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Lehmann B, Bräuninger L, Cho Y, Falck F, Jayadeva S, Katell M, Nguyen T, Perini A, Tallman S, Mackintosh M, Silver M, Kuchenbäcker K, Leslie D, Chatterjee N, Holmes C. Methodological opportunities in genomic data analysis to advance health equity. Nat Rev Genet 2025:10.1038/s41576-025-00839-w. [PMID: 40369311 DOI: 10.1038/s41576-025-00839-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2025] [Indexed: 05/16/2025]
Abstract
The causes and consequences of inequities in genomic research and medicine are complex and widespread. However, it is widely acknowledged that underrepresentation of diverse populations in human genetics research risks exacerbating existing health disparities. Efforts to improve diversity are ongoing, but an often-overlooked source of inequity is the choice of analytical methods used to process, analyse and interpret genomic data. This choice can influence all areas of genomic research, from genome-wide association studies and polygenic score development to variant prioritization and functional genomics. New statistical and machine learning techniques to understand, quantify and correct for the impact of biases in genomic data are emerging within the wider genomic research and genomic medicine ecosystems. At this crucial time point, it is important to clarify where improvements in methods and practices can, or cannot, have a role in improving equity in genomics. Here, we review existing approaches to promote equity and fairness in statistical analysis for genomics, and propose future methodological developments that are likely to yield the most impact for equity.
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Affiliation(s)
- Brieuc Lehmann
- Department of Statistical Science, University College London, London, UK.
| | - Leandra Bräuninger
- Department of Statistical Science, University College London, London, UK
- The Alan Turing Institute, London, UK
| | - Yoonsu Cho
- Genomics England, London, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Fabian Falck
- The Alan Turing Institute, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | - Matt Silver
- Genomics England, London, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Karoline Kuchenbäcker
- Genomics England, London, UK
- Division of Psychiatry, University College London, London, UK
| | | | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Chris Holmes
- Department of Statistics, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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2
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Bravo JI, Zhang L, Benayoun BA. Multi-ancestry GWAS reveals loci linked to human variation in LINE-1- and Alu-insertion numbers. TRANSLATIONAL MEDICINE OF AGING 2025; 9:25-40. [PMID: 40051556 PMCID: PMC11883834 DOI: 10.1016/j.tma.2025.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2025] Open
Abstract
LINE-1 (L1) and Alu are two families of transposable elements (TEs) occupying ~17% and ~11% of the human genome, respectively. Though only a small fraction of L1 copies is able to produce the machinery to mobilize autonomously, Alu and degenerate L1s can hijack their functional machinery and mobilize in trans. The expression and subsequent mobilization of L1 and Alu can exert pathological effects on their hosts. These features have made them promising focus subjects in studies of aging where they can become active. However, mechanisms regulating TE activity are incompletely characterized, especially in diverse human populations. To address these gaps, we leveraged genomic data from the 1000 Genomes Project to carry out a trans-ethnic GWAS of L1/Alu insertion singletons. These are rare, recently acquired insertions observed in only one person and which we used as proxies for variation in L1/Alu insertion numbers. Our approach identified SNVs in genomic regions containing genes with potential and known TE regulatory properties, and it enriched for SNVs in regions containing known regulators of L1 expression. Moreover, we identified reference TE copies and structural variants that associated with L1/Alu singletons, suggesting their potential contribution to TE insertion number variation. Finally, a transcriptional analysis of lymphoblastoid cells highlighted potential cell cycle alterations in a subset of samples harboring L1/Alu singletons. Collectively, our results suggest that known TE regulatory mechanisms may be active in diverse human populations, expand the list of loci implicated in TE insertion number variability, and reinforce links between TEs and disease.
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Affiliation(s)
- Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Lucia Zhang
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Quantitative and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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3
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Bravo JI, Zhang L, Benayoun BA. Multi-ancestry GWAS reveals loci linked to human variation in LINE-1- and Alu-insertion numbers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.09.10.612283. [PMID: 39314493 PMCID: PMC11419044 DOI: 10.1101/2024.09.10.612283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
LINE-1 (L1) and Alu are two families of transposable elements (TEs) occupying ~17% and ~11% of the human genome, respectively. Though only a small fraction of L1 copies is able to produce the machinery to mobilize autonomously, Alu and degenerate L1s can hijack their functional machinery and mobilize in trans. The expression and subsequent mobilization of L1 and Alu can exert pathological effects on their hosts. These features have made them promising focus subjects in studies of aging where they can become active. However, mechanisms regulating TE activity are incompletely characterized, especially in diverse human populations. To address these gaps, we leveraged genomic data from the 1000 Genomes Project to carry out a trans-ethnic GWAS of L1/Alu insertion singletons. These are rare, recently acquired insertions observed in only one person and which we used as proxies for variation in L1/Alu insertion numbers. Our approach identified SNVs in genomic regions containing genes with potential and known TE regulatory properties, and it enriched for SNVs in regions containing known regulators of L1 expression. Moreover, we identified reference TE copies and structural variants that associated with L1/Alu singletons, suggesting their potential contribution to TE insertion number variation. Finally, a transcriptional analysis of lymphoblastoid cells highlighted potential cell cycle alterations in a subset of samples harboring L1/Alu singletons. Collectively, our results suggest that known TE regulatory mechanisms may be active in diverse human populations, expand the list of loci implicated in TE insertion number variability, and reinforce links between TEs and disease.
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Affiliation(s)
- Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Lucia Zhang
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Quantitative and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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Jiang Z, Sullivan PF, Li T, Zhao B, Wang X, Luo T, Huang S, Guan PY, Chen J, Yang Y, Stein JL, Li Y, Liu D, Sun L, Zhu H. The X chromosome's influences on the human brain. SCIENCE ADVANCES 2025; 11:eadq5360. [PMID: 39854466 PMCID: PMC11759047 DOI: 10.1126/sciadv.adq5360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 12/23/2024] [Indexed: 01/26/2025]
Abstract
Genes on the X chromosome are extensively expressed in the human brain. However, little is known for the X chromosome's impact on the brain anatomy, microstructure, and functional networks. We examined 1045 complex brain imaging traits from 38,529 participants in the UK Biobank. We unveiled potential autosome-X chromosome interactions while proposing an atlas outlining dosage compensation for brain imaging traits. Through extensive association studies, we identified 72 genome-wide significant trait-locus pairs (including 29 new associations) that share genetic architectures with brain-related disorders, notably schizophrenia. Furthermore, we found unique sex-specific associations and assessed variations in genetic effects between sexes. Our research offers critical insights into the X chromosome's role in the human brain, underscoring its contribution to the differences observed in brain structure and functionality between sexes.
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Affiliation(s)
- Zhiwen Jiang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Patrick F. Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tengfei Li
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bingxin Zhao
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xifeng Wang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tianyou Luo
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shuai Huang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Peter Y. Guan
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jie Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yue Yang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason L. Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dajiang Liu
- Department of Public Health Sciences, Penn State University, Hershey, PA 17033, USA
- Department of Biochemistry and Molecular Biology, Penn State University, Hershey, PA 17033, USA
| | - Lei Sun
- Department of Statistical Sciences, University of Toronto, Toronto, ON M5G 1Z5, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Hongtu Zhu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Biomedical Research Imaging Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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5
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Ahmed S, Vaden KI, Leitao D, Dubno JR, Drögemöller BI. Large-scale audiometric phenotyping identifies distinct genes and pathways involved in hearing loss subtypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.01.14.24318673. [PMID: 39867375 PMCID: PMC11759831 DOI: 10.1101/2025.01.14.24318673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Age-related hearing loss affects one-third of the population over 65 years. However, the diverse pathologies underlying these heterogenous phenotypes complicate genetic studies. To overcome challenges associated with accurate phenotyping for older adults with hearing loss, we applied computational phenotyping approaches based on audiometrically measured hearing loss. This novel phenotyping strategy uncovered distinct genetic variants associated with sensory and metabolic hearing loss. Sex-stratified analyses of these sexually dimorphic hearing loss phenotypes revealed a novel locus of relevance to sensory hearing loss in males, but not females. Enrichment analyses revealed that genes involved in frontotemporal dementia were implicated in metabolic hearing loss, while genes relating to sensory processing of sound by hair cells were implicated in sensory hearing loss. Our study has enhanced our understanding of these two distinct hearing loss phenotypes, representing the first step in the development of more precise treatments for these pathologically distinct hearing loss phenotypes.
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Affiliation(s)
- Samah Ahmed
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kenneth I Vaden
- Hearing Research Program, Department of Otolaryngology-Head and Neck Surgery, Medical University of South Carolina, South Carolina, Charleston, USA
| | - Darren Leitao
- Department of Otolaryngology-Head and Neck Surgery, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Judy R Dubno
- Hearing Research Program, Department of Otolaryngology-Head and Neck Surgery, Medical University of South Carolina, South Carolina, Charleston, USA
| | - Britt I Drögemöller
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- The Children's Hospital Foundation of Manitoba, Winnipeg, Manitoba, Canada
- CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
- Centre on Aging, Winnipeg, Manitoba, Canada
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Mendes M, Chen DZ, Engchuan W, Leal TP, Thiruvahindrapuram B, Trost B, Howe JL, Pellecchia G, Nalpathamkalam T, Alexandrova R, Salazar NB, McKee EA, Rivera-Alfaro N, Lai MC, Bandres-Ciga S, Roshandel D, Bradley CA, Anagnostou E, Sun L, Scherer SW. Chromosome X-wide common variant association study in autism spectrum disorder. Am J Hum Genet 2025; 112:135-153. [PMID: 39706197 PMCID: PMC11739886 DOI: 10.1016/j.ajhg.2024.11.008] [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: 08/05/2024] [Revised: 11/19/2024] [Accepted: 11/19/2024] [Indexed: 12/23/2024] Open
Abstract
Autism spectrum disorder (ASD) displays a notable male bias in prevalence. Research into rare (<0.1) genetic variants on the X chromosome has implicated over 20 genes in ASD pathogenesis, such as MECP2, DDX3X, and DMD. The "female protective effect" in ASD suggests that females may require a higher genetic burden to manifest symptoms similar to those in males, yet the mechanisms remain unclear. Despite technological advances in genomics, the complexity of the biological nature of sex chromosomes leaves them underrepresented in genome-wide studies. Here, we conducted an X-chromosome-wide association study (XWAS) using whole-genome sequencing data from 6,873 individuals with ASD (82% males) across Autism Speaks MSSNG, Simons Simplex Collection (SSC), and Simons Powering Autism Research (SPARK), alongside 8,981 population controls (43% males). We analyzed 418,652 X chromosome variants, identifying 59 associated with ASD (p values 7.9 × 10-6 to 1.51 × 10-5), surpassing Bonferroni-corrected thresholds. Key findings include significant regions on Xp22.2 (lead SNP rs12687599, p = 3.57 × 10-7) harboring ASB9/ASB11 and another encompassing DDX53 and the PTCHD1-AS long non-coding RNA (lead SNP rs5926125, p = 9.47 × 10-6). When mapping genes within 10 kb of the 59 most significantly associated SNPs, 91 genes were found, 17 of which yielded association with ASD (GRPR, AP1S2, DDX53, HDAC8, PCDH19, PTCHD1, PCDH11X, PTCHD1-AS, DMD, SYAP1, CNKSR2, GLRA2, OFD1, CDKL5, GPRASP2, NXF5, and SH3KBP1). FGF13 emerged as an X-linked ASD candidate gene, highlighted by sex-specific differences in minor allele frequencies. These results reveal significant insights into X chromosome biology in ASD, confirming and nominating genes and pathways for further investigation.
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Affiliation(s)
- Marla Mendes
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.
| | - Desmond Zeya Chen
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 3E3, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Thiago Peixoto Leal
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Brett Trost
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jennifer L Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Roumiana Alexandrova
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nelson Bautista Salazar
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ethan A McKee
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Natalia Rivera-Alfaro
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Meng-Chuan Lai
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5G 2C1, Canada; Department of Psychiatry, The Hospital for Sick Children, Toronto, ON M5G 1E8, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Sara Bandres-Ciga
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD 20892, USA
| | - Delnaz Roshandel
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Clarrisa A Bradley
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Evdokia Anagnostou
- Autism Research Centre, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada; Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Lei Sun
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 3E3, Canada; Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, ON M5G 1X6, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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7
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Grunin M, Igo Jr RP, Song YE, Blanton SH, Pericak-Vance MA, Haines JL, International Age-related Macular Degeneration Genomics Consortium. Identifying X-chromosome variants associated with age-related macular degeneration. Hum Mol Genet 2024; 33:2085-2093. [PMID: 39324238 PMCID: PMC11630753 DOI: 10.1093/hmg/ddae141] [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: 05/13/2024] [Revised: 08/14/2024] [Accepted: 09/16/2024] [Indexed: 09/27/2024] Open
Abstract
PURPOSE In genome-wide association studies (GWAS), X chromosome (ChrX) variants are often not investigated. Sex-specific effects and ChrX-specific quality control (QC) are needed to examine these effects. Previous GWAS identified 52 autosomal variants associated with age-related macular degeneration (AMD) via the International AMD Genomics Consortium (IAMDGC), but did not analyze ChrX. Therefore¸ our goal was to investigate ChrX variants for association with AMD. METHODS We genotyped 29 629 non-Hispanic White (NHW) individuals (M/F:10404/18865; AMD12,087/14723) via a custom chip and imputed after ChrX-specific QC (XWAS 3.0) using the Michigan Imputation Server. Imputation generated 1 221 623 variants on ChrX. Age, informative PCs, and subphenotypes were covariates for logistic association analyses with Fisher's correction. Gene/pathway analyses were performed with VEGAS, GSEASNP, ICSNPathway, DAVID, and mirPath. RESULTS Logistic association on NHW individuals with sex correction identified variants in/near the genes SLITRK4, ARHGAP6, FGF13 and DMD associated with AMD (P < 1 × 10-6,Fisher's combined-corrected). Association testing of the subphenotypes of choroidal neovascularization and geographic atrophy (GA), identified variants in DMD associated with GA (P < 1 × 10-6, Fisher's combined-corrected). Via gene-based analysis with VEGAS, several genes were associated with AMD (P < 0.05, both truncated tail strength/truncated product P) including SLITRK4 and BHLHB9. Pathway analysis using GSEASNP and DAVID identified genes associated with nervous system development (FDR: P:0.02), and blood coagulation (FDR: P:0.03). Variants in the region of a microRNA (miR) were associated with AMD (P < 0.05, truncated tail strength/truncated product P). Via DIANA mirPath analysis, downstream targets of miRs showed association with brain disorders and fatty acid elongation (P < 0.05). A long noncoding RNA on ChrX near the DMD locus was also associated with AMD (P = 4 × 10-7). Epistatic analysis (t-statistic) for a quantitative trait of AMD vs control including covariates found a suggestive association in the XG gene (P = 2 × 10^-5). CONCLUSIONS Analysis of ChrX variation identifies several potential new locifor AMD risk and these variants nominate novel AMD pathways. Further analysis is needed to refine these results and to understand their biological significance and relationship with AMD development in worldwide populations.
