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Bhattacharyya U, John J, Lencz T, Lam M. Dissecting Schizophrenia Biology Using Pleiotropy with Cognitive Genomics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.16.24305885. [PMID: 38699340 PMCID: PMC11065000 DOI: 10.1101/2024.04.16.24305885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Given the increasingly large number of loci discovered by psychiatric GWAS, specification of the key biological pathways underlying these loci has become a priority for the field. We have previously leveraged the pleiotropic genetic relationships between schizophrenia and two cognitive phenotypes (educational attainment and cognitive task performance) to differentiate two subsets of illness-relevant SNPs: (1) those with "concordant" alleles, which are associated with reduced cognitive ability/education and increased schizophrenia risk; and (2) those with "discordant" alleles linked to reduced educational and/or cognitive levels but lower schizophrenia susceptibility. In the present study, we extend our prior work, utilizing larger input GWAS datasets and a more powerful statistical approach to pleiotropic meta-analysis, the Pleiotropic Locus Exploration and Interpretation using Optimal test (PLEIO). Our pleiotropic meta-analysis of schizophrenia and the two cognitive phenotypes revealed 768 significant loci (159 novel). Among these, 347 loci harbored concordant SNPs, 270 encompassed discordant SNPs, and 151 "dual" loci contained concordant and discordant SNPs. Competitive gene-set analysis using MAGMA related concordant SNP loci with neurodevelopmental pathways (e.g., neurogenesis), whereas discordant loci were associated with mature neuronal synaptic functions. These distinctions were also observed in BrainSpan analysis of temporal enrichment patterns across developmental periods, with concordant loci containing more prenatally expressed genes than discordant loci. Dual loci were enriched for genes related to mRNA translation initiation, representing a novel finding in the schizophrenia literature.
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2
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Pineda SS, Lee H, Ulloa-Navas MJ, Linville RM, Garcia FJ, Galani K, Engelberg-Cook E, Castanedes MC, Fitzwalter BE, Pregent LJ, Gardashli ME, DeTure M, Vera-Garcia DV, Hucke ATS, Oskarsson BE, Murray ME, Dickson DW, Heiman M, Belzil VV, Kellis M. Single-cell dissection of the human motor and prefrontal cortices in ALS and FTLD. Cell 2024; 187:1971-1989.e16. [PMID: 38521060 PMCID: PMC11086986 DOI: 10.1016/j.cell.2024.02.031] [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: 02/16/2023] [Revised: 11/09/2023] [Accepted: 02/23/2024] [Indexed: 03/25/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) share many clinical, pathological, and genetic features, but a detailed understanding of their associated transcriptional alterations across vulnerable cortical cell types is lacking. Here, we report a high-resolution, comparative single-cell molecular atlas of the human primary motor and dorsolateral prefrontal cortices and their transcriptional alterations in sporadic and familial ALS and FTLD. By integrating transcriptional and genetic information, we identify known and previously unidentified vulnerable populations in cortical layer 5 and show that ALS- and FTLD-implicated motor and spindle neurons possess a virtually indistinguishable molecular identity. We implicate potential disease mechanisms affecting these cell types as well as non-neuronal drivers of pathogenesis. Finally, we show that neuron loss in cortical layer 5 tracks more closely with transcriptional identity rather than cellular morphology and extends beyond previously reported vulnerable cell types.
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Affiliation(s)
- S Sebastian Pineda
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Hyeseung Lee
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Raleigh M Linville
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Francisco J Garcia
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kyriakitsa Galani
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | | | - Brent E Fitzwalter
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Luc J Pregent
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Michael DeTure
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Andre T S Hucke
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Melissa E Murray
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Myriam Heiman
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | | | - Manolis Kellis
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.
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3
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Gorman BR, Francis M, Nealon CL, Halladay CW, Duro N, Markianos K, Genovese G, Hysi PG, Choquet H, Afshari NA, Li YJ, Gaziano JM, Hung AM, Wu WC, Greenberg PB, Pyarajan S, Lass JH, Peachey NS, Iyengar SK. A multi-ancestry GWAS of Fuchs corneal dystrophy highlights the contributions of laminins, collagen, and endothelial cell regulation. Commun Biol 2024; 7:418. [PMID: 38582945 PMCID: PMC10998918 DOI: 10.1038/s42003-024-06046-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 03/13/2024] [Indexed: 04/08/2024] Open
Abstract
Fuchs endothelial corneal dystrophy (FECD) is a leading indication for corneal transplantation, but its molecular etiology remains poorly understood. We performed genome-wide association studies (GWAS) of FECD in the Million Veteran Program followed by multi-ancestry meta-analysis with the previous largest FECD GWAS, for a total of 3970 cases and 333,794 controls. We confirm the previous four loci, and identify eight novel loci: SSBP3, THSD7A, LAMB1, PIDD1, RORA, HS3ST3B1, LAMA5, and COL18A1. We further confirm the TCF4 locus in GWAS for admixed African and Hispanic/Latino ancestries and show an enrichment of European-ancestry haplotypes at TCF4 in FECD cases. Among the novel associations are low frequency missense variants in laminin genes LAMA5 and LAMB1 which, together with previously reported LAMC1, form laminin-511 (LM511). AlphaFold 2 protein modeling, validated through homology, suggests that mutations at LAMA5 and LAMB1 may destabilize LM511 by altering inter-domain interactions or extracellular matrix binding. Finally, phenome-wide association scans and colocalization analyses suggest that the TCF4 CTG18.1 trinucleotide repeat expansion leads to dysregulation of ion transport in the corneal endothelium and has pleiotropic effects on renal function.
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Affiliation(s)
- Bryan R Gorman
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA, USA
- Booz Allen Hamilton, McLean, VA, USA
| | - Michael Francis
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA, USA
- Booz Allen Hamilton, McLean, VA, USA
| | - Cari L Nealon
- Eye Clinic, VA Northeast Ohio Healthcare System, Cleveland, OH, USA
| | - Christopher W Halladay
- Center of Innovation in Long Term Services and Supports, Providence VA Medical Center, Providence, RI, USA
| | - Nalvi Duro
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA, USA
- Booz Allen Hamilton, McLean, VA, USA
| | - Kyriacos Markianos
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA, USA
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Pirro G Hysi
- Department of Ophthalmology, King's College London, London, UK
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
- UCL Great Ormond Street Hospital Institute of Child Health, King's College London, London, UK
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California (KPNC), Oakland, CA, USA
| | - Natalie A Afshari
- Shiley Eye Institute, Viterbi Family Department of Ophthalmology, University of California, San Diego, La Jolla, CA, USA
| | - Yi-Ju Li
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Division of Aging, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Adriana M Hung
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN, USA
- VA Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Wen-Chih Wu
- Cardiology Section, Medical Service, Providence VA Medical Center, Providence, RI, USA
| | - Paul B Greenberg
- Ophthalmology Section, Providence VA Medical Center, Providence, RI, USA
- Division of Ophthalmology, Alpert Medical School, Brown University, Providence, RI, USA
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA, USA
| | - Jonathan H Lass
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Neal S Peachey
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, OH, USA.
- Cole Eye Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA.
| | - Sudha K Iyengar
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, OH, USA.
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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Tsartsalis S, Sleven H, Fancy N, Wessely F, Smith AM, Willumsen N, Cheung TKD, Rokicki MJ, Chau V, Ifie E, Khozoie C, Ansorge O, Yang X, Jenkyns MH, Davey K, McGarry A, Muirhead RCJ, Debette S, Jackson JS, Montagne A, Owen DR, Miners JS, Love S, Webber C, Cader MZ, Matthews PM. A single nuclear transcriptomic characterisation of mechanisms responsible for impaired angiogenesis and blood-brain barrier function in Alzheimer's disease. Nat Commun 2024; 15:2243. [PMID: 38472200 DOI: 10.1038/s41467-024-46630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Brain perfusion and blood-brain barrier (BBB) integrity are reduced early in Alzheimer's disease (AD). We performed single nucleus RNA sequencing of vascular cells isolated from AD and non-diseased control brains to characterise pathological transcriptional signatures responsible for this. We show that endothelial cells (EC) are enriched for expression of genes associated with susceptibility to AD. Increased β-amyloid is associated with BBB impairment and a dysfunctional angiogenic response related to a failure of increased pro-angiogenic HIF1A to increased VEGFA signalling to EC. This is associated with vascular inflammatory activation, EC senescence and apoptosis. Our genomic dissection of vascular cell risk gene enrichment provides evidence for a role of EC pathology in AD and suggests that reducing vascular inflammatory activation and restoring effective angiogenesis could reduce vascular dysfunction contributing to the genesis or progression of early AD.
