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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2
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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] [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.
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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
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3
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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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Paganini J, Faux P, Beley S, Picard C, Chiaroni J, Di Cristofaro J. HLA-F transcriptional and protein differential expression according to its genetic polymorphisms. HLA 2023; 102:578-589. [PMID: 37166140 DOI: 10.1111/tan.15087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/21/2023] [Accepted: 04/20/2023] [Indexed: 05/12/2023]
Abstract
Many specificities single out HLA-F: its structure, expression regulation at cell membrane and function. HLA-F mRNA is detected in the most cell types and the protein is localized in the ER and Golgi apparatus. When expressed at cell surface, HLA-F may be associated to β2-microglobulin and peptide or expressed as an open-conformer molecule. HLA-F reaches the membrane upon activation of different primary cell types and cell-lines. HLA-F has its highest affinity for the KIR3DS1-activating NK receptor, but also binds inhibitory immune receptors. Some studies reported that HLA-F expression is associated with its genotype. Higher HLA-F mRNA expression associated with F*01:01:02, and 3 noncoding SNPs, rs1362126, rs2523405, and rs2523393, located in HLA-F-AS1 or upstream the HLA-F sequence were associated with HLA-F mRNA expression. Given the implication of HLA-F in many clinical setting, and the undisclosed process of its expression regulation, we aim to confirm the effect of the aforementioned SNPs with HLA-F transcriptional and protein expression. We analyzed the distribution, frequency and linkage disequilibrium of these SNPs at worldwide scale in the 1000 Genomes Project samples. Influence on the genotype of each SNP on HLA-F expression was explored using RNAseq data from the 1000 Genomes Project, and using Q-PCR and intracellular cytometry in PBMC from healthy individuals. Our results show that the SNPs under studied displayed remarkably different allelic proportion according to geography and confirm that rs1362126, rs2523405, and rs2523393 displayed the most concordant results, with the highest effect size and a double-dose effect.
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Affiliation(s)
| | - Pierre Faux
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, Castanet Tolosan, France
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
| | - Sophie Beley
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Christophe Picard
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Jacques Chiaroni
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Julie Di Cristofaro
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
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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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Castelli EC, Paes GS, da Silva IM, Moreau P, Donadi EA. The + 3010/C single nucleotide polymorphism (rs1710) at the HLA-G 3' untranslated region is associated with a short transcript exhibiting a deletion of 92 nucleotides. Immunogenetics 2023; 75:155-160. [PMID: 36879172 DOI: 10.1007/s00251-023-01297-6] [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: 11/30/2022] [Accepted: 02/06/2023] [Indexed: 03/08/2023]
Abstract
The physiological expression of HLA-G is mainly observed in the placenta, playing an essential role in maternal-fetal tolerance. Among the HLA-G mRNA alternative transcripts, the one lacking 92 bases at the HLA-G 3' untranslated region (3'UTR), the 92bDel transcript, is more stable, is associated with increased HLA-G soluble levels, and was observed in individuals presenting a 14 bp insertion (14 bp+) at the 3'UTR. We investigated the presence of the 92bDel transcript in placenta samples, correlating its expression levels with the HLA-G polymorphisms at the 3'UTR. The 14 bp+ allele correlates with the presence of the 92bDel transcript. However, the polymorphism triggering this alternative splicing is the + 3010/C allele (rs1710, allele C). Most 14 bp+ haplotypes (UTR-2/-5/-7) present allele + 3010/C. However, 14 bp- haplotypes such as UTR-3 are also associated with + 3010/C, and the 92bDel transcript can be detected in homozygous samples for the 14 bp- allele carrying at least one copy of UTR-3. The UTR-3 haplotype is associated with alleles G*01:04 and the HLA-G lineage HG0104, which is a high-expressing lineage. The only HLA-G lineage that is not likely to produce this transcript is HG010101, associated with the + 3010/G allele. This functional difference may be advantageous, considering the high worldwide frequency of the HG010101 lineage. Therefore, HLA-G lineages are functionally distinct regarding the 92bDel transcript expression, and the 3010/C allele triggers the alternative splicing that produces this shorter and more stable transcript.
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Affiliation(s)
- Erick C Castelli
- Department of Pathology, School of Medicine, São Paulo State University (Unesp), Botucatu, Brazil.