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Affiliation(s)
- Michelle Grunin
- Population and Quantitative Health Sciences, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, United States
- Cleveland Institute for Computational Biology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106 United States
| | - Robert P Igo Jr
- Population and Quantitative Health Sciences, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, United States
- Cleveland Institute for Computational Biology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106 United States
| | - Yeunjoo E Song
- Population and Quantitative Health Sciences, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, United States
- Cleveland Institute for Computational Biology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106 United States
| | - Susan H Blanton
- Dr. John T Macdonald Department of Human Genetics, University of Miami School of Medicine, 1600 NW 10th Ave, Miami, FL 33136, United States
- The John P Hussman Institute for Human Genomics, University of Miami School of Medicine, Miami, 1600 NW 10th Ave, FL 33136, United States
| | - Margaret A Pericak-Vance
- Dr. John T Macdonald Department of Human Genetics, University of Miami School of Medicine, 1600 NW 10th Ave, Miami, FL 33136, United States
- The John P Hussman Institute for Human Genomics, University of Miami School of Medicine, Miami, 1600 NW 10th Ave, FL 33136, United States
| | - Jonathan L Haines
- Population and Quantitative Health Sciences, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, United States
- Cleveland Institute for Computational Biology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106 United States
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8
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Nurkkala J, Vaura F, Toivonen J, Niiranen T. Genetics of hypertension-related sex differences and hypertensive disorders of pregnancy. Blood Press 2024; 33:2408574. [PMID: 39371034 DOI: 10.1080/08037051.2024.2408574] [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: 06/21/2024] [Revised: 09/16/2024] [Accepted: 09/19/2024] [Indexed: 10/08/2024]
Abstract
Background: Hypertension and hypertensive disorders of pregnancy (HDP) cause a significant burden of disease on societies and individuals by increasing cardiovascular disease risk. Environmental risk factors alone do not explain the observed sexual dimorphism in lifetime blood pressure (BP) trajectories nor inter-individual variation in HDP risk. Methods: In this short review, we focus on the genetics of hypertension-related sex differences and HDP and discuss the importance of genetics utilization for sex-specific hypertension risk prediction. Results: Population and twin studies estimate that 28-66% of variation in BP levels and HDP is explained by genetic variation, while genomic wide association studies suggest that BP traits and HDP partly share a common genetic background. Moreover, environmental and epigenetic regulation of these genes differ by sex and oestrogen receptors in particular are shown to convey cardio- and vasculoprotective effects through epigenetic regulation of DNA. The majority of known genetic variation in hypertension and HDP is polygenic. Polygenic risk scores for BP display stronger associations with hypertension risk in women than in men and are associated with sex-specific age of hypertension onset. Monogenic forms of hypertension are rare and mostly present equally in both sexes. Conclusion: Despite recent genetic discoveries providing new insights into HDP and sex differences in BP traits, further research is needed to elucidate the underlying biology. Emphasis should be placed on demonstrating the added clinical value of these genetic discoveries, which may eventually facilitate genomics-based personalized treatments for hypertension and HDP.
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Affiliation(s)
- Jouko Nurkkala
- Division of Perioperative Services, Intensive Care and Pain Medicine, Turku University Hospital, Turku, Finland
- Department of Anesthesiology and Intensive Care, University of Turku, Turku, Finland
| | - Felix Vaura
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Jenni Toivonen
- Division of Perioperative Services, Intensive Care and Pain Medicine, Turku University Hospital, Turku, Finland
- Department of Anesthesiology and Intensive Care, University of Turku, Turku, Finland
| | - Teemu Niiranen
- Department of Internal Medicine, University of Turku, Turku, Finland
- Division of Medicine, Turku University Hospital, Turku, Finland
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Turku, Finland
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9
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Main LR, Song YE, Lynn A, Laux RA, Miskimen KL, Osterman MD, Cuccaro ML, Ogrocki PK, Lerner AJ, Vance JM, Fuzzell D, Fuzzell SL, Hochstetler SD, Dorfsman DA, Caywood LJ, Prough MB, Adams LD, Clouse JE, Herington SD, Scott WK, Pericak-Vance MA, Haines JL. Genetic analysis of cognitive preservation in the midwestern Amish reveals a novel locus on chromosome 2. Alzheimers Dement 2024; 20:7453-7464. [PMID: 39376159 PMCID: PMC11567819 DOI: 10.1002/alz.14045] [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: 11/21/2023] [Revised: 04/17/2024] [Accepted: 05/13/2024] [Indexed: 10/09/2024]
Abstract
INTRODUCTION Alzheimer's disease (AD) remains a debilitating condition with limited treatments and additional therapeutic targets needed. Identifying AD protective genetic loci may identify new targets and accelerate identification of therapeutic treatments. We examined a founder population to identify loci associated with cognitive preservation into advanced age. METHODS Genome-wide association and linkage analyses were performed on 946 examined and sampled Amish individuals, aged 76-95, who were either cognitively unimpaired (CU) or impaired (CI). RESULTS A total of 12 single nucleotide polymorphisms (SNPs) demonstrated suggestive association (P ≤ 5 × 10-4) with cognitive preservation. Genetic linkage analyses identified > 100 significant (logarithm of the odds [LOD] ≥ 3.3) SNPs, some which overlapped with the association results. Only one locus on chromosome 2 retained significance across multiple analyses. DISCUSSION A novel significant result for cognitive preservation on chromosome 2 includes the genes LRRTM4 and CTNNA2. Additionally, the lead SNP, rs1402906, impacts the POU3F2 transcription factor binding affinity, which regulates LRRTM4 and CTNNA2. HIGHLIGHTS GWAS and linkage identified over 100 loci associated with cognitive preservation. One locus on Chromosome 2 retained significance over multiple analyses. Predicted TFBSs near rs1402906 regulate genes associated with neurocognition.
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Affiliation(s)
- Leighanne R Main
- Departments of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Renee A Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Kristy L Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Michael D Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Michael L Cuccaro
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Paula K Ogrocki
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
- Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Alan J Lerner
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
- Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Jeffery M Vance
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Sarada L Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Sherri D Hochstetler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Daniel A Dorfsman
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Laura J Caywood
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Michael B Prough
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Larry D Adams
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jason E Clouse
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Sharlene D Herington
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - William K Scott
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Margaret A Pericak-Vance
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jonathan L Haines
- Departments of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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10
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Buckley RF, Seto M. How Is the X Chromosome Involved in Alzheimer Disease? JAMA Neurol 2024; 81:1028-1029. [PMID: 39250122 DOI: 10.1001/jamaneurol.2024.2831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Affiliation(s)
- Rachel F Buckley
- Department of Neurology, Massachusetts General Hospital, Boston
- Center for Alzheimer's Research and Therapy, Brigham & Women's Hospital, Boston, Massachusetts
- Melbourne School of Psychological Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Mabel Seto
- Center for Alzheimer's Research and Therapy, Brigham & Women's Hospital, Boston, Massachusetts
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11
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Mendes M, Chen DZ, Engchuan W, Leal TP, Thiruvahindrapuram B, Trost B, Howe JL, Pellecchia G, Nalpathamkalam T, Alexandrova R, Salazar NB, McKee EA, Alfaro NR, Lai MC, Bandres-Ciga S, Roshandel D, Bradley CA, Anagnostou E, Sun L, Scherer SW. Chromosome X-Wide Common Variant Association Study (XWAS) in Autism Spectrum Disorder. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.18.24310640. [PMID: 39108515 PMCID: PMC11302709 DOI: 10.1101/2024.07.18.24310640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
Autism Spectrum Disorder (ASD) displays a notable male bias in prevalence. Research into rare (<0.1) genetic variants on the X chromosome has implicated over 20 genes in ASD pathogenesis, such as MECP2, DDX3X, and DMD. The "female protective effect" in ASD suggests that females may require a higher genetic burden to manifest similar symptoms as males, yet the mechanisms remain unclear. Despite technological advances in genomics, the complexity of the biological nature of sex chromosomes leave them underrepresented in genome-wide studies. Here, we conducted an X chromosome-wide association study (XWAS) using whole-genome sequencing data from 6,873 individuals with ASD (82% males) across Autism Speaks MSSNG, Simons Simplex Cohort SSC, and Simons Foundation Powering Autism Research SPARK, alongside 8,981 population controls (43% males). We analyzed 418,652 X-chromosome variants, identifying 59 associated with ASD (p-values 7.9×10-6 to 1.51×10-5), surpassing Bonferroni-corrected thresholds. Key findings include significant regions on chrXp22.2 (lead SNP=rs12687599, p=3.57×10-7) harboring ASB9/ASB11, and another encompassing DDX53/PTCHD1-AS long non-coding RNA (lead SNP=rs5926125, p=9.47×10-6). When mapping genes within 10kb of the 59 most significantly associated SNPs, 91 genes were found, 17 of which yielded association with ASD (GRPR, AP1S2, DDX53, HDAC8, PCDH19, PTCHD1, PCDH11X, PTCHD1-AS, DMD, SYAP1, CNKSR2, GLRA2, OFD1, CDKL5, GPRASP2, NXF5, SH3KBP1). FGF13 emerged as a novel X-linked ASD candidate gene, highlighted by sex-specific differences in minor allele frequencies. These results reveal significant new insights into X chromosome biology in ASD, confirming and nominating genes and pathways for further investigation.
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Affiliation(s)
- Marla Mendes
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Desmond Zeya Chen
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, ON, M5G 1X6, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Thiago Peixoto Leal
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, OH, 44106, USA
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Brett Trost
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jennifer L. Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Roumiana Alexandrova
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Nelson Bautista Salazar
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Ethan Alexander McKee
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Natalia Rivera Alfaro
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Meng-Chuan Lai
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5G 2C1, Canada
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, M5G 1E8, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Sara Bandres-Ciga
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Delnaz Roshandel
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Clarrisa A. Bradley
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Evdokia Anagnostou
- Autism Research Centre, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, M4G 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Lei Sun
- Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, ON, M5G 1X6, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, M5S 3E3, Canada
| | - Stephen W. Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
- McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
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12
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Neale N, Lona-Durazo F, Ryten M, Gagliano Taliun SA. Leveraging sex-genetic interactions to understand brain disorders: recent advances and current gaps. Brain Commun 2024; 6:fcae192. [PMID: 38894947 PMCID: PMC11184352 DOI: 10.1093/braincomms/fcae192] [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: 04/03/2024] [Revised: 04/11/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
It is established that there are sex differences in terms of prevalence, age of onset, clinical manifestations, and response to treatment for a variety of brain disorders, including neurodevelopmental, psychiatric, and neurodegenerative disorders. Cohorts of increasing sample sizes with diverse data types collected, including genetic, transcriptomic and/or phenotypic data, are providing the building blocks to permit analytical designs to test for sex-biased genetic variant-trait associations, and for sex-biased transcriptional regulation. Such molecular assessments can contribute to our understanding of the manifested phenotypic differences between the sexes for brain disorders, offering the future possibility of delivering personalized therapy for females and males. With the intention of raising the profile of this field as a research priority, this review aims to shed light on the importance of investigating sex-genetic interactions for brain disorders, focusing on two areas: (i) variant-trait associations and (ii) transcriptomics (i.e. gene expression, transcript usage and regulation). We specifically discuss recent advances in the field, current gaps and provide considerations for future studies.
