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Proteins: Structure, Function, and bioinformatics 2018年第5期86卷

作者： J. C. Gaines S. Acebes A. Virrueta M. Butler L. Regan C. S. O'Hern Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 Integrated Graduate Program in Physical and Engineering Biology (IGPPEB) Yale University New Haven Connecticut 06520 Department of Mechanical Engineering and Materials Science Yale University New Haven Connecticut 06520 Department of Physics and Astronomy University of Southern California Los Angeles California 90007 Department of Molecular Biophysics & Biochemistry Yale University New Haven Connecticut 06520 Department of Chemistry Yale University New Haven Connecticut 06520 Department of Physics Yale University New Haven Connecticut 06520 Department of Applied Physics Yale University New Haven Connecticut 06520

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Front Cover: Design, Synthesis, and Characterization of Novel Styryl Dyes as Fluorescent Probes for Tau Aggregate Detectionin Vitroand in Cells (Chem. Asian J. 6/2024)

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Chemistry – An Asian Journal 2024年第6期19卷

作者： Withsakorn Sangsuwan Kriangsak Faikhruea Kotchakorn Supabowornsathit Don Sangsopon Praewphan Ingrungruanglert Hathaichanok Chuntakaruk Napatsaporn Nuntavanotayan Kittiporn Nakprasit Nipan Israsena Thanyada Rungrotmongkol Pitak Chuawong Tirayut Vilaivan Chanat Aonbangkhen Center of Excellence in Natural Products Chemistry (CENP) Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand Department of Chemistry and Center of Excellence for Innovation in Chemistry Faculty of Science Special Research Unit for Advanced Magnetic Resonance (AMR) Kasetsart University Bangkok 10900 Thailand These authors are contributed equally. Organic Synthesis Research Unit Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand Stem Cell and Cell Therapy Research Unit and Department of Pharmacology Faculty of Medicine Chulalongkorn University Bangkok 10330 Thailand Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok 10330 Thailand Center of Excellence in Structural and Computational Biology Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand

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A systems biology approach uncovers novel disease mechanisms in age-related macular degeneration

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Cell Genomics 2023年第6期3卷 100302-100302页

作者： Orozco, Luz D. Owen, Leah A. Hofmann, Jeffrey Stockwell, Amy D. Tao, Jianhua Haller, Susan Mukundan, Vineeth T. Clarke, Christine Lund, Jessica Sridhar, Akshayalakshmi Mayba, Oleg Barr, Julie L. Zavala, Rylee A. Graves, Elijah C. Zhang, Charles Husami, Nadine Finley, Robert Au, Elizabeth Lillvis, John H. Farkas, Michael H. Shakoor, Akbar Sherva, Richard Kim, Ivana K. Kaminker, Joshua S. Townsend, Michael J. Farrer, Lindsay A. Yaspan, Brian L. Chen, Hsu-Hsin DeAngelis, Margaret M. Department of Bioinformatics and Computational Biology Genentech South San Francisco 94080 CA United States Department of Ophthalmology and Visual Sciences University of Utah School of Medicine The University of Utah Salt Lake City 84132 UT United States Department of Population Health Sciences University of Utah School of Medicine The University of Utah Salt Lake City 84132 UT United States Department of Obstetrics and Gynecology University of Utah School of Medicine The University of Utah Salt Lake City 84132 UT United States Department of Ophthalmology Ross Eye Institute Jacobs School of Medicine and Biomedical Sciences State University of New York University at Buffalo Buffalo 14203 NY United States Department of Pathology Genentech South San Francisco 94080 CA United States Department of Human Genetics Genentech South San Francisco 94080 CA United States Departments of Microchemistry Proteomics and Lipidomics Genentech South San Francisco 94080 CA United States Department of Human Pathobiology & OMNI Reverse Translation Genentech South San Francisco 94080 CA United States Neuroscience Graduate Program Jacobs School of Medicine and Biomedical Sciences State University of New York University at Buffalo Buffalo 14203 NY United States Department of Biochemistry Jacobs School of Medicine and Biomedical Sciences State University of New York University at Buffalo Buffalo 14203 NY United States Veterans Administration Western New York Healthcare System Buffalo 14212 NY United States Department of Medicine Biomedical Genetics Boston University School of Medicine Boston 02118 MA United States Retina Service Massachusetts Eye & Ear Department of Ophthalmology Harvard Medical School Boston 02114 MA United States Genetics Genomics and Bioinformatics Graduate Program Jacobs School of Medicine and Biomedical Sciences State University of New York University at Buffalo Buffalo 14203 NY United States

