1
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Laue HE, Bonham KS, Coker MO, Moroishi Y, Pathmasiri W, McRitchie S, Sumner S, Hoen AG, Karagas MR, Klepac-Ceraj V, Madan JC. Prospective association of the infant gut microbiome with social behaviors in the ECHO consortium. Mol Autism 2024; 15:21. [PMID: 38760865 PMCID: PMC11101342 DOI: 10.1186/s13229-024-00597-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/11/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Identifying modifiable risk factors of autism spectrum disorders (ASDs) may inform interventions to reduce financial burden. The infant/toddler gut microbiome is one such feature that has been associated with social behaviors, but results vary between cohorts. We aimed to identify consistent overall and sex-specific associations between the early-life gut microbiome and autism-related behaviors. METHODS Utilizing the Environmental influences on Children Health Outcomes (ECHO) consortium of United States (U.S.) pediatric cohorts, we gathered data on 304 participants with fecal metagenomic sequencing between 6-weeks to 2-years postpartum (481 samples). ASD-related social development was assessed with the Social Responsiveness Scale (SRS-2). Linear regression, PERMANOVA, and Microbiome Multivariable Association with Linear Models (MaAsLin2) were adjusted for sociodemographic factors. Stratified models estimated sex-specific effects. RESULTS Genes encoding pathways for synthesis of short-chain fatty acids were associated with higher SRS-2 scores, indicative of ASDs. Fecal concentrations of butyrate were also positively associated with ASD-related SRS-2 scores, some of which may be explained by formula use. LIMITATIONS The distribution of age at outcome assessment differed in the cohorts included, potentially limiting comparability between cohorts. Stool sample collection methods also differed between cohorts. Our study population reflects the general U.S. population, and thus includes few participants who met the criteria for being at high risk of developing ASD. CONCLUSIONS Our study is among the first multicenter studies in the U.S. to describe prospective microbiome development from infancy in relation to neurodevelopment associated with ASDs. Our work contributes to clarifying which microbial features associate with subsequent diagnosis of neuropsychiatric outcomes. This will allow for future interventional research targeting the microbiome to change neurodevelopmental trajectories.
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Affiliation(s)
- Hannah E Laue
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Kevin S Bonham
- Department of Biological Sciences, Wellesley College, 106 Central Street, Wellesley, MA, 02481, USA
| | - Modupe O Coker
- School of Dental Medicine, Rutgers University, Newark, NJ, USA
| | - Yuka Moroishi
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Wimal Pathmasiri
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan McRitchie
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan Sumner
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anne G Hoen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, 106 Central Street, Wellesley, MA, 02481, USA.
| | - Juliette C Madan
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.
- Departments of Pediatrics and Psychiatry, One Medical Center Drive, Dartmouth Hitchcock Medical Center, Lebanon, NH, 03756, USA.
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2
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Philip N, Yun X, Pi H, Murray S, Hill Z, Fonticella J, Perez P, Zhang C, Pathmasiri W, Sumner S, Servinsky L, Jiang H, Huetsch JC, Oldham WM, Visovatti S, Leary PJ, Gharib SA, Brittain E, Simpson CE, Le A, Shimoda LA, Suresh K. Fatty acid metabolism promotes TRPV4 activity in lung microvascular endothelial cells in pulmonary arterial hypertension. Am J Physiol Lung Cell Mol Physiol 2024; 326:L252-L265. [PMID: 38226418 DOI: 10.1152/ajplung.00199.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/07/2023] [Indexed: 01/17/2024] Open
Abstract
Pulmonary arterial hypertension (PAH) is a morbid disease characterized by significant lung endothelial cell (EC) dysfunction. Prior work has shown that microvascular endothelial cells (MVECs) isolated from animals with experimental PAH and patients with PAH exhibit significant abnormalities in metabolism and calcium signaling. With regards to metabolism, we and others have shown evidence of increased aerobic glycolysis and evidence of increased utilization of alternate fuel sources (such as fatty acids) in PAH EC. In the realm of calcium signaling, our prior work linked increased activity of the transient receptor potential vanilloid-4 (TRPV4) channel to increased proliferation of MVECs isolated from the Sugen/Hypoxia rat model of PAH (SuHx-MVECs). However, the relationship between metabolic shifts and calcium abnormalities was not clear. Specifically, whether shifts in metabolism were responsible for increasing TRPV4 channel activity in SuHx-MVECs was not known. In this study, using human data, serum samples from SuHx rats, and SuHx-MVECs, we describe the consequences of increased MVEC fatty acid oxidation in PAH. In human samples, we observed an increase in long-chain fatty acid levels that was associated with PAH severity. Next, using SuHx rats and SuHx-MVECs, we observed increased intracellular levels of lipids. We also show that increasing intracellular lipid content increases TRPV4 activity, whereas inhibiting fatty acid oxidation normalizes basal calcium levels in SuHx-MVECs. By exploring the fate of fatty acid-derived carbons, we observed that the metabolite linking increased intracellular lipids to TRPV4 activity was β-hydroxybutyrate (BOHB), a product of fatty acid oxidation. Finally, we show that BOHB supplementation alone is sufficient to sensitize the TRPV4 channel in rat and mouse MVECs. Returning to humans, we observe a transpulmonary BOHB gradient in human patients with PAH. Thus, we establish a link between fatty acid oxidation, BOHB production, and TRPV4 activity in MVECs in PAH. These data provide new insight into metabolic regulation of calcium signaling in lung MVECs in PAH.NEW & NOTEWORTHY In this paper, we explore the link between metabolism and intracellular calcium levels in microvascular endothelial cells (MVECs) in pulmonary arterial hypertension (PAH). We show that fatty acid oxidation promotes sensitivity of the transient receptor potential vanilloid-4 (TRPV4) calcium channel in MVECs isolated from a rodent model of PAH.
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Affiliation(s)
- Nicolas Philip
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Xin Yun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Hongyang Pi
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States
| | - Samuel Murray
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Zack Hill
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Jay Fonticella
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Preston Perez
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Cissy Zhang
- Gigantest, Inc., Baltimore, Maryland, United States
| | - Wimal Pathmasiri
- Department of Nutrition, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina, United States
| | - Susan Sumner
- Department of Nutrition, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina, United States
| | - Laura Servinsky
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Haiyang Jiang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - John C Huetsch
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - William M Oldham
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - Scott Visovatti
- Department of Cardiology, Ohio State University School of Medicine, Columbus, Ohio, United States
| | - Peter J Leary
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States
| | - Sina A Gharib
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States
| | - Evan Brittain
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States
| | - Catherine E Simpson
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Anne Le
- Gigantest, Inc., Baltimore, Maryland, United States
| | - Larissa A Shimoda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Karthik Suresh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
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3
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Nieman DC, Sakaguchi CA, Pelleigrini M, Thompson MJ, Sumner S, Zhang Q. Healthy lifestyle linked to innate immunity and lipoprotein metabolism: a cross-sectional comparison using untargeted proteomics. Sci Rep 2023; 13:16728. [PMID: 37794065 PMCID: PMC10550951 DOI: 10.1038/s41598-023-44068-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/03/2023] [Indexed: 10/06/2023] Open
Abstract
This study used untargeted proteomics to compare blood proteomic profiles in two groups of adults that differed widely in lifestyle habits. A total of 52 subjects in the lifestyle group (LIFE) (28 males, 24 females) and 52 in the control group (CON) (27 males, 25 females) participated in this cross-sectional study. Age, education level, marital status, and height did not differ significantly between LIFE and CON groups. The LIFE and CON groups differed markedly in body composition, physical activity patterns, dietary intake patterns, disease risk factor prevalence, blood measures of inflammation, triglycerides, HDL-cholesterol, glucose, and insulin, weight-adjusted leg/back and handgrip strength, and mood states. The proteomics analysis showed strong group differences for 39 of 725 proteins identified in dried blood spot samples. Of these, 18 were downregulated in the LIFE group and collectively indicated a lower innate immune activation signature. A total of 21 proteins were upregulated in the LIFE group and supported greater lipoprotein metabolism and HDL remodeling. Lifestyle-related habits and biomarkers were probed and the variance (> 50%) in proteomic profiles was best explained by group contrasts in indicators of adiposity. This cross-sectional study established that a relatively small number of proteins are associated with good lifestyle habits.
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Affiliation(s)
- David C Nieman
- Human Performance Laboratory, Biology Department, Appalachian State University, North Carolina Research Campus, Kannapolis, NC, USA.
| | - Camila A Sakaguchi
- Human Performance Laboratory, Biology Department, Appalachian State University, North Carolina Research Campus, Kannapolis, NC, USA
| | - Matteo Pelleigrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael J Thompson
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Susan Sumner
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, 28081, USA
| | - Qibin Zhang
- UNCG Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, USA
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4
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Zeitler EM, Li Y, Schroder M, Falk RJ, Sumner S. Characterizing the metabolic response of the zebrafish kidney to overfeeding. Am J Physiol Renal Physiol 2023; 325:F491-F502. [PMID: 37589050 PMCID: PMC10639026 DOI: 10.1152/ajprenal.00113.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023] Open
Abstract
Obesity is a global epidemic and risk factor for the development of chronic kidney disease. Obesity induces systemic changes in metabolism, but how it affects kidney metabolism specifically is not known. Zebrafish have previously been shown to develop obesity-related kidney pathology and dysfunction when fed hypercaloric diets. To understand the direct effects of obesity on kidney metabolic function, we treated zebrafish for 8 wk with a control and an overfeeding diet. At the end of treatment, we assessed changes in kidney and fish weights and used electron microscopy to evaluate cell ultrastructure. We then performed an untargeted metabolomic analysis on the kidney tissue of fish using ultra-high performance liquid chromatography coupled with high-resolution mass spectrometry and used mummichog and gene set enrichment analysis to uncover differentially affected metabolic pathways. Kidney metabolomes differed significantly and consistently between the control and overfed diets. Among 9,593 features, we identified 235 that were significantly different (P < 0.05) between groups (125 upregulated in overfed diet, 110 downregulated). Pathway analysis demonstrated perturbations in glycolysis and fatty acid synthesis pathways, and analysis of specific metabolites points to perturbations in tryptophan metabolism. Our key findings show that diet-induced obesity leads to metabolic changes in the kidney tissue itself and implicates specific metabolic pathways, including glycolysis and tryptophan metabolism in the pathogenesis of obesity-related kidney disease, demonstrating the power of untargeted metabolomics to identify pathways of interest by directly interrogating kidney tissue.NEW & NOTEWORTHY Obesity causes systemic metabolic dysfunction, but how this affects kidney metabolism is less understood. This study used ultra-high performance liquid chromatography coupled with high-resolution mass spectrometry to analyze the kidneys of overfed zebrafish. Metabolites in the kidneys of obese zebrafish revealed perturbations in metabolic pathways including glycolysis and tryptophan metabolism. These data suggest obesity alters metabolism within the kidney, which may play an important role in obesity-related kidney dysfunction.
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Affiliation(s)
- Evan M Zeitler
- Division of Nephrology and Hypertension, Department of Medicine, UNC Kidney Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Yuanyuan Li
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Madison Schroder
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Ronald J Falk
- Division of Nephrology and Hypertension, Department of Medicine, UNC Kidney Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Susan Sumner
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
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5
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Rushing BR, Molina S, Sumner S. Metabolomics Analysis Reveals Altered Metabolic Pathways and Response to Doxorubicin in Drug-Resistant Triple-Negative Breast Cancer Cells. Metabolites 2023; 13:865. [PMID: 37512572 PMCID: PMC10383792 DOI: 10.3390/metabo13070865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/07/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
This study aimed to investigate metabolic changes following the acquisition of resistance to doxorubicin in the triple-negative breast cancer (TNBC) cell line MDA-MB-231. Two drug-resistant cell lines, DOX-RES-50 and DOX-RES-100, were generated by treating MDA-MB-231 cells with doxorubicin for 24 h and allowing them to recover for six weeks. Both drug-resistant cell lines demonstrated an increase in doxorubicin IC50 values, indicating acquired drug resistance. Metabolomics analysis showed clear separation between the parental MDA-MB-231 cell line and the drug-resistant cell lines. Pathway analysis revealed that arginine and proline metabolism, glutathione metabolism, and beta-alanine metabolism were significantly perturbed in the drug-resistant cell lines compared to the parental cell line. After matching signals to an in-house library of reference standards, significant decreases in short- and medium-chain acylcarnitines and significant increases in long-chain acylcarnitines, 5-oxoproline, and 7-ketodeoxycholic acid were observed in the resistant cell lines as compared to the parental MDA-MB-231 cell line. In addition to baseline metabolic differences, we also investigated differences in metabolic responses in resistant cell lines upon a second exposure at multiple concentrations. Results indicate that whereas the parental MDA-MB-231 cell line had many metabolites that responded to doxorubicin in a dose-dependent manner, the two resistant cell lines lost a dose-dependent response for the majority of these metabolites. The study's findings provide insight into how metabolism is altered during the acquisition of resistance in TNBC cells and how the metabolic response to doxorubicin changes upon repeated treatment. This information can potentially identify novel targets to prevent or reverse multi-drug resistance in TNBC, and also demonstrate the usefulness of metabolomics technology in identifying new mechanisms of drug resistance in cancer and potential drug targets.
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Affiliation(s)
- Blake R Rushing
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC 28081, USA
| | - Sabrina Molina
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC 28081, USA
| | - Susan Sumner
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC 28081, USA
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6
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Bhayana S, Zhao Y, Merchant M, Cummins T, Dougherty JA, Kamigaki Y, Pathmasiri W, McRitchie S, Mariani LH, Sumner S, Klein JB, Li L, Smoyer WE. Multiomics Analysis of Plasma Proteomics and Metabolomics of Steroid Resistance in Childhood Nephrotic Syndrome Using a "Patient-Specific" Approach. Kidney Int Rep 2023; 8:1239-1254. [PMID: 37284673 PMCID: PMC10239920 DOI: 10.1016/j.ekir.2023.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/20/2023] [Indexed: 06/08/2023] Open
Abstract
Introduction Nephrotic syndrome (NS) occurs commonly in children with glomerular disease and glucocorticoids (GCs) are the mainstay treatment. Steroid resistant NS (SRNS) develops in 15% to 20% of children, increasing the risk of chronic kidney disease compared to steroid sensitive NS (SSNS). NS pathogenesis is unclear in most children, and no biomarkers exist that predict the development of pediatric SRNS. Methods We studied a unique patient cohort with plasma specimens collected before GC treatment, yielding a disease-only sample not confounded by steroid-induced gene expression changes (SSNS n = 8; SRNS n = 7). A novel "patient-specific" bioinformatic approach merged paired pretreatment and posttreatment proteomic and metabolomic data and identified candidate SRNS biomarkers and altered molecular pathways in SRNS versus SSNS. Results Joint pathway analyses revealed perturbations in nicotinate or nicotinamide and butanoate metabolic pathways in patients with SRNS. Patients with SSNS had perturbations of lysine degradation, mucin type O-glycan biosynthesis, and glycolysis or gluconeogenesis pathways. Molecular analyses revealed frequent alteration of molecules within these pathways that had not been observed by separate proteomic and metabolomic studies. We observed upregulation of NAMPT, NMNAT1, and SETMAR in patients with SRNS, in contrast to upregulation of ALDH1B1, ACAT1, AASS, ENPP1, and pyruvate in patients with SSNS. Pyruvate regulation was the change seen in our previous analysis; all other targets were novel. Immunoblotting confirmed increased NAMPT expression in SRNS and increased ALDH1B1 and ACAT1 expression in SSNS, following GC treatment. Conclusion These studies confirmed that a novel "patient-specific" bioinformatic approach can integrate disparate omics datasets and identify candidate SRNS biomarkers not observed by separate proteomic or metabolomic analysis.