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Affiliation(s)
- Nikita Neale
- Faculty of Medicine, Université de Montréal, Québec, H3C 3J7 Canada
| | - Frida Lona-Durazo
- Faculty of Medicine, Université de Montréal, Québec, H3C 3J7 Canada
- Research Centre, Montreal Heart Institute, Québec, H1T 1C8 Canada
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, WC1N 1EH London, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, 20815 MD, USA
- NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, Bloomsbury, WC1N 1EH London, UK
| | - Sarah A Gagliano Taliun
- Research Centre, Montreal Heart Institute, Québec, H1T 1C8 Canada
- Department of Medicine & Department of Neurosciences, Faculty of Medicine, Université de Montréal, Québec, H3C 3J7 Canada
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13
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Bravo JI, Mizrahi CR, Kim S, Zhang L, Suh Y, Benayoun BA. An eQTL-based approach reveals candidate regulators of LINE-1 RNA levels in lymphoblastoid cells. PLoS Genet 2024; 20:e1011311. [PMID: 38848448 PMCID: PMC11189215 DOI: 10.1371/journal.pgen.1011311] [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: 12/27/2023] [Revised: 06/20/2024] [Accepted: 05/21/2024] [Indexed: 06/09/2024] Open
Abstract
Long interspersed element 1 (LINE-1; L1) are a family of transposons that occupy ~17% of the human genome. Though a small number of L1 copies remain capable of autonomous transposition, the overwhelming majority of copies are degenerate and immobile. Nevertheless, both mobile and immobile L1s can exert pleiotropic effects (promoting genome instability, inflammation, or cellular senescence) on their hosts, and L1's contributions to aging and aging diseases is an area of active research. However, because of the cell type-specific nature of transposon control, the catalogue of L1 regulators remains incomplete. Here, we employ an eQTL approach leveraging transcriptomic and genomic data from the GEUVADIS and 1000Genomes projects to computationally identify new candidate regulators of L1 RNA levels in lymphoblastoid cell lines. To cement the role of candidate genes in L1 regulation, we experimentally modulate the levels of top candidates in vitro, including IL16, STARD5, HSD17B12, and RNF5, and assess changes in TE family expression by Gene Set Enrichment Analysis (GSEA). Remarkably, we observe subtle but widespread upregulation of TE family expression following IL16 and STARD5 overexpression. Moreover, a short-term 24-hour exposure to recombinant human IL16 was sufficient to transiently induce subtle, but widespread, upregulation of L1 subfamilies. Finally, we find that many L1 expression-associated genetic variants are co-associated with aging traits across genome-wide association study databases. Our results expand the catalogue of genes implicated in L1 RNA control and further suggest that L1-derived RNA contributes to aging processes. Given the ever-increasing availability of paired genomic and transcriptomic data, we anticipate this new approach to be a starting point for more comprehensive computational scans for regulators of transposon RNA levels.
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Affiliation(s)
- Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, California, United States of America
| | - Chanelle R. Mizrahi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- USC Gerontology Enriching MSTEM to Enhance Diversity in Aging Program, University of Southern California, Los Angeles, California, United States of America
| | - Seungsoo Kim
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Lucia Zhang
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- Quantitative and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California, United States of America
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California, United States of America
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, California, United States of America
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, California, United States of America
- USC Stem Cell Initiative, Los Angeles, California, United States of America
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14
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Bellavance J, Wang L, Gagliano Taliun SA. Eight quick tips for including chromosome X in genome-wide association studies. PLoS Comput Biol 2024; 20:e1012160. [PMID: 38843110 PMCID: PMC11156303 DOI: 10.1371/journal.pcbi.1012160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024] Open
Affiliation(s)
- Justin Bellavance
- Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
- Research Centre, Montréal Heart Institute, Montréal, Québec, Canada
| | - Linda Wang
- Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
- Research Centre, Montréal Heart Institute, Montréal, Québec, Canada
| | - Sarah A. Gagliano Taliun
- Research Centre, Montréal Heart Institute, Montréal, Québec, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
- Department of Neurosciences, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
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15
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Jiang Z, Sullivan PF, Li T, Zhao B, Wang X, Luo T, Huang S, Guan PY, Chen J, Yang Y, Stein JL, Li Y, Liu D, Sun L, Zhu H. The pivotal role of the X-chromosome in the genetic architecture of the human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.08.30.23294848. [PMID: 37693466 PMCID: PMC10491353 DOI: 10.1101/2023.08.30.23294848] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Genes on the X-chromosome are extensively expressed in the human brain. However, little is known for the X-chromosome's impact on the brain anatomy, microstructure, and functional network. We examined 1,045 complex brain imaging traits from 38,529 participants in the UK Biobank. We unveiled potential autosome-X-chromosome interactions, while proposing an atlas outlining dosage compensation (DC) for brain imaging traits. Through extensive association studies, we identified 72 genome-wide significant trait-locus pairs (including 29 new associations) that share genetic architectures with brain-related disorders, notably schizophrenia. Furthermore, we discovered unique sex-specific associations and assessed variations in genetic effects between sexes. Our research offers critical insights into the X-chromosome's role in the human brain, underscoring its contribution to the differences observed in brain structure and functionality between sexes.
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16
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Lopez-Lee C, Torres ERS, Carling G, Gan L. Mechanisms of sex differences in Alzheimer's disease. Neuron 2024; 112:1208-1221. [PMID: 38402606 PMCID: PMC11076015 DOI: 10.1016/j.neuron.2024.01.024] [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: 07/31/2023] [Revised: 11/01/2023] [Accepted: 01/23/2024] [Indexed: 02/27/2024]
Abstract
Alzheimer's disease (AD) and the mechanisms underlying its etiology and progression are complex and multifactorial. The higher AD risk in women may serve as a clue to better understand these complicated processes. In this review, we examine aspects of AD that demonstrate sex-dependent effects and delve into the potential biological mechanisms responsible, compiling findings from advanced technologies such as single-cell RNA sequencing, metabolomics, and multi-omics analyses. We review evidence that sex hormones and sex chromosomes interact with various disease mechanisms during aging, encompassing inflammation, metabolism, and autophagy, leading to unique characteristics in disease progression between men and women.
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Affiliation(s)
- Chloe Lopez-Lee
- Helen and Robert Appel Alzheimer's Disease Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA; Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Eileen Ruth S Torres
- Helen and Robert Appel Alzheimer's Disease Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Gillian Carling
- Helen and Robert Appel Alzheimer's Disease Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA; Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Li Gan
- Helen and Robert Appel Alzheimer's Disease Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA; Neuroscience Graduate Program, Weill Cornell Medicine, New York, NY, USA.
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17
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French JN, Pua VB, Laboulaye R, Leal TP, Olivas MC, Lima-Costa MF, Horta BL, Barreto ML, Tarazona-Santos E, Mata I, O’Connor TD. Comparing the effect of imputation reference panel composition in four distinct Latin American cohorts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589057. [PMID: 38659746 PMCID: PMC11042191 DOI: 10.1101/2024.04.11.589057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Genome-wide association studies have been useful in identifying genetic risk factors for various phenotypes. These studies rely on imputation and many existing panels are largely composed of individuals of European ancestry, resulting in lower levels of imputation quality in underrepresented populations. We aim to analyze how the composition of imputation reference panels affects imputation quality in four target Latin American cohorts. We compared imputation quality for chromosomes 7 and X when altering the imputation reference panel by: 1) increasing the number of Latin American individuals; 2) excluding either Latin American, African, or European individuals, or 3) increasing the Indigenous American (IA) admixture proportions of included Latin Americans. We found that increasing the number of Latin Americans in the reference panel improved imputation quality in the four populations; however, there were differences between chromosomes 7 and X in some cohorts. Excluding Latin Americans from analysis resulted in worse imputation quality in every cohort, while differential effects were seen when excluding Europeans and Africans between and within cohorts and between chromosomes 7 and X. Finally, increasing IA-like admixture proportions in the reference panel increased imputation quality at different levels in different populations. The difference in results between populations and chromosomes suggests that existing and future reference panels containing Latin American individuals are likely to perform differently in different Latin American populations.
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Affiliation(s)
- Jennifer N French
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | - Victor Borda Pua
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
- University of Maryland Institute for Health Computing, Rockville, MD
| | - Roland Laboulaye
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | - Thiago Peixoto Leal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Mario Cornejo Olivas
- Neurogenetics Working Group, Universidad Cientifica del Sur, Lima, Peru
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
| | | | - Bernardo L Horta
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Mauricio L Barreto
- Center for Data and Knowledge Integration for Health (CIDACS), Gonçalo Moniz Institute (IGM), Oswaldo Cruz Foundation (FIOCRUZ-BA), Salvador, Bahia, Brazil
- Collective Health Institute, Federal University of Bahia (UFBA), Salvador, Bahia, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Ignacio Mata
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
- Program in Health Equity and Population Health, University of Maryland School of Medicine
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18
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Caduff M, Eckel R, Leuenberger C, Wegmann D. Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data. Mol Ecol Resour 2024; 24:e13913. [PMID: 38173222 DOI: 10.1111/1755-0998.13913] [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: 09/16/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
The identification of sex-linked scaffolds and the genetic sex of individuals, i.e. their sex karyotype, is a fundamental step in population genomic studies. If sex-linked scaffolds are known, single individuals may be sexed based on read counts of next-generation sequencing data. If both sex-linked scaffolds as well as sex karyotypes are unknown, as is often the case for non-model organisms, they have to be jointly inferred. For both cases, current methods rely on arbitrary thresholds, which limits their power for low-depth data. In addition, most current methods are limited to euploid sex karyotypes (XX and XY). Here we develop BeXY, a fully Bayesian method to jointly infer the posterior probabilities for each scaffold to be autosomal, X- or Y-linked and for each individual to be any of the sex karyotypes XX, XY, X0, XXX, XXY, XYY and XXYY. If the sex-linked scaffolds are known, it also identifies autosomal trisomies and estimates the sex karyotype posterior probabilities for single individuals. As we show with downsampling experiments, BeXY has higher power than all existing methods. It accurately infers the sex karyotype of ancient human samples with as few as 20,000 reads and accurately infers sex-linked scaffolds from data sets of just a handful of samples or with highly imbalanced sex ratios, also in the case of low-quality reference assemblies. We illustrate the power of BeXY by applying it to both whole-genome shotgun and target enrichment sequencing data of ancient and modern humans, as well as several non-model organisms.
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Affiliation(s)
- Madleina Caduff
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Raphael Eckel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Christoph Leuenberger
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
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McAusland L, Burton CL, Bagnell A, Boylan K, Hatchard T, Lingley-Pottie P, Al Maruf A, McGrath P, Newton AS, Rowa K, Schachar RJ, Shaheen SM, Stewart S, Arnold PD, Crosbie J, Mattheisen M, Soreni N, Stewart SE, Meier S. The genetic architecture of youth anxiety: a study protocol. BMC Psychiatry 2024; 24:159. [PMID: 38395805 PMCID: PMC10885620 DOI: 10.1186/s12888-024-05583-9] [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: 01/17/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Anxiety disorders are the most common psychiatric problems among Canadian youth and typically have an onset in childhood or adolescence. They are characterized by high rates of relapse and chronicity, often resulting in substantial impairment across the lifespan. Genetic factors play an important role in the vulnerability toward anxiety disorders. However, genetic contribution to anxiety in youth is not well understood and can change across developmental stages. Large-scale genetic studies of youth are needed with detailed assessments of symptoms of anxiety disorders and their major comorbidities to inform early intervention or preventative strategies and suggest novel targets for therapeutics and personalization of care. METHODS The Genetic Architecture of Youth Anxiety (GAYA) study is a Pan-Canadian effort of clinical and genetic experts with specific recruitment sites in Calgary, Halifax, Hamilton, Toronto, and Vancouver. Youth aged 10-19 (n = 13,000) will be recruited from both clinical and community settings and will provide saliva samples, complete online questionnaires on demographics, symptoms of mental health concerns, and behavioural inhibition, and complete neurocognitive tasks. A subset of youth will be offered access to a self-managed Internet-based cognitive behavioral therapy resource. Analyses will focus on the identification of novel genetic risk loci for anxiety disorders in youth and assess how much of the genetic risk for anxiety disorders is unique or shared across the life span. DISCUSSION Results will substantially inform early intervention or preventative strategies and suggest novel targets for therapeutics and personalization of care. Given that the GAYA study will be the biggest genomic study of anxiety disorders in youth in Canada, this project will further foster collaborations nationally and across the world.
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Affiliation(s)
- Laina McAusland
- The Mathison Centre for Mental Health Research & Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Psychiatry, University of Calgary, Calgary, AB, Canada.
