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Li W, Ballard J, Zhao Y, Long Q. Knowledge-guided learning methods for integrative analysis of multi-omics data. Comput Struct Biotechnol J 2024; 23:1945-1950. [PMID: 38736693 PMCID: PMC11087912 DOI: 10.1016/j.csbj.2024.04.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/14/2024] Open
Abstract
Integrative analysis of multi-omics data has the potential to yield valuable and comprehensive insights into the molecular mechanisms underlying complex diseases such as cancer and Alzheimer's disease. However, a number of analytical challenges complicate multi-omics data integration. For instance, -omics data are usually high-dimensional, and sample sizes in multi-omics studies tend to be modest. Furthermore, when genes in an important pathway have relatively weak signal, it can be difficult to detect them individually. There is a growing body of literature on knowledge-guided learning methods that can address these challenges by incorporating biological knowledge such as functional genomics and functional proteomics into multi-omics data analysis. These methods have been shown to outperform their counterparts that do not utilize biological knowledge in tasks including prediction, feature selection, clustering, and dimension reduction. In this review, we survey recently developed methods and applications of knowledge-guided multi-omics data integration methods and discuss future research directions.
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Affiliation(s)
- Wenrui Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Drive, Philadelphia, 19104, PA, USA
| | - Jenna Ballard
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, 19104, PA, USA
| | - Yize Zhao
- Department of Biostatistics, School of Public Health, Yale University, 60 College Street, New Haven, 06510, CT, USA
| | - Qi Long
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Drive, Philadelphia, 19104, PA, USA
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2
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Marín-Sáez J, Hernández-Mesa M, Cano-Sancho G, García-Campaña AM. Analytical challenges and opportunities in the study of endocrine disrupting chemicals within an exposomics framework. Talanta 2024; 279:126616. [PMID: 39067205 DOI: 10.1016/j.talanta.2024.126616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/11/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Exposomics aims to measure human exposures throughout the lifespan and the changes they produce in the human body. Exposome-scale studies have significant potential to understand the interplay of environmental factors with complex multifactorial diseases widespread in our society and whose origin remain unclear. In this framework, the study of the chemical exposome aims to cover all chemical exposures and their effects in human health but, today, this goal still seems unfeasible or at least very challenging, which makes the exposome for now only a concept. Furthermore, the study of the chemical exposome faces several methodological challenges such as moving from specific targeted methodologies towards high-throughput multitargeted and non-targeted approaches, guaranteeing the availability and quality of biological samples to obtain quality analytical data, standardization of applied analytical methodologies, as well as the statistical assignment of increasingly complex datasets, or the identification of (un)known analytes. This review discusses the various steps involved in applying the exposome concept from an analytical perspective. It provides an overview of the wide variety of existing analytical methods and instruments, highlighting their complementarity to develop combined analytical strategies to advance towards the chemical exposome characterization. In addition, this review focuses on endocrine disrupting chemicals (EDCs) to show how studying even a minor part of the chemical exposome represents a great challenge. Analytical strategies applied in an exposomics context have shown great potential to elucidate the role of EDCs in health outcomes. However, translating innovative methods into etiological research and chemical risk assessment will require a multidisciplinary effort. Unlike other review articles focused on exposomics, this review offers a holistic view from the perspective of analytical chemistry and discuss the entire analytical workflow to finally obtain valuable results.
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Affiliation(s)
- Jesús Marín-Sáez
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Campus Fuentenueva s/n, E-18071, Granada, Spain; Research Group "Analytical Chemistry of Contaminants", Department of Chemistry and Physics, Research Centre for Mediterranean Intensive Agrosystems and Agri-Food Biotechnology (CIAIMBITAL), University of Almeria, Agrifood Campus of International Excellence, ceiA3, E-04120, Almeria, Spain.
| | - Maykel Hernández-Mesa
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Campus Fuentenueva s/n, E-18071, Granada, Spain.
| | | | - Ana M García-Campaña
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Campus Fuentenueva s/n, E-18071, Granada, Spain
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3
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Kuligowski J, Moreno-Torres M, Quintás G. Improving insights from metabolomic functional analysis combining multivariate tools. Anal Chim Acta 2024; 1323:343062. [PMID: 39182979 DOI: 10.1016/j.aca.2024.343062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/31/2024] [Accepted: 08/05/2024] [Indexed: 08/27/2024]
Abstract
BACKGROUND Metabolomics is a scientific field that relies on the comprehensive analysis of metabolites to provide direct insights into functional processes in biological systems. Metabolomic data provides valuable insights into the functional processes of biological systems, often analyzed through univariate and multivariate approaches, and well as with functional or pathway analysis using different methods such as mummichog. Yet, the integration of results from these sources to aid the interpretation of their biological significance remains challenging. This represents a significant bottleneck limiting the applicability of multivariate analysis of metabolomic data, despite its potential for providing deep biological insights. RESULTS In this work we propose two straightforward methods to facilitate the interpretation of results from multivariate analysis and functional metabolic analysis using: i) p-values from multivariate tests as input in functional analysis, and ii) cluster-CV to assess the impact on the predictive performance of a multivariate model at the pathway level. Four simulated data sets were analyzed including a data set with no class separation, and three data sets with a statistically significant discrimination between classes by including either univariate, multivariate, or both types of discriminant effects. The data sets were analyzed using univariate tests and OPLS-DA. Furthermore, p-values for each feature estimated by univariate analysis and OPLS-DA were used as input for functional analysis in mummichog. Cluster-CV was then used to assess the effect of detected metabolic pathways on the class separation observed by OPLS-DA. SIGNIFICANCE Through simulated data, we show how these approaches enhance the interpretation of biological effects driving multivariate models and support the identification of altered pathways not detected by univariate analysis. By providing a deeper understanding of metabolic phenotypes, these methods might improve the biological insights derived from statistical and functional analysis of future or previous studies.
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Affiliation(s)
- Julia Kuligowski
- Neonatal Research Group, Health Research Institute La Fe (IISLAFE), Avda Fernando Abril Martorell 106, 46026, Valencia, Spain; Primary Care Interventions to Prevent Maternal and Child Chronic Diseases of Perinatal and Developmental Origin Network (RICORS-SAMID), Instituto de Salud Carlos III, Madrid, Spain; Servicio de Análisis de Vesículas Extracelulares (SAVE), Health Research Institute La Fe (IISLAFE), Avda Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Marta Moreno-Torres
- Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Valencia, Spain; Unit for Experimental Hepatology, Health Research Institute La Fe (IISLAFE), Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Guillermo Quintás
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Health and Biomedicine Department, Leitat Technological Center, Barcelona, Spain.
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Suthar H, Tanghal RB, Chatzi L, Goodrich JA, Morello-Frosch R, Aung M. Metabolic Perturbations Associated with both PFAS Exposure and Perinatal/Antenatal Depression in Pregnant Individuals: A Meet-in-the-Middle Scoping Review. Curr Environ Health Rep 2024; 11:404-415. [PMID: 38898328 PMCID: PMC11324697 DOI: 10.1007/s40572-024-00451-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2024] [Indexed: 06/21/2024]
Abstract
PURPOSE OF REVIEW Depression during the perinatal or antenatal period affects at least 1 in 10 women worldwide, with long term health implications for the mother and child. Concurrently, there is increasing evidence associating maternal exposure to per- and poly-fluoroalkyl substances (PFAS) to adverse pregnancy outcomes. We reviewed the body of evidence examining both the associations between PFAS exposure and perturbations in the maternal metabolome, and the associations between the maternal metabolome and perinatal/antenatal depression. Through this, we sought to explore existing evidence of the perinatal metabolome as a potential mediation pathway linking PFAS exposure and perinatal/antenatal depression. RECENT FINDINGS There are few studies examining the metabolomics of PFAS exposure-specifically in pregnant women-and the metabolomics of perinatal/antenatal depression, let alone studies examining both simultaneously. Of the studies reviewed (N = 11), the majority were cross sectional, based outside of the US, and conducted on largely homogenous populations. Our review identified 23 metabolic pathways in the perinatal metabolome common to both PFAS exposure and perinatal/antenatal depression. Future studies may consider findings from our review to conduct literature-derived hypothesis testing focusing on fatty acid metabolism, alanine metabolism, glutamate metabolism, and tyrosine metabolism when exploring the biochemical mechanisms conferring the risk of perinatal/antenatal depression due to PFAS exposure. We recommend that researchers also utilize heterogenous populations, longitudinal study designs, and mediation approaches to elucidate key pathways linking PFAS exposures to perinatal/antenatal depression.
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Affiliation(s)
- Himal Suthar
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, SSB 225R, 1845 N Soto St., Los Angeles, CA, 90032, USA
| | - Roselyn B Tanghal
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, SSB 225R, 1845 N Soto St., Los Angeles, CA, 90032, USA
| | - Lida Chatzi
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, SSB 225R, 1845 N Soto St., Los Angeles, CA, 90032, USA
| | - Jesse A Goodrich
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, SSB 225R, 1845 N Soto St., Los Angeles, CA, 90032, USA
| | - Rachel Morello-Frosch
- Department of Environmental Science, Policy, and Management, University of California, 130 Mulford Hall #3114, Berkeley, CA, 94720, USA
| | - Max Aung
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, SSB 225R, 1845 N Soto St., Los Angeles, CA, 90032, USA.
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Anbazhagan AN, Ge Y, Priyamvada S, Kumar A, Jayawardena D, Palani ARV, Husain N, Kulkarni N, Kapoor S, Kaur P, Majumder A, Lin YD, Maletta L, Gill RK, Alrefai WA, Saksena S, Zadeh K, Hong S, Mohamadzadeh M, Dudeja PK. A Direct Link Implicating Loss of SLC26A6 to Gut Microbial Dysbiosis, Compromised Barrier Integrity, and Inflammation. Gastroenterology 2024; 167:704-717.e3. [PMID: 38735402 DOI: 10.1053/j.gastro.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/27/2024] [Accepted: 05/02/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND & AIMS Putative anion transporter-1 (PAT1, SLC26A6) plays a key role in intestinal oxalate and bicarbonate secretion. PAT1 knockout (PKO) mice exhibit hyperoxaluria and nephrolithiasis. Notably, diseases such as inflammatory bowel disease are also associated with higher risk of hyperoxaluria and nephrolithiasis. However, the potential role of PAT1 deficiency in gut-barrier integrity and susceptibility to colitis is currently elusive. METHODS Age-matched PKO and wild-type littermates were administered 3.5% dextran sulfate sodium in drinking water for 6 days. Ileum and colon of control and treated mice were harvested. Messenger RNA and protein expression of tight junction proteins were determined by reverse transcription polymerase chain reaction and western blotting. Severity of inflammation was assessed by measuring diarrheal phenotype, cytokine expression, and hematoxylin and eosin staining. Gut microbiome and associated metabolome were analyzed by 16S ribosomal RNA sequencing and mass spectrometry, respectively. RESULTS PKO mice exhibited significantly higher loss of body weight, gut permeability, colonic inflammation, and diarrhea in response to dextran sulfate sodium treatment. In addition, PKO mice showed microbial dysbiosis and significantly reduced levels of butyrate and butyrate-producing microbes compared with controls. Co-housing wild-type and PKO mice for 4 weeks resulted in PKO-like signatures on the expression of tight junction proteins in the colons of wild-type mice. CONCLUSIONS Our data demonstrate that loss of PAT1 disrupts gut microbiome and related metabolites, decreases gut-barrier integrity, and increases host susceptibility to intestinal inflammation. These findings, thus, highlight a novel role of the oxalate transporter PAT1 in promoting gut-barrier integrity, and its deficiency appears to contribute to the pathogenesis of inflammatory bowel diseases.
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Affiliation(s)
- Arivarasu N Anbazhagan
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Yong Ge
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health, San Antonio, Texas
| | - Shubha Priyamvada
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Anoop Kumar
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Dulari Jayawardena
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Arvind Raj Vishnu Palani
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Nazim Husain
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Neelkanth Kulkarni
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Shaunik Kapoor
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Prabhdeep Kaur
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Apurba Majumder
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Yang-Ding Lin
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health, San Antonio, Texas
| | - Leeany Maletta
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health, San Antonio, Texas
| | - Ravinder K Gill
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Waddah A Alrefai
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Seema Saksena
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Kimia Zadeh
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Sungmo Hong
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health, San Antonio, Texas
| | - Mansour Mohamadzadeh
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health, San Antonio, Texas; South Texas Veterans Health Care System, San Antonio, Texas
| | - Pradeep K Dudeja
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois.
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Du NH, Sinturel F, Nowak N, Gosselin P, Saini C, Guessous I, Jornayvaz FR, Philippe J, Rey G, Dermitzakis ET, Zenobi R, Dibner C, Brown SA. Multi-omics correlates of insulin resistance and circadian parameters mapped directly from human serum. Eur J Neurosci 2024. [PMID: 39205434 DOI: 10.1111/ejn.16486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/30/2024] [Accepted: 07/15/2024] [Indexed: 09/04/2024]
Abstract
While it is generally known that metabolic disorders and circadian dysfunction are intertwined, how the two systems affect each other is not well understood, nor are the genetic factors that might exacerbate this pathological interaction. Blood chemistry is profoundly changed in metabolic disorders, and we have previously shown that serum factors change cellular clock properties. To investigate if circulating factors altered in metabolic disorders have circadian modifying effects, and whether these effects are of genetic origin, we measured circadian rhythms in U2OS cell in the presence of serum collected from diabetic, obese or control subjects. We observed that circadian period lengthening in U2OS cells was associated with serum chemistry that is characteristic of insulin resistance. Characterizing the genetic variants that altered circadian period length by genome-wide association analysis, we found that one of the top variants mapped to the E3 ubiquitin ligase MARCH1 involved in insulin sensitivity. Confirming our data, the serum circadian modifying variants were also enriched in type 2 diabetes and chronotype variants identified in the UK Biobank cohort. Finally, to identify serum factors that might be involved in period lengthening, we performed detailed metabolomics and found that the circadian modifying variants are particularly associated with branched chain amino acids, whose levels are known to correlate with diabetes and insulin resistance. Overall, our multi-omics data showed comprehensively that systemic factors serve as a path through which metabolic disorders influence circadian system, and these can be examined in human populations directly by simple cellular assays in common cultured cells.
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Affiliation(s)
- Ngoc-Hien Du
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Flore Sinturel
- Department of Surgery, Division of Thoracic and Endocrine Surgery, University Hospitals of Geneva, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Nora Nowak
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Pauline Gosselin
- Department of Surgery, Division of Thoracic and Endocrine Surgery, University Hospitals of Geneva, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department and Division of Primary Care Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Camille Saini
- Department of Surgery, Division of Thoracic and Endocrine Surgery, University Hospitals of Geneva, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department and Division of Primary Care Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Idris Guessous
- Department and Division of Primary Care Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - François R Jornayvaz
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Medicine, Division of Endocrinology, Diabetes, Nutrition, and Therapeutic Education of Patient, University Hospitals of Geneva, Geneva, Switzerland
| | - Jacques Philippe
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Medicine, Division of Endocrinology, Diabetes, Nutrition, and Therapeutic Education of Patient, University Hospitals of Geneva, Geneva, Switzerland
| | - Guillaume Rey
- Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Emmanouil T Dermitzakis
- Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Charna Dibner
- Department of Surgery, Division of Thoracic and Endocrine Surgery, University Hospitals of Geneva, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
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7
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Ropri AS, Lam TG, Kalia V, Buchanan HM, Bartosch AMW, Youth EHH, Xiao H, Ross SK, Jain A, Chakrabarty JK, Kang MS, Boyett D, Spinazzi EF, Iodice G, McGovern RA, Honig LS, Brown LM, Miller GW, McKhann GM, Teich AF. Alzheimer's disease CSF biomarkers correlate with early pathology and alterations in neuronal and glial gene expression. Alzheimers Dement 2024. [PMID: 39192661 DOI: 10.1002/alz.14194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 08/29/2024]
Abstract
INTRODUCTION Normal pressure hydrocephalus (NPH) patients undergoing cortical shunting frequently show early Alzheimer's disease (AD) pathology on cortical biopsy, which is predictive of progression to clinical AD. The objective of this study was to use samples from this cohort to identify cerebrospinal fluid (CSF) biomarkers for AD-related central nervous system (CNS) pathophysiologic changes using tissue and fluids with early pathology, free of post mortem artifact. METHODS We analyzed Simoa, proteomic, and metabolomic CSF data from 81 patients with previously documented pathologic and transcriptomic changes. RESULTS AD pathology on biopsy correlates with CSF β-amyloid-42/40, neurofilament light chain (NfL), and phospho-tau-181(p-tau181)/β-amyloid-42, while several gene expression modules correlate with NfL. Proteomic analysis highlights seven core proteins that correlate with pathology and gene expression changes on biopsy, and metabolomic analysis of CSF identifies disease-relevant groups that correlate with biopsy data. DISCUSSION As additional biomarkers are added to AD diagnostic panels, our work provides insight into the CNS pathophysiology these markers are tracking. HIGHLIGHTS AD CSF biomarkers correlate with CNS pathology and transcriptomic changes. Seven proteins correlate with CNS pathology and gene expression changes. Inflammatory and neuronal gene expression changes correlate with YKL-40 and NPTXR, respectively. CSF metabolomic analysis identifies pathways that correlate with biopsy data. Fatty acid metabolic pathways correlate with β-amyloid pathology.