Age-related macular degeneration (AMD) is a leading cause of blindness, affecting 200 million people worldwide. To identify genes that could be targeted for treatment, we created a molecular atlas at different stages of AMD. Our resource is comprised of RNA sequencing (RNA-seq) and DNA methylation microarrays from bulk macular retinal pigment epithelium (RPE)/choroid of clinically phenotyped normal and AMD donor eyes (n = 85), single-nucleus RNA-seq (164,399 cells), and single-nucleus assay for transposase-accessible chromatin (ATAC)-seq (125,822 cells) from the retina, RPE, and choroid of 6 AMD and 7 control donors. We identified 23 genome-wide significant loci differentially methylated in AMD, over 1,000 differentially expressed genes across different disease stages, and an AMD Müller state distinct from normal or gliosis. Chromatin accessibility peaks in genome-wide association study (GWAS) loci revealed putative causal genes for AMD, including HTRA1 and C6orf223. Our systems biology approach uncovered molecular mechanisms underlying AMD, including regulators of WNT signaling, FRZB and TLE2, as mechanistic players in disease. © 2023 The Authors

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Publisher Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers

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Nature genetics 2023年第5期55卷 893页

作者： Yuan Yuan Young Seok Ju Youngwook Kim Jun Li Yumeng Wang Christopher J Yoon Yang Yang Inigo Martincorena Chad J Creighton John N Weinstein Yanxun Xu Leng Han Hyung-Lae Kim Hidewaki Nakagawa Keunchil Park Peter J Campbell Han Liang Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon Korea. Department of Health Science and Technology Samsung Advanced Institute for Health Science and Technology Sungkyunkwan University School of Medicine Seoul Korea. Quantitative and Computational Biosciences Graduate Program Baylor College of Medicine Houston TX USA. Division of Biostatistics The University of Texas Health Science Center at Houston School of Public Health Houston TX USA. Department of Medicine and Dan L. Duncan Cancer Center Division of Biostatistics Baylor College of Medicine Houston TX USA. Department of Systems Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Department of Applied Mathematics and Statistics Johns Hopkins University Baltimore MD USA. Department of Biochemistry and Molecular Biology The University of Texas Health Science Center at Houston McGovern Medical School Houston TX USA. Department of Biochemistry Ewha Womans University School of Medicine Seoul Korea. Laboratory for Cancer Genomics RIKEN Center for Integrative Medical Sciences Yokohama Japan. Division of Hematology/Oncology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Korea. kpark@skku.edu. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK. pc8@sanger.ac.uk. Cambridge University Hospitals NHS Foundation Trust Cambridge UK. pc8@sanger.ac.uk. Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston TX USA. hliang1@***. Quantitative and Computational Biosciences Graduate Program Baylor College of Medicine Houston TX USA. hliang1@***. Department of Systems Biology The University of Texas MD Anderson Cancer Center Houston TX USA. hliang1@mdanderson

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Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers

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Nature genetics 2023年第6期55卷 1078页

