1
|
Wang Q, Antone J, Alsop E, Reiman R, Funk C, Bendl J, Dudley JT, Liang WS, Karr TL, Roussos P, Bennett DA, De Jager PL, Serrano GE, Beach TG, Van Keuren-Jensen K, Mastroeni D, Reiman EM, Readhead BP. Single cell transcriptomes and multiscale networks from persons with and without Alzheimer's disease. Nat Commun 2024; 15:5815. [PMID: 38987616 PMCID: PMC11237088 DOI: 10.1038/s41467-024-49790-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/13/2024] [Indexed: 07/12/2024] Open
Abstract
The emergence of single nucleus RNA sequencing (snRNA-seq) offers to revolutionize the study of Alzheimer's disease (AD). Integration with complementary multiomics data such as genetics, proteomics and clinical data provides powerful opportunities to link cell subpopulations and molecular networks with a broader disease-relevant context. We report snRNA-seq profiles from superior frontal gyrus samples from 101 well characterized subjects from the Banner Brain and Body Donation Program in combination with whole genome sequences. We report findings that link common AD risk variants with CR1 expression in oligodendrocytes as well as alterations in hematological parameters. We observed an AD-associated CD83(+) microglial subtype with unique molecular networks and which is associated with immunoglobulin IgG4 production in the transverse colon. Our major observations were replicated in two additional, independent snRNA-seq data sets. These findings illustrate the power of multi-tissue molecular profiling to contextualize snRNA-seq brain transcriptomics and reveal disease biology.
Collapse
Affiliation(s)
- Qi Wang
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Jerry Antone
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Eric Alsop
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Rebecca Reiman
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Cory Funk
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jaroslav Bendl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joel T Dudley
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Winnie S Liang
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Timothy L Karr
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Philip L De Jager
- Department of Neurology, Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, 85351, USA
| | | | - Diego Mastroeni
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA
| | - Eric M Reiman
- Banner Alzheimer's Institute, Phoenix, AZ, 85006, USA
| | - Benjamin P Readhead
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, 85281, USA.
| |
Collapse
|
2
|
Ray NR, Kunkle BW, Hamilton-Nelson K, Kurup JT, Rajabli F, Qiao M, Vardarajan BN, Cosacak MI, Kizil C, Jean-Francois M, Cuccaro M, Reyes-Dumeyer D, Cantwell L, Kuzma A, Vance JM, Gao S, Hendrie HC, Baiyewu O, Ogunniyi A, Akinyemi RO, Lee WP, Martin ER, Wang LS, Beecham GW, Bush WS, Xu W, Jin F, Wang L, Farrer LA, Haines JL, Byrd GS, Schellenberg GD, Mayeux R, Pericak-Vance MA, Reitz C. Extended genome-wide association study employing the African genome resources panel identifies novel susceptibility loci for Alzheimer's disease in individuals of African ancestry. Alzheimers Dement 2024. [PMID: 38958117 DOI: 10.1002/alz.13880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 04/03/2024] [Accepted: 04/12/2024] [Indexed: 07/04/2024]
Abstract
INTRODUCTION Despite a two-fold risk, individuals of African ancestry have been underrepresented in Alzheimer's disease (AD) genomics efforts. METHODS Genome-wide association studies (GWAS) of 2,903 AD cases and 6,265 controls of African ancestry. Within-dataset results were meta-analyzed, followed by functional genomics analyses. RESULTS A novel AD-risk locus was identified in MPDZ on chromosome (chr) 9p23 (rs141610415, MAF = 0.002, P = 3.68×10-9). Two additional novel common and nine rare loci were identified with suggestive associations (P < 9×10-7). Comparison of association and linkage disequilibrium (LD) patterns between datasets with higher and lower degrees of African ancestry showed differential association patterns at chr12q23.2 (ASCL1), suggesting that this association is modulated by regional origin of local African ancestry. DISCUSSION These analyses identified novel AD-associated loci in individuals of African ancestry and suggest that degree of African ancestry modulates some associations. Increased sample sets covering as much African genetic diversity as possible will be critical to identify additional loci and deconvolute local genetic ancestry effects. HIGHLIGHTS Genetic ancestry significantly impacts risk of Alzheimer's Disease (AD). Although individuals of African ancestry are twice as likely to develop AD, they are vastly underrepresented in AD genomics studies. The Alzheimer's Disease Genetics Consortium has previously identified 16 common and rare genetic loci associated with AD in African American individuals. The current analyses significantly expand this effort by increasing the sample size and extending ancestral diversity by including populations from continental Africa. Single variant meta-analysis identified a novel genome-wide significant AD-risk locus in individuals of African ancestry at the MPDZ gene, and 11 additional novel loci with suggestive genome-wide significance at P < 9×10-7. Comparison of African American datasets with samples of higher degree of African ancestry demonstrated differing patterns of association and linkage disequilibrium at one of these loci, suggesting that degree and/or geographic origin of African ancestry modulates the effect at this locus. These findings illustrate the importance of increasing number and ancestral diversity of African ancestry samples in AD genomics studies to fully disentangle the genetic architecture underlying AD, and yield more effective ancestry-informed genetic screening tools and therapeutic interventions.
Collapse
Affiliation(s)
- Nicholas R Ray
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Brian W Kunkle
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Kara Hamilton-Nelson
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Jiji T Kurup
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Farid Rajabli
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Min Qiao
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Badri N Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | | | - Caghan Kizil
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Melissa Jean-Francois
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Michael Cuccaro
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Laura Cantwell
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Amanda Kuzma
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jeffery M Vance
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Sujuan Gao
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Hugh C Hendrie
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | | | | | - Wan-Ping Lee
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Eden R Martin
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, University of Miami, Miami, Florida, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Gary W Beecham
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - William S Bush
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Biomedical Research, Cleveland, Ohio, USA
- Department of Population and Quantitative Health Sciences and Cleveland Institute for Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Wanying Xu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Biomedical Research, Cleveland, Ohio, USA
| | - Fulai Jin
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Biomedical Research, Cleveland, Ohio, USA
- Department of Population and Quantitative Health Sciences and Cleveland Institute for Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Liyong Wang
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Lindsay A Farrer
- Department of Medicine, Biomedical Genetics Section, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
- Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences and Cleveland Institute for Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Goldie S Byrd
- Maya Angelou Center for Health Equity, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Gerard D Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
- Department of Neurology, Columbia University, New York, New York, USA
- Department of Psychiatry, Columbia University, New York, New York, USA
- Epidemiology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, University of Miami, Miami, Florida, USA
| | - Christiane Reitz
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
- Department of Neurology, Columbia University, New York, New York, USA
- Epidemiology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| |
Collapse
|
3
|
Hudgins AD, Zhou S, Arey RN, Rosenfeld MG, Murphy CT, Suh Y. A systems biology-based identification and in vivo functional screening of Alzheimer's disease risk genes reveal modulators of memory function. Neuron 2024; 112:2112-2129.e4. [PMID: 38692279 PMCID: PMC11223975 DOI: 10.1016/j.neuron.2024.04.009] [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: 07/16/2022] [Revised: 10/18/2023] [Accepted: 04/08/2024] [Indexed: 05/03/2024]
Abstract
Genome-wide association studies (GWASs) have uncovered over 75 genomic loci associated with risk for late-onset Alzheimer's disease (LOAD), but identification of the underlying causal genes remains challenging. Studies of induced pluripotent stem cell (iPSC)-derived neurons from LOAD patients have demonstrated the existence of neuronal cell-intrinsic functional defects. Here, we searched for genetic contributions to neuronal dysfunction in LOAD using an integrative systems approach that incorporated multi-evidence-based gene mapping and network-analysis-based prioritization. A systematic perturbation screening of candidate risk genes in Caenorhabditis elegans (C. elegans) revealed that neuronal knockdown of the LOAD risk gene orthologs vha-10 (ATP6V1G2), cmd-1 (CALM3), amph-1 (BIN1), ephx-1 (NGEF), and pho-5 (ACP2) alters short-/intermediate-term memory function, the cognitive domain affected earliest during LOAD progression. These results highlight the impact of LOAD risk genes on evolutionarily conserved memory function, as mediated through neuronal endosomal dysfunction, and identify new targets for further mechanistic interrogation.
Collapse
Affiliation(s)
- Adam D Hudgins
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Shiyi Zhou
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Rachel N Arey
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael G Rosenfeld
- Department of Medicine, School of Medicine, University of California, La Jolla, CA, USA; Howard Hughes Medical Institute, University of California, La Jolla, CA, USA
| | - Coleen T Murphy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA; LSI Genomics, Princeton University, Princeton, NJ, USA.
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
4
|
Zhang Y, Xu F, Wang T, Han Z, Shang H, Han K, Zhu P, Gao S, Wang X, Xue Y, Huang C, Chen Y, Liu G. Shared genetics and causal association between plasma levels of SARS-CoV-2 entry receptor ACE2 and Alzheimer's disease. CNS Neurosci Ther 2024; 30:e14873. [PMID: 39056224 PMCID: PMC11273102 DOI: 10.1111/cns.14873] [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: 04/04/2024] [Revised: 06/26/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is the highest risk of COVID-19 infection, hospitalization, and mortality. However, it remains largely unclear about the link between AD and COVID-19 outcomes. ACE2 is an entry receptor for SARS-CoV-2. Circulating ACE2 is a novel biomarker of death and associated with COVID-19 outcomes. METHODS Here, we explored the shared genetics and causal association between AD and plasma ACE2 levels using large-scale genome-wide association study, gene expression, expression quantitative trait loci, and high-throughput plasma proteomic profiling datasets. RESULTS We found a significant causal effect of genetically increased circulating ACE2 on increased risk of AD. Cross-trait association analysis identified 19 shared genetic variants, and three variants rs3104412, rs2395166, and rs3135344 at chromosome 6p21.32 were associated with COVID-19 infection, hospitalization, and severity. We mapped 19 variants to 117 genes, which were significantly upregulated in lung, spleen, and small intestine, downregulated in brain tissues, and involved in immune system, immune disease, and infectious disease pathways. The plasma proteins corresponding to LST1, AGER, TNXB, and APOC1 were predominantly associated with COVID-19 infection, ventilation, and death. CONCLUSION Together, our findings suggest the shared genetics and causal association between AD and plasma ACE2 levels, which may partially explain the link between AD and COVID-19.
Collapse
Affiliation(s)
- Yan Zhang
- Department of PathologyThe Affiliated Hospital of Weifang Medical UniversityWeifangChina
| | - Fang Xu
- Department of Neurology, Xuanwu Hospital, National Center for Neurological DisordersCapital Medical UniversityBeijingChina
| | - Tao Wang
- Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
- Chinese Institute for Brain ResearchBeijingChina
| | - Zhifa Han
- Center of Respiratory Medicine, China–Japan Friendship Hospital, National Center for Respiratory Medicine, Institute of Respiratory MedicineChinese Acadamy of Medical Sciences, National Clinical Research Center for Respiratory DiseasesBeijingChina
| | - Hong Shang
- Department of NeurologyThe Fourth Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Kevin Han
- Department of StatisticsStanford UniversityStanfordCaliforniaUSA
| | - Ping Zhu
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain DisordersCapital Medical UniversityBeijingChina
| | - Shan Gao
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain DisordersCapital Medical UniversityBeijingChina
| | - Xiaojie Wang
- Department of NeurologyShenzhen Qianhai Shekou Free Trade Zone HospitalShenzhenChina
| | - Yanli Xue
- School of Biomedical EngineeringCapital Medical UniversityBeijingChina
| | - Chen Huang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese MedicineMacau University of Science and TechnologyMacao SARChina
| | - Yan Chen
- Department of Epidemiology and Biostatistics, School of Public HealthWannan Medical CollegeWuhuChina
- Institute of Chronic Disease Prevention and ControlWannan Medical CollegeWuhuChina
| | - Guiyou Liu
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain DisordersCapital Medical UniversityBeijingChina
- Department of Epidemiology and Biostatistics, School of Public HealthWannan Medical CollegeWuhuChina
- Institute of Chronic Disease Prevention and ControlWannan Medical CollegeWuhuChina
- Beijing Key Laboratory of Hypoxia Translational Medicine, National Engineering Laboratory of Internet Medical Diagnosis and Treatment Technology, Xuanwu HospitalCapital Medical UniversityBeijingChina
- Taishan Vocational College of NursingTaianChina
- Brain HospitalShengli Oilfield Central HospitalDongyingChina
| |
Collapse
|
5
|
Qiu Y, Hou Y, Gohel D, Zhou Y, Xu J, Bykova M, Yang Y, Leverenz JB, Pieper AA, Nussinov R, Caldwell JZK, Brown JM, Cheng F. Systematic characterization of multi-omics landscape between gut microbial metabolites and GPCRome in Alzheimer's disease. Cell Rep 2024; 43:114128. [PMID: 38652661 DOI: 10.1016/j.celrep.2024.114128] [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: 12/22/2023] [Revised: 03/06/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Shifts in the magnitude and nature of gut microbial metabolites have been implicated in Alzheimer's disease (AD), but the host receptors that sense and respond to these metabolites are largely unknown. Here, we develop a systems biology framework that integrates machine learning and multi-omics to identify molecular relationships of gut microbial metabolites with non-olfactory G-protein-coupled receptors (termed the "GPCRome"). We evaluate 1.09 million metabolite-protein pairs connecting 408 human GPCRs and 335 gut microbial metabolites. Using genetics-derived Mendelian randomization and integrative analyses of human brain transcriptomic and proteomic profiles, we identify orphan GPCRs (i.e., GPR84) as potential drug targets in AD and that triacanthine experimentally activates GPR84. We demonstrate that phenethylamine and agmatine significantly reduce tau hyperphosphorylation (p-tau181 and p-tau205) in AD patient induced pluripotent stem cell-derived neurons. This study demonstrates a systems biology framework to uncover the GPCR targets of human gut microbiota in AD and other complex diseases if broadly applied.
