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Fortuno C, Feng BJ, Carroll C, Innella G, Kohlmann W, Lázaro C, Brunet J, Feliubadaló L, Iglesias S, Menéndez M, Teulé A, Ballinger ML, Thomas DM, Campbell A, Field M, Harris M, Kirk J, Pachter N, Poplawski N, Susman R, Tucker K, Wallis M, Williams R, Cops E, Goldgar D, James PA, Spurdle AB. Cancer Risks Associated With TP53 Pathogenic Variants: Maximum Likelihood Analysis of Extended Pedigrees for Diagnosis of First Cancers Beyond the Li-Fraumeni Syndrome Spectrum. JCO Precis Oncol 2024; 8:e2300453. [PMID: 38412388 PMCID: PMC10914239 DOI: 10.1200/po.23.00453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/23/2023] [Accepted: 12/21/2023] [Indexed: 02/29/2024] Open
Abstract
PURPOSE Establishing accurate age-related penetrance figures for the broad range of cancer types that occur in individuals harboring a pathogenic germline variant in the TP53 gene is essential to determine the most effective clinical management strategies. These figures also permit optimal use of cosegregation data for classification of TP53 variants of unknown significance. Penetrance estimation can easily be affected by bias from ascertainment criteria, an issue not commonly addressed by previous studies. MATERIALS AND METHODS We performed a maximum likelihood penetrance estimation using full pedigree data from a multicenter study of 146 TP53-positive families, incorporating adjustment for the effect of ascertainment and population-specific background cancer risks. The analysis included pedigrees from Australia, Spain, and United States, with phenotypic information for 4,028 individuals. RESULTS Core Li-Fraumeni syndrome (LFS) cancers (breast cancer, adrenocortical carcinoma, brain cancer, osteosarcoma, and soft tissue sarcoma) had the highest hazard ratios of all cancers analyzed in this study. The analysis also detected a significantly increased lifetime risk for a range of cancers not previously formally associated with TP53 pathogenic variant status, including colorectal, gastric, lung, pancreatic, and ovarian cancers. The cumulative risk of any cancer type by age 50 years was 92.4% (95% CI, 82.2 to 98.3) for females and 59.7% (95% CI, 39.9 to 81.3) for males. Females had a 63.3% (95% CI, 35.6 to 90.1) cumulative risk of developing breast cancer by age 50 years. CONCLUSION The results from maximum likelihood analysis confirm the known high lifetime risk for the core LFS-associated cancer types providing new risk estimates and indicate significantly increased lifetime risks for several additional cancer types. Accurate cancer risk estimates will help refine clinical recommendations for TP53 pathogenic variant carriers and improve TP53 variant classification.
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Affiliation(s)
- Cristina Fortuno
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Bing-Jian Feng
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Courtney Carroll
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Giovanni Innella
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Wendy Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
- Hereditary Cancer Program, ONCOBELL, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
- Hereditary Cancer Program, ONCOBELL, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
- Precision Oncology in Girona, IDIBGI, Girona, Spain
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
- Hereditary Cancer Program, ONCOBELL, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Silvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Mireia Menéndez
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Alex Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
- Hereditary Cancer Program, ONCOBELL, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Mandy L. Ballinger
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, New South Wales, Australia
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - David M. Thomas
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Centre for Molecular Oncology, Faculty of Medicine, University of New South Wales, New South Wales, Australia
| | - Ainsley Campbell
- Department of Clinical Genetics, Austin Health, Melbourne, Victoria, Australia
| | - Mike Field
- Familial Cancer Service, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Marion Harris
- Monash Health Familial Cancer Service, Melbourne, Victoria, Australia
| | - Judy Kirk
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Westmead, New South Wales, Australia
| | - Nicholas Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia, Australia
| | - Nicola Poplawski
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Kathy Tucker
- Hereditary Cancer Clinic, Prince of Wales Hospital, Randwick, New South Wales, Australia
- Prince of Wales Clinical School, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Royal Hobart Hospital, Hobart, Tasmania, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Rachel Williams
- Prince of Wales Clinical School, UNSW Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
- Prince of Wales Hereditary Cancer Centre, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Elisa Cops
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - David Goldgar
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - kConFab Investigators
- kConFab, Research Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Paul A. James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Amanda B. Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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Archer DB, Eissman JM, Mukherjee S, Lee ML, Choi S, Scollard P, Trittschuh EH, Mez JB, Bush WS, Kunkle BW, Naj AC, Gifford KA, Cuccaro ML, Pericak‐Vance MA, Farrer LA, Wang L, Schellenberg GD, Mayeux RP, Haines JL, Jefferson AL, Kukull WA, Keene CD, Saykin AJ, Thompson PM, Martin ER, Bennett DA, Barnes LL, Schneider JA, Crane PK, Dumitrescu L, Hohman TJ. Longitudinal change in memory performance as a strong endophenotype for Alzheimer's disease. Alzheimers Dement 2024; 20:1268-1283. [PMID: 37985223 PMCID: PMC10896586 DOI: 10.1002/alz.13508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 11/22/2023]
Abstract
INTRODUCTION Although large-scale genome-wide association studies (GWAS) have been conducted on AD, few have been conducted on continuous measures of memory performance and memory decline. METHODS We conducted a cross-ancestry GWAS on memory performance (in 27,633 participants) and memory decline (in 22,365 participants; 129,201 observations) by leveraging harmonized cognitive data from four aging cohorts. RESULTS We found high heritability for two ancestry backgrounds. Further, we found a novel ancestry locus for memory decline on chromosome 4 (rs6848524) and three loci in the non-Hispanic Black ancestry group for memory performance on chromosomes 2 (rs111471504), 7 (rs4142249), and 15 (rs74381744). In our gene-level analysis, we found novel genes for memory decline on chromosomes 1 (SLC25A44), 11 (BSX), and 15 (DPP8). Memory performance and memory decline shared genetic architecture with AD-related traits, neuropsychiatric traits, and autoimmune traits. DISCUSSION We discovered several novel loci, genes, and genetic correlations associated with late-life memory performance and decline. HIGHLIGHTS Late-life memory has high heritability that is similar across ancestries. We discovered four novel variants associated with late-life memory. We identified four novel genes associated with late-life memory. Late-life memory shares genetic architecture with psychiatric/autoimmune traits.
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Greenfest‐Allen E, Valladares O, Kuksa PP, Gangadharan P, Lee W, Cifello J, Katanic Z, Kuzma AB, Wheeler N, Bush WS, Leung YY, Schellenberg G, Stoeckert CJ, Wang L. NIAGADS Alzheimer's GenomicsDB: A resource for exploring Alzheimer's disease genetic and genomic knowledge. Alzheimers Dement 2024; 20:1123-1136. [PMID: 37881831 PMCID: PMC10916966 DOI: 10.1002/alz.13509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/25/2023] [Accepted: 09/21/2023] [Indexed: 10/27/2023]
Abstract
INTRODUCTION The National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site Alzheimer's Genomics Database (GenomicsDB) is a public knowledge base of Alzheimer's disease (AD) genetic datasets and genomic annotations. METHODS GenomicsDB uses a custom systems architecture to adopt and enforce rigorous standards that facilitate harmonization of AD-relevant genome-wide association study summary statistics datasets with functional annotations, including over 230 million annotated variants from the AD Sequencing Project. RESULTS GenomicsDB generates interactive reports compiled from the harmonized datasets and annotations. These reports contextualize AD-risk associations in a broader functional genomic setting and summarize them in the context of functionally annotated genes and variants. DISCUSSION Created to make AD-genetics knowledge more accessible to AD researchers, the GenomicsDB is designed to guide users unfamiliar with genetic data in not only exploring but also interpreting this ever-growing volume of data. Scalable and interoperable with other genomics resources using data technology standards, the GenomicsDB can serve as a central hub for research and data analysis on AD and related dementias. HIGHLIGHTS The National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS) offers to the public a unique, disease-centric collection of AD-relevant GWAS summary statistics datasets. Interpreting these data is challenging and requires significant bioinformatics expertise to standardize datasets and harmonize them with functional annotations on genome-wide scales. The NIAGADS Alzheimer's GenomicsDB helps overcome these challenges by providing a user-friendly public knowledge base for AD-relevant genetics that shares harmonized, annotated summary statistics datasets from the NIAGADS repository in an interpretable, easily searchable format.
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Affiliation(s)
- Emily Greenfest‐Allen
- Penn Neurodegeneration Genomics CenterPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Institute for Biomedical InformaticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Pathology and Laboratory MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Otto Valladares
- Penn Neurodegeneration Genomics CenterPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Institute for Biomedical InformaticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Pathology and Laboratory MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Pavel P. Kuksa
- Penn Neurodegeneration Genomics CenterPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Institute for Biomedical InformaticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Pathology and Laboratory MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Prabhakaran Gangadharan
- Penn Neurodegeneration Genomics CenterPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Institute for Biomedical InformaticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Pathology and Laboratory MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Wan‐Ping Lee
- Penn Neurodegeneration Genomics CenterPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Institute for Biomedical InformaticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Pathology and Laboratory MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jeffrey Cifello
- Penn Neurodegeneration Genomics CenterPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Pathology and Laboratory MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Zivadin Katanic
- Penn Neurodegeneration Genomics CenterPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Institute for Biomedical InformaticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Pathology and Laboratory MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Amanda B. Kuzma
- Penn Neurodegeneration Genomics CenterPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Institute for Biomedical InformaticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Pathology and Laboratory MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Nicholas Wheeler
- Cleveland Institute for Computational BiologyDepartment of Population and Quantitative Health SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - William S. Bush
- Cleveland Institute for Computational BiologyDepartment of Population and Quantitative Health SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics CenterPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Institute for Biomedical InformaticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Pathology and Laboratory MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Gerard Schellenberg
- Penn Neurodegeneration Genomics CenterPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Institute for Biomedical InformaticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Pathology and Laboratory MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Christian J. Stoeckert
- Institute for Biomedical InformaticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of GeneticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Li‐San Wang
- Penn Neurodegeneration Genomics CenterPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Institute for Biomedical InformaticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Pathology and Laboratory MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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Ishikawa Y, Tanaka N, Asano Y, Kodera M, Shirai Y, Akahoshi M, Hasegawa M, Matsushita T, Saito K, Motegi SI, Yoshifuji H, Yoshizaki A, Kohmoto T, Takagi K, Oka A, Kanda M, Tanaka Y, Ito Y, Nakano K, Kasamatsu H, Utsunomiya A, Sekiguchi A, Niiro H, Jinnin M, Makino K, Makino T, Ihn H, Yamamoto M, Suzuki C, Takahashi H, Nishida E, Morita A, Yamamoto T, Fujimoto M, Kondo Y, Goto D, Sumida T, Ayuzawa N, Yanagida H, Horita T, Atsumi T, Endo H, Shima Y, Kumanogoh A, Hirata J, Otomo N, Suetsugu H, Koike Y, Tomizuka K, Yoshino S, Liu X, Ito S, Hikino K, Suzuki A, Momozawa Y, Ikegawa S, Tanaka Y, Ishikawa O, Takehara K, Torii T, Sato S, Okada Y, Mimori T, Matsuda F, Matsuda K, Amariuta T, Imoto I, Matsuo K, Kuwana M, Kawaguchi Y, Ohmura K, Terao C. GWAS for systemic sclerosis identifies six novel susceptibility loci including one in the Fcγ receptor region. Nat Commun 2024; 15:319. [PMID: 38296975 PMCID: PMC10830486 DOI: 10.1038/s41467-023-44541-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 12/18/2023] [Indexed: 02/02/2024] Open
Abstract
Here we report the largest Asian genome-wide association study (GWAS) for systemic sclerosis performed to date, based on data from Japanese subjects and comprising of 1428 cases and 112,599 controls. The lead SNP is in the FCGR/FCRL region, which shows a penetrating association in the Asian population, while a complete linkage disequilibrium SNP, rs10917688, is found in a cis-regulatory element for IRF8. IRF8 is also a significant locus in European GWAS for systemic sclerosis, but rs10917688 only shows an association in the presence of the risk allele of IRF8 in the Japanese population. Further analysis shows that rs10917688 is marked with H3K4me1 in primary B cells. A meta-analysis with a European GWAS detects 30 additional significant loci. Polygenic risk scores constructed with the effect sizes of the meta-analysis suggest the potential portability of genetic associations beyond populations. Prioritizing the top 5% of SNPs of IRF8 binding sites in B cells improves the fitting of the polygenic risk scores, underscoring the roles of B cells and IRF8 in the development of systemic sclerosis. The results also suggest that systemic sclerosis shares a common genetic architecture across populations.
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Affiliation(s)
- Yuki Ishikawa
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Nao Tanaka
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshihide Asano
- Department of Dermatology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Dermatology, The University of Tokyo, Tokyo, Japan
| | - Masanari Kodera
- Department of Dermatology, Chukyo Hospital, Japan Community Health Care Organization, Nagoya, Japan
| | - Yuichiro Shirai
- Department of Allergy and Rheumatology, Nippon Medical School Graduate School of Medicine, Tokyo, Japan
| | - Mitsuteru Akahoshi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
- Department of Rheumatology, Saga University Hospital, Saga, Japan
| | - Minoru Hasegawa
- Faculty of Medical Sciences, Department of Dermatology, University of Fukui, Fukui, Japan
| | - Takashi Matsushita
- Department of Dermatology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Saito
- The First Department of Internal Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
| | - Sei-Ichiro Motegi
- Department of Dermatology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hajime Yoshifuji
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ayumi Yoshizaki
- Department of Dermatology, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Kohmoto
- Aichi Cancer Center Research Institute, Division of Molecular Genetics, Nagoya, Japan
| | - Kae Takagi
- Tokyo Women's Medical University, Adachi Medical Center, Tokyo, Japan
| | - Akira Oka
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Miho Kanda
- Department of Dermatology, Chukyo Hospital, Japan Community Health Care Organization, Nagoya, Japan
| | - Yoshihito Tanaka
- Department of Dermatology, Chukyo Hospital, Japan Community Health Care Organization, Nagoya, Japan
| | - Yumi Ito
- Department of Dermatology, Chukyo Hospital, Japan Community Health Care Organization, Nagoya, Japan
| | - Kazuhisa Nakano
- The First Department of Internal Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
| | - Hiroshi Kasamatsu
- Faculty of Medical Sciences, Department of Dermatology, University of Fukui, Fukui, Japan
| | - Akira Utsunomiya
- Faculty of Medical Sciences, Department of Dermatology, University of Fukui, Fukui, Japan
| | - Akiko Sekiguchi
- Department of Dermatology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hiroaki Niiro
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Masatoshi Jinnin
- Department of Dermatology, Wakayama Medical University Graduate School of Medicine, Wakayama, Japan
| | - Katsunari Makino
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takamitsu Makino
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hironobu Ihn
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Motohisa Yamamoto
- Department of Rheumatology and Allergy, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Chisako Suzuki
- Department of Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroki Takahashi
- Department of Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Emi Nishida
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
- Department of Dermatology, Okazaki City Hospital, Okazaki, Japan
| | - Akimichi Morita
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Toshiyuki Yamamoto
- Department of Dermatology, Fukushima Medical University, School of Medicine, Fukushima, Japan
| | - Manabu Fujimoto
- Department of Dermatology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuya Kondo
- Department of Rheumatology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Daisuke Goto
- Department of Rheumatology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Takayuki Sumida
- Department of Rheumatology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Naho Ayuzawa
- Department of Clinical Immunology, National Hospital Organization, Utano National Hospital, Kyoto, Japan
| | - Hidetoshi Yanagida
- Department of Clinical Immunology, National Hospital Organization, Utano National Hospital, Kyoto, Japan
| | - Tetsuya Horita
- Faculty of Medicine and Graduate School of Medicine, Department of Rheumatology, Endocrinology and Nephrology, Hokkaido University, Sapporo, Japan
| | - Tatsuya Atsumi
- Faculty of Medicine and Graduate School of Medicine, Department of Rheumatology, Endocrinology and Nephrology, Hokkaido University, Sapporo, Japan
| | - Hirahito Endo
- Omori Medical Center, Toho University, Rheumatic Disease Center, Tokyo, Japan
| | - Yoshihito Shima
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Jun Hirata
- Immunology Frontier Center, Osaka University, Statistical Immunology, Osaka, Japan
| | - Nao Otomo
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Hiroyuki Suetsugu
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Yoshinao Koike
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Kohei Tomizuka
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Soichiro Yoshino
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Xiaoxi Liu
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Shuji Ito
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Keiko Hikino
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Pharmacogenomics, Yokohama, Japan
| | - Akari Suzuki
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Autoimmune Diseases, Yokohama, Japan
| | - Yukihide Momozawa
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Genotyping Development, Yokohama, Japan
| | - Shiro Ikegawa
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Bone and Joint Diseases, Yokohama, Japan
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
| | - Osamu Ishikawa
- Department of Dermatology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kazuhiko Takehara
- Department of Dermatology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | | | - Shinichi Sato
- Department of Dermatology, The University of Tokyo, Tokyo, Japan
| | - Yukinori Okada
- Immunology Frontier Center, Osaka University, Statistical Immunology, Osaka, Japan
| | - Tsuneyo Mimori
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Ijinkai Takeada General Hospital, Kyoto, Japan
| | - Fumihiko Matsuda
- Graduate School of Medicine, Kyoto University, Center for Genomic Medicine, Kyoto, Japan
| | - Koichi Matsuda
- Institute of Medical Science, The University of Tokyo, Laboratory of Genome Technology, Human Genome Center, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tiffany Amariuta
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Issei Imoto
- Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Keitaro Matsuo
- Aichi Cancer Center Research Institute, Division of Cancer Epidemiology and Prevention, Nagoya, Japan
| | - Masataka Kuwana
- Department of Allergy and Rheumatology, Nippon Medical School Graduate School of Medicine, Tokyo, Japan
| | - Yasushi Kawaguchi
- Tokyo Women's Medical University, Division of Rheumatology, Department of Internal Medicine, Tokyo, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan.