作者： Yuan Yuan Young Seok Ju Youngwook Kim Jun Li Yumeng Wang Christopher J Yoon Yang Yang Inigo Martincorena Chad J Creighton John N Weinstein Yanxun Xu Leng Han Hyung-Lae Kim Hidewaki Nakagawa Keunchil Park Peter J Campbell Han Liang Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon Korea. Department of Health Science and Technology Samsung Advanced Institute for Health Science and Technology Sungkyunkwan University School of Medicine Seoul Korea. Samsung Genome Institute Samsung Medical Center Seoul Korea. Quantitative and Computational Biosciences Graduate Program Baylor College of Medicine Houston TX USA. Division of Biostatistics The University of Texas Health Science Center at Houston School of Public Health Houston TX USA. Department of Medicine and Dan L. Duncan Cancer Center Division of Biostatistics Baylor College of Medicine Houston TX USA. Department of Systems Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Department of Applied Mathematics and Statistics Johns Hopkins University Baltimore MD USA. Department of Biochemistry and Molecular Biology The University of Texas Health Science Center at Houston McGovern Medical School Houston TX USA. Department of Biochemistry Ewha Womans University School of Medicine Seoul Korea. Laboratory for Cancer Genomics RIKEN Center for Integrative Medical Sciences Yokohama Japan. Division of Hematology/Oncology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Korea. kpark@skku.edu. Samsung Advanced Institute for Health Sciences and Technology Sungkyunkwan University School of Medicine Seoul South Korea. kpark@skku.edu. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK. pc8@sanger.ac.uk. Department of Haematology University of Cambridge Cambridge UK. pc8@sanger.ac.uk. Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston TX USA. hliang1@mdanderson.org. Quantitative and Comp

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Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data

Research Square

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Research Square 2021年

作者： Zhang, Martin Jinye Hou, Kangcheng Pasaniuc, Bogdan Price, Alkes L. Dey, Kushal K. Jagadeesh, Karthik A. Weinand, Kathryn Sakaue, Saori Taychameekiatchai, Aris Rao, Poorvi Pisco, Angela Oliveira Zou, James Wang, Bruce Gandal, Michael Raychaudhuri, Soumya Harvard University United States Osaka University Japan Department of Epidemiology Harvard T.H. Chan School of Public Health BostonMA United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard CambridgeMA United States Bioinformatics Interdepartmental Program University of California Los Angeles Los AngelesCA United States Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Department of Computational Medicine David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Center for Data Sciences Brigham and Women’s Hospital BostonMA United States Division of Genetics Department of Medicine Brigham and Women’s Hospital Harvard Medical School BostonMA United States Division of Rheumatology Inflammation and Immunity Department of Medicine Brigham and Women’s Hospital Harvard Medical School BostonMA United States Department of Biomedical Informatics Harvard Medical School BostonMA United States Department of Medicine and Liver Center University of California San Francisco San FranciscoCA United States Developmental and Stem Cell Biology Graduate Program University of California San Francisco San FranciscoCA United States Chan Zuckerberg Biohub San FranciscoCA United States Department of Electrical Engineering Stanford University Palo AltoCA United States Department of Biomedical Data Science Stanford University Palo AltoCA United States Department of Psychiatry David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Program in Neurobehavioral Genetics Semel Institute David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Versus Arthritis Centre for Genetics and Genomic

Gene expression at the individual cell-level resolution, as quantified by single-cell RNA-sequencing (scRNA-seq), can provide unique insights into the pathology and cellular origin of diseases and complex traits. Here, we introduce single-cell Disease Relevance Score (scDRS), an approach that links scRNA-seq with polygenic risk of disease at individual cell resolution;scDRS identifies individual cells that show excess expression levels for genes in a disease-specific gene set constructed from GWAS data. We determined via simulations that scDRS is well-calibrated and powerful in identifying individual cells associated to disease. We applied scDRS to GWAS data from 74 diseases and complex traits (average N =341K) in conjunction with 16 scRNA-seq data sets spanning 1.3 million cells from 31 tissues and organs. At the cell type level, scDRS broadly recapitulated known links between classical cell types and disease, and also produced novel biologically plausible findings. At the individual cell level, scDRS identified subpopulations of disease-associated cells that are not captured by existing cell type labels, including subpopulations of CD4+ T cells associated with inflammatory bowel disease, partially characterized by their effector-like states;subpopulations of hippocampal CA1 pyramidal neurons associated with schizophrenia, partially characterized by their spatial location at the proximal part of the hippocampal CA1 region;and subpopulations of hepatocytes associated with triglyceride levels, partially characterized by their higher ploidy levels. At the gene level, we determined that genes whose expression across individual cells was correlated with the scDRS score (thus reflecting co-expression with GWAS disease genes) were strongly enriched for gold-standard drug target and Mendelian disease genes. © 2021, CC BY.

