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Liu X, Peng T, Xu M, Lin S, Hu B, Chu T, Liu B, Xu Y, Ding W, Li L, Cao C, Wu P. Spatial multi-omics: deciphering technological landscape of integration of multi-omics and its applications. J Hematol Oncol 2024; 17:72. [PMID: 39182134 PMCID: PMC11344930 DOI: 10.1186/s13045-024-01596-9] [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: 05/22/2024] [Accepted: 08/09/2024] [Indexed: 08/27/2024] Open
Abstract
The emergence of spatial multi-omics has helped address the limitations of single-cell sequencing, which often leads to the loss of spatial context among cell populations. Integrated analysis of the genome, transcriptome, proteome, metabolome, and epigenome has enhanced our understanding of cell biology and the molecular basis of human diseases. Moreover, this approach offers profound insights into the interactions between intracellular and intercellular molecular mechanisms involved in the development, physiology, and pathogenesis of human diseases. In this comprehensive review, we examine current advancements in multi-omics technologies, focusing on their evolution and refinement over the past decade, including improvements in throughput and resolution, modality integration, and accuracy. We also discuss the pivotal contributions of spatial multi-omics in revealing spatial heterogeneity, constructing detailed spatial atlases, deciphering spatial crosstalk in tumor immunology, and advancing translational research and cancer therapy through precise spatial mapping.
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Affiliation(s)
- Xiaojie Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ting Peng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Miaochun Xu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shitong Lin
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bai Hu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tian Chu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Binghan Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yashi Xu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wencheng Ding
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Li Li
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Canhui Cao
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Peng Wu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Downie CG, Highland HM, Alotaibi M, Welch BM, Howard AG, Cheng S, Miller N, Jain M, Kaplan RC, Lilly AG, Long T, Sofer T, Thyagarajan B, Yu B, North KE, Avery CL. Genome-wide association study reveals shared and distinct genetic architecture underlying fatty acid and bioactive oxylipin metabolites in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.21.24307719. [PMID: 38826448 PMCID: PMC11142272 DOI: 10.1101/2024.05.21.24307719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Bioactive fatty acid-derived oxylipin molecules play key roles in mediating inflammation and oxidative stress, which underlie many chronic diseases. Circulating levels of fatty acids and oxylipins are influenced by both environmental and genetic factors; characterizing the genetic architecture of bioactive lipids could yield new insights into underlying biological pathways. Thus, we performed a genome wide association study (GWAS) of n=81 fatty acids and oxylipins in n=11,584 Hispanic Community Health Study/Study of Latinos (HCHS/SOL) participants with genetic and lipidomic data measured at study baseline (58.6% female, mean age = 46.1 years, standard deviation = 13.8 years). Additionally, given the effects of central obesity on inflammation, we examined interactions with waist circumference using two-degree-of-freedom joint tests. Heritability estimates ranged from 0% to 47.9%, and 48 of the 81oxylipins and fatty acids were significantly heritable. Moreover, 40 (49.4%) of the 81 oxylipins and fatty acids had at least one genome-wide significant (p< 6.94E-11) variant resulting in 19 independent genetic loci involved in fatty acid and oxylipin synthesis, as well as downstream pathways. Four loci (lead variant minor allele frequency [MAF] range: 0.08-0.50), including the desaturase-encoding FADS and the OATP1B1 transporter protein-encoding SLCO1B1, exhibited associations with four or more fatty acids and oxylipins. The majority of the 15 remaining loci (87.5%) (lead variant MAF range = 0.03-0.45, mean = 0.23) were only associated with one oxylipin or fatty acid, demonstrating evidence of distinct genetic effects. Finally, while most loci identified in two-degree-of-freedom tests were previously identified in our main effects analyses, we also identified an additional rare variant (MAF = 0.002) near CARS2, a locus previously implicated in inflammation. Our analyses revealed shared and distinct genetic architecture underlying fatty acids and oxylipins, providing insights into genetic factors and motivating future multi-omics work to characterize these compounds and elucidate their roles in disease pathways.
