LABORATORY
Fiehn
LAST_NAME
Kind
FIRST_NAME
Tobias
ADDRESS
451 E. Health Sci. Drive, Davis, California 95616, USA
This experiment tests the effect of individual mutations on the metabolome of The standardized growth conditions are as follows: 1. Seeds (between 14 and 16) sown on media in 100 x 100 x 15mm square Falcon Petri Dishes (Fisher catalogue #08-757-11A). Seeds were arranged on the plates in a single line at the 1-cm mark from the top of the plate. 2. Each plate contains between and 25-ml of sterile MS media containing 0.1% (w/v) sucrose. 3. Prior to seeds were sterilized by treating for 1-minute at room temperature with a 300-l of 50% (v/v) ethanol, this solution was removed and replaced with a 300-l consisting of 1% (v/v) Tween 20 (Fischer BioReagents, catalogue #BP33750), and (v/v) bleach solution (Clorox), and incubated at room temperature for The seeds were then washed with three changes of 0.3-ml of sterile water. 4. sowing with seeds, the plates were wrapped with Micropore tape (3M Health Care, #1530-0), and then stored horizontally for 4-days at 4 °C, with of 1 mol/m2. 5. On the 5th day, plates were moved to the growth room, and held a vertical position in Plexi-glass holders for 17-days this growth room is labeled in Table I. 6. On 18th day Petri plates were opened and the aerial of these plants were harvested immediately upon plate opening. 7. Upon plant material was quenched by immersion in liquid nitrogen and stored at 70
INSTITUTE
University of California, Davis
DEPARTMENT
Davis Genome Center
LABORATORY
Fiehn
LAST_NAME
Kind
FIRST_NAME
Tobias
ADDRESS
451 E. Health Sci. Drive, Davis, California 95616, USA
To determine the basis of running capacity and health differences in outbread N/NIH rats selected for high capacity (HCR) and low capacity (LCR) running (a for VO2max) (see:Science. 2005 Jan 21;307(5708):418-20). Plasma collected at 12 of age in generation 28 rats after ad lib feeding or 40% caloric restriction at week 8 of age. All animals fasted 4 hours prior to collection between 5-8
Metabolomics Analysis of Thermally Challenged Mayfly Larvae (GCMS analysis)
STUDY_TYPE
Metabolomic analysis of mayflies
STUDY_SUMMARY
The purpose of this study was to examine the metabolic profiles of mayfly triangulifer) larvae subjected to thermal challenge. This species is unusual in of its ease of culture, and its suitability as a laboratory test organism. Our here was to examine how an environmentally realistic thermal challenge affects physiology of this organism. In this study, we obtained several types of insect and we were able to show that GC-MS Metabolomics could be used to distinguish the different types of larvae.
Human subjects were given high PUFA diet for 21 days then converted to high diet for another 21 days. Plasma samples were drawn during the feeding process 7 visits.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Plasma metabolomics: Comparison of non-diabetic controls with T1D patients
STUDY_TYPE
Drug effect study
STUDY_SUMMARY
Non-diabetic controls whose metabolites were compared to T1D patients with and insulin. Seven C-peptide?negative T1D subjects were studied on two occasions: during insulin treatment and the other following withdrawal of insulin for 8 h compared with matched healthy ND participants
Identification of altered metabolic pathways in Alzheimer's disease, mild impairment and cognitively normals using Metabolomics (plasma)
STUDY_TYPE
1
STUDY_SUMMARY
Criteria for the diagnosis of amnestic MCI included: (i) memory complaint by the patient and collateral source; (ii) impairment in 1 or more of the 4 domains (memory, executive functioning/attention, visuospatial, or language); essentially normal functional activities of daily living; and (iv) absence of In general, the amnestic MCI determination is made when the memory measures 1.0â??1.5 SD below the means for age and education appropriate individuals our community; however, rigid cutoffs on psychometric scores were not used to the diagnosis of amnestic MCI which was made on clinical grounds. The diagnosis dementia was made using DSM-IV criteria, and the diagnosis of AD was made using criteria. Subjects were considered to be CN if they performed within the range and did not meet criteria for MCI or dementia.
Identification of altered metabolic pathways in Alzheimer's disease, mild impairment and cognitively normals using Metabolomics (CSF)
STUDY_TYPE
MS
STUDY_SUMMARY
Criteria for the diagnosis of amnestic MCI included: (i) memory complaint by the patient and collateral source; (ii) impairment in 1 or more of the 4 domains (memory, executive functioning/attention, visuospatial, or language); essentially normal functional activities of daily living; and (iv) absence of In general, the amnestic MCI determination is made when the memory measures 1.0?1.5 SD below the means for age and education appropriate individuals in community; however, rigid cutoffs on psychometric scores were not used to the diagnosis of amnestic MCI which was made on clinical grounds. The diagnosis dementia was made using DSM-IV criteria, and the diagnosis of AD was made using criteria. Subjects were considered to be CN if they performed within the range and did not meet criteria for MCI or dementia.
Metabolomic & lipidomic profiles in response to exogenous insulin & GLP-1 during prolonged fasting (GCMS)
STUDY_TYPE
Timecourse
STUDY_SUMMARY
This application requests funding to access state-of-the-art metabolomics and platforms at the NIH West Coast Metabolomics Center to analyze plasma samples recent insulin and glucagon-like peptide-1 (GLP-1) infusion experiments in prolong-fasted elephant seals. This suite of studies was designed to better the mechanisms contributing to the onset of an insulin resistantlike condition by prolonged food deprivation/starvation in mammals. Because elephant seals evolved robust physiological mechanisms that have allowed them to naturally such protracted bouts of fasting, they provide an ideal model to address our hypothesis that increased lipid utilization late in the fast contributes to resistance in elephant seals. Insulin resistance is a common consequence of in mammals and, while the mechanisms by which it manifests are still unclear, a shift favoring increased mobilization and utilization of lipids during food deprivation may be a principal causative factor. Insulin resistance has a connotation due to its association with obesity and diabetes among humans, but has been suggested to be an adaptive response to food deprivation.
INSTITUTE
University of California, Davis
DEPARTMENT
GBSF
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
451 Health Sci Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
1-530-752-8258
NUM_GROUPS
5
TOTAL_SUBJECTS
117
STUDY_COMMENTS
5 general classes are designed in the experiment:#1 - A=No GLP1/ Late GTT#2 - (Low Dose)#3 - C=GLP1 (High Dose)#4 - IL- Early Fasting Insulin Infusion#5 - Late Fasting Insulin InfusionEach of the 5 classes has 6 timepoints (5x6):T1 - minT2 - 10 minT3 - 30 minT4 - 60 minT5 - 120 minEach timepoint had 5 animals (5 x 5 classes x 6 timepoints = 150 totalBecause certain animals and timepoints to be excluded 108 measurments remain.The experiment also contains 9 technical of pooled samples (pool)The total sample number is 108 (biological) + 9 pooled = 117
Effect of kinase inhibitors on FLT3-ITD AML cell metabolomes
STUDY_TYPE
Metabolomics analysis on the effect of kinase inhibitors on FLT3-ITD AML cell to identify changes in cell signaling networks
STUDY_SUMMARY
FLT3-ITD AML cells (MR2) obtained from mice were treated with two MEK kinase (GSK and AZD) at 10 uM versus media only control. Conditioned media aliquots cellular fractions comprised of two aliquots (tecnical replicates) for LC-MS and one for Western blot analyses were collected at 0, 4, 24, and 48 hours. The was repeated three times. HPLC-MS data were acquired for 24 samples from one experiment.
Combined Metabolomics and Lipidomics of Type 1 Diabetes (GCMS)
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project granted to Bell (University of Chicago) and collaborator Manami Hara uses a multi-omics to investigate the metabolome (primary metabolites), lipidome (complex lipids) signaling lipids (oxylipins) in the plasma of Non-obese Diabetic (NOD) mice progressed to Type 1 Diabetes Mellitus (T1D) and those that did not. NOD Mice were assessed as diabetic or non-diabetic based on their fasting (4hr) blood levels at sacrifice, which defined 30 hyperglycemic (glucose = 250 mg/dL) and normoglycemic animals. The primary objective of this study was to identify biomarkers associated with beta-cell destruction/survival and T1D progression.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolite changes associated with methionine stress sensitivity of cancer (GC MS analysis)
STUDY_TYPE
timecourse study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project granted to Kaiser (UC Irvine), aims to achieve understanding of a unique metabolic of cancer cells to explore development of novel unconventional therapeutic that exploit dependence of cancer cells on methyl-donor abundance. The past few have highlighted the role of altered metabolism in cancer. While mechanistic into changed metabolism in cancer is very limited, the importance of the pathway surrounding homocysteine and methionine for cancer cell proliferation been known for over 30 years.These findings, generally summarized as or methionine stress sensitivity, describe the phenomenon that most cancer cannot proliferate in growth medium where the amino acid methionine is replaced its direct metabolic precursor homocysteine. Importantly, non-tumorigenic cells unaffected by replacing methionine with homocysteine in the growth medium. For past years we have been studying methionine dependence of breast and prostate and demonstrated that methionine-dependence is caused by insufficient flux this pathway to sustain synthesis of the downstream metabolite and the methyl-donor S-adenosylmethionine (SAM).We have isolated rare cell clones from breast cancer cells (referred to as MB468RES) that are no longer methionine and proliferate in homocysteine medium. Interestingly, MB468RES have lost their for anchorage independent growth, a hallmark of cancer. The MB468 and MB468RES line pair confirms other observations showing that methionine dependence is linked to tumorigenicity. Importantly, this cell line pair is an ideal model to metabolite signatures linked to cancer cell methionine dependence. We propose characterize the metabolic changes triggered by the shift from normal growth to homocysteine medium in MB468 breast cancer cells and the methionine stress MB468RES derivatives. In addition we have developed cancer cell lines with shRNAs targeting methionine adenosyltransferase (MAT), the enzyme catalyzing of SAM from methionine and ATP. Inducible knockdown of MAT allows us to reduce SAM synthesis. Our previous results suggest that SAM limitation is the trigger for cancer cell methionine dependence. Thus metabolite profiling using MAT knockdown system will provide an independent dataset that together with profiles from the MB468 and MB468RES cell line pair will define critical profiles related to cancer cell methionine dependence. In the current untargeted analysis of primary metabolites and complex lipids, coupled with analysis of methionine pathway intermediates (folate and respective s-adenosylmethoinine, s-adenosylhomocysteine, choline, betaine) and metabolic will be conducted on MB468, MB468RES and MB468shRNA following the switch from containing media to homocysteine containing media over the course of 0, 2, 4, 12, 24 and 48 hours. The primary objectives were to 1) characterize the response to methionine stress and SAM limitation and 2) correlate the metabolic with cancer cell proliferation arrest and death.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolic Profiling of Visceral and Subcutaneous Adipose Tissue from Colorectal Patients: GC-TOF MS analyis of subcutaneous and visceral adipose tissue samples
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Johanna Lampe (Fred Hutchinson Cancer Research Center at Univ. of Washington, In the current investigation, unbiased profiling of the metabolome and lipidome adipose tissue samples (visceral(VAT) and subcutaenous (SAT)) and serum of 50 patients, including stages I-IV, from the Fred Hutchinson Cancer Center and the German Cancer Research Center (Heidelberg, Germany) was conducted. The and metabolome of adipose tissue (VAT/SAT) and serum were analyzed using UPLC-QTOFMS analysis and GC-TOFMS analyses, respectively. The primary of this project were to 1) compare the metabolome and lipidome SAT adipose tissue of n=50 Colorectal Cancer Cell (CRC) patients, 2) the associations between the lipidome and metabolome in adipose tissue and serum of n=50 CRC patients and 3) test the associations between the of VAT and serum with the tumor stage of CRC patients.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Biomarkers for Depression in Human Plasma in a Population Sample
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Roel Ophoff (UC Los Angeles ) and Steve Horwath (UC Los Angeles ) . Major disorder (MDD) is one of the most debilitating disorders in the United States a 12-month prevalence of 6.7% in the adult population. The disorder affects of Americans daily and is a major health concern with enormous economic cost society at large. Criteria for MDD diagnosis and treatment are based on various and symptoms not always fitting into strict diagnostic categories such as Despite various known risk factors (such as family history, age, and gender), markers supporting diagnosis or prediction of MDD are unavailable. We have cerebrospinal fluid (CSF) and peripheral blood of more than 600 subjects from general population. For each of the participants we also obtained biometric as well as behavioral trait measures. One of the measures is the Beck Inventory (BDI), a well-established questionnaire for measuring severity of Based on the BDI, roughly 5% of participants suffer from severe depressive while most of these subjects are not under treatment or receiving any for depression In the current investigation, untargeted analysis of primary was conducted on age and gender matched human cerebrospinal fluid (CSF) and from subjects suffering with MDD ( n=50) and control subjects (n=50). were diagnosed as having MDD based on the Beck Depression Inventory.The primary of this study were to 1) identify metabolites which discriminate between with and without depression symptoms in the CSF and plasma and 2) how changes between CSF and plasma.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Biomarkers for Depression in Human Cerebrospinal Fluid in a Population Sample
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Roel Ophoff (UC Los Angeles ) and Steve Horwath (UC Los Angeles ) . Major disorder (MDD) is one of the most debilitating disorders in the United States a 12-month prevalence of 6.7% in the adult population. The disorder affects of Americans daily and is a major health concern with enormous economic cost society at large. Criteria for MDD diagnosis and treatment are based on various and symptoms not always fitting into strict diagnostic categories such as Despite various known risk factors (such as family history, age, and gender), markers supporting diagnosis or prediction of MDD are unavailable. We have cerebrospinal fluid (CSF) and peripheral blood of more than 600 subjects from general population. For each of the participants we also obtained biometric as well as behavioral trait measures. One of the measures is the Beck Inventory (BDI), a well-established questionnaire for measuring severity of Based on the BDI, roughly 5% of participants suffer from severe depressive while most of these subjects are not under treatment or receiving any for depression In the current investigation, untargeted analysis of primary was conducted on age and gender matched human cerebrospinal fluid (CSF) and from subjects suffering with MDD ( n=50) and control subjects (n=50). were diagnosed as having MDD based on the Beck Depression Inventory.The primary of this study were to 1) identify metabolites which discriminate between with and without depression symptoms in the CSF and plasma and 2) how changes between CSF and plasma.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolic Profiling of Visceral and Subcutaneous Adipose Tissue from Colorectal Patients: GC-TOF MS analyis of serum samples
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Johanna Lampe (Fred Hutchinson Cancer Research Center at Univ. of Washington, In the current investigation, unbiased profiling of the metabolome and lipidome adipose tissue samples (visceral(VAT) and subcutaenous (SAT)) and serum of 50 patients, including stages I-IV, from the Fred Hutchinson Cancer Center and the German Cancer Research Center (Heidelberg, Germany) was conducted. The and metabolome of adipose tissue (VAT/SAT) and serum were analyzed using UPLC-QTOFMS analysis and GC-TOFMS analyses, respectively. The primary of this project were to 1) compare the metabolome and lipidome SAT adipose tissue of n=50 Colorectal Cancer Cell (CRC) patients, 2) the associations between the lipidome and metabolome in adipose tissue and serum of n=50 CRC patients and 3) test the associations between the of VAT and serum with the tumor stage of CRC patients.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolomic profiling of influenza: a 2009 pandemic H1N1 influenza in lean and mice (via blood and tissue)
STUDY_TYPE
Metabolomics analysis on the effec of diet-related obesity on the immune to pH1N1 infection
STUDY_SUMMARY
Lung samples were obtained at 15 weeks from 56 mice that had received either a low fat diet, or a high fat diet and that were uninfected, 4 days or 8 days post-infection.
Effect of diet and age on ovarian metabolome (via tissue)
STUDY_TYPE
Metabolomics analysis on the ovarian metabolome
STUDY_SUMMARY
Ovarian samples from twenty-one adult, female Cynomolgus monkeys were studied, of which were fed the Western #907 diet, and 13 of which were fed the Prudent diet. HPLC-MS data were acquired for the 21 samples.
Effect of diet and age on ovarian metabolome (serum metabolome compared to
STUDY_TYPE
Metabolomics analysis on the serum metabolome for comparison against the metabolome
STUDY_SUMMARY
Serum samples from twenty-one adult, female Cynomolgus monkeys were studied, of which were fed the Western #907 diet, and 13 of which were fed the Prudent diet. HPLC-MS data were acquired for the 21 samples.
Genetic effects of high fat diet on mouse fecal metabolomics
STUDY_TYPE
Metabolomics analysis on the effect of genetics and diet on the metabolism of GI tract and obesity
STUDY_SUMMARY
This study includes 72 female mice with 4 mice from each of the 18 mice Two mice from each strain were fed a high fat diet and two mice were fed a fat diet. The 36 mice fed a normal fat diet will serve as the controls. All are age 27.6 weeks or older at the time of sacrifice. UPLC-MS data was for all 72 samples.
Metabolite changes associated with methionine stress sensitivity of cancer (CSH MS analysis)
STUDY_TYPE
timecourse study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project granted to Peter Kaiser (UC Irvine), aims to achieve understanding of a unique metabolic dependence of cancer cells to explore development of novel unconventional therapeutic strategies that exploit dependence of cancer cells on methyl-donor abundance. The past few years have highlighted the role of altered metabolism in cancer. While mechanistic insight into changed metabolism in cancer is very limited, the importance of the metabolic pathway surrounding homocysteine and methionine for cancer cell proliferation has been known for over 30 years. These findings, generally summarized as methionine-dependence or methionine stress sensitivity, describe the phenomenon that most cancer cells cannot proliferate in growth medium where the amino acid methionine is replaced with its direct metabolic precursor homocysteine. Importantly, non-tumorigenic cells are unaffected by replacing methionine with homocysteine in the growth medium. For the past years we have been studying methionine dependence of breast and prostate cancer and demonstrated that methionine-dependence is caused by insufficient flux through this pathway to sustain synthesis of the downstream metabolite and the principal methyl-donor S-adenosylmethionine (SAM). We have isolated rare cell clones from MDA-MB468 breast cancer cells (referred to as MB468RES) that are no longer methionine dependent and proliferate in homocysteine medium. Interestingly, MB468RES have lost their ability for anchorage independent growth, a hallmark of cancer. The MB468 and MB468RES cell line pair confirms other observations showing that methionine dependence is tightly linked to tumorigenicity. Importantly, this cell line pair is an ideal model to identify metabolite signatures linked to cancer cell methionine dependence. We propose to characterize the metabolic changes triggered by the shift from normal growth medium to homocysteine medium in MB468 breast cancer cells and the methionine stress insensitive MB468RES derivatives. In addition we have developed cancer cell lines with inducible shRNAs targeting methionine adenosyltransferase (MAT), the enzyme catalyzing synthesis of SAM from methionine and ATP. Inducible knockdown of MAT allows us to specifically reduce SAM synthesis. Our previous results suggest that SAM limitation is the critical trigger for cancer cell methionine dependence. Thus metabolite profiling using the MAT knockdown system will provide an independent dataset that together with metabolite profiles from the MB468 and MB468RES cell line pair will define critical metabolic profiles related to cancer cell methionine dependence. In the current investigation, untargeted analysis of primary metabolites and complex lipids, coupled with quantitative analysis of methionine pathway intermediates (folate and respective derivatives, s-adenosylmethoinine, s-adenosylhomocysteine, choline, betaine) and metabolic flux will be conducted on MB468, MB468RES and MB468shRNA following the switch from methionine containing media to homocysteine containing media over the course of 0, 2, 4, 8, 12, 24 and 48 hours. The primary objectives were to 1) characterize the metabolic response to methionine stress and SAM limitation and 2) correlate the metabolic signatures with cancer cell proliferation arrest and death.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
Metabolic Profiling of Visceral and Subcutaneous Adipose Tissue from Colorectal Patients: UHPLC-QTOF MS analyis of subcutaneous and visceral adipose tissue
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Johanna Lampe (Fred Hutchinson Cancer Research Center at Univ. of Washington, In the current investigation, unbiased profiling of the metabolome and lipidome adipose tissue samples (visceral(VAT) and subcutaenous (SAT)) and serum of 50 patients, including stages I-IV, from the Fred Hutchinson Cancer Center and the German Cancer Research Center (Heidelberg, Germany) was conducted. The and metabolome of adipose tissue (VAT/SAT) and serum were analyzed using UPLC-QTOFMS analysis and GC-TOFMS analyses, respectively. The primary of this project were to 1) compare the metabolome and lipidome SAT adipose tissue of n=50 Colorectal Cancer Cell (CRC) patients, 2) the associations between the lipidome and metabolome in adipose tissue and serum of n=50 CRC patients and 3) test the associations between the of VAT and serum with the tumor stage of CRC patients.Â
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
NUM_GROUPS
2
TOTAL_SUBJECTS
59
STUDY_COMMENTS
Lipidomics profiles for studyThis is the SAT and VAT part of the studyLabel-ID conserved for all parts of the study---The samples had to be diluted for mode measurements (therefore 2 dilutions are measured for the same sample). are then combined and scaling factor is used for final results.
Metabolic Profiling of Visceral and Subcutaneous Adipose Tissue from Colorectal Patients: UHPLC-QTOF MS analyis of serum samples
STUDY_TYPE
biomarker study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Johanna Lampe (Fred Hutchinson Cancer Research Center at Univ. of Washington, In the current investigation, unbiased profiling of the metabolome and lipidome adipose tissue samples (visceral(VAT) and subcutaenous (SAT)) and serum of 50 patients, including stages I-IV, from the Fred Hutchinson Cancer Center and the German Cancer Research Center (Heidelberg, Germany) was conducted. The and metabolome of adipose tissue (VAT/SAT) and serum were analyzed using UPLC-QTOFMS analysis and GC-TOFMS analyses, respectively. The primary of this project were to 1) compare the metabolome and lipidome SAT adipose tissue of n=50 Colorectal Cancer Cell (CRC) patients, 2) the associations between the lipidome and metabolome in adipose tissue and serum of n=50 CRC patients and 3) test the associations between the of VAT and serum with the tumor stage of CRC patients.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
NUM_GROUPS
1
TOTAL_SUBJECTS
59
STUDY_COMMENTS
Lipidomics profiles for studyThis is the serum part of the studyLabel-ID os for all parts of the study---
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of activation
STUDY_TYPE
growth condition, timecourse
STUDY_SUMMARY
Macrophages are central players in immune response, manifesting divergent to control inflammation and innate immunity through release of cytokines and signaling factors. Recently, the focus on metabolism has been reemphasized as signaling and regulatory pathways of human pathophysiology, ranging from cancer aging, often converge on metabolic responses. Here, we used genome-scale and multi-omics (transcriptomics, proteomics, and metabolomics) analysis to metabolic features that are critical for macrophage activation. A genome-scale network for the RAW 264.7 cell line was constructed to determine metabolic of activation. Metabolites well-known to be associated with immunoactivation and arginine) and immunosuppression (tryptophan and vitamin D3) were among the critical effectors. Intracellular metabolic mechanisms were assessed, a suppressive role for de-novo nucleotide synthesis. Finally, underlying mechanisms of macrophage activation were identified by analyzing multi-omic obtained from LPS-stimulated RAW cells in the context of our flux-based This study demonstrates that the role of metabolism in regulating activation be greater than previously anticipated and elucidates underlying connections activation and metabolic effectors. This submission corresponds to the data from this study.
Salmonella Modulates Metabolism during Growth under Conditions that Induce of Virulence Genes
STUDY_TYPE
growth conditions, timecourse
STUDY_SUMMARY
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a facultative that uses complex mechanisms to invade and proliferate within mammalian host To investigate possible contributions of metabolic processes to virulence in S. grown under conditions known to induce expression of virulence genes, we used a systems biology approach coupled with genome scale modeling. First, we distinct metabolite profiles associated with bacteria grown in either rich or media and report the most comprehensive coverage of the S. Typhimurium to date. Second, we applied an omics-informed genome scale modeling analysis of functional consequences of adaptive alterations in S. Typhimurium metabolism growth under our conditions. Modeling efforts highlighted a decreased cellular to both produce and utilize intracellular amino acids during stationary phase in virulence conditions, despite significant abundance increases for these as observed by our metabolomics measurements. Furthermore, analyses of omics in the context of the metabolic model indicated rewiring of the metabolic to support pathways associated with virulence. For example, cellular of polyamines were perturbed, as well as the predicted capacity for secretion uptake.
A study of changes in lipid metabolism of ovarian cancer cells co-cultured with GC-TOF MS analysis
STUDY_TYPE
timecourse study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Ernst Lengyel (University of Chicago).The biology of ovarian cancer (OvCa) is distinct from that of most epithelial tumors, in that hematogenous metastases rare, and ovarian tumors remain confined to the peritoneal cavity. The omentum, large pad of fat tissue (20x13x3cm) covering the bowel, is the most common site OvCa metastasis. It consists primarily of adipocytes, which become the microenvironment for the OvCa cells. The underlying hypothesis for this is that, in the presence of adipocytes, the metabolism of OvCa cells is and shifts towards lipid utilization, which provides energy that facilitates growth and metastasis. Preliminary results suggest that primary human omental secrete cytokines which promote the metastasis of OvCa cells to the omentum and subsequent invasion. Once metastasis has occurred, OvCa cells induce lipolysis omental adipocytes, and use the energy derived from these lipids to study the metabolic changes in the tumor microenvironment we have established a organotypic culture of the human omentum using primary human cells established patient tissue. Metabolic studies will be performed on adipocytes and OvCa individually, on conditioned media and on adipocytes and OvCa cells co-cultured our 3D model, with the goal of arriving at a comprehensive analysis of primary and lipids in the tumor microenvironment.In the current investigation, analysis of primary metabolites and complex lipids were conducted on adipocytes OvCa cells individually, on conditioned media and on adipocytes and OvCa cells in our 3D model. Analysis of oxylipins was conducted on conditioned media. To better understanding of the dynamic regulation of metabolic pathways we will perform metabolic flux analysis using labeled cells (13C-glucose, in the 3D culture model.The primary objective of this study is to gain insight the dynamic interactions between OvCa cells and human adipocytes with the of elucidating targets of therapeutic intervention.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
NUM_GROUPS
2
TOTAL_SUBJECTS
14
STUDY_COMMENTS
Lipidomics profiles for studyFor the co-culture Human Adipocytes were grown in of SKOV3ip1 ovarian cancer cellsFor control samples the adipocytes were grown the absence of SKOV3ip1 ovarian cancer cells---Exp design 2 x 14Final result is by merging results from both files and applying dilution factor.Reason was high concentration in positive mode onlyRaw Data File (Positive Mode_TGs) Data File (Positive Mode_Non-TGs) (dilution2)
A study of changes in lipid metabolism of ovarian cancer cells co-cultured with UHPLC-QTOF MS analysis
STUDY_TYPE
timecourse study
STUDY_SUMMARY
This West Coast Metabolomics Center pilot and feasibility project was granted Ernst Lengyel (University of Chicago).The biology of ovarian cancer (OvCa) is distinct from that of most epithelial tumors, in that hematogenous metastases rare, and ovarian tumors remain confined to the peritoneal cavity. The omentum, large pad of fat tissue (20x13x3cm) covering the bowel, is the most common site OvCa metastasis. It consists primarily of adipocytes, which become the microenvironment for the OvCa cells. The underlying hypothesis for this is that, in the presence of adipocytes, the metabolism of OvCa cells is and shifts towards lipid utilization, which provides energy that facilitates growth and metastasis. Preliminary results suggest that primary human omental secrete cytokines which promote the metastasis of OvCa cells to the omentum and subsequent invasion. Once metastasis has occurred, OvCa cells induce lipolysis omental adipocytes, and use the energy derived from these lipids to study the metabolic changes in the tumor microenvironment we have established a organotypic culture of the human omentum using primary human cells established patient tissue. Metabolic studies will be performed on adipocytes and OvCa individually, on conditioned media and on adipocytes and OvCa cells co-cultured our 3D model, with the goal of arriving at a comprehensive analysis of primary and lipids in the tumor microenvironment.In the current investigation, analysis of primary metabolites and complex lipids were conducted on adipocytes OvCa cells individually, on conditioned media and on adipocytes and OvCa cells in our 3D model. Analysis of oxylipins was conducted on conditioned media. To better understanding of the dynamic regulation of metabolic pathways we will perform metabolic flux analysis using labeled cells (13C-glucose, in the 3D culture model.The primary objective of this study is to gain insight the dynamic interactions between OvCa cells and human adipocytes with the of elucidating targets of therapeutic intervention.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility451 Health Sciences DriveDavis, CA
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
NUM_GROUPS
2
TOTAL_SUBJECTS
14
STUDY_COMMENTS
Lipidomics profiles for studyFor the co-culture Human Adipocytes were grown in of SKOV3ip1 ovarian cancer cellsFor control samples the adipocytes were grown the absence of SKOV3ip1 ovarian cancer cells---Exp design 2 x 14Final result is by merging results from both files and applying dilution factor.Reason was high concentration in positive mode onlyRaw Data File (Positive Mode_TGs) Data File (Positive Mode_Non-TGs) (dilution2)
Quantitative Metabolomics by 1H-NMR and LC-MS/MS Confirms Altered Metabolic Pathways in Diabetes
STUDY_TYPE
Pre- and Post- insulin study with matched controls
STUDY_SUMMARY
We obtained plasma samples from 7 c-peptide negative type 1 diabetic individuals (T1D) and 7 non-diabetic controls (Con) that were matched for age (T1D = 31.1±2.9 yrs, Con = 30.2±3.4 yrs), body mass (T1D = 80.2±4.7kg, Con = 81.9±7.4 kg) and BMI (T1D = 26.5±1.2 kg/m2, Con = 25.2±1.3 kg/m2). Type 1 diabetic people were studied while treated with insulin and also after 8 hours of insulin deprivation
A statistical analysis of the effects of urease pre-treatment on the of the urinary metabolome by gas chromatographymass spectrometry
STUDY_TYPE
Analytical Comparison
STUDY_SUMMARY
Urease pre-treatment of urine has been utilized since the early 1960s to remove levels of urea from samples prior to further processing and analysis by gas spectrometry (GCMS). Aside from the obvious depletion or elimination of urea, effect, if any, of urease pre-treatment on the urinary metabolome has not been in detail. Here, we report the results of three separate but related that were designed to assess possible indirect effects of urease pre-treatment the urinary metabolome as measured by GCMS. In total, 235 GCMS analyses performed and over 106 identified and 200 unidentified metabolites were across the three experiments. The results showed that data from urease samples (1) had the same or lower coefficients of variance among reproducibly metabolites, (2) more accurately reflected quantitative differences and the ratios among different urine volumes, and (3) increased the number of identifications. Overall, we observed no negative consequences of urease In contrast, urease pre-treatment enhanced the ability to distinguish between and biological sample types compared to no treatment. Taken together, these show that urease pre-treatment of urine offers multiple beneficial effects that any artifacts that may be introduced to the data in urinary metabolomics
Metabolomics Analysis of Frontal Fibrosing Alopecia
STUDY_TYPE
Unaffected and Affected patient scalp biopsies
STUDY_SUMMARY
Scarring alopecia consists of a collection of disorders characterized by of hair follicles, replacement with fibrous scar tissue, and irreversible hair Alopecia affects men and women worldwide and can be a significant source of stress and depression for affected individuals. The purpose of this study was explore metabolic profiles in scalp tissue samples from normal control subjects and in matched samples obtained from affected (n=12) and unaffected (n=12) of the scalp in patients with lymphocytic Frontal Fibrosing Alopecia (FFA). fibrosing alopecia results from destruction of hair follicles by an lymphocytic infiltrate that is localized around the upper portion of the hair
INSTITUTE
Case Western Reserve University
DEPARTMENT
Dermatology
LABORATORY
Karnik Lab
LAST_NAME
Karnik
FIRST_NAME
Pratima
ADDRESS
-
EMAIL
psk11@case.edu
PHONE
216-368-0209
NUM_GROUPS
3 groups-Paired unaffected and affected (n=12),Normals(n=6)
TOTAL_SUBJECTS
Patients (N=12), Normals (N=6)
STUDY_COMMENTS
Affected scalp biopsies were obtained from frontal scalp, Unaffected from scalp. Normal scalp biopsies were obtained from the occipital scalp.
A study of changes in lipid metabolism of ovarian cancer cells co-cultured with adipocytes: UPLC-QTRAP MS analysis
STUDY_TYPE
Timecourse
STUDY_SUMMARY
The study investigated the interaction between omental adipocytes and OvCa cells, as a follow up to preliminary data indicating this leads to reprograming of metabolic (especially lipid) profiles in both adipocytes and OvCa cells as ovarian cancer cells (OvCa) readily metastasize to the omental fat pad in the abdomen and stimulate the release of fatty acids. In order to mimic the interaction between OvCa and omental adipocytes during metastasis, a coculture system was used that employed OvCa cells and primary human adipocytes isolated from omentum. Human primary adipocytes were isolated from omental explants from patients undergoing surgery for benign conditions. After surgical removal, omental tissue was digested with collagenase I, and primary cultures of adipocytes were established, characterized, and incorporated into the co-culture. The primary adipocytes were isolated and co-cultured with the OvCa cell line Skov3ip1. In this current submission, the the samples will be collected at 4, 18 and 24 hour time points post co-culture to determine the time dependent effect on lipid mediators, including oxylipins and ceramides. The study results included in this DRCC submission were the 18 hour time point data for oxylipins and ceramides from targeted metabolomic analysis of lipid mediators performed by the Newman lab.
This experiment is investigating the metabolome of men, healthy women, and with Polycystic Ovary Syndrome (PCOS) with and without Obstructive Sleep Apnea
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomic and lipidomic profiles in response to exogenous insulin and GLP-1 during prolonged fasting
STUDY_TYPE
Timecourse
STUDY_SUMMARY
Seventeen northern elephant seal pups constituting four different cohorts at Nuevo State Reserve were studied at two post-weaning periods: early (1-2 wk weaning; n=5) and late (6-7 weeks post weaning; n=12). Study #1: Prior to each protocol, plasma U/kg). Following the infusion, blood samples were collected at determine the effects of prolonged fasting on peripheral insulin activity and samples were collected. Ten fasting seal pups (n=5 early, n=5 late) were (i.v.) with a mass-specific dose of insulin (0.065 U/kg). Following the blood samples were collected at 10, 30, 60, 90, and 120 minutes. Study #2: late-fasted seal pups were administered either a low (LDG; 10 pmol/kg; n=3) or (HDG; 100 pmol/kg; n=4) dose of GLP-1 immediately following a glucose bolus g/kg) (i.v.) infused within 2 mins. the infusions, blood samples were collected 10, 30, 60, 90, 120, and 150 minutes.
SIRM Analysis of human P493 cells under hypoxia in [U-13C/15N] labeled medium (Positive ion mode FTMS)
STUDY_TYPE
tracer
STUDY_SUMMARY
SIRM Analysis of MYC inducible P493 cells under normoxia and hypoxia in labeled Glutamine medium
INSTITUTE
University of Kentucky
DEPARTMENT
Toxicology
LAST_NAME
Fan
FIRST_NAME
Teresa
ADDRESS
-
EMAIL
twmfan@gmail.com
PHONE
-
NUM_GROUPS
4
TOTAL_SUBJECTS
8
STUDY_COMMENTS
For protocols and additional information, see Le, A., Lane, A.N., Hamaker, M., S., Barbi, J., Tsukamoto, T., Rojas, C.J., Slusher, B.S., Zhang, H., Zimmerman. Liebler, D.C., Slebos, R.J.C., Lorkiewicz, P.K., Higashi, R.M., Fan, T.W-M., Dang, C.V. Cell Metabolism 15, 110 (2012). 13C/15N Gln was used as the tracer this study, even though the analysis did not explicity look for 15N
Disruption of Zinc homeostasis can impair maternal glucocorticoid metabolism: on the developing fetus
STUDY_TYPE
steroid panel in pregnant rats
STUDY_SUMMARY
Steroids play a broad and vital role in regulation of gene expression, sexual characteristics, maturation, reproduction, and neurological functions; an imbalance in steroid metabolism is also linked to development and of many diseases including autism. Prenatal stress of different nature has been to affect both the mother and the offspring. Adverse nutritional conditions gestation can impair the maternal hypothalamic-pituitary-adrenal axis (HPA) and the fetus to high levels of glucocorticoids (GC). Evenwhen GC are required for brain development; an increased exposure of the fetus to GC as a consequence of stress can affect fetal hypothalamic-pituitary-gonad axis (HPG) development, neurogenesis, and have a long term impact on the offsprings mental health. zinc availability can occur during pregnancy as a consequence of different (nutritional deficiency, infections, diabetes, alcohol consumption, and to certain toxicants). Importantly, several of these gestational conditions been linked to autism. In fact, alterations in maternal zinc homeostasis upon to select environmental stressors (e.g. the phthalate plasticizer phthalate (DEHP)) that have become increasingly common since the industrial may underlie the recent rise in the incidence of autism.Alterations in maternal homeostasis could expose the fetus to high GC concentrations secondary to a maternal GC production and/or to a decreased capacity of the placenta to GC to inactive metabolites. The overall goal of this proposal is to investigate alterations in zinc homeostasis during gestation triggered by either a marginal nutrition or exposure to an environmental pollutant (the phthalate plasticizer phthalate (DEHP)) can impair maternal and fetal endocrine signaling leading to fetal brain development.
Impact of anesthesia and euthanasia on metabolomics of mammalian tissues: in a C57BL/6J mouse model
STUDY_TYPE
Anesthesia effect study
STUDY_SUMMARY
We examined the effect of several commonly-used methods of anesthesia and for collection of skeletal muscle, liver, heart, adipose and serum of C57BL/6J The data revealed tissue-specific impacts of different anesthesia and strategies. Based on these findings, we present a more optimal collection mammalian tissues and recommend that rodent tissues intended for metabolomics be collected under anesthesia rather than post-euthanasia.
INSTITUTE
University of Michigan
DEPARTMENT
Internal Medicine
LABORATORY
Evans Lab / Burant Lab
LAST_NAME
Charles
FIRST_NAME
Evans
ADDRESS
6321 Brehm Tower, 1000 Wall Street, Ann Arbor MI 48105
Monitoring In Vitro Response of Selenium-Treated Prostate Cells by 1H NMR Spectroscopy
STUDY_TYPE
Metabolite level response after treatment with organoselenium
STUDY_SUMMARY
Metabolomics analysis was performed on DU145 prostate cancer cells and PNT1A non-tumorigenic prostate cells after treatment with selenomethionine and Se-methylselenocysteine using 800 MHz Bruker NMR spectrometer on 18 cell samples.
Metabolic analysis of Normal Mouse Lung Fiboblasts with/without TGFbeta treatment (Part 1)
STUDY_TYPE
Glycolysis/TCA/Nucleotide analysis (tissue/cells)
STUDY_SUMMARY
This study is a part of series performed for the same researcher through pilot/feasibility grant program, so the publication is relevant reference for other studies, see the project for this study. This specific experiment is a small pilot study to establish method performance, it includes four biological replicas of identical cell cultures after the identical treatment and a single tissue sample.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Labeling of cells was carried out in triplicate with each unstimulated sample containing 20e6 cells and stimulated cells containing 12.8e6 cells. Cells were deprived of glucose or glutamine for 1 h then resuspended in 10mM [13C1,2] D-glucose labeled medium. At this time cells were also activated with 1 ug/ml anti-CD3 and anti-CD28. Cells were labeled (and activated) for 12 h when 1 ml of spent medium was collected and cells were resuspended in 200 ul ice cold methanol. All samples were immediately stored in -80°C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Cells were deprived of glucose or glutamine for 1 h then resuspended in 10mM [13C1,2] D-glucose labeled or 4 mM [13C5]-U-glutamine labeled medium, respectively. At this time cells were also activated with 5 ug/ml anti-CD3 and anti-CD28. Cells were labeled (and activated) for 12 h when samples were spun down, and cells were resuspended in 200 ul ice cold methanol
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Jurkat parental cells (JP6) or cells stably expressing the pCDNA Noxa vector (N5) cells were cultured to confluence and counted. 20E6 cells in triplicate were resuspended in glucose free or glutamine free medium for 2 hours. Cells were then pelleted and resuspended in 13C-1,2 Glucose (10mM) or 13C-U-glutamine (4mM) for 24 hours. Cells were pelleted and spent medium was collected. Cell pellets were washed 1X with ice cold PBS and cell pellets were resuspended in 400ul -20 methanol. Cells and media were snap frozen in liquid nitrogen and stored at -80.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Association of Metabolic Profile and Microbiome in Chronic Pressure Ulcer Wounds
STUDY_SUMMARY
Chronic, non-healing wounds contribute significantly to the suffering of patients with co-morbidities in the clinical population with mild to severely compromised immune systems. Normal wound healing proceeds through a well-described process. However, in chronic wounds this process seems to become dysregulated at the transition between resolution of inflammation and re-epithelialization. Bioburden in the form of colonizing bacteria is a major contributor to the delayed headlining in chronic wounds such as pressure ulcers. However how the microbiome influences the wound metabolic landscape is unknown. Here, we have used a Systems Biology approach to determine the association between the taxonomic and metabolomic profile of wounds colonized by bacteria. Pressure ulcer biopsies were harvested from primary chronic wounds and bisected into top and bottom sections prior to analysis of microbiome by pyrosequencing and analysis of metabolome using 1H nuclear magnetic resonance (NMR) spectroscopy. Bacterial taxonomy revealed that wounds were colonized predominantly by three main phyla, but differed significantly at the genus level. While taxonomic profiles demonstrated significant variability between wounds, metabolic profiles shared significant similarity based on the depth of the wound biopsy. Association between taxonomy and metabolic landscape indicated significant wound-to-wound similarity in metabolite enrichment sets and metabolic pathway impacts, especially with regard to amino acid metabolism. To our knowledge, this is the first demonstration of a statistically robust correlation between bacterial colonization and metabolic landscape within the chronic wound environment.