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Affiliation(s)
- Stergios Tsartsalis
- Department of Brain Sciences, Imperial College London, London, UK
- Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Hannah Sleven
- Nuffield Department of Clinical Neurosciences, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Sherrington Road, University of Oxford, Oxford, UK
| | - Nurun Fancy
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Frank Wessely
- UK Dementia Research Institute Centre, Cardiff University, Cardiff, UK
| | - Amy M Smith
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
- Centre for Brain Research and Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
| | - Nanet Willumsen
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - To Ka Dorcas Cheung
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Michal J Rokicki
- UK Dementia Research Institute Centre, Cardiff University, Cardiff, UK
| | - Vicky Chau
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Eseoghene Ifie
- Neuropathology Unit, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Combiz Khozoie
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Olaf Ansorge
- Neuropathology Unit, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Xin Yang
- Department of Brain Sciences, Imperial College London, London, UK
- St Edmund Hall, University of Oxford, Oxford, UK
| | - Marion H Jenkyns
- Department of Brain Sciences, Imperial College London, London, UK
| | - Karen Davey
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Aisling McGarry
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Robert C J Muirhead
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Stephanie Debette
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, Team ELEANOR, UMR 1219, 33000, Bordeaux, France
| | - Johanna S Jackson
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Axel Montagne
- Centre for Clinical Brain Sciences, and UK Dementia Research Institute, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - David R Owen
- Department of Brain Sciences, Imperial College London, London, UK
| | - J Scott Miners
- Dementia Research Group, University of Bristol, Bristol, UK
| | - Seth Love
- Dementia Research Group, University of Bristol, Bristol, UK
| | - Caleb Webber
- UK Dementia Research Institute Centre, Cardiff University, Cardiff, UK
| | - M Zameel Cader
- Nuffield Department of Clinical Neurosciences, Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Sherrington Road, University of Oxford, Oxford, UK
| | - Paul M Matthews
- Department of Brain Sciences, Imperial College London, London, UK.
- UK Dementia Research Institute Centre, Imperial College London, London, UK.
- St Edmund Hall, University of Oxford, Oxford, UK.
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Puvogel S, Alsema A, North HF, Webster MJ, Weickert CS, Eggen BJL. Single-Nucleus RNA-Seq Characterizes the Cell Types Along the Neuronal Lineage in the Adult Human Subependymal Zone and Reveals Reduced Oligodendrocyte Progenitor Abundance with Age. eNeuro 2024; 11:ENEURO.0246-23.2024. [PMID: 38351133 PMCID: PMC10913050 DOI: 10.1523/eneuro.0246-23.2024] [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: 07/12/2023] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 03/06/2024] Open
Abstract
The subependymal zone (SEZ), also known as the subventricular zone (SVZ), constitutes a neurogenic niche that persists during postnatal life. In humans, the neurogenic potential of the SEZ declines after the first year of life. However, studies discovering markers of stem and progenitor cells highlight the neurogenic capacity of progenitors in the adult human SEZ, with increased neurogenic activity occurring under pathological conditions. In the present study, the complete cellular niche of the adult human SEZ was characterized by single-nucleus RNA sequencing, and compared between four youth (age 16-22) and four middle-aged adults (age 44-53). We identified 11 cellular clusters including clusters expressing marker genes for neural stem cells (NSCs), neuroblasts, immature neurons, and oligodendrocyte progenitor cells. The relative abundance of NSC and neuroblast clusters did not differ between the two age groups, indicating that the pool of SEZ NSCs does not decline in this age range. The relative abundance of oligodendrocyte progenitors and microglia decreased in middle-age, indicating that the cellular composition of human SEZ is remodeled between youth and adulthood. The expression of genes related to nervous system development was higher across different cell types, including NSCs, in youth as compared with middle-age. These transcriptional changes suggest ongoing central nervous system plasticity in the SEZ in youth, which declined in middle-age.
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Affiliation(s)
- Sofía Puvogel
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen 9700 AD, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen 6500 HB, The Netherlands
| | - Astrid Alsema
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen 9700 AD, The Netherlands
| | - Hayley F North
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, New South Wales 2031, Australia
- School of Psychiatry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Maree J Webster
- Laboratory of Brain Research, Stanley Medical Research Institute, Rockville 20850, Maryland
| | - Cynthia Shannon Weickert
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Sydney, New South Wales 2031, Australia
- School of Psychiatry, University of New South Wales, Sydney, New South Wales 2052, Australia
- Department of Neuroscience and Physiology, Upstate Medical University, Syracuse, New York 13201
| | - Bart J L Eggen
- Section Molecular Neurobiology, Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen 9700 AD, The Netherlands
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Genovese G, Rockweiler NB, Gorman BR, Bigdeli TB, Pato MT, Pato CN, Ichihara K, McCarroll SA. BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies. Bioinformatics 2024; 40:btae038. [PMID: 38261650 PMCID: PMC10832354 DOI: 10.1093/bioinformatics/btae038] [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: 10/16/2023] [Revised: 12/07/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024] Open
Abstract
MOTIVATION Many genetics studies report results tied to genomic coordinates of a legacy genome assembly. However, as assemblies are updated and improved, researchers are faced with either realigning raw sequence data using the updated coordinate system or converting legacy datasets to the updated coordinate system to be able to combine results with newer datasets. Currently available tools to perform the conversion of genetic variants have numerous shortcomings, including poor support for indels and multi-allelic variants, that lead to a higher rate of variants being dropped or incorrectly converted. As a result, many researchers continue to work with and publish using legacy genomic coordinates. RESULTS Here we present BCFtools/liftover, a tool to convert genomic coordinates across genome assemblies for variants encoded in the variant call format with improved support for indels represented by different reference alleles across genome assemblies and full support for multi-allelic variants. It further supports variant annotation fields updates whenever the reference allele changes across genome assemblies. The tool has the lowest rate of variants being dropped with an order of magnitude less indels dropped or incorrectly converted and is an order of magnitude faster than other tools typically used for the same task. It is particularly suited for converting variant callsets from large cohorts to novel telomere-to-telomere assemblies as well as summary statistics from genome-wide association studies tied to legacy genome assemblies. AVAILABILITY AND IMPLEMENTATION The tool is written in C and freely available under the MIT open source license as a BCFtools plugin available at http://github.com/freeseek/score.
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Affiliation(s)
- Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Nicole B Rockweiler
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Bryan R Gorman
- Center for Data and Computational Sciences, VA Boston HealthCare System, Boston, MA 02130, United States
- Booz Allen Hamilton Inc, McLean, VA 22102, United States
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, United States
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, United States
- Cooperative Studies Program, VA New York Harbor Healthcare System, Brooklyn, NY 11209, United States
| | - Michelle T Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, New Brunswick, NJ 08901, United States
| | - Carlos N Pato
- Department of Psychiatry, Robert Wood Johnson Medical School, New Brunswick, NJ 08901, United States
| | - Kiku Ichihara
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Stanley Center, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
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7
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Akçimen F, Chia R, Saez-Atienzar S, Ruffo P, Rasheed M, Ross JP, Liao C, Ray A, Dion PA, Scholz SW, Rouleau GA, Traynor BJ. Genomic analysis identifies risk factors in restless legs syndrome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.19.23300211. [PMID: 38168192 PMCID: PMC10760278 DOI: 10.1101/2023.12.19.23300211] [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
Restless legs syndrome (RLS) is a neurological condition that causes uncomfortable sensations in the legs and an irresistible urge to move them, typically during periods of rest. The genetic basis and pathophysiology of RLS are incompletely understood. Here, we present a whole-genome sequencing and genome-wide association meta-analysis of RLS cases (n = 9,851) and controls (n = 38,957) in three population-based biobanks (All of Us, Canadian Longitudinal Study on Aging, and CARTaGENE). Genome-wide association analysis identified nine independent risk loci, of which eight had been previously reported, and one was a novel risk locus (LMX1B, rs35196838, OR = 1.14, 95% CI = 1.09-1.19, p-value = 2.2 × 10-9). A genome-wide, gene-based common variant analysis identified GLO1 as an additional risk gene (p-value = 8.45 × 10-7). Furthermore, a transcriptome-wide association study also identified GLO1 and a previously unreported gene, ELFN1. A genetic correlation analysis revealed significant common variant overlaps between RLS and neuroticism (rg = 0.40, se = 0.08, p-value = 5.4 × 10-7), depression (rg = 0.35, se = 0.06, p-value = 2.17 × 10-8), and intelligence (rg = -0.20, se = 0.06, p-value = 4.0 × 10-4). Our study expands the understanding of the genetic architecture of RLS and highlights the contributions of common variants to this prevalent neurological disorder.
