1
|
Bian S, Guo X, Yang X, Wei Y, Yang Z, Cheng S, Yan J, Chen Y, Chen GB, Du X, Francis SS, Shu Y, Liu S. Genetic determinants of IgG antibody response to COVID-19 vaccination. Am J Hum Genet 2024; 111:181-199. [PMID: 38181733 PMCID: PMC10806743 DOI: 10.1016/j.ajhg.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 01/07/2024] Open
Abstract
Human humoral immune responses to SARS-CoV-2 vaccines exhibit substantial inter-individual variability and have been linked to vaccine efficacy. To elucidate the underlying mechanism behind this variability, we conducted a genome-wide association study (GWAS) on the anti-spike IgG serostatus of UK Biobank participants who were previously uninfected by SARS-CoV-2 and had received either the first dose (n = 54,066) or the second dose (n = 46,232) of COVID-19 vaccines. Our analysis revealed significant genome-wide associations between the IgG antibody serostatus following the initial vaccine and human leukocyte antigen (HLA) class II alleles. Specifically, the HLA-DRB1∗13:02 allele (MAF = 4.0%, OR = 0.75, p = 2.34e-16) demonstrated the most statistically significant protective effect against IgG seronegativity. This protective effect was driven by an alteration from arginine (Arg) to glutamic acid (Glu) at position 71 on HLA-DRβ1 (p = 1.88e-25), leading to a change in the electrostatic potential of pocket 4 of the peptide binding groove. Notably, the impact of HLA alleles on IgG responses was cell type specific, and we observed a shared genetic predisposition between IgG status and susceptibility/severity of COVID-19. These results were replicated within independent cohorts where IgG serostatus was assayed by two different antibody serology tests. Our findings provide insights into the biological mechanism underlying individual variation in responses to COVID-19 vaccines and highlight the need to consider the influence of constitutive genetics when designing vaccination strategies for optimizing protection and control of infectious disease across diverse populations.
Collapse
Affiliation(s)
- Shengzhe Bian
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Xinxin Guo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Xilai Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Yuandan Wei
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Zijing Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Shiyao Cheng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Jiaqi Yan
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Yongkun Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Guo-Bo Chen
- Center for General Practice Medicine, Department of General Practice Medicine, Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310059, Zhejiang, P.R. China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou 310063, Zhejiang, P.R. China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Stephen S Francis
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China; Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, P.R. China.
| | - Siyang Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China; School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, P.R. China.
| |
Collapse
|
3
|
Vinoy N, Sheeja N, Kumar S, Biswas L. Class II HLA (DRB1, & DQB1) alleles and IL7R (rs6897932) variants and the risk for Multiple Sclerosis in Kerala, India. Mult Scler Relat Disord 2021; 50:102848. [PMID: 33657520 DOI: 10.1016/j.msard.2021.102848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/04/2021] [Accepted: 02/17/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND Different human leukocyte antigen (HLA) variants are known to modulate the risk of multiple sclerosis. The main objective of this study was to identify HLA-DRB1 and HLA-DQB1 alleles and Non -HLA gene IL7R (rs6897932) variants associated with MS. METHODS Patients attending the MS clinic, diagnosed with Multiple Sclerosis as per Mc Donald diagnostic criteria were the subjects in the study. The association of the highly polymorphic HLA-DRB1 and HLA-DQB1 loci was determined by high resolution tissue typing and the genotyping of the IL7R (rs6897932) variants was performed by Sanger sequencing in MS patients (n = 81) and healthy individuals (n = 82). RESULTS HLA-DRB1*15:01/15:02 alleles (OR = 3.65; p< 0.0001) and HLA-DQB1*06:02 (OR=4.19, p<0.0001) were found to be positively associated while HLA-DRB1*14:04:01 (OR = 0.21; p = 0.0009) was found to be negatively associated with MS. The most significant predisposing HLA haplotype was found to be DRB1*15:01-DQB1*06:02 (OR=5.69, p<0.0001). Univariate analysis of IL7R SNP (rs6897932) showed no significant association with MS in our population whereas analysis of HLA-DRB1 alleles and IL7R (rs6897932) genotypes showed significant association between the HLA-DRB1*15:01/15:02 and the IL7R (rs6897932) CC genotype (OR = 3.58, p = 0.0002). CONCLUSION HLA-DRB1*15:01, 15:02 and DQB1*06:02 are the predisposing alleles while HLA-DRB1*14:04 is the protective allele for MS in our population.
Collapse
Affiliation(s)
- Navia Vinoy
- Centre for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, Kerala 682041, India
| | - Neethu Sheeja
- Centre for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, Kerala 682041, India
| | - Suresh Kumar
- Department of Neurology, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi, Kerala 682041, India.
| | - Lalitha Biswas
- Centre for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, Kerala 682041, India.
