1
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Silva NSB, Bourguiba-Hachemi S, Ciriaco VAO, Knorst SHY, Carmo RT, Masotti C, Meyer D, Naslavsky MS, Duarte YAO, Zatz M, Gourraud PA, Limou S, Castelli EC, Vince N. A multi-ethnic reference panel to impute HLA classical and non-classical class I alleles in admixed samples: Testing imputation accuracy in an admixed sample from Brazil. HLA 2024; 103:e15543. [PMID: 38837862 DOI: 10.1111/tan.15543] [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: 01/23/2024] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024]
Abstract
The MHC class I region contains crucial genes for the innate and adaptive immune response, playing a key role in susceptibility to many autoimmune and infectious diseases. Genome-wide association studies have identified numerous disease-associated SNPs within this region. However, these associations do not fully capture the immune-biological relevance of specific HLA alleles. HLA imputation techniques may leverage available SNP arrays by predicting allele genotypes based on the linkage disequilibrium between SNPs and specific HLA alleles. Successful imputation requires diverse and large reference panels, especially for admixed populations. This study employed a bioinformatics approach to call SNPs and HLA alleles in multi-ethnic samples from the 1000 genomes (1KG) dataset and admixed individuals from Brazil (SABE), utilising 30X whole-genome sequencing data. Using HIBAG, we created three reference panels: 1KG (n = 2504), SABE (n = 1171), and the full model (n = 3675) encompassing all samples. In extensive cross-validation of these reference panels, the multi-ethnic 1KG reference exhibited overall superior performance than the reference with only Brazilian samples. However, the best results were achieved with the full model. Additionally, we expanded the scope of imputation by developing reference panels for non-classical, MICA, MICB and HLA-H genes, previously unavailable for multi-ethnic populations. Validation in an independent Brazilian dataset showcased the superiority of our reference panels over the Michigan Imputation Server, particularly in predicting HLA-B alleles among Brazilians. Our investigations underscored the need to enhance or adapt reference panels to encompass the target population's genetic diversity, emphasising the significance of multiethnic references for accurate imputation across different populations.
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Affiliation(s)
- Nayane S B Silva
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University, Botucatu, State of São Paulo, Brazil
- Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, State of São Paulo, Brazil
| | - Sonia Bourguiba-Hachemi
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
| | - Viviane A O Ciriaco
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University, Botucatu, State of São Paulo, Brazil
| | - Stefan H Y Knorst
- Department of Molecular Oncology, Hospital Sírio-Libanes, São Paulo, Brazil
| | - Ramon T Carmo
- Department of Molecular Oncology, Hospital Sírio-Libanes, São Paulo, Brazil
| | - Cibele Masotti
- Department of Molecular Oncology, Hospital Sírio-Libanes, São Paulo, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, State of São Paulo, Brazil
| | - Michel S Naslavsky
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, State of São Paulo, Brazil
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, State of São Paulo, Brazil
| | - Yeda A O Duarte
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, State of São Paulo, Brazil
- Medical-Surgical Nursing Department, School of Nursing, University of São Paulo, São Paulo, State of São Paulo, Brazil
| | - Mayana Zatz
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, State of São Paulo, Brazil
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, State of São Paulo, Brazil
| | - Pierre-Antoine Gourraud
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
| | - Sophie Limou
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University, Botucatu, State of São Paulo, Brazil
- Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, State of São Paulo, Brazil
| | - Nicolas Vince
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