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Affiliation(s)
- Ali S Ropri
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
| | - Tiffany G Lam
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
| | - Vrinda Kalia
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Heather M Buchanan
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
| | - Anne Marie W Bartosch
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
| | - Elliot H H Youth
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
| | - Harrison Xiao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
| | - Sophie K Ross
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
| | - Anu Jain
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Jayanta K Chakrabarty
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Min Suk Kang
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Deborah Boyett
- Department of Neurosurgery, Columbia University Irving Medical Center, New York, New York, USA
| | - Eleonora F Spinazzi
- Department of Neurosurgery, Columbia University Irving Medical Center, New York, New York, USA
| | - Gail Iodice
- Ankyra Therapeutics, Cambridge, Massachusetts, USA
| | - Robert A McGovern
- Department of Neurosurgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Lawrence S Honig
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Lewis M Brown
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Gary W Miller
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Guy M McKhann
- Department of Neurosurgery, Columbia University Irving Medical Center, New York, New York, USA
| | - Andrew F Teich
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
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8
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Kranidioti E, Ricaño-Ponce I, Antonakos N, Kyriazopoulou E, Kotsaki A, Tsangaris I, Markopoulou D, Rovina N, Antoniadou E, Koutsodimitropoulos I, Dalekos GN, Vlachogianni G, Akinosoglou K, Koulouras V, Komnos A, Kontopoulou T, Dimopoulos G, Netea MG, Kumar V, Giamarellos-Bourboulis EJ. Modulation of Metabolomic Profile in Sepsis According to the State of Immune Activation. Crit Care Med 2024:00003246-990000000-00367. [PMID: 39178163 DOI: 10.1097/ccm.0000000000006391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2024]
Abstract
OBJECTIVE To investigate the metabolomic profiles associated with different immune activation states in sepsis patients. DESIGN Subgroup analysis of the PROVIDE (a Personalized Randomized trial of Validation and restoration of Immune Dysfunction in severe infections and Sepsis) prospective clinical study. SETTING Results of the PROVIDE study showed that patients with sepsis may be classified into three states of immune activation: 1) macrophage-activation-like syndrome (MALS) characterized by hyperinflammation, sepsis-induced immunoparalysis, and 3) unclassified or intermediate patients without severe immune dysregulation. PATIENTS OR SUBJECTS Two hundred ten patients from 14 clinical sites in Greece meeting the Sepsis-3 definitions with lung infection, acute cholangitis, or primary bacteremia. INTERVENTIONS During our comparison, we did not perform any intervention. MEASUREMENTS AND MAIN RESULTS Untargeted metabolomics analysis was performed on plasma samples from 210 patients (a total of 1394 products). Differential abundance analysis identified 221 significantly different metabolites across the immune states. Metabolites were enriched in pathways related to ubiquinone biosynthesis, tyrosine metabolism, and tryptophan metabolism when comparing MALS to immunoparalysis and unclassified patients. When comparing MALS to unclassified, 312 significantly different metabolites were found, and pathway analysis indicated enrichment in multiple pathways. Comparing immunoparalysis to unclassified patients revealed only two differentially regulated metabolites. CONCLUSIONS Findings suggest distinct metabolic dysregulation patterns associated with different immune dysfunctions in sepsis: the strongest metabolic dysregulation is associated with MALS.
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Affiliation(s)
- Eleftheria Kranidioti
- First Department of Internal Medicine, Evangelismos General Hospital, Athens, Greece
| | - Isis Ricaño-Ponce
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nikolaos Antonakos
- Fourth Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Evdoxia Kyriazopoulou
- Fourth Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Antigone Kotsaki
- Fourth Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Iraklis Tsangaris
- Second Department of Critical Care Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Nikoleta Rovina
- First Department of Pulmonary Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Eleni Antoniadou
- Intensive Care Unit, "G. Gennimatas" Thessaloniki General Hospital, Thessaloniki, Greece
| | | | - George N Dalekos
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, Full Member of the European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | - Glykeria Vlachogianni
- Intensive Care Unit, "Aghios Dimitrios" Thessaloniki General Hospital, Thessaloniki, Greece
| | | | - Vasilios Koulouras
- Department of Critical Care Medicine, University of Ioannina, Ioannina, Greece
| | | | - Theano Kontopoulou
- First Department of Internal Medicine, Evangelismos General Hospital, Athens, Greece
| | - George Dimopoulos
- Third Department of Critical Care Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Vinod Kumar
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Evangelos J Giamarellos-Bourboulis
- Fourth Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Hellenic Institute for the Study of Sepsis, Athens, Greece
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9
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Elmsjö A, Ward LJ, Horioka K, Watanabe S, Kugelberg FC, Druid H, Green H. Biomarker patterns and mechanistic insights into hypothermia from a postmortem metabolomics investigation. Sci Rep 2024; 14:18972. [PMID: 39152132 PMCID: PMC11329508 DOI: 10.1038/s41598-024-68973-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 07/30/2024] [Indexed: 08/19/2024] Open
Abstract
Postmortem metabolomics holds promise for identifying crucial biological markers relevant to death investigations and clinical scenarios. We aimed to assess its applicability in diagnosing hypothermia, a condition lacking definitive biomarkers. Our retrospective analysis involved 1095 postmortem femoral blood samples, including 150 hypothermia cases, 278 matched controls, and 667 randomly selected test cases, analyzed using UHPLC-QTOF mass spectrometry. The model demonstrated robustness with an R2 and Q2 value of 0.73 and 0.68, achieving 94% classification accuracy, 92% sensitivity, and 96% specificity. Discriminative metabolite patterns, including acylcarnitines, stress hormones, and NAD metabolites, along with identified pathways, suggest that metabolomics analysis can be helpful to diagnose fatal hypothermia. Exposure to cold seems to trigger a stress response in the body, increasing cortisol production to maintain core temperature, possibly explaining the observed upregulation of cortisol levels and alterations in metabolic markers related to renal function. In addition, thermogenesis seems to increase metabolism in brown adipose tissue, contributing to changes in nicotinamide metabolism and elevated levels of ketone bodies and acylcarnitines, these findings highlight the effectiveness of UHPLC-QTOF mass spectrometry, multivariate analysis, and pathway identification of postmortem samples in identifying metabolite markers with forensic and clinical significance. The discovered patterns may offer valuable clinical insights and diagnostic markers, emphasizing the broader potential of postmortem metabolomics in understanding critical states or diseases.
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Affiliation(s)
- Albert Elmsjö
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.
| | - Liam J Ward
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Kie Horioka
- Forensic Medicine Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
- Department of Forensic Medicine, Research Unit of Internal Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Shimpei Watanabe
- Forensic Science Group, Photon Science Research Division, RIKEN SPring-8 Center, Sayo-Gun, Japan
| | - Fredrik C Kugelberg
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Henrik Druid
- Forensic Medicine Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Henrik Green
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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10
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Jeon J, He X, Shinde A, Meister M, Barnett L, Zhang Q, Black M, Shannahan J, Wright C. The role of puff volume in vaping emissions, inhalation risks, and metabolic perturbations: a pilot study. Sci Rep 2024; 14:18949. [PMID: 39147784 PMCID: PMC11327287 DOI: 10.1038/s41598-024-69985-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024] Open
Abstract
Secondhand vaping exposure is an emerging public health concern that remains understudied. In this study, saliva and exhaled emissions from ENDS users (secondhand) and non-ENDS users (baseline) were collected, firsthand emissions were generated using an automated ENDS aerosol generation system programmed to simulate puffing topography profiles collected from ENDS users. Particulate concentrations and sizes along with volatile organic compounds were characterized. We revealed puffing topography metrics as potential mediators of firsthand and secondhand particle and chemical exposures, as well as metabolic and respiratory health outcomes. Particle deposition modeling revealed that while secondhand emissions displayed smaller deposited mass, total and pulmonary particle deposition fractions were higher than firsthand deposition levels, possibly due to smaller secondhand emission particle diameters. Lastly, untargeted metabolomic profiling of salivary biomarkers of lung injury due to firsthand ENDS exposures revealed potential early indicators of respiratory distress that may also be relevant in bystanders exposed to secondhand vaping scenarios. By leveraging system toxicology, we identified 10 metabolites, including leukotriene D4, that could potentially serve as biomarkers for ENDS use, exposure estimation, and the prediction of vaping-related disease. This study highlights characterization of vaping behavior is an important exposure component in advancing our understanding of potential health effects in ENDS users and bystanders.
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Affiliation(s)
- Jennifer Jeon
- Chemical Insights Research Institute of UL Research Institutes, Marietta, GA, 30367, USA
| | - Xiaojia He
- Chemical Insights Research Institute of UL Research Institutes, Marietta, GA, 30367, USA
| | - Akshada Shinde
- School of Health Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Maureen Meister
- Chemical Insights Research Institute of UL Research Institutes, Marietta, GA, 30367, USA
| | - Lillie Barnett
- Chemical Insights Research Institute of UL Research Institutes, Marietta, GA, 30367, USA
| | - Qian Zhang
- Chemical Insights Research Institute of UL Research Institutes, Marietta, GA, 30367, USA
| | - Marilyn Black
- Chemical Insights Research Institute of UL Research Institutes, Marietta, GA, 30367, USA
| | - Jonathan Shannahan
- School of Health Sciences, Purdue University, West Lafayette, IN, 47907, USA.
| | - Christa Wright
- Chemical Insights Research Institute of UL Research Institutes, Marietta, GA, 30367, USA.
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11
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Shi D, Grey AC, Guo G. An isotopically-labelled temporal mass spectrometry imaging data analysis workflow to reveal glucose spatial metabolism patterns in bovine lens tissue. Sci Rep 2024; 14:18843. [PMID: 39138264 PMCID: PMC11322647 DOI: 10.1038/s41598-024-69507-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/06/2024] [Indexed: 08/15/2024] Open
Abstract
Application of stable isotopically labelled (SIL) molecules in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) over a series of time points allows the temporal and spatial dynamics of biochemical reactions to be tracked in a biological system. However, these large kinetic MSI datasets and the inherent variability of biological replicates presents significant challenges to the rapid analysis of the data. In addition, manual annotation of downstream SIL metabolites involves human input to carefully analyse the data based on prior knowledge and personal expertise. To overcome these challenges to the analysis of spatiotemporal MALDI-MSI data and improve the efficiency of SIL metabolite identification, a bioinformatics pipeline has been developed and demonstrated by analysing normal bovine lens glucose metabolism as a model system. The pipeline consists of spatial alignment to mitigate the impact of sample variability and ensure spatial comparability of the temporal data, dimensionality reduction to rapidly map regional metabolic distinctions within the tissue, and metabolite annotation coupled with pathway enrichment modules to summarise and display the metabolic pathways induced by the treatment. This pipeline will be valuable for the spatial metabolomics community to analyse kinetic MALDI-MSI datasets, enabling rapid characterisation of spatio-temporal metabolic patterns from tissues of interest.
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Affiliation(s)
- Dingchang Shi
- Department of Physiology, School of Medical Sciences, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
| | - Angus C Grey
- Department of Physiology, School of Medical Sciences, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand.
| | - George Guo
- Department of Physiology, School of Medical Sciences, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand
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12
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Huang H, Liu RQ, Chen Y, Liu Y, Dong GH, Hou J, Li S, Guo Y, Wang C, Chen G. Metabolic pathways altered by air pollutant exposure in association with coagulation function among the rural elderly. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135507. [PMID: 39182293 DOI: 10.1016/j.jhazmat.2024.135507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/11/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
Air pollution exposure has been linked with coagulation function. However, evidence is limited for the relationships between air pollution, coagulation function and metabolomics in humans. We recruited a panel of 130 rural elderly from the Chayashan township in China, all of whom were free of pre-existing cardiovascular diseases and had provided residential address information. We conducted clinical examinations and collected blood samples from these rural elderly for the detection of coagulation biomarkers (e.g, activated partial thromboplastin time, fibrinogen, thrombin time, and prothrombin time) and untargeted metabolites in both December 2021 and August 2022. We used mini ambient air quality monitor to measure the mean levels of five air pollutants (e.g., PM2.5, SO2, NO2, CO and O3) during 1 to 2 weeks before blood sample collection. The Mummichog pathway analysis was used to identified potential metabolic features and pathways. In this study, we identified 5 pathways associated with both air pollution and coagulation function, and further pinpointed eight metabolic features within these pathways. The majority of these features were lipids, including arachidonic acid and linoleic acid. Overall, the findings of this study offer insights into potential mechanisms, particularly lipid metabolism, that may underlie the association between air pollution and coagulation function.
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Affiliation(s)
- Haoyu Huang
- Joint International Research Laboratory of Environment and Health, Ministry of Education, Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Ru-Qing Liu
- Joint International Research Laboratory of Environment and Health, Ministry of Education, Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Yan Chen
- Joint International Research Laboratory of Environment and Health, Ministry of Education, Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuewei Liu
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangdong 510080, China
| | - Guang-Hui Dong
- Joint International Research Laboratory of Environment and Health, Ministry of Education, Guangdong Provincial Engineering Technology Research Center of Environmental Pollution and Health Risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Jian Hou
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shanshan Li
- Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Yuming Guo
- Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Chongjian Wang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Gongbo Chen
- Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia.
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13
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Rahman ML, Shu XO, Jones DP, Hu W, Ji BT, Blechter B, Wong JYY, Cai Q, Yang G, Gao YT, Zheng W, Rothman N, Walker D, Lan Q. A nested case-control study of untargeted plasma metabolomics and lung cancer among never-smoking women within the prospective Shanghai Women's Health Study. Int J Cancer 2024; 155:508-518. [PMID: 38651675 PMCID: PMC11284831 DOI: 10.1002/ijc.34929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/27/2024] [Accepted: 02/12/2024] [Indexed: 04/25/2024]
Abstract
The etiology of lung cancer in never-smokers remains elusive, despite 15% of lung cancer cases in men and 53% in women worldwide being unrelated to smoking. Here, we aimed to enhance our understanding of lung cancer pathogenesis among never-smokers using untargeted metabolomics. This nested case-control study included 395 never-smoking women who developed lung cancer and 395 matched never-smoking cancer-free women from the prospective Shanghai Women's Health Study with 15,353 metabolic features quantified in pre-diagnostic plasma using liquid chromatography high-resolution mass spectrometry. Recognizing that metabolites often correlate and seldom act independently in biological processes, we utilized a weighted correlation network analysis to agnostically construct 28 network modules of correlated metabolites. Using conditional logistic regression models, we assessed the associations for both metabolic network modules and individual metabolic features with lung cancer, accounting for multiple testing using a false discovery rate (FDR) < 0.20. We identified a network module of 121 features inversely associated with all lung cancer (p = .001, FDR = 0.028) and lung adenocarcinoma (p = .002, FDR = 0.056), where lyso-glycerophospholipids played a key role driving these associations. Another module of 440 features was inversely associated with lung adenocarcinoma (p = .014, FDR = 0.196). Individual metabolites within these network modules were enriched in biological pathways linked to oxidative stress, and energy metabolism. These pathways have been implicated in previous metabolomics studies involving populations exposed to known lung cancer risk factors such as traffic-related air pollution and polycyclic aromatic hydrocarbons. Our results suggest that untargeted plasma metabolomics could provide novel insights into the etiology and risk factors of lung cancer among never-smokers.