- Shizuoka General Hospital, The Clinical Research Center, Shizuoka, Japan.
- The Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
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105
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Singh H, Shipra, Gupta M, Gupta N, Gupta G, Pandita AK, Sharma R, Pandita S, Singh V, Garg B, Rai E, Sharma S. SOX9 gene shows association with adolescent idiopathic scoliosis predisposition in Northwest Indians. Eur J Med Res 2024; 29:66. [PMID: 38245767 PMCID: PMC10799485 DOI: 10.1186/s40001-024-01635-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Adolescent idiopathic scoliosis (AIS) is a common structural deformity of the spine affecting adolescent individuals globally. The disorder is polygenic and is accompanied by the association of various genetic loci. Genetic studies in Chinese and Japanese populations have shown the association of genetic variants of SOX9 with AIS curve severity. However, no genetic study evaluating the association of SRY-Box Transcription Factor 9 (SOX9) variants with AIS predisposition has been conducted in any Indian population. Thus, we aimed to investigate the association of the genetic variants of the SOX9 along with 0.88 Mb upstream region with AIS susceptibility in the population of Northwest India. METHODS In total, 113 AIS cases and 500 non-AIS controls were recruited from the population of Northwest India in the study and screened for 155 genetic variants across the SOX9 gene and 0.88 Mb upstream region of the gene using Global Screening Array-24 v3.0 chip (Illumina). The statistical significance of the Bonferroni threshold was set at 0.000322. RESULT The results showed the association of 11 newly identified variants; rs9302936, rs7210997, rs77736349, rs12940821, rs9302937, rs77447012, rs8071904, rs74898711, rs9900249, rs2430514, and rs1042667 with the AIS susceptibility in the studied population. Only one variant, rs2430514, was inversely associated with AIS in the population, while the ten variants were associated with the AIS risk. Moreover, 47 variants clustered in the gene desert region of the SOX9 gene were associated at a p-value ≤ 0.05. CONCLUSION The present study is the first to demonstrate the association of SOX9 enhancer locus variants with AIS in any South Asian Indian population. The results are interesting as rs1042667, a 3' untranslated region (UTR) variant in the exon 3 and upstream variants of the SOX9 gene, were associated with AIS susceptibility in the Northwest Indian population. This provides evidence that the variants in the enhancer region of SOX9 might regulate its gene expression, thus leading to AIS pathology and might act as an important gene for AIS susceptibility.
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Affiliation(s)
- Hemender Singh
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Shipra
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Manish Gupta
- Department of Orthopaedics, All India Institute of Medical Sciences, New Delhi, India
| | - Nital Gupta
- District Hospital Poonch, Poonch, Jammu and Kashmir, India
| | - Geetanjali Gupta
- Department of Radiology, Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, Jammu and Kashmir, India
| | - Ajay K Pandita
- Accidental Hospital, Chowki Choura, Jammu, Jammu and Kashmir, India
| | - Rajesh Sharma
- Government Medical College, Jammu, Jammu and Kashmir, India
| | - Sarla Pandita
- Chest Disease Hospital, Bakshi Nagar, Jammu, Jammu and Kashmir, India
| | - Vinod Singh
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Bhavuk Garg
- Department of Orthopaedics, All India Institute of Medical Sciences, New Delhi, India
| | - Ekta Rai
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India.
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
| | - Swarkar Sharma
- Human Genetics Research Lab, Centre for Molecular Biology, Central University of Jammu, Jammu, India.
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Sarsani V, Brotman SM, Xianyong Y, Fernandes Silva L, Laakso M, Spracklen CN. A cross-ancestry genome-wide meta-analysis, fine-mapping, and gene prioritization approach to characterize the genetic architecture of adiponectin. HGG Adv 2024; 5:100252. [PMID: 37859345 PMCID: PMC10652123 DOI: 10.1016/j.xhgg.2023.100252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023] Open
Abstract
Previous genome-wide association studies (GWASs) for adiponectin, a complex trait linked to type 2 diabetes and obesity, identified >20 associated loci. However, most loci were identified in populations of European ancestry, and many of the target genes underlying the associations remain unknown. We conducted a cross-ancestry adiponectin GWAS meta-analysis in ≤46,434 individuals from the Metabolic Syndrome in Men (METSIM) cohort and the ADIPOGen and AGEN consortiums. We combined study-specific association summary statistics using a fixed-effects, inverse variance-weighted approach. We identified 22 loci associated with adiponectin (p < 5×10-8), including 15 known and seven previously unreported loci. Among individuals of European ancestry, Genome-wide Complex Traits Analysis joint conditional analysis (GCTA-COJO) identified 14 additional distinct signals at the ADIPOQ, CDH13, HCAR1, and ZNF664 loci. Leveraging the cross-ancestry data, FINEMAP + SuSiE identified 45 causal variants (PP > 0.9), which also exhibited potential pleiotropy for cardiometabolic traits. To prioritize target genes at associated loci, we propose a combinatorial likelihood scoring formalism (Gene Priority Score [GPScore]) based on measures derived from 11 gene prioritization strategies and the physical distance to the transcription start site. With GPScore, we prioritize the 30 most probable target genes underlying the adiponectin-associated variants in the cross-ancestry analysis, including well-known causal genes (e.g., ADIPOQ, CDH13) and additional genes (e.g., CSF1, RGS17). Functional association networks revealed complex interactions of prioritized genes, their functionally connected genes, and their underlying pathways centered around insulin and adiponectin signaling, indicating an essential role in regulating energy balance in the body, inflammation, coagulation, fibrinolysis, insulin resistance, and diabetes. Overall, our analyses identify and characterize adiponectin association signals and inform experimental interrogation of target genes for adiponectin.
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Affiliation(s)
- Vishal Sarsani
- Department of Mathematics and Statistics, University of Massachusetts Amherst, Amherst, MA, USA
| | - Sarah M Brotman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yin Xianyong
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Lillian Fernandes Silva
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Cassandra N Spracklen
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst, Amherst, MA, USA.
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107
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de Andrade KC, Strande NT, Kim J, Haley JS, Hatton JN, Frone MN, Khincha PP, Thone GM, Mirshahi UL, Schneider C, Desai H, Dove JT, Smelser DT, Levine AJ, Maxwell KN, Stewart DR, Carey DJ, Savage SA. Genome-first approach of the prevalence and cancer phenotypes of pathogenic or likely pathogenic germline TP53 variants. HGG Adv 2024; 5:100242. [PMID: 37777824 PMCID: PMC10589747 DOI: 10.1016/j.xhgg.2023.100242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/02/2023] Open
Abstract
Pathogenic or likely pathogenic (P/LP) germline TP53 variants are the primary cause of Li-Fraumeni syndrome (LFS), a hereditary cancer predisposition disorder characterized by early-onset cancers. The population prevalence of P/LP germline TP53 variants is estimated to be approximately one in every 3,500 to 20,000 individuals. However, these estimates are likely impacted by ascertainment biases and lack of clinical and genetic data to account for potential confounding factors, such as clonal hematopoiesis. Genome-first approaches of cohorts linked to phenotype data can further refine these estimates by identifying individuals with variants of interest and then assessing their phenotypes. This study evaluated P/LP germline (variant allele fraction ≥30%) TP53 variants in three cohorts: UK Biobank (UKB, n = 200,590), Geisinger (n = 170,503), and Penn Medicine Biobank (PMBB, n = 43,731). A total of 109 individuals were identified with P/LP germline TP53 variants across the three databases. The TP53 p.R181H variant was the most frequently identified (9 of 109 individuals, 8%). A total of 110 cancers, including 47 hematologic cancers (47 of 110, 43%), were reported in 71 individuals. The prevalence of P/LP germline TP53 variants was conservatively estimated as 1:10,439 in UKB, 1:3,790 in Geisinger, and 1:2,983 in PMBB. These estimates were calculated after excluding related individuals and accounting for the potential impact of clonal hematopoiesis by excluding heterozygotes who ever developed a hematologic cancer. These varying estimates likely reflect intrinsic selection biases of each database, such as healthcare or population-based contexts. Prospective studies of diverse, young cohorts are required to better understand the population prevalence of germline TP53 variants and their associated cancer penetrance.
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Affiliation(s)
- Kelvin C de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Natasha T Strande
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jeremy S Haley
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Jessica N Hatton
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Megan N Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Payal P Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gretchen M Thone
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Uyenlinh L Mirshahi
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Cynthia Schneider
- Division of Hematology/Oncology, Department of Medicine and Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Heena Desai
- Division of Hematology/Oncology, Department of Medicine and Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - James T Dove
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Diane T Smelser
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Kara N Maxwell
- Division of Hematology/Oncology, Department of Medicine and Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David J Carey
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Venema WJ, Hiddingh S, van Loosdregt J, Bowes J, Balliu B, de Boer JH, Ossewaarde-van Norel J, Thompson SD, Langefeld CD, de Ligt A, van der Veken LT, Krijger PHL, de Laat W, Kuiper JJW. A cis-regulatory element regulates ERAP2 expression through autoimmune disease risk SNPs. Cell Genom 2024; 4:100460. [PMID: 38190099 PMCID: PMC10794781 DOI: 10.1016/j.xgen.2023.100460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/04/2023] [Accepted: 11/09/2023] [Indexed: 01/09/2024]
Abstract
Single-nucleotide polymorphisms (SNPs) near the ERAP2 gene are associated with various autoimmune conditions, as well as protection against lethal infections. Due to high linkage disequilibrium, numerous trait-associated SNPs are correlated with ERAP2 expression; however, their functional mechanisms remain unidentified. We show by reciprocal allelic replacement that ERAP2 expression is directly controlled by the splice region variant rs2248374. However, disease-associated variants in the downstream LNPEP gene promoter are independently associated with ERAP2 expression. Allele-specific conformation capture assays revealed long-range chromatin contacts between the gene promoters of LNPEP and ERAP2 and showed that interactions were stronger in patients carrying the alleles that increase susceptibility to autoimmune diseases. Replacing the SNPs in the LNPEP promoter by reference sequences lowered ERAP2 expression. These findings show that multiple SNPs act in concert to regulate ERAP2 expression and that disease-associated variants can convert a gene promoter region into a potent enhancer of a distal gene.
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Affiliation(s)
- Wouter J Venema
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Sanne Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jorg van Loosdregt
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Brunilda Balliu
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joke H de Boer
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | | | - Susan D Thompson
- Department of Pediatrics, University of Cincinnati College of Medicine, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Aafke de Ligt
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lars T van der Veken
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
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109
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Hodonsky CJ, Turner AW, Khan MD, Barrientos NB, Methorst R, Ma L, Lopez NG, Mosquera JV, Auguste G, Farber E, Ma WF, Wong D, Onengut-Gumuscu S, Kavousi M, Peyser PA, van der Laan SW, Leeper NJ, Kovacic JC, Björkegren JLM, Miller CL. Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci. Cell Genom 2024; 4:100465. [PMID: 38190101 PMCID: PMC10794848 DOI: 10.1016/j.xgen.2023.100465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/07/2023] [Accepted: 11/19/2023] [Indexed: 01/09/2024]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWASs, and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotypes to identify quantitative trait loci for expression (eQTLs) and splicing (sQTLs) in coronary arteries from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary artery; 19% exhibited cell-type-specific expression. Colocalization revealed subgroups of eGenes unique to CAD and blood pressure GWAS. Fine-mapping highlighted additional eGenes, including TBX20 and IL5. We also identified sQTLs for 1,690 genes, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing to accurately identify disease-relevant isoform expression. Our work provides a patient-derived coronary artery eQTL resource and exemplifies the need for diverse study populations and multifaceted approaches to characterize gene regulation in disease processes.
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Affiliation(s)
- Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Nelson B Barrientos
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ruben Methorst
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicolas G Lopez
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Jose Verdezoto Mosquera
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Gaëlle Auguste
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Emily Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Wei Feng Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Medical Scientist Training Program, Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48019, USA
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Nicholas J Leeper
- Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Clint L Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Division of Vascular Surgery, Department of Surgery, Stanford University, Stanford, CA 94305, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA.
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110
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Dulski J, Ross OA, Wszolek ZK. Genetics of Parkinson's Disease: state-of-the-art and role in clinical settings. Neurol Neurochir Pol 2024; 58:38-46. [PMID: 38175148 DOI: 10.5603/pjnns.97806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/21/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024]
Abstract
INTRODUCTION Advances in sequencing technologies have enabled extensive genetic testing on an individual basis. Genome-wide association studies (GWAS) have provided insight into the pathophysiology of PD. Additionally, direct-to-consumer genetic testing has enabled the identification of genetic diseases and risk factors without genetic counselling. As genetics increasingly permeates clinical practice, this paper aims to summarise the most important information on genetics in PD forclinical practitioners. STATE-OF-THE-ART LRRK2 mutations may be found in c.1% of all PD patients with an indistinguishable phenotype from sporadic PD. LRRK2-PD is more prevalent in patients with a positive family history (5-6%) and among certain populations (e.g. up to 41% in North Africans and Ashkenazi Jews). Other familial forms include PRKN (patients with early onset, EOPD), VPS35 (Western European ancestry), PINK1 (EOPD), DJ-1 (EOPD), and SNCA. GBA mutations are found in a large number of PD patients and are associated with faster progression and a poorer prognosis. GWAS have identified 90 genetic risk variants for developing PD and several genetic modifiers for the age at onset, disease progression, and response to treatment. CLINICAL IMPLICATIONS Multigene panels using next-generation sequencing (NGS) are the first choice for genetic testing in clinical settings. Whole exome sequencing is increasingly being used, particularly as the second-tier testing in patients with negative results of multigene panels. NGS may not detect accurately copy number variants (CNV), meaning that additional analysis is warranted. In a case of a variant of unknown significance (VUS), we suggest firstly searching the up-to-date literature. Segregation studies and in silico predictions may shed more light on the character of the VUS; however, functional studies remain the gold standard. Several interventional clinical trials are active for carriers of LRRK2 and/or GBA mutations. FUTURE DIRECTIONS Application of artificial intelligence and machine learning will enable high-throughput analysis of large sets of multimodal data. We speculate that, in the future, the treatment landscape for PD will be similar to that in oncological conditions, in which the presence of certain gene mutations or gene overexpression determines the prognosis and treatment decision-making.
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Affiliation(s)
- Jarosław Dulski
- Department of Neurology, Mayo Clinic, Jacksonville, Florida, USA.
- Division of Neurological and Psychiatric Nursing, Faculty of Health Sciences, Medical University of Gdansk, Gdansk, Poland.
- Neurology Department, St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland.
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA.