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Affiliation(s)
- Sagar Bhayana
- Center for Clinical and Translational Research, Nationwide Children’s Hospital; Columbus, Ohio, USA
| | - Yue Zhao
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Michael Merchant
- Department of Medicine, Division of Nephrology and Hypertension, University of Louisville; Louisville, Kentucky, USA
| | - Timothy Cummins
- Department of Medicine, Division of Nephrology and Hypertension, University of Louisville; Louisville, Kentucky, USA
| | - Julie A. Dougherty
- Center for Clinical and Translational Research, Nationwide Children’s Hospital; Columbus, Ohio, USA
| | - Yu Kamigaki
- Center for Clinical and Translational Research, Nationwide Children’s Hospital; Columbus, Ohio, USA
| | - Wimal Pathmasiri
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill; Kannapolis, North Carolina, USA
| | - Susan McRitchie
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill; Kannapolis, North Carolina, USA
| | - Laura H. Mariani
- Division of Nephrology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Susan Sumner
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill; Kannapolis, North Carolina, USA
| | - Jon B. Klein
- Department of Medicine, Division of Nephrology and Hypertension, University of Louisville; Louisville, Kentucky, USA
- Robley Rex VA Medical Center, Louisville, Kentucky, USA
| | - Lang Li
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - William E. Smoyer
- Center for Clinical and Translational Research, Nationwide Children’s Hospital; Columbus, Ohio, USA
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
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7
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Howard AG, Mhatre S, Sha W, Lloyd-Jones D, Rushing B, McRitchie S, Du X, Li Y, Sumner S, Avery CL, North KE, Gordon-Larsen P. Abstract P207: Heterogeneity in Obesity in Relation to Related to Hypertension: Investigating the Role of Metabolic Pathways. Circulation 2023. [DOI: 10.1161/circ.147.suppl_1.p207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Background:
While obesity is associated with hypertension, there is heterogeneity in risk by weight status and we know little about whether and which metabolic pathways play a role in exacerbating differential risk across weight status categories.
Methods:
Fasting blood was collected at the Yr. 20 follow-up exam in the Coronary Artery Risk Development in Young Adults (CARDIA) Study. We conducted Ultra-High-Performance Liquid Chromatography high resolution mass spectrometry untargeted metabolomics in 1,769 individuals (ages 37-54, 58% female, 66% Black) classified as normotensive (no hypertension diagnosis or medication and SBP/DBP ≤ 130/80). We identified 7,522 metabolomic peaks and 8 principal components, which we included in a multivariable-adjusted proportional hazards model with an interaction term to assess whether the association between these metabolite measures and incident hypertension (HTN) varied by BMI. We then employed multivariate analysis using Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) models using 70% of the sample within each obesity category to predict incident HTN at ten years in normal weight, overweight and obese groups based on the high dimensional metabolomics data. The remaining 30% of individuals in each obesity category were then used to evaluate the predictive value of the OPLS-DA models. Finally, we used mummichog software and Fisher’s exact tests, to conduct pathway enrichment analysis using data from both the individual peak and the OPLS-DA models.
Results:
We identified 723 metabolites where the association with long term risk of HTN differed by BMI, although none were statistically significant after adjustment for multiple comparisons. However, we found strong evidence of effect modification for metabolites via principal components and OPLS-DA. For the 3
rd
principal component, which explained 5% of the variation across all peaks, we found a significant interaction with BMI (p-value = 0.0043). In external test data sets, OPLS-DA models predicted incident HTN relatively well in normal weight individuals (AUC of 77%) but not well in overweight and obese individuals (AUC of 49% and 56% respectively). We identified several pathways with a differential HTN risk by BMI shown in the OPLS-DA and proportional hazards models. In the phenylamine pathway there was substantial differentiation between those with and without incident HTN risk for normal weight only and across the lysine degradation pathway only for individuals who were obese.
Conclusions:
Our findings identify variation in hypertension risk by BMI, with suggestive evidence for a role of metabolomic pathways and combinations of metabolites. Overall, metabolites predicted 10-year incident hypertension very well in individuals of normal weight (but not obese status), indicating heterogeneity in hypertension risk by weight status.
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Affiliation(s)
| | | | - Wei Sha
- Atrium Health, Greensboro, NC
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8
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Hullings AG, Howard AG, Meyer KA, Avery CL, North KE, Mhatre S, Sha W, Du X, Li Y, Rushing B, Sumner S, Lewis CE, Gordon-Larsen P. Abstract P414: Modification of Diet-Metabolite Associations by Race and Sex in the Coronary Artery Risk Development in Young Adults Study. Circulation 2023. [DOI: 10.1161/circ.147.suppl_1.p414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Objective:
There is known heterogeneity in the relationship between diet quality and cardiovascular disease by self-reported race and sex, which may underlie inequities in cardiovascular health.
Methods:
We used data from 2,832 participants in the Coronary Artery Risk Development in Young Adults (CARDIA) study (2005-06, aged 37-55, 57% women, 45% Black). Using fasted blood samples, we obtained ultra-high-performance liquid chromatography high resolution mass spectrometry untargeted metabolomics and derived an
a priori
diet quality score using a validated diet history questionnaire, based on classification of 46 food groups with potential beneficial (n=20), adverse (n=13), or neutral (n=13) implications for cardiovascular health. We tested effect modification of associations between metabolites and diet quality by race and sex, separately, using multivariable-adjusted linear regression for 7,522 metabolite peaks, accounting for multiple comparisons, adjusted for batch, field center, demographics, lifestyle behaviors, total energy intake, hypertension and diabetes status, medication use, and BMI. We also used race- and sex-stratified multivariate Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) analyses to examine how metabolites distinguish by diet quality 1
st
and 4
th
quartiles. We identified differing metabolite pathways by race and sex through biochemical pathway analysis (Mummichog version 1.0.10) from regression and OPLS-DA models.
Results:
In linear regression, race significantly modified metabolite-diet quality associations for 231 metabolite peaks; sex modified associations for 1 peak (FDR<0.1). OPLS-DA pathway analysis identified cysteine, methionine, histidine, and alpha-linoleic metabolism and terpenoid backbone biosynthesis as significantly associated with diet quality in Black, but not White, race. Linear regression and OPLS-DA pathway analysis found differences (p<0.05) in arginine biosynthesis by sex. OPLS-DA also found aminoacyl-tRNA and arginine biosynthesis, nitrogen, porphyrin, and chlorophyll metabolism were significantly associated with diet quality in men only.
Conclusions:
Metabolite pathways were statistically different by self-reported race, and to a lesser extent, by sex. Differences in metabolite-diet quality associations may reflect differences in contextual or social variables, and potentially, heterogeneity in metabolism.
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Affiliation(s)
| | | | | | | | | | - Sachin Mhatre
- Levine Cancer Institute, Atrium Health, Charlotte, NC
| | - Wei Sha
- Levine Cancer Institute, Atrium Health, Charlotte, NC
| | - Xiuxia Du
- Univ of North Carolina, Charlotte, NC
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9
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Yeum D, Gilbert-Diamond D, Doherty B, Coker M, Stewart D, Kirchner D, McRitchie S, Sumner S, Karagas MR, Hoen AG. Associations of maternal plasma and umbilical cord plasma metabolomics profiles with birth anthropometric measures. Pediatr Res 2023:10.1038/s41390-022-02449-2. [PMID: 36627359 DOI: 10.1038/s41390-022-02449-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/11/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND The metabolomics profiles of maternal plasma during pregnancy and cord plasma at birth might influence fetal growth and birth anthropometry. The objective was to examine how maternal plasma and umbilical cord plasma metabolites are associated with newborn anthropometric measures, a known predictor of future health outcomes. METHODS Pregnant women between 24 and 28 weeks of gestation were recruited as part of a prospective cohort study. Blood samples from 413 women at enrollment and 787 infant cord blood samples were analyzed using the Biocrates AbsoluteIDQ® p180 kit. Multivariable linear regression models were used to examine associations of cord and maternal metabolites with infant anthropometry at birth. RESULTS In cord blood samples from this rural cohort from New Hampshire of largely white residents, 13 metabolites showed negative associations, and 10 metabolites showed positive associations with birth weight Z-score. Acylcarnitine C5 showed negative association, and 4 lysophosphatidylcholines showed positive associations with birth length Z-score. Maternal blood metabolites did not significantly correlate with birth weight and length Z-scores. CONCLUSIONS Consistent findings were observed for several acylcarnitines that play a role in utilization of energy sources, and a lysophosphatidylcholine that is part of oxidative stress and inflammatory response pathways in cord plasma samples. IMPACT The metabolomics profiles of maternal plasma during pregnancy and cord plasma at birth may influence fetal growth and birth anthropometry. This study examines the independent effects of maternal gestational and infant cord blood metabolomes across different classes of metabolites on birth anthropometry. Acylcarnitine species were negatively associated and glycerophospholipids species were positively associated with weight and length Z-scores at birth in the cord plasma samples, but not in the maternal plasma samples. This study identifies lipid metabolites in infants that possibly may affect early growth.
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Affiliation(s)
- Dabin Yeum
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
| | - Diane Gilbert-Diamond
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Children's Environmental Health and Disease Prevention Center at Dartmouth, Hanover, NH, USA
| | - Brett Doherty
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Modupe Coker
- Department of Oral Biology, Rutgers School of Dental Medicine, Rutgers State University of New Jersey, Newark, NJ, USA
| | - Delisha Stewart
- Department of Nutrition, Gillings School of Global Public Health, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - David Kirchner
- Department of Nutrition, Gillings School of Global Public Health, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Susan McRitchie
- Department of Nutrition, Gillings School of Global Public Health, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Susan Sumner
- Department of Nutrition, Gillings School of Global Public Health, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Margaret R Karagas
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Children's Environmental Health and Disease Prevention Center at Dartmouth, Hanover, NH, USA
| | - Anne G Hoen
- Department of Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Biomedical Data Science, Geisel School of Medicine, Lebanon, NH, USA
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10
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Rushing BR, Fogle HM, Sharma J, You M, McCormac JP, Molina S, Sumner S, Krupenko NI, Krupenko SA. Exploratory Metabolomics Underscores the Folate Enzyme ALDH1L1 as a Regulator of Glycine and Methylation Reactions. Molecules 2022; 27:molecules27238394. [PMID: 36500483 PMCID: PMC9740053 DOI: 10.3390/molecules27238394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022]
Abstract
Folate (vitamin B9) is involved in one-carbon transfer reactions and plays a significant role in nucleic acid synthesis and control of cellular proliferation, among other key cellular processes. It is now recognized that the role of folates in different stages of carcinogenesis is complex, and more research is needed to understand how folate reactions become dysregulated in cancers and the metabolic consequences that occur as a result. ALDH1L1 (cytosolic 10-formyltetrahydrofolate dehydrogenase), an enzyme of folate metabolism expressed in many tissues, is ubiquitously downregulated in cancers and is not expressed in cancer cell lines. The RT4 cell line (derived from papillary bladder cancer) which expresses high levels of ALDH1L1 represents an exception, providing an opportunity to explore the metabolic consequences of the loss of this enzyme. We have downregulated this protein in RT4 cells (shRNA driven knockdown or CRISPR driven knockout) and compared metabolomes of ALDH1L1-expressing and -deficient cells to determine if metabolic changes linked to the loss of this enzyme might provide proliferative and/or survival advantages for cancer cells. In this study, cell extracts were analyzed using Ultra High Performance Liquid Chromatography High Resolution Mass Spectrometry (UHPLC-HR-MS). A total of 13,339 signals were identified or annotated using an in-house library and public databases. Supervised and unsupervised multivariate analysis revealed metabolic differences between RT4 cells and ALDH1L1-deficient clones. Glycine (8-fold decrease) and metabolites derived from S-adenosylmethionine utilizing pathways were significantly decreased in the ALDH1L1-deficient clones, compared with RT4 cells. Other changes linked to ALDH1L1 downregulation include decreased levels of amino acids, Krebs cycle intermediates, and ribose-5-phosphate, and increased nicotinic acid. While the ALDH1L1-catalyzed reaction is directly linked to glycine biosynthesis and methyl group flux, its overall effect on cellular metabolism extends beyond immediate metabolic pathways controlled by this enzyme.
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Affiliation(s)
- Blake R. Rushing
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
- Department of Nutrition, UNC Chapel Hill, Chapel Hill, NC 27599, USA
| | - Halle M. Fogle
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
- Department of Nutrition, UNC Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jaspreet Sharma
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
| | - Mikyoung You
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
| | | | - Sabrina Molina
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
| | - Susan Sumner
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
- Department of Nutrition, UNC Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence: (S.S.); (S.A.K.)
| | - Natalia I. Krupenko
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
- Department of Nutrition, UNC Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sergey A. Krupenko
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
- Department of Nutrition, UNC Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence: (S.S.); (S.A.K.)
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11
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Li Y, Rushing B, Schroder M, Sumner S, Kay CD. Exploring the Contribution of (Poly)phenols to the Dietary Exposome Using High Resolution Mass Spectrometry Untargeted Metabolomics. Mol Nutr Food Res 2022; 66:e2100922. [PMID: 35106906 PMCID: PMC9343475 DOI: 10.1002/mnfr.202100922] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/11/2022] [Indexed: 12/30/2022]
Abstract
SCOPE This study presents a workflow to construct a Dietary Exposome Library (DEL) comprised of phytochemicals and their metabolites derived from host and gut microbiome metabolism for use in peak identification/annotation of untargeted metabolomics datasets. METHODS AND RESULTS An evidence mapping initiative established target analytes related to the consumption of phytochemical-rich foods. Analytes were confirmed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS(n)) analysis of human biospecimens from dietary intervention studies of (poly)phenol-rich diets. One hundred and sixty six verified compounds were subsequently analyzed on an untargeted metabolomics platform to acquire chromatographic and high-resolution mass spectral data for construction of a DEL. The DEL facilitated identification/annotation of 123 metabolites associate with exposure to (poly)phenol enriched diets, which included aromatic ketones, benzoic acids, ellagic acids, caffeoylquinic acids, catecholamines, coumarins, hippuric acid, hydroxytoluenes, phenylamines, stilbenes, urolithins, valerolactones, and xanthonoids, in untargeted metabolomics datasets acquire from human plasma and urine reference materials. CONCLUSIONS The DEL focusing on (poly)phenols and their metabolites of dietary exposure facilitated identification/annotation of ingested food components and their associated pathways in untargeted metabolomics datasets acquired from human biospecimens. The DEL continues to expand with the aim to provide evidence-based data for dietary metabolites in exposome research and inform the development of dietary intervention strategies.