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Affiliation(s)
- Mohammad L Rahman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Vanderbilt University, Nashville, Tennessee, USA
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Wei Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Batel Blechter
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Jason Y Y Wong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Qiuyin Cai
- Division of Epidemiology, Vanderbilt University, Nashville, Tennessee, USA
| | - Gong Yang
- Division of Epidemiology, Vanderbilt University, Nashville, Tennessee, USA
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt University, Nashville, Tennessee, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Douglas Walker
- Division of Environmental Health, School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
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14
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Alijagic A, Sinisalu L, Duberg D, Kotlyar O, Scherbak N, Engwall M, Orešič M, Hyötyläinen T. Metabolic and phenotypic changes induced by PFAS exposure in two human hepatocyte cell models. ENVIRONMENT INTERNATIONAL 2024; 190:108820. [PMID: 38906088 DOI: 10.1016/j.envint.2024.108820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 06/23/2024]
Abstract
PFAS are ubiquitous industrial chemicals with known adverse health effects, particularly on the liver. The liver, being a vital metabolic organ, is susceptible to PFAS-induced metabolic dysregulation, leading to conditions such as hepatotoxicity and metabolic disturbances. In this study, we investigated the phenotypic and metabolic responses of PFAS exposure using two hepatocyte models, HepG2 (male cell line) and HepaRG (female cell line), aiming to define phenotypic alterations, and metabolic disturbances at the metabolite and pathway levels. The PFAS mixture composition was selected based on epidemiological data, covering a broad concentration spectrum observed in diverse human populations. Phenotypic profiling by Cell Painting assay disclosed predominant effects of PFAS exposure on mitochondrial structure and function in both cell models as well as effects on F-actin, Golgi apparatus, and plasma membrane-associated measures. We employed comprehensive metabolic characterization using liquid chromatography combined with high-resolution mass spectrometry (LC-HRMS). We observed dose-dependent changes in the metabolic profiles, particularly in lipid, steroid, amino acid and sugar and carbohydrate metabolism in both cells as well as in cell media, with HepaRG cell line showing a stronger metabolic response. In cells, most of the bile acids, acylcarnitines and free fatty acids showed downregulation, while medium-chain fatty acids and carnosine were upregulated, while the cell media showed different response especially in relation to the bile acids in HepaRG cell media. Importantly, we observed also nonmonotonic response for several phenotypic features and metabolites. On the pathway level, PFAS exposure was also associated with pathways indicating oxidative stress and inflammatory responses. Taken together, our findings on PFAS-induced phenotypic and metabolic disruptions in hepatocytes shed light on potential mechanisms contributing to the broader comprehension of PFAS-related health risks.
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Affiliation(s)
- Andi Alijagic
- Man-Technology-Environment (MTM) Research Centre, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden; Inflammatory Response and Infection Susceptibility Centre (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro SE-701 82, Sweden; School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden
| | - Lisanna Sinisalu
- Man-Technology-Environment (MTM) Research Centre, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden
| | - Daniel Duberg
- Man-Technology-Environment (MTM) Research Centre, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden
| | - Oleksandr Kotlyar
- Man-Technology-Environment (MTM) Research Centre, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden; Centre for Applied Autonomous Sensor Systems (AASS), Mobile Robotics and Olfaction Lab (MRO), Örebro University, SE-701 82 Örebro, Sweden
| | - Nikolai Scherbak
- Man-Technology-Environment (MTM) Research Centre, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden
| | - Magnus Engwall
- Man-Technology-Environment (MTM) Research Centre, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden
| | - Matej Orešič
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland; Department of Life Technologies, University of Turku, FI-20014 Turku, Finland
| | - Tuulia Hyötyläinen
- Man-Technology-Environment (MTM) Research Centre, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden.
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15
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Black B, da Silva LBR, Hu G, Qu X, Smith DFQ, Magaña AA, Horianopoulos LC, Caza M, Attarian R, Foster LJ, Casadevall A, Kronstad JW. Glutathione-mediated redox regulation in Cryptococcus neoformans impacts virulence. Nat Microbiol 2024; 9:2084-2098. [PMID: 38956248 DOI: 10.1038/s41564-024-01721-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 05/07/2024] [Indexed: 07/04/2024]
Abstract
The fungal pathogen Cryptococcus neoformans is well adapted to its host environment. It has several defence mechanisms to evade oxidative and nitrosative agents released by phagocytic host cells during infection. Among them, melanin production is linked to both fungal virulence and defence against harmful free radicals that facilitate host innate immunity. How C. neoformans manipulates its redox environment to facilitate melanin formation and virulence is unclear. Here we show that the antioxidant glutathione is inextricably linked to redox-active processes that facilitate melanin and titan cell production, as well as survival in macrophages and virulence in a murine model of cryptococcosis. Comparative metabolomics revealed that disruption of glutathione biosynthesis leads to accumulation of reducing and acidic compounds in the extracellular environment of mutant cells. Overall, these findings highlight the importance of redox homeostasis and metabolic compensation in pathogen adaptation to the host environment and suggest new avenues for antifungal drug development.
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Affiliation(s)
- Braydon Black
- The Michael Smith Laboratories, Departments of Microbiology and Immunology, and Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leandro Buffoni Roque da Silva
- The Michael Smith Laboratories, Departments of Microbiology and Immunology, and Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guanggan Hu
- The Michael Smith Laboratories, Departments of Microbiology and Immunology, and Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xianya Qu
- The Michael Smith Laboratories, Departments of Microbiology and Immunology, and Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel F Q Smith
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Armando Alcázar Magaña
- The Michael Smith Laboratories, Departments of Microbiology and Immunology, and Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Metabolomics Core Facility, Life Sciences Institute, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Linda C Horianopoulos
- The Michael Smith Laboratories, Departments of Microbiology and Immunology, and Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Mélissa Caza
- The Michael Smith Laboratories, Departments of Microbiology and Immunology, and Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Larissa Yarr Medical Microbiology Laboratory, Kelowna General Hospital, Kelowna, British Columbia, Canada
| | - Rodgoun Attarian
- The Michael Smith Laboratories, Departments of Microbiology and Immunology, and Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Pfizer Canada, Kirkland, Quebec, Canada
| | - Leonard J Foster
- The Michael Smith Laboratories, Departments of Microbiology and Immunology, and Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- Metabolomics Core Facility, Life Sciences Institute, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arturo Casadevall
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - James W Kronstad
- The Michael Smith Laboratories, Departments of Microbiology and Immunology, and Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
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16
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van Aubel G, Van Cutsem E, Emond A, Métillon G, Cordier É, Van Cutsem P. Dual Transcriptomic and Metabolomic Analysis of Elicited Flax Sheds Light on the Kinetics of Immune Defense Activation Against the Biotrophic Pathogen Oidium lini. PHYTOPATHOLOGY 2024; 114:1904-1916. [PMID: 38748518 DOI: 10.1094/phyto-02-24-0070-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2024]
Abstract
Flax (Linum usitatissimum) grown under controlled conditions displayed genotype-dependent resistance to powdery mildew (Oidium lini) following COS-OGA (comprising chitosan- and pectin-derived oligomers) elicitor application. The present study reveals a two-step immune response in plants preventively challenged with the elicitor: an initial, rapid response characterized by the transcription of defense genes whose protein products act in contact with or within the cell wall, where biotrophic pathogens initially thrive, followed by a prolonged activation of cell wall peroxidases and accumulation of secondary metabolites. Thus, dozens of genes encoding membrane receptors, pathogenesis-related proteins, and wall peroxidases were initially overexpressed. Repeated COS-OGA treatments had a transient effect on the transcriptome response while cumulatively remodeling the metabolome over time, with a minimum of two applications required for maximal metabolomic shifts. Secondary metabolites, in particular terpenoids and phenylpropanoids, emerged as major components of this secondary defense response alongside pathogenesis-related proteins and wall peroxidases. The sustained accumulation of secondary metabolites, even after cessation of elicitation, contrasted with the short-lived transcriptomic response. Wall peroxidase enzyme activity also exhibited cumulative effects, increasing strongly for weeks after a third elicitor treatment. This underscores the plasticity of the plant immune response in the face of a potential infection, and the need for repeated preventive applications to achieve the full protective potential of the elicitor.
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Affiliation(s)
- Géraldine van Aubel
- Biology Department, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
- FytoFend S.A., 5032 Isnes, Belgium
| | | | - Amélie Emond
- Biology Department, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | | | - Émilie Cordier
- Biology Department, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Pierre Van Cutsem
- Biology Department, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
- FytoFend S.A., 5032 Isnes, Belgium
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17
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Gundogan K, Nellis MM, Ozer NT, Ergul SS, Sahin GG, Temel S, Yuksel RC, Teeny S, Alvarez JA, Sungur M, Jones DP, Ziegler TR. High-resolution plasma metabolomics and thiamine status in critically Ill adult patients. Metabolomics 2024; 20:83. [PMID: 39066851 PMCID: PMC11283406 DOI: 10.1007/s11306-024-02144-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 06/24/2024] [Indexed: 07/30/2024]
Abstract
INTRODUCTION Thiamine (Vitamin B1) is an essential micronutrient and is classically considered a co-factor in energy metabolism. The association between thiamine status and whole-body metabolism in critical illness has not been studied. OBJECTIVES To determine association between whole blood thiamine pyrophosphate (TPP) concentrations and plasma metabolites and connected metabolic pathways using high resolution metabolomics (HRM) in critically ill patients. METHODS Cross-sectional study performed at Erciyes University Hospital, Kayseri, Turkey and Emory University, Atlanta, GA, USA. Participants were critically ill adults with an expected length of intensive care unit stay longer than 48 h and receiving chronic furosemide therapy. A total of 76 participants were included. Mean age was 69 years (range 33-92 years); 65% were female. Blood for TPP and metabolomics was obtained on the day of ICU admission. Whole blood TPP was measured by HPLC and plasma HRM was performed using liquid chromatography/mass spectrometry. Data was analyzed using regression analysis of TPP levels against all plasma metabolomic features in metabolome-wide association studies (MWAS). MWAS using the highest and lowest TPP concentration tertiles was performed as a secondary analysis. RESULTS Specific metabolic pathways associated with whole blood TPP levels in regression and tertile analysis included pentose phosphate, fructose and mannose, branched chain amino acid, arginine and proline, linoleate, and butanoate pathways. CONCLUSIONS Plasma HRM revealed that thiamine status, determined by whole blood TPP concentrations, was significantly associated with metabolites and metabolic pathways related to metabolism of energy, carbohydrates, amino acids, lipids, and the gut microbiome in adult critically ill patients.
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Affiliation(s)
- Kursat Gundogan
- Division of Intensive Care Medicine, Department of Internal Medicine, Erciyes University School of Medicine, Melikgazi, 38039, Kayseri, Turkey.
- Division of Clinical Nutrition, Erciyes University Health Sciences Institute, Kayseri, Turkey.
| | - Mary M Nellis
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Nurhayat T Ozer
- Division of Clinical Nutrition, Erciyes University Health Sciences Institute, Kayseri, Turkey
| | - Serap S Ergul
- Division of Clinical Nutrition, Erciyes University Health Sciences Institute, Kayseri, Turkey
| | - Gulsah G Sahin
- Division of Clinical Nutrition, Erciyes University Health Sciences Institute, Kayseri, Turkey
| | - Sahin Temel
- Division of Intensive Care Medicine, Department of Internal Medicine, Erciyes University School of Medicine, Melikgazi, 38039, Kayseri, Turkey
| | - Recep C Yuksel
- Division of Intensive Care Medicine, Department of Internal Medicine, Erciyes University School of Medicine, Melikgazi, 38039, Kayseri, Turkey
| | - Sami Teeny
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Jessica A Alvarez
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Medicine, Emory Center for Clinical and Molecular Nutrition, Emory University School of Medicine, Atlanta, GA, USA
| | - Murat Sungur
- Division of Intensive Care Medicine, Department of Internal Medicine, Erciyes University School of Medicine, Melikgazi, 38039, Kayseri, Turkey
- Division of Clinical Nutrition, Erciyes University Health Sciences Institute, Kayseri, Turkey
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, GA, 30322, USA
- Department of Medicine, Emory Center for Clinical and Molecular Nutrition, Emory University School of Medicine, Atlanta, GA, USA
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas R Ziegler
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Medicine, Emory Center for Clinical and Molecular Nutrition, Emory University School of Medicine, Atlanta, GA, USA
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18
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Albores-Méndez EM, Carrasco-Vargas H, Alaniz Monreal S, Mayen Quinto RD, López García ED, Gutierrez Salmean G, Medina-Quero K, Vargas-Hernández MA, Ferreira Batista CV, López-Hernández Y, Winkler R. An intense 60-day weight-loss course leads to an 18 kg body weight reduction and metabolic reprogramming of soldiers with obesity. PeerJ 2024; 12:e17757. [PMID: 39076775 PMCID: PMC11285361 DOI: 10.7717/peerj.17757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/25/2024] [Indexed: 07/31/2024] Open
Abstract
Soldiers of the Mexican Army with obesity were subjected to an intense 60-day weight-loss course consisting of a controlled diet, daily physical training, and psychological sessions. The nutritional treatment followed the European Society of Cardiology (ESC) recommendations, incorporating elements of the traditional milpa diet in the nutritional intervention. The total energy intake was reduced by 200 kcal every 20 days, starting with 1,800 kcal and ending with 1,400 kcal daily. On average, the participants reduced their body weight by 18 kg. We employed an innovative approach to monitor the progress of the twelve soldiers who completed the entire program. We compared the untargeted metabolomics profiles of their urine samples, taken before and after the course. The data obtained through liquid chromatography and high-resolution mass spectrometry (LC-MS) provided insightful results. Classification models perfectly separated the profiles pre and post-course, indicating a significant reprogramming of the participants' metabolism. The changes were observed in the C1-, vitamin, amino acid, and energy metabolism pathways, primarily affecting the liver, biliary system, and mitochondria. This study not only demonstrates the potential of rapid weight loss and metabolic pathway modification but also introduces a non-invasive method for monitoring the metabolic state of individuals through urine mass spectrometry data.
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Affiliation(s)
- Exsal M. Albores-Méndez
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | - Humberto Carrasco-Vargas
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | | | - Rodolfo David Mayen Quinto
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | - Ernesto Diderot López García
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | | | - Karen Medina-Quero
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | - Marco A. Vargas-Hernández
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | - Cesar Vicente Ferreira Batista
- Escuela Militar de Graduados de Sanidad, Universidad del Ejército y Fuerza Aérea Mexicanos, Secretaría de la Defensa Nacional, Mexico City, Mexico
| | - Yamilé López-Hernández
- Laboratorio de Proteómica y Metabolómica de la Unidad de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
| | - Robert Winkler
- Unidad de Genómica Avanzada, Cinvestav, Irapuato, Mexico
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19
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Francis EC, Kechris K, Johnson RK, Rawal S, Pathmasiri W, Rushing BR, Du X, Jansson T, Dabelea D, Sumner SJ, Perng W. Maternal Serum Metabolomics in Mid-Pregnancy Identifies Lipid Pathways as a Key Link to Offspring Obesity in Early Childhood. Int J Mol Sci 2024; 25:7620. [PMID: 39062861 PMCID: PMC11276882 DOI: 10.3390/ijms25147620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/29/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Maternal metabolism during pregnancy shapes offspring health via in utero programming. In the Healthy Start study, we identified five subgroups of pregnant women based on conventional metabolic biomarkers: Reference (n = 360); High HDL-C (n = 289); Dyslipidemic-High TG (n = 149); Dyslipidemic-High FFA (n = 180); Insulin Resistant (IR)-Hyperglycemic (n = 87). These subgroups not only captured metabolic heterogeneity among pregnant participants but were also associated with offspring obesity in early childhood, even among women without obesity or diabetes. Here, we utilize metabolomics data to enrich characterization of the metabolic subgroups and identify key compounds driving between-group differences. We analyzed fasting blood samples from 1065 pregnant women at 18 gestational weeks using untargeted metabolomics. We used weighted gene correlation network analysis (WGCNA) to derive a global network based on the Reference subgroup and characterized distinct metabolite modules representative of the different metabolomic profiles. We used the mummichog algorithm for pathway enrichment and identified key compounds that differed across the subgroups. Eight metabolite modules representing pathways such as the carnitine-acylcarnitine translocase system, fatty acid biosynthesis and activation, and glycerophospholipid metabolism were identified. A module that included 189 compounds related to DHA peroxidation, oxidative stress, and sex hormone biosynthesis was elevated in the Insulin Resistant-Hyperglycemic vs. the Reference subgroup. This module was positively correlated with total cholesterol (R:0.10; p-value < 0.0001) and free fatty acids (R:0.07; p-value < 0.05). Oxidative stress and inflammatory pathways may underlie insulin resistance during pregnancy, even below clinical diabetes thresholds. These findings highlight potential therapeutic targets and strategies for pregnancy risk stratification and reveal mechanisms underlying the developmental origins of metabolic disease risk.