INSTITUTE
Montana State University
DEPARTMENT
Chemistry and Biochemistry
LABORATORY
Ammons
LAST_NAME
Ammons
FIRST_NAME
Mary Cloud
ADDRESS
103 CBB, Montana State University, Bozeman, MT 59717
The human acute lymphoblastic leukemia cell line (Jurkat) was used to isolate a clones based on Noxa expression. JP6 is low Noxa, JP3 is high Noxa. Furthermore, a Noxa expressing plasmid was tranfected and stable clones were selected for a Noxa high model (N5). 10E6 cells were starved of glucose (A) or glutamine (B&C) for 3 hours and then fed 13C 1,2 glucose (A), 15N alpha nitrogen glutamine (B) or 15N amide nitrogen glutamine (C) for 24 hours. Cells were washed 1X in ice cold PBS and resuspended in -20C methanol. Quenched cells were snap frozen and stored at -80. For experiment A we would like to observe the contribution of labeled glucose into the synthesis of amino acids, specifically glycine and serine. For experiment B we are most interested in the nitrogen incorporation into aspartate. SCB edits: This fluxomics study requires measuring amino acids for M, M+1, M+2, and M+3 prioritizing glycine, serine, aspartate, asparagine, ornithine, citrulline, then as many as possible using a diamond hydride column and LCMS method (see CEvans).
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Flies were fed a normal diet or high-sugar (30% sucrose) diet for 7 days. of flies fasted for 24h or sated were microdissected and immediately frozen in ice. The microdissection process from taking the fly out of the vial to the brain took less than a minute. Each brain microdissected piece contains 50K cells.We dissected 40 brains per condition (4 conditions total) and 4-5 replicates
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
13C mass isotopomer analysis (LCMS flux studies) MLL-AF9 (part II)
STUDY_TYPE
timecourse
STUDY_SUMMARY
How cancer cells adapt to metabolically adverse conditions in patients and to proliferate is a fundamental question in cancer biology. Here we show that protein kinase (AMPK), a metabolic checkpoint kinase, confers metabolic stress to leukemia-initiating cells (LICs) and promotes leukemogenesis. Upon dietary MLL-AF9-induced murine acute myeloid leukemia (AML) activated AMPK and leukemogenic potential. AMPK deletion significantly delayed leukemogenesis and LICs by reducing the expression of glucose transporter 1 (Glut1), compromising flux, and increasing oxidative stress and DNA damage. LICs were particularly on AMPK to suppress oxidative stress in the hypoglycemic bone marrow Strikingly, AMPK inhibition synergized with physiological metabolic stress by dietary restriction and profoundly suppressed leukemogenesis. Our results that AMPK protects LICs from metabolic stress and that combining AMPK with physiological metabolic stress potently suppresses AML by inducing stress and DNA damage.
INSTITUTE
University of Michigan
DEPARTMENT
Molecular and Human genetics (Baylor College of Medicine)
Human fecal bile acid profiles before and after fecal transplant
STUDY_TYPE
Understand the bile acid profiles from the feces of fecal microbiota transplant patients that successfully recover from recurrent C. difficile infection
STUDY_SUMMARY
Understand the bile acid profiles from the feces of fecal microbiota transplant patients that successfully recover from recurrent C. difficile infection
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
U13C-Glutamine and U13C-Glucose Flux Analysis (MFA SiHa B16F10)
STUDY_TYPE
SiHa_NT and SiHa_L are 2 experimental group, control and treatment incubated with U13Cglutamine before lysis for 2 hours. SiHa_WT and SiHa_F3 are different cell isogenic clones to incubated before lysis with U13C glucose for Similarly, B1610 and B16M4 are 2 cell lines incubated before lysis with U13C for 2hours
STUDY_SUMMARY
SiHa_NT and SiHa_L are 2 experimental group, control and treatment incubated with U13Cglutamine before lysis for 2 hours. SiHa_WT and SiHa_F3 are different cell isogenic clones to incubated before lysis with U13C glucose for Similarly, B1610 and B16M4 are 2 cell lines incubated before lysis with U13C for 2hours
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Metabolomic analysis of normal and diabetic mouse bone marrow under PBS or treatment
STUDY_TYPE
Untargeted Metabolomics
STUDY_SUMMARY
Wild type and diabetic (MKR) mice were treated daily with intraperitoneal of 50 microliters of PBS (control) or metformin (200 mg/kg body weight) for 14 Their bone marrow cells were collected and compared by untargeted metabolomics.
INSTITUTE
New York University
DEPARTMENT
College of Dentistry, Basic Science and Craniofacial Biology
LABORATORY
Xin Li Laboratory
LAST_NAME
Xin
FIRST_NAME
Li
ADDRESS
345 East 24th Street, Room 901D, New York, NY 10010
EMAIL
xl15@nyu.edu
PHONE
1-(212)992-7009
NUM_GROUPS
4
TOTAL_SUBJECTS
15 samples
STUDY_COMMENTS
each sample with 3 technical replicates in each mode
Effect of Insulin Sensitizer Therapy on Amino Acids and Their Metabolites
STUDY_TYPE
drug + time course
STUDY_SUMMARY
We previously reported the overall study design for the parent study [29]. The report primarily examines the effect of three months of insulin sensitizer on plasma concentrations of BCAA, AAA, and AA metabolites in overweight/obese with fasting hyperglycemia, defined as either impaired fasting glucose or diabetes [29]. Briefly, 25 drug naïve, Northern European American participants fasting blood glucose concentrations of 108?180 mg/dL were randomized to either 45 mg of pioglitazone per day plus 1 g of metformin twice per day (n = or placebo (n = 13) for 12 weeks. We chose metformin based on its proven effect hepatic insulin sensitivity and pioglitazone based on its effect on peripheral sensitivity. Current use of hypoglycemic medications excluded participants from present study.
13C mass isotopomer analysis (LCMS flux studies) MLL-AF9 (part III)
STUDY_TYPE
Glycolysis/TCA/Nucleotide analysis (tissue/cells)
STUDY_SUMMARY
How cancer cells adapt to metabolically adverse conditions in patients and to proliferate is a fundamental question in cancer biology. Here we show that protein kinase (AMPK), a metabolic checkpoint kinase, confers metabolic stress to leukemia-initiating cells (LICs) and promotes leukemogenesis. Upon dietary MLL-AF9-induced murine acute myeloid leukemia (AML) activated AMPK and leukemogenic potential. AMPK deletion significantly delayed leukemogenesis and LICs by reducing the expression of glucose transporter 1 (Glut1), compromising flux, and increasing oxidative stress and DNA damage. LICs were particularly on AMPK to suppress oxidative stress in the hypoglycemic bone marrow Strikingly, AMPK inhibition synergized with physiological metabolic stress by dietary restriction and profoundly suppressed leukemogenesis. Our results that AMPK protects LICs from metabolic stress and that combining AMPK with physiological metabolic stress potently suppresses AML by inducing stress and DNA damage.
INSTITUTE
University of Michigan
DEPARTMENT
Molecular and Human genetics (Baylor College of Medicine)
THP-1 Human Monocyte cells (10^6) were seeded in RPMI 1640 with 0.5% FBS. The were incubated for 30 minutes in either no citrate, 1 mM citrate, or 6 mM Separately, cells were either incubated in 1 mM 13C6 citrate or 6mM 13C6 (Sigma-Aldrich #606081). After the 30 minute pre-incubation time, the cells harvested or stimulated with lipopolysaccharide (LPS) for 1 h or 30 min. Cells subsequently spun down and washed in 150mM ammonium acetate. Cell were respun the supernatant was discarded. Cells were flash frozen in liquid nitrogen and on dry ice.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Comparative metabolomics study of WT and iButOH tolerant E. coli
STUDY_SUMMARY
This study aims to elucidate metabolic mechanisms of tolerance to isobutanol in coli. Two strains are utilized: WT parental strain EcHW24, and isobutanol strain 38-20-4 created via multiplex genome engineering. The metabolic response growth with isobutanol (0.7% w/v) and without (0% w/v) on NG50 minimal media be compared for each strain. 3 replicates for each strain/iButOH concentration been submitted, excpet for WT/0.7%; we have observed high growth phenotype for this combination, and have corresponding submitted 5x replicates. Strain contains mutations in the TCA cycle (gltA SNP) and amino acid metabolism indels in glnE, gltD, and tnaA), thus our hypothesis is that tolerance arises rewiring of TCA cycle and amino acid metabolism, possibly resulting in intracellular ratio of glutamine:glutamate
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
The experiment was done on 4/2/2014 and consists of 7 experimental conditions x replicates per condition = 14 samples. The experimental duplicates are numbered (i.e. 1 and 2, 3 and 4, etc.). All samples are primary mouse macrophages from bone marrow. 12 million cells were plated in each 10 cm tissue culture plate (Corning) and the following day the cells were stimulated with LPS, CL097 and/or Gardiquimod in 10 mls of 2% FBS 25 mM HEPES IMDM. After 60 minutes medium was aspirated and the cells were rapidly wahsed with 15 mls of 150 mM acetate and after aspiration liquid nitrogen was poured on top of the cells and to -80 C freezer. Sample pairs 7 - 8 and 9-10 were treated identically except the rinse was done with ammonium acetate (7 and 8) or distilled water (9 and to evaluate the effect of the rinse solution in the quality of the obtained
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
T cell metabolism during graft-versus-host disease (CAB 307)-PART I
STUDY_TYPE
Glycolysis/TCA/Nucleotide analysis (tissue/cells)
STUDY_SUMMARY
T cells were injected into mice to model graft-versus-host disease. On day 7 after bone marrow transplantation (BMT), cells were recovered and CD8 T cells were purified to > 90% purity over magnetic columns. Naïve T cells were used as control. Cells were then plated at 5x10^6 cells/ml onto plates coated with anti-CD3/CD28 antibodies in the presence of 300µM 13C-palmitate conjugated to BSA (in PBS). Cells were incubated at 37oC for 60min, after which time they were removed from the plates, counted, and an equal number (2.5x10^6) were placed into a 1.7 ml micro-centrifuge tubes and spun down. Cells were washed once with ammonium chloride, residual volume was removed by a second brief spin, cell pellets were flash frozen in liquid nitrogen and stored at -80oC until analysis. Several mice lines were used in this study.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
We recently reported superior right ventricle (RV) performance in response to acute afterload challenge in lambs with a model of congenital heart disease with chronic left-to-right cardiac shunts. Compared with control animals, shunt lambs demonstrated increased contractility because of an enhanced Anrep effect (the slow increase in contractility following myocyte stretch). This advantageous physiological response may reflect preservation of a fetal phenotype, since the RV of shunt lambs remains exposed to increased pressure postnatally. Nitric oxide (NO) production by NO synthase (NOS) is activated by myocyte stretch and is a necessary intermediary of the Anrep response. The purpose of this study was to test the hypothesis that NO signaling is increased in the RV of fetal lambs compared with controls and shunt lambs have persistence of this fetal pattern. An 8-mm graft was placed between the pulmonary artery and aorta in fetal lambs (shunt). NOS isoform expression, activity, and association with activating cofactors were determined in fetal tissue obtained during late-gestation and in 4-wk-old juvenile shunt and control lambs. We demonstrated increased RNA and protein expression of NOS isoforms and increased total NOS activity in the RV of both shunt and fetal lambs compared with control. We also found increased NOS activation and association with cofactors in shunt and fetal RV compared with control. These data demonstrate preserved fetal NOS phenotype and NO signaling in shunt RV, which may partially explain the mechanism underlying the adaptive response to increased afterload seen in the RV of shunt lambs. Research is published, core data not used but project description is relevant: http://ajpheart.physiology.org/content/309/1/H157.long
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Lanthanide-mineral induced alteration of bile acid metabolism in a murine model steatohepatitis
STUDY_SUMMARY
120 mice (equal number of males and females) were randomized into 3 equal One group is on a HFWD alone, a second group is on HFWD supplemented with and calcium, and a third control group is supplemented with calcium alone. At termination (18 months) we will harvest hepatocytes and colonic enterocytes for of epithelial gene expression patterns. We will also harvest cecal contents and for microbial profiling by 16S rRNA pyrosequencing. For this small pilot we wish to add an untargeted metabolomic analysis component. We will harvest (right medial lobe with gall bladder), serum, and feces. We will assay liver/gall bladder samples (8 from the HFWD group and 8 from the supplemented group). Remaining liver samples and the serum and feces will be for future investigation. Liver is being targeted first since both and hepatocellular carcinoma were seen in our previous study in mice on HFWD Additionally, alterations of bile acid profiles and bile acid metabolism have associated with both steatohepatitis and hepatic cancers.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Understand the differences in Bile Acid composition between knockout and floxed at each intestinal segment. Also difference in metabolites between these two at each level of the intestine.
STUDY_SUMMARY
Understand the differences in Bile Acid composition between knockout and floxed at each intestinal segment. Also difference in metabolites between these two at each level of the intestine.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Murine gastrointestinal bile acid profiles before and after antibiotics
STUDY_SUMMARY
Mice were treated with cefoperazone for 10 days and then allowed 6 weeks to off of the antibiotic. Other antibiotic treatments included IP clindamycin the 6 week recovery, IP clindamycin alone, vancomycin alone, kanamycin alone metronidazole. Gut luminal contents of these mice were collected at the time of and included both ileal and cecal content. Paired samples will be used for both analysis and targeted bile acid analysis to define how gut bacteria alter bile profiles in the gut and in turn how this affects C. difficle spore germination outgrowth.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
THP-1 Human Monocyte cells (10^6) were seeded in RPMI 1640 with 0.5% FBS. The were incubated for 30 minutes in either no citrate, 1 mM citrate, or 6 mM Separately, cells were either incubated in 1 mM 13C6 citrate or 6mM 13C6 (Sigma-Aldrich #606081). After the 30 minute pre-incubation time, the cells harvested or stimulated with lipopolysaccharide (LPS) for 1 h or 30 min. Cells subsequently spun down and washed in 150mM ammonium acetate. Cell were respun the supernatant was discarded. Cells were flash frozen in liquid nitrogen and on dry ice.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Wild type and AMPK KO bone marrow derived macrophage were stimulated with LPS for various time period and plates were frozen in liquid nitrogen after washing sodium acetate (200uM) solution and kept in deep freezer for further analysis.
STUDY_SUMMARY
Wild type and AMPK KO bone marrow derived macrophage were stimulated with LPS for various time period and plates were frozen in liquid nitrogen after washing sodium acetate (200uM) solution and kept in deep freezer for further analysis.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Liver and Plasma metaboites for 13C-glucose load in wild type, LIRKO GTT 1 mice
STUDY_TYPE
13C mass isotopomer analysis (flux studies)
STUDY_SUMMARY
Mice were fasted for 18 hr overnight then sacrificed or treated with 13C-U-glucose (2 g/kg ip) and sacrificed 1 hr later by decapitation and liver was immediately freeze-clamped and stored in liquid N2 and then at -80 C. Wild type (IR and IR/FoxO1 floxed) mice were sacrificed after fasting and 1 hr post-glucose treatment. Liver-specific insulin receptor knockout (LIRKO) and insulin receptor/FoxO1 double knockout (LIRFKO) mice were sacrificed 1 hr post glucose treatment. http://www.nature.com/ncomms/2015/150512/ncomms8079/full/ncomms8079.html
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Comparison of normal, lung adenocarcinoma and SCLC tissue metabolomes
STUDY_SUMMARY
In addition to the generation and analysis of metabolomics data on cell lines, of normal lung tissue, adenocarcinoma lung tissue and small cell lung carcinoma (seven samples/group) were processed and evaluated metabolite profile under the scope of the pilot and feasibility study. These data can be to the metabolite profiles defined in the SCLC and NSCLC cell lines and with the ABPP-determined metabolic kinases to identify distinct metabolic or biomarkers (?oncometabolites?) that distinguish small cell lung cancer from cell lung cancer.
Normal plasma cells,Low proliferation multiple myeloma and High proliferation myeloma cells
STUDY_TYPE
differential metabolomics
STUDY_SUMMARY
CD138 sorted bone marrow plasma cell were obtained from a normal patient, a myelow with slow proliferation and a multiple myelow with rapid proliferation.
Untargeted metabolomic analysis of the small intestinal content of malnourished
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
A total of 8 samples from 6 week old, female C57BL/6 mice, treated for 3 weeks a malnourished diet or a control-fed isocaloric diet. Samples were taken from small intestinal fecal content at the terminus of the ileum.
INSTITUTE
University of Victoria
DEPARTMENT
The Uvic Proteomics and Metabolomics Innovation Centre
LAST_NAME
Borchers
FIRST_NAME
Christoph
ADDRESS
#3101-4464 Markham St Victoria, BC Canada, V8Z 7X8
Adult (14 weeks old) Sprague-Dawley rats showing at least three consecutive periods (4 day) of estrous cycles were randomly assigned to four groups: 1: 2: nicotine (6 mg/kg), 3: OC and 4: nicotine (6 mg/kg) + OC. Rats were exposed these treatments for a month. At the end of treatments, hippocampus was immediately frozen in liquid nitrogen. We are sending one side of hippocampi to Center for Integrated Metabolomics for analysis at the University of Florida.
Quick Comparison of Urine Metabolites in Human and SD Rats of Different Sex by UPLC-TOFMS and In-house Software Platform
STUDY_TYPE
Biomarker Discovery
STUDY_SUMMARY
Human urine samples were collected before breakfast from 14 male and 13 female post-graduate students, age from 23 to 29, on the morning of sample collection Male (n=8) and female (n=8) SD rats weighing between 220 and 250g were used. On morning of sample collection day, each rat was deprived of food and put in cage for 24h urine collection. All urine samples were frozen at -80°C prior to
Quick Comparison of Serum Metabolites in SD Rats of Different Sex by Untargeted and In-house Software Platform
STUDY_TYPE
Biomarker Discovery
STUDY_SUMMARY
Male (n=8) and female (n=8) SD rats weighing between 220 and 250g were used. On morning of sample collection day, each rat was deprived of food and put in cage for 24h urine collection. Then a blood sample (3-5ml) was collected from aorta of the rat under anesthesia and centrifuged to obtain serum. All urine serum samples were frozen at -80°C prior to analysis.
Sexual antagonism in exuded non-volatile metabolites in C. purpureus
STUDY_TYPE
male - female
STUDY_SUMMARY
The experimental approach seeks to test for sexual dimorphism in exuded metabolites in C. purpureus. The proposed research is creative and original in its inter-disciplinary approach and its use of a biochemically tractable to develop a much-needed link between natural selection for sexual dimorphism the molecular targets of that selection pressure.
Cyclobutene- and cyclobutane-functionalized fatty acids as novel biochemical of structure and function in HepG2 cells
STUDY_TYPE
Lipid analysis novel C18 fatty acid anologues in complex lipids
STUDY_SUMMARY
Human hepatoma HepG2 cells (American Type Culture Collection; HB-8065) were in 75 ml tissue cell culture flasks in Eagle's minimal essential medium (EMEM) with 10% fetal bovine serum at 37°C in a humidified atmosphere with 5% CO2. treatment with fatty acids or analogues, the cells were seeded at a density of × 106 cells in a T25-cm2 flask for 24 h. Each FA or analogue was added to the medium as a fatty acid-bovine serum albumin (BSA) complex (2.5:1, FA:BSA) to the desired final concentration. The controls in these experiments were HepG2 with BSA alone. After 24 h treatment, the media was collected, cells were twice with PBS and cells were harvested for analysis. To each cell suspension to lipid extraction a standard mixture of 25 µg C15:0 PE, C17:0 PC and C71:1 was added as standards. Extraction of lipids was performed according to the method. For metabolomics analysis, the lipid extracts were resuspended in 2:1 (v/v).All analyses were carried out using an Agilent 1200 Series HPLC, ACE C8-300 column (2.1 x 100 mm) and linear gradient elution at a flow rate of 0.1 Mobile phase A and B consisted of 0.1% formic acid; 10 mM ammonium acetate in and 0.1% formic acid; 10 mM ammonium acetate in ACN/isopropanol (50/50; v/v), The injection volume was 4 µL. Separation of metabolites was achieved at the gradient: T=0 min: 30% B; T=1 min: 30% B; T=25 min: 100% B; T=45 min: 100% B; min: 30% B; and T=60 min: 30% B (re-equilibration). The HPLC system was coupled to a Bruker Soalrix 70 Hybrid FTMS instrument equipped with ionization source (ESI) (Bruker Daltonics). The system was controlled by HyStar software. MS data was collected with resolving power of 78,000 (at m/z 400) in or negative mode under following conditions: a capillary voltage of (+/-) 4,500 and an end plate offset of -500 V. The dry temperature was set at 180°C. Dry flow was maintained 4 L/min. Acquisition range was 244-1,800 m/z with 0.2 s ion time. LC-MS data was converted into mzXML format using CompassXport v. 3.0.6 processed by mzMine v.2.10 [25] or XCMS data analysis software. Data processing mass detection, chromatographic peak detection and deconvolution, isotopic grouping, normalization and peak alignment. Metabolite data were mean-centered unit-variance scaled to remove the offsets and adjust the importance of high low abundance metabolites to an equal level. Significantly altered metabolites defined by a fold change (FC) >2 and p<0.05. Principal component analysis (PCA) hierarchical clustering analysis (HCA) of signature metabolites altered in treated cells compared to control were performed in the Metaboanalyst web (www.metaboanalyst.ca).
INSTITUTE
University of Nebraska - Lincoln
DEPARTMENT
Biochemistry
LABORATORY
DiRusso Black FATTT Lab
LAST_NAME
DiRusso
FIRST_NAME
Concetta
ADDRESS
Department of Biochemistry, University of Nebraska-Lincoln, N241 Beadle Center Vine St.
EMAIL
cdirusso2@unl.edu
PHONE
402-472-6504 or 402-613-9293
NUM_GROUPS
8
TOTAL_SUBJECTS
24+24=48
STUDY_COMMENTS
8 groups in triplicate ran in both negative and positive mode
Whole unconditioned medium (Defined culture media, M199),Whole M1 medium,Whole medium
STUDY_TYPE
differential metabolomics
STUDY_SUMMARY
Media was flash frozen with N2 and stored at -80 C. Samples can be stored at C until use. ~1 ml aliquots. The following media has been provided to the core in biological triplicates.Complete (Whole) Media:1) Whole unconditioned (Defined culture media, M199)2) Whole M1 medium3) Whole M2 medium
Metabolomic-based investigation on the effects of antifungal agents in Candida
STUDY_TYPE
in vitro study/drug dosage
STUDY_SUMMARY
Our aim is to determine the metabolic effects of increasing doses of an agent on C. albicans metabolism (untargeted, steady state metabolomics). We culture in vitro Candida cells to the mid-logarithmic growth in liquid media at 37°C and then inoculate biological replicates (1ml) onto 22mm filters under vocuum filtration in sterile conditions. Subsequently, isolates be cultivated to midlogarithmic phase of growth on the same agar (RPMI-1640) to the antifungal agent has been added at a range of concentrations to achieve equivalent to 0 MIC (no drug), 0.0625 MIC, 0.125 MIC, 0.25 MIC, 0.5 MIC and 1.0 at 37°C. At mid-logarithmic phase of growth (12h) replicates will be quenched by immersion into a solvent mixture of 40% acetonitrile: 40% methanol: water precooled at -40°C. The resulting quenched isolate/solvent mixtrue will mechanically lysed by bead-beating with 0.1mm Zirconia beads in a tissue and then centrifuged to seperate out cell wall components. Supernatants will be and stored at -80°C until they will be sent to SECIM facility.
In this project we will investigate the feasibility of metabolomics and to the diversity of ?metabotypes? in the horse, towards discovery of markers and associated with obesity and insulin resistance in the equine model. The team of researchers assembled for this work have identified horses severely with Equine Metabolic syndrome, often characterized by obesity and These animals are all from the Arabian breed, to control for some genetic Horses are age, sex and farm of residence matched with a control animal possible. Carefully controlled collection protocols were utilized to ensure variability in sample age and quality. Blood plasma is submitted for both LC-MS analysis through the SECIM core facilities. This discovery-based approach begin to generate new targets for the development of novel therapeutic for the treatment and prevention of obesity, type-2 diabetes as well as related conditions in both humans and horses. Finally, as the first dataset of its kind the horse, we may also be able to highlight promising new biomarkers for diagnostic use.
Impact of recurrent hypoglycemia on brain metabolite profile
STUDY_TYPE
Insulin treatment in diabetic rats
STUDY_SUMMARY
The goal of this study is to determine the effect of mild / moderate on brain metabolism. To achieve this goal insulin-treated diabetic rats will be to recurrent mild / moderate hypoglycemia.
INSTITUTE
University of Florida
DEPARTMENT
SECIM
LAST_NAME
Dave
FIRST_NAME
Kunjan
ADDRESS
-
EMAIL
Kdave@med.miami.edu
PHONE
305-243-3590
NUM_GROUPS
2
TOTAL_SUBJECTS
40
STUDY_COMMENTS
Two groups (i) Insulin treated diabetic + Recurrent hypoglycemia, (ii) Insulin diabetic + Recurrent hypoglycemia (only insulin injection) + Glucose infusion maintain glucose to baseline levels.Total 40 samples. Description: Ten samples and 10 hypothalamus sample from ITD+RH group of rats.Similarly, Ten samples and 10 hypothalamus sample from ITD+RH+Glucose group of rats.
NIH WCMC Pilot & Feasibility Project: Metabolite changes associated with loss
STUDY_TYPE
Feeding study
STUDY_SUMMARY
Targeted metabolomic analyses of oxylipins, endocannabinoids, and ceramides performed on 18 mouse liver, adipose, hypothalamus, plasma, and muscle samples from mice euthanized at 18 weeks following consumption of three diet regimens induced lean, obese, and weight loss phenotypes. Samples were analyzed by using a Waters Acquity UPLC and detected on an API 4000 QTrap (AB Sciex, MA, USA) by multiple reaction monitoring (MRM) after negative mode electrospray
Metabolic contribution of pSymA and pSymB megaplasmid/chromid for multipartite meliloti cultured in minimal M9 medium
STUDY_TYPE
megaplasmid deletion
STUDY_SUMMARY
To understand the contribution of pSymA and pSymB to the metabolism of S. the intracellular metabolome was analyzed at five time points (exponential and growth phases) across the growth curve of strains with or without pSymA and/or grown in a defined, minimal medium (M9).
INSTITUTE
McMaster University
DEPARTMENT
Department of Biology
LAST_NAME
Finan
FIRST_NAME
Turlough
ADDRESS
Department of Biology, McMaster University, Hamilton, Canada L8S4K1
metabolic contriubtion of pSymA and pSymB megaplasmid/chromid for multipartite meliloti cultured in rich LBmc medium
STUDY_TYPE
megaplasmid deletion
STUDY_SUMMARY
We wished to evaluate the contribution of pSymA and pSymB towards the of various metabolites in a nutritionally complex environment and to examine S. meliloti influences its surrounding environment.
INSTITUTE
McMaster University
DEPARTMENT
Department of Biology
LAST_NAME
Finan
FIRST_NAME
Turlough
ADDRESS
Department of Biology, McMaster University, Hamilton, Canada L8S4K1
We analyzed metabolites in the brains of wild type mice and DJ-1 knockout mice. DJ-1 knockout mouse is a model of an inherited form of Parkinson's disease.
INSTITUTE
National Institute on Aging
DEPARTMENT
Laboratory of Neurogenetics
LABORATORY
Cell Biology and Gene Expression Section
LAST_NAME
Hauser
FIRST_NAME
David
ADDRESS
35 Lincoln Drive, BLDG 35, Room 1A-1012, Bethesda, MD 20892
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv1016
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3280
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
NUM_GROUPS
3 replicates X 3 timepoints
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv3722c
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in M. tuberculosis genome with whole-cell lysate and assaying changes in levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might
INSTITUTE
Weill Cornell Medical College
DEPARTMENT
Microbiology and Immunology
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 Avenue, New York, NY
EMAIL
kyr9001@med.cornell.edu
PHONE
-
STUDY_COMMENTS
The timepoints in the datafiles refer the amount of time (in minutes) that each was incubated with lysate.The units for 'mzmed' are mass/charge.The units for are seconds (retention time).The units for all the other data columns in the are arbitrary; they are integrated peak counts.In this study, Rv1713 was with lysate with and without 1mM GTP added as a co-factor.
Mice were fed with a TFD for 8 or 24 weeks to induce NAFLD or NASH, Targeted analyses examined diacylglycerols and ceramides in 6-8 mice per group 4 groups including 8 week control, 24 week control, 8 week TFD, and 24 week Samples were analyzed via UHPLC-HRMS
INSTITUTE
University of Florida
DEPARTMENT
Chemistry
LABORATORY
Yost Laboratory
LAST_NAME
Patterson
FIRST_NAME
Rainey
ADDRESS
214 Leigh Hall, University of Florida, Gainesville, FL 32611
Serum samples from Mla patients responsive or not responsive to chemotherapy
STUDY_SUMMARY
In the current study we will perform global metabolic profiling on serum samples obtained at diagnosis from pediatric AML patients (n=20) treated under St. Jude AML02 clinical trial to identify potential biomarkers of clinical significance. These patients include 10 responders and 10 non responders. In a subset of patients (n=7), we have matched samples that were obtained at remission allowing us to determine the change in serum metabolome at diagnosis and after remission followed by investigation of the metabolome change analysis with clinical response.
Pyruvate isotopically labeled by 13C either at position 1 or 2 was used to carbon flux in 3T3-L1 mouse cells line in the presence of various combinations drugs
INSTITUTE
University of Michigan
DEPARTMENT
Molecular and Integrative Physiology (MCTP)
LABORATORY
Macdougald Lab (MCTP)
LAST_NAME
MacDougald
FIRST_NAME
Ormond
ADDRESS
University Michigan, 2900 Huron Parkway, Ann Arbor, MI 48105
Lung contusion is a major risk factor for the development of acute respiratory syndrome. Hypoxia-inducible factor-1? is the primary transcription factor that responsible for regulating the cellular response to changes in oxygen tension. set to determine if hypoxia-inducible factor-1? plays a role in the of acute inflammatory response and injury in lung contusion.Nonlethal unilateral lung contusion was induced in a hypoxia reporter mouse model and 2 cell-specific hypoxia-inducible factor-1? conditional knockout mice. The mice killed at 5-, 24-, 48-, and 72-hour time points, and the extent of systemic and hypoxia was assessed. In addition, injury and inflammation were assessed by bronchoalveolar lavage cells (flow cytometry and cytospin), albumin injury), and cytokines (inflammation). Isolated type 2 cells from the factor-1? conditional knockout mice were isolated and evaluated for cytokines following lung contusion. Finally, the role of nuclear factor-?B and as intermediates in this interaction was studied.
INSTITUTE
University of Michigan
DEPARTMENT
Surgery
LABORATORY
Raghavendran Lab
LAST_NAME
Thomas
FIRST_NAME
Bivin
ADDRESS
Ann Arbor, MI
EMAIL
bthomas@umich.edu
PHONE
734-615-7142
NUM_GROUPS
4
TOTAL_SUBJECTS
8
STUDY_COMMENTS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245055/ : HIF1 (+/+) stands for reporter mouse modelHIF1 (-/-) stands for type 2 cell-specific factor-1? conditional knockout
Metabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fiboblasts and Human & Normal Lung Fiboblasts (Part 2)
STUDY_TYPE
Glycolysis/TCA/Nucleotide analysis. Ceramide analysis for parp1 wild type lung after saline or bleomycin treatment.
STUDY_SUMMARY
This study is a part of series performed for the same researcher through grant program, so the publication is relevant reference for other studies ST000183)This specific experiment is a small pilot study to establish method it includes four biological replicas of identical cell cultures after the treatment and a single tissue sample.
This study is a part of series performed for the same researcher through pilot/feasibility grant program, so the publication is relevant reference for other studies (ST000199)This specific experiment is a pilot study to compare the metabolism of cells transformed using empty vector against cells transformed with vector carrying short hairpin RNA (shRNA) targeted to silence isocitrate dehydrogenase-1 (IDH1) gene.
The goal of the study was to compare the influence of Ileal pouch-anal (IPAA) surgical treatment on patients with ulcerative colitis (UC) vs those familial adenomatous polyposis (FAP). Stool samples were obtained at the time clinic visit, immediately frozen and stored at -80oC until the assay. There no exclusion criteria.
Small airway epithelial cell (SAEC) (Lonza Walkersville, Inc., MD) were grown according to the manufacturer's instructions in growth medium (SAGM) containing 0.03 mg/ml bovine pituitary extract (BPE), 0.5 µg/ml hydrocortisone, 0.5 ng/ml hEGF, 0.5 µg/ml epinephrine, 10 µg/ml transferrin, 5 µg/ml insulin, 0.1 ng/ml retinoic acid, 6.5ng/ml triiodothyronine, 50 µg/ml gentamicin and 50ng/ml Amphotericin-B, and 0.5 mg/ml bovine serum albumin (BSA, fatty acid free). When SAE grew to around 80 to 90% confluence, the cells were put into basal medium not supplemented with growth factors 3hours. Then the cell monolayers were infected with naïve hMPV at multiplicity of infection (MOI) of 3 to certain time. The supernatant was saved and cells were harvested and stored exactly according to the protocol provided by University of Michigan Metabolomics Core Facility for metabolomics analysis. 50mM ammonium acetate in water was used for rinse buffer.
Small airway epithelial cell (SAEC) (Lonza Walkersville, Inc., MD) were grown according to the manufacturer's instructions in growth medium (SAGM) containing 0.03 mg/ml bovine pituitary extract (BPE), 0.5 µg/ml hydrocortisone, 0.5 ng/ml hEGF, 0.5 µg/ml epinephrine, 10 µg/ml transferrin, 5 µg/ml insulin, 0.1 ng/ml retinoic acid, 6.5ng/ml triiodothyronine, 50 µg/ml gentamicin and 50ng/ml Amphotericin-B, and 0.5 mg/ml bovine serum albumin (BSA, fatty acid free). When SAE grew to around 80 to 90% confluence, the cells were put into basal medium not supplemented with growth factors 3hours. Then the cell monolayers were infected with naïve hMPV at multiplicity of infection (MOI) of 3 to certain time. The supernatant was saved and cells were harvested and stored exactly according to the protocol provided by University of Michigan Metabolomics Core Facility for metabolomics analysis. 50mM ammonium acetate in water was used for rinse buffer.
Pilot Study 13C flux effects when RhoC or RhoA perturbed (13C BCs)
STUDY_TYPE
13C mass isotopomer analysis (flux studies)
STUDY_SUMMARY
Rho-GTPases are small GTP-binding proteins that contribute to the epithelial-to-mesenchymal transition by regulating several cellular processes including organization of the actin cytoskeleton, cell motility, transcription, and cell proliferation. Overexpression of RhoC-GTPases (RhoC) in breast cancer has been implicated in poor disease prognosis due to increased cancer cells invasion, migration, and motility, which warranted its consideration as a therapeutic target for inhibiting breast cancer metastasis. Using silencing RNA (siRNA) molecules to knockdown RhoC expression is a promising approach to inhibit breast cancer metastases.
INSTITUTE
University of Michigan
DEPARTMENT
Internal Medicine
LABORATORY
Merajver Lab
LAST_NAME
Wynn
FIRST_NAME
Michelle
ADDRESS
University Michigan, 2900 Huron Parkway, Ann Arbor, MI 48105
Colorectal Cancer Detection Using Targeted Serum Metabolic Profiling
STUDY_SUMMARY
Colorectal cancer (CRC) is one of the most prevalent and deadly cancers in the Despite an expanding knowledge of its molecular pathogenesis during the past decades, robust biomarkers to enable screening, surveillance, and therapy of CRC are still lacking. In this study, we present a targeted liquid mass spectrometry-based metabolic profiling approach for identifying biomarker that could enable highly sensitive and specific CRC detection using human serum In this targeted approach, 158 metabolites from 25 metabolic pathways of significance were monitored in 234 serum samples from three groups of patients CRC patients, 76 polyp patients, and 92 healthy controls). Partial least analysis (PLS-DA) models were established, which proved to be powerful for CRC patients from both healthy controls and polyp patients. Receiver operating curves generated based on these PLS-DA models showed high sensitivities (0.96 0.89, respectively, for differentiating CRC patients from healthy controls or patients); good specificities (0.80 and 0.88), and excellent areas under the (0.93 and 0.95) were also obtained. Monte Carlo cross validation (MCCV) was applied, demonstrating the robust diagnostic power of this metabolic profiling
Postprandial lipids are lower after vertical sleeve gastrectomy (VSG) surgery and this efect is independent of lipid absorption and chylomicron production. This poses a question of where the lipids are going. In order to test the hypothesis that intestinal oxidation of lipids is increased, Sham or VSG animals were gavaged with glycerol trioleate or water and sacrificed 2h later.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Conjugated linoleic acid (CLA) study in LDLR-/- mice
STUDY_TYPE
Acylcarnitine analysis
STUDY_SUMMARY
LDLR-/- mice were fed a high fat high sucrose diet with either 9,11 CLA or 10,12 CLA. Control groups included no supplementation or caloric restriction to mirror weight loss seen in CLA group. Mice were sacrificed and blood was collected into EDTA tubes. Isolated plasma was immediately frozen at -80C. Adipose tissue from gonadal fat (epididymal white adipose tissue, EWAT) and subcutaneous fat (inguinal white adipose tissue, IWAT) and liver were harvested, snap frozen in liquid nitrogen, and immediately frozen at -80C. An aliquot of thawed plasma was prepared for this project and frozen in an eppendorf tube. Small pieces of frozen tissue were cut and weighed on dry ice and packaged in individual foil packets for this project. **Note: tissue weight is approximate**
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Cecal samples were isolated directly from the ceca of dissected chickens that were either experimentally infected with C. jejuni DRH212 or mock-infected with PBS. Cecal samples were re-suspended in Life Technologies 1X PBS based on weight of sample (1 ml/100 mg = 10-1 dilution) and stored at -80C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Tumor neurospheres were grown in culture until ~90% confluent. Media was changed to contain 1mM acetate. After 24h, 0h time points were collected and media was changed on all other cells to 1mM 13C-acetate containing media. Cells were then collected at their various time points, 1, 3, 24, 48, or 72 hours. Cells were collected into 15mL tubes, spun down at 100xg for 1min and media aspirated. Pellet was washed (not resuspended) in 150mM ammonium acetate. This was then aspirated off and the cells snap frozen and stored at -80C until all time points complete to ship on dry ice. 0h, 1h, and 3h A, B, and C samples will have gTn by HILIC + TCA by GCMS done on them, while 0h, 1h, and 3h D, E, and F will have FAMES and DG & PC analysis done on them. 24h, 48h, and 72h A, B, and C samples will have FAMES analysis done on them.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Role of medium in bacterial growth (HILIC chromatography)
STUDY_SUMMARY
Experiment to test how different growth mediums affect bacterial growth. The supernatants of 17 strains of bacteria (10 grown in one medium and 7 grown in another medium) were submitted for metabolite analysis.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Characterization and Plasticity of the Metabolome in Peripheral Cells in Bipolar I Disorder
STUDY_TYPE
Broad Spectrum LCMS
STUDY_SUMMARY
Patients with Bipolar I Disorder (BPI) and matched non-affected controls were recruited. Males and females from all races and ethnicities between the ages of 19-65 participated in the research. Skin biopsies were obtained and fibroblasts were isolated from each of these biopsies. A total of 1 x 〖10〗^7 fibroblasts cells were used for metabolomics. Cell pellets were flash frozen in liquid nitrogen and shipped on dry ice to the NIH Eastern Regional Comprehensive Metabolomic Resource Core at RTI International in North Carolina. Metabolomics will be determined using a broad spectrum metabolomics protocol by RTI
Investigation of metabolomic blood biomarkers for detection of adenocarcinoma lung cancer
STUDY_TYPE
Lung cancer case control biomarker discovery
STUDY_SUMMARY
Recently, the National Lung Cancer Screen Trial (NLST) demonstrated that low-dose CT (LDCT) screening could reduce mortality due to lung cancer by 20%. However, LDCT screening is largely hindered by high false-positive rates (96%), particularly in high-risk populations (heavy smokers), due to the low prevalence rates (less than 2%) of malignant tumors and high incidence of benign lung nodules. Consequently, complementary biomarkers that can be used in conjunction with LDCT screening to improve diagnostic capacities and reduce false-positive rates are highly desirable. Preferably, such complementary tools should be noninvasive and exhibit high sensitivity and specificity. The application of “-omic” sciences (genomics, transcriptomics, proteomics, and metabolomics) represents valuable tools for the discovery and validation of potential biomarkers that can be used for detection of NSCLC. Of these omic sciences, metabolomics has received considerable attention for its application in cancer. Metabolomics is the assessment of small molecules and biochemical intermediates (metabolites) using analytic instrumentation. Metabolites in blood are the product of all cellular processes, which are highly responsive to conditions of disease and environment, and represent the final output products of all organs forming a detailed systemic representation of an individual's current physiologic state. In this study, we used an untargeted metabolomics approach using gas chromatography time-of-flight mass spectrometry (GCTOFMS) to analyze the metabolome of serum and plasma samples both collected from the same patients that were organized into two independent case–control studies (ADC1 and ADC2). In both studies, only NSCLC adenocarcinoma was investigated. The overall objectives were to (i) determine whether individual or combinations of metabolites could be used as a diagnostic test to distinguish NSCLC adenocarcinoma from controls and (ii) to determine which, plasma or serum, provides more accurate classifiers for the detection of lung cancer. We developed individual and multimetabolite classifiers using a training test from the ADC1 study and evaluated the performance of the constructed classifiers, individually or in combination, in an independent test/validation study (ADC2). This study shows the potential of metabolite-based diagnostic tests for detection of lung adenocarcinoma. Further validation in a larger pool of samples is warranted.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
SS = Sigma sample and is used as a quality control The first set (ADC1) used for biomarker development consisted of serum and plasma samples obtained from 52 stages I–IV NSCLC adenocarcinoma patients (52 plasma and 49 serum), and 31 healthy controls (31 pairs of serum and plasma) for a total of 163 samples. This set was regarded as the training set for biomarker discovery and classifier development. A second, independent case–control study (ADC2) consisting of serum and plasma samples collected from 43 stage I–IV NSCLC adenocarcinoma patients and 43 healthy controls (total 172 samples) was used as an independent test set for biomarker evaluation. A limitation of this study is the relatively small sample size for each cohort (52 cases, 31 controls for ADC1, and 43 cases and 43 controls for ADC2) because patient variability can be a big factor in smaller studies.