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Affiliation(s)
- Yuan‐Yuan Li
- Nutrition Research InstituteUNC Chapel Hill500 Laureate WayKannapolisNC28081USA,North Carolina Human Health Exposure Analysis Resource (NC HHEAR) HubNC28081USA
| | - Blake Rushing
- Nutrition Research InstituteUNC Chapel Hill500 Laureate WayKannapolisNC28081USA,North Carolina Human Health Exposure Analysis Resource (NC HHEAR) HubNC28081USA
| | - Madison Schroder
- Nutrition Research InstituteUNC Chapel Hill500 Laureate WayKannapolisNC28081USA,North Carolina Human Health Exposure Analysis Resource (NC HHEAR) HubNC28081USA
| | - Susan Sumner
- Nutrition Research InstituteUNC Chapel Hill500 Laureate WayKannapolisNC28081USA,North Carolina Human Health Exposure Analysis Resource (NC HHEAR) HubNC28081USA
| | - Colin D. Kay
- North Carolina Human Health Exposure Analysis Resource (NC HHEAR) HubNC28081USA,Food Bioprocessing and Nutrition Sciences DepartmentPlants for Human Health InstituteNorth Carolina State UniversityKannapolisNC28081USA
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12
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Rushing BR, Tilley S, Molina S, Schroder M, Sumner S. Commonalities in Metabolic Reprogramming between Tobacco Use and Oral Cancer. Int J Environ Res Public Health 2022; 19:10261. [PMID: 36011897 PMCID: PMC9408724 DOI: 10.3390/ijerph191610261] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
Tobacco use is a major public health concern and is linked to myriad diseases, including cancer. The link between tobacco use and oral cancer, specifically, is very strong, making tobacco use one of the primary risk factors for oral cancer. While this association is well known, the underlying biochemical changes that result from tobacco use, and how this links to metabolic phenotypes of oral cancer, is not well understood. To address this knowledge gap, a combination of literature reviews and metabolomics studies were performed to identify commonalities in metabolic perturbations between tobacco use and oral cancers. Metabolomics analysis was performed on pooled reference urine from smokers and non-smokers, healthy and malignant oral tissues, and cultured oral cells with or without treatment of the well-known tobacco carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Alterations in amino acid metabolism, carbohydrates/oxidative phosphorylation, fatty acid oxidation, nucleotide metabolism, steroid metabolism, and vitamin metabolism were found to be shared between tobacco use and oral cancer. These results support the conclusion that tobacco use metabolically reprograms oral cells to support malignant transformation through these pathways. These metabolic reprogramming events may be potential targets to prevent or treat oral cancers that arise from tobacco use.
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Affiliation(s)
- Blake R. Rushing
- Department of Nutrition, University of North Carolina at Chapel Hill, Durham, NC 27599, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC 28081, USA
| | - Spencer Tilley
- Department of Nutrition, University of North Carolina at Chapel Hill, Durham, NC 27599, USA
| | - Sabrina Molina
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC 28081, USA
| | - Madison Schroder
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC 28081, USA
| | - Susan Sumner
- Department of Nutrition, University of North Carolina at Chapel Hill, Durham, NC 27599, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC 28081, USA
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13
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Lynch DH, Spangler HB, Franz JR, Krupenevich RL, Kim H, Nissman D, Zhang J, Li YY, Sumner S, Batsis JA. Multimodal Diagnostic Approaches to Advance Precision Medicine in Sarcopenia and Frailty. Nutrients 2022; 14:nu14071384. [PMID: 35405997 PMCID: PMC9003228 DOI: 10.3390/nu14071384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 12/12/2022] Open
Abstract
Sarcopenia, defined as the loss of muscle mass, strength, and function with aging, is a geriatric syndrome with important implications for patients and healthcare systems. Sarcopenia increases the risk of clinical decompensation when faced with physiological stressors and increases vulnerability, termed frailty. Sarcopenia develops due to inflammatory, hormonal, and myocellular changes in response to physiological and pathological aging, which promote progressive gains in fat mass and loss of lean mass and muscle strength. Progression of these pathophysiological changes can lead to sarcopenic obesity and physical frailty. These syndromes independently increase the risk of adverse patient outcomes including hospitalizations, long-term care placement, mortality, and decreased quality of life. This risk increases substantially when these syndromes co-exist. While there is evidence suggesting that the progression of sarcopenia, sarcopenic obesity, and frailty can be slowed or reversed, the adoption of broad-based screening or interventions has been slow to implement. Factors contributing to slow implementation include the lack of cost-effective, timely bedside diagnostics and interventions that target fundamental biological processes. This paper describes how clinical, radiographic, and biological data can be used to evaluate older adults with sarcopenia and sarcopenic obesity and to further the understanding of the mechanisms leading to declines in physical function and frailty.
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Affiliation(s)
- David H. Lynch
- Division of Geriatric Medicine, Center for Aging and Health, University of North Carolina, Chapel Hill, NC 27599, USA;
- Correspondence: ; Tel.: +919-966-5945; Fax: +919-962-9795
| | - Hillary B. Spangler
- Division of Medicine and Pediatrics, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Jason R. Franz
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC 27599, USA; (J.R.F.); (R.L.K.); (H.K.)
| | - Rebecca L. Krupenevich
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC 27599, USA; (J.R.F.); (R.L.K.); (H.K.)
| | - Hoon Kim
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC 27599, USA; (J.R.F.); (R.L.K.); (H.K.)
| | - Daniel Nissman
- Department of Radiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; (D.N.); (J.Z.)
| | - Janet Zhang
- Department of Radiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; (D.N.); (J.Z.)
| | - Yuan-Yuan Li
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA; (Y.-Y.L.); (S.S.)
| | - Susan Sumner
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA; (Y.-Y.L.); (S.S.)
| | - John A. Batsis
- Division of Geriatric Medicine, Center for Aging and Health, University of North Carolina, Chapel Hill, NC 27599, USA;
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA; (Y.-Y.L.); (S.S.)
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14
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Anklam E, Bahl MI, Ball R, Beger RD, Cohen J, Fitzpatrick S, Girard P, Halamoda-Kenzaoui B, Hinton D, Hirose A, Hoeveler A, Honma M, Hugas M, Ishida S, Kass GEN, Kojima H, Krefting I, Liachenko S, Liu Y, Masters S, Marx U, McCarthy T, Mercer T, Patri A, Pelaez C, Pirmohamed M, Platz S, Ribeiro AJS, Rodricks JV, Rusyn I, Salek RM, Schoonjans R, Silva P, Svendsen CN, Sumner S, Sung K, Tagle D, Tong L, Tong W, van den Eijnden-van-Raaij J, Vary N, Wang T, Waterton J, Wang M, Wen H, Wishart D, Yuan Y, Slikker Jr. W. Emerging technologies and their impact on regulatory science. Exp Biol Med (Maywood) 2022; 247:1-75. [PMID: 34783606 PMCID: PMC8749227 DOI: 10.1177/15353702211052280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
There is an evolution and increasing need for the utilization of emerging cellular, molecular and in silico technologies and novel approaches for safety assessment of food, drugs, and personal care products. Convergence of these emerging technologies is also enabling rapid advances and approaches that may impact regulatory decisions and approvals. Although the development of emerging technologies may allow rapid advances in regulatory decision making, there is concern that these new technologies have not been thoroughly evaluated to determine if they are ready for regulatory application, singularly or in combinations. The magnitude of these combined technical advances may outpace the ability to assess fit for purpose and to allow routine application of these new methods for regulatory purposes. There is a need to develop strategies to evaluate the new technologies to determine which ones are ready for regulatory use. The opportunity to apply these potentially faster, more accurate, and cost-effective approaches remains an important goal to facilitate their incorporation into regulatory use. However, without a clear strategy to evaluate emerging technologies rapidly and appropriately, the value of these efforts may go unrecognized or may take longer. It is important for the regulatory science field to keep up with the research in these technically advanced areas and to understand the science behind these new approaches. The regulatory field must understand the critical quality attributes of these novel approaches and learn from each other's experience so that workforces can be trained to prepare for emerging global regulatory challenges. Moreover, it is essential that the regulatory community must work with the technology developers to harness collective capabilities towards developing a strategy for evaluation of these new and novel assessment tools.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Reza M Salek
- International Agency for Research on Cancer, France
| | | | | | | | | | | | | | - Li Tong
- Universities of Georgia Tech and Emory, USA
| | | | | | - Neil Vary
- Canadian Food Inspection Agency, Canada
| | - Tao Wang
- National Medical Products Administration, China
| | | | - May Wang
- Universities of Georgia Tech and Emory, USA
| | - Hairuo Wen
- National Institutes for Food and Drug Control, China
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15
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Krupenko NI, Sharma J, Fogle HM, Pediaditakis P, Strickland KC, Du X, Helke KL, Sumner S, Krupenko SA. Knockout of Putative Tumor Suppressor Aldh1l1 in Mice Reprograms Metabolism to Accelerate Growth of Tumors in a Diethylnitrosamine (DEN) Model of Liver Carcinogenesis. Cancers (Basel) 2021; 13:cancers13133219. [PMID: 34203215 PMCID: PMC8268287 DOI: 10.3390/cancers13133219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Cancers often loose the enzyme of folate metabolism ALDH1L1. We proposed that such loss is advantageous for the malignant tumor growth and tested this hypothesis in mice proficient or deficient (gene knockout) in ALDH1L1 expression. Liver cancer in both groups was induced by injection of chemical carcinogen diethylnitrosamine. While the number of tumors observed in ALDH1L1 proficient and deficient mice was similar, tumors grew faster and to a larger size in the knockout mice. We conclude that the ALDH1L1 loss promotes liver tumor growth without affecting tumor initiation or multiplicity. Accelerated growth of tumors lacking the enzyme was linked to several metabolic pathways, which are beneficial for rapid proliferation. Abstract Cytosolic 10-formyltetrahydrofolate dehydrogenase (ALDH1L1) is commonly downregulated in human cancers through promoter methylation. We proposed that ALDH1L1 loss promotes malignant tumor growth. Here, we investigated the effect of the Aldh1l1 mouse knockout (Aldh1l1−/−) on hepatocellular carcinoma using a chemical carcinogenesis model. Fifteen-day-old male Aldh1l1 knockout mice and their wild-type littermate controls (Aldh1l1+/+) were injected intraperitoneally with 20 μg/g body weight of DEN (diethylnitrosamine). Mice were sacrificed 10, 20, 28, and 36 weeks post-DEN injection, and livers were examined for tumor multiplicity and size. We observed that while tumor multiplicity did not differ between Aldh1l1−/− and Aldh1l1+/+ animals, larger tumors grew in Aldh1l1−/− compared to Aldh1l1+/+ mice at 28 and 36 weeks. Profound differences between Aldh1l1−/− and Aldh1l1+/+ mice in the expression of inflammation-related genes were seen at 10 and 20 weeks. Of note, large tumors from wild-type mice showed a strong decrease of ALDH1L1 protein at 36 weeks. Metabolomic analysis of liver tissues at 20 weeks showed stronger differences in Aldh1l1+/+ versus Aldh1l1−/− metabotypes than at 10 weeks, which underscores metabolic pathways that respond to DEN in an ALDH1L1-dependent manner. Our study indicates that Aldh1l1 knockout promoted liver tumor growth without affecting tumor initiation or multiplicity.
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Affiliation(s)
- Natalia I. Krupenko
- Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599, USA; (N.I.K.); (S.S.)
- Nutrition Research Institute, University of North Carolina, Kannapolis, NC 28081, USA; (J.S.); (H.M.F.); (P.P.)
| | - Jaspreet Sharma
- Nutrition Research Institute, University of North Carolina, Kannapolis, NC 28081, USA; (J.S.); (H.M.F.); (P.P.)
| | - Halle M. Fogle
- Nutrition Research Institute, University of North Carolina, Kannapolis, NC 28081, USA; (J.S.); (H.M.F.); (P.P.)
| | - Peter Pediaditakis
- Nutrition Research Institute, University of North Carolina, Kannapolis, NC 28081, USA; (J.S.); (H.M.F.); (P.P.)
| | | | - Xiuxia Du
- Department of Bioinformatics & Genomics, UNC Charlotte, Charlotte, NC 28223, USA;
| | - Kristi L. Helke
- Department of Comparative Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Susan Sumner
- Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599, USA; (N.I.K.); (S.S.)
- Nutrition Research Institute, University of North Carolina, Kannapolis, NC 28081, USA; (J.S.); (H.M.F.); (P.P.)
| | - Sergey A. Krupenko
- Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599, USA; (N.I.K.); (S.S.)
- Nutrition Research Institute, University of North Carolina, Kannapolis, NC 28081, USA; (J.S.); (H.M.F.); (P.P.)
- Correspondence:
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16
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Sharma J, Rushing B, Krupenko N, Sumner S, Krupenko S. Effect of Folate Diet on Liver Metabolomics in Wild Type and Aldh1l1 Knockout Mice. Curr Dev Nutr 2021. [DOI: 10.1093/cdn/nzab050_016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Objectives
The goal of the present study was to investigate whether dietary folate restriction exacerbates the metabotype associated with the KO.
Methods
Hepatic tissues from wildtype (Aldh1l1+/+) and KO (Aldh1l1−/−) mice fed a control (CD), or folate deficient diet (FDD) for 16 weeks were profiled using untargeted metabolomics to identify metabolite changes and affected pathways.
Results
PCA plots of the 6595 peaks in the preprocessed liver datasets show tight clustering of samples within the groups and clear separation between genotypes, and diets. OPLS-DA analysis showed strong separation between pairwise comparisons of the groups with model statistics (R2X, R2Y, and Q2) all greater than 0.5, indicating that dietary folate and Aldh1l1 alone or in combination have a significant effect on the liver metabolomes in male and female mice. Using MetaboAnalyst for pathway analysis significant differences in bile acid metabolism, nucleotide metabolism, and protein synthesis/amino acid metabolism (aminoacyl-tRNA biosynthesis; alanine, aspartate and glutamate metabolism; valine, leucine and isoleucine biosynthesis) were observed in males. Similarly, in females many perturbations in amino acid metabolism, nucleotide metabolism, carbohydrate metabolism (pyruvate metabolism; fructose and mannose metabolism), sphingolipid metabolism, bile acid metabolism and microbiome metabolism (propanoate metabolism; butanoate metabolism) were noted.
Conclusions
Dietary folate elicits liver metabolome response depending on Aldh1l1 genotype.
Funding Sources
NIH, R01
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Affiliation(s)
| | - Blake Rushing
- UNC Nutrition Research Institute, University of North Carolina at Chapel Hill
| | - Natalia Krupenko
- UNC Nutrition Research Institute, University of North Carolina at Chapel Hill
| | - Susan Sumner
- UNC Nutrition Research Institute, University of North Carolina at Chapel Hill
| | - Sergey Krupenko
- UNC Nutrition Research Institute, University of North Carolina at Chapel Hill
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17
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Rushing B, McRitchie S, Arbeeva L, Nelson A, Azcarate-Peril MA, Li YY, Qian Y, Sumner S, Loeser R. Untargeted Fecal Metabolomics to Investigate the Role of the Microbiome and Nutrients in Osteoarthritis. Curr Dev Nutr 2021. [DOI: 10.1093/cdn/nzab033_047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Objectives
The objective of this study was to determine if perturbations in gut microbial composition and the gut metabolome could be linked to individuals with obesity and osteoarthritis (OA).
Methods
Fecal samples were collected from 92 participants with obesity recruited from the Johnston County Osteoarthritis Project. OA cases (n = 59) had radiographic hand plus knee OA, defined as involvement of at least 3 joints across both hands, and a Kellgren-Lawrence (KL) grade 2–4 in at least one knee. Controls (n = 33) were without hand OA and with KL grade 0–1 knees. Fecal metabolomes were analyzed by a UHPLC/Q Exactive HFx mass spectrometer. Microbiome composition was determined in fecal samples by 16S ribosomal RNA amplicon sequencing (rRNA-seq). Stepwise logistic regression models were built to determine predictors of OA status.
Spearman correlations were performed to determine associations between metabolites and microbiota in OA or healthy individuals.
Results
Untargeted metabolomics analysis indicated that OA cases had significantly higher levels of di- and tri-peptides (P < 0.05), and significant perturbations (P < 0.1) in microbial metabolites. Pathway analysis revealed several significantly perturbed pathways (P < 0.05) associated with OA, including leukotriene metabolism, amino acid metabolism and fatty acid utilization. Logistic regression models selected metabolites associated with the microbiota and leaky gut syndrome as significant predictors of OA status, particularly when combined with the 16S rRNA sequencing data. Omega-3/6 polyunsaturated fatty acids (PUFAs) levels were significantly correlated with the phyla Bacteriodetes and Firmicutes.
Conclusions
Adults with obesity and OA have distinct fecal metabolomes characterized by perturbations in microbial metabolites, PUFAs, and protein digestion compared with healthy controls. These metabolic perturbations suggest a role of intestinal inflammation and leaky gut in OA.