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Affiliation(s)
- Carolina G Downie
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Mona Alotaibi
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, San Diego, San Diego, CA
| | - Barrett M Welch
- School of Public Health, University of Nevada, Reno, Reno, NV
| | - Annie Green Howard
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Mohit Jain
- Sapient Bioanalytics, San Diego, CA
- Departments of Medicine and Pharmacology, University of California, San Diego, San Diego, CA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY; Public Health Sciences Division, Fred Hutchison Cancer Center, Seattle, WA
| | - Adam G Lilly
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Tao Long
- Sapient Bioanalytics, San Diego, CA
| | - Tamar Sofer
- CardioVascular Institute (CVI), Beth Israel Deaconess Medical Center, Boston, MA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical Center, Minneapolis, MN
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health, Houston, TX
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
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3
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Joshi AD, Rahnavard A, Kachroo P, Mendez KM, Lawrence W, Julián-Serrano S, Hua X, Fuller H, Sinnott-Armstrong N, Tabung FK, Shutta KH, Raffield LM, Darst BF. An epidemiological introduction to human metabolomic investigations. Trends Endocrinol Metab 2023; 34:505-525. [PMID: 37468430 PMCID: PMC10527234 DOI: 10.1016/j.tem.2023.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/17/2023] [Accepted: 06/19/2023] [Indexed: 07/21/2023]
Abstract
Metabolomics holds great promise for uncovering insights around biological processes impacting disease in human epidemiological studies. Metabolites can be measured across biological samples, including plasma, serum, saliva, urine, stool, and whole organs and tissues, offering a means to characterize metabolic processes relevant to disease etiology and traits of interest. Metabolomic epidemiology studies face unique challenges, such as identifying metabolites from targeted and untargeted assays, defining standards for quality control, harmonizing results across platforms that often capture different metabolites, and developing statistical methods for high-dimensional and correlated metabolomic data. In this review, we introduce metabolomic epidemiology to the broader scientific community, discuss opportunities and challenges presented by these studies, and highlight emerging innovations that hold promise to uncover new biological insights.
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Affiliation(s)
- Amit D Joshi
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ali Rahnavard
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin M Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wayne Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sachelly Julián-Serrano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Public Health, University of Massachusetts Lowell, Lowell, MA, USA
| | - Xinwei Hua
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Department of Cardiology, Peking University Third Hospital, Beijing, China
| | - Harriett Fuller
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nasa Sinnott-Armstrong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Fred K Tabung
- The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH, USA
| | - Katherine H Shutta
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Burcu F Darst
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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Smith CJ, Sinnott-Armstrong N, Cichońska A, Julkunen H, Fauman EB, Würtz P, Pritchard JK. Integrative analysis of metabolite GWAS illuminates the molecular basis of pleiotropy and genetic correlation. eLife 2022; 11:e79348. [PMID: 36073519 PMCID: PMC9536840 DOI: 10.7554/elife.79348] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 09/06/2022] [Indexed: 11/15/2022] Open
Abstract
Pleiotropy and genetic correlation are widespread features in genome-wide association studies (GWAS), but they are often difficult to interpret at the molecular level. Here, we perform GWAS of 16 metabolites clustered at the intersection of amino acid catabolism, glycolysis, and ketone body metabolism in a subset of UK Biobank. We utilize the well-documented biochemistry jointly impacting these metabolites to analyze pleiotropic effects in the context of their pathways. Among the 213 lead GWAS hits, we find a strong enrichment for genes encoding pathway-relevant enzymes and transporters. We demonstrate that the effect directions of variants acting on biology between metabolite pairs often contrast with those of upstream or downstream variants as well as the polygenic background. Thus, we find that these outlier variants often reflect biology local to the traits. Finally, we explore the implications for interpreting disease GWAS, underscoring the potential of unifying biochemistry with dense metabolomics data to understand the molecular basis of pleiotropy in complex traits and diseases.