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Sangphukieo A, Thongkumkoon P, Noisagul P, Lo Piccolo L, O’Brien TE, Chaowattanapanit S, Choonhakarn C, Amornpinyo W, Chaiwarith R, Kiratikanon S, Rujiwetpongstorn R, Tovanabutra N, Chiewchanvit S, Kantaputra P, Intachai W, Dissook S, Chuamanochan M. Human Leukocyte Antigen Markers for Distinguishing Pustular Psoriasis and Adult-Onset Immunodeficiency with Pustular Reaction. Genes (Basel) 2024; 15:278. [PMID: 38540337 PMCID: PMC10970016 DOI: 10.3390/genes15030278] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 06/15/2024] Open
Abstract
Pustular skin diseases, with pustular psoriasis (PP) being the prototype, are immune-mediated diseases characterized by the presence of multiple pustules, resulting from neutrophil accumulation in the layer of epidermis. Sterile skin pustular eruption, like PP, is also observed in 20-30% of patients with adult-onset immunodeficiency syndrome (AOID) and anti-interferon γ autoantibodies (IFN-γ), leading to challenges in classification and diagnosis. While the mechanism underlying this similar phenotype remains unknown, genetic factors in relation to the immune system are suspected of playing an important role. Here, the association between human leukocyte antigen (HLA) genes, which play essential roles in antigen presentation, contributing to immune response, and the presence of skin pustules in AOID and PP was revealed. HLA genotyping of 41 patients from multiple centers in Thailand who presented with multiple sterile skin pustules (17 AOID patients and 24 PP patients) was conducted using a next-generation-sequencing-based approach. In comparison to healthy controls, HLA-B*13:01 (OR = 3.825, 95%CI: 2.08-7.035), C*03:04 (OR = 3.665, 95%CI: 2.102-6.39), and DQB1*05:02 (OR = 2.134, 95%CI: 1.326-3.434) were significantly associated with the group of aforementioned conditions having sterile cutaneous pustules, suggesting a common genetic-related mechanism. We found that DPB1*05:01 (OR = 3.851, p = 0.008) and DRB1*15:02 (OR = 3.195, p = 0.033) have a significant association with pustular reaction in AOID patients, with PP patients used as a control. A variant in the DRB1 gene, rs17885482 (OR = 9.073, p = 0.005), was observed to be a risk factor for PP when using AOID patients who had pustular reactions as a control group. DPB1*05:01 and DRB1*15:02 alleles, as well as the rs17885482 variant in the DRB1 gene, were proposed as novel biomarkers to differentiate PP and AOID patients who first present with multiple sterile skin pustules without known documented underlying conditions.
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Affiliation(s)
- Apiwat Sangphukieo
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (A.S.); (P.T.); (P.N.); (L.L.P.)
| | - Patcharawadee Thongkumkoon
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (A.S.); (P.T.); (P.N.); (L.L.P.)
| | - Pitiporn Noisagul
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (A.S.); (P.T.); (P.N.); (L.L.P.)
| | - Luca Lo Piccolo
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (A.S.); (P.T.); (P.N.); (L.L.P.)
| | - Timothy E. O’Brien
- Applied and Environmental Statistics, Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL 60153, USA;
| | - Suteeraporn Chaowattanapanit
- Division of Dermatology, Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (C.C.)
| | - Charoen Choonhakarn
- Division of Dermatology, Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (S.C.); (C.C.)
| | - Warayuwadee Amornpinyo
- Division of Dermatology, Department of Internal Medicine, Khon Kaen Hospital, Ministry of Public Health, Khon Kaen 40002, Thailand;
| | - Romanee Chaiwarith
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Salin Kiratikanon
- Division of Dermatology, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (S.K.); (R.R.); (N.T.); (S.C.)
| | - Rujira Rujiwetpongstorn
- Division of Dermatology, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (S.K.); (R.R.); (N.T.); (S.C.)
| | - Napatra Tovanabutra
- Division of Dermatology, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (S.K.); (R.R.); (N.T.); (S.C.)
| | - Siri Chiewchanvit
- Division of Dermatology, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (S.K.); (R.R.); (N.T.); (S.C.)
| | - Piranit Kantaputra
- Center of Excellence in Medical Genetics Research, Chiang Mai University, Chiang Mai 50200, Thailand; (P.K.); (W.I.)
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Worrachet Intachai
- Center of Excellence in Medical Genetics Research, Chiang Mai University, Chiang Mai 50200, Thailand; (P.K.); (W.I.)
| | - Sivamoke Dissook
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Mati Chuamanochan
- Division of Dermatology, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (S.K.); (R.R.); (N.T.); (S.C.)