Study 2 Investigation of metabolomic blood biomarkers for detection of adenocarcinoma lung cancer (test/validation)
STUDY_SUMMARY
Recently, the National Lung Cancer Screen Trial (NLST) demonstrated that low-dose CT (LDCT) screening could reduce mortality due to lung cancer by 20%. However, LDCT screening is largely hindered by high false-positive rates (96%), particularly in high-risk populations (heavy smokers), due to the low prevalence rates (less than 2%) of malignant tumors and high incidence of benign lung nodules. Consequently, complementary biomarkers that can be used in conjunction with LDCT screening to improve diagnostic capacities and reduce false-positive rates are highly desirable. Preferably, such complementary tools should be noninvasive and exhibit high sensitivity and specificity. The application of “-omic” sciences (genomics, transcriptomics, proteomics, and metabolomics) represents valuable tools for the discovery and validation of potential biomarkers that can be used for detection of NSCLC. Of these omic sciences, metabolomics has received considerable attention for its application in cancer. Metabolomics is the assessment of small molecules and biochemical intermediates (metabolites) using analytic instrumentation. Metabolites in blood are the product of all cellular processes, which are highly responsive to conditions of disease and environment, and represent the final output products of all organs forming a detailed systemic representation of an individual's current physiologic state. In this study, we used an untargeted metabolomics approach using gas chromatography time-of-flight mass spectrometry (GCTOFMS) to analyze the metabolome of serum and plasma samples both collected from the same patients that were organized into two independent case–control studies (ADC1 and ADC2). In both studies, only NSCLC adenocarcinoma was investigated. The overall objectives were to (i) determine whether individual or combinations of metabolites could be used as a diagnostic test to distinguish NSCLC adenocarcinoma from controls and (ii) to determine which, plasma or serum, provides more accurate classifiers for the detection of lung cancer. We developed individual and multimetabolite classifiers using a training test from the ADC1 study and evaluated the performance of the constructed classifiers, individually or in combination, in an independent test/validation study (ADC2). This study shows the potential of metabolite-based diagnostic tests for detection of lung adenocarcinoma. Further validation in a larger pool of samples is warranted.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
EMAIL
ofiehn@ucdavis.edu
PHONE
(530) 754-8258
STUDY_COMMENTS
SS = Sigma sample and is used as a quality control The first set (ADC1) used for biomarker development consisted of serum and plasma samples obtained from 52 stages I–IV NSCLC adenocarcinoma patients (52 plasma and 49 serum), and 31 healthy controls (31 pairs of serum and plasma) for a total of 163 samples. This set was regarded as the training set for biomarker discovery and classifier development. A second, independent case–control study (ADC2) consisting of serum and plasma samples collected from 43 stage I–IV NSCLC adenocarcinoma patients and 43 healthy controls (total 172 samples) was used as an independent test set for biomarker evaluation. A limitation of this study is the relatively small sample size for each cohort (52 cases, 31 controls for ADC1, and 43 cases and 43 controls for ADC2) because patient variability can be a big factor in smaller studies.
Changes in the metabalome and lipidome in response to exercise training
STUDY_TYPE
HERITAGE (HEalth, RIsk factors, exercise Training And GEnetics) family study
STUDY_SUMMARY
The overall objective of the Heritage Family Study is to study the role of the genotype in cardiovascular, metabolic, and hormonal responses to aerobic exercise training and the contribution of regular exercise to changes in several cardiovascular disease and diabetes risk factors. The study cohort used in this analysis was derived from the pool of 473 Caucasian subjects (230 male and 243 female) from 99 nuclear families who completed ≥58 of the prescribed 60 exercise-training sessions. Utilizing a subsample of this Caucasian cohort, we selected family members from the Quebec center (N=125) to assess the metabolome and lipidome of circulating plasma under two well-defined environmental conditions, the pre- and post-training conditions.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
Health Sciences Drive, Davis, California, 95616, USA
Serum phosphatidylethanolamine levels distinguish benign from malignant solitary pulmonary nodules and represent a potential diagnostic biomarker for lung cancer (part I)
STUDY_SUMMARY
Recent computed tomography (CT) screening trials showed that it is effective for early detection of lung cancer, but were plagued by high false positive rates. Additional blood biomarker tests designed to complement CT screening and reduce false positive rates are highly desirable. In the current study, we expand upon our initial experimental findings as part of the discovery phase by evaluating metabolites in serum from subjects with benign or malignant SPNs using a combined approach of gas chromatography time-of-flight mass spectrometry (GC-TOFMS) and hydrophilic liquid chromatography accurate mass quadrupole time-of-flight mass spectrometry (HILIC-qTOFMS). Furthermore, we evaluated serum collected pre-diagnosis and at-diagnosis of lung cancer in addition to samples obtained post-surgical intervention from subjects with malignant SPNs (post-diagnosis). We hypothesize that our systems biology approach to identify candidate metabolomics biomarkers will ultimately lead to improved early detection of lung cancer and can be used in as a companion blood test to LDCT screening.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Serum phosphatidylethanolamine levels distinguish benign from malignant solitary pulmonary nodules and represent a potential diagnostic biomarker for lung cancer (part II)
STUDY_SUMMARY
Recent computed tomography (CT) screening trials showed that it is effective for early detection of lung cancer, but were plagued by high false positive rates. Additional blood biomarker tests designed to complement CT screening and reduce false positive rates are highly desirable. In the current study, we expand upon our initial experimental findings as part of the discovery phase by evaluating metabolites in serum from subjects with benign or malignant SPNs using a combined approach of gas chromatography time-of-flight mass spectrometry (GC-TOFMS) and hydrophilic liquid chromatography accurate mass quadrupole time-of-flight mass spectrometry (HILIC-qTOFMS). Furthermore, we evaluated serum collected pre-diagnosis and at-diagnosis of lung cancer in addition to samples obtained post-surgical intervention from subjects with malignant SPNs (post-diagnosis). We hypothesize that our systems biology approach to identify candidate metabolomics biomarkers will ultimately lead to improved early detection of lung cancer and can be used in as a companion blood test to LDCT screening.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
Metabolic profiling during ex vivo machine perfusion of the human liver
STUDY_SUMMARY
As donor organ shortages persist, functional machine perfusion is under investigation to improve preservation of the donor liver. The transplantation of donation after circulatory death (DCD) livers is limited by poor outcomes, but its application may be expanded by ex vivo repair and assessment of the organ before transplantation. Here we employed subnormothermic (21 °C) machine perfusion of discarded human livers combined with metabolomics to gain insight into metabolic recovery during machine perfusion. Improvements in energetic cofactors and redox shifts were observed, as well as reversal of ischemia-induced alterations in selected pathways, including lactate metabolism and increased TCA cycle intermediates. We next evaluated whether DCD livers with steatotic and severe ischemic injury could be discriminated from ‘transplantable’ DCD livers. Metabolomic profiling was able to cluster livers with similar metabolic patterns based on the degree of injury. Moreover, perfusion parameters combined with differences in metabolic factors suggest variable mechanisms that result in poor energy recovery in injured livers. We conclude that machine perfusion combined with metabolomics has significant potential as a clinical instrument for the assessment of preserved livers.
INSTITUTE
University of California, Davis
DEPARTMENT
Genome and Biomedical Sciences Facility
LABORATORY
WCMC Metabolomics Core
LAST_NAME
Fiehn
FIRST_NAME
Oliver
ADDRESS
1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616
CHEAR Urine Reference Material Proficiency Test Biocrates
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
CHEAR Reference Material Urine. The material was prepared and analyzed by way of LC-MS and Biocrates workflow employed by the Eastern Regional Metabolomics Resource Core (protocols available in metabolomics workbench). Six samples were injected of the sample reference material prepared in replicate.
CHEAR Plasma Reference Material Proficiency Test Biocrates
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
CHEAR Reference Material Plasma was provided by Emory University. The material was prepared and analyzed by way of LC-MS and Biocrates workflow employed by the Eastern Regional Metabolomics Resource Core (protocols available in metabolomics workbench). Six samples were injected of the sample reference material prepared in replicate.
Maize plants were grown under three different temperature regimes: 1) normal day / normal night; 2) hot day / normal night; 3) hot day / hot night. Kernels from developing ears were taken 14, 16, 18, 22, 26 and 40 days after pollination.
AH and TM samples were obtained from young-normotensive DBA/2J (3 and 7.5 months) and old-hypertensive DBA/2J mice (8-8.5, 10 and 12 month). Lipids were extracted using modified Bligh and Dyer method and subjected to mass spectrometric identification using appropriate class-specific lipid standards and ratiometric quantification. Corresponding aqueous phase (of extraction) protein concentrations were measured using Bradford method.
INSTITUTE
University of Miami
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
McKnight Vision Research Building, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Room 706A, Miami, Florida 33136
Human Aqueous Humor Phospholipids in Control and Glaucomatous eyes
STUDY_SUMMARY
An analysis of phospholipid (phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine and phosphatidylinositol) classes in human control and glaucomatous aqueous humor (AH). Lipid extraction was performed using a modification of the Bligh and Dyer method, protein concentrations were determined using the Bradford’s method, and select samples were confirmed with Densitometry of PHAST gels. Lipids were identified and subjected to ratiometric quantification using a TSQ Quantum Access Max triple quadrupole mass spectrometer utilizing precursor ion scan (PIS) or neutral ion loss scan (NLS) using appropriate class specific lipid standards in a two-step quantification process. Mass spectrometer data were analyzed using MzMine 2.23.
Non-targeted Metabolomics Analysis of Golden Retriever Muscular Dystrophy-Affected Muscles Reveals Alterations in Arginine and Proline Metabolism, and Elevations in Glutamic and Oleic Acid In Vivo
STUDY_SUMMARY
Like Duchenne muscular dystrophy (DMD), the Golden Retriever Muscular Dystrophy (GRMD) dog model of DMD exhibits is characterized by muscle necrosis, progressive paralysis, and pseudohypertrophy in specific skeletal muscles. This severe GRMD phenotype included atrophy of the biceps femoris (BF) and compared to unaffected normal dogs, while the long digital extensor (LDE) of the pelvic limb, serving as a hip flex and stifle extensor, is unaffected. A recent microarray analysis of GRMD identified alterations in genes associated with lipid metabolism and energy production. We, therefore, undertook a non-targeted metabolomics analysis of the GRMD BF (affected) and LDE (unaffected) using GC-MS to identify underlying metabolic defects specific for affected GRMD skeletal muscle. Of the 134 metabolites identified in BF, eight were significantly altered in GRMD BF compared to control BF (Glutamic Acid (2.48 fold vs. controls); Oleic Acid (1.76 fold vs. controls); Proline (1.73 fold vs. controls); Myoinositol-2- Phosphate (0.44 fold vs. controls); Fumaric Acid (0.40 fold vs. controls); Carnosine (0.40 fold vs. controls); Lactamide (0.33 fold vs. controls); and Stearamide (0.23 fold vs. controls). Pathway analysis of the T-test significant metabolites identified BF muscle metabolites significantly enriched for Arginine and proline metabolism (p=5.8E-4, FDR=0.04) and Alanine, aspartate, and glutamate metabolism (p=1.3E-3, FDR=0.05). The GRMD LDE previously reported to be unaffected, in contrast, had only one significantly altered metabolite (3-Phosphoglyceric Acid (0.35 Fold vs. controls)).The identification of elevated BF Oleic acid (a long-chain fatty acid) is consistent with recent microarray studies identifying altered lipid metabolism genes, while alterations in Arginine and Proline metabolism are consistent with recent studies identifying elevated L-arginine in DMD patient sera as a biomarker of disease (alterations in DMD or GRMD muscle itself have not previously been reported).Together, these studies demonstrate muscle-specific alterations in GRMD-affected muscle, which illustrate previously unidentified metabolic changes.
INSTITUTE
University of North Carolina
DEPARTMENT
McAllister heart Institute, Department of Internal medicine, Department of Pathology & Laboratory, Department of Pharmacology
LABORATORY
Multiple Centers
LAST_NAME
Willis
FIRST_NAME
Monte
ADDRESS
111 Mason Farm Road, MBRB 2336, Chapel Hill, North Carolina, 27599-7126, USA
EMAIL
monte_willis@med.unc.edu
PHONE
(984) 999-5431
STUDY_COMMENTS
Skeletal Muscle (Biceps femoris (BF), long digital extensor(LDE))
Human trabecular meshowrk phospholipid profiles of control and glaucomatous eyes
STUDY_SUMMARY
We compared phospholipid (phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, and phosphatidylinositol) profiles of control and glaucomatous trabecular meshwork (TM) derived from human donors.Lipid extraction was performed using a modification of the Bligh and Dyer method, protein concentrations were determined using the Bradford method, and for select samples confirmed with densitometry of PHAST gels. Lipids were identified and subjected to ratiometric quantification using a TSQ quantum Access Max triple quadrupole mass spectrometer with precursor ion scan (PIS) or neutral ion loss scan (NLS), using appropriate class specific lipid standards.
INSTITUTE
University of Miami
LAST_NAME
Bhattacharya
FIRST_NAME
Sanjoy
ADDRESS
McKnight Vision Research Building, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 1638 NW 10th Avenue, Room 706A, Miami, Florida 33136
SJGBM2 and MGG8 glioma cells were stable transfected with IDH1-R132H mutated. The expression of IDH1-R132H was confirmed by Western Blot assay. The aim of this project is analyze the production of 2HG in the stable transfected cells (SJGBM-IDH1m and MGG8-IDH1m) compared with the control group WT.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Purine and TCA measurements in salt sensitive (SS) hypertension
STUDY_TYPE
MS analysis
STUDY_SUMMARY
SS rats were surgically implanted with a chronic servo-control cuff, the purpose of which is to maintain normal pressure to the left kidney while the right kidney is exposed to high blood pressure. After 7 days of high salt treatment, which induces high blood pressure in the SS rat, rats were anesthetized with pentobarbital, kidneys were flushed and removed. The renal medulla was separated from the cortex using scissors, and the renal medullas were frozen in liquid nitrogen and stored at -80 C.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Kachman
FIRST_NAME
Maureen
ADDRESS
6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
In this study, two independent large cohorts of mature dates exhibiting substantial diversity in origin, varieties and fruit processing conditions were measured by metabolomics techniques in order to identify major determinants of the fruit metabotype. Additional samples reflecting different stages of date fruit ripening process has been included for 10 different fruit varieties. This study includes updated date photographs and combined results data (GCMS/LCMS) and technical validation data, see downloadable files section to access this information.
Mechanism Behind Stay Green Trait in Bread Wheat (Triticum aestivum L.)
STUDY_TYPE
Comparison
STUDY_SUMMARY
Two different wheat genotypes were treated with the high temperature and control conditions under full irrigated condition. Leaf tissues were collected for all 2-different treatments with six replicates after 7 and 10 days of high temperature treatment.
Biomarkers of NAFLD progression: a lipidomics approach to an epidemic. Part 3:Urine
STUDY_TYPE
Lipidomics Study
STUDY_SUMMARY
The spectrum of nonalcoholic fatty liver disease (NAFLD) includes steatosis, nonalcoholic steatohepatitis (NASH), and cirrhosis. Recognition and timely diagnosis of these different stages, particularly NASH, is important for both potential reversibility and limitation of complications. Liver biopsy remains the clinical standard for definitive diagnosis. Diagnostic tools minimizing the need for invasive procedures or that add information to histologic data are important in novel management strategies for the growing epidemic of NAFLD. We describe an 'omics' approach to detecting a reproducible signature of lipid metabolites, aqueous intracellular metabolites, SNPs, and mRNA transcripts in a double-blinded study of patients with different stages of NAFLD that involves profiling liver biopsies, plasma, and urine samples. Using linear discriminant analysis, a panel of 20 plasma metabolites that includes glycerophospholipids, sphingolipids, sterols, and various aqueous small molecular weight components involved in cellular metabolic pathways, can be used to differentiate between NASH and steatosis. This identification of differential biomolecular signatures has the potential to improve clinical diagnosis and facilitate therapeutic intervention of NAFLD.
Plasma metabolic fingerprint for breast cancer (MS) - part I
STUDY_TYPE
control - case
STUDY_SUMMARY
Breast cancer is a highly heterogeneous disease associated with metabolic reprogramming. The shifts in the metabolome caused by breast cancer still lack data from Latin populations of Hispanic origin. In this pilot study, metabolomic and lipidomic approaches were performed to establish a plasma metabolic fingerprint of Colombian Hispanic women with breast cancer. NMR, GC-MS and LC-MS datasets were combined and compared. Statistics showed discrimination between breast cancer and healthy subjects on all analytical platforms.
Longitudinal Metabolomics of the Human Microbiome in Inflammatory Bowel Disease
STUDY_SUMMARY
A number of factors contribute to the complex array of small molecules that occur in stool; including diet, gut flora, and gut function. Comprehensive profiling of the stool metabolome therefore can provide detailed phenotypic information on health status, metabolic interactions between the host and the microbiome, and interactions among gut microbes. Here, we applied metabolomics to characterize stool samples collected longitudinally from inflammatory bowel disease (IBD) patients and non-IBD controls who participated in the Integrative Human Microbiome Project (iHMP). A total of 546 stool samples were analyzed using a platform comprised of four complementary liquid chromatography tandem mass spectrometry (LC-MS) methods designed to measure polar metabolites and lipids. Each method used high resolution/accurate mass (HRAM) profiling to measure both metabolites of confirmed identity and yet to be identified metabolite peaks. 81,867 de-isotoped LC-MS peaks were measured, out of which 597 were annotated based on confirmation with authentic reference standards. Pooled stool extracts inserted and analyzed throughout the analysis queues to evaluate analytical reproducibility showed a median coefficient of variation of 5.1% among known metabolites and 24.2% across all 81,867 features. Owing to differences in water content and heterogeneity among stool samples, total median scaling was used to standardize the metabolomics data. In addition to being accessible at the Metabolomics Workbench repository, these metabolomics data will be incorporated into a multi’omic database (https://www.hmpdacc.org/ihmp/) that will enable the study of associations between the gut microbiome and IBD.
Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv2553c
STUDY_TYPE
timecourse
STUDY_SUMMARY
These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.
INSTITUTE
Weill Cornell Medical College, NY
LAST_NAME
Rhee
FIRST_NAME
Kyu
ADDRESS
Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY
Aspirin Metabolomics in Colorectal Cancer Chemoprevention (part 1 - Colon)
STUDY_TYPE
Untargeted high-resolution mass spectrometry profiling
STUDY_SUMMARY
Substantial evidence supports the effectiveness of aspirin for cancer chemoprevention in addition to its well established role in cardiovascular protection. In recent meta-analyses of randomized controlled trials in humans, daily aspirin use reduced incidence, metastasis and mortality from several common types of cancer, especially colorectal cancer. The mechanism(s) by which aspirin exerts an anticancer benefit is uncertain; numerous effects have been described involving both cyclooxygenase-dependent and -independent pathways. The goal of this research is to elucidate the key metabolic changes that are responsible for the anticancer effects of aspirin in humans using untargeted metabolomics analysis. Metabolomics, or global metabolite profiling, is an emerging discipline that has the potential to transform the study of pharmaceutical agents. Our innovative approach will use high-resolution mass spectroscopy to detect thousands of metabolites in blood plasma and normal colon mucosa biopsies that were collected from participants in the Aspirin/Folate Polyp Prevention Study, a randomized, double-blind, placebo-controlled trial of aspirin and/or folic acid supplementation for the prevention of colorectal adenomas. Participants in the trial were assigned with equal probability to three aspirin treatment arms (placebo, 81 mg, or 325 mg daily). Over the three-year treatment period, 81 mg/day of aspirin reduced the risk of adenomas, whereas the 325 mg/day dose had less effect. The aims of the current proposal are to identify metabolomic signatures, including specific metabolites and metabolic pathways, that are associated with aspirin treatment in blood and normal colon mucosal tissue of participants after three years of randomized aspirin treatment; and then to assess the associations of these metabolic signatures with adenoma risk and whether they mediate the reductions in risk due to 81 mg/day aspirin treatment. We will prioritize metabolites for study by evaluating metabolite levels in patients from the placebo and treatment arms while controlling the false discovery rate, use correlation analysis to enhance identification of relevant metabolic modules associated with these prioritized metabolites, and apply pathway mapping with post-hoc application of ion dissociation spectroscopy to representative metabolites to confirm pathway identification. Because aspirin is a multifunctional drug that is thought to modify numerous pathways with potential roles in carcinogenesis, a global discovery-based metabolomics approach is the best way to identify its key activities. The public health significance of this work is substantial because understanding the mechanism of aspirin’s anticancer effects is key to optimizing its use and to the development of novel drugs targeting the metabolic pathways identified.
INSTITUTE
Emory University
DEPARTMENT
School of Medicine
LABORATORY
Clincal Biomarkers Laboratory
LAST_NAME
Uppal
FIRST_NAME
Karan
ADDRESS
615 Michael Street, Atlanta, GA, 30322, USA
EMAIL
kuppal2@emory.edu
PHONE
(404) 727 5027
NUM_GROUPS
3
TOTAL_SUBJECTS
325
NUM_MALES
214
NUM_FEMALES
111
STUDY_COMMENTS
Both pooled colon tissue samples and Clinical Biomarker Laboratory pooled plasma samples were used
Data resource for fully 13C labelled and non-labelled plant tissues (part-I)
STUDY_SUMMARY
LC-MS/MS data files of fully 13C labelled and 12C plant tissues, which were utilized to determine the carbon element number for metabolite characterizations.
Lipidomics of Newborn Heart Tissue Exposed to Excess Maternal Cortisol in Late Gestation (part-1)
STUDY_SUMMARY
Cardiac tissue from newborn hearts from animals exposed to excess maternal cortisol in late gestation and untreated was compared via MS lipidomic analysis
INSTITUTE
University of Florida
DEPARTMENT
Biochemsitry & Molecular Biology
LAST_NAME
Walejko
FIRST_NAME
Jacquelyn
ADDRESS
R3-226 Academic Research Building, Department of Biochemistry and Molecular Biology, PO Box 100245, Gainesville, FL 32610-0245
Microbial depletion and ozone exposure - Lung tissue (part I)
STUDY_SUMMARY
Global biochemical profiles were determined in lung tissue collected from untreated control mice and mice treated for two weeks with untreated drinking water or water containing an antibiotic cocktail (ampicillin, neomycin, metronidazole, and vancomycin), followed by a three hour exposure to ambient air or ozone (2ppm). Sample collection occurred 24 hours post-ozone exposure.
Multi-omics analysis demonstrates unique mode of action of a potent new antimalarial compound, JPC-3210, against Plasmodium falciparum
STUDY_SUMMARY
The increasing incidence of antimalarial drug resistance to the first-line artemisinins, and their combination partner drugs, underpins an urgent need for new antimalarial drugs, ideally with a novel mechanism of action. The recently developed 2-aminomethylphenol, JPC-3210, (MMV 892646) is an erythrocytic schizonticide with potent in vitro antimalarial activity against multidrug-resistant Plasmodium falciparum, low cytotoxicity, potent in vivo efficacy against murine malaria, and favourable preclinical pharmacokinetics, including a lengthy plasma elimination half-life. This study demonstrates the application of a “multi-omics” workflow based on high resolution orbitrap mass spectrometry to investigate the impact of JPC-3210 on biochemical pathways within P. falciparum infected red blood cells. Metabolomics and peptidomics analysis revealed a perturbation in hemoglobin metabolism following JPC-3210 exposure. The metabolomics data demonstrated a depletion in short hemoglobin-derived peptides, while peptidomics analysis showed a depletion in longer hemoglobin-derived peptides. In order to further elucidate the mechanism responsible for inhibition of hemoglobin metabolism, we used in vitro β-hematin polymerisation assays and showed JPC-3210 to be an intermediate inhibitor of β-hematin polymerisation, about 10-fold less potent then the quinoline antimalarials. Furthermore, quantitative proteomics analysis showed that JPC-3210 treatment results in a distinct proteomic signature in comparison to other known antimalarials. Whilst JPC-3210 clustered closely with mefloquine in the metabolomics and proteomics analyses, a key differentiating signature for JPC-3210 was the significant enrichment of parasite proteins involved in regulation of translation. In conclusion, multi-omics studies using high resolution mass spectrometry revealed JPC-3210 to possess a unique mechanism of action involving inhibition of hemoglobin digestion, depletion of DNA replication and synthesis proteins, and elevation of regulators of protein translation. Importantly, this mechanism is distinct from currently-used antimalarials, suggesting that JPC-3210 warrants further investigation as a potentially useful new antimalarial agent.
Correlations between LC-MS/MS-detected Glycomics and NMR-detected Metabolomics in Caenorhabditis (part -I) elegans Development.
STUDY_SUMMARY
This study examines the relationship between glycans, metabolites, and development in C. elegans. Samples of N2 animals were synchronized and grown to five different time points that ranged from L1 to a mixed population of adults, gravid adults, and offspring.
Correlations between LC-MS/MS-detected Glycomics and NMR-detected Metabolomics in Caenorhabditis elegans Development.
STUDY_SUMMARY
This study examines the relationship between glycans, metabolites, and development in C. elegans. Samples of N2 animals were synchronized and grown to five different time points that ranged from L1 to a mixed population of adults, gravid adults, and offspring.
We propose to evaluate microbial and metabolic profiles in baseline and endpoint colonic mucosal, fecal, and serum samples from human patients at risk for CRC and enrolled in a 90-day phase I clinical trial. Patients will receive daily supplementation with calcium alone, a calcium-rich multimineral (Aquamin?), or placebo (maltodextrin) (n=10 per group). We hypothesize that dietary supplementation will correlate with CRC-protective metabolic profiles and that multimineral supplementation will generate more favorable profiles than calcium supplementation alone.
Metabolic responses to PD1 immune-checkpoint blockade and association with therapeutic benefits - Part III
STUDY_SUMMARY
Inhibition of immune-checkpoint targets including PD1 is clinically effective in a variety of cancers. However, only a subset of patients respond and complete response remains uncommon. Given the known role of metabolites in modulating immunity, we sought to understand how individual patients’ metabolic activities adapt to PD1 immune checkpoint blockade and how they associate with therapeutic benefits. To this end, we profiled metabolites in pre- and multiple on-treatment patient serum samples from three independent immunotherapy trials using hydrophilic interaction liquid chromatography coupled with either triple quadrupole MS multiple reaction monitoring or high resolution full scan MS detection. The study consisted of two Phase I trials (CA209-038, NCT01621490; CA209-009, NCT01358721) which included 78 patients with advanced melanoma and 91 patients with metastatic renal cell carcinoma (RCC) treated with nivolumab. To investigate the generalizability of our results, we also analyzed a large randomized Phase III trial (CheckMate 025, NCT01668784) with 743 RCC patients, among which 394 received nivolumab and 349 received everolimus.
Determining secondary metabolite profile of Ilyonectria spp. pathogenic to ginseng root
STUDY_SUMMARY
This experiment aims to ascertain a profile of secondary metabolites produced by Ilyonectria species capable of causing disappearing root rot in ginseng. Ilyonectria isolates were grown on potato dextrose agar for 20 days, then plugs were taken from the cultures and extracted with ethyl acetate. Extracts were analyzed by LC-HRMS and tandem HRMS. Data were analyzed by Principal component analysis and molecular networking with GNPS.
Retargeting azithromycin-like compounds as antimalarials with dual modality
STUDY_SUMMARY
Resistance to front-line antimalarials (artemisinin combination therapies) is spreading, and development of new drug treatment strategies to rapidly kill Plasmodium parasites that cause malaria are urgently needed. Here, we show that azithromycin—a clinically used macrolide antibiotic that targets the bacterium-like ribosome of the malaria parasites apicoplast organelle and causes a slow-killing ‘delayed death’ phenotype—can also rapidly kill parasites throughout the asexual blood-stages of the lifecycle via a ‘quick-killing’ mechanism of action. Investigation of 84 azithromycin analogues revealed nanomolar quick-killing potency that is directed against the very earliest stage of parasite development within red blood cells. Indeed, the best analogue exhibited 1600-fold higher potency than azithromycin for in vitro treatment windows less than 48 hours. Analogues were also effective against the zoonotic malaria parasite P. knowlesi, and against both multi-drug and artemisinin resistant P. falciparum lines. Metabolomic profiles of azithromycin analogue treated parasites were similar to those of chloroquine treated parasites, suggesting that the quick-killing mechanism of action may in part be localised to the parasite food vacuole. However, metabolomic signatures associated with mitochondrial disruption were also present. In addition, unlike chloroquine, azithromycin and analogues were active across blood stage development, including merozoite invasion, suggesting that these macrolides have a multi-factorial mechanism of quick-killing activity. The positioning of functional groups added to azithromycin and its quick-killing analogues altered their activity against bacterial-like ribosomes but had minimal change on quick-killing activity, which suggests that apicoplast-targeting, delayed-death activity can either be preserved or removed independently of quick-killing. Apicoplast minus parasites remained susceptible to both azithromycin and its analogues, further demonstrating that quick-killing is independent of apicoplast-targeting, delayed-death activity. Therefore, development of azithromycin and analogues as antimalarials offers the possibility of targeting parasites through both a quick-killing and delayed death mechanism of action in a single, multifactorial chemotype.
INSTITUTE
Monash University
LAST_NAME
Siddiqui
FIRST_NAME
Ghizal
ADDRESS
381 Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
To perform an untargeted metabolomics analysis of urine samples, matrix blanks and quality control samples. The metabolomics approach will be performed using both reverse phase (RP) and HILIC chromatography (ZHP) separations coupled to high-resolution mass spectrometry. Samples were received and stored at -80°C until processing. In total, 315 samples had sufficient sample volume for metabolomics analysis.
INSTITUTE
Icahn School of Medicine at Mount Sinai
LAST_NAME
Petrick
FIRST_NAME
Lauren
ADDRESS
Department of Environmental Medicine and Public Health, Atran Building 3rd floor, 101st St. between Madison and 5th Ave, New York, New York, 10029, USA
Ontogeny related changes in the pediatric liver metabolome (part-II)
STUDY_SUMMARY
A major challenge in implementing personalized medicine in pediatrics is identifying appropriate drug dosages for children. The majority of drug dosing studies have been based on adult populations, often with modification of the dosing for children based on size and weight. However, the growth and development experienced by children between birth and adulthood represents a dynamically changing biological system, with implications for effective drug dosing, efficacy as well as potential drug toxicity. The purpose of this study was to apply a metabolomics approach to gain preliminary insights into the ontogeny of liver function from newborn to adolescent.
Ontogeny related changes in the pediatric liver metabolome (part-III)
STUDY_SUMMARY
A major challenge in implementing personalized medicine in pediatrics is identifying appropriate drug dosages for children. The majority of drug dosing studies have been based on adult populations, often with modification of the dosing for children based on size and weight. However, the growth and development experienced by children between birth and adulthood represents a dynamically changing biological system, with implications for effective drug dosing, efficacy as well as potential drug toxicity. The purpose of this study was to apply a metabolomics approach to gain preliminary insights into the ontogeny of liver function from newborn to adolescent.
Metabolomics of lung injury after allogeneic hematopoietic cell transplantation - Colon NMR 1D
STUDY_TYPE
preliminary data
STUDY_SUMMARY
Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative treatment option for a variety of hematological malignancies. Interactions between the donor immune system and the patient tissue result in a disease, called GVHD. The pathophysiology of acute GVHD can be hypothesized in three sequential phases: cytokine storm and activation of the antigen-presenting cells (APC), donor T cell activation and effector cell phase. Idiopathic pneumonia syndrome (IPS) is one of the most deleterious complications after allogeneic HCT and is considered not only to be related to conditioning regimen toxicity but also represents an end organ damage caused by allo-reactive T cells, therefore making the lung susceptible to a two-pronged attack, one of which overlaps with GVHD causing other target organ injury. IPS results in mortality of up to 90% of patients. We will use a murine model of IPS and GVHD which is well established in our group, and in which disease evolves either across disparities in major histocompatibility complex (MCH) class I and II, minor histocompatibility antigens (miHags) or both. Metabolomics changes following syngeneic and allogeneic HCT at post-transplantation Days +7 (cytokine storm phase) and Days +42 (cellular effector phase) are compared to baseline wild-type (naive) controls. Prior to analysis, naïve - and experimental mice (N=3 from each group) were fed with semi-liquid diet supplemented with tracers (13C6-glucose ) over 24 hours. At the end of 7 days or 42 days, respectively, feces and aGVHD target organs (colon, liver and lung) were collected from all groups and further processed and / or analyzed. We expect to reveal metabolic pathways affected after allo-HCT which contribute to immune cell mediated lung injury (IPS) and will potentially identify different metabolic pathways in other GVHD target organs.
INSTITUTE
University of Kentucky
DEPARTMENT
MCC
LAST_NAME
Hildebrandt
FIRST_NAME
Gerhard
ADDRESS
CTW-453, 900 South Limestone street. UKY. Lexington, Kentucky-40536
Metabolomics of lung injury after allogeneic hematopoietic cell transplantation - Lung DI-FTMS
STUDY_TYPE
preliminary data
STUDY_SUMMARY
Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative treatment option for a variety of hematological malignancies. Interactions between the donor immune system and the patient tissue result in a disease, called GVHD. The pathophysiology of acute GVHD can be hypothesized in three sequential phases: cytokine storm and activation of the antigen-presenting cells (APC), donor T cell activation and effector cell phase. Idiopathic pneumonia syndrome (IPS) is one of the most deleterious complications after allogeneic HCT and is considered not only to be related to conditioning regimen toxicity but also represents an end organ damage caused by allo-reactive T cells, therefore making the lung susceptible to a two-pronged attack, one of which overlaps with GVHD causing other target organ injury. IPS results in mortality of up to 90% of patients. We will use a murine model of IPS and GVHD which is well established in our group, and in which disease evolves either across disparities in major histocompatibility complex (MCH) class I and II, minor histocompatibility antigens (miHags) or both. Metabolomics changes following syngeneic and allogeneic HCT at post-transplantation Days +7 (cytokine storm phase) and Days +42 (cellular effector phase) are compared to baseline wild-type (naive) controls. Prior to analysis, naïve - and experimental mice (N=3 from each group) were fed with semi-liquid diet supplemented with tracers (13C6-glucose ) over 24 hours. At the end of 7 days or 42 days, respectively, feces and aGVHD target organs (colon, liver and lung) were collected from all groups and further processed and / or analyzed. We expect to reveal metabolic pathways affected after allo-HCT which contribute to immune cell mediated lung injury (IPS) and will potentially identify different metabolic pathways in other GVHD target organs.
INSTITUTE
University of Kentucky
DEPARTMENT
MCC
LAST_NAME
Hildebrandt
FIRST_NAME
Gerhard
ADDRESS
CTW-453, 900 South Limestone street. UKY. Lexington, Kentucky-40536
Metabolomics of lung injury after allogeneic hematopoietic cell transplantation - Lung ICMS
STUDY_TYPE
preliminary data
STUDY_SUMMARY
Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative treatment option for a variety of hematological malignancies. Interactions between the donor immune system and the patient tissue result in a disease, called GVHD. The pathophysiology of acute GVHD can be hypothesized in three sequential phases: cytokine storm and activation of the antigen-presenting cells (APC), donor T cell activation and effector cell phase. Idiopathic pneumonia syndrome (IPS) is one of the most deleterious complications after allogeneic HCT and is considered not only to be related to conditioning regimen toxicity but also represents an end organ damage caused by allo-reactive T cells, therefore making the lung susceptible to a two-pronged attack, one of which overlaps with GVHD causing other target organ injury. IPS results in mortality of up to 90% of patients. We will use a murine model of IPS and GVHD which is well established in our group, and in which disease evolves either across disparities in major histocompatibility complex (MCH) class I and II, minor histocompatibility antigens (miHags) or both. Metabolomics changes following syngeneic and allogeneic HCT at post-transplantation Days +7 (cytokine storm phase) and Days +42 (cellular effector phase) are compared to baseline wild-type (naive) controls. Prior to analysis, naïve - and experimental mice (N=3 from each group) were fed with semi-liquid diet supplemented with tracers (13C6-glucose ) over 24 hours. At the end of 7 days or 42 days, respectively, feces and aGVHD target organs (colon, liver and lung) were collected from all groups and further processed and / or analyzed. We expect to reveal metabolic pathways affected after allo-HCT which contribute to immune cell mediated lung injury (IPS) and will potentially identify different metabolic pathways in other GVHD target organs.