关键词： RNA

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Chronic obstructive pulmonary disease and related phenotypes: polygenic risk scores in population-based and case-control cohorts

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The Lancet Respiratory Medicine 2020年第7期8卷 696-708页

作者： Moll, Matthew Sakornsakolpat, Phuwanat Shrine, Nick Hobbs, Brian D DeMeo, Dawn L John, Catherine Guyatt, Anna L McGeachie, Michael J Gharib, Sina A Obeidat, Ma'en Lahousse, Lies Wijnant, Sara R A Brusselle, Guy Meyers, Deborah A Bleecker, Eugene R Li, Xingnan Tal-Singer, Ruth Manichaikul, Ani Rich, Stephen S Won, Sungho Kim, Woo Jin Do, Ah Ra Washko, George R Barr, R Graham Psaty, Bruce M Bartz, Traci M Hansel, Nadia N Barnes, Kathleen Hokanson, John E Crapo, James D Lynch, David Bakke, Per Gulsvik, Amund Hall, Ian P Wain, Louise Soler Artigas, María Jackson, Victoria E Strachan, David P Hui, Jennie James, Alan L Kerr, Shona M Polasek, Ozren Vitart, Veronique Marten, Jonathan Rudan, Igor Kähönen, Mika Surakka, Ida Gieger, Christian Karrasch, Stefan Rawal, Rajesh Schulz, Holger Deary, Ian J Harris, Sarah E Enroth, Stefan Gyllensten, Ulf Imboden, Medea Probst-Hensch, Nicole M Lehtimäki, Terho Raitakari, Olli T Langenberg, Claudia Luan, Jian'an Wareham, Nick Zhao, Jing Hua Hayward, Caroline Murray, Alison Porteous, David J Smith, Blair H Jarvelin, Marjo-Riitta Wielscher, Matthias Joshi, Peter K Kentistou, Katherine A Timmers, Paul RHJ Wilson, James F Cook, James P Lind, Lars Mahajan, Anubha Morris, Andrew P Ewert, Ralf Homuth, Georg Stubbe, Beate Weiss, Stefan Zeggini, Eleftheria Weiss, Scott T Silverman, Edwin K Dudbridge, Frank Tobin, Martin D Cho, Michael H Channing Division of Network Medicine Brigham and Women's Hospital Boston MA United States Division of Pulmonary and Critical Care Medicine Brigham and Women's Hospital Boston MA United States Department of Medicine Faculty of Medicine Siriraj Hospital Mahidol University Bangkok Thailand Genetic Epidemiology Group Department of Health Sciences University of Leicester Leicester United Kingdom Computational Medicine Core Center for Lung Biology Department of Medicine University of Washington Seattle WA United States Division of Pulmonary Critical Care and Sleep Medicine Department of Medicine University of Washington Seattle WA United States Cardiovascular Health Research Unit Department of Medicine University of Washington Seattle WA United States University of British Columbia Center for Heart Lung Innovation St Paul's Hospital Vancouver BC Canada Department of Epidemiology Erasmus Medical Centre Rotterdam Netherlands Department of Respiratory Medicine Erasmus Medical Centre Rotterdam Netherlands Department of Bioanalysis Faculty of Pharmaceutical Sciences Ghent University Ghent Belgium Department of Respiratory Medicine Ghent University Hospital Ghent Belgium Department of Medicine University of Arizona Tucson AZ United States GlaxoSmithKline Research and Development Collegeville PA United States Center for Public Health Genomics University of Virginia Charlottesville VA United States Department of Public Health Sciences University of Virginia Charlottesville VA United States Department of Public Health Sciences Graduate School of Public Health Seoul National University Seoul South Korea Interdisciplinary Program of Bioinformatics College of National Sciences Seoul National University Seoul South Korea Institute of Health and Environment Seoul National University Seoul South Korea Department of Internal Medicine Kangwon National University Chuncheon South Korea Department of Medicine and Department of Epidemiology Columbia Universit