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Affiliation(s)
- Fulya Akçimen
- Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Ruth Chia
- Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sara Saez-Atienzar
- Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Paola Ruffo
- Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Memoona Rasheed
- Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Jay P. Ross
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Calwing Liao
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anindita Ray
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Patrick A. Dion
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Sonja W. Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Guy A. Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Montreal Neurological Institute, McGill University, Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Bryan J. Traynor
- Neuromuscular Diseases Research Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
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8
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Wang J, Cheng X, Liang Q, Owen LA, Lu J, Zheng Y, Wang M, Chen S, DeAngelis MM, Li Y, Chen R. Single-cell multiomics of the human retina reveals hierarchical transcription factor collaboration in mediating cell type-specific effects of genetic variants on gene regulation. Genome Biol 2023; 24:269. [PMID: 38012720 PMCID: PMC10680294 DOI: 10.1186/s13059-023-03111-8] [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: 11/11/2022] [Accepted: 11/15/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Systematic characterization of how genetic variation modulates gene regulation in a cell type-specific context is essential for understanding complex traits. To address this question, we profile gene expression and chromatin accessibility in cells from healthy retinae of 20 human donors through single-cell multiomics and genomic sequencing. RESULTS We map eQTL, caQTL, allelic-specific expression, and allelic-specific chromatin accessibility in major retinal cell types. By integrating these results, we identify and characterize regulatory elements and genetic variants effective on gene regulation in individual cell types. The majority of identified sc-eQTLs and sc-caQTLs display cell type-specific effects, while the cis-elements containing genetic variants with cell type-specific effects are often accessible in multiple cell types. Furthermore, the transcription factors whose binding sites are perturbed by genetic variants tend to have higher expression levels in the cell types where the variants exert their effects, compared to the cell types where the variants have no impact. We further validate our findings with high-throughput reporter assays. Lastly, we identify the enriched cell types, candidate causal variants and genes, and cell type-specific regulatory mechanism underlying GWAS loci. CONCLUSIONS Overall, genetic effects on gene regulation are highly context dependent. Our results suggest that cell type-dependent genetic effect is driven by precise modulation of both trans-factor expression and chromatin accessibility of cis-elements. Our findings indicate hierarchical collaboration among transcription factors plays a crucial role in mediating cell type-specific effects of genetic variants on gene regulation.
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Affiliation(s)
- Jun Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xuesen Cheng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Qingnan Liang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Leah A Owen
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
| | - Jiaxiong Lu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yiqiao Zheng
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, MO, USA
| | - Meng Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, MO, USA
- Department of Developmental Biology, Washington University in St Louis, Saint Louis, MO, USA
| | - Margaret M DeAngelis
- Department of Ophthalmology, University at Buffalo the State University of New York, Buffalo, NY, USA
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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9
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Li J, Wang J, Ibarra IL, Cheng X, Luecken MD, Lu J, Monavarfeshani A, Yan W, Zheng Y, Zuo Z, Colborn SLZ, Cortez BS, Owen LA, Tran NM, Shekhar K, Sanes JR, Stout JT, Chen S, Li Y, DeAngelis MM, Theis FJ, Chen R. Integrated multi-omics single cell atlas of the human retina. RESEARCH SQUARE 2023:rs.3.rs-3471275. [PMID: 38014002 PMCID: PMC10680922 DOI: 10.21203/rs.3.rs-3471275/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Single-cell sequencing has revolutionized the scale and resolution of molecular profiling of tissues and organs. Here, we present an integrated multimodal reference atlas of the most accessible portion of the mammalian central nervous system, the retina. We compiled around 2.4 million cells from 55 donors, including 1.4 million unpublished data points, to create a comprehensive human retina cell atlas (HRCA) of transcriptome and chromatin accessibility, unveiling over 110 types. Engaging the retina community, we annotated each cluster, refined the Cell Ontology for the retina, identified distinct marker genes, and characterized cis-regulatory elements and gene regulatory networks (GRNs) for these cell types. Our analysis uncovered intriguing differences in transcriptome, chromatin, and GRNs across cell types. In addition, we modeled changes in gene expression and chromatin openness across gender and age. This integrated atlas also enabled the fine-mapping of GWAS and eQTL variants. Accessible through interactive browsers, this multimodal cross-donor and cross-lab HRCA, can facilitate a better understanding of retinal function and pathology.
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Affiliation(s)
- Jin Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Jun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Ignacio L Ibarra
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Xuesen Cheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Malte D Luecken
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Lung Health & Immunity, Helmholtz Munich; Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Jiaxiong Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States
| | - Aboozar Monavarfeshani
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Wenjun Yan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Yiqiao Zheng
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, United States
| | - Zhen Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | | | | | - Leah A Owen
- John A. Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, Utah, United States
| | - Nicholas M Tran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Karthik Shekhar
- Department of Chemical and Biomolecular Engineering; Helen Wills Neuroscience Institute; Center for Computational Biology; California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, California, United States
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - J Timothy Stout
- Department of Ophthalmology, Cullen Eye Institute, Baylor College of Medicine, Houston, Texas, United States
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University in St Louis, Saint Louis, Missouri, United States
- Department of Developmental Biology, Washington University in St Louis, Saint Louis, Missouri, United States
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Margaret M DeAngelis
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, United States
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States
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10
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Alvarado CX, Weller CA, Johnson N, Leonard HL, Singleton AB, Reed X, Blauewendraat C, Nalls MA. Human brain single nucleus cell type enrichments in neurodegenerative diseases. RESEARCH SQUARE 2023:rs.3.rs-3390225. [PMID: 38014237 PMCID: PMC10680930 DOI: 10.21203/rs.3.rs-3390225/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Background Single-cell RNA sequencing has opened a window into clarifying the complex underpinnings of disease, particularly in quantifying the relevance of tissue- and cell-type-specific gene expression. Methods To identify the cell types and genes important to therapeutic target development across the neurodegenerative disease spectrum, we leveraged genome-wide association studies, recent single-cell sequencing data, and bulk expression studies in a diverse series of brain region tissues. Results We were able to identify significant immune-related cell types in the brain across three major neurodegenerative diseases: Alzheimer's disease, amyotrophic lateral sclerosis, and Parkinson's disease. Subsequently, putative roles of 30 fine-mapped loci implicating seven genes in multiple neurodegenerative diseases and their pathogenesis were identified. Conclusions We have helped refine the genetic regions and cell types effected across multiple neurodegenerative diseases, helping focus future translational research efforts.
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11
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Cifello J, Kuksa PP, Saravanan N, Valladares O, Wang LS, Leung YY. hipFG: high-throughput harmonization and integration pipeline for functional genomics data. Bioinformatics 2023; 39:btad673. [PMID: 37947320 PMCID: PMC10660288 DOI: 10.1093/bioinformatics/btad673] [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: 05/16/2023] [Revised: 09/20/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023] Open
Abstract
SUMMARY Preparing functional genomic (FG) data with diverse assay types and file formats for integration into analysis workflows that interpret genome-wide association and other studies is a significant and time-consuming challenge. Here we introduce hipFG (Harmonization and Integration Pipeline for Functional Genomics), an automatically customized pipeline for efficient and scalable normalization of heterogenous FG data collections into standardized, indexed, rapidly searchable analysis-ready datasets while accounting for FG datatypes (e.g. chromatin interactions, genomic intervals, quantitative trait loci). AVAILABILITY AND IMPLEMENTATION hipFG is freely available at https://bitbucket.org/wanglab-upenn/hipFG. A Docker container is available at https://hub.docker.com/r/wanglab/hipfg.