| |
Collapse
|
5
|
Savage SA, Viard M, O'hUigin C, Zhou W, Yeager M, Li SA, Wang T, Ramsuran V, Vince N, Vogt A, Hicks B, Burdett L, Chung C, Dean M, de Andrade KC, Freedman ND, Berndt SI, Rothman N, Lan Q, Cerhan JR, Slager SL, Zhang Y, Teras LR, Haagenson M, Chanock SJ, Spellman SR, Wang Y, Willis A, Askar M, Lee SJ, Carrington M, Gadalla SM. Genome-wide Association Study Identifies HLA-DPB1 as a Significant Risk Factor for Severe Aplastic Anemia. Am J Hum Genet 2020; 106:264-271. [PMID: 32004448 PMCID: PMC7010969 DOI: 10.1016/j.ajhg.2020.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 01/07/2020] [Indexed: 12/20/2022] Open
Abstract
Severe aplastic anemia (SAA) is a rare disorder characterized by hypoplastic bone marrow and progressive pancytopenia. The etiology of acquired SAA is not understood but is likely related to abnormal immune responses and environmental exposures. We conducted a genome-wide association study of individuals with SAA genetically matched to healthy controls in discovery (359 cases, 1,396 controls) and validation sets (175 cases, 1,059 controls). Combined analyses identified linked SNPs in distinct blocks within the major histocompatibility complex on 6p21. The top SNP encodes p.Met76Val in the P4 binding pocket of the HLA class II gene HLA-DPB1 (rs1042151A>G, odds ratio [OR] 1.75, 95% confidence interval [CI] 1.50-2.03, p = 1.94 × 10-13) and was associated with HLA-DP cell surface expression in healthy individuals (p = 2.04 × 10-6). Phylogenetic analyses indicate that Val76 is not monophyletic and likely occurs in conjunction with different HLA-DP binding groove conformations. Imputation of HLA-DPB1 alleles revealed increased risk of SAA associated with Val76-encoding alleles DPB1∗03:01, (OR 1.66, p = 1.52 × 10-7), DPB1∗10:01 (OR 2.12, p = 0.0003), and DPB1∗01:01 (OR 1.60, p = 0.0008). A second SNP near HLA-B, rs28367832G>A, reached genome-wide significance (OR 1.49, 95% CI 1.22-1.78, p = 7.27 × 10-9) in combined analyses; the association remained significant after excluding cases with clonal copy-neutral loss-of-heterozygosity affecting class I HLA genes (8.6% of cases and 0% of controls). SNPs in the HLA class II gene HLA-DPB1 and possibly class I (HLA-B) are associated with SAA. The replacement of Met76 to Val76 in certain HLA-DPB1 alleles might influence risk of SAA through mechanisms involving DP peptide binding specificity, expression, and/or other factors affecting DP function.
Collapse
Affiliation(s)
- Sharon A Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Colm O'hUigin
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Weiyin Zhou
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Meredith Yeager
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shengchao Alfred Li
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Veron Ramsuran
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nicolas Vince
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Aurelie Vogt
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Belynda Hicks
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Laurie Burdett
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Charles Chung
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kelvin C de Andrade
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55902, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55902, USA
| | - Yawei Zhang
- Section of Surgical Outcomes and Epidemiology, Department of Surgery, Yale Medical School, New Haven, CT 06520, USA
| | - Lauren R Teras
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, 30303, USA
| | - Michael Haagenson
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Youjin Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Amanda Willis
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, TX 76798, USA
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, TX 76798, USA
| | - Stephanie J Lee
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Shahinaz M Gadalla
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| |
Collapse
|
6
|
Zheng W, Chen Y, Chen H, Xiao W, Liang Y, Wang N, Jiang X, Wen S. Identification of key target genes and biological pathways in multiple sclerosis brains using microarray data obtained from the Gene Expression Omnibus database. Neurol Res 2018; 40:883-891. [PMID: 30074468 DOI: 10.1080/01616412.2018.1497253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The purpose of this study was to investigate critical genes in multiple sclerosis (MS) using microarray data from brain tissue in MS. MATERIALS The expression profile data set of MS (GSE38010) downloaded from the Gene Expression Omnibus database contained gene information from five plaque tissues from MS brains and two white matter tissues from healthy controls. An R package was applied to process these raw chip data. Gene Ontology (GO) functional analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and protein-protein interaction (PPI) network analysis were performed to investigate interactions between differentially expressed genes (DEGs) in MS brain tissues. RESULTS This study identified a total of 1065 DEGs, including 530 up-regulated genes and 535 down-regulated genes, in MS brain tissue samples compared to those in normal white matter tissue samples. GO and KEGG pathway enrichment analyses showed that the up-regulated DEGs were mainly related to neuron development, neuron projection morphogenesis and neuron differentiation. Furthermore, the down-regulated DEGs were largely related to axon ensheathment, ensheathment of neurons and nervous system development. Seven key genes were found as hub genes in the maintenance of the PPI network. CONCLUSION Several key target genes and their GO and KEGG pathway enrichment identified in the present study may serve as feasible targets for MS therapies.
Collapse
Affiliation(s)
- Weipeng Zheng
- a Department of Orthopedics, Guangzhou First People's Hospital , Guangzhou Medical University , Guangzhou , People's Republic of China
| | - Yimin Chen
- b First Clinical College of Guangzhou Medical University , Guangzhou Medical University , Guangzhou , People's Republic of China
| | - Haoyi Chen
- a Department of Orthopedics, Guangzhou First People's Hospital , Guangzhou Medical University , Guangzhou , People's Republic of China
| | - Wende Xiao
- a Department of Orthopedics, Guangzhou First People's Hospital , Guangzhou Medical University , Guangzhou , People's Republic of China
| | - YingJie Liang
- a Department of Orthopedics, Guangzhou First People's Hospital , Guangzhou Medical University , Guangzhou , People's Republic of China
| | - Ning Wang
- a Department of Orthopedics, Guangzhou First People's Hospital , Guangzhou Medical University , Guangzhou , People's Republic of China
| | - Xin Jiang
- a Department of Orthopedics, Guangzhou First People's Hospital , Guangzhou Medical University , Guangzhou , People's Republic of China
| | - Shifeng Wen
- a Department of Orthopedics, Guangzhou First People's Hospital , Guangzhou Medical University , Guangzhou , People's Republic of China
| |
Collapse
|