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Affiliation(s)
- Courtney J Smith
- Department of Genetics, Stanford University School of MedicineStanfordUnited States
| | - Nasa Sinnott-Armstrong
- Department of Genetics, Stanford University School of MedicineStanfordUnited States
- Herbold Computational Biology Program, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | | | | | - Eric B Fauman
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and MedicalCambridgeUnited States
| | | | - Jonathan K Pritchard
- Department of Genetics, Stanford University School of MedicineStanfordUnited States
- Department of Biology, Stanford UniversityStanfordUnited States
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5
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Evidence of a genetically driven metabolomic signature in actively inflamed Crohn's disease. Sci Rep 2022; 12:14101. [PMID: 35982195 PMCID: PMC9388636 DOI: 10.1038/s41598-022-18178-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/08/2022] [Indexed: 11/09/2022] Open
Abstract
Crohn's disease (CD) is characterised by chronic inflammation. We aimed to identify a relationship between plasma inflammatory metabolomic signature and genomic data in CD using blood plasma metabolic profiles. Proton NMR spectroscopy were achieved for 228 paediatric CD patients. Regression (OPLS) modelling and machine learning (ML) approaches were independently applied to establish the metabolic inflammatory signature, which was correlated against gene-level pathogenicity scores generated for all patients and functional enrichment was analysed. OPLS modelling of metabolomic spectra from unfasted patients revealed distinctive shifts in plasma metabolites corresponding to regions of the spectrum assigned to N-acetyl glycoprotein, glycerol and phenylalanine that were highly correlated (R2 = 0.62) with C-reactive protein levels. The same metabolomic signature was independently identified using ML to predict patient inflammation status. Correlation of the individual peaks comprising this metabolomic signature of inflammation with pathogenic burden across 15,854 unselected genes identified significant enrichment for genes functioning within 'intrinsic component of membrane' (p = 0.003) and 'inflammatory bowel disease (IBD)' (p = 0.003). The seven genes contributing IBD enrichment are critical regulators of pro-inflammatory signaling. Overall, a metabolomic signature of inflammation can be detected from blood plasma in CD. This signal is correlated with pathogenic mutation in pro-inflammatory immune response genes.
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Ali S, Nedvědová Š, Badshah G, Afridi MS, Abdullah, Dutra LM, Ali U, Faria SG, Soares FL, Rahman RU, Cançado FA, Aoyanagi MM, Freire LG, Santos AD, Barison A, Oliveira CA. NMR spectroscopy spotlighting immunogenicity induced by COVID-19 vaccination to mitigate future health concerns. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:199-214. [PMID: 36032416 PMCID: PMC9393187 DOI: 10.1016/j.crimmu.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
In this review, the disease and immunogenicity affected by COVID-19 vaccination at the metabolic level are described considering the use of nuclear magnetic resonance (NMR) spectroscopy for the analysis of different biological samples. Consistently, we explain how different biomarkers can be examined in the saliva, blood plasma/serum, bronchoalveolar-lavage fluid (BALF), semen, feces, urine, cerebrospinal fluid (CSF) and breast milk. For example, the proposed approach for the given samples can allow one to detect molecular biomarkers that can be relevant to disease and/or vaccine interference in a system metabolome. The analysis of the given biomaterials by NMR often produces complex chemical data which can be elucidated by multivariate statistical tools, such as PCA and PLS-DA/OPLS-DA methods. Moreover, this approach may aid to improve strategies that can be helpful in disease control and treatment management in the future. NMR analysis of various bio-samples can explore disease course and vaccine interaction. Immunogenicity and reactogenicity caused by COVID-19 vaccination can be studied by NMR. Vaccine interaction alters metabolic pathway(s) at a certain stage, and this mechanism can be probed at the metabolic level.
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Sönmez Flitman R, Khalili B, Kutalik Z, Rueedi R, Brümmer A, Bergmann S. Untargeted Metabolome- and Transcriptome-Wide Association Study Suggests Causal Genes Modulating Metabolite Concentrations in Urine. J Proteome Res 2021; 20:5103-5114. [PMID: 34699229 PMCID: PMC9286311 DOI: 10.1021/acs.jproteome.1c00585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
Gene products can
affect the concentrations of small molecules
(aka “metabolites”), and conversely, some metabolites
can modulate the concentrations of gene transcripts. While many specific
instances of this interplay have been revealed, a global approach
to systematically uncover human gene-metabolite interactions is still
lacking. We performed a metabolome- and transcriptome-wide association
study to identify genes influencing the human metabolome using untargeted
metabolome features, extracted from 1H nuclear magnetic
resonance spectroscopy (NMR) of urine samples, and gene expression
levels, quantified from RNA-Seq of lymphoblastoid cell lines (LCL)
from 555 healthy individuals. We identified 20 study-wide significant
associations corresponding to 15 genes, of which 5 associations (with
2 genes) were confirmed with follow-up NMR data. Using metabomatching,
we identified the metabolites corresponding to metabolome features
associated with the genes, namely, N-acetylated compounds with ALMS1 and trimethylamine (TMA) with HPS1. Finally, Mendelian randomization analysis supported a potential
causal link between the expression of genes in both the ALMS1- and HPS1-loci and their associated metabolite
concentrations. In the case of HPS1, we additionally
observed that TMA concentration likely exhibits a reverse causal effect
on HPS1 expression levels, indicating a negative
feedback loop. Our study highlights how the integration of metabolomics,
gene expression, and genetic data can pinpoint causal genes modulating
metabolite concentrations.
