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Forutan M, Engle BN, Chamberlain AJ, Ross EM, Nguyen LT, D'Occhio MJ, Snr AC, Kho EA, Fordyce G, Speight S, Goddard ME, Hayes BJ. Genome-wide association and expression quantitative trait loci in cattle reveals common genes regulating mammalian fertility. Commun Biol 2024; 7:724. [PMID: 38866948 PMCID: PMC11169601 DOI: 10.1038/s42003-024-06403-2] [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: 04/20/2023] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
Most genetic variants associated with fertility in mammals fall in non-coding regions of the genome and it is unclear how these variants affect fertility. Here we use genome-wide association summary statistics for Heifer puberty (pubertal or not at 600 days) from 27,707 Bos indicus, Bos taurus and crossbred cattle; multi-trait GWAS signals from 2119 indicine cattle for four fertility traits, including days to calving, age at first calving, pregnancy status, and foetus age in weeks (assessed by rectal palpation of the foetus); and expression quantitative trait locus for whole blood from 489 indicine cattle, to identify 87 putatively functional genes affecting cattle fertility. Our analysis reveals a significant overlap between the set of cattle and previously reported human fertility-related genes, impling the existence of a shared pool of genes that regulate fertility in mammals. These findings are crucial for developing approaches to improve fertility in cattle and potentially other mammals.
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Affiliation(s)
- Mehrnush Forutan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
| | - Bailey N Engle
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- USDA,ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Amanda J Chamberlain
- Agriculture Victoria, Centre for AgriBiosciences, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Elizabeth M Ross
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Loan T Nguyen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Michael J D'Occhio
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Alf Collins Snr
- Collins Belah Valley Brahman Stud, Marlborough, 4705, QLD, Australia
| | - Elise A Kho
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Geoffry Fordyce
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | | | - Michael E Goddard
- Agriculture Victoria, Centre for AgriBiosciences, Bundoora, VIC, Australia
- University of Melbourne, Melbourne, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
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2
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Asiimwe IG, Walker L, Sofat R, Jorgensen AL, Pirmohamed M. Genetic Determinants of Thiazide-Induced Hyperuricemia, Hyperglycemia, and Urinary Electrolyte Disturbances - A Genome-Wide Evaluation of the UK Biobank. Clin Pharmacol Ther 2024; 115:1408-1417. [PMID: 38425181 DOI: 10.1002/cpt.3229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
Thiazide diuretics, widely used in hypertension, cause a variety of adverse reactions, including hyperglycemia, hyperuricemia, and electrolyte abnormalities. In this study, we aimed to identify genetic variants that interact with thiazide-use to increase the risk of these adverse reactions. Using UK Biobank data, we first performed genomewide variance quantitative trait locus (vQTL) analysis of ~ 6.2 million SNPs on 95,493 unrelated hypertensive White British participants (24,313 on self-reported bendroflumethiazide treatment at recruitment) for 2 blood (glucose and urate) and 2 urine (potassium and sodium) biomarkers. Second, we conducted direct gene-environment interaction (GEI) tests on the significant (P < 2.5 × 10-9) vQTLs, included a second UK Biobank cohort comprising 13,647 unrelated hypertensive White British participants (3,478 on thiazides other than bendroflumethiazide) and set significance at P = 0.05 divided by the number of vQTL SNPs tested for GEIs. The vQTL analysis identified eight statistically significant SNPs for blood glucose (5 SNPs) and serum urate (3 SNPs), with none being identified for the urinary biomarkers. Two of the SNPs (1 glucose SNP: CDKAL1 intron rs35612982, GEI P = 6.24 × 10-3; and 1 serum urate SNP: SLC2A9 intron rs938564, GEI P = 4.51 × 10-4) demonstrated significant GEI effects in the first, but not the second, cohort. Both genes are biologically plausible candidates, with the SLC2A9-mediated interaction having been previously reported. In conclusion, we used a two-stage approach to detect two biologically plausible genetic loci that can interact with thiazides to increase the risk of thiazide-associated biochemical abnormalities. Understanding how environmental exposures (including medications such as thiazides) and genetics interact, is an important step toward precision medicine and improved patient outcomes.
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Affiliation(s)
- Innocent G Asiimwe
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lauren Walker
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Reecha Sofat
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Andrea L Jorgensen
- Department of Health Data Science, Institute of Population Health Sciences, University of Liverpool, Liverpool, UK
| | - Munir Pirmohamed
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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Smith HM, Ng HK, Moodie JE, Gadd DA, McCartney DL, Bernabeu E, Campbell A, Redmond P, Taylor A, Page D, Corley J, Harris SE, Tay D, Deary IJ, Evans KL, Robinson MR, Chambers JC, Loh M, Cox SR, Marioni RE, Hillary RF. Methylome-wide studies of six metabolic traits. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.29.24308103. [PMID: 38853823 PMCID: PMC11160850 DOI: 10.1101/2024.05.29.24308103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Exploring the molecular correlates of metabolic health measures may identify the shared and unique biological processes and pathways that they track. Here, we performed epigenome-wide association studies (EWASs) of six metabolic traits: body mass index (BMI), body fat percentage, waist-hip ratio (WHR), and blood-based measures of glucose, high-density lipoprotein (HDL) cholesterol, and total cholesterol. We considered blood-based DNA methylation (DNAm) from >750,000 CpG sites in over 17,000 volunteers from the Generation Scotland (GS) cohort. Linear regression analyses identified between 304 and 11,815 significant CpGs per trait at P<3.6×10-8, with 37 significant CpG sites across all six traits. Further, we performed a Bayesian EWAS that jointly models all CpGs simultaneously and conditionally on each other, as opposed to the marginal linear regression analyses. This identified between 3 and 27 CpGs with a posterior inclusion probability ≥ 0.95 across the six traits. Next, we used elastic net penalised regression to train epigenetic scores (EpiScores) of each trait in GS, which were then tested in the Lothian Birth Cohort 1936 (LBC1936; European ancestry) and Health for Life in Singapore (HELIOS; Indian-, Malay- and Chinese-ancestries). A maximum of 27.1% of the variance in BMI was explained by the BMI EpiScore in the subset of Malay-ancestry Singaporeans. Four metabolic EpiScores were associated with general cognitive function in LBC1936 in models adjusted for vascular risk factors (Standardised βrange: 0.08 - 0.12, PFDR < 0.05). EpiScores of metabolic health are applicable across ancestries and can reflect differences in brain health.
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Affiliation(s)
- Hannah M. Smith
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Hong Kiat Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Joanna E. Moodie
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Danni A. Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Elena Bernabeu
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Paul Redmond
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Adele Taylor
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Danielle Page
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Janie Corley
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Sarah E. Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Darwin Tay
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Ian J. Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Matthew R. Robinson
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - John C. Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Simon R. Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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Hillary RF, Ng HK, McCartney DL, Elliott HR, Walker RM, Campbell A, Huang F, Direk K, Welsh P, Sattar N, Corley J, Hayward C, McIntosh AM, Sudlow C, Evans KL, Cox SR, Chambers JC, Loh M, Relton CL, Marioni RE, Yousefi PD, Suderman M. Blood-based epigenome-wide analyses of chronic low-grade inflammation across diverse population cohorts. CELL GENOMICS 2024; 4:100544. [PMID: 38692281 PMCID: PMC11099341 DOI: 10.1016/j.xgen.2024.100544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/09/2024] [Accepted: 04/03/2024] [Indexed: 05/03/2024]
Abstract
Chronic inflammation is a hallmark of age-related disease states. The effectiveness of inflammatory proteins including C-reactive protein (CRP) in assessing long-term inflammation is hindered by their phasic nature. DNA methylation (DNAm) signatures of CRP may act as more reliable markers of chronic inflammation. We show that inter-individual differences in DNAm capture 50% of the variance in circulating CRP (N = 17,936, Generation Scotland). We develop a series of DNAm predictors of CRP using state-of-the-art algorithms. An elastic-net-regression-based predictor outperformed competing methods and explained 18% of phenotypic variance in the Lothian Birth Cohort of 1936 (LBC1936) cohort, doubling that of existing DNAm predictors. DNAm predictors performed comparably in four additional test cohorts (Avon Longitudinal Study of Parents and Children, Health for Life in Singapore, Southall and Brent Revisited, and LBC1921), including for individuals of diverse genetic ancestry and different age groups. The best-performing predictor surpassed assay-measured CRP and a genetic score in its associations with 26 health outcomes. Our findings forge new avenues for assessing chronic low-grade inflammation in diverse populations.
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Affiliation(s)
- Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Hong Kiat Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; School of Psychology, University of Exeter, Exeter EX4 4QG, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Felicia Huang
- MRC Unit for Lifelong Health and Ageing, University College London, London WC1E 7HB, UK
| | - Kenan Direk
- Imperial Clinical Trials Unit, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Paul Welsh
- School of Cardiovascular and Metabolic Health, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - Naveed Sattar
- School of Cardiovascular and Metabolic Health, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - Janie Corley
- Lothian Birth Cohort Studies, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Caroline Hayward
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK; Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh EH10 5HF, UK
| | - Cathie Sudlow
- Centre for Clinical Brain Sciences, Edinburgh Imaging and UK Dementia Research Institute, University of Edinburgh, Edinburgh EH16 4SB, UK; British Heart Foundation Data Science Centre, Health Data Research UK, London NW1 2BE, UK; Health Data Research UK, London NW1 2BE, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Simon R Cox
- Lothian Birth Cohort Studies, Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - John C Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore; Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London W2 1PG, UK
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore; Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St Mary's Campus, London W2 1PG, UK; National Skin Centre, Singapore 308205, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK.
| | - Paul D Yousefi
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK.
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK.
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Kemper KE, Sidorenko J, Wang H, Hayes BJ, Wray NR, Yengo L, Keller MC, Goddard M, Visscher PM. Genetic influence on within-person longitudinal change in anthropometric traits in the UK Biobank. Nat Commun 2024; 15:3776. [PMID: 38710707 PMCID: PMC11074304 DOI: 10.1038/s41467-024-47802-7] [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: 05/11/2023] [Accepted: 04/10/2024] [Indexed: 05/08/2024] Open
Abstract
The causes of temporal fluctuations in adult traits are poorly understood. Here, we investigate the genetic determinants of within-person trait variability of 8 repeatedly measured anthropometric traits in 50,117 individuals from the UK Biobank. We found that within-person (non-directional) variability had a SNP-based heritability of 2-5% for height, sitting height, body mass index (BMI) and weight (P ≤ 2.4 × 10-3). We also analysed longitudinal trait change and show a loss of both average height and weight beyond about 70 years of age. A variant tracking the Alzheimer's risk APOE- E 4 allele (rs429358) was significantly associated with weight loss ( β = -0.047 kg per yr, s.e. 0.007, P = 2.2 × 10-11), and using 2-sample Mendelian Randomisation we detected a relationship consistent with causality between decreased lumbar spine bone mineral density and height loss (bxy = 0.011, s.e. 0.003, P = 3.5 × 10-4). Finally, population-level variance quantitative trait loci (vQTL) were consistent with within-person variability for several traits, indicating an overlap between trait variability assessed at the population or individual level. Our findings help elucidate the genetic influence on trait-change within an individual and highlight disease risks associated with these changes.
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Affiliation(s)
- Kathryn E Kemper
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.
| | - Julia Sidorenko
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Huanwei Wang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Loic Yengo
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Matthew C Keller
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
| | - Michael Goddard
- Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, VIC, Australia
- Biosciences Research Division, Agriculture Victoria, Bundoora, VIC, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
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Davyson E, Shen X, Huider F, Adams M, Borges K, McCartney D, Barker L, Van Dongen J, Boomsma D, Weihs A, Grabe H, Kühn L, Teumer A, Völzke H, Zhu T, Kaprio J, Ollikainen M, David FS, Meinert S, Stein F, Forstner AJ, Dannlowski U, Kircher T, Tapuc A, Czamara D, Binder EB, Brückl T, Kwong A, Yousefi P, Wong C, Arseneault L, Fisher HL, Mill J, Cox S, Redmond P, Russ TC, van den Oord E, Aberg KA, Penninx B, Marioni RE, Wray NR, McIntosh AM. Antidepressant Exposure and DNA Methylation: Insights from a Methylome-Wide Association Study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.01.24306640. [PMID: 38746357 PMCID: PMC11092700 DOI: 10.1101/2024.05.01.24306640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Importance Understanding antidepressant mechanisms could help design more effective and tolerated treatments. Objective Identify DNA methylation (DNAm) changes associated with antidepressant exposure. Design Case-control methylome-wide association studies (MWAS) of antidepressant exposure were performed from blood samples collected between 2006-2011 in Generation Scotland (GS). The summary statistics were tested for enrichment in specific tissues, gene ontologies and an independent MWAS in the Netherlands Study of Depression and Anxiety (NESDA). A methylation profile score (MPS) was derived and tested for its association with antidepressant exposure in eight independent cohorts, alongside prospective data from GS. Setting Cohorts; GS, NESDA, FTC, SHIP-Trend, FOR2107, LBC1936, MARS-UniDep, ALSPAC, E-Risk, and NTR. Participants Participants with DNAm data and self-report/prescription derived antidepressant exposure. Main Outcomes and Measures Whole-blood DNAm levels were assayed by the EPIC/450K Illumina array (9 studies, N exposed = 661, N unexposed = 9,575) alongside MBD-Seq in NESDA (N exposed = 398, N unexposed = 414). Antidepressant exposure was measured by self- report and/or antidepressant prescriptions. Results The self-report MWAS (N = 16,536, N exposed = 1,508, mean age = 48, 59% female) and the prescription-derived MWAS (N = 7,951, N exposed = 861, mean age = 47, 59% female), found hypermethylation at seven and four DNAm sites (p < 9.42x10 -8 ), respectively. The top locus was cg26277237 ( KANK1, p self-report = 9.3x10 -13 , p prescription = 6.1x10 -3 ). The self-report MWAS found a differentially methylated region, mapping to DGUOK-AS1 ( p adj = 5.0x10 -3 ) alongside significant enrichment for genes expressed in the amygdala, the "synaptic vesicle membrane" gene ontology and the top 1% of CpGs from the NESDA MWAS (OR = 1.39, p < 0.042). The MPS was associated with antidepressant exposure in meta-analysed data from external cohorts (N studies = 9, N = 10,236, N exposed = 661, f3 = 0.196, p < 1x10 -4 ). Conclusions and Relevance Antidepressant exposure is associated with changes in DNAm across different cohorts. Further investigation into these changes could inform on new targets for antidepressant treatments. 3 Key Points Question: Is antidepressant exposure associated with differential whole blood DNA methylation?Findings: In this methylome-wide association study of 16,536 adults across Scotland, antidepressant exposure was significantly associated with hypermethylation at CpGs mapping to KANK1 and DGUOK-AS1. A methylation profile score trained on this sample was significantly associated with antidepressant exposure (pooled f3 [95%CI]=0.196 [0.105, 0.288], p < 1x10 -4 ) in a meta-analysis of external datasets. Meaning: Antidepressant exposure is associated with hypermethylation at KANK1 and DGUOK-AS1 , which have roles in mitochondrial metabolism and neurite outgrowth. If replicated in future studies, targeting these genes could inform the design of more effective and better tolerated treatments for depression.