Funding Sources
Supported by the Arthritis Foundation, the National Center for Advancing Translational Sciences (NCATS) (UL1TR002489), and the National Institute of Arthritis and Musculoskeletal and Skin Diseases (P30AR072580).
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Affiliation(s)
- Blake Rushing
- UNC Nutrition Research Institute, University of North Carolina at Chapel Hill
| | | | | | | | | | | | | | - Susan Sumner
- UNC Nutrition Research Institute, University of North Carolina at Chapel Hill
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Coleman MF, O’Flanagan CH, Pfeil AJ, Chen X, Pearce JB, Sumner S, Krupenko SA, Hursting SD. Metabolic Response of Triple-Negative Breast Cancer to Folate Restriction. Nutrients 2021; 13:nu13051637. [PMID: 34068120 PMCID: PMC8152779 DOI: 10.3390/nu13051637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Triple-negative breast cancers (TNBCs), accounting for approximately 15% of breast cancers, lack targeted therapy. A hallmark of cancer is metabolic reprogramming, with one-carbon metabolism essential to many processes altered in tumor cells, including nucleotide biosynthesis and antioxidant defenses. We reported that folate deficiency via folic acid (FA) withdrawal in several TNBC cell lines results in heterogenous effects on cell growth, metabolic reprogramming, and mitochondrial impairment. To elucidate underlying drivers of TNBC sensitivity to folate stress, we characterized in vivo and in vitro responses to FA restriction in two TNBC models differing in metastatic potential and innate mitochondrial dysfunction. Methods: Metastatic MDA-MB-231 cells (high mitochondrial dysfunction) and nonmetastatic M-Wnt cells (low mitochondrial dysfunction) were orthotopically injected into mice fed diets with either 2 ppm FA (control), 0 ppm FA, or 12 ppm FA (supplementation; in MDA-MB-231 only). Tumor growth, metabolomics, and metabolic gene expression were assessed. MDA-MB-231 and M-Wnt cells were also grown in media with 0 or 2.2 µM FA; metabolic alterations were assessed by extracellular flux analysis, flow cytometry, and qPCR. Results: Relative to control, dietary FA restriction decreased MDA-MB-231 tumor weight and volume, while FA supplementation minimally increased MDA-MB-231 tumor weight. Metabolic studies in vivo and in vitro using MDA-MB-231 cells showed FA restriction remodeled one-carbon metabolism, nucleotide biosynthesis, and glucose metabolism. In contrast to findings in the MDA-MB-231 model, FA restriction in the M-Wnt model, relative to control, led to accelerated tumor growth, minimal metabolic changes, and modest mitochondrial dysfunction. Increased mitochondrial dysfunction in M-Wnt cells, induced via chloramphenicol, significantly enhanced responsiveness to the cytotoxic effects of FA restriction. Conclusions: Given the lack of targeted treatment options for TNBC, uncovering metabolic vulnerabilities that can be exploited as therapeutic targets is an important goal. Our findings suggest that a major driver of TNBC sensitivity to folate restriction is a high innate level of mitochondrial dysfunction, which can increase dependence on one-carbon metabolism. Thus, folate deprivation or antifolate therapy for TNBCs with metabolic inflexibility due to their elevated levels of mitochondrial dysfunction may represent a novel precision-medicine strategy.
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Affiliation(s)
- Michael F. Coleman
- Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599, USA; (M.F.C.); (C.H.O.); (A.J.P.); (X.C.); (J.B.P.); (S.S.); (S.A.K.)
| | - Ciara H. O’Flanagan
- Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599, USA; (M.F.C.); (C.H.O.); (A.J.P.); (X.C.); (J.B.P.); (S.S.); (S.A.K.)
| | - Alexander J. Pfeil
- Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599, USA; (M.F.C.); (C.H.O.); (A.J.P.); (X.C.); (J.B.P.); (S.S.); (S.A.K.)
| | - Xuewen Chen
- Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599, USA; (M.F.C.); (C.H.O.); (A.J.P.); (X.C.); (J.B.P.); (S.S.); (S.A.K.)
| | - Jane B. Pearce
- Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599, USA; (M.F.C.); (C.H.O.); (A.J.P.); (X.C.); (J.B.P.); (S.S.); (S.A.K.)
| | - Susan Sumner
- Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599, USA; (M.F.C.); (C.H.O.); (A.J.P.); (X.C.); (J.B.P.); (S.S.); (S.A.K.)
- Nutrition Research Institute, University of North Carolina, Kannapolis, NC 28081, USA
| | - Sergey A. Krupenko
- Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599, USA; (M.F.C.); (C.H.O.); (A.J.P.); (X.C.); (J.B.P.); (S.S.); (S.A.K.)
- Nutrition Research Institute, University of North Carolina, Kannapolis, NC 28081, USA
| | - Stephen D. Hursting
- Department of Nutrition, University of North Carolina, Chapel Hill, NC 27599, USA; (M.F.C.); (C.H.O.); (A.J.P.); (X.C.); (J.B.P.); (S.S.); (S.A.K.)
- Nutrition Research Institute, University of North Carolina, Kannapolis, NC 28081, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
- Correspondence:
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Sharma J, Krupenko N, Sumner S, Krupenko S. Metabolic Effects of ALDH1L1 Knockout in Diethylnitrosamine‐Induced Model of Liver Carcinogenesis. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.04079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Susan Sumner
- Department of NutritionUNC‐Chapel HillChapel HillNC
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20
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Kennedy P, Sumner S, Botha P, Welton NJ, Higginson AD, Radford AN. Diminishing returns drive altruists to help extended family. Nat Ecol Evol 2021; 5:468-479. [PMID: 33589803 PMCID: PMC7610556 DOI: 10.1038/s41559-020-01382-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/10/2020] [Indexed: 11/09/2022]
Abstract
Altruism between close relatives can be easily explained. However, paradoxes arise when organisms divert altruism towards more distantly related recipients. In some social insects, workers drift extensively between colonies and help raise less related foreign brood, seemingly reducing inclusive fitness. Since being highlighted by W. D. Hamilton, three hypotheses (bet hedging, indirect reciprocity and diminishing returns to cooperation) have been proposed for this surprising behaviour. Here, using inclusive fitness theory, we show that bet hedging and indirect reciprocity could only drive cooperative drifting under improbable conditions. However, diminishing returns to cooperation create a simple context in which sharing workers is adaptive. Using a longitudinal dataset comprising over a quarter of a million nest cell observations, we quantify cooperative payoffs in the Neotropical wasp Polistes canadensis, for which drifting occurs at high levels. As the worker-to-brood ratio rises in a worker's home colony, the predicted marginal benefit of a worker for expected colony productivity diminishes. Helping related colonies can allow effort to be focused on related brood that are more in need of care. Finally, we use simulations to show that cooperative drifting evolves under diminishing returns when dispersal is local, allowing altruists to focus their efforts on related recipients. Our results indicate the power of nonlinear fitness effects to shape social organization, and suggest that models of eusocial evolution should be extended to include neglected social interactions within colony networks.
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Affiliation(s)
- P. Kennedy
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK,Correspondence:
| | - S. Sumner
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - P. Botha
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - N. J. Welton
- Population Health Sciences, Bristol Medical School, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol, BS8 2PS, UK
| | - A. D. Higginson
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, EX4 4QG, UK
| | - A. N. Radford
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
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21
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Harville EW, Li YY, Pan K, McRitchie S, Pathmasiri W, Sumner S. Untargeted analysis of first trimester serum to reveal biomarkers of pregnancy complications: a case-control discovery phase study. Sci Rep 2021; 11:3468. [PMID: 33568690 PMCID: PMC7876105 DOI: 10.1038/s41598-021-82804-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/15/2021] [Indexed: 11/23/2022] Open
Abstract
Understanding of causal biology and predictive biomarkers are lacking for hypertensive disorders of pregnancy (HDP) and preterm birth (PTB). First-trimester serum specimens from 51 cases of HDP, including 18 cases of pre-eclampsia (PE) and 33 cases of gestational hypertension (GH); 53 cases of PTB; and 109 controls were obtained from the Global Alliance to Prevent Prematurity and Stillbirth repository. Metabotyping was conducted using liquid chromatography high resolution mass spectroscopy and nuclear magnetic resonance spectroscopy. Multivariable logistic regression was used to identify signals that differed between groups after controlling for confounders. Signals important to predicting HDP and PTB were matched to an in-house physical standards library and public databases. Pathway analysis was conducted using GeneGo MetaCore. Over 400 signals for endogenous and exogenous metabolites that differentiated cases and controls were identified or annotated, and models that included these signals produced substantial improvements in predictive power beyond models that only included known risk factors. Perturbations of the aminoacyl-tRNA biosynthesis, L-threonine, and renal secretion of organic electrolytes pathways were associated with both HDP and PTB, while pathways related to cholesterol transport and metabolism were associated with HDP. This untargeted metabolomics analysis identified signals and common pathways associated with pregnancy complications.
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Affiliation(s)
- E W Harville
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, Epidemiology #8318, 1440 Canal St. Ste. 2001, New Orleans, LA, 70112, USA.
| | - Y-Y Li
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, CB#74612, Chapel Hill, NC, 27599-7461, USA
| | - K Pan
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, Epidemiology #8318, 1440 Canal St. Ste. 2001, New Orleans, LA, 70112, USA
| | - S McRitchie
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, CB#74612, Chapel Hill, NC, 27599-7461, USA
| | - W Pathmasiri
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, CB#74612, Chapel Hill, NC, 27599-7461, USA
| | - S Sumner
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, CB#74612, Chapel Hill, NC, 27599-7461, USA.
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22
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Krupenko NI, Sharma J, Pediaditakis P, Helke KL, Hall MS, Du X, Sumner S, Krupenko SA. Aldh1l2 knockout mouse metabolomics links the loss of the mitochondrial folate enzyme to deregulation of a lipid metabolism observed in rare human disorder. Hum Genomics 2020; 14:41. [PMID: 33168096 PMCID: PMC7654619 DOI: 10.1186/s40246-020-00291-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/14/2020] [Indexed: 12/29/2022] Open
Abstract
Background Mitochondrial folate enzyme ALDH1L2 (aldehyde dehydrogenase 1 family member L2) converts 10-formyltetrahydrofolate to tetrahydrofolate and CO2 simultaneously producing NADPH. We have recently reported that the lack of the enzyme due to compound heterozygous mutations was associated with neuro-ichthyotic syndrome in a male patient. Here, we address the role of ALDH1L2 in cellular metabolism and highlight the mechanism by which the enzyme regulates lipid oxidation. Methods We generated Aldh1l2 knockout (KO) mouse model, characterized its phenotype, tissue histology, and levels of reduced folate pools and applied untargeted metabolomics to determine metabolic changes in the liver, pancreas, and plasma caused by the enzyme loss. We have also used NanoString Mouse Inflammation V2 Code Set to analyze inflammatory gene expression and evaluate the role of ALDH1L2 in the regulation of inflammatory pathways. Results Both male and female Aldh1l2 KO mice were viable and did not show an apparent phenotype. However, H&E and Oil Red O staining revealed the accumulation of lipid vesicles localized between the central veins and portal triads in the liver of Aldh1l2-/- male mice indicating abnormal lipid metabolism. The metabolomic analysis showed vastly changed metabotypes in the liver and plasma in these mice suggesting channeling of fatty acids away from β-oxidation. Specifically, drastically increased plasma acylcarnitine and acylglycine conjugates were indicative of impaired β-oxidation in the liver. Our metabolomics data further showed that mechanistically, the regulation of lipid metabolism by ALDH1L2 is linked to coenzyme A biosynthesis through the following steps. ALDH1L2 enables sufficient NADPH production in mitochondria to maintain high levels of glutathione, which in turn is required to support high levels of cysteine, the coenzyme A precursor. As the final outcome, the deregulation of lipid metabolism due to ALDH1L2 loss led to decreased ATP levels in mitochondria. Conclusions The ALDH1L2 function is important for CoA-dependent pathways including β-oxidation, TCA cycle, and bile acid biosynthesis. The role of ALDH1L2 in the lipid metabolism explains why the loss of this enzyme is associated with neuro-cutaneous diseases. On a broader scale, our study links folate metabolism to the regulation of lipid homeostasis and the energy balance in the cell. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-020-00291-3.
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Affiliation(s)
- Natalia I Krupenko
- Nutrition Research Institute, University of North Carolina, Chapel Hill, NC, USA.,Department of Nutrition, University of North Carolina, Chapel Hill, NC, USA
| | - Jaspreet Sharma
- Nutrition Research Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Peter Pediaditakis
- Nutrition Research Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Kristi L Helke
- Department of Comparative Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Madeline S Hall
- Nutrition Research Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Xiuxia Du
- Department of Bioinformatics & Genomics, UNC Charlotte, Charlotte, NC, USA
| | - Susan Sumner
- Nutrition Research Institute, University of North Carolina, Chapel Hill, NC, USA.,Department of Nutrition, University of North Carolina, Chapel Hill, NC, USA
| | - Sergey A Krupenko
- Nutrition Research Institute, University of North Carolina, Chapel Hill, NC, USA. .,Department of Nutrition, University of North Carolina, Chapel Hill, NC, USA.
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23
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Xue J, Hutchins EK, Elnagheeb M, Li Y, Valdar W, McRitchie S, Sumner S, Ideraabdullah FY. Maternal Liver Metabolic Response to Chronic Vitamin D Deficiency Is Determined by Mouse Strain Genetic Background. Curr Dev Nutr 2020; 4:nzaa106. [PMID: 32851199 PMCID: PMC7439094 DOI: 10.1093/cdn/nzaa106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/08/2020] [Accepted: 06/16/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Liver metabolite concentrations have the potential to be key biomarkers of systemic metabolic dysfunction and overall health. However, for most conditions we do not know the extent to which genetic differences regulate susceptibility to metabolic responses. This limits our ability to detect and diagnose effects in heterogeneous populations. OBJECTIVES Here, we investigated the extent to which naturally occurring genetic differences regulate maternal liver metabolic response to vitamin D deficiency (VDD), particularly during perinatal periods when such changes can adversely affect maternal and fetal health. METHODS We used a panel of 8 inbred Collaborative Cross (CC) mouse strains, each with a different genetic background (72 dams, 3-6/treatment group, per strain). We identified robust maternal liver metabolic responses to vitamin D depletion before and during gestation and lactation using a vitamin-D-deficient (VDD; 0 IU vitamin D3/kg) or -sufficient diet (1000 IU vitamin D3/kg). We then identified VDD-induced metabolite changes influenced by strain genetic background. RESULTS We detected a significant VDD effect by orthogonal partial least squares discriminant analysis (Q2 = 0.266, pQ2 = 0.002): primarily, altered concentrations of 78 metabolites involved in lipid, amino acid, and nucleotide metabolism (variable importance to projection score ≥1.5). Metabolites in unsaturated fatty acid and glycerophospholipid metabolism pathways were significantly enriched [False Discovery Rate (FDR) <0.05]. VDD also significantly altered concentrations of putative markers of uremic toxemia, acylglycerols, and dipeptides. The extent of the metabolic response to VDD was strongly dependent on genetic strain, ranging from robustly responsive to nonresponsive. Two strains (CC017/Unc and CC032/GeniUnc) were particularly sensitive to VDD; however, each strain altered different pathways. CONCLUSIONS These novel findings demonstrate that maternal VDD induces different liver metabolic effects in different genetic backgrounds. Strains with differing susceptibility and metabolic response to VDD represent unique tools to identify causal susceptibility factors and further elucidate the role of VDD-induced metabolic changes in maternal and/or fetal health for ultimately translating findings to human populations.