INSTITUTE
University of Kentucky
DEPARTMENT
MCC
LAST_NAME
Hildebrandt
FIRST_NAME
Gerhard
ADDRESS
CTW-453, 900 South Limestone street. UKY. Lexington, Kentucky-40536
Metabolomics of lung injury after allogeneic hematopoietic cell transplantation - Small Intestines ICMS
STUDY_TYPE
preliminary data
STUDY_SUMMARY
Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative treatment option for a variety of hematological malignancies. Interactions between the donor immune system and the patient tissue result in a disease, called GVHD. The pathophysiology of acute GVHD can be hypothesized in three sequential phases: cytokine storm and activation of the antigen-presenting cells (APC), donor T cell activation and effector cell phase. Idiopathic pneumonia syndrome (IPS) is one of the most deleterious complications after allogeneic HCT and is considered not only to be related to conditioning regimen toxicity but also represents an end organ damage caused by allo-reactive T cells, therefore making the lung susceptible to a two-pronged attack, one of which overlaps with GVHD causing other target organ injury. IPS results in mortality of up to 90% of patients. We will use a murine model of IPS and GVHD which is well established in our group, and in which disease evolves either across disparities in major histocompatibility complex (MCH) class I and II, minor histocompatibility antigens (miHags) or both. Metabolomics changes following syngeneic and allogeneic HCT at post-transplantation Days +7 (cytokine storm phase) and Days +42 (cellular effector phase) are compared to baseline wild-type (naive) controls. Prior to analysis, naïve - and experimental mice (N=3 from each group) were fed with semi-liquid diet supplemented with tracers (13C6-glucose ) over 24 hours. At the end of 7 days or 42 days, respectively, feces and aGVHD target organs (colon, liver and lung) were collected from all groups and further processed and / or analyzed. We expect to reveal metabolic pathways affected after allo-HCT which contribute to immune cell mediated lung injury (IPS) and will potentially identify different metabolic pathways in other GVHD target organs.
INSTITUTE
University of Kentucky
DEPARTMENT
MCC
LAST_NAME
Hildebrandt
FIRST_NAME
Gerhard
ADDRESS
CTW-453, 900 South Limestone street. UKY. Lexington, Kentucky-40536
Plasma metabolites of known identity profiled using hybrid nontargeted methods (part-III)
STUDY_SUMMARY
We determined the effect of diet on the composition and metabolic function of human gut microbiome using a controlled feeding experiment with three divergent diets (vegan, omnivore, and an exclusive enteral nutrition diet (EEN) devoid of dietary fiber) in the Food And Resulting Microbial Metabolites (FARMM) study. The study included an antibiotic and polyethylene glycol (Abx/PEG) intervention to dynamically assess the effect of diet on the reconstitution of the gut microbiota and its associated fecal and plasma metabolome. Samples from thirty healthy volunteers between the ages of 18 and 60, 10 mper diet group were analyzed. Self-reported vegans were required to have followed a vegan diet for a minimum of 6 months prior to enrollment. Key exclusion criteria included inflammatory bowel disease, celiac disease, or other chronic intestinal disorders; prior bowel resection surgery other than appendectomy; baseline bowel frequency less than every 2 days or greater than 3 times daily; creatinine concentration greater than the upper limit of normal; diabetes mellitus; currently smoking; body mass index (BMI) <18.5 or >35; and use of antibiotics and probiotics in the prior 6 months. The 10 vegans continued to follow their usual diet as outpatients. All participants completed the Diet History Questionnaire II (DHQ II), a food frequency questionnaire developed by the Risk Factor Monitoring and Methods Branch of the National Cancer Institute. The vegan participants also completed three 24 hour diet recalls with a dietitian in the week prior to starting antibiotics. We randomly assigned the 20 omnivores to receive an omnivore diet or EEN (Modulen® IBD) while residing in an inpatient research unit. The macronutrient composition of Modulen® is protein 36g, fat 47g, and carbohydrate 110g per 1000 Kcal. The two omnivore diets were engineered to have a similar composition to EEN. All the subjects consumed the menu A on day 11 and menu B on days 4 and 14. Diets for omnivores were constructed to provide the expected total calories required per day for the participant to maintain their current weight and were adjusted if there was weight gain or loss of more than 2.5 pounds. On days 6, 7, and 8, inpatients participants received vancomycin 500mg orally every 6 hours and neomycin 1000mg orally every 6 hours. On day 7, participants consumed 4L of polyethylene glycol (PEG) based bowel purgative (GoLytely®). Participants in the omnivore and EEN arms left the inpatient research unit only under the direct supervision of a research staff member. The vegan outpatients reported to the hospital twice on days 6,7 and 8 to receive antibiotics and to consume PEG on day 7. The first stool sample of each day of the inpatient groups was collected, aliquoted and frozen immediately at -80oC. Blood was collected on days 1, 5, 9, 12 and 15 from which plasma aliquots were immediately isolated and frozen at -80oC. The outpatient participants following the vegan diet also had blood collected on days 1, 5, 9, 12, and 15 from which plasma aliquots were immediately isolated and frozen at -80oC. Among these participants, the first stool of the day was collected at home daily and kept on ice packs until it was brought to the research unit where it could be aliquoted and frozen. Samples from vegans were received for aliquoting within 24 hours and on average within 4 hours (Wu et al., 2010). Day 0 stool was not collected from vegans since their diet did not change. The aliquoted amounts for all samples ranged from 500 mg to 1 g. The aliquots were taken from different areas of the sample. Remaining sample was then collected into one residual 50 ml conical tube with a tongue depressor. Any remaining stool was discarded. The University of Pennsylvania Institutional Review Board (IRB) approved the research protocol.
This study explored models predictive of staging and chemotherapy response based on metabolomic analysis of fresh, patient-derived non-small cell lung cancer (NSCLC) core biopsies. Prospectively collected tissue samples before initial treatment were evaluated with high-resolution 2DLC-MS/MS and 13C-glucose enrichment, and the data were comprehensively analyzed with machine learning techniques. Patients were categorized as Disease-Control (DC) [encompassing complete-response (CR), partial-response (PR), and stable-disease (SD)] and Progressive-Disease (PD). Four major types of learning methods (partial least squares discriminant analysis (PLS-DA), support vector machines (SVM), artificial neural networks, and random forests) were applied to differentiate between positive (DC and CR/PR) and poor (PD and SD/PD) responses, and between stage I/II/III and stage IV disease. Models were trained with forward feature selection based on variable importance and tested on validation subsets.
Aromatic amino acid metabolism by the anaerobic gut bacterium Clostridium sporogenes (part-II)
STUDY_SUMMARY
Germ-free MCAD-/- mice or MCAD+/+ controls were mono-colonized with wild-type Clostridium sporogenes. Urine was collected for untargeted LC-QTOF analysis.
Plasma Metabolomic signatures of COPD in a SPIROMICS cohort
STUDY_SUMMARY
The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) (ClinicalTrials.gov Identifier: NCT01969344) includes 2,771 subjects, aged 40-80 years with at least 20 pack-years of smoking. An additional 202 subjects were never smokers. Fasting blood drawn at the enrollment visit using a p100 tube. The first 649 subjects who returned for a 5-7 year visit (Visit 5) were selected for this study. The blood profiled were from the year 1 visit.
A cross-sectional study of functional and metabolic changes during aging through the lifespan in male mice (Liver) part-III
STUDY_SUMMARY
Aging is associated with distinct phenotypical, physiological, and functional changes, leading to the onset of disease and death. The progression of aging-related traits varies widely among individuals, influenced by their environment, lifestyle, and genetics. In this study, we performed physiologic and functional tests cross-sectionally throughout the entire lifespan of male C57BL/6N mice. In parallel, metabolomics analyses in serum, brain, liver, heart, and skeletal muscle were also performed to identify signatures associated with frailty and age-dependent functional decline. Our findings indicate that the decline in gait speed as a function of age and frailty is associated with dramatic increases in the energetic cost of physical activity and decreases in working capacity. Aging and functional decline prompt organs to rewire their substrate selection and metabolism towards redox-related pathways, mainly in liver and heart. Collectively, the data provide a framework to further understand and characterize processes of aging at the individual and organ levels.
INSTITUTE
National Institutes of Health
DEPARTMENT
NIA
LABORATORY
Experimental Gerontology Section and Translational Gerontology Branch
LAST_NAME
de Cabo
FIRST_NAME
Rafael
ADDRESS
251 Bayview Blvd. Suite 100/Room 5C214. Baltimore, MD 21224
Optimization of redox metabolite detection in mammalian cells (part I)
STUDY_SUMMARY
Conditions were tested to optimize number of cells and extraction buffer for the detection of redox reactive metabolites from mammalian cells. Four different extraction buffers were compared. Derivatization of glutathione was explored as a condition as well. This is an independent repeat.
INSTITUTE
Boston Children's Hospital, Harvard Medical School
Application of the redox metabolite detection method for mammalian tissues (part I)
STUDY_SUMMARY
This study was aimed at optimizing redox metabolites detection from mammalian tissues. Three different chromatographic conditions were compared as well as three different extraction conditions. This study was run on LUNA NH2 HILIC chromatography
INSTITUTE
Boston Children's Hospital, Harvard Medical School
Plasma metabolomics of diverse mouse strains infected with Plasmodium chabaudi
STUDY_SUMMARY
To uncover links between metabolism and disease severity in murine malaria, we performed plasma metabolomics via Metabolon on eight inbred, Plasmodium chabaudi-infected mouse strains with diverse disease phenotypes. We sacrificed and collected plasma from >=3 mice per strain per day of acute infection alongside uninfected control mice (approximately days 5-12 depending on mouse strain). We collected disease severity data, e.g. weight loss, liver enzymes, and anemia, concurrently. Together, these data enable 1) a picture of strain-specific and conserved metabolic responses during acute malaria, and 2) a comparison between metabolic responses and disease severity.
Untargeted Metabolomics analysis of A549 treated with 0.5 mM extracellular ATP and 10 ng/ml TGF-beta
STUDY_SUMMARY
Control, 0.5 mM extracellular ATP and 10 ng/ml TGF-beta were used to treated 5 million A549 lung cancer cells in vitro for 2, 6 and 12 hours. The untargeted metabolomics analysis was performed on the cell lysates. The main objective of the study was to determine changes in metabolite abundances in lung cancer after treatment with extracellular ATP and TGF-beta (a known EMT inducer).
INSTITUTE
Ohio University
DEPARTMENT
Biological Sciences
LABORATORY
Dr. Xiaozhuo Chen, Edison biotechnology Institute
LAST_NAME
Shriwas
FIRST_NAME
Pratik
ADDRESS
Room 425, Parks Hall, College of Pharmacy, Ohio State University, Columbus Ohio. 43210
EMAIL
ps774614@ohio.edu
NUM_GROUPS
7
STUDY_TYPE
Untargeted metabolomics analysis in lung cancer cells
The study population includes 844 healthy volunteers of which 183 women and 661 men, with a median age of 43 ± 12 yrs and 40 ± 11 yrs, respectively. The participants in this study were selected from the Tus-cany section of the Italian Association of Blood Donors (AVIS) in the Transfusion Service of the Pistoia Hospital. Plasma samples were obtained according to the Italian guidelines for blood donations. How age and sex influence the human metabolome and lipidome were investigated.
Impact of high intensity and moderate exercise on genomic and metabolic remodeling with age in male mice
STUDY_SUMMARY
How skeletal muscle adapts to different types of exercise intensity with age is not known. Young and old C57BL/6 male mice were assigned to either a sedentary or two types of exercise regimes consisting of daily high-intensity intermittent (HIIT) or moderate intensity continuous (MICT) training for 4 weeks, compatible with the older group’s exercise capacity. Body composition, fasting blood glucose levels, and muscle strength were improved in exercised old mice compared to sedentary controls, while the exercise benefits were absent in younger animals. Skeletal muscle exhibited structural and functional adaptations in response to exercise, as revealed by electron microscopy, OXPHOS assays, respirometry, and PGC-1 and LC3-II protein levels. Transcriptomics analysis of gastrocnemius muscle combined with liver and serum metabolomics unveiled an age-dependent metabolic remodeling provoked by exercise through mitochondrial biogenesis, energy metabolism, and cellular plasticity. These results are supportive of a tailored exercise prescription approach with the goal of improving health and ameliorating age-associated loss of muscle mass, strength and function in the elderly.
INSTITUTE
National Institutes of Health
DEPARTMENT
Experimental Gerontology Section and Translational Gerontology Branch, NIA
LAST_NAME
de Cabo
FIRST_NAME
Rafael
ADDRESS
251 Bayview Blvd. Suite 100/Room 5C214. Baltimore, MD 21224
Metabolic Markers of Methotrexate Response in Juvenile Idiopathic Arthritis
STUDY_TYPE
Clinical
STUDY_SUMMARY
Plasma from children with juvenile idiopathic arthritis collected pre-treatment and following 3 months of treatment with methotrexate were submitted for metabolomic profiling to the NIH West Coast Metabolomics Center.
The pregnancy metabolome from a multi-ethnic pregnancy cohort
STUDY_SUMMARY
The PRogramming of Intergenerational Stress Mechanisms (PRISM) study is an urban, ethnically diverse pregnancy cohort that was designed to study a range of chemical and non-chemical stressors in relation to maternal health, pregnancy outcomes, and child development. Pregnant women were enrolled from Boston and New York City hospitals and affiliated prenatal clinics beginning in 2011. Eligibility criteria included English or Spanish-speaking, over 18 years of age at enrollment, and singleton pregnancy. Exclusion criteria included HIV+ status or self-reported drinking ≥7 alcoholic drinks per week before pregnancy or any alcohol after pregnancy recognition
The metabolomic resetting effect of FG4592 in AKI to CKD transition-day 21
STUDY_SUMMARY
C57BL/6 mice were anesthetized using isoflurane. UIR was induced by clamping the right renal pedicle for 45 minutes and then releasing it to allow reperfusion, leaving the left kidney intact. Sham treated mice served as controls. Each mouse was located supine on a thermostatic pad (37 °C) to maintain its body temperature throughout the whole process. After 3 days of recovery, the mice received a daily intraperitoneal (i.p.) injection of FG4592 (10 mg/kg) or vehicle for 18 consecutive days. After treatment, the mice were sacrificed. Non-target metabolomics analysis was carried out using the kidney tissues of mice sacrificed at day 21 after UIR.
Effects of GP130 Antagonism on Right Ventricular Metabolism in Monocrotaline Rats
STUDY_SUMMARY
We used global metabolomics profiling to evaluate right ventricular metabolism in control, monocrotaline rats treated with vehicle, and monocrotaline rats treated with SC144 (GP130 antagonists).
Metabolomics analysis of multiple samples on Agilent 6546-Part 2
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
Metabolomics analysis of multiple samples from mouse, trying to annotate the metabolites in them. Agilent 6546 LC-QTOF was used for metabolomics detection.
INSTITUTE
Dalian Institute Of Chemical Physics
LABORATORY
Laboratory of High Resolution Separation/Analysis and Metabonomics
LAST_NAME
Zheng
FIRST_NAME
Fujian
ADDRESS
No. 457 Zhongshan Road, Shahekou District, Dalian, Liaoning Province, China
The study comprehends two consecutive LC-QqQ/MS analyses of Babesia divergens merozoite extracts isolated from B. divergens infected red blood cell cultures performed under identical chromatographic conditions and targeting distinct transitions corresponding to metabolites from specific pathways including the glycolysis, the TCA cycle, the pentose phosphate pathway, purine and pyrimidine biosynthesis and amino acid metabolism.
Mitochondrial-Derived Compartments Facilitate Cellular Adaptation to Amino Acid Stress
STUDY_SUMMARY
Amino acids are essential building blocks of life. However, increasing evidence suggests that elevated amino acids cause cellular toxicity associated with numerous metabolic disorders. How cells cope with elevated amino acids remains poorly understood. Here, we show that a previously identified cellular structure, the mitochondrial-derived compartment (MDC), functions to protect cells from amino acid stress. In response to amino acid elevation, MDCs are generated from mitochondria, where they selectively sequester and deplete SLC25A nutrient carriers and their associated import receptor Tom70 from the organelle. Generation of MDCs promotes amino acid catabolism, and their formation occurs simultaneously with transporter removal at the plasma membrane via the multi-vesicular body (MVB) pathway. Combined loss of vacuolar amino acid storage, MVBs and MDCs renders cells sensitive to high amino acid stress. Thus, we propose that MDCs operate as part of a coordinated cell network that facilitates amino acid homoeostasis through post-translational nutrient transporter remodeling.
INSTITUTE
University of Utah School of Medicine
DEPARTMENT
Biochemistry
LABORATORY
Hughes Lab
LAST_NAME
Hughes
FIRST_NAME
Adam
ADDRESS
15 N Medical Drive East, RM 4100, Salt Lake City, UT, 84112, USA
Sublytic membrane attack complex drives glycolysis and mitochondrial dysfunction with inflammatory consequences in human monocyte-derived macrophages
STUDY_SUMMARY
The terminal stage in the complement activation pathways, the membrane attack complex (MAC), is upregulated in diabetic and rheumatoid arthritis patients, contributing pathologically by increasing inflammation. Previous research has highlighted that a sublytic dose of MAC can initiate NLRP3 inflammasome activation via calcium influx and loss of mitochondrial membrane potential. Here, we show that sublytic concentrations of MAC mediate a previously undescribed perturbation in cellular energy metabolism in human monocyte-derived macrophages, by phenotypic skewing towards glycolysis and upregulation of glycolysis-promoting genes. Sublytic MAC concentrations drive mitochondrial dysfunction, characterised by a fragmented mitochondrial morphology, loss of maximal respiratory response, depleted mitochondrial membrane potential as well as increased mitochondrial reactive oxygen species production. The consequences of these alterations in glycolytic metabolism and mitochondrial dysfunction lead to NLRP3 inflammasome activation, driving gasdermin D formation and IL-18 release. This novel link between sublytic MAC and immunometabolism, with direct consequences for downstream inflammatory processes, is important for development of novel therapeutics for areas where MAC may mediate disease.
Fungal consortium of two Beauveria bassiana strains increases their virulence, growth, and resistance to stress: a metabolomic approach.
STUDY_TYPE
Untargeted Metabolomics
STUDY_SUMMARY
Entomopathogenic fungi have been successfully used to control agricultural pests. They infect insects by coming into direct contact with their cuticle or when feeding on contaminated leaves or fruits. After contact with the insect, the entomopathogenic fungus penetrates its body cavity, where it grows and colonizes it from within, causing its death The use of two or more microorganisms in a microbial consortium has been increasingly applied in the biological control of diseases and pests. Beauveria bassiana is one of the most widely studied fungal species in biological control, yet little is known about its role in fungal consortiums. In a previous study, our group found that a consortium formed by two strains of B. bassiana had significantly greater biocontrol potential against the polyphagous caterpillars Duponchelia fovealis (Lepidoptera: Crambidae) than either strain on its own. Despite recent developments and growing efforts to better understand fungal metabolism and metabolites, much remains unknown. Metabolomics therefore represents an important field for evaluating the metabolites produced or modified by an organism or its relationship with the environment. In the present study, we aim to use untargeted metabolomics with gas and liquid chromatography coupled to mass spectrometers (GC-MS and LC-MS/MS) to evaluate the metabolic alterations caused by the co-cultivation of these strains and to correlate the metabolites produced by this consortium with the increased mortality in D. fovealis observed previosly.
INSTITUTE
Universidade Federal do Paraná
DEPARTMENT
Patologia Básica
LABORATORY
Laboratório de Microbiologia e Biologia Molecular
LAST_NAME
Stuart
FIRST_NAME
Andressa
ADDRESS
Av. Cel. Francisco Heráclito dos Santos, 100, 81530000, Jardim das Américas, Curitiba, Paraná, Brasil
Plasma Metabolome Normalization in Rheumatoid Arthritis following initiation of Methotrexate and the Identification of Metabolic Biomarkers of Efficacy
STUDY_TYPE
Clinical
STUDY_SUMMARY
Methotrexate (MTX) efficacy in the treatment of rheumatoid arthritis (RA) is variable and unpredictable, resulting in a need to identify biomarkers to guide drug therapy. This study evaluates changes in the plasma metabolome associated with response to MTX in RA with the goal of understanding the metabolic basis for MTX efficacy towards the identification of potential metabolic biomarkers of MTX response.
Metabolomic Fingerprinting of Human High Grade Serous Ovarian Carcinoma Cell Lines
STUDY_SUMMARY
Focusing on defining the metabolomic basis of intratumoral heterogeneity in ovarian cancer, the metabolic diversity of a panel of high grade serous ovarian carcinoma (HGSOC) cell-lines we investigated using a metabolomics platform that interrogate 731 compounds. Metabolic fingerprinting followed by 2-dimensional and 3-dimensional principal component analysis defined the heterogeneity of the HGSOC cells and clustered them into five distinct metabolic groups. An overall increase in the metabolites associated with aerobic glycolysis and phospholipid metabolism were observed in the majority of the cancer cells. A preponderant increase in the levels of metabolites involved in trans-sulfuration and glutathione synthesis was also observed. Subsets of HGSOC cells showed an increase in the levels of 5-Hydroxytryptamine, gamma-aminobutyric acid, or glutamate, pointing to their potential role as oncometabolites. In summary, our results identify increased glycolysis, phospholipid metabolism and amino acid metabolism with the resultant increase in the levels of 5-Hydoxytryptamine, GABA, and Glutamate as metabolomic correlates underlying the heterogeneity of ovarian cancer cell lines.
INSTITUTE
University of Oklahoma Health Sciences Center
DEPARTMENT
Cell Biology
LABORATORY
Danny N Dhanasekaran
LAST_NAME
Jayaraman
FIRST_NAME
Muralidharan
ADDRESS
975 NE 10th street, BRC1470, Oklahoma City, Oklahoma, 73104, USA
Metabolomics of the interaction between a consortium of entomopathogenic fungi and their target insect: mechanisms of attack and survival
STUDY_TYPE
Untargeted Metabolomics
STUDY_SUMMARY
One of the most concerning pests that attack strawberries in Brazil is Duponchelia fovealis, a non-native moth with no registered control methods to date. Our group recently observed that a fungal consortium formed by two strains of Beauveria bassiana increased the mortality of D. fovealis more than inoculation with each strain on its own. However, the molecular interaction between the fungal consortium and the caterpillars is unknown, raising several questions about the enhanced pest control observed. Furthermore, concerns over the emergency of resistance and the selection for resistance to chemical and biological products that are constantly applied in agriculture highlight the need for careful examination of novel pest control methods. Thus, in this work, we sought to pioneer the evaluation of the molecular interaction between a fungal consortium of B. bassiana and D. fovealis caterpillars. We aimed to understand the biocontrol process involved in this interaction and the defense system of the caterpillar. Therefore, seven days after D. fovealis caterpillars were inoculated with the B. bassiana consortium, the dead and surviving caterpillars were analyzed using GC-MS and LC-MS/MS.
INSTITUTE
Universidade Federal do Paraná
DEPARTMENT
Patologia Básica
LABORATORY
Laboratório de Microbiologia e Biologia Molecular
LAST_NAME
Katiski da Costa Stuart
FIRST_NAME
Andressa
ADDRESS
Av. Cel. Francisco Heráclito dos Santos, 100, Curitiba, Paraná, 81530-000, Brazil
Isotope tracing analysis of stress erythroid progenitors
STUDY_SUMMARY
Isotope tracing analysis to study the intracellular metabolic changes of progenitors during the expansion stage of stress erythropoiesis and assess the effect of 1400w treatment.
INSTITUTE
Pennsylvania State University
DEPARTMENT
Veterinary and Biomedical Sciences
LABORATORY
Paulson Lab
LAST_NAME
Ruan
FIRST_NAME
Baiye
ADDRESS
228 AVBS Building Shortlidge Road University Park, PA 16802
Untargeted primary metabolite profiling in Arabidopsis thaliana
STUDY_SUMMARY
The goal of this project is to compare the primary metabolite profile in different tissue types of the model plant Arabidopsis thaliana. Specifically, plants were grown hydroponically under the long-day (16hr light/day) condition at 21C. Tissue samples, including leaves, inflorescences, and roots were harvest 4 1/2 weeks post sowing. Untargeted primary metabolites profiling was carried out using GCTOF.
Untargeted metabolite analysis was performed on a Thermo Orbitrap IDX Tribrid MS to understand changes in metabolites due to COVID severity.
INSTITUTE
University of Virginia
DEPARTMENT
1Department of Biochemistry & Molecular Genetics; School of Medicine Core Facilities; Department of Microbiology, Immunology, and Cancer Biology; Department of Biomedical Engineering
LABORATORY
Biomolecular Analysis Facility, Univ of Virginia School of Medicine
LAST_NAME
Wase
FIRST_NAME
Nishikant
ADDRESS
Biomolecular Analysis Facility, Pinn Hall Room No 1105B
Algal bacterial interactions in phycosphere microbial communities have important implications for the stability and productivity of algal biofuel systems, and algal metabolites are important mediators of those interactions. We characterized exometabolites and cell associated metabolites from the model diatom Phaeodactylum tricornutum across different growth stages.
Defining the mammalian coactivation of hepatic 12-hour clock and lipid metabolism
STUDY_SUMMARY
The 12-hour clock coordinates lipid homeostasis, energy metabolism and stress rhythms via the transcriptional regulator XBP1. However, the biochemical and physiological basis for integrated control of the 12-hour clock and diverse metabolic pathways remains unclear. Here, we show that steroid receptor coactivator SRC-3 coactivates XBP1 transcription and regulates hepatic 12-hour cistrome and gene rhythmicity. Mice lacking SRC-3 show abnormal 12-hour rhythms in hepatic transcription, metabolic functions, systemic energetics, and rate-limiting lipid metabolic processes including triglyceride, phospholipid and cardiolipin pathways. Notably, 12-hour clock coactivation is not only preserved, with its cistromic activation priming ahead of the zeitgeber cue of light, but concomitant with rhythmic remodeling in the absence of food. These findings reveal that SRC-3 integrates the mammalian 12-hour clock, energy metabolism, and membrane and lipid homeostasis, and demonstrates a role for the 12-hour clock machinery as an active transcriptional mechanism in anticipating physiological and metabolic energy needs and stresses.
Predicting dying: a study of the metabolic changes and the dying process in patients with lung cancer
STUDY_TYPE
Observational study
STUDY_SUMMARY
Background: Accurately recognising that a person may be dying is central for improving their experience of care. Yet recognising dying is difficult and predicting dying frequently inaccurate. Methods: Serial urine samples from patients (n=112) with lung cancer were analysed using high resolution untargeted mass spectrometry. ANOVA and volcano plot analysis demonstrated metabolites that changed in the last weeks of life. Further analysis identified potential biological pathways affected. Cox lasso logistic regression was engaged to develop a multivariable model predicting the probability of survival within the last 30 days of life. Results: In total 124 metabolites changed. ANOVA analysis identified 93 metabolites and volcano plot analysis 85 metabolites. 53 metabolites changed using both approaches. Pathways altered in the last weeks included those associated with decreased oral intake, muscle loss, decreased RNA and protein synthesis, mitochondrial dysfunction, disrupted β-oxidation and one carbon metabolism. Epinephrine and cortisol increased in the last 2 weeks and week respectively. A model predicting time to death using 7 metabolites had excellent accuracy (AUC= 0.86 at day 30, 0.88 at day 20 and 0.85 at day 10) and enabled classification of patients at low, medium and high risk of dying on a Kaplan-Meier survival curve. Conclusions: Metabolomic analysis identified metabolites and their associated pathways that change in the last weeks and days of life in patients with lung cancer. Prognostic tests based on the metabolites identified have the potential to change clinical practice and improve the care of dying patients.
INSTITUTE
University of Liverpool Institute of Life Course & Medical Sciences
LAST_NAME
Norman
FIRST_NAME
Brendan
ADDRESS
William Henry Duncan Building, 6 West Derby Street, Liverpool, UK. L7 8TX
Plasma Metabolomic signatures of COPD in a SPIROMICS cohort
STUDY_TYPE
Observational Cohort
STUDY_SUMMARY
Plasma Metabolomic signatures of COPD in a SPIROMICS cohort The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) (ClinicalTrials.gov Identifier: NCT01969344) includes 2,771 subjects, aged 40-80 years with at least 20 pack-years of smoking. An additional 202 subjects were never smokers. Fasting blood drawn at the enrollment visit using a p100 tube. The first 648 subjects who returned for a 5-7 year visit (Visit 5) were selected for this study. The blood profiled were from the year 1 visit.
The NIH sponsored multicenter Genetic Epidemiology of COPD (COPDGene (ClinicalTrials.gov Identifier: NCT01969344) study was approved and reviewed by the institutional review board at all participating centers (1). All study participants provided written informed consent. This study enrolled 10,198 non-Hispanic white (NHW) and African American (AA) individuals from January 2008 until April 2011 (Phase 1) who were aged 45-80 with ≥10 pack-year smoking history and no exacerbations for greater than 30 days. In addition, 465 age and gender matched healthy individuals with no history of smoking were enrolled as controls (mostly at Phase 2). From July 2013 to July 2017, 5,697 subjects returned for an in-person 5-year visit. Each in-person visit included spirometry before and after albuterol, quantitative CT imaging of the chest, and blood sampling. From two clinical centers (National Jewish Health and University of Iowa) 1,136 subjects (1,040 NHW, 96 AA) participated in an ancillary study in which they provided fresh frozen plasma collected using an 8.5 ml p100 tube (Becton Dickinson) at Phase 2.
Commensal intestinal microbiota regulates host luminal proteolytic activity and intestinal barrier integrity through β-glucuronidase activity (Part 2)
STUDY_SUMMARY
Proteases constitute the largest enzyme gene family in vertebrates with intracellular and secreted proteases having critical roles in cellular and organ physiology. Intestinal tract contains diverse set of proteases mediating digestion, microbial responses, epithelial and immune signaling. Transit of chyme through the intestinal tract results in significant suppression of proteases. Although endogenous protease inhibitors have been identified, the broader mechanisms underlying protease regulation in the intestinal tract remains unclear. The objective of this study was to determine microbial regulation of proteolytic activity in intestinal tract using phenotype of post-infection irritable bowel syndrome, a condition characterized by high fecal proteolytic activity. Proteases of host pancreatic origin (chymotrypsin like pancreatic elastase 2A, 3B and trypsin 2) drove proteolytic activity. Of the 14 differentially abundant taxa, high proteolytic activity state was characterized by complete absence of the commensal Alistipes putredinis. Germ free mice had very high proteolytic activity (10-fold of specific-pathogen free mice) which dropped significantly upon humanization with microbiota from healthy volunteers. In contrast, high proteolytic activity microbiota failed to inhibit it, a defect that corrected with fecal microbiota transplant as well as addition of A. putredinis. These mice also had increased intestinal permeability similar to that seen in patients. Microbiota β-glucuronidases mediate bilirubin deconjugation and unconjugated bilirubin is an inhibitor of serine proteases. We found that high proteolytic activity patients had lower urobilinogen levels, a product of bilirubin deconjugation. Mice colonized with β-glucuronidase overexpressing E. coli demonstrated significant inhibition of proteolytic activity and treatment with β-glucuronidase inhibitors increased it. The findings establish that specific commensal microbiota mediates effective inhibition of host pancreatic proteases and maintains intestinal barrier function through the production of β-glucuronidases. This suggests an important homeostatic role for commensal intestinal microbiota.
Towards a mechanistic understanding of patient response to neoadjuvant SBRT with anti-PDL1 in human HPV-unrelated locally advanced HNSCC: Phase I/Ib trial results (Part 2)
STUDY_SUMMARY
Five-year survival for HPV-unrelated head and neck squamous cell carcinomas (HNSCC) remains below 50%. We assessed the safety of administering combination hypofractionated stereotactic body radiation therapy (SBRT) with anti-PDL-1 neoadjuvantly followed by adjuvant anti-PDL-1 with standard of care therapy (n=21). The primary endpoint of the study was safety, which was met. Secondary endpoints included radiographic, pathologic, and objective response, locoregional control (LRC), progression-free survival (PFS), and overall survival (OS). Among evaluable patients at early median follow-up of 16 months (448 days), OS was 83.3%, LRC and PFS were 83.3%, and major pathological response (MPR) or complete response (CR) was 75%. Circulating CD8/Treg ratio, CD4 effector memory T cells, and TCR repertoire emerged as biologic correlates of response to therapy. Using high-dimensional multi-omics and spatial data as well as biological correlatives pre- and post-treatment, three major changes were noted in responders within the tumor microenvironment (TME) (and within the blood) post-treatment: 1) an increase in effector T cells; 2) a decrease in immunosuppressive cells; and 3) an increase in antigen presentation. Non-responders appeared to fail due to a lack of one of these three identified steps needed for priming and maintaining activation of T cells. Multiple correlates for response, along with subsets of non-responders that may benefit from additional or alternative immunotherapies, were identified. This treatment is being tested in an ongoing phase II trial with a similar design, where we hope to confirm and expand on our understanding of the mechanisms underlying resistance to therapy.
INSTITUTE
University of Colorado Denver
LAST_NAME
Culp-Hill
FIRST_NAME
Rachel
ADDRESS
12801 E 17th Ave L18-9403D, Aurora, Colorado, 80045, USA
GCN2 regulates mitochondrial OXPHOS in HSPCs under proliferation conditions.
STUDY_SUMMARY
Our results revealed that among all 273 metabolites detected, the levels of metabolites involved in glucose-related glycolysis and gluconeogenesis were elevated in GCN2 deleted HSPCs. Moreover, GCN2 deletion specifically increased mitochondrial OXPHOS and suppressed anaerobic glycolysis in HSPCs.
Amino acids and TCA substrates in hematopoietic cells (Part1)
STUDY_SUMMARY
This study uses [13C,15N] labeled amino acids to study the amino acid consumption and their catabolism into tricarboxylic acid cycle substrates in hematopoietic stem cells, hemopoietic progenitors, and differentiated hematopoietic cells under different conditions, such as homeostasis and proliferation and with drug treatment.
Amino acids and TCA substrates in hematopoietic cells (Part2)
STUDY_SUMMARY
This study uses [13C,15N] labeled amino acids to study the amino acid consumption and their catabolism into tricarboxylic acid cycle substrates in hematopoietic stem cells, hemopoietic progenitors, and differentiated hematopoietic cells under different conditions, such as homeostasis and proliferation and with drug treatment.
Amino acids and TCA substrates in hematopoietic cells (Part3)
STUDY_SUMMARY
This study uses [13C,15N] labeled amino acids to study the amino acid consumption and their catabolism into tricarboxylic acid cycle substrates in hematopoietic stem cells, hemopoietic progenitors, and differentiated hematopoietic cells under different conditions, such as homeostasis and proliferation and with drug treatment.
Amino acids and TCA substrates in hematopoietic cells (Part4)
STUDY_SUMMARY
This study uses [13C,15N] labeled amino acids to study the amino acid consumption and their catabolism into tricarboxylic acid cycle substrates in hematopoietic stem cells, hemopoietic progenitors, and differentiated hematopoietic cells under different conditions, such as homeostasis and proliferation and with drug treatment.
Metabolic effect of the loss of mitochondrial-specific aspartyl-tRNA synthetase Das2 on mouse intestinal epithelial cells
STUDY_SUMMARY
We analysed the intestinal epithelial cell (IEC) from Dars2 fl/fl ; VillinCreERT2 tg/wt mice (n=15) and and Dars2 fl/fl ; VillinCreERT2 wt/wt mice (n=9) at 8 days upon tamoxifen injection to assess the metabolic effect of Das2 loss. Isolated IECs were divided into three technical replicates (n=69) and analysed with two analytical repeats (n=138).
Metabolic profiling at COVID-19 onset shows disease severity and sex-specific dysregulation
STUDY_SUMMARY
In this study CE-MS and GC-MS based metabolomics was used to analyze COVID-19 disease. In total, 144 individuals classified as healthy, asymptomatic/mils, moderate and severe according to the highest COVID-19 severity status, were analyzed.
The metabolomics effect of Foxa2 knockdown on FH-deficient cells
STUDY_SUMMARY
To assess whether there is a functional convergence between the two proteins, we performed metabolomics on Fh1fl/fl, Fh1-/-CL1 and Fh1-/-CL19 cells treated with either siNT or siFoxa2. 5 x 104 Fh1fl/fl, 1 x 105 Fh1-/-CL1 and 1 x 105 Fh1-/-CL19 cells were plated the onto 6-well plate and reverse transfected with siRNA. Before extraction, cells were counted using a separate counting plate. There are a total of 30 samples prepared from three cell lines and 6 biological conditions.
Analysis of metabolite relative abundance in blood plasma from 316 individuals with trisomy 21 (T21, Down syndrome) and 103 euploid controls. This dataset is part of the Human Trisome Project run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/
INSTITUTE
University of Colorado Denver
LABORATORY
PIs - Joaquin Espinosa and Angelo D'Alessandro
LAST_NAME
Haines
FIRST_NAME
Julie
ADDRESS
12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA
Estrogen receptor a deficiency in cardiac myocytes reprograms heart-derived extracellular vesicle proteome and induces obesity in female mice (Part 2)
STUDY_SUMMARY
Dysregulation of ERα has been linked with increased metabolic and cardiovascular disease risk. Uncovering the impact of ERα deficiency in specific tissues has implications for understanding the role of ERα in normal physiology and disease, the increased disease risk in postmenopausal women, and the design of tissue-specific ERα-based therapies for a range of pathologies including cardiac disease and cancer. Cardiac myocyte-specific ER knockout mice (ERαHKO) were generated to assess the role of ERα in the heart. Female ERαHKO mice displayed a modest cardiac phenotype, but unexpectedly, the most striking phenotype was obesity in female ERαHKO but not male ERHKO mice. In female ERαHKO mice we identified cardiac dysfunction, mild glucose and insulin intolerance, and reduced ERα gene expression in skeletal muscle and white adipose tissue (WAT). Gene expression, protein, lipidomic and metabolomic analyses showed evidence of contractile and/or metabolic dysregulation in heart, skeletal muscle and WAT. We also show that extracellular vesicles (EVs) collected from the perfusate of isolated hearts from female ERαHKO mice have a distinct proteome, and these EVs have the capacity to reprogram the proteome of a skeletal muscle cell including proteins linked with ERα, fatty acid regulation, lipid metabolism and mitochondrial function. This study uncovers a cardiac-initiated and sex-specific cardiometabolic phenotype that is regulated by ERα.
INSTITUTE
Baker Heart and Diabetes Institute
DEPARTMENT
Discovery and Preclinical Science
LABORATORY
Cardiac Hypertrophy
LAST_NAME
Tham
FIRST_NAME
Yow Keat
ADDRESS
75 Commercial Rd, Melbourne, Victoria, 3004, Australia
Application of Artificial Intelligence to Plasma Metabolomics Profiles to Predict Response to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer
STUDY_SUMMARY
Summary: There is a need for biomarkers predictive of response to neoadjuvant chemotherapy (NACT) in triple-negative breast cancer (TNBC). We previously obtained evidence that a polyamine signature in the blood is associated with TNBC development and progression. In this study, we evaluated whether plasma polyamines and other metabolites may identify TNBC patients who are unlikely to respond to NACT. Pre-treatment plasma levels of acetylated polyamines were elevated in TNBC patients that had moderate to extensive tumor burden (RCB-II/III) following NACT compared to those that achieved a complete pathological response (pCR/RCB-0) or had minimal residual disease (RCB-I). We further applied artificial intelligence to comprehensive metabolic profiles to identify additional metabolites associated with treatment response. A deep learning model (DLM) consisting of two polyamines as well as nine additional metabolites was developed for improved prediction of RCB-II/III. The DLM has potential clinical value for identifying TNBC patients who are unlikely to respond to NACT and who may benefit from other treatment modalities.
Hypoxia promotes osteogenesis via regulating the acetyl-CoA-mediated mito-nuclear communication.
STUDY_SUMMARY
Bone-mesenchymal stem cells (MSCs) reside in a hypoxic niche that maintains their differentiation potential. Although the role of hypoxia (low oxygen concentration) in the regulation of stem cell function has been previously reported, with normoxia (high oxygen concentration) leading to impaired osteogenesis, the molecular events triggering changes in stem cell fate decisions in response to high oxygen remain elusive. Here, we study the impact of normoxia on the mito-nuclear communication with regards to stem cell differentiation. We show that normoxia-cultured MSCs undergo profound transcriptional alterations which cause irreversible osteogenesis defects. Mechanistically, high oxygen promotes chromatin compaction and histone hypo-acetylation, particularly on promoters and enhancers of osteogenic genes. Although normoxia induces metabolic rewiring resulting in high acetyl-CoA levels, histone hypo-acetylation occurs due to trapping of acetyl-CoA inside mitochondria, owing to lower CiC activity. Strikingly, restoring the cytosolic acetyl-CoA pool remodels the chromatin landscape and rescues the osteogenic defects. Collectively, our results demonstrate that the metabolism-chromatin-osteogenesis axis is heavily perturbed in response to high oxygen and identify CiC as a novel, oxygen-sensitive regulator of the MSC function.
