1
|
Douillard V, Dos Santos Brito Silva N, Bourguiba-Hachemi S, Naslavsky MS, Scliar MO, Duarte YAO, Zatz M, Passos-Bueno MR, Limou S, Gourraud PA, Launay É, Castelli EC, Vince N. Optimal population-specific HLA imputation with dimension reduction. HLA 2024; 103:e15282. [PMID: 37950640 DOI: 10.1111/tan.15282] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/29/2023] [Accepted: 10/14/2023] [Indexed: 11/13/2023]
Abstract
Human genomics has quickly evolved, powering genome-wide association studies (GWASs). SNP-based GWASs cannot capture the intense polymorphism of HLA genes, highly associated with disease susceptibility. There are methods to statistically impute HLA genotypes from SNP-genotypes data, but lack of diversity in reference panels hinders their performance. We evaluated the accuracy of the 1000 Genomes data as a reference panel for imputing HLA from admixed individuals of African and European ancestries, focusing on (a) the full dataset, (b) 10 replications from 6 populations, and (c) 19 conditions for the custom reference panels. The full dataset outperformed smaller models, with a good F1-score of 0.66 for HLA-B. However, custom models outperformed the multiethnic or population models of similar size (F1-scores up to 0.53, against up to 0.42). We demonstrated the importance of using genetically specific models for imputing populations, which are currently underrepresented in public datasets, opening the door to HLA imputation for every genetic population.
Collapse
Affiliation(s)
- Venceslas Douillard
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Nayane Dos Santos Brito Silva
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
- São Paulo State University, Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, Brazil
| | - Sonia Bourguiba-Hachemi
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Marilia O Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Yeda A O Duarte
- Medical-Surgical Nursing Department, School of Nursing, University of São Paulo, São Paulo, Brazil
- Epidemiology Department, Public Health School, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Sophie Limou
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Pierre-Antoine Gourraud
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Élise Launay
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
- Department of Pediatrics and Pediatric Emergency, Hôpital Femme Enfant Adolescent, CHU de Nantes, Nantes, France
| | - Erick C Castelli
- São Paulo State University, Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, Brazil
| | - Nicolas Vince
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| |
Collapse
|
2
|
da Silva Antunes R, Weiskopf D, Sidney J, Rubiro P, Peters B, Arlehamn CSL, Grifoni A, Sette A. The MegaPool Approach to Characterize Adaptive CD4+ and CD8+ T Cell Responses. Curr Protoc 2023; 3:e934. [PMID: 37966108 PMCID: PMC10662678 DOI: 10.1002/cpz1.934] [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] [Indexed: 11/16/2023]
Abstract
Epitopes recognized by T cells are a collection of short peptide fragments derived from specific antigens or proteins. Immunological research to study T cell responses is hindered by the extreme degree of heterogeneity of epitope targets, which are usually derived from multiple antigens; within a given antigen, hundreds of different T cell epitopes can be recognized, differing from one individual to the next because T cell epitope recognition is restricted by the epitopes' ability to bind to MHC molecules, which are extremely polymorphic in different individuals. Testing large pools encompassing hundreds of peptides is technically challenging because of logistical considerations regarding solvent-induced toxicity. To address this issue, we developed the MegaPool (MP) approach based on sequential lyophilization of large numbers of peptides that can be used in a variety of assays to measure T cell responses, including ELISPOT, intracellular cytokine staining, and activation-induced marker assays, and that has been validated in the study of infectious diseases, allergies, and autoimmunity. Here, we describe the procedures for generating and testing MPs, starting with peptide synthesis and lyophilization, as well as a step-by-step guide and recommendations for their handling and experimental usage. Overall, the MP approach is a powerful strategy for studying T cell responses and understanding the immune system's role in health and disease. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Generation of peptide pools ("MegaPools") Basic Protocol 2: MegaPool testing and quantitation of antigen-specific T cell responses.