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida, USA
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Waterink L, Masselink LA, van der Lee SJ, Visser LNC, Cleutjens S, van der Schaar J, van Harten AC, Scheltens P, Sikkes SAM, van der Flier WM, Zwan MD. Interest in genetic susceptibility testing and disclosure of AD dementia risk in cognitively normal adults: a survey study. Alzheimers Res Ther 2024; 16:1. [PMID: 38167083 PMCID: PMC10759504 DOI: 10.1186/s13195-023-01364-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Apolipoprotein-E (APOE) genetic testing for Alzheimer's disease is becoming more important as clinical trials are increasingly targeting individuals carrying APOE-ε4 alleles. Little is known about the interest in finding out one's genetic risk for Alzheimer's disease in the general population. Our objective was to examine this in a sample of cognitively normal (CN) adults within a population-based online research registry with the goal to implement APOE-ε4 status for trial recruitment. METHODS An online survey was completed by 442 CN participants between the age of 49 and 75 years (56% female) from the Dutch Brain Research Registry. The survey assessed interest in participation in research into, and disclosure of, genetic risk for dementia. The survey assessed interest in participation in research into, and disclosure of, genetic risk for dementia and knowing their genetic risk in different hypothetical risk scenarios (10%, 30%, and 50% genetic risk for dementia at age 85, corresponding to APOEε2/ε2 or ε2/ε3, APOEε3/ε4 or ε2ε4, and APOE-ε4/ε4 genotypes). Cochran's Q and post hoc McNemar tests were used to analyse differences in frequencies across scenarios. RESULTS Most participants were interested in participating in research into and disclosure of their genetic risk (81%). The most reported reason was to contribute to scientific research (94%). Interest was higher in males, whilst lower-educated participants were more often undecided. When provided with different risk scenarios, interest in knowing their risk was somewhat higher in the scenarios with higher risk, i.e. in the 50% (79%) compared to the 10% scenario (73%;χ2(2) = 7.98; p = .005). Most individuals expected they would share their genetic risk with close relatives (77-89%), would participate in medication trials (79-88%), and would make long-term arrangements, e.g. retirement, health care, will (69-82%), with larger proportions for scenarios with higher hypothetical genetic risk. CONCLUSIONS Our findings indicate that the vast majority of CN adults participating in a research registry expresses interest in AD genetic risk research and disclosure. Interest in genetic risk disclosure is higher in scenarios corresponding to the APOE-ε4 genotype. This suggests APOE-ε4 screening within an online research registry is potentially a well-received method to accelerate inclusion for trials.
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Affiliation(s)
- Lisa Waterink
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands.
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081, HV, The Netherlands.
| | - Larissa A Masselink
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Sven J van der Lee
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081, HV, The Netherlands
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, The Netherlands
| | - Leonie N C Visser
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081, HV, The Netherlands
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, 171 77, Stockholm, Sweden
- Department of Medical Psychology, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, 1105, AZ, the Netherlands
- Amsterdam Public Health research Institute, Quality of Care, Amsterdam, 1105, BP, The Netherlands
| | - Solange Cleutjens
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Jetske van der Schaar
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081, HV, The Netherlands
| | - Argonde C van Harten
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Philip Scheltens
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- EQT Life Sciences Partners, Amsterdam, 1071, DV, The Netherlands
| | - Sietske A M Sikkes
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Faculty of Behavioural and Movement Sciences, Department of Clinical, Neuro and Developmental Psychology, Vrije Universiteit, Amsterdam, 1081, HV, The Netherlands
| | - Wiesje M van der Flier
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081, HV, The Netherlands
- Department of Epidemiology and Data Science, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Amsterdam, 1081, HZ, The Netherlands
| | - Marissa D Zwan
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, 1081, HV, The Netherlands
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Nuytemans K, Rajabli F, Jean-Francois M, Kurup JT, Adams LD, Starks TD, Whitehead PL, Kunkle BW, Caban-Holt A, Haines JL, Cuccaro ML, Vance JM, Byrd GS, Beecham GW, Reitz C, Pericak-Vance MA. Genetic analyses in multiplex families confirms chromosome 5q35 as a risk locus for Alzheimer's Disease in individuals of African Ancestry. Neurobiol Aging 2024; 133:125-133. [PMID: 37952397 DOI: 10.1016/j.neurobiolaging.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023]
Abstract
There is a paucity of genetic studies of Alzheimer Disease (AD) in individuals of African Ancestry, despite evidence suggesting increased risk of AD in the African American (AA) population. We performed whole-genome sequencing (WGS) and multipoint linkage analyses in 51 multi-generational AA AD families ascertained through the Research in African American Alzheimer Disease Initiative (REAAADI) and the National Institute on Aging Late Onset Alzheimer's disease (NIA-LOAD) Family Based Study. Variants were prioritized on minor allele frequency (<0.01), functional potential of coding and noncoding variants, co-segregation with AD and presence in multi-ancestry ADSP release 3 WGS data. We identified a significant linkage signal on chromosome 5q35 (HLOD=3.3) driven by nine families. Haplotype segregation analysis in the family with highest LOD score identified a 3'UTR variant in INSYN2B with the most functional evidence. Four other linked AA families harbor within-family shared variants located in INSYN2B's promoter or enhancer regions. This AA family-based finding shows the importance of diversifying population-level genetic data to better understand the genetic determinants of AD on a global scale.
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Affiliation(s)
- Karen Nuytemans
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA; Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA; Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Melissa Jean-Francois
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jiji Thulaseedhara Kurup
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Takiyah D Starks
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, NC, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Brian W Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA; Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Allison Caban-Holt
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, NC, USA
| | - Jonathan L Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA; Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA; Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Goldie S Byrd
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, NC, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA; Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Christiane Reitz
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA; Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA.
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Lv Y, Wen L, Hu WJ, Deng C, Ren HW, Bao YN, Su BW, Gao P, Man ZY, Luo YY, Li CJ, Xiang ZX, Wang B, Luan ZL. Schizophrenia in the genetic era: a review from development history, clinical features and genomic research approaches to insights of susceptibility genes. Metab Brain Dis 2024; 39:147-171. [PMID: 37542622 DOI: 10.1007/s11011-023-01271-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023]
Abstract
Schizophrenia is a devastating neuropsychiatric disorder affecting 1% of the world population and ranks as one of the disorders providing the most severe burden for society. Schizophrenia etiology remains obscure involving multi-risk factors, such as genetic, environmental, nutritional, and developmental factors. Complex interactions of genetic and environmental factors have been implicated in the etiology of schizophrenia. This review provides an overview of the historical origins, pathophysiological mechanisms, diagnosis, clinical symptoms and corresponding treatment of schizophrenia. In addition, as schizophrenia is a polygenic, genetic disorder caused by the combined action of multiple micro-effective genes, we further detail several approaches, such as candidate gene association study (CGAS) and genome-wide association study (GWAS), which are commonly used in schizophrenia genomics studies. A number of GWASs about schizophrenia have been performed with the hope to identify novel, consistent and influential risk genetic factors. Finally, some schizophrenia susceptibility genes have been identified and reported in recent years and their biological functions are also listed. This review may serve as a summary of past research on schizophrenia genomics and susceptibility genes (NRG1, DISC1, RELN, BDNF, MSI2), which may point the way to future schizophrenia genetics research. In addition, depending on the above discovery of susceptibility genes and their exact function, the development and application of antipsychotic drugs will be promoted in the future.
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Affiliation(s)
- Ye Lv
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Lin Wen
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Wen-Juan Hu
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Chong Deng
- Department of Neurosurgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116027, China
| | - Hui-Wen Ren
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Ya-Nan Bao
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Bo-Wei Su
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Ping Gao
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Zi-Yue Man
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Yi-Yang Luo
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Cheng-Jie Li
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Zhi-Xin Xiang
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Bing Wang
- Department of Endocrinology and Metabolism, The Central hospital of Dalian University of Technology, Dalian, 116000, China.
| | - Zhi-Lin Luan
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, 116044, China.
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Lafi And ZK, Mohammed BJ. Relationship between vitamin D receptor genotypes (FOK1rs2228570) and IL18 gene expression in sample of multiple sclerosis Iraqi patients. Hum Antibodies 2024; 32:1-8. [PMID: 38339924 DOI: 10.3233/hab-230010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
BACKGROUND Multiple Sclerosis known as MS, this chronic inflammatory demyelinating condition affects the nervous system. It is a heterogenic and multifactorial disease. The goal of the current study was to investigate the relationship between MS patients' IL18 gene expression and the vitamin D receptor gene polymorphism (FOK1rs2228570). OBJECTIVE The aim of the study to investigate the association of vitamin D receptor (FOK1rs2228570) gene polymorphism and pro inflammatory cytokine (IL18) gene expression among multiple sclerosis Iraqi patients. Detection VDR polymorphism and determine whether this SNP is involved in susceptibility to multiple sclerosis and estimation IL18 gene expression and explore its relation with multiple sclerosis susceptibility. METHODS Blood samples were taken from 75 MS patients in Iraq (30 men and 45 women), as well as from 75 volunteers who seemed to be in a favorable state of health and fell within the age range of 20 to 50 years. Tetra-ARMS Polymerase Chain Reaction (Tetra-ARMS PCR) was used to find polymorphisms in the vitamin D receptor (VDR) gene, and Real-time Polymerase Chain Reaction (RT-PCR) was used to measure IL18 gene expression. RESULTS The findings from the analysis of VDR gene polymorphism in patients with MS indicated that the wild-type genotype T/T was present in 8 individuals, accounting for 10.6%, the heterogeneous genotype TC was 36 (48%), and the homogeneous genotype CC was 31 (41.3%), whilst T allele frequency was 52(34.6%) and C allele was 98(65.3%) with (P⩽ 0.01) significant difference and even as in control T/T genotype was 49(65.3%), TC genotype was 21(28%), CC genotype was 5(6.66%), T allele frequency was 119(79.3%) and C allele was 31(20.6%) with significant difference (P⩽ 0.001). While estimation of IL18 expression showed high elevation in patients' group (2.59 ± 0.51 fold) by significance difference (P⩽ 0.5) when compared to control group (1.35 ± 0.14 fold). The relationship between IL18 gene expression with VDR variant in MS patients demonstrated a significant rise (2.9 ± 0.51 fold) at CC genotype patients in IL18 folding gene expression, followed by (4.6 ± 0.17 fold) in TC genotype patients and finally (1.4 ± 0.08 fold) in TT genotype patients with highly significant (P⩽ 0.01). CONCLUSION The VDR(FOK1rs2228570) genotype was significantly correlated with IL18 expression in MS patients from Iraq.
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Mufford MS, van der Meer D, Kaufmann T, Frei O, Ramesar R, Thompson PM, Jahanshad N, Morey RA, Andreassen OA, Stein DJ, Dalvie S. The Genetic Architecture of Amygdala Nuclei. Biol Psychiatry 2024; 95:72-84. [PMID: 37391117 DOI: 10.1016/j.biopsych.2023.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 07/02/2023]
Abstract
BACKGROUND Whereas genetic variants influencing total amygdala volume have been identified, the genetic architecture of its distinct nuclei has yet to be explored. We aimed to investigate whether increased phenotypic specificity through nuclei segmentation aids genetic discoverability and elucidates the extent of shared genetic architecture and biological pathways with related disorders. METHODS T1-weighted brain magnetic resonance imaging scans (N = 36,352, 52% female) from the UK Biobank were segmented into 9 amygdala nuclei with FreeSurfer (version 6.1). Genome-wide association analyses were performed on the entire sample, a European-only subset (n = 31,690), and a generalization (transancestry) subset (n = 4662). We estimated single nucleotide polymorphism-based heritability; derived polygenicity, discoverability, and power estimates; and investigated genetic correlations and shared loci with psychiatric disorders. RESULTS The heritability of the nuclei ranged from 0.17 to 0.33. Across the whole amygdala and the nuclei volumes, we identified 28 novel genome-wide significant (padj < 5 × 10-9) loci in the European analysis, with significant en masse replication for the whole amygdala and central nucleus volumes in the generalization analysis, and we identified 10 additional candidate loci in the combined analysis. The central nucleus had the highest statistical power for discovery. The significantly associated genes and pathways showed unique and shared effects across the nuclei, including immune-related pathways. Shared variants were identified between specific nuclei and autism spectrum disorder, Alzheimer's disease, Parkinson's disease, bipolar disorder, and schizophrenia. CONCLUSIONS Through investigation of amygdala nuclei volumes, we have identified novel candidate loci in the neurobiology of amygdala volume. These nuclei volumes have unique associations with biological pathways and genetic overlap with psychiatric disorders.
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Affiliation(s)
- Mary S Mufford
- South African Medical Research Council Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Global Initiative for Neuropsychiatric Genetics Education in Research program, Harvard T.H. Chan School of Public Health and the Stanley Center for Psychiatric Research at the Broad Institute of Harvard and MIT, Boston, Massachusetts; South African Medical Research Council Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa.
| | - Dennis van der Meer
- Norwegian Centre for Mental Disorders Research Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway; School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands
| | - Tobias Kaufmann
- Norwegian Centre for Mental Disorders Research Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, Tübingen, Germany
| | - Oleksandr Frei
- Norwegian Centre for Mental Disorders Research Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Raj Ramesar
- South African Medical Research Council Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Paul M Thompson
- Imaging Genetics Center, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of the University of Southern California, Marina del Rey, California
| | - Neda Jahanshad
- Imaging Genetics Center, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of the University of Southern California, Marina del Rey, California
| | - Rajendra A Morey
- Duke-UNC Brain Imaging and Analysis Center, Duke University, Durham, North Carolina
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research Centre, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway; KG Jebsen Centre for Neurodevelopmental Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Dan J Stein
- South African Medical Research Council Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Shareefa Dalvie
- South African Medical Research Council Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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Paniri A, Hosseini MM, Fattahi S, Amiribozorgi G, Asouri M, Maadi M, Motamed N, Zamani F, Akhavan‐Niaki H. Genetic variations in IKZF3, LET7-a2, and CDKN2B-AS1: Exploring associations with metabolic syndrome susceptibility and clinical manifestations. J Clin Lab Anal 2024; 38:e24999. [PMID: 38193570 PMCID: PMC10829692 DOI: 10.1002/jcla.24999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 11/23/2023] [Accepted: 12/24/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND AND AIM Metabolic syndrome (MetS) increases the risk of atherosclerosis and diabetes, but there are no approved predictive markers. This study assessed the role of specific genetic variations in MetS susceptibility and their impact on clinical manifestations. METHOD In this study, a genotype-phenotype assessment was performed for IKZF3 (rs907091), microRNA-let-7a-2 (rs1143770), and lncRNA-CDKN2B-AS1 (rs1333045). RESULTS Analyses indicate that while rs907091 and rs1143770 may have potential associations with MetS susceptibility and an increased risk of atherosclerosis and diabetes, there is an observed trend suggesting that the rs1333045 CC genotype may be associated with a decreased risk of MetS. The genotypes and allele frequencies of rs1333045 were significantly different between studied groups (OR = 0.56, 95% CI 0.38-0.81, p = 0.002, and OR = 0.71, 95% CI 0.55-0.92, p = 0.008), with the CC genotype displaying increased levels of HDL. Furthermore, the rs907091 TT genotype was associated with increased triglyceride, cholesterol, and HOMA index in MetS patients. Subjects with the CC genotype for rs1143770 had higher HbA1c and BMI. In silico analyses illustrated that rs907091 C remarkably influences the secondary structure and the target site of a broad spectrum of microRNAs, especially hsa-miR-4497. Moreover, rs1333045 creates a binding site for seven different microRNAs. CONCLUSION Further studies on other populations may help confirm these SNPs as useful predictive markers in assessing the MetS risk.
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Affiliation(s)
- Alireza Paniri
- Genetics Department, Faculty of MedicineBabol University of Medical SciencesBabolIran
- Zoonoses Research CenterPasteur Institute of IranAmolIran
| | | | - Sadegh Fattahi
- Zoonoses Research CenterPasteur Institute of IranAmolIran
| | | | - Mohsen Asouri
- Zoonoses Research CenterPasteur Institute of IranAmolIran
| | - Mansooreh Maadi
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical SciencesTehranIran
| | - Nima Motamed
- Department of Social MedicineZanjan University of Medical SciencesZanjanIran
| | - Farhad Zamani
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical SciencesTehranIran
| | - Haleh Akhavan‐Niaki
- Genetics Department, Faculty of MedicineBabol University of Medical SciencesBabolIran
- Zoonoses Research CenterPasteur Institute of IranAmolIran
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Zhou DY, Su X, Wu Y, Yang Y, Zhang L, Cheng S, Shao M, Li W, Zhang Z, Wang L, Lv L, Li M, Song M. Decreased CNNM2 expression in prefrontal cortex affects sensorimotor gating function, cognition, dendritic spine morphogenesis and risk of schizophrenia. Neuropsychopharmacology 2024; 49:433-442. [PMID: 37715107 PMCID: PMC10724213 DOI: 10.1038/s41386-023-01732-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 08/15/2023] [Accepted: 08/31/2023] [Indexed: 09/17/2023]
Abstract
Genome-wide association studies (GWASs) have reported multiple single nucleotide polymorphisms (SNPs) associated with schizophrenia, yet the underlying molecular mechanisms are largely unknown. In this study, we aimed to identify schizophrenia relevant genes showing alterations in mRNA and protein expression associated with risk SNPs at the 10q24.32-33 GWAS locus. We carried out the quantitative trait loci (QTL) and summary data-based Mendelian randomization (SMR) analyses, using the PsychENCODE dorsolateral prefrontal cortex (DLPFC) expression QTL (eQTL) database, as well as the ROSMAP and Banner DLPFC protein QTL (pQTL) datasets. The gene CNNM2 (encoding a magnesium transporter) at 10q24.32-33 was identified to be a robust schizophrenia risk gene, and was highly expressed in human neurons according to single cell RNA-seq (scRNA-seq) data. We further revealed that reduced Cnnm2 in the mPFC of mice led to impaired cognition and compromised sensorimotor gating function, and decreased Cnnm2 in primary cortical neurons altered dendritic spine morphogenesis, confirming the link between CNNM2 and endophenotypes of schizophrenia. Proteomics analyses showed that reduced Cnnm2 level changed expression of proteins associated with neuronal structure and function. Together, these results identify a robust gene in the pathogenesis of schizophrenia.