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Affiliation(s)
- Jeffrey Cifello
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Pavel P Kuksa
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Naveensri Saravanan
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Otto Valladares
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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12
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Gao H, Zheng S, Yuan X, Xie J, Xu L. Causal association between inflammatory bowel disease and 32 site-specific extracolonic cancers: a Mendelian randomization study. BMC Med 2023; 21:389. [PMID: 37817217 PMCID: PMC10566178 DOI: 10.1186/s12916-023-03096-y] [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: 12/10/2022] [Accepted: 09/27/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND The risk of extracolonic cancer is increased in inflammatory bowel disease (IBD) patients, but it is not clear whether there is a causal relationship. We aimed to systematically estimate the causal relationship between IBD and extracolonic cancers. METHODS Independent genetic variants strongly associated with IBD were extracted as instrumental variables from genome-wide association study (GWAS) conducted by the International IBD Genetics Consortium including 12,882 IBD patients, 5956 Crohn's disease (CD) patients, and 6968 ulcerative colitis (UC) patients. Three sources of cancer GWAS were selected as outcome data. Two-sample Mendelian randomization (MR) analysis was conducted to assess the causal effects of IBD on 32 extracolonic cancers. The meta-analysis was applied to assess the combined causal effect with multiple MR results. RESULTS IBD, CD, and UC have potential causal associations with oral cavity cancer (IBD: OR = 1.180, 95% CI: 1.059 to 1.316, P = 0.003; CD: OR = 1.112, 95% CI: 1.008 to 1.227, P = 0.034; UC: OR = 1.158, 95% CI: 1.041 to 1.288, P = 0.007). Meta-analysis showed a significant positive causal relationship between IBD and breast cancer (OR = 1.059; 95% CI: 1.033 to 1.086; P < 0.0001) as well as a potential causal relationship between CD and breast cancer (OR = 1.029; 95% CI: 1.002 to 1.055; P = 0.032) based on combining multiple MR results. CONCLUSIONS This comprehensive MR analysis suggested that genetically predicted IBD, as well as its subtypes, may be a risk factor in the development of oral cavity and breast cancer.
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Affiliation(s)
- Hui Gao
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo, ZheJiang, 315010, China
- Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Shuhao Zheng
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo, ZheJiang, 315010, China
- Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Xin Yuan
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo, ZheJiang, 315010, China
| | - Jiarong Xie
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo, ZheJiang, 315010, China
| | - Lei Xu
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo, ZheJiang, 315010, China.
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13
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Chen X, Hu G. Correlation study of malignant lymphoma and breast Cancer in different gender European populations: mendelian randomization analysis. BMC Genom Data 2023; 24:59. [PMID: 37814219 PMCID: PMC10561426 DOI: 10.1186/s12863-023-01162-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/29/2023] [Indexed: 10/11/2023] Open
Abstract
BACKGROUND Previous research has already indicated an elevated risk of breast cancer (BC) among survivors of malignant lymphoma, but the underlying reasons remain unknown. Our objective is to elucidate the causal relationship between malignant lymphoma and BC through Mendelian randomization (MR). Genome-wide association studies (GWAS) data from 181,125 Hodgkin lymphoma (HL) patients and 181,289 non-Hodgkin lymphoma (NHL) patients from the FinnGen Consortium were utilized as exposure. We selected single nucleotide polymorphisms (SNPs) strongly associated with the exposure as instrumental variables to investigate their relationship with BC in a cohort of 107,722 participants. Subsequently, we obtained data from the UK Biobank containing gender-stratified information on HL, NHL, and BC. We validated the findings from our analysis and explored the impact of gender. The Inverse-Variance Weighted (IVW) method served as the primary reference for the two-sample MR, accompanied by tests for heterogeneity and pleiotropy. RESULTS The analysis results from the FinnGen consortium indicate that there is no causal relationship between HL and NHL with BC. HL (OR = 1.01, 95% CI = 0.98-1.04, p = 0.29), NHL (OR = 1.01, 95% CI = 0.96-1.05, p = 0.64). When utilizing GWAS data from the UK Biobank that includes different gender cohorts, the lack of association between HL, NHL, and BC remains consistent. HL (OR = 1.08, 95% CI = 0.74-1.56, p = 0.69), HL-Female (OR = 0.84, 95% CI = 0.59-1.19, p = 0.33), NHL (OR = 0.89, 95% CI = 0.66-1.19, p = 0.44), and NHL-Female (OR = 0.81, 95% CI = 0.58-1.11, p = 0.18). CONCLUSIONS The two-sample MR analysis indicates that there is no significant causal relationship between malignant lymphoma (HL and NHL) and BC. The association between malignant lymphoma and breast cancer requires further in-depth research and exploration.
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Affiliation(s)
- Xiong Chen
- Department of General Surgery, Affiliated Changsha Hospital of Hunan Normal University, Changsha, 410000 China
| | - GuoHuang Hu
- Department of General Surgery, Affiliated Changsha Hospital of Hunan Normal University, Changsha, 410000 China
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14
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Xu H, Sun Y, Francis M, Cheng CF, Modulla NT, Brenna JT, Chiang CWK, Ye K. Shared genetic basis informs the roles of polyunsaturated fatty acids in brain disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.03.23296500. [PMID: 37873425 PMCID: PMC10593041 DOI: 10.1101/2023.10.03.23296500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The neural tissue is rich in polyunsaturated fatty acids (PUFAs), components that are indispensable for the proper functioning of neurons, such as neurotransmission. PUFA nutritional deficiency and imbalance have been linked to a variety of chronic brain disorders, including major depressive disorder (MDD), anxiety, and anorexia. However, the effects of PUFAs on brain disorders remain inconclusive, and the extent of their shared genetic determinants is largely unknown. Here, we used genome-wide association summary statistics to systematically examine the shared genetic basis between six phenotypes of circulating PUFAs (N = 114,999) and 20 brain disorders (N = 9,725-762,917), infer their potential causal relationships, identify colocalized regions, and pinpoint shared genetic variants. Genetic correlation and polygenic overlap analyses revealed a widespread shared genetic basis for 77 trait pairs between six PUFA phenotypes and 16 brain disorders. Two-sample Mendelian randomization analysis indicated potential causal relationships for 16 pairs of PUFAs and brain disorders, including alcohol consumption, bipolar disorder (BIP), and MDD. Colocalization analysis identified 40 shared loci (13 unique) among six PUFAs and ten brain disorders. Twenty-two unique variants were statistically inferred as candidate shared causal variants, including rs1260326 (GCKR), rs174564 (FADS2) and rs4818766 (ADARB1). These findings reveal a widespread shared genetic basis between PUFAs and brain disorders, pinpoint specific shared variants, and provide support for the potential effects of PUFAs on certain brain disorders, especially MDD, BIP, and alcohol consumption.