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada.
| | - Christie L Burton
- Neurosciences & Mental Health, Hospital for Sick Children, Toronto, ON, Canada
| | - Alexa Bagnell
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - Khrista Boylan
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
- Offord Center for Child Studies, Hamilton, ON, Canada
- Child and Youth Mental Health Program, Hamilton Health Sciences, Hamilton, ON, Canada
| | - Taylor Hatchard
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
- Youth Wellness Center, St. Joseph's Healthcare, Hamilton, ON, Canada
| | - Patricia Lingley-Pottie
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
- Department of Psychiatry, IWK Health Centre, Halifax, NS, Canada
| | - Abdullah Al Maruf
- The Mathison Centre for Mental Health Research & Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Psychiatry, University of Calgary, Calgary, AB, Canada
- College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Patrick McGrath
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - Amanda S Newton
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Karen Rowa
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
- Anxiety Treatment and Research Clinic, St. Joseph's Healthcare Hamilton, Hamilton, ON, Canada
- Department of Psychology, Neuroscience, and Behaviour, McMaster University, Hamilton, ON, Canada
| | - Russell J Schachar
- Neurosciences & Mental Health, Hospital for Sick Children, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - S-M Shaheen
- The Mathison Centre for Mental Health Research & Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Psychiatry, University of Calgary, Calgary, AB, Canada
| | - Sam Stewart
- Department of Epidemiology and Community Health, Dalhousie University, Halifax, NS, Canada
| | - Paul D Arnold
- The Mathison Centre for Mental Health Research & Education, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Psychiatry, University of Calgary, Calgary, AB, Canada
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Jennifer Crosbie
- Neurosciences & Mental Health, Hospital for Sick Children, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Manuel Mattheisen
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
- Department of Epidemiology and Community Health, Dalhousie University, Halifax, NS, Canada
- Department of Computer Science, Dalhousie University, Halifax, NS, Canada
| | - Noam Soreni
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
- Offord Center for Child Studies, Hamilton, ON, Canada
- Anxiety Treatment and Research Clinic, St. Joseph's Healthcare Hamilton, Hamilton, ON, Canada
- Pediatric OCD Consultation Service, St. Joseph's Healthcare Hamilton, Hamilton, ON, Canada
| | - S Evelyn Stewart
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Sandra Meier
- Department of Psychiatry, Dalhousie University, Halifax, NS, Canada
- Department of Epidemiology and Community Health, Dalhousie University, Halifax, NS, Canada
- Department of Computer Science, Dalhousie University, Halifax, NS, Canada
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20
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Bayram E, Reho P, Litvan I, Ding J, Gibbs JR, Dalgard CL, Traynor BJ, Scholz SW, Chia R. Genetic analysis of the X chromosome in people with Lewy body dementia nominates new risk loci. NPJ Parkinsons Dis 2024; 10:39. [PMID: 38378815 PMCID: PMC10879525 DOI: 10.1038/s41531-024-00649-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Sex influences the prevalence and symptoms of Lewy body dementia (LBD). However, genome-wide association studies typically focus on autosomal variants and exclude sex-specific risk factors. We addressed this gap by performing an X chromosome-wide association study using whole-genome sequence data from 2591 LBD cases and 4391 controls. We identified a significant risk locus within intron 1 of MAP3K15 (rs141773145, odds ratio = 2.42, 95% confidence interval = 1.65-3.56, p-value = 7.0 × 10-6) in female LBD cases conditioned for APOE ε4 dosage. The locus includes an enhancer region that regulates MAP3K15 expression in ganglionic eminence cells derived from primary cultured neurospheres. Rare variant burden testing showed differential enrichment of missense mutations in TEX13A in female LBD cases, that did not reach significance (p-value = 1.34 × 10-4). These findings support the sex-specific effects of genetic factors and a potential role of Alzheimer's-related risk for females with LBD.
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Affiliation(s)
- Ece Bayram
- Department of Neurosciences, Parkinson and Other Movement Disorders Center, University of California San Diego, La Jolla, CA, USA
| | - Paolo Reho
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Irene Litvan
- Department of Neurosciences, Parkinson and Other Movement Disorders Center, University of California San Diego, La Jolla, CA, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - J Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Bryan J Traynor
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA
- Therapeutics Development Laboratory, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Ruth Chia
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA.
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21
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Singh K, Wendt FR. Effects of sex and gender on the etiologies and presentation of select internalizing psychopathologies. Transl Psychiatry 2024; 14:73. [PMID: 38307846 PMCID: PMC10837201 DOI: 10.1038/s41398-024-02730-4] [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: 01/03/2023] [Revised: 12/19/2023] [Accepted: 01/02/2024] [Indexed: 02/04/2024] Open
Abstract
The internalizing spectrum encompasses a subset of psychopathologies characterized by emotional liability, anhedonia, anxiousness, distress, and fear, and includes, among others, diagnoses of major depressive disorder (MDD), generalized anxiety disorder (GAD), and posttraumatic stress disorder (PTSD). In this review, we describe the vast body of work highlighting a role for sex and gender in the environment, symptom onset, genetic liability, and disorder progression and comorbidities of MDD, GAD, and PTSD. We also point the reader to different language used in diverse fields to describe sexual and gender minorities that may complicate the interpretation of emerging literature from the social sciences, psychiatric and psychological sciences, and genetics. Finally, we identify several gaps in knowledge that we hope serve as launch-points for expanding the scope of psychiatric studies beyond binarized sex-stratification. Despite being under-represented in genomics studies, placing emphasis on inclusion of sexual and gender diverse participants in these works will hopefully improve our understanding of disorder etiology using genetics as one tool to inform how biology (e.g., hormone concentration) and environmental variables (e.g., exposure to traumatic events) contribute to differences in symptom onset, pattern, and long-term trajectory.
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Affiliation(s)
- Kritika Singh
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Frank R Wendt
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada.
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22
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Main LR, Song YE, Lynn A, Laux RA, Miskimen KL, Osterman MD, Cuccaro ML, Ogrocki PK, Lerner AJ, Vance JM, Fuzzell MD, Fuzzell SL, Hochstetler SD, Dorfsman DA, Caywood LJ, Prough MB, Adams LD, Clouse JE, Herington SD, Scott WK, Pericak-Vance MA, Haines JL. Genetic analysis of cognitive preservation in the midwestern Amish reveals a novel locus on chromosome 2. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.13.23299932. [PMID: 38168325 PMCID: PMC10760262 DOI: 10.1101/2023.12.13.23299932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
INTRODUCTION Alzheimer disease (AD) remains a debilitating condition with limited treatments and additional therapeutic targets needed. Identifying AD protective genetic loci may identify new targets and accelerate identification of therapeutic treatments. We examined a founder population to identify loci associated with cognitive preservation into advanced age. METHODS Genome-wide association and linkage analyses were performed on 946 examined and sampled Amish individuals, aged 76-95, who were either cognitively unimpaired (CU) or impaired (CI). RESULTS 12 SNPs demonstrated suggestive association (P≤5×10-4) with cognitive preservation. Genetic linkage analyses identified >100 significant (LOD≥3.3) SNPs, some which overlapped with the association results. Only one locus on chromosome 2 retained significance across multiple analyses. DISCUSSION A novel significant result for cognitive preservation on chromosome 2 includes the genes LRRTM4 and CTNNA2. Additionally, the lead SNP, rs1402906, impacts the POU3F2 transcription factor binding affinity, which regulates LRRTM4 and CTNNA2.
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Affiliation(s)
- Leighanne R Main
- Departments of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, USA, 44106
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Renee A Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Kristy L Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Michael D Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Michael L Cuccaro
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Paula K Ogrocki
- Department of Neurology, University Hospitals Cleveland Medical Center, 11100 Euclid Ave, Cleveland, OH, USA, 44106
- Department of Neurology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Alan J Lerner
- Department of Neurology, University Hospitals Cleveland Medical Center, 11100 Euclid Ave, Cleveland, OH, USA, 44106
- Department of Neurology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Jeffery M Vance
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - M Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Sarada L Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Sherri D Hochstetler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Daniel A Dorfsman
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Laura J Caywood
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Michael B Prough
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Larry D Adams
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Jason E Clouse
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Sharlene D Herington
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - William K Scott
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Margaret A Pericak-Vance
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Jonathan L Haines
- Departments of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, USA, 44106
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
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23
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Li W, Zhou H, Thygesen JH, Heydtmann M, Smith I, Degenhardt F, Nöthen M, Morgan MY, Kranzler HR, Gelernter J, Bass N, McQuillin A. Genome-wide association study of antisocial personality disorder diagnostic criteria provides evidence for shared risk factors across disorders. Psychiatr Genet 2023; 33:233-242. [PMID: 37756443 PMCID: PMC10635348 DOI: 10.1097/ypg.0000000000000352] [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: 06/29/2022] [Accepted: 06/19/2023] [Indexed: 09/29/2023]
Abstract
INTRODUCTION While progress has been made in determining the genetic basis of antisocial behaviour, little progress has been made for antisocial personality disorder (ASPD), a condition that often co-occurs with other psychiatric conditions including substance use disorders, attention deficit hyperactivity disorder (ADHD), and anxiety disorders. This study aims to improve the understanding of the genetic risk for ASPD and its relationship with other disorders and traits. METHODS We conducted a genome-wide association study (GWAS) of the number of ASPD diagnostic criteria data from 3217 alcohol-dependent participants recruited in the UK (UCL, N = 644) and the USA (Yale-Penn, N = 2573). RESULTS We identified rs9806493, a chromosome 15 variant, that showed a genome-wide significant association ( Z -score = -5.501, P = 3.77 × 10 -8 ) with ASPD criteria. rs9806493 is an eQTL for SLCO3A1 (Solute Carrier Organic Anion Transporter Family Member 3A1), a ubiquitously expressed gene with strong expression in brain regions that include the anterior cingulate and frontal cortices. Polygenic risk score analysis identified positive correlations between ASPD and smoking, ADHD, depression traits, and posttraumatic stress disorder. Negative correlations were observed between ASPD PRS and alcohol intake frequency, reproductive traits, and level of educational attainment. CONCLUSION This study provides evidence for an association between ASPD risk and SLCO3A1 and provides insight into the genetic architecture and pleiotropic associations of ASPD.
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Affiliation(s)
- Wenqianglong Li
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - Hang Zhou
- Department of Psychiatry, Yale School of Medicine, New Haven
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
| | - Johan H. Thygesen
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
- Institute of Health Informatics, University College London, London, UK
| | - Mathis Heydtmann
- Royal Alexandria Hospital, NHS Greater Glasgow and Clyde, Paisley, UK
- Department of Gastroenterology, Dumfries & Galloway Royal Infirmary, Cargenbridge, Dumfries, Scotland
| | - Iain Smith
- Substance misuse service, Mayfield Centre, St Ninians, Stirling, UK
| | - Franziska Degenhardt
- Department of Child and Adolescent Psychiatry, University of Duisburg-Essen, Essen
| | - Markus Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Marsha Y. Morgan
- UCL Institute for Liver & Digestive Health, Division of Medicine, Royal Free Campus, University College London, London, UK
| | - Henry R. Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine
- Crescenz Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - Joel Gelernter
- Department of Psychiatry, Yale School of Medicine, New Haven
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
- Departments of Genetics and Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nicholas Bass
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
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24
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Bravo JI, Mizrahi CR, Kim S, Zhang L, Suh Y, Benayoun BA. An eQTL-based Approach Reveals Candidate Regulators of LINE-1 RNA Levels in Lymphoblastoid Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.15.553416. [PMID: 37645920 PMCID: PMC10461994 DOI: 10.1101/2023.08.15.553416] [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
Long interspersed element 1 (L1) are a family of autonomous, actively mobile transposons that occupy ~17% of the human genome. A number of pleiotropic effects induced by L1 (promoting genome instability, inflammation, or cellular senescence) have been observed, and L1's contributions to aging and aging diseases is an area of active research. However, because of the cell type-specific nature of transposon control, the catalogue of L1 regulators remains incomplete. Here, we employ an eQTL approach leveraging transcriptomic and genomic data from the GEUVADIS and 1000Genomes projects to computationally identify new candidate regulators of L1 RNA levels in lymphoblastoid cell lines. To cement the role of candidate genes in L1 regulation, we experimentally modulate the levels of top candidates in vitro, including IL16, STARD5, HSDB17B12, and RNF5, and assess changes in TE family expression by Gene Set Enrichment Analysis (GSEA). Remarkably, we observe subtle but widespread upregulation of TE family expression following IL16 and STARD5 overexpression. Moreover, a short-term 24-hour exposure to recombinant human IL16 was sufficient to transiently induce subtle, but widespread, upregulation of L1 subfamilies. Finally, we find that many L1 expression-associated genetic variants are co-associated with aging traits across genome-wide association study databases. Our results expand the catalogue of genes implicated in L1 RNA control and further suggest that L1-derived RNA contributes to aging processes. Given the ever-increasing availability of paired genomic and transcriptomic data, we anticipate this new approach to be a starting point for more comprehensive computational scans for transposon transcriptional regulators.
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Affiliation(s)
- Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Chanelle R. Mizrahi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- USC Gerontology Enriching MSTEM to Enhance Diversity in Aging Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Seungsoo Kim
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lucia Zhang
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Quantitative and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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25
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Trebes H, Wang Y, Reynolds E, Tiplady K, Harland C, Lopdell T, Johnson T, Davis S, Harris B, Spelman R, Couldrey C. Identification of candidate novel production variants on the Bos taurus chromosome X. J Dairy Sci 2023; 106:7799-7815. [PMID: 37562645 DOI: 10.3168/jds.2022-23095] [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: 12/01/2022] [Accepted: 04/26/2023] [Indexed: 08/12/2023]
Abstract
Chromosome X is often excluded from bovine genetic studies due to complications caused by the sex specific nature of the chromosome. As chromosome X is the second largest cattle chromosome and makes up approximately 6% of the female genome, finding ways to include chromosome X in dairy genetic studies is important. Using female animals and treating chromosome X as an autosome, we performed X chromosome inclusive genome-wide association studies in the selective breeding environment of the New Zealand dairy industry, aiming to identify chromosome X variants associated with milk production traits. We report on the findings of these genome-wide association studies and their potential effect within the dairy industry. We identify missense mutations in the MOSPD1 and CCDC160 genes that are associated with decreased milk volume and protein production and increased fat production. Both of these mutations are exonic SNP that are more prevalent in the Jersey breed than in Holstein-Friesians. Of the 2 candidates proposed it is likely that only one is causal, though we have not been able to identify which is more likely.
