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Pirastu N, McDonnell C, Grzeszkowiak EJ, Mounier N, Imamura F, Merino J, Day FR, Zheng J, Taba N, Concas MP, Repetto L, Kentistou KA, Robino A, Esko T, Joshi PK, Fischer K, Ong KK, Gaunt TR, Kutalik Z, Perry JRB, Wilson JF. Using genetic variation to disentangle the complex relationship between food intake and health outcomes. PLoS Genet 2022; 18:e1010162. [PMID: 35653391 PMCID: PMC9162356 DOI: 10.1371/journal.pgen.1010162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 03/22/2022] [Indexed: 02/02/2023] Open
Abstract
Diet is considered as one of the most important modifiable factors influencing human health, but efforts to identify foods or dietary patterns associated with health outcomes often suffer from biases, confounding, and reverse causation. Applying Mendelian randomization in this context may provide evidence to strengthen causality in nutrition research. To this end, we first identified 283 genetic markers associated with dietary intake in 445,779 UK Biobank participants. We then converted these associations into direct genetic effects on food exposures by adjusting them for effects mediated via other traits. The SNPs which did not show evidence of mediation were then used for MR, assessing the association between genetically predicted food choices and other risk factors, health outcomes. We show that using all associated SNPs without omitting those which show evidence of mediation, leads to biases in downstream analyses (genetic correlations, causal inference), similar to those present in observational studies. However, MR analyses using SNPs which have only a direct effect on the exposure on food exposures provided unequivocal evidence of causal associations between specific eating patterns and obesity, blood lipid status, and several other risk factors and health outcomes.
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Affiliation(s)
- Nicola Pirastu
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Human Technopole, Milan, Italy
- * E-mail:
| | - Ciara McDonnell
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Centre for Cardiovascular Sciences, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Eryk J. Grzeszkowiak
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Ninon Mounier
- Centre for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Fumiaki Imamura
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Jordi Merino
- Diabetes Unit and Centre for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Felix R. Day
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Jie Zheng
- MRC Integrative Epidemiology Unit, Bristol Medical School, Bristol, United Kingdom
| | - Nele Taba
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Maria Pina Concas
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Linda Repetto
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Katherine A. Kentistou
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Centre for Cardiovascular Sciences, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Antonietta Robino
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Peter K. Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Krista Fischer
- Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Ken K. Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Tom R. Gaunt
- MRC Integrative Epidemiology Unit, Bristol Medical School, Bristol, United Kingdom
| | - Zoltán Kutalik
- Centre for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - John R. B. Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - James F. Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland, United Kingdom
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May-Wilson S, Matoba N, Wade KH, Hottenga JJ, Concas MP, Mangino M, Grzeszkowiak EJ, Menni C, Gasparini P, Timpson NJ, Veldhuizen MG, de Geus E, Wilson JF, Pirastu N. Large-scale GWAS of food liking reveals genetic determinants and genetic correlations with distinct neurophysiological traits. Nat Commun 2022; 13:2743. [PMID: 35585065 PMCID: PMC9117208 DOI: 10.1038/s41467-022-30187-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 04/20/2022] [Indexed: 12/15/2022] Open
Abstract
We present the results of a GWAS of food liking conducted on 161,625 participants from the UK-Biobank. Liking was assessed over 139 specific foods using a 9-point scale. Genetic correlations coupled with structural equation modelling identified a multi-level hierarchical map of food-liking with three main dimensions: “Highly-palatable”, “Acquired” and “Low-caloric”. The Highly-palatable dimension is genetically uncorrelated from the other two, suggesting that independent processes underlie liking high reward foods. This is confirmed by genetic correlations with MRI brain traits which show with distinct associations. Comparison with the corresponding food consumption traits shows a high genetic correlation, while liking exhibits twice the heritability. GWAS analysis identified 1,401 significant food-liking associations which showed substantial agreement in the direction of effects with 11 independent cohorts. In conclusion, we created a comprehensive map of the genetic determinants and associated neurophysiological factors of food-liking. Genetic determinants of food consumption and food liking are likely to be distinct, although it has not been well studied. Here, the authors identify genetic variants associated with food-liking, finding that different food-liking traits correlate with different brain areas and other food consumption traits.