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Affiliation(s)
- Huifang Xu
- Department of Genetics, University of Georgia, Athens, Georgia
| | - Yitang Sun
- Department of Genetics, University of Georgia, Athens, Georgia
| | - Michael Francis
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
| | - Claire F. Cheng
- Department of Genetics, University of Georgia, Athens, Georgia
| | | | - J. Thomas Brenna
- Dell Pediatric Research Institute and Department of Pediatrics, The University of Texas at Austin, Texas
- Dell Pediatric Research Institute and Department of Chemistry, The University of Texas at Austin, Texas
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Texas
| | - Charleston W. K. Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California
| | - Kaixiong Ye
- Department of Genetics, University of Georgia, Athens, Georgia
- Institute of Bioinformatics, University of Georgia, Athens, Georgia
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15
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Westergaard D, Steinthorsdottir V, Stefansdottir L, Rohde PD, Wu X, Geller F, Tyrmi J, Havulinna AS, Navais PS, Flatley C, Ostrowski SR, Pedersen OB, Erikstrup C, Sørensen E, Mikkelsen C, Brun MT, Jensen BA, Brodersen T, Ullum H, Magnus P, Andreassen OA, Njolstad PR, Kolte AM, Krebs L, Nyegaard M, Hansen TF, Fenstra B, Daly M, Lindgren CM, Thorleifsson G, Stefansson OA, Sveinbjornsson G, Gudbjartsson DF, Thorsteinsdottir U, Banasik K, Jacobsson B, Laisk T, Laivuori H, Stefansson K, Brunak S, Nielsen HS. Pregnancy-Associated Bleeding and Genetics: Five Sequence Variants in the Myometrium and Progesterone Signaling Pathway are associated with postpartum hemorrhage. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.10.23293932. [PMID: 37645979 PMCID: PMC10462219 DOI: 10.1101/2023.08.10.23293932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Bleeding in early pregnancy and postpartum hemorrhage (PPH) bear substantial risks, with the former closely associated with pregnancy loss and the latter being the foremost cause of maternal death, underscoring the severity of these complications in maternal-fetal health. Here, we investigated the genetic variation underlying aspects of pregnancy-associated bleeding and identified five loci associated with PPH through a meta-analysis of 21,512 cases and 259,500 controls. Functional annotation analysis indicated candidate genes, HAND2, TBX3, and RAP2C/FRMD7, at three loci and showed that at each locus, associated variants were located within binding sites for progesterone receptors (PGR). Furthermore, there were strong genetic correlations with birth weight, gestational duration, and uterine fibroids. Early bleeding during pregnancy (28,898 cases and 302,894 controls) yielded no genome-wide association signals, but showed strong genetic correlation with a variety of human traits, indicative of polygenic and pleiotropic effects. Our results suggest that postpartum bleeding is related to myometrium dysregulation, whereas early bleeding is a complex trait related to underlying health and possibly socioeconomic status.
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Affiliation(s)
- David Westergaard
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | | | | | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Gistrup, Denmark
| | - Xiaoping Wu
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Frank Geller
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jaakko Tyrmi
- Centre for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare - THL, Helsinki, Finland
| | - Pol Sole Navais
- Department of Obstetrics and Gynaecology, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | - Christopher Flatley
- Department of Obstetrics and Gynaecology, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
| | - Sisse Rye Ostrowski
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Birger Pedersen
- Department of Clinical immunology, Zealand University Hospital, Køge, Denmark
- Department of Clinical medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Erik Sørensen
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Christina Mikkelsen
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Mie Topholm Brun
- Clinical Immunological Research Unit, Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | | | - Thorsten Brodersen
- Department of Clinical immunology, Zealand University Hospital, Køge, Denmark
| | - Henrik Ullum
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Per Magnus
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Ole A Andreassen
- NORMENT Centre, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Pål R Njolstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
| | - Astrid Marie Kolte
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Lone Krebs
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Department of Clinical medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Gistrup, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Danish Headache Center, Department of neurology, Copenhagen University Hospital, Glostrup, Denmark
| | - Bjarke Fenstra
- Department of Clinical immunology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Mark Daly
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cecilia M Lindgren
- Big Data Institute Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Wellcome Trust Centre Human Genetics, University of Oxford, Oxford, UK
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, Reykjavik University, Reykjavik, Iceland
| | - Karina Banasik
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bo Jacobsson
- Department of Obstetrics and Gynaecology, Institute of Clinical Science, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics and Gynaecology, Tampere University Hospital, Tampere, Finland
- Centre for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kari Stefansson
- deCODE genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, Reykjavik University, Reykjavik, Iceland
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henriette Svarre Nielsen
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Department of Clinical medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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16
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Rasooly D, Peloso GM, Pereira AC, Dashti H, Giambartolomei C, Wheeler E, Aung N, Ferolito BR, Pietzner M, Farber-Eger EH, Wells QS, Kosik NM, Gaziano L, Posner DC, Bento AP, Hui Q, Liu C, Aragam K, Wang Z, Charest B, Huffman JE, Wilson PWF, Phillips LS, Whittaker J, Munroe PB, Petersen SE, Cho K, Leach AR, Magariños MP, Gaziano JM, Langenberg C, Sun YV, Joseph J, Casas JP. Genome-wide association analysis and Mendelian randomization proteomics identify drug targets for heart failure. Nat Commun 2023; 14:3826. [PMID: 37429843 PMCID: PMC10333277 DOI: 10.1038/s41467-023-39253-3] [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: 12/08/2022] [Accepted: 06/05/2023] [Indexed: 07/12/2023] Open
Abstract
We conduct a large-scale meta-analysis of heart failure genome-wide association studies (GWAS) consisting of over 90,000 heart failure cases and more than 1 million control individuals of European ancestry to uncover novel genetic determinants for heart failure. Using the GWAS results and blood protein quantitative loci, we perform Mendelian randomization and colocalization analyses on human proteins to provide putative causal evidence for the role of druggable proteins in the genesis of heart failure. We identify 39 genome-wide significant heart failure risk variants, of which 18 are previously unreported. Using a combination of Mendelian randomization proteomics and genetic cis-only colocalization analyses, we identify 10 additional putatively causal genes for heart failure. Findings from GWAS and Mendelian randomization-proteomics identify seven (CAMK2D, PRKD1, PRKD3, MAPK3, TNFSF12, APOC3 and NAE1) proteins as potential targets for interventions to be used in primary prevention of heart failure.
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Affiliation(s)
- Danielle Rasooly
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St., Boston, MA, 02130, USA.
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, 150. S. Huntington Ave, Boston, MA, 02130, USA.
| | - Gina M Peloso
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, 150. S. Huntington Ave, Boston, MA, 02130, USA
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Ave Crosstown Centre, Boston, MA, 02118, USA
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo, Av Dr Eneas de Carvalho Aguiar 54, São Paulo, 5403000, Brazil
- Genetics Department, Harvard Medical School, Harvard University, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Hesam Dashti
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St., Boston, MA, 02130, USA
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA, 02142, USA
| | - Claudia Giambartolomei
- Health Data Science Centre, Human Technopole, V.le Rita Levi-Montalcini, 1, Milan, 20157, Italy
- Central RNA Lab, Non-coding RNAs and RNA-based Therapeutics, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Eleanor Wheeler
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Addenbrookes Hospital, IMS, Box 285, Cambridge, CB2 0QQ, UK
| | - Nay Aung
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, West Smithfield, London, UK
| | - Brian R Ferolito
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, 150. S. Huntington Ave, Boston, MA, 02130, USA
| | - Maik Pietzner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Addenbrookes Hospital, IMS, Box 285, Cambridge, CB2 0QQ, UK
- Computational Medicine, Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Kapelle Ufer 2, Berlin, 10117, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Eric H Farber-Eger
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quinn Stanton Wells
- Vanderbilt University Med. Ctr., Departments of Medicine (Cardiology), Biomedical Informatics, and Pharmacology, Nashville, TN, USA
| | - Nicole M Kosik
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, 150. S. Huntington Ave, Boston, MA, 02130, USA
| | - Liam Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, 150. S. Huntington Ave, Boston, MA, 02130, USA
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge, CB1 8RN, UK
| | - Daniel C Posner
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, 150. S. Huntington Ave, Boston, MA, 02130, USA
| | - A Patrícia Bento
- Department of Chemical Biology, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Qin Hui
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Rd NE, Atlanta, GA, 30322, USA
- Atlanta VA Health Care System, 1670 Clairmont Road, Decatur, GA, 30033, USA
| | - Chang Liu
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Rd NE, Atlanta, GA, 30322, USA
| | - Krishna Aragam
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, 150. S. Huntington Ave, Boston, MA, 02130, USA
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA, 02142, USA
- Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Zeyuan Wang
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Rd NE, Atlanta, GA, 30322, USA
| | - Brian Charest
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, 150. S. Huntington Ave, Boston, MA, 02130, USA
| | - Jennifer E Huffman
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, 150. S. Huntington Ave, Boston, MA, 02130, USA
| | - Peter W F Wilson
- Atlanta VA Health Care System, 1670 Clairmont Road, Decatur, GA, 30033, USA
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, 1639 Pierce Dr NE, Atlanta, GA, 30322, USA
| | - Lawrence S Phillips
- Atlanta VA Health Care System, 1670 Clairmont Road, Decatur, GA, 30033, USA
- Division of Endocrinology, Emory University, 101 Woodruff Circle, WMRB 1027, Atlanta, GA, 30322, USA
| | - John Whittaker
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, United Kingdom
| | - Patricia B Munroe
- William Harvey Research Institute, Barts and The London Faculty of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
- National Institute for Health Research, Barts Biomedical Research Centre, Queen Mary University of London, London, UK
| | - Steffen E Petersen
- Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, West Smithfield, London, UK
- William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London, Charterhouse Square, London, EC1M 68Q, UK
| | - Kelly Cho
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St., Boston, MA, 02130, USA
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, 150. S. Huntington Ave, Boston, MA, 02130, USA
| | - Andrew R Leach
- Department of Chemical Biology, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - María Paula Magariños
- Department of Chemical Biology, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - John Michael Gaziano
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St., Boston, MA, 02130, USA
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, 150. S. Huntington Ave, Boston, MA, 02130, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Addenbrookes Hospital, IMS, Box 285, Cambridge, CB2 0QQ, UK
- Computational Medicine, Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Kapelle Ufer 2, Berlin, 10117, Germany
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK
| | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, 1518 Clifton Rd NE, Atlanta, GA, 30322, USA
- Atlanta VA Health Care System, 1670 Clairmont Road, Decatur, GA, 30033, USA
- Department of Biomedical Informatics, Emory University School of Medicine, 1639 Pierce Dr NE, Atlanta, GA, 30332, USA
| | - Jacob Joseph
- Cardiology Section, VA Providence Healthcare System, 830 Chalkstone Avenue, Providence, RI, 02908, USA.