Collapse
Affiliation(s)
- Yunguang Qiu
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yuan Hou
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Dhruv Gohel
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yadi Zhou
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jielin Xu
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Marina Bykova
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yuxin Yang
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - James B Leverenz
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Andrew A Pieper
- Brain Health Medicines Center, Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA; Department of Psychiatry, Case Western Reserve University, Cleveland, OH 44106, USA; Geriatric Psychiatry, GRECC, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA; Institute for Transformative Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA; Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jessica Z K Caldwell
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Las Vegas, NV 89106, USA
| | - J Mark Brown
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Department of Cancer Biology, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Feixiong Cheng
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA.
| |
Collapse
|
6
|
Cary GA, Wiley JC, Gockley J, Keegan S, Amirtha Ganesh SS, Heath L, Butler RR, Mangravite LM, Logsdon BA, Longo FM, Levey A, Greenwood AK, Carter GW. Genetic and multi-omic risk assessment of Alzheimer's disease implicates core associated biological domains. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2024; 10:e12461. [PMID: 38650747 PMCID: PMC11033838 DOI: 10.1002/trc2.12461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/23/2024] [Accepted: 02/09/2024] [Indexed: 04/25/2024]
Abstract
INTRODUCTION Alzheimer's disease (AD) is the predominant dementia globally, with heterogeneous presentation and penetrance of clinical symptoms, variable presence of mixed pathologies, potential disease subtypes, and numerous associated endophenotypes. Beyond the difficulty of designing treatments that address the core pathological characteristics of the disease, therapeutic development is challenged by the uncertainty of which endophenotypic areas and specific targets implicated by those endophenotypes to prioritize for further translational research. However, publicly funded consortia driving large-scale open science efforts have produced multiple omic analyses that address both disease risk relevance and biological process involvement of genes across the genome. METHODS Here we report the development of an informatic pipeline that draws from genetic association studies, predicted variant impact, and linkage with dementia associated phenotypes to create a genetic risk score. This is paired with a multi-omic risk score utilizing extensive sets of both transcriptomic and proteomic studies to identify system-level changes in expression associated with AD. These two elements combined constitute our target risk score that ranks AD risk genome-wide. The ranked genes are organized into endophenotypic space through the development of 19 biological domains associated with AD in the described genetics and genomics studies and accompanying literature. The biological domains are constructed from exhaustive Gene Ontology (GO) term compilations, allowing automated assignment of genes into objectively defined disease-associated biology. This rank-and-organize approach, performed genome-wide, allows the characterization of aggregations of AD risk across biological domains. RESULTS The top AD-risk-associated biological domains are Synapse, Immune Response, Lipid Metabolism, Mitochondrial Metabolism, Structural Stabilization, and Proteostasis, with slightly lower levels of risk enrichment present within the other 13 biological domains. DISCUSSION This provides an objective methodology to localize risk within specific biological endophenotypes and drill down into the most significantly associated sets of GO terms and annotated genes for potential therapeutic targets.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Frank M. Longo
- Stanford University School of MedicineStanfordCaliforniaUSA
| | | | | | | |
Collapse
|
7
|
Wyatt-Johnson SK, Afify R, Brutkiewicz RR. The immune system in neurological diseases: What innate-like T cells have to say. J Allergy Clin Immunol 2024; 153:913-923. [PMID: 38365015 PMCID: PMC10999338 DOI: 10.1016/j.jaci.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/26/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024]
Abstract
The immune system classically consists of 2 lines of defense, innate and adaptive, both of which interact with one another effectively to protect us against any pathogenic threats. Importantly, there is a diverse subset of cells known as innate-like T cells that act as a bridge between the innate and adaptive immune systems and are pivotal players in eliciting inflammatory immune responses. A growing body of evidence has demonstrated the regulatory impact of these innate-like T cells in central nervous system (CNS) diseases and that such immune cells can traffic into the brain in multiple pathological conditions, which can be typically attributed to the breakdown of the blood-brain barrier. However, until now, it has been poorly understood whether innate-like T cells have direct protective or causative properties, particularly in CNS diseases. Therefore, in this review, our attention is focused on discussing the critical roles of 3 unique subsets of unconventional T cells, namely, natural killer T cells, γδ T cells, and mucosal-associated invariant T cells, in the context of CNS diseases, disorders, and injuries and how the interplay of these immune cells modulates CNS pathology, in an attempt to gain a better understanding of their complex functions.
Collapse
Affiliation(s)
- Season K Wyatt-Johnson
- Department of Microbiology and Immunology, Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Ind
| | - Reham Afify
- Department of Microbiology and Immunology, Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Ind
| | - Randy R Brutkiewicz
- Department of Microbiology and Immunology, Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Ind.
| |
Collapse
|
8
|
Zachariou M, Loizidou EM, Spyrou GM. Immediate-Early Genes as Influencers in Genetic Networks and their Role in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.586739. [PMID: 38585978 PMCID: PMC10996630 DOI: 10.1101/2024.03.29.586739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Immediate-early genes (IEGs) are a class of activity-regulated genes (ARGs) that are transiently and rapidly activated in the absence of de novo protein synthesis in response to neuronal activity. We explored the role of IEGs in genetic networks to pinpoint potential drug targets for Alzheimer's disease (AD). Using a combination of network analysis and genome-wide association study (GWAS) summary statistics we show that (1) IEGs exert greater topological influence across different human and mouse gene networks compared to other ARGs, (2) ARGs are sparsely involved in diseases and significantly more mutational constrained compared to non-ARGs, (3) Many AD-linked variants are in ARGs gene regions, mainly in MARK4 near FOSB, with an AD risk eQTL that increases MARK4 expression in cortical areas, (4) MARK4 holds an influential place in a dense AD multi-omic network and a high AD druggability score. Our work on IEGs' influential network role is a valuable contribution to guiding interventions for diseases marked by dysregulation of their downstream targets and highlights MARK4 as a promising underexplored AD-target.
Collapse
Affiliation(s)
| | - Eleni M Loizidou
- biobank.cy, Center of Excellence in Biobanking and Biomedical Research, University of Cyprus
| | - George M Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics
| |
Collapse
|
9
|
Gaynor-Gillett SC, Cheng L, Shi M, Liu J, Wang G, Spector M, Flaherty M, Wall M, Hwang A, Gu M, Chen Z, Chen Y, Consortium P, Moran JR, Zhang J, Lee D, Gerstein M, Geschwind D, White KP. Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.585066. [PMID: 38562832 PMCID: PMC10983874 DOI: 10.1101/2024.03.14.585066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Genome-wide association studies (GWAS) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. We performed capture STARR-sequencing of over 78,000 candidate regions to identify active enhancers in primary human neural progenitor cells (phNPCs). We selected candidate regions by integrating data from NPCs, prefrontal cortex, developmental timepoints, and GWAS. Over 8,000 regions demonstrated enhancer activity in the phNPCs, and we linked these regions to over 2,200 predicted target genes. These genes are involved in neuronal and psychiatric disease-associated pathways, including dopaminergic synapse, axon guidance, and schizophrenia. We functionally validated a subset of these enhancers using mutation STARR-sequencing and CRISPR deletions, demonstrating the effects of genetic variation on enhancer activity and enhancer deletion on gene expression. Overall, we identified thousands of highly active enhancers and functionally validated a subset of these enhancers, improving our understanding of regulatory networks underlying brain function and disease.
Collapse
Affiliation(s)
- Sophia C. Gaynor-Gillett
- Tempus Labs, Inc.; Chicago, IL, 60654, USA
- Department of Biology, Cornell College; Mount Vernon, IA, 52314, USA
| | | | - Manman Shi
- Tempus Labs, Inc.; Chicago, IL, 60654, USA
| | - Jason Liu
- Computational Biology and Bioinformatics Program, Yale University; New Haven, CT, 06511, USA
| | - Gaoyuan Wang
- Computational Biology and Bioinformatics Program, Yale University; New Haven, CT, 06511, USA
| | | | | | | | - Ahyeon Hwang
- Department of Computer Science, University of California Irvine; Irvine, CA, 92697, USA
| | - Mengting Gu
- Computational Biology and Bioinformatics Program, Yale University; New Haven, CT, 06511, USA
| | - Zhanlin Chen
- Computational Biology and Bioinformatics Program, Yale University; New Haven, CT, 06511, USA
| | - Yuhang Chen
- Computational Biology and Bioinformatics Program, Yale University; New Haven, CT, 06511, USA
| | | | | | - Jing Zhang
- Department of Computer Science, University of California Irvine; Irvine, CA, 92697, USA
| | - Donghoon Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University; New Haven, CT, 06511, USA
- Department of Statistics and Data Science, Yale University; New Haven, CT, 06511, USA
- Department of Molecular Biophysics and Biochemistry, Yale University; New Haven, CT, 06511, USA
- Department of Computer Science, Yale University; New Haven, CT, 06511, USA
| | - Daniel Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry and Semel Institute, David Geffen School of Medicine, University of California Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles; Los Angeles, CA, 90095, USA
| | - Kevin P. White
- Yong Loo Lin School of Medicine, National University of Singapore; Singapore, 117597
| |
Collapse
|
10
|
Boltz T, Schwarz T, Bot M, Hou K, Caggiano C, Lapinska S, Duan C, Boks MP, Kahn RS, Zaitlen N, Pasaniuc B, Ophoff R. Cell-type deconvolution of bulk-blood RNA-seq reveals biological insights into neuropsychiatric disorders. Am J Hum Genet 2024; 111:323-337. [PMID: 38306997 PMCID: PMC10870131 DOI: 10.1016/j.ajhg.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 02/04/2024] Open
Abstract
Genome-wide association studies (GWASs) have uncovered susceptibility loci associated with psychiatric disorders such as bipolar disorder (BP) and schizophrenia (SCZ). However, most of these loci are in non-coding regions of the genome, and the causal mechanisms of the link between genetic variation and disease risk is unknown. Expression quantitative trait locus (eQTL) analysis of bulk tissue is a common approach used for deciphering underlying mechanisms, although this can obscure cell-type-specific signals and thus mask trait-relevant mechanisms. Although single-cell sequencing can be prohibitively expensive in large cohorts, computationally inferred cell-type proportions and cell-type gene expression estimates have the potential to overcome these problems and advance mechanistic studies. Using bulk RNA-seq from 1,730 samples derived from whole blood in a cohort ascertained from individuals with BP and SCZ, this study estimated cell-type proportions and their relation with disease status and medication. For each cell type, we found between 2,875 and 4,629 eGenes (genes with an associated eQTL), including 1,211 that are not found on the basis of bulk expression alone. We performed a colocalization test between cell-type eQTLs and various traits and identified hundreds of associations that occur between cell-type eQTLs and GWASs but that are not detected in bulk eQTLs. Finally, we investigated the effects of lithium use on the regulation of cell-type expression loci and found examples of genes that are differentially regulated according to lithium use. Our study suggests that applying computational methods to large bulk RNA-seq datasets of non-brain tissue can identify disease-relevant, cell-type-specific biology of psychiatric disorders and psychiatric medication.
Collapse
Affiliation(s)
- Toni Boltz
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| | - Tommer Schwarz
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Merel Bot
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kangcheng Hou
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Christa Caggiano
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Sandra Lapinska
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Chenda Duan
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Marco P Boks
- Department of Psychiatry, Brain Center, University Medical Center Utrecht, University Utrecht, Utrecht, the Netherlands
| | - Rene S Kahn
- Department of Psychiatry, Brain Center, University Medical Center Utrecht, University Utrecht, Utrecht, the Netherlands; Department of Psychiatry, Icahn School of Medicine, Mount Sinai, NY, USA
| | - Noah Zaitlen
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA; Department of Neurology, University of California Los Angeles, Los Angeles, Los Angeles, CA, USA
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA; Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Roel Ophoff
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA; Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry, Erasmus University Medical Center, Rotterdam, the Netherlands.
| |
Collapse
|
11
|
Han Y, Huang C, Pan Y, Gu X. Single Cell Sequencing Technology and Its Application in Alzheimer's Disease. J Alzheimers Dis 2024; 97:1033-1050. [PMID: 38217599 DOI: 10.3233/jad-230861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
Alzheimer's disease (AD) involves degeneration of cells in the brain. Due to insidious onset and slow progression, AD is often not diagnosed until it gets progressed to a more severe stage. The diagnosis and treatment of AD has been a challenge. In recent years, high-throughput sequencing technologies have exhibited advantages in exploring the pathogenesis of diseases. However, the types of cells of the central nervous system are complex and traditional bulk sequencing cannot reflect their heterogeneity. Single-cell sequencing technology enables study at the individual cell level and has an irreplaceable advantage in the study of complex diseases. In recent years, this field has expanded rapidly and several types of single-cell sequencing technologies have emerged, including transcriptomics, epigenomics, genomics and proteomics. This review article provides an overview of these single-cell sequencing technologies and their application in AD.
Collapse
Affiliation(s)
- Yuru Han
- Shanghai Key Laboratory of Molecular Imaging, Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, China
- School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Congying Huang
- Shanghai Key Laboratory of Molecular Imaging, Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, China
- School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yuhui Pan
- Center for Disease Control and Prevention of Harbin, Harbin, China
| | - Xuefeng Gu
- Shanghai Key Laboratory of Molecular Imaging, Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, China
- School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| |
Collapse
|
12
|
Chemparathy A, Guen YL, Zeng Y, Gorzynski J, Jensen T, Yang C, Kasireddy N, Talozzi L, Belloy ME, Stewart I, Gitler AD, Wagner AD, Mormino E, Henderson VW, Wyss-Coray T, Ashley E, Cruchaga C, Greicius MD. A 3'UTR Insertion Is a Candidate Causal Variant at the TMEM106B Locus Associated with Increased Risk for FTLD-TDP. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.06.23292312. [PMID: 37461476 PMCID: PMC10350161 DOI: 10.1101/2023.07.06.23292312] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Background and Objectives Single nucleotide variants near TMEM106B associate with risk of frontotemporal lobar dementia with TDP-43 inclusions (FTLD-TDP) and Alzheimer's disease (AD) in genome-wide association studies (GWAS), but the causal variant at this locus remains unclear. Here we asked whether a novel structural variant on TMEM106B is the causal variant. Methods An exploratory analysis identified structural variants on neurodegeneration-related genes. Subsequent analyses focused on an Alu element insertion on the 3'UTR of TMEM106B. This study included data from longitudinal aging and neurogenerative disease cohorts at Stanford University, case-control cohorts in the Alzheimer's Disease Sequencing Project (ADSP), and expression and proteomics data from Washington University in St. Louis (WUSTL). 432 individuals from two Stanford aging cohorts were whole-genome long-read and short-read sequenced. 16,906 samples from ADSP were short-read sequenced. Genotypes, transcriptomics, and proteomics data were available in 1,979 participants from an aging and dementia cohort at WUSTL. Selection criteria were specific to each cohort. In primary analyses, the linkage disequilibrium between the TMEM106B locus variants in the FTLD-TDP GWAS and the 3'UTR insertion was estimated. We then estimated linkage by ancestry in the ADSP and evaluated the effect of the TMEM106B lead variant on mRNA and protein levels. Results The primary analysis included 432 participants (52.5% females, age range 45-92 years old). We identified a 316 bp Alu insertion overlapping the TMEM106B 3'UTR tightly linked with top GWAS variants rs3173615(C) and rs1990622(A). In ADSP European-ancestry participants, this insertion is in equivalent linkage with rs1990622(A) (R2=0.962, D'=0.998) and rs3173615(C) (R2=0.960, D'=0.996). In African-ancestry participants, the insertion is in stronger linkage with rs1990622(A) (R2=0.992, D'=0.998) than with rs3173615(C) (R2=0.811, D'=0.994). In public datasets, rs1990622 was consistently associated with TMEM106B protein levels but not with mRNA expression. In the WUSTL dataset, rs1990622 is associated with TMEM106B protein levels in plasma and cerebrospinal fluid, but not with TMEM106B mRNA expression. Discussion We identified a novel Alu element insertion in the 3'UTR of TMEM106B in tight linkage with the lead FTLD-TDP risk variant. The lead variant is associated with TMEM106B protein levels, but not expression. The 3'UTR insertion is a lead candidate for the causal variant at this complex locus, pending confirmation with functional studies.
Collapse
Affiliation(s)
- Augustine Chemparathy
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
- Quantitative Sciences Unit, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Yi Zeng
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - John Gorzynski
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
- Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Tanner Jensen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Chengran Yang
- Neurogenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO
| | - Nandita Kasireddy
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Lia Talozzi
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Michael E. Belloy
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Ilaria Stewart
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Anthony D. Wagner
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - Elizabeth Mormino
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - Victor W. Henderson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| | - Euan Ashley
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
- Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Carlos Cruchaga
- Neurogenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO
| | - Michael D. Greicius
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
| |
Collapse
|
13
|
Chandrashekar PB, Alatkar S, Wang J, Hoffman GE, He C, Jin T, Khullar S, Bendl J, Fullard JF, Roussos P, Wang D. DeepGAMI: deep biologically guided auxiliary learning for multimodal integration and imputation to improve genotype-phenotype prediction. Genome Med 2023; 15:88. [PMID: 37904203 PMCID: PMC10617196 DOI: 10.1186/s13073-023-01248-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Genotypes are strongly associated with disease phenotypes, particularly in brain disorders. However, the molecular and cellular mechanisms behind this association remain elusive. With emerging multimodal data for these mechanisms, machine learning methods can be applied for phenotype prediction at different scales, but due to the black-box nature of machine learning, integrating these modalities and interpreting biological mechanisms can be challenging. Additionally, the partial availability of these multimodal data presents a challenge in developing these predictive models. METHOD To address these challenges, we developed DeepGAMI, an interpretable neural network model to improve genotype-phenotype prediction from multimodal data. DeepGAMI leverages functional genomic information, such as eQTLs and gene regulation, to guide neural network connections. Additionally, it includes an auxiliary learning layer for cross-modal imputation allowing the imputation of latent features of missing modalities and thus predicting phenotypes from a single modality. Finally, DeepGAMI uses integrated gradient to prioritize multimodal features for various phenotypes. RESULTS We applied DeepGAMI to several multimodal datasets including genotype and bulk and cell-type gene expression data in brain diseases, and gene expression and electrophysiology data of mouse neuronal cells. Using cross-validation and independent validation, DeepGAMI outperformed existing methods for classifying disease types, and cellular and clinical phenotypes, even using single modalities (e.g., AUC score of 0.79 for Schizophrenia and 0.73 for cognitive impairment in Alzheimer's disease). CONCLUSION We demonstrated that DeepGAMI improves phenotype prediction and prioritizes phenotypic features and networks in multiple multimodal datasets in complex brains and brain diseases. Also, it prioritized disease-associated variants, genes, and regulatory networks linked to different phenotypes, providing novel insights into the interpretation of gene regulatory mechanisms. DeepGAMI is open-source and available for general use.