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Affiliation(s)
- Ellen C. Francis
- Department of Biostatistics & Epidemiology, Rutgers School of Public Health, Piscataway, NJ 08854, USA
| | - Katerina Kechris
- Department of Biostatistics & Informatics, Colorado School of Public Health, Aurora, CO 80045, USA;
| | - Randi K. Johnson
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (D.D.); (W.P.)
| | - Shristi Rawal
- Department of Clinical and Preventive Nutrition Sciences, School of Health Professions, Rutgers University, Newark, NJ 07102, USA;
| | - Wimal Pathmasiri
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (W.P.); (B.R.R.)
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Blake R. Rushing
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (W.P.); (B.R.R.)
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xiuxia Du
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA;
| | - Thomas Jansson
- Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (D.D.); (W.P.)
- The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Susan J. Sumner
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (W.P.); (B.R.R.)
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wei Perng
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (D.D.); (W.P.)
- The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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20
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Pang Z, Lu Y, Zhou G, Hui F, Xu L, Viau C, Spigelman A, MacDonald P, Wishart D, Li S, Xia J. MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation. Nucleic Acids Res 2024; 52:W398-W406. [PMID: 38587201 PMCID: PMC11223798 DOI: 10.1093/nar/gkae253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024] Open
Abstract
We introduce MetaboAnalyst version 6.0 as a unified platform for processing, analyzing, and interpreting data from targeted as well as untargeted metabolomics studies using liquid chromatography - mass spectrometry (LC-MS). The two main objectives in developing version 6.0 are to support tandem MS (MS2) data processing and annotation, as well as to support the analysis of data from exposomics studies and related experiments. Key features of MetaboAnalyst 6.0 include: (i) a significantly enhanced Spectra Processing module with support for MS2 data and the asari algorithm; (ii) a MS2 Peak Annotation module based on comprehensive MS2 reference databases with fragment-level annotation; (iii) a new Statistical Analysis module dedicated for handling complex study design with multiple factors or phenotypic descriptors; (iv) a Causal Analysis module for estimating metabolite - phenotype causal relations based on two-sample Mendelian randomization, and (v) a Dose-Response Analysis module for benchmark dose calculations. In addition, we have also improved MetaboAnalyst's visualization functions, updated its compound database and metabolite sets, and significantly expanded its pathway analysis support to around 130 species. MetaboAnalyst 6.0 is freely available at https://www.metaboanalyst.ca.
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Affiliation(s)
- Zhiqiang Pang
- Institute of Parasitology, McGill University,Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Yao Lu
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Guangyan Zhou
- Institute of Parasitology, McGill University,Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Fiona Hui
- Institute of Parasitology, McGill University,Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Lei Xu
- Institute of Parasitology, McGill University,Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Charles Viau
- Institute of Parasitology, McGill University,Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Aliya F Spigelman
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Patrick E MacDonald
- Department of Pharmacology and Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
| | - David S Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, Canada
| | - Shuzhao Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- University of Connecticut School of Medicine, Farmington, CT, USA
| | - Jianguo Xia
- Institute of Parasitology, McGill University,Sainte-Anne-de-Bellevue, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
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21
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Hood RB, Nelson J, Minguez-Alarcon L, Ford JB, Hauser R, Jones D, Liang D, Gaskins AJ. The associations between pre-conception urinary phthalate concentrations, the serum metabolome, and live birth among women undergoing assisted reproduction. ENVIRONMENTAL RESEARCH 2024; 252:119149. [PMID: 38754604 PMCID: PMC11219194 DOI: 10.1016/j.envres.2024.119149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND Phthalates are ubiquitous endocrine disruptors. Past studies have shown an association between higher preconception urinary concentrations of phthalate metabolites and lower fertility in women; however, the biological mechanisms remain unclear. Our exploratory study aimed to understand the metabolites and pathways associated with maternal preconception phthalate exposure and examine if any may underline the association between phthalate exposure and live birth using untargeted metabolomics. METHODS Participants (n = 183) were part of the Environment and Reproductive Health (EARTH) study, a prospective cohort that followed women undergoing in vitro fertilization (IVF) at the Massachusetts General Hospital Fertility Center (2005-2016). On the same day, women provided a serum sample during controlled ovarian stimulation, which was analyzed for metabolomics using liquid chromatography coupled with high-resolution mass spectrometry and two chromatography columns, and a urine sample, which was analyzed for 11 phthalate metabolites using targeted approaches. We used multivariable generalized linear models to identified metabolic features associated with urinary phthalate metabolite concentrations and live birth, followed by enriched pathway analysis. We then used a meet-in-the-middle approach to identify overlapping pathways and features. RESULTS Metabolic pathway enrichment analysis revealed 43 pathways in the C18 negative and 32 pathways in the HILIC positive columns that were significantly associated (p < 0.05) with at least one of the 11 urinary phthalate metabolites or molar sum of di-2-ethylhexyl phthalate metabolites. Lipid, amino acid, and carbohydrate metabolism were the most common pathways associated with phthalate exposure. Five pathways, tryptophan metabolism, tyrosine metabolism, biopterin metabolism, carnitine shuttle, and vitamin B6 metabolism, were also identified as being associated with at least one phthalate metabolite and live birth following IVF. CONCLUSION Our study provides further insight into the metabolites and metabolomics pathways, including amino acid, lipid, and vitamin metabolism that may underlie the observed associations between phthalate exposures and lower fertility in women.
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Affiliation(s)
- Robert B Hood
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA.
| | - Jillian Nelson
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Lidia Minguez-Alarcon
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jennifer B Ford
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Russ Hauser
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Dean Jones
- Division of Pulmonary, Allergy, & Critical Care Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Donghai Liang
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Audrey J Gaskins
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
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22
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Ropri AS, Lam TG, Kalia V, Buchanan HM, Bartosch AMW, Youth EHH, Xiao H, Ross SK, Jain A, Chakrabarty JK, Kang MS, Boyett D, Spinazzi EF, Iodice G, McGovern RA, Honig LS, Brown LM, Miller GW, McKhann GM, Teich AF. Alzheimer's disease CSF biomarkers correlate with early pathology and alterations in neuronal and glial gene expression. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.11.24308706. [PMID: 38947015 PMCID: PMC11213077 DOI: 10.1101/2024.06.11.24308706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
INTRODUCTION Normal pressure hydrocephalus (NPH) patients undergoing cortical shunting frequently show early AD pathology on cortical biopsy, which is predictive of progression to clinical AD. The objective of this study was to use samples from this cohort to identify CSF biomarkers for AD-related CNS pathophysiologic changes using tissue and fluids with early pathology, free of post-mortem artifact. METHODS We analyzed Simoa, proteomic, and metabolomic CSF data from 81 patients with previously documented pathologic and transcriptomic changes. RESULTS AD pathology on biopsy correlates with CSF β-amyloid-40/42, neurofilament light chain (NfL), and phospho-tau-181(p-tau181)/β-amyloid-42, while several gene expression modules correlate with NfL. Proteomic analysis highlights 7 core proteins that correlate with pathology and gene expression changes on biopsy, and metabolomic analysis of CSF identifies disease-relevant groups that correlate with biopsy data.. DISCUSSION As additional biomarkers are added to AD diagnostic panels, our work provides insight into the CNS pathophysiology these markers are tracking.
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Affiliation(s)
- Ali S. Ropri
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tiffany G. Lam
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vrinda Kalia
- Dept. of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Heather M. Buchanan
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Anne Marie W. Bartosch
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Elliot H. H. Youth
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Harrison Xiao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sophie K. Ross
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Anu Jain
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Jayanta K. Chakrabarty
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Min Suk Kang
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Deborah Boyett
- Department of Neurosurgery, Columbia University, New York, NY 10032, USA
| | | | - Gail Iodice
- Ankyra Therapeutics, Cambridge, MA 02142, USA
| | - Robert A. McGovern
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lawrence S. Honig
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Lewis M. Brown
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Gary W. Miller
- Dept. of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Guy M. McKhann
- Department of Neurosurgery, Columbia University, New York, NY 10032, USA
| | - Andrew F. Teich
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY 10032, USA
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23
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Pathmasiri W, Rushing BR, McRitchie S, Choudhari M, Du X, Smirnov A, Pelleigrini M, Thompson MJ, Sakaguchi CA, Nieman DC, Sumner SJ. Untargeted metabolomics reveal signatures of a healthy lifestyle. Sci Rep 2024; 14:13630. [PMID: 38871777 DOI: 10.1038/s41598-024-64561-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024] Open
Abstract
This cross-sectional study investigated differences in the plasma metabolome in two groups of adults that were of similar age but varied markedly in body composition and dietary and physical activity patterns. Study participants included 52 adults in the lifestyle group (LIFE) (28 males, 24 females) and 52 in the control group (CON) (27 males, 25 females). The results using an extensive untargeted ultra high-performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS) metabolomics analysis with 10,535 metabolite peaks identified 486 important metabolites (variable influence on projections scores of VIP ≥ 1) and 16 significantly enriched metabolic pathways that differentiated LIFE and CON groups. A novel metabolite signature of positive lifestyle habits emerged from this analysis highlighted by lower plasma levels of numerous bile acids, an amino acid profile characterized by higher histidine and lower glutamic acid, glutamine, β-alanine, phenylalanine, tyrosine, and proline, an elevated vitamin D status, higher levels of beneficial fatty acids and gut microbiome catabolism metabolites from plant substrates, and reduced levels of N-glycan degradation metabolites and environmental contaminants. This study established that the plasma metabolome is strongly associated with body composition and lifestyle habits. The robust lifestyle metabolite signature identified in this study is consistent with an improved life expectancy and a reduced risk for chronic disease.
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Affiliation(s)
- Wimal Pathmasiri
- 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
| | - 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
| | - Susan McRitchie
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, 28081, USA
| | - Mansi Choudhari
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, 28081, USA
| | - Xiuxia Du
- College of Computing and Informatics, University of North Carolina at Charlotte, Kannapolis, NC, 28081, USA
| | - Alexsandr Smirnov
- College of Computing and Informatics, University of North Carolina at Charlotte, Kannapolis, NC, 28081, 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
| | - Camila A Sakaguchi
- Human Performance Laboratory, Department of Biology, Appalachian State University, North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - David C Nieman
- Human Performance Laboratory, Department of Biology, Appalachian State University, North Carolina Research Campus, Kannapolis, NC, 28081, USA.
| | - Susan J 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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24
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Ali ML, Ferrieres L, Jass J, Hyötyläinen T. Metabolic Changes in Pseudomonas oleovorans Isolated from Contaminated Construction Material Exposed to Varied Biocide Treatments. Metabolites 2024; 14:326. [PMID: 38921461 PMCID: PMC11205842 DOI: 10.3390/metabo14060326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/27/2024] Open
Abstract
Biocide resistance poses a significant challenge in industrial processes, with bacteria like Pseudomonas oleovorans exhibiting intrinsic resistance to traditional antimicrobial agents. In this study, the impact of biocide exposure on the metabolome of two P. oleovorans strains, namely, P. oleovorans P4A, isolated from contaminated coating material, and P. oleovorans 1045 reference strain, were investigated. The strains were exposed to 2-Methylisothiazol-3(2H)-one (MI) MIT, 1,2-Benzisothiazol-3(2H)-one (BIT), and 5-chloro-2-methyl-isothiazol-3-one (CMIT) at two different sub-inhibitory concentrations and the lipids and polar and semipolar metabolites were analyzed by ultra-high performance liquid chromatography quadrupole time-of-flight mass spectrometry UPLC-Q-TOF/MS. Exposure to the BIT biocide induced significant metabolic modifications in P. oleovorans. Notable changes were observed in lipid and metabolite profiles, particularly in phospholipids, amino acid metabolism, and pathways related to stress response and adaptation. The 1045 strain showed more pronounced metabolic alterations than the P4A strain, suggesting potential implications for lipid, amino acid metabolism, energy metabolism, and stress adaptation. Improving our understanding of how different substances interact with bacteria is crucial for making antimicrobial chemicals more effective and addressing the challenges of resistance. We observed that different biocides trigged significantly different metabolic responses in these strains. Our study shows that metabolomics can be used as a tool for the investigation of metabolic mechanisms underlying biocide resistance, and thus in the development of targeted biocides. This in turn can have implications in combating biocide resistance in bacteria such as P. oleovorans.
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Affiliation(s)
- Muatasem Latif Ali
- School of Science and Technology, Örebro University, Fakultetsgatan 1, SE 701 82 Örebro, Sweden; (M.L.A.); (J.J.)
- Saint-Gobain SWEDEN AB, SCANSPAC, Kemivägen 7, SE 705 97 Glanshammar, Sweden
| | - Lionel Ferrieres
- Saint-Gobain Recherche, 39 Quai Lucien Lefranc, FR-93303 Aubervilliers Cedex, France;
| | - Jana Jass
- School of Science and Technology, Örebro University, Fakultetsgatan 1, SE 701 82 Örebro, Sweden; (M.L.A.); (J.J.)
| | - Tuulia Hyötyläinen
- School of Science and Technology, Örebro University, Fakultetsgatan 1, SE 701 82 Örebro, Sweden; (M.L.A.); (J.J.)
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Cabello-Pinedo S, Abdulla H, Mas S, Fraire A, Maroto B, Seth-Smith M, Escriba M, Teruel J, Crespo J, Munné S, Horcajadas JA. Development of a Novel Non-invasive Metabolomics Assay to Predict Implantation Potential of Human Embryos. Reprod Sci 2024:10.1007/s43032-024-01583-y. [PMID: 38834841 DOI: 10.1007/s43032-024-01583-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/29/2024] [Indexed: 06/06/2024]
Abstract
Can a set of metabolites present in embryo culture media correlate with embryo implantation? Case-control study in two phases: discovery phase (101 samples) and validation phase (169 samples), collected between 2018 and 2022, with a total of 218 participants. Culture media samples with known implantation outcomes were collected after blastocyst embryo transfer (including both PGT and non-PGT cycles) and were analyzed using chromatography followed by mass spectrometry. The spectra were processed and analyzed using statistical and machine learning techniques to identify biomarkers associated with embryo implantation, and to develop a predictive model. In the discovery phase, 148 embryo implantation biomarkers were identified using high resolution equipment, and 47 of them were characterized. Our results indicate a significant enrichment of tryptophan metabolism, arginine and proline metabolism, and lysine degradation biochemical pathways. After transferring the method to a lower resolution equipment, a model able to assign a Metabolite Pregnancy Index (MPI) to each embryo culture media was developed, taking the concentration of 36 biomarkers as input. Applying this model to 20% of the validation samples (N=34) used as the test set, an accuracy of 85.29% was achieved, with a PPV (Positive Predictive Value) of 88% and a NPV (Negative Predictive Value) of 77.78%. Additionally, informative results were obtained for all the analyzed samples. Metabolite concentration in the media after in vitro culture shows correlation with embryo implantation potential. Furthermore, the mathematical combination of biomarker concentrations using Artificial Intelligence techniques can be used to predict embryo implantation outcome with an accuracy of around 85%.
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Affiliation(s)
| | - H Abdulla
- Texas A&M University Corpus Christi, Corpus Christi, Texas, 78412, USA
| | - S Mas
- Overture Life, 28108, Alcobendas, Madrid, Spain
| | - A Fraire
- Overture Life, 28108, Alcobendas, Madrid, Spain
| | - B Maroto
- Overture Life, 28108, Alcobendas, Madrid, Spain
| | | | - M Escriba
- Juana Crespo Clinic, 46015, Valencia, Spain
| | - J Teruel
- Juana Crespo Clinic, 46015, Valencia, Spain
| | - J Crespo
- Juana Crespo Clinic, 46015, Valencia, Spain
| | - S Munné
- Overture Life, 28108, Alcobendas, Madrid, Spain
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26
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Dunn F, Paquette SE, Pennell KD, Plavicki JS, Manz KE. Metabolomic changes following GenX and PFBS exposure in developing zebrafish. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 271:106908. [PMID: 38608566 PMCID: PMC11209921 DOI: 10.1016/j.aquatox.2024.106908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024]
Abstract
Short chain per- and polyfluoroalkyl substances (PFAS), including hexafluoropropylene oxide dimer acid (GenX) and perfluorobutane sulfonate (PFBS), are replacement chemicals for environmentally persistent, long-chain PFAS. Although GenX and PFBS have been detected in surface and ground water worldwide, few studies provide information on the metabolic alterations or risks associated with their exposures. In this study, larval zebrafish were used to investigate the toxicity of early-life exposure to GenX or PFBS. Zebrafish were chronically exposed from 4 h post-fertilization (hpf) to 6 days post-fertilization (dpf) to 150 µM GenX or 95.0 µM PFBS. Ultra-high-performance liquid chromatography paired with high-resolution mass spectrometry was used to quantify uptake of GenX and PFBS into zebrafish larvae and perform targeted and untargeted metabolomics. Our results indicate that PFBS was 20.4 % more readily absorbed into the zebrafish larvae compared to GenX. Additionally, PFBS exposure significantly altered 13 targeted metabolites and 21 metabolic pathways, while GenX exposure significantly altered 1 targeted metabolite and 17 metabolic pathways. Exposure to GenX, and to an even greater extent PFBS, resulted in a number of altered metabolic pathways in the amino acid metabolism, with other significant alterations in the carbohydrate, lipid, cofactors and vitamins, nucleotide, and xenobiotics metabolisms. Our results indicate that GenX and PFBS impact the zebrafish metabolome, with implications of global metabolic dysregulation, particularly in metabolic pathways relating to growth and development.