Longitudinal fecal metabolomic profiles from mothers and their infants in the EDIA study
STUDY_SUMMARY
In a cohort consisting of 32 mother-infant dyads, we profiled the fecal metabolome at birth and at 3 and 6 months of infant age. Metagenomes from the same samples were also generated.
Metabolomics and metagenomics of pediatric obesity (Serum)
STUDY_SUMMARY
Pediatric obesity has grown as important global health problem in the world. The pediatric obesity affects all the organs and it is closely linked to risks of metabolic diseases such as diabetes, cardiovascular disease, and mental disease. However, the mechanism of both the pediatric obesity and treatment of the obesity remains unclear. Therefore, we investigated metabolomic pathways related to the pediatric obesity and the treatment through metabolomics and metagenomics approaches.
INSTITUTE
Seoul National University College of Medicine and Hospital
LAST_NAME
Lee
FIRST_NAME
Yujin
ADDRESS
101, Daehak-ro, Jongno-gu, Seoul, Republic of Korea
Intermittent fasting induces rapid hepatocyte proliferation to maintain the hepatostat
STUDY_SUMMARY
Nutrient availability fluctuates in most natural populations, forcing organisms to undergo periods of fasting and re-feeding. It is unknown how dietary change influences liver homeostasis. Here, we show that a switch from ad libitum feeding to intermittent fasting (IF) promotes rapid hepatocyte proliferation. Mechanistically, IF- induced hepatocyte proliferation is driven by the combined action of intestinally produced, systemic endocrine FGF15 and localized WNT signaling. IF proliferation re-establishes a constant liver-to-body-mass ratio during periods of fasting and re-feeding, a process termed the hepatostat. This study provides the first example of dietary influence on adult hepatocyte proliferation, and challenges the widely held view that liver tissue is mostly quiescent unless chemically or mechanically injured.
Stage 41 tadpoles were injected with 4 nmol of the glycolysis inhibitor, 2-deoxyglucose (2DG), or a tracer control to evaluate consequences of inhibition on metabolites 24 hours after treatment began. Similarly, tadpoles were incubated in DMSO control or 1 of 2 G6PD inhibitors (Dehydroepiandrosterone and g6pdi), to similarly assess the consequences of inhibiting the pentose phosphate pathway. We find that inhibition of glucose metabolism with 2DG results in a decrease in downstream glycolytic intermediates, confirming a reduction in activity of this pathway. G6PD inhibition was not as clear as changes were less consistent across treatments and downstream metabolites did not behave in a coordinated way, though impacts on other metabolic processes by these inhibitors may be fruitful for exploring how they perturb metabolism in the tadpoles.
INSTITUTE
University of Washington
LAST_NAME
Patel
FIRST_NAME
Jeet
ADDRESS
1705 NE Pacific St., HSB J-Wing, J405, Seattle, Washington, 98195, USA
To identify changes in metabolites that correlate with progression of tail regeneration, we collected a timecourse of tissues containing 250 um of tissue anterior to the wound site as well as all regenerating tissue at 0, 3, and 24 hours post amputation. We also collected the posterior 500 um of the developing tail to represent the metabolic profile of uninjured tissues. Tissues from 25 individuals were collected and frozen in more than 5-8 minutes per replicate before processing as in the methods. 104 metabolites were identified in these samples and relative peak intensities were compared to identify changes in abundance corresponding to regeneration. 42 differentially abundant metabolites were found using MetaboAnalyst, the majority of which were increased 24 hours post amputation. Further investigation of these 24 hours post amputation enriched metabolites revealed that these metabolites were largely associated with increased growth and nucleotide metabolism. This finding is in line with the growth of new tissue seen at this timepoint and also suggests that generation of nucleotides are a major factor in sustaining this growth.
INSTITUTE
University of Washington
LAST_NAME
Patel
FIRST_NAME
Jeet
ADDRESS
1705 NE Pacific St., HSB J-Wing, J405, Seattle, Washington, 98195, USA
Metabolomics study comparing SCAP KO and WT B cells
STUDY_TYPE
Purified mouse B cells, stimulated ex vivo
STUDY_SUMMARY
Splenic B cells isolated from SCAP+/+ CD19-Cre (WT) and SCAPfl/fl CD19-Cre (KO) mice were stimulated with LPS or anti-CD40 for 24 and 48 hours. Cells were then analyzed by metabolomics. Metabolomics reveals global metabolic changes in SCAP deficient B cells.
Metabolome and transcriptome analysis of oral mucosa of HIV+ patients reveal a role for polyamine metabolic pathway in T cell dysfunction
STUDY_SUMMARY
Metabolic changes of immune cells contribute to both physiological and pathophysiological outcomes of immune reactions. How viruses alter the metabolic states of mucosal T cells and the precise mechanisms underlying the persisting immune dysfunction during chronic viral infections are key questions that have not been fully addressed. Here, by comparing transcriptome and salivary metabolome profiles of the uninfected individuals and people living with HIV (PLWH) on treatment, we found a role of polyamine metabolism in immune perturbations of the oral mucosa of HIV+ patients. Flow cytometry analysis confirmed the higher expression of ornithine decarboxylase (ODC-1) and eukaryotic translation initiation factor 5A (EIF5A), the polyamine metabolism intermediates in CD4+ T cells in PLWH. Mechanistic studies using an in vitro human tonsil organoid infection model revealed that HIV infection of activated T cells also resulted in increased polyamine synthesis, which was dependent on the activities of caspase-1, IL-1β, and ODC-1. HIV-1 also led to elevated dysfunctional regulatory T cells (TregDys) /Thelper 17 (Th17) cell ratios as well as heightened expression of ODC-1, EIF5A, and hypusinated EIF5A. Blockade of caspase-1, ODC-1, and EIF5A hypusination and not HIF-1⍺ or NLRP3 reversed the frequency of TregDys showing the direct impact of polyamine pathway in Treg dysfunction during HIV-1 infection. The addition of exogenous polyamines increased TregDys percentages independent of HIV-1 infection in vitro. Finally, oral mucosal TregDys/Th17 ratios and CD4 hyperactivation positively correlated with the increases in salivary putrescine levels, which were found to be elevated in the saliva of PLWH. Thus, by revealing the role of aberrantly increased polyamine synthesis during HIV infection, our study unveils a new mechanism by which chronic viral infections could drive distinct T cell effector programs and Treg dysfunction.
INSTITUTE
Case Western Reserve University
DEPARTMENT
Biological Sciences
LABORATORY
Pushpa Pandiyan
LAST_NAME
Pandiyan
FIRST_NAME
Pushpa
ADDRESS
Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, Cleveland, Ohio, 44106
Comparative metabolite profiling of glycolytic and sulfoglycolytic E. coli
STUDY_SUMMARY
Glycolytic E. coli (E. coli grown on glucose as a sole carbon source) and sulfoglycolytic E. coli (E. coli grown on the sulfosugar sulfoquinovose as a sole carbon source) were grown to mid-log phase in M9 minimal medium. Samples were harvested at mid-log phase and analysed using GC-EI-QqQ-MS.
INSTITUTE
University of Melbourne
LAST_NAME
Williams
FIRST_NAME
Spencer
ADDRESS
05, 532, David Penington Building, Parkville, 3010, VIC, Australia
UCP2-dependent redox-sensing in POMC neurons regulates feeding
STUDY_SUMMARY
Paradoxically, glucose, the primary driver of satiety, activates a small population of anorexigenic POMC neurons. Here we show that lactate levels in the circulation and in the cerebrospinal fluid are elevated in fed state and addition of lactate to glucose activates the majority of POMC neurons while increasing cytosolic NADH generation, mitochondrial respiration and extracellular pyruvate levels. Inhibition of lactate dehydrogenases diminishes mitochondrial respiration, NADH production, and POMC neuronal activity. However, inhibition of the mitochondrial pyruvate carrier has no effect. POMC-specific downregulation of Ucp2 (Ucp2PomcKO), a molecule regulated by fatty acid metabolism and shown to play a role as transporter in the malate-aspartate shuttle, abolishes lactate- and glucose-sensing of POMC neurons. Ucp2PomcKO mice have impaired glucose metabolism and are prone to obesity on a high fat diet. Altogether, our data show that lactate through redox signaling and blocking mitochondrial glucose utilization activates POMC neurons to regulate feeding and glucose metabolism.
INSTITUTE
Columbia University
LAST_NAME
Diano
FIRST_NAME
Sabrina
ADDRESS
1150 St. Nicholas Avenue Russ Berrie Medical Science Pavilion Rm 405 New York, NY, 10032
The impact of acute Colony Stimulating Factor 1 treatment on serum and liver metabolites in fed and fasted mice LIVER
STUDY_TYPE
Drug treatment
STUDY_SUMMARY
The aim of the study was to investigate the impact of expanding tissue macrophage populations on systemic metabolism. Groups of male mice were treated with 4 x daily injections of Colony Stimulating Factor (1), followed by normal feeding or a 24 h fast from day 6 to day 7. Serum and liver were collected for GC-MS metabolomic analysis on a Shimadzu TQ8050.
High-resolution metabolomics analysis of NLRP3 inflammasome activated macrophages
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Activating macrophage NLRP3 inflammasome can promote excessive inflammation, with severe cell and tissue damage and organ dysfunction. Here, we show that pharmacological or genetic inhibition of pyruvate dehydrogenase kinase (PDHK) significantly attenuates NLRP3 inflammasome activation in murine and human macrophages and septic mice by lowering caspase-1 cleavage and IL-1beta secretion. Inhibiting PDHK reverses NLRP3 inflammasome-induced metabolic reprogramming, enhances autophagy, promotes mitochondrial fusion over fission, preserves cristae ultrastructure, and attenuates mitochondrial ROS production. The suppressive effect of PDHK inhibition on the NLRP3 inflammasome is independent of its canonical role as a pyruvate dehydrogenase regulator. We suggest that PDHK inhibition improves mitochondrial fitness by reversing NLRP3 inflammasome activation in acutely inflamed macrophages.
Targeted metabolomics analysis of WT and GSDMDKO macrophages
STUDY_TYPE
MS analysis
STUDY_SUMMARY
Activating macrophage NLRP3 inflammasome can promote excessive inflammation, with severe cell and tissue damage and organ dysfunction. Here, we show that pharmacological or genetic inhibition of pyruvate dehydrogenase kinase (PDHK) significantly attenuates NLRP3 inflammasome activation in murine and human macrophages and septic mice by lowering caspase-1 cleavage and IL-1beta secretion. Inhibiting PDHK reverses NLRP3 inflammasome-induced metabolic reprogramming, enhances autophagy, promotes mitochondrial fusion over fission, preserves cristae ultrastructure, and attenuates mitochondrial ROS production. The suppressive effect of PDHK inhibition on the NLRP3 inflammasome is independent of its canonical role as a pyruvate dehydrogenase regulator. We suggest that PDHK inhibition improves mitochondrial fitness by reversing NLRP3 inflammasome activation in acutely inflamed macrophages.
Metabolomic and Cultivation Insights into the Tolerance of the Spacecraft-Associated Acinetobacter Towards Kleenol 30, a Cleanroom Floor Detergent
STUDY_TYPE
research
STUDY_SUMMARY
To ensure cleanliness, NASA spacecraft are assembled in cleanroom facilities, where floors are routinely cleansed with Kleenol 30 (K30), an alkaline detergent. Through metabolomic and cultivation approaches, we show that cultures of spacecraft-associated Acinetobacter tolerate up to 1% v/v K30 and are fully inhibited at ≥2%; in comparison, NASA cleanrooms are cleansed with 0.8% K30. For A. johnsonii 2P08AA (isolated from a cleanroom floor), cultivations with 0.1% v/v K30 yield (1) limited changes in the intracellular metabolome and (2) increases in extracellular sugar acids, monosaccharides, organic acids, and fatty acids. For A. radioresistens 50v1 (isolated from a spacecraft surface), cultivations yield (1) differential changes in intracellular amino acids, compatible solutes, nucleotide-related metabolites, dicarboxylic acids, and saturated fatty acids and (2) substantial yet differential impacts to extracellular sugar acids, monosaccharides, and organic acids. These combined results suggest that (1) K30 manifests strain-dependent impacts on the intracellular metabolomes and (2) K30 influences extracellular trace element acquisition in both strains. Hence, this work lends support towards the hypothesis that repeated cleansing during spacecraft assembly serve as selective pressures that promote tolerances towards the cleaning conditions.
Metabolomics of B-cell Acute Lymphoblastic Leukemia in Response to Adipocyte Conditioned Media
STUDY_TYPE
Untargeted MS
STUDY_SUMMARY
Adipocyte conditioned media (ACM), stromal cell conditioned media (SCM) and unconditioned media (UCM) were added to B-cell Acute Lymphoblastic Leukemia cells (REH and RCH-AcV) either with or without methotrexate (MTX). The metabolomic profiles of the cells was determined by mass spectrometry.
Evaluation of Two Simultaneous Metabolomic and Proteomic Extraction Protocols Assessed by Ultra-High-Performance Liquid Chromatography Tandem Mass Spectrometry
STUDY_SUMMARY
Untargeted multi-omics analysis of plasma is an emerging tool for the identification of novel biomarkers for evaluating disease prognosis and for a better understanding of molecular mechanisms underlying human disease. The successful application of metabolomic and proteomic approaches relies on reproducibly quantifying a wide range of metabolites and proteins. Herein, we report the results of untargeted metabolomic and proteomic analyses from blood plasma samples following analyte extraction by two frequently used solvent systems: chloro-form/methanol and methanol-only. Whole blood samples were collected from participants (n=6) at University Hospital Sharjah (UHS) hospital, then plasma was separated and extracted by two methods i. methanol precipitation and, ii. 4:3 methanol:chloroform extraction. The coverage and reproducibility of the two methods were assessed by ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). The study revealed that metabolite extraction by methanol-only showed greater reproducibility for both metabolomic and proteomic quantifications than did methanol/chloroform, while yielding similar peptide coverage. However, coverage of extracted metabolites was higher with the methanol/chloroform precipitation.
INSTITUTE
Sharjah Institute for Medical Research
LAST_NAME
Facility
FIRST_NAME
Core
ADDRESS
M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah
Metabolomics of Adipocyte-Conditioned Media Compared to Stromal Cell- and Un-conditioned Media
STUDY_TYPE
Untargeted MS
STUDY_SUMMARY
The metabolomics profiles of adipocyte conditioned media (ACM), stromal cell conditioned media (SCM) and unconditioned media (UCM) were analyzed by untargeted mass spectrometry.
Spatial, temporal, and inter-subject variation of the metabolome along the human upper intestinal tract (MS HILIC negative data)
STUDY_SUMMARY
Most utilization of human diets occurs in the small intestine, which remains largely unstudied. Here, we used a novel non-invasive, ingestible sampling device to probe the spatiotemporal variation of upper intestinal luminal contents during routine daily digestion in 15 healthy subjects. We analyzed 274 intestinal samples and 60 corresponding stool homogenates by combining five metabolomics assays and 16S rRNA sequencing. We identified 1,909 metabolites, including sulfonolipids and novel bile acids. Stool and intestinal metabolomes differed dramatically. Food metabolites displayed known differences and trends in dietary biomarkers, unexpected increases in dicarboxylic acids along the intestinal tract, and a positive association between luminal keto acids and fruit intake. Diet-derived and microbially linked metabolites accounted for the largest inter-subject differences. Interestingly, subjects exhibited large variation in levels of bioactive fatty acid esters of hydroxy fatty acids (FAHFAs) and sulfonolipids. Two subjects who had taken antibiotics within 6 months prior to sampling showed markedly different patterns in these and other microbially related metabolites; from this variation, we identified Blautia species as most likely to be involved in FAHFA metabolism. Thus, in vivo sampling of the human small intestine under physiologic conditions can reveal links between diet, host and microbial metabolism.
Elucidating dynamic anaerobe metabolism with HRMAS 13C NMR and genome-scale modeling
STUDY_SUMMARY
Anaerobic microbial metabolism drives critical functions within global ecosystems, host-microbiota interactions, and industrial applications, yet remains ill-defined. Here we advance a versatile approach to elaborate cellular metabolism in obligate anaerobes using the pathogen Clostridioides difficile, an amino acid and carbohydrate-fermenting Clostridia. High-Resolution Magic Angle Spinning (HRMAS) Nuclear Magnetic Resonance (NMR) spectroscopy of C. difficile, grown with fermentable 13C substrates, informed dynamic flux balance analysis (dFBA) of the pathogen’s genome-scale metabolism. Analyses identified dynamic recruitment of oxidative and supporting reductive pathways, with integration of high-flux amino acid and glycolytic metabolism at alanine’s biosynthesis to support efficient energy generation, nitrogen handling, and biomass generation. Model predictions informed an approach leveraging the sensitivity of 13C NMR spectroscopy to simultaneously track cellular carbon and nitrogen flow from [U-13C]glucose and [15N]leucine, confirming the formation of [13C,15N]alanine. Findings identify metabolic strategies used by C. difficile to support its rapid colonization and expansion in gut ecosystems.
INSTITUTE
Brigham and Women's Hospital
DEPARTMENT
Pathology
LABORATORY
Bry Lab, Massachusetts Host-Microbiome Center; Cheng Lab, Massachusetts General Hospital
LAST_NAME
Pavao
FIRST_NAME
Aidan
ADDRESS
221 Longwood Ave, EBRC-411, Boston, MA, 02115, USA
Zebrafish Optic Nerve Regeneration Metabolomics - 3 Days Post Crush
STUDY_SUMMARY
Zebrafish (Danio Rerio) have the capacity for successful adult optic nerve regeneration. In contrast, mammals lack this intrinsic ability and undergo irreversible neurodegeneration seen in glaucoma and other optic neuropathies. Optic nerve regeneration is often studied using optic nerve crush, a mechanical neurodegenerative model. Untargeted metabolomic studies within successful regenerative models are deficient. Evaluation of tissue metabolomic changes in active zebrafish optic nerve regeneration can elucidate prioritized metabolite pathways that can be targeted in mammalian systems for therapeutic development. Female and male (6 month to 1 year old) right Zebrafish (Tg(gap43:GFP)) optic nerves were crushed and collected three days after. Contralateral, uninjured optic nerves were collected as controls. The tissue was dissected from euthanized fish and frozen on dry ice. Samples were pooled for each category (female crush, female control, male crush, male control) and pooled at n = 31 to obtain sufficient metabolite concentrations for analysis. Optic nerve regeneration was verified by microscope visualization of GFP fluorescence. Metabolites were extracted using a Precellys Homogenizer and a serial extraction method: (1) 1:1 Methanol/Water and (2) 8:1:1 Acetonitrile/Methanol/Acetone. Metabolites were analyzed by untargeted liquid chromatography-mass spectrometry (LC MS-MS) profiling using a Q-Exactive Orbitrap instrument coupled with Vanquish Horizon Binary UHPLC LC-MS system. Metabolites were identified and quantified using Compound Discoverer 3.3 and isotopic internal metabolites standards.
Metabolic analysis of primary HPV18-genome containing human foreskin keratinocytes compared to untransfected donor-matched controls.
STUDY_SUMMARY
Six primary HPV18-genome containing human foreskin keratinocyte cell populations and six donor-matched primary untransfected human foreskin keratinocyte cell populations were grown on lethally-irradiated 3T3-J2 fibroblasts. Before harvesting the keratinocytes, the 3T3-J2 fibroblasts were washed off. Cells and spent media were harvested and frozen at -80°C until processing.
INSTITUTE
University of Birmingham, UK
DEPARTMENT
Institute of Cancer and Genomic Sciences
LABORATORY
Joanna Parish
LAST_NAME
Parish
FIRST_NAME
Joanna
ADDRESS
IBR Wolfson Drive Medical School, University of Birmingham, Edgbaston
Untargeted metabolomics of HUVECs subjected to hypoxia-reoxygenation
STUDY_SUMMARY
Acute hemorrhage commonly leads to coagulopathy and organ dysfunction or failure. Recent evidence suggests that damage to the endothelial glycocalyx contributes to these adverse outcomes. The physiological events mediating acute glycocalyx shedding are undefined, however. Here, we show that succinate accumulation within endothelial cells drives glycocalyx degradation through a membrane reorganization-mediated mechanism. We investigated this mechanism in a cultured endothelial cell hypoxia-reoxygenation model, in a rat model of hemorrhage, and in trauma patient plasma samples. We found that succinate metabolism by succinate dehydrogenase mediates glycocalyx damage through lipid oxidation and phospholipase A2-mediated membrane reorganization (increasing lysophospholipids), promoting the interaction of MMP24 and MMP25 with glycocalyx constituents. In trauma patients, we found that succinate levels were associated with glycocalyx damage and the development of coagulopathy, and that interaction of MMP24 and syndecan-1 were elevated compared to healthy controls. This establishes a novel metabolic cascade mediating the endotheliopathy of traumatic hemorrhage.
INSTITUTE
Tulane University School of Medicine
DEPARTMENT
Surgery
LABORATORY
Tulane Trauma and Critical Care Research Lab
LAST_NAME
Jackson-Weaver
FIRST_NAME
Olan
ADDRESS
1430 Tulane Ave, Department of Surgery, School of Medicine
Map of microbially induced metabolic changes across diverse body sites in mice - Mouse Data
STUDY_SUMMARY
Tissue samples from contents along the intestinal tract and systemic sites in mice that did not have any bacteria (germ free) or colonized with a simplified microbiota or more complex microbiota.
Linking bacterial metabolites to disease-associated microbes to uncover mechanisms of host-microbial interactions in intestinal inflammation. Veillonella parvula media profiling of IBD drug metabolites
STUDY_SUMMARY
Understanding the role of the gut microbiome in inflammatory and autoimmune diseases requires the identification of microbial molecular effectors and their link to host pathophysiology. Here, we present a framework to identify and characterize novel microbial metabolites in patient samples and to directly link their production to disease-associated microbes. We applied this approach to investigate the spectrum of disease severity and treatment response in ulcerative colitis (UC) using longitudinal metabolite and strain profiles combined with paired plasma profiles.
High body temperature increases gut microbiota-dependent host resistance to influenza A virus and SARS-CoV-2 infection (Mouse)
STUDY_SUMMARY
While a common symptom of influenza and coronavirus disease 2019 (COVID-19) is fever, its physiological role on host resistance to viral infection remains less clear. Here, we demonstrate that exposure of mice to the high ambient temperature of 36 °C increase host resistance to viral pathogens including influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). High heat-exposed mice increase basal body temperature over 38 °C to enable more bile acids production in a gut microbiota-dependent manner. The gut microbiota-derived deoxycholic acid (DCA) and its plasma membrane-bound receptor Takeda G-protein-coupled receptor 5 (TGR5) signaling increase host resistance to influenza virus infection by suppressing virus replication and neutrophil-dependent tissue damage. Furthermore, the DCA and its nuclear farnesoid X receptor (FXR) agonist protect Syrian hamster from lethal SARS-CoV-2 infection. Moreover, we demonstrate that certain bile acids are reduced in the plasma of COVID-19 patients who developed moderate I/II disease compared with minor illness group. These findings uncover an unexpected mechanism by which virus-induced high fever increases host resistance to influenza virus and SARS-CoV-2 in a gut microbiota-dependent manner.
INSTITUTE
Keio University
LAST_NAME
Fukuda
FIRST_NAME
Shinji
ADDRESS
Kakuganji 246-2, Mizukami, Tsuruoka City Yamagata,Japan
Metabolomic analysis of maternal mid-gestation plasma and cord blood: primary metabolism
STUDY_SUMMARY
Metabolomic analysis of maternal mid-gestation plasma and cord blood reveals evidence in autism spectrum disorder of inflammation, disruption of membrane integrity, and impaired neurotransmission and neurotoxicity. The discovery of prenatal and neonatal molecular biomarkers has the potential to yield insights into autism spectrum disorder (ASD) and facilitate early diagnosis. We characterized metabolomic profiles in ASD using plasma samples collected in the Norwegian Autism Birth Cohort from mothers at weeks 17-21 gestation (maternal mid-gestation, MMG, n=408) and from children on the day of birth (cord blood, CB, n=418). We analyzed associations using sex-stratified adjusted logistic regression models with Bayesian analyses. Chemical enrichment analyses (ChemRICH) were performed to determine altered chemical clusters. We also employed machine learning algorithms to assess the utility of metabolomics as ASD biomarkers. We identified ASD associations with a variety of chemical compounds including arachidonic acid, glutamate, and glutamine, and metabolite clusters including hydroxy eicospentaenoic acids, phosphatidylcholines, and ceramides in MMG and CB plasma that are consistent with inflammation, disruption of membrane integrity, and impaired neurotransmission and neurotoxicity. Girls with ASD have disruption of ether/non-ether phospholipid balance in the MMG plasma that is similar to that found in other neurodevelopmental disorders. ASD boys in the CB analyses had the highest number of dysregulated chemical clusters. Machine learning classifiers distinguished ASD cases from controls with AUC values ranging from 0.710 to 0.853. Predictive performance was better in CB analyses than in MMG. These findings may provide new insights into the sex-specific differences in ASD and have implications for discovery of biomarkers that may enable early diagnosis and intervention.
The goal of this study was to use metabolomics as a platform to elucidate the chemical composition of plants in order to increase their resolution and in turn use the identified chemicals to reveal potential health impacts. 20 plant foods were studied: apple, banana, tomato, lettuce, strawberry, carrot, peach, onion, spinach, pepper, corn, garlic, basil, potato, soybean, black bean, olive, chickpea, sugarbeet, and pear.
INSTITUTE
Northeastern University; Massachusets Institute of Technology
DEPARTMENT
Department of Physics
LABORATORY
BarabasiLab
LAST_NAME
Barabasi
FIRST_NAME
Albert-Laszlo
ADDRESS
177 Huntington Ave, 11th Floor, Boston, MA, 02115, USA
Composition of raw plant-based food items Pilot Study
STUDY_TYPE
Composition of food
STUDY_SUMMARY
The goal of this pilot study was to be a preliminary metabolomics study on the platforms used to elucidate the chemical composition of plants in order to increase their resolution and in turn use the identified chemicals to reveal potential health impacts. In this pilot we focused on 6 food items: apple, basil, lettuce, strawberry, tomato, and garlic.
INSTITUTE
Northeastern University; Massachusets Institute of Technology
DEPARTMENT
Department of Physics
LABORATORY
BarabasiLab
LAST_NAME
Barabasi
FIRST_NAME
Albert-Laszlo
ADDRESS
177 Huntington Ave, 11th Floor, Boston, MA, 02115, USA
Study of environmental toxicants and gut microbiome in relation to obesity and insulin resistance
STUDY_SUMMARY
Background & Aims: Environmental toxicants (ETs) associate with various adverse health outcomes. Here, we hypothesized that exposures to ETs are associated with obesity and insulin resistance via a dysbiotic gut microbiota and derived alterations in microbiome-mediated bile acid (BA) synthesis. Methods: Serum BAs, per- and polyfluoroalkyl substances (PFAS) and additional twenty-seven ETs were measured by mass spectrometry in 264 Danes (121 women and 143 men, age 56.6 ± 7.3 years, BMI 29.7 ± 6.0 kg/m2). Bacterial species were identified based on whole-genome shotgun (WGS) sequencing of DNA extracted from purified stool samples. Personalized genome-scale metabolic models (GEMs) of gut microbial communities were developed to elucidate regulation of BA pathways. Subsequently, we compared findings in the human study with metabolic implications of perfluorooctanoic acid (PFOA) exposure in a PPAR-humanized murine model. Results: Fasting serum concentrations of twelve ETs associated directly with measures of obesity and insulin resistance. Several bacterial species including Dorea longicatena, Dorea formicigenerans, Subdoligranulum spp., Veillonella spp., and Roseburia intestinalis associated positively and in a sex-dimorphic manner, particularly in women, with high exposure to ETs. Moreover, high serum concentrations of ETs were linked with higher fasting serum levels of microbiome-synthesized secondary BAs such as lithocholic acid (LCA) and ursodeoxycholic acid (UDCA). These findings were substantiated by the outcome of a murine exposure study. Conclusion: Serum concentrations of ETs, particularly in women, were associated with an altered gut microbiome-mediated secondary BA biosynthesis, linked with obesity and insulin resistance.
INSTITUTE
Örebro University
DEPARTMENT
Department of Medical Sciences
LABORATORY
Systems Medicine
LAST_NAME
Orešič
FIRST_NAME
Matej
ADDRESS
School of Medical Sciences, Örebro, Örebro, 70281, Sweden
Time course 1: Growth of Eggerthella lenta in defined media
STUDY_TYPE
Untargeted LC-MS
STUDY_SUMMARY
This dataset contains untargeted metabolomics analysis of supernatants from 3 strains of Eggerthella lenta grown in defined EDM1 media with varying acetate concentrations.
INSTITUTE
University of California, San Francisco
LAST_NAME
Noecker
FIRST_NAME
Cecilia
ADDRESS
513 Parnassus Ave HSW1501, San Francisco, CA 94143
Strain supernatants: Strain diversity of Eggerthella lenta metabolites in defined media
STUDY_TYPE
Untargeted LC-MS
STUDY_SUMMARY
This dataset contains untargeted metabolomics analysis of supernatants from stationary phase of a collection of 30 strains of Eggerthella lenta grown in defined EDM1 media.
INSTITUTE
University of California, San Francisco
LAST_NAME
Noecker
FIRST_NAME
Cecilia
ADDRESS
513 Parnassus Ave HSW1501, San Francisco, CA 94143
Gnotobiotic mice: Metabolites in intestinal contents of germ-free mice colonized with strains of gut bacterium Eggerthella lenta
STUDY_TYPE
Untargeted LC-MS
STUDY_SUMMARY
This dataset contains untargeted metabolomics analysis of intestinal contents of gnotobiotic mice either colonized with different strains of Eggerthella lenta for 2 weeks, or germ-free controls.
INSTITUTE
University of California, San Francisco
LAST_NAME
Noecker
FIRST_NAME
Cecilia
ADDRESS
513 Parnassus Ave HSW1501, San Francisco, CA 94143
Gnotobiotic mice: Metabolites in serum of germ-free mice colonized with strains of gut bacterium Eggerthella lenta
STUDY_TYPE
Untargeted LC-MS
STUDY_SUMMARY
This dataset contains untargeted metabolomics analysis of serum of gnotobiotic mice either colonized with different strains of Eggerthella lenta for 2 weeks, or germ-free controls.
INSTITUTE
University of California, San Francisco
LAST_NAME
Noecker
FIRST_NAME
Cecilia
ADDRESS
513 Parnassus Ave HSW1501, San Francisco, CA 94143
Time course 2: Growth of Eggerthella lenta in defined media with some samples receiving 13C2 stable isotope labeled acetate
STUDY_TYPE
Untargeted LC-MS
STUDY_SUMMARY
This dataset contains untargeted metabolomics analysis of supernatants from 3 strains of Eggerthella lenta grown in defined EDM1 media with varying acetate concentrations. One set of samples grew in EDM1 containing 13C2 stable isotope labeled acetate.
INSTITUTE
University of California, San Francisco
LAST_NAME
Noecker
FIRST_NAME
Cecilia
ADDRESS
513 Parnassus Ave HSW1501, San Francisco, CA 94143
Time course 2: Growth of Eggerthella lenta in defined media with some samples receiving 13C2 stable isotope labeled acetate (intracellular samples)
STUDY_TYPE
Untargeted LC-MS
STUDY_SUMMARY
This dataset contains untargeted metabolomics analysis of supernatants from 3 strains of Eggerthella lenta grown in defined EDM1 media with varying acetate concentrations. One set of samples grew in EDM1 containing 13C2 stable isotope labeled acetate. Samples were collected at a subset of time points for extraction of intracellular metabolites.
INSTITUTE
University of California, San Francisco
LAST_NAME
Noecker
FIRST_NAME
Cecilia
ADDRESS
513 Parnassus Ave HSW1501, San Francisco, CA 94143
Deriving Schwann Cells from hPSCs Enables Disease Modeling and Drug Discovery for Diabetic Peripheral Neuropathy
STUDY_SUMMARY
Schwann cells (SCs) are the major glia of the peripheral nervous system (PNS) and are essential for its function. Defects in SCs are associated with many PNS disorders including diabetic peripheral neuropathy (DPN), a condition affecting millions of patients. We have developed a strategy for deriving SCs from human pluripotent stem cells (hPSCs) which recapitulate the molecular features of primary SCs and are capable of engrafting efficiently and producing myelin in vitro and in injured sciatic nerves in rats. We further established an hPSC-based model of DPN that revealed the selective vulnerability of human SCs to hyperglycemia-induced cytotoxicity. By high-throughput screening we found bupropion counteracts glucose-mediated cytotoxicity in SCs and normalizes glucose-induced transcriptional and metabolic abnormalities in SCs. Treatment of hyperglycemic mice with bupropion rescued sensory function, prevented SC death, and counteracted myelin damage in sciatic nerves. Our retrospective analysis of patient health records revealed that bupropion treatment was associated with a lower incidence of neuropathy among diabetic patients that receive antidepressant medications.
Methionine restriction constrains lipoylation and activates mitochondria for nitrogenic synthesis of amino acids (Part 1)
STUDY_SUMMARY
Methionine restriction (MR) provides metabolic benefits in many organisms. However, mechanisms underlying the MR-induced effect remain incompletely understood. Here, we show in the budding yeast S. cerevisiae that MR relays a signal of S-adenosylmethionine (SAM) deprivation to adapt bioenergetic mitochondria to nitrogenic anabolism. In particular, decreases in cellular SAM constrain lipoate metabolism and protein lipoylation required for the operation of the tricarboxylic acid (TCA) cycle in the mitochondria, leading to incomplete glucose oxidation with an exit of acetyl-CoA and alpha-ketoglutarate from the TCA cycle to the syntheses of amino acids, such as arginine and leucine. This mitochondrial SAM-induced response, namely mitoSIR, promotes cell fitness through the coordination of mitochondrial fuel metabolism with the nitrogenic synthesis of amino acids.
Methionine restriction constrains lipoylation and activates mitochondria for nitrogenic synthesis of amino acids (Part 2)
STUDY_SUMMARY
Methionine restriction (MR) provides metabolic benefits in many organisms. However, mechanisms underlying the MR-induced effect remain incompletely understood. Here, we show in the budding yeast S. cerevisiae that MR relays a signal of S-adenosylmethionine (SAM) deprivation to adapt bioenergetic mitochondria to nitrogenic anabolism. In particular, decreases in cellular SAM constrain lipoate metabolism and protein lipoylation required for the operation of the tricarboxylic acid (TCA) cycle in the mitochondria, leading to incomplete glucose oxidation with an exit of acetyl-CoA and alpha-ketoglutarate from the TCA cycle to the syntheses of amino acids, such as arginine and leucine. This mitochondrial SAM-induced response, namely mitoSIR, promotes cell fitness through the coordination of mitochondrial fuel metabolism with the nitrogenic synthesis of amino acids.
Metabolomics dataset of CNTF induced axon regeneration in mice post optic nerve crush
STUDY_SUMMARY
Axons are processes or extensions of a neuron that help connect one neuron with the next. In the eye all retinal ganglion cells (RGCs) reside within the retina but their axons travel a very long distance traversing through the optic nerve they connect with other neurons in the lateral geniculate nucleus in the brain. Loss of axons results in blindness in glaucoma and traumatic optic neuropathies. Optic nerve crush (ONC) is mouse is an assay system that enable pharmacological induction of axon regeneration from existing RGCs. Lipids form the outer boundary of axons, their synthesis or alterations are associated with metabolite changes. Our motivation was to understand what metabolite changes occurred when ONC axons regenerated due to ciliary neurotrophic factor (CNTF) treatment. We found metabolite profile changes associated with regeneration after crush induced by CNTF. This metabolite dataset was collected from C57Bl/6 mice expressing either AAV2-CNTF to promote regeneration or AAV2-Green Lantern as a control. Animals were subjected to optic nerve crush injury and allowed to recover for either 7 days or 14 days. At the respective time points, animals were euthanized and optic nerves were collected. Nerves underwent two rounds of extraction using a Precellys 24 Touch Homogenizer and a two solvent system of 1:1 Methanol/Water and 8:1:1 Acetonitrile/Methanol/Acetone. Metabolites were analyzed by untargeted liquid chromatography-mass spectrometry (LC MS-MS) using a Vanquish Horizon Binary HPLC coupled to a Q Exactive Orbitrap mass spectrometer. Metabolites were identified using Compound Discoverer 3.3 and quantified using isotopic internal metabolite standards.
Blood metabolomics and impacted cellular mechanisms during transition into lactation in dairy cows that develop metritis
STUDY_TYPE
Case-Control Study
STUDY_SUMMARY
The objective of this study was to identify metabolites associated with metritis and use them for identification of cellular mechanisms affected during transition into lactation. Holstein cows (n = 104) had blood collected in the prepartum period (d-14 ± 6), at calving (d0), and at the day of metritis diagnosis (d7 ± 2). Cows with reddish or brownish, watery, and fetid discharge were diagnosed with metritis (n = 52). Cows with metritis were paired with herdmates without metritis (n = 52) based on DIM. The metabolome of plasma samples was evaluated using untargeted gas chromatography time-of-flight mass spectrometry. Univariate analyses included t-tests and fold change analyses. Metabolites with false discovery rate (FDR) adjusted P ≤ 0.10 on t-tests were used for partial least squares – discriminant analysis PLS-DA coupled with permutational analysis using 2,000 permutations. Metabolites with FDR adjusted P ≤ 0.10 on t-tests were also used for enriched pathway analyses and identification of cellular processes. Cows that developed metritis had affected cellular processes associated with lower amino acid metabolism in the prepartum period, greater lipolysis, cell death, and oxidative stress at calving and at metritis diagnosis, and greater leukocyte activation at calving, but lower immune cell activation at metritis diagnosis. In summary, cows that developed metritis had plasma metabolomic changes associated with greater lipolysis, oxidative stress, and a dysregulated immune response which may predispose cows to metritis development.
Stable isotope tracer analysis (SITA) using 13C6-glucose and 13C5-glutamine measured by GC/MS in BIN-67 cells ± SMARCA4 restoration
STUDY_SUMMARY
SMARCA4/2-loss drives the metabolic shift preferring glutamine than glucose to sustain the TCA cycle. SITA using 13C6-glucose confirmed that glucose uptake was increased in BIN-67 cells upon SMARCA4-restoration, leading to overall increased metabolic flux through glucose (lactate) and TCA cycle intermediates (citrate, fumarate, malate, aspartate) via pyruvate carboxylation.Conversely, the 13C5-glutamine SITA in BIN-67 cells revealed that SMARCA4-restoration decreased glutamine uptake and utilization via glutaminolysis to fuel the TCA cycle as indicated by reduced glutamine metabolites (glutamate, α-KG, m+5 metabolites) and TCA cycle intermediates (succinate, fumarate, malate, aspartate, m+4 metabolites)
INSTITUTE
McGill University
DEPARTMENT
Biochemistry
LABORATORY
Sidong Huang Lab
LAST_NAME
Fu
FIRST_NAME
Zheng
ADDRESS
McIntyre Medical Sciences Building, 3655 promenade Sir-William-Osler
Stable isotope tracer analysis (SITA) using 13C6-glucose and 13C5-glutamine measured by GC/MS in H1703 cells ± SMARCA4/A2 restoration
STUDY_SUMMARY
SMARCA4/2-loss drives the metabolic shift preferring glutamine than glucose to sustain the TCA cycle. SITA using 13C6-glucose confirmed that glucose uptake was increased in H1703 cells upon SMARCA4/A2-restoration. Conversely, the 13C5-glutamine SITA in H1703 cells revealed that SMARCA4/A2-restoration decreased glutamine uptake and utilization via glutaminolysis to fuel the TCA cycle as indicated by reduced glutamine metabolites (glutamate, α-KG, metabolites) and TCA cycle intermediates (succinate, fumarate, malate, aspartate, metabolites)
INSTITUTE
McGill University
DEPARTMENT
Biochemistry
LABORATORY
Sidong Huang Lab
LAST_NAME
Fu
FIRST_NAME
Zheng
ADDRESS
McIntyre Medical Sciences Building, 3655 promenade Sir-William-Osler
MoTrPAC: Endurance exercise training study in young adult rats, Tissue:Plasma - Untargeted HILIC-Positive
STUDY_SUMMARY
The goal of the endurance exercise training study in young adult rats (internal code: PASS1B-06) was to perform exercise training studies in adult (6 month) F344 rats, and from these rats collect as many tissues as feasible in order to provide high quality samples for detailed analysis by chemical analysis sites. Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups. The 8-week training group and controls were from the same cohort and same age at euthanasia (either 8). For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program. Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max as outlined in the Table on the next page. Training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max (see tables) and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31. This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved. If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized. It is important to note that the starting treadmill speed varied depending on the sex and age of the rat. The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats. Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.