Collapse
Affiliation(s)
- Pramod Bharadwaj Chandrashekar
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53076, USA
| | - Sayali Alatkar
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, 53076, USA
| | - Jiebiao Wang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Department of Psychiatry and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chenfeng He
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53076, USA
| | - Ting Jin
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53076, USA
| | - Saniya Khullar
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53076, USA
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Department of Psychiatry and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Department of Psychiatry and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Department of Psychiatry and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research, Education and Clinical Centers, James J. Peters VA Medical Center, Bronx, NY, 10468, USA
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, 10962, USA
| | - Daifeng Wang
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53076, USA.
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, 53076, USA.
| |
Collapse
|
14
|
Wang Q, Antone J, Alsop E, Reiman R, Funk C, Bendl J, Dudley JT, Liang WS, Karr TL, Roussos P, Bennett DA, De Jager PL, Serrano GE, Beach TG, Keuren-Jensen KV, Mastroeni D, Reiman EM, Readhead BP. A public resource of single cell transcriptomes and multiscale networks from persons with and without Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563319. [PMID: 37961404 PMCID: PMC10634692 DOI: 10.1101/2023.10.20.563319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The emergence of technologies that can support high-throughput profiling of single cell transcriptomes offers to revolutionize the study of brain tissue from persons with and without Alzheimer's disease (AD). Integration of these data with additional complementary multiomics data such as genetics, proteomics and clinical data provides powerful opportunities to link observed cell subpopulations and molecular network features within a broader disease-relevant context. We report here single nucleus RNA sequencing (snRNA-seq) profiles generated from superior frontal gyrus cortical tissue samples from 101 exceptionally well characterized, aged subjects from the Banner Brain and Body Donation Program in combination with whole genome sequences. We report findings that link common AD risk variants with CR1 expression in oligodendrocytes as well as alterations in peripheral hematological lab parameters, with these observations replicated in an independent, prospective cohort study of ageing and dementia. We also observed an AD-associated CD83(+) microglial subtype with unique molecular networks that encompass many known regulators of AD-relevant microglial biology, and which are associated with immunoglobulin IgG4 production in the transverse colon. These findings illustrate the power of multi-tissue molecular profiling to contextualize snRNA-seq brain transcriptomics and reveal novel disease biology. The transcriptomic, genetic, phenotypic, and network data resources described within this study are available for access and utilization by the scientific community.
Collapse
|
15
|
Gu XJ, Su WM, Dou M, Jiang Z, Duan QQ, Yin KF, Cao B, Wang Y, Li GB, Chen YP. Expanding causal genes for Parkinson's disease via multi-omics analysis. NPJ Parkinsons Dis 2023; 9:146. [PMID: 37865667 PMCID: PMC10590374 DOI: 10.1038/s41531-023-00591-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/12/2023] [Indexed: 10/23/2023] Open
Abstract
Genome‑wide association studies (GWASs) have revealed numerous loci associated with Parkinson's disease (PD). However, some potential causal/risk genes were still not revealed and no etiological therapies are available. To find potential causal genes and explore genetically supported drug targets for PD is urgent. By integrating the expression quantitative trait loci (eQTL) and protein quantitative trait loci (pQTL) datasets from multiple tissues (blood, cerebrospinal fluid (CSF) and brain) and PD GWAS summary statistics, a pipeline combing Mendelian randomization (MR), Steiger filtering analysis, Bayesian colocalization, fine mapping, Protein-protein network and enrichment analysis were applied to identify potential causal genes for PD. As a result, GPNMB displayed a robust causal role for PD at the protein level in the blood, CSF and brain, and transcriptional level in the brain, while the protective role of CD38 (in brain pQTL and eQTL) was also identified. We also found inconsistent roles of DGKQ on PD between protein and mRNA levels. Another 9 proteins (CTSB, ARSA, SEC23IP, CD84, ENTPD1, FCGR2B, BAG3, SNCA, FCGR2A) were associated with the risk for PD based on only a single pQTL after multiple corrections. We also identified some proteins' interactions with known PD causative genes and therapeutic targets. In conclusion, this study suggested GPNMB, CD38, and DGKQ may act in the pathogenesis of PD, but whether the other proteins involved in PD needs more evidence. These findings would help to uncover the genes underlying PD and prioritize targets for future therapeutic interventions.
Collapse
Affiliation(s)
- Xiao-Jing Gu
- Mental Health Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wei-Ming Su
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Meng Dou
- Chengdu Institute of Computer Application, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Zheng Jiang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qing-Qing Duan
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Kang-Fu Yin
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bei Cao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yi Wang
- Department of Pathophysiology, West China College of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, China
| | - Yong-Ping Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| |
Collapse
|
16
|
Johansen N, Somasundaram S, Travaglini KJ, Yanny AM, Shumyatcher M, Casper T, Cobbs C, Dee N, Ellenbogen R, Ferreira M, Goldy J, Guzman J, Gwinn R, Hirschstein D, Jorstad NL, Keene CD, Ko A, Levi BP, Ojemann JG, Pham T, Shapovalova N, Silbergeld D, Sulc J, Torkelson A, Tung H, Smith K, Lein ES, Bakken TE, Hodge RD, Miller JA. Interindividual variation in human cortical cell type abundance and expression. Science 2023; 382:eadf2359. [PMID: 37824649 DOI: 10.1126/science.adf2359] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 07/30/2023] [Indexed: 10/14/2023]
Abstract
Single-cell transcriptomic studies have identified a conserved set of neocortical cell types from small postmortem cohorts. We extended these efforts by assessing cell type variation across 75 adult individuals undergoing epilepsy and tumor surgeries. Nearly all nuclei map to one of 125 robust cell types identified in the middle temporal gyrus. However, we found interindividual variance in abundances and gene expression signatures, particularly in deep-layer glutamatergic neurons and microglia. A minority of donor variance is explainable by age, sex, ancestry, disease state, and cell state. Genomic variation was associated with expression of 150 to 250 genes for most cell types. This characterization of cellular variation provides a baseline for cell typing in health and disease.
Collapse
Affiliation(s)
| | | | | | | | | | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Charles Cobbs
- Swedish Neuroscience Institute, Seattle,WA 98122, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Richard Ellenbogen
- Department of Neurological Surgery, University of Washington, Seattle, WA 98104, USA
| | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA 98104, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Junitta Guzman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ryder Gwinn
- Swedish Neuroscience Institute, Seattle,WA 98122, USA
| | | | | | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98104, USA
| | - Andrew Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA 98104, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA 98104, USA
| | - Thanh Pham
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Daniel Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA 98104, USA
| | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Amy Torkelson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kimberly Smith
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | |
Collapse
|
17
|
Girdhar K, Bendl J, Baumgartner A, Therrien K, Venkatesh S, Mathur D, Dong P, Rahman S, Kleopoulos SP, Misir R, Reach SM, Auluck PK, Marenco S, Lewis DA, Haroutunian V, Funk C, Voloudakis G, Hoffman GE, Fullard JF, Roussos P. The neuronal chromatin landscape in adult schizophrenia brains is linked to early fetal development. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.02.23296067. [PMID: 37873320 PMCID: PMC10593028 DOI: 10.1101/2023.10.02.23296067] [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
Non-coding variants increase risk of neuropsychiatric disease. However, our understanding of the cell-type specific role of the non-coding genome in disease is incomplete. We performed population scale (N=1,393) chromatin accessibility profiling of neurons and non-neurons from two neocortical brain regions: the anterior cingulate cortex and dorsolateral prefrontal cortex. Across both regions, we observed notable differences in neuronal chromatin accessibility between schizophrenia cases and controls. A per-sample disease pseudotime was positively associated with genetic liability for schizophrenia. Organizing chromatin into cis- and trans-regulatory domains, identified a prominent neuronal trans-regulatory domain (TRD1) active in immature glutamatergic neurons during fetal development. Polygenic risk score analysis using genetic variants within chromatin accessibility of TRD1 successfully predicted susceptibility to schizophrenia in the Million Veteran Program cohort. Overall, we present the most extensive resource to date of chromatin accessibility in the human cortex, yielding insights into the cell-type specific etiology of schizophrenia.
Collapse
Affiliation(s)
- Kiran Girdhar
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Karen Therrien
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, New York, 10468, USA
| | - Sanan Venkatesh
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, New York, 10468, USA
| | - Deepika Mathur
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, New York, 10468, USA
| | - Pengfei Dong
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Samir Rahman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Steven P Kleopoulos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruth Misir
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sarah M Reach
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pavan K Auluck
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, MD, USA
| | - Stefano Marenco
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, MD, USA
| | - David A Lewis
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vahram Haroutunian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, New York, 10468, USA
| | - Cory Funk
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Georgios Voloudakis
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, New York, 10468, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, New York, 10468, USA
| |
Collapse
|
18
|
Wingo AP, Liu Y, Gerasimov ES, Vattathil SM, Liu J, Cutler DJ, Epstein MP, Blokland GAM, Thambisetty M, Troncoso JC, Duong DM, Bennett DA, Levey AI, Seyfried NT, Wingo TS. Sex differences in brain protein expression and disease. Nat Med 2023; 29:2224-2232. [PMID: 37653343 PMCID: PMC10504083 DOI: 10.1038/s41591-023-02509-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
Most complex human traits differ by sex, but we have limited insight into the underlying mechanisms. Here, we investigated the influence of biological sex on protein expression and its genetic regulation in 1,277 human brain proteomes. We found that 13.2% (1,354) of brain proteins had sex-differentiated abundance and 1.5% (150) of proteins had sex-biased protein quantitative trait loci (sb-pQTLs). Among genes with sex-biased expression, we found 67% concordance between sex-differentiated protein and transcript levels; however, sex effects on the genetic regulation of expression were more evident at the protein level. Considering 24 psychiatric, neurologic and brain morphologic traits, we found that an average of 25% of their putatively causal genes had sex-differentiated protein abundance and 12 putatively causal proteins had sb-pQTLs. Furthermore, integrating sex-specific pQTLs with sex-stratified genome-wide association studies of six psychiatric and neurologic conditions, we uncovered another 23 proteins contributing to these traits in one sex but not the other. Together, these findings begin to provide insights into mechanisms underlying sex differences in brain protein expression and disease.
Collapse
Affiliation(s)
- Aliza P Wingo
- Veterans Affairs Atlanta Health Care System, Decatur, GA, USA.
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA.
| | - Yue Liu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Selina M Vattathil
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jiaqi Liu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Gabriëlla A M Blokland
- Department of Psychiatry and Neuropsychology, Maastricht University School for Mental Health and Neuroscience, Maastricht, the Netherlands
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
- Goizueta Alzheimer's Disease Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas S Wingo
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
- Goizueta Alzheimer's Disease Center, Emory University School of Medicine, Atlanta, GA, USA.
| |
Collapse
|
19
|
Walker KA, Chen J, Shi L, Yang Y, Fornage M, Zhou L, Schlosser P, Surapaneni A, Grams ME, Duggan MR, Peng Z, Gomez GT, Tin A, Hoogeveen RC, Sullivan KJ, Ganz P, Lindbohm JV, Kivimaki M, Nevado-Holgado AJ, Buckley N, Gottesman RF, Mosley TH, Boerwinkle E, Ballantyne CM, Coresh J. Proteomics analysis of plasma from middle-aged adults identifies protein markers of dementia risk in later life. Sci Transl Med 2023; 15:eadf5681. [PMID: 37467317 PMCID: PMC10665113 DOI: 10.1126/scitranslmed.adf5681] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/28/2023] [Indexed: 07/21/2023]
Abstract
A diverse set of biological processes have been implicated in the pathophysiology of Alzheimer's disease (AD) and related dementias. However, there is limited understanding of the peripheral biological mechanisms relevant in the earliest phases of the disease. Here, we used a large-scale proteomics platform to examine the association of 4877 plasma proteins with 25-year dementia risk in 10,981 middle-aged adults. We found 32 dementia-associated plasma proteins that were involved in proteostasis, immunity, synaptic function, and extracellular matrix organization. We then replicated the association between 15 of these proteins and clinically relevant neurocognitive outcomes in two independent cohorts. We demonstrated that 12 of these 32 dementia-associated proteins were associated with cerebrospinal fluid (CSF) biomarkers of AD, neurodegeneration, or neuroinflammation. We found that eight of these candidate protein markers were abnormally expressed in human postmortem brain tissue from patients with AD, although some of the proteins that were most strongly associated with dementia risk, such as GDF15, were not detected in these brain tissue samples. Using network analyses, we found a protein signature for dementia risk that was characterized by dysregulation of specific immune and proteostasis/autophagy pathways in adults in midlife ~20 years before dementia onset, as well as abnormal coagulation and complement signaling ~10 years before dementia onset. Bidirectional two-sample Mendelian randomization genetically validated nine of our candidate proteins as markers of AD in midlife and inferred causality of SERPINA3 in AD pathogenesis. Last, we prioritized a set of candidate markers for AD and dementia risk prediction in midlife.
Collapse
Affiliation(s)
- Keenan A. Walker
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD 21224, USA
| | - Jingsha Chen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21210, USA
| | - Liu Shi
- Novo Nordisk Research Centre Oxford (NNRCO), Oxford OX3 7FZ, UK
| | - Yunju Yang
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School and Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School and Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Linda Zhou
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21210, USA
| | - Pascal Schlosser
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21210, USA
| | - Aditya Surapaneni
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21210, USA
| | - Morgan E. Grams
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21210, USA
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21210, USA
| | - Michael R. Duggan
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD 21224, USA
| | - Zhongsheng Peng
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD 21224, USA
| | - Gabriela T. Gomez
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21210, USA
| | - Adrienne Tin
- MIND Center and Division of Nephrology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Ron C. Hoogeveen
- Section of Cardiovascular Research, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin J. Sullivan
- Department of Medicine, Division of Geriatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Peter Ganz
- Department of Medicine, University of California-San Francisco, San Francisco, CA 94115, USA
| | - Joni V. Lindbohm
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Mika Kivimaki
- Department of Mental Health of Older People, Faculty of Brain Sciences, University College London, London WC1E 6BT, UK
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki 00100, Finland
| | | | - Noel Buckley
- Department of Psychiatry, University of Oxford, Oxford OX1 2JD, UK
| | - Rebecca F. Gottesman
- National Institute of Neurological Disorders and Stroke, Intramural Research Program, Bethesda, MD 20892, USA
| | - Thomas H. Mosley
- Department of Medicine, Division of Geriatrics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christie M. Ballantyne
- Section of Cardiovascular Research, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21210, USA
| |
Collapse
|
20
|
Ursini G, Di Carlo P, Mukherjee S, Chen Q, Han S, Kim J, Deyssenroth M, Marsit CJ, Chen J, Hao K, Punzi G, Weinberger DR. Prioritization of potential causative genes for schizophrenia in placenta. Nat Commun 2023; 14:2613. [PMID: 37188697 PMCID: PMC10185564 DOI: 10.1038/s41467-023-38140-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Our earlier work has shown that genomic risk for schizophrenia converges with early life complications in affecting risk for the disorder and sex-biased neurodevelopmental trajectories. Here, we identify specific genes and potential mechanisms that, in placenta, may mediate such outcomes. We performed TWAS in healthy term placentae (N = 147) to derive candidate placental causal genes that we confirmed with SMR; to search for placenta and schizophrenia-specific associations, we performed an analogous analysis in fetal brain (N = 166) and additional placenta TWAS for other disorders/traits. The analyses in the whole sample and stratifying by sex ultimately highlight 139 placenta and schizophrenia-specific risk genes, many being sex-biased; the candidate molecular mechanisms converge on the nutrient-sensing capabilities of placenta and trophoblast invasiveness. These genes also implicate the Coronavirus-pathogenesis pathway and showed increased expression in placentae from a small sample of SARS-CoV-2-positive pregnancies. Investigating placental risk genes for schizophrenia and candidate mechanisms may lead to opportunities for prevention that would not be suggested by study of the brain alone.