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Affiliation(s)
- Dan-Yang Zhou
- Yunnan Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xi Su
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yong Wu
- Research Center for Mental Health and Neuroscience, Wuhan Mental Health Center, Wuhan, Hubei, China
- Affiliated Wuhan Mental Health Center, Jianghan University, Wuhan, Hubei, China
| | - Yongfeng Yang
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Luwen Zhang
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Shumin Cheng
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Minglong Shao
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Wenqiang Li
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
| | - Zhaohui Zhang
- Department of Psychiatry, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Lu Wang
- Yunnan Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Luxian Lv
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China
- Henan Province People's Hospital, Zhengzhou, Henan, China
| | - Ming Li
- Yunnan Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China.
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Meng Song
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China.
- Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China.
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Khaled M, Al-Jamal H, Tajer L, El-Mir R. Alzheimer's Disease in Lebanon: Exploring Genetic and Environmental Risk Factors-A Comprehensive Review. J Alzheimers Dis 2024; 99:21-40. [PMID: 38640157 DOI: 10.3233/jad-231432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative condition that displays a high prevalence in Lebanon causing a local burden in healthcare and socio-economic sectors. Unfortunately, the lack of prevalence studies and clinical trials in Lebanon minimizes the improvement of AD patient health status. In this review, we include over 155 articles to cover the different aspects of AD ranging from mechanisms to possible treatment and management tools. We highlight some important modifiable and non-modifiable risk factors of the disease including genetics, age, cardiovascular diseases, smoking, etc. Finally, we propose a hypothetical genetic synergy model between APOE4 and TREM2 genes which constitutes a potential early diagnostic tool that helps in reducing the risk of AD based on preventative measures decades before cognitive decline. The studies on AD in Lebanon and the Middle East are scarce. This review points out the importance of genetic mapping in the understanding of disease pathology which is crucial for the emergence of novel diagnostic tools. Hence, we establish a rigid basis for further research to identify the most influential genetic and environmental risk factors for the purpose of using more specific diagnostic tools and possibly adopting a local management protocol.
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Affiliation(s)
| | - Hadi Al-Jamal
- Faculty of Public Health III, Lebanese University, Tripoli, Lebanon
| | - Layla Tajer
- Faculty of Public Health III, Lebanese University, Tripoli, Lebanon
| | - Reem El-Mir
- Faculty of Public Health III, Lebanese University, Tripoli, Lebanon
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Hutchcraft ML, Zhang S, Lin N, Pickarski JC, Belcher EA, Wei S, Bocklage T, Miller RW, Villano JL, Cavnar MJ, Kim J, Arnold SM, Ueland FR, Kolesar JM. Feasibility and Clinical Utility of Reporting Hereditary Cancer Predisposition Pathogenic Variants Identified in Research Germline Sequencing: A Prospective Interventional Study. JCO Precis Oncol 2024; 8:e2300266. [PMID: 38295319 PMCID: PMC10843325 DOI: 10.1200/po.23.00266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 11/02/2023] [Accepted: 12/04/2023] [Indexed: 02/02/2024] Open
Abstract
PURPOSE Patients with cancer frequently undergo research-grade germline sequencing but clinically actionable results are not routinely disclosed. The objective of this study is to evaluate the feasibility of reporting clinically relevant secondary findings (SF) identified in germline research sequencing using the institutional molecular tumor board (MTB) and the treating oncology physician. METHODS This prospective, interventional cohort study enrolled Total Cancer Care participants with any cancer diagnosis at a single institution. Patients underwent research-grade germline whole-exome sequencing, with bioinformatic analysis in a Clinical Laboratory Improvement Amendments-certified laboratory to verify pathogenic/likely pathogenic germline variants (PGVs) in any American College of Medical Genomics and Genetics SF v2.0 genes. After a protocol modification in consenting patients, the MTB reported PGVs to treating oncology physicians with recommendations for referral to a licensed genetic counselor and clinical confirmatory testing. RESULTS Of the 781 enrolled participants, 32 (4.1%) harbored cancer predisposition PGVs, 24 (3.1%) were heterozygous carriers of an autosomal recessive cancer predisposition syndrome, and 14 (1.8%) had other hereditary disease PGVs. Guideline-directed testing would have missed 37.5% (12/32) of the inherited cancer predisposition PGVs, which included BRCA1, BRCA2, MSH6, SDHAF2, SDHB, and TP53 variants. Three hundred fifteen participants consented to reporting results; results for all living patients were reported to the clinical team with half referred to a licensed genetic counselor. There was concordance between all research variants identified in patients (n = 9) who underwent clinical confirmatory sequencing. CONCLUSION MTB reporting of research-grade germline sequencing to the clinical oncology team is feasible. Over a third of PGVs identified using a universal testing strategy would have been missed by guideline-based approach, suggesting a role for expanding germline testing.
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Affiliation(s)
- Megan L. Hutchcraft
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Shulin Zhang
- Department of Pathology and Laboratory Medicine University of Kentucky Chandler Medical Center, Lexington, KY
- Markey Comprehensive Cancer Center, University of Kentucky, Lexington, KY
| | - Nan Lin
- Department of Pharmacy Practice and Science, University of Kentucky College of Pharmacy, Lexington, KY
| | | | - Elizabeth A. Belcher
- Department of Clinical Research, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Sainan Wei
- Department of Pathology and Laboratory Medicine University of Kentucky Chandler Medical Center, Lexington, KY
| | - Thèrése Bocklage
- Department of Pathology and Laboratory Medicine University of Kentucky Chandler Medical Center, Lexington, KY
| | - Rachel W. Miller
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - John L. Villano
- Division of Medical Oncology, Department of Internal Medicine, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Michael J. Cavnar
- Division of Surgical Oncology, Department of Surgery, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Joseph Kim
- Division of Surgical Oncology, Department of Surgery, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Susanne M. Arnold
- Division of Medical Oncology, Department of Internal Medicine, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Frederick R. Ueland
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Kentucky Markey Comprehensive Cancer Center, Lexington, KY
| | - Jill M. Kolesar
- Markey Comprehensive Cancer Center, University of Kentucky, Lexington, KY
- Department of Pharmacy Practice and Science, University of Kentucky College of Pharmacy, Lexington, KY
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Kaabi YA. MTNR 1B (rs10830963) Gene Polymorphism, but not MTNR 1A (rs2119882), Associated with Type 2 Diabetes Mellitus Risk in Saudi Arabia. Clin Lab 2024; 70. [PMID: 38213225 DOI: 10.7754/clin.lab.2023.230651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
BACKGROUND Disrupted circadian rhythm has been linked to the pathogenesis of type 2 diabetes mellitus (T2DM). Single nucleotide polymorphisms (SNPs) in melatonin receptors (MTNR), MTNR 1A rs2119882 (T>C) and MTNR 1B rs10830963 (C>G) may interfere with the normal function of melatonin and increase the risk of T2DM. This study investigated the prevalence of MTNR 1A rs2119882 (T>C) and MTNR 1B rs10830963 (C>G) SNPs and tested their association with T2DM in Saudi Arabian population. METHODS A total of 459 Saudi Arabian participants from Jazan Province, Saudi Arabia, were selected and included 227 T2DM patients and 232 control subjects. DNA was extracted from all participants and genotyped for rs2119882 and rs10830963 SNPs using TaqMan technology. Genotype frequencies were determined for both SNPs, and logistic regression was fitted to test the association with T2DM. RESULTS No association was found between MTNR 1A rs2119882 (T>C) SNP and T2DM (odds ratio (OR) = 0.69; 95% confidence interval (CI) = 0.44 - 1.08; p-value = 0.111). However, the MTNR 1B rs10830963 (C>G) SNP was significantly associated with T2DM (OR = 1.73; 95% CI = 1.18 - 2.55; p-value = 0.0065). Co-inheritance of the MTNR 1B rs10830963 G allele and MTNR 1A rs2119882 T allele further increased the risk of T2DM (OR = 2.80; 95% CI = 1.71 - 4.57; p-value < 0.0001). CONCLUSIONS The minor G allele of the MTNR 1B rs10830963 SNP was significantly associated with T2DM in our population. This association further intensified with the presence of the T allele in MTNR 1A rs2119882 locus. This study sheds light on the importance of melatonin receptor polymorphisms as genetic candidates for the development of T2DM in Saudi Arabia.
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Starling S. How a common NAFLD genetic risk variant affects human metabolism. Nat Rev Endocrinol 2024; 20:2. [PMID: 37964025 DOI: 10.1038/s41574-023-00924-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
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Zhang X, Gomez L, Below JE, Naj AC, Martin ER, Kunkle BW, Bush WS. An X Chromosome Transcriptome Wide Association Study Implicates ARMCX6 in Alzheimer's Disease. J Alzheimers Dis 2024; 98:1053-1067. [PMID: 38489177 DOI: 10.3233/jad-231075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Background The X chromosome is often omitted in disease association studies despite containing thousands of genes that may provide insight into well-known sex differences in the risk of Alzheimer's disease (AD). Objective To model the expression of X chromosome genes and evaluate their impact on AD risk in a sex-stratified manner. Methods Using elastic net, we evaluated multiple modeling strategies in a set of 175 whole blood samples and 126 brain cortex samples, with whole genome sequencing and RNA-seq data. SNPs (MAF > 0.05) within the cis-regulatory window were used to train tissue-specific models of each gene. We apply the best models in both tissues to sex-stratified summary statistics from a meta-analysis of Alzheimer's Disease Genetics Consortium (ADGC) studies to identify AD-related genes on the X chromosome. Results Across different model parameters, sample sex, and tissue types, we modeled the expression of 217 genes (95 genes in blood and 135 genes in brain cortex). The average model R2 was 0.12 (range from 0.03 to 0.34). We also compared sex-stratified and sex-combined models on the X chromosome. We further investigated genes that escaped X chromosome inactivation (XCI) to determine if their genetic regulation patterns were distinct. We found ten genes associated with AD at p < 0.05, with only ARMCX6 in female brain cortex (p = 0.008) nearing the significance threshold after adjusting for multiple testing (α = 0.002). Conclusions We optimized the expression prediction of X chromosome genes, applied these models to sex-stratified AD GWAS summary statistics, and identified one putative AD risk gene, ARMCX6.
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Affiliation(s)
- Xueyi Zhang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adam C Naj
- Department of Biostatistics, Epidemiology, and Informatics, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Brian W Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
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Beatriz González-Castro T, Alfonso Tovilla-Zárate C, Esther Juárez-Rojop I, Hernández-Díaz Y, Lilia López-Narváez M, Felicita Ortiz-Ojeda R. The association of cytokines genes (IL-6 and IL-10) with the susceptibility to schizophrenia: A systematic review and meta-analysis. Brain Res 2024; 1822:148667. [PMID: 37923001 DOI: 10.1016/j.brainres.2023.148667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/19/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
Cytokines are among the important effectors and messenger molecules for restoring the homeostasis tissue after an inflammatory response. The association between IL-6 and IL-10 genes polymorphisms with the schizophrenia susceptibility have yielded controversial results. To reconcile the results, a systematic review followed by meta-analysis was performed to assess the association. We carried out literature searches of PubMed, Scopus, EBSCO, and Web of Sciences databases. Pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated to assess the strength of the association. Subgroup analysis, heterogeneity analyses, and publication bias were also calculated in the meta-analysis. A total of 22 case-control studies, consisting of 4,993 schizophrenic patients and 5,195 healthy controls, were included in the meta-analysis. The meta-analysis suggests that the IL-6 rs1800795 polymorphism displays a protective role against schizophrenia, while the IL-10 rs1800896 and rs1800872 polymorphisms confer an increased risk of schizophrenia. Similar results were found in subgroup analysis by ethnicity. We did not find association between IL-10 rs1800871 polymorphism and schizophrenia susceptibility. Finally, this meta-analysis suggested that the dysregulation of cytokines could lead to the pathogenesis of the schizophrenia.
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Affiliation(s)
- Thelma Beatriz González-Castro
- División Académica Multidisciplinaria de Jalpa de Méndez, Universidad Juárez Autónoma de Tabasco, Jalpa de Méndez, Tabasco, México
| | - Carlos Alfonso Tovilla-Zárate
- División Académica Multidisciplinaria de Comalcalco, Universidad Juárez Autónoma de Tabasco, Comalcalco, Tabasco, México.
| | - Isela Esther Juárez-Rojop
- División Académica de Ciencias de la Salud, Universidad Juárez Autónoma de Tabasco, Villahermosa, Tabasco, México
| | - Yazmín Hernández-Díaz
- División Académica Multidisciplinaria de Jalpa de Méndez, Universidad Juárez Autónoma de Tabasco, Jalpa de Méndez, Tabasco, México.
| | | | - Rosa Felicita Ortiz-Ojeda
- División Académica Multidisciplinaria de Jalpa de Méndez, Universidad Juárez Autónoma de Tabasco, Jalpa de Méndez, Tabasco, México
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Elam KK, Su J, Kutzner J, Trevino A. Individual Trajectories of Depressive Symptoms Within Racially-Ethnically Diverse Youth: Associations with Polygenic Risk for Depression and Substance Use Intent and Perceived Harm. Behav Genet 2024; 54:86-100. [PMID: 38097814 DOI: 10.1007/s10519-023-10167-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/10/2023] [Indexed: 01/30/2024]
Abstract
There are distinct individual trajectories of depressive symptoms across adolescence which are most often differentiated into low, moderate/stable, and high/increasing groups. Research has found genetic predisposition for depression associated with trajectories characterized by greater depressive symptoms. However, the majority of this research has been conducted in White youth. Moreover, a separate literature indicates that trajectories with elevated depressive symptoms can result in substance use. It is critical to identify depressive symptom trajectories, genetic predictors, and substance use outcomes in diverse samples in early adolescence to understand distinct processes and convey equitable benefits from research. Using data from the Adolescent Cognitive Brain Development Study (ABCD), we examined parent-reported depressive symptom trajectories within Black/African American (AA, n = 1783), White/European American (EA, n = 6179), and Hispanic/Latinx (LX, n = 2410) youth across four annual assessments in early adolescence (age 9-10 to 12-13). We examined racially/ethnically aligned polygenic scores (Dep-PGS) as predictors of trajectories as well as substance use intent and perceived substance use harm as outcomes at age 12-13. Differential trajectories were found in AA, EA, and LX youth but low and high trajectories were represented within each group. In EA youth, greater Dep-PGS were broadly associated with membership in trajectories with greater depressive symptoms. Genetic effects were not significant in AA and LX youth. In AA youth, membership in the low trajectory was associated with greater substance use intent. In EA youth, membership in trajectories with higher depressive symptoms was associated with greater substance use intent and less perceived harm. There were no associations between trajectories and substance use intent and perceived harm in LX youth. These findings indicate that there are distinct depressive symptom trajectories in AA, EA, and LX youth, accompanied by unique associations with genetic predisposition for depressive symptoms and substance use outcomes.
