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Feofanova EV, Brown MR, Alkis T, Manuel AM, Li X, Tahir UA, Li Z, Mendez KM, Kelly RS, Qi Q, Chen H, Larson MG, Lemaitre RN, Morrison AC, Grieser C, Wong KE, Gerszten RE, Zhao Z, Lasky-Su J, Yu B. Whole-Genome Sequencing Analysis of Human Metabolome in Multi-Ethnic Populations. Nat Commun 2023; 14:3111. [PMID: 37253714 PMCID: PMC10229598 DOI: 10.1038/s41467-023-38800-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/16/2023] [Indexed: 06/01/2023] Open
Abstract
Circulating metabolite levels may reflect the state of the human organism in health and disease, however, the genetic architecture of metabolites is not fully understood. We have performed a whole-genome sequencing association analysis of both common and rare variants in up to 11,840 multi-ethnic participants from five studies with up to 1666 circulating metabolites. We have discovered 1985 novel variant-metabolite associations, and validated 761 locus-metabolite associations reported previously. Seventy-nine novel variant-metabolite associations have been replicated, including three genetic loci located on the X chromosome that have demonstrated its involvement in metabolic regulation. Gene-based analysis have provided further support for seven metabolite-replicated loci pairs and their biologically plausible genes. Among those novel replicated variant-metabolite pairs, follow-up analyses have revealed that 26 metabolites have colocalized with 21 tissues, seven metabolite-disease outcome associations have been putatively causal, and 7 metabolites might be regulated by plasma protein levels. Our results have depicted the genetic contribution to circulating metabolite levels, providing additional insights into understanding human disease.
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Affiliation(s)
- Elena V Feofanova
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA
| | - Michael R Brown
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA
| | - Taryn Alkis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA
| | - Astrid M Manuel
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Usman A Tahir
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kevin M Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Retina Service, Massachusetts Eye and Ear, Harvard Medical School, 243 Charles Street, Boston, MA, USA
| | - Rachel S Kelly
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Han Chen
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Martin G Larson
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Rozenn N Lemaitre
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Alanna C Morrison
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA
| | | | | | - Robert E Gerszten
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Zhongming Zhao
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Bing Yu
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA.
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2
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Hoshi RA, Liu Y, Luttmann-Gibson H, Tiwari S, Giulianini F, Andres AM, Watrous JD, Cook NR, Costenbader KH, Okereke OI, Ridker PM, Manson JE, Lee IM, Vinayagamoorthy M, Cheng S, Copeland T, Jain M, Chasman DI, Demler OV, Mora S. Association of Physical Activity With Bioactive Lipids and Cardiovascular Events. Circ Res 2022; 131:e84-e99. [PMID: 35862024 PMCID: PMC9357171 DOI: 10.1161/circresaha.122.320952] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND To clarify the mechanisms underlying physical activity (PA)-related cardioprotection, we examined the association of PA with plasma bioactive lipids (BALs) and cardiovascular disease (CVD) events. We additionally performed genome-wide associations. METHODS PA-bioactive lipid associations were examined in VITAL (VITamin D and OmegA-3 TriaL)-clinical translational science center (REGISTRATION: URL: https://www. CLINICALTRIALS gov; Unique identifier: NCT01169259; N=1032) and validated in JUPITER (Justification for the Use of statins in Prevention: an Intervention Trial Evaluating Rosuvastatin)-NC (REGISTRATION: URL: https://www. CLINICALTRIALS gov; Unique identifier: NCT00239681; N=589), using linear models adjusted for age, sex, race, low-density lipoprotein-cholesterol, total-C, and smoking. Significant BALs were carried over to examine associations with incident CVD in 2 nested CVD case-control studies: VITAL-CVD (741 case-control pairs) and JUPITER-CVD (415 case-control pairs; validation). RESULTS We detected 145 PA-bioactive lipid validated associations (false discovery rate <0.1). Annotations were found for 6 of these BALs: 12,13-diHOME, 9,10-diHOME, lysoPC(15:0), oxymorphone-3b-D-glucuronide, cortisone, and oleoyl-glycerol. Genetic analysis within JUPITER-NC showed associations of 32 PA-related BALs with 22 single-nucleotide polymorphisms. From PA-related BALs, 12 are associated with CVD. CONCLUSIONS We identified a PA-related bioactive lipidome profile out of which 12 BALs also had opposite associations with incident CVD events.