MoTrPAC: Endurance exercise training study in young adult rats, Rat Plasma - Untargeted Lipidomics, Reversed-Phase Negative
STUDY_SUMMARY
The goal of the endurance exercise training study in young adult rats (internal code: PASS1B-06) was to perform exercise training studies in adult (6 month) F344 rats, and from these rats collect as many tissues as feasible in order to provide high quality samples for detailed analysis by chemical analysis sites. Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups. The 8-week training group and controls were from the same cohort and same age at euthanasia (either 8). For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program. Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max as outlined in the Table on the next page. Training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max (see tables) and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31. This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved. If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized. It is important to note that the starting treadmill speed varied depending on the sex and age of the rat. The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats. Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.
MoTrPAC: Endurance exercise training study in young adult rats, Tissue:Plasma - Untargeted Lipidomics, Reversed-Phase Positive
STUDY_SUMMARY
The goal of the endurance exercise training study in young adult rats (internal code: PASS1B-06) was to perform exercise training studies in adult (6 month) F344 rats, and from these rats collect as many tissues as feasible in order to provide high quality samples for detailed analysis by chemical analysis sites. Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups. The 8-week training group and controls were from the same cohort and same age at euthanasia (either 8). For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program. Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max as outlined in the Table on the next page. Training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max (see tables) and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31. This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved. If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized. It is important to note that the starting treadmill speed varied depending on the sex and age of the rat. The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats. Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.
MoTrPAC: Endurance exercise training study in young adult rats, Rat Gastrocnemius Powder - Untargeted Lipidomics, Reversed-Phase Positive
STUDY_SUMMARY
The goal of the endurance exercise training study in young adult rats (internal code: PASS1B-06) was to perform exercise training studies in adult (6 month) F344 rats, and from these rats collect as many tissues as feasible in order to provide high quality samples for detailed analysis by chemical analysis sites. Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups. The 8-week training group and controls were from the same cohort and same age at euthanasia (either 8). For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program. Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max as outlined in the Table on the next page. Training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max (see tables) and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31. This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved. If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized. It is important to note that the starting treadmill speed varied depending on the sex and age of the rat. The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats. Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.
MoTrPAC: Endurance exercise training study in young adult rats, Rat Kidney Powder - Untargeted Lipidomics, Reversed-Phase Negative
STUDY_SUMMARY
The goal of the endurance exercise training study in young adult rats (internal code: PASS1B-06) was to perform exercise training studies in adult (6 month) F344 rats, and from these rats collect as many tissues as feasible in order to provide high quality samples for detailed analysis by chemical analysis sites. Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups. The 8-week training group and controls were from the same cohort and same age at euthanasia (either 8). For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program. Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max as outlined in the Table on the next page. Training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max (see tables) and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31. This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved. If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized. It is important to note that the starting treadmill speed varied depending on the sex and age of the rat. The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats. Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.
MoTrPAC: Endurance exercise training study in young adult rats, Rat Gastrocnemius Powder - Targeted Acyl-CoA
STUDY_SUMMARY
The goal of the endurance exercise training study in young adult rats (internal code: PASS1B-06) was to perform exercise training studies in adult (6 month) F344 rats, and from these rats collect as many tissues as feasible in order to provide high quality samples for detailed analysis by chemical analysis sites. Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups. The 8-week training group and controls were from the same cohort and same age at euthanasia (either 8). For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program. Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max as outlined in the Table on the next page. Training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max (see tables) and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31. This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved. If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized. It is important to note that the starting treadmill speed varied depending on the sex and age of the rat. The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats. Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.
MoTrPAC: Endurance exercise training study in young adult rats, Tissue:Lung - Untargeted Reversed-Phase Negative
STUDY_SUMMARY
The goal of the endurance exercise training study in young adult rats (internal code: PASS1B-06) was to perform exercise training studies in adult (6 month) F344 rats, and from these rats collect as many tissues as feasible in order to provide high quality samples for detailed analysis by chemical analysis sites. Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups. The 8-week training group and controls were from the same cohort and same age at euthanasia (either 8). For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program. Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max as outlined in the Table on the next page. Training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max (see tables) and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31. This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved. If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized. It is important to note that the starting treadmill speed varied depending on the sex and age of the rat. The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats. Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Burant
FIRST_NAME
Charles
ADDRESS
6120 Brehm Tower,1000 Wall St., Ann Arbor, MI, 48105-5714
MoTrPAC: Endurance exercise training study in young adult rats, Tissue:White Adipose - Untargeted Lipidomics, Reversed-Phase Negative
STUDY_SUMMARY
The goal of the endurance exercise training study in young adult rats (internal code: PASS1B-06) was to perform exercise training studies in adult (6 month) F344 rats, and from these rats collect as many tissues as feasible in order to provide high quality samples for detailed analysis by chemical analysis sites. Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups. The 8-week training group and controls were from the same cohort and same age at euthanasia (either 8). For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program. Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max as outlined in the Table on the next page. Training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max (see tables) and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31. This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved. If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized. It is important to note that the starting treadmill speed varied depending on the sex and age of the rat. The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats. Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.
MoTrPAC: Endurance exercise training study in young adult rats, Rat White Adipose Powder - Untargeted Reversed-Phase Negative
STUDY_SUMMARY
The goal of the endurance exercise training study in young adult rats (internal code: PASS1B-06) was to perform exercise training studies in adult (6 month) F344 rats, and from these rats collect as many tissues as feasible in order to provide high quality samples for detailed analysis by chemical analysis sites. Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups. The 8-week training group and controls were from the same cohort and same age at euthanasia (either 8). For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program. Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max as outlined in the Table on the next page. Training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max (see tables) and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31. This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved. If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized. It is important to note that the starting treadmill speed varied depending on the sex and age of the rat. The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats. Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Burant
FIRST_NAME
Charles
ADDRESS
6120 Brehm Tower,1000 Wall St., Ann Arbor, MI, 48105-5714
Systemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites
STUDY_TYPE
Biomedical research
STUDY_SUMMARY
We found that host inflammation altered the plasma environment surrounding Plasmodium falciparum parasites in vivo, and that this altered plasma environment contained inhibitory factors that directly impaired maturation of early trophozoite stages. We demonstrated with LPS-conditioning that systemic host inflammation alone, in the absence of confounding factors such as ongoing infection, slowed the rate at which parasites transited from one generation of RBC to the next. While this is consistent with the idea that host inflammatory responses can impair parasite maturation, other TLR agonists, CpG and Poly I:C, did not elicit such a response. Metabolomics also identified 1-methylhypoxanthine as elevated in both LPS conditioned and acutely-infected plasma. Plasmodium survival depends on host hypoxanthine, inosine and xanthine for purine synthesis. 1-Methylhypoxanthine can bind effectively to and possibly limit the action of hypoxanthine-guanine phosphoribosyl transferase (HGPRTase)25, an enzyme critical for purine synthesis. Interestingly, hypoxanthine, inosine and xanthine were also all reduced in the plasma of LPS-conditioned and acutely infected mice supporting the possibility that inhibition of purine synthesis by 1-methylhypoxanthine might have been partly aided by the lack of substrates for this pathway.
INSTITUTE
Peter Doherty Institute for Infection and Immunity
DEPARTMENT
Department of Microbiology and Immunology
LABORATORY
Ashraful Haque lab
LAST_NAME
Skinner
FIRST_NAME
Oliver
ADDRESS
792 Elizabeth Street, The University of Melbourne, Victoria 3000 Australia
Comparison of metabolic of A549 cells before and after Gossypol acetate (GAA) treatment
STUDY_SUMMARY
GAA is a natural product with anti-cancer application prospect, but its anti-tumor molecular mechanism is still controversial. Previous studies have showed that GAA can suppress the expression of mitochondrial DNA encoded proteins by targeting LRPPRC, suggesting that GAA may affect mitochondrial metabolism. Here, metabonomics was applied to study of effect of GAA on central carbon metabolism in A549 cells. The metabolomic data showed that GAA significantly decreased tricarboxylic acid cycle ralated metabolites and significantly increased glycolysis-related metabolites. These results indicated that GAA could inhibite oxidative phosphorylation in A549 cells.
INSTITUTE
Hangzhou Institute of Medicine, Chinese Academy of Sciences
LABORATORY
University of Chinese Academy of Sciences (Zhejiang Cancer Hospital)
Improved Endurance Capacity of Diabetic Mice during SGLT2 Inhibition: Potential Role of AICARP, an Endogenous AMPK Activator.
STUDY_SUMMARY
Diabetes is associated with an increased risk of deleterious changes in muscle mass and function or sarcopenia, leading to physical inactivity and worsening glycemic control. Given the negative energy balance during sodium-glucose cotransporter 2 (SGLT2) inhibition, whether SGLT2 inhibitors affect skeletal muscle mass and function is a matter of concern. However, how SGLT2 inhibition affects the skeletal muscle function in patients with diabetes remains insufficiently explored. We aimed to explore the effects of canagliflozin (CANA), an SGLT2 inhibitor, on skeletal muscles in genetically diabetic db/db mice.
INSTITUTE
Medical Institute of Bioregulation, Kyushu University
LAST_NAME
Takahashi
FIRST_NAME
Masatomo
ADDRESS
Maidashi 3-1-1, Higashi-ku, Fukuoka, Fukuoka, 8128582, Japan
In this study we used LC-MS and MS/MS to characterize the metabolomes of the input mouse liver metabolites used in the first two studies of this submission.
100μl serum of 11-12 weeks old male mice with a background from various diet groups were processed in Metabolon (https://www.metabolon.com) for metabolics analysis.Diet groups are CDm CDl CD, CDm CDl HFD, CDmHFDl HFD, HFDm CDl CD, HFDm CDl HFD, HFDm HFDl CD and HFDm CDl CD. (m: maternal diet, l: lactation)
Day-night fluctuations in Cerebrospinal fluid metabolomics
STUDY_TYPE
Circadian (Naïve animals)
STUDY_SUMMARY
This study was designed to investigate whether the molecular drivers underlying the diurnal fluctuation of CSF secretion rate could be found in either the choroid plexus tissue itself and/or in the CSF surrounding it. Male Sprague-Dawley rats, kept in light-controlled 12:12 conditions, presented with diurnally modulated CSF metabolite composition. This change was accompanied with differential expression of 2778 genes within the choroid plexus, with several plasma membrane transporters and CLOCK-associated genes diurnally modulated.
INSTITUTE
University of Copenhagen
DEPARTMENT
Department of Neuroscience
LABORATORY
MacAulay Group
LAST_NAME
Edelbo
FIRST_NAME
Beatriche
ADDRESS
Blegdamsvej 3B
EMAIL
beatriche.henriksen@sund.ku.dk
PHONE
+4527697585
NUM_GROUPS
2
TOTAL_SUBJECTS
25
NUM_MALES
25
STUDY_COMMENTS
2 night animals were excluded due to comments regarding sampling/behavior (N4 and N11)
PUBLICATIONS
Day-night fluctuations in choroid plexus transcriptomics and cerebrospinal fluid metabolomics
Metabolomics studies on L4-5 Dorsal Root Ganglia of Ctrl and cKO mice
STUDY_SUMMARY
Metabolomics studies on Dorsal Root Ganglia (DRGs) (Ctrl and cKO).The specific knockout of PP2Cm in the DRG was achieved by intracellular injection of AAV9-Pirt-Cre (1.0×1013 vg/ml) or AAV9-Pirt (1.0×1013 vg/ml)) as control. Mice were used for experiments at 4 weeks after the injection.
INSTITUTE
West China Hospital of Sichuan University
LAST_NAME
Li
FIRST_NAME
Tao
ADDRESS
No. 37 Guoxue Road, Wuhou District, Chendu 610041, Sichuan, China
Lipidomics analysis of maternal obesity model - wild type
STUDY_SUMMARY
10μl liver tissue of 11-12 weeks old male mice from various diet groups with various genetic background were homogenized and lipids were extracted for shotgun lipidomics experiments. Raw files were converted to .mzml files and imported into and analyzed by LipidXplorer software using custom mfql files to identify sample lipids and internal standards. For further data processing, absolute amounts were calculated using the internal standard intensities followed by the calculated mol% of the identified lipids. For wild-type C57BL/6JRcc mice, diet groups are CDm CDl CD, CDm CDl HFD, CDm HFDl HFD, HFDm CDl CD, HFDm CDl HFD, HFDm HFDl CD and HFDm CDl CD. m: maternal diet, l: lactation phase diet.
Resource competition predicts assembly of in vitro gut bacterial communities- HILIC
STUDY_SUMMARY
Microbiota dynamics arise from a plethora of interspecies interactions, including resource competition, cross-feeding, and pH modulation. The individual contributions of these mechanisms are challenging to untangle, especially in natural or complex laboratory environments where the landscape of resource competition is unclear. Here, we developed a framework to estimate the extent of multi-species niche overlaps by combining metabolomics data of individual species, growth measurements in pairwise spent media, and mathematical models. When applied to an in vitro model system of human gut commensals in complex media, our framework revealed that a simple model of resource competition described most pairwise interactions. By grouping metabolomic features depleted by the same set of species, we constructed a coarse-grained consumer-resource model that predicted assembly compositions to reasonable accuracy. Moreover, deviations from model predictions enabled us to identify and incorporate into the model additional interactions, including pH-mediated effects and cross-feeding, which improved model performance. In sum, our work provides an experimental and theoretical framework to dissect microbial interactions in complex in vitro environments.
Investigation of FGFR signaling controlled metabolism in FGFR2-fusion+ intrahepatic cholangiocarcinoma
STUDY_SUMMARY
Genomic alterations that activate FGFR2 are common in intrahepatic cholangiocarcinoma (ICC) and confer sensitivity to treatment with FGFR inhibitors. However, the depth and duration of responses are often limited. Elucidating the FGFR2-driven oncogenic program and the adaptions to FGFR inhibition is needed to gain insight into the biology of these tumors and inform future therapeutic development. Here, we conducted metabolomic analysis of patient-derived models to define the pathways that fuel tumor growth downstream of oncogenic FGFR2 signaling in ICC and to uncover compensatory mechanisms associated with pathway inhibition. We find FGFR2-fusion+ ICC maintains a highly glycolytic phenotype in FGFR2+ ICC. Conversely, FGFR inhibition blocks glucose uptake and glycolysis, while inciting a series of adaptive changes. Thus, we show that glycolysis is a key downstream effector of oncogenic FGFR2 signaling in ICC, and that pronounced metabolic reprogramming in response to FGFR inhibition confers new targetable vulnerabilities.
Targeting Pancreatic Cancer Metabolic Dependencies through Glutamine Antagonism.
STUDY_SUMMARY
Pancreatic ductal adenocarcinoma (PDAC) cells utilize glutamine (Gln) to support proliferation and redox balance. Earlier attempts to inhibit Gln metabolism using glutaminase inhibitors resulted in rapid metabolic reprogramming and therapeutic resistance. Here, we demonstrated that treating PDAC cells with a Gln antagonist, 6-Diazo-5-oxo-L-norleucine (DON), led to a metabolic crisis in vitro. In addition, we observed a profound decrease in tumor growth in various in vivo models using DRP-104 (sirpiglenastat), a pro-drug version of DON that was designed to circumvent DON associated toxicity. We found that ERK signaling is increased as a compensatory mechanism. Combinatorial treatment of DRP-104 and Trametinib led to a significant increase in survival in a syngeneic model PDAC. These proof-of-concept studies suggested that broadly targeting Gln metabolism could provide a therapeutic avenue for PDAC. The combination with an ERK signaling pathway inhibitor could further improve the therapeutic outcome.
INSTITUTE
New York University
LAST_NAME
Encarnacion Rosado
FIRST_NAME
Joel
ADDRESS
Smilow Research Building Room 907G New York, NY 10016
Intracerebroventricular Transplantation of Foetal Allogeneic Neural Stem Cells in Patients with Secondary Progressive Multiple Sclerosis (hNSC-SPMS): a phase I dose-escalation clinical trial - Metabolomics Analysis of Human CSF
STUDY_SUMMARY
This is an open-label, first-in-human, dose-escalation phase I study (NCT03282760, EudraCT2015‐004855‐37) to determine the feasibility, safety, and tolerability of the transplantation of allogeneic human neural stem/progenitor cells (hNSCs) for the treatment of progressive multiple sclerosis. We report the analysis of 1 year of data from the first cohort of 15 patients from two trial sites that received increasing numbers of allogeneic hNSCs delivered via intracerebroventricular injection in combination with an immunosuppressive regimen. No treatment-related deaths nor serious adverse events (AEs) were observed over the 12-month follow-up. Participants displayed stability of clinical and laboratory parameters, as well as lesion load and activity at the brain MRIs, compared to study entry. Longitudinal metabolomics and lipidomics analyses of cerebrospinal fluid and serum from these patients identified time and dose-dependent responses, with increased levels of free fatty acids and acylcarnitines in the CSF, especially at the highest dose of injected hNSCs at the one-year follow-up time point. Finally, a significant inverse correlation was found between the highest dose of injected hNSCs and the smaller parenchymal brain volume change (PBVC; Spearman’s rho= -0.7, p= 0.03), clinical covariates that correlated with CSF levels of free fatty acids, acyl-carnitines, oxylipins, conjugated bile acids and purine breakdown and deamination products, such as hypoxanthine. The absence of AEs and the stability of functional and structural outcomes is reassuring in terms of risks and represent a main milestone to rigorously address the challenges for the safe translation of key principles of stem cell biology into effective regenerative medicines.
INSTITUTE
University of Colorado
DEPARTMENT
Department of Biochemistry and Molecular Genetics
LABORATORY
Angelo D’Alessandro
LAST_NAME
Stephenson
FIRST_NAME
Daniel
ADDRESS
Research 1 South L18-1303 12801 E. 17th Ave., Aurora, Colorado, 80045, USA
Gut Microbiota-associated Metabolites Affected the Susceptibility to Heart Health Abnormality in Young Migrants at High-altitude-Human Serum Metabolomics
STUDY_SUMMARY
Background: Young migrants in plateau are susceptible to heart health abnormality and even high-altitude heart disease (HAHD). Though the gut microbial community was found to be drastically affected when exposed to a hypobaric hypoxia environment, there is limited knowledge about the roles of gut microbiota and gut microbiota-associated serum metabolites (GMSMs) in high-altitude associated heart diseases. Hence, we performed multi-omics integration analysis of 230 graduates from the same university in this study (163 who migrated to Tibet Plateau and 67 matched controls currently living in Chengdu Plain) to explore how the gut microbiota affect the development of high-altitude associated heart health abnormality. Results: Here, we found 206 differential metabolites (82 from serum and 124 from feces) and 369 differential species among the plateau migrants and plain controls. Of these, 27 differential microbial species and 4 differential metabolites (L-Asp, betaine, 3-GUA, and α-KG) that both existed in serum and feces were related to the plateau migrants with undermined heart health (HH-A), which were diagnosed by biomedical detection, electrocardiography (ECG), frequency-domain Cardiogram (FCG) and ultrasonic cardiogram (UCG). Moreover, the abundances of Streptococcus rubneri and Veillonella rogosae were related with the serum levels of L-Asp, betaine, and α-KG in HH-A individuals. And lower these microbiome biomarkers and GMSMs abundances were validated in an independent cohort, both of which together had an excellent discernibility efficacy of heart health abnormality in plateau migrants, with a higher AUC value of 0.7857. Besides, supplement with the two species or each of GMSMs were confirmed to effectively attenuate hypobaric hypoxia-induced higher serum lactic acid, glycolysis, myocardial damage and cardiac hypertrophy. Integrated analysis revealed significant shift in gut microbiome exerted negative regulations in Malate-Aspartate (MA) shuttle, Tricarboxylic acid cycle (TCA) and oxidative phosphorylation in HH-A individuals. Conclusion: Plateau migration altered profoundly the signatures of gut microbiome and metabolome in young migrants. Hypobaric hypoxia-induced lower abundances of Veillonella rogosae, Streptococcus rubneri, and related GMSMs promoted the remodeling of metabolic processes, resulting in higher susceptibility to heart health abnormality in high-altitude. Our findings not only presented elaborate microbial mechanisms, but also provided potential early risk prediction and therapeutic interventions for HAHD.
INSTITUTE
Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University
DEPARTMENT
Shanghai Center for Systems Biomedicine
LABORATORY
Lu Group
LAST_NAME
Liu
FIRST_NAME
Jingjing
ADDRESS
800 Dongchuan RD. Minhang District, Shanghai, Shanghai, 200240, China
Gut Microbiota-associated Metabolites Affected the Susceptibility to Heart Health Abnormality in Young Migrants at High-altitude-Human Faeces Metabolomics
STUDY_SUMMARY
Background: Young migrants in plateau are susceptible to heart health abnormality and even high-altitude heart disease (HAHD). Though the gut microbial community was found to be drastically affected when exposed to a hypobaric hypoxia environment, there is limited knowledge about the roles of gut microbiota and gut microbiota-associated serum metabolites (GMSMs) in high-altitude associated heart diseases. Hence, we performed multi-omics integration analysis of 230 graduates from the same university in this study (163 who migrated to Tibet Plateau and 67 matched controls currently living in Chengdu Plain) to explore how the gut microbiota affect the development of high-altitude associated heart health abnormality. Results: Here, we found 206 differential metabolites (82 from serum and 124 from feces) and 369 differential species among the plateau migrants and plain controls. Of these, 27 differential microbial species and 4 differential metabolites (L-Asp, betaine, 3-GUA, and α-KG) that both existed in serum and feces were related to the plateau migrants with undermined heart health (HH-A), which were diagnosed by biomedical detection, electrocardiography (ECG), frequency-domain Cardiogram (FCG) and ultrasonic cardiogram (UCG). Moreover, the abundances of Streptococcus rubneri and Veillonella rogosae were related with the serum levels of L-Asp, betaine, and α-KG in HH-A individuals. And lower these microbiome biomarkers and GMSMs abundances were validated in an independent cohort, both of which together had an excellent discernibility efficacy of heart health abnormality in plateau migrants, with a higher AUC value of 0.7857. Besides, supplement with the two species or each of GMSMs were confirmed to effectively attenuate hypobaric hypoxia-induced higher serum lactic acid, glycolysis, myocardial damage and cardiac hypertrophy. Integrated analysis revealed significant shift in gut microbiome exerted negative regulations in Malate-Aspartate (MA) shuttle, Tricarboxylic acid cycle (TCA) and oxidative phosphorylation in HH-A individuals. Conclusion: Plateau migration altered profoundly the signatures of gut microbiome and metabolome in young migrants. Hypobaric hypoxia-induced lower abundances of Veillonella rogosae, Streptococcus rubneri, and related GMSMs promoted the remodeling of metabolic processes, resulting in higher susceptibility to heart health abnormality in high-altitude. Our findings not only presented elaborate microbial mechanisms, but also provided potential early risk prediction and therapeutic interventions for HAHD.
INSTITUTE
Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University
DEPARTMENT
Shanghai Center for Systems Biomedicine
LABORATORY
Lu Group
LAST_NAME
Liu
FIRST_NAME
Jingjing
ADDRESS
800 Dongchuan RD. Minhang District, Shanghai, Shanghai, 200240, China
The role of PFAS exposures in nonalcoholic fatty liver disease and hepatocellular carcinoma in the Multiethnic Cohort
STUDY_SUMMARY
Funding was approved by the NIH HHEAR Program (Study #2020-0500), and analysis was performed within the Mount Sinai HHEAR Laboratories (U2C ES030859 and U2CES026561). 2,952 plasma samples collected from the Multiethnic Cohort (MEC) were provided by the PI (Veronica Setiawan, PhD) and analyzed using liquid chromatography with high-resolution mass spectrometry (LC-HRMS) using a hybrid targeted and untargeted method that provides quantitation of known poly- and per-fluoroalkyl substances (PFAS), as well as untargeted detection of small molecules. Results were reported in terms of untargeted mass spectral signals (Level 5), identified small molecules (Level 1), and computational annotations (Level 3 or 4) according to the MSI Annotation Schemes
INSTITUTE
University of Southern California
LAST_NAME
Veronica
FIRST_NAME
Setiawan
ADDRESS
Genetic Epidemiology NRT 1502 1450 Biggy Street Health Sciences Campus Los Angeles
Comparative multi-omics analyses of cardiac mitochondrial stress in three mouse models of frataxin deficiency
STUDY_SUMMARY
Cardiomyopathy is often fatal in Friedreich Ataxia (FA). However, the FA heart maintains adequate function until disease end stage, suggesting that it can initially adapt to the loss of frataxin (FXN). Conditional knockout mouse models with no Fxn expression show transcriptional and metabolic profiles of cardiomyopathy and mitochondrial integrated stress response (ISRmt). However, ISRmt has not been investigated in models with disease-relevant, partial decrease of FXN. We characterized the heart transcriptomes and metabolomes of three mouse models of partial FXN loss, YG8-800, KIKO-700, and FxnG127V. Few metabolites were significantly changed in YG8-800 mice and did not provide a signature of cardiomyopathy or ISRmt. Instead, several metabolites were altered in FxnG127V and KIKO-700 hearts. Transcriptional changes were found in all models, but differentially expressed genes consistent with cardiomyopathy and ISRmt were only identified in FxnG127V hearts. However, these changes were surprisingly mild even at an advanced age (18-months), despite a severe decrease in FXN levels to 1% of WT. These findings indicate that the mouse heart has extremely low reliance on FXN, highlighting the difficulty in modeling genetically relevant FA cardiomyopathy.
High Level Expression of NSD2 Creates a Metabolic Dependency in Multiple Myeloma
STUDY_SUMMARY
Multiple myeloma (MM) is a malignancy of plasma cells with several molecular subtypes and variable prognosis. Despite therapeutic advances, most patients ultimately relapse due to drug resistance. Frontline treatments for MM target malignant cells based on their differentiated B cell nature, but not the underlying genetic lesions. Chromosomal translocation t(4;14), observed in 15% of MM patients, results in overexpression of the histone methyltransferase NSD2, which contributes to MM pathogenesis by promoting an oncogenic transcriptional program and is associated with a worse prognosis. A genome-wide CRISPR based functional screen in isogenic MM cell lines with high and low NSD2 expression identified the mitochondrial enzyme adenylate kinase 2 (AK2) as a NSD2-driven MM cell dependency. AK2 loss in t(4;14) MM cells induced apoptosis and inhibited cell growth in vitro and in vivo. Consistent with a defect in shuttling ATP from the mitochondria to intracellular utilization sites, AK2 depletion impaired ATP-dependent protein folding in the ER and increased MM cell sensitivity to the proteasome inhibitor bortezomib. Furthermore, AK2 suppression decreased intracellular NAD(H) phosphorylation resulting in lower NADP(H) levels. Cytosolic NADPH is necessary for reducing thioredoxin, an essential cofactor for ribonucleotide reductase which is critical for deoxyribonucleotides (dNTP) synthesis. Consequently, AK2 deficiency in MM cells resulted in dNTP pool depletion and induced DNA replication stress. Creatine phosphorylation by mitochondrial creatine kinase is an alternative route for shuttling ATP from the mitochondria to the cytosol. Metabolomics analysis revealed decreased levels of creatine and accumulation of its precursor guanadoacetate in NSD2 high cells, in association with elevated levels of S-adenosyl homocysteine (SAH) indicating consumption of the carbon donor S-Adenosyl methionine (SAM). This along with the 6-fold increase in genome wide H3K36me2 levels and 40% increase in DNA methylation levels in NSD2 high cells suggested that overexpression of NSD2 redirected one-carbon metabolism to the epigenome and away from the SAM-dependent creatine synthesis. Therefore, decreased creatine levels in NSD2 overexpressing cells underlie the increased reliance on AK2. Correspondingly, supplementation with exogenous creatine restored NADP(H) levels and rescued AK2 deficient cells from apoptosis. These findings revealed a novel metabolic susceptibility in t(4;14) MM and provided insight into a novel therapeutic strategy to improve patient prognosis. We performed metabolomic analysis of multiple myeloma cell lines with either high or low NSD2 levels with or without NSD2 knockdown.
Identification and targeting of microbial putrescine acetylation in bloodstream infections
STUDY_TYPE
comparison of septic shock versus control plasma
STUDY_SUMMARY
To identify bacterial metabolites elevated in human plasma during infection, we performed metabolomics on an existing cohort of patient plasma samples from 21 septic shock patients admitted to the intensive care unit (ICU) with culture positive gram-negative BSIs (Escherichia coli, Klebsiella spp., Pseudomonas spp.) who had banked blood samples drawn contemporaneously or near-contemporaneously with their positive blood cultures as well from 22 controls admitted to the ICU for other reasons.
MoTrPAC: Endurance exercise training study in young adult rats, Rat Kidney Powder - Untargeted Reversed-Phase Negative
STUDY_SUMMARY
The goal of the endurance exercise training study in young adult rats (internal code: PASS1B-06) was to perform exercise training studies in adult (6 month) F344 rats, and from these rats collect as many tissues as feasible in order to provide high quality samples for detailed analysis by chemical analysis sites. Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups. The 8-week training group and controls were from the same cohort and same age at euthanasia (either 8). For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program. Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max as outlined in the Table on the next page. Training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max (see tables) and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31. This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved. If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized. It is important to note that the starting treadmill speed varied depending on the sex and age of the rat. The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats. Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Burant
FIRST_NAME
Charles
ADDRESS
6120 Brehm Tower,1000 Wall St., Ann Arbor, MI, 48105-5714
MoTrPAC: Endurance exercise training study in young adult rats, Rat Heart Powder - Untargeted Reversed-Phase Negative
STUDY_SUMMARY
The goal of the endurance exercise training study in young adult rats (internal code: PASS1B-06) was to perform exercise training studies in adult (6 month) F344 rats, and from these rats collect as many tissues as feasible in order to provide high quality samples for detailed analysis by chemical analysis sites. Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups. The 8-week training group and controls were from the same cohort and same age at euthanasia (either 8). For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program. Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max as outlined in the Table on the next page. Training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max (see tables) and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31. This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved. If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized. It is important to note that the starting treadmill speed varied depending on the sex and age of the rat. The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats. Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.
INSTITUTE
University of Michigan
DEPARTMENT
Biomedical Research Core Facilities
LABORATORY
Metabolomics core
LAST_NAME
Burant
FIRST_NAME
Charles
ADDRESS
6120 Brehm Tower,1000 Wall St., Ann Arbor, MI, 48105-5714
Investigate the impact of feeding time on the hexosamine biosynthetic pathway (HBP) in the mouse liver and heart using targeted metabolomics: biogenic amines
STUDY_SUMMARY
The overall goal of this project is to advance our understanding of post-translational mechanisms that mediate metabolic regulation of time-of-day-specific protein functions to orchestrate daily rhythms and maintain homeostasis in animals. Robust daily biological rhythms over the 24-hour (h) day-night cycles are key hallmarks of animal health span and are strongly regulated by circadian clocks. Circadian clocks are cell autonomous molecular timers present in the brain and in peripheral organs that enable animals to adapt to predictable daily changes in environment and regulate rhythmic processes such as sleep-wake cycles, feeding-fasting cycles, metabolism, hormonal signaling and neuronal excitability. Besides light, the dominant time cue for the brain clock, metabolic signals from clock-controlled feeding-fasting cycles represent the most potent time cue to entrain and synchronize peripheral clocks in key organs. Much effort has been dedicated to understanding the metabolic regulation of daily biological rhythms, but many important mechanisms are only just emerging. We recently established that metabolic signals from feeding-fasting cycles regulate daily biological rhythms in Drosophila through rhythmic O-linked-N-acetylglucosaminylation (O-GlcNAcylation). Protein O-GlcNAcylation is a nutrient sensitive posttranslational modification (PTM) that is tightly linked to metabolic status, as UDP-GlcNAc, the substrate of O-GlcNAcylation, is produced from hexosamine biosynthetic pathway (HBP), which integrates the metabolites from glucose, amino acid, lipid and nucleotide metabolism. We now propose to investigate whether feeding activity can regulate daily O-GlcNAcylation rhythm in mouse liver and heart and whether the levels of HBP metabolites in mouse liver and heart are affected by different feeding time within a day/night cycle. Here, we restricted the feeding time of C57BL/6 male mice to ZT12-24 (RF12-24. ZT, zeitgeber time; ZT0 indicates light on, while ZT12 indicates light off) v.s. ZT0-12 (RF0-12) for 3 weeks and collected liver and heart tissues every 4 hours over a 24-hour period. The liver and heart samples were subjected to targeted metabolomic analysis for HBP metabolites.
INSTITUTE
University of California, Davis
DEPARTMENT
Department of Entomology and Nematology
LABORATORY
Chiu lab
LAST_NAME
Chiu
FIRST_NAME
Joanna
ADDRESS
6352 Storer Hall, One Shields Avenue, Davis, CA 95616, USA
Metabolite flux from temperature-acclimated diatom strains (drawdown experiment)
STUDY_SUMMARY
The temperature increase occurring in the surface ocean has fundamental implications for physiological rates and processes of marine microbes. Here we asked whether the temperature at which a marine diatom strain is acclimated affects carbon transfer to a co-cultured heterotrophic bacterium. Model systems were established in which the diatom Thalassiosira pseudonana was acclimated for three months at temperatures below (14°C), equal to (20°C), and above (28°C) the temperature of optimal growth, and then inoculated with the heterotrophic bacterium Ruegeria pomeroyi. This deposition is for results obtained from a drawdown experiment of phytoplankton metabolites using R. pomeroyi conducted during this study.
Automated preparation of plasma lipids, metabolites, and proteins for LC/MS-based analysis of a high-fat diet in mice
STUDY_TYPE
Method Development
STUDY_SUMMARY
We designed an automated liquid-liquid extraction method with minimal contamination and human intervention. This approach enables accurate and precise collection of metabolite, lipid fractions, and protein pellet from a small volume of mice plasma for multiomic analysis.
Integrating uterine microbiome and metabolome to advance the understanding of the uterine environment in dairy cows with metritis
STUDY_SUMMARY
Background: Metritis is a prevalent uterine disease that affects the welfare, fertility, and survival of dairy cows. The uterine microbiome from cows that develop metritis and those that remain healthy do not differ from calving until 2 days after calving, after which there is a dysbiosis of the uterine microbiome characterized by a shift towards opportunistic pathogens such as Fusobacteriota and Bacteroidota. Whether these opportunistic pathogens proliferate and overtake the uterine commensals could be determined by the type of substrates present in the uterus. The objective of this study was to integrate uterine metabolome and microbiome data to advance the understanding of metritis development in dairy cows. Holstein cows (n = 104) had uterine fluid collected at calving and at the day of metritis diagnosis. Cows with metritis (n = 52) were paired with cows without metritis (n = 52) based on days after calving. First, the uterine metabolome and microbiome were evaluated individually, and then integrated using network analyses. Results: The uterine metabolome differed both at calving and on the day of metritis diagnosis between cows with and without metritis. The uterine microbiome did not differ at calving but differed on the day of metritis diagnosis between cows with and without metritis. Omics integration was performed between 153 significant metabolites and 6 significant bacteria genera on the day of metritis diagnosis. A total of 49 metabolites were correlated with 3 bacteria genera (i.e. Fusobacteria, Porphyromonas and Bacteroides) on the day of metritis diagnosis. The main metabolites have been associated with attenuation of biofilm formation by commensal bacteria, pathogenic bacterial overgrowth, defense mechanisms against the immune system, tissue damage and inflammation, and immune dysregulation. Conclusions: The data integration presented herein helps advance the understanding of metritis development in dairy cows. The identified metabolites may be promising targets for future interventions aiming to reduce pathogenic bacterial growth in the uterus, and therefore, reducing the incidence of metritis.
The role of gut microbiota in muscle mitochondria function, colon health, and sarcopenia: from clinical to bench (2)
STUDY_SUMMARY
Gut microbes produce metabolites in the intestinal lumen, which can travel systemically to affect organs. Metagenomic analysis was performed on liquid chromatographyâmass spectrometry (LC-MS) to detect differential metabolites between people with or without sarcopenia.
Multi-Omics Plasma Signatures of Severe Injury with Influence of REBOA Intervention in a Swine Model.
STUDY_TYPE
Original Research
STUDY_SUMMARY
Swine experienced controlled severe injury involving combinations of trauma, hemorrhagic shock, and disseminated complex blast injury (DCBI). After a period of hemorrhagic shock, resuscitation was performed using Resuscitative Endovascular Balloon Occlusion of the Aorta (REBOA) and shed blood transfusion. Blood samples were collected from sham and experiment swine. Blood samples for experiment swine were collected at baseline and periodically through the monitored time course. The plasma fraction were then subjected to mass spectrometry based metabolomics. Results indicated intervention using REBOA following polytrauma in our swine model induced distinct multi-omics alterations as a function of placement location. Namely, aortic balloon placement in Zone-1 worsened ischemic damage and mitochondrial dysfunction, patterns that continued through the monitored time course.
Plasma instead of serum avoids critical confounding of clinical metabolomics studies by platelets (Part 2/3 - Eicosadomics of isolated platelets)
STUDY_SUMMARY
Metabolomics is an emerging and powerful molecular profiling method supporting clinical investigations. Serum and plasma are commonly used without rational prioritization. Serum is collected after blood coagulation, a complex biochemical process involving active platelet metabolism. This may affect the metabolome and increase the variance as platelet counts and function may vary substantially in individuals. A multi-omics approach systematically investigating the suitability of serum and plasma for clinical studies demonstrated that metabolites correlated well (n=461, R2=0.991), whereas lipid mediators (n=104, R2=0.906) and proteins (n=322, R2=0.860) differed substantially between specimen. Independently, analysis of platelet releasates identified most biomolecules significantly enriched in serum when compared to plasma. A prospective, randomized, controlled parallel group metabolomics trial with acetylsalicylic acid administered for 7 days demonstrated that the apparent drug effects significantly differ depending on analyzed specimen. Only serum analyses of healthy individuals suggested a significant downregulation of TXB2 and 12-HETE, which were specifically formed during coagulation in vitro. Plasma analyses reliably identified acetylsalicylic acid effects on metabolites and lipids occurring in vivo such as a decrease in polyunsaturated fatty acids. The present data suggests that plasma should be preferred above serum for clinical metabolomics studies as the serum metabolome may be substantially confounded by platelets.
Plasma instead of serum avoids critical confounding of clinical metabolomics studies by platelets (Part 1/3 - Plasma and serum eicosadomics)
STUDY_SUMMARY
Metabolomics is an emerging and powerful molecular profiling method supporting clinical investigations. Serum and plasma are commonly used without rational prioritization. Serum is collected after blood coagulation, a complex biochemical process involving active platelet metabolism. This may affect the metabolome and increase the variance as platelet counts and function may vary substantially in individuals. A multi-omics approach systematically investigating the suitability of serum and plasma for clinical studies demonstrated that metabolites correlated well (n=461, R2=0.991), whereas lipid mediators (n=104, R2=0.906) and proteins (n=322, R2=0.860) differed substantially between specimen. Independently, analysis of platelet releasates identified most biomolecules significantly enriched in serum when compared to plasma. A prospective, randomized, controlled parallel group metabolomics trial with acetylsalicylic acid administered for 7 days demonstrated that the apparent drug effects significantly differ depending on analyzed specimen. Only serum analyses of healthy individuals suggested a significant downregulation of TXB2 and 12-HETE, which were specifically formed during coagulation in vitro. Plasma analyses reliably identified acetylsalicylic acid effects on metabolites and lipids occurring in vivo such as a decrease in polyunsaturated fatty acids. The present data suggests that plasma should be preferred above serum for clinical metabolomics studies as the serum metabolome may be substantially confounded by platelets.