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Affiliation(s)
- Fiona Dunn
- School of Engineering, Brown University, 184 Hope Street, Providence, RI, 02912, United States
| | - Shannon E Paquette
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Providence, RI, 02903, United States
| | - Kurt D Pennell
- School of Engineering, Brown University, 184 Hope Street, Providence, RI, 02912, United States
| | - Jessica S Plavicki
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Providence, RI, 02903, United States.
| | - Katherine E Manz
- School of Engineering, Brown University, 184 Hope Street, Providence, RI, 02912, United States; Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, United States.
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27
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Li YY, Madduri SS, Rezeli ET, Santos C, Freeman III H, Peng J, McRitchie SL, Pathmasiri W, Hursting SD, Sumner SJ, Stewart DA. Macronutrient-differential dietary pattern impacts on body weight, hepatic inflammation, and metabolism. Front Nutr 2024; 11:1356038. [PMID: 38868554 PMCID: PMC11168494 DOI: 10.3389/fnut.2024.1356038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/24/2024] [Indexed: 06/14/2024] Open
Abstract
Introduction Obesity is a multi-factorial disease frequently associated with poor nutritional habits and linked to many detrimental health outcomes. Individuals with obesity are more likely to have increased levels of persistent inflammatory and metabolic dysregulation. The goal of this study was to compare four dietary patterns differentiated by macronutrient content in a postmenopausal model. Dietary patterns were high carbohydrate (HC), high fat (HF), high carbohydrate plus high fat (HCHF), and high protein (HP) with higher fiber. Methods Changes in body weight and glucose levels were measured in female, ovariectomized C57BL/6 mice after 15 weeks of feeding. One group of five mice fed the HCHF diet was crossed over to the HP diet on day 84, modeling a 21-day intervention. In a follow-up study comparing the HCHF versus HP dietary patterns, systemic changes in inflammation, using an 80-cytokine array and metabolism, by untargeted liquid chromatography-mass spectrometry (LCMS)-based metabolomics were evaluated. Results Only the HF and HCHF diets resulted in obesity, shown by significant differences in body weights compared to the HP diet. Body weight gains during the two-diet follow-up study were consistent with the four-diet study. On Day 105 of the 4-diet study, glucose levels were significantly lower for mice fed the HP diet than for those fed the HC and HF diets. Mice switched from the HCHF to the HP diet lost an average of 3.7 grams by the end of the 21-day intervention, but this corresponded with decreased food consumption. The HCHF pattern resulted in dramatic inflammatory dysregulation, as all 80 cytokines were elevated significantly in the livers of these mice after 15 weeks of HCHF diet exposure. Comparatively, only 32 markers changed significantly on the HP diet (24 up, 8 down). Metabolic perturbations in several endogenous biological pathways were also observed based on macronutrient differences and revealed dysfunction in several nutritionally relevant biosynthetic pathways. Conclusion Overall, the HCHF diet promoted detrimental impacts and changes linked to several diseases, including arthritis or breast neoplasms. Identification of dietary pattern-specific impacts in this model provides a means to monitor the effects of disease risk and test interventions to prevent poor health outcomes through nutritional modification.
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Affiliation(s)
- Yuan-yuan Li
- Metabolomics and Exposome Laboratory, Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Supradeep S. Madduri
- Metabolomics and Exposome Laboratory, Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Erika T. Rezeli
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Charlene Santos
- Animal Studies Core Lab, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Herman Freeman III
- Metabolomics and Exposome Laboratory, Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
| | - Jing Peng
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Susan L. McRitchie
- Metabolomics and Exposome Laboratory, Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Wimal Pathmasiri
- Metabolomics and Exposome Laboratory, Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Stephen D. Hursting
- Metabolomics and Exposome Laboratory, Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Susan J. Sumner
- Metabolomics and Exposome Laboratory, Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Delisha A. Stewart
- Metabolomics and Exposome Laboratory, Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill, Kannapolis, NC, United States
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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28
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Cochran SJ, Dunigan-Russell K, Hutton GM, Nguyen H, Schladweiler MC, Jones DP, Williams WC, Fisher AA, Gilmour MI, Dye JA, Smith MR, Miller CN, Gowdy KM. Repeated exposure to eucalyptus wood smoke alters pulmonary gene and metabolic profiles in male Long-Evans rats. Toxicol Sci 2024; 199:332-348. [PMID: 38544285 PMCID: PMC11131017 DOI: 10.1093/toxsci/kfae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024] Open
Abstract
Exposure to wildfire smoke is associated with both acute and chronic cardiopulmonary illnesses, which are of special concern for wildland firefighters who experience repeated exposure to wood smoke. It is necessary to better understand the underlying pathophysiology by which wood smoke exposure increases pulmonary disease burdens in this population. We hypothesize that wood smoke exposure produces pulmonary dysfunction, lung inflammation, and gene expression profiles associated with future pulmonary complications. Male Long-Evans rats were intermittently exposed to smoldering eucalyptus wood smoke at 2 concentrations, low (11.0 ± 1.89 mg/m3) and high (23.7 ± 0.077 mg/m3), over a 2-week period. Whole-body plethysmography was measured intermittently throughout. Lung tissue and lavage fluid were collected 24 h after the final exposure for transcriptomics and metabolomics. Increasing smoke exposure upregulated neutrophils and select cytokines in the bronchoalveolar lavage fluid. In total, 3446 genes were differentially expressed in the lungs of rats in the high smoke exposure and only 1 gene in the low smoke exposure (Cd151). Genes altered in the high smoke group reflected changes to the Eukaryotic Initiation Factor 2 stress and oxidative stress responses, which mirrored metabolomics analyses. xMWAS-integrated analysis revealed that smoke exposure significantly altered pathways associated with oxidative stress, lung morphogenesis, and tumor proliferation pathways. These results indicate that intermittent, 2-week exposure to eucalyptus wood smoke leads to transcriptomic and metabolic changes in the lung that may predict future lung disease development. Collectively, these findings provide insight into cellular signaling pathways that may contribute to the chronic pulmonary conditions observed in wildland firefighters.
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Affiliation(s)
- Samuel J Cochran
- Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio 43210, USA
| | - Katelyn Dunigan-Russell
- Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio 43210, USA
| | - Grace M Hutton
- Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio 43210, USA
| | - Helen Nguyen
- Oak Ridge Institute for Science and Education, U.S. Environmental Protection Agency, Center for Public Health and Environmental Assessment, Research Triangle Park, North Carolina 27711, USA
| | - Mette C Schladweiler
- Cardiopulmonary and Immunotoxicology Branch, Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - Dean P Jones
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322, USA
| | - Wanda C Williams
- Cardiopulmonary and Immunotoxicology Branch, Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - Anna A Fisher
- Cardiopulmonary and Immunotoxicology Branch, Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - M Ian Gilmour
- Cardiopulmonary and Immunotoxicology Branch, Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - Janice A Dye
- Cardiopulmonary and Immunotoxicology Branch, Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - M Ryan Smith
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322, USA
- Atlanta Veterans Affairs Healthcare System, Decatur, Georgia 30033, USA
| | - Colette N Miller
- Cardiopulmonary and Immunotoxicology Branch, Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - Kymberly M Gowdy
- Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, Ohio 43210, USA
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29
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Cheng SL, Hedges M, Keski-Rahkonen P, Chatziioannou AC, Scalbert A, Chung KF, Sinharay R, Green DC, de Kok TMCM, Vlaanderen J, Kyrtopoulos SA, Kelly F, Portengen L, Vineis P, Vermeulen RCH, Chadeau-Hyam M, Dagnino S. Multiomic Signatures of Traffic-Related Air Pollution in London Reveal Potential Short-Term Perturbations in Gut Microbiome-Related Pathways. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8771-8782. [PMID: 38728551 PMCID: PMC11112755 DOI: 10.1021/acs.est.3c09148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/12/2024]
Abstract
This randomized crossover study investigated the metabolic and mRNA alterations associated with exposure to high and low traffic-related air pollution (TRAP) in 50 participants who were either healthy or were diagnosed with chronic pulmonary obstructive disease (COPD) or ischemic heart disease (IHD). For the first time, this study combined transcriptomics and serum metabolomics measured in the same participants over multiple time points (2 h before, and 2 and 24 h after exposure) and over two contrasted exposure regimes to identify potential multiomic modifications linked to TRAP exposure. With a multivariate normal model, we identified 78 metabolic features and 53 mRNA features associated with at least one TRAP exposure. Nitrogen dioxide (NO2) emerged as the dominant pollutant, with 67 unique associated metabolomic features. Pathway analysis and annotation of metabolic features consistently indicated perturbations in the tryptophan metabolism associated with NO2 exposure, particularly in the gut-microbiome-associated indole pathway. Conditional multiomics networks revealed complex and intricate mechanisms associated with TRAP exposure, with some effects persisting 24 h after exposure. Our findings indicate that exposure to TRAP can alter important physiological mechanisms even after a short-term exposure of a 2 h walk. We describe for the first time a potential link between NO2 exposure and perturbation of the microbiome-related pathways.
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Affiliation(s)
- Sibo Lucas Cheng
- NIHR
HPRU in Environmental Exposures and Health, Imperial College London, London W12 0BZ, U.K.
- MRC
Centre for Environment and Health, Department of Epidemiology and
Biostatistics, School of Public Health, Imperial College London, London W12 7TA, U.K.
| | - Michael Hedges
- MRC
Centre for Environment and Health, Environmental Research Group, Imperial College London, London W12 0BZ, U.K.
| | | | | | - Augustin Scalbert
- International
Agency for Research on Cancer (IARC), Lyon 69366 Cedex, France
| | - Kian Fan Chung
- National
Heart & Lung Institute, Imperial College
London, London SW7 2AZ, U.K.
- Royal Brompton
& Harefield NHS Trust, London SW3 6NP, U.K.
| | - Rudy Sinharay
- National
Heart & Lung Institute, Imperial College
London, London SW7 2AZ, U.K.
- Imperial
College Healthcare NHS Trust, London W2 1NY, U.K.
| | - David C. Green
- NIHR
HPRU in Environmental Exposures and Health, Imperial College London, London W12 0BZ, U.K.
- MRC
Centre for Environment and Health, Environmental Research Group, Imperial College London, London W12 0BZ, U.K.
| | - Theo M. C. M. de Kok
- Department
of Toxicogenomics, GROW School for Oncology and Reproduction, Maastricht University, Maastricht 6229 ER, The Netherlands
| | - Jelle Vlaanderen
- Division
of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CS, The Netherlands
| | | | - Frank Kelly
- NIHR
HPRU in Environmental Exposures and Health, Imperial College London, London W12 0BZ, U.K.
- MRC
Centre for Environment and Health, Environmental Research Group, Imperial College London, London W12 0BZ, U.K.
| | - Lützen Portengen
- Division
of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CS, The Netherlands
| | - Paolo Vineis
- MRC
Centre for Environment and Health, Department of Epidemiology and
Biostatistics, School of Public Health, Imperial College London, London W12 7TA, U.K.
| | - Roel C. H. Vermeulen
- Division
of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CS, The Netherlands
- Julius Centre for Health Sciences and Primary Care, University
Medical
Centre, Utrecht University, Utrecht 3584 CG, The Netherlands
| | - Marc Chadeau-Hyam
- NIHR
HPRU in Environmental Exposures and Health, Imperial College London, London W12 0BZ, U.K.
- MRC
Centre for Environment and Health, Department of Epidemiology and
Biostatistics, School of Public Health, Imperial College London, London W12 7TA, U.K.
| | - Sonia Dagnino
- MRC
Centre for Environment and Health, Department of Epidemiology and
Biostatistics, School of Public Health, Imperial College London, London W12 7TA, U.K.
- Transporters
in Imaging and Radiotherapy in Oncology (TIRO), School
of Medicine, Direction de la Recherche Fondamentale (DRF), Institut
des Sciences du Vivant Fréderic Joliot, Commissariat à
l’Energie Atomique et aux Énergies Alternatives (CEA), Université Côte d’Azur (UniCA), Nice 06107, France
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30
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Li S, Lin Y, Jones D, Walker DI, Duarte Folle A, Del Rosario I, Yu Y, Zhang K, Keener AM, Bronstein J, Ritz B, Paul KC. Untargeted serum metabolic profiling of diabetes mellitus among Parkinson's disease patients. NPJ Parkinsons Dis 2024; 10:100. [PMID: 38730245 PMCID: PMC11087477 DOI: 10.1038/s41531-024-00711-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a common comorbidity among Parkinson's disease (PD) patients. Yet, little is known about dysregulated pathways that are unique in PD patients with T2DM. We applied high-resolution metabolomic profiling in serum samples of 636 PD and 253 non-PD participants recruited from Central California. We conducted an initial discovery metabolome-wide association and pathway enrichment analysis. After adjusting for multiple testing, in positive (or negative) ion mode, 30 (25) metabolic features were associated with T2DM in both PD and non-PD participants, 162 (108) only in PD participants, and 32 (7) only in non-PD participants. Pathway enrichment analysis identified 17 enriched pathways associated with T2DM in both the PD and non-PD participants, 26 pathways only in PD participants, and 5 pathways only in non-PD participants. Several amino acid, nucleic acids, and fatty acid metabolisms were associated with T2DM only in the PD patient group suggesting a possible link between PD and T2DM.
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Affiliation(s)
- Shiwen Li
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Yuyuan Lin
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Dean Jones
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, USA
| | - Douglas I Walker
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Aline Duarte Folle
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Irish Del Rosario
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Yu Yu
- Center for Health Policy Research, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Keren Zhang
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Adrienne M Keener
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jeff Bronstein
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Beate Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Kimberly C Paul
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA.
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31
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Sivalogan K, Liang D, Accardi C, Diaz-Artiga A, Hu X, Mollinedo E, Ramakrishnan U, Teeny SN, Tran V, Clasen TF, Thompson LM, Sinharoy SS. Human Milk Composition Is Associated with Maternal Body Mass Index in a Cross-Sectional, Untargeted Metabolomics Analysis of Human Milk from Guatemalan Mothers. Curr Dev Nutr 2024; 8:102144. [PMID: 38726027 PMCID: PMC11079463 DOI: 10.1016/j.cdnut.2024.102144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/12/2024] [Accepted: 03/19/2024] [Indexed: 05/12/2024] Open
Abstract
Background Maternal overweight and obesity has been associated with poor lactation performance including delayed lactogenesis and reduced duration. However, the effect on human milk composition is less well understood. Objectives We evaluated the relationship of maternal BMI on the human milk metabolome among Guatemalan mothers. Methods We used data from 75 Guatemalan mothers who participated in the Household Air Pollution Intervention Network trial. Maternal BMI was measured between 9 and <20 weeks of gestation. Milk samples were collected at a single time point using aseptic collection from one breast at 6 mo postpartum and analyzed using high-resolution mass spectrometry. A cross-sectional untargeted high-resolution metabolomics analysis was performed by coupling hydrophilic interaction liquid chromatography (HILIC) and reverse phase C18 chromatography with mass spectrometry. Metabolic features associated with maternal BMI were determined by a metabolome-wide association study (MWAS), adjusting for baseline maternal age, education, and dietary diversity, and perturbations in metabolic pathways were identified by pathway enrichment analysis. Results The mean age of participants at baseline was 23.62 ± 3.81 y, and mean BMI was 24.27 ± 4.22 kg/m2. Of the total metabolic features detected by HILIC column (19,199 features) and by C18 column (11,594 features), BMI was associated with 1026 HILIC and 500 C18 features. Enriched pathways represented amino acid metabolism, galactose metabolism, and xenobiotic metabolic metabolism. However, no significant features were identified after adjusting for multiple comparisons using the Benjamini-Hochberg false discovery rate procedure (FDRBH < 0.2). Conclusions Findings from this untargeted MWAS indicate that maternal BMI is associated with metabolic perturbations of galactose metabolism, xenobiotic metabolism, and xenobiotic metabolism by cytochrome p450 and biosynthesis of amino acid pathways. Significant metabolic pathway alterations detected in human milk were associated with energy metabolism-related pathways including carbohydrate and amino acid metabolism.This trial was registered at clinicaltrials.gov as NCT02944682.