Collapse
Affiliation(s)
- Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Paul Rubiro
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | | | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| |
Collapse
|
3
|
Zhou XJ, Su T, Xie J, Xie QH, Wang LZ, Hu Y, Chen G, Jia Y, Huang JW, Li G, Liu Y, Yu XJ, Nath SK, Tsoi LC, Patrick MT, Berthier CC, Liu G, Wang SX, Xu H, Chen N, Hao CM, Zhang H, Yang L. Genome-Wide Association Study in Acute Tubulointerstitial Nephritis. J Am Soc Nephrol 2023; 34:895-908. [PMID: 36749126 PMCID: PMC10125656 DOI: 10.1681/asn.0000000000000091] [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: 07/21/2022] [Accepted: 12/28/2022] [Indexed: 02/08/2023] Open
Abstract
SIGNIFICANCE STATEMENT Polymorphisms of HLA genes may confer susceptibility to acute tubulointerstitial nephritis (ATIN), but small sample sizes and candidate gene design have hindered their investigation. The first genome-wide association study of ATIN identified two significant loci, risk haplotype DRB1*14-DQA1*0101-DQB1*0503 (DR14 serotype) and protective haplotype DRB1*1501-DQA1*0102-DQB1*0602 (DR15 serotype), with amino acid position 60 in the peptide-binding groove P10 of HLA-DR β 1 key. Risk alleles were shared among different causes of ATIN and HLA genotypes associated with kidney injury and immune therapy response. HLA alleles showed the strongest association. The findings suggest that a genetically conferred risk of immune dysregulation is part of the pathogenesis of ATIN. BACKGROUND Acute tubulointerstitial nephritis (ATIN) is a rare immune-related disease, accounting for approximately 10% of patients with unexplained AKI. Previous elucidation of the relationship between genetic factors that contribute to its pathogenesis was hampered because of small sample sizes and candidate gene design. METHODS We undertook the first two-stage genome-wide association study and meta-analysis involving 544 kidney biopsy-defined patients with ATIN and 2346 controls of Chinese ancestry. We conducted statistical fine-mapping analysis, provided functional annotations of significant variants, estimated single nucleotide polymorphism (SNP)-based heritability, and checked genotype and subphenotype correlations. RESULTS Two genome-wide significant loci, rs35087390 of HLA-DQA1 ( P =3.01×10 -39 ) on 6p21.32 and rs2417771 of PLEKHA5 on 12p12.3 ( P =2.14×10 -8 ), emerged from the analysis. HLA imputation using two reference panels suggested that HLA-DRB1*14 mainly drives the HLA risk association . HLA-DRB1 residue 60 belonging to pocket P10 was the key amino acid position. The SNP-based heritability estimates with and without the HLA locus were 20.43% and 10.35%, respectively. Different clinical subphenotypes (drug-related or tubulointerstitial nephritis and uveitis syndrome) seemed to share the same risk alleles. However, the HLA risk genotype was associated with disease severity and response rate to immunosuppressive therapy. CONCLUSIONS We identified two candidate genome regions associated with susceptibility to ATIN. The findings suggest that a genetically conferred risk of immune dysregulation is involved in the pathogenesis of ATIN.
Collapse
Affiliation(s)
- Xu-Jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Tao Su
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Jingyuan Xie
- Department of Nephrology, Institute of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiong-Hong Xie
- Division of Nephrology, Huashan Hospital, Fudan University, Shanghai, China
| | - Li-Zhong Wang
- WeGene, Shenzhen Zaozhidao Technology Co., Ltd., Shenzhen, China
- Human Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
- Shenzhen WeGene Clinical Laboratory, Shenzhen, China
| | - Yong Hu
- Beijing Institute of Biotechnology, Beijing, China
| | - Gang Chen
- WeGene, Shenzhen Zaozhidao Technology Co., Ltd., Shenzhen, China
- Human Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
- Shenzhen WeGene Clinical Laboratory, Shenzhen, China
| | - Yan Jia
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Jun-Wen Huang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Gui Li
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Yang Liu
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Xiao-Juan Yu
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Lam C. Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Matthew T. Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Celine C. Berthier
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Gang Liu
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Su-Xia Wang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China
- School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Nan Chen
- Department of Nephrology, Institute of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chuan-Ming Hao
- Division of Nephrology, Huashan Hospital, Fudan University, Shanghai, China
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Li Yang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| |
Collapse
|