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Affiliation(s)
- Reyhan Sönmez Flitman
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Bita Khalili
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Zoltan Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,University Center for Primary Care and Public Health, University of Lausanne, Lausanne 1010, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Anneke Brümmer
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.,Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.,Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7700, South Africa
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Gupta J, Care A, Goodfellow L, Alfirevic Z, Lian LY, Müller-Myhsok B, Alfirevic A, Phelan M. Metabolic profiling of maternal serum of women at high-risk of spontaneous preterm birth using NMR and MGWAS approach. Biosci Rep 2021; 41:BSR20210759. [PMID: 34402867 PMCID: PMC8415214 DOI: 10.1042/bsr20210759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/28/2021] [Accepted: 08/17/2021] [Indexed: 12/26/2022] Open
Abstract
Preterm birth (PTB) is a leading global cause of infant mortality. Risk factors include genetics, lifestyle choices and infection. Understanding the mechanism of PTB could aid the development of novel approaches to prevent PTB. This study aimed to investigate the metabolic biomarkers of PTB in early pregnancy and the association of significant metabolites with participant genotypes. Maternal sera collected at 16 and 20 weeks of gestation, from women who previously experienced PTB (high-risk) and women who did not (low-risk controls), were analysed using 1H nuclear magnetic resonance (NMR) metabolomics and genome-wide screening microarray. ANOVA and probabilistic neural network (PNN) modelling were performed on the spectral bins. Metabolomics genome-wide association (MGWAS) of the spectral bins and genotype data from the same participants was applied to determine potential metabolite-gene pathways. Phenylalanine, acetate and lactate metabolite differences between PTB cases and controls were obtained by ANOVA and PNN showed strong prediction at week 20 (AUC = 0.89). MGWAS identified several metabolite bins with strong genetic associations. Cis-eQTL analysis highlighted TRAF1 (involved in the inflammatory pathway) local to a non-coding SNP associated with lactate at week 20 of gestation. MGWAS of a well-defined cohort of participants highlighted a lactate-TRAF1 relationship that could potentially contribute to PTB.
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Affiliation(s)
- Juhi K. Gupta
- Wolfson Centre for Personalised Medicine, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3GL, UK
- Harris-Wellbeing Research Centre, University Department, Liverpool Women’s Hospital, Liverpool, L8 7SS, UK
| | - Angharad Care
- Harris-Wellbeing Research Centre, University Department, Liverpool Women’s Hospital, Liverpool, L8 7SS, UK
| | - Laura Goodfellow
- Harris-Wellbeing Research Centre, University Department, Liverpool Women’s Hospital, Liverpool, L8 7SS, UK
| | - Zarko Alfirevic
- Harris-Wellbeing Research Centre, University Department, Liverpool Women’s Hospital, Liverpool, L8 7SS, UK
| | - Lu-Yun Lian
- NMR Centre for Structural Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Bertram Müller-Myhsok
- Wolfson Centre for Personalised Medicine, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3GL, UK
- Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Ana Alfirevic
- Wolfson Centre for Personalised Medicine, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3GL, UK
- Harris-Wellbeing Research Centre, University Department, Liverpool Women’s Hospital, Liverpool, L8 7SS, UK
| | - Marie M. Phelan
- NMR Centre for Structural Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
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9
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Edison AS, Colonna M, Gouveia GJ, Holderman NR, Judge MT, Shen X, Zhang S. NMR: Unique Strengths That Enhance Modern Metabolomics Research. Anal Chem 2020; 93:478-499. [DOI: 10.1021/acs.analchem.0c04414] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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10
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Linke V, Overmyer KA, Miller IJ, Brademan DR, Hutchins PD, Trujillo EA, Reddy TR, Russell JD, Cushing EM, Schueler KL, Stapleton DS, Rabaglia ME, Keller MP, Gatti DM, Keele GR, Pham D, Broman KW, Churchill GA, Attie AD, Coon JJ. A large-scale genome-lipid association map guides lipid identification. Nat Metab 2020; 2:1149-1162. [PMID: 32958938 PMCID: PMC7572687 DOI: 10.1038/s42255-020-00278-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 08/11/2020] [Indexed: 12/13/2022]
Abstract
Despite the crucial roles of lipids in metabolism, we are still at the early stages of comprehensively annotating lipid species and their genetic basis. Mass spectrometry-based discovery lipidomics offers the potential to globally survey lipids and their relative abundances in various biological samples. To discover the genetics of lipid features obtained through high-resolution liquid chromatography-tandem mass spectrometry, we analysed liver and plasma from 384 diversity outbred mice, and quantified 3,283 molecular features. These features were mapped to 5,622 lipid quantitative trait loci and compiled into a public web resource termed LipidGenie. The data are cross-referenced to the human genome and offer a bridge between genetic associations in humans and mice. Harnessing this resource, we used genome-lipid association data as an additional aid to identify a number of lipids, for example gangliosides through their association with B4galnt1, and found evidence for a group of sex-specific phosphatidylcholines through their shared locus. Finally, LipidGenie's ability to query either mass or gene-centric terms suggests acyl-chain-specific functions for proteins of the ABHD family.