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Hatton AA, Cheng FF, Lin T, Shen RJ, Chen J, Zheng Z, Qu J, Lyu F, Harris SE, Cox SR, Jin ZB, Martin NG, Fan D, Montgomery GW, Yang J, Wray NR, Marioni RE, Visscher PM, McRae AF. Genetic control of DNA methylation is largely shared across European and East Asian populations. Nat Commun 2024; 15:2713. [PMID: 38548728 PMCID: PMC10978881 DOI: 10.1038/s41467-024-47005-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
DNA methylation is an ideal trait to study the extent of the shared genetic control across ancestries, effectively providing hundreds of thousands of model molecular traits with large QTL effect sizes. We investigate cis DNAm QTLs in three European (n = 3701) and two East Asian (n = 2099) cohorts to quantify the similarities and differences in the genetic architecture across populations. We observe 80,394 associated mQTLs (62.2% of DNAm probes with significant mQTL) to be significant in both ancestries, while 28,925 mQTLs (22.4%) are identified in only a single ancestry. mQTL effect sizes are highly conserved across populations, with differences in mQTL discovery likely due to differences in allele frequency of associated variants and differing linkage disequilibrium between causal variants and assayed SNPs. This study highlights the overall similarity of genetic control across ancestries and the value of ancestral diversity in increasing the power to detect associations and enhancing fine mapping resolution.
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Affiliation(s)
- Alesha A Hatton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Fei-Fei Cheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ren-Juan Shen
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jie Chen
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhili Zheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jia Qu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Fan Lyu
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Sarah E Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, 100008, Beijing, China
- School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Nicholas G Martin
- Queensland Institute of Medical Research Berghofer, Brisbane, QLD, 4006, Australia
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, 100191, Beijing, China
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang, China
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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8
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Vasileva SS, Yang Y, Baker A, Siskind D, Gratten J, Eyles D. Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia. JAMA Psychiatry 2024; 81:292-302. [PMID: 38294805 PMCID: PMC10831632 DOI: 10.1001/jamapsychiatry.2023.5371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/09/2023] [Indexed: 02/01/2024]
Abstract
Importance There is growing interest in the role of gut microbiome composition in schizophrenia. However, lifestyle factors are often neglected, and few studies have investigated microbiome composition in treatment-resistant schizophrenia. Objective To explore associations between the gut microbiome and schizophrenia diagnosis, treatment resistance, clozapine response, and treatment-related adverse effects while adjusting for demographic and lifestyle factors. Design, Setting, and Participants In this case-control study of adults aged 20 to 63 years, stool samples and data on demographic characteristics, lifestyle, and medication use were collected and gut microbiome measures obtained using shotgun metagenomics. Participants with a schizophrenia diagnosis were referred through psychiatric inpatient units and outpatient clinics. Data were collected for 4 distinct groups: control individuals without a psychiatric diagnosis (past or present), individuals with treatment-responsive schizophrenia taking nonclozapine antipsychotic medications, clozapine-responsive individuals with treatment-resistant schizophrenia, and clozapine-nonresponsive individuals with treatment-resistant schizophrenia. Participants were recruited between November 2020 and November 2021. Control individuals were recruited in parallel through posters and online advertisements and matched for age, sex, and body mass index (BMI) to the individuals with schizophrenia. Participants were excluded if taking antibiotics in the past 2 months, if unable to communicate in English or otherwise follow study instructions, were pregnant or planning to become pregnant, or had any concomitant disease or condition making them unsuited to the study per investigator assessment. Data were analyzed from January 2022 to March 2023. Main Outcomes and Measures Omics relationship matrices, α and β diversity, and relative abundance of microbiome features. Results Data were collected for 97 individuals (71 [74%] male; mean [SD] age, 40.4 [10.3] years; mean [SD] BMI, 32.8 [7.4], calculated as weight in kilograms divided by height in meters squared). Significant microbiome associations with schizophrenia were observed at multiple taxonomic and functional levels (eg, common species: b2, 30%; SE, 13%; adjusted P = .002) and treatment resistance (eg, common species: b2, 27%; SE, 16%; adjusted P = .03). In contrast, limited evidence was found for microbiome associations with clozapine response, constipation, or metabolic syndrome. Significantly decreased microbial richness was found in individuals with schizophrenia compared to control individuals (t95 = 4.25; P < .001; mean [SD] for control individuals, 151.8 [32.31]; mean [SD] for individuals with schizophrenia, 117.00 [36.2]; 95% CI, 18.6-51.0), which remained significant after a covariate and multiple comparison correction. However, limited evidence was found for differences in β diversity (weighted UniFrac) for schizophrenia diagnosis (permutational multivariate analysis of variance [PERMANOVA]: R2, 0.03; P = .02), treatment resistance (R2, 0.02; P = .18), or clozapine response (R2, 0.04; P = .08). Multiple differentially abundant bacterial species (19) and metabolic pathways (162) were found in individuals with schizophrenia, which were primarily associated with treatment resistance and clozapine exposure. Conclusions and Relevance The findings in this study are consistent with the idea that clozapine induces alterations to gut microbiome composition, although the possibility that preexisting microbiome differences contribute to treatment resistance cannot be ruled out. These findings suggest that prior reports of microbiome alterations in individuals with chronic schizophrenia may be due to medication or lifestyle factors and that future studies should incorporate these variables in their design and interpretation.
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Affiliation(s)
- Svetlina S. Vasileva
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Queensland Centre for Mental Health Research, Wacol, Queensland, Australia
| | - Yuanhao Yang
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Andrea Baker
- Queensland Centre for Mental Health Research, Wacol, Queensland, Australia
- Metro South Addiction and Mental Health Service, Metro South Health, Brisbane, Brisbane South, Queensland, Australia
| | - Dan Siskind
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Queensland Centre for Mental Health Research, Wacol, Queensland, Australia
- Metro South Addiction and Mental Health Service, Metro South Health, Brisbane, Brisbane South, Queensland, Australia
- University of Queensland School of Clinical Medicine, Brisbane, Queensland, Australia
| | - Jacob Gratten
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Darryl Eyles
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Queensland Centre for Mental Health Research, Wacol, Queensland, Australia
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9
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Garrett ME, Dennis MF, Bourassa KJ, Hauser MA, Kimbrel NA, Beckham JC, Ashley-Koch AE. Genome-wide DNA methylation analysis of cannabis use disorder in a veteran cohort enriched for posttraumatic stress disorder. Psychiatry Res 2024; 333:115757. [PMID: 38309009 PMCID: PMC10922626 DOI: 10.1016/j.psychres.2024.115757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/05/2024]
Abstract
Cannabis use has been increasing over the past decade, not only in the general US population, but particularly among military veterans. With this rise in use has come a concomitant increase in cannabis use disorder (CUD) among veterans. Here, we performed an epigenome-wide association study for lifetime CUD in an Iraq/Afghanistan era veteran cohort enriched for posttraumatic stress disorder (PTSD) comprising 2,310 total subjects (1,109 non-Hispanic black and 1,201 non-Hispanic white). We also investigated CUD interactions with current PTSD status and examined potential indirect effects of DNA methylation (DNAm) on the relationship between CUD and psychiatric diagnoses. Four CpGs were associated with lifetime CUD, even after controlling for the effects of current smoking (AHRR cg05575921, LINC00299 cg23079012, VWA7 cg22112841, and FAM70A cg08760398). Importantly, cg05575921, a CpG strongly linked to smoking, remained associated with lifetime CUD even when restricting the analysis to veterans who reported never smoking cigarettes. Moreover, CUD interacted with current PTSD to affect cg05575921 and cg23079012 such that those with both CUD and PTSD displayed significantly lower DNAm compared to the other groups. Finally, we provide preliminary evidence that AHRR cg05575921 helps explain the association between CUD and any psychiatric diagnoses, specifically mood disorders.
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Affiliation(s)
- Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, 300N Duke St, Durham, NC 27701, USA
| | - Michelle F Dennis
- Durham Veterans Affairs (VA) Health Care System, Durham, NC, USA; VA Mid-Atlantic Mental Illness Research, Education, and Clinical Center, Durham, NC, USA; Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Kyle J Bourassa
- Durham Veterans Affairs (VA) Health Care System, Durham, NC, USA; VA Mid-Atlantic Mental Illness Research, Education, and Clinical Center, Durham, NC, USA; Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, NC, USA
| | - Michael A Hauser
- Duke Molecular Physiology Institute, Duke University Medical Center, 300N Duke St, Durham, NC 27701, USA
| | - Nathan A Kimbrel
- Durham Veterans Affairs (VA) Health Care System, Durham, NC, USA; VA Mid-Atlantic Mental Illness Research, Education, and Clinical Center, Durham, NC, USA; Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Jean C Beckham
- Durham Veterans Affairs (VA) Health Care System, Durham, NC, USA; VA Mid-Atlantic Mental Illness Research, Education, and Clinical Center, Durham, NC, USA; Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, 300N Duke St, Durham, NC 27701, USA.
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10
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Maliar NL, Talbot EJ, Edwards AR, Khoronenkova SV. Microglial inflammation in genome instability: A neurodegenerative perspective. DNA Repair (Amst) 2024; 135:103634. [PMID: 38290197 DOI: 10.1016/j.dnarep.2024.103634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/08/2024] [Accepted: 01/21/2024] [Indexed: 02/01/2024]
Abstract
The maintenance of genome stability is crucial for cell homeostasis and tissue integrity. Numerous human neuropathologies display chronic inflammation in the central nervous system, set against a backdrop of genome instability, implying a close interplay between the DNA damage and immune responses in the context of neurological disease. Dissecting the molecular mechanisms of this crosstalk is essential for holistic understanding of neuroinflammatory pathways in genome instability disorders. Non-neuronal cell types, specifically microglia, are major drivers of neuroinflammation in the central nervous system with neuro-protective and -toxic capabilities. Here, we discuss how persistent DNA damage affects microglial homeostasis, zooming in on the cytosolic DNA sensing cGAS-STING pathway and the downstream inflammatory response, which can drive neurotoxic outcomes in the context of genome instability.
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Affiliation(s)
- Nina L Maliar
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Emily J Talbot
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Abigail R Edwards
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
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11
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Jia X, Kang Z, Wang G, Zhang K, Fu X, Li C, Lai S, Chen SY. Long-read sequencing-based transcriptomic landscape in longissimus dorsi and transcriptome-wide association studies for growth traits of meat rabbits. Front Vet Sci 2024; 11:1320484. [PMID: 38318148 PMCID: PMC10839001 DOI: 10.3389/fvets.2024.1320484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
Rabbits are an attractive meat livestock species that can efficiently convert human-indigestible plant biomass, and have been commonly used in biological and medical researches. Yet, transcriptomic landscape in muscle tissue and association between gene expression level and growth traits have not been specially studied in meat rabbits. In this study Oxford Nanopore Technologies (ONT) long-read sequencing technology was used for comprehensively exploring transcriptomic landscape in Longissimus dorsi for 115 rabbits at 84 days of age, and transcriptome-wide association studies (TWAS) were performed for growth traits, including body weight at 84 days of age and average daily gain during three growth periods. The statistical analysis of TWAS was performed using a mixed linear model, in which polygenic effect was fitted as a random effect according to gene expression level-based relationships. A total of 18,842 genes and 42,010 transcripts were detected, among which 35% of genes and 47% of transcripts were novel in comparison with the reference genome annotation. Furthermore, 45% of genes were widely expressed among more than 90% of individuals. The proportions (±SE) of phenotype variance explained by genome-wide gene expression level ranged from 0.501 ± 0.216 to 0.956 ± 0.209, and the similar results were obtained when explained by transcript expression level. In contrast, neither gene nor transcript was detected by TWAS to be statistically significantly associated with these growth traits. In conclusion, these novel genes and transcripts that have been extensively profiled in a single muscle tissue using long-read sequencing technology will greatly improve our understanding on transcriptional diversity in rabbits. Our results with a relatively small sample size further revealed the important contribution of global gene expression to phenotypic variation on growth performance, but it seemed that no single gene has an outstanding effect; this knowledge is helpful to include intermediate omics data for implementing genetic evaluation of growth traits in meat rabbits.
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Affiliation(s)
- Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhe Kang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Guozhi Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Kai Zhang
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xiangchao Fu
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Congyan Li
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Songjia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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12
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Han L, Shen B, Wu X, Zhang J, Wen YJ. Compressed variance component mixed model reveals epistasis associated with flowering in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2024; 14:1283642. [PMID: 38259933 PMCID: PMC10800901 DOI: 10.3389/fpls.2023.1283642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024]
Abstract
Introduction Epistasis is currently a topic of great interest in molecular and quantitative genetics. Arabidopsis thaliana, as a model organism, plays a crucial role in studying the fundamental biology of diverse plant species. However, there have been limited reports about identification of epistasis related to flowering in genome-wide association studies (GWAS). Therefore, it is of utmost importance to conduct epistasis in Arabidopsis. Method In this study, we employed Levene's test and compressed variance component mixed model in GWAS to detect quantitative trait nucleotides (QTNs) and QTN-by-QTN interactions (QQIs) for 11 flowering-related traits of 199 Arabidopsis accessions with 216,130 markers. Results Our analysis detected 89 QTNs and 130 pairs of QQIs. Around these loci, 34 known genes previously reported in Arabidopsis were confirmed to be associated with flowering-related traits, such as SPA4, which is involved in regulating photoperiodic flowering, and interacts with PAP1 and PAP2, affecting growth of Arabidopsis under light conditions. Then, we observed significant and differential expression of 35 genes in response to variations in temperature, photoperiod, and vernalization treatments out of unreported genes. Functional enrichment analysis revealed that 26 of these genes were associated with various biological processes. Finally, the haplotype and phenotypic difference analysis revealed 20 candidate genes exhibiting significant phenotypic variations across gene haplotypes, of which the candidate genes AT1G12990 and AT1G09950 around QQIs might have interaction effect to flowering time regulation in Arabidopsis. Discussion These findings may offer valuable insights for the identification and exploration of genes and gene-by-gene interactions associated with flowering-related traits in Arabidopsis, that may even provide valuable reference and guidance for the research of epistasis in other species.
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Affiliation(s)
- Le Han
- College of Science, Nanjing Agricultural University, Nanjing, China
| | - Bolin Shen
- College of Science, Nanjing Agricultural University, Nanjing, China
| | - Xinyi Wu
- College of Science, Nanjing Agricultural University, Nanjing, China
| | - Jin Zhang
- College of Science, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yang-Jun Wen
- College of Science, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
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13
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Yang N, Wang Y, Liu X, Jin M, Vallebueno-Estrada M, Calfee E, Chen L, Dilkes BP, Gui S, Fan X, Harper TK, Kennett DJ, Li W, Lu Y, Ding J, Chen Z, Luo J, Mambakkam S, Menon M, Snodgrass S, Veller C, Wu S, Wu S, Zhuo L, Xiao Y, Yang X, Stitzer MC, Runcie D, Yan J, Ross-Ibarra J. Two teosintes made modern maize. Science 2023; 382:eadg8940. [PMID: 38033071 DOI: 10.1126/science.adg8940] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/02/2023] [Indexed: 12/02/2023]
Abstract
The origins of maize were the topic of vigorous debate for nearly a century, but neither the current genetic model nor earlier archaeological models account for the totality of available data, and recent work has highlighted the potential contribution of a wild relative, Zea mays ssp. mexicana. Our population genetic analysis reveals that the origin of modern maize can be traced to an admixture between ancient maize and Zea mays ssp. mexicana in the highlands of Mexico some 4000 years after domestication began. We show that variation in admixture is a key component of maize diversity, both at individual loci and for additive genetic variation underlying agronomic traits. Our results clarify the origin of modern maize and raise new questions about the anthropogenic mechanisms underlying dispersal throughout the Americas.