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Silva NSB, Bourguiba-Hachemi S, Douillard V, Koskela S, Degenhardt F, Clancy J, Limou S, Meyer D, Masotti C, Knorst S, Naslavsky MS, Franke A, Castelli EC, Gourraud PA, Vince N. 18th International HLA and Immunogenetics Workshop: Report on the SNP-HLA Reference Consortium (SHLARC) component. HLA 2024; 103:e15293. [PMID: 37947386 DOI: 10.1111/tan.15293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
The SNP-HLA Reference Consortium (SHLARC), a component of the 18th International HLA and Immunogenetics Workshop, is aimed at collecting diverse and extensive human leukocyte antigen (HLA) data to create custom reference panels and enhance HLA imputation techniques. Genome-wide association studies (GWAS) have significantly contributed to identifying genetic associations with various diseases. The HLA genomic region has emerged as the top locus in GWAS, particularly in immune-related disorders. However, the limited information provided by single nucleotide polymorphisms (SNPs), the hallmark of GWAS, poses challenges, especially in the HLA region, where strong linkage disequilibrium (LD) spans several megabases. HLA imputation techniques have been developed using statistical inference in response to these challenges. These techniques enable the prediction of HLA alleles from genotyped GWAS SNPs. Here we present the SHLARC activities, a collaborative effort to create extensive, and multi-ethnic reference panels to enhance HLA imputation accuracy.
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Affiliation(s)
- Nayane S B Silva
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, Brazil
| | - Sonia Bourguiba-Hachemi
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
| | - Venceslas Douillard
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
| | - Satu Koskela
- Finnish Red Cross Blood Service Biobank, Helsinki, Finland
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, University Hospital Schleswig Holstein - Campus Kiel, Kiel, Germany
| | - Jonna Clancy
- Finnish Red Cross Blood Service Biobank, Helsinki, Finland
| | - Sophie Limou
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Cibele Masotti
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Stefan Knorst
- Molecular Oncology Center, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Michel Satya Naslavsky
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, University Hospital Schleswig Holstein - Campus Kiel, Kiel, Germany
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, Brazil
| | - Pierre-Antoine Gourraud
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
| | - Nicolas Vince
- Center for Research in Transplantation and Translational Immunology, Nantes Université, INSERM, Ecole Centrale Nantes, Nantes, France
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4
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Velastegui E, Vera E, Vanden Berghe W, Muñoz MS, Orellana-Manzano A. "HLA-C: evolution, epigenetics, and pathological implications in the major histocompatibility complex". Front Genet 2023; 14:1206034. [PMID: 37465164 PMCID: PMC10350511 DOI: 10.3389/fgene.2023.1206034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
HLA-C, a gene located within the major histocompatibility complex, has emerged as a prominent target in biomedical research due to its involvement in various diseases, including cancer and autoimmune disorders; even though its recent addition to the MHC, the interaction between HLA-C and KIR is crucial for immune responses, particularly in viral infections. This review provides an overview of the structure, origin, function, and pathological implications of HLA-C in the major histocompatibility complex. In the last decade, we systematically reviewed original publications from Pubmed, ScienceDirect, Scopus, and Google Scholar. Our findings reveal that genetic variations in HLA-C can determine susceptibility or resistance to certain diseases. However, the first four exons of HLA-C are particularly susceptible to epigenetic modifications, which can lead to gene silencing and alterations in immune function. These alterations can manifest in diseases such as alopecia areata and psoriasis and can also impact susceptibility to cancer and the effectiveness of cancer treatments. By comprehending the intricate interplay between genetic and epigenetic factors that regulate HLA-C expression, researchers may develop novel strategies for preventing and treating diseases associated with HLA-C dysregulation.
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Affiliation(s)
- Erick Velastegui
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Edwin Vera
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Wim Vanden Berghe
- Epigenetic Signaling Lab, Faculty Biomedical Sciences, PPES, University of Antwerp, Antwerp, Belgium
| | - Mindy S. Muñoz
- Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Andrea Orellana-Manzano
- Escuela Superior Politécnica del Litoral, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la Vida (FCV), Guayaquil, Ecuador
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5
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Silva NDSB, Souza ADS, Andrade HDS, Pereira RN, Castro CFB, Vince N, Limou S, Naslavsky MS, Zatz M, Duarte YADO, Mendes-Junior CT, Castelli EDC. Immunogenetics of HLA-B: SNP, allele, and haplotype diversity in populations from different continents and ancestry backgrounds. HLA 2023; 101:634-646. [PMID: 37005006 DOI: 10.1111/tan.15043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 04/04/2023]
Abstract
HLA-B is among the most variable gene in the human genome. This gene encodes a key molecule for antigen presentation to CD8+ T lymphocytes and NK cell modulation. Despite the myriad of studies evaluating its coding region (with an emphasis on exons 2 and 3), few studies evaluated introns and regulatory sequences in real population samples. Thus, HLA-B variability is probably underestimated. We applied a bioinformatics pipeline tailored for HLA genes on 5347 samples from 80 different populations, which includes more than 1000 admixed Brazilians, to evaluate the HLA-B variability (SNPs, indels, MNPs, alleles, and haplotypes) in exons, introns, and regulatory regions. We observed 610 variable sites throughout HLA-B; the most frequent variants are shared worldwide. However, the haplotype distribution is geographically structured. We detected 920 full-length haplotypes (exons, introns, and untranslated regions) encoding 239 different protein sequences. HLA-B gene diversity is higher in admixed populations and Europeans while lower in African ancestry individuals. Each HLA-B allele group is associated with specific promoter sequences. This HLA-B variation resource may improve HLA imputation accuracy and disease-association studies and provide evolutionary insights regarding HLA-B genetic diversity in human populations.