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Affiliation(s)
- Kasthuri Sivalogan
- Nutrition and Health Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Donghai Liang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Carolyn Accardi
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Anaite Diaz-Artiga
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Xin Hu
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Erick Mollinedo
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Usha Ramakrishnan
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
- Department of Environmental Health, College of Public Health, University of Georgia, Athens, GA, United States
| | - Sami Nadeem Teeny
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, GA, United States
| | - ViLinh Tran
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, GA, United States
| | - Thomas F Clasen
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Lisa M Thompson
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, United States
| | - Sheela S Sinharoy
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
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Pang Z, Xu L, Viau C, Lu Y, Salavati R, Basu N, Xia J. MetaboAnalystR 4.0: a unified LC-MS workflow for global metabolomics. Nat Commun 2024; 15:3675. [PMID: 38693118 PMCID: PMC11063062 DOI: 10.1038/s41467-024-48009-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 04/18/2024] [Indexed: 05/03/2024] Open
Abstract
The wide applications of liquid chromatography - mass spectrometry (LC-MS) in untargeted metabolomics demand an easy-to-use, comprehensive computational workflow to support efficient and reproducible data analysis. However, current tools were primarily developed to perform specific tasks in LC-MS based metabolomics data analysis. Here we introduce MetaboAnalystR 4.0 as a streamlined pipeline covering raw spectra processing, compound identification, statistical analysis, and functional interpretation. The key features of MetaboAnalystR 4.0 includes an auto-optimized feature detection and quantification algorithm for LC-MS1 spectra processing, efficient MS2 spectra deconvolution and compound identification for data-dependent or data-independent acquisition, and more accurate functional interpretation through integrated spectral annotation. Comprehensive validation studies using LC-MS1 and MS2 spectra obtained from standards mixtures, dilution series and clinical metabolomics samples have shown its excellent performance across a wide range of common tasks such as peak picking, spectral deconvolution, and compound identification with good computing efficiency. Together with its existing statistical analysis utilities, MetaboAnalystR 4.0 represents a significant step toward a unified, end-to-end workflow for LC-MS based global metabolomics in the open-source R environment.
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Affiliation(s)
- Zhiqiang Pang
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Lei Xu
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Charles Viau
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Yao Lu
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Reza Salavati
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada.
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
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Jiang Y, Zhu X, Shen Y, He Y, Fan H, Xu X, Zhou L, Zhu Y, Xue X, Zhang Q, Du X, Zhang L, Zhang Y, Liu C, Niu Y, Cai J, Kan H, Chen R. Mechanistic insights into cardiovascular effects of ultrafine particle exposure: A longitudinal panel study. ENVIRONMENT INTERNATIONAL 2024; 187:108714. [PMID: 38718674 DOI: 10.1016/j.envint.2024.108714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/16/2024] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Ultrafine particle (UFP) has been linked with higher risks of cardiovascular diseases; however, the biological mechanisms remain to be fully elucidated. OBJECTIVES This study aims to investigate the cardiovascular responses to short-term UFP exposure and the biological pathways involved. METHODS A longitudinal panel study was conducted among 32 healthy, non-smoking young adults in Shanghai, China, who were engaged in five rounds of follow-ups between December 2020 and November 2021. Individual exposures were calculated based on the indoor and outdoor real-time measurements. Blood pressure, arterial stiffness, targeted biomarkers, and untargeted proteomics and metabolomics were examined during each follow-up. Linear mixed-effect models were applied to analyze the exposure and health data. The differential proteins and metabolites were used for pathway enrichment analyses. RESULTS Short-term UFP exposure was associated with significant increases in blood pressure and arterial stiffness. For example, systolic blood pressure increased by 2.10 % (95 % confidence interval: 0.63 %, 3.59 %) corresponding to each interquartile increase in UFP concentrations at lag 0-3 h, while pulse wave velocity increased by 2.26 % (95 % confidence interval: 0.52 %, 4.04 %) at lag 7-12 h. In addition, dozens of molecular biomarkers altered significantly. These effects were generally present within 24 h after UFP exposure, and were robust to the adjustment of co-pollutants. Molecular changes detected in proteomics and metabolomics analyses were mainly involved in systemic inflammation, oxidative stress, endothelial dysfunction, coagulation, and disturbance in lipid transport and metabolism. DISCUSSION This study provides novel and compelling evidence on the detrimental subclinical cardiovascular effects in response to short-term UFP exposure. The multi-omics profiling further offers holistic insights into the underlying biological pathways.
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Affiliation(s)
- Yixuan Jiang
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Xinlei Zhu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Yang Shen
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Yu He
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Hao Fan
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Xueyi Xu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Lu Zhou
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Yixiang Zhu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Xiaowei Xue
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Qingli Zhang
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Xihao Du
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Lina Zhang
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yang Zhang
- Department of Systems Biology for Medicine, and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cong Liu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Yue Niu
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Jing Cai
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
| | - Haidong Kan
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China; Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China.
| | - Renjie Chen
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China; School of Public Health, Hengyang Medical School, University of South China, Hengyang, China.
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Carpenter AD, Li Y, Fatanmi OO, Wise SY, Petrus SA, Janocha BL, Cheema AK, Singh VK. Metabolomic Profiles in Tissues of Nonhuman Primates Exposed to Either Total- or Partial-Body Radiation. Radiat Res 2024; 201:371-383. [PMID: 38253059 DOI: 10.1667/rade-23-00091.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/27/2023] [Indexed: 01/24/2024]
Abstract
A complex cascade of systemic and tissue-specific responses induced by exposure to ionizing radiation can lead to functional impairment over time in the surviving population. Current methods for management of survivors of unintentional radiation exposure episodes rely on monitoring individuals over time for the development of adverse clinical symptoms due to the lack of predictive biomarkers for tissue injury. In this study, we report on changes in metabolomic and lipidomic profiles in multiple tissues of nonhuman primates (NHPs) that received either 4.0 Gy or 5.8 Gy total-body irradiation (TBI) of 60Co gamma rays, and 4.0 or 5.8 Gy partial-body irradiation (PBI) from LINAC-derived photons and were treated with a promising radiation countermeasure, gamma-tocotrienol (GT3). These include small molecule alterations that correlate with radiation effects in the jejunum, lung, kidney, and spleen of animals that either survived or succumbed to radiation toxicities over a 30-day period. Radiation-induced metabolic changes in tissues were observed in animals exposed to both doses and types of radiation, but were partially alleviated in GT3-treated and irradiated animals, with lung and spleen being most responsive. The majority of the pathways protected by GT3 treatment in these tissues were related to glucose metabolism, inflammation, and aldarate metabolism, suggesting GT3 may exert radioprotective effects in part by sparing these pathways from radiation-induced dysregulation. Taken together, the results of our study demonstrate that the prophylactic administration of GT3 results in metabolic and lipidomic shifts that likely provide an overall advantage against radiation injury. This investigation is among the first to highlight the use of a molecular phenotyping approach in a highly translatable NHP model of partial- and total-body irradiation to determine the underlying physiological mechanisms involved in the radioprotective efficacy of GT3.
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Affiliation(s)
- Alana D Carpenter
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Yaoxiang Li
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Oluseyi O Fatanmi
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Stephen Y Wise
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Sarah A Petrus
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Brianna L Janocha
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Amrita K Cheema
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington DC
| | - Vijay K Singh
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland
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Ewald JD, Zhou G, Lu Y, Kolic J, Ellis C, Johnson JD, Macdonald PE, Xia J. Web-based multi-omics integration using the Analyst software suite. Nat Protoc 2024; 19:1467-1497. [PMID: 38355833 DOI: 10.1038/s41596-023-00950-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 11/21/2023] [Indexed: 02/16/2024]
Abstract
The growing number of multi-omics studies demands clear conceptual workflows coupled with easy-to-use software tools to facilitate data analysis and interpretation. This protocol covers three key components involved in multi-omics analysis, including single-omics data analysis, knowledge-driven integration using biological networks and data-driven integration through joint dimensionality reduction. Using the dataset from a recent multi-omics study of human pancreatic islet tissue and plasma samples, the first section introduces how to perform transcriptomics/proteomics data analysis using ExpressAnalyst and lipidomics data analysis using MetaboAnalyst. On the basis of significant features detected in these workflows, the second section demonstrates how to perform knowledge-driven integration using OmicsNet. The last section illustrates how to perform data-driven integration from the normalized omics data and metadata using OmicsAnalyst. The complete protocol can be executed in ~2 h. Compared with other available options for multi-omics integration, the Analyst software suite described in this protocol enables researchers to perform a wide range of omics data analysis tasks via a user-friendly web interface.
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Affiliation(s)
- Jessica D Ewald
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Guangyan Zhou
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Yao Lu
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Jelena Kolic
- Life Sciences Institute, Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Cara Ellis
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - James D Johnson
- Life Sciences Institute, Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick E Macdonald
- Department of Pharmacology, University of Alberta, Edmonton, Alberta, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada.
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.
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Ge Y, Yang C, Zadeh M, Sprague SM, Lin YD, Jain HS, Determann BF, Roth WH, Palavicini JP, Larochelle J, Candelario-Jalil E, Mohamadzadeh M. Functional regulation of microglia by vitamin B12 alleviates ischemic stroke-induced neuroinflammation in mice. iScience 2024; 27:109480. [PMID: 38715940 PMCID: PMC11075062 DOI: 10.1016/j.isci.2024.109480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/14/2023] [Accepted: 03/08/2024] [Indexed: 05/12/2024] Open
Abstract
Ischemic stroke is the second leading cause of death and disability worldwide, and efforts to prevent stroke, mitigate secondary neurological damage, and promote neurological recovery remain paramount. Recent findings highlight the critical importance of microbiome-related metabolites, including vitamin B12 (VB12), in alleviating toxic stroke-associated neuroinflammation. Here, we showed that VB12 tonically programmed genes supporting microglial cell division and activation and critically controlled cellular fatty acid metabolism in homeostasis. Intriguingly, VB12 promoted mitochondrial transcriptional and metabolic activities and significantly restricted stroke-associated gene alterations in microglia. Furthermore, VB12 differentially altered the functions of microglial subsets during the acute phase of ischemic stroke, resulting in reduced brain damage and improved neurological function. Pharmacological depletion of microglia before ischemic stroke abolished VB12-mediated neurological improvement. Thus, our preclinical studies highlight the relevance of VB12 in the functional programming of microglia to alleviate neuroinflammation, minimize ischemic injury, and improve host neurological recovery after ischemic stroke.
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Affiliation(s)
- Yong Ge
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health, San Antonio, TX, USA
| | - Changjun Yang
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Mojgan Zadeh
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health, San Antonio, TX, USA
| | - Shane M. Sprague
- Department of Neurosurgery, University of Texas Health, San Antonio, TX, USA
| | - Yang-Ding Lin
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health, San Antonio, TX, USA
| | - Heetanshi Sanjay Jain
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health, San Antonio, TX, USA
| | | | - William H. Roth
- Department of Neurology, University of Chicago Medical Center, Chicago, IL, USA
| | - Juan Pablo Palavicini
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health, San Antonio, TX, USA
| | - Jonathan Larochelle
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Eduardo Candelario-Jalil
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Mansour Mohamadzadeh
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health, San Antonio, TX, USA
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Pristner M, Wasinger D, Seki D, Klebermaß-Schrehof K, Berger A, Berry D, Wisgrill L, Warth B. Neuroactive metabolites and bile acids are altered in extremely premature infants with brain injury. Cell Rep Med 2024; 5:101480. [PMID: 38518769 PMCID: PMC11031385 DOI: 10.1016/j.xcrm.2024.101480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/02/2023] [Accepted: 02/27/2024] [Indexed: 03/24/2024]
Abstract
The gut microbiome is associated with pathological neurophysiological evolvement in extremely premature infants suffering from brain injury. The exact underlying mechanism and its associated metabolic signatures in infants are not fully understood. To decipher metabolite profiles linked to neonatal brain injury, we investigate the fecal and plasma metabolome of samples obtained from a cohort of 51 extremely premature infants at several time points, using liquid chromatography (LC)-high-resolution mass spectrometry (MS)-based untargeted metabolomics and LC-MS/MS-based targeted analysis for investigating bile acids and amidated bile acid conjugates. The data are integrated with 16S rRNA gene amplicon gut microbiome profiles as well as patient cytokine, growth factor, and T cell profiles. We find an early onset of differentiation in neuroactive metabolites between infants with and without brain injury. We detect several bacterially derived bile acid amino acid conjugates in plasma and feces. These results provide insights into the early-life metabolome of extremely premature infants.
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Affiliation(s)
- Manuel Pristner
- Department of Food Chemistry and Toxicology, University of Vienna, 1090 Vienna, Austria
| | - Daniel Wasinger
- Department of Food Chemistry and Toxicology, University of Vienna, 1090 Vienna, Austria
| | - David Seki
- Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1090 Vienna, Austria
| | - Katrin Klebermaß-Schrehof
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Angelika Berger
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - David Berry
- Center for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria; Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1090 Vienna, Austria
| | - Lukas Wisgrill
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Benedikt Warth
- Department of Food Chemistry and Toxicology, University of Vienna, 1090 Vienna, Austria.
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Fairley JK, Ferreira JA, Fraga LAO, Lyon S, Valadão Cardoso TM, Boson VC, Madureira Nunes AC, Medeiros Cinha EH, de Oliveira LBP, Magueta Silva EB, Marçal PHF, Branco AC, Grossi MAF, Jones DP, Ziegler TR, Collins JM. High-Resolution Plasma Metabolomics Identifies Alterations in Fatty Acid, Energy, and Micronutrient Metabolism in Adults Across the Leprosy Spectrum. J Infect Dis 2024; 229:1189-1199. [PMID: 37740551 PMCID: PMC11011203 DOI: 10.1093/infdis/jiad410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND High-resolution metabolomics (HRM) is an innovative tool to study challenging infectious diseases like leprosy, where the pathogen cannot be grown with standard methods. Here, we use HRM to better understand associations between disease manifestations, nutrition, and host metabolism. METHODS From 2018 to 2019, adults with leprosy and controls were recruited in Minas Gerais, Brazil. Plasma metabolites were detected using an established HRM workflow and characterized by accurate mass, mass to charge ratio m/z and retention time. The mummichog informatics package compared metabolic pathways between cases and controls and between multibacillary (MB) and paucibacillary (PB) leprosy. Additionally, select individual metabolites were quantified and compared. RESULTS Thirty-nine cases (62% MB and 38% PB) and 25 controls were enrolled. We found differences (P < .05) in several metabolic pathways, including fatty acid metabolism, carnitine shuttle, retinol, vitamin D3, and C-21 steroid metabolism, between cases and controls with lower retinol and associated metabolites in cases. Between MB and PB, leukotrienes, prostaglandins, tryptophan, and cortisol were all found to be lower in MB (P < .05). DISCUSSION Metabolites associated with several nutrient-related metabolic pathways appeared differentially regulated in leprosy, especially MB versus PB. This pilot study demonstrates the metabolic interdependency of these pathways, which may play a role in the pathophysiology of disease.