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Affiliation(s)
- Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Miguel Vallebueno-Estrada
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, 36821 Guanajuato, México
| | - Erin Calfee
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Lu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Brian P Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650200, China
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Ziqi Chen
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Sowmya Mambakkam
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Mitra Menon
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
| | - Samantha Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Carl Veller
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Shenshen Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Siying Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Zhuo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Michelle C Stitzer
- Institute for Genomic Diversity and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Daniel Runcie
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Yazhouwan National Laboratory, Sanya 572024, China
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Genome Center, University of California, Davis, CA 95616, USA
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14
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Hatton AA, Hillary RF, Bernabeu E, McCartney DL, Marioni RE, McRae AF. Blood-based genome-wide DNA methylation correlations across body-fat- and adiposity-related biochemical traits. Am J Hum Genet 2023; 110:1564-1573. [PMID: 37652023 PMCID: PMC10502853 DOI: 10.1016/j.ajhg.2023.08.004] [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: 03/28/2023] [Revised: 08/04/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
The recent increase in obesity levels across many countries is likely to be driven by nongenetic factors. The epigenetic modification DNA methylation (DNAm) may help to explore this, as it is sensitive to both genetic and environmental exposures. While the relationship between DNAm and body-fat traits has been extensively studied, there is limited literature on the shared associations of DNAm variation across such traits. Akin to genetic correlation estimates, here, we introduce an approach to evaluate the similarities in DNAm associations between traits: DNAm correlations. As DNAm can be both a cause and consequence of complex traits, DNAm correlations have the potential to provide insights into trait relationships above that currently obtained from genetic and phenotypic correlations. Utilizing 7,519 unrelated individuals from Generation Scotland with DNAm from the EPIC array, we calculated DNAm correlations between body-fat- and adiposity-related traits by using the bivariate OREML framework in the OSCA software. For each trait, we also estimated the shared contribution of DNAm between sexes. We identified strong, positive DNAm correlations between each of the body-fat traits (BMI, body-fat percentage, and waist-to-hip ratio, ranging from 0.96 to 1.00), finding larger associations than those identified by genetic and phenotypic correlations. We identified a significant deviation from 1 in the DNAm correlations for BMI between males and females, with sex-specific DNAm changes associated with BMI identified at eight DNAm probes. Employing genome-wide DNAm correlations to evaluate the similarities in the associations of DNAm with complex traits has provided insight into obesity-related traits beyond that provided by genetic correlations.
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Affiliation(s)
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Elena Bernabeu
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, Brisbane, Australia.
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15
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Ren J, Loughnan R, Xu B, Thompson WK, Fan CC. Estimating the Total Variance Explained by Whole-Brain Imaging for Zero-inflated Outcomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553270. [PMID: 37645753 PMCID: PMC10462013 DOI: 10.1101/2023.08.14.553270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Zero-inflated outcomes are very common in behavioral data, particularly for responses to psychological questionnaires. Modeling these challenging distributions is further exacerbated by the absence of established statistical models capable of characterizing total signals attributed to whole-brain imaging features, making the accurate assessment of brain-behavior relationships particularly formidable. Given this critical need, we have developed a novel variational Bayes algorithm that characterizes the total signal captured by whole-brain imaging features for zero-inflated outcomes . Our zero-inflated variance (ZIV) estimator robustly estimates the fraction of variance explained (FVE) and the proportion of non-null effects from large-scale imaging data. In simulations, ZIV outperformed other linear prediction algorithms. Applying ZIV to data from one of the largest neuroimaging studies, the Adolescent Brain Cognitive Development SM (ABCD) Study, we found that whole-brain imaging features have a larger FVE for externalizing compared to internalizing behavior. We also demonstrate that the ZIV estimator, especially applied to focal sub-scales, can localize key neurocircuitry associated with human behavior.
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16
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Mortlock S, Houshdaran S, Kosti I, Rahmioglu N, Nezhat C, Vitonis AF, Andrews SV, Grosjean P, Paranjpe M, Horne AW, Jacoby A, Lager J, Opoku-Anane J, Vo KC, Manvelyan E, Sen S, Ghukasyan Z, Collins F, Santamaria X, Saunders P, Kober K, McRae AF, Terry KL, Vallvé-Juanico J, Becker C, Rogers PAW, Irwin JC, Zondervan K, Montgomery GW, Missmer S, Sirota M, Giudice L. Global endometrial DNA methylation analysis reveals insights into mQTL regulation and associated endometriosis disease risk and endometrial function. Commun Biol 2023; 6:780. [PMID: 37587191 PMCID: PMC10432557 DOI: 10.1038/s42003-023-05070-z] [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: 02/09/2023] [Accepted: 06/23/2023] [Indexed: 08/18/2023] Open
Abstract
Endometriosis is a leading cause of pain and infertility affecting millions of women globally. Herein, we characterize variation in DNA methylation (DNAm) and its association with menstrual cycle phase, endometriosis, and genetic variants through analysis of genotype data and methylation in endometrial samples from 984 deeply-phenotyped participants. We estimate that 15.4% of the variation in endometriosis is captured by DNAm and identify significant differences in DNAm profiles associated with stage III/IV endometriosis, endometriosis sub-phenotypes and menstrual cycle phase, including opening of the window for embryo implantation. Menstrual cycle phase was a major source of DNAm variation suggesting cellular and hormonally-driven changes across the cycle can regulate genes and pathways responsible for endometrial physiology and function. DNAm quantitative trait locus (mQTL) analysis identified 118,185 independent cis-mQTLs including 51 associated with risk of endometriosis, highlighting candidate genes contributing to disease risk. Our work provides functional evidence for epigenetic targets contributing to endometriosis risk and pathogenesis. Data generated serve as a valuable resource for understanding tissue-specific effects of methylation on endometrial biology in health and disease.
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Affiliation(s)
- Sally Mortlock
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Sahar Houshdaran
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Idit Kosti
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Nilufer Rahmioglu
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women's and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Camran Nezhat
- Stanford University Medical Center, Palo Alto, CA, USA
- University of California San Francisco, San Francisco, CA, USA
- Camran Nezhat Institute, Center for Special Minimally Invasive and Robotic Surgery, Woodside, CA, USA
| | - Allison F Vitonis
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shan V Andrews
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Parker Grosjean
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Manish Paranjpe
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Andrew W Horne
- MRC Centre for Reproductive Health, University of Edinburgh, QMRI, Edinburgh, UK
| | - Alison Jacoby
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Jeannette Lager
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Opoku-Anane
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kim Chi Vo
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Evelina Manvelyan
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sushmita Sen
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Zhanna Ghukasyan
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Frances Collins
- MRC Centre for Reproductive Health, University of Edinburgh, QMRI, Edinburgh, UK
| | - Xavier Santamaria
- Carlos Simon Foundation, Health Research Institute, Valencia, Spain
- Group of Biomedical Research in Gynecology, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Philippa Saunders
- Centre for Inflammation Research, Institute for Regeneration and Repair University of Edinburgh, Edinburgh, UK
| | - Kord Kober
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Physiological Nursing, University of California San Francisco, San Francisco, CA, USA
| | - Allan F McRae
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kathryn L Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Boston Center for Endometriosis, Boston Children's Hospital and Brigham and Women's Hospital, Boston, MA, USA
| | - Júlia Vallvé-Juanico
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Group of Biomedical Research in Gynecology, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Christian Becker
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women's and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Peter A W Rogers
- University of Melbourne Department of Obstetrics and Gynaecology, Royal Women's Hospital, Melbourne, Australia
| | - Juan C Irwin
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Krina Zondervan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women's and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Grant W Montgomery
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Stacey Missmer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Boston Center for Endometriosis, Boston Children's Hospital and Brigham and Women's Hospital, Boston, MA, USA
- Division of Adolescent and Young Adult Medicine, Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Division of Neonatology, University of California San Francisco, San Francisco, CA, USA
| | - Linda Giudice
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA.
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17
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Guo H, Cao P, Wang C, Lai J, Deng Y, Li C, Hao Y, Wu Z, Chen R, Qiang Q, Fernie AR, Yang J, Wang S. Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1888-1902. [PMID: 36971992 DOI: 10.1007/s11427-022-2299-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/17/2023] [Indexed: 03/29/2023]
Abstract
DNA methylation is an important epigenetic marker, yet its diversity and consequences in tomato breeding at the population level are largely unknown. We performed whole-genome bisulfite sequencing (WGBS), RNA sequencing, and metabolic profiling on a population comprising wild tomatoes, landraces, and cultivars. A total of 8,375 differentially methylated regions (DMRs) were identified, with methylation levels progressively decreasing from domestication to improvement. We found that over 20% of DMRs overlapped with selective sweeps. Moreover, more than 80% of DMRs in tomato were not significantly associated with single-nucleotide polymorphisms (SNPs), and DMRs had strong linkages with adjacent SNPs. We additionally profiled 339 metabolites from 364 diverse accessions and further performed a metabolic association study based on SNPs and DMRs. We detected 971 and 711 large-effect loci via SNP and DMR markers, respectively. Combined with multi-omics, we identified 13 candidate genes and updated the polyphenol biosynthetic pathway. Our results showed that DNA methylation variants could complement SNP profiling of metabolite diversity. Our study thus provides a DNA methylome map across diverse accessions and suggests that DNA methylation variation can be the genetic basis of metabolic diversity in plants.
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Affiliation(s)
- Hao Guo
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Peng Cao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Chao Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Jun Lai
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Yuan Deng
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Chun Li
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Yingchen Hao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Zeyong Wu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Ridong Chen
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Qi Qiang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, 144776, Germany
| | - Jun Yang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Shouchuang Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
- College of Tropical Crops, Hainan University, Haikou, 572208, China.
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18
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Zhou Y, Zhou K, Lin X, Wei Y, Ma B, Lu S, Xie G, Zhang Z, Liang J. Association of gut microbiota, plasma and fecal metabolite profiles with intellectual development in school-age children. Transl Pediatr 2023; 12:1292-1304. [PMID: 37575906 PMCID: PMC10416130 DOI: 10.21037/tp-22-610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/18/2023] [Indexed: 08/15/2023] Open
Abstract
Background Little is known about how the gut microbiota and metabolic profiles are related to cognitive outcomes in young children until now. It was hypothesized that the gut microbiota, the plasma and fecal metabolites significantly correlated with intelligence quotient (IQ) in school-age children in current study. Methods This cross-sectional study enrolled 452 children aged 6-9 years old. IQ was measured using the Wechsler Intelligence Scale for Children-Fourth Edition. Fecal microbiota, plasma and fecal metabolites were analyzed using 16S rRNA amplicon sequencing and targeted metabolomic technologies, respectively. Results Restricted maximum likelihood (REML) analyses showed that microbiota composition and fecal metabolites were associated with neither subscale nor full-scale IQ (P: 0.059-0.500). However, plasma metabolites were significantly correlated with the processing speed (P=0.008). In multiple regression analysis after adjusting for confounders and multiple test correction, benzoic acid, azelaic acid, adipic acid, suberic acid and malonic acid selected by the multivariate methods with unbiased variable selection were positively associated with processing speed index (PSI) [Pfalse discovery rate (FDR): 0.006-0.024], whereas pyruvic acid was negatively associated with the PSI and full-scale IQ (PFDR: 0.014-0.030). Conclusions In normal school-age children, certain plasma metabolites concentrations but not the gut microbiota composition nor fecal metabolites are correlated with intelligence.
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Affiliation(s)
- Yingyu Zhou
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Kejun Zhou
- Human Metabolomics Institute, Inc., Shenzhen, China
| | - Xiaoping Lin
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yuanhuan Wei
- Department of Clinical Nutrition, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Bingjie Ma
- Department of Child Health Care, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Shaomin Lu
- Department of Child Health Care, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Guoxiang Xie
- Human Metabolomics Institute, Inc., Shenzhen, China
| | - Zheqing Zhang
- Department of Nutrition and Food Hygiene, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jingjing Liang
- Department of Child Health Care, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
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19
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Allaire P, He J, Mayer J, Moat L, Gerstenberger P, Wilhorn R, Strutz S, Kim DS, Zeng C, Cox N, Shay JW, Denny J, Bastarache L, Hebbring S. Genetic and clinical determinants of telomere length. HGG ADVANCES 2023; 4:100201. [PMID: 37216007 PMCID: PMC10199259 DOI: 10.1016/j.xhgg.2023.100201] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
Many epidemiologic studies have identified important relationships between leukocyte telomere length (LTL) with genetics and health. Most of these studies have been significantly limited in scope by focusing predominantly on individual diseases or restricted to GWAS analysis. Using two large patient populations derived from Vanderbilt University and Marshfield Clinic biobanks linked to genomic and phenomic data from medical records, we investigated the inter-relationship between LTL, genomics, and human health. Our GWAS confirmed 11 genetic loci previously associated with LTL and two novel loci in SCNN1D and PITPNM1. PheWAS of LTL identified 67 distinct clinical phenotypes associated with both short and long LTL. We demonstrated that several diseases associated with LTL were related to one another but were largely independent from LTL genetics. Age of death was correlated with LTL independent of age. Those with very short LTL (<-1.5 standard deviation [SD]) died 10.4 years (p < 0.0001) younger than those with average LTL (±0.5 SD; mean age of death = 74.2 years). Likewise, those with very long LTL (>1.5 SD) died 1.9 years (p = 0.0175) younger than those with average LTL. This is consistent with the PheWAS results showing diseases associating with both short and long LTL. Finally, we estimated that the genome (12.8%) and age (8.5%) explain the largest proportion of LTL variance, whereas the phenome (1.5%) and sex (0.9%) explained a smaller fraction. In total, 23.7% of LTL variance was explained. These observations provide the rationale for expanded research to understand the multifaceted correlations between TL biology and human health over time, leading to effective LTL usage in medical applications.
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Affiliation(s)
- Patrick Allaire
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield, WI, USA
| | - Jing He
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John Mayer
- Marshfield Clinic Research Institute, Office of Research Computing and Analytics, Marshfield, WI, USA
| | - Luke Moat
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield, WI, USA
| | - Peter Gerstenberger
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield, WI, USA
| | - Reynor Wilhorn
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield, WI, USA
| | - Sierra Strutz
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield, WI, USA
| | - David S.L. Kim
- Marshfield Clinic Health System, Pathology, Marshfield, WI, USA
| | - Chenjie Zeng
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nancy Cox
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jerry W. Shay
- University of Texas Southwestern Medical Center, Department of Cell Biology and the Simmons Comprehensive Cancer Center, Dallas, TX, USA
| | - Joshua Denny
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lisa Bastarache
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott Hebbring
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield, WI, USA
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20
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Hillary RF, McCartney DL, Smith HM, Bernabeu E, Gadd DA, Chybowska AD, Cheng Y, Murphy L, Wrobel N, Campbell A, Walker RM, Hayward C, Evans KL, McIntosh AM, Marioni RE. Blood-based epigenome-wide analyses of 19 common disease states: A longitudinal, population-based linked cohort study of 18,413 Scottish individuals. PLoS Med 2023; 20:e1004247. [PMID: 37410739 PMCID: PMC10325072 DOI: 10.1371/journal.pmed.1004247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/25/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND DNA methylation is a dynamic epigenetic mechanism that occurs at cytosine-phosphate-guanine dinucleotide (CpG) sites. Epigenome-wide association studies (EWAS) investigate the strength of association between methylation at individual CpG sites and health outcomes. Although blood methylation may act as a peripheral marker of common disease states, previous EWAS have typically focused only on individual conditions and have had limited power to discover disease-associated loci. This study examined the association of blood DNA methylation with the prevalence of 14 disease states and the incidence of 19 disease states in a single population of over 18,000 Scottish individuals. METHODS AND FINDINGS DNA methylation was assayed at 752,722 CpG sites in whole-blood samples from 18,413 volunteers in the family-structured, population-based cohort study Generation Scotland (age range 18 to 99 years). EWAS tested for cross-sectional associations between baseline CpG methylation and 14 prevalent disease states, and for longitudinal associations between baseline CpG methylation and 19 incident disease states. Prevalent cases were self-reported on health questionnaires at the baseline. Incident cases were identified using linkage to Scottish primary (Read 2) and secondary (ICD-10) care records, and the censoring date was set to October 2020. The mean time-to-diagnosis ranged from 5.0 years (for chronic pain) to 11.7 years (for Coronavirus Disease 2019 (COVID-19) hospitalisation). The 19 disease states considered in this study were selected if they were present on the World Health Organisation's 10 leading causes of death and disease burden or included in baseline self-report questionnaires. EWAS models were adjusted for age at methylation typing, sex, estimated white blood cell composition, population structure, and 5 common lifestyle risk factors. A structured literature review was also conducted to identify existing EWAS for all 19 disease states tested. The MEDLINE, Embase, Web of Science, and preprint servers were searched to retrieve relevant articles indexed as of March 27, 2023. Fifty-four of approximately 2,000 indexed articles met our inclusion criteria: assayed blood-based DNA methylation, had >20 individuals in each comparison group, and examined one of the 19 conditions considered. First, we assessed whether the associations identified in our study were reported in previous studies. We identified 69 associations between CpGs and the prevalence of 4 conditions, of which 58 were newly described. The conditions were breast cancer, chronic kidney disease, ischemic heart disease, and type 2 diabetes mellitus. We also uncovered 64 CpGs that associated with the incidence of 2 disease states (COPD and type 2 diabetes), of which 56 were not reported in the surveyed literature. Second, we assessed replication across existing studies, which was defined as the reporting of at least 1 common site in >2 studies that examined the same condition. Only 6/19 disease states had evidence of such replication. The limitations of this study include the nonconsideration of medication data and a potential lack of generalizability to individuals that are not of Scottish and European ancestry. CONCLUSIONS We discovered over 100 associations between blood methylation sites and common disease states, independently of major confounding risk factors, and a need for greater standardisation among EWAS on human disease.