Collapse
Affiliation(s)
- Gianluca Ursini
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Pasquale Di Carlo
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
- Group of Psychiatric Neuroscience, Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Sreya Mukherjee
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Qiang Chen
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Shizhong Han
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Jiyoung Kim
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Maya Deyssenroth
- Departments of Environmental Medicine and Public Health, Icahn School of Public Health at Mount Sinai, New York, NY, USA
| | - Carmen J Marsit
- Departments of Environmental Health and Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jia Chen
- Departments of Environmental Medicine and Public Health, Icahn School of Public Health at Mount Sinai, New York, NY, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Giovanna Punzi
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| |
Collapse
|
21
|
Zhang P, Hou Y, Tu W, Campbell N, Pieper AA, Leverenz JB, Gao S, Cummings J, Cheng F. Population-based discovery and Mendelian randomization analysis identify telmisartan as a candidate medicine for Alzheimer's disease in African Americans. Alzheimers Dement 2023; 19:1876-1887. [PMID: 36331056 PMCID: PMC10156891 DOI: 10.1002/alz.12819] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/11/2022] [Accepted: 09/02/2022] [Indexed: 11/06/2022]
Abstract
INTRODUCTION African Americans (AAs) and European Americans (EAs) differ in Alzheimer's disease (AD) prevalence, risk factors, and symptomatic presentation and AAs are less likely to enroll in AD clinical trials. METHODS We conducted race-conscious pharmacoepidemiologic studies of 5.62 million older individuals (age ≥60) to investigate the association of telmisartan exposure and AD outcome using Cox analysis, Kaplan-Meier analysis, and log-rank test. We performed Mendelian randomization (MR) analysis of large ethnically diverse genetic data to test likely causal relationships between telmisartan's target and AD. RESULTS We identified that moderate/high telmisartan exposure was significantly associated with a reduced incidence of AD in the AAs compared to low/no telmisartan exposure (hazard ratio [HR] = 0.77, 95% CI: 0.65-0.91, p-value = 0.0022), but not in the non-Hispanic EAs (HR = 0.97, 95% CI: 0.89-1.05, p-value = 0.4110). Sensitivity and sex-/age-stratified patient subgroup analyses identified that telmisartan's medication possession ratio (MPR) and average hypertension daily dosage were significantly associated with a stronger reduction in the incidence of both AD and dementia in AAs. Using MR analysis from large genome-wide association studies (GWAS) (over 2 million individuals) across AD, hypertension, and diabetes, we further identified AA-specific beneficial effects of telmisartan for AD. DISCUSSION Randomized controlled trials with ethnically diverse patient cohorts are warranted to establish causality and therapeutic outcomes of telmisartan and AD. HIGHLIGHTS Telmisartan is associated with lower risk of Alzheimer's disease (AD) in African Americans (AAs). Telmisartan is the only angiotensin II receptor blockers having PPAR-γ agonistic properties with beneficial anti-diabetic and renal function effects, which mitigate AD risk in AAs. Mendelian randomization (MR) analysis demonstrates the specificity of telmisartan's protective mechanism to AAs.
Collapse
Affiliation(s)
- Pengyue Zhang
- Department of Biostatistics and Health Data Science, Indiana University, Indianapolis, Indiana, USA
| | - Yuan Hou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Wanzhu Tu
- Department of Biostatistics and Health Data Science, Indiana University, Indianapolis, Indiana, USA
| | - Noll Campbell
- Department of Pharmacy Practice, Purdue University, West Lafayette, Indiana, USA
| | - Andrew A. Pieper
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
- Department of Psychiatry, Case Western Reserve University, Cleveland, Ohio, USA
- Geriatric Psychiatry, GRECC, Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, USA
- Institute for Transformative Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Neuroscience, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA
| | - James B. Leverenz
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sujuan Gao
- Department of Biostatistics and Health Data Science, Indiana University, Indianapolis, Indiana, USA
| | - Jeffrey Cummings
- Chambers-Grundy Center for Transformative Neuroscience, Department of Brain Health, School of Integrated Health Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| |
Collapse
|
22
|
Balusu S, Praschberger R, Lauwers E, De Strooper B, Verstreken P. Neurodegeneration cell per cell. Neuron 2023; 111:767-786. [PMID: 36787752 DOI: 10.1016/j.neuron.2023.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/12/2022] [Accepted: 01/18/2023] [Indexed: 02/16/2023]
Abstract
The clinical definition of neurodegenerative diseases is based on symptoms that reflect terminal damage of specific brain regions. This is misleading as it tells little about the initial disease processes. Circuitry failures that underlie the clinical symptomatology are themselves preceded by clinically mostly silent, slowly progressing multicellular processes that trigger or are triggered by the accumulation of abnormally folded proteins such as Aβ, Tau, TDP-43, and α-synuclein, among others. Methodological advances in single-cell omics, combined with complex genetics and novel ways to model complex cellular interactions using induced pluripotent stem (iPS) cells, make it possible to analyze the early cellular phase of neurodegenerative disorders. This will revolutionize the way we study those diseases and will translate into novel diagnostics and cell-specific therapeutic targets, stopping these disorders in their early track before they cause difficult-to-reverse damage to the brain.
Collapse
Affiliation(s)
- Sriram Balusu
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Roman Praschberger
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Elsa Lauwers
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Bart De Strooper
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium; UK Dementia Research Institute, London, UK.
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium.
| |
Collapse
|
23
|
Bressan E, Reed X, Bansal V, Hutchins E, Cobb MM, Webb MG, Alsop E, Grenn FP, Illarionova A, Savytska N, Violich I, Broeer S, Fernandes N, Sivakumar R, Beilina A, Billingsley KJ, Berghausen J, Pantazis CB, Pitz V, Patel D, Daida K, Meechoovet B, Reiman R, Courtright-Lim A, Logemann A, Antone J, Barch M, Kitchen R, Li Y, Dalgard CL, Rizzu P, Hernandez DG, Hjelm BE, Nalls M, Gibbs JR, Finkbeiner S, Cookson MR, Van Keuren-Jensen K, Craig DW, Singleton AB, Heutink P, Blauwendraat C. The Foundational Data Initiative for Parkinson Disease: Enabling efficient translation from genetic maps to mechanism. CELL GENOMICS 2023; 3:100261. [PMID: 36950378 PMCID: PMC10025424 DOI: 10.1016/j.xgen.2023.100261] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/22/2022] [Accepted: 01/12/2023] [Indexed: 02/08/2023]
Abstract
The Foundational Data Initiative for Parkinson Disease (FOUNDIN-PD) is an international collaboration producing fundamental resources for Parkinson disease (PD). FOUNDIN-PD generated a multi-layered molecular dataset in a cohort of induced pluripotent stem cell (iPSC) lines differentiated to dopaminergic (DA) neurons, a major affected cell type in PD. The lines were derived from the Parkinson's Progression Markers Initiative study, which included participants with PD carrying monogenic PD variants, variants with intermediate effects, and variants identified by genome-wide association studies and unaffected individuals. We generated genetic, epigenetic, regulatory, transcriptomic, and longitudinal cellular imaging data from iPSC-derived DA neurons to understand molecular relationships between disease-associated genetic variation and proximate molecular events. These data reveal that iPSC-derived DA neurons provide a valuable cellular context and foundational atlas for modeling PD genetic risk. We have integrated these data into a FOUNDIN-PD data browser as a resource for understanding the molecular pathogenesis of PD.
Collapse
Affiliation(s)
| | - Xylena Reed
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
| | - Vikas Bansal
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Elizabeth Hutchins
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Melanie M. Cobb
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Michelle G. Webb
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
| | - Eric Alsop
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Francis P. Grenn
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Natalia Savytska
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ivo Violich
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
| | - Stefanie Broeer
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Noémia Fernandes
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ramiyapriya Sivakumar
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
| | - Alexandra Beilina
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Kimberley J. Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Joos Berghausen
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Caroline B. Pantazis
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
| | - Vanessa Pitz
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Dhairya Patel
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Kensuke Daida
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Bessie Meechoovet
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Rebecca Reiman
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Amanda Courtright-Lim
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Amber Logemann
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jerry Antone
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Mariya Barch
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Robert Kitchen
- Massachusetts General Hospital, Cardiovascular Research Center, Charlestown, MA, USA
| | - Yan Li
- Protein/Peptide Sequencing Facility, National Institute of Neurological, Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - The American Genome Center
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
- Division of Neurogenomics, The Translational Genomics Research Institute, Phoenix, AZ, USA
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
- Massachusetts General Hospital, Cardiovascular Research Center, Charlestown, MA, USA
- Protein/Peptide Sequencing Facility, National Institute of Neurological, Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Data Tecnica International, Washington, DC, USA
- Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Dena G. Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Brooke E. Hjelm
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, USA
| | - Mike Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
- Data Tecnica International, Washington, DC, USA
| | - J. Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA, USA
| | - Mark R. Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - David W. Craig
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA, 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 (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Peter Heutink
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- 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
| |
Collapse
|
24
|
Dai Q, Zhou G, Zhao H, Võsa U, Franke L, Battle A, Teumer A, Lehtimäki T, Raitakari OT, Esko T, Epstein MP, Yang J. OTTERS: a powerful TWAS framework leveraging summary-level reference data. Nat Commun 2023; 14:1271. [PMID: 36882394 PMCID: PMC9992663 DOI: 10.1038/s41467-023-36862-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] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Most existing TWAS tools require individual-level eQTL reference data and thus are not applicable to summary-level reference eQTL datasets. The development of TWAS methods that can harness summary-level reference data is valuable to enable TWAS in broader settings and enhance power due to increased reference sample size. Thus, we develop a TWAS framework called OTTERS (Omnibus Transcriptome Test using Expression Reference Summary data) that adapts multiple polygenic risk score (PRS) methods to estimate eQTL weights from summary-level eQTL reference data and conducts an omnibus TWAS. We show that OTTERS is a practical and powerful TWAS tool by both simulations and application studies.
Collapse
Affiliation(s)
- Qile Dai
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA, 30322, USA
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Geyu Zhou
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA
| | - Hongyu Zhao
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 50090, Tartu, Estonia
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands
- Oncode Institute, 3521 AL, Utrecht, The Netherlands
| | - Alexis Battle
- Department of Computer Science, and Departments of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, 17489, Greifswald, Germany
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Centre for Cardiovascular Disease Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, 20520, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20521, Turku, Finland
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 50090, Tartu, Estonia
| | - Michael P Epstein
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Jingjing Yang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| |
Collapse
|
25
|
Leonard HL, Murtadha R, Martinez-Carrasco A, Jama A, Müller-Nedebock AC, Gil-Martinez AL, Illarionova A, Moore A, Bustos BI, Jadhav B, Huxford B, Storm C, Towns C, Vitale D, Chetty D, Yu E, Grenn FP, Salazar G, Rateau G, Iwaki H, Elsayed I, Foote IF, Jansen van Rensburg Z, Kim JJ, Yuan J, Lake J, Brolin K, Senkevich K, Wu L, Tan MMX, Periñán MT, Makarious MB, Ta M, Pillay NS, Betancor OL, Reyes-Pérez PR, Alvarez Jerez P, Saini P, Al-Ouran R, Sivakumar R, Real R, Reynolds RH, Hu R, Abrahams S, Rao SC, Antar T, Leal TP, Iankova V, Scotton WJ, Song Y, Singleton A, Nalls MA, Dey S, Bandres-Ciga S, Blauwendraat C, Noyce AJ. The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson's disease data. NPJ Parkinsons Dis 2023; 9:33. [PMID: 36871034 PMCID: PMC9984758 DOI: 10.1038/s41531-023-00472-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Open science and collaboration are necessary to facilitate the advancement of Parkinson's disease (PD) research. Hackathons are collaborative events that bring together people with different skill sets and backgrounds to generate resources and creative solutions to problems. These events can be used as training and networking opportunities, thus we coordinated a virtual 3-day hackathon event, during which 49 early-career scientists from 12 countries built tools and pipelines with a focus on PD. Resources were created with the goal of helping scientists accelerate their own research by having access to the necessary code and tools. Each team was allocated one of nine different projects, each with a different goal. These included developing post-genome-wide association studies (GWAS) analysis pipelines, downstream analysis of genetic variation pipelines, and various visualization tools. Hackathons are a valuable approach to inspire creative thinking, supplement training in data science, and foster collaborative scientific relationships, which are foundational practices for early-career researchers. The resources generated can be used to accelerate research on the genetics of PD.