- Department of Medicine, Warren Alpert Medical School of Brown University, 222 Richmond Street, Providence, RI, 02903, USA.
| | - Juan P Casas
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, 75 Francis St., Boston, MA, 02130, USA
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, 150. S. Huntington Ave, Boston, MA, 02130, USA
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17
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Alvarado CX, Weller CA, Johnson N, Leonard HL, Singleton AB, Reed X, Blauewendraat C, Nalls M. Human brain single nucleus cell type enrichments in neurodegenerative diseases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.30.23292084. [PMID: 37577689 PMCID: PMC10418576 DOI: 10.1101/2023.06.30.23292084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Single cell RNA sequencing has opened a window into clarifying the complex underpinnings of disease, particularly in quantifying the relevance of tissue- and cell-type-specific gene expression. To identify the cell types and genes important to therapeutic target development across the neurodegenerative disease spectrum, we leveraged genome-wide association studies, recent single cell sequencing data, and bulk expression studies in a diverse series of brain region tissues. We were able to identify significant immune-related cell types in the brain across three major neurodegenerative diseases: Alzheimer's Disease, Amyotrophic Lateral Sclerosis, and Parkinson's Diseases. Subsequently, we identified the major role of 30 fine-mapped loci implicating seven genes in multiple neurodegenerative diseases and their pathogenesis.
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Affiliation(s)
- Chelsea X. Alvarado
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Cory A. Weller
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Nicholas Johnson
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Hampton L. Leonard
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
| | - Andrew B. Singleton
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Xylena Reed
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Cornelis Blauewendraat
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Mike Nalls
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
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18
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Lake J, Warly Solsberg C, Kim JJ, Acosta-Uribe J, Makarious MB, Li Z, Levine K, Heutink P, Alvarado CX, Vitale D, Kang S, Gim J, Lee KH, Pina-Escudero SD, Ferrucci L, Singleton AB, Blauwendraat C, Nalls MA, Yokoyama JS, Leonard HL. Multi-ancestry meta-analysis and fine-mapping in Alzheimer's disease. Mol Psychiatry 2023; 28:3121-3132. [PMID: 37198259 PMCID: PMC10615750 DOI: 10.1038/s41380-023-02089-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 05/19/2023]
Abstract
Genome-wide association studies (GWAS) of Alzheimer's disease are predominantly carried out in European ancestry individuals despite the known variation in genetic architecture and disease prevalence across global populations. We leveraged published GWAS summary statistics from European, East Asian, and African American populations, and an additional GWAS from a Caribbean Hispanic population using previously reported genotype data to perform the largest multi-ancestry GWAS meta-analysis of Alzheimer's disease and related dementias to date. This method allowed us to identify two independent novel disease-associated loci on chromosome 3. We also leveraged diverse haplotype structures to fine-map nine loci with a posterior probability >0.8 and globally assessed the heterogeneity of known risk factors across populations. Additionally, we compared the generalizability of multi-ancestry- and single-ancestry-derived polygenic risk scores in a three-way admixed Colombian population. Our findings highlight the importance of multi-ancestry representation in uncovering and understanding putative factors that contribute to risk of Alzheimer's disease and related dementias.
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Affiliation(s)
- Julie Lake
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Caroline Warly Solsberg
- Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonggeol Jeffrey Kim
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Preventive Neurology Unit, Centre for Prevention Diagnosis and Detection, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Juliana Acosta-Uribe
- Neuroscience Research Institute and the department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
- Neuroscience Group of Antioquia, University of Antioquia, Medellín, Colombia
| | - Mary B Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
| | - Zizheng Li
- Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kristin Levine
- Data Tecnica International LLC, Washington, DC, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Peter Heutink
- Alector, Inc. 131 Oyster Point Blvd, Suite 600, South San Francisco, CA, 94080, USA
| | - Chelsea X Alvarado
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Dan Vitale
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Sarang Kang
- Gwangju Alzheimer's disease and Related Dementia Cohort Research Center, Chosun University, Gwangju, 61452, Korea
- BK FOUR Department of Integrative Biological Sciences, Chosun University, Gwangju, 61452, Korea
| | - Jungsoo Gim
- Gwangju Alzheimer's disease and Related Dementia Cohort Research Center, Chosun University, Gwangju, 61452, Korea
- BK FOUR Department of Integrative Biological Sciences, Chosun University, Gwangju, 61452, Korea
- Department of Biomedical Science, Chosun University, Gwangju, 61452, Korea
| | - Kun Ho Lee
- Gwangju Alzheimer's disease and Related Dementia Cohort Research Center, Chosun University, Gwangju, 61452, Korea
- BK FOUR Department of Integrative Biological Sciences, Chosun University, Gwangju, 61452, Korea
- Department of Biomedical Science, Chosun University, Gwangju, 61452, Korea
- Korea Brain Research Institute, Daegu, 41062, Korea
| | - Stefanie D Pina-Escudero
- Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Data Tecnica International LLC, Washington, DC, USA
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer S Yokoyama
- Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Memory and Aging Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
- Data Tecnica International LLC, Washington, DC, USA.
- Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD, USA.
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
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19
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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 DOI: 10.1016/j.ajhg.2023.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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20
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Demela P, Pirastu N, Soskic B. Cross-disorder genetic analysis of immune diseases reveals distinct gene associations that converge on common pathways. Nat Commun 2023; 14:2743. [PMID: 37173304 PMCID: PMC10182075 DOI: 10.1038/s41467-023-38389-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Genome-wide association studies (GWAS) have mapped thousands of susceptibility loci associated with immune-mediated diseases. To assess the extent of the genetic sharing across nine immune-mediated diseases we apply genomic structural equation modelling to GWAS data from European populations. We identify three disease groups: gastrointestinal tract diseases, rheumatic and systemic diseases, and allergic diseases. Although loci associated with the disease groups are highly specific, they converge on perturbing the same pathways. Finally, we test for colocalization between loci and single-cell eQTLs derived from peripheral blood mononuclear cells. We identify the causal route by which 46 loci predispose to three disease groups and find evidence for eight genes being candidates for drug repurposing. Taken together, here we show that different constellations of diseases have distinct patterns of genetic associations, but that associated loci converge on perturbing different nodes in T cell activation and signalling pathways.