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Affiliation(s)
- Sebastian May-Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kaitlin H Wade
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Jouke-Jan Hottenga
- Dept of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Maria Pina Concas
- Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, Trieste, Italy
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.,NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Eryk J Grzeszkowiak
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Paolo Gasparini
- Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, Trieste, Italy.,Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Nicholas J Timpson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,Medical Research Council (MRC) Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, UK
| | - Maria G Veldhuizen
- Department of Anatomy, Faculty of Medicine, Mersin University, Mersin, Turkey
| | - Eco de Geus
- Dept of Biological Psychology, FGB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Public Health research institute, Amsterdam, UMC, The Netherlands
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Nicola Pirastu
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK. .,Human Technopole, Milan, Italy.
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Kennedy OJ, Pirastu N, Poole R, Fallowfield JA, Hayes PC, Grzeszkowiak EJ, Taal MW, Wilson JF, Parkes J, Roderick PJ. Coffee Consumption and Kidney Function: A Mendelian Randomization Study. Am J Kidney Dis 2019; 75:753-761. [PMID: 31837886 DOI: 10.1053/j.ajkd.2019.08.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 08/20/2019] [Indexed: 12/21/2022]
Abstract
RATIONALE & OBJECTIVE Chronic kidney disease (CKD) is a leading cause of morbidity and mortality worldwide, with limited strategies for prevention and treatment. Coffee is a complex mixture of chemicals, and consumption has been associated with mostly beneficial health outcomes. This work aimed to determine the impact of coffee consumption on kidney function. STUDY DESIGN Genome-wide association study (GWAS) and Mendelian randomization. SETTING & PARTICIPANTS UK Biobank baseline data were used for a coffee consumption GWAS and included 227,666 participants. CKDGen Consortium data were used for kidney outcomes and included 133,814 participants (12,385 cases of CKD) of mostly European ancestry across various countries. EXPOSURE Coffee consumption. OUTCOMES Estimated glomerular filtration rate (eGFR), CKD GFR categories 3 to 5 (G3-G5; eGFR<60mL/min/1.73m2), and albuminuria. ANALYTICAL APPROACH GWAS to identify single-nucleotide polymorphisms (SNPs) associated with coffee consumption in UK Biobank and use of those SNPs in Mendelian randomization analyses of coffee consumption and kidney outcomes in CKDGen. RESULTS 2,126 SNPs were associated with coffee consumption (P<5×10-8), 25 of which were independent and available in CKDGen. Drinking an extra cup of coffee per day conferred a protective effect against CKD G3-G5 (OR, 0.84; 95% CI, 0.72-0.98; P=0.03) and albuminuria (OR, 0.81; 95% CI, 0.67-0.97; P=0.02). An extra cup was also associated with higher eGFR (β=0.022; P=1.6×10-6) after removal of 3 SNPs responsible for significant heterogeneity (Cochran Q P = 3.5×10-15). LIMITATIONS Assays used to measure creatinine and albumin varied between studies that contributed data and a sex-specific definition was used for albuminuria rather than KDIGO guideline recommendations. CONCLUSIONS This study provides evidence of a beneficial effect of coffee on kidney function. Given widespread coffee consumption and limited interventions to prevent CKD incidence and progression, this could have significant implications for global public health in view of the increasing burden of CKD worldwide.
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Affiliation(s)
- Oliver J Kennedy
- Primary Care & Population Sciences Faculty of Medicine, University of Southampton, Southampton, United Kingdom.
| | - Nicola Pirastu
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Robin Poole
- Primary Care & Population Sciences Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jonathan A Fallowfield
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Peter C Hayes
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh BioQuarter, Edinburgh, United Kingdom
| | - Eryk J Grzeszkowiak
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Maarten W Taal
- Division of Medical Sciences and Graduate Entry Medicine, University of Nottingham, Nottingham, United Kingdom
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom; MRC Human Genetic Unit, Institute of Genetic and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Julie Parkes
- Primary Care & Population Sciences Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Paul J Roderick
- Primary Care & Population Sciences Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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