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Affiliation(s)
- Vanessa Linke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Katherine A Overmyer
- Morgridge Institute for Research, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ian J Miller
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Dain R Brademan
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Paul D Hutchins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Edna A Trujillo
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Thiru R Reddy
- Morgridge Institute for Research, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Emily M Cushing
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Donald S Stapleton
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Mary E Rabaglia
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Duy Pham
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Karl W Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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11
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Khalili B, Tomasoni M, Mattei M, Mallol Parera R, Sonmez R, Krefl D, Rueedi R, Bergmann S. Automated Analysis of Large-Scale NMR Data Generates Metabolomic Signatures and Links Them to Candidate Metabolites. J Proteome Res 2019; 18:3360-3368. [PMID: 31318216 DOI: 10.1021/acs.jproteome.9b00295] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Identification of metabolites in large-scale 1H NMR data from human biofluids remains challenging due to the complexity of the spectra and their sensitivity to pH and ionic concentrations. In this work, we tested the capacity of three analysis tools to extract metabolite signatures from 968 NMR profiles of human urine samples. Specifically, we studied sets of covarying features derived from principal component analysis (PCA), the iterative signature algorithm (ISA), and averaged correlation profiles (ACP), a new method we devised inspired by the STOCSY approach. We used our previously developed metabomatching method to match the sets generated by these algorithms to NMR spectra of individual metabolites available in public databases. On the basis of the number and quality of the matches, we concluded that ISA and ACP can robustly identify ten and nine metabolites, respectively, half of which were shared, while PCA did not produce any signatures with robust matches.
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Affiliation(s)
- Bita Khalili
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Mattia Tomasoni
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Mirjam Mattei
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Roger Mallol Parera
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Reyhan Sonmez
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Daniel Krefl
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Rico Rueedi
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Sven Bergmann
- Department of Computational Biology , University of Lausanne , 1015 Lausanne , Switzerland.,Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland.,Department of Integrative Biomedical Sciences , University of Cape Town , Cape Town 7700 , South Africa
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12
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Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Günther UL, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JTM, Peluso A, Piras ME, Pireddu L, Reed MAC, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C. PhenoMeNal: processing and analysis of metabolomics data in the cloud. Gigascience 2019; 8:giy149. [PMID: 30535405 PMCID: PMC6377398 DOI: 10.1093/gigascience/giy149] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/19/2018] [Accepted: 11/20/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution. FINDINGS PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm. CONCLUSIONS PhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and 'omics research domains.