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Affiliation(s)
- Jing Xue
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Elizabeth K Hutchins
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marwa Elnagheeb
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Yi Li
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William Valdar
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan McRitchie
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan Sumner
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Folami Y Ideraabdullah
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
- Department of Nutrition, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Lee SE, Li YY, Sumner S, McRitchie S, Wu L, Labrique A, Christian P, West Jr K, Schulze K. Plasma Untargeted Metabolomic Profile Associated with Vitamin A Status in Pregnant Women in Rural Bangladesh. Curr Dev Nutr 2020. [DOI: 10.1093/cdn/nzaa041_022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Objectives
Vitamin A status during pregnancy is important for visual health, immune function and fetal growth and development. However, little is known about how vitamin A may affect systemic metabolic function of undernourished pregnant women. The objective of this study is to characterize metabolic signatures and pathways associated with vitamin A status in pregnant women.
Methods
This study was nested into JiVitA-3, a community-based antenatal multiple micronutrient vs. iron-folic acid supplementation trial in rural Bangladesh. In plasma samples of 150 women at ∼32 weeks of gestation, retinol had been measured by HPLC and relative abundances of metabolites were measured by UPLC Q-Exactive HF-X mass spectrometer. Univariate linear regression was used to determine metabolites associated with plasma retinol. Multiple testing was corrected using a false discovery rate threshold of 5%.
Results
Among 2985 peak features included in data analysis, 97 known metabolites were positively or negatively associated with plasma retinol concentrations. Among the top 11 positive correlates, seven metabolites are tryptophan or its metabolic catabolites including 5-methoxy tryptophan, tryptamine, 5-methoxytryptamine, N-formylkynureine, indole, 2-indolecarboxylic acid, and 3-methylene-indolenine (r = 0.32∼0.42, p-value < 8 × 10−5). Pathway analysis demonstrated that metabolic pathways of tryptophan, nicotinamide (vitamin B3), lysine, arginine and proline were significantly enriched (gamma p-value < 0.05).
Conclusions
An untargeted plasma metabolomics platform revealed associations of microbial catabolites of tryptophan and other amino acids with vitamin A status of undernourished pregnant women. These metabolites have been implicated in activation of intestinal immune cells and anti-inflammatory and anti-oxidative functions. The results suggest novel mechanisms by which vitamin A may influence immune system and systemic homeostasis, prompting a need for confirmatory studies.
Funding Sources
The JiVitA-3 trial and micronutrient status assessments were funded by the Bill and Melinda Gates Foundation (West, PI). Metabolomics analysis was funded from the NIH Common Fund Metabolomics Program (Sumner, PI).
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Affiliation(s)
| | - Yuan-yuan Li
- NIH Eastern Regional Comprehensive Metabolomics Resource Core, Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill
| | - Susan Sumner
- NIH Eastern Regional Comprehensive Metabolomics Resource Core, Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill
| | - Susan McRitchie
- NIH Eastern Regional Comprehensive Metabolomics Resource Core, Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill
| | - Lee Wu
- Center for Human Nutrition, Department of International Health, Johns Hopkins Bloomberg School of Public Health
| | - Alain Labrique
- Center for Human Nutrition, Department of International Health, Johns Hopkins Bloomberg School of Public Health
| | - Parul Christian
- Center for Human Nutrition, Department of International Health, Johns Hopkins Bloomberg School of Public Health
| | - Keith West Jr
- Center for Human Nutrition, Department of International Health, Johns Hopkins Bloomberg School of Public Health
| | - Kerry Schulze
- Center for Human Nutrition, Department of International Health, Johns Hopkins Bloomberg School of Public Health
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Colgan TJ, Carolan JC, Sumner S, Blaxter ML, Brown MJF. Infection by the castrating parasitic nematode Sphaerularia bombi changes gene expression in Bombus terrestris bumblebee queens. Insect Mol Biol 2020; 29:170-182. [PMID: 31566835 DOI: 10.1111/imb.12618] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/20/2019] [Accepted: 09/13/2019] [Indexed: 06/10/2023]
Abstract
Parasitism can result in dramatic changes in host phenotype, which are themselves underpinned by genes and their expression. Understanding how hosts respond at the molecular level to parasites can therefore reveal the molecular architecture of an altered host phenotype. The entomoparasitic nematode Sphaerularia bombi is a parasite of bumblebee (Bombus) hosts where it induces complex behavioural changes and host castration. To examine this interaction at the molecular level, we performed genome-wide transcriptional profiling using RNA-Sequencing (RNA-Seq) of S. bombi-infected Bombus terrestris queens at two critical time-points: during and just after overwintering diapause. We found that infection by S. bombi affects the transcription of genes underlying host biological processes associated with energy usage, translation, and circadian rhythm. We also found that the parasite affects the expression of immune genes, including members of the Toll signalling pathway providing evidence for a novel interaction between the parasite and the host immune response. Taken together, our results identify host biological processes and genes affected by an entomoparasitic nematode providing the first steps towards a molecular understanding of this ecologically important host-parasite interaction.
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Affiliation(s)
- T J Colgan
- Department of Zoology, School of Natural Sciences, University of Dublin, Trinity College, Dublin, Ireland
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - J C Carolan
- Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland
| | - S Sumner
- Centre for Biodiversity and Environment Research, University College London, London, UK
| | - M L Blaxter
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - M J F Brown
- Centre of Ecology, Evolution and Behaviour, Department of Biological Sciences, Royal Holloway University of London, Egham, UK
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Sharma J, Krupenko NI, Sumner S, Helke KL, Krupenko SA. Effects of
Aldh1l2
Knockout on the Metabolic Profile of Mouse Liver. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.06482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
The informatics pipeline for making sense of untargeted LC-MS or GC-MS data starts with preprocessing the raw data. Results from data preprocessing undergo statistical analysis and subsequently mapped to metabolic pathways for placing untargeted metabolomics data in the biological context. ADAP is a suite of computational algorithms that has been developed specifically for preprocessing LC-MS and GC-MS data. It consists of two separate computational workflows that extract compound-relevant information from raw LC-MS and GC-MS data, respectively. Computational steps include construction of extracted ion chromatograms, detection of chromatographic peaks, spectral deconvolution, and alignment. The two workflows have been incorporated into the cross-platform and graphical MZmine 2 framework and ADAP-specific graphical user interfaces have been developed for using ADAP with ease. This chapter summarizes the algorithmic principles underlying key steps in the two workflows and illustrates how to apply ADAP to preprocess LC-MS and GC-MS data.
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Affiliation(s)
- Xiuxia Du
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Aleksandr Smirnov
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Wei Jia
- University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Susan Sumner
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
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Abstract
In this chapter, we summarize data preprocessing and data analysis strategies used for analysis of NMR data for metabolomics studies. Metabolomics consists of the analysis of the low molecular weight compounds in cells, tissues, or biological fluids, and has been used to reveal biomarkers for early disease detection and diagnosis, to monitor interventions, and to provide information on pathway perturbations to inform mechanisms and identifying targets. Metabolic profiling (also termed metabotyping) involves the analysis of hundreds to thousands of molecules using mainly state-of-the-art mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy technologies. While NMR is less sensitive than mass spectrometry, NMR does provide a wealth of complex and information rich metabolite data. NMR data together with the use of conventional statistics, modeling methods, and bioinformatics tools reveals biomarker and mechanistic information. A typical NMR spectrum, with up to 64k data points, of a complex biological fluid or an extract of cells and tissues consists of thousands of sharp signals that are mainly derived from small molecules. In addition, a number of advanced NMR spectroscopic methods are available for extracting information on high molecular weight compounds such as lipids or lipoproteins. There are numerous data preprocessing, data reduction, and analysis methods developed and evolving in the field of NMR metabolomics. Our goal is to provide an extensive summary of NMR data preprocessing and analysis strategies by providing examples and open source and commercially available analysis software and bioinformatics tools.
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Affiliation(s)
- Wimal Pathmasiri
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA.
| | - Kristine Kay
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Susan McRitchie
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Susan Sumner
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
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Gooding J, Cao L, Ahmed F, Mwiza JM, Fernander M, Whitaker C, Acuff Z, McRitchie S, Sumner S, Ongeri EM. LC-MS-based metabolomics analysis to identify meprin-β-associated changes in kidney tissue from mice with STZ-induced type 1 diabetes and diabetic kidney injury. Am J Physiol Renal Physiol 2019; 317:F1034-F1046. [PMID: 31411076 PMCID: PMC6843037 DOI: 10.1152/ajprenal.00166.2019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/04/2019] [Accepted: 08/06/2019] [Indexed: 01/22/2023] Open
Abstract
Meprin metalloproteases have been implicated in the pathophysiology of diabetic kidney disease (DKD). Single-nucleotide polymorphisms in the meprin-β gene have been associated with DKD in Pima Indians, a Native American ethnic group with an extremely high prevalence of DKD. In African American men with diabetes, urinary meprin excretion positively correlated with the severity of kidney injury. In mice, meprin activity decreased at the onset of diabetic kidney injury. Several studies have identified meprin targets in the kidney. However, it is not known how proteolytic processing of the targets by meprins impacts the metabolite milieu in kidneys. In the present study, global metabolomics analysis identified differentiating metabolites in kidney tissues from wild-type and meprin-β knockout mice with streptozotocin (STZ)-induced type 1 diabetes. Kidney tissues were harvested at 8 wk post-STZ and analyzed by hydrophilic interaction liquid chromatography ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. Principal component analysis identified >200 peaks associated with diabetes. Meprin expression-associated metabolites with strong variable importance of projection scores were indoxyl sulfate, N-γ-l-glutamyl-l-aspartic acid, N-methyl-4-pyridone-3-carboxamide, inosine, and cis-5-decenedioic acid. N-methyl-4-pyridone-3-carboxamide has been previously implicated in kidney injury, and its isomers, 4-PY and 2-PY, are markers of peroxisome proliferation and inflammation that correlate with creatinine clearance and glucose tolerance. Meprin deficiency-associated differentiating metabolites with high variable importance of projection scores were cortisol, hydroxymethoxyphenylcarboxylic acid-O-sulfate, and isovaleryalanine. The data suggest that meprin-β activity enhances diabetic kidney injury in part by altering the metabolite balance in kidneys, favoring high levels of uremic toxins such as indoxyl sulfate and N-methyl-pyridone-carboxamide.
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Affiliation(s)
- Jessica Gooding
- National Institutes of Health Common Fund Eastern Regional Comprehensive Metabolomics Resource Core, RTI International, Research Park, North Carolina
| | - Lei Cao
- Department of Biology, North Carolina A&T State University, Greensboro, North Carolina
| | - Faihaa Ahmed
- Department of Biology, North Carolina A&T State University, Greensboro, North Carolina
| | - Jean-Marie Mwiza
- Department of Biology, North Carolina A&T State University, Greensboro, North Carolina
| | - Mizpha Fernander
- Department of Biology, North Carolina A&T State University, Greensboro, North Carolina
| | - Courtney Whitaker
- National Institutes of Health Common Fund Eastern Regional Comprehensive Metabolomics Resource Core, RTI International, Research Park, North Carolina
| | - Zach Acuff
- National Institutes of Health Common Fund Eastern Regional Comprehensive Metabolomics Resource Core, RTI International, Research Park, North Carolina
| | - Susan McRitchie
- National Institutes of Health Common Fund Eastern Regional Comprehensive Metabolomics Resource Core, RTI International, Research Park, North Carolina
- Department of Nutrition, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Susan Sumner
- National Institutes of Health Common Fund Eastern Regional Comprehensive Metabolomics Resource Core, RTI International, Research Park, North Carolina
- Department of Nutrition, School of Public Health, University of North Carolina, Chapel Hill, North Carolina
| | - Elimelda Moige Ongeri
- Department of Biology, North Carolina A&T State University, Greensboro, North Carolina
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Carter RA, Pan K, Harville EW, McRitchie S, Sumner S. Metabolomics to reveal biomarkers and pathways of preterm birth: a systematic review and epidemiologic perspective. Metabolomics 2019; 15:124. [PMID: 31506796 PMCID: PMC7805080 DOI: 10.1007/s11306-019-1587-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/03/2019] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Most known risk factors for preterm birth, a leading cause of infant morbidity and mortality, are not modifiable. Advanced molecular techniques are increasingly being applied to identify biomarkers and pathways important in disease development and progression. OBJECTIVES We review the state of the literature and assess it from an epidemiologic perspective. METHODS PubMed, Embase, CINAHL, and Cochrane Central were searched on January 31, 2019 for original articles published after 1998 that utilized an untargeted metabolomic approach to identify markers of preterm birth. Eligible manuscripts were peer-reviewed and included original data from untargeted metabolomics analyses of maternal tissue derived from human studies designed to determine mechanisms and predictors of preterm birth. RESULTS Of 2823 results, 14 articles met the inclusion requirements. There was little consistency in study design, outcome definition, type of biospecimen, or the inclusion of covariates and confounding factors, and few consistent associations with metabolites were identified in this review. CONCLUSION Studies to date on metabolomic predictors of preterm birth are highly heterogeneous in both methodology and resulting metabolite identification. There is an urgent need for larger studies in well-defined populations, to determine biomarkers predictive of preterm birth, and to reveal mechanisms and targets for development of intervention strategies.
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Affiliation(s)
- R A Carter
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, 1440 Canal Street, New Orleans, LA, 70112, USA
| | - K Pan
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, 1440 Canal Street, New Orleans, LA, 70112, USA.
| | - E W Harville
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, 1440 Canal Street, New Orleans, LA, 70112, USA
| | - S McRitchie
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, 500 Laureate Way, Kannapolis, NC, 28081, USA
| | - S Sumner
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, 500 Laureate Way, Kannapolis, NC, 28081, USA
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Anzmann AF, Pinto S, Busa V, Carlson J, McRitchie S, Sumner S, Pandey A, Vernon HJ. Multi-omics studies in cellular models of methylmalonic acidemia and propionic acidemia reveal dysregulation of serine metabolism. Biochim Biophys Acta Mol Basis Dis 2019; 1865:165538. [PMID: 31449969 DOI: 10.1016/j.bbadis.2019.165538] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/06/2019] [Accepted: 08/21/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Methylmalonic acidemia (MMA) and propionic acidemia (PA) are related disorders of mitochondrial propionate metabolism, caused by defects in methylmalonyl-CoA mutase (MUT) and propionyl-CoA carboxylase (PCC), respectively. These biochemical defects lead to a complex cascade of downstream metabolic abnormalities, and identification of these abnormal pathways has important implications for understanding disease pathophysiology. Using a multi-omics approach in cellular models of MMA and PA, we identified serine and thiol metabolism as important areas of metabolic dysregulation. METHODS We performed global proteomic analysis of fibroblasts and untargeted metabolomics analysis of plasma from individuals with MMA to identify novel pathways of dysfunction. We probed these novel pathways in CRISPR-edited, MUT and PCCA null HEK293 cell lines via targeted metabolomics, gene expression analysis, and flux metabolomics tracing utilization of 13C-glucose. RESULTS Proteomic analysis of fibroblasts identified upregulation of multiple proteins involved in serine synthesis and thiol metabolism including: phosphoserine amino transferase (PSAT1), cystathionine beta synthase (CBS), and mercaptopyruvate sulfurtransferase (MPST). Metabolomics analysis of plasma revealed significantly increased levels of cystathionine and glutathione, central metabolites in thiol metabolism. CRISPR-edited MUT and PCCA HEK293 cells recapitulate primary defects of MMA and PA and have upregulation of transcripts associated with serine and thiol metabolism including PSAT1. 13C-glucose flux metabolomics in MUT and PCCA null HEK293 cells identified increases in serine de novo biosynthesis, serine transport, and abnormal downstream TCA cycle utilization. CONCLUSION We identified abnormal serine metabolism as a novel area of cellular dysfunction in MMA and PA, thus introducing a potential new target for therapeutic investigation.