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Affiliation(s)
- H Trebes
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand.
| | - Y Wang
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - E Reynolds
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - K Tiplady
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - C Harland
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - T Lopdell
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - T Johnson
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - S Davis
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - B Harris
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - R Spelman
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - C Couldrey
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
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Khrom M, Li D, Naito T, Lee HS, Botwin GJ, Potdar AA, Boucher G, NIDDK Inflammatory Bowel Disease Genetics Consortium, International Inflammatory Bowel Disease Genetics Consortium, Yang S, Mengesha E, Dube S, Song K, McGovern DPB, Haritunians T. Sex-Dimorphic Analyses Identify Novel and Sex-Specific Genetic Associations in Inflammatory Bowel Disease. Inflamm Bowel Dis 2023; 29:1622-1632. [PMID: 37262302 PMCID: PMC10547236 DOI: 10.1093/ibd/izad089] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Indexed: 06/03/2023]
Abstract
BACKGROUND Sex is an integral variable often overlooked in complex disease genetics. Differences between sexes have been reported in natural history, disease complications, and age of onset in inflammatory bowel disease (IBD). While association studies have identified >230 IBD loci, there have been a limited number of studies investigating sex differences underlying these genetic associations. METHODS We report the first investigation of sex-dimorphic associations via meta-analysis of a sex-stratified association study (34 579 IBD cases, 39 125 controls). In addition, we performed chromosome (chr) X-specific analyses, considering models of X inactivation (XCI) and XCI escape. Demographic and clinical characteristics were also compared between sexes. RESULTS We identified significant differences between sexes for disease location and perianal complication in Crohn's disease and disease extent in ulcerative colitis. We observed genome-wide-significant sex-dimorphic associations (P < 5 × 10-8) at loci not previously reported in large-scale IBD genetic studies, including at chr9q22, CARMIL1, and UBASH3A. We identified variants in known IBD loci, including in chr2p15 and within the major histocompatibility complex on chr6, exhibiting sex-specific patterns of association (P < 5 × 10-7 in one sex only). We identified 3 chrX associations with IBD, including a novel Crohn's disease susceptibility locus at Xp22. CONCLUSIONS These analyses identified novel IBD loci, in addition to characterizing sex-specific patterns of associations underlying sex-dimorphic associations. By elucidating the role of sex in IBD genetics, our study will help enhance our understanding of the differences between the sexes in IBD biology and underscores a need to move beyond conventional sex-combined analyses to appreciate the genetic architecture of IBD more comprehensively.
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Affiliation(s)
- Michelle Khrom
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dalin Li
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Takeo Naito
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Gregory J Botwin
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alka A Potdar
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | | | - Shaohong Yang
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Emebet Mengesha
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shishir Dube
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Talin Haritunians
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Sun L, Wang Z, Lu T, Manolio TA, Paterson AD. eXclusionarY: 10 years later, where are the sex chromosomes in GWASs? Am J Hum Genet 2023; 110:903-912. [PMID: 37267899 PMCID: PMC10257007 DOI: 10.1016/j.ajhg.2023.04.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
10 years ago, a detailed analysis showed that only 33% of genome-wide association study (GWAS) results included the X chromosome. Multiple recommendations were made to combat such exclusion. Here, we re-surveyed the research landscape to determine whether these earlier recommendations had been translated. Unfortunately, among the genome-wide summary statistics reported in 2021 in the NHGRI-EBI GWAS Catalog, only 25% provided results for the X chromosome and 3% for the Y chromosome, suggesting that the exclusion phenomenon not only persists but has also expanded into an exclusionary problem. Normalizing by physical length of the chromosome, the average number of studies published through November 2022 with genome-wide-significant findings on the X chromosome is ∼1 study/Mb. By contrast, it ranges from ∼6 to ∼16 studies/Mb for chromosomes 4 and 19, respectively. Compared with the autosomal growth rate of ∼0.086 studies/Mb/year over the last decade, studies of the X chromosome grew at less than one-seventh that rate, only ∼0.012 studies/Mb/year. Among the studies that reported significant associations on the X chromosome, we noted extreme heterogeneities in data analysis and reporting of results, suggesting the need for clear guidelines. Unsurprisingly, among the 430 scores sampled from the PolyGenic Score Catalog, 0% contained weights for sex chromosomal SNPs. To overcome the dearth of sex chromosome analyses, we provide five sets of recommendations and future directions. Finally, until the sex chromosomes are included in a whole-genome study, instead of GWASs, we propose such studies would more properly be referred to as "AWASs," meaning "autosome-wide scans."
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Affiliation(s)
- Lei Sun
- Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, ON, Canada; Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
| | - Zhong Wang
- Department of Statistics and Data Science, Faculty of Science, National University of Singapore, Singapore
| | - Tianyuan Lu
- Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, ON, Canada; Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Andrew D Paterson
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada; Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
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Khramtsova EA, Wilson MA, Martin J, Winham SJ, He KY, Davis LK, Stranger BE. Quality control and analytic best practices for testing genetic models of sex differences in large populations. Cell 2023; 186:2044-2061. [PMID: 37172561 PMCID: PMC10266536 DOI: 10.1016/j.cell.2023.04.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 01/31/2023] [Accepted: 04/07/2023] [Indexed: 05/15/2023]
Abstract
Phenotypic sex-based differences exist for many complex traits. In other cases, phenotypes may be similar, but underlying biology may vary. Thus, sex-aware genetic analyses are becoming increasingly important for understanding the mechanisms driving these differences. To this end, we provide a guide outlining the current best practices for testing various models of sex-dependent genetic effects in complex traits and disease conditions, noting that this is an evolving field. Insights from sex-aware analyses will not only teach us about the biology of complex traits but also aid in achieving the goals of precision medicine and health equity for all.
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Affiliation(s)
- Ekaterina A Khramtsova
- Population Analytics and Insights, Data Science Analytics & Insights, Janssen R&D, Lower Gwynedd Township, PA, USA.
| | - Melissa A Wilson
- School of Life Sciences, Center for Evolution and Medicine, Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85282, USA
| | - Joanna Martin
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Stacey J Winham
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Karen Y He
- Population Analytics and Insights, Data Science Analytics & Insights, Janssen R&D, Lower Gwynedd Township, PA, USA
| | - Lea K Davis
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Barbara E Stranger
- Center for Genetic Medicine, Department of Pharmacology, Northwestern University, Chicago, IL, USA.
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29
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Romanowska J, Nustad HE, Page CM, Denault WRP, Lee Y, Magnus MC, Haftorn KL, Gjerdevik M, Novakovic B, Saffery R, Gjessing HK, Lyle R, Magnus P, Håberg SE, Jugessur A. The X-factor in ART: does the use of assisted reproductive technologies influence DNA methylation on the X chromosome? Hum Genomics 2023; 17:35. [PMID: 37085889 PMCID: PMC10122315 DOI: 10.1186/s40246-023-00484-6] [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: 01/09/2023] [Accepted: 04/10/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Assisted reproductive technologies (ART) may perturb DNA methylation (DNAm) in early embryonic development. Although a handful of epigenome-wide association studies of ART have been published, none have investigated CpGs on the X chromosome. To bridge this knowledge gap, we leveraged one of the largest collections of mother-father-newborn trios of ART and non-ART (natural) conceptions to date to investigate sex-specific DNAm differences on the X chromosome. The discovery cohort consisted of 982 ART and 963 non-ART trios from the Norwegian Mother, Father, and Child Cohort Study (MoBa). To verify our results from the MoBa cohort, we used an external cohort of 149 ART and 58 non-ART neonates from the Australian 'Clinical review of the Health of adults conceived following Assisted Reproductive Technologies' (CHART) study. The Illumina EPIC array was used to measure DNAm in both datasets. In the MoBa cohort, we performed a set of X-chromosome-wide association studies ('XWASs' hereafter) to search for sex-specific DNAm differences between ART and non-ART newborns. We tested several models to investigate the influence of various confounders, including parental DNAm. We also searched for differentially methylated regions (DMRs) and regions of co-methylation flanking the most significant CpGs. Additionally, we ran an analogous model to our main model on the external CHART dataset. RESULTS In the MoBa cohort, we found more differentially methylated CpGs and DMRs in girls than boys. Most of the associations persisted after controlling for parental DNAm and other confounders. Many of the significant CpGs and DMRs were in gene-promoter regions, and several of the genes linked to these CpGs are expressed in tissues relevant for both ART and sex (testis, placenta, and fallopian tube). We found no support for parental DNAm-dependent features as an explanation for the observed associations in the newborns. The most significant CpG in the boys-only analysis was in UBE2DNL, which is expressed in testes but with unknown function. The most significant CpGs in the girls-only analysis were in EIF2S3 and AMOT. These three loci also displayed differential DNAm in the CHART cohort. CONCLUSIONS Genes that co-localized with the significant CpGs and DMRs associated with ART are implicated in several key biological processes (e.g., neurodevelopment) and disorders (e.g., intellectual disability and autism). These connections are particularly compelling in light of previous findings indicating that neurodevelopmental outcomes differ in ART-conceived children compared to those naturally conceived.
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Affiliation(s)
- Julia Romanowska
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.
| | - Haakon E Nustad
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- DeepInsight, 0154, Oslo, Norway
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - William R P Denault
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Yunsung Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Kristine L Haftorn
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Miriam Gjerdevik
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Computer Science, Electrical Engineering and Mathematical Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Boris Novakovic
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Robert Lyle
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
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30
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Kong YF, Li SZ, Wang KW, Zhu B, Yuan YX, Li MK, Zhou JY. An Efficient Bayesian Method for Estimating the Degree of the Skewness of X Chromosome Inactivation Based on the Mixture of General Pedigrees and Unrelated Females. Biomolecules 2023; 13:543. [PMID: 36979477 PMCID: PMC10046098 DOI: 10.3390/biom13030543] [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: 02/04/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Skewed X chromosome inactivation (XCI-S) has been reported to be associated with some X-linked diseases. Several methods have been proposed to estimate the degree of XCI-S (denoted as γ) for quantitative and qualitative traits based on unrelated females. However, there is no method available for estimating γ based on general pedigrees. Therefore, in this paper, we propose a Bayesian method to obtain the point estimate and the credible interval of γ based on the mixture of general pedigrees and unrelated females (called mixed data for brevity), which is also suitable for only general pedigrees. We consider the truncated normal prior and the uniform prior for γ. Further, we apply the eigenvalue decomposition and Cholesky decomposition to our proposed methods to accelerate the computation speed. We conduct extensive simulation studies to compare the performances of our proposed methods and two existing Bayesian methods which are only applicable to unrelated females. The simulation results show that the incorporation of general pedigrees can improve the efficiency of the point estimation and the precision and the accuracy of the interval estimation of γ. Finally, we apply the proposed methods to the Minnesota Center for Twin and Family Research data for their practical use.
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Affiliation(s)
- Yi-Fan Kong
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Shi-Zhu Li
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Kai-Wen Wang
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Bin Zhu
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Yu-Xin Yuan
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Meng-Kai Li
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Ji-Yuan Zhou
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
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31
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Wendt FR, Pathak GA, Singh K, Stein MB, Koenen KC, Krystal JH, Gelernter J, Davis LK, Polimanti R. Sex-Specific Genetic and Transcriptomic Liability to Neuroticism. Biol Psychiatry 2023; 93:243-252. [PMID: 36244801 PMCID: PMC10508260 DOI: 10.1016/j.biopsych.2022.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/08/2022] [Accepted: 07/13/2022] [Indexed: 01/06/2023]
Abstract
BACKGROUND The presentation, etiology, and relative risk of psychiatric disorders are strongly influenced by biological sex. Neuroticism is a transdiagnostic feature of psychiatric disorders displaying prominent sex differences. We performed genome-wide association studies of neuroticism separately in males and females to identify sex-specific genetic and transcriptomic profiles. METHODS Neuroticism scores were derived from the Eysenck Personality Inventory Neuroticism scale. Genome-wide association studies were performed in 145,669 females and 129,229 males from the UK Biobank considering autosomal and X chromosomal variation. Two-sided z tests were used to test for sex-specific effects of discovered loci, genetic correlates (n = 673 traits), tissue and gene transcriptomic profiles, and polygenic associations across health outcomes in the Vanderbilt University Biobank (39,692 females and 31,268 males). RESULTS The single nucleotide polymorphism heritability of neuroticism was not statistically different between males (h2 = 10.6%) and females (h2 = 11.85%). Four female-specific (rs10736549-CNTN5, rs6507056-ASXL3, rs2087182-MMS22L, and rs72995548-HSPB2) and 2 male-specific (rs10507274-MED13L and rs7984597) neuroticism risk loci reached genome-wide significance. Male- and female-specific neuroticism polygenic scores were most significantly associated with mood disorders (males: odds ratio = 1.11, p = 1.40 × 10-9; females: odds ratio = 1.14, p = 6.05 × 10-22). They also associated with sex-specific laboratory measurements related to erythrocyte count, distribution, and hemoglobin concentration. Gene expression variation in the pituitary was enriched for neuroticism loci in males (male: b = 0.026, p = .002), and genetically regulated transcriptomic changes highlighted the effect of SHISHA9, TEX26, and NCOA6. CONCLUSIONS Through a comprehensive assessment of genetic risk for neuroticism and the associated biological processes, this study identified several molecular pathways that can partially explain the known sex differences in neurotic symptoms and their psychiatric comorbidities.