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Affiliation(s)
- Jessica K Fairley
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - José A Ferreira
- Faculdade da Saúde e Écologia Humana, FASEH, Vespasiano, Minas Gerais, Brazil
| | - Lucia A O Fraga
- Department of Health Sciences, Universidade Federal de Juiz de Fora, Governador Valadares, Minas Gerais, Brazil
| | - Sandra Lyon
- Faculdade da Saúde e Écologia Humana, FASEH, Vespasiano, Minas Gerais, Brazil
- Fundação Hospitalar do Estado de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Victor Campos Boson
- Faculdade da Saúde e Écologia Humana, FASEH, Vespasiano, Minas Gerais, Brazil
| | | | - Eloisa H Medeiros Cinha
- Department of Health Sciences, Universidade Federal de Juiz de Fora, Governador Valadares, Minas Gerais, Brazil
| | - Lorena B P de Oliveira
- Department of Health Sciences, Universidade Federal de Juiz de Fora, Governador Valadares, Minas Gerais, Brazil
| | - Erica B Magueta Silva
- Department of Health Sciences, Universidade Federal de Juiz de Fora, Governador Valadares, Minas Gerais, Brazil
| | - Pedro H F Marçal
- Department of Health Sciences, Universidade Federal de Juiz de Fora, Governador Valadares, Minas Gerais, Brazil
| | - Alexandre C Branco
- Centro de Referência em Doenças Endêmicas e Programs Especiais, Governador Valadares, Minas Gerais, Brazil
| | | | - Dean P Jones
- Division of Pulmonary, Critical Care, and Allergy, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Thomas R Ziegler
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jeffrey M Collins
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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Ricciutelli M, Angeloni S, Conforti S, Corneli M, Caprioli G, Sagratini G, Alabed HBR, D'Amato Tóthová J, Pellegrino RM. An untargeted metabolomics approach to study changes of the medium during human cornea culture. Metabolomics 2024; 20:44. [PMID: 38581549 DOI: 10.1007/s11306-024-02102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/15/2024] [Indexed: 04/08/2024]
Abstract
INTRODUCTION Two main approaches (organ culture and hypothermia) for the preservation and storage of human donor corneas are globally adopted for corneal preservation before the transplant. Hypothermia is a hypothermic storage which slows down cellular metabolism while organ culture, a corneal culture performed at 28-37 °C, maintains an active corneal metabolism. Researchers, till now, have just studied the impact of organ culture on human cornea after manipulating and disrupting tissues. OBJECTIVES The aim of the current work was to optimize an analytical procedure which can be useful for discovering biomarkers capable of predicting tissue health status. For the first time, this research proposed a preliminary metabolomics study on medium for organ culture without manipulating and disrupting the valuable human tissues which could be still used for transplantation. METHODS In particular, the present research proposed a method for investigating changes in the medium, over a storage period of 20 days, in presence and absence of a human donor cornea. An untargeted metabolomics approach using UHPLC-QTOF was developed to deeply investigate the differences on metabolites and metabolic pathways and the influence of the presence of the cornea inside the medium. RESULTS Differences in the expression of some compounds emerged from this preliminary metabolomics approach, in particular in medium maintained for 10 and 20 days in presence but also in the absence of cornea. A total of 173 metabolites have been annotated and 36 pathways were enriched by pathway analysis. CONCLUSION The results revealed a valuable untargeted metabolomics approach which can be applied in organ culture metabolomics.
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Affiliation(s)
- Massimo Ricciutelli
- Chemistry Interdisciplinary Project (ChIP), School of Pharmacy, University of Camerino, I-62032, Camerino, Italy
| | - Simone Angeloni
- Chemistry Interdisciplinary Project (ChIP), School of Pharmacy, University of Camerino, I-62032, Camerino, Italy.
| | - Silvia Conforti
- The Marche Region Eye Bank, AST Ancona - E. Profili Hospital, 60044, Fabriano, Italy
| | - Massimiliano Corneli
- The Marche Region Eye Bank, AST Ancona - E. Profili Hospital, 60044, Fabriano, Italy
| | - Giovanni Caprioli
- Chemistry Interdisciplinary Project (ChIP), School of Pharmacy, University of Camerino, I-62032, Camerino, Italy
| | - Gianni Sagratini
- Chemistry Interdisciplinary Project (ChIP), School of Pharmacy, University of Camerino, I-62032, Camerino, Italy
| | - Husam B R Alabed
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06100, Perugia, Italy
| | | | - Roberto Maria Pellegrino
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06100, Perugia, Italy
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40
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Meier L, Bruginski E, Marafiga JR, Caus LB, Pasquetti MV, Calcagnotto ME, Campos FR. Hippocampal metabolic profile during epileptogenesis in the pilocarpine model of epilepsy. Biomed Chromatogr 2024; 38:e5820. [PMID: 38154955 DOI: 10.1002/bmc.5820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/30/2023]
Abstract
Temporal lobe epilepsy (TLE) is a common form of refractory epilepsy in adulthood. The metabolic profile of epileptogenesis is still poorly investigated. Elucidation of such a metabolic profile using animal models of epilepsy could help identify new metabolites and pathways involved in the mechanisms of epileptogenesis process. In this study, we evaluated the metabolic profile during the epileptogenesis periods. Using a pilocarpine model of epilepsy, we analyzed the global metabolic profile of hippocampal extracts by untargeted metabolomics based on ultra-performance liquid chromatography-high-resolution mass spectrometry, at three time points (3 h, 1 week, and 2 weeks) after status epilepticus (SE) induction. We demonstrated that epileptogenesis periods presented different hippocampal metabolic profiles, including alterations of metabolic pathways of amino acids and lipid metabolism. Six putative metabolites (tryptophan, N-acetylornithine, N-acetyl-L-aspartate, glutamine, adenosine, and cholesterol) showed significant different levels during epileptogenesis compared to their respective controls. These putative metabolites could be associated with the imbalance of neurotransmitters, mitochondrial dysfunction, and cell loss observed during both epileptogenesis and epilepsy. With these findings, we provided an overview of hippocampal metabolic profiles during different stages of epileptogenesis that could help investigate pathways and respective metabolites as predictive tools in epilepsy.
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Affiliation(s)
- Letícia Meier
- Biosciences and Mass Spectrometry Laboratory, Department of Pharmacy, Universidade Federal do Paraná, Curitiba, PR, Brazil
- Graduate Program in Pharmaceutical Science, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Estevan Bruginski
- Biosciences and Mass Spectrometry Laboratory, Department of Pharmacy, Universidade Federal do Paraná, Curitiba, PR, Brazil
- Graduate Program in Pharmaceutical Science, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Joseane Righes Marafiga
- Neurophysiology and Neurochemistry of Neuronal Excitability and Synaptic Plasticity Laboratory (NNNESP Lab.), Department of Biochemistry, ICBS, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Graduate Program in Biological Science: Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Letícia Barbieri Caus
- Neurophysiology and Neurochemistry of Neuronal Excitability and Synaptic Plasticity Laboratory (NNNESP Lab.), Department of Biochemistry, ICBS, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Mayara Vendramin Pasquetti
- Neurophysiology and Neurochemistry of Neuronal Excitability and Synaptic Plasticity Laboratory (NNNESP Lab.), Department of Biochemistry, ICBS, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Elisa Calcagnotto
- Neurophysiology and Neurochemistry of Neuronal Excitability and Synaptic Plasticity Laboratory (NNNESP Lab.), Department of Biochemistry, ICBS, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Graduate Program in Biological Science: Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Francinete Ramos Campos
- Biosciences and Mass Spectrometry Laboratory, Department of Pharmacy, Universidade Federal do Paraná, Curitiba, PR, Brazil
- Graduate Program in Pharmaceutical Science, Universidade Federal do Paraná, Curitiba, PR, Brazil
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Sahu U, Villa E, Reczek CR, Zhao Z, O'Hara BP, Torno MD, Mishra R, Shannon WD, Asara JM, Gao P, Shilatifard A, Chandel NS, Ben-Sahra I. Pyrimidines maintain mitochondrial pyruvate oxidation to support de novo lipogenesis. Science 2024; 383:1484-1492. [PMID: 38547260 PMCID: PMC11325697 DOI: 10.1126/science.adh2771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 02/20/2024] [Indexed: 04/02/2024]
Abstract
Cellular purines, particularly adenosine 5'-triphosphate (ATP), fuel many metabolic reactions, but less is known about the direct effects of pyrimidines on cellular metabolism. We found that pyrimidines, but not purines, maintain pyruvate oxidation and the tricarboxylic citric acid (TCA) cycle by regulating pyruvate dehydrogenase (PDH) activity. PDH activity requires sufficient substrates and cofactors, including thiamine pyrophosphate (TPP). Depletion of cellular pyrimidines decreased TPP synthesis, a reaction carried out by TPP kinase 1 (TPK1), which reportedly uses ATP to phosphorylate thiamine (vitamin B1). We found that uridine 5'-triphosphate (UTP) acts as the preferred substrate for TPK1, enabling cellular TPP synthesis, PDH activity, TCA-cycle activity, lipogenesis, and adipocyte differentiation. Thus, UTP is required for vitamin B1 utilization to maintain pyruvate oxidation and lipogenesis.
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Affiliation(s)
- Umakant Sahu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Elodie Villa
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Colleen R Reczek
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Brendan P O'Hara
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Michael D Torno
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | | | | | - John M Asara
- Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Peng Gao
- Metabolomics Core Facility, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Navdeep S Chandel
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
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Ma G, Kang J, Yu T. Bayesian functional analysis for untargeted metabolomics data with matching uncertainty and small sample sizes. Brief Bioinform 2024; 25:bbae141. [PMID: 38581417 PMCID: PMC10998539 DOI: 10.1093/bib/bbae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/28/2024] [Accepted: 03/13/2024] [Indexed: 04/08/2024] Open
Abstract
Untargeted metabolomics based on liquid chromatography-mass spectrometry technology is quickly gaining widespread application, given its ability to depict the global metabolic pattern in biological samples. However, the data are noisy and plagued by the lack of clear identity of data features measured from samples. Multiple potential matchings exist between data features and known metabolites, while the truth can only be one-to-one matches. Some existing methods attempt to reduce the matching uncertainty, but are far from being able to remove the uncertainty for most features. The existence of the uncertainty causes major difficulty in downstream functional analysis. To address these issues, we develop a novel approach for Bayesian Analysis of Untargeted Metabolomics data (BAUM) to integrate previously separate tasks into a single framework, including matching uncertainty inference, metabolite selection and functional analysis. By incorporating the knowledge graph between variables and using relatively simple assumptions, BAUM can analyze datasets with small sample sizes. By allowing different confidence levels of feature-metabolite matching, the method is applicable to datasets in which feature identities are partially known. Simulation studies demonstrate that, compared with other existing methods, BAUM achieves better accuracy in selecting important metabolites that tend to be functionally consistent and assigning confidence scores to feature-metabolite matches. We analyze a COVID-19 metabolomics dataset and a mouse brain metabolomics dataset using BAUM. Even with a very small sample size of 16 mice per group, BAUM is robust and stable. It finds pathways that conform to existing knowledge, as well as novel pathways that are biologically plausible.
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Affiliation(s)
- Guoxuan Ma
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jian Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tianwei Yu
- Shenzhen Research Institute of Big Data, School of Data Science, The Chinese University of Hong Kong - Shenzhen (CUHK-Shenzhen), Shenzhen, Guangdong 518172, China
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Bai J, Eldridge R, Houser M, Martin M, Powell C, Sutton KS, Noh HI, Wu Y, Olson T, Konstantinidis KT, Bruner DW. Multi-omics analysis of the gut microbiome and metabolites associated with the psychoneurological symptom cluster in children with cancer receiving chemotherapy. J Transl Med 2024; 22:256. [PMID: 38461265 PMCID: PMC10924342 DOI: 10.1186/s12967-024-05066-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/05/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Children with cancer receiving chemotherapy commonly report a cluster of psychoneurological symptoms (PNS), including pain, fatigue, anxiety, depression, and cognitive dysfunction. The role of the gut microbiome and its functional metabolites in PNS is rarely studied among children with cancer. This study investigated the associations between the gut microbiome-metabolome pathways and PNS in children with cancer across chemotherapy as compared to healthy children. METHODS A case-control study was conducted. Cancer cases were recruited from Children's Healthcare of Atlanta and healthy controls were recruited via flyers. Participants reported PNS using the Pediatric Patient-Reported Outcomes Measurement Information System. Data for cases were collected pre-cycle two chemotherapy (T0) and post-chemotherapy (T1), whereas data for healthy controls were collected once. Gut microbiome and its metabolites were measured using fecal specimens. Gut microbiome profiling was performed using 16S rRNA V4 sequencing, and metabolome was performed using an untargeted liquid chromatography-mass spectrometry approach. A multi-omics network integration program analyzed microbiome-metabolome pathways of PNS. RESULTS Cases (n = 21) and controls (n = 14) had mean ages of 13.2 and 13.1 years. For cases at T0, PNS were significantly associated with microbial genera (e.g., Ruminococcus, Megasphaera, and Prevotella), which were linked with carnitine shuttle (p = 0.0003), fatty acid metabolism (p = 0.001) and activation (p = 0.001), and tryptophan metabolism (p = 0.008). Megasphaera, clustered with aspartate and asparagine metabolism (p = 0.034), carnitine shuttle (p = 0.002), and tryptophan (p = 0.019), was associated with PNS for cases at T1. Gut bacteria with potential probiotic functions, along with fatty acid metabolism, tryptophan, and carnitine shuttle, were more clustered in cancer cases than the control network and this linkage with PNS needs further studies. CONCLUSIONS Using multi-omics approaches, this study indicated specific microbiome-metabolome pathways linked with PNS in children with cancer across chemotherapy. Due to limitations such as antibiotic use in cancer cases, these findings need to be further confirmed in a larger cohort.
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Affiliation(s)
- Jinbing Bai
- Nell Hodgson Woodruff School of Nursing, Emory University, 1520 Clifton Road NE, Atlanta, GA, 30322, USA.
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.
| | - Ronald Eldridge
- Nell Hodgson Woodruff School of Nursing, Emory University, 1520 Clifton Road NE, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Madelyn Houser
- Nell Hodgson Woodruff School of Nursing, Emory University, 1520 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Melissa Martin
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Christie Powell
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Kathryn S Sutton
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- School of Medicine, Emory University, Atlanta, GA, USA
| | - Hye In Noh
- Nell Hodgson Woodruff School of Nursing, Emory University, 1520 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Yuhua Wu
- Nell Hodgson Woodruff School of Nursing, Emory University, 1520 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Thomas Olson
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- School of Medicine, Emory University, Atlanta, GA, USA
| | | | - Deborah W Bruner
- Nell Hodgson Woodruff School of Nursing, Emory University, 1520 Clifton Road NE, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
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Santiago KAA, Wong WC, Goh YK, Tey SH, Ting ASY. Pathogenicity of monokaryotic and dikaryotic mycelia of Ganoderma boninense revealed via LC-MS-based metabolomics. Sci Rep 2024; 14:5330. [PMID: 38438519 PMCID: PMC10912678 DOI: 10.1038/s41598-024-56129-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/01/2024] [Indexed: 03/06/2024] Open
Abstract
This study compared the pathogenicity of monokaryotic (monokaryon) and dikaryotic (dikaryon) mycelia of the oil palm pathogen Ganoderma boninense via metabolomics approach. Ethyl acetate crude extracts of monokaryon and dikaryon were analysed by liquid chromatography quadrupole/time-of-flight-mass spectrometry (LC-Q/TOF-MS) coupled with multivariate data analysis using MetaboAnalyst. The mummichog algorithm was also used to identify the functional activities of monokaryon and dikaryon without a priori identification of all their secondary metabolites. Results revealed that monokaryon produced lesser fungal metabolites than dikaryon, suggesting that monokaryon had a lower possibility of inducing plant infection. These findings were further supported by the identified functional activities. Monokaryon exhibits tyrosine, phenylalanine, and tryptophan metabolism, which are important for fungal growth and development and to produce toxin precursors. In contrast, dikaryon exhibits the metabolism of cysteine and methionine, arginine and proline, and phenylalanine, which are important for fungal growth, development, virulence, and pathogenicity. As such, monokaryon is rendered non-pathogenic as it produces growth metabolites and toxin precursors, whereas dikaryon is pathogenic as it produces metabolites that are involved in fungal growth and pathogenicity. The LC-MS-based metabolomics approach contributes significantly to our understanding of the pathogenesis of Ganoderma boninense, which is essential for disease management in oil palm plantations.