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Affiliation(s)
- Pietro Demela
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Nicola Pirastu
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Blagoje Soskic
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy.
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21
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Peachey N, Gorman B, Francis M, Nealon C, Halladay C, Duro N, Markianos K, Genovese G, Hysi P, Choquet H, Afshari N, Li YJ, Gaziano JM, Hung A, Wu WC, Greenberg P, Pyarajan S, Lass J, Iyengar S. Multi-ancestry GWAS of Fuchs corneal dystrophy highlights roles of laminins, collagen, and endothelial cell regulation. RESEARCH SQUARE 2023:rs.3.rs-2762003. [PMID: 37205546 PMCID: PMC10187421 DOI: 10.21203/rs.3.rs-2762003/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Fuchs endothelial corneal dystrophy (FECD) is a leading indication for corneal transplantation, but its molecular pathophysiology remains poorly understood. We performed genome-wide association studies (GWAS) of FECD in the Million Veteran Program (MVP) and meta-analyzed with the previous largest FECD GWAS, finding twelve significant loci (eight novel). We further confirmed the TCF4 locus in admixed African and Hispanic/Latino ancestries, and found an enrichment of European-ancestry haplotypes at TCF4 in FECD cases. Among the novel associations are low frequency missense variants in laminin genes LAMA5 and LAMB1 which, together with previously reported LAMC1, form laminin-511 (LM511). AlphaFold 2 protein modeling suggests that mutations at LAMA5 and LAMB1 may destabilize LM511 by altering inter-domain interactions or extracellular matrix binding. Finally, phenome-wide association scans and co-localization analyses suggest that the TCF4 CTG18.1 trinucleotide repeat expansion leads to dysregulation of ion transport in the corneal endothelium and has pleiotropic effects on renal function.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California
| | | | | | | | | | | | | | - Saiju Pyarajan
- Center for Data and Computational Sciences, Veterans Affairs Boston Healthcare System
| | - Jonathan Lass
- Case Western Reserve University and University Hospitals Case Medical Center
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22
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Cifello J, Kuksa PP, Saravanan N, Valladares O, Leung YY, Wang LS. hipFG: High-throughput harmonization and integration pipeline for functional genomics data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537695. [PMID: 37162864 PMCID: PMC10168270 DOI: 10.1101/2023.04.21.537695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Preparing functional genomic (FG) data with diverse assay types and file formats for integration into analysis workflows that interpret genome-wide association and other studies is a significant and time-consuming challenge. Here we introduce hipFG, an automatically customized pipeline for efficient and scalable normalization of heterogenous FG data collections into standardized, indexed, rapidly searchable analysis-ready datasets while accounting for FG datatypes (e.g., chromatin interactions, genomic intervals, quantitative trait loci).
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Affiliation(s)
- Jeffrey Cifello
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania
| | - Pavel P. Kuksa
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania
| | - Naveensri Saravanan
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania
| | - Otto Valladares
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania
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Zhang Q, Li Q, Zhao H, Shu M, Luo M, Li Y, Ding Y, Shi S, Cheng X, Niu Q. Neurodegenerative disease and antioxidant biomarkers: A bidirectional Mendelian randomization study. Front Neurol 2023; 14:1158366. [PMID: 37034095 PMCID: PMC10076659 DOI: 10.3389/fneur.2023.1158366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/07/2023] [Indexed: 04/11/2023] Open
Abstract
Objective Previous observational studies have suggested that antioxidant imbalance is correlated with neurodegenerative diseases, while its cause-effect remains unclear. Thus, the goal of the present study is to explore the causal relationship between 11 antioxidant biomarkers and 3 most common neurodegenerative diseases [Alzheimer's disease (AD), Amyotrophic Lateral Sclerosis (ALS) and Parkinson's disease (PD)]. Methods A bidirectional Mendelian randomization (MR) study was performed to investigate the causal effects by using 3 main methods (Variance Weighted (IVW), Weighted Median (WM), and MR-Egger regression) in the European population. The data of 11 antioxidant biomarkers were obtained from the open database by the most up-to-date Genome-Wide Association Studies (GWAS), the summary statistics of PD and ALS were obtained from the International Parkinson's Disease Genomics Consortium (IPDGC) (33,674 cases, and 449,056 controls), and the International Amyotrophic Lateral Sclerosis Genomics Consortium (IALSC) (20,806 cases and 59,804 controls), respectively. For AD, we specifically used two recently published GWAS data, one from the International Genomics of Alzheimer's Project (IGAP) (21,982 cases and 41,944 controls), and the other from a large meta-analysis (71,880 cases and 383,378 controls) as validation data. Results Based on the Bonferroni correction p < 0.0015, there was no significant causal evidence for the antioxidant biomarkers on neurodegenerative diseases, however, the reverse analysis found that AD was significantly related to the decrease in retinol (IVW: beta = -0.023, p = 0.0007; WM: beta = -0.025, p = 0.0121), while the same analysis was carried out between the AD validation database and retinol, the results were consistent (IVW: beta = -0.064, p = 0.025). Moreover, AD on Glutathione S-transferase (GST), PD on Glutathione Peroxidase (GPX) as well as PD on uric acid (UA) also indicated potential causal-and-effect associations (IVW: p = 0.025; p = 0.027; p = 0.021, respectively). Conclusions There was no sufficient evidence that antioxidant imbalance has a significant causal effect on neurodegenerative diseases. However, this study revealed that genetically predicted AD was significantly related to the decrease in retinol, which provides a new insight into previous research and indicates the possibility to regard retinol as potential biomarker for the diagnosis and progress of AD.
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Kim M, Vo DD, Kumagai ME, Jops CT, Gandal MJ. GeneticsMakie.jl: a versatile and scalable toolkit for visualizing locus-level genetic and genomic data. Bioinformatics 2023; 39:6887175. [PMID: 36495218 PMCID: PMC9825774 DOI: 10.1093/bioinformatics/btac786] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 10/29/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
SUMMARY With the continued deluge of results from genome-wide association and functional genomic studies, it has become increasingly imperative to quickly combine and visualize different layers of genetic and genomic data within a given locus to facilitate exploratory and integrative data analyses. While several tools have been developed to visualize locus-level genetic results, the limited speed, scalability and flexibility of current approaches remain a significant bottleneck. Here, we present a Julia package for high-performance genetics and genomics-related data visualization that enables fast, simultaneous plotting of hundreds of association results along with multiple relevant genomic annotations. Leveraging the powerful plotting and layout utilities from Makie.jl facilitates the customization and extensibility of every component of a plot, enabling generation of publication-ready figures. AVAILABILITY AND IMPLEMENTATION The GeneticsMakie.jl package is open source and distributed under the MIT license via GitHub (https://github.com/mmkim1210/GeneticsMakie.jl). The GitHub repository contains installation instructions as well as examples and documentation for built-in functions. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Minsoo Kim
- To whom correspondence should be addressed. or
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25
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Matushyn M, Bose M, Mahmoud AA, Cuthbertson L, Tello C, Bircan KO, Terpolovsky A, Bamunusinghe V, Khan U, Novković B, Grabherr MG, Yazdi PG. SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration. BMC Bioinformatics 2022; 23:443. [PMID: 36284273 PMCID: PMC9594936 DOI: 10.1186/s12859-022-04920-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/06/2022] [Indexed: 11/23/2022] Open
Abstract
Background Generating polygenic risk scores for diseases and complex traits requires high quality GWAS summary statistic files. Often, these files can be difficult to acquire either as a result of unshared or incomplete data. To date, bioinformatics tools which focus on restoring missing columns containing identification and association data are limited, which has the potential to increase the number of usable GWAS summary statistics files. Results SumStatsRehab was able to restore rsID, effect/other alleles, chromosome, base pair position, effect allele frequencies, beta, standard error, and p-values to a better extent than any other currently available tool, with minimal loss. Conclusions SumStatsRehab offers a unique tool utilizing both functional programming and pipeline-like architecture, allowing users to generate accurate data restorations for incomplete summary statistics files. This in turn, increases the number of usable GWAS summary statistics files, which may be invaluable for less researched health traits.
