|
1
|
Chu X, Jaeger M, Beumer J, Bakker OB, Aguirre-Gamboa R, Oosting M, Smeekens SP, Moorlag S, Mourits VP, Koeken VACM, de Bree C, Jansen T, Mathews IT, Dao K, Najhawan M, Watrous JD, Joosten I, Sharma S, Koenen HJPM, Withoff S, Jonkers IH, Netea-Maier RT, Xavier RJ, Franke L, Xu CJ, Joosten LAB, Sanna S, Jain M, Kumar V, Clevers H, Wijmenga C, Netea MG, Li Y. Integration of metabolomics, genomics, and immune phenotypes reveals the causal roles of metabolites in disease. Genome Biol 2021; 22:198. [PMID: 34229738 PMCID: PMC8259168 DOI: 10.1186/s13059-021-02413-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/21/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Recent studies highlight the role of metabolites in immune diseases, but it remains unknown how much of this effect is driven by genetic and non-genetic host factors. RESULT We systematically investigate circulating metabolites in a cohort of 500 healthy subjects (500FG) in whom immune function and activity are deeply measured and whose genetics are profiled. Our data reveal that several major metabolic pathways, including the alanine/glutamate pathway and the arachidonic acid pathway, have a strong impact on cytokine production in response to ex vivo stimulation. We also examine the genetic regulation of metabolites associated with immune phenotypes through genome-wide association analysis and identify 29 significant loci, including eight novel independent loci. Of these, one locus (rs174584-FADS2) associated with arachidonic acid metabolism is causally associated with Crohn's disease, suggesting it is a potential therapeutic target. CONCLUSION This study provides a comprehensive map of the integration between the blood metabolome and immune phenotypes, reveals novel genetic factors that regulate blood metabolite concentrations, and proposes an integrative approach for identifying new disease treatment targets.
Collapse
Affiliation(s)
- Xiaojing Chu
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Joep Beumer
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584, CT, Utrecht, the Netherlands
| | - Olivier B Bakker
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Raul Aguirre-Gamboa
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Sanne P Smeekens
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Simone Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Vera P Mourits
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Valerie A C M Koeken
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Charlotte de Bree
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Trees Jansen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Ian T Mathews
- Departments of Medicine and Pharmacology, University of California, San Diego, CA, USA
- La Jolla Institute, La Jolla, CA, USA
| | - Khoi Dao
- Departments of Medicine and Pharmacology, University of California, San Diego, CA, USA
| | - Mahan Najhawan
- Departments of Medicine and Pharmacology, University of California, San Diego, CA, USA
| | - Jeramie D Watrous
- Departments of Medicine and Pharmacology, University of California, San Diego, CA, USA
| | - Irma Joosten
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Center, 6525, GA, Nijmegen, the Netherlands
| | | | - Hans J P M Koenen
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Center, 6525, GA, Nijmegen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Iris H Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Romana T Netea-Maier
- Department of Internal Medicine, Division of Endocrinology, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology and Gastrointestinal Unit, Massachusetts General Hospital, Harvard School of Medicine, Boston, MA, 02114, USA
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Cheng-Jian Xu
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Mohit Jain
- Departments of Medicine and Pharmacology, University of California, San Diego, CA, USA
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584, CT, Utrecht, the Netherlands
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584, CS, Utrecht, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands.
- Department of Immunology, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372, Oslo, Norway.
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands.
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115, Bonn, Germany.
| | - Yang Li
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700, RB, Groningen, the Netherlands.
- Department of Computational Biology for Individualised Medicine, Centre for Individualised Infection Medicine, CiiM, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands.
| |
Collapse
|