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Affiliation(s)
- Kit K Elam
- Department of Applied Health Science, Indiana University, 1025 E. 7th St., Suite 116, Bloomington, IN, 47405, USA.
| | - Jinni Su
- Department of Psychology, Arizona State University, Phoenix, USA
| | - Jodi Kutzner
- Department of Applied Health Science, Indiana University, 1025 E. 7th St., Suite 116, Bloomington, IN, 47405, USA
| | - Angel Trevino
- Department of Psychology, Arizona State University, Phoenix, USA
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Hayat S, Asad A, Munni MA, Nayeem MAJ, Mostafa MG, Jahan I, Howlader MZH, Mohammad QD, Islam Z. Interleukin-10 promoter polymorphisms and haplotypes in patients with Guillain-Barré syndrome. Ann Clin Transl Neurol 2024; 11:133-142. [PMID: 37955408 PMCID: PMC10791015 DOI: 10.1002/acn3.51939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/17/2023] [Accepted: 10/19/2023] [Indexed: 11/14/2023] Open
Abstract
OBJECTIVE Interleukin-10 (IL-10) is a multifunctional cytokine that exerts both pro- and anti-inflammatory effects on the immune system as well as in the pathogenesis of Guillain-Barré syndrome (GBS). We investigated whether the three common polymorphisms -1082 G/A(rs1800896), -819 C/T(rs1800871), and -592 C/A(rs1800872) in the promoter region of IL-10 have any influence on the susceptibility, severity, and clinical outcome of GBS. METHODS IL-10 promoter polymorphisms were investigated in 152 patients with GBS and 152 healthy controls from Bangladesh using polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP), and allele-specific oligonucleotide-PCR (ASO-PCR). Haplotype patterns and frequencies were analyzed using Heatmaply R-package, chi-square, and Fisher's exact test. The serum level of IL-10 was measured through enzyme-linked immunosorbent assays. p-values < 0.05 were considered statistically significant. RESULTS IL-10 promoter polymorphisms -1082 G/A, -819 C/T, and -592 C/A were not associated with GBS susceptibility. The homozygous -819 TT genotype showed a tendency with susceptibility (p = 0.029; pc = 0.08) and was prevalent in axonal variants of GBS compared to demyelinating subtypes and controls (p = 0.042, OR = 8.67, 95% CI = 1.03-72.97; pc = 0.123 and p = 0.005, OR = 4.2, 95% CI = 1.55-11.40; pc = 0.015, respectively). Haplotype analysis revealed 19 patterns of genotypes and high IL-10 expression haplotype combinations (GCC/GTA, GCC/ATA, and GCC/GCA) may have influence on disease severity (p = 0.026; pc = 0.078). Serum expression of IL-10 was elevated in GBS patients ([GBS, 12.16 ± 45.71] vs. [HC, 0.65 ± 5.17] pg/mL; p = 0.0027) and varied with disease severity ([severe-GBS, 15.25 ± 51.72] vs. [mild-GBS, 3.59 ± 19.79] pg/mL, p = 0.046). INTERPRETATION The -819 TT genotypes influence axonal GBS, and high frequency of IL-10 expression haplotype combination with elevated serum IL-10 may play an important role in disease severity.
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Affiliation(s)
- Shoma Hayat
- Laboratory of Gut‐Brain AxisInfectious Diseases Division (IDD), icddr,bDhakaBangladesh
| | - Asaduzzaman Asad
- Laboratory of Gut‐Brain AxisInfectious Diseases Division (IDD), icddr,bDhakaBangladesh
| | - Moriam Akter Munni
- Laboratory of Gut‐Brain AxisInfectious Diseases Division (IDD), icddr,bDhakaBangladesh
| | - Md. Abu Jaher Nayeem
- Laboratory of Gut‐Brain AxisInfectious Diseases Division (IDD), icddr,bDhakaBangladesh
| | - Md. Golam Mostafa
- Laboratory of Gut‐Brain AxisInfectious Diseases Division (IDD), icddr,bDhakaBangladesh
| | - Israt Jahan
- Laboratory of Gut‐Brain AxisInfectious Diseases Division (IDD), icddr,bDhakaBangladesh
| | | | | | - Zhahirul Islam
- Laboratory of Gut‐Brain AxisInfectious Diseases Division (IDD), icddr,bDhakaBangladesh
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Cetinsoy O, Anyanwu I, Krishnanand H, Natarajan G, Ramachandran N, Thomas A, Brookes KJ. Gene Association Study of the Urokinase Plasminogen Activator and Its Receptor Gene in Alzheimer's Disease. J Alzheimers Dis 2024; 99:241-250. [PMID: 38669542 DOI: 10.3233/jad-231383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Background The role of the innate immune system has long been associated with Alzheimer's disease (AD). There is now accumulating evidence that the soluble Urokinase Plasminogen Activator Receptor pathway, and its genes, PLAU and PLAUR may be important in AD, and yet there have been few genetic association studies to explore this. Objective This study utilizes the DNA bank of the Brains for Dementia Research cohort to investigate the genetic association of common polymorphisms across the PLAU and PLAUR genes with AD. Methods TaqMan genotyping assays were used with standard procedures followed by association analysis in PLINK. Results No association was observed between the PLAU gene and AD; however, two SNPs located in the PLAUR gene were indicative of a trend towards association but did not surpass multiple testing significance thresholds. Conclusions Further genotyping studies and exploration of the consequences of these SNPs on gene expression and alternative splicing are warranted to fully uncover the role this system may have in AD.
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Affiliation(s)
- Ozde Cetinsoy
- Biosciences, Clifton Campus, Nottingham Trent University, Nottingham, UK
| | - Ijeoma Anyanwu
- Biosciences, Clifton Campus, Nottingham Trent University, Nottingham, UK
| | | | | | | | - Alan Thomas
- Brains for Dementia Research, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Keeley J Brookes
- Biosciences, Clifton Campus, Nottingham Trent University, Nottingham, UK
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Gao Y, Su B, Luo Y, Tian Y, Hong S, Gao S, Xie J, Zheng X. HLA-C*07:01 and HLA-DQB1*02:01 protect against white matter hyperintensities and deterioration of cognitive function: A population-based cohort study. Brain Behav Immun 2024; 115:250-257. [PMID: 37884160 DOI: 10.1016/j.bbi.2023.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/14/2023] [Accepted: 10/22/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Neuroinflammation and aberrant immune regulation are increasingly implicated in the pathophysiology of white matter hyperintensities (WMH), an imaging marker of cerebrovascular pathologies and predictor of cognitive impairment. The role of human leukocyte antigen (HLA) genes, critical in immunoregulation and associated with susceptibility to neurodegenerative diseases, in WMH pathophysiology remains unexplored. METHODS We performed association analyses between classical HLA alleles and WMH volume, derived from MRI scans of 38 302 participants in the UK Biobank. To identify independent functional alleles driving these associations, we conducted conditional forward stepwise regression and lasso regression. We further investigated whether these functional alleles showed consistent associations with WMH across subgroups characterized by varying levels of clinical determinants. Additionally, we validated the clinical relevance of the identified alleles by examining their association with cognitive function (n = 147 549) and dementia (n = 460 029) in a larger cohort. FINDINGS Four HLA alleles (DQB1*02:01, DRB1*03:01, C*07:01, and B*08:01) showed an association with reduced WMH volume after Bonferroni correction for multiple comparisons. Among these alleles, DQB1*02:01 exhibited the most significant association (β = -0.041, 95 % CI: -0.060 to -0.023, p = 1.04 × 10-5). Forward selection and lasso regression analyses indicated that DQB1*02:01 and C*07:01 primarily drove this association. The protective effect against WMH conferred by DQB1*02:01 and C*07:01 persisted in clinically relevant subgroups, with a stronger effect observed in older participants. Carrying DQB1*02:01 and C*07:01 was associated with higher cognitive function, but no association with dementia was found. INTERPRETATION Our population-based findings support the involvement of immune-associated mechanisms, particularly both HLA class I and class II genes, in the pathogenesis of WMH and subsequent consequence of cognitive functions.
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Affiliation(s)
- Yaqing Gao
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Binbin Su
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China
| | - Yanan Luo
- Department of Global Health, School of Public Health, Peking University, Beijing, China
| | - Yaohua Tian
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shenda Hong
- National Institute of Health Data Science, Peking University, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Song Gao
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Junqing Xie
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK.
| | - Xiaoying Zheng
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China; HeSAY, Peking University, Beijing, China.
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Hughley RW, Matejcic M, Song Z, Sheng X, Wan P, Xia L, Hart SN, Hu C, Yadav S, Lubmawa A, Kiddu V, Asiimwe F, Amanya C, Mutema G, Job K, Ssebakumba MK, Ingles SA, Hamilton AS, Couch FJ, Watya S, Conti DV, Darst BF, Haiman CA. Polygenic Risk Score Modifies Prostate Cancer Risk of Pathogenic Variants in Men of African Ancestry. Cancer Res Commun 2023; 3:2544-2550. [PMID: 38014910 PMCID: PMC10720390 DOI: 10.1158/2767-9764.crc-23-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/17/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
Prostate cancer risk is influenced by rare and common germline variants. We examined the aggregate association of rare germline pathogenic/likely pathogenic/deleterious (P/LP/D) variants in ATM, BRCA2, PALB2, and NBN with a polygenic risk score (PRS) on prostate cancer risk among 1,796 prostate cancer cases (222 metastatic) and 1,424 controls of African ancestry. Relative to P/LP/D non-carriers at average genetic risk (33%-66% of PRS), men with low (0%-33%) and high (66%-100%) PRS had Odds Ratios (ORs) for overall prostate cancer of 2.08 [95% confidence interval (CI) = 0.58-7.49] and 18.06 (95% CI = 4.24-76.84) among P/LP/D carriers and 0.57 (95% CI = 0.46-0.71) and 3.02 (95% CI = 2.53-3.60) among non-carriers, respectively. The OR for metastatic prostate cancer was 2.73 (95% CI = 0.24-30.54) and 28.99 (95% CI = 4.39-191.43) among P/LP/D carriers and 0.54 (95% CI = 0.31-0.95) and 3.22 (95% CI = 2.20-4.73) among non-carriers, for men with low and high PRS, respectively. Lifetime absolute risks of overall prostate cancer increased with PRS (low to high) from 9.8% to 51.5% in P/LP/D carriers and 5.5% to 23.9% in non-carriers. Lifetime absolute risks of metastatic prostate cancer increased with PRS from 1.9% to 18.1% in P/LP/D carriers and 0.3% to 2.2% in non-carriers These findings suggest that assessment of prostate cancer risk for rare variant carriers should include PRS status. SIGNIFICANCE These findings highlight the importance of considering rare and common variants to comprehensively assess prostate cancer risk in men of African ancestry.
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Affiliation(s)
- Raymond W. Hughley
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Marco Matejcic
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ziwei Song
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Xin Sheng
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Peggy Wan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Lucy Xia
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Steven N. Hart
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | - Colline Amanya
- Makerere University College of Health Sciences, Kampala, Uganda
| | | | | | | | - Sue A. Ingles
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ann S. Hamilton
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Fergus J. Couch
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Stephen Watya
- Uro Care, Kampala, Uganda
- Makerere University College of Health Sciences, Kampala, Uganda
| | - David V. Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Burcu F. Darst
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
- Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California
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129
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Li D, Farrell JJ, Mez J, Martin ER, Bush WS, Ruiz A, Boada M, de Rojas I, Mayeux R, Haines JL, Vance MAP, Wang LS, Schellenberg GD, Lunetta KL, Farrer LA. Novel loci for Alzheimer's disease identified by a genome-wide association study in Ashkenazi Jews. Alzheimers Dement 2023; 19:5550-5562. [PMID: 37260021 PMCID: PMC10689571 DOI: 10.1002/alz.13117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 06/02/2023]
Abstract
INTRODUCTION Most Alzheimer's disease (AD) loci have been discovered in individuals with European ancestry (EA). METHODS We applied principal component analysis using Gaussian mixture models and an Ashkenazi Jewish (AJ) reference genome-wide association study (GWAS) data set to identify Ashkenazi Jews ascertained in GWAS (n = 42,682), whole genome sequencing (WGS, n = 16,815), and whole exome sequencing (WES, n = 20,504) data sets. The association of AD was tested genome wide (GW) in the GWAS and WGS data sets and exome wide (EW) in all three data sets (EW). Gene-based analyses were performed using aggregated rare variants. RESULTS In addition to apolipoprotein E (APOE), GW analyses (1355 cases and 1661 controls) revealed associations with TREM2 R47H (p = 9.66 × 10-9 ), rs541586606 near RAB3B (p = 5.01 × 10-8 ), and rs760573036 between SPOCK3 and ANXA10 (p = 6.32 × 10-8 ). In EW analyses (1504 cases and 2047 controls), study-wide significant association was observed with rs1003710 near SMAP2 (p = 1.91 × 10-7 ). A significant gene-based association was identified with GIPR (p = 7.34 × 10-7 ). DISCUSSION Our results highlight the efficacy of founder populations for AD genetic studies.
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Affiliation(s)
- Donghe Li
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Jesse Mez
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Eden R. Martin
- Dr. John T. Macdonald Foundation, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - William S. Bush
- Department of Population & Quantitative Health Science and Cleveland Institute for Computational Biology, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Agustin Ruiz
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Mercè Boada
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Itziar de Rojas
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Richard Mayeux
- Taub Institute on Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center Department of Neurology, Columbia University, 710 West 168th Street, New York, NY 10032, USA
| | - Jonathan L. Haines
- Department of Population & Quantitative Health Science and Cleveland Institute for Computational Biology, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Margaret A. Pericak Vance
- Dr. John T. Macdonald Foundation, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
- Department of Neurology, University of Miami, Miami, FL 33136, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
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Yu H, Armstrong N, Pavela G, Kaiser K. Sex and Race Differences in Obesity-Related Genetic Susceptibility and Risk of Cardiometabolic Disease in Older US Adults. JAMA Netw Open 2023; 6:e2347171. [PMID: 38064210 PMCID: PMC10709778 DOI: 10.1001/jamanetworkopen.2023.47171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/29/2023] [Indexed: 12/18/2023] Open
Abstract
Importance The fat mass and obesity-associated gene (FTO) is associated with obesity phenotypes, but the association is inconsistent across populations. Within-population differences may explain some of the variability observed. Objective To investigate sex differences in the association between FTO single-nucleotide variants (SNVs) and obesity traits among self-identified non-Hispanic Black and non-Hispanic White US adults, to examine whether the SNVs were associated with cardiometabolic diseases, and to evaluate whether obesity mediated the association between FTO SNVs and cardiometabolic diseases. Design, Setting, and Participants This cross-sectional study used data from the Reasons for Geographic and Racial Differences in Stroke (REGARDS) study, a US population-based cohort study with available genetic data (assayed in 2018) and phenotypic data at baseline (enrolled 2003-2007). Participants were aged 45 to 98 years at baseline. Data were analyzed from October 2021 to October 2022. Exposures Eleven SNVs in the FTO gene present among both Black and White participants. Main Outcomes and Measures Objectively measured obesity indicators (body mass index and waist-to-height ratio), objectively measured and/or self-reported cardiometabolic diseases (hypertension, stroke history, heart disease, and diabetes), and self-reported social-economic and psychosocial status. Results A total of 10 447 participants (mean [SD] age, 64.4 [9.7] years; 5276 [55.8%] women; 8743 [83.7%] Black and 1704 [16.3%] White) were included. In the White group, 11 FTO SNVs were significantly associated with obesity, hypertension, and diabetes using linear models (eg, body mass index: β = 0.536; 95% CI, 0.197-0.875), but none of the FTO SNVs were associated with obesity traits in the Black group. White males had a higher risk of obesity while White females had a higher risk of hypertension and diabetes. However, 1 FTO SNV (rs1121980) was associated with a direct increase in the risk of heart disease in Black participants not mediated by obesity (c' = 0.145 [SE, 0.0517]; P = .01). Conclusions and Relevance In this cross-sectional study of obesity phenotypes and their association with cardiometabolic diseases, the tested FTO SNVs reflected sex differences in White participants. Different patterns of associations were observed among self-identified Black participants. Therefore, these results could inform future work discovering risk alleles or risk scores unique to Black individuals or further investigating genetic risk in all US residents.
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Affiliation(s)
- Hairui Yu
- Department of Health Behavior, School of Public Health, University of Alabama at Birmingham
- Department of Family and Community Medicine, School of Medicine, University of Alabama at Birmingham
| | - Nicole Armstrong
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham
| | - Greg Pavela
- Department of Health Behavior, School of Public Health, University of Alabama at Birmingham
| | - Kathryn Kaiser
- Department of Health Behavior, School of Public Health, University of Alabama at Birmingham
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131
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Iqbal MS, Peng K, Sardar N, Iqbal MH, Ghani MU, Tanvir F, Gu D, Guohua Z, Duan X. Interleukins-6 -174G/C (rs1800795) and -572C/G (rs1800796) polymorphisms and prostate cancer risk. Mol Immunol 2023; 164:88-97. [PMID: 37989067 DOI: 10.1016/j.molimm.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/23/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023]
Abstract
Prostate cancer (PCa) is an aggressive cancer influenced by a complex interplay of genetic and environmental factors. Amongst these risk factors, the impact of Interleukin6 (IL6) gene polymorphisms in PCa risk has received a lot of attention. IL-6 is a cytokine that has been implicated in the pathogenesis of several malignancies, including PCa. Two IL-6 gene polymorphisms, - 174 G/C (rs1800795) and - 572 C/G (rs1800796), have received intellectual attention due to their potential role as modulators of prostate cancer risk. The main objective of this research was to comprehensively explore the potential associations between IL-6 rs1800795 and rs1800796 polymorphisms, and their impact on the occurrence of PCa. A case-control study was carried out with a well-defined cohort comprising 110 PCa cases and 110 controls (total n = 220). The genotyping of rs1800795 and rs1800796 was carefully performed using the highly sensitive and accurate Polymerase Chain Reaction-High Resolution Melting Curve (PCR-HRM) technique. The assessment of genetic associations was evaluated using various R packages, such as Haplo-Stats, SNP stat, pheatmap, and LD heatmap. The present study applied odds ratio (OR) analysis to reveal significant evidence of strong associations between the genotypes of rs1800795 and rs1800796 and the susceptibility to PCa. The findings of this study underscore the noteworthy impact of genetic variations in the IL-6 gene on the development of prostate cancer. Specifically, the C/G and G/G genotypes of rs1800795 demonstrated increased PCa risk, with odds ratios (OR) of 1.650 (95% CI = 1.068-2.549, p = 0.032) and 2.475 (95% CI = 1.215-5.043, p < 0.001), respectively. Similarly, the G/C genotype of rs1800796 exhibited an OR of 2.374 (95% CI = 1.363-4.130, p = 0.012) for elevated prostate cancer risk, while the C/C genotype had an OR of 1.81 (95% CI = 1.02-3.22, p = 0.7). Furthermore, our haplotype analysis have revealed an association between haplotype 4 (C-G) and increased risk of PCa (OR = 1.69, 95% CI = 1.05-2.73, p = 0.032). In conclusion, this case-control analysis presents compelling evidence for a significant association between IL-6 variants (rs1800795 and rs1800796) and increased susceptibility to prostate cancer.