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Affiliation(s)
- Rosangela A. Hoshi
- Center for Lipid Metabolomics, Division of Preventive Medicine, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yanyan Liu
- Center for Lipid Metabolomics, Division of Preventive Medicine, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Heike Luttmann-Gibson
- Center for Lipid Metabolomics, Division of Preventive Medicine, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Saumya Tiwari
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92037, USA
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Allen M. Andres
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92037, USA
| | - Jeramie D. Watrous
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92037, USA
| | - Nancy R. Cook
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Karen H. Costenbader
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Olivia I. Okereke
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Paul M Ridker
- Center for Lipid Metabolomics, Division of Preventive Medicine, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - JoAnn E. Manson
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - I-Min Lee
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Susan Cheng
- Smidt Heart Institute, Cedars-Sinai Medical Ctr, Los Angeles, CA 90048, USA
| | - Trisha Copeland
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mohit Jain
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Olga V. Demler
- Center for Lipid Metabolomics, Division of Preventive Medicine, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Computer Science, ETH Zurich, Zurich 8092, Switzerland
| | - Samia Mora
- Center for Lipid Metabolomics, Division of Preventive Medicine, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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Bomba L, Walter K, Guo Q, Surendran P, Kundu K, Nongmaithem S, Karim MA, Stewart ID, Langenberg C, Danesh J, Di Angelantonio E, Roberts DJ, Ouwehand WH, Dunham I, Butterworth AS, Soranzo N. Whole-exome sequencing identifies rare genetic variants associated with human plasma metabolites. Am J Hum Genet 2022; 109:1038-1054. [PMID: 35568032 PMCID: PMC9247822 DOI: 10.1016/j.ajhg.2022.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/13/2022] [Indexed: 12/11/2022] Open
Abstract
Metabolite levels measured in the human population are endophenotypes for biological processes. We combined sequencing data for 3,924 (whole-exome sequencing, WES, discovery) and 2,805 (whole-genome sequencing, WGS, replication) donors from a prospective cohort of blood donors in England. We used multiple approaches to select and aggregate rare genetic variants (minor allele frequency [MAF] < 0.1%) in protein-coding regions and tested their associations with 995 metabolites measured in plasma by using ultra-high-performance liquid chromatography-tandem mass spectrometry. We identified 40 novel associations implicating rare coding variants (27 genes and 38 metabolites), of which 28 (15 genes and 28 metabolites) were replicated. We developed algorithms to prioritize putative driver variants at each locus and used mediation and Mendelian randomization analyses to test directionality at associations of metabolite and protein levels at the ACY1 locus. Overall, 66% of reported associations implicate gene targets of approved drugs or bioactive drug-like compounds, contributing to drug targets' validating efforts.
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Affiliation(s)
- Lorenzo Bomba
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Klaudia Walter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Qi Guo
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Kousik Kundu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Suraj Nongmaithem
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Mohd Anisul Karim
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Isobel D Stewart
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0SL, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0SL, UK; Computational Medicine, Berlin Institute of Health at Charité - Utniversitätsmedizin Berlin, Berlin 10117, Germany
| | - John Danesh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB2 0QQ, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB10 1SA, UK
| | - Emanuele Di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB2 0QQ, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB10 1SA, UK; Human Technopole, Palazzo Italia, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - David J Roberts
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; NHS Blood and Transplant-Oxford Centre, Level 2, John Radcliffe Hospital, Oxford OX3 9BQ, UK; Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9BQ, UK
| | - Willem H Ouwehand
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | | | - Ian Dunham
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB2 0QQ, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge CB10 1SA, UK
| | - Nicole Soranzo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Open Targets, Wellcome Genome Campus, Hinxton CB10 1SD, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge CB2 0QQ, UK; National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge CB1 8RN, UK; Human Technopole, Palazzo Italia, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy.