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Affiliation(s)
- Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Hannah M. Smith
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Elena Bernabeu
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Danni A. Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Aleksandra D. Chybowska
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Yipeng Cheng
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, United Kingdom
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, United Kingdom
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Rosie M. Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- School of Psychology, University of Exeter, Exeter, United Kingdom
| | - Caroline Hayward
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew M. McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, United Kingdom
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
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21
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Babu M, Snyder M. Multi-Omics Profiling for Health. Mol Cell Proteomics 2023; 22:100561. [PMID: 37119971 PMCID: PMC10220275 DOI: 10.1016/j.mcpro.2023.100561] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/01/2023] Open
Abstract
The world has witnessed a steady rise in both non-infectious and infectious chronic diseases, prompting a cross-disciplinary approach to understand and treating disease. Current medical care focuses on treating people after they become patients rather than preventing illness, leading to high costs in treating chronic and late-stage diseases. Additionally, a "one-size-fits all" approach to health care does not take into account individual differences in genetics, environment, or lifestyle factors, decreasing the number of people benefiting from interventions. Rapid advances in omics technologies and progress in computational capabilities have led to the development of multi-omics deep phenotyping, which profiles the interaction of multiple levels of biology over time and empowers precision health approaches. This review highlights current and emerging multi-omics modalities for precision health and discusses applications in the following areas: genetic variation, cardio-metabolic diseases, cancer, infectious diseases, organ transplantation, pregnancy, and longevity/aging. We will briefly discuss the potential of multi-omics approaches in disentangling host-microbe and host-environmental interactions. We will touch on emerging areas of electronic health record and clinical imaging integration with muti-omics for precision health. Finally, we will briefly discuss the challenges in the clinical implementation of multi-omics and its future prospects.
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Affiliation(s)
- Mohan Babu
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.
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22
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Kimbrel NA, Garrett ME, Evans MK, Mellows C, Dennis MF, Hair LP, Hauser MA, Ashley-Koch AE, Beckham JC. Large epigenome-wide association study identifies multiple novel differentially methylated CpG sites associated with suicidal thoughts and behaviors in veterans. Front Psychiatry 2023; 14:1145375. [PMID: 37398583 PMCID: PMC10311443 DOI: 10.3389/fpsyt.2023.1145375] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/28/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction The U.S. suicide mortality rate has steadily increased during the past two decades, particularly among military veterans; however, the epigenetic basis of suicidal thoughts and behaviors (STB) remains largely unknown. Methods To address this issue, we conducted an epigenome-wide association study of DNA methylation (DNAm) of peripheral blood samples obtained from 2,712 U.S. military veterans. Results Three DNAm probes were significantly associated with suicide attempts, surpassing the multiple testing threshold (FDR q-value <0.05), including cg13301722 on chromosome 7, which lies between the genes SLC4A2 and CDK5; cg04724646 in PDE3A; and cg04999352 in RARRES3. cg13301722 was also found to be differentially methylated in the cerebral cortex of suicide decedents in a publicly-available dataset (p = 0.03). Trait enrichment analysis revealed that the CpG sites most strongly associated with STB in the present sample were also associated with smoking, alcohol consumption, maternal smoking, and maternal alcohol consumption, whereas pathway enrichment analysis revealed significant associations with circadian rhythm, adherens junction, insulin secretion, and RAP-1 signaling, each of which was recently associated with suicide attempts in a large, independent genome-wide association study of suicide attempts of veterans. Discussion Taken together, the present findings suggest that SLC4A2, CDK5, PDE3A, and RARRES3 may play a role in STB. CDK5, a member of the cyclin-dependent kinase family that is highly expressed in the brain and essential for learning and memory, appears to be a particularly promising candidate worthy of future study; however, additional work is still needed to replicate these finding in independent samples.
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Affiliation(s)
- Nathan A. Kimbrel
- Durham Veterans Affairs (VA) Health Care System, Durham, NC, United States
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham, NC, United States
- VA Health Services Research and Development Center of Innovation to Accelerate Discovery and Practice Transformation, Durham, NC, United States
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, United States
| | | | - Mariah K. Evans
- Durham Veterans Affairs (VA) Health Care System, Durham, NC, United States
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, United States
| | - Clara Mellows
- Department of Psychology and Neuroscience, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Michelle F. Dennis
- Durham Veterans Affairs (VA) Health Care System, Durham, NC, United States
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, United States
| | - Lauren P. Hair
- Durham Veterans Affairs (VA) Health Care System, Durham, NC, United States
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, United States
| | | | | | - Jean C. Beckham
- Durham Veterans Affairs (VA) Health Care System, Durham, NC, United States
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham, NC, United States
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, United States
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23
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Queen K, Nguyen MN, Gilliland FD, Chun S, Raby BA, Millstein J. ACDC: a general approach for detecting phenotype or exposure associated co-expression. Front Med (Lausanne) 2023; 10:1118824. [PMID: 37275375 PMCID: PMC10235619 DOI: 10.3389/fmed.2023.1118824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Background Existing module-based differential co-expression methods identify differences in gene-gene relationships across phenotype or exposure structures by testing for consistent changes in transcription abundance. Current methods only allow for assessment of co-expression variation across a singular, binary or categorical exposure or phenotype, limiting the information that can be obtained from these analyses. Methods Here, we propose a novel approach for detection of differential co-expression that simultaneously accommodates multiple phenotypes or exposures with binary, ordinal, or continuous data types. Results We report an application to two cohorts of asthmatic patients with varying levels of asthma control to identify associations between gene co-expression and asthma control test scores. Results suggest that both expression levels and covariances of ADORA3, ALOX15, and IDO1 are associated with asthma control. Conclusion ACDC is a flexible extension to existing methodology that can detect differential co-expression across varying external variables.
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Affiliation(s)
- Katelyn Queen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - My-Nhi Nguyen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Frank D. Gilliland
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Sung Chun
- Division of Pulmonary Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - Benjamin A. Raby
- Division of Pulmonary Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Joshua Millstein
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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24
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Gao C, Amador C, Walker RM, Campbell A, Madden RA, Adams MJ, Bai X, Liu Y, Li M, Hayward C, Porteous DJ, Shen X, Evans KL, Haley CS, McIntosh AM, Navarro P, Zeng Y. Phenome-wide analyses identify an association between the parent-of-origin effects dependent methylome and the rate of aging in humans. Genome Biol 2023; 24:117. [PMID: 37189164 PMCID: PMC10184337 DOI: 10.1186/s13059-023-02953-6] [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: 10/05/2022] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND The variation in the rate at which humans age may be rooted in early events acting through the genomic regions that are influenced by such events and subsequently are related to health phenotypes in later life. The parent-of-origin-effect (POE)-regulated methylome includes regions enriched for genetically controlled imprinting effects (the typical type of POE) and regions influenced by environmental effects associated with parents (the atypical POE). This part of the methylome is heavily influenced by early events, making it a potential route connecting early exposures, the epigenome, and aging. We aim to test the association of POE-CpGs with early and later exposures and subsequently with health-related phenotypes and adult aging. RESULTS We perform a phenome-wide association analysis for the POE-influenced methylome using GS:SFHS (Ndiscovery = 5087, Nreplication = 4450). We identify and replicate 92 POE-CpG-phenotype associations. Most of the associations are contributed by the POE-CpGs belonging to the atypical class where the most strongly enriched associations are with aging (DNAmTL acceleration), intelligence, and parental (maternal) smoking exposure phenotypes. A proportion of the atypical POE-CpGs form co-methylation networks (modules) which are associated with these phenotypes, with one of the aging-associated modules displaying increased within-module methylation connectivity with age. The atypical POE-CpGs also display high levels of methylation heterogeneity, fast information loss with age, and a strong correlation with CpGs contained within epigenetic clocks. CONCLUSIONS These results identify the association between the atypical POE-influenced methylome and aging and provide new evidence for the "early development of origin" hypothesis for aging in humans.
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Affiliation(s)
- Chenhao Gao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Carmen Amador
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rosie M Walker
- Centre for Clinical Brain Sciences, Chancellor's Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- School of Psychology, University of Exeter, Perry Road, Exeter, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | | | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - Xiaomeng Bai
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Ying Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xueyi Shen
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Chris S Haley
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - Yanni Zeng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
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25
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Yap CX, Henders AK, Alvares GA, Giles C, Huynh K, Nguyen A, Wallace L, McLaren T, Yang Y, Hernandez LM, Gandal MJ, Hansell NK, Cleary D, Grove R, Hafekost C, Harun A, Holdsworth H, Jellett R, Khan F, Lawson LP, Leslie J, Levis Frenk M, Masi A, Mathew NE, Muniandy M, Nothard M, Miller JL, Nunn L, Strike LT, Cadby G, Moses EK, de Zubicaray GI, Thompson PM, McMahon KL, Wright MJ, Visscher PM, Dawson PA, Dissanayake C, Eapen V, Heussler HS, Whitehouse AJO, Meikle PJ, Wray NR, Gratten J. Interactions between the lipidome and genetic and environmental factors in autism. Nat Med 2023; 29:936-949. [PMID: 37076741 PMCID: PMC10115648 DOI: 10.1038/s41591-023-02271-1] [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: 05/27/2022] [Accepted: 02/22/2023] [Indexed: 04/21/2023]
Abstract
Autism omics research has historically been reductionist and diagnosis centric, with little attention paid to common co-occurring conditions (for example, sleep and feeding disorders) and the complex interplay between molecular profiles and neurodevelopment, genetics, environmental factors and health. Here we explored the plasma lipidome (783 lipid species) in 765 children (485 diagnosed with autism spectrum disorder (ASD)) within the Australian Autism Biobank. We identified lipids associated with ASD diagnosis (n = 8), sleep disturbances (n = 20) and cognitive function (n = 8) and found that long-chain polyunsaturated fatty acids may causally contribute to sleep disturbances mediated by the FADS gene cluster. We explored the interplay of environmental factors with neurodevelopment and the lipidome, finding that sleep disturbances and unhealthy diet have a convergent lipidome profile (with potential mediation by the microbiome) that is also independently associated with poorer adaptive function. In contrast, ASD lipidome differences were accounted for by dietary differences and sleep disturbances. We identified a large chr19p13.2 copy number variant genetic deletion spanning the LDLR gene and two high-confidence ASD genes (ELAVL3 and SMARCA4) in one child with an ASD diagnosis and widespread low-density lipoprotein-related lipidome derangements. Lipidomics captures the complexity of neurodevelopment, as well as the biological effects of conditions that commonly affect quality of life among autistic people.
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Affiliation(s)
- Chloe X Yap
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia.
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Gail A Alvares
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Corey Giles
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kevin Huynh
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anh Nguyen
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Tiana McLaren
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Yuanhao Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Leanna M Hernandez
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Lifespan Brain Institute at Penn Medicine and The Children's Hospital of Philadelphia, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Narelle K Hansell
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Dominique Cleary
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Rachel Grove
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Faculty of Health, University of Technology Sydney, Sydney, New South Wales, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Claire Hafekost
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Alexis Harun
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Helen Holdsworth
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Rachel Jellett
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, Victoria, Australia
| | - Feroza Khan
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Lauren P Lawson
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Department of Psychology, Counselling and Therapy, La Trobe University, Melbourne, Victoria, Australia
| | - Jodie Leslie
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Mira Levis Frenk
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Anne Masi
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Nisha E Mathew
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Melanie Muniandy
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, Victoria, Australia
| | - Michaela Nothard
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, Victoria, Australia
| | - Jessica L Miller
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Lorelle Nunn
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Lachlan T Strike
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Gemma Cadby
- School of Population and Global Health, The University of Western Australia, Perth, Western Australia, Australia
| | - Eric K Moses
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Greig I de Zubicaray
- School of Psychology and Counselling, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Katie L McMahon
- School of Clinical Sciences, Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Margaret J Wright
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Paul A Dawson
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Cheryl Dissanayake
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, Victoria, Australia
| | - Valsamma Eapen
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Academic Unit of Child Psychiatry South West Sydney, Ingham Institute for Applied Medical Research, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Helen S Heussler
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Child Development Program, Children's Health Queensland, Brisbane, Queensland, Australia
| | - Andrew J O Whitehouse
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Jacob Gratten
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia.
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26
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Genome-Wide Analysis of Dental Caries Variability Reveals Genotype-by-Environment Interactions. Genes (Basel) 2023; 14:genes14030736. [PMID: 36981009 PMCID: PMC10048401 DOI: 10.3390/genes14030736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/09/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Genotype-by-environment interactions (GEI) may influence dental caries, although their effects are difficult to detect. Variance quantitative trait loci (vQTL) may serve as an indicator of underlying GEI effects. The aim of this study was to investigate GEI effects on dental caries by prioritizing variants from genome-wide vQTL analysis. First, we identified vQTLs from ~4.3 M genome-wide variants in three cohorts of white children aged 3–5 (n = 396, n = 328, n = 773) using Levene’s test. A total of 39 independent vQTLs with p < 1 × 10−6 were identified, some of which were located in or near genes with plausible biological roles in dental caries (IGFBP7, SLC5A8, and SHH involved in tooth development and enamel mineralization). Next, we used linear regression to test GEI effects on dental caries with the 39 prioritized variants and self-reported environmental factors (demographic, socioeconomic, behavioral, and dietary factors) in the three cohorts separately. We identified eight significant GEIs indicating that children with vQTL risk genotypes had higher caries experience if they had less educated parents, lower household/parental income, brushed their teeth less frequently, consumed sugar-sweetened beverages more frequently, were not breastfed, and were female. We reported the first genome-wide vQTL analysis of dental caries in children nominating several novel genes and GEI for further investigations.