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Affiliation(s)
- Frank R Wendt
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut; VA CT Healthcare System, West Haven, Connecticut; Department of Anthropology, University of Toronto, Mississauga, Ontario, Canada; Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.
| | - Gita A Pathak
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut; VA CT Healthcare System, West Haven, Connecticut
| | - Kritika Singh
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Murray B Stein
- Psychiatry Service, VA San Diego Healthcare System, San Diego, California; Department of Psychiatry, University of California, San Diego, San Diego, California; Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, San Diego, California
| | - Karestan C Koenen
- Stanley Center for Psychiatry Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Psychiatry and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts; Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - John H Krystal
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut
| | - Joel Gelernter
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut; Department of Genetics, Yale School of Medicine, New Haven, Connecticut; Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut; VA CT Healthcare System, West Haven, Connecticut
| | - Lea K Davis
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut; VA CT Healthcare System, West Haven, Connecticut.
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32
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Gorlov IP, Amos CI. Why does the X chromosome lag behind autosomes in GWAS findings? PLoS Genet 2023; 19:e1010472. [PMID: 36848382 PMCID: PMC9997976 DOI: 10.1371/journal.pgen.1010472] [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: 10/12/2022] [Revised: 03/09/2023] [Accepted: 02/15/2023] [Indexed: 03/01/2023] Open
Abstract
The X-chromosome is among the largest human chromosomes. It differs from autosomes by a number of important features including hemizygosity in males, an almost complete inactivation of one copy in females, and unique patterns of recombination. We used data from the Catalog of Published Genome Wide Association Studies to compare densities of the GWAS-detected SNPs on the X-chromosome and autosomes. The density of GWAS-detected SNPs on the X-chromosome is 6-fold lower compared to the density of the GWAS-detected SNPs on autosomes. Differences between the X-chromosome and autosomes cannot be explained by differences in the overall SNP density, lower X-chromosome coverage by genotyping platforms or low call rate of X-chromosomal SNPs. Similar differences in the density of GWAS-detected SNPs were found in female-only GWASs (e.g. ovarian cancer GWASs). We hypothesized that the lower density of GWAS-detected SNPs on the X-chromosome compared to autosomes is not a result of a methodological bias, e.g. differences in coverage or call rates, but has a real underlying biological reason-a lower density of functional SNPs on the X-chromosome versus autosomes. This hypothesis is supported by the observation that (i) the overall SNP density of X-chromosome is lower compared to the SNP density on autosomes and that (ii) the density of genic SNPs on the X-chromosome is lower compared to autosomes while densities of intergenic SNPs are similar.
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Affiliation(s)
- Ivan P. Gorlov
- Baylor College of Medicine, Institute for Clinical & Translational Research, One Baylor Plaza, Houston, Texas, United States of America
| | - Christopher I. Amos
- Baylor College of Medicine, Institute for Clinical & Translational Research, One Baylor Plaza, Houston, Texas, United States of America
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Garcia AX, Xu J, Cheng F, Ruppin E, Schäffer AA. Altered gene expression in excitatory neurons is associated with Alzheimer's disease and its higher incidence in women. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2023; 9:e12373. [PMID: 36873924 PMCID: PMC9983144 DOI: 10.1002/trc2.12373] [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] [Received: 09/12/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 02/11/2023]
Abstract
Introduction Alzheimer's disease (AD) is a neurodegenerative disorder involving interactions between different cell types in the brain. Previous single-cell and bulk expression Alzheimer's studies have reported conflicting findings about the key cell types and cellular pathways whose expression is primarily altered in this disease. We re-analyzed these data in a uniform, coherent manner aiming to resolve and extend past findings. Our analysis sheds light on the observation that females have higher AD incidence than males. Methods We re-analyzed three single-cell transcriptomics datasets. We used the software Model-based Analysis of Single-cell Transcriptomics (MAST) to seek differentially expressed genes comparing AD cases to matched controls for both sexes together and each sex separately. We used the GOrilla software to search for enriched pathways among the differentially expressed genes. Motivated by the male/female difference in incidence, we studied genes on the X-chromosome, focusing on genes in the pseudoautosomal region (PAR) and on genes that are heterogeneous across individuals or tissues for X-inactivation. We validated findings by analyzing bulk AD datasets from the cortex in the Gene Expression Omnibus. Results Our results resolve a contradiction in the literature, showing that by comparing AD patients to unaffected controls, excitatory neurons have more differentially expressed genes than do other cell types. Synaptic transmission and related pathways are altered in a sex-specific analysis of excitatory neurons. PAR genes and X-chromosome heterogeneous genes, including, for example, BEX1 and ELK1, may contribute to the difference in sex incidence of Alzheimer's disease. GRIN1, stood out as an overexpressed autosomal gene in cases versus controls in all three single-cell datasets and as a functional candidate gene contributing to pathways upregulated in cases. Discussion Taken together, these results point to a potential linkage between two longstanding questions concerning AD pathogenesis, involving which cell type is the most important and why females have a higher incidence than males. Highlights By reanalyzing three, published, single-cell RNAseq datasets, we resolved a contradiction in the literature and showed that when comparing AD patients to unaffected controls, excitatory neurons have more differentially expressed genes than do other cell types.Further analysis of the published single-cell datasets showed that synaptic transmission and related pathways are altered in a sex-specific analysis of excitatory neurons.Combining analysis of single-cell datasets and publicly available bulk transcriptomics datasets revealed that X-chromosome genes, such as BEX1, ELK1, and USP11, whose X-inactivation status is heterogeneous may contribute to the higher incidence in females of Alzheimer's disease.
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Affiliation(s)
- A. Xavier Garcia
- Cancer Data Science LaboratoryCenter for Cancer ResearchNational Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
- Present address:
Weill Cornell/Rockefeller/Sloan Kettering Tri‐Institutional MD‐PhD ProgramNew YorkNYUSA
| | - Jielin Xu
- Genomic Medicine InstituteLerner Research InstituteCleveland ClinicClevelandOhioUSA
| | - Feixiong Cheng
- Genomic Medicine InstituteLerner Research InstituteCleveland ClinicClevelandOhioUSA
- Department of Molecular MedicineCleveland Clinic Lerner College of MedicineCase Western Reserve UniversityClevelandOhioUSA
- Case Comprehensive Cancer CenterCase Western Reserve University School of MedicineClevelandOhioUSA
| | - Eytan Ruppin
- Cancer Data Science LaboratoryCenter for Cancer ResearchNational Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Alejandro A. Schäffer
- Cancer Data Science LaboratoryCenter for Cancer ResearchNational Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
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Keur N, Ricaño-Ponce I, Kumar V, Matzaraki V. A systematic review of analytical methods used in genetic association analysis of the X-chromosome. Brief Bioinform 2022; 23:6651325. [PMID: 35901513 DOI: 10.1093/bib/bbac287] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/07/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic association studies have been very successful at elucidating the genetic background of many complex diseases/traits. However, the X-chromosome is often neglected in these studies because of technical difficulties and the fact that most tools only utilize genetic data from autosomes. In this review, we aim to provide an overview of different practical approaches that are followed to incorporate the X-chromosome in association analysis, such as Genome-Wide Association Studies and Expression Quantitative Trait Loci Analysis. In general, the choice of which test statistics is most appropriate will depend on three main criteria: (1) the underlying X-inactivation model, (2) if Hardy-Weinberg equilibrium holds and sex-specific allele frequencies are expected and (3) whether adjustment for confounding variables is required. All in all, it is recommended that a combination of different association tests should be used for the analysis of X-chromosome.
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Affiliation(s)
- Nick Keur
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 HP, Nijmegen, The Netherlands
| | - Isis Ricaño-Ponce
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 HP, Nijmegen, The Netherlands
| | - Vinod Kumar
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 HP, Nijmegen, The Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700RB, Groningen, The Netherlands
| | - Vasiliki Matzaraki
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 HP, Nijmegen, The Netherlands
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Abstract
Sex is a key risk factor for many types of cardiovascular disease. It is imperative to understand the mechanisms underlying sex differences to devise optimal preventive and therapeutic approaches for all individuals. Both biological sex (determined by sex chromosomes and gonadal hormones) and gender (social and cultural behaviors associated with femininity or masculinity) influence differences between men and women in disease susceptibility and pathology. Here, we focus on the application of experimental mouse models that elucidate the influence of 2 components of biological sex-sex chromosome complement (XX or XY) and gonad type (ovaries or testes). These models have revealed that in addition to well-known effects of gonadal hormones, sex chromosome complement influences cardiovascular risk factors, such as plasma cholesterol levels and adiposity, as well as the development of atherosclerosis and pulmonary hypertension. One mechanism by which sex chromosome dosage influences cardiometabolic traits is through sex-biased expression of X chromosome genes that escape X inactivation. These include chromatin-modifying enzymes that regulate gene expression throughout the genome. The identification of factors that determine sex-biased gene expression and cardiometabolic traits will expand our mechanistic understanding of cardiovascular disease processes and provide insight into sex differences that remain throughout the lifespan as gonadal hormone levels alter with age.
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Affiliation(s)
- Karen Reue
- Department of Human Genetics, David Geffen School of Medicine at UCLA
- Department of Medicine, David Geffen School of Medicine at UCLA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
| | - Carrie B. Wiese
- Department of Human Genetics, David Geffen School of Medicine at UCLA
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Yu WY, Zhang Y, Li MK, Yang ZY, Fung WK, Zhao PZ, Zhou JY. BEXCIS: Bayesian methods for estimating the degree of the skewness of X chromosome inactivation. BMC Bioinformatics 2022; 23:193. [PMID: 35610583 PMCID: PMC9128296 DOI: 10.1186/s12859-022-04721-y] [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: 01/24/2022] [Accepted: 05/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND X chromosome inactivation (XCI) is an epigenetic phenomenon that one of two X chromosomes in females is transcriptionally silenced during early embryonic development. Skewed XCI has been reported to be associated with some X-linked diseases. There have been several methods measuring the degree of the skewness of XCI. However, these methods may still have several limitations. RESULTS We propose a Bayesian method to obtain the point estimate and the credible interval of the degree of XCI skewing by incorporating its prior information of being between 0 and 2. We consider a normal prior and a uniform prior for it (respectively denoted by BN and BU). We also propose a penalized point estimate based on the penalized Fieller's method and derive the corresponding confidence interval. Simulation results demonstrate that the BN and BU methods can solve the problems of extreme point estimates, noninformative intervals, empty sets and discontinuous intervals. The BN method generally outperforms other methods with the lowest mean squared error in the point estimation, and well controls the coverage probability with the smallest median and the least variation of the interval width in the interval estimation. We apply all the methods to the Graves' disease data and the Minnesota Center for Twin and Family Research data, and find that SNP rs3827440 in the Graves' disease data may undergo skewed XCI towards the allele C. CONCLUSIONS We recommend the BN method for measuring the degree of the skewness of XCI in practice. The R package BEXCIS is publicly available at https://github.com/Wen-YiYu/BEXCIS .
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Affiliation(s)
- Wen-Yi Yu
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Yu Zhang
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Meng-Kai Li
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Zi-Ying Yang
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
| | - Wing Kam Fung
- Department of Statistics and Actuarial Science, The University of Hong Kong, Hong Kong, China
| | - Pei-Zhen Zhao
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Ji-Yuan Zhou
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou, China
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Carey SB, Lovell JT, Jenkins J, Leebens-Mack J, Schmutz J, Wilson MA, Harkess A. Representing sex chromosomes in genome assemblies. CELL GENOMICS 2022; 2. [PMID: 35720975 PMCID: PMC9205529 DOI: 10.1016/j.xgen.2022.100132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sex chromosomes have evolved hundreds of independent times across eukaryotes. As genome sequencing, assembly, and scaffolding techniques rapidly improve, it is now feasible to build fully phased sex chromosome assemblies. Despite technological advances enabling phased assembly of whole chromosomes, there are currently no standards for representing sex chromosomes when publicly releasing a genome. Furthermore, most computational analysis tools are unable to efficiently investigate their unique biology relative to autosomes. We discuss a diversity of sex chromosome systems and consider the challenges of representing sex chromosome pairs in genome assemblies. By addressing these issues now as technologies for full phasing of chromosomal assemblies are maturing, we can collectively ensure that future genome analysis toolkits can be broadly applied to all eukaryotes with diverse types of sex chromosome systems. Here we provide best practice guidelines for presenting a genome assembly that contains sex chromosomes. These guidelines can also be applied to other non-recombining genomic regions, such as S-loci in plants and mating-type loci in fungi and algae.
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Affiliation(s)
- Sarah B Carey
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.,US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Melissa A Wilson
- School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Alex Harkess
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL 36849, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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XCMAX4: A Robust X Chromosomal Genetic Association Test Accounting for Covariates. Genes (Basel) 2022; 13:genes13050847. [PMID: 35627231 PMCID: PMC9141238 DOI: 10.3390/genes13050847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 04/30/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022] Open
Abstract
Although the X chromosome accounts for about 5% of the human genes, it is routinely excluded from genome-wide association studies probably due to its unique structure and complex biological patterns. While some statistical methods have been proposed for testing the association between X chromosomal markers and diseases, very a few of them can adjust for covariates. Unfortunately, those methods that can incorporate covariates either need to specify an X chromosome inactivation model or require the permutation procedure to compute the p value. In this article, we proposed a novel analytic approach based on logistic regression that allows for covariates and does not need to specify the underlying X chromosome inactivation pattern. Simulation studies showed that our proposed method controls the size well and has robust performance in power across various practical scenarios. We applied the proposed method to analyze Graves’ disease data to show its usefulness in practice.