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4
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Shu X, Chen Z, Long J, Guo X, Yang Y, Qu C, Ahn YO, Cai Q, Casey G, Gruber SB, Huyghe JR, Jee SH, Jenkins MA, Jia WH, Jung KJ, Kamatani Y, Kim DH, Kim J, Kweon SS, Le Marchand L, Matsuda K, Matsuo K, Newcomb PA, Oh JH, Ose J, Oze I, Pai RK, Pan ZZ, Pharoah PD, Playdon MC, Ren ZF, Schoen RE, Shin A, Shin MH, Shu XO, Sun X, Tangen CM, Tanikawa C, Ulrich CM, van Duijnhoven FJ, Van Guelpen B, Wolk A, Woods MO, Wu AH, Peters U, Zheng W. Large-scale Integrated Analysis of Genetics and Metabolomic Data Reveals Potential Links Between Lipids and Colorectal Cancer Risk. Cancer Epidemiol Biomarkers Prev 2022; 31:1216-1226. [PMID: 35266989 PMCID: PMC9354799 DOI: 10.1158/1055-9965.epi-21-1008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/12/2021] [Accepted: 03/04/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The etiology of colorectal cancer is not fully understood. METHODS Using genetic variants and metabolomics data including 217 metabolites from the Framingham Heart Study (n = 1,357), we built genetic prediction models for circulating metabolites. Models with prediction R2 > 0.01 (Nmetabolite = 58) were applied to predict levels of metabolites in two large consortia with a combined sample size of approximately 46,300 cases and 59,200 controls of European and approximately 21,700 cases and 47,400 controls of East Asian (EA) descent. Genetically predicted levels of metabolites were evaluated for their associations with colorectal cancer risk in logistic regressions within each racial group, after which the results were combined by meta-analysis. RESULTS Of the 58 metabolites tested, 24 metabolites were significantly associated with colorectal cancer risk [Benjamini-Hochberg FDR (BH-FDR) < 0.05] in the European population (ORs ranged from 0.91 to 1.06; P values ranged from 0.02 to 6.4 × 10-8). Twenty one of the 24 associations were replicated in the EA population (ORs ranged from 0.26 to 1.69, BH-FDR < 0.05). In addition, the genetically predicted levels of C16:0 cholesteryl ester was significantly associated with colorectal cancer risk in the EA population only (OREA: 1.94, 95% CI, 1.60-2.36, P = 2.6 × 10-11; OREUR: 1.01, 95% CI, 0.99-1.04, P = 0.3). Nineteen of the 25 metabolites were glycerophospholipids and triacylglycerols (TAG). Eighteen associations exhibited significant heterogeneity between the two racial groups (PEUR-EA-Het < 0.005), which were more strongly associated in the EA population. This integrative study suggested a potential role of lipids, especially certain glycerophospholipids and TAGs, in the etiology of colorectal cancer. CONCLUSIONS This study identified potential novel risk biomarkers for colorectal cancer by integrating genetics and circulating metabolomics data. IMPACT The identified metabolites could be developed into new tools for risk assessment of colorectal cancer in both European and EA populations.