Background: Genetic factors influence chronic obstructive pulmonary disease (COPD) risk, but the individual variants that have been identified have small effects. We hypothesised that a polygenic risk score using additional variants would predict COPD and associated phenotypes. Methods: We constructed a polygenic risk score using a genome-wide association study of lung function (FEV₁ and FEV₁/forced vital capacity [FVC]) from the UK Biobank and SpiroMeta. We tested this polygenic risk score in nine cohorts of multiple ethnicities for an association with moderate-to-severe COPD (defined as FEV₁/FVC <0·7 and FEV₁ <80% of predicted). Associations were tested using logistic regression models, adjusting for age, sex, height, smoking pack-years, and principal components of genetic ancestry. We assessed predictive performance of models by area under the curve. In a subset of studies, we also studied quantitative and qualitative CT imaging phenotypes that reflect parenchymal and airway pathology, and patterns of reduced lung growth. Findings: The polygenic risk score was associated with COPD in European (odds ratio [OR] per SD 1·81 [95% CI 1·74–1·88] and non-European (1·42 [1·34–1·51]) populations. Compared with the first decile, the tenth decile of the polygenic risk score was associated with COPD, with an OR of 7·99 (6·56–9·72) in European ancestry and 4·83 (3·45–6·77) in non-European ancestry cohorts. The polygenic risk score was superior to previously described genetic risk scores and, when combined with clinical risk factors (ie, age, sex, and smoking pack-years), showed improved prediction for COPD compared with a model comprising clinical risk factors alone (AUC 0·80 [0·79–0·81] vs 0·76 [0·75–0·76]). The polygenic risk score was associated with CT imaging phenotypes, including wall area percent, quantitative and qualitative measures of emphysema, local histogram emphysema patterns, and destructive emphysema subtypes. The po

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Correction to: Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD

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Conservation Genetics 2021年第4期22卷 537-539页

作者： Laikre, Linda Hohenlohe, Paul A. Allendorf, Fred W. Bertola, Laura D. Breed, Martin F. Bruford, Michael W. Funk, W. Chris Gajardo, Gonzalo González-Rodríguez, Antonio Grueber, Catherine E. Hedrick, Philip W. Heuertz, Myriam Hunter, Margaret E. Johannesson, Kerstin Liggins, Libby MacDonald, Anna J. Mergeay, Joachim Moharrek, Farideh O’Brien, David Ogden, Rob Orozco-terWengel, Pablo Palma-Silva, Clarisse Pierson, Jennifer Paz-Vinas, Ivan Russo, Isa-Rita M. Ryman, Nils Segelbacher, Gernot Sjögren-Gulve, Per Waits, Lisette P. Vernesi, Cristiano Hoban, Sean Division of Population Genetics Department of Zoology Stockholm University Stockholm Sweden Institute for Bioinformatics and Evolutionary Studies Department of Biological Sciences University of Idaho Moscow USA Division of Biological Sciences University of Montana Missoula USA City College of New York New York USA College of Science and Engineering Flinders University Bedford Park Australia School of Biosciences Cardiff University Cardiff Wales UK Graduate Degree Program in Ecology Department of Biology Colorado State University Fort Collins USA Universidad de Los Lagos Lab Genetics Aquaculture & Biodiversity Osorno Chile Instituto de Investigaciones en Ecosistemas y Sustentabilidad Universidad Nacional Autónoma de México Morelia Mexico School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia School of Life Sciences Arizona State University Tempe USA INRAE Univ. Bordeaux Biogeco Cestas France U.S. Geological Survey Wetland and Aquatic Research Center Gainesville USA Department of Marine Sciences University of Gothenburg Tjärnö Strömstad Sweden School of Natural and Computational Sciences Massey University Auckland New Zealand The John Curtin School of Medical Research/Research School of Biology The Australian National University Acton Australia Research Institute for Nature and Forest Geraardsbergen Belgium Aquatic Ecology Evolution and Conservation KULeuven Leuven Belgium Novo Nordisk Foundation Center for Basic Metabolic Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Faculty of Biological Sciences Tarbiat Modares University Tehran Iran Scottish Natural Heritage Inverness UK Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Midlothian UK Department of Plant Science Institute of Biology University of Campinas Campinas Brazil Australian Wildlife Conservancy Subiaco East Australia Laboratoire Evolution & Div