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27
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Rahmioglu N, Mortlock S, Ghiasi M, Møller PL, Stefansdottir L, Galarneau G, Turman C, Danning R, Law MH, Sapkota Y, Christofidou P, Skarp S, Giri A, Banasik K, Krassowski M, Lepamets M, Marciniak B, Nõukas M, Perro D, Sliz E, Sobalska-Kwapis M, Thorleifsson G, Topbas-Selcuki NF, Vitonis A, Westergaard D, Arnadottir R, Burgdorf KS, Campbell A, Cheuk CSK, Clementi C, Cook J, De Vivo I, DiVasta A, Dorien O, Donoghue JF, Edwards T, Fontanillas P, Fung JN, Geirsson RT, Girling JE, Harkki P, Harris HR, Healey M, Heikinheimo O, Holdsworth-Carson S, Hostettler IC, Houlden H, Houshdaran S, Irwin JC, Jarvelin MR, Kamatani Y, Kennedy SH, Kepka E, Kettunen J, Kubo M, Kulig B, Kurra V, Laivuori H, Laufer MR, Lindgren CM, MacGregor S, Mangino M, Martin NG, Matalliotaki C, Matalliotakis M, Murray AD, Ndungu A, Nezhat C, Olsen CM, Opoku-Anane J, Padmanabhan S, Paranjpe M, Peters M, Polak G, Porteous DJ, Rabban J, Rexrode KM, Romanowicz H, Saare M, Saavalainen L, Schork AJ, Sen S, Shafrir AL, Siewierska-Górska A, Słomka M, Smith BH, Smolarz B, Szaflik T, Szyłło K, Takahashi A, Terry KL, Tomassetti C, Treloar SA, Vanhie A, Vincent K, Vo KC, Werring DJ, Zeggini E, Zervou MI, Adachi S, Buring JE, Ridker PM, D’Hooghe T, Goulielmos GN, Hapangama DK, Hayward C, Horne AW, Low SK, Martikainen H, Chasman DI, Rogers PAW, Saunders PT, Sirota M, Spector T, Strapagiel D, Tung JY, Whiteman DC, Giudice LC, Velez-Edwards DR, Uimari O, Kraft P, Salumets A, Nyholt DR, Mägi R, Stefansson K, Becker CM, Yurttas-Beim P, Steinthorsdottir V, Nyegaard M, Missmer SA, Montgomery GW, Morris AP, Zondervan KT. The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions. Nat Genet 2023; 55:423-436. [PMID: 36914876 PMCID: PMC10042257 DOI: 10.1038/s41588-023-01323-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/27/2023] [Indexed: 03/16/2023]
Abstract
Endometriosis is a common condition associated with debilitating pelvic pain and infertility. A genome-wide association study meta-analysis, including 60,674 cases and 701,926 controls of European and East Asian descent, identified 42 genome-wide significant loci comprising 49 distinct association signals. Effect sizes were largest for stage 3/4 disease, driven by ovarian endometriosis. Identified signals explained up to 5.01% of disease variance and regulated expression or methylation of genes in endometrium and blood, many of which were associated with pain perception/maintenance (SRP14/BMF, GDAP1, MLLT10, BSN and NGF). We observed significant genetic correlations between endometriosis and 11 pain conditions, including migraine, back and multisite chronic pain (MCP), as well as inflammatory conditions, including asthma and osteoarthritis. Multitrait genetic analyses identified substantial sharing of variants associated with endometriosis and MCP/migraine. Targeted investigations of genetically regulated mechanisms shared between endometriosis and other pain conditions are needed to aid the development of new treatments and facilitate early symptomatic intervention.
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Affiliation(s)
- Nilufer Rahmioglu
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women’s and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Sally Mortlock
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Marzieh Ghiasi
- Department of Epidemiology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Peter L Møller
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | | | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rebecca Danning
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston MA, USA
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Biomedical Sciences, Faculty of Health, and Institute of health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland, Australia
| | - Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Paraskevi Christofidou
- Department of Twin Research and Genetic Epidemiology, St. Thomas’ Hospital, Kings College London, London, UK
| | - Sini Skarp
- Northern Finland Birth Cohorts, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Ayush Giri
- Department of Obstetrics and Gynecology, Institute of Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michal Krassowski
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women’s and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Maarja Lepamets
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Błażej Marciniak
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Margit Nõukas
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Danielle Perro
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women’s and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Eeva Sliz
- Computational Medicine and Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | | | - Nura F Topbas-Selcuki
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women’s and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Allison Vitonis
- Boston Center for Endometriosis, Boston Children’s Hospital and Brigham and Women’s Hospital, Boston, MA, USA
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ragnheidur Arnadottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, Iceland
| | - Kristoffer S Burgdorf
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Cecilia SK Cheuk
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women’s and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | | | - James Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Amy DiVasta
- Boston Center for Endometriosis, Boston Children’s Hospital and Brigham and Women’s Hospital, Boston, MA, USA
- Division of Adolescent and Young Adult Medicine, Department of Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - O Dorien
- Department of Obstetrics and Gynaecology, Leuven University Fertility Centre, University Hospital Leuven, Leuven, Belgium
- KULeuven (University of Leuven), Department of Development and Regeneration, Organ systems, Leuven, Belgium
| | - Jacqueline F Donoghue
- University of Melbourne Department of Obstetrics and Gynaecology, Royal Women’s Hospital, Melbourne, Australia
| | - Todd Edwards
- Department of Obstetrics and Gynecology, Institute of Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Jenny N Fung
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Reynir T Geirsson
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, Iceland
| | - Jane E Girling
- University of Melbourne Department of Obstetrics and Gynaecology, Royal Women’s Hospital, Melbourne, Australia
- Department of Anatomy, School of Biomedical Sciences, University of Otago, New Zealand
| | - Paivi Harkki
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Holly R Harris
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Martin Healey
- University of Melbourne Department of Obstetrics and Gynaecology, Royal Women’s Hospital, Melbourne, Australia
| | - Oskari Heikinheimo
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sarah Holdsworth-Carson
- University of Melbourne Department of Obstetrics and Gynaecology, Royal Women’s Hospital, Melbourne, Australia
| | - Isabel C Hostettler
- Stroke Research Centre, University College London, Institute of Neurology, London, UK
- Neurogenetics Laboratory, The National Hospital of Neurology and Neurosurgery, London, UK
- Department of Neurosurgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Henry Houlden
- Neurogenetics Laboratory, The National Hospital of Neurology and Neurosurgery, London, UK
| | - Sahar Houshdaran
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Juan C Irwin
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Computational Medicine and Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, Middlesex, UK
| | | | - Stephen H Kennedy
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women’s and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Ewa Kepka
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Johannes Kettunen
- Computational Medicine and Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Institute for Health and Welfare, Helsinki, Finland
| | - Michiaki Kubo
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Bartosz Kulig
- Department of Operative Gynecology and Oncological Gynecology, Polish Mother’s Memorial Hospital - Research Institute, Łódź, Poland
| | - Venla Kurra
- Department of Obstetrics and Gynecology, Tampere University Hospital, Tampere, Finland
- Faculty of Medicine and Health Technology, University of Tampere, Tampere, Finland
| | - Hannele Laivuori
- Department of Obstetrics and Gynecology, Tampere University Hospital, Tampere, Finland
- Faculty of Medicine and Health Technology, University of Tampere, Tampere, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Marc R Laufer
- Boston Center for Endometriosis, Boston Children’s Hospital and Brigham and Women’s Hospital, Boston, MA, USA
- Division of Adolescent and Young Adult Medicine, Department of Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gynecology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Cecilia M Lindgren
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women’s and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Big Data Institute at the Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, University of Queensland, Queensland, Australia
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, St. Thomas’ Hospital, Kings College London, London, UK
- NIHR Biomedical Research Centre at Guy’s and St Thomas’ Foundation Trust, London, UK
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Charoula Matalliotaki
- Third Department of Obstetrics and Gynecology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Michail Matalliotakis
- Third Department of Obstetrics and Gynecology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Alison D Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, UK
| | - Anne Ndungu
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women’s and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Camran Nezhat
- Center For Special Minimally Invasive and Robotic Surgery, Camran Nezhat Institute, Palo Alto, CA, USA
| | - Catherine M Olsen
- Department of Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jessica Opoku-Anane
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Manish Paranjpe
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Maire Peters
- Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Grzegorz Polak
- 1st Department of Oncological Gynecology and Gynecology, Medical University of Lublin, Poland
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Joseph Rabban
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Kathyrn M Rexrode
- Division of Women’s Health, Brigham and Women’s Hospital, Boston MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Hanna Romanowicz
- Laboratory of Cancer Genetics, Department of Clinical Pathomorphology, Polish Mother’s Memorial Hospital - Research Institute, Łódź, Poland
| | - Merli Saare
- Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Liisu Saavalainen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Andrew J Schork
- Institute of Biological Psychiatry, Mental Health Center, Sct. Hans, Mental Health Services, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Sushmita Sen
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Amy L Shafrir
- Boston Center for Endometriosis, Boston Children’s Hospital and Brigham and Women’s Hospital, Boston, MA, USA
- Division of Adolescent and Young Adult Medicine, Department of Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Anna Siewierska-Górska
- Computational Medicine and Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Marcin Słomka
- Computational Medicine and Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Beata Smolarz
- Laboratory of Cancer Genetics, Department of Clinical Pathomorphology, Polish Mother’s Memorial Hospital - Research Institute, Łódź, Poland
| | - Tomasz Szaflik
- Department of Operative Gynecology and Oncological Gynecology, Polish Mother’s Memorial Hospital - Research Institute, Łódź, Poland
| | - Krzysztof Szyłło
- Department of Operative Gynecology and Oncological Gynecology, Polish Mother’s Memorial Hospital - Research Institute, Łódź, Poland
| | - Atsushi Takahashi
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Research Institute, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Kathryn L Terry
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Boston Center for Endometriosis, Boston Children’s Hospital and Brigham and Women’s Hospital, Boston, MA, USA
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Carla Tomassetti
- Department of Obstetrics and Gynaecology, Leuven University Fertility Centre, University Hospital Leuven, Leuven, Belgium
- KULeuven (University of Leuven), Department of Development and Regeneration, Organ systems, Leuven, Belgium
| | - Susan A Treloar
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Arne Vanhie
- Department of Obstetrics and Gynaecology, Leuven University Fertility Centre, University Hospital Leuven, Leuven, Belgium
- KULeuven (University of Leuven), Department of Development and Regeneration, Organ systems, Leuven, Belgium
| | - Katy Vincent
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women’s and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Kim C Vo
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - David J Werring
- Stroke Research Centre, University College London, Institute of Neurology, London, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Wellcome Sanger Institute, Hinxton, United Kingdom
- TUM School of Medicine, Technical University of Munich and Klinikum Rechts der Isar, Munich, Germany
| | - Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | | | | | | | | | - Sosuke Adachi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Thomas D’Hooghe
- KULeuven (University of Leuven), Department of Development and Regeneration, Organ systems, Leuven, Belgium
- Global Medical Affairs Fertility, Research and Development, Merck, Darmstadt, Germany
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Dharani K Hapangama
- Department of Women’s and Children’s Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Andrew W Horne
- MRC Centre for Reproductive Health, University of Edinburgh, Institute for Regeneration and Repair, Edinburgh, UK
| | - Siew-Kee Low
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hannu Martikainen
- Department of Obstetrics and Gynecology, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Peter AW Rogers
- University of Melbourne Department of Obstetrics and Gynaecology, Royal Women’s Hospital, Melbourne, Australia
| | - Philippa T Saunders
- Centre for Inflammation Research, University of Edinburgh, Institute for Regeneration and Repair, Edinburgh, UK
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, St. Thomas’ Hospital, Kings College London, London, UK
| | - Dominik Strapagiel
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | | | - David C Whiteman
- Department of Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Linda C Giudice
- Center for Reproductive Sciences, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Digna R Velez-Edwards
- Department of Obstetrics and Gynecology, Institute of Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Outi Uimari
- Department of Obstetrics and Gynecology, Oulu University Hospital, Oulu, Finland
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andres Salumets
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Dale R Nyholt
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Biomedical Sciences, Faculty of Health, and Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kari Stefansson
- deCODE genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Christian M Becker
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women’s and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | | | | | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Health, Science and Technology, Aalborg University, Aalborg, Denmark
| | - Stacey A Missmer
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Boston Center for Endometriosis, Boston Children’s Hospital and Brigham and Women’s Hospital, Boston, MA, USA
- Division of Adolescent and Young Adult Medicine, Department of Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Grant W Montgomery
- The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Krina T Zondervan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Endometriosis CaRe Centre, Nuffield Department of Women’s and Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, UK
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Nabais MF, Gadd DA, Hannon E, Mill J, McRae AF, Wray NR. An overview of DNA methylation-derived trait score methods and applications. Genome Biol 2023; 24:28. [PMID: 36797751 PMCID: PMC9936670 DOI: 10.1186/s13059-023-02855-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 01/17/2023] [Indexed: 02/18/2023] Open
Abstract
Microarray technology has been used to measure genome-wide DNA methylation in thousands of individuals. These studies typically test the associations between individual DNA methylation sites ("probes") and complex traits or diseases. The results can be used to generate methylation profile scores (MPS) to predict outcomes in independent data sets. Although there are many parallels between MPS and polygenic (risk) scores (PGS), there are key differences. Here, we review motivations, methods, and applications of DNA methylation-based trait prediction, with a focus on common diseases. We contrast MPS with PGS, highlighting where assumptions made in genetic modeling may not hold in epigenetic data.
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Affiliation(s)
- Marta F Nabais
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Eilis Hannon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Jonathan Mill
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
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29
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Gao C, Amador C, Walker RM, Campbell A, Madden RA, Adams MJ, Bai X, Liu Y, Li M, Hayward C, Porteous DJ, Shen X, Evans KL, Haley CS, McIntosh AM, Navarro P, Zeng Y. Phenome-wide analysis identifies parent-of-origin effects on the human methylome associated with changes in the rate of aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524653. [PMID: 36711749 PMCID: PMC9882261 DOI: 10.1101/2023.01.18.524653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Variation in the rate at which humans age may be rooted in early life events acting through genomic regions that are influenced by such events and subsequently are related to health phenotypes in later life. The parent-of-origin-effect (POE)-regulated methylome includes regions either enriched for genetically controlled imprinting effects (the typical type of POE) or atypical POE introduced by environmental effects associated with parents. This part of the methylome is heavily influenced by early life events, making it a potential route connecting early environmental exposures, the epigenome and the rate of aging. Here, we aim to test the association of POE-influenced methylation of CpG dinucleotides (POE-CpG sites) with early and later environmental exposures and subsequently with health-related phenotypes and adult aging phenotypes. We do this by performing phenome-wide association analyses of the POE-influenced methylome using a large family-based population cohort (GS:SFHS, Ndiscovery=5,087, Nreplication=4,450). At the single CpG level, 92 associations of POE-CpGs with phenotypic variation were identified and replicated. Most of the associations were contributed by POE-CpGs belonging to the atypical class and the most strongly enriched associations were with aging (DNAmTL acceleration), intelligence and parental (maternal) smoking exposure phenotypes. We further found that a proportion of the atypical-POE-CpGs formed co-methylation networks (modules) which are associated with these phenotypes, with one of the aging-associated modules displaying increased internal module connectivity (strength of methylation correlation across constituent CpGs) with age. Atypical POE-CpGs also displayed high levels of methylation heterogeneity and epigenetic drift (i.e. information loss with age) and a strong correlation with CpGs contained within epigenetic clocks. These results identified associations between the atypical-POE-influenced methylome and aging and provided new evidence for the "early development of origin" hypothesis for aging in humans.
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Affiliation(s)
- Chenhao Gao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Carmen Amador
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rosie M. Walker
- Centre for Clinical Brain Sciences, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- School of Psychology, University of Exeter, Perry Road, Exeter, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Rebecca A Madden
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Mark J. Adams
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Xiaomeng Bai
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Ying Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - David J. Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Xueyi Shen
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Chris S. Haley
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Andrew M. McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Yanni Zeng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
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30
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Fürtjes AE, Cole JH, Couvy-Duchesne B, Ritchie SJ. A quantified comparison of cortical atlases on the basis of trait morphometricity. Cortex 2023; 158:110-126. [PMID: 36516597 DOI: 10.1016/j.cortex.2022.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Many different brain atlases exist that subdivide the human cortex into dozens or hundreds of regions-of-interest (ROIs). Inconsistency across studies using one or another cortical atlas may contribute to the replication crisis across the neurosciences. METHODS Here, we provide a quantitative comparison between seven popular cortical atlases (Yeo, Desikan-Killiany, Destrieux, Jülich-Brain, Gordon, Glasser, Schaefer) and vertex-wise measures (thickness, surface area, and volume), to determine which parcellation retains the most information in the analysis of behavioural traits (incl. age, sex, body mass index, and cognitive ability) in the UK Biobank sample (N∼40,000). We use linear mixed models to compare whole-brain morphometricity; the proportion of trait variance accounted for when using a given atlas. RESULTS Commonly-used atlases resulted in a considerable loss of information compared to vertex-wise representations of cortical structure. Morphometricity increased linearly as a function of the log-number of ROIs included in an atlas, indicating atlas-based analyses miss many true associations and yield limited prediction accuracy. Likelihood ratio tests revealed that low-dimensional atlases accounted for unique trait variance rather than variance common between atlases, suggesting that previous studies likely returned atlas-specific findings. Finally, we found that the commonly-used atlases yielded brain-behaviour associations on par with those obtained with random parcellations, where specific region boundaries were randomly generated. DISCUSSION Our findings motivate future structural neuroimaging studies to favour vertex-wise cortical representations over coarser atlases, or to consider repeating analyses across multiple atlases, should the use of low-dimensional atlases be necessary. The insights uncovered here imply that cortical atlas choices likely contribute to the lack of reproducibility in ROI-based studies.