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Affiliation(s)
- Xiang Shu
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Yoon-Ok Ahn
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Stephen B. Gruber
- Department of Preventive Medicine & USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jeroen R. Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Korea
| | - Mark A. Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Keum Ji Jung
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Korea
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan,Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Dong-Hyun Kim
- Department of Social and Preventive Medicine, Hallym University College of Medicine, Okcheon-dong, Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Gyeonggi-do, South Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | | | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan,Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Polly A. Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA,School of Public Health, University of Washington, Seattle, Washington, USA
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center Hospital, National Cancer Center, Gyeonggi-do, South Korea
| | - Jennifer Ose
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Isao Oze
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Rish K. Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Zhi-Zhong Pan
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Paul D.P. Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mary C. Playdon
- Cancer Control and Population Sciences, Huntsman Cancer Institute and Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, Utah, USA
| | - Ze-Fang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Robert E. Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Aesun Shin
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea,Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Xiao-ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Xiaohui Sun
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Epidemiology, Zhejiang Chinese Medical University, Zhejiang, China
| | - Catherine M. Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Cornelia M. Ulrich
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Michael O. Woods
- Memorial University of Newfoundland, Discipline of Genetics, St. John's, Canada
| | - Anna H. Wu
- University of Southern California, Preventative Medicine, Los Angeles, California, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA,Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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5
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Zhang C, Hansen MEB, Tishkoff SA. Advances in integrative African genomics. Trends Genet 2022; 38:152-168. [PMID: 34740451 PMCID: PMC8752515 DOI: 10.1016/j.tig.2021.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022]
Abstract
There has been a rapid increase in human genome sequencing in the past two decades, resulting in the identification of millions of previously unknown genetic variants. However, African populations are under-represented in sequencing efforts. Additional sequencing from diverse African populations and the construction of African-specific reference genomes is needed to better characterize the full spectrum of variation in humans. However, sequencing alone is insufficient to address the molecular and cellular mechanisms underlying variable phenotypes and disease risks. Determining functional consequences of genetic variation using multi-omics approaches is a fundamental post-genomic challenge. We discuss approaches to close the knowledge gaps about African genomic diversity and review advances in African integrative genomic studies and their implications for precision medicine.
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Affiliation(s)
- Chao Zhang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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6
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Lightning TA, Gesteira TF, Mueller JW. Steroid disulfates - Sulfation double trouble. Mol Cell Endocrinol 2021; 524:111161. [PMID: 33453296 DOI: 10.1016/j.mce.2021.111161] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/24/2020] [Accepted: 01/05/2021] [Indexed: 02/08/2023]
Abstract
Sulfation pathways have recently come into the focus of biomedical research. For steroid hormones and related compounds, sulfation represents an additional layer of regulation as sulfated steroids are more water-soluble and tend to be biologically less active. For steroid diols, an additional sulfation is possible, carried out by the same sulfotransferases that catalyze the first sulfation step. The steroid disulfates that are formed are the focus of this review. We discuss both their biochemical production as well as their putative biological function. Steroid disulfates have also been linked to various clinical conditions in numerous untargeted metabolomics studies. New analytical techniques exploring the biosynthetic routes of steroid disulfates have led to novel insights, changing our understanding of sulfation in human biology. They promise a bright future for research into sulfation pathways, hopefully too for the diagnosis and treatment of several associated diseases.
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Affiliation(s)
- Thomas Alec Lightning
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Tarsis F Gesteira
- College of Optometry, University of Houston, Houston, TX, USA; Optimvia, LLC, Batavia, OH, USA
| | - Jonathan Wolf Mueller
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK; Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, UK.