A correction to this paper has been published: https://***/10.1007/s10592-021-01376-9

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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge CB2 1EW UK Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge UK Ludwig Center at Harvard Medical School Boston MA USA School of Mathematical Sciences and Center for Statistical Science Peking University Beijing 100871 China Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Bioi

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Immunity geneIFITM3variant: relation to cognition and Alzheimer pathology

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Alzheimer's & Dementia 2023年第S1期19卷

作者： Jung-Min Pyun Young Ho Park Moon-ku Han Angela Hodges Jae-Won Jang Paula Bice SangYun Kim Andrew J. Saykin Kwangsik Nho Seoul National University Bundang Hospital Seongnam Korea Republic of South Korea Soonchunhyang University Seoul Hospital Seoul Korea Republic of South Korea King’s College London London United Kingdom Interdisciplinary Graduate Program in Medical Bigdata Convergence Kangwon National University Chuncheon Korea Republic of South Korea Indiana University School of Medicine Indianapolis IN USA Seoul National University Bundang Hospital Seoul National University College of Medicine Seongnam Korea Republic of South Korea Indiana Alzheimer’s Disease Research Center Indiana University School of Medicine Indianapolis IN USA Department of Radiology and Imaging Sciences Indiana University School of Medicine Indianapolis IN USA Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN USA Center for Computational Biology and Bioinformatics Indiana University School of Medicine Indianapolis IN USA Indiana Alzheimer’s Disease Research Center Indianapolis IN USA

Background IFITM3, an innate immune response protein and inhibitor of viral infection, was reported to modulate amyloid-β production in Alzheimer’s disease (AD). We aimed to identify single-nucleotide polymorphisms (SNPs) in IFITM3 associated with cognition and AD biomarkers. Method We used genetic, longitudinal cognition and AD biomarker data from Alzheimer’s Disease Neuroimaging Initiative (ADNI; N = 1,565) and AddNeuroMed (N = 633) as discovery and replication samples, respectively. First, we performed gene-based association analysis of SNPs in IFITM3 with cognitive performance. Second, we performed SNP-based association analysis in IFITM3 with cognitive decline and AD biomarkers from amyloid positron emission tomography (PET), cerebrospinal fluid (CSF), and magnetic resonance imaging (MRI). Result Gene-based association analysis showed that IFITM3 was significantly associated with cognitive performance (permutation-corrected p = 1.25×10 −3 ). Particularly, among two SNPs (rs10751647, rs2091850) in IFITM3 significantly associated with cognitive performance, rs10751647 was associated with cognitive decline in ADNI, which was replicated in AddNeuroMed. In addition, rs10751647 was significantly associated with amyloid-β deposition measured by amyloid PET scan, CSF phosphorylated tau levels, and entorhinal cortical thickness measured by MRI scan in ADNI. The association of rs10751647 with entorhinal cortical thickness was replicated in AddNeuroMed. Participants with minor alleles (C) of rs10751647 have less cognitive decline, less amyloid and tau burden, and less brain atrophy. eQTL analysis showed that rs10751647 is associated with IFITM3 expression levels in blood and brain. Conclusion This suggests that rs10751647 in IFITM3 is associated with less vulnerability for cognitive decline and AD biomarkers, providing mechanistic insight regarding involvement of immune activity and infection in AD.

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