Collapse
Affiliation(s)
- Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA. .,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. .,Data Tecnica International LLC, Washington, DC, USA. .,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
| | - Ruqaya Murtadha
- 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
| | - Alejandro Martinez-Carrasco
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Alina Jama
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Amica Corda Müller-Nedebock
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
| | - Ana-Luisa Gil-Martinez
- Department of Neurodegenerative Disease, University College London, London, UK.,Great Ormond Street Institute of Child Health, Genetics and Genomic Medicine, University College London, London, UK
| | | | - Anni Moore
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Bernabe I Bustos
- The Ken & Ruth Davee Department of Neurology and Simpson Querrey Center of Neurogenetics, Feinberg Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Bharati Jadhav
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, New York, NY, 10029, USA
| | - Brook Huxford
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Catherine Storm
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Clodagh Towns
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Dan Vitale
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.,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.,Data Tecnica International LLC, Washington, DC, USA
| | - Devina Chetty
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Eric Yu
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada
| | - Francis P Grenn
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Gabriela Salazar
- INNCOSYS, Col. Morelos Second Section, 50120, Toluca de Lerdo, México
| | - Geoffrey Rateau
- Institut du Cerveau - Institute of Brain and Spine (ICM), Hôpital Pitié, 47 Bd de l'Hôpital, 75013, Paris, France
| | - Hirotaka Iwaki
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.,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.,Data Tecnica International LLC, Washington, DC, USA
| | - Inas Elsayed
- Faculty of pharmacy, University of Gezira, Wad Medani, P.O. Box 20, Sudan.,International Parkinson Disease Genomics Consortium (IPDGC)-Africa, University of Gezira, Wad Medani, P.O. Box 20, Sudan
| | - Isabelle Francesca Foote
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, New York, NY, 10029, USA.,Unit for Psychological Medicine, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Zuné Jansen van Rensburg
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Jonggeol Jeff Kim
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.,Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, New York, NY, 10029, USA
| | - Jie Yuan
- Center for Advanced Parkinson Research, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Julie Lake
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Kajsa Brolin
- Translational Neurogenetics Unit, Wallenberg Neuroscience Center, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Konstantin Senkevich
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Lesley Wu
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Manuela M X Tan
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK.,Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - María Teresa Periñán
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,CIBERNED, Madrid, Spain
| | - 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, University College London, London, UK
| | - Michael Ta
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Nikita Simone Pillay
- South African National Bioinformatics Institute (SANBI), South African Medical Research Council Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
| | - Oswaldo Lorenzo Betancor
- Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA.,Department of Neurology, University of Washington School of Medicine, Seattle, WA, USA
| | - Paula R Reyes-Pérez
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de, México, Juriquilla, México
| | - Pilar Alvarez Jerez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.,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
| | - Prabhjyot Saini
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Rami Al-Ouran
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Raquel Real
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Regina H Reynolds
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa.,Department of Neurodegenerative Disease, University College London, London, UK
| | - Ruifneg Hu
- Center for Advanced Parkinson Research, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Shameemah Abrahams
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Shilpa C Rao
- Department of Genomic Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA.,Department of Molecular Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Tarek Antar
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Thiago Peixoto Leal
- Department of Genomic Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Vassilena Iankova
- Department of Neurology With Friedrich Baur Institut, University Hospital of Ludwig-Maximilians-Universität München, Munich, Germany
| | - William J Scotton
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
| | - Yeajin Song
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.,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
| | - Andrew Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.,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
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.,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.,Data Tecnica International LLC, Washington, DC, USA
| | - Sumit Dey
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, New York, NY, 10029, USA
| | - Sara Bandres-Ciga
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.,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
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.,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
| | - Alastair J Noyce
- Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount, Hess Center for Science and Medicine, New York, NY, 10029, USA
| | | |
Collapse
|
26
|
Hansson O, Kumar A, Janelidze S, Stomrud E, Insel PS, Blennow K, Zetterberg H, Fauman E, Hedman ÅK, Nagle MW, Whelan CD, Baird D, Mälarstig A, Mattsson‐Carlgren N. The genetic regulation of protein expression in cerebrospinal fluid. EMBO Mol Med 2023; 15:e16359. [PMID: 36504281 PMCID: PMC9832827 DOI: 10.15252/emmm.202216359] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022] Open
Abstract
Studies of the genetic regulation of cerebrospinal fluid (CSF) proteins may reveal pathways for treatment of neurological diseases. 398 proteins in CSF were measured in 1,591 participants from the BioFINDER study. Protein quantitative trait loci (pQTL) were identified as associations between genetic variants and proteins, with 176 pQTLs for 145 CSF proteins (P < 1.25 × 10-10 , 117 cis-pQTLs and 59 trans-pQTLs). Ventricular volume (measured with brain magnetic resonance imaging) was a confounder for several pQTLs. pQTLs for CSF and plasma proteins were overall correlated, but CSF-specific pQTLs were also observed. Mendelian randomization analyses suggested causal roles for several proteins, for example, ApoE, CD33, and GRN in Alzheimer's disease, MMP-10 in preclinical Alzheimer's disease, SIGLEC9 in amyotrophic lateral sclerosis, and CD38, GPNMB, and ADAM15 in Parkinson's disease. CSF levels of GRN, MMP-10, and GPNMB were altered in Alzheimer's disease, preclinical Alzheimer's disease, and Parkinson's disease, respectively. These findings point to pathways to be explored for novel therapies. The novel finding that ventricular volume confounded pQTLs has implications for design of future studies of the genetic regulation of the CSF proteome.
Collapse
Affiliation(s)
- Oskar Hansson
- Clinical Memory Research Unit, Faculty of MedicineLund UniversityLundSweden
- Memory ClinicSkåne University Hospital, Lund UniversityLundSweden
| | - Atul Kumar
- Clinical Memory Research Unit, Faculty of MedicineLund UniversityLundSweden
| | - Shorena Janelidze
- Clinical Memory Research Unit, Faculty of MedicineLund UniversityLundSweden
| | - Erik Stomrud
- Clinical Memory Research Unit, Faculty of MedicineLund UniversityLundSweden
- Memory ClinicSkåne University Hospital, Lund UniversityLundSweden
| | - Philip S Insel
- Clinical Memory Research Unit, Faculty of MedicineLund UniversityLundSweden
- Department of Psychiatry and Behavioral SciencesUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Kaj Blennow
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska AcademyUniversity of GothenburgMölndalSweden
| | - Henrik Zetterberg
- Clinical Neurochemistry LaboratorySahlgrenska University HospitalMölndalSweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska AcademyUniversity of GothenburgMölndalSweden
- Department of Neurodegenerative DiseaseUCL Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLLondonUK
- Hong Kong Center for Neurodegenerative DiseasesHong KongChina
| | - Eric Fauman
- Internal Medicine Research UnitPfizer Worldwide Research, Development and MedicalCambridgeMAUSA
| | - Åsa K Hedman
- Pfizer Worldwide Research, Development and MedicalStockholmSweden
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Michael W Nagle
- Neurogenomics, Genetics‐Guided Dementia DiscoveryEisai, IncCambridgeMAUSA
| | | | - Denis Baird
- Department of Neurology, Skåne University HospitalLund UniversityLundSweden
| | - Anders Mälarstig
- Pfizer Worldwide Research, Development and MedicalStockholmSweden
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Niklas Mattsson‐Carlgren
- Clinical Memory Research Unit, Faculty of MedicineLund UniversityLundSweden
- Department of Neurology, Skåne University HospitalLund UniversityLundSweden
- Wallenberg Center for Molecular MedicineLund UniversityLundSweden
| |
Collapse
|
27
|
Gedik H, Peterson RE, Riley BP, Vladimirov VI, Bacanu SA. Integrative Post-Genome-Wide Association Study Analyses Relevant to Psychiatric Disorders: Imputing Transcriptome and Proteome Signals. Complex Psychiatry 2023; 9:130-144. [PMID: 37588130 PMCID: PMC10425719 DOI: 10.1159/000530223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 03/09/2023] [Indexed: 08/18/2023] Open
Abstract
Background The genome-wide association study (GWAS) is a common tool to identify genetic variants associated with complex traits, including psychiatric disorders (PDs). However, post-GWAS analyses are needed to extend the statistical inference to biologically relevant entities, e.g., genes, proteins, and pathways. To achieve this goal, researchers developed methods that incorporate biologically relevant intermediate molecular phenotypes, such as gene expression and protein abundance, which are posited to mediate the variant-trait association. Transcriptome-wide association study (TWAS) and proteome-wide association study (PWAS) are commonly used methods to test the association between these molecular mediators and the trait. Summary In this review, we discuss the most recent developments in TWAS and PWAS. These methods integrate existing "omic" information with the GWAS summary statistics for trait(s) of interest. Specifically, they impute transcript/protein data and test the association between imputed gene expression/protein level with phenotype of interest by using (i) GWAS summary statistics and (ii) reference transcriptomic/proteomic/genomic datasets. TWAS and PWAS are suitable as analysis tools for (i) primary association scan and (ii) fine-mapping to identify potentially causal genes for PDs. Key Messages As post-GWAS analyses, TWAS and PWAS have the potential to highlight causal genes for PDs. These prioritized genes could indicate targets for the development of novel drug therapies. For researchers attempting such analyses, we recommend Mendelian randomization tools that use GWAS statistics for both trait and reference datasets, e.g., summary Mendelian randomization (SMR). We base our recommendation on (i) being able to use the same tool for both TWAS and PWAS, (ii) not requiring the pre-computed weights (and thus easier to update for larger reference datasets), and (iii) most larger transcriptome reference datasets are publicly available and easy to transform into a compatible format for SMR analysis.
Collapse
Affiliation(s)
- Huseyin Gedik
- Integrative Life Sciences, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Roseann E. Peterson
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Brien P. Riley
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Vladimir I. Vladimirov
- Department of Psychiatry, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Silviu-Alin Bacanu
- Institute for Genomics in Health, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| |
Collapse
|
28
|
Mijalkov M, Veréb D, Jamialahmadi O, Canal-Garcia A, Gómez-Ruiz E, Vidal-Piñeiro D, Romeo S, Volpe G, Pereira JB. Sex differences in multilayer functional network topology over the course of aging in 37543 UK Biobank participants. Netw Neurosci 2023; 7:351-376. [PMID: 37334001 PMCID: PMC10275214 DOI: 10.1162/netn_a_00286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/06/2022] [Indexed: 07/27/2023] Open
Abstract
Aging is a major risk factor for cardiovascular and neurodegenerative disorders, with considerable societal and economic implications. Healthy aging is accompanied by changes in functional connectivity between and within resting-state functional networks, which have been associated with cognitive decline. However, there is no consensus on the impact of sex on these age-related functional trajectories. Here, we show that multilayer measures provide crucial information on the interaction between sex and age on network topology, allowing for better assessment of cognitive, structural, and cardiovascular risk factors that have been shown to differ between men and women, as well as providing additional insights into the genetic influences on changes in functional connectivity that occur during aging. In a large cross-sectional sample of 37,543 individuals from the UK Biobank cohort, we demonstrate that such multilayer measures that capture the relationship between positive and negative connections are more sensitive to sex-related changes in the whole-brain connectivity patterns and their topological architecture throughout aging, when compared to standard connectivity and topological measures. Our findings indicate that multilayer measures contain previously unknown information on the relationship between sex and age, which opens up new avenues for research into functional brain connectivity in aging.
Collapse
Affiliation(s)
- Mite Mijalkov
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Dániel Veréb
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Oveis Jamialahmadi
- Department of Molecular and Clinical Medicine, Goteborg University, Goteborg, Sweden
| | - Anna Canal-Garcia
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Stefano Romeo
- Department of Molecular and Clinical Medicine, Goteborg University, Goteborg, Sweden
- Cardiology Department, Sahlgrenska University Hospital, Gothenburg, Sweden
- Clinical Nutrition Unit, University Magna Graecia, Catanzaro, Italy
| | - Giovanni Volpe
- Department of Physics, Goteborg University, Goteborg, Sweden
| | - Joana B. Pereira
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
- Memory Research Unit, Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
| |
Collapse
|
29
|
Ren M, Yang Y, Heng KHY, Ng LY, Chong CYY, Ng YT, Gorur-Shandilya S, Lee RMQ, Lim KL, Zhang J, Koh TW. MED13 and glycolysis are conserved modifiers of α-synuclein-associated neurodegeneration. Cell Rep 2022; 41:111852. [PMID: 36543134 DOI: 10.1016/j.celrep.2022.111852] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 10/04/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
α-Synuclein (α-syn) is important in synucleinopathies such as Parkinson's disease (PD). While genome-wide association studies (GWASs) of synucleinopathies have identified many risk loci, the underlying genes have not been shown for most loci. Using Drosophila, we screened 3,471 mutant chromosomes for genetic modifiers of α-synuclein and identified 12 genes. Eleven modifiers have human orthologs associated with diseases, including MED13 and CDC27, which lie within PD GWAS loci. Drosophila Skd/Med13 and glycolytic enzymes are co-upregulated by α-syn-associated neurodegeneration. While elevated α-syn compromises mitochondrial function, co-expressing skd/Med13 RNAi and α-syn synergistically increase the ratio of oxidized-to-reduced glutathione. The resulting neurodegeneration can be suppressed by overexpressing a glycolytic enzyme or treatment with deferoxamine, suggesting that compensatory glycolysis is neuroprotective. In addition, the functional relationship between α-synuclein, MED13, and glycolytic enzymes is conserved between flies and mice. We propose that hypoxia-inducible factor and MED13 are part of a druggable pathway for PD.
Collapse
Affiliation(s)
- Mengda Ren
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308207, Singapore; National Neuroscience Institute, Singapore 308433, Singapore
| | - Ying Yang
- Department of Pathology, Zhejiang University First Affiliated Hospital and School of Medicine, Hangzhou, Zhejiang 310002, China
| | | | - Lu Yi Ng
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | | | - Yan Ting Ng
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore
| | | | - Rachel Min Qi Lee
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Kah Leong Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308207, Singapore; National Neuroscience Institute, Singapore 308433, Singapore
| | - Jing Zhang
- Department of Pathology, Zhejiang University First Affiliated Hospital and School of Medicine, Hangzhou, Zhejiang 310002, China; China National Health and Disease Human Brain Tissue Resource Center, Hangzhou, Zhejiang 310002, China
| | - Tong-Wey Koh
- Temasek Life Sciences Laboratory, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore.
| |
Collapse
|
30
|
Oatman SR, Ertekin-Taner N. Dementia risk variants - hunting needles in a haystack. Nat Rev Neurol 2022; 18:705-706. [PMID: 36329345 DOI: 10.1038/s41582-022-00739-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA. .,Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
| |
Collapse
|
31
|
Jin C, Lee B, Shen L, Long Q. Integrating multi-omics summary data using a Mendelian randomization framework. Brief Bioinform 2022; 23:bbac376. [PMID: 36094096 PMCID: PMC9677504 DOI: 10.1093/bib/bbac376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 12/14/2022] Open
Abstract
Mendelian randomization is a versatile tool to identify the possible causal relationship between an omics biomarker and disease outcome using genetic variants as instrumental variables. A key theme is the prioritization of genes whose omics readouts can be used as predictors of the disease outcome through analyzing GWAS and QTL summary data. However, there is a dearth of study of the best practice in probing the effects of multiple -omics biomarkers annotated to the same gene of interest. To bridge this gap, we propose powerful combination tests that integrate multiple correlated $P$-values without assuming the dependence structure between the exposures. Our extensive simulation experiments demonstrate the superiority of our proposed approach compared with existing methods that are adapted to the setting of our interest. The top hits of the analyses of multi-omics Alzheimer's disease datasets include genes ABCA7 and ATP1B1.
Collapse
Affiliation(s)
- Chong Jin
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brian Lee
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qi Long
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | |
Collapse
|
32
|
Song W, Yuan K, Liu Z, Cai W, Chen J, Yu S, Zhao M, Lin GN. Locus-level antagonistic selection shaped the polygenic architecture of human complex diseases. Hum Genet 2022; 141:1935-1947. [PMID: 35943608 DOI: 10.1007/s00439-022-02471-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND We aimed to evaluate the potential role of antagonistic selection in polygenic diseases: if one variant increases the risk of one disease and decreases the risk of another disease, the signals of genetic risk elimination by natural selection will be distorted, which leads to a higher frequency of risk alleles. METHODS We applied local genetic correlations and transcriptome-wide association studies to identify genomic loci and genes adversely associated with at least two diseases. Then, we used different population genetic metrics to measure the signals of natural selection for these loci and genes. RESULTS First, we identified 2120 cases of antagonistic pleiotropy (negative local genetic correlation) among 87 diseases in 716 genomic loci (antagonistic loci). Next, by comparing with non-antagonistic loci, we observed that antagonistic loci explained an excess proportion of disease heritability (median 6%), showed enhanced signals of balancing selection, and reduced signals of directional polygenic adaptation. Then, at the gene expression level, we identified 31,991 cases of antagonistic pleiotropy among 98 diseases at 4368 genes. However, evidence of altered signals of selection pressure and heritability distribution at the gene expression level is limited. CONCLUSION We conclude that antagonistic pleiotropy is widespread among human polygenic diseases, and it has distorted the evolutionary signal and genetic architecture of diseases at the locus level.