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Affiliation(s)
- Arianna Franca Anzmann
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Sneha Pinto
- Institute of Bioinformatics, Bengalaru, India; Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Veronica Busa
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - James Carlson
- LECO Corporation, St. Joseph, MI, United States of America; RTI International, Research Triangle Park, NC, USA
| | - Susan McRitchie
- RTI International, Research Triangle Park, NC, USA; University of North Carolina at Chapel Hill, Nutrition Research Institute, Eastern Regional Comprehensive Metabolomics Resource Core, University of North Carolina at Chapel Hill, United States of America
| | - Susan Sumner
- RTI International, Research Triangle Park, NC, USA; University of North Carolina at Chapel Hill, Nutrition Research Institute, Eastern Regional Comprehensive Metabolomics Resource Core, University of North Carolina at Chapel Hill, United States of America
| | - Akhilesh Pandey
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Hilary J Vernon
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America; Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, United States of America.
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Sarret C, Ashkavand Z, Paules E, Dorboz I, Pediaditakis P, Sumner S, Eymard-Pierre E, Francannet C, Krupenko NI, Boespflug-Tanguy O, Krupenko SA. Deleterious mutations in ALDH1L2 suggest a novel cause for neuro-ichthyotic syndrome. NPJ Genom Med 2019; 4:17. [PMID: 31341639 PMCID: PMC6650503 DOI: 10.1038/s41525-019-0092-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/03/2019] [Indexed: 01/06/2023] Open
Abstract
Neuro-ichthyotic syndromes are a group of rare genetic diseases mainly associated with perturbations in lipid metabolism, intracellular vesicle trafficking, or glycoprotein synthesis. Here, we report a patient with a neuro-ichthyotic syndrome associated with deleterious mutations in the ALDH1L2 (aldehyde dehydrogenase 1 family member L2) gene encoding for mitochondrial 10-formyltetrahydrofolate dehydrogenase. Using fibroblast culture established from the ALDH1L2-deficient patient, we demonstrated that the enzyme loss impaired mitochondrial function affecting both mitochondrial morphology and the pool of metabolites relevant to β-oxidation of fatty acids. Cells lacking the enzyme had distorted mitochondria, accumulated acylcarnitine derivatives and Krebs cycle intermediates, and had lower ATP and increased ADP/AMP indicative of a low energy index. Re-expression of functional ALDH1L2 enzyme in deficient cells restored the mitochondrial morphology and the metabolic profile of fibroblasts from healthy individuals. Our study underscores the role of ALDH1L2 in the maintenance of mitochondrial integrity and energy balance of the cell, and suggests the loss of the enzyme as the cause of neuro-cutaneous disease.
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Affiliation(s)
- Catherine Sarret
- IGCNC, Institut Pascal, UMR CNRS-UCA-SIGMA, Aubière, France.,2Department of Clinical Genetics and Medical Cytogenetics, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, France
| | - Zahra Ashkavand
- 3Nutrition Research Institute, University of North Carolina, Chapel Hill, NC USA
| | - Evan Paules
- 3Nutrition Research Institute, University of North Carolina, Chapel Hill, NC USA.,4Department of Nutrition, University of North Carolina, Chapel Hill, NC USA
| | - Imen Dorboz
- 5INSERM UMR1141, DHU PROTECT, PARIS-DIDEROT, University Sorbonne Paris-Cite, Paris, France
| | - Peter Pediaditakis
- 3Nutrition Research Institute, University of North Carolina, Chapel Hill, NC USA
| | - Susan Sumner
- 3Nutrition Research Institute, University of North Carolina, Chapel Hill, NC USA.,4Department of Nutrition, University of North Carolina, Chapel Hill, NC USA
| | - Eléonore Eymard-Pierre
- 2Department of Clinical Genetics and Medical Cytogenetics, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, France
| | - Christine Francannet
- 2Department of Clinical Genetics and Medical Cytogenetics, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, France
| | - Natalia I Krupenko
- 3Nutrition Research Institute, University of North Carolina, Chapel Hill, NC USA.,4Department of Nutrition, University of North Carolina, Chapel Hill, NC USA
| | - Odile Boespflug-Tanguy
- 5INSERM UMR1141, DHU PROTECT, PARIS-DIDEROT, University Sorbonne Paris-Cite, Paris, France.,6Department of Child Neurology and Metabolic Disorders, LEUKOFRANCE, Hôpital Robert Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sergey A Krupenko
- 3Nutrition Research Institute, University of North Carolina, Chapel Hill, NC USA.,4Department of Nutrition, University of North Carolina, Chapel Hill, NC USA
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Schulfer AF, Schluter J, Zhang Y, Brown Q, Pathmasiri W, McRitchie S, Sumner S, Li H, Xavier JB, Blaser MJ. The impact of early-life sub-therapeutic antibiotic treatment (STAT) on excessive weight is robust despite transfer of intestinal microbes. ISME J 2019; 13:1280-1292. [PMID: 30651608 PMCID: PMC6474226 DOI: 10.1038/s41396-019-0349-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 12/07/2018] [Accepted: 12/31/2018] [Indexed: 01/12/2023]
Abstract
The high-fat, high-calorie diets of westernized cultures contribute to the global obesity epidemic, and early life exposure to antibiotics may potentiate those dietary effects. Previous experiments with mice had shown that sub-therapeutic antibiotic treatment (STAT)-even restricted to early life-affected the gut microbiota, altered host metabolism, and increased adiposity throughout the lifetime of the animals. Here we carried out a large-scale cohousing experiment to investigate whether cohousing STAT and untreated (Control) mice would transfer the STAT-perturbed microbiota and transmit its impact on weight. We exposed pregnant dams and their young offspring to either low-dose penicillin (STAT) or water (Control) until weaning, and then followed the offspring as they grew and endured a switch from normal to high-fat diet at week 17 of life. Cohousing, which started at week 4, rapidly approximated the microbiota within cages, lowering the weight of STAT mice relative to non-cohoused mice. The effect, however, varied between cages, and was restricted to the first 16 weeks when diet consisted of normal chow. Once mice switched to high-fat diet, the microbiota α- and β-diversity expanded and the effect of cohousing faded: STAT mice, again, were heavier than control mice independently of cohousing. Metabolomics revealed serum metabolites associated with STAT exposure, but no significant differences were detected in glucose or insulin tolerance. Our results show that cohousing can partly ameliorate the impact of STAT on the gut microbiota but not prevent increased weight with high-fat diet. These observations have implications for microbiota therapies aimed to resolve the collateral damage of antibiotics and their load on human obesity.
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Affiliation(s)
- Anjelique F Schulfer
- Department of Medicine, New York University Langone Medical Center, New York, NY, 10016, USA
| | - Jonas Schluter
- Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Yilong Zhang
- Department of Population Health, New York University Langone Medical Center, New York, NY, 10016, USA
| | - Quincy Brown
- Department of Medicine, New York University Langone Medical Center, New York, NY, 10016, USA
| | - Wimal Pathmasiri
- Eastern Regional Comprehensive Metabolomics Resource Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan McRitchie
- Eastern Regional Comprehensive Metabolomics Resource Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan Sumner
- Eastern Regional Comprehensive Metabolomics Resource Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Huilin Li
- Department of Population Health, New York University Langone Medical Center, New York, NY, 10016, USA
| | - Joao B Xavier
- Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.
| | - Martin J Blaser
- Department of Medicine, New York University Langone Medical Center, New York, NY, 10016, USA.
- New York Harbor Veterans Affairs Medical Center, New York, NY, 10010, USA.
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Ghanbari R, Pathmasiri W, McRitchie S, Stewart D, Etemadi A, Abnet C, Pollock J, Malekzadeh R, Sumner S. Metabolomics Analysis of Opiate Abusers from Golestan Cohort Study (GCS). FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.lb235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Reza Ghanbari
- Nutrition Research InstituteUniversity of North Carolina at Chapel HillKannapolisNC
| | - Wimal Pathmasiri
- Nutrition Research InstituteUniversity of North Carolina at Chapel HillKannapolisNC
| | - Susan McRitchie
- Nutrition Research InstituteUniversity of North Carolina at Chapel HillKannapolisNC
| | - Delisha Stewart
- Nutrition Research InstituteUniversity of North Carolina at Chapel HillKannapolisNC
| | - Arash Etemadi
- Division of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMD
| | - Christian Abnet
- Division of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMD
| | - Jonathan Pollock
- Genetics, Epigenetics and Developmental Neuroscience BranchNational Institute on Drug AbuseRockvilleMD
| | - Reza Malekzadeh
- Digestive Diseases Research InstituteTehran University of Medical SciencesTehranIran
| | - Susan Sumner
- Nutrition Research InstituteUniversity of North Carolina at Chapel HillKannapolisNC
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Hemnes AR, Luther JM, Rhodes CJ, Burgess JP, Carlson J, Fan R, Fessel JP, Fortune N, Gerszten RE, Halliday SJ, Hekmat R, Howard L, Newman JH, Niswender KD, Pugh ME, Robbins IM, Sheng Q, Shibao CA, Shyr Y, Sumner S, Talati M, Wharton J, Wilkins MR, Ye F, Yu C, West J, Brittain EL. Human PAH is characterized by a pattern of lipid-related insulin resistance. JCI Insight 2019; 4:e123611. [PMID: 30626738 PMCID: PMC6485674 DOI: 10.1172/jci.insight.123611] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/27/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is a deadly disease of the small pulmonary vasculature with an increased prevalence of insulin resistance (IR). Insulin regulates both glucose and lipid homeostasis. We sought to quantify glucose- and lipid-related IR in human PAH, testing the hypothesis that lipoprotein indices are more sensitive indices of IR in PAH. METHODS Oral glucose tolerance testing in PAH patients and triglyceride-matched (TG-matched) controls and proteomic, metabolomics, and lipoprotein analyses were performed in PAH and controls. Results were validated in an external cohort and in explanted human PAH lungs. RESULTS PAH patients were similarly glucose intolerant or IR by glucose homeostasis metrics compared with control patients when matched for the metabolic syndrome. Using the insulin-sensitive lipoprotein index, TG/HDL ratio, PAH patients were more commonly IR than controls. Proteomic and metabolomic analysis demonstrated separation between PAH and controls, driven by differences in lipid species. We observed a significant increase in long-chain acylcarnitines, phosphatidylcholines, insulin metabolism-related proteins, and in oxidized LDL receptor 1 (OLR1) in PAH plasma in both a discovery and validation cohort. PAH patients had higher lipoprotein axis-related IR and lipoprotein-based inflammation scores compared with controls. PAH patient lung tissue showed enhanced OLR1 immunostaining within plexiform lesions and oxidized LDL accumulation within macrophages. CONCLUSIONS IR in PAH is characterized by alterations in lipid and lipoprotein homeostasis axes, manifest by elevated TG/HDL ratio, and elevated circulating medium- and long-chain acylcarnitines and lipoproteins. Oxidized LDL and its receptor OLR1 may play a role in a proinflammatory phenotype in PAH. FUNDING NIH DK096994, HL060906, UL1 RR024975-01, UL1 TR000445-06, DK020593, P01 HL108800-01A1, and UL1 TR002243; American Heart Association 13FTF16070002.
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Affiliation(s)
- Anna R. Hemnes
- Division of Allergy, Pulmonary and Critical Care Medicine and
| | - J. Matthew Luther
- Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christopher J. Rhodes
- Centre for Pharmacology and Therapeutics, Department of Medicine, Hammersmith Campus, Imperial College, London, United Kingdom
| | | | - James Carlson
- RTI International, Research Triangle Park, North Carolina, USA
| | - Run Fan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Niki Fortune
- Division of Allergy, Pulmonary and Critical Care Medicine and
| | - Robert E. Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Rezzan Hekmat
- Cardiovascular Medicine Division, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Luke Howard
- National Heart and Lung Institute, Imperial College, London and National Pulmonary Hypertension Service, Hammersmith Hospital, London, United Kingdom
| | - John H. Newman
- Division of Allergy, Pulmonary and Critical Care Medicine and
| | | | | | - Ivan M. Robbins
- Division of Allergy, Pulmonary and Critical Care Medicine and
| | - Quanhu Sheng
- Division of Cancer Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Cyndya A. Shibao
- Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yu Shyr
- Division of Cancer Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Susan Sumner
- NIH Common Fund Eastern Regional Comprehensive Metabolomics Resource Core, School of Public Health, University of North Carolina at Chapel Hill, Kannapolis, North Carolina, USA
| | - Megha Talati
- Division of Allergy, Pulmonary and Critical Care Medicine and
| | - John Wharton
- Centre for Pharmacology and Therapeutics, Department of Medicine, Hammersmith Campus, Imperial College, London, United Kingdom
| | - Martin R. Wilkins
- Centre for Pharmacology and Therapeutics, Department of Medicine, Hammersmith Campus, Imperial College, London, United Kingdom
| | - Fei Ye
- Division of Cancer Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Chang Yu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James West
- Division of Allergy, Pulmonary and Critical Care Medicine and
| | - Evan L. Brittain
- Cardiovascular Medicine Division, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Rock KD, Horman B, Phillips AL, McRitchie SL, Watson S, Deese-Spruill J, Jima D, Sumner S, Stapleton HM, Patisaul HB. EDC IMPACT: Molecular effects of developmental FM 550 exposure in Wistar rat placenta and fetal forebrain. Endocr Connect 2018; 7:305-324. [PMID: 29351906 PMCID: PMC5817967 DOI: 10.1530/ec-17-0373] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/19/2018] [Indexed: 12/13/2022]
Abstract
Firemaster 550 (FM 550) is a flame retardant (FR) mixture that has become one of the most commonly used FRs in foam-based furniture and baby products. Human exposure to this commercial mixture, composed of brominated and organophosphate components, is widespread. We have repeatedly shown that developmental exposure can lead to sex-specific behavioral effects in rats. Accruing evidence of endocrine disruption and potential neurotoxicity has raised concerns regarding the neurodevelopmental effects of FM 550 exposure, but the specific mechanisms of action remains unclear. Additionally, we observed significant, and in some cases sex-specific, accumulation of FM 550 in placental tissue following gestational exposure. Because the placenta is an important source of hormones and neurotransmitters for the developing brain, it may be a critical target of toxicity to consider in the context of developmental neurotoxicity. Using a mixture of targeted and exploratory approaches, the goal of the present study was to identify possible mechanisms of action in the developing forebrain and placenta. Wistar rat dams were orally exposed to FM 550 (0, 300 or 1000 µg/day) for 10 days during gestation and placenta and fetal forebrain tissue collected for analysis. In placenta, evidence of endocrine, inflammatory and neurotransmitter signaling pathway disruption was identified. Notably, 5-HT turnover was reduced in placental tissue and fetal forebrains indicating that 5-HT signaling between the placenta and the embryonic brain may be disrupted. These findings demonstrate that environmental contaminants, like FM 550, have the potential to impact the developing brain by disrupting normal placental functions.