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Affiliation(s)
- Kristian Peters
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
| | - James Bradbury
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marco Capuccini
- Division of Scientific Computing, Department of Information Technology, Uppsala University, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Spain
| | - Pedro de Atauri
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Spain
| | - Timothy M D Ebbels
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Carles Foguet
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Spain
| | - Robert Glen
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB21EW, United Kingdom
| | - Alejandra Gonzalez-Beltran
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
| | - Ulrich L Günther
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Evangelos Handakas
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Thomas Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, 2333 CC, The Netherlands
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Stephanie Herman
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, Sweden
| | | | - Massimiliano Izzo
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
| | - Daniel Jacob
- INRA, University of Bordeaux, Plateforme Métabolome Bordeaux-MetaboHUB, 33140 Villenave d'Ornon, France
| | - David Johnson
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
- Department of Informatics and Media, Uppsala University, Box 513, 751 20 Uppsala, Sweden
| | - Fabien Jourdan
- INRA - French National Institute for Agricultural Research, UMR1331, Toxalim, Research Centre in Food Toxicology, Toulouse, France
| | - Namrata Kale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ibrahim Karaman
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St. Mary's Campus, Norfolk Place, W2 1PG, London, United Kingdom
| | - Bita Khalili
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Payam Emami Khonsari
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, Sweden
| | - Kim Kultima
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, Sweden
| | - Samuel Lampa
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
| | - Anders Larsson
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Christian Ludwig
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Jon Ander Novella
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Jake T M Pearce
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Alina Peluso
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | | | | | - Michelle A C Reed
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
| | - Pierrick Roger
- CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, France
| | - Antonio Rosato
- Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence and CIRMMP, 50019 Sesto Fiorentino, Florence, Italy
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christoph Ruttkies
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
| | - Noureddin Sadawi
- Department of Computer Science, College of Engineering, Design and Physical Sciences, Brunel University, London, UK
- Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Reza M Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, United Kingdom
| | - Vitaly Selivanov
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Spain
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
| | - Daniel Schober
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
| | - Etienne A Thévenot
- CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, France
| | - Mattia Tomasoni
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Merlijn van Rijswijk
- Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands
- ELIXIR-NL, Dutch Techcentre for Life Sciences, Utrecht, 3503 RM, Netherlands
| | - Michael van Vliet
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, 2333 CC, The Netherlands
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | | | - Christoph Steinbeck
- Cheminformatics and Computational Metabolomics, Institute for Analytical Chemistry, Lessingstr. 8, 07743 Jena, Germany
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13
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Köttgen A, Raffler J, Sekula P, Kastenmüller G. Genome-Wide Association Studies of Metabolite Concentrations (mGWAS): Relevance for Nephrology. Semin Nephrol 2019; 38:151-174. [PMID: 29602398 DOI: 10.1016/j.semnephrol.2018.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Metabolites are small molecules that are intermediates or products of metabolism, many of which are freely filtered by the kidneys. In addition, the kidneys have a central role in metabolite anabolism and catabolism, as well as in active metabolite reabsorption and/or secretion during tubular passage. This review article illustrates how the coupling of genomics and metabolomics in genome-wide association analyses of metabolites can be used to illuminate mechanisms underlying human metabolism, with a special focus on insights relevant to nephrology. First, genetic susceptibility loci for reduced kidney function and chronic kidney disease (CKD) were reviewed systematically for their associations with metabolite concentrations in metabolomics studies of blood and urine. Second, kidney function and CKD-associated metabolites reported from observational studies were interrogated for metabolite-associated genetic variants to generate and discuss complementary insights. Finally, insights originating from the simultaneous study of both blood and urine or by modeling intermetabolite relationships are summarized. We also discuss methodologic questions related to the study of metabolite concentrations in urine as well as among CKD patients. In summary, genome-wide association analyses of metabolites using metabolite concentrations quantified from blood and/or urine are a promising avenue of research to illuminate physiological and pathophysiological functions of the kidney.
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Affiliation(s)
- Anna Köttgen
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany.
| | - Johannes Raffler
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
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14
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Bingol K. Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods. High Throughput 2018; 7:E9. [PMID: 29670016 PMCID: PMC6023270 DOI: 10.3390/ht7020009] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 12/23/2022] Open
Abstract
Metabolomics has made significant progress in multiple fronts in the last 18 months. This minireview aimed to give an overview of these advancements in the light of their contribution to targeted and untargeted metabolomics. New computational approaches have emerged to overcome the manual absolute quantitation step of metabolites in one-dimensional (1D) ¹H nuclear magnetic resonance (NMR) spectra. This provides more consistency between inter-laboratory comparisons. Integration of two-dimensional (2D) NMR metabolomics databases under a unified web server allowed for very accurate identification of the metabolites that have been catalogued in these databases. For the remaining uncatalogued and unknown metabolites, new cheminformatics approaches have been developed by combining NMR and mass spectrometry (MS). These hybrid MS/NMR approaches accelerated the identification of unknowns in untargeted studies, and now they are allowing for profiling ever larger number of metabolites in application studies.
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Affiliation(s)
- Kerem Bingol
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
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