Collapse
Affiliation(s)
- Weichen Song
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Kai Yuan
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhe Liu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxiang Cai
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jue Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Shunying Yu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Min Zhao
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China.
| | - Guan Ning Lin
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China.
| |
Collapse
|
33
|
Integrative Analyses of Transcriptomes to Explore Common Molecular Effects of Antipsychotic Drugs. Int J Mol Sci 2022; 23:ijms23147508. [PMID: 35886854 PMCID: PMC9325239 DOI: 10.3390/ijms23147508] [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: 06/14/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 01/27/2023] Open
Abstract
There is little understanding of the underlying molecular mechanism(s) involved in the clinical efficacy of antipsychotics for schizophrenia. This study integrated schizophrenia-associated transcriptional perturbations with antipsychotic-induced gene expression profiles to detect potentially relevant therapeutic targets shared by multiple antipsychotics. Human neuronal-like cells (NT2-N) were treated for 24 h with one of the following antipsychotic drugs: amisulpride, aripiprazole, clozapine, risperidone, or vehicle controls. Drug-induced gene expression patterns were compared to schizophrenia-associated transcriptional data in post-mortem brain tissues. Genes regulated by each of four antipsychotic drugs in the reverse direction to schizophrenia were identified as potential therapeutic-relevant genes. A total of 886 genes were reversely expressed between at least one drug treatment (versus vehicle) and schizophrenia (versus healthy control), in which 218 genes were commonly regulated by all four antipsychotic drugs. The most enriched biological pathways include Wnt signaling and action potential regulation. The protein-protein interaction (PPI) networks found two main clusters having schizophrenia expression quantitative trait loci (eQTL) genes such as PDCD10, ANK2, and AKT3, suggesting further investigation on these genes as potential novel treatment targets.
Collapse
|
34
|
Andirkó A, Boeckx C. Brain region-specific effects of nearly fixed sapiens-derived alleles. BMC Genom Data 2022; 23:36. [PMID: 35546225 PMCID: PMC9097168 DOI: 10.1186/s12863-022-01048-8] [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: 12/02/2021] [Accepted: 04/05/2022] [Indexed: 11/10/2022] Open
Abstract
The availability of high-coverage genomes of our extinct relatives, the Neanderthals and Denisovans, and the emergence of large, tissue-specific databases of modern human genetic variation, offer the possibility of probing the effects of modern-derived alleles in specific tissues, such as the brain, and its specific regions. While previous research has explored the effects of introgressed variants in gene expression, the effects of Homo sapiens-specific gene expression variability are still understudied. Here we identify derived, Homo sapiens-specific high-frequency (≥90%) alleles that are associated with differential gene expression across 15 brain structures derived from the GTEx database. We show that regulation by these derived variants targets regions under positive selection more often than expected by chance, and that high-frequency derived alleles lie in functional categories related to transcriptional regulation. Our results highlight the role of these variants in gene regulation in specific regions like the cerebellum and pituitary.
Collapse
Affiliation(s)
- Alejandro Andirkó
- University of Barcelona, Barcelona, Spain.,University of Barcelona Institute of Complex Systems, Barcelona, Spain
| | - Cedric Boeckx
- University of Barcelona, Barcelona, Spain. .,University of Barcelona Institute of Complex Systems, Barcelona, Spain. .,ICREA, Barcelona, Spain.
| |
Collapse
|
35
|
Reagan AM, Onos KD, Heuer SE, Sasner M, Howell GR. Improving mouse models for the study of Alzheimer's disease. Curr Top Dev Biol 2022; 148:79-113. [PMID: 35461569 DOI: 10.1016/bs.ctdb.2021.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disease whose risk is influenced by genetic and environmental factors. Although a number of pathological hallmarks have been extensively studied over the last several decades, a complete picture of disease initiation and progression remains unclear. We now understand that numerous cell types and systems are involved in AD pathogenesis, and that this cellular profile may present differently for each individual, making the creation of relevant mouse models challenging. However, with increasingly diverse data made available by genome-wide association studies, we can identify and examine new genes and pathways involved in genetic risk for AD, many of which involve vascular health and inflammation. When developing mouse models, it is critical to assess (1) an aging timeline that represents onset and progression in humans, (2) genetic variants and context, (3) environmental factors present in human populations that result in both neuropathological and functional changes-themes that we address in this chapter.
Collapse
Affiliation(s)
| | | | - Sarah E Heuer
- The Jackson Laboratory, Bar Harbor, ME, United States; Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, United States
| | | | - Gareth R Howell
- The Jackson Laboratory, Bar Harbor, ME, United States; Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, United States; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, United States.
| |
Collapse
|
36
|
He L, Loika Y, Kulminski AM. Allele-specific analysis reveals exon- and cell-type-specific regulatory effects of Alzheimer's disease-associated genetic variants. Transl Psychiatry 2022; 12:163. [PMID: 35436980 PMCID: PMC9016079 DOI: 10.1038/s41398-022-01913-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 01/20/2023] Open
Abstract
Elucidating regulatory effects of Alzheimer's disease (AD)-associated genetic variants is critical for unraveling their causal pathways and understanding the pathology. However, their cell-type-specific regulatory mechanisms in the brain remain largely unclear. Here, we conducted an analysis of allele-specific expression quantitative trait loci (aseQTLs) for 33 AD-associated variants in four brain regions and seven cell types using ~3000 bulk RNA-seq samples and >0.25 million single nuclei. We first develop a flexible hierarchical Poisson mixed model (HPMM) and demonstrate its superior statistical power to a beta-binomial model achieved by unifying samples in both allelic and genotype-level expression data. Using the HPMM, we identified 24 (~73%) aseQTLs in at least one brain region, including three new eQTLs associated with CA12, CHRNE, and CASS4. Notably, the APOE ε4 variant reduces APOE expression across all regions, even in AD-unaffected controls. Our results reveal region-dependent and exon-specific effects of multiple aseQTLs, such as rs2093760 with CR1, rs7982 with CLU, and rs3865444 with CD33. In an attempt to pinpoint the cell types responsible for the observed tissue-level aseQTLs using the snRNA-seq data, we detected many aseQTLs in microglia or monocytes associated with immune-related genes, including HLA-DQB1, HLA-DQA2, CD33, FCER1G, MS4A6A, SPI1, and BIN1, highlighting the regulatory role of AD-associated variants in the immune response. These findings provide further insights into potential causal pathways and cell types mediating the effects of the AD-associated variants.
Collapse
Affiliation(s)
- Liang He
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA.
| | - Yury Loika
- grid.26009.3d0000 0004 1936 7961Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC USA
| | - Alexander M. Kulminski
- grid.26009.3d0000 0004 1936 7961Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC USA
| |
Collapse
|
37
|
Song W, Lin GN, Yu S, Zhao M. Genome-wide identification of the shared genetic basis of cannabis and cigarette smoking and schizophrenia implicates NCAM1 and neuronal abnormality. Psychiatry Res 2022; 310:114453. [PMID: 35235886 DOI: 10.1016/j.psychres.2022.114453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/31/2022] [Accepted: 02/15/2022] [Indexed: 01/02/2023]
Abstract
OBJECTIVES Confirming the existence and composition of the shared genetic basis of Schizophrenia and cannabis and cigarette smoking has critical values for the clinical prevention and intervention of psychosis. METHODS To achieve this goal, we leveraged Genome-Wide summary statistics of Schizophrenia (n = 99,934), cigarette smoking (n = 518,633) and cannabis usage (n = 162,082). We applied Causal Analysis Using Summary Effect Estimates (CAUSE) and genomic structural equation modeling (GenomicSEM) to quantify the contribution of a common genetic factor of cannabis and cigarette smoking and schizophrenia (referred to as SCZ_SMO), then identified genome-wide loci that made up SCZ_SMO. RESULTS We estimated that SCZ_SMO explained 8.6% of Schizophrenia heritability (Z score <-2.5 in CAUSE, p<10-20 in Genomic SEM). There were 20 independent loci showing association with SCZ_SMO at the genome-wide threshold of p<5 × 10-8. At the top locus on chromosome 11, fine-mapping identified rs7945073 (posterior inclusion probability =0.12, p = 2.24 × 10-32) as the top risk variants. Gene-level association and fine-mapping highlighted NCAM1, PHC2, and SEMA6D as risk genes of SCZ_SMO. Other risk genes were enriched in cortex, neuron, and dendritic spines (adjusted p<0.05). SCZ_SMO showed significant positive correlation (p<10-6) with the genetic risk of attention deficit hyperactivity disorder (r = 0.50), lifestyle problems (r = 0.83), social deprivation (r = 0.58) and all-cause pregnant loss (r = 0.60). CONCLUSION Our result provided new evidence on the shared genetic basis model for the association between Schizophrenia and smoking and provided genetic and biological insights into their shared mechanism.
Collapse
Affiliation(s)
- Weichen Song
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Guan Ning Lin
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Shunying Yu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Min Zhao
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China; CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
38
|
Seto M, Mahoney ER, Dumitrescu L, Ramanan VK, Engelman CD, Deming Y, Albert M, Johnson SC, Zetterberg H, Blennow K, Vemuri P, Jefferson AL, Hohman TJ. Exploring common genetic contributors to neuroprotection from amyloid pathology. Brain Commun 2022; 4:fcac066. [PMID: 35425899 PMCID: PMC9006043 DOI: 10.1093/braincomms/fcac066] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/13/2022] [Accepted: 03/15/2022] [Indexed: 01/25/2023] Open
Abstract
Preclinical Alzheimer's disease describes some individuals who harbour Alzheimer's pathologies but are asymptomatic. For this study, we hypothesized that genetic variation may help protect some individuals from Alzheimer's-related neurodegeneration. We therefore conducted a genome-wide association study using 5 891 064 common variants to assess whether genetic variation modifies the association between baseline beta-amyloid, as measured by both cerebrospinal fluid and positron emission tomography, and neurodegeneration defined using MRI measures of hippocampal volume. We combined and jointly analysed genotype, biomarker and neuroimaging data from non-Hispanic white individuals who were enrolled in four longitudinal ageing studies (n = 1065). Using regression models, we examined the interaction between common genetic variants (Minor Allele Frequency >0.01), including APOE-ɛ4 and APOE-ɛ2, and baseline cerebrospinal levels of amyloid (CSF Aβ42) on baseline hippocampal volume and the longitudinal rate of hippocampal atrophy. For targeted replication of top findings, we analysed an independent dataset (n = 808) where amyloid burden was assessed by Pittsburgh Compound B ([11C]-PiB) positron emission tomography. In this study, we found that APOE-ɛ4 modified the association between baseline CSF Aβ42 and hippocampal volume such that APOE-ɛ4 carriers showed more rapid atrophy, particularly in the presence of enhanced amyloidosis. We also identified a novel locus on chromosome 3 that interacted with baseline CSF Aβ42. Minor allele carriers of rs62263260, an expression quantitative trait locus for the SEMA5B gene (P = 1.46 × 10-8; 3:122675327) had more rapid neurodegeneration when amyloid burden was high and slower neurodegeneration when amyloid was low. The rs62263260 × amyloid interaction on longitudinal change in hippocampal volume was replicated in an independent dataset (P = 0.0112) where amyloid burden was assessed by positron emission tomography. In addition to supporting the established interaction between APOE and amyloid on neurodegeneration, our study identifies a novel locus that modifies the association between beta-amyloid and hippocampal atrophy. Annotation results may implicate SEMA5B, a gene involved in synaptic pruning and axonal guidance, as a high-quality candidate for functional confirmation and future mechanistic analysis.
Collapse
Affiliation(s)
- Mabel Seto
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, 1207 17th Ave S, Nashville, TN 37212, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37212, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Emily R. Mahoney
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, 1207 17th Ave S, Nashville, TN 37212, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37212, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, 1207 17th Ave S, Nashville, TN 37212, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37212, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | | - Corinne D. Engelman
- Department of Population Health Sciences, University of Wisconsin, School of Medicine and Public Health, Madison, WI 53726, USA
- Alzheimer’s Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
- Geriatric Education and Clinical Center, Wm.S.Middleton VA Hospital, Madison, WI 53705, USA
| | - Yuetiva Deming
- Department of Population Health Sciences, University of Wisconsin, School of Medicine and Public Health, Madison, WI 53726, USA
- Alzheimer’s Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
- Geriatric Education and Clinical Center, Wm.S.Middleton VA Hospital, Madison, WI 53705, USA
| | - Marilyn Albert
- Department of Neurology, the Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sterling C. Johnson
- Alzheimer’s Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
- Geriatric Education and Clinical Center, Wm.S.Middleton VA Hospital, Madison, WI 53705, USA
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal 413 90, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal 413 45, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK
- UK Dementia Research Institute at UCL, London WC1E 6BT, UK
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at University of Gothenburg, Mölndal 413 90, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal 413 45, Sweden
| | | | - Angela L. Jefferson
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, 1207 17th Ave S, Nashville, TN 37212, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Timothy J. Hohman
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center, 1207 17th Ave S, Nashville, TN 37212, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37212, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | | |
Collapse
|
39
|
Vialle RA, de Paiva Lopes K, Bennett DA, Crary JF, Raj T. Integrating whole-genome sequencing with multi-omic data reveals the impact of structural variants on gene regulation in the human brain. Nat Neurosci 2022; 25:504-514. [PMID: 35288716 PMCID: PMC9245608 DOI: 10.1038/s41593-022-01031-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 02/07/2022] [Indexed: 11/09/2022]
Abstract
Structural variants (SVs), genomic rearrangements of >50 bp, are an important source of genetic diversity and have been linked to many diseases. However, it remains unclear how they modulate human brain function and disease risk. Here, we report 170,996 SVs discovered using 1,760 short-read whole genomes from aged adults and Alzheimer’s disease individuals. By applying quantitative trait locus (SV-xQTL) analyses, we quantified the impact of cis-acting SVs on histone modifications, gene expression, splicing, and protein abundance in post-mortem brain tissues. More than 3,200 SVs were associated with at least one molecular phenotype. We found reproducibility of 65–99% SV-eQTLs across cohorts and brain regions. SV associations with mRNA and proteins shared the same direction of effect in more than 87% of SV-gene pairs. Mediation analysis showed ~8% of SV-eQTLs mediated by histone acetylation, and ~11% by splicing. Additionally, associations of SVs with progressive supranuclear palsy identified previously known and novel SVs.
Collapse
Affiliation(s)
- Ricardo A Vialle
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Katia de Paiva Lopes
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - John F Crary
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
40
|
Wang M, Song WM, Ming C, Wang Q, Zhou X, Xu P, Krek A, Yoon Y, Ho L, Orr ME, Yuan GC, Zhang B. Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application. Mol Neurodegener 2022; 17:17. [PMID: 35236372 PMCID: PMC8889402 DOI: 10.1186/s13024-022-00517-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 01/18/2022] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic studies have revealed biomarkers, risk factors, pathways, and targets of AD in the past decade. However, the exact molecular basis of AD development and progression remains elusive. The emerging single-cell sequencing technology can potentially provide cell-level insights into the disease. Here we systematically review the state-of-the-art bioinformatics approaches to analyze single-cell sequencing data and their applications to AD in 14 major directions, including 1) quality control and normalization, 2) dimension reduction and feature extraction, 3) cell clustering analysis, 4) cell type inference and annotation, 5) differential expression, 6) trajectory inference, 7) copy number variation analysis, 8) integration of single-cell multi-omics, 9) epigenomic analysis, 10) gene network inference, 11) prioritization of cell subpopulations, 12) integrative analysis of human and mouse sc-RNA-seq data, 13) spatial transcriptomics, and 14) comparison of single cell AD mouse model studies and single cell human AD studies. We also address challenges in using human postmortem and mouse tissues and outline future developments in single cell sequencing data analysis. Importantly, we have implemented our recommended workflow for each major analytic direction and applied them to a large single nucleus RNA-sequencing (snRNA-seq) dataset in AD. Key analytic results are reported while the scripts and the data are shared with the research community through GitHub. In summary, this comprehensive review provides insights into various approaches to analyze single cell sequencing data and offers specific guidelines for study design and a variety of analytic directions. The review and the accompanied software tools will serve as a valuable resource for studying cellular and molecular mechanisms of AD, other diseases, or biological systems at the single cell level.