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Affiliation(s)
- Kylie D Rock
- Department of Biological SciencesNorth Carolina State University, Raleigh, North Carolina, USA
| | - Brian Horman
- Department of Biological SciencesNorth Carolina State University, Raleigh, North Carolina, USA
| | - Allison L Phillips
- Nicholas School of the EnvironmentDuke University, Durham, North Carolina, USA
| | - Susan L McRitchie
- NIH Eastern Regional Comprehensive Metabolomics Res. CoreUniv. of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Scott Watson
- NIH Eastern Regional Comprehensive Metabolomics Res. CoreUniv. of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jocelin Deese-Spruill
- NIH Eastern Regional Comprehensive Metabolomics Res. CoreUniv. of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dereje Jima
- Center for Human Health and the EnvironmentNorth Carolina State University, Raleigh, North Carolina, USA
- Bioinformatics Research CenterNorth Carolina State University, Raleigh, North Carolina, USA
| | - Susan Sumner
- NIH Eastern Regional Comprehensive Metabolomics Res. CoreUniv. of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Center for Human Health and the EnvironmentNorth Carolina State University, Raleigh, North Carolina, USA
| | - Heather M Stapleton
- Nicholas School of the EnvironmentDuke University, Durham, North Carolina, USA
| | - Heather B Patisaul
- Department of Biological SciencesNorth Carolina State University, Raleigh, North Carolina, USA
- Center for Human Health and the EnvironmentNorth Carolina State University, Raleigh, North Carolina, USA
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Abstract
Drug addiction has been associated with an increased risk for cancer, psychological complications, heart, liver, and lung disease, as well as infection. While genes have been identified that can mark individuals at risk for substance abuse, the initiation step of addiction is attributed to persistent metabolic disruptions occurring following the first instance of narcotic drug use. Advances in analytical technologies can enable the detection of thousands of signals in body fluids and excreta that can be used to define biochemical profiles of addiction. Today, these approaches hold promise for determining how exposure to drugs, in the absence or presence of other environmentally relevant factors, can impact human metabolism. We posit that these can lead to candidate biomarkers of drug dependence, treatment, withdrawal, or relapse.
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Affiliation(s)
- Reza Ghanbari
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Susan Sumner
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Saggi SJ, Mercier K, Gooding JR, Friedman E, Vyas U, Ranganathan N, Ranganathan P, McRitchie S, Sumner S. Metabolic profiling of a chronic kidney disease cohort reveals metabolic phenotype more likely to benefit from a probiotic. Int J Probiotics Prebiotics 2017; 12:43-54. [PMID: 30774576 PMCID: PMC6377160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
SCOPE Persistent reduction in Glomerular Filtration Rate (GFR) is a hallmark of Chronic Kidney Disease (CKD) and is associated with an elevation of Blood Urea Nitrogen (BUN). This metabolomics pilot study sought to identify metabolites that differentiated patients with CKD whose BUN decreased on a probiotic and possible mechanisms. METHODS AND RESULTS Metabolomics was used to analyze baseline plasma samples previously diagnosed with CKD Stage III-IV. Patients had participated in a dose escalation study of the probiotic Renadyl™. A total of 24 samples were categorized depending on whether BUN increased or decreased from baseline after 4 months of probiotic use. Multivariate analysis was used to analyze the data and determine the metabolites that best differentiated the phenotypic groups. The sixteen patients who had a decrease in BUN were not significantly different based on demographic and clinical measures from those whose BUN increased or did not change with the exception of age. Eleven of the fourteen metabolites that differentiated the groups were known to be modulated by gut microflora, which may eventually provide a mechanistic link between probiotic and outcomes. CONCLUSIONS Metabolomics revealed metabolites at baseline that may predict individuals with CKD that would most benefit from a probiotics.
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Affiliation(s)
- Subodh J. Saggi
- Divisions of Nephrology and Transplantation, SUNY Downstate Medical Center, 450 Clarkson Ave., Brooklyn, NY 11203, USA
| | - Kelly Mercier
- NIH Eastern Regional Comprehensive Metabolomics Resource Core, RTI International, 3040 E Cornwallis Rd., Durham, NC 27709, USA
| | - Jessica R. Gooding
- NIH Eastern Regional Comprehensive Metabolomics Resource Core, RTI International, 3040 E Cornwallis Rd., Durham, NC 27709, USA
| | - Eli Friedman
- Divisions of Nephrology and Transplantation, SUNY Downstate Medical Center, 450 Clarkson Ave., Brooklyn, NY 11203, USA
| | - Usha Vyas
- Kibow Biotech Inc., 4781 West Chester Pike, Newtown Square, PA 19073, USA
| | | | - Pari Ranganathan
- Kibow Biotech Inc., 4781 West Chester Pike, Newtown Square, PA 19073, USA
| | - Susan McRitchie
- NIH Eastern Regional Comprehensive Metabolomics Resource Core, RTI International, 3040 E Cornwallis Rd., Durham, NC 27709, USA
| | - Susan Sumner
- NIH Eastern Regional Comprehensive Metabolomics Resource Core, RTI International, 3040 E Cornwallis Rd., Durham, NC 27709, USA
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Chou H, Pathmasiri W, Deese-Spruill J, Sumner S, Buchwalter DB. Metabolomics reveal physiological changes in mayfly larvae (Neocloeon triangulifer) at ecological upper thermal limits. J Insect Physiol 2017; 101:107-112. [PMID: 28733240 PMCID: PMC5575740 DOI: 10.1016/j.jinsphys.2017.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 06/07/2023]
Abstract
Aquatic insects play critical roles in freshwater ecosystems and temperature is a fundamental driver of species performance and distributions. However, the physiological mechanisms that determine the thermal performance of species remain unclear. Here we used a metabolomics approach to gain insights into physiological changes associated with a short-term, sublethal thermal challenge in the mayfly Neocloeon triangulifer (Ephemeroptera: Baetidae). Larvae were subjected to a thermal ramp (from 22 to 30°C at a rate of 1°C/h) and metabolomics analysis (both Nuclear Magnetic Resonance (NMR) Spectroscopy and Gas Chromatography coupled Time-of-Flight Mass Spectrometry (GC-TOF-MS)) indicated that processes related to energetics (sugar metabolism) and membrane stabilization primarily differentiated heat treated larvae from controls. Limited evidence of anaerobic metabolism was observed in the heat treated larvae at 30°C, a temperature that is chronically lethal to larvae.
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Affiliation(s)
- Hsuan Chou
- Graduate Toxicology Program, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, United States.
| | - Wimal Pathmasiri
- Systems and Translational Sciences, RTI International, Research Triangle Park, NC 27709, United States
| | - Jocelin Deese-Spruill
- Systems and Translational Sciences, RTI International, Research Triangle Park, NC 27709, United States
| | - Susan Sumner
- Systems and Translational Sciences, RTI International, Research Triangle Park, NC 27709, United States
| | - David B Buchwalter
- Graduate Toxicology Program, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, United States
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Szabo DT, Pathmasiri W, Sumner S, Birnbaum LS. Serum Metabolomic Profiles in Neonatal Mice following Oral Brominated Flame Retardant Exposures to Hexabromocyclododecane (HBCD) Alpha, Gamma, and Commercial Mixture. Environ Health Perspect 2017; 125:651-659. [PMID: 27814246 PMCID: PMC5381977 DOI: 10.1289/ehp242] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/30/2015] [Accepted: 09/19/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Hexabromocyclododecane (HBCD) is a high production volume brominated flame retardant added to building insulation foams, electronics, and textiles. HBCD is a commercial mixture (CM-HBCD) composed of three main stereoisomers: α-HBCD (10%), β-HBCD (10%), and γ-HBCD (80%). A shift from the dominant stereoisomer γ-HBCD to α-HBCD is detected in humans and wildlife. OBJECTIVES Considering CM-HBCD has been implicated in neurodevelopment and endocrine disruption, with expected metabolism perturbations, we performed metabolomics on mice serum obtained during a window-of-developmental neurotoxicity to draw correlations between early-life exposures and developmental outcomes and to predict health risks. METHODS Six female C57BL/6 mice at postnatal day (PND) 10 were administered a single gavage dose of α-, γ-, or CM-HBCD at 3, 10, and 30 mg/kg. Nuclear magnetic resonance metabolomics was used to analyze 60 μL serum aliquots of blood collected 4 days post-oral exposure. RESULTS Infantile mice exposed to α-, γ-, or CM-HBCD demonstrated differences in endogenous metabolites by treatment and dose groups, including metabolites involved in glycolysis, gluconeogenesis, lipid metabolism, citric acid cycle, and neurodevelopment. Ketone bodies, 3-hydroxybutyrate, and acetoacetate, were nonstatistically elevated, when compared with mean control levels, in all treatment and dose groups, while glucose, pyruvate, and alanine varied. Acetoacetate was significantly increased in the 10 mg/kg α-HBCD and was nonsignificantly decreased with CM-HBCD. A third ketone body, acetone, was significantly lower in the 30 mg/kg α-HBCD group with significant increases in pyruvate at the same treatment and dose group. Metabolites significant in differentiating treatment and dose groups were also identified, including decreases in amino acids glutamate (excitatory neurotransmitter in learning and memory) and phenylalanine (neurotransmitter precursor) after α-HBCD and γ-HBCD exposure, respectively. CONCLUSIONS We demonstrated that 4 days following a single neonatal oral exposure to α-, γ-, and CM-HBCD resulted in different serum metabolomic profiles, indicating stereoisomer- and mixture-specific effects and possible mechanisms of action.
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Affiliation(s)
- David T. Szabo
- National Human Environmental Exposure Research Laboratory, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina, USA
- Curriculum in Toxicology, University of North Carolina–Chapel Hill, Chapel Hill, North Carolina, USA
- Address correspondence to D.T. Szabo, U.S. Environmental Protection Agency, National Human Environmental Exposure Research Laboratory; and University of North Carolina–Chapel Hill, Curriculum in Toxicology, 130 Finsbury Street, Durham, NC 27703 USA. Telephone: (352) 615-2415. E-mail:
| | - Wimal Pathmasiri
- Discovery Sciences, Research Triangle Institute International, Research Triangle Park, North Carolina, USA
| | - Susan Sumner
- Discovery Sciences, Research Triangle Institute International, Research Triangle Park, North Carolina, USA
| | - Linda S. Birnbaum
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services, Research Triangle Park, North Carolina, USA
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Dhungana S, Carlson JE, Pathmasiri W, McRitchie S, Davis M, Sumner S, Appt SE. Impact of a western diet on the ovarian and serum metabolome. Maturitas 2016; 92:134-142. [DOI: 10.1016/j.maturitas.2016.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/25/2016] [Accepted: 07/07/2016] [Indexed: 11/26/2022]
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Dennis KK, Auerbach SS, Balshaw DM, Cui Y, Fallin MD, Smith MT, Spira A, Sumner S, Miller GW. The Importance of the Biological Impact of Exposure to the Concept of the Exposome. Environ Health Perspect 2016; 124:1504-1510. [PMID: 27258438 PMCID: PMC5047763 DOI: 10.1289/ehp140] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/23/2016] [Accepted: 05/12/2016] [Indexed: 05/11/2023]
Abstract
BACKGROUND The term "exposome" was originally coined in 2005 and defined as the totality of exposures throughout the lifetime. The exposome provides an excellent scientific framework for studying human health and disease. Recently, it has been suggested that how exposures affect our biology and how our bodies respond to such exposures should be part of the exposome. OBJECTIVES The authors describe the biological impact of the exposome and outline many of the targets and processes that can be assessed as part of a comprehensive analysis of the exposome. DISCUSSION The processes that occur downstream from the initial interactions with exogenous and endogenous compounds determine the biological impact of exposures. If the effects are not considered in the same context as the exposures, it will be difficult to determine cause and effect. The exposome and biology are interactive-changes in biology due to the environment change one's vulnerability to subsequent exposures. Additionally, highly resilient individuals are able to withstand environmental exposures with minimal effects to their health. We expect that the vast majority of exposures are transient, and chemicals underlying exposures that occurred weeks, months, or years ago are long gone from the body. However, these past chemical exposures often leave molecular fingerprints that may be able to provide information on these past exposures. CONCLUSIONS Through linking exposures to specific biological responses, exposome research could serve to improve understanding of the mechanistic connections between exposures and health to help mitigate adverse health outcomes across the lifespan. CITATION Dennis KK, Auerbach SS, Balshaw DM, Cui Y, Fallin MD, Smith MT, Spira A, Sumner S, Miller GW. 2016. The importance of the biological impact of exposure to the concept of the exposome. Environ Health Perspect 124:1504-1510; http://dx.doi.org/10.1289/EHP140.
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Affiliation(s)
- Kristine K. Dennis
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Scott S. Auerbach
- Biomolecular Screening Branch, Division of the National Toxicology Program, and
| | - David M. Balshaw
- Exposure, Response, and Technology Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Resources, Research Triangle Park, North Carolina, USA
| | - Yuxia Cui
- Exposure, Response, and Technology Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Resources, Research Triangle Park, North Carolina, USA
| | - Margaret Daniele Fallin
- Department of Mental Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Martyn T. Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Avrum Spira
- Division of Computational Biomedicine, School of Medicine, Boston University, Boston, Massachusetts, USA
| | - Susan Sumner
- Discovery Sciences, RTI International, Research Triangle Park, North Carolina, USA
| | - Gary W. Miller
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
- Address correspondence to G.W. Miller, Department of Environmental Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd. NE, Mailstop: 1518-002-8BB, Atlanta, GA 30322 USA. Telephone: (404) 712-8582. E-mail:
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Livanos AE, Greiner TU, Vangay P, Pathmasiri W, Stewart D, McRitchie S, Li H, Chung J, Sohn J, Kim S, Gao Z, Barber C, Kim J, Ng S, Rogers AB, Sumner S, Zhang XS, Cadwell K, Knights D, Alekseyenko A, Bäckhed F, Blaser MJ. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nat Microbiol 2016; 1:16140. [PMID: 27782139 PMCID: PMC5808443 DOI: 10.1038/nmicrobiol.2016.140] [Citation(s) in RCA: 234] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 07/12/2016] [Indexed: 12/15/2022]
Abstract
The early life microbiome plays important roles in host immunological and metabolic development. Because the incidence of type 1 diabetes (T1D) has been increasing substantially in recent decades, we hypothesized that early-life antibiotic use alters gut microbiota, which predisposes to disease. Using non-obese diabetic mice that are genetically susceptible to T1D, we examined the effects of exposure to either continuous low-dose antibiotics or pulsed therapeutic antibiotics (PAT) early in life, mimicking childhood exposures. We found that in mice receiving PAT, T1D incidence was significantly higher, and microbial community composition and structure differed compared with controls. In pre-diabetic male PAT mice, the intestinal lamina propria had lower Th17 and Treg proportions and intestinal SAA expression than in controls, suggesting key roles in transducing the altered microbiota signals. PAT affected microbial lipid metabolism and host cholesterol biosynthetic gene expression. These findings show that early-life antibiotic treatments alter the gut microbiota and its metabolic capacities, intestinal gene expression and T-cell populations, accelerating T1D onset in non-obese diabetic mice.