- Molecular Genetics and Bioinformatics Laboratory (GeMBio) - Experimental Research Unit, School of Medicine, São Paulo State University (Unesp), Botucatu, Brazil.
| | - Gabriela Sato Paes
- Molecular Genetics and Bioinformatics Laboratory (GeMBio) - Experimental Research Unit, School of Medicine, São Paulo State University (Unesp), Botucatu, Brazil
| | - Isabelle Mira da Silva
- Molecular Genetics and Bioinformatics Laboratory (GeMBio) - Experimental Research Unit, School of Medicine, São Paulo State University (Unesp), Botucatu, Brazil
| | - Philippe Moreau
- Commissariat À L'Energie Atomique Et Aux Energies Alternatives, Direction de La Recherche Fondamentale, Institut de Biologie François Jacob, Service de Recherches en Hémato-ImmunologieHôpital Saint-Louis, Paris, France
- U976 HIPI Unit, ISRL, Université Paris Cité, Paris, France
| | - Eduardo A Donadi
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, CEP, 14049-900, Brazil
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7
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Evidence for Epistatic Interaction between HLA-G and LILRB1 in the Pathogenesis of Nonsegmental Vitiligo. Cells 2023; 12:cells12040630. [PMID: 36831297 PMCID: PMC9954564 DOI: 10.3390/cells12040630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/31/2022] [Accepted: 01/29/2023] [Indexed: 02/18/2023] Open
Abstract
Vitiligo is the most frequent cause of depigmentation worldwide. Genetic association studies have discovered about 50 loci associated with disease, many with immunological functions. Among them is HLA-G, which modulates immunity by interacting with specific inhibitory receptors, mainly LILRB1 and LILRB2. Here we investigated the LILRB1 and LILRB2 association with vitiligo risk and evaluated the possible role of interactions between HLA-G and its receptors in this pathogenesis. We tested the association of the polymorphisms of HLA-G, LILRB1, and LILRB2 with vitiligo using logistic regression along with adjustment by ancestry. Further, methods based on the multifactor dimensionality reduction (MDR) approach (MDR v.3.0.2, GMDR v.0.9, and MB-MDR) were used to detect potential epistatic interactions between polymorphisms from the three genes. An interaction involving rs9380142 and rs2114511 polymorphisms was identified by all methods used. The polymorphism rs9380142 is an HLA-G 3'UTR variant (+3187) with a well-established role in mRNA stability. The polymorphism rs2114511 is located in the exonic region of LILRB1. Although no association involving this SNP has been reported, ChIP-Seq experiments have identified this position as an EBF1 binding site. These results highlight the role of an epistatic interaction between HLA-G and LILRB1 in vitiligo pathogenesis.
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8
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Aguiar VRC, Castelli EC, Single RM, Bashirova A, Ramsuran V, Kulkarni S, Augusto DG, Martin MP, Gutierrez-Arcelus M, Carrington M, Meyer D. Comparison between qPCR and RNA-seq reveals challenges of quantifying HLA expression. Immunogenetics 2023; 75:249-262. [PMID: 36707444 PMCID: PMC9883133 DOI: 10.1007/s00251-023-01296-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/11/2023] [Indexed: 01/29/2023]
Abstract
Human leukocyte antigen (HLA) class I and II loci are essential elements of innate and acquired immunity. Their functions include antigen presentation to T cells leading to cellular and humoral immune responses, and modulation of NK cells. Their exceptional influence on disease outcome has now been made clear by genome-wide association studies. The exons encoding the peptide-binding groove have been the main focus for determining HLA effects on disease susceptibility/pathogenesis. However, HLA expression levels have also been implicated in disease outcome, adding another dimension to the extreme diversity of HLA that impacts variability in immune responses across individuals. To estimate HLA expression, immunogenetic studies traditionally rely on quantitative PCR (qPCR). Adoption of alternative high-throughput technologies such as RNA-seq has been hampered by technical issues due to the extreme polymorphism at HLA genes. Recently, however, multiple bioinformatic methods have been developed to accurately estimate HLA expression from RNA-seq data. This opens an exciting opportunity to quantify HLA expression in large datasets but also brings questions on whether RNA-seq results are comparable to those by qPCR. In this study, we analyze three classes of expression data for HLA class I genes for a matched set of individuals: (a) RNA-seq, (b) qPCR, and (c) cell surface HLA-C expression. We observed a moderate correlation between expression estimates from qPCR and RNA-seq for HLA-A, -B, and -C (0.2 ≤ rho ≤ 0.53). We discuss technical and biological factors which need to be accounted for when comparing quantifications for different molecular phenotypes or using different techniques.