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Affiliation(s)
- Mykyta Matushyn
- SelfDecode.Com, 1031 Ives Dairy Road Suite 228 - 1047, Miami, FL, 33179, USA
| | - Madhuchanda Bose
- SelfDecode.Com, 1031 Ives Dairy Road Suite 228 - 1047, Miami, FL, 33179, USA
| | | | - Lewis Cuthbertson
- SelfDecode.Com, 1031 Ives Dairy Road Suite 228 - 1047, Miami, FL, 33179, USA
| | - Carlos Tello
- SelfDecode.Com, 1031 Ives Dairy Road Suite 228 - 1047, Miami, FL, 33179, USA
| | - Karatuğ Ozan Bircan
- SelfDecode.Com, 1031 Ives Dairy Road Suite 228 - 1047, Miami, FL, 33179, USA
| | - Andrew Terpolovsky
- SelfDecode.Com, 1031 Ives Dairy Road Suite 228 - 1047, Miami, FL, 33179, USA
| | - Varuna Bamunusinghe
- SelfDecode.Com, 1031 Ives Dairy Road Suite 228 - 1047, Miami, FL, 33179, USA
| | - Umar Khan
- SelfDecode.Com, 1031 Ives Dairy Road Suite 228 - 1047, Miami, FL, 33179, USA
| | - Biljana Novković
- SelfDecode.Com, 1031 Ives Dairy Road Suite 228 - 1047, Miami, FL, 33179, USA
| | - Manfred G Grabherr
- SelfDecode.Com, 1031 Ives Dairy Road Suite 228 - 1047, Miami, FL, 33179, USA
| | - Puya G Yazdi
- SelfDecode.Com, 1031 Ives Dairy Road Suite 228 - 1047, Miami, FL, 33179, USA.
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Pan S, Kang H, Liu X, Lin S, Yuan N, Zhang Z, Bao Y, Jia P. Brain Catalog: a comprehensive resource for the genetic landscape of brain-related traits. Nucleic Acids Res 2022; 51:D835-D844. [PMID: 36243988 PMCID: PMC9825493 DOI: 10.1093/nar/gkac895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/13/2022] [Accepted: 10/08/2022] [Indexed: 01/30/2023] Open
Abstract
A broad range of complex phenotypes are related to dysfunctions in brain (hereafter referred to as brain-related traits), including various mental and behavioral disorders and diseases of the nervous system. These traits in general share overlapping symptoms, pathogenesis, and genetic components. Here, we present Brain Catalog (https://ngdc.cncb.ac.cn/braincatalog), a comprehensive database aiming to delineate the genetic components of more than 500 GWAS summary statistics datasets for brain-related traits from multiple aspects. First, Brain Catalog provides results of candidate causal variants, causal genes, and functional tissues and cell types for each trait identified by multiple methods using comprehensive annotation datasets (58 QTL datasets spanning 6 types of QTLs). Second, Brain Catalog estimates the SNP-based heritability, the partitioning heritability based on functional annotations, and genetic correlations among traits. Finally, through bidirectional Mendelian randomization analyses, Brain Catalog presents inference of risk factors that are likely causal to each trait. In conclusion, Brain Catalog presents a one-stop shop for the genetic components of brain-related traits, potentially serving as a valuable resource for worldwide researchers to advance the understanding of how GWAS signals may contribute to the biological etiology of brain-related traits.
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Affiliation(s)
| | | | | | - Shiqi Lin
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Na Yuan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhang Zhang
- Correspondence may also be addressed to Zhang Zhang.
| | - Yiming Bao
- Correspondence may also be addressed to Yiming Bao.
| | - Peilin Jia
- To whom correspondence should be addressed. Tel: +86 1084097798; ;
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Coales I, Tsartsalis S, Fancy N, Weinert M, Clode D, Owen D, Matthews PM. Alzheimer's disease-related transcriptional sex differences in myeloid cells. J Neuroinflammation 2022; 19:247. [PMID: 36199077 PMCID: PMC9535846 DOI: 10.1186/s12974-022-02604-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 09/21/2022] [Indexed: 11/30/2022] Open
Abstract
Sex differences have been identified in many diseases associated with dysregulated immune responses, including Alzheimer's disease (AD), for which approximately two-thirds of patients are women. An accumulating body of research indicates that microglia may play a causal role in the pathogenesis of this disease. We hypothesised that sex differences in the transcriptome of human myeloid cells may contribute to the sex difference observed in AD prevalence. To explore this, we assessed bulk and single-nuclear RNA sequencing data sets generated from four human derived myeloid cell populations: post-mortem microglial nuclei, peripheral monocytes, monocyte-derived macrophages (MDMs) and induced pluripotent stem cell derived microglial-like cells (MGLs). We found that expression of AD risk genes, gene signatures associated with the inflammatory response in AD, and genes related to proinflammatory immune responses were enriched in microglial nuclei isolated from aged female donors without ante-mortem neurological disease, relative to those from males. In addition, these inflammation-associated gene sets were found to be enriched in peripheral monocytes isolated from postmenopausal women and in MDMs obtained from premenopausal individuals relative to age-matched males. Expression of these gene sets did not differ in MDMs derived from women whose blood was sampled across the menstrual cycle or in MGLs cultured with 17β-oestradiol. This suggests that the observed gene set enrichments in myeloid cells from women were not being driven by acute hormonal influences. Together, these data support the hypothesis that the increased prevalence of AD in women may be partly explained by a myeloid cell phenotype biased towards expression of biological processes relevant to AD.
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Affiliation(s)
- Isabelle Coales
- Department of Brain Sciences, Imperial College London, London, UK
- Centre for Host Microbiome Interactions, King's College London, London, SE1 9RT, UK
| | - Stergios Tsartsalis
- Department of Brain Sciences, Imperial College London, London, UK
- Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Nurun Fancy
- Department of Brain Sciences, Imperial College London, London, UK
- UK Dementia Research Centre at Imperial College London, London, UK
| | - Maria Weinert
- Department of Brain Sciences, Imperial College London, London, UK
| | - Daniel Clode
- UK Dementia Research Centre at Imperial College London, London, UK
| | - David Owen
- Department of Brain Sciences, Imperial College London, London, UK.
- Clinical Research Facility, Hammersmith Hospital, ICTM Building, DuCane Road, London, W12 0NN, UK.
| | - Paul M Matthews
- Department of Brain Sciences, Imperial College London, London, UK.
- UK Dementia Research Centre at Imperial College London, London, UK.
- Hammersmith Hospital, E502, Burlington Danes Building, DuCane Road, London, W12 0NN, UK.
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Schilder BM, Navarro E, Raj T. Multi-omic insights into Parkinson's Disease: From genetic associations to functional mechanisms. Neurobiol Dis 2021; 163:105580. [PMID: 34871738 PMCID: PMC10101343 DOI: 10.1016/j.nbd.2021.105580] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/17/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Genome-Wide Association Studies (GWAS) have elucidated the genetic components of Parkinson's Disease (PD). However, because the vast majority of GWAS association signals fall within non-coding regions, translating these results into an interpretable, mechanistic understanding of the disease etiology remains a major challenge in the field. In this review, we provide an overview of the approaches to prioritize putative causal variants and genes as well as summarise the primary findings of previous studies. We then discuss recent efforts to integrate multi-omics data to identify likely pathogenic cell types and biological pathways implicated in PD pathogenesis. We have compiled full summary statistics of cell-type, tissue, and phentoype enrichment analyses from multiple studies of PD GWAS and provided them in a standardized format as a resource for the research community (https://github.com/RajLabMSSM/PD_omics_review). Finally, we discuss the experimental, computational, and conceptual advances that will be necessary to fully elucidate the effects of functional variants and genes on cellular dysregulation and disease risk.
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Affiliation(s)
- Brian M Schilder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; UK Dementia Research Institute at Imperial College London, London, United Kingdom.
| | - Elisa Navarro
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Sección Departamental de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
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