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Affiliation(s)
- Muhammad Sarfaraz Iqbal
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, Guangzhou Urology Research Institute, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Kaoqing Peng
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, Guangzhou Urology Research Institute, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Nimra Sardar
- Department of Microbiology and Molecular Genetics, School of Applied Sciences, University of Okara, Punjab, Pakistan.
| | | | - Muhammad Usman Ghani
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan.
| | - Fouzia Tanvir
- Department of Molecularbiology, Institute of Pure and Applied Zoology, University of Okara, Punjab, Pakistan
| | - Di Gu
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, Guangzhou Urology Research Institute, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Zeng Guohua
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, Guangzhou Urology Research Institute, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Xiaolu Duan
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, Guangzhou Urology Research Institute, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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132
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Mas-Bermejo P, Papiol S, Via M, Rovira P, Torrecilla P, Kwapil TR, Barrantes-Vidal N, Rosa A. Schizophrenia polygenic risk score in psychosis proneness. Eur Arch Psychiatry Clin Neurosci 2023; 273:1665-1675. [PMID: 37301774 PMCID: PMC10713704 DOI: 10.1007/s00406-023-01633-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Schizophrenia (SZ) is a complex disorder with a highly polygenic inheritance. It can be conceived as the extreme expression of a continuum of traits that are present in the general population often broadly referred to as schizotypy. However, it is still poorly understood how these traits overlap genetically with the disorder. We investigated whether polygenic risk for SZ is associated with these disorder-related phenotypes (schizotypy, psychotic-like experiences, and subclinical psychopathology) in a sample of 253 non-clinically identified participants. Polygenic risk scores (PRSs) were constructed based on the latest SZ genome-wide association study using the PRS-CS method. Their association with self-report and interview measures of SZ-related traits was tested. No association with either schizotypy or psychotic-like experiences was found. However, we identified a significant association with the Motor Change subscale of the Comprehensive Assessment of At-Risk Mental States (CAARMS) interview. Our results indicate that the genetic overlap of SZ with schizotypy and psychotic-like experiences is less robust than previously hypothesized. The relationship between high PRS for SZ and motor abnormalities could reflect neurodevelopmental processes associated with psychosis proneness and SZ.
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Affiliation(s)
- Patricia Mas-Bermejo
- Secció de Zoologia i Antropologia Biològica. Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals. Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal 643, 08028, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
| | - Sergi Papiol
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, 80336, Munich, Germany
- Max Planck Institute of Psychiatry, Munich, Germany
- CIBER de Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
| | - Marc Via
- Brainlab, Cognitive Neuroscience Research Group, Department of Clinical Psychology and Psychobiology, Universitat de Barcelona, Barcelona, Spain
- Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Paula Rovira
- Vicerectorat de Recerca, Investigadora Postdoctoral Margarita Salas, Universitat de Barcelona, Barcelona, Spain
- Instituto de Neurociencias, Centro de Investigación Biomédica (CIBM), Universidad de Granada, Granada, Spain
- Departamento de Psiquiatría, Facultad de Medicina, Universidad de Granada, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
| | - Pilar Torrecilla
- Department of Clinical and Health Psychology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Thomas R Kwapil
- Department of Psychology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Neus Barrantes-Vidal
- CIBER de Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
- Department of Clinical and Health Psychology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Sant Pere Claver-Fundació Sanitària, Barcelona, Spain
| | - Araceli Rosa
- Secció de Zoologia i Antropologia Biològica. Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals. Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal 643, 08028, Barcelona, Spain.
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain.
- CIBER de Salud Mental, Instituto de Salud Carlos III, Madrid, Spain.
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Dulski J, Soto-Beasley AI, Uitti RJ, Wszolek ZK, Ross OA. PTPA variants are rare in early-onset and familial Parkinson's disease. Brain 2023; 146:e125-e127. [PMID: 37448355 DOI: 10.1093/brain/awad244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Affiliation(s)
- Jarosław Dulski
- Department of Neurology, Mayo Clinic, Jacksonville, FL 32224, USA
- Division of Neurological and Psychiatric Nursing, Faculty of Health Sciences, Medical University of Gdansk, 80-211 Gdansk, Poland
- Neurology Department, St Adalbert Hospital, Copernicus PL Ltd., 80-462 Gdansk, Poland
| | | | - Ryan J Uitti
- Department of Neurology, Mayo Clinic, Jacksonville, FL 32224, USA
| | | | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
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134
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Jie J, Wu T. Single-nucleotide polymorphisms of TLR4 and GAS7 linked to primary open-angle glaucoma among patients of Shenyang, China. Exp Biol Med (Maywood) 2023; 248:2319-2324. [PMID: 38240248 PMCID: PMC10903258 DOI: 10.1177/15353702231214254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/30/2023] [Indexed: 01/23/2024] Open
Abstract
The potential for adverse outcomes and classifications of glaucoma differ among race, country, gender, and family medical history. Nearly, 50 represent candidate genes are considered as potential contributors to the happening for the primary open-angle glaucoma (POAG) since the advent of GWASs. Our investigation is the first to report the Toll-like receptor 4 (TLR4) and growth arrest-specific 7 (GAS7) among people in Shenyang, China; to investigate whether single-nucleotide polymorphisms (SNPs) in (TLR4) or GAS7 gene are risk factors for POAG among people in Shenyang, China; and also to explore their potential pathogenic mechanisms. POAG patients from July 2015 to June 2019 at Shenyang Fourth People's Hospital were selected. A total of 218 POAG patients and 252 controls were enrolled. Eight potentially functional SNPs of TLR4 (rs7868859, rs7873784, rs77358523, and rs752998) and GAS7 (rs8012311, rs11656696, rs74629981, and rs9900085) were genotyped. Multifactor analysis was conducted to evaluate the correlation between TLR4, GAS7, and POAG. The allele frequency of rs7873784 of TLR4 demonstrated that the GC (P = 0.030), CC (P = 0.040), and GC + CC genotypes (P = 0.009) were significantly higher compared with CC genotype for POAG patients than that for controls. The rs8072311 and rs9900085 of GAS7 gene also were significantly associated with POAG. Haplotype analysis found that the C-A-T-A haplotype (order: rs7873784-rs77358523-rs752998-rs7868859) of TLR4 gene and the two haplotypes A-C-C-A and C-C-A-C of GAS7 (order: rs9900085-rs74629981-rs8072311-rs11656696) were associated with an elevated susceptibility to POAG (P < 0.05). In this study, rs7868859 of TLR4 and rs8012311 and rs9900085 polymorphisms of GAS7 were first identified to be related to POAG among people in Shenyang, China.
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Affiliation(s)
- Jiao Jie
- Department of Ophthalmology, The Fourth People’s Hospital of Shenyang, Shenyang 110031, P.R. China
| | - Tengfei Wu
- Department of Laboratory Animal Science, China Medical University, Shenyang, Liaoning 110122, P.R. China
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Chen L, Zhao M, Zhou M, Luo J, Li S, Liu X, Cheng Z, Zhuo Y, Zeng W, Zhang Z, Zhou L. LncRNA RP1-276N6.2 Expression and RP1-276N6.2 Gene Polymorphisms Contribute to the Risk of Coronary Artery Disease in Chinese Han Population. DNA Cell Biol 2023; 42:746-752. [PMID: 37843894 DOI: 10.1089/dna.2023.0202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have been implicated in coronary artery disease (CAD) processes. However, the relationship between the gene polymorphisms of lncRNA RP1-276N6.2 as a novel molecule and susceptibility to CAD remains unclear. In our case-control study, 949 CAD patients and 892 healthy controls were genotyped using the TaqMan genotyping assay. The quantitative real-time polymerase chain reaction and enzyme-linked immunosorbent assay were performed to examine the expression levels of RP1-276N6.2 and SLC22A3(OCT3). We observed that CAD patients had significantly lower RP1-276N6.2 levels than those healthy participants (p < 0.05). Compared to the wild-type genotype, the rs611950 T allele and the rs10499313 AG genotype and G allele significantly increased the premature CAD risk (p = 0.02, p = 0.002, and p = 0.01, respectively), while the rs505000 G allele reduced this risk (p = 0.01); moreover, the rs505000 CG genotype significantly enhanced the delayed CAD risk (p = 0.03), and the rs505000 G allele reduced the expression levels of RP1-276N6.2 and SLC22A3 (p < 0.05 and p < 0.05, respectively). In addition, RP1-276N6.2 positively regulated the mRNA and secreted protein levels of SLC22A3 (p < 0.05). In conclusion, the RP1-276N6.2 gene polymorphisms were closely associated with CAD risk. LncRNA RP1-276N6.2 may be a potential genetic target for CAD early diagnosis and treatment.
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Affiliation(s)
- Lijuan Chen
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Mingming Zhao
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Mingsha Zhou
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Jia Luo
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Shan Li
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Xing Liu
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Zheng Cheng
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Yang Zhuo
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Weiqi Zeng
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Zhiyu Zhang
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Li Zhou
- Department of Epidemiology, School of Public Health, Chongqing Medical University, Chongqing, China
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136
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Ostrožovičová M, Mecheri Y, Al-Mubarak BR, Al-Tassan N, Makarious MB, Periñan MT, Bandres-Ciga S. PTPA variants and the risk for Parkinson's disease in diverse ancestry populations. Brain 2023; 146:e120-e124. [PMID: 37467482 PMCID: PMC10689897 DOI: 10.1093/brain/awad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023] Open
Affiliation(s)
- Miriam Ostrožovičová
- Department of Neurology, P.J. Safarik University, Kosice 04011, Slovak Republic
- Department of Neurology, University Hospital of L. Pasteur, Kosice 04011, Slovak Republic
| | - Yasser Mecheri
- Neurology Department, Dr Benbadis University Hospital, Constantine 25018, Algeria
| | - Bashayer R Al-Mubarak
- Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Nada Al-Tassan
- Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Mary B Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
- UCL Movement Disorders Centre, University College London, WC1N 3BG London, UK
| | - Maria Teresa Periñan
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clínica, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Sevilla, 41013 Seville, Spain
- Preventive Neurology Unit, Centre for Prevention, Detection and Diagnosis, Wolfson Institute of Population Health, Queen Mary University of London, EC1M 6BQ London, UK
| | - Sara Bandres-Ciga
- 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 20892, USA
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137
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Li A, Xiong C, Gong C, Gou M, Wang Y, Yang Y, Xu H. Genetic polymorphisms of purinergic P2Y 2 receptor were associated with the susceptibility to essential hypertension in Chinese postmenopausal women. Purinergic Signal 2023; 19:663-671. [PMID: 36653592 PMCID: PMC10754786 DOI: 10.1007/s11302-023-09921-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/07/2023] [Indexed: 01/20/2023] Open
Abstract
Hypertension has become a prominent public health concern. Essential hypertension (EH) is a polygenic disorder caused by multiple susceptibility genes. It has been previously shown that the purinergic P2Y2 receptor (P2Y2R) regulates blood pressure; however, whether P2Y2R genetic polymorphisms correlate with EH has not been investigated in Chinese. Our study included 500 EH cases and 504 controls who are Chinese postmenopausal women. We used allele-specific polymerase chain reaction (ASPCR) to genotype five single-nucleotide polymorphism (SNPs) in the P2Y2R gene, i.e., rs4944831, rs12366239, rs1783596, rs4382936, and rs10898909. We assessed the association of P2Y2R genetic polymorphisms with EH susceptibility. The results demonstrated that P2Y2R rs4382936A was correlated with a high risk of EH; particularly, the participants with the rs4382936A allele and CA/AA/(CA+AA) genotypes were at higher risks to EH compared to the subjects with the rs4382936C allele and CC genotype. Moreover, haplotype CAG combined by rs1783596-rs4382936-rs10898909 was a susceptible haplotype for EH, whereas haplotype CCG was a protective haplotype for EH. These results may provide new evidence for applying P2Y2R genetic polymorphisms as useful markers in clinic screening or monitoring potential EH cases in a population of Chinese postmenopausal women.
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Affiliation(s)
- Ao Li
- Department of Physiology, Jiangxi Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
- Joint Program of Nanchang University and Queen Mary University of London, Jiangxi Medical College of Nanchang University, Nanchang, Jiangxi, China
| | - Chaopeng Xiong
- Department of Intervention Center, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, China
| | - Chengxin Gong
- Department of Science and Education, Chest Hospital of Jiangxi Province, Nanchang, Jiangxi, China
| | - Mengyang Gou
- Department of Physiology, Jiangxi Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Yaqun Wang
- Department of Physiology, Jiangxi Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China
| | - Yuping Yang
- Medical Examination Center, The Fourth Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Hong Xu
- Department of Physiology, Jiangxi Medical College of Nanchang University, Nanchang, Jiangxi, 330006, People's Republic of China.
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138
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Waszczuk MA, Jonas KG, Bornovalova M, Breen G, Bulik CM, Docherty AR, Eley TC, Hettema JM, Kotov R, Krueger RF, Lencz T, Li JJ, Vassos E, Waldman ID. Dimensional and transdiagnostic phenotypes in psychiatric genome-wide association studies. Mol Psychiatry 2023; 28:4943-4953. [PMID: 37402851 PMCID: PMC10764644 DOI: 10.1038/s41380-023-02142-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/17/2023] [Accepted: 06/16/2023] [Indexed: 07/06/2023]
Abstract
Genome-wide association studies (GWAS) provide biological insights into disease onset and progression and have potential to produce clinically useful biomarkers. A growing body of GWAS focuses on quantitative and transdiagnostic phenotypic targets, such as symptom severity or biological markers, to enhance gene discovery and the translational utility of genetic findings. The current review discusses such phenotypic approaches in GWAS across major psychiatric disorders. We identify themes and recommendations that emerge from the literature to date, including issues of sample size, reliability, convergent validity, sources of phenotypic information, phenotypes based on biological and behavioral markers such as neuroimaging and chronotype, and longitudinal phenotypes. We also discuss insights from multi-trait methods such as genomic structural equation modelling. These provide insight into how hierarchical 'splitting' and 'lumping' approaches can be applied to both diagnostic and dimensional phenotypes to model clinical heterogeneity and comorbidity. Overall, dimensional and transdiagnostic phenotypes have enhanced gene discovery in many psychiatric conditions and promises to yield fruitful GWAS targets in the years to come.