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Affiliation(s)
- Nayane Dos Santos Brito Silva
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
- INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes Université, UMR 1064, F-44000, Nantes, France
| | - Andreia da Silva Souza
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
| | - Heloisa de Souza Andrade
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, São Paulo, Brazil
| | - Raphaela Neto Pereira
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
| | - Camila Ferreira Bannwart Castro
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
- UniFSP, Centro Universitário Sudoeste Paulista, Itapetininga, São Paulo, Brazil
| | - Nicolas Vince
- INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes Université, UMR 1064, F-44000, Nantes, France
| | - Sophie Limou
- INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes Université, UMR 1064, F-44000, Nantes, France
| | - Michel Satya Naslavsky
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, São Paulo, Brazil
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Celso Teixeira Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Erick da Cruz Castelli
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine, São Paulo State University - Unesp, Botucatu, São Paulo, Brazil
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6
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Oliveira MLG, Castelli EC, Veiga‐Castelli LC, Pereira ALE, Marcorin L, Carratto TMT, Souza AS, Andrade HS, Simões AL, Donadi EA, Courtin D, Sabbagh A, Giuliatti S, Mendes‐Junior CT. Genetic diversity of the
LILRB1
and
LILRB2
coding regions in an admixed Brazilian population sample. HLA 2022; 100:325-348. [DOI: 10.1111/tan.14725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/02/2022] [Accepted: 06/24/2022] [Indexed: 11/27/2022]
Affiliation(s)
| | - Erick C. Castelli
- Pathology Department, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Luciana C. Veiga‐Castelli
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Alison Luis E. Pereira
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Letícia Marcorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Thássia M. T. Carratto
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Andreia S. Souza
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Heloisa S. Andrade
- Molecular Genetics and Bioinformatics Laboratory, School of Medicine São Paulo State University (UNESP) Botucatu State of São Paulo Brazil
| | - Aguinaldo L. Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Eduardo A. Donadi
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | | | | | - Silvana Giuliatti
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
| | - Celso Teixeira Mendes‐Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Ribeirão Preto SP Brazil
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7
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Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil. Nat Commun 2022; 13:1004. [PMID: 35246524 PMCID: PMC8897431 DOI: 10.1038/s41467-022-28648-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/21/2022] [Indexed: 02/07/2023] Open
Abstract
As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly admixed elderly Brazilians from a census-based cohort, providing over 76 million variants, of which ~2 million are absent from large public databases. WGS enables identification of ~2,000 previously undescribed mobile element insertions without previous description, nearly 5 Mb of genomic segments absent from the human genome reference, and over 140 alleles from HLA genes absent from public resources. We reclassify and curate pathogenicity assertions for nearly four hundred variants in genes associated with dominantly-inherited Mendelian disorders and calculate the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observe that whole-genome and HLA imputation could be significantly improved compared to available datasets since rare variation represents the largest proportion of input from WGS. These results demonstrate that even smaller sample sizes of underrepresented populations bring relevant data for genomic studies, especially when exploring analyses allowed only by WGS. Whole genome sequencing (WGS) data on non-European and admixed individuals remains scarce. Here, the authors analyse WGS data from 1,171 admixed elderly Brazilians from a census cohort, characterising population-specific genetic variation and exploring the clinical utility of this expanded dataset.
