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Gadd DA, Hillary RF, McCartney DL, Shi L, Stolicyn A, Robertson NA, Walker RM, McGeachan RI, Campbell A, Xueyi S, Barbu MC, Green C, Morris SW, Harris MA, Backhouse EV, Wardlaw JM, Steele JD, Oyarzún DA, Muniz-Terrera G, Ritchie C, Nevado-Holgado A, Chandra T, Hayward C, Evans KL, Porteous DJ, Cox SR, Whalley HC, McIntosh AM, Marioni RE. Integrated methylome and phenome study of the circulating proteome reveals markers pertinent to brain health. Nat Commun 2022; 13:4670. [PMID: 35945220 PMCID: PMC9363452 DOI: 10.1038/s41467-022-32319-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 07/25/2022] [Indexed: 12/04/2022] Open
Abstract
Characterising associations between the methylome, proteome and phenome may provide insight into biological pathways governing brain health. Here, we report an integrated DNA methylation and phenotypic study of the circulating proteome in relation to brain health. Methylome-wide association studies of 4058 plasma proteins are performed (N = 774), identifying 2928 CpG-protein associations after adjustment for multiple testing. These are independent of known genetic protein quantitative trait loci (pQTLs) and common lifestyle effects. Phenome-wide association studies of each protein are then performed in relation to 15 neurological traits (N = 1,065), identifying 405 associations between the levels of 191 proteins and cognitive scores, brain imaging measures or APOE e4 status. We uncover 35 previously unreported DNA methylation signatures for 17 protein markers of brain health. The epigenetic and proteomic markers we identify are pertinent to understanding and stratifying brain health.
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Affiliation(s)
- Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Liu Shi
- Department of Psychiatry, University of Oxford, Oxford, OX3 7JX, UK
| | - Aleks Stolicyn
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF, UK
| | - Neil A Robertson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Rosie M Walker
- Centre for Clinical Brain Sciences, Chancellor's Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB, UK
| | - Robert I McGeachan
- Centre for Discovery Brain Sciences, University of Edinburgh, 1 George Square, Edinburgh, EH8 9JZ, UK
- The Hospital for Small Animals, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Edinburgh, EH25 9RG, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Shen Xueyi
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF, UK
| | - Miruna C Barbu
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF, UK
| | - Claire Green
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF, UK
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Mathew A Harris
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF, UK
| | - Ellen V Backhouse
- Centre for Clinical Brain Sciences, Chancellor's Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB, UK
| | - Joanna M Wardlaw
- Centre for Clinical Brain Sciences, Chancellor's Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB, UK
- Edinburgh Imaging, University of Edinburgh, Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - J Douglas Steele
- Division of Imaging Science and Technology, Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Diego A Oyarzún
- School of Informatics, University of Edinburgh, Edinburgh, EH8 9AB, UK
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH3 3JF, UK
- The Alan Turing Institute, 96 Euston Road, London, NW1 2DB, UK
| | - Graciela Muniz-Terrera
- Centre for Clinical Brain Sciences, Edinburgh Dementia Prevention, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Department of Social Medicine, Ohio University, Athens, OH, 45701, USA
| | - Craig Ritchie
- Centre for Clinical Brain Sciences, Edinburgh Dementia Prevention, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | | | - Tamir Chandra
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Caroline Hayward
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Simon R Cox
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Heather C Whalley
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.
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Hillary RF, Gadd DA, McCartney DL, Shi L, Campbell A, Walker RM, Ritchie CW, Deary IJ, Evans KL, Nevado‐Holgado AJ, Hayward C, Porteous DJ, McIntosh AM, Lovestone S, Robinson MR, Marioni RE. Genome- and epigenome-wide studies of plasma protein biomarkers for Alzheimer's disease implicate TBCA and TREM2 in disease risk. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2022; 14:e12280. [PMID: 35475137 PMCID: PMC9019629 DOI: 10.1002/dad2.12280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 11/24/2022]
Abstract
Introduction The levels of many blood proteins are associated with Alzheimer's disease (AD) or its pathological hallmarks. Elucidating the molecular factors that control circulating levels of these proteins may help to identify proteins associated with disease risk mechanisms. Methods Genome-wide and epigenome-wide studies (nindividuals ≤1064) were performed on plasma levels of 282 AD-associated proteins, identified by a structured literature review. Bayesian penalized regression estimated contributions of genetic and epigenetic variation toward inter-individual differences in plasma protein levels. Mendelian randomization (MR) and co-localization tested associations between proteins and disease-related phenotypes. Results Sixty-four independent genetic and 26 epigenetic loci were associated with 45 proteins. Novel findings included an association between plasma triggering receptor expressed on myeloid cells 2 (TREM2) levels and a polymorphism and cytosine-phosphate-guanine (CpG) site within the MS4A4A locus. Higher plasma tubulin-specific chaperone A (TBCA) and TREM2 levels were significantly associated with lower AD risk. Discussion Our data inform the regulation of biomarker levels and their relationships with AD.
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Affiliation(s)
- Robert F. Hillary
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
| | - Danni A. Gadd
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
| | - Daniel L. McCartney
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
| | - Liu Shi
- Department of PsychiatryUniversity of OxfordOxfordUK
| | - Archie Campbell
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
| | - Rosie M. Walker
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
- Centre for Clinical Brain Sciences, Chancellor's Building, 49 Little France CrescentUniversity of EdinburghEdinburghUK
| | - Craig W. Ritchie
- Edinburgh Dementia Prevention, Centre for Clinical Brain SciencesUniversity of EdinburghEdinburghUK
| | - Ian J. Deary
- Lothian Birth Cohorts, Department of PsychologyUniversity of EdinburghEdinburghUK
| | - Kathryn L. Evans
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
| | | | - Caroline Hayward
- MRC Human Genetics UnitInstitute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - David J. Porteous
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
| | - Andrew M. McIntosh
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
- Division of Psychiatry, Centre for Clinical Brain SciencesUniversity of EdinburghEdinburghUK
| | - Simon Lovestone
- Department of PsychiatryUniversity of OxfordOxfordUK
- NeurodegenerationJohnson and Johnson Medical LtdWokinghamUK
| | - Matthew R. Robinson
- Medical Genomics GroupInstitute of Science and Technology AustriaKlosterneuburgAustria
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Cancer, University of EdinburghEdinburghUK
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