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Affiliation(s)
- Anna E Fürtjes
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK.
| | - James H Cole
- Department of Neuroimaging, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK; Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK; Dementia Research Centre, Institute of Neurology, University College London, London, UK
| | - Baptiste Couvy-Duchesne
- Paris Brain Institute (ICM), Inserm (U 1127), CNRS (UMR 7225), Sorbonne University, Inria Paris, Aramis Project-team, Paris, France; Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Stuart J Ritchie
- Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
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31
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Lu T, Forgetta V, Richards JB, Greenwood CMT. Genetic determinants of polygenic prediction accuracy within a population. Genetics 2022; 222:6762086. [PMID: 36250789 PMCID: PMC9713421 DOI: 10.1093/genetics/iyac158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/10/2022] [Indexed: 11/15/2022] Open
Abstract
Genomic risk prediction is on the emerging path toward personalized medicine. However, the accuracy of polygenic prediction varies strongly in different individuals. Based on up to 352,277 European ancestry participants in the UK Biobank, we constructed polygenic risk scores for 15 physiological and biochemical quantitative traits. We identified a total of 185 polygenic prediction variability quantitative trait loci for 11 traits by Levene's test among 254,376 unrelated individuals. We validated the effects of prediction variability quantitative trait loci using an independent test set of 58,927 individuals. For instance, a score aggregating 51 prediction variability quantitative trait locus variants for triglycerides had the strongest Spearman correlation of 0.185 (P-value <1.0 × 10-300) with the squared prediction errors. We found a strong enrichment of complex genetic effects conferred by prediction variability quantitative trait loci compared to risk loci identified in genome-wide association studies, including 89 prediction variability quantitative trait loci exhibiting dominance effects. Incorporation of dominance effects into polygenic risk scores significantly improved polygenic prediction for triglycerides, low-density lipoprotein cholesterol, vitamin D, and platelet. In conclusion, we have discovered and profiled genetic determinants of polygenic prediction variability for 11 quantitative biomarkers. These findings may assist interpretation of genomic risk prediction in various contexts and encourage novel approaches for constructing polygenic risk scores with complex genetic effects.
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Affiliation(s)
- Tianyuan Lu
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.,Quantitative Life Sciences Program, McGill University, Montreal, QC H3A 0G4, Canada
| | - Vincenzo Forgetta
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - John Brent Richards
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.,Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada.,Department of Twin Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Celia M T Greenwood
- Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.,Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC H3A 0G4, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
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32
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Alamin M, Sultana MH, Lou X, Jin W, Xu H. Dissecting Complex Traits Using Omics Data: A Review on the Linear Mixed Models and Their Application in GWAS. PLANTS (BASEL, SWITZERLAND) 2022; 11:3277. [PMID: 36501317 PMCID: PMC9739826 DOI: 10.3390/plants11233277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Genome-wide association study (GWAS) is the most popular approach to dissecting complex traits in plants, humans, and animals. Numerous methods and tools have been proposed to discover the causal variants for GWAS data analysis. Among them, linear mixed models (LMMs) are widely used statistical methods for regulating confounding factors, including population structure, resulting in increased computational proficiency and statistical power in GWAS studies. Recently more attention has been paid to pleiotropy, multi-trait, gene-gene interaction, gene-environment interaction, and multi-locus methods with the growing availability of large-scale GWAS data and relevant phenotype samples. In this review, we have demonstrated all possible LMMs-based methods available in the literature for GWAS. We briefly discuss the different LMM methods, software packages, and available open-source applications in GWAS. Then, we include the advantages and weaknesses of the LMMs in GWAS. Finally, we discuss the future perspective and conclusion. The present review paper would be helpful to the researchers for selecting appropriate LMM models and methods quickly for GWAS data analysis and would benefit the scientific society.
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Affiliation(s)
- Md. Alamin
- Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | | | - Xiangyang Lou
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Wenfei Jin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Haiming Xu
- Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
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33
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Chuong M, Adams MJ, Kwong ASF, Haley CS, Amador C, McIntosh AM. Genome-by-Trauma Exposure Interactions in Adults With Depression in the UK Biobank. JAMA Psychiatry 2022; 79:1110-1117. [PMID: 36169986 PMCID: PMC9520433 DOI: 10.1001/jamapsychiatry.2022.2983] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Self-reported trauma exposure has consistently been found to be a risk factor for major depressive disorder (MDD), and several studies have reported interactions with genetic liability. To date, most studies have examined gene-environment interactions with trauma exposure using genome-wide variants (single-nucleotide variations [SNVs]) or polygenic scores, both typically capturing less than 3% of phenotypic risk variance. Objective To reexamine genome-by-trauma interaction associations using genetic measures using all available genotyped data and thus, maximizing accounted variance. Design, Setting, and Participants The UK Biobank study was conducted from April 2007 to May 1, 2016 (follow-up mental health questionnaire). The current study used available cross-sectional genomic and trauma exposure data from UK Biobank. Participants who completed the mental health questionnaire and had available genetic, trauma experience, depressive symptoms, and/or neuroticism information were included. Data were analyzed from April 1 to August 30, 2021. Exposures Trauma and genome-by-trauma exposure interactions. Main Outcomes and Measures Measures of self-reported depression, neuroticism, and trauma exposure with whole-genome SNV data are available from the UK Biobank study. Here, a mixed-model statistical approach using genetic, trauma exposure, and genome-by-trauma exposure interaction similarity matrices was used to explore sources of variation in depression and neuroticism. Results Analyses were conducted on 148 129 participants (mean [SD] age, 56 [7] years) of which 76 995 were female (52.0%). The study approach estimated the heritability (SE) of MDD to be approximately 0.160 (0.016). Subtypes of self-reported trauma exposure (catastrophic, adult, childhood, and full trauma) accounted for a significant proportion of the variance of MDD, with heritability (SE) ranging from 0.056 (0.013) to 0.176 (0.025). The proportion of MDD risk variance accounted for by significant genome-by-trauma interaction revealed estimates (SD) ranging from 0.074 (0.006) to 0.201 (0.009). Results from sex-specific analyses found genome-by-trauma interaction variance estimates approximately 5-fold greater for MDD in male participants (0.441 [0.018]) than in female participants (0.086 [0.009]). Conclusions and Relevance This cross-sectional study used an approach combining all genome-wide SNV data when exploring genome-by-trauma interactions in individuals with MDD; findings suggest that such interactions were associated with depression manifestation. Genome-by-trauma interaction accounts for greater trait variance in male individuals, which points to potential differences in depression etiology between the sexes. The methodology used in this study can be extrapolated to other environmental factors to identify modifiable risk environments and at-risk groups to target with interventions.
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Affiliation(s)
- Melisa Chuong
- Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom.,Department of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Mark J Adams
- Department of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Alex S F Kwong
- Department of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Chris S Haley
- Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Carmen Amador
- Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew M McIntosh
- Department of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
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34
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Derks EM, Thorp JG, Gerring ZF. Ten challenges for clinical translation in psychiatric genetics. Nat Genet 2022; 54:1457-1465. [PMID: 36138228 DOI: 10.1038/s41588-022-01174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/27/2022] [Indexed: 11/09/2022]
Abstract
Genome-wide association studies have identified hundreds of robust genetic associations underlying psychiatric disorders and provided important biological insights into disease onset and progression. There is optimism that genetic findings will pave the way to precision psychiatry by facilitating the development of more effective treatments and the identification of groups of patients that these treatments should be targeted toward. However, there are several challenges that must be addressed before genetic findings can be translated into the clinic. In this Perspective, we highlight ten challenges for the field of psychiatric genetics, focused on the robust and generalizable detection of genetic risk factors, improved definition and assessment of psychopathology and achieving better clinical indicators. We discuss recent advancements in the field that will improve the explanatory and predictive power of genetic data and ultimately contribute to improving the management and treatment of patients with a psychiatric disorder.
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Affiliation(s)
- Eske M Derks
- Translational Neurogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
| | - Jackson G Thorp
- Translational Neurogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Zachary F Gerring
- Translational Neurogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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35
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Couvy-Duchesne B, Zhang F, Kemper KE, Sidorenko J, Wray NR, Visscher PM, Colliot O, Yang J. Parsimonious model for mass-univariate vertexwise analysis. J Med Imaging (Bellingham) 2022; 9:052404. [PMID: 35610986 PMCID: PMC9122091 DOI: 10.1117/1.jmi.9.5.052404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/26/2022] [Indexed: 11/14/2022] Open
Abstract
Purpose: Covariance between gray-matter measurements can reflect structural or functional brain networks though it has also been shown to be influenced by confounding factors (e.g., age, head size, and scanner), which could lead to lower mapping precision (increased size of associated clusters) and create distal false positives associations in mass-univariate vertexwise analyses. Approach: We evaluated this concern by performing state-of-the-art mass-univariate analyses (general linear model, GLM) on traits simulated from real vertex-wise gray matter data (including cortical and subcortical thickness and surface area). We contrasted the results with those from linear mixed models (LMMs), which have been shown to overcome similar issues in omics association studies. Results: We showed that when performed on a large sample ( N = 8662 , UK Biobank), GLMs yielded greatly inflated false positive rate (cluster false discovery rate > 0.6 ). We showed that LMMs resulted in more parsimonious results: smaller clusters and reduced false positive rate but at a cost of increased computation. Next, we performed mass-univariate association analyses on five real UKB traits (age, sex, BMI, fluid intelligence, and smoking status) and LMM yielded fewer and more localized associations. We identified 19 significant clusters displaying small associations with age, sex, and BMI, which suggest a complex architecture of at least dozens of associated areas with those phenotypes. Conclusions: The published literature could contain a large proportion of redundant (possibly confounded) associations that are largely prevented using LMMs. The parsimony of LMMs results from controlling for the joint effect of all vertices, which prevents local and distal redundant associations from reaching significance.
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Affiliation(s)
- Baptiste Couvy-Duchesne
- University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland, Australia.,Sorbonne University, Paris Brain Institute (ICM), CNRS, INRIA, INSERM, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Futao Zhang
- University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland, Australia
| | - Kathryn E Kemper
- University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland, Australia
| | - Julia Sidorenko
- University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland, Australia
| | - Naomi R Wray
- University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland, Australia
| | - Peter M Visscher
- University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland, Australia
| | - Olivier Colliot
- Sorbonne University, Paris Brain Institute (ICM), CNRS, INRIA, INSERM, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Jian Yang
- University of Queensland, Institute for Molecular Bioscience, St. Lucia, Queensland, Australia.,Westlake University, School of Life Sciences, Hangzhou, China.,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
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36
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Pihlstrøm L, Shireby G, Geut H, Henriksen SP, Rozemuller AJM, Tunold JA, Hannon E, Francis P, Thomas AJ, Love S, Mill J, van de Berg WDJ, Toft M. Epigenome-wide association study of human frontal cortex identifies differential methylation in Lewy body pathology. Nat Commun 2022; 13:4932. [PMID: 35995800 PMCID: PMC9395387 DOI: 10.1038/s41467-022-32619-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are closely related progressive disorders with no available disease-modifying therapy, neuropathologically characterized by intraneuronal aggregates of misfolded α-synuclein. To explore the role of DNA methylation changes in PD and DLB pathogenesis, we performed an epigenome-wide association study (EWAS) of 322 postmortem frontal cortex samples and replicated results in an independent set of 200 donors. We report novel differentially methylated replicating loci associated with Braak Lewy body stage near TMCC2, SFMBT2, AKAP6 and PHYHIP. Differentially methylated probes were independent of known PD genetic risk alleles. Meta-analysis provided suggestive evidence for a differentially methylated locus within the chromosomal region affected by the PD-associated 22q11.2 deletion. Our findings elucidate novel disease pathways in PD and DLB and generate hypotheses for future molecular studies of Lewy body pathology.
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Affiliation(s)
- Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway.
| | - Gemma Shireby
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Hanneke Geut
- Amsterdam UMC, Vrije Universiteit, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Netherlands Brain Bank, Netherlands Institute of Neurosciences, Amsterdam, The Netherlands
| | | | - Annemieke J M Rozemuller
- Amsterdam UMC, Vrije Universiteit, Department of Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Jon-Anders Tunold
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Paul Francis
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Alan J Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Seth Love
- Dementia Research Group, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Wilma D J van de Berg
- Amsterdam UMC, Vrije Universiteit, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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37
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Schaffner SL, Kobor MS. DNA methylation as a mediator of genetic and environmental influences on Parkinson's disease susceptibility: Impacts of alpha-Synuclein, physical activity, and pesticide exposure on the epigenome. Front Genet 2022; 13:971298. [PMID: 36061205 PMCID: PMC9437223 DOI: 10.3389/fgene.2022.971298] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder with a complex etiology and increasing prevalence worldwide. As PD is influenced by a combination of genetic and environment/lifestyle factors in approximately 90% of cases, there is increasing interest in identification of the interindividual mechanisms underlying the development of PD as well as actionable lifestyle factors that can influence risk. This narrative review presents an outline of the genetic and environmental factors contributing to PD risk and explores the possible roles of cytosine methylation and hydroxymethylation in the etiology and/or as early-stage biomarkers of PD, with an emphasis on epigenome-wide association studies (EWAS) of PD conducted over the past decade. Specifically, we focused on variants in the SNCA gene, exposure to pesticides, and physical activity as key contributors to PD risk. Current research indicates that these factors individually impact the epigenome, particularly at the level of CpG methylation. There is also emerging evidence for interaction effects between genetic and environmental contributions to PD risk, possibly acting across multiple omics layers. We speculated that this may be one reason for the poor replicability of the results of EWAS for PD reported to date. Our goal is to provide direction for future epigenetics studies of PD to build upon existing foundations and leverage large datasets, new technologies, and relevant statistical approaches to further elucidate the etiology of this disease.
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Affiliation(s)
- Samantha L. Schaffner
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
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38
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Genetic control of RNA splicing and its distinct role in complex trait variation. Nat Genet 2022; 54:1355-1363. [PMID: 35982161 PMCID: PMC9470536 DOI: 10.1038/s41588-022-01154-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/08/2022] [Indexed: 12/11/2022]
Abstract
Most genetic variants identified from genome-wide association studies (GWAS) in humans are noncoding, indicating their role in gene regulation. Previous studies have shown considerable links of GWAS signals to expression quantitative trait loci (eQTLs) but the links to other genetic regulatory mechanisms, such as splicing QTLs (sQTLs), are underexplored. Here, we introduce an sQTL mapping method, testing for heterogeneity between isoform-eQTLeffects (THISTLE), with improved power over competing methods. Applying THISTLE together with a complementary sQTL mapping strategy to brain transcriptomic (n = 2,865) and genotype data, we identified 12,794 genes with cis-sQTLs at P < 5 × 10−8, approximately 61% of which were distinct from eQTLs. Integrating the sQTL data into GWAS for 12 brain-related complex traits (including diseases), we identified 244 genes associated with the traits through cis-sQTLs, approximately 61% of which could not be discovered using the corresponding eQTL data. Our study demonstrates the distinct role of most sQTLs in the genetic regulation of transcription and complex trait variation. A powerful method for splicing quantitative trait loci (sQTL) mapping, THISTLE, is presented and applied to a collection of 2,865 brain samples. Integration with GWAS identifies 244 genes associated via cis-sQTLs, of which 61% were not identified using expression QTLs.