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Li MK, Yuan YX, Zhu B, Wang KW, Fung WK, Zhou JY. Gene-Based Methods for Estimating the Degree of the Skewness of X Chromosome Inactivation. Genes (Basel) 2022; 13:genes13050827. [PMID: 35627212 PMCID: PMC9140558 DOI: 10.3390/genes13050827] [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: 04/14/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022] Open
Abstract
Skewed X chromosome inactivation (XCI-S) has been reported to be associated with some X-linked diseases, and currently several methods have been proposed to estimate the degree of the XCI-S (denoted as γ) for a single locus. However, no method has been available to estimate γ for genes. Therefore, in this paper, we first propose the point estimate and the penalized point estimate of γ for genes, and then derive its confidence intervals based on the Fieller’s and penalized Fieller’s methods, respectively. Further, we consider the constraint condition of γ∈[0, 2] and propose the Bayesian methods to obtain the point estimates and the credible intervals of γ, where a truncated normal prior and a uniform prior are respectively used (denoted as GBN and GBU). The simulation results show that the Bayesian methods can avoid the extreme point estimates (0 or 2), the empty sets, the noninformative intervals ([0, 2]) and the discontinuous intervals to occur. GBN performs best in both the point estimation and the interval estimation. Finally, we apply the proposed methods to the Minnesota Center for Twin and Family Research data for their practical use. In summary, in practical applications, we recommend using GBN to estimate γ of genes.
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Affiliation(s)
- Meng-Kai Li
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (M.-K.L.); (Y.-X.Y.); (B.Z.); (K.-W.W.)
- Guangdong-Hong Hong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Yu-Xin Yuan
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (M.-K.L.); (Y.-X.Y.); (B.Z.); (K.-W.W.)
- Guangdong-Hong Hong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Bin Zhu
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (M.-K.L.); (Y.-X.Y.); (B.Z.); (K.-W.W.)
- Guangdong-Hong Hong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Kai-Wen Wang
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (M.-K.L.); (Y.-X.Y.); (B.Z.); (K.-W.W.)
- Guangdong-Hong Hong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
| | - Wing Kam Fung
- Department of Statistics and Actuarial Science, The University of Hong Kong, Hong Kong, China;
| | - Ji-Yuan Zhou
- Department of Biostatistics, State Key Laboratory of Organ Failure Research, Ministry of Education, and Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China; (M.-K.L.); (Y.-X.Y.); (B.Z.); (K.-W.W.)
- Guangdong-Hong Hong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangzhou 510006, China
- Correspondence:
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40
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Wang Z, Sun L, Paterson AD. Major sex differences in allele frequencies for X chromosomal variants in both the 1000 Genomes Project and gnomAD. PLoS Genet 2022; 18:e1010231. [PMID: 35639794 PMCID: PMC9187127 DOI: 10.1371/journal.pgen.1010231] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 06/10/2022] [Accepted: 05/03/2022] [Indexed: 12/19/2022] Open
Abstract
An unexpectedly high proportion of SNPs on the X chromosome in the 1000 Genomes Project phase 3 data were identified with significant sex differences in minor allele frequencies (sdMAF). sdMAF persisted for many of these SNPs in the recently released high coverage whole genome sequence of the 1000 Genomes Project that was aligned to GRCh38, and it was consistent between the five super-populations. Among the 245,825 common (MAF>5%) biallelic X-chromosomal SNPs in the phase 3 data presumed to be of high quality, 2,039 have genome-wide significant sdMAF (p-value <5e-8). sdMAF varied by location: non-pseudo-autosomal region (NPR) = 0.83%, pseudo-autosomal regions (PAR1) = 0.29%, PAR2 = 13.1%, and X-transposed region (XTR)/PAR3 = 0.85% of SNPs had sdMAF, and they were clustered at the NPR-PAR boundaries, among others. sdMAF at the NPR-PAR boundaries are biologically expected due to sex-linkage, but have generally been ignored in association studies. For comparison, similar analyses found only 6, 1 and 0 SNPs with significant sdMAF on chromosomes 1, 7 and 22, respectively. Similar sdMAF results for the X chromosome were obtained from the high coverage whole genome sequence data from gnomAD V 3.1.2 for both the non-Finnish European and African/African American samples. Future X chromosome analyses need to take sdMAF into account.
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Affiliation(s)
- Zhong Wang
- Department of Statistics and Data Science, Faculty of Science, National University of Singapore, Singapore
| | - Lei Sun
- Department of Statistic Sciences, Faculty of Arts and Science, University of Toronto, Ontario, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
| | - Andrew D. Paterson
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
- Genetics and Genome Biology, The Hospital for Sick Children, Ontario, Canada
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Ontario, Canada
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Gerussi A, Paraboschi EM, Cappadona C, Caime C, Binatti E, Cristoferi L, Asselta R, Invernizzi P. The Role of Epigenetics in Primary Biliary Cholangitis. Int J Mol Sci 2022; 23:4873. [PMID: 35563266 PMCID: PMC9105933 DOI: 10.3390/ijms23094873] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/12/2022] Open
Abstract
Primary Biliary Cholangitis (PBC) is a rare autoimmune disease of the liver, affecting mostly females. There is evidence that epigenetic changes have a pathogenic role in PBC. Epigenetic modifications are related to methylation of CpG DNA islands, post-translational modifications of histone proteins, and non-coding RNAs. In PBC, there are data showing a dysregulation of all these levels, especially in immune cells. In addition, epigenetics seems to be involved in complex phenomena such as X monosomy or abnormalities in the process of X chromosome inactivation, which have been reported in PBC and appear to influence its sex imbalance and pathogenesis. We review here historical data on epigenetic modifications in PBC, present new data, and discuss possible links among X-chromosome abnormalities at a genetic and epigenetic level, PBC pathogenesis, and PBC sex imbalance.
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Affiliation(s)
- Alessio Gerussi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (A.G.); (C.C.); (E.B.); (L.C.)
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, 20900 Monza, Italy
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (E.M.P.); (C.C.); (R.A.)
- Humanitas Clinical and Research Center, IRCCS, Via Manzoni 56, 20089 Rozzano, Italy
| | - Claudio Cappadona
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (E.M.P.); (C.C.); (R.A.)
- Humanitas Clinical and Research Center, IRCCS, Via Manzoni 56, 20089 Rozzano, Italy
| | - Chiara Caime
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (A.G.); (C.C.); (E.B.); (L.C.)
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, 20900 Monza, Italy
| | - Eleonora Binatti
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (A.G.); (C.C.); (E.B.); (L.C.)
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, 20900 Monza, Italy
| | - Laura Cristoferi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (A.G.); (C.C.); (E.B.); (L.C.)
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, 20900 Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (E.M.P.); (C.C.); (R.A.)
- Humanitas Clinical and Research Center, IRCCS, Via Manzoni 56, 20089 Rozzano, Italy
| | - Pietro Invernizzi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (A.G.); (C.C.); (E.B.); (L.C.)
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, 20900 Monza, Italy
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Wren G, Davies W. Sex-linked genetic mechanisms and atrial fibrillation risk. Eur J Med Genet 2022; 65:104459. [PMID: 35189376 DOI: 10.1016/j.ejmg.2022.104459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/11/2022] [Accepted: 02/16/2022] [Indexed: 01/14/2023]
Abstract
Atrial fibrillation (AF) is a cardiac condition characterised by an irregular heartbeat, atrial pathology and an elevated downstream risk of thrombosis and heart failure, as well as neurological sequelae including stroke and dementia. The prevalence and presentation of, risk factors for, and therapeutic responses to, AF differ by sex, and this sex bias may be partially explained in terms of genetics. Here, we consider four sex-linked genetic mechanisms that may influence sex-biased phenotypes related to AF and provide examples of each: X-linked gene dosage, X-linked genomic imprinting, sex-biased autosomal gene expression, and male-limited Y-linked gene expression. We highlight novel candidate risk genes and pathways that warrant further investigation in clinical and preclinical studies. Understanding the biological basis of sex differences in AF should allow better prediction of disease risk, identification of novel risk/protective factors, and the development of more effective sex-tailored interventions.
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Affiliation(s)
| | - William Davies
- School of Psychology, Cardiff University, UK; School of Medicine, Cardiff University, UK.
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Vaura F, Palmu J, Aittokallio J, Kauko A, Niiranen T. Genetic, Molecular, and Cellular Determinants of Sex-Specific Cardiovascular Traits. Circ Res 2022; 130:611-631. [PMID: 35175841 DOI: 10.1161/circresaha.121.319891] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite the well-known sex dimorphism in cardiovascular disease traits, the exact genetic, molecular, and cellular underpinnings of these differences are not well understood. A growing body of evidence currently points at the links between cardiovascular disease traits and the genome, epigenome, transcriptome, and metabolome. However, the sex-specific differences in these links remain largely unstudied due to challenges in bioinformatic methods, inadequate statistical power, analytic costs, and paucity of valid experimental models. This review article provides an overview of the literature on sex differences in genetic architecture, heritability, epigenetic changes, transcriptomic signatures, and metabolomic profiles in relation to cardiovascular disease traits. We also review the literature on the associations between sex hormones and cardiovascular disease traits and discuss the potential mechanisms underlying these associations, focusing on human studies.
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Affiliation(s)
- Felix Vaura
- Department of Internal Medicine (F.V., J.P., A.K., T.N.), University of Turku, Finland
| | - Joonatan Palmu
- Department of Internal Medicine (F.V., J.P., A.K., T.N.), University of Turku, Finland
| | - Jenni Aittokallio
- Department of Anesthesiology and Intensive Care (J.A.), University of Turku, Finland.,Division of Perioperative Services, Intensive Care and Pain Medicine (J.A.), Turku University Hospital, Finland
| | - Anni Kauko
- Department of Internal Medicine (F.V., J.P., A.K., T.N.), University of Turku, Finland
| | - Teemu Niiranen
- Department of Internal Medicine (F.V., J.P., A.K., T.N.), University of Turku, Finland.,Division of Medicine (T.N.), Turku University Hospital, Finland.,Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland (T.N.)
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Lopez-Lee C, Kodama L, Gan L. Sex Differences in Neurodegeneration: The Role of the Immune System in Humans. Biol Psychiatry 2022; 91:72-80. [PMID: 33715827 PMCID: PMC8263798 DOI: 10.1016/j.biopsych.2021.01.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 01/03/2023]
Abstract
Growing evidence supports significant involvement of immune dysfunction in the etiology of neurodegenerative diseases, several of which also display prominent sex differences across prevalence, pathology, and symptomology. In this review, we summarize evidence from human studies of established and recent findings of sex differences in multiple sclerosis, Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis and discuss how sex-specific central nervous system innate immune activity could contribute to downstream sex differences in these diseases. We examine human genomic and transcriptomics studies in each neurodegenerative disease through the lens of sex differences in the neuroimmune system and highlight the importance of stratifying sex in clinical and translational research studies. Finally, we discuss the limitations of the existing studies and outline recommendations for further advancing sex-based analyses to uncover novel disease mechanisms that could ultimately help treat both sexes.
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Affiliation(s)
- Chloe Lopez-Lee
- Neuroscience Graduate Program, Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York; Helen and Robert Appel Alzheimer's Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York
| | - Lay Kodama
- Helen and Robert Appel Alzheimer's Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York; Medical Scientist Training Program and Neuroscience Graduate Program, University of California San Francisco, San Francisco, California.
| | - Li Gan
- Neuroscience Graduate Program, Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York; Helen and Robert Appel Alzheimer's Disease Research Institute, Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York.
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Cappadona C, Paraboschi EM, Ziliotto N, Bottaro S, Rimoldi V, Gerussi A, Azimonti A, Brenna D, Brunati A, Cameroni C, Campanaro G, Carloni F, Cavadini G, Ciravegna M, Composto A, Converso G, Corbella P, D’Eugenio D, Dal Rì G, Di Giorgio SM, Grondelli MC, Guerrera L, Laffoucriere G, Lando B, Lopedote L, Maizza B, Marconi E, Mariola C, Matronola GM, Menga LM, Montorsi G, Papatolo A, Patti R, Profeta L, Rebasti V, Smidili A, Tarchi SM, Tartaglia FC, Tettamanzi G, Tinelli E, Stuani R, Bolchini C, Pattini L, Invernizzi P, Degenhardt F, Franke A, Duga S, Asselta R. MEDTEC Students against Coronavirus: Investigating the Role of Hemostatic Genes in the Predisposition to COVID-19 Severity. J Pers Med 2021; 11:1166. [PMID: 34834519 PMCID: PMC8622845 DOI: 10.3390/jpm11111166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the coronavirus disease 2019 (COVID-19) pandemic. Besides virus intrinsic characteristics, the host genetic makeup is predicted to account for the extreme clinical heterogeneity of the disease, which is characterized, among other manifestations, by a derangement of hemostasis associated with thromboembolic events. To date, large-scale studies confirmed that genetic predisposition plays a role in COVID-19 severity, pinpointing several susceptibility genes, often characterized by immunologic functions. With these premises, we performed an association study of common variants in 32 hemostatic genes with COVID-19 severity. We investigated 49,845 single-nucleotide polymorphism in a cohort of 332 Italian severe COVID-19 patients and 1668 controls from the general population. The study was conducted engaging a class of students attending the second year of the MEDTEC school (a six-year program, held in collaboration between Humanitas University and the Politecnico of Milan, allowing students to gain an MD in Medicine and a Bachelor's Degree in Biomedical Engineering). Thanks to their willingness to participate in the fight against the pandemic, we evidenced several suggestive hits (p < 0.001), involving the PROC, MTHFR, MTR, ADAMTS13, and THBS2 genes (top signal in PROC: chr2:127192625:G:A, OR = 2.23, 95%CI = 1.50-3.34, p = 8.77 × 10-5). The top signals in PROC, MTHFR, MTR, ADAMTS13 were instrumental for the construction of a polygenic risk score, whose distribution was significantly different between cases and controls (p = 1.62 × 10-8 for difference in median levels). Finally, a meta-analysis performed using data from the Regeneron database confirmed the contribution of the MTHFR variant chr1:11753033:G:A to the predisposition to severe COVID-19 (pooled OR = 1.21, 95%CI = 1.09-1.33, p = 4.34 × 10-14 in the weighted analysis).