Collapse
Affiliation(s)
- Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Chen Ming
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Peng Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Yonejung Yoon
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Lap Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Miranda E. Orr
- Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| |
Collapse
|
41
|
Johnson ECB, Carter EK, Dammer EB, Duong DM, Gerasimov ES, Liu Y, Liu J, Betarbet R, Ping L, Yin L, Serrano GE, Beach TG, Peng J, De Jager PL, Haroutunian V, Zhang B, Gaiteri C, Bennett DA, Gearing M, Wingo TS, Wingo AP, Lah JJ, Levey AI, Seyfried NT. Large-scale deep multi-layer analysis of Alzheimer's disease brain reveals strong proteomic disease-related changes not observed at the RNA level. Nat Neurosci 2022; 25:213-225. [PMID: 35115731 PMCID: PMC8825285 DOI: 10.1038/s41593-021-00999-y] [Citation(s) in RCA: 183] [Impact Index Per Article: 91.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 12/08/2021] [Indexed: 12/16/2022]
Abstract
The biological processes that are disrupted in the Alzheimer's disease (AD) brain remain incompletely understood. In this study, we analyzed the proteomes of more than 1,000 brain tissues to reveal new AD-related protein co-expression modules that were highly preserved across cohorts and brain regions. Nearly half of the protein co-expression modules, including modules significantly altered in AD, were not observed in RNA networks from the same cohorts and brain regions, highlighting the proteopathic nature of AD. Two such AD-associated modules unique to the proteomic network included a module related to MAPK signaling and metabolism and a module related to the matrisome. The matrisome module was influenced by the APOE ε4 allele but was not related to the rate of cognitive decline after adjustment for neuropathology. By contrast, the MAPK/metabolism module was strongly associated with the rate of cognitive decline. Disease-associated modules unique to the proteome are sources of promising therapeutic targets and biomarkers for AD.
Collapse
Affiliation(s)
- Erik C B Johnson
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
| | - E Kathleen Carter
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Duc M Duong
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Yue Liu
- Department of Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jiaqi Liu
- Department of Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ranjita Betarbet
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lingyan Ping
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Luming Yin
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Taub Institute, Columbia University Irving Medical Center, New York Presbyterian Hospital, New York, NY, USA
| | - Vahram Haroutunian
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center MIRECC, Bronx, NY, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Marla Gearing
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas S Wingo
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Aliza P Wingo
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA
- Division of Mental Health, Atlanta VA Medical Center, Atlanta, GA, USA
| | - James J Lah
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Nicholas T Seyfried
- Goizueta Alzheimer's Disease Research Center, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.
| |
Collapse
|
42
|
Meta-imputation of transcriptome from genotypes across multiple datasets by leveraging publicly available summary-level data. PLoS Genet 2022; 18:e1009571. [PMID: 35100255 PMCID: PMC8830793 DOI: 10.1371/journal.pgen.1009571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 02/10/2022] [Accepted: 01/07/2022] [Indexed: 11/22/2022] Open
Abstract
Transcriptome wide association studies (TWAS) can be used as a powerful method to identify and interpret the underlying biological mechanisms behind GWAS by mapping gene expression levels with phenotypes. In TWAS, gene expression is often imputed from individual-level genotypes of regulatory variants identified from external resources, such as Genotype-Tissue Expression (GTEx) Project. In this setting, a straightforward approach to impute expression levels of a specific tissue is to use the model trained from the same tissue type. When multiple tissues are available for the same subjects, it has been demonstrated that training imputation models from multiple tissue types improves the accuracy because of shared eQTLs between the tissues and increase in effective sample size. However, existing joint-tissue methods require access of genotype and expression data across all tissues. Moreover, they cannot leverage the abundance of various expression datasets across various tissues for non-overlapping individuals. Here, we explore the optimal way to combine imputed levels across training models from multiple tissues and datasets in a flexible manner using summary-level data. Our proposed method (SWAM) combines arbitrary number of transcriptome imputation models to linearly optimize the imputation accuracy given a target tissue. By integrating models across tissues and/or individuals, SWAM can improve the accuracy of transcriptome imputation or to improve power to TWAS while only requiring individual-level data from a single reference cohort. To evaluate the accuracy of SWAM, we combined 49 tissue-specific gene expression imputation models from the GTEx Project as well as from a large eQTL study of Depression Susceptibility Genes and Networks (DGN) Project and tested imputation accuracy in GEUVADIS lymphoblastoid cell lines samples. We also extend our meta-imputation method to meta-TWAS to leverage multiple tissues in TWAS analysis with summary-level statistics. Our results capitalize on the importance of integrating multiple tissues to unravel regulatory impacts of genetic variants on complex traits. The gene expression levels within a cell are affected by various factors, including DNA variation, cell type, cellular microenvironment, disease status, and other environmental factors surrounding the individual. The genetic component of gene expression is known to explain a substantial fraction of transcriptional variation among individuals and can be imputed from genotypes in a tissue-specific manner, by training from population-scale transcriptomic profiles designed to identify expression quantitative loci (eQTLs). Imputing gene expression levels is shown to help understand the genetic basis of human disease through Transcriptome-wide association analysis (TWAS) and Mendelian Randomization (MR). However, it has been unclear how to integrate multiple imputation models trained from individual datasets to maximize their accuracy without having to access individual genotypes and expression levels that are often protected for privacy concerns. We developed SWAM (Smartly Weighted Averaging across Multiple datasets), a meta-imputation framework which can accurately impute gene expression levels from genotypes by integrating multiple imputation models without requiring individual-level data. Our method examines the similarity or differences between resources and borrowing information most relevant to the tissue of interest. We demonstrate that SWAM outperforms existing single-tissue and multi-tissue imputation models and continue to increase accuracy when integrating additional imputation models.
Collapse
|
43
|
Hwang R, Dang LH, Chen J, Lee JH, Marquer C. Triplication of Synaptojanin 1 in Alzheimer's Disease Pathology in Down Syndrome. Curr Alzheimer Res 2022; 19:795-807. [PMID: 36464875 DOI: 10.2174/1567205020666221202102832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/29/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022]
Abstract
Down Syndrome (DS), caused by triplication of human chromosome 21 (Hsa21) is the most common form of intellectual disability worldwide. Recent progress in healthcare has resulted in a dramatic increase in the lifespan of individuals with DS. Unfortunately, most will develop Alzheimer's disease like dementia (DS-AD) as they age. Understanding similarities and differences between DSAD and the other forms of the disease - i.e., late-onset AD (LOAD) and autosomal dominant AD (ADAD) - will provide important clues for the treatment of DS-AD. In addition to the APP gene that codes the precursor of the main component of amyloid plaques found in the brain of AD patients, other genes on Hsa21 are likely to contribute to disease initiation and progression. This review focuses on SYNJ1, coding the phosphoinositide phosphatase synaptojanin 1 (SYNJ1). First, we highlight the function of SYNJ1 in the brain. We then summarize the involvement of SYNJ1 in the different forms of AD at the genetic, transcriptomic, proteomic and neuropathology levels in humans. We further examine whether results in humans correlate with what has been described in murine and cellular models of the disease and report possible mechanistic links between SYNJ1 and the progression of the disease. Finally, we propose a set of questions that would further strengthen and clarify the role of SYNJ1 in the different forms of AD.
Collapse
Grants
- U19 AG068054, U01 AG051412, UL1TR001873, R01 AG058918, R01 AG058918 S1, P30AG10161, P30AG72975, R01AG15819, R01AG17917, R01AG03-6836, U01AG46152, U01AG61356, U01AG046139, P50 AG016574, R01 AG032990, U01AG046139, R01AG01-8023, U01AG006576, U01AG006786, R01AG025711, R01AG017216, R01AG003949, R01NS080820, U24NS07-2026, P30AG19610, U01AG046170, RF1AG057440, U24AG061340 NIH/NIA , National Institutes of Health
Collapse
Affiliation(s)
- Robert Hwang
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY, 10032, USA
| | - Lam-Ha Dang
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY, 10032, USA
- G.H. Sergievsky Center, Columbia University Medical Center, New York, NY 10032, USA
- Departments of Epidemiology and Neurology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Jacinda Chen
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY, 10032, USA
| | - Joseph H Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY, 10032, USA
- G.H. Sergievsky Center, Columbia University Medical Center, New York, NY 10032, USA
- Departments of Epidemiology and Neurology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Catherine Marquer
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY, 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, NY, 10032, USA
| |
Collapse
|
44
|
Kuksa PP, Liu CL, Fu W, Qu L, Zhao Y, Katanic Z, Clark K, Kuzma AB, Ho PC, Tzeng KT, Valladares O, Chou SY, Naj AC, Schellenberg GD, Wang LS, Leung YY. Alzheimer's Disease Variant Portal: A Catalog of Genetic Findings for Alzheimer's Disease. J Alzheimers Dis 2022; 86:461-477. [PMID: 35068457 PMCID: PMC9028687 DOI: 10.3233/jad-215055] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Recent Alzheimer's disease (AD) genetics findings from genome-wide association studies (GWAS) span progressively larger and more diverse populations and outcomes. Currently, there is no up-to-date resource providing harmonized and searchable information on all AD genetic associations found by GWAS, nor linking the reported genetic variants and genes with functional and genomic annotations. OBJECTIVE Create an integrated/harmonized, and literature-derived collection of population-specific AD genetic associations. METHODS We developed the Alzheimer's Disease Variant Portal (ADVP), an extensive collection of associations curated from >200 GWAS publications from Alzheimer's Disease Genetics Consortium and other consortia. Genetic associations were systematically extracted, harmonized, and annotated from both the genome-wide significant and suggestive loci reported in these publications. To ensure consistent representation of AD genetic findings, all the extracted genetic association information was harmonized across specifically designed publication, variant, and association categories. RESULTS ADVP V1.0 (February 2021) catalogs 6,990 associations related to disease-risk, expression quantitative traits, endophenotypes, or neuropathology. This extensive harmonization effort led to a catalog containing >900 loci, >1,800 variants, >80 cohorts, and 8 populations. Besides, ADVP provides investigators with a seamless integration of genomic and publicly available functional annotations across multiple databases per harmonized variant and gene records, thus facilitating further understanding and analyses of these genetics findings. CONCLUSION ADVP is a valuable resource for investigators to quickly and systematically explore high-confidence AD genetic findings and provides insights into population-specific AD genetic architecture. ADVP is continually maintained and enhanced by NIAGADS and is freely accessible at https://advp.niagads.org.
Collapse
Affiliation(s)
- Pavel P. Kuksa
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Chia-Lun Liu
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Wei Fu
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Liming Qu
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Yi Zhao
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Zivadin Katanic
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Kaylyn Clark
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Amanda B. Kuzma
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Pei-Chuan Ho
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Kai-Teh Tzeng
- Department of Economics, Lehigh University, Bethlehem, PA, USA
| | - Otto Valladares
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Shin-Yi Chou
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Economics, Lehigh University, Bethlehem, PA, USA
| | - Adam C. Naj
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| |
Collapse
|
45
|
Farrell K, Kim S, Han N, Iida MA, Gonzalez EM, Otero-Garcia M, Walker JM, Richardson TE, Renton AE, Andrews SJ, Fulton-Howard B, Humphrey J, Vialle RA, Bowles KR, de Paiva Lopes K, Whitney K, Dangoor DK, Walsh H, Marcora E, Hefti MM, Casella A, Sissoko CT, Kapoor M, Novikova G, Udine E, Wong G, Tang W, Bhangale T, Hunkapiller J, Ayalon G, Graham RR, Cherry JD, Cortes EP, Borukov VY, McKee AC, Stein TD, Vonsattel JP, Teich AF, Gearing M, Glass J, Troncoso JC, Frosch MP, Hyman BT, Dickson DW, Murray ME, Attems J, Flanagan ME, Mao Q, Mesulam MM, Weintraub S, Woltjer RL, Pham T, Kofler J, Schneider JA, Yu L, Purohit DP, Haroutunian V, Hof PR, Gandy S, Sano M, Beach TG, Poon W, Kawas CH, Corrada MM, Rissman RA, Metcalf J, Shuldberg S, Salehi B, Nelson PT, Trojanowski JQ, Lee EB, Wolk DA, McMillan CT, Keene CD, Latimer CS, Montine TJ, Kovacs GG, Lutz MI, Fischer P, Perrin RJ, Cairns NJ, Franklin EE, Cohen HT, Raj T, Cobos I, Frost B, Goate A, White Iii CL, Crary JF. Genome-wide association study and functional validation implicates JADE1 in tauopathy. Acta Neuropathol 2022; 143:33-53. [PMID: 34719765 PMCID: PMC8786260 DOI: 10.1007/s00401-021-02379-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/13/2021] [Accepted: 10/24/2021] [Indexed: 01/07/2023]
Abstract
Primary age-related tauopathy (PART) is a neurodegenerative pathology with features distinct from but also overlapping with Alzheimer disease (AD). While both exhibit Alzheimer-type temporal lobe neurofibrillary degeneration alongside amnestic cognitive impairment, PART develops independently of amyloid-β (Aβ) plaques. The pathogenesis of PART is not known, but evidence suggests an association with genes that promote tau pathology and others that protect from Aβ toxicity. Here, we performed a genetic association study in an autopsy cohort of individuals with PART (n = 647) using Braak neurofibrillary tangle stage as a quantitative trait. We found some significant associations with candidate loci associated with AD (SLC24A4, MS4A6A, HS3ST1) and progressive supranuclear palsy (MAPT and EIF2AK3). Genome-wide association analysis revealed a novel significant association with a single nucleotide polymorphism on chromosome 4 (rs56405341) in a locus containing three genes, including JADE1 which was significantly upregulated in tangle-bearing neurons by single-soma RNA-seq. Immunohistochemical studies using antisera targeting JADE1 protein revealed localization within tau aggregates in autopsy brains with four microtubule-binding domain repeats (4R) isoforms and mixed 3R/4R, but not with 3R exclusively. Co-immunoprecipitation in post-mortem human PART brain tissue revealed a specific binding of JADE1 protein to four repeat tau lacking N-terminal inserts (0N4R). Finally, knockdown of the Drosophila JADE1 homolog rhinoceros (rno) enhanced tau-induced toxicity and apoptosis in vivo in a humanized 0N4R mutant tau knock-in model, as quantified by rough eye phenotype and terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) in the fly brain. Together, these findings indicate that PART has a genetic architecture that partially overlaps with AD and other tauopathies and suggests a novel role for JADE1 as a modifier of neurofibrillary degeneration.