Providing insight into the mechanism of action of Cationic Lipidated Oligomers (CLOs) using metabolomics
STUDY_TYPE
Biomedical research
STUDY_SUMMARY
The increasing resistance of clinically relevant microbes against current commercially available antimicrobials underpins the urgent need for alternative and novel treatment strategies. Cationic lipidated oligomers (CLOs) are innovative alternatives to antimicrobial peptides, and have reported antimicrobial potential. An understanding of their antimicrobial mechanism of action is required to rationally design future treatment strategies for CLOs, either in monotherapy or synergistic combinations. In the present study, metabolomics was used to investigate the potential metabolic pathways involved in the mechanisms of antibacterial activity of one CLO, C12-o-(BG-D)-10, which we have previously shown to be effective against methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43300. The metabolomes of MRSA ATCC 43300 at 1, 3 and 6 h following treatment with C12-o-(BG-D)-10 (48 µg/mL i.e., 3x MIC) were compared to those of the untreated controls. Our findings reveal that the studied CLO, C12-o-(BG-D)-10, disorganized the bacterial membrane as the first step towards its antimicrobial effect, as evidenced by marked perturbations in the bacterial membrane lipids and peptidoglycan biosynthesis observed at early time points i.e., 1, and 3 h. Central carbon metabolism, and biosynthesis of DNA, RNA, and arginine were also vigorously perturbed, mainly at early time points. Moreover, bacterial cells were under osmotic and oxidative stress across all time points, evident by perturbations of trehalose biosynthesis and pentose phosphate shunt. Overall, this metabolomics study has, for the first time, revealed that the antimicrobial action of C12-o-(BG-D)-10 may potentially stem from the dysregulation of multiple metabolic pathways.
INSTITUTE
Monash University
DEPARTMENT
Drug Delivery, Disposition and Dynamics
LABORATORY
Cornelia Landersdorfer
LAST_NAME
Hussein
FIRST_NAME
Maytham
ADDRESS
Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
Untargeted MS analysis of maternal liver, CSF, serum, and embryonic CSF and liver, with saline and PolyI:C administrated to mother. Metabolome changes in embryonic CSF 3 hours prior to PolyI:C injection in mother. Metabolome changes in embryonic CSF, maternal and embryonic liver 48 hours following PolyI:C injection in mother.
INSTITUTE
Boston Children's Hospital, Harvard Medical School
Lactiplantibacillus plantarum intervention on fecal bile acids of gestational fecal microbiome transplant germ-free mice
STUDY_SUMMARY
The study aims to investigate whether administration of probiotic L. plantarum could influence profiling of fecal bile acids of germ-free mice. L. plantarum during gestation of humanized GF mice showed that α-MCA, UCA, ACA, β-UDCA, and isoLCA were significantly increased. Other bile acids showed no significant difference.
Parallel pheromonal, metabolite, and lipid analyses reveal patterns associated with early life transitions and ovary activation in honey bee (Apis mellifera) queens
STUDY_SUMMARY
We used a novel pheromone detection method to quantify retinue pheromone (QRP) concurrently with shotgun metabolomics and lipidomics analysis to determine what changes in pheromones and small molecules may underpin differences in age, laying status, and acceptance by workers in honey bee queens.
INSTITUTE
University of British Columbia
DEPARTMENT
Life Sciences Institute
LAST_NAME
Alcazar Magana
FIRST_NAME
Armando
ADDRESS
2350 Health Sciences Mall, Vancouver, BC, V6T1Z3, Canada
Cellular adaptation to cancer therapy along a resistance continuum
STUDY_SUMMARY
Recent research has shed light on the role of non-genetic plasticity in transient drug tolerance and the acquisition of stable resistance. However, the dynamics of cell state transitions occurring in the adaptation to cancer therapies remain elusive and require a systems-level longitudinal framework. Here we demonstrate that resistance develops through trajectories of cell state transitions accompanied by a progressive increase in cell fitness, which we denote the ‘resistance continuum’. This cellular adaptation involves a step-wise assembly of gene expression programs and epigenetically reinforced cell states underpinned by phenotypic plasticity stress adaptation and metabolic reprogramming. Through systematic genetic perturbations, we identify an acquisition of progressive metabolic dependencies, exposing a spectrum of vulnerabilities that can be potentially exploited therapeutically. The concept of the resistance continuum highlights the dynamic nature of cellular adaptation and calls for complementary therapies directed at the mechanisms underlying adaptive cell state transitions.
Effect of high fat diet on serum fatty acids, lipidome and metabolome in CHCHD10 mutant mice
STUDY_SUMMARY
Mutations in CHCHD10, a mitochondrial protein with undefined functions, are associated with autosomal dominant mitochondrial diseases. Chchd10 knock-in mice harboring a heterozygous S55L mutation (equivalent to human pathogenic S59L) develop a fatal mitochondrial cardiomyopathy caused by CHCHD10 aggregation and proteotoxic mitochondrial integrated stress response (mtISR). In mutant hearts, mtISR is accompanied by a metabolic rewiring characterized by increased reliance on glycolysis rather than fatty acid oxidation. To counteract this metabolic rewiring, heterozygous S55L mice were subjected to chronic high fat diet (HFD) to decrease insulin sensitivity and glucose uptake and enhance fatty acid utilization in the heart. HFD ameliorated the ventricular dysfunction of mutant hearts and significantly extended the survival of mutant female mice affected by severe pregnancy-induced cardiomyopathy. Gene expression profiles confirmed that HFD increased fatty acid utilization and ameliorated cardiomyopathy markers. Importantly, HFD also decreased accumulation of aggregated CHCHD10 in the S55L heart, suggesting activation of quality control mechanisms. Overall, our findings indicate that metabolic therapy can be effective in mitochondrial cardiomyopathies associated with proteotoxic stress.
While there is strong evidence for interactions between the microbiota-gut-brain axis and host physiology in the context of chronic stress, limited research has investigated the role of the microbiome in host response to acute stress. Determining the underlying mechanisms by which stress-induced microbiota changes may provoke functional changes in the gut and brain is critical for developing future therapeutics to alleviate the adverse consequences of traumatic stress. Here, we aimed to identify a biological signature of gut metabolites that are significantly altered following exposure to acute restraint stress. Adult male C57Bl/6 conventional, germ-free and colonized germ-free mice underwent a 15-minute restraint stress exposure. Caecal contents were collected from naïve mice and stressed mice, either immediately or 45 minutes following stress. Caecal contents underwent untargeted metabolomics analysis.
While there is strong evidence for interactions between the microbiota-gut-brain axis and host physiology in the context of chronic stress, limited research has investigated the role of the microbiome in host response to acute stress. Determining the underlying mechanisms by which stress-induced microbiota changes may provoke functional changes in the gut and brain is critical for developing future therapeutics to alleviate the adverse consequences of traumatic stress. Here, we aimed to identify a biological signature of gut metabolites that are significantly altered following exposure to acute restraint stress. Adult male C57Bl/6 conventional, germ-free and colonized germ-free mice underwent a 15-minute restraint stress exposure. Caecal contents were collected from naïve mice and stressed mice, either immediately or 45 minutes following stress. Colonic mucosa underwent untargeted metabolomics analysis.
Exploring The Impact of Two Novel DNA Minor Groove Binders on HCT-116 Cells: A Comprehensive Multi-Omics Analysis Using Mass Spectrometry
STUDY_TYPE
LC/MS/MS
STUDY_SUMMARY
Colorectal cancer (CRC) poses a significant global health challenge, necessitating innovative therapeutic approaches. Despite advancements, current treatments encounter obstacles such as chemotherapy resistance and adverse effects due to non-selective targeting. DNA Minor Groove Binders (MGBs) present promising alternatives, targeting DNA structure without causing permanent damage. In this study, two novel MGB compounds were synthesized, MGB30 and MGB32, resembling distamycin, a natural DNA-binding agent. These compounds bind reversibly to the DNA minor groove, influencing DNA structure and inhibiting cancer growth-related enzymes. Our study aims to explore the unique effects of MGB30 and MGB32 on the metabolomic profiles of treated HCT-116 cells using TIMS-QTOF-UHPLC-MS. Objectives include comprehensive analysis, comparison of effects, identification of altered pathways, and insights into MGB compound mechanisms. Additionally, we established four biological replicates for each treatment condition. Advanced statistical analyses, including the two-tailed independent Student's t-test and one-way analysis of variance (ANOVA), were utilized to minimize false discoveries. Our analysis generated a comprehensive dataset from 12 samples, identifying 75 distinct metabolites. The significance of this study lies in elucidating the molecular mechanisms of action of MGB30 and MGB32, crucial for their development as CRC drug candidates.
INSTITUTE
Sharjah Institute for Medical Research
LAST_NAME
Facility
FIRST_NAME
Core
ADDRESS
M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah, Sharjah, UAE, Sharjah, 000, United Arab Emirates
BT-474 cells fed with [13C2] acetate and treated with 1 uM Fasnall or 1 uM GSK2194069 for 24 h
STUDY_TYPE
Intracellular metabolomics, [13C2] acetate
STUDY_SUMMARY
BT-474 breast cancer cells fed with [13C2] acetate and treated with 1 uM Fasnall or 1 uM GSK2194069 for 24 h. Cells were grown in RPMI-1640 with 10% dialyzed FBS.
INSTITUTE
Wistar Institute
DEPARTMENT
Molecular and Cellular Oncogenesis Program, Ellen and Ronald Caplan Cancer Center
Metabolomics of Murine WT or MCJ KO CD19-BBz CD8 CAR-T cells
STUDY_SUMMARY
MCJ/DnaJC15 is an endogenous negative regulator of Complex I and mitochondrial respiration. The goal of these experiments are to characterize the metabolic profile of murine WT or MCJ KO CD8 CD19-BBz CAR-T cells after 3 expansions (6 days) with IL-2 (60IU/ml).
INSTITUTE
University of Colorado School of Medicine
LABORATORY
Laboratory of Angelo D'Alessandro in collaboration with Mercedes Rincon
LAST_NAME
Cendali
FIRST_NAME
Francesca
ADDRESS
13199 East Montview Boulevard, Aurora, CO, 80045, USA
Metabolism of chimeric antigen receptor (CAR) T cells is emerging as an important area to improve CAR-T cell therapy in cancer treatment. Mitochondrial respiration is essential for survival and function of CAR-T cells, but developing strategies to specifically enhance mitochondrial respiration has been challenging. Here we identify MCJ/DnaJC15, an endogenous negative regulator of mitochondrial Complex I, as a metabolic target to enhance mitochondrial respiration in CD8 CAR-T cells. Loss of MCJ in CD8 CAR-T cells increases their in vitro and in vivo efficacy against mouse B cell leukemias. MCJ deficiency in TCR- specific CD8 cells also increases their efficacy against solid tumors in vivo. Furthermore, we reveal that human CD8 cells express MCJ and that silencing MCJ expression increases mitochondrial metabolism and anti-tumor activity of human CAR-T cells. Thus, targeting MCJ to enhance mitochondrial metabolism is a promising therapeutic strategy to improve the efficacy of adoptive T cell therapies.
INSTITUTE
University of Colorado School of Medicine
LABORATORY
Laboratory of Angelo D'Alessandro in collaboration with Mercedes Rincon
LAST_NAME
Cendali
FIRST_NAME
Francesca
ADDRESS
13199 East Montview Boulevard, Aurora, CO, 80045, USA
Fetal growth delay caused by loss of non-canonical imprinting is resolved late in pregnancy and culminates in offspring overgrowth
STUDY_SUMMARY
Germline epigenetic programming, including genomic imprinting, substantially influences offspring development. Polycomb Repressive Complex 2 (PRC2) plays an important role in Histone 3 Lysine 27 trimethylation (H3K27me3)-dependent imprinting, loss of which leads to growth and developmental changes in mouse offspring. In this study, we show that offspring from mouse oocytes lacking the PRC2 protein Embryonic Ectoderm Development (EED) were initially developmentally delayed, characterised by low blastocyst cell counts and substantial growth delay in mid-gestation embryos. This initial developmental delay was resolved as offspring underwent accelerated fetal development and growth in late gestation resulting in offspring that were similar stage and weight to controls at birth. The accelerated development and growth in offspring from Eed-null oocytes was associated with remodelling of the placenta, which involved an increase in fetal and maternal tissue size, conspicuous expansion of the glycogen enriched cell population and delayed parturition. Despite placental remodelling and accelerated offspring fetal growth and development, placental efficiency and fetal blood glucose levels were low, and the fetal blood metabolome was unchanged. Moreover, while expression of the H3K27me3-imprinted gene and amino acid transporter Slc38a4 was increased, fetal blood levels of individual amino acids were similar to controls, indicating that placental amino acid transport was not enhanced. Genome-wide analyses identified extensive transcriptional dysregulation and DNA methylation changes in affected placentas, including a range of imprinted and non-imprinted genes. Together, while deletion of Eed in growing oocytes resulted in fetal growth and developmental delay and placental hyperplasia, our data indicate a remarkable capacity for offspring fetal growth to be normalised despite inefficient placental function and the loss of H3K27me3-dependent genomic imprinting.
Exploration of Zeb1-dependent changes in the redox-lipidome of MDA-MB-231 cells
STUDY_SUMMARY
Human breast cancer MDA-MB-231 wildtype (WT) cells and the stably transduced MDA-MB-231 shZeb1 (stable Zeb1 knockdown) and shCtrl cell lines (control cell line for the stable Zeb1 knockdown) (Spaderna et al. 2008, DOI: 10.1158/0008-5472.CAN-07-5682) were treated with DMSO or RSL3 (1 or 10 µM) for 2 h, 4 h, 6 h or 24 h. The cell pellets were collected and analyzed for their oxidized phospholipid profile by UPLC-MS/MS. Please note that one sample set was measured three times with the same sample-ID, but with different methods (Ox-PE, Ox-PC, Ox-PI), therefore each sub-class has their own raw-data file marked by their corresponding abbreviation (Ox-PE, Ox-PC, Ox-PI; e.g. "210514_MDA_ZEB1_oxPE_dil_UD_std_1ul_JZ_oxPE_MRM_003.wiff", "210514_MDA_ZEB1_oxPC_dil_UD_std_1ul_JZ_oxPC_MRM_002.wiff" or "210514_MDA_ZEB1_oxPI_dil_UD_std_1ul_JZ_oxPI_MRM_001.wiff").
A Covalent Creatine Kinase Inhibitor Ablates Glioblastoma Migration and Sensitizes Tumors to Oxidative Stress.
STUDY_TYPE
Cki treatment on glioblastoma
STUDY_SUMMARY
Glioblastoma is a Grade 4 primary brain tumor defined by therapy resistance, diffuse infiltration, and near-uniform lethality. The underlying mechanisms are unknown, and no treatment has been curative. Using a recently developed kinase inhibitor (CKi), we explored the role of this inhibitor on GBM biology in vitro. While CKi minimally impacted GBM cell proliferation and viability, it significantly affected migration. In established GBM cell lines and patient-derived xenografts, CKi ablated both the migration and invasion of GBM cells. CKi also hindered radiation-induced migration. RNA-seq revealed a decrease in invasion-related genes, with an unexpected increase in glutathione metabolism and ferroptosis protection genes post-CKi treatment. The effects of CKi could be reversed by the addition of cell-permeable glutathione. Carbon-13 metabolite tracing indicated heightened glutathione biosynthesis post-CKi treatment. Combinatorial CKi blockade and glutathione inhibition or ferroptosis activation abrogated cell survival. Our data demonstrated that CKi perturbs promigratory and anti-ferroptotic roles in GBM, identifying the creatine kinase axis as a druggable target for GBM treatment.
INSTITUTE
Northwestern University, Feinberg School of Medicine
Malic Enzyme 2 maintains metabolic state and anti-tumor immunity of CD8+ T cells
STUDY_SUMMARY
For metabolite analysis, naive ME2+/+ and ME2-/- CD8+ T cells were isolated and activated with anti-CD3 (4μg/ml) and anti-CD28 (1μg/ml). Cells were washed twice with ice-cold PBS and metabolites were extracted with ice-cold 80% methanol. The extracts were analyzed by LC-MS/MS.
Metabolomics analysis of human spermatozoa reveals impaired metabolic pathways in asthenozoospermia (MS data)
STUDY_SUMMARY
Background: Infertility is a major health issue, affecting 15% of reproductive-age couples with male factors contributing to 50% of cases. Asthenozoospermia, or low sperm motility, is a common cause of male infertility with complex etiology, involving genetic and metabolic alterations, inflammation, and oxidative stress. However, the molecular mechanisms behind low motility are unclear. In this study, we used a metabolomics approach to identify metabolic biomarkers and pathways involved in sperm motility. Methods: We compared the metabolome and lipidome of spermatozoa of men with normozoospermia (n = 44) and asthenozoospermia (n = 22) using untargeted LC-MS and the metabolome of seminal fluid using 1H-NMR. Additionally, we evaluated the seminal fluid redox status to assess the oxidative stress in the ejaculate. Results: We identified 112 metabolites and 209 lipids in spermatozoa and 27 metabolites in the seminal fluid of normozoospermic and asthenozoospermic men. PCA analysis of the spermatozoa’s metabolomics and lipidomics data showed a clear separation between groups. Spermatozoa of asthenozoospermic men presented lower levels of several amino acids, and increased levels of energetic substrates and lysophospholipids. However, the metabolome and redox status of the seminal fluid was not altered in asthenozoospermia. Conclusions: Our results indicate impaired metabolic pathways associated with redox homeostasis and amino acid, energy, and lipid metabolism in asthenozoospermia. Taken together, these findings suggest that the metabolome and lipidome of human spermatozoa are key factors influencing their motility and that oxidative stress exposure during spermatogenesis or sperm maturation may be in the etiology of decreased motility in asthenozoospermia.
INSTITUTE
University of Aveiro
DEPARTMENT
Department of Chemistry
LAST_NAME
Guerra-Carvalho
FIRST_NAME
Bárbara
ADDRESS
Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
FDX2-KO induces global down-regulation of iron-sulfur cluster-containing proteins and senescence-like growth arrest or death in ovarian cancer cells
STUDY_SUMMARY
Recent studies report molecular mechanisms underlying iron-sulfur cluster (Fe-S) biosynthesis and suggest its importance in health and disease. However, a role for Fe-S biosynthesis in cancer contexts remains unclear. Here we report that FDX2, an Fe-S assembly factor, is indispensable for maintenance of cellular Fe-S-containing proteins (Fe-S protein(s)) and proliferation of ovarian cancer (OVC) cells. CRISPR-screening of all metabolism-related genes in OVC cells identified several Fe-S assembly genes as essential for OVC growth. Using an inducible FDX2-KO OVC line, we found that FDX2 loss promotes either senescence-like growth arrest or cell death, depending on TP53 status. Mechanistically, FDX2-loss caused global but differential post transcriptional down-regulation of Fe-S proteins, in turn perturbing respiration, iron-regulation and redox homeostasis, all associated with DNA damage. These results demonstrate significant roles for Fe-S biosynthesis in OVC proliferation and survival and provide information about how the cellular Fe-S-protein network responds to disruptions in Fe-S assembly.
INSTITUTE
Tohoku University
DEPARTMENT
Graduate School of Medicine
LABORATORY
Department of Biochemical Oncology
LAST_NAME
Tanuma
FIRST_NAME
Nobu-hiro
ADDRESS
2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
Tracing diversion of waste derived carbon to omega fatty acid: a comparative metabolomics approach
STUDY_TYPE
Untargeted GC-MS metabolomics
STUDY_SUMMARY
Thraustochytrids are leading producers of docosahexaenoic acid (DHA); an essential Ï-3 fatty acid with several health benefits. In this study, we evaluated the potential of Schizochytrium limacinum SR21 to convert waste streams such as biodiesel derived glycerol, volatile fatty acid, and waste cooking oil (WCO) into DHA. Maximum DHA was obtained for SR21 when cultivated in combination of glucose, glycerol, and acetic acid (AA). Further, GC-MS based comparative metabolomics was performed for twelve combinations of carbon substrates to understand the participating precursors.
Effect of ACC inhibition on the proportion of PUFAs in phosphatidylcholines in stressed fibroblasts
STUDY_SUMMARY
Consequences of acetyl-CoA carboxylase inhibition by 5-(tetradecyloxy)-2-furoic acid (TOFA) on the phosphatidylcholine fatty acid composition of NIH-3T3 fibroblasts treated with cytotoxic stressors (staurosporine, cycloheximide, etoposide, thapsigargin, valinomycin, myrtucommulone), exposed to tumor necrosis factor α, or deprived of serum for 48 h.
An integrated LC-MS analysis of the biometric characteristics of different time cohorts of race walkers - untargeted
STUDY_SUMMARY
To obtain metabolic changes during endurance exercise, we conducted a metabolomics study in which 19 race walkers were recruited to collect blood at four time points: before, during, after, and after rest until day two using both non-targeted and targeted methods. A total of 859 metabolites and 411 lipids were identified by non-targeted methods, and 465 metabolites were quantitatively identified by targeted methods. This extensive data set provides a valuable resource for understanding systemic metabolic changes caused by race walking and helps researchers identify biomarkers of exercise performance.
INSTITUTE
The First Affiliated Hospital of Dalian Medical University
LAST_NAME
Zhang
FIRST_NAME
yunshu
ADDRESS
No.222 Zhongshan Road, Xigang District, Dalian City, Liaoning Province
Dissecting the Genetic Basis of UV-B Responsive Metabolites in Rice
STUDY_SUMMARY
UV-B, an important environmental factor, has been shown to affect the yield and quality of rice (Oryza sativa) worldwide. However, the biochemical and genetic basis of the metabolome underlying the response to UV-B stress remain elusive in rice. In this study, we performed comprehensive metabolic profiling of leaves from 160 diverse rice accessions under UV-B and normal-light conditions using a widely targeted metabolomics approach. Our results revealed substantial differences in the accumulation of metabolites between the two major rice subspecies indica and japonica, especially after UV-B treatment, shedding light on the possible role and mechanism of metabolome changes in subspecies differentiation and the stress response.
INSTITUTE
Industrial Crops Institute of Hubei Academy of Agricultural Sciences
Malate dehydrogenase (MDH) inhibition assay: Fasnall does not affect MDH activity in vitro
STUDY_TYPE
Intracellular metabolomics, medium metabolomics
STUDY_SUMMARY
The enzymatic activity of porcine malate dehydrogenase (MDH) was reconstructed using NADH and oxaloacetate as substrates. LC-MS/MS was used to monitor the reaction by measuring the accumulation of malic acid and NAD+, as well as the consumption of oxaloacetate and NADH. Fasnall does not affect MDH activity in vitro.
INSTITUTE
Wistar Institute
DEPARTMENT
Molecular and Cellular Oncogenesis Program, Ellen and Ronald Caplan Cancer Center
Incorporation of oleate-d9 and elaidate-d17 in broader lipidome of Huh7 cells.
STUDY_SUMMARY
We analyzed several lipid classes including LPC, LPE, PC, PE, DG, and TG in Huh7 cells treated with BSA-oleate-d9 or BSA-elaidate-d17 to determine their incorporation into the broader lipidome.
Incorporation of oleate-d9 and elaidate-d17 in sphingolipids in Huh7 cells while modulating SPT flux.
STUDY_SUMMARY
We analyzed sphingolipids in Huh7 cells treated with BSA-oleate-d9 or BSA-elaidate-d17 to determine their incorporation into the long-chain base (LCB) of intact sphingolipids. We validated their reduction in abundance through pharmacological inhibition of SPT with myriocin.
Incorporation of oleate-d9 and elaidate-d17 in sphingolipids in Huh7 cells while modulating SPT flux.
STUDY_SUMMARY
We analyzed sphingolipids in Huh7 cells treated with BSA-oleate-d9 or BSA-elaidate-d17 to determine their incorporation into the long-chain base (LCB) of intact sphingolipids. We validated their reduction in abundance through pharmacological inhibition of SPT with myriocin.
Sphingolipid secretory flux from Huh7 SPTLC3 KO cells
STUDY_SUMMARY
We analyzed 13C labeling on sphingolipids in fresh and spent media from Huh7 control and SPTLC3 KO cells treated with BSA-palmitate and the stable isotope tracers [13C]serine and [13C]glycine to measure sphingolipid secretory flux.
Obesity and fatty liver diseases-metabolic dysfunction-associated steatotic liver disease (MASLD and MASH) affect over a third of the global population and are exacerbated in individuals with reduced functional aldehyde dehydrogenase 2 (ALDH2), observed in approximately 560 million people. Current treatment to prevent disease progression to cancer remains inadequate, requiring innovative approaches. We observe that Aldh2-/- and Aldh2-/-Sptbn1+/- mice develop phenotypes of human Metabolic Syndrome (MetS) and MASH with a striking accumulation of endogenous aldehydes such as 4-hydroxynonenal (4-HNE). While phospholipids are often modified by reactive aldehydes that accumulate in the absence of ALDH2, to understand the mechanisms for the differences in liver metabolism in ASKO mice, we analyzed liver metabolomics and lipidomics from mice models. Briefly, C57BL/6 mice (n=15) were from 3 groups (WT, Aldh2-/-(ko), Aldh2-/-Sptbn1+/-(double), n=5 per group) and fed normal chow diet for 10 months. For quality control, 6 QC samples were also included in the analysis (total 21 samples). We observed that livers of Aldh2-/-Sptbn1+/- mice had substantially higher levels of all investigated phospholipids, including ⥠2-fold increase in 26% of phosphatidylethanolamine (PE) lipid types and ⥠2-fold increase in 32% of phosphatidylserine (PS) lipid types, compared to livers of WT mice. Similarly, increased abundances of TGs and diacylglycerides (DGs) lipid types were also observed in the livers of Aldh2-/-Sptbn1+/- mice. These results demonstrated that Aldehydes altered lipid metabolism which may be implicated in the progression of liver MetS, MASLD/MASH in Aldh2-/-Sptbn1+/- mice.
Sphingolipid biosynthetic flux in Huh7 SPTLC3 KO cells
STUDY_SUMMARY
We analyzed 13C labeling on sphingolipids in Huh7 control and SPTLC3 KO cells treated with BSA-palmitate and the stable isotope tracers [13C]serine and [13C]glycine to measure intracellular sphingolipid biosynthetic flux.
Impact of high-fat diet enriched in cis or trans fatty acids and myriocin on the plasma lipoprotein profile of sphingolipids in Ldlr-/- mice
STUDY_SUMMARY
We analyzed sphingolipids in plasma lipoprotein fractions of Ldlr-/- mice fed 1) Cis HFD, 2) Cis HFD + Myriocin, 3) Trans HFD, or 4) Trans HFD + Myriocin. We aimed to determine how dietary cis and trans monounsaturated fatty acids impact sphingolipid enrichment in circulating lipoproteins while pharmacologically inhibiting the initial rate-limiting enzyme of sphingolipid biosynthesis, serine palmitoyltransferase (SPT), via myriocin.
In-depth profiling of biosignatures for Type 2 diabetes mellitus cohort utilizing an integrated targeted LC-MS platform
STUDY_TYPE
Observational study
STUDY_SUMMARY
A cohort of 200 healthy individuals and 100 newly diagnosed Type 2 diabetes mellitus patients from the northern region of China were conducted to profiling the metabolic abnormalities in the condition of diabetes.Then, the data by methods M1-M6 was merged and uploaded as a whole file. The overall differential analysis results were summarized, indicating an obvious metabolic disturbance in amino acid, fatty acids, lysophosphatidyl choline (LysoPC), and triacylglycerol (TAG) under T2DM.
INSTITUTE
The First Affiliated Hospital of Dalian Medical University
LABORATORY
Laboratory of Integrative Medicine
LAST_NAME
Ma
FIRST_NAME
Shurong
ADDRESS
No.222 Zhongshan Road, Xigang District, Dalian City, Liaoning Province
Untargeted analysis of urine samples in a Longitudinal analysis of environmental exposures in pregnancy.
STUDY_SUMMARY
Untargeted analysis of urine samples to measure environmental toxins (inclusive of PAH analytes and untargeted panels which include phenols, parabens, flame retardants, and pesticides) in a longitudinal cohort to determine how levels vary in pregnancy.
Metabolomic and transcriptomic remodeling of bone marrow myeloid cells in response to maternal obesity
STUDY_SUMMARY
Maternal obesity puts the offspring at high risk of developing obesity and cardio-metabolic diseases in adulthood. Here, using a mouse model of maternal high-fat diet-induced obesity, we show that whole body fat content of the Off-HFD increases significantly from very early age when compared to the Off-RD. We have previously shown significant metabolic and immune perturbations in the bone marrow of newly weaned offspring of obese mothers. Therefore, we hypothesized that lipid metabolism is altered in the bone marrow Off-HFD in newly weaned offspring of obese mothers when compared to the Off-RD. To test this hypothesis, we investigated the lipidomic profile of bone marrow cells collected from three-week-old offspring of regular and high fat diet-fed mothers. Diacylgycerols (DAGs), triacylglycerols (TAGs), sphingolipids and phospholipids, including plasmalogen, and lysophospholipids were remarkably different between the groups, independent of fetal sex. Levels of cholesteryl esters were significantly decreased in offspring of obese mothers, suggesting reduced delivery of cholesterol to bone marrow cells. This was accompanied by age-dependent progression of mitochondrial dysfunction in bone marrow cells. We subsequently isolated CD11b+ myeloid cells from three-week-old mice and conducted metabolomics, lipidomics, and transcriptomics analyses. The lipidomic profiles of these bone marrow myeloid cells were largely similar to that seen in bone marrow cells and included increases in DAGs and phospholipids alongside decreased TAGs, except for long-chain TAGs, which were significantly increased. Our data also revealed significant sex-dependent changes in amino acids and metabolites related to energy metabolism. Transcriptomic analysis revealed altered expression of genes related to major immune pathways including macrophage alternative activation, B-cell receptor signaling, TGF signaling, and communication between the innate and adaptive immune systems. All told, this study revealed lipidomic, metabolomic, and gene expression abnormalities in bone marrow cells broadly, and in bone marrow myeloid cells particularly, in the newly-weaned offspring of obese mothers, which might at least partially explain the progression of metabolic and cardiovascular diseases in their adulthood.
INSTITUTE
Oregon Health and Science University
LABORATORY
Maloyan Laboratory
LAST_NAME
Maloyan
FIRST_NAME
Alina
ADDRESS
3181 S.W. Sam Jackson Park Road, Portland, Oregon, 97239-3098, USA
Metabolomics analysis of breast cancer cell lines treated with dimethylmalonate (DMM), GSK2194069, and their combination.
STUDY_SUMMARY
Seven breast cancer cell lines (MDA-MB-468, SUM159PT, MCF7, HCC1806, MDA-MB-231, HS578T, CAL120) were treated with 5 mM DMM, 1 uM GSK2194069, and their combination, for 24 h. Intracellular samples were collected for the metabolomics analysis.
INSTITUTE
Wistar Institute
DEPARTMENT
Molecular and Cellular Oncogenesis Program, Ellen and Ronald Caplan Cancer Center
Plasma concentrations of Fasnall in mice after a bolus of 10 mg/kg administered intraperitoneally.
STUDY_TYPE
Plasma metabolomics
STUDY_SUMMARY
A single dose of 10 mg/kg (drug/body weight) Fasnall was injected intraperitoneally (~50 ul of solution in 1:1 DMSO:PBS), and plasma samples were collected. Blood was collected through a cardiac puncture. EDTA was used as an anticoagulant.
INSTITUTE
Wistar Institute
DEPARTMENT
Molecular and Cellular Oncogenesis Program, Ellen and Ronald Caplan Cancer Center
Metabolomics analysis of zebrafish embryos treated with rotenone, Fasnall, TVB-2640, and GSK2194069
STUDY_SUMMARY
To compare the metabolic effects and toxicity of Fasnall with rotenone in vivo, zebrafish embryos 48 h post-fertilization were exposed to a drug-containing medium for 6 h. Rotenone at 25 nM is lethal to fish embryos, while 5 nM concentration leads to a ~15-fold lactate accumulation. Similarly, Fasnall treatment increases lactate content, although the magnitude of the effect is significantly lower. Unlike 5 nM rotenone, Fasnall treatment does not cause visible phenotypic changes in the yolk. The zebrafish model suggests that Fasnall acts as a Complex I inhibitor in vivo.
INSTITUTE
Wistar Institute
DEPARTMENT
Molecular and Cellular Oncogenesis Program, Ellen and Ronald Caplan Cancer Center
Metabolomics of human serum to support understanding of early metabolic shift in presymptomatic sepsis patients. (Part1 human metabolites)
STUDY_SUMMARY
Sepsis, a life-threatening organ dysfunction caused by a dysregulated response to infection, is a critical medical condition with significant global impact, responsible for 48.9 million cases and 11 million deaths annually. Metabolic dysregulation in sepsis is a critical determinant of disease outcome, yet most studies focus on patients after severe illness onset, comparing septic versus non-septic groups or survivors versus non-survivors. To truly understand this complex disease, it is essential to investigate early metabolic shifts, capturing the transition from simple infection to sepsis. Our untargeted serum metabolome analysis of 152 presymptomatic patients undergoing major elective surgery revealed early metabolic signals in sepsis.
INSTITUTE
Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute
Hypoxia-inducible factor 1α (HIF1α) is a master regulator of biological processes in hypoxia. Yet, the mechanisms and biological consequences of aerobic HIF1α activation by intrinsic factors, particularly in normal (primary) cells, remain elusive. Here, we show that HIF1α signalling is activated in several human primary vascular cells in normoxia, and in vascular smooth muscle cells (VSMCs) of normal human lungs. Mechanistically, aerobic HIF1α activation is mediated by paracrine secretion of three branched chain α-ketoacids (BCKAs), which suppress PHD2 activity via direct inhibition and via LDHA-mediated generation of L-2-hydroxyglutarate. BCKA-mediated HIF1α signalling activation stimulated glycolytic activity and governed a phenotypic switch of pulmonary artery SMCs, which correlated with BCKA metabolic dysregulation and pathophenotypic changes in pulmonary arterial hypertension patients and male rat models. We thus identify BCKAs as novel signalling metabolites that aerobically activate HIF1α and that the BCKA-HIF1α pathway modulates VSMC function, an effect that may be relevant to pulmonary vascular pathobiology.
INSTITUTE
Peking University
DEPARTMENT
Department of Toxicology
LAST_NAME
Xiao
FIRST_NAME
Wusheng
ADDRESS
38 Xueyuan Rd, Haidian District, Beijing, Beijing, 100191, China
Metabolic alterations in pulmonary artery smooth muscle cells of idiopathic pulmonary arterial hypertension (IPAH) patients.
STUDY_SUMMARY
Hypoxia-inducible factor 1α (HIF1α) is a master regulator of biological processes in hypoxia. Yet, the mechanisms and biological consequences of aerobic HIF1α activation by intrinsic factors, particularly in normal (primary) cells, remain elusive. Here, we show that HIF1α signalling is activated in several human primary vascular cells in normoxia, and in vascular smooth muscle cells (VSMCs) of normal human lungs. Mechanistically, aerobic HIF1α activation is mediated by paracrine secretion of three branched chain α-ketoacids (BCKAs), which suppress PHD2 activity via direct inhibition and via LDHA-mediated generation of L-2-hydroxyglutarate. BCKA-mediated HIF1α signalling activation stimulated glycolytic activity and governed a phenotypic switch of pulmonary artery SMCs, which correlated with BCKA metabolic dysregulation and pathophenotypic changes in pulmonary arterial hypertension patients and male rat models. We thus identify BCKAs as novel signalling metabolites that aerobically activate HIF1α and that the BCKA-HIF1α pathway modulates VSMC function, an effect that may be relevant to pulmonary vascular pathobiology.
INSTITUTE
Peking University
DEPARTMENT
Department of Toxicology
LAST_NAME
Xiao
FIRST_NAME
Wusheng
ADDRESS
38 Xueyuan Rd, Haidian District, Beijing, Beijing, 100191, China
Highly reliable LC-MS lipidomics database for efficient human plasma profiling based on NIST SRM 1950
STUDY_SUMMARY
Liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS)-based methods have become the gold standard methodology for the comprehensive profiling of the human plasma lipidome. However, both the complexity of lipid chemistry and LC-HRMS-associated data pose challenges to the characterization of this biological matrix. In accordance with the current consensus of quality requirements for LC-HRMS lipidomics data, we aimed to characterize the NIST® Standard Reference Material for Human Plasma (SRM 1950) using an LC-ESI(+/–)-MS method compatible with high-throughput lipidome profiling. We generated a highly curated lipid database with increased coverage, quality, and consistency, including additional quality assurance procedures involving adduct formation, within-method m/z evaluation, retention behavior of species within lipid chain isomers, and expert-driven resolution of isomeric and isobaric interferences. As a proof-of-concept, we showed the utility of our in-house LC-MS lipidomic database –consisting of 592 lipid entries– for the fast, comprehensive, and reliable lipidomic profiling of the human plasma from healthy human volunteers. We are confident that the implementation of this robust resource and methodology will have a significant impact by reducing data redundancy and the current delays and bottlenecks in untargeted plasma lipidomic studies.
INSTITUTE
Universidad CEU San Pablo
DEPARTMENT
Chemistry and Biochemistry
LABORATORY
CEMBIO
LAST_NAME
Martínez
FIRST_NAME
Sara
ADDRESS
Urbanización Montepríncipe, 28660, Boadilla del Monte, Madrid, Spain
Identify key lipid species in CAF-PDAC crosstalk under hypoxia
STUDY_SUMMARY
This study ran lipidomic profiling to identify the lipids enriched in CAF-conditioned media and depleted in PDAC cell culture under hypoxia at 72 hours.
Effect of insluin on metabolism of ex vivo ischemia heart
STUDY_SUMMARY
Ex vivo hearts were pre-perfused with or without insulin, followed by ischemia induced by the cessation of perfusion. After 25 minutes of ischemia, hearts underwent 30 minutes of reperfusion. Right atrial tissue was then collected for IC-MS analysis. Three groups were included: a control group without ischemia, a group with 25 minutes of ischemia followed by reperfusion, and a group pre-perfused with insulin for 30 minutes prior to ischemia and reperfusion.
INSTITUTE
Mayo Clinic
LAST_NAME
Qiu
FIRST_NAME
Huiliang
ADDRESS
5951 E Mayo Blvd, RE 1-408, Zhu Lab, Phoenix, AZ 85054
Nutrient intervention protects against retinal dysfunction caused by disrupted peroxisomal fatty acid oxidation
STUDY_SUMMARY
Dyslipidemia is a significant contributor to many eye diseases, but the lipid processing pathways are not fully understood. Peroxisomes oxidize very long-chain fatty acids and generate docosahexaenoic acid. Mutations in peroxisomal genes can result in severe neural retinal dysfunction. However, therapeutic approaches for peroxisomal diseases remain scarce. In this study, we found impaired retinal function and altered retinal metabolism in mice lacking the first enzyme of peroxisomal fatty acid oxidation (ACOX1). Supplementation of the depleted metabolite pyruvate or the depleted omega-3 fatty acid docosahexaenoic acid mitigated the progression of retinal dysfunction in Acox1 KO mice. Nutrient intervention may therefore offer a promising therapeutic approach for peroxisomal diseases.
Enoyl-acyl carrier protein reductase (ZmENR1) expression level is critical for de novo fatty acid biosynthesis and anther cuticle and pollen exine formation in maize.
STUDY_SUMMARY
Lipid metabolism is very important for plant male reproduction. Many lipid metabolism genes, male sterility (GMS) genes play a role in the endoplasmic reticulum of anther tapetum, but little is known about GMS genes involved in the de novo synthesis of fatty acids in anther tapetum. Using gene mapping, we cloned a new GMS gene, enoyl-acyl carrier protein (ACP) reductase (ZmENR1). enr1 (mutation of enoyl-ACP reductase gene) has early tapetum degradation, anther epidermis and pollen exine defects. In order to further study the function of ZmENR1, we compared the changes of lipid content in anthers of wild-type (WT) and enr1 mutants at maturity. The expression of ZmENR1 significantly affected the contents of cutin, wax and total fatty acids (TFA) in anthers. In addition, enr1 mutant reduced the expression of cutin/wax and sporopollen related genes to inhibit the formation of anther epidermis and pollen exine. Therefore, our researches provide a new insight into the synthesis of fatty acids mediated by ZmENR1, and provide an insight into the molecular mechanism of ZmENR1 regulating maize male sterility.