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Affiliation(s)
- Claudio Cappadona
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
- Humanitas Clinical and Research Center, IRCCS, Via Manzoni 56, 20089 Rozzano, Italy
| | - Nicole Ziliotto
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Sandro Bottaro
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
- Humanitas Clinical and Research Center, IRCCS, Via Manzoni 56, 20089 Rozzano, Italy
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Alessio Gerussi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (A.G.); (P.I.)
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, 20900 Monza, Italy
| | - Andrea Azimonti
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Daniele Brenna
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Andrea Brunati
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Charlotte Cameroni
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Giovanni Campanaro
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Francesca Carloni
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Giacomo Cavadini
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Martina Ciravegna
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Antonio Composto
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Giuseppe Converso
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Pierluigi Corbella
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Davide D’Eugenio
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Giovanna Dal Rì
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Sofia Maria Di Giorgio
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Maria Chiara Grondelli
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Lorenza Guerrera
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Georges Laffoucriere
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Beatrice Lando
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Leandro Lopedote
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Benedetta Maizza
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Elettra Marconi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Carlotta Mariola
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Guia Margherita Matronola
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Luca Maria Menga
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Giulia Montorsi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Antonio Papatolo
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Riccardo Patti
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Lorenzo Profeta
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Vera Rebasti
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Alice Smidili
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Sofia Maria Tarchi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Francesco Carlo Tartaglia
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Gaia Tettamanzi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Elena Tinelli
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Riccardo Stuani
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
| | - Cristiana Bolchini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy; (C.B.); (L.P.)
| | - Linda Pattini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy; (C.B.); (L.P.)
| | - Pietro Invernizzi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (A.G.); (P.I.)
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, 20900 Monza, Italy
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, 24105 Kiel, Germany; (F.D.); (A.F.)
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, 24105 Kiel, Germany; (F.D.); (A.F.)
- University Hospital Schleswig-Holstein (UKSH), 24105 Kiel, Germany
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
- Humanitas Clinical and Research Center, IRCCS, Via Manzoni 56, 20089 Rozzano, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (C.C.); (E.M.P.); (N.Z.); (S.B.); (V.R.); (A.A.); (D.B.); (A.B.); (C.C.); (G.C.); (F.C.); (G.C.); (M.C.); (A.C.); (G.C.); (P.C.); (D.D.); (G.D.R.); (S.M.D.G.); (M.C.G.); (L.G.); (G.L.); (B.L.); (L.L.); (B.M.); (E.M.); (C.M.); (G.M.M.); (L.M.M.); (G.M.); (A.P.); (R.P.); (L.P.); (V.R.); (A.S.); (S.M.T.); (F.C.T.); (G.T.); (E.T.); (R.S.); (S.D.)
- Humanitas Clinical and Research Center, IRCCS, Via Manzoni 56, 20089 Rozzano, Italy
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Mielke MM, Miller VM. Improving clinical outcomes through attention to sex and hormones in research. Nat Rev Endocrinol 2021; 17:625-635. [PMID: 34316045 PMCID: PMC8435014 DOI: 10.1038/s41574-021-00531-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/24/2021] [Indexed: 02/07/2023]
Abstract
Biological sex, fluctuations in sex steroid hormones throughout life and gender as a social construct all influence every aspect of health and disease. Yet, for decades, most basic and clinical studies have included only male individuals. As modern health care moves towards personalized medicine, it is clear that considering sex and hormonal status in basic and clinical studies will bring precision to the development of novel therapeutics and treatment paradigms. To this end, funding, regulatory and policy agencies now require inclusion of female animals and women in basic and clinical studies. However, inclusion of female animals and women often does not mean that information regarding potential hormonal interactions with pharmacological treatments or clinical outcomes is available. All sex steroid hormones can interact with receptors for drug targets, metabolism and transport. Genetic variation in receptors or in enzymatic function might contribute to sex differences in therapeutic efficacy and adverse drug reactions. Outcomes from clinical trials are often not reported by sex, and, if the data are available, they are not translated into clinical practice guidelines. This Review will provide a historical perspective for the current state of research related to hormone trials and provide concrete strategies that, if implemented, will improve the health of all people.
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Affiliation(s)
- Michelle M Mielke
- Division of Epidemiology, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA.
- Mayo Clinic Specialized Center of Research Excellence, Mayo Clinic, Rochester, MN, USA.
- Department of Neurology, Mayo Clinic, Rochester, MN, USA.
| | - Virginia M Miller
- Mayo Clinic Specialized Center of Research Excellence, Mayo Clinic, Rochester, MN, USA
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Women's Health Research Center, Mayo Clinic, Rochester, MN, USA
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Chen B, Craiu RV, Strug LJ, Sun L. The X factor: A robust and powerful approach to X-chromosome-inclusive whole-genome association studies. Genet Epidemiol 2021; 45:694-709. [PMID: 34224641 PMCID: PMC9292551 DOI: 10.1002/gepi.22422] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/14/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022]
Abstract
The X‐chromosome is often excluded from genome‐wide association studies because of analytical challenges. Some of the problems, such as the random, skewed, or no X‐inactivation model uncertainty, have been investigated. Other considerations have received little to no attention, such as the value in considering nonadditive and gene–sex interaction effects, and the inferential consequence of choosing different baseline alleles (i.e., the reference vs. the alternative allele). Here we propose a unified and flexible regression‐based association test for X‐chromosomal variants. We provide theoretical justifications for its robustness in the presence of various model uncertainties, as well as for its improved power when compared with the existing approaches under certain scenarios. For completeness, we also revisit the autosomes and show that the proposed framework leads to a more robust approach than the standard method. Finally, we provide supporting evidence by revisiting several published association studies. Supporting Information for this article are available online.
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Affiliation(s)
- Bo Chen
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Radu V Craiu
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Lisa J Strug
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada.,Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lei Sun
- Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada.,Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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A statistical measure for the skewness of X chromosome inactivation for quantitative traits and its application to the MCTFR data. BMC Genom Data 2021; 22:24. [PMID: 34215184 PMCID: PMC8254321 DOI: 10.1186/s12863-021-00978-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 06/17/2021] [Indexed: 11/24/2022] Open
Abstract
Background X chromosome inactivation (XCI) is that one of two chromosomes in mammalian females is silenced during early development of embryos. There has been a statistical measure for the degree of the skewness of XCI for qualitative traits. However, no method is available for such task at quantitative trait loci. Results In this article, we extend the existing statistical measure for the skewness of XCI for qualitative traits, and the likelihood ratio, Fieller’s and delta methods for constructing the corresponding confidence intervals, and make them accommodate quantitative traits. The proposed measure is a ratio of two linear regression coefficients when association exists. Noting that XCI may cause variance heterogeneity of the traits across different genotypes in females, we obtain the point estimate and confidence intervals of the measure by incorporating such information. The hypothesis testing of the proposed methods is also investigated. We conduct extensive simulation studies to assess the performance of the proposed methods. Simulation results demonstrate that the median of the point estimates of the measure is very close to the pre-specified true value. The likelihood ratio and Fieller’s methods control the size well, and have the similar test power and accurate coverage probability, which perform better than the delta method. So far, we are not aware of any association study for the X-chromosomal loci in the Minnesota Center for Twin and Family Research data. So, we apply our proposed methods to these data for their practical use and find that only the rs792959 locus, which is simultaneously associated with the illicit drug composite score and behavioral disinhibition composite score, may undergo XCI skewing. However, this needs to be confirmed by molecular genetics. Conclusions We recommend the Fieller’s method in practical use because it is a non-iterative procedure and has the similar performance to the likelihood ratio method. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00978-z.
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Vergara C, Valencia A, Thio CL, Goedert JJ, Mangia A, Piazzolla V, Johnson E, Kral AH, O’Brien TR, Mehta SH, Kirk GD, Kim AY, Lauer GM, Chung RT, Cox AL, Peters MG, Khakoo SI, Alric L, Cramp ME, Donfield SM, Edlin BR, Busch MP, Alexander G, Rosen HR, Murphy EL, Wojcik GL, Taub MA, Thomas DL, Duggal P. A Multiancestry Sex-Stratified Genome-Wide Association Study of Spontaneous Clearance of Hepatitis C Virus. J Infect Dis 2021; 223:2090-2098. [PMID: 33119750 PMCID: PMC8205624 DOI: 10.1093/infdis/jiaa677] [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: 07/27/2020] [Accepted: 10/28/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Spontaneous clearance of acute hepatitis C virus (HCV) infection is more common in women than in men, independent of known risk factors. METHODS To identify sex-specific genetic loci, we studied 4423 HCV-infected individuals (2903 male, 1520 female) of European, African, and Hispanic ancestry. We performed autosomal, and X chromosome sex-stratified and combined association analyses in each ancestry group. RESULTS A male-specific region near the adenosine diphosphate-ribosylation factor-like 5B (ARL5B) gene was identified. Individuals with the C allele of rs76398191 were about 30% more likely to have chronic HCV infection than individuals with the T allele (OR, 0.69; P = 1.98 × 10-07), and this was not seen in females. The ARL5B gene encodes an interferon-stimulated gene that inhibits immune response to double-stranded RNA viruses. We also identified suggestive associations near septin 6 and ribosomal protein L39 genes on the X chromosome. In box sexes, allele G of rs12852885 was associated with a 40% increase in HCV clearance compared with the A allele (OR, 1.4; P = 2.46 × 10-06). Septin 6 facilitates HCV replication via interaction with the HCV NS5b protein, and ribosomal protein L39 acts as an HCV core interactor. CONCLUSIONS These novel gene associations support differential mechanisms of HCV clearance between the sexes and provide biological targets for treatment or vaccine development.
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Affiliation(s)
- Candelaria Vergara
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ana Valencia
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
- Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Chloe L Thio
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Alessandra Mangia
- Liver Unit IRCCS “Casa Sollievo della Sofferenza,” San Giovanni Rotondo, Italy
| | - Valeria Piazzolla
- Liver Unit IRCCS “Casa Sollievo della Sofferenza,” San Giovanni Rotondo, Italy
| | - Eric Johnson
- RTI International, Research Triangle Park, North Carolina, USA
| | - Alex H Kral
- RTI International, Research Triangle Park, North Carolina, USA
| | - Thomas R O’Brien
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Shruti H Mehta
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Gregory D Kirk
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Arthur Y Kim
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Georg M Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea L Cox
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Marion G Peters
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California, San Francisco, California, USA
| | - Salim I Khakoo
- University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Laurent Alric
- Department of Internal Medicine and Digestive Diseases, CHU Rangueil, UMR 152 IRD, Toulouse 3 University, France
| | | | | | - Brian R Edlin
- SUNY Downstate College of Medicine, Brooklyn, New York, USA
| | - Michael P Busch
- University of California and Vitalant Research Institute, San Francisco, California, USA
| | - Graeme Alexander
- UCL Institute for Liver and Digestive Health, Royal Free Hospital, Hampstead, London, United Kingdom
| | | | - Edward L Murphy
- University of California and Vitalant Research Institute, San Francisco, California, USA
| | - Genevieve L Wojcik
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Margaret A Taub
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - David L Thomas
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Priya Duggal
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
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50
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Song Y, Biernacka JM, Winham SJ. Testing and estimation of X-chromosome SNP effects: Impact of model assumptions. Genet Epidemiol 2021; 45:577-592. [PMID: 34082482 PMCID: PMC8453908 DOI: 10.1002/gepi.22393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/30/2021] [Accepted: 05/18/2021] [Indexed: 12/16/2022]
Abstract
Interest in analyzing X chromosome single nucleotide polymorphisms (SNPs) is growing and several approaches have been proposed. Prior studies have compared power of different approaches, but bias and interpretation of coefficients have received less attention. We performed simulations to demonstrate the impact of X chromosome model assumptions on effect estimates. We investigated the coefficient biases of SNP and sex effects with commonly used models for X chromosome SNPs, including models with and without assumptions of X chromosome inactivation (XCI), and with and without SNP–sex interaction terms. Sex and SNP coefficient biases were observed when assumptions made about XCI and sex differences in SNP effect in the analysis model were inconsistent with the data‐generating model. However, including a SNP–sex interaction term often eliminated these biases. To illustrate these findings, estimates under different genetic model assumptions are compared and interpreted in a real data example. Models to analyze X chromosome SNPs make assumptions beyond those made in autosomal variant analysis. Assumptions made about X chromosome SNP effects should be stated clearly when reporting and interpreting X chromosome associations. Fitting models with SNP × Sex interaction terms can avoid reliance on assumptions, eliminating coefficient bias even in the absence of sex differences in SNP effect.
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Affiliation(s)
- Yilin Song
- Department of Biostatistics, University of Washington, Seattle, Washington, USA.,Department of Mathematics, Statistics, and Computer Science, St. Olaf College, Northfield, Minnesota, USA
| | - Joanna M Biernacka
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Stacey J Winham
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
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