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Affiliation(s)
- Krystle Angelique A Santiago
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Wei Chee Wong
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - You Keng Goh
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Seng Heng Tey
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Adeline Su Yien Ting
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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Fall F, Mamede L, Vast M, De Tullio P, Hayette MP, Michels PAM, Frédérich M, Govaerts B, Quetin-Leclercq J. First comprehensive untargeted metabolomics study of suramin-treated Trypanosoma brucei: an integrated data analysis workflow from multifactor data modelling to functional analysis. Metabolomics 2024; 20:25. [PMID: 38393408 DOI: 10.1007/s11306-024-02094-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/26/2024] [Indexed: 02/25/2024]
Abstract
INTRODUCTION Human African trypanosomiasis, commonly known as sleeping sickness, is a vector-borne parasitic disease prevalent in sub-Saharan Africa and transmitted by the tsetse fly. Suramin, a medication with a long history of clinical use, has demonstrated varied modes of action against Trypanosoma brucei. This study employs a comprehensive workflow to investigate the metabolic effects of suramin on T. brucei, utilizing a multimodal metabolomics approach. OBJECTIVES The primary aim of this study is to comprehensively analyze the metabolic impact of suramin on T. brucei using a combined liquid chromatography-mass spectrometry (LC-MS) and nuclear magnetic resonance spectroscopy (NMR) approach. Statistical analyses, encompassing multivariate analysis and pathway enrichment analysis, are applied to elucidate significant variations and metabolic changes resulting from suramin treatment. METHODS A detailed methodology involving the integration of high-resolution data from LC-MS and NMR techniques is presented. The study conducts a thorough analysis of metabolite profiles in both suramin-treated and control T. brucei brucei samples. Statistical techniques, including ANOVA-simultaneous component analysis (ASCA), principal component analysis (PCA), ANOVA 2 analysis, and bootstrap tests, are employed to discern the effects of suramin treatment on the metabolomics outcomes. RESULTS Our investigation reveals substantial differences in metabolic profiles between the control and suramin-treated groups. ASCA and PCA analysis confirm distinct separation between these groups in both MS-negative and NMR analyses. Furthermore, ANOVA 2 analysis and bootstrap tests confirmed the significance of treatment, time, and interaction effects on the metabolomics outcomes. Functional analysis of the data from LC-MS highlighted the impact of treatment on amino-acid, and amino-sugar and nucleotide-sugar metabolism, while time effects were observed on carbon intermediary metabolism (notably glycolysis and di- and tricarboxylic acids of the succinate production pathway and tricarboxylic acid (TCA) cycle). CONCLUSION Through the integration of LC-MS and NMR techniques coupled with advanced statistical analyses, this study identifies distinctive metabolic signatures and pathways associated with suramin treatment in T. brucei. These findings contribute to a deeper understanding of the pharmacological impact of suramin and have the potential to inform the development of more efficacious therapeutic strategies against African trypanosomiasis.
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Affiliation(s)
- Fanta Fall
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Avenue E. Mounier, B1 72.03, 1200, Brussels, Belgium.
| | - Lucia Mamede
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Liège, Belgium
| | - Madeline Vast
- Institute of Statistics, Biostatistics and Actuarial Sciences (ISBA/LIDAM), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Pascal De Tullio
- Clinical Metabolomics Group (CliMe), Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Liège, Belgium
| | - Marie-Pierre Hayette
- Department of Clinical Microbiology, Centre Hospitalier Universitaire de Liège, Domaine Universitaire, 4000, Liège, Belgium
| | - Paul A M Michels
- School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland
| | - Michel Frédérich
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Liège, Belgium
| | - Bernadette Govaerts
- Institute of Statistics, Biostatistics and Actuarial Sciences (ISBA/LIDAM), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Joëlle Quetin-Leclercq
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Avenue E. Mounier, B1 72.03, 1200, Brussels, Belgium
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Ferrell M, Wang Z, Anderson JT, Li XS, Witkowski M, DiDonato JA, Hilser JR, Hartiala JA, Haghikia A, Cajka T, Fiehn O, Sangwan N, Demuth I, König M, Steinhagen-Thiessen E, Landmesser U, Tang WHW, Allayee H, Hazen SL. A terminal metabolite of niacin promotes vascular inflammation and contributes to cardiovascular disease risk. Nat Med 2024; 30:424-434. [PMID: 38374343 DOI: 10.1038/s41591-023-02793-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 12/22/2023] [Indexed: 02/21/2024]
Abstract
Despite intensive preventive cardiovascular disease (CVD) efforts, substantial residual CVD risk remains even for individuals receiving all guideline-recommended interventions. Niacin is an essential micronutrient fortified in food staples, but its role in CVD is not well understood. In this study, untargeted metabolomics analysis of fasting plasma from stable cardiac patients in a prospective discovery cohort (n = 1,162 total, n = 422 females) suggested that niacin metabolism was associated with incident major adverse cardiovascular events (MACE). Serum levels of the terminal metabolites of excess niacin, N1-methyl-2-pyridone-5-carboxamide (2PY) and N1-methyl-4-pyridone-3-carboxamide (4PY), were associated with increased 3-year MACE risk in two validation cohorts (US n = 2,331 total, n = 774 females; European n = 832 total, n = 249 females) (adjusted hazard ratio (HR) (95% confidence interval) for 2PY: 1.64 (1.10-2.42) and 2.02 (1.29-3.18), respectively; for 4PY: 1.89 (1.26-2.84) and 1.99 (1.26-3.14), respectively). Phenome-wide association analysis of the genetic variant rs10496731, which was significantly associated with both 2PY and 4PY levels, revealed an association of this variant with levels of soluble vascular adhesion molecule 1 (sVCAM-1). Further meta-analysis confirmed association of rs10496731 with sVCAM-1 (n = 106,000 total, n = 53,075 females, P = 3.6 × 10-18). Moreover, sVCAM-1 levels were significantly correlated with both 2PY and 4PY in a validation cohort (n = 974 total, n = 333 females) (2PY: rho = 0.13, P = 7.7 × 10-5; 4PY: rho = 0.18, P = 1.1 × 10-8). Lastly, treatment with physiological levels of 4PY, but not its structural isomer 2PY, induced expression of VCAM-1 and leukocyte adherence to vascular endothelium in mice. Collectively, these results indicate that the terminal breakdown products of excess niacin, 2PY and 4PY, are both associated with residual CVD risk. They also suggest an inflammation-dependent mechanism underlying the clinical association between 4PY and MACE.
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Affiliation(s)
- Marc Ferrell
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Systems Biology and Bioinformatics Program, Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Zeneng Wang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - James T Anderson
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xinmin S Li
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Marco Witkowski
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiology, Angiology and Intensive Care, Deutsches Herzzentrum der Charité, Campus Benjamin Franklin, Berlin, Germany
| | - Joseph A DiDonato
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - James R Hilser
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jaana A Hartiala
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Arash Haghikia
- Department of Cardiology, Angiology and Intensive Care, Deutsches Herzzentrum der Charité, Campus Benjamin Franklin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Friede Springer Cardiovascular Prevention Center at Charité, Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tomas Cajka
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA
| | - Naseer Sangwan
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ilja Demuth
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Maximilian König
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Ulf Landmesser
- Department of Cardiology, Angiology and Intensive Care, Deutsches Herzzentrum der Charité, Campus Benjamin Franklin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Friede Springer Cardiovascular Prevention Center at Charité, Berlin, Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - W H Wilson Tang
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Hooman Allayee
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stanley L Hazen
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Department of Cardiovascular Medicine, Heart, Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH, USA.
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Martinez-Morata I, Wu H, Galvez-Fernandez M, Ilievski V, Bottiglieri T, Niedzwiecki MM, Goldsmith J, Jones DP, Kioumourtzoglou MA, Pierce B, Walker DI, Gamble MV. Metabolomic Effects of Folic Acid Supplementation in Adults: Evidence from the FACT Trial. J Nutr 2024; 154:670-679. [PMID: 38092151 PMCID: PMC10900167 DOI: 10.1016/j.tjnut.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/31/2023] Open
Abstract
BACKGROUND Folic acid (FA) is the oxidized form of folate found in supplements and FA-fortified foods. Most FA is reduced by dihydrofolate reductase to 5-methyltetrahydrofolate (5mTHF); the latter is the form of folate naturally found in foods. Ingestion of FA increases the plasma levels of both 5mTHF and unmetabolized FA (UMFA). Limited information is available on the downstream metabolic effects of FA supplementation, including potential effects associated with UMFA. OBJECTIVE We aimed to assess the metabolic effects of FA-supplementation, and the associations of plasma 5mTHF and UMFA with the metabolome in FA-naïve Bangladeshi adults. METHODS Sixty participants were selected from the Folic Acid and Creatine Trial; half received 800 μg FA/day for 12 weeks and half placebo. Plasma metabolome profiles were measured by high-resolution mass spectrometry, including 170 identified metabolites and 26,541 metabolic features. Penalized regression methods were used to assess the associations of targeted metabolites with FA-supplementation, plasma 5mTHF, and plasma UMFA. Pathway analyses were conducted using Mummichog. RESULTS In penalized models of identified metabolites, FA-supplementation was associated with higher choline. Changes in 5mTHF concentrations were positively associated with metabolites involved in amino acid metabolism (5-hydroxyindoleacetic acid, acetylmethionine, creatinine, guanidinoacetate, hydroxyproline/n-acetylalanine) and 2 fatty acids (docosahexaenoic acid and linoleic acid). Changes in 5mTHF concentrations were negatively associated with acetylglutamate, acetyllysine, carnitine, propionyl carnitine, cinnamic acid, homogentisate, arachidonic acid, and nicotine. UMFA concentrations were associated with lower levels of arachidonic acid. Together, metabolites selected across all models were related to lipids, aromatic amino acid metabolism, and the urea cycle. Analyses of nontargeted metabolic features identified additional pathways associated with FA supplementation. CONCLUSION In addition to the recapitulation of several expected metabolic changes associated with 5mTHF, we observed additional metabolites/pathways associated with FA-supplementation and UMFA. Further studies are needed to confirm these associations and assess their potential implications for human health. TRIAL REGISTRATION NUMBER This trial was registered at https://clinicaltrials.gov as NCT01050556.
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Affiliation(s)
- Irene Martinez-Morata
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Haotian Wu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Marta Galvez-Fernandez
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Vesna Ilievski
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Teodoro Bottiglieri
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, United States
| | - Megan M Niedzwiecki
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jeff Goldsmith
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Dean P Jones
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States; Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
| | - Marianthi-Anna Kioumourtzoglou
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Brandon Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, IL, United States; Department of Human Genetics, University of Chicago, Chicago, IL, United States; Comprehensive Cancer Center, University of Chicago, Chicago, IL, United States
| | - Douglas I Walker
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Mary V Gamble
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States.
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Costello E, Goodrich JA, Patterson WB, Walker DI, Chen J(C, Baumert BO, Rock S, Gilliland FD, Goran MI, Chen Z, Alderete TL, Conti DV, Chatzi L. Proteomic and Metabolomic Signatures of Diet Quality in Young Adults. Nutrients 2024; 16:429. [PMID: 38337712 PMCID: PMC10857402 DOI: 10.3390/nu16030429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
The assessment of "omics" signatures may contribute to personalized medicine and precision nutrition. However, the existing literature is still limited in the homogeneity of participants' characteristics and in limited assessments of integrated omics layers. Our objective was to use post-prandial metabolomics and fasting proteomics to identify biological pathways and functions associated with diet quality in a population of primarily Hispanic young adults. We conducted protein and metabolite-wide association studies and functional pathway analyses to assess the relationships between a priori diet indices, Healthy Eating Index-2015 (HEI) and Dietary Approaches to Stop Hypertension (DASH) diets, and proteins (n = 346) and untargeted metabolites (n = 23,173), using data from the MetaAIR study (n = 154, 61% Hispanic). Analyses were performed for each diet quality index separately, adjusting for demographics and BMI. Five proteins (ACY1, ADH4, AGXT, GSTA1, F7) and six metabolites (undecylenic acid, betaine, hyodeoxycholic acid, stearidonic acid, iprovalicarb, pyracarbolid) were associated with both diets (p < 0.05), though none were significant after adjustment for multiple comparisons. Overlapping proteins are involved in lipid and amino acid metabolism and in hemostasis, while overlapping metabolites include amino acid derivatives, bile acids, fatty acids, and pesticides. Enriched biological pathways were involved in macronutrient metabolism, immune function, and oxidative stress. These findings in young Hispanic adults contribute to efforts to develop precision nutrition and medicine for diverse populations.
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Affiliation(s)
- Elizabeth Costello
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Jesse A. Goodrich
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - William B. Patterson
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA; (W.B.P.); (T.L.A.)
| | - Douglas I. Walker
- Gangarosa Department of Environmental Health, Emory University, Atlanta, GA 30329, USA;
| | - Jiawen (Carmen) Chen
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Brittney O. Baumert
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Sarah Rock
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Frank D. Gilliland
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Michael I. Goran
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
- Department of Pediatrics, Children’s Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA
| | - Zhanghua Chen
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Tanya L. Alderete
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA; (W.B.P.); (T.L.A.)
| | - David V. Conti
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
| | - Lida Chatzi
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA; (J.A.G.); (J.C.); (B.O.B.); (S.R.); (F.D.G.); (M.I.G.); (Z.C.); (D.V.C.); (L.C.)
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Xu R, Zhang H, Crowder MW, Zhu J. Multiple and Optimal Screening Subset: a method selecting global characteristic congeners for robust foodomics analysis. Brief Bioinform 2024; 25:bbae046. [PMID: 38385875 PMCID: PMC10883140 DOI: 10.1093/bib/bbae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/04/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
Metabolomics and foodomics shed light on the molecular processes within living organisms and the complex food composition by leveraging sophisticated analytical techniques to systematically analyze the vast array of molecular features. The traditional feature-picking method often results in arbitrary selections of the model, feature ranking, and cut-off, which may lead to suboptimal results. Thus, a Multiple and Optimal Screening Subset (MOSS) approach was developed in this study to achieve a balance between a minimal number of predictors and high predictive accuracy during statistical model setup. The MOSS approach compares five commonly used models in the context of food matrix analysis, specifically bourbons. These models include Student's t-test, receiver operating characteristic curve, partial least squares-discriminant analysis (PLS-DA), random forests, and support vector machines. The approach employs cross-validation to identify promising subset feature candidates that contribute to food characteristic classification. It then determines the optimal subset size by comparing it to the corresponding top-ranked features. Finally, it selects the optimal feature subset by traversing all possible feature candidate combinations. By utilizing MOSS approach to analyze 1406 mass spectral features from a collection of 122 bourbon samples, we were able to generate a subset of features for bourbon age prediction with 88% accuracy. Additionally, MOSS increased the area under the curve performance of sweetness prediction to 0.898 with only four predictors compared with the top-ranked four features at 0.681 based on the PLS-DA model. Overall, we demonstrated that MOSS provides an efficient and effective approach for selecting optimal features compared with other frequently utilized methods.
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Affiliation(s)
- Rui Xu
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, Ohio, USA 43210
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA 43210
| | - Huan Zhang
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, Ohio, USA 43210
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA 43210
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA 45056
| | - Jiangjiang Zhu
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, Ohio, USA 43210
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA 43210
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50
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Vazquez-Medina A, Rodriguez-Trujillo N, Ayuso-Rodriguez K, Marini-Martinez F, Angeli-Morales R, Caussade-Silvestrini G, Godoy-Vitorino F, Chorna N. Exploring the interplay between running exercises, microbial diversity, and tryptophan metabolism along the microbiota-gut-brain axis. Front Microbiol 2024; 15:1326584. [PMID: 38318337 PMCID: PMC10838991 DOI: 10.3389/fmicb.2024.1326584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
The emergent recognition of the gut-brain axis connection has shed light on the role of the microbiota in modulating the gut-brain axis's functions. Several microbial metabolites, such as serotonin, kynurenine, tryptamine, indole, and their derivatives originating from tryptophan metabolism have been implicated in influencing this axis. In our study, we aimed to investigate the impact of running exercises on microbial tryptophan metabolism using a mouse model. We conducted a multi-omics analysis to obtain a comprehensive insight into the changes in tryptophan metabolism along the microbiota-gut-brain axis induced by running exercises. The analyses integrated multiple components, such as tryptophan changes and metabolite levels in the gut, blood, hippocampus, and brainstem. Fecal microbiota analysis aimed to examine the composition and diversity of the gut microbiota, and taxon-function analysis explored the associations between specific microbial taxa and functional activities in tryptophan metabolism. Our findings revealed significant alterations in tryptophan metabolism across multiple sites, including the gut, blood, hippocampus, and brainstem. The outcomes indicate a shift in microbiota diversity and tryptophan metabolizing capabilities within the running group, linked to increased tryptophan transportation to the hippocampus and brainstem through circulation. Moreover, the symbiotic association between Romboutsia and A. muciniphila indicated their potential contribution to modifying the gut microenvironment and influencing tryptophan transport to the hippocampus and brainstem. These findings have potential applications for developing microbiota-based approaches in the context of exercise for neurological diseases, especially on mental health and overall well-being.
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Affiliation(s)
- Alejandra Vazquez-Medina
- Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | - Nicole Rodriguez-Trujillo
- Nutrition and Dietetics Program, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
| | - Kiara Ayuso-Rodriguez
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
| | | | - Roberto Angeli-Morales
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
| | | | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | - Nataliya Chorna
- Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
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