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Tabassum R, Ripatti S. Integrating lipidomics and genomics: emerging tools to understand cardiovascular diseases. Cell Mol Life Sci 2021; 78:2565-2584. [PMID: 33449144 PMCID: PMC8004487 DOI: 10.1007/s00018-020-03715-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/09/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of mortality and morbidity worldwide leading to 31% of all global deaths. Early prediction and prevention could greatly reduce the enormous socio-economic burden posed by CVDs. Plasma lipids have been at the center stage of the prediction and prevention strategies for CVDs that have mostly relied on traditional lipids (total cholesterol, total triglycerides, HDL-C and LDL-C). The tremendous advancement in the field of lipidomics in last two decades has facilitated the research efforts to unravel the metabolic dysregulation in CVDs and their genetic determinants, enabling the understanding of pathophysiological mechanisms and identification of predictive biomarkers, beyond traditional lipids. This review presents an overview of the application of lipidomics in epidemiological and genetic studies and their contributions to the current understanding of the field. We review findings of these studies and discuss examples that demonstrates the potential of lipidomics in revealing new biology not captured by traditional lipids and lipoprotein measurements. The promising findings from these studies have raised new opportunities in the fields of personalized and predictive medicine for CVDs. The review further discusses prospects of integrating emerging genomics tools with the high-dimensional lipidome to move forward from the statistical associations towards biological understanding, therapeutic target development and risk prediction. We believe that integrating genomics with lipidome holds a great potential but further advancements in statistical and computational tools are needed to handle the high-dimensional and correlated lipidome.
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Affiliation(s)
- Rubina Tabassum
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, PO Box 20, 00014, Helsinki, Finland.
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, PO Box 20, 00014, Helsinki, Finland.
- Department of Public Health, Clinicum, University of Helsinki, Helsinki, Finland.
- Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
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Feofanova EV, Chen H, Dai Y, Jia P, Grove ML, Morrison AC, Qi Q, Daviglus M, Cai J, North KE, Laurie CC, Kaplan RC, Boerwinkle E, Yu B. A Genome-wide Association Study Discovers 46 Loci of the Human Metabolome in the Hispanic Community Health Study/Study of Latinos. Am J Hum Genet 2020; 107:849-863. [PMID: 33031748 PMCID: PMC7675000 DOI: 10.1016/j.ajhg.2020.09.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/10/2020] [Indexed: 02/08/2023] Open
Abstract
Variation in levels of the human metabolome reflect changes in homeostasis, providing a window into health and disease. The genetic impact on circulating metabolites in Hispanics, a population with high cardiometabolic disease burden, is largely unknown. We conducted genome-wide association analyses on 640 circulating metabolites in 3,926 Hispanic Community Health Study/Study of Latinos participants. The estimated heritability for 640 metabolites ranged between 0%-54% with a median at 2.5%. We discovered 46 variant-metabolite pairs (p value < 1.2 × 10-10, minor allele frequency ≥ 1%, proportion of variance explained [PEV] mean = 3.4%, PEVrange = 1%-22%) with generalized effects in two population-based studies and confirmed 301 known locus-metabolite associations. Half of the identified variants with generalized effect were located in genes, including five nonsynonymous variants. We identified co-localization with the expression quantitative trait loci at 105 discovered and 151 known loci-metabolites sets. rs5855544, upstream of SLC51A, was associated with higher levels of three steroid sulfates and co-localized with expression levels of SLC51A in several tissues. Mendelian randomization (MR) analysis identified several metabolites associated with coronary heart disease (CHD) and type 2 diabetes. For example, two variants located in or near CYP4F2 (rs2108622 and rs79400241, respectively), involved in vitamin E metabolism, were associated with the levels of octadecanedioate and vitamin E metabolites (gamma-CEHC and gamma-CEHC glucuronide); MR analysis showed that genetically high levels of these metabolites were associated with lower odds of CHD. Our findings document the genetic architecture of circulating metabolites in an underrepresented Hispanic/Latino community, shedding light on disease etiology.
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Affiliation(s)
- Elena V Feofanova
- Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Han Chen
- Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA; Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Megan L Grove
- Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Alanna C Morrison
- Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Martha Daviglus
- Institute for Minority Health Research, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina Gilling School of Global Public Health, Chapel Hill, NC 27599, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina Gilling School of Global Public Health, Chapel Hill, NC 27599, USA; Carolina Center of Genome Sciences, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Bing Yu
- Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA.
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