Collapse
Affiliation(s)
- Kurt Farrell
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - SoongHo Kim
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalia Han
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Megan A Iida
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elias M Gonzalez
- Department of Cell Systems and Anatomy, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, the Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Marcos Otero-Garcia
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of California, Los Angeles, CA, USA
| | - Jamie M Walker
- Department of Pathology and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Timothy E Richardson
- Department of Pathology and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Alan E Renton
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shea J Andrews
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Fulton-Howard
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ricardo A Vialle
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathryn R Bowles
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katia de Paiva Lopes
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen Whitney
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diana K Dangoor
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hadley Walsh
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marco M Hefti
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | - Alicia Casella
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cheick T Sissoko
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manav Kapoor
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gloriia Novikova
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Evan Udine
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Garrett Wong
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Weijing Tang
- Department of Pathology, Stanford University, Palo Alto, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, South San Francisco, CA, USA
| | - Julie Hunkapiller
- Department of Human Genetics, Genentech, South San Francisco, CA, USA
| | - Gai Ayalon
- Neumora Therapeutics, South San Francisco, CA, USA
| | | | - Jonathan D Cherry
- Department of Pathology (Neuropathology), VA Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Etty P Cortes
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Valeriy Y Borukov
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ann C McKee
- Department of Pathology (Neuropathology), VA Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Thor D Stein
- Department of Pathology (Neuropathology), VA Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Jean-Paul Vonsattel
- Department of Pathology and Cell Biology, Department of Neurology, and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Andy F Teich
- Department of Pathology and Cell Biology, Department of Neurology, and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Marla Gearing
- Department of Pathology and Laboratory Medicine (Neuropathology) and Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jonathan Glass
- Department of Pathology and Laboratory Medicine (Neuropathology) and Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Juan C Troncoso
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew P Frosch
- Department of Neurology and Pathology, Harvard Medical School and Massachusetts General Hospital, Charlestown, MA, USA
| | - Bradley T Hyman
- Department of Neurology and Pathology, Harvard Medical School and Massachusetts General Hospital, Charlestown, MA, USA
| | | | | | - Johannes Attems
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Margaret E Flanagan
- Department of Pathology (Neuropathology), Northwestern Cognitive Neurology and Alzheimer Disease Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Qinwen Mao
- Department of Pathology (Neuropathology), Northwestern Cognitive Neurology and Alzheimer Disease Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - M-Marsel Mesulam
- Department of Pathology (Neuropathology), Northwestern Cognitive Neurology and Alzheimer Disease Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sandra Weintraub
- Department of Pathology (Neuropathology), Northwestern Cognitive Neurology and Alzheimer Disease Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Randy L Woltjer
- Department of Pathology, Oregon Health Sciences University, Portland, OR, USA
| | - Thao Pham
- Department of Pathology, Oregon Health Sciences University, Portland, OR, USA
| | - Julia Kofler
- Department of Pathology (Neuropathology), University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Julie A Schneider
- Departments of Pathology (Neuropathology) and Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Lei Yu
- Departments of Pathology (Neuropathology) and Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Dushyant P Purohit
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Department of Psychiatry, Alzheimer's Disease Research Center, James J. Peters VA Medical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vahram Haroutunian
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Alzheimer's Disease Research Center, James J. Peters VA Medical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patrick R Hof
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sam Gandy
- Department of Psychiatry, Alzheimer's Disease Research Center, James J. Peters VA Medical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Center for Cognitive Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mary Sano
- Department of Psychiatry, Alzheimer's Disease Research Center, James J. Peters VA Medical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas G Beach
- Department of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Wayne Poon
- Department of Neurology, Department of Epidemiology, Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA, USA
| | - Claudia H Kawas
- Department of Neurology, Department of Neurobiology and Behavior, Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA, USA
| | - María M Corrada
- Department of Neurology, Department of Epidemiology, Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA, USA
| | - Robert A Rissman
- Department of Neurosciences University of California and the Veterans Affairs San Diego Healthcare System, La Jolla, San Diego, California, USA
| | - Jeff Metcalf
- Department of Neurosciences University of California and the Veterans Affairs San Diego Healthcare System, La Jolla, San Diego, California, USA
| | - Sara Shuldberg
- Department of Neurosciences University of California and the Veterans Affairs San Diego Healthcare System, La Jolla, San Diego, California, USA
| | - Bahar Salehi
- Department of Neurosciences University of California and the Veterans Affairs San Diego Healthcare System, La Jolla, San Diego, California, USA
| | - Peter T Nelson
- Department of Pathology (Neuropathology) and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - John Q Trojanowski
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward B Lee
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David A Wolk
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Corey T McMillan
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of f Medicine, Seattle, WA, USA
| | - Caitlin S Latimer
- Department of Laboratory Medicine and Pathology, University of f Medicine, Seattle, WA, USA
| | - Thomas J Montine
- Department of Laboratory Medicine and Pathology, University of f Medicine, Seattle, WA, USA
- Department of Pathology, Stanford University, Palo Alto, USA
| | - Gabor G Kovacs
- Laboratory Medicine Program, Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Disease and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Mirjam I Lutz
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Peter Fischer
- Department of Psychiatry, Danube Hospital, Vienna, Austria
| | - Richard J Perrin
- Department of Pathology and Immunology, Department of Neurology, Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Nigel J Cairns
- College of Medicine and Health, University of Exeter, Exeter, UK
| | - Erin E Franklin
- Department of Pathology and Immunology, Department of Neurology, Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Herbert T Cohen
- Departments of Medicine, Pathology, and Pharmacology, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Towfique Raj
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Inma Cobos
- Department of Pathology, Stanford University, Palo Alto, USA
| | - Bess Frost
- Department of Cell Systems and Anatomy, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, the Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Alison Goate
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles L White Iii
- Department of Pathology (Neuropathology), University of Texas Southwestern Medical School, Dallas, TX, USA
| | - John F Crary
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA.
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
46
|
He Z, Le Guen Y, Liu L, Lee J, Ma S, Yang AC, Liu X, Rutledge J, Losada PM, Song B, Belloy ME, Butler RR, Longo FM, Tang H, Mormino EC, Wyss-Coray T, Greicius MD, Ionita-Laza I. Genome-wide analysis of common and rare variants via multiple knockoffs at biobank scale, with an application to Alzheimer disease genetics. Am J Hum Genet 2021; 108:2336-2353. [PMID: 34767756 PMCID: PMC8715147 DOI: 10.1016/j.ajhg.2021.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Knockoff-based methods have become increasingly popular due to their enhanced power for locus discovery and their ability to prioritize putative causal variants in a genome-wide analysis. However, because of the substantial computational cost for generating knockoffs, existing knockoff approaches cannot analyze millions of rare genetic variants in biobank-scale whole-genome sequencing and whole-genome imputed datasets. We propose a scalable knockoff-based method for the analysis of common and rare variants across the genome, KnockoffScreen-AL, that is applicable to biobank-scale studies with hundreds of thousands of samples and millions of genetic variants. The application of KnockoffScreen-AL to the analysis of Alzheimer disease (AD) in 388,051 WG-imputed samples from the UK Biobank resulted in 31 significant loci, including 14 loci that are missed by conventional association tests on these data. We perform replication studies in an independent meta-analysis of clinically diagnosed AD with 94,437 samples, and additionally leverage single-cell RNA-sequencing data with 143,793 single-nucleus transcriptomes from 17 control subjects and AD-affected individuals, and proteomics data from 735 control subjects and affected indviduals with AD and related disorders to validate the genes at these significant loci. These multi-omics analyses show that 79.1% of the proximal genes at these loci and 76.2% of the genes at loci identified only by KnockoffScreen-AL exhibit at least suggestive signal (p < 0.05) in the scRNA-seq or proteomics analyses. We highlight a potentially causal gene in AD progression, EGFR, that shows significant differences in expression and protein levels between AD-affected individuals and healthy control subjects.
Collapse
Affiliation(s)
- Zihuai He
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA; Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA; Institut du Cerveau - Paris Brain Institute - ICM, Paris 75013, France
| | - Linxi Liu
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Justin Lee
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Shiyang Ma
- Department of Biostatistics, Columbia University, New York, NY 10032, USA
| | - Andrew C Yang
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Xiaoxia Liu
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Jarod Rutledge
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Patricia Moran Losada
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Bowen Song
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Michael E Belloy
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Robert R Butler
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Frank M Longo
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Hua Tang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth C Mormino
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | | |
Collapse
|
47
|
Wang B, Yang J, Qiu S, Bai Y, Qin ZS. Systematic Exploration in Tissue-Pathway Associations of Complex Traits Using Comprehensive eQTLs Catalog. Front Big Data 2021; 4:719737. [PMID: 34805976 PMCID: PMC8595594 DOI: 10.3389/fdata.2021.719737] [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: 06/03/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
The collection of expression quantitative trait loci (eQTLs) is an important resource to study complex traits through understanding where and how transcriptional regulations are controlled by genetic variations in the non-coding regions of the genome. Previous studies have focused on associating eQTLs with traits to identify the roles of trait-related eQTLs and their corresponding target genes involved in trait determination. Since most genes function as a part of pathways in a systematic manner, it is crucial to explore the pathways’ involvements in complex traits to test potentially novel hypotheses and to reveal underlying mechanisms of disease pathogenesis. In this study, we expanded and applied loci2path software to perform large-scale eQTLs enrichment [i.e., eQTLs’ target genes (eGenes) enrichment] analysis at pathway level to identify the tissue-specific enriched pathways within trait-related genomic intervals. By utilizing 13,791,909 eQTLs cataloged in the Genotype-Tissue Expression (GTEx) V8 data for 49 tissue types, 2,893 pathway sets reported from MSigDB, and query regions derived from the Phenotype-Genotype Integrator (PheGenI) catalog, we identified intriguing biological pathways that are likely to be involved in ten traits [Alzheimer’s disease (AD), body mass index, Parkinson’s disease (PD), schizophrenia, amyotrophic lateral sclerosis, non-small cell lung cancer (NSCLC), stroke, blood pressure, autism spectrum disorder, and myocardial infarction]. Furthermore, we extracted the most significant pathways for AD, such as BioCarta D4-GDI pathway and WikiPathways sulfation biotransformation reaction and viral acute myocarditis pathways, to study specific genes within pathways. Our data presented new hypotheses in AD pathogenesis supported by previous studies, like the increased level of caspase-3 in the amygdala that cleaves GDP dissociation inhibitor and binds to beta-amyloid, leading to increased apoptosis and neuronal loss. Our findings also revealed potential pathogenesis mechanisms for PD, schizophrenia, NSCLC, blood pressure, autism spectrum disorder, and myocardial infarction, which were consistent with past studies. Our results indicated that loci2path′s eQTLs enrichment test was valuable in unveiling novel biological mechanisms of complex traits. The discovered mechanisms of disease pathogenesis and traits require further in-depth analysis and experimental validation.
Collapse
Affiliation(s)
- Boqi Wang
- Emory University, Atlanta, GA, United States
| | - James Yang
- Carmel High School, Carmel, IN, United States
| | - Steven Qiu
- James Martin High School, Arlington, TX, United States
| | - Yongsheng Bai
- Next-Gen Intelligent Science Training, Ann Arbor, MI, United States
| | - Zhaohui S Qin
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, United States
| |
Collapse
|
48
|
Horimoto ARVR, Xue D, Thornton TA, Blue EE. Admixture mapping reveals the association between Native American ancestry at 3q13.11 and reduced risk of Alzheimer's disease in Caribbean Hispanics. Alzheimers Res Ther 2021; 13:122. [PMID: 34217363 PMCID: PMC8254995 DOI: 10.1186/s13195-021-00866-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/20/2021] [Indexed: 02/02/2023]
Abstract
BACKGROUND Genetic studies have primarily been conducted in European ancestry populations, identifying dozens of loci associated with late-onset Alzheimer's disease (AD). However, much of AD's heritability remains unexplained; as the prevalence of AD varies across populations, the genetic architecture of the disease may also vary by population with the presence of novel variants or loci. METHODS We conducted genome-wide analyses of AD in a sample of 2565 Caribbean Hispanics to better understand the genetic contribution to AD in this population. Statistical analysis included both admixture mapping and association testing. Evidence for differential gene expression within regions of interest was collected from independent transcriptomic studies comparing AD cases and controls in samples with primarily European ancestry. RESULTS Our genome-wide association study of AD identified no loci reaching genome-wide significance. However, a genome-wide admixture mapping analysis that tests for association between a haplotype's ancestral origin and AD status detected a genome-wide significant association with chromosome 3q13.11 (103.7-107.7Mb, P = 8.76E-07), driven by a protective effect conferred by the Native American ancestry (OR = 0.58, 95%CI = 0.47-0.73). Within this region, two variants were significantly associated with AD after accounting for the number of independent tests (rs12494162, P = 2.33E-06; rs1731642, P = 6.36E-05). The significant admixture mapping signal is composed of 15 haplotype blocks spanning 5 protein-coding genes (ALCAM, BBX, CBLB, CCDC54, CD47) and four brain-derived topologically associated domains, and includes markers significantly associated with the expression of ALCAM, BBX, CBLB, and CD47 in the brain. ALCAM and BBX were also significantly differentially expressed in the brain between AD cases and controls with European ancestry. CONCLUSION These results provide multiethnic evidence for a relationship between AD and multiple genes at 3q13.11 and illustrate the utility of leveraging genetic ancestry diversity via admixture mapping for new insights into AD.
Collapse
Affiliation(s)
| | - Diane Xue
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Elizabeth E Blue
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA.
- Division of Medical Genetics, University of Washington, BOX 357720, Seattle, WA, 98195-7720, USA.
| |
Collapse
|
49
|
Wingo TS, Liu Y, Gerasimov ES, Gockley J, Logsdon BA, Duong DM, Dammer EB, Lori A, Kim PJ, Ressler KJ, Beach TG, Reiman EM, Epstein MP, De Jager PL, Lah JJ, Bennett DA, Seyfried NT, Levey AI, Wingo AP. Brain proteome-wide association study implicates novel proteins in depression pathogenesis. Nat Neurosci 2021; 24:810-817. [PMID: 33846625 PMCID: PMC8530461 DOI: 10.1038/s41593-021-00832-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 03/04/2021] [Indexed: 02/01/2023]
Abstract
Depression is a common condition, but current treatments are only effective in a subset of individuals. To identify new treatment targets, we integrated depression genome-wide association study (GWAS) results (N = 500,199) with human brain proteomes (N = 376) to perform a proteome-wide association study of depression followed by Mendelian randomization. We identified 19 genes that were consistent with being causal in depression, acting via their respective cis-regulated brain protein abundance. We replicated nine of these genes using an independent depression GWAS (N = 307,353) and another human brain proteomic dataset (N = 152). Eleven of the 19 genes also had cis-regulated mRNA levels that were associated with depression, based on integration of the depression GWAS with human brain transcriptomes (N = 888). Meta-analysis of the discovery and replication proteome-wide association study analyses identified 25 brain proteins consistent with being causal in depression, 20 of which were not previously implicated in depression by GWAS. Together, these findings provide promising brain protein targets for further mechanistic and therapeutic studies.
Collapse
Affiliation(s)
- Thomas S Wingo
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
| | - Yue Liu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | | | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Adriana Lori
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA
| | - Paul J Kim
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | - Eric M Reiman
- Banner Alzheimer's Institute, Arizona State University and University of Arizona, Phoenix, AZ, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - James J Lah
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Aliza P Wingo
- Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, USA.
- Division of Mental Health, Atlanta VA Medical Center, Decatur, GA, USA.
| |
Collapse
|
50
|
A Genetic Study of Cerebral Atherosclerosis Reveals Novel Associations with NTNG1 and CNOT3. Genes (Basel) 2021; 12:genes12060815. [PMID: 34073619 PMCID: PMC8228534 DOI: 10.3390/genes12060815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 11/17/2022] Open
Abstract
Cerebral atherosclerosis is a leading cause of stroke and an important contributor to dementia. Yet little is known about its genetic basis. To examine the association of common single nucleotide polymorphisms with cerebral atherosclerosis severity, we conducted a genomewide association study (GWAS) using data collected as part of two community-based cohort studies in the United States, the Religious Orders Study (ROS) and Rush Memory and Aging Project (MAP). Both studies enroll older individuals and exclude participants with signs of dementia at baseline. From our analysis of 1325 participants of European ancestry who had genotype and neuropathologically assessed cerebral atherosclerosis measures available, we found a novel locus for cerebral atherosclerosis in NTNG1. The locus comprises eight SNPs, including two independent significant SNPs: rs6664221 (β = -0.27, 95% CI = (-0.35, -0.19), p = 1.29 × 10-10) and rs10881463 (β = -0.20, 95% CI = (-0.27, -0.13), p = 3.40 × 10-8). We further found that the SNPs may influence cerebral atherosclerosis by regulating brain protein expression of CNOT3. CNOT3 is a subunit of CCR4-NOT, which has been shown to be a master regulator of mRNA stability and translation and an important complex for cholesterol homeostasis. In summary, we identify a novel genetic locus for cerebral atherosclerosis and a potential mechanism linking this variation to cerebral atherosclerosis progression. These findings offer insights into the genetic effects on cerebral atherosclerosis.
Collapse
|