INSTITUTE
University of Science and Technology Beijing
LAST_NAME
Zhang
FIRST_NAME
Shaowei
ADDRESS
30 XUEYUAN ROAD, HAIDIAN DISTRICT, BEIJING 100083, CHINA
To examine whether a molecule associated with metabolic liver zonation has an effect on systemic metabolism, we first administer adenoviruses expressing Rspo3 or LacZ (control) into the murine liver. Then, by performing metabolome analyses, we compare the results of Rspo3-mice with those of LacZ-mice.
Candida auris planktonic and dispersed cells Chromatographic analysis using GC-MS
STUDY_SUMMARY
The emerging Candida auris (C. auris) has caused several outbreaks globally. While several studies explored the resistant biofilm formed by C. auris, little is known regarding the cells dispersed following biofilm formation. Herein, I investigated and characterized the cells dispersed from C. auris biofilms. Cells dispersed from biofilm developed in 96 well plate were isolated and counted. GC-MS analysis indicated that dispersed cells exhibit altered metabolic profile that enhance cells survivability under stress and nutrient limit condition. The presented study is the first to explore C. auris dispersed cells and indicated that they are not able to revert to the planktonic mode once released from the biofilm.
Multilevel Plasticity and Altered Glycosylation Drive Aggressiveness in Hypoxic and Glucose-Deprived Bladder Cancer Cells
STUDY_TYPE
MS quantitative analysis
STUDY_SUMMARY
Bladder tumours with aggressive characteristics often present microenvironmental niches marked by low oxygen levels (hypoxia) and limited glucose supply due to inadequate vascularization. The molecular mechanisms facilitating cellular adaptation to these stimuli remain largely elusive. Employing a multi-omics approach, we discovered that hypoxic and glucose-deprived cancer cells enter a quiescent state supported by mitophagy, fatty acid β-oxidation, and amino acid catabolism, concurrently enhancing their invasive capabilities. Reoxygenation and glucose restoration efficiently reversed cell quiescence without affecting cellular viability, highlighting significant molecular plasticity in adapting to microenvironmental challenges. Furthermore, cancer cells exhibited substantial perturbation of protein O-glycosylation, leading to simplified glycophenotypes with shorter glycosidic chains. Exploiting glycoengineered cell models, we established that immature glycosylation contributes to reduced cell proliferation and increased invasion. Our findings collectively indicate that hypoxia and glucose deprivation trigger cancer aggressiveness, reflecting an adaptive escape mechanism underpinned by altered metabolism and protein glycosylation, providing grounds for clinical intervention.
INSTITUTE
Portuguese Oncology Institute of Porto (IPO-Porto)
Untargeted metabolomics of Human embryonic kidney cells (HEK293) infected by Human adenovirus serotype 5 during early and late infection.
STUDY_SUMMARY
Human adenoviruses overtake the DNA replication machinery of the infected host, rewiring mitotic events. Infection leads to the elevations in glucose and glutamine consumption rates, while also increasing lactate production rate. Fibroblast lineages are normally quiescent cells that display a repertoire of responses to certain agonists. Data on the shifts in fibroblast metabolism in response to human adenoviral infection are lacking. Specifically, knowledge pertaining to metabolic shifts aside from those involved in glycolytic metabolism after human adenoviral infection remains sparse. We used an untargeted metabolomic approach to better understand the dynamic metabolic changes to fibroblasts in response to 3 viral dosages, across 4 time points post-infection. Cells were infected for the following periods: 6, 12, 24, and 36 hours. Noninfected cells cultured for 24 hours were used as a negative control. Cells were subjected to the following viral dosages: 0.5, 1.0, and 2.0 multiplicity of infection (MOI) and 6 replicates were used for each experimental condition. Cellular pellets were collected at each time point following the removal of media. Samples were sent to the UC Davis Metabolomics Core for analysis of primary carbons using GC-TOF-MS. Profound shifts were seen in cysteine, purine, and unsaturated fatty acid metabolites. This analysis provides a global perspective and highlights previously underappreciated aspects of how human adenovirus alters host metabolism.
Lipidomics facilitates the discovery of diagnostic biomarkers in patients with chronic total occlusion during the perioperative period
STUDY_SUMMARY
Chronic total occlusion (CTO) is a subtype of cardiovascular disease associated with high mortality and an increased risk of ventricular arrhythmia. This study aimed to investigate lipidomic changes in CTO patients undergoing percutaneous coronary intervention (PCI) using a tandem-lipidomic strategy. We first applied a global lipidomic approach to identify the serum lipidomes of CTO-PCI patients during the perioperative period, successfully separating and identifying over 1,500 lipids. Based on these results, a Multiple Reaction Monitoring (MRM) quantification method was developed and employed for targeted lipidomic analysis. Using a high-throughput MRM tandem liquid chromatography-mass spectrometry approach, 613 lipids were successfully quantified in CTO-PCI patients and control donors. PA 18:2/11:0 emerged as a potential biomarker for distinguishing CTO patients from those suspected of having the condition. Notably, patients with different prognostic outcomes exhibited significantly distinct serum lipidomes in both pre- and post-CTO-PCI samples. This finding suggests that lipidomic data hold significant potential not only for monitoring postoperative prognosis but also for predicting surgical outcomes
Metabolic and Morphometric Analysis of Allometric and Total Liver Growth in Post-Hatch Chickens
STUDY_SUMMARY
This study was designed to characterize the liver and plasma metabolome of Ross 708 broiler chickens. Liver and plasma samples were obtained at necropsy on days 4,6,8,10,12,14,16,18 and 20 post-hatch and frozen in liquid nitrogen. Samples were submitted to the University of Carlifornia Davis campus for metabolomic analysis. Analysis revealed three distinct metabolic periods, A (days 4,6,8), B (days 10,12,14) and C (days 16,18,20). Period A corresponded to metabolism driven by yolk nutrients. Period B was a transition period during which yolk resources were being exhausted, and nutrients from feed were metabolized. Period C corresponded to the metabolism of a mature liver.
FOLFIRINOX effects on lipidomics in pancreatic cancer cells
STUDY_SUMMARY
To understand the effects of FOLFIRINOX treatment on lipid metabolism in PDAC cells, MiaPaCa2 cells were treated with the mFOLFIRINOX cocktail consisted of 5-FU, SN-38 (metabolic product of Irenocan responsible for its inhibitory activity toward DNA topoisomerase I) and oxaliplatin at 10 uM, 5uM and 10 uM, respectively, for 24 hours. The lipids were extracted, and targeted metabolomics screening were carried out to determine the effects of lomitapide treatment.
Metabolomics studies on mouse cecum samples on a Western diet
STUDY_SUMMARY
Targeted metabolomics was performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS).to measure polar metabolites in both positive and negative ionization mode on cecummice tissue acquired after a 30 week dietary intervention.
Lipid Metabolite Profiling of nontuberculous mycobacterial pulmonary disease
STUDY_SUMMARY
In this study, we conducted lipidomic analyses of NTM-PD using lung tissues and serum. First, we aimed to identify characteristic lipid profiles associated with diverse geospatial lesions, enabling correlations with specific pathological findings. Next, we examined how these lesion-specific lipidomic profiles are reflected in serum relative to disease severity. Through these analyses, we sought to deepen our understanding of the role of lipid profiles in the pathophysiology of NTM-PD.
INSTITUTE
Seoul National University College of Medicine and Hospital
Metabolomic analysis of skeletal muscle from fed, starved and tumor-bearing mice.
STUDY_SUMMARY
Improving muscle wasting in cachexia, a complex syndrome of severe muscle wasting associated with diseases such as cancer, is important in reducing resistance to cancer treatment and precocious death. However, the techniques to treat or reverse cancer cachexia have not been identified due to the complexity and opacity of the molecular mechanisms underlying muscle wasting. To better understand the metabolic changes in skeletal muscle during starvation and cancer cachexia, we performed a metabolomic analysis of skeletal muscle (gastrocnemius muscle) from 4-month-old LLC tumor-bearing C57BL/6J male mice, 4-month-old C57BL/6J male mice fasted for 48 hours (starved mice), and 4-month-old control male mice using CE-TOFMS. Our data show that cancer cachexia and starvation induce dynamic metabolomic remodeling of the skeletal muscle, with a particular impact on polyamine metabolism.
INSTITUTE
Kyoto Prefectural University
LAST_NAME
Kamei
FIRST_NAME
Yasutomi
ADDRESS
1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan
Metabolomic analysis of skeletal muscle from control WT, immobilized WT, control mFoxO1,3,4-/- and immobilized mFoxO1,3,4-/- mice.
STUDY_SUMMARY
The Forkhead box O (FoxO) transcription factors have been reported to be critical factors for muscle atrophy in a variety of pathological and physiological conditions, and triple-knockout of FoxO1,3,4 prevented immobilization-induced muscle atrophy in mice. To better understand the FoxO-dependent metabolic changes in skeletal muscle during immobilization, we performed a metabolomic analysis of skeletal muscle (gastrocnemius muscle) from control and 11-day immobilized 4-month-old WT (FoxO1,3,4flox/flox) male mice and age-matched mFoxO1,3,4-/- male mice using CE-TOFMS. Our data show that triple knockout of FoxO1,3,4 prevented the metabolomic remodeling in skeletal muscles caused by immobilization.
INSTITUTE
Kyoto Prefectural University
LAST_NAME
Kamei
FIRST_NAME
Yasutomi
ADDRESS
1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto, 606-8522, Japan
The Chromosome-Scale Assembly and Multi-Omics Analysis Reveal Adaptive Evolution and Nitrogen Utilization Mechanisms in Edible Grass (Rumex patientia L.Ã Rumex tianschanicus A. LOS)
STUDY_SUMMARY
Edible grass (Rumex patientia L.à Rumex tianschanicus A. LOS), a perennial herbaceous plant from the Polygonaceae family, boasts a high protein content and rapid growth rate, making it a promising solution to feed shortages as a forage protein source. In this study, we utilized the PacBio sequencing platform and integrated methods including Hi-C to achieve a chromosomal-scale assembly of the R. patientia genome. The assembled genome spans 2.19 Gb with an N50 of 18.84 Mb, and 93.61% (2.05 Gb) of the assembly has been allocated to 30 pseudochromosomes. Comparative genomic analysis has revealed significant expansion of gene families involved in nitrogen metabolism and D-glutamine and D-glutamate metabolism pathways, which are responsible for the plant's strong nitrogen utilization capabilities and high protein content. Additionally, expansions in gene families associated with the Wnt signaling pathway, ubiquitin-mediated proteolysis, Toll and Imd signaling pathways, TGF-β signaling pathway, protein processing in the endoplasmic reticulum, photosynthesis-antenna proteins, circadian rhythm, and cell cycle pathways are closely related to the rapid growth and development of R. patientia. We have also identified the rhizosphere microbiome of R. patientia and, by integrating metabolomic data from root tissues and soil, found that during rapid growth phases, the plant secretes various apigenin-like compounds into the soil, enhancing the symbiotic nitrogen-fixing capabilities and potentially providing nitrogen sources to the leaves through symbiotic nitrogen fixation. Our research provides crucial insights into the genetic basis of R. patientia 's utility as a forage protein source.
INSTITUTE
Hunan Agricultural University
LAST_NAME
li
FIRST_NAME
zhu
ADDRESS
1 Nongda Road, Changsha City, Hunan Province, Changsha, Hunan, 410128, China
Cardiac metabolome signatures of hepato-cardiac FGF21 signaling in pressure overload-induced cardiac hypertrophy
STUDY_SUMMARY
This study investigates the early (3 days) mid- (2 weeks) and late (8 weeks) cardiac metabolome changes driven by FGF21 signaling in the context of pressure overload-induced cardiac hypertrophy. Targeted NMR-based metabolomic profiling was performed on cardiac tissue from control mice at 3 days, 2 weeks, and 8 weeks following transverse aortic constriction (TAC), as well as from hepatocyte-specific (HEP-FGF21) and cardiomyocyte specific (CM-FGF21) Fgf21 knockout mice at the 8-week post-TAC timepoint. Sham-operated wild type mice and mice expressing Cre in hepatocytes or cardiomyocytes served as controls for each timepoint. The early and mid-timepoints were selected to capture transient and potentially triggering metabolic adaptations that precede overt cardiac remodeling, while the late timepoint allowed assessment of established metabolic reprogramming in advanced hypertrophy. Inclusion of the knockout models at 8 weeks enabled dissection of the respective contributions of endocrine (hepatocyte-derived) and autocrine (cardiomyocyte-derived) FGF21 signaling to the cardiac metabolome phenotype. The analysis revealed time-dependent alterations in the metabolic profile, with lower glucose and glucose derived metabolites in early timepoints and accumulation of Branched-Chain Amino Acids when pathological hypertrophy has fully developed (8 weeks). Ablation of Fgf21 in either the hepatocytes or cardiomyocytes mitigated maladaptive metabolic remodeling at 8 weeks, highlighting distinct and cooperative roles of hepatic and cardiac FGF21 in the progression of hypertrophy.
INSTITUTE
University of Cincinnati College of Medicine
LAST_NAME
Siokatas
FIRST_NAME
Georgios
ADDRESS
231 ALBERT SABIN WAY, University of Cincinnati, Cincinnati, OH, 45267-2827
Screen potential marker proteins influencing spermatogenesis in the testes of Shandong Black Cattle bulls via multi-omics integrated analysis.
STUDY_SUMMARY
This study was designed to identify candidate marker proteins that influence the growth and development of Shandong Black Cattle bull testes through a multi-omics joint analysis, thereby providing a certain theoretical basis for testis growth and development as well as bull selection. Eight 12-month-old Shandong Black Cattle bulls were selected, and testes tissues were collected. The testes were categorized into two groups based on their morphological characteristics: Group 1 (weight > 120 g) and Group 2 (weight < 120 g). Group 2 was employed as the control group to construct a protein and metabolite library for joint analysis to screen candidate marker proteins that affect testis growth and development. The results revealed that 1553 differential proteins (DEPs) were differentially expressed between the large and small testes of Black Bleykett bulls, with 1219 being upregulated and 334 being downregulated. The KEGG enrichment results manifested that the upregulated DEPs were primarily involved in the cell cycle (CDK1, CCNB, MCM4), DNA replication (MCM3, MCM4), etc. The downregulated DEPs were mainly associated with metabolic pathways (ACSM1, IMPDH1), etc. The GO enrichment results disclosed that the DEPs were significantly enriched in the categories of cytoskeleton movement. The weighted gene co-expression analysis suggested that the testis weight was significantly correlated with MCM, STRADA, and SEC31B. After integrating the DEPs, a PPI analysis was performed, and 10 key regulatory proteins were identified, including MCM3, MCM4, CDK1, and CDK2. Metabolomics demonstrated that 59 upregulated metabolites were enriched in the glucose metabolism pathway (uridine diphosphate glucose), and 14 downregulated metabolites were significantly enriched in metabolic pathways (hypoxanthine).
Human to mouse microbiota transfer model demonstrates disease-modifying effects of the short-chain fatty acid biotherapy modified microbiota
STUDY_TYPE
Biomedical research
STUDY_SUMMARY
We used a human-to-mouse fecal microbiota transfer model to investigate whether the functional changes in the human microbiota present after the Short-chain fatty acid biotherapy (SCFA-biotherapy) could modify gut microbiome and thus stool metabolome in pups. Oral delivery of a SCFA-yielding biotherapy in adults with T1D was followed by increased SCFAs, altered gut microbiota and immunoregulation, as well as delaying diabetes in preclinical models. Fecal microbiota transfer demonstrated that the microbiota of SCFA-responders modified gut bacteria metabolism in humanized gnotobiotic mice.
Lactate activates trained immunity by fueling the tricarboxylic acid cycle and regulating histone lactylation
STUDY_SUMMARY
Using 13C-based metabolic tracers, we investigate the role of physiologic carbon sources (PCSs) on glucose metabolism in trained immunity. β-glucan treatment led to the rapid conversion of 13C-glucose into lactate and intracellular TCA cycle intermediates (e.g., citrate and fumarate) within the first 8 hours in monocytes. As expected, glucose and glutamine were consumed within 12-24 hrs during the trained immunity process, and PCS treatment mildly affected glucose and glutamine consumption in β-glucan treated monocytes. A slower decrease of other carbon sources, including βOHB, citrate, and pyruvate, was observed in the PCS-supplemented medium compared to the glucose-supplemented medium.
INSTITUTE
Wuhan University
LAST_NAME
Liu
FIRST_NAME
Shi
ADDRESS
Luojia Hill, Wuchang District, Wuhan, Hubei, 430072, China
Metabolomics Analysis of the Silkworm Cocoon Shell
STUDY_TYPE
metabolomics
STUDY_SUMMARY
In this study we conducted metabolomics analyses of historical and contemporary Bombyx mori cocoon shells to case-study the human-driven introduction and diversification of this species in Europe. We employed LC-MS/MS analyses protocols for 80 cocoon shell samples to identify that the cocoon shell of this species contains 141 metabolites in 80% of the samples. Our metabolomics datasets provide a valuable foundation for advancing further exploitations of silkworm cocoon shells in multiple scientific perspectives.
Untargeted metabolome analysis of control and disease intervertebral disc tissue
STUDY_TYPE
UHPLC-MS/MS untargeted Metabolomics
STUDY_SUMMARY
Intervertebral disc degeneration (IVDD) is a multifactorial disease which causes structural and biochemical changes that leads to disability. Identifying the molecular signatures in the intervertebral disc (IVD) during degeneration is crucial to understand the disease pathogenesis. The study aims to identify the metabolic alterations during IVD degeneration. Control and disease IVD tissues were collected and the metabolites were extracted from nucleus pulposus tissue (NP) using triple solvent mixture (Methanol: Acetonitrile: Methanol with 2:2:1 ratio) and profiled using UHPLC-ESI-MS/MS. Untargeted metabolomics identified 832 metabolites from control and disease samples. Differential analysis revealed alterations in amino acids and lipids predominantly. Pathway analysis showed altered metabolites are associated to amino acids category and Phenylalanine and proline are the top upregulated metabolites. Phenylalanine metabolism is the enriched pathway for the upregulated metabolites. In case of lipids, fatty acyl, sphingolipids, glycerophospholipids, prenol lipids were altered during disease. Further large scale analysis are necessary to validate the findings.
INSTITUTE
Ganga Orthopaedic Research and Education Foundation
DEPARTMENT
Proteomics
LABORATORY
Proteomics
LAST_NAME
Tangavel
FIRST_NAME
Dr. Chitraa
ADDRESS
Ganga Research Centre, 442, Vattamalaipalayam, NGGO Colony, Coimbatore-641022, Coimbatore, Tamil Nadu, 641022, India
Respiration defects limit serine synthesis required for lung cancer growth and survival - Effect of Polg mutation in NSCLC Em tumor derived cell lines (TDCLs)
STUDY_SUMMARY
This study investigates the impact of mtDNA mutation burden induced by the PolGD256A mutation in NSCLC tumor derived cell lines (TDCLs). We characterized the metabolic profile of TDCLs harboring this mutation compared to controls. KP: NSCLC TDCLs generated from conditional animals PGKP: NSCLC TDCLs generated from conditional animals bearing PolG mutation. Here, we show that PolG mutation causes mitochondrial dysfunction, impacting serine/glycine metabolism as well as energy metabolism through glycolysis due intensive usage of glucose over time.
Respiration defects limit serine synthesis required for lung cancer growth and survival - NSCLC rewires glycolytic metabolism to synthesize more serine from glucose (Tumors)
STUDY_TYPE
In vivo Isotope Tracing
STUDY_SUMMARY
This study investigates the impact of mtDNA mutation burden induced by the PolGD256A mutation in Non-Small cell lung cancer (NSCLC). Using in vivo, we characterized the metabolic profile of NSCLC harboring this mutation compared to controls after submit the animals to 12 weeks of special diet and 2h30 of [U-13C]D-Glucose infusion. Here we found that mitochondria impairment causes more use of glucose to synthesize serine in NSCLC tumors but not in other tissues (lungs, liver, plasma, and muscle. Due the lack of carbons from glucose to TCA (Tricarboxylic acid cycle) the PGKP cells have an energetic imbalance. WT: Wild Type animals KP: NSCLC conditional animals PolG: Animals with PolG mutation PGKP: NSCLC conditional animals with PolG mutation
G1P promotes pentose phosphate pathway in CD8+ memory T cells via glycogen-G6PD phase separation and compartmentalization
STUDY_SUMMARY
Glucose-6-phosphate (G6P) is a key metabolic molecule that regulates reactive oxygen species (ROS) homeostasis by initiating the pentose phosphate pathway (PPP) to generate NADPH that converts H2O2 to water by providing hydrogen. While both glucose phosphorylation and glycogenolysis result in G6P production, here we show that G6P derived from glycogenolysis, rather than glucose phosphorylation, flows to PPP for ROS clearance in CD8+ memory T (Tm) cells and inflammatory macrophages. Mechanistically, glycogenolysis-produced G1P allosterically induces G6P dehydrogenase (G6PD) binding to glycogen, which together undergo liquid-liquid phase separation (LLPS) and recruit PPP enzymes, resulting in a compartmentalized reaction cascade. Based on mechanistic elucidation, we demonstrated that G1P can act as an antitumor immunotherapeutic agent by modulating memory fitness and maintenance of tumor-reactive CD8+ T cells in mice. These findings revealed an unusual function of glycogen metabolism, which is of paramount importance in the regulation of PPP and redox homeostasis in cells.
NMR-based Urinary Biomarkers in Pediatric Primary Mitochondrial Disorders and Chronic Kidney Disease: Shared Mitochondrial Dysfunction, Diverging Biosignatures
STUDY_TYPE
Prospective
STUDY_SUMMARY
Background: Renal involvement is a frequent manifestation of primary mitochondrial disorders (PMD), either as a presenting feature or during the disease course. Simultaneously, the metabolomic profile of chronic kidney disease (CKD) is often associated with underlying mitochondrial dysfunction. This study aimed to characterize urinary metabolic signatures in genetically confirmed paediatric PMD without chronic kidney disease, comparing them to healthy controls, suspected (unconfirmed) mitochondrial disease (SMD), and non-mitochondrial CKD. Methods: We performed untargeted 1H-NMR metabolomic profiling of 76 urine samples from 61 paediatric patients. Outlier samples and patients undergoing acute decompensation were excluded from the main analyses. Final comparisons included genetically confirmed PMD without CKD (n = 13);, SMD (n = 10), non-mitochondrial CKD (n = 28; 17 at stages 1–2 and 9 at stages 3–5), and healthy controls (n = 10). Spectral data was analysed using multivariate (PCA, PLS-DA) and univariate approaches after normalization to urinary creatinine or total spectral area. Results: Correlations between normalization strategies varied across metabolites (Pearson r ranging from –0.32 to 0.98), underscoring the need for cautious interpretation of normalization-dependent findings. PMD patients exhibited distinct urinary metabolic profiles compared to controls (high predictive value, Q² = 0.52), with significantly elevated levels of several metabolites, including 4-aminohippurate, homovanillic acid (HVA), cis-aconitate, and fumarate were significantly elevated in PMD patients and remained discriminative compared to both CKD and control groups. A multimetabolite panel comprising 4-aminohippurate, HVA, histidine, and cis-aconitate achieved high diagnostic accuracy for distinguishing PMD from CKD stage 3–5 (AUC = 0.944), integrating complementary metabolic pathways related to energy metabolism, amino acid handling, and tubular function. Conclusion: Urinary metabolomic profiling by 1H-NMR revealed a distinct biosignature in paediatric PMD patients without renal involvement, characterized by elevated levels of 4-aminohippurate, HVA, and TCA cycle intermediates. The consistent increase in 4-aminohippurate and HVA—both reliant on energy-dependent proximal tubular excretion—points to impaired mitochondrial modulation of tubular function, even in the absence of overt renal disease. These findings support the use of urinary 1H-NMR metabolomics as a non-invasive tool for biomarker discovery in PMD and highlight the potential of integrated, multiparametric metabolic fingerprints for diagnostic refinement and patient stratification.
INSTITUTE
University of Aveiro
DEPARTMENT
Reference Center for Inherited Metabolic Disorders, Centro Hospitalar Universitario de Santo António
LABORATORY
Department of Chemistry and CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
LAST_NAME
Paiva Coelho
FIRST_NAME
Margarida
ADDRESS
Largo da Maternindade, S/N 4050 Porto
EMAIL
mmargaridacoelho.dca@chporto.min-saude.pt
PHONE
+351913448849
NUM_GROUPS
6
TOTAL_SUBJECTS
60
NUM_MALES
35
NUM_FEMALES
25
STUDY_COMMENTS
Raw NMR data (.fid, acqus, pdata/1) and processed spectral matrices included. Spectra acquired using Bruker AVANCE III 500 MHz spectrometer and normalized to total area. Ocasional urine samples irrespective of fasting period
Effect of Desiccation of Mycobacterium tuberculosis metabolism
STUDY_TYPE
Metabolomics
STUDY_SUMMARY
Mycobacterium tuberculosis (Mtb) is an obligate human pathogen that depends on its ability to spread from host-to-host to survive as a species. Yet, knowledge of transmission-specific traits remains lacking. Here, we report the discovery of a specific adaptive response to desiccation, a stress intrinsically linked to the generation of the aerosol droplets within which Mtb transmits. We show that desiccation inflicts oxidative damage and activates Mtb’s DNA repair responses but that this repair is imperfect and results in mutations. We further show that activation of these DNA repair responses is accompanied by increased expression of the transcription-coupled repair factor, mfd, but that this expression serves to buffer the fitness cost of specific resistance-conferring mutations in rpoB, the target of the frontline drug rifampin, rather than to facilitate transcription-coupled DNA repair. Silencing mfd during aerosolization impairs survival of strains harboring the rifampin resistance allele S450L. This function is further supported by whole genome sequence data from over 50,000 clinically circulating strains. These studies indicate that Mtb has evolved transmission-specific stress responses that have enabled it to leverage desiccation-induced DNA damage as a potential source of genetic diversification and drug resistance.
INSTITUTE
Weill Cornell Medicine
DEPARTMENT
Department of Medicine, Division of Infectious Diseases
Trehalose catalytic shift inherently enhances phenotypic heterogeneity and multidrug resistance in Mycobacterium tuberculosis
STUDY_SUMMARY
Drug-resistance (DR) in bacteria often develops through the repetitive formation of drug-tolerant persister cells, which survive antibiotics without genetic changes. It is unclear whether Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis (TB), undergoes a similar transitioning process. Recent studies highlight changes in trehalose metabolism as crucial for Mtb persister formation and drug resistance. In this study, we observe that mutants lacking trehalose catalytic shift activity exhibited fewer DR mutants due to decreased persisters. This shift enhances Mtb survival during antibiotic treatment by increasing metabolic heterogeneity and drug tolerance, facilitating drug-resistance. Rifampicin (RIF)-resistant bacilli display cross-resistance to other antibiotics linked to higher trehalose catalytic shift, explaining how multidrug resistance (MDR) can follow RIF-resistance. In particular, the HN878 W-Beijing strain exhibits higher trehalose catalytic shift, increasing MDR risk. Both genetic and pharmacological inactivation of this shift reduces persister formation and MDR development, suggesting trehalose catalytic shift as a potential therapeutic target to combat TB resistance.
INSTITUTE
University of Southern California
LAST_NAME
Eoh
FIRST_NAME
Hyungjin
ADDRESS
1501 San Pablo Street, Los Angeles, CA, 90033, USA
Measuring PC lipids in HCMV infected fibroblasts treated with phosphonoacetic acid (PAA).
STUDY_SUMMARY
HCMV viral gene expression is classified into three kinetic classes, immediate early (IE), early (E) and late genes (L). HCMV promotes PC lipids by 48 hpi relative to uninfected cells, suggesting the involvement of an IE or E viral protein in regulating PC lipid levels. Viral DNA synthesis initiates L viral gene expression. Phosphonoacetic acid (PAA) inhibits HCMV genome replication and consequentially, L gene expression. Therefore, we used PAA to test whether L gene expression was required to reprogram PC lipid levels in HCMV infection. We find that PAA-treated cells contain similar levels of PC lipids to vehicle-treated conditions thus, L HCMV gene expression is not required to promote PC levels.
Measuring de novo PC synthesis in HCMV infected fibroblasts using 13C-choline.
STUDY_SUMMARY
The host de novo PC pathway is the canonical pathway for PC synthesis. We determined if the de novo PC pathway was active in HCMV infection. Our findings demonstrate that infection promotes the de novo PC pathway to increase PC lipids.
Measuring PC synthesis via Land Cycle in HCMV infected fibroblasts using labeled LPC(17:0).
STUDY_TYPE
Experimental design: isotopic MS labeling and MS/MS abundance data.
STUDY_SUMMARY
The Lands Cycle remodels and synthesizes PC lipids via the addition of a fatty acid tail to a one-tailed Lyso PC (LPC) lipid. Here, we measure the synthesis of PC lipids using a deuterium-labeled LPC(17:0) to track the conversion of LPC to PC in HCMV infection. d5-LPC(17:0) produces a mass shift of Δ5.0313 and contained a mass spectral peak of 269.249 m/z corresponding to the C17:0 fatty acid of exogenously supplied d5-LPC(17:0). We find that HCMV-infected and uninfected cells exhibit similar levels of constitutive pathway activity.
Experimental design: isotopic MS labeling and MS/MS abundance data.
STUDY_SUMMARY
The levels of PC lipids are reported to increase in HCMV-infected cells. These studies were performed using growth conditions previously used in the HCMV field but are limited in their conclusions regarding our understanding of host and virus factors that influence the PC lipid phenotype observed in HCMV infection. Therefore, we tested several growth conditions including, cell type confluency, presence of serum, MOI, etc., that could impact the increase in PC lipids observed in HCMV infection. We find that HCMV promotes the levels of most PC lipids, including PC-VLCFAs.
Competitive inhibition of SNAT2-dependent MeAIB uptake by saturating concentrations of L-alanine.
STUDY_SUMMARY
MeAIB uptake in SNAT2-expressing HY15549 cells was inhibited by co-treating with a concentration gradient of L-alanine from 20 mM to 0.04 mM and 0.5 mM of MeAIB.
INSTITUTE
University of British Columbia
DEPARTMENT
Biochemistry & Molecular Biology
LABORATORY
Parker laboratory
LAST_NAME
Parker
FIRST_NAME
Seth
ADDRESS
950 W 28th Ave, Vancouver, British Columbia, V6H 0B3, Canada
Targeted Stable Isotope Labeling (SIL) LCMS/MS Methods for Uniformly Labeled Glucose and Glutamine through Glycolysis, TCA Cycle, Hexosamine Biosynthetic Pathway, and Glutaminolysis
STUDY_SUMMARY
The goal of this study was to generate targeted LCMS/MS methods for stable isotope labeling (SIL) through glycolysis, tricarboxylic acid cycle, glutaminolysis, and the hexosamine biosynthetic pathway using either uniformly carbon-13 labeled glucose or glutamine. This method generation included the visualization of carbon-13 labeling through detailed labeling maps; identification of carbon-13 labeled metabolite masses and fragmentation patterns, including chemical structures; and confirmatory experiments detailing the efficacy of the method. The data in this project was used to confirm targeted SIL methods over a time course and after treatment with glycolytic and glutaminolysis inhibitors. All metabolites were converted to nmol using the area ratio of the peak area of analyte to the peak area of the internal standard (100 nmol for each sample) before normalization to protein concentration.
Untargeted Metabolomics Identifies Oncometabolites Induced by P2-HNF4α Overexpression in Hepatocytes
STUDY_SUMMARY
This study explores the metabolic impact of P2-HNF4α overexpression in primary mouse hepatocytes. Using untargeted metabolomics, we compared metabolite profiles between control and P2-HNF4α-overexpressing cells to identify metabolic pathways potentially altered in liver disease and HCC.
LC-TOFMS-based metabolomic analysis of serum from Normal and High-fat diet-fed mice
STUDY_SUMMARY
To investigate diet-induced changes in serum metabolites, especially lipids related to ovarian cancer proliferation, we analyzed blood serum samples from ten mice—five fed a Normal diet and five fed a High-fat diet. Samples were subjected to LC-TOFMS in both positive and negative ion modes. A total of 210 metabolite peaks were detected (115 in positive mode, 95 in negative mode), and putative compound identities were assigned using the Human Metabolome Technologies (HMT) library. Metabolome analysis revealed that serum cholesterol (C₂₇H₄₆O) levels were significantly elevated in the High-fat diet group. Cholesterol exhibited the highest Variable Importance in Projection (VIP) score in partial least squares discriminant analysis, indicating its strong contribution to the metabolic differences between diet groups. Principal Component Analysis (PCA) and hierarchical clustering further demonstrated clear separation between Normal and High-fat diet samples, confirming distinct metabolic profiles induced by diet. The data will be used to identify metabolites differentially expressed in the HFD group that may influence ovarian cancer cell behavior.
The secreted metabolite sensor CtBP2 links metabolism to healthy lifespan
STUDY_SUMMARY
While metabolic homeostasis is coordinated by metabolite-sensing molecules within a cell, their roles in horizontal regulation across cells remain underexplored. Here, we describe a system regulated by a metabolite sensor CtBP2. CtBP2 is secreted via exosomes in response to reductive metabolism, which is suppressed by oxidative stress. A series of pro-longevity agents induce CtBP2 secretion, and administration of exosomal CtBP2 extends lifespan of aged mice. Consistently, serum CtBP2 concentrations are higher in human subjects from families with a history of longevity and exhibit an age-dependent decline. Healthspan is also improved by exosomal CtBP2, as exemplified by protection against frailty in mice and negative associations between serum CtBP2 levels and cardiovascular diseases in humans. These health benefits could be attributed to the proper channeling of reducing equivalents into a chain of activation of CYB5R3 and AMPK. Our findings illustrate a previously uncharacterized metabolic system that provides insights into the regulation of human health and holds promise for future clinical applications.
Metabolite profiling in the glycerol kinase (GK), GPD1 and GAPDH genes into the reconstituted ChREBPα-MLX HEK293T system alongside green fluorescent protein (GFP).
STUDY_SUMMARY
To distinguish between potential ChREBP-activating ligands, we introduced glycerol kinase (GK), GPD1 and GAPDH genes into the reconstituted ChREBP MLX HEK293T system alongside green fluorescent protein (GFP).Relative quantification of 137 metabolites showed that in these cells, GPD1 strongly depressed levels of GA3P and DHAP, while elevating G3P.
Cytosolic Acetyl-Coenzyme A is a signaling metabolite to control mitophagy
STUDY_SUMMARY
Acetyl-Coenzyme A (AcCoA) sits at the nexus of nutrient metabolism and shuttles between the canonical and non-canonical tricarboxylic acid cycle (TCA ) cycle, which is dynamically regulated by nutritional status, such as fasting. We found that reducing cytosolic acetyl-CoA levels triggers mitophagy by short-term fasting, and ATP-Citrate Lyase (ACLY), mitochondrial citrate/malate antiporter (SLC25A1) or acyl-CoA synthetase short chain family member 2 (ACSS2) inhibition, which can be counteracted by acetate supplementation. Interestingly, NOD-like receptor family member X1 (NLRX1) is identified to mediate this effect. Disrupting NLRX1 abrogates cytosolic AcCoA reduction-induced mitophagy both in vitro and in vivo. Mechanically, the mitochondria outer membrane-localized NLRX1 directly binds to cytosolic AcCoA within a conserved pocket on its leucine-rich repeat (LRR) domain. In addition, AcCoA binds to the LRR domain and enhances its interaction with the nucleotide-binding and oligomerization (NACHT) domain, which helps to maintain NLRX1 in an auto-inhibited state and prevents the association between NLRX1 and light chain 3 (LC3). Furthermore, we discover that the AcCoA-NLRX1 axis underlies KRAS inhibitor-induced mitophagy response and promotes drug resistance, providing a metabolic mechanism of KRAS inhibitor resistance. Collectively, cytosolic AcCoA is a signaling metabolite connecting metabolism to mitophagy through its receptor NLRX1.
INSTITUTE
Fudan University
LAST_NAME
Lei
FIRST_NAME
Qun-ying
ADDRESS
131 Dongan Road, Shanghai, Shanghai, 200032, China
Equilibrative Nucleoside Transporter 2 Modulates Inosine Catabolism to Influence Astrocyte Metabolism and Reactivity
STUDY_SUMMARY
In this study, we demonstrate that inosine functions as an essential energy substrate for astrocytes under inflammatory conditions. Targeted metabolomic datasets were generated from mouse primary astrocytes after 24 hours of cytokine cocktail treatment. Metabolomic profiling, combined with pharmacological approaches, revealed that Ent2 regulates inosine efflux and is critical for maintaining astrocytic energy balance. Pharmacological inhibition of inosine utilization in energy-producing pathways with Forodesine led to disrupted energy homeostasis and increased astrocytic reactivity. The datasets include both raw and processed metabolomic files. Metabolomic analyses were performed at the Metabolomics Core Facility, Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
INSTITUTE
Institute of Biomedical Sciences, Academia Sinica
LAST_NAME
Chern
FIRST_NAME
Yijuang
ADDRESS
128 Section 2, Academia Road, Nankang, Taipei, 115201, Taiwan
Discovery and Validation of Metabolic Biomarkers for 'Liver Qi Stagnation' and 'Liver-Gallbladder Damp-Heat' Syndromes in Cholelithiasis: Blood targeted
STUDY_TYPE
Observational study
STUDY_SUMMARY
This study employed three targeted metabolomics methods on the blood of patients with gallstones of different traditional Chinese medicine syndromes. A total of 210 metabolites were detected.
INSTITUTE
The First Affiliated Hospital of Dalian Medical University
LABORATORY
Laboratory of Integrative Medicine
LAST_NAME
Zhang
FIRST_NAME
Yunshu
ADDRESS
No.222 Zhongshan Road, Xigang District, Dalian City, Liaoning Province
Cell state-specific metabolic networks govern ferroptosis versus apoptosis in small cell lung cancer
STUDY_TYPE
LC/MS
STUDY_SUMMARY
LC/MS metabolomics was performed on neuroendocrine (ASCL1 high) and non-neuroendocrine (ASCL1 low) small cell lung cancer cells isolated from the RPR2 genetically engineered mouse model (Rb1 flox/flox; Trp53 flox/flox; Rbl2 flox/flox; Hes1GFP). Cancer cell states were separated based on in vivo Hes1 expression, with ASCL1 high neuroendocrine cells enriched as cells with low/no Hes1 expression and ASCL1 low non-neuroendocrine cells as cells with high Hes1. Agilent 1290 Infinity LC system coupled to an Agilent 6545 Q-TOF mass spectrometer with an Agilent Jet Stream Source was used to detect 1296 entities, of which 474 were significantly altered between the two cell states. Pathway analysis revealed differences in purine metabolism, sphingolipid metabolism, tRNA charging, and glutathione-related redox pathways. These data provide insights into metabolic heterogeneity and redox regulation in SCLC cell states.
Lipidomic analysis of the perigonadal adipose tissue of Control, HSL KO and ATGL KO mice.
STUDY_SUMMARY
AdipoCreERT2⁺ and AdipoCreERT2⁻ (control) mice carrying floxed alleles of Lipe (HSL) or Pnpla2 (ATGL) were treated with 4-hydroxy-tamoxifen to induce adipocyte-specific depletion of HSL or ATGL. Following gene deletion, white adipose tissue (WAT) samples were collected, and lipids were extracted. The hexane phases were isolated and analyzed by LC–MS/MS to quantify the complete triacylglycerol (TG) profile. While all TG species were measured, we specifically focused on short- and medium-chain fatty acid–containing TGs (SMCFA-TGs), where we detected marked differences in abundance between genotypes depending on the presence or absence of HSL or ATGL.
The metabolic effects of succinylation and desuccinylation of HADHB at lysine 292
STUDY_SUMMARY
To elucidate the metabolic effects of succinylation and desuccinylation at lysine 292 (K292) of HADHB, we generated stable H9C2 rat cardiomyocyte cell lines expressing HADHB mutants. Specifically, lysine 292 was substituted with arginine (K292R) to mimic the desuccinylated state and with glutamic acid (K292E) to mimic the negatively charged succinylated modification. Non-targeted metabolomic profiling was performed on three groups—wild-type (WT), desuccinylation-mimic (K292R), and succinylation-mimic (K292E)—with six biological replicates per group. The metabolomic analysis revealed that succinylation at K292 of HADHB in cardiomyocytes leads to distinct metabolic alterations, particularly affecting the fatty acid β-oxidation pathway.