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39
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Hillary RF, McCartney DL, McRae AF, Campbell A, Walker RM, Hayward C, Horvath S, Porteous DJ, Evans KL, Marioni RE. Identification of influential probe types in epigenetic predictions of human traits: implications for microarray design. Clin Epigenetics 2022; 14:100. [PMID: 35948928 PMCID: PMC9367152 DOI: 10.1186/s13148-022-01320-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND CpG methylation levels can help to explain inter-individual differences in phenotypic traits. Few studies have explored whether identifying probe subsets based on their biological and statistical properties can maximise predictions whilst minimising array content. Variance component analyses and penalised regression (epigenetic predictors) were used to test the influence of (i) the number of probes considered, (ii) mean probe variability and (iii) methylation QTL status on the variance captured in eighteen traits by blood DNA methylation. Training and test samples comprised ≤ 4450 and ≤ 2578 unrelated individuals from Generation Scotland, respectively. RESULTS As the number of probes under consideration decreased, so too did the estimates from variance components and prediction analyses. Methylation QTL status and mean probe variability did not influence variance components. However, relative effect sizes were 15% larger for epigenetic predictors based on probes with known or reported methylation QTLs compared to probes without reported methylation QTLs. Relative effect sizes were 45% larger for predictors based on probes with mean Beta-values between 10 and 90% compared to those based on hypo- or hypermethylated probes (Beta-value ≤ 10% or ≥ 90%). CONCLUSIONS Arrays with fewer probes could reduce costs, leading to increased sample sizes for analyses. Our results show that reducing array content can restrict prediction metrics and careful attention must be given to the biological and distribution properties of CpG probes in array content selection.
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Affiliation(s)
- Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK.
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Australia
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK.,Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095-7088, USA.,Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095-1772, USA
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
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40
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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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41
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Westerman KE, Majarian TD, Giulianini F, Jang DK, Miao J, Florez JC, Chen H, Chasman DI, Udler MS, Manning AK, Cole JB. Variance-quantitative trait loci enable systematic discovery of gene-environment interactions for cardiometabolic serum biomarkers. Nat Commun 2022; 13:3993. [PMID: 35810165 PMCID: PMC9271055 DOI: 10.1038/s41467-022-31625-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 06/24/2022] [Indexed: 11/29/2022] Open
Abstract
Gene-environment interactions represent the modification of genetic effects by environmental exposures and are critical for understanding disease and informing personalized medicine. These often induce differential phenotypic variance across genotypes; these variance-quantitative trait loci can be prioritized in a two-stage interaction detection strategy to greatly reduce the computational and statistical burden and enable testing of a broader range of exposures. We perform genome-wide variance-quantitative trait locus analysis for 20 serum cardiometabolic biomarkers by multi-ancestry meta-analysis of 350,016 unrelated participants in the UK Biobank, identifying 182 independent locus-biomarker pairs (p < 4.5×10-9). Most are concentrated in a small subset (4%) of loci with genome-wide significant main effects, and 44% replicate (p < 0.05) in the Women's Genome Health Study (N = 23,294). Next, we test each locus-biomarker pair for interaction across 2380 exposures, identifying 847 significant interactions (p < 2.4×10-7), of which 132 are independent (p < 0.05) after accounting for correlation between exposures. Specific examples demonstrate interaction of triglyceride-associated variants with distinct body mass- versus body fat-related exposures as well as genotype-specific associations between alcohol consumption and liver stress at the ADH1B gene. Our catalog of variance-quantitative trait loci and gene-environment interactions is publicly available in an online portal.
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Affiliation(s)
- Kenneth E Westerman
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, USA.
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Timothy D Majarian
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dong-Keun Jang
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jenkai Miao
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
| | - Jose C Florez
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Miriam S Udler
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alisa K Manning
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Joanne B Cole
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA.
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
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42
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Freydenzon A, Nabais MF, Lin T, Williams KL, Wallace L, Henders AK, Blair IP, Wray NR, Pamphlett R, McRae AF. Association between DNA methylation variability and self-reported exposure to heavy metals. Sci Rep 2022; 12:10582. [PMID: 35732753 PMCID: PMC9217962 DOI: 10.1038/s41598-022-13892-w] [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: 07/29/2021] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
Individuals encounter varying environmental exposures throughout their lifetimes. Some exposures such as smoking are readily observed and have high personal recall; others are more indirect or sporadic and might only be inferred from long occupational histories or lifestyles. We evaluated the utility of using lifetime-long self-reported exposures for identifying differential methylation in an amyotrophic lateral sclerosis cases-control cohort of 855 individuals. Individuals submitted paper-based surveys on exposure and occupational histories as well as whole blood samples. Genome-wide DNA methylation levels were quantified using the Illumina Infinium Human Methylation450 array. We analyzed 15 environmental exposures using the OSCA software linear and MOA models, where we regressed exposures individually by methylation adjusted for batch effects and disease status as well as predicted scores for age, sex, cell count, and smoking status. We also regressed on the first principal components on clustered environmental exposures to detect DNA methylation changes associated with a more generalised definition of environmental exposure. Five DNA methylation probes across three environmental exposures (cadmium, mercury and metalwork) were significantly associated using the MOA models and seven through the linear models, with one additionally across a principal component representing chemical exposures. Methylome-wide significance for four of these markers was driven by extreme hyper/hypo-methylation in small numbers of individuals. The results indicate the potential for using self-reported exposure histories in detecting DNA methylation changes in response to the environment, but also highlight the confounded nature of environmental exposure in cohort studies.
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Affiliation(s)
- Anna Freydenzon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Marta F Nabais
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,University of Exeter Medical School, Exeter, EX2 5DW, Devon, UK
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Macquarie University, Exeter, NSW, 2109, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Macquarie University, Exeter, NSW, 2109, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Roger Pamphlett
- Brain and Mind Centre, The University of Sydney, Sydney, NSW, 2050, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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43
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Johnson R, Sotoudeh R, Conley D. Polygenic Scores for Plasticity: A New Tool for Studying Gene-Environment Interplay. Demography 2022; 59:1045-1070. [PMID: 35553650 DOI: 10.1215/00703370-9957418] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Fertility, health, education, and other outcomes of interest to demographers are the product of an individual's genetic makeup and their social environment. Yet, gene × environment (G×E) research deploys a limited toolkit on the genetic side to study the gene-environment interplay, relying on polygenic scores (PGSs) that reflect the influence of genetics on levels of an outcome. In this article, we develop a genetic summary measure better suited for G×E research: variance polygenic scores (vPGSs), which are PGSs that reflect genetic contributions to plasticity in outcomes. First, we use the UK Biobank (N ∼ 408,000 in the analytic sample) and the Health and Retirement Study (N ∼ 5,700 in the analytic sample) to compare four approaches to constructing PGSs for plasticity. The results show that widely used methods for discovering which genetic variants affect outcome variability fail to serve as distinctive new tools for G×E. Second, using the PGSs that do capture distinctive genetic contributions to plasticity, we analyze heterogeneous effects of a UK education reform on health and educational attainment. The results show the properties of a useful new tool for population scientists studying the interplay of nature and nurture and for population-based studies that are releasing PGSs to applied researchers.
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Affiliation(s)
- Rebecca Johnson
- McCourt School of Public Policy, Georgetown University, Washington, DC, USA
| | | | - Dalton Conley
- Department of Sociology and Office of Population Research, Princeton University, Princeton, NJ, USA
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44
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Yousefi PD, Suderman M, Langdon R, Whitehurst O, Davey Smith G, Relton CL. DNA methylation-based predictors of health: applications and statistical considerations. Nat Rev Genet 2022; 23:369-383. [PMID: 35304597 DOI: 10.1038/s41576-022-00465-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 12/12/2022]
Abstract
DNA methylation data have become a valuable source of information for biomarker development, because, unlike static genetic risk estimates, DNA methylation varies dynamically in relation to diverse exogenous and endogenous factors, including environmental risk factors and complex disease pathology. Reliable methods for genome-wide measurement at scale have led to the proliferation of epigenome-wide association studies and subsequently to the development of DNA methylation-based predictors across a wide range of health-related applications, from the identification of risk factors or exposures, such as age and smoking, to early detection of disease or progression in cancer, cardiovascular and neurological disease. This Review evaluates the progress of existing DNA methylation-based predictors, including the contribution of machine learning techniques, and assesses the uptake of key statistical best practices needed to ensure their reliable performance, such as data-driven feature selection, elimination of data leakage in performance estimates and use of generalizable, adequately powered training samples.
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Affiliation(s)
- Paul D Yousefi
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Matthew Suderman
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Ryan Langdon
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Oliver Whitehurst
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Bristol, UK.
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45
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Rand A, Zimny P, Nagel R, Telang C, Mollison J, Bruns A, Leff E, Reisner WW, Dunbar WB. Electronic Mapping of a Bacterial Genome with Dual Solid-State Nanopores and Active Single-Molecule Control. ACS NANO 2022; 16:5258-5273. [PMID: 35302746 PMCID: PMC9048701 DOI: 10.1021/acsnano.1c09575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
We present an electronic mapping of a bacterial genome using solid-state nanopore technology. A dual-nanopore architecture and active control logic are used to produce single-molecule data that enables estimation of distances between physical tags installed at sequence motifs within double-stranded DNA. Previously developed "DNA flossing" control logic generates multiple scans of each captured DNA. We extended this logic in two ways: first, to automate "zooming out" on each molecule to progressively increase the number of tags scanned during flossing, and second, to automate recapture of a molecule that exited flossing to enable interrogation of the same and/or different regions of the molecule. Custom analysis methods were developed to produce consensus alignments from each multiscan event. The combined multiscanning and multicapture method was applied to the challenge of mapping from a heterogeneous mixture of single-molecule fragments that make up the Escherichia coli (E. coli) chromosome. Coverage of 3.1× across 2355 resolvable sites of the E. coli genome was achieved after 5.6 h of recording time. The recapture method showed a 38% increase in the merged-event alignment length compared to single-scan alignments. The observed intertag resolution was 150 bp in engineered DNA molecules and 166 bp natively within fragments of E. coli DNA, with detection of 133 intersite intervals shorter than 200 bp in the E. coli reference map. We present results on estimating distances in repetitive regions of the E. coli genome. With an appropriately designed array, higher throughput implementations could enable human-sized genome and epigenome mapping applications.
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Affiliation(s)
- Arthur Rand
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Philip Zimny
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Roland Nagel
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Chaitra Telang
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Justin Mollison
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Aaron Bruns
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Emily Leff
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Walter W. Reisner
- Department
of Physics, McGill University, 3600 Rue University, Montreal, QC, Canada H3A 2T8
| | - William B. Dunbar
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
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46
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Shen X, Caramaschi D, Adams MJ, Walker RM, Min JL, Kwong A, Hemani G, Barbu MC, Whalley HC, Harris SE, Deary IJ, Morris SW, Cox SR, Relton CL, Marioni RE, Evans KL, McIntosh AM. DNA methylome-wide association study of genetic risk for depression implicates antigen processing and immune responses. Genome Med 2022; 14:36. [PMID: 35354486 PMCID: PMC8969265 DOI: 10.1186/s13073-022-01039-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 03/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Depression is a disabling and highly prevalent condition where genetic and epigenetic, such as DNA methylation (DNAm), differences contribute to disease risk. DNA methylation is influenced by genetic variation but the association between polygenic risk of depression and DNA methylation is unknown. METHODS We investigated the association between polygenic risk scores (PRS) for depression and DNAm by conducting a methylome-wide association study (MWAS) in Generation Scotland (N = 8898, mean age = 49.8 years) with replication in the Lothian Birth Cohorts of 1921 and 1936 and adults in the Avon Longitudinal Study of Parents and Children (ALSPAC) (Ncombined = 2049, mean age = 79.1, 69.6 and 47.2 years, respectively). We also conducted a replication MWAS in the ALSPAC children (N = 423, mean age = 17.1 years). Gene ontology analysis was conducted for the cytosine-guanine dinucleotide (CpG) probes significantly associated with depression PRS, followed by Mendelian randomisation (MR) analysis to infer the causal relationship between depression and DNAm. RESULTS Widespread associations (NCpG = 71, pBonferroni < 0.05, p < 6.3 × 10-8) were found between PRS constructed using genetic risk variants for depression and DNAm in CpG probes that localised to genes involved in immune responses and neural development. The effect sizes for the significant associations were highly correlated between the discovery and replication samples in adults (r = 0.79) and in adolescents (r = 0.82). Gene Ontology analysis showed that significant CpG probes are enriched in immunological processes in the human leukocyte antigen system. Additional MWAS was conducted for each lead genetic risk variant. Over 47.9% of the independent genetic risk variants included in the PRS showed associations with DNAm in CpG probes located in both the same (cis) and distal (trans) locations to the genetic loci (pBonferroni < 0.045). Subsequent MR analysis showed that there are a greater number of causal effects found from DNAm to depression than vice versa (DNAm to depression: pFDR ranged from 0.024 to 7.45 × 10-30; depression to DNAm: pFDR ranged from 0.028 to 0.003). CONCLUSIONS PRS for depression, especially those constructed from genome-wide significant genetic risk variants, showed methylome-wide differences associated with immune responses. Findings from MR analysis provided evidence for causal effect of DNAm to depression.
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Affiliation(s)
- Xueyi Shen
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh, EH10 5HF, UK.
| | - Doretta Caramaschi
- College of Life and Environmental Sciences, Psychology, University of Exeter, Exeter, UK
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh, EH10 5HF, UK
| | - Rosie M Walker
- Centre for Clinical Brain Sciences, Chancellor's Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, UK
| | - Josine L Min
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Alex Kwong
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh, EH10 5HF, UK
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Gibran Hemani
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Miruna C Barbu
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh, EH10 5HF, UK
| | - Heather C Whalley
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh, EH10 5HF, UK
| | - Sarah E Harris
- Lothian Birth Cohorts group, Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Lothian Birth Cohorts group, Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Lothian Birth Cohorts group, Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Morningside Park, Edinburgh, EH10 5HF, UK.