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Affiliation(s)
- Monika A Waszczuk
- Department of Psychology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA.
| | - Katherine G Jonas
- Department of Psychiatry, Stony Brook University School of Medicine, Stony Brook, NY, USA
| | | | - Gerome Breen
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- UK National Institute for Health and Care Research (NIHR) Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
| | - Cynthia M Bulik
- Department of Psychiatry, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Anna R Docherty
- Huntsman Mental Health Institute, Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Thalia C Eley
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- UK National Institute for Health and Care Research (NIHR) Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
| | - John M Hettema
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
- Department of Psychiatry, Texas A&M Health Sciences Center, Bryan, TX, USA
| | - Roman Kotov
- Department of Psychiatry, Stony Brook University School of Medicine, Stony Brook, NY, USA
| | - Robert F Krueger
- Psychology Department, University of Minnesota, Minneapolis, MN, USA
| | - Todd Lencz
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY, USA
- Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - James J Li
- Department of Psychology, University of Wisconsin, Madison, WI, USA
- Waisman Center, University of Wisconsin, Madison, WI, USA
| | - Evangelos Vassos
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- UK National Institute for Health and Care Research (NIHR) Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
| | - Irwin D Waldman
- Department of Psychology, Emory University, Atlanta, GA, USA
- Center for Computational and Quantitative Genetics, Emory University, Atlanta, GA, USA
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139
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Ma DR, Li SJ, Shi JJ, Liang YY, Hu ZW, Hao XY, Li MJ, Guo MN, Zuo CY, Yu WK, Mao CY, Tang MB, Zhang C, Xu YM, Wu J, Sun SL, Shi CH. Shared Genetic Architecture between Parkinson's Disease and Brain Structural Phenotypes. Mov Disord 2023; 38:2258-2268. [PMID: 37990409 DOI: 10.1002/mds.29598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/02/2023] [Accepted: 08/21/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Patients with Parkinson's disease (PD) have consistently demonstrated brain structure abnormalities, indicating the presence of shared etiological and pathological processes between PD and brain structures; however, the genetic relationship remains poorly understood. OBJECTIVE The aim of this study was to investigate the extent of shared genetic architecture between PD and brain structural phenotypes (BSPs) and to identify shared genomic loci. METHODS We used the summary statistics from genome-wide association studies to conduct MiXeR and conditional/conjunctional false discovery rate analyses to investigate the shared genetic signatures between PD and BSPs. Subsequent expression quantitative trait loci mapping in the human brain and enrichment analyses were also performed. RESULTS MiXeR analysis identified genetic overlap between PD and various BSPs, including total cortical surface area, average cortical thickness, and specific brain volumetric structures. Further analysis using conditional false discovery rate (FDR) identified 21 novel PD risk loci on associations with BSPs at conditional FDR < 0.01, and the conjunctional FDR analysis demonstrated that PD shared several genomic loci with certain BSPs at conjunctional FDR < 0.05. Among the shared loci, 16 credible mapped genes showed high expression in the brain tissues and were primarily associated with immune function-related biological processes. CONCLUSIONS We confirmed the polygenic overlap with mixed directions of allelic effects between PD and BSPs and identified multiple shared genomic loci and risk genes, which are likely related to immune-related biological processes. These findings provide insight into the complex genetic architecture associated with PD. © 2023 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Dong-Rui Ma
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Shuang-Jie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Jing-Jing Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yuan-Yuan Liang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Zheng-Wei Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Xiao-Yan Hao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Meng-Jie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Meng-Nan Guo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Chun-Yan Zuo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Wen-Kai Yu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Cheng-Yuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Mi-Bo Tang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Chan Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yu-Ming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
| | - Jun Wu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
| | - Shi-Lei Sun
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
| | - Chang-He Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
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140
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Nath M, Swarnkar P, Misra S, Kumar P. Phosphodiesterase 4 D (PDE4D) gene polymorphisms and risk of ischemic stroke: A systematic review and meta-analysis. Acta Neurol Belg 2023; 123:2085-2110. [PMID: 36862303 DOI: 10.1007/s13760-023-02218-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 02/16/2023] [Indexed: 03/03/2023]
Abstract
BACKGROUND AND PURPOSE Studies on the relationship between Phosphodiesterase 4 D (PDE4D) gene polymorphism with the risk of ischemic stroke (IS) have shown discordant results. The present meta-analysis was aimed to clarify the relationship between PDE4D gene polymorphism with the risk of IS by estimating pooled analysis of published epidemiological studies. METHODS A comprehensive literature search for all the published articles was performed in various electronic databases, including PubMed, EMbase, Cochrane Library, Trip Database, Worldwide Science, CINAHL, and Google Scholar up to 22nd December 2021. Pooled Odds ratios (ORs) with 95% Confidence Intervals (CIs) under dominant, recessive, and allelic models were calculated. Subgroup analysis based on ethnicity (Caucasian vs. Asian) was performed to examine the reliability of these findings. Sensitivity analysis was also performed to detect the heterogeneity between studies. Finally, Begg's funnel plot was used to assess the potential for publication bias. RESULTS In our meta-analysis, we identified a total of 47 case-control studies with 20,644 ischemic stroke (IS) cases and 23,201 control subjects, including 17 studies of Caucasian descent and 30 studies of Asian descent. Our findings suggest that there was a significant relationship between SNP45 gene polymorphism and risk of IS (Recessive model: OR = 2.06, 95% CI 1.31-3.23), SNP83 overall (allelic model: OR = 1.22, 95% CI 1.04-1.42), Asian (allelic model: OR = 1.20, 95% CI 1.05-1.37), and SNP89 Asian (Dominant model: OR = 1.43, 95% CI 1.29-1.59, recessive model: OR = 1.42, 95% CI 1.28-1.58) respectively. However, no significant relationship was found between SNP32, SNP41, SNP26, SNP56, and SNP87 gene polymorphisms and risk of IS. CONCLUSION Findings of this meta-analysis conclude that SNP45, SNP83, and SNP89 polymorphism could be capable of increasing stroke susceptibility in Asians but not in the Caucasian population. Genotyping of SNP 45, 83, 89 polymorphisms may be used as a predictor for the occurrence of IS.
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Affiliation(s)
- Manabesh Nath
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Priyanka Swarnkar
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Shubham Misra
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, 110029, India
- Department of Neurology, Yale University School of Medicine, New Heaven, USA
| | - Pradeep Kumar
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, 110029, India.
- Clinical Research Unit, All India Institute of Medical Sciences, New Delhi, India.
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141
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Humphries EM, Ahn K, Kember RL, Lopes FL, Mocci E, Peralta JM, Blangero J, Glahn DC, Goes FS, Zandi PP, Kochunov P, Van Hout C, Shuldiner AR, Pollin TI, Mitchell BD, Bucan M, Hong LE, McMahon FJ, Ament SA. Genome-wide significant risk loci for mood disorders in the Old Order Amish founder population. Mol Psychiatry 2023; 28:5262-5271. [PMID: 36882501 PMCID: PMC10483025 DOI: 10.1038/s41380-023-02014-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
Genome-wide association studies (GWAS) of mood disorders in large case-control cohorts have identified numerous risk loci, yet pathophysiological mechanisms remain elusive, primarily due to the very small effects of common variants. We sought to discover risk variants with larger effects by conducting a genome-wide association study of mood disorders in a founder population, the Old Order Amish (OOA, n = 1,672). Our analysis revealed four genome-wide significant risk loci, all of which were associated with >2-fold relative risk. Quantitative behavioral and neurocognitive assessments (n = 314) revealed effects of risk variants on sub-clinical depressive symptoms and information processing speed. Network analysis suggested that OOA-specific risk loci harbor novel risk-associated genes that interact with known neuropsychiatry-associated genes via gene interaction networks. Annotation of the variants at these risk loci revealed population-enriched, non-synonymous variants in two genes encoding neurodevelopmental transcription factors, CUX1 and CNOT1. Our findings provide insight into the genetic architecture of mood disorders and a substrate for mechanistic and clinical studies.
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Affiliation(s)
- Elizabeth M Humphries
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Molecular Epidemiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kwangmi Ahn
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Rachel L Kember
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Fabiana L Lopes
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Evelina Mocci
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Juan M Peralta
- University of Texas Rio Grande Valley, Harlingen, TX, USA
| | - John Blangero
- University of Texas Rio Grande Valley, Harlingen, TX, USA
| | | | - Fernando S Goes
- Departments of Epidemiology and Mental Health, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Peter P Zandi
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Peter Kochunov
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Cristopher Van Hout
- Regeneron Genetics Center, Tarrytown, NY, USA
- Laboratorio Internacional de Investigatión sobre el Genoma Humano, Campus Juriquilla de la Universidad Nacional Autónoma de México, Querétaro, Querétaro, 76230, Mexico
| | - Alan R Shuldiner
- Regeneron Genetics Center, Tarrytown, NY, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Toni I Pollin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maja Bucan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - L Elliot Hong
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Francis J McMahon
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA.
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Kendler KS, Ohlsson H, Sundquist J, Sundquist K. Selecting cases of major psychiatric and substance use disorders in Swedish national registries on the basis of clinical features to maximize the strength or specificity of the genetic risk. Mol Psychiatry 2023; 28:5195-5205. [PMID: 37414926 PMCID: PMC10832579 DOI: 10.1038/s41380-023-02156-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 07/08/2023]
Abstract
We investigate how selection of psychiatric cases by phenotypic criteria can alter the strength and specificity of their genetic risk by examining samples from national Swedish registries for five disorders: major depression (MD, N = 158,557), drug use disorder (DUD, N = 69,841), bipolar disorder (BD, N = 13,530)) ADHD (N = 54,996) and schizophrenia (N = 11,227)). We maximized the family genetic risk score (FGRS) for each disorder and then the specificity of the FGRS in six disorder pairs by univariable and multivariable regression. We use split-half methods to divide our cases for each disorder into deciles for prediction of genetic risk magnitude and quintiles for prediction of specificity by FGRS differences between two disorders. We utilized seven predictor groups: demography/sex, # registrations, site of diagnosis, severity, comorbidity, treatment, and educational/social variables. The ratio of the FGRS in the upper vs two lower deciles from our multivariable prediction model was, in order, DUD - 12.6, MD - 4.9, BD - 4.5, ADHD - 3.3 and schizophrenia 1.4. From the lowest to highest quintile, our measures of genetic specificity increased more than five-fold for i) MD vs. Anxiety Disorders, ii) MD vs BD, iii) MD versus alcohol use disorder (AUD), iv) BD vs schizophrenia and v) DUD vs AUD. This increase was nearly two-fold for ADHD vs DUD. We conclude that the level of genetic liability for our psychiatric disorders could be substantially enriched by selection of cases with our predictors. Specificity of genetic risk could also be substantially impacted by these same predictors.
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Affiliation(s)
- Kenneth S Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA.
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA.
| | - Henrik Ohlsson
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Jan Sundquist
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Departments of Family Medicine, Community Health and Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristina Sundquist
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
- Departments of Family Medicine, Community Health and Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Kenny J, Mullin BH, Tomlinson W, Robertson B, Yuan J, Chen W, Zhao J, Pavlos NJ, Walsh JP, Wilson SG, Tickner J, Morahan G, Xu J. Age-dependent genetic regulation of osteoarthritis: independent effects of immune system genes. Arthritis Res Ther 2023; 25:232. [PMID: 38041181 PMCID: PMC10691153 DOI: 10.1186/s13075-023-03216-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023] Open
Abstract
OBJECTIVES Osteoarthritis (OA) is a joint disease with a heritable component. Genetic loci identified via genome-wide association studies (GWAS) account for an estimated 26.3% of the disease trait variance in humans. Currently, there is no method for predicting the onset or progression of OA. We describe the first use of the Collaborative Cross (CC), a powerful genetic resource, to investigate knee OA in mice, with follow-up targeted multi-omics analysis of homologous regions of the human genome. METHODS We histologically screened 275 mice for knee OA and conducted quantitative trait locus (QTL) mapping in the complete cohort (> 8 months) and the younger onset sub-cohort (8-12 months). Multi-omic analysis of human genetic datasets was conducted to investigate significant loci. RESULTS We observed a range of OA phenotypes. QTL mapping identified a genome-wide significant locus on mouse chromosome 19 containing Glis3, the human equivalent of which has been identified as associated with OA in recent GWAS. Mapping the younger onset sub-cohort identified a genome-wide significant locus on chromosome 17. Multi-omic analysis of the homologous region of the human genome (6p21.32) indicated the presence of pleiotropic effects on the expression of the HLA - DPB2 gene and knee OA development risk, potentially mediated through the effects on DNA methylation. CONCLUSIONS The significant associations at the 6p21.32 locus in human datasets highlight the value of the CC model of spontaneous OA that we have developed and lend support for an immune role in the disease. Our results in mice also add to the accumulating evidence of a role for Glis3 in OA.
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Affiliation(s)
- Jacob Kenny
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia.
| | - Benjamin H Mullin
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - William Tomlinson
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Brett Robertson
- Australian Institute of Robotic Orthopaedics, Crawley, WA, Australia
| | - Jinbo Yuan
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Weiwei Chen
- Research Centre for Regenerative Medicine, and Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Guangxi, China
| | - Jinmin Zhao
- Research Centre for Regenerative Medicine, and Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Guangxi, China
| | - Nathan J Pavlos
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - John P Walsh
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
- Medical School, University of Western Australia, Crawley, WA, Australia
| | - Scott G Wilson
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jennifer Tickner
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute for Medical Research, Nedlands, WA, Australia.
| | - Jiake Xu
- School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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Noda Y, Miyoshi H, Benucci S, Gonzalez A, Bandschapp O, Girard T, Treves S, Zorzato F. Functional characterization of RYR1 variants identified in malignant hyperthermia susceptible individuals. Neuromuscul Disord 2023; 33:951-963. [PMID: 37996280 DOI: 10.1016/j.nmd.2023.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/25/2023]
Abstract
Malignant hyperthermia is a pharmacogenetic disorder triggered by halogenated anesthetic agents in genetically predisposed individuals. Approximately 70 % of these individuals carry mutations in RYR1, the gene encoding the ryanodine receptor calcium channel of skeletal muscle. In this study, we performed functional analysis of 5 RYR1 variants identified in members from 8 families who had been diagnosed by the IVCT. Of the 68 individuals enrolled in the study, 43 were diagnosed as MHS, 23 as MHN, and 2 individuals were not tested. Here we demonstrate that the 5 RyR1 variants cause hypersensitivity to RyR1 agonist-mediated calcium release. According to the EMHG scoring matrix these five genetic variants can be classified as follows: c.8638G>A (p.E2880K) and c.11314C>T (p.R3772W) likely pathogenic, c.11416G>A (p.G3806R), c.14627A>G (p.K4876R) and c.14813T>C (p.I4938T), pathogenic (RefSeq NM_000540.3). We propose that the newly functionally characterized RYR1 variants, be included in the panel of variants to be used for the molecular diagnosis of MHS.
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Affiliation(s)
- Yuko Noda
- Departments of Biomedicine and Neurology, Basel University Hospital, Hebelstrasse 20, Basel 4031, Switzerland; Department of Anesthesiology, Hiroshima University Hospital, 1-2-3 Kasumi Minami-ku Hiroshima, 734-8551, Japan
| | - Hirotsugu Miyoshi
- Department of Anesthesiology, Hiroshima University Hospital, 1-2-3 Kasumi Minami-ku Hiroshima, 734-8551, Japan
| | - Sofia Benucci
- Departments of Biomedicine and Neurology, Basel University Hospital, Hebelstrasse 20, Basel 4031, Switzerland
| | | | | | - Thierry Girard
- Anesthesiology, Spitalstrasse 21, Basel 4031, Switzerland
| | - Susan Treves
- Departments of Biomedicine and Neurology, Basel University Hospital, Hebelstrasse 20, Basel 4031, Switzerland; Department of Life Science and Biotechnology, University of Ferrara, Via Borsari 46, Ferrara 44100, Italy.
| | - Francesco Zorzato
- Departments of Biomedicine and Neurology, Basel University Hospital, Hebelstrasse 20, Basel 4031, Switzerland; Department of Life Science and Biotechnology, University of Ferrara, Via Borsari 46, Ferrara 44100, Italy.
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145
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Talebi T, Masoumi T, Heshmatzad K, Hesami M, Maleki M, Kalayinia S. Genetic Variations in the Human Angiotensin-ConvertingEnzyme 2 and Susceptibility to Coronavirus Disease-19. Genet Res (Camb) 2023; 2023:2593199. [PMID: 38074420 PMCID: PMC10699955 DOI: 10.1155/2023/2593199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 11/06/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Background Health and economies are both affected by the coronavirus disease-19 (COVID-19) global pandemic. Angiotensin-converting enzyme 2 (ACE2) is a polymorphic enzyme that is a part of the renin-angiotensin system, and it plays a crucial role in viral entry. Previous investigations and studies revealed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and ACE2 have a considerable association. Recently, ACE2 variants have been described in human populations in association with cardiovascular and pulmonary conditions. In this study, genetic susceptibility to COVID-19 in different populations was investigated. Methods and Results We evaluated the identified variants based on the predictive performance of 5 deleteriousness-scoring methods and the 2015 American College of Medical Genetics and Genomics (ACMG) guidelines. The results indicated 299 variants within the ACE2 gene. The variants were analyzed by different in-silico analysis tools to assess their functional effects. Ultimately, 5 more deleterious variants were found in the ACE2 gene. Conclusions Collecting more information about the variations in binding affinity between SARS-CoV-2 and host-cell receptors due to ACE2 variants leads to progress in treatment strategies for COVID-19. The evidence accumulated in this study showed that ACE2 variants in different populations may be associated with the genetic susceptibility, symptoms, and outcome of SARS-CoV-2 infection.