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8
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Di D, Nunes JM, Jiang W, Sanchez-Mazas A. Like Wings of a Bird: Functional Divergence and Complementarity between HLA-A and HLA-B Molecules. Mol Biol Evol 2021; 38:1580-1594. [PMID: 33320202 PMCID: PMC8355449 DOI: 10.1093/molbev/msaa325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Human leukocyte antigen (HLA) genes are among the most polymorphic of our genome, as a likely consequence of balancing selection related to their central role in adaptive immunity. HLA-A and HLA-B genes were recently suggested to evolve through a model of joint divergent asymmetric selection conferring all human populations, including those with severe loss of diversity, an equivalent immune potential. However, the mechanisms by which these two genes might undergo joint evolution while displaying very distinct allelic profiles in populations are still unknown. To address this issue, we carried out extensive data analyses (among which factorial correspondence analysis and linear modeling) on 2,909 common and rare HLA-A, HLA-B, and HLA-C alleles and 200,000 simulated pathogenic peptides by taking into account sequence variation, predicted peptide-binding affinity and HLA allele frequencies in 123 populations worldwide. Our results show that HLA-A and HLA-B (but not HLA-C) molecules maintain considerable functional divergence in almost all populations, which likely plays an instrumental role in their immune defense. We also provide robust evidence of functional complementarity between HLA-A and HLA-B molecules, which display asymmetric relationships in terms of amino acid diversity at both inter- and intraprotein levels and in terms of promiscuous or fastidious peptide-binding specificities. Like two wings of a flying bird, the functional complementarity of HLA-A and HLA-B is a perfect example, in our genome, of duplicated genes sharing their capacity of assuming common vital functions while being submitted to complex and sometimes distinct environmental pressures.
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Affiliation(s)
- Da Di
- Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - Jose Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), Geneva, Switzerland
| | - Wei Jiang
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History (AGP Lab), Department of Genetics and Evolution-Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva Medical Centre (CMU), Geneva, Switzerland
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Weiss E, Andrade HS, Lara JR, Souza AS, Paz MA, Lima THA, Porto IOP, S B Silva N, Castro CFB, Grotto RMT, Donadi EA, Mendes-Junior CT, Castelli EC. KIR2DL4 genetic diversity in a Brazilian population sample: implications for transcription regulation and protein diversity in samples with different ancestry backgrounds. Immunogenetics 2021; 73:227-241. [PMID: 33595694 DOI: 10.1007/s00251-021-01206-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/22/2021] [Indexed: 11/30/2022]
Abstract
KIR2DL4 is an important immune modulator expressed in natural killer cells; HLA-G is its main ligand. We have characterized the KIR2DL4 genetic diversity by considering the promoter, all exons, and all introns in a highly admixed Brazilian population sample and by using massively parallel sequencing. We introduce a molecular method to amplify and to sequence the complete KIR2DL4 gene. To avoid the mapping bias and genotype errors commonly observed in gene families, we have developed and validated a bioinformatic pipeline designed to minimize these errors and applied it to survey the variability of 220 individuals from the State of São Paulo, southeastern Brazil. We have also compared the KIR2DL4 genetic diversity in the Brazilian cohort with the diversity previously reported by the 1000Genomes consortium. KIR2DL4 presents high linkage disequilibrium throughout the gene, with coding sequences associated with specific promoters. There are few but divergent promoter haplotypes. We have also detected many new KIR2DL4 sequences, all bearing nucleotide exchanges in introns and encoding previously described proteins. Exons 3 and 4, which encode the external domains, are the most variable. The ancestry background influences the KIR2DL4 allele frequencies and must be considered for association studies regarding KIR2DL4.
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Affiliation(s)
- Emiliana Weiss
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Heloisa S Andrade
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Juliana Rodrigues Lara
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Andreia S Souza
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Michelle A Paz
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Thálitta H A Lima
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Iane O P Porto
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Nayane S B Silva
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Camila F Bannwart Castro
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Rejane M T Grotto
- Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.,School of Agronomical Sciences, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil
| | - Eduardo A Donadi
- Department of Medicine, Ribeirão, Preto Medical School, University of São Paulo (USP), Ribeirao Preto, State of Sao Paulo, Brazil
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências E Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil. .,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil. .,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, State of Sao Paulo, Brazil.
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