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47
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Hop PJ, Zwamborn RA, Hannon E, Shireby GL, Nabais MF, Walker EM, van Rheenen W, van Vugt JJ, Dekker AM, Westeneng HJ, Tazelaar GH, van Eijk KR, Moisse M, Baird D, Khleifat AA, Iacoangeli A, Ticozzi N, Ratti A, Cooper-Knock J, Morrison KE, Shaw PJ, Basak AN, Chiò A, Calvo A, Moglia C, Canosa A, Brunetti M, Grassano M, Gotkine M, Lerner Y, Zabari M, Vourc’h P, Corcia P, Couratier P, Pardina JSM, Salas T, Dion P, Ross JP, Henderson RD, Mathers S, McCombe PA, Needham M, Nicholson G, Rowe DB, Pamphlett R, Mather KA, Sachdev PS, Furlong S, Garton FC, Henders AK, Lin T, Ngo ST, Steyn FJ, Wallace L, Williams KL, Neto MM, Cauchi RJ, Blair IP, Kiernan MC, Drory V, Povedano M, de Carvalho M, Pinto S, Weber M, Rouleau GA, Silani V, Landers JE, Shaw CE, Andersen PM, McRae AF, van Es MA, Pasterkamp RJ, Wray NR, McLaughlin RL, Hardiman O, Kenna KP, Tsai E, Runz H, Al-Chalabi A, van den Berg LH, Van Damme P, Mill J, Veldink JH. Genome-wide study of DNA methylation shows alterations in metabolic, inflammatory, and cholesterol pathways in ALS. Sci Transl Med 2022; 14:eabj0264. [PMID: 35196023 PMCID: PMC10040186 DOI: 10.1126/scitranslmed.abj0264] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an estimated heritability between 40 and 50%. DNA methylation patterns can serve as proxies of (past) exposures and disease progression, as well as providing a potential mechanism that mediates genetic or environmental risk. Here, we present a blood-based epigenome-wide association study meta-analysis in 9706 samples passing stringent quality control (6763 patients, 2943 controls). We identified a total of 45 differentially methylated positions (DMPs) annotated to 42 genes, which are enriched for pathways and traits related to metabolism, cholesterol biosynthesis, and immunity. We then tested 39 DNA methylation-based proxies of putative ALS risk factors and found that high-density lipoprotein cholesterol, body mass index, white blood cell proportions, and alcohol intake were independently associated with ALS. Integration of these results with our latest genome-wide association study showed that cholesterol biosynthesis was potentially causally related to ALS. Last, DNA methylation at several DMPs and blood cell proportion estimates derived from DNA methylation data were associated with survival rate in patients, suggesting that they might represent indicators of underlying disease processes potentially amenable to therapeutic interventions.
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Affiliation(s)
- Paul J. Hop
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Ramona A.J. Zwamborn
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Gemma L. Shireby
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Marta F. Nabais
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Emma M. Walker
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Wouter van Rheenen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Joke J.F.A. van Vugt
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Annelot M. Dekker
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Henk-Jan Westeneng
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Gijs H.P. Tazelaar
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Kristel R. van Eijk
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Matthieu Moisse
- KU Leuven–University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven 3000, Belgium
- VIB, Center for Brain and Disease Research, Leuven 3000, Belgium
- University Hospitals Leuven, Department of Neurology, Leuven 3000, Belgium
| | - Denis Baird
- Translational Biology, Biogen, Boston, MA 02142, USA
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol BS8 2BN, UK
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- National Institute for Health Research Biomedical Research Centre and Dementia Unit, South London and Maudsley NHS Foundation Trust and King’s College London, London SE5 8AZ, UK
| | - Nicola Ticozzi
- Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan 20149, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan 20122, Italy
| | - Antonia Ratti
- Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan 20149, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milano 20145, Italy
| | - Jonathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - Karen E. Morrison
- School of Medicine, Dentistry, and Biomedical Sciences, Queen’s University Belfast, Belfast BT9 7BL, UK
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield S10 2HQ, UK
| | - A. Nazli Basak
- Koc University, School of Medicine, Translational Medicine Research Center, NDAL, Istanbul, 34450, Turkey
| | - Adriano Chiò
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, SC Neurologia 1U, Turin 10126, Italy
| | - Andrea Calvo
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, SC Neurologia 1U, Turin 10126, Italy
| | - Cristina Moglia
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, SC Neurologia 1U, Turin 10126, Italy
| | - Antonio Canosa
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, SC Neurologia 1U, Turin 10126, Italy
| | - Maura Brunetti
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
| | - Maurizio Grassano
- “Rita Levi Montalcini” Department of Neuroscience, ALS Centre, University of Torino, Turin 10126, Italy
| | - Marc Gotkine
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center, Jerusalem 91120, Israel
| | - Yossef Lerner
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center, Jerusalem 91120, Israel
| | - Michal Zabari
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Agnes Ginges Center for Human Neurogenetics, Department of Neurology, Hadassah Medical Center, Jerusalem 91120, Israel
| | - Patrick Vourc’h
- Service de Biochimie et Biologie moléculaire, CHU de Tours, Tours 37044, France
- UMR 1253, Université de Tours, Inserm, Tours 37044, France
| | - Philippe Corcia
- UMR 1253, Université de Tours, Inserm, Tours 37044, France
- Centre de référence sur la SLA, CHU de Tours, Tours 37044, France
| | - Philippe Couratier
- Centre de référence sur la SLA, CHRU de Limoges, Limoges 87042, France
- UMR 1094, Université de Limoges, Inserm, Limoges 87025, France
| | | | - Teresa Salas
- Department of Neurology, Hospital La Paz-Carlos III, Madrid 28046, Spain
| | - Patrick Dion
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC H3A 2B4, Canada
| | - Jay P. Ross
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC H3A 2B4, Canada
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Robert D. Henderson
- Department of Neurology, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
| | - Susan Mathers
- Calvary Health Care Bethlehem, Parkdale, VIC 3195, Australia
| | - Pamela A. McCombe
- Centre for Clinical Research, University of Queensland, Brisbane, QLD 4019, Australia
| | - Merrilee Needham
- Fiona Stanley Hospital, Perth, WA 6150, Australia
- Notre Dame University, Fremantle, WA 6160, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - Garth Nicholson
- ANZAC Research Institute, Concord Repatriation General Hospital, Sydney, NSW 2139, Australia
| | - Dominic B. Rowe
- Centre for Motor Neuron Disease Research, Macquarie University, NSW 2109, Australia
| | - Roger Pamphlett
- Discipline of Pathology and Department of Neuropathology, Brain and Mind Centre, University of Sydney, Sydney, NSW 2050, Australia
| | - Karen A. Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2031, Australia
- Neuroscience Research Australia Institute, Randwick, NSW 2031, Australia
| | - Perminder S. Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2031, Australia
- Neuropsychiatric Institute, Prince of Wales Hospital, UNSW, Randwick, NSW 2031, Australia
| | - Sarah Furlong
- Centre for Motor Neuron Disease Research, Macquarie University, NSW 2109, Australia
| | - Fleur C. Garton
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Anjali K. Henders
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Tian Lin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Shyuan T. Ngo
- Centre for Clinical Research, University of Queensland, Brisbane, QLD 4019, Australia
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Frederik J. Steyn
- Centre for Clinical Research, University of Queensland, Brisbane, QLD 4019, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Kelly L. Williams
- Centre for Motor Neuron Disease Research, Macquarie University, NSW 2109, Australia
| | | | | | | | - Ruben J. Cauchi
- Center for Molecular Medicine and Biobanking and Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, 2023 Msida, Malta
| | - Ian P. Blair
- Centre for Motor Neuron Disease Research, Macquarie University, NSW 2109, Australia
| | - Matthew C. Kiernan
- Brain and Mind Centre, University of Sydney, Sydney, NSW, 2050, Australia
- Department of Neurology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Vivian Drory
- Department of Neurology, Tel-Aviv Sourasky Medical Centre, Tel-Aviv 64239, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Monica Povedano
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, L’Hospitalet de Llobregat, Barcelona 08907, Spain
| | - Mamede de Carvalho
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon 1649-028, Portugal
| | - Susana Pinto
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon 1649-028, Portugal
| | - Markus Weber
- Neuromuscular Diseases Unit/ALS Clinic, Kantonsspital St. Gallen, 9007 St. Gallen, Switzerland
| | - Guy A. Rouleau
- Montréal Neurological Institute and Hospital, McGill University, Montréal, QC H3A 2B4, Canada
| | - Vincenzo Silani
- Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan 20149, Italy
- Department of Pathophysiology and Transplantation, “Dino Ferrari” Center, Università degli Studi di Milano, Milan 20122, Italy
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Christopher E. Shaw
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Peter M. Andersen
- Department of Clinical Science, Umeå University, Umeå SE-901 85, Sweden
| | - Allan F. McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
| | - Michael A. van Es
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - R. Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, 3584 CX, Netherlands
| | - Naomi R. Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD4072, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Russell L. McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Kevin P. Kenna
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, 3584 CX, Netherlands
| | - Ellen Tsai
- Translational Biology, Biogen, Boston, MA 02142, USA
| | - Heiko Runz
- Translational Biology, Biogen, Boston, MA 02142, USA
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- King’s College Hospital, Denmark Hill, London SE5 9RS, UK
| | - Leonard H. van den Berg
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Philip Van Damme
- KU Leuven–University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), Leuven 3000, Belgium
- VIB, Center for Brain and Disease Research, Leuven 3000, Belgium
- University Hospitals Leuven, Department of Neurology, Leuven 3000, Belgium
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter EX1 2LU, UK
| | - Jan H. Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
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48
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A Gadd D, I McGeachan R, F Hillary R, L McCartney D, E Harris S, A Sherwood R, Abbott NJ, R Cox S, E Marioni R. The genetic and epigenetic profile of serum S100β in the Lothian Birth Cohort 1936 and its relationship to Alzheimer’s disease. Wellcome Open Res 2022; 6:306. [PMID: 35028426 PMCID: PMC8686327 DOI: 10.12688/wellcomeopenres.17322.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Circulating S100 calcium-binding protein (S100β) is a marker of brain inflammation that has been associated with a range of neurological conditions. To provide insight into the molecular regulation of S100β and its potential causal associations with Alzheimer’s disease, we carried out genome- and epigenome-wide association studies (GWAS/EWAS) of serum S100β levels in older adults and performed Mendelian randomisation with Alzheimer’s disease. Methods: GWAS (N=769, mean age 72.5 years, sd = 0.7) and EWAS (N=722, mean age 72.5 years, sd = 0.7) of S100β levels were performed in participants from the Lothian Birth Cohort 1936. Conditional and joint analysis (COJO) was used to identify independent loci. Expression quantitative trait locus (eQTL) analyses were performed for lead loci that had genome-wide significant associations with S100β. Bidirectional, two-sample Mendelian randomisation was used to test for causal associations between S100β and Alzheimer’s disease. Colocalisation between S100β and Alzheimer’s disease GWAS loci was also examined. Results: We identified 154 SNPs from chromosome 21 that associated (P<5x10-8) with S100β protein levels. The lead variant was located in the S100β gene (rs8128872, P=5.0x10-17). We found evidence that two independent causal variants existed for both transcription of S100β and S100β protein levels in our eQTL analyses. No CpG sites were associated with S100β levels at the epigenome-wide significant level (P<3.6x10-8); the lead probe was cg06833709 (P=5.8x10-6), which mapped to the LGI1 gene. There was no evidence of a causal association between S100β levels and Alzheimer’s disease or vice versa and no evidence for colocalisation between S100β and Alzheimer’s disease loci. Conclusions: These data provide insight into the molecular regulators of S100β levels. This context may aid in understanding the role of S100β in brain inflammation and neurological disease.
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Affiliation(s)
- Danni A Gadd
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
| | - Robert I McGeachan
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
| | - Robert F Hillary
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
| | - Daniel L McCartney
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
| | - Sarah E Harris
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
| | - Roy A Sherwood
- Department of Clinical Biochemistry, King's College Hospital NHS Foundation Trust, London, Other (Non-U.S.), SE5 9RS, UK
| | - N Joan Abbott
- Institute of Pharmaceutical Science, King's College London, London, Other (Non-U.S.), WC2R 2LS, UK
| | - Simon R Cox
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
| | - Riccardo E Marioni
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
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49
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McCartney DL, Hillary RF, Conole ELS, Banos DT, Gadd DA, Walker RM, Nangle C, Flaig R, Campbell A, Murray AD, Maniega SM, Valdés-Hernández MDC, Harris MA, Bastin ME, Wardlaw JM, Harris SE, Porteous DJ, Tucker-Drob EM, McIntosh AM, Evans KL, Deary IJ, Cox SR, Robinson MR, Marioni RE. Blood-based epigenome-wide analyses of cognitive abilities. Genome Biol 2022; 23:26. [PMID: 35039062 PMCID: PMC8762878 DOI: 10.1186/s13059-021-02596-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Blood-based markers of cognitive functioning might provide an accessible way to track neurodegeneration years prior to clinical manifestation of cognitive impairment and dementia. RESULTS Using blood-based epigenome-wide analyses of general cognitive function, we show that individual differences in DNA methylation (DNAm) explain 35.0% of the variance in general cognitive function (g). A DNAm predictor explains ~4% of the variance, independently of a polygenic score, in two external cohorts. It also associates with circulating levels of neurology- and inflammation-related proteins, global brain imaging metrics, and regional cortical volumes. CONCLUSIONS As sample sizes increase, the ability to assess cognitive function from DNAm data may be informative in settings where cognitive testing is unreliable or unavailable.
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Affiliation(s)
- Daniel L. McCartney
- 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
| | - Eleanor L. S. Conole
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Daniel Trejo Banos
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Biomedical Informatics, University Hospital of Zurich, Zurich, Switzerland
| | - Danni A. Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Rosie M. Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Cliff Nangle
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Robin Flaig
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Alison D. Murray
- Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, Scotland, UK
| | - Susana Muñoz Maniega
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - María del C. Valdés-Hernández
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Mathew A. Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - Mark E. Bastin
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Joanna M. Wardlaw
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Sarah E. Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - David J. Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Elliot M. Tucker-Drob
- Department of Psychology, University of Texas, Austin, TX USA
- Population Research Center and Center on Aging and Population Sciences, University of Texas, Austin, TX USA
| | - Andrew M. McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Ian J. Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - Simon R. Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ 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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50
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A Gadd D, I McGeachan R, F Hillary R, L McCartney D, E Harris S, A Sherwood R, Abbott NJ, R Cox S, E Marioni R. The genetic and epigenetic profile of serum S100β in the Lothian Birth Cohort 1936 and its relationship to Alzheimer's disease. Wellcome Open Res 2022; 6:306. [PMID: 35028426 DOI: 10.12688/wellcomeopenres.17322.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Circulating S100 calcium-binding protein (S100β) is a marker of brain inflammation that has been associated with a range of neurological conditions. To provide insight into the molecular regulation of S100β and its potential causal associations with Alzheimer's disease, we carried out genome- and epigenome-wide association studies (GWAS/EWAS) of serum S100β levels in older adults and performed Mendelian randomisation with Alzheimer's disease. Methods: GWAS (N=769, mean age 72.5 years, sd = 0.7) and EWAS (N=722, mean age 72.5 years, sd = 0.7) of S100β levels were performed in participants from the Lothian Birth Cohort 1936. Conditional and joint analysis (COJO) was used to identify independent loci. Expression quantitative trait locus (eQTL) analyses were performed for lead loci that had genome-wide significant associations with S100β. Bidirectional, two-sample Mendelian randomisation was used to test for causal associations between S100β and Alzheimer's disease. Colocalisation between S100β and Alzheimer's disease GWAS loci was also examined. Results: We identified 154 SNPs from chromosome 21 that associated (P<5x10 -8) with S100β protein levels. The lead variant was located in the S100β gene (rs8128872, P=5.0x10 -17). We found evidence that two independent causal variants existed for both transcription of S100β and S100β protein levels in our eQTL analyses . No CpG sites were associated with S100β levels at the epigenome-wide significant level (P<3.6x10 -8); the lead probe was cg06833709 (P=5.8x10 -6), which mapped to the LGI1 gene. There was no evidence of a causal association between S100β levels and Alzheimer's disease or vice versa and no evidence for colocalisation between S100β and Alzheimer's disease loci. Conclusions: These data provide insight into the molecular regulators of S100β levels. This context may aid in understanding the role of S100β in brain inflammation and neurological disease.
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Affiliation(s)
- Danni A Gadd
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
| | - Robert I McGeachan
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
| | - Robert F Hillary
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
| | - Daniel L McCartney
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
| | - Sarah E Harris
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK.,Department of Psychology, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
| | - Roy A Sherwood
- Department of Clinical Biochemistry, King's College Hospital NHS Foundation Trust, London, Other (Non-U.S.), SE5 9RS, UK
| | - N Joan Abbott
- Institute of Pharmaceutical Science, King's College London, London, Other (Non-U.S.), WC2R 2LS, UK
| | - Simon R Cox
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK.,Department of Psychology, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH8 9JZ, UK
| | - Riccardo E Marioni
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Other (Non-U.S.), EH4 2XU, UK
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