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Affiliation(s)
- Taravat Talebi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Tannaz Masoumi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Katayoun Heshmatzad
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mahshid Hesami
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
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146
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Nogawa S, Kanamori H, Tokuda K, Kawafune K, Chijiiwa M, Saito K, Takahashi S. A web-based genome-wide association study reveals the susceptibility loci of common adverse events following COVID-19 vaccination in the Japanese population. Sci Rep 2023; 13:20820. [PMID: 38012279 PMCID: PMC10682012 DOI: 10.1038/s41598-023-47632-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has spread rapidly worldwide. To prevent its spread, mRNA-based vaccines made by Pfizer/BioNTech (BNT162b1) and Moderna (mRNA-1273) have been widely used, including in Japan. Various adverse events have been reported following the COVID-19 mRNA vaccination, with differences observed among individuals. However, analyses of the genetic background associated with the susceptibility to side effects have been limited. In the present study, we performed genome-wide association studies (GWAS) for self-reported adverse events of the COVID-19 mRNA vaccination in 4545 Japanese individuals and identified 14 associated loci. Among these, 6p21 was associated with 37.5 °C or higher fever, 38 °C or higher fever, and muscle pain. HLA allele association analysis revealed that various HLA alleles were associated with the adverse effects; HLA-DQA1*03:01 and HLA-A*11:01 were more reliably associated with the adverse effects. Our results may enable the preparation and management of adverse effects by identifying the susceptibility to these adverse events. Furthermore, we obtained valuable data that may lead to a better understanding of the mechanisms of action of the COVID-19 mRNA vaccines.
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Affiliation(s)
- Shun Nogawa
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Hajime Kanamori
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
- Division of Infection Control, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Koichi Tokuda
- Department of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
- Division of Infection Control, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Kaoru Kawafune
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Miyuki Chijiiwa
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Kenji Saito
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan
| | - Shoko Takahashi
- Genequest Inc., Siba 5-29-11, Minato-ku, Tokyo, 108-0014, Japan.
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147
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Jain PR, Burch M, Martinez M, Mir P, Fichna JP, Zekanowski C, Rizzo R, Tümer Z, Barta C, Yannaki E, Stamatoyannopoulos J, Drineas P, Paschou P. Can polygenic risk scores help explain disease prevalence differences around the world? A worldwide investigation. BMC Genom Data 2023; 24:70. [PMID: 37986041 PMCID: PMC10662565 DOI: 10.1186/s12863-023-01168-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/20/2023] [Indexed: 11/22/2023] Open
Abstract
Complex disorders are caused by a combination of genetic, environmental and lifestyle factors, and their prevalence can vary greatly across different populations. The extent to which genetic risk, as identified by Genome Wide Association Study (GWAS), correlates to disease prevalence in different populations has not been investigated systematically. Here, we studied 14 different complex disorders and explored whether polygenic risk scores (PRS) based on current GWAS correlate to disease prevalence within Europe and around the world. A clear variation in GWAS-based genetic risk was observed based on ancestry and we identified populations that have a higher genetic liability for developing certain disorders. We found that for four out of the 14 studied disorders, PRS significantly correlates to disease prevalence within Europe. We also found significant correlations between worldwide disease prevalence and PRS for eight of the studied disorders with Multiple Sclerosis genetic risk having the highest correlation to disease prevalence. Based on current GWAS results, the across population differences in genetic risk for certain disorders can potentially be used to understand differences in disease prevalence and identify populations with the highest genetic liability. The study highlights both the limitations of PRS based on current GWAS but also the fact that in some cases, PRS may already have high predictive power. This could be due to the genetic architecture of specific disorders or increased GWAS power in some cases.
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Affiliation(s)
- Pritesh R Jain
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Myson Burch
- Department of Computer Sciences, Purdue University, West Lafayette, IN, USA
| | - Melanie Martinez
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Pablo Mir
- Unidad de Trastornos del Movimiento, Instituto de Biomedicina de Sevilla (IBiS). Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Jakub P Fichna
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Neurogenetics and Functional Genomics, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Cezary Zekanowski
- Department of Neurogenetics and Functional Genomics, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Renata Rizzo
- Child and Adolescent Neurology and Psychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Zeynep Tümer
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Csaba Barta
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Evangelia Yannaki
- Hematology Department- Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, Thessaloniki, Greece
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Medicine, Division of Oncology, University of Washington, Seattle, WA, USA
| | - Petros Drineas
- Department of Computer Sciences, Purdue University, West Lafayette, IN, USA
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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148
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Nehring P, Gromadzka G, Jastrzębski M, Przybyłkowski A. Genetic Variants in Matrix Metalloproteinases MMP3 (rs3025058) and MMP9 (rs3918242) Associated with Colonic Diverticulosis. Medicina (Kaunas) 2023; 59:2031. [PMID: 38004080 PMCID: PMC10673370 DOI: 10.3390/medicina59112031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Background and Objectives: Diverticulosis affects a significant portion of the elderly population, with age and lifestyle being established risk factors. Additionally, genetic predisposition is gaining recognition as a contributing factor. This pilot study sought to explore the frequency of genetic variants in matrix metalloproteinases (MMPs) 3, 9, and 12 in a population of colonic diverticulosis patients. Materials and Methods: The study encompassed 134 participants: 59 diagnosed with colon diverticulosis during colonoscopy and 75 healthy controls. The cases and controls were meticulously matched in terms of age and gender. We assessed the distribution of genetic variants MMP3 rs3025058, MMP9 rs3918242, and MMP12 rs2276109 using the polymerase chain reaction-restriction fragments length polymorphism technique. Results: The MMP9 rs3918242 allele T was notably more frequent in individuals with diverticulosis when compared with the control group (p < 0.03). Furthermore, it was associated with dominant (OR = 2.62; 95% CI: 1.24-5.56; p < 0.01) and co-dominant (OR = 2.10; 95% CI: 1.06-4.13; p < 0.03) genetic models. The MMP3 rs3025058 5A/5A genotype was nearly twice as frequent in patients with diverticulosis, while the 6A/6A genotype was only half as common in this group. Conversely, no significant correlation was established between MMP12 rs2276109 and colonic diverticulosis. Conclusions: Our study offers the first insight into a potential connection between genetic variants in MMPs and colon diverticulosis. Specifically, allele T of MMP9 rs3918242 and allele 5A of MMP3 rs3025058 appear to be linked to this condition. These findings indirectly suggest a role for extracellular matrix proteins in the pathogenesis of diverticulosis.
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Affiliation(s)
- Piotr Nehring
- Department of Gastroenterology and Internal Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland (M.J.)
| | - Grażyna Gromadzka
- Faculty of Medicine, Collegium Medicum, Cardinal Stefan Wyszyński University in Warsaw, Wóycickiego 1/3, 01-938 Warsaw, Poland;
| | - Miłosz Jastrzębski
- Department of Gastroenterology and Internal Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland (M.J.)
| | - Adam Przybyłkowski
- Department of Gastroenterology and Internal Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland (M.J.)
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149
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Makarious MB, Lake J, Pitz V, Ye Fu A, Guidubaldi JL, Solsberg CW, Bandres-Ciga S, Leonard HL, Kim JJ, Billingsley KJ, Grenn FP, Jerez PA, Alvarado CX, Iwaki H, Ta M, Vitale D, Hernandez D, Torkamani A, Ryten M, Hardy J, Scholz SW, Traynor BJ, Dalgard CL, Ehrlich DJ, Tanaka T, Ferrucci L, Beach TG, Serrano GE, Real R, Morris HR, Ding J, Gibbs JR, Singleton AB, Nalls MA, Bhangale T, Blauwendraat C. Large-scale rare variant burden testing in Parkinson's disease. Brain 2023; 146:4622-4632. [PMID: 37348876 PMCID: PMC10629770 DOI: 10.1093/brain/awad214] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/01/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Parkinson's disease has a large heritable component and genome-wide association studies have identified over 90 variants with disease-associated common variants, providing deeper insights into the disease biology. However, there have not been large-scale rare variant analyses for Parkinson's disease. To address this gap, we investigated the rare genetic component of Parkinson's disease at minor allele frequencies <1%, using whole genome and whole exome sequencing data from 7184 Parkinson's disease cases, 6701 proxy cases and 51 650 healthy controls from the Accelerating Medicines Partnership Parkinson's disease (AMP-PD) initiative, the National Institutes of Health, the UK Biobank and Genentech. We performed burden tests meta-analyses on small indels and single nucleotide protein-altering variants, prioritized based on their predicted functional impact. Our work identified several genes reaching exome-wide significance. Two of these genes, GBA1 and LRRK2, have variants that have been previously implicated as risk factors for Parkinson's disease, with some variants in LRRK2 resulting in monogenic forms of the disease. We identify potential novel risk associations for variants in B3GNT3, AUNIP, ADH5, TUBA1B, OR1G1, CAPN10 and TREML1 but were unable to replicate the observed associations across independent datasets. Of these, B3GNT3 and TREML1 could provide new evidence for the role of neuroinflammation in Parkinson's disease. To date, this is the largest analysis of rare genetic variants in Parkinson's disease.
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Affiliation(s)
- Mary B Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
| | - Julie Lake
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Vanessa Pitz
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Allen Ye Fu
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Joseph L Guidubaldi
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, 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 20814, USA
| | - Caroline Warly Solsberg
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
- Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Sara Bandres-Ciga
- 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 20814, USA
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, 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 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Jonggeol Jeffrey Kim
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Kimberley J Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, 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 20814, USA
| | - Francis P Grenn
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Pilar Alvarez Jerez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, 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 20814, USA
| | - Chelsea X Alvarado
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Hirotaka Iwaki
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, 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 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Michael Ta
- 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 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Dan Vitale
- 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 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mina Ryten
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - John Hardy
- UK Dementia Research Institute and Department of Neurodegenerative Disease and Reta Lila Weston Institute, UCL Queen Square Institute of Neurology and UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | | | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20814, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD 21287, USA
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD 21287, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Debra J Ehrlich
- Parkinson’s Disease Clinic, Office of the Clinical Director, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20814, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Raquel Real
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
| | - Jinhui Ding
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, 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 20814, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, 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 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, 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 20814, USA
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150
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Rizig M, Bandres-Ciga S, Makarious MB, Ojo OO, Crea PW, Abiodun OV, Levine KS, Abubakar SA, Achoru CO, Vitale D, Adeniji OA, Agabi OP, Koretsky MJ, Agulanna U, Hall DA, Akinyemi RO, Xie T, Ali MW, Shamim EA, Ani-Osheku I, Padmanaban M, Arigbodi OM, Standaert DG, Bello AH, Dean MN, Erameh CO, Elsayed I, Farombi TH, Okunoye O, Fawale MB, Billingsley KJ, Imarhiagbe FA, Jerez PA, Iwuozo EU, Baker B, Komolafe MA, Malik L, Nwani PO, Daida K, Nwazor EO, Miano-Burkhardt A, Nyandaiti YW, Fang ZH, Obiabo YO, Kluss JH, Odeniyi OA, Hernandez DG, Odiase FE, Tayebi N, Ojini FI, Sidranksy E, Onwuegbuzie GA, D'Souza AM, Osaigbovo GO, Berhe B, Osemwegie N, Reed X, Oshinaike OO, Leonard HL, Otubogun FM, Alvarado CX, Oyakhire SI, Ozomma SI, Samuel SC, Taiwo FT, Wahab KW, Zubair YA, Iwaki H, Kim JJ, Morris HR, Hardy J, Nalls MA, Heilbron K, Norcliffe-Kaufmann L, Blauwendraat C, Houlden H, Singleton A, Okubadejo NU. Identification of genetic risk loci and causal insights associated with Parkinson's disease in African and African admixed populations: a genome-wide association study. Lancet Neurol 2023; 22:1015-1025. [PMID: 37633302 PMCID: PMC10593199 DOI: 10.1016/s1474-4422(23)00283-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/15/2023] [Accepted: 07/18/2023] [Indexed: 08/28/2023]
Abstract
BACKGROUND An understanding of the genetic mechanisms underlying diseases in ancestrally diverse populations is an important step towards development of targeted treatments. Research in African and African admixed populations can enable mapping of complex traits, because of their genetic diversity, extensive population substructure, and distinct linkage disequilibrium patterns. We aimed to do a comprehensive genome-wide assessment in African and African admixed individuals to better understand the genetic architecture of Parkinson's disease in these underserved populations. METHODS We performed a genome-wide association study (GWAS) in people of African and African admixed ancestry with and without Parkinson's disease. Individuals were included from several cohorts that were available as a part of the Global Parkinson's Genetics Program, the International Parkinson's Disease Genomics Consortium Africa, and 23andMe. A diagnosis of Parkinson's disease was confirmed clinically by a movement disorder specialist for every individual in each cohort, except for 23andMe, in which it was self-reported based on clinical diagnosis. We characterised ancestry-specific risk, differential haplotype structure and admixture, coding and structural genetic variation, and enzymatic activity. FINDINGS We included 197 918 individuals (1488 cases and 196 430 controls) in our genome-wide analysis. We identified a novel common risk factor for Parkinson's disease (overall meta-analysis odds ratio for risk of Parkinson's disease 1·58 [95% CI 1·37-1·80], p=2·397 × 10-14) and age at onset at the GBA1 locus, rs3115534-G (age at onset β=-2·00 [SE=0·57], p=0·0005, for African ancestry; and β=-4·15 [0·58], p=0·015, for African admixed ancestry), which was rare in non-African or non-African admixed populations. Downstream short-read and long-read whole-genome sequencing analyses did not reveal any coding or structural variant underlying the GWAS signal. The identified signal seems to be associated with decreased glucocerebrosidase activity. INTERPRETATION Our study identified a novel genetic risk factor in GBA1 in people of African ancestry, which has not been seen in European populations, and it could be a major mechanistic basis of Parkinson's disease in African populations. This population-specific variant exerts substantial risk on Parkinson's disease as compared with common variation identified through GWAS and it was found to be present in 39% of the cases assessed in this study. This finding highlights the importance of understanding ancestry-specific genetic risk in complex diseases, a particularly crucial point as the Parkinson's disease field moves towards targeted treatments in clinical trials. The distinctive genetics of African populations highlights the need for equitable inclusion of ancestrally diverse groups in future trials, which will be a valuable step towards gaining insights into novel genetic determinants underlying the causes of Parkinson's disease. This finding opens new avenues towards RNA-based and other therapeutic strategies aimed at reducing lifetime risk of Parkinson's disease. FUNDING The Global Parkinson's Genetics Program, which is funded by the Aligning Science Across Parkinson's initiative, and The Michael J Fox Foundation for Parkinson's Research.
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Affiliation(s)
- Mie Rizig
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Sara Bandres-Ciga
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Mary B Makarious
- UCL Movement Disorders Centre, University College London, London, UK; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Peter Wild Crea
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Kristin S Levine
- Center for Alzheimer's and Related Dementias, 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
| | | | | | - Dan Vitale
- Data Tecnica International, Washington, DC, USA
| | | | - Osigwe Paul Agabi
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria
| | - Mathew J Koretsky
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Uchechi Agulanna
- Lagos University Teaching Hospital, Idi Araba, Lagos State, Nigeria
| | - Deborah A Hall
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Rufus Olusola Akinyemi
- Neuroscience and Ageing Research Unit, Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Tao Xie
- Department of Neurology, University of Chicago Medicine, Chicago, IL, USA
| | | | - Ejaz A Shamim
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Kaiser Permanente Mid-Atlantic States, Largo, MD, USA; MidAtlantic Permanente Research Institute, Rockville, MD, USA
| | | | - Mahesh Padmanaban
- Department of Neurology, University of Chicago Medicine, Chicago, IL, USA
| | | | - David G Standaert
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Marissa N Dean
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Inas Elsayed
- Faculty of Pharmacy, University of Gezira, Wadmadani, Sudan
| | | | - Olaitan Okunoye
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | | | - Kimberley J Billingsley
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Pilar Alvarez Jerez
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK; Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Breeana Baker
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Laksh Malik
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Paul Osemeke Nwani
- Nnamdi Azikiwe University Teaching Hospital, Nnewi, Anambra State, Nigeria
| | - Kensuke Daida
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Abigail Miano-Burkhardt
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Zih-Hua Fang
- German Center for Neurodegenerative Diseases, Tuebingen, Germany
| | | | - Jillian H Kluss
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Nahid Tayebi
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Francis Ibe Ojini
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria
| | - Ellen Sidranksy
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Andrea M D'Souza
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Bahafta Berhe
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xylena Reed
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Hampton L Leonard
- Center for Alzheimer's and Related Dementias, 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
| | | | - Chelsea X Alvarado
- Center for Alzheimer's and Related Dementias, 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
| | | | | | | | | | - Kolawole Wasiu Wahab
- University of Ilorin Teaching Hospital, Ilorin, Kwara State, Nigeria; University of Ilorin, Ilorin, Kwara State, Nigeria
| | | | - Hirotaka Iwaki
- Center for Alzheimer's and Related Dementias, 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
| | - Jonggeol Jeffrey Kim
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Huw R Morris
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - John Hardy
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | | | | | | | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Andrew Singleton
- Center for Alzheimer's and Related Dementias, National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
| | - Njideka Ulunma Okubadejo
- College of Medicine, University of Lagos, Idi Araba, Lagos State, Nigeria; Lagos University Teaching Hospital, Idi Araba, Lagos State, Nigeria.
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