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Affiliation(s)
- Alexandra E. Livanos
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Thomas U. Greiner
- Department of Molecular and Clinical Medicine, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Pajau Vangay
- Biomedical Informatics and Computational Biology Program, University of Minnesota, Minneapolis, Minneapolis 55455, USA
| | - Wimal Pathmasiri
- Systems and Translational Sciences, RTI International, Research Triangle Park, North Carolina 27709, USA
| | - Delisha Stewart
- Systems and Translational Sciences, RTI International, Research Triangle Park, North Carolina 27709, USA
| | - Susan McRitchie
- Systems and Translational Sciences, RTI International, Research Triangle Park, North Carolina 27709, USA
| | - Huilin Li
- Departments of Population Health, New York University Langone Medical Center, New York, New York 10016, USA
| | - Jennifer Chung
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Jiho Sohn
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Sara Kim
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Zhan Gao
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Cecily Barber
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Joanne Kim
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Sandy Ng
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Arlin B. Rogers
- Department of Biomedical Sciences, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, USA
| | - Susan Sumner
- Systems and Translational Sciences, RTI International, Research Triangle Park, North Carolina 27709, USA
| | - Xue-Song Zhang
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Ken Cadwell
- Department of Microbiology, New York University Langone Medical Center, New York, New York 10016, USA
- Skirball Institute, New York University Langone Medical Center, New York, New York 10016, USA
| | - Dan Knights
- Computer Science and Engineering, University of Minnesota, Minneapolis, Minneapolis 55455, USA
- Biotechnology Institute, University of Minnesota, Saint Paul, Minneapolis 55108, USA
| | - Alexander Alekseyenko
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
- CHIBI, New York University Langone Medical Center, New York, New York 10016, USA
| | - Fredrik Bäckhed
- Department of Molecular and Clinical Medicine, University of Gothenburg, 40530 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, Faculty of Health Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Martin J. Blaser
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
- New York Harbor Veterans Affairs Medical Center, New York, New York 10010, USA
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Sandlers Y, Mercier K, Pathmasiri W, Carlson J, McRitchie S, Sumner S, Vernon HJ. Metabolomics Reveals New Mechanisms for Pathogenesis in Barth Syndrome and Introduces Novel Roles for Cardiolipin in Cellular Function. PLoS One 2016; 11:e0151802. [PMID: 27015085 PMCID: PMC4807847 DOI: 10.1371/journal.pone.0151802] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/04/2016] [Indexed: 02/07/2023] Open
Abstract
Barth Syndrome is the only known Mendelian disorder of cardiolipin remodeling, with characteristic clinical features of cardiomyopathy, skeletal myopathy, and neutropenia. While the primary biochemical defects of reduced mature cardiolipin and increased monolysocardiolipin are well-described, much of the downstream biochemical dysregulation has not been uncovered, and biomarkers are limited. In order to further expand upon the knowledge of the biochemical abnormalities in Barth Syndrome, we analyzed metabolite profiles in plasma from a cohort of individuals with Barth Syndrome compared to age-matched controls via 1H nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectrometry. A clear distinction between metabolite profiles of individuals with Barth Syndrome and controls was observed, and was defined by an array of metabolite classes including amino acids and lipids. Pathway analysis of these discriminating metabolites revealed involvement of mitochondrial and extra-mitochondrial biochemical pathways including: insulin regulation of fatty acid metabolism, lipid metabolism, biogenic amine metabolism, amino acid metabolism, endothelial nitric oxide synthase signaling, and tRNA biosynthesis. Taken together, this data indicates broad metabolic dysregulation in Barth Syndrome with wide cellular effects.
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Affiliation(s)
- Yana Sandlers
- Department of Chemistry, Cleveland State University, Cleveland, OH, United States of America
| | - Kelly Mercier
- Research Triangle International, Durham, NC, United States of America
| | - Wimal Pathmasiri
- Research Triangle International, Durham, NC, United States of America
| | - Jim Carlson
- Research Triangle International, Durham, NC, United States of America
| | - Susan McRitchie
- Research Triangle International, Durham, NC, United States of America
| | - Susan Sumner
- Research Triangle International, Durham, NC, United States of America
| | - Hilary J. Vernon
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, United States of America
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, United States of America
- * E-mail:
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Sud M, Fahy E, Cotter D, Azam K, Vadivelu I, Burant C, Edison A, Fiehn O, Higashi R, Nair KS, Sumner S, Subramaniam S. Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Res 2015; 44:D463-70. [PMID: 26467476 PMCID: PMC4702780 DOI: 10.1093/nar/gkv1042] [Citation(s) in RCA: 445] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 09/30/2015] [Indexed: 11/18/2022] Open
Abstract
The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund's Metabolomics Program, provides data from the Common Fund's Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world.
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Affiliation(s)
- Manish Sud
- San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Eoin Fahy
- San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Dawn Cotter
- San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Kenan Azam
- San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Ilango Vadivelu
- San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Charles Burant
- University of Michigan, 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105, USA
| | - Arthur Edison
- University of Florida, 2250 Shealy Drive, Gainesville, FL 32608, USA
| | - Oliver Fiehn
- University of California, Davis, 451 Health Sciences Dr, Davis, CA 95616, USA
| | - Richard Higashi
- University of Kentucky, 789 S. Limestone, 521 Biopharm Bldg, Lexington, KY 40536, USA
| | | | - Susan Sumner
- RTI International, 3040 Cornwallis Rd, Research Triangle Park, NC 27709, USA
| | - Shankar Subramaniam
- San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA Departments of Bioengineering, Computer Science and Engineering, Cellular and Molecular Medicine, and Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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Stewart DA, Winnike J, McRitchie S, Pathmasiri W, Sumner S. Abstract 1836: Triple negative breast cancer: Metabolomics and flux analysis to identify targets for drug development. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
To date, no targeted therapies are clinically available to treat triple negative breast cancer (TNBC). This highly aggressive form of breast cancer (BCa) derives its name from the absence of estrogen receptor (ER+), progesterone receptor (PR+), and HER2/neu receptor (HER2+). These receptors are expressed in other subtypes of BCa (i.e. Luminal, HER2-enriched) and have been successfully targeted with therapeutics such as Tamoxifen and Herceptin. New therapeutics are needed to improve the prognosis for patients with TNBC. Metabolomics and metabolic flux analysis (MFA) were conducted to reveal differences in TNBC cell lines compared with hormone receptor-positive cell lines (ER+ and +/-HER2+) prior to and following treatment with chemotherapy drugs. Two triple-negative (MDA-MB-231 and MDA-MB-468) and two hormone-responsive (BT474 and MCF-7) cell lines were compared before and after treatment with Taxol®/Paclitaxel. The metabolic profiles were assessed using 1H NMR broad spectrum metabolomics, MFA using [U-13C]-glucose and [U-13C]-glutamine enriched media, and cytokine profiling of the media. Broad spectrum metabolomics analysis demonstrated differences in the metabolic profiles between the TNBC and hormone-responsive cell lines in the absence of treatment, with a higher level of amino acids (e.g. alanine, glutamate, glutamine, glutathione), short chain fatty acids (isobutyrate, β-hydroxybutyrate), and nucleotides and nucleotide sugars (ADP, ATP, UDP-glucose, UDP-glucuronate) in the TNBC cell lines. Further, MFA demonstrated that glucose utilization was greater in the TNBC cells (MDA-MB-468) compared to the hormone-responsive cells (MCF-7). In addition, 13C-labeled glycine and 13C-labeled glutathione were only observed in TNBC cell lines treated in the presence of [U-13C]-glucose. In response to Taxol treatment, more metabolites were altered in the hormone-responsive cell lines compared with the TNBC cells. Profiling of 80 inflammatory cytokines (RayBiotech arrays) also demonstrated different responses in secreted inflammatory signals following treatment. We observed significant upregulation in interleukins-4 and -16 in MDA-MB-468 cells, while there was a downregulation of osteoprotegerin in all four cell lines after treatment with Taxol. This approach holds promise for identifying biomarkers which may be leveraged for development of targeted treatments.
Citation Format: Delisha A. Stewart, Jason Winnike, Susan McRitchie, Wimal Pathmasiri, Susan Sumner. Triple negative breast cancer: Metabolomics and flux analysis to identify targets for drug development. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1836. doi:10.1158/1538-7445.AM2015-1836
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Affiliation(s)
| | - Jason Winnike
- 2David H. Murdock Research Institute, Kannapolis, NC
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Stewart PA, Li J, Fisher KJ, Dhungana S, Stewart D, Sumner S, Gardner E, Poirier J, Rudin CM, Welsh EA, Eschrich S, Chen A, Haura EB. Abstract 3752: Integrating proteomics and metabolomics characterizes active pathways and potential drug targets in small cell lung cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-3752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Small cell lung cancer (SCLC) accounts for 13-15% of all new lung cancer cases and represents the sixth most commonly diagnosed cancer in the US. However, it is an understudied cancer for which no molecularly targeted approaches have shown benefit. Using high-throughput techniques such as proteomics and metabolomics we can provide a more global, unbiased characterization to the inner workings of this disease. Integrating disparate data is a challenge in data analysis and bioinformatics, but this challenge is worth confronting due to the potential for combined proteomics / metabolomics analyses to better interrogate and capture the global landscape of active pathways and networks in SCLC than either technology alone. We accomplished this by comparing SCLC cell lines with non-small cell lung cancer (NSCLC) cell lines, differentiating characteristics of these two lung cancer cell types. We first used activity-based protein profiling (ABPP) combined with LC-MS/MS to profile the ATP-binding proteome of SCLC cell lines (n = 18) and NSCLC cell lines (n = 18). ABPP uses chemical probes that are directed against the active sites of enzymes to interrogate the functional state of ATP-binding enzymes, particularly kinases, in biological samples. These experiments identified 6937 peptides (2319 proteins), of which 3891 peptides (1543 proteins) were differentially expressed. Several pathways related to metabolism, such as purine biosynthesis and glycolysis / gluconeogenesis, were identified as over-represented in this list. These results led us to perform broad spectrum UPLC-TOF-MS metabolomics on ten SCLC and ten NSCLC cell lines. Multivariate analysis demonstrated distinct metabolite profiles for SCLC and NSCLC. Over 100 metabolites with variable importance to projection greater than 1 contributed to the differentiation of the two groups. These included metabolites related to purine metabolism such as inosinic acid and adenosine monophosphate and suggest a connection between our proteomics and metabolomics results. Statistical modeling approaches such as linear modeling, nonparametric nonlinear correlation, and Bayesian network analysis were used to integrate proteomics and metabolomics data to jointly characterize the key pathways and constituent components in SCLC. Multiple regression revealed a statistically significant interaction between endoglin (ENG) and phosphatidylethanolamine (PE), both of which are involved in angiogenesis. These findings and other statistical modeling results have the potential to facilitate the identification of new subtypes in SCLC and allow for the identification of novel targeted therapies. Future work will use these results to help characterize SCLC patient-derived xenograft models and surgically resected patient tissue samples. Funded, in part, by NIH Common Fund, 1U24DK097193.
Citation Format: Paul A. Stewart, Jiannong Li, Kate J. Fisher, Suraj Dhungana, Delisha Stewart, Susan Sumner, Eric Gardner, John Poirier, Charles M. Rudin, Eric A. Welsh, Steven Eschrich, Ann Chen, Eric B. Haura. Integrating proteomics and metabolomics characterizes active pathways and potential drug targets in small cell lung cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3752. doi:10.1158/1538-7445.AM2015-3752
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Affiliation(s)
| | | | | | | | | | | | - Eric Gardner
- 3Memorial Sloan-Kettering Cancer Center, New York, NY
| | - John Poirier
- 3Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | | | | | - Ann Chen
- 1Moffitt Cancer Center, Tampa, FL
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Pratt KJ, McRitchie S, Collier DN, Lutes LD, Sumner S. Parent & Family Influences on Adopting Healthy Weight-Related Behaviors: Views and Perceptions of Obese African-American Female Adolescents. J Natl Med Assoc 2015; 107:74-9. [DOI: 10.1016/s0027-9684(15)30027-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Sumner LW, Styczynski M, McLean J, Fiehn O, Jander G, Liao J, Sumner S, Britz-McKibbin P, Welti R, Jones AD, Dorrestein PC, Bearden D, Kaddurah-Daouk R. Introducing the USA Plant, Algae and Microbial Metabolomics Research Coordination Network (PAMM-NET). Metabolomics 2015; 11:3-5. [PMID: 28018159 PMCID: PMC5178969 DOI: 10.1007/s11306-014-0755-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | | | | | | | - Georg Jander
- Boyce Thompson Institute for Plant Research, Ithaca
| | | | | | | | | | | | | | - Dan Bearden
- National Institute of Standards and Technology, Charleston
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Mazagova M, Wang L, Anfora AT, Wissmueller M, Lesley SA, Miyamoto Y, Eckmann L, Dhungana S, Pathmasiri W, Sumner S, Westwater C, Brenner DA, Schnabl B. Commensal microbiota is hepatoprotective and prevents liver fibrosis in mice. FASEB J 2014; 29:1043-55. [PMID: 25466902 DOI: 10.1096/fj.14-259515] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Translocation of bacteria and their products across the intestinal barrier is common in patients with liver disease, and there is evidence that experimental liver fibrosis depends on bacterial translocation. The purpose of our study was to investigate liver fibrosis in conventional and germ-free (GF) C57BL/6 mice. Chronic liver injury was induced by administration of thioacetamide (TAA) in the drinking water for 21 wk or by repeated intraperitoneal injections of carbon tetrachloride (CCl4). Increased liver fibrosis was observed in GF mice compared with conventional mice. Hepatocytes showed more toxin-induced oxidative stress and cell death. This was accompanied by increased activation of hepatic stellate cells, but hepatic mediators of inflammation were not significantly different. Similarly, a genetic model using Myd88/Trif-deficient mice, which lack downstream innate immunity signaling, had more severe fibrosis than wild-type mice. Isolated Myd88/Trif-deficient hepatocytes were more susceptible to toxin-induced cell death in culture. In conclusion, the commensal microbiota prevents fibrosis upon chronic liver injury in mice. This is the first study describing a beneficial role of the commensal microbiota in maintaining liver homeostasis and preventing liver fibrosis.
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Affiliation(s)
- Magdalena Mazagova
- *Department of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, California, USA; Genomics Institute of the Novartis Research Foundation, San Diego, California, USA; Systems and Translational Science, RTI International, Research Triangle Park, North Carolina, USA; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Lirui Wang
- *Department of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, California, USA; Genomics Institute of the Novartis Research Foundation, San Diego, California, USA; Systems and Translational Science, RTI International, Research Triangle Park, North Carolina, USA; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Andrew T Anfora
- *Department of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, California, USA; Genomics Institute of the Novartis Research Foundation, San Diego, California, USA; Systems and Translational Science, RTI International, Research Triangle Park, North Carolina, USA; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Max Wissmueller
- *Department of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, California, USA; Genomics Institute of the Novartis Research Foundation, San Diego, California, USA; Systems and Translational Science, RTI International, Research Triangle Park, North Carolina, USA; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Scott A Lesley
- *Department of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, California, USA; Genomics Institute of the Novartis Research Foundation, San Diego, California, USA; Systems and Translational Science, RTI International, Research Triangle Park, North Carolina, USA; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Yukiko Miyamoto
- *Department of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, California, USA; Genomics Institute of the Novartis Research Foundation, San Diego, California, USA; Systems and Translational Science, RTI International, Research Triangle Park, North Carolina, USA; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Lars Eckmann
- *Department of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, California, USA; Genomics Institute of the Novartis Research Foundation, San Diego, California, USA; Systems and Translational Science, RTI International, Research Triangle Park, North Carolina, USA; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Suraj Dhungana
- *Department of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, California, USA; Genomics Institute of the Novartis Research Foundation, San Diego, California, USA; Systems and Translational Science, RTI International, Research Triangle Park, North Carolina, USA; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Wimal Pathmasiri
- *Department of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, California, USA; Genomics Institute of the Novartis Research Foundation, San Diego, California, USA; Systems and Translational Science, RTI International, Research Triangle Park, North Carolina, USA; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Susan Sumner
- *Department of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, California, USA; Genomics Institute of the Novartis Research Foundation, San Diego, California, USA; Systems and Translational Science, RTI International, Research Triangle Park, North Carolina, USA; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Caroline Westwater
- *Department of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, California, USA; Genomics Institute of the Novartis Research Foundation, San Diego, California, USA; Systems and Translational Science, RTI International, Research Triangle Park, North Carolina, USA; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - David A Brenner
- *Department of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, California, USA; Genomics Institute of the Novartis Research Foundation, San Diego, California, USA; Systems and Translational Science, RTI International, Research Triangle Park, North Carolina, USA; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Bernd Schnabl
- *Department of Medicine, University of California, San Diego, La Jolla, California, USA; Department of Medicine, VA San Diego Healthcare System, San Diego, California, USA; Genomics Institute of the Novartis Research Foundation, San Diego, California, USA; Systems and Translational Science, RTI International, Research Triangle Park, North Carolina, USA; and Department of Oral Health Sciences, Medical University of South Carolina, Charleston, South Carolina, USA
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