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Affiliation(s)
- Vitor R. C. Aguiar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP Brazil ,Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA ,Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Erick C. Castelli
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University, Botucatu, SP Brazil
| | - Richard M. Single
- Department of Mathematics and Statistics, University of Vermont, Burlington, VT USA
| | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD USA ,Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD USA
| | - Veron Ramsuran
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD USA ,Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD USA ,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa ,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Smita Kulkarni
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD USA ,Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD USA ,Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX USA
| | - Danillo G. Augusto
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD USA ,Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD USA ,Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC USA ,Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR Brazil
| | - Maureen P. Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD USA ,Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD USA
| | - Maria Gutierrez-Arcelus
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA ,Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD USA ,Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD USA ,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP Brazil
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9
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de Castro MV, Silva MVR, Naslavsky MS, Scliar MO, Nunes K, Passos-Bueno MR, Castelli EC, Magawa JY, Adami FL, Moretti AIS, de Oliveira VL, Boscardin SB, Cunha-Neto E, Kalil J, Jouanguy E, Bastard P, Casanova JL, Quiñones-Vega M, Sosa-Acosta P, Guedes JDS, de Almeida NP, Nogueira FCS, Domont GB, Santos KS, Zatz M. The oldest unvaccinated Covid-19 survivors in South America. Immun Ageing 2022; 19:57. [PMID: 36384671 PMCID: PMC9666972 DOI: 10.1186/s12979-022-00310-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Although older adults are at a high risk of severe or critical Covid-19, there are many cases of unvaccinated centenarians who had a silent infection or recovered from mild or moderate Covid-19. We studied three Brazilian supercentenarians, older than 110 years, who survived Covid-19 in 2020 before being vaccinated. RESULTS Despite their advanced age, humoral immune response analysis showed that these individuals displayed robust levels of IgG and neutralizing antibodies (NAbs) against SARS-CoV-2. Enrichment of plasma proteins and metabolites related to innate immune response and host defense was also observed. None presented autoantibodies (auto-Abs) to type I interferon (IFN). Furthermore, these supercentenarians do not carry rare variants in genes underlying the known inborn errors of immunity, including particular inborn errors of type I IFN. CONCLUSION These observations suggest that their Covid-19 resilience might be a combination of their genetic background and their innate and adaptive immunity.
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Affiliation(s)
- Mateus V de Castro
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Monize V R Silva
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Marilia O Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Erick C Castelli
- Department of Pathology, School of Medicine, UNESP - São Paulo State University, Botucatu, São Paulo, Brazil
| | - Jhosiene Y Magawa
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia-Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
- Departamento de Clínica Médica, Disciplina de Imunologia Clínica e Alergia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Flávia L Adami
- Laboratory of Antigen Targeting to Dendritic Cells, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana I S Moretti
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
| | - Vivian L de Oliveira
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
| | - Silvia B Boscardin
- Laboratory of Antigen Targeting to Dendritic Cells, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Edecio Cunha-Neto
- Instituto de Investigação em Imunologia-Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
- Departamento de Clínica Médica, Disciplina de Imunologia Clínica e Alergia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Jorge Kalil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia-Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris, Paris, France
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris, Paris, France
| | - Jean-Laurent Casanova
- Imagine Institute, University of Paris, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Mauricio Quiñones-Vega
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics (LabProt), Institute of Chemistry, LADETEC, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia Sosa-Acosta
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics (LabProt), Institute of Chemistry, LADETEC, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jéssica de S Guedes
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics (LabProt), Institute of Chemistry, LADETEC, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Natália P de Almeida
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics (LabProt), Institute of Chemistry, LADETEC, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fábio C S Nogueira
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Proteomics (LabProt), Institute of Chemistry, LADETEC, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gilberto B Domont
- Proteomics Unit, Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Keity S Santos
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia-Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
- Departamento de Clínica Médica, Disciplina de Imunologia Clínica e Alergia, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, São Paulo, Brazil.
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil.
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10
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Castelli EC, de Castro MV, Naslavsky MS, Scliar MO, Silva NSB, Pereira RN, Ciriaco VAO, Castro CFB, Mendes-Junior CT, Silveira EDS, de Oliveira IM, Antonio EC, Vieira GF, Meyer D, Nunes K, Matos LRB, Silva MVR, Wang JYT, Esposito J, Cória VR, Magawa JY, Santos KS, Cunha-Neto E, Kalil J, Bortolin RH, Hirata MH, Dell’Aquila LP, Razuk-Filho A, Batista-Júnior PB, Duarte-Neto AN, Dolhnikoff M, Saldiva PHN, Passos-Bueno MR, Zatz M. MUC22, HLA-A, and HLA-DOB variants and COVID-19 in resilient super-agers from Brazil. Front Immunol 2022; 13:975918. [PMID: 36389712 PMCID: PMC9641602 DOI: 10.3389/fimmu.2022.975918] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/15/2022] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Although aging correlates with a worse prognosis for Covid-19, super elderly still unvaccinated individuals presenting mild or no symptoms have been reported worldwide. Most of the reported genetic variants responsible for increased disease susceptibility are associated with immune response, involving type I IFN immunity and modulation; HLA cluster genes; inflammasome activation; genes of interleukins; and chemokines receptors. On the other hand, little is known about the resistance mechanisms against SARS-CoV-2 infection. Here, we addressed polymorphisms in the MHC region associated with Covid-19 outcome in super elderly resilient patients as compared to younger patients with a severe outcome. METHODS SARS-CoV-2 infection was confirmed by RT-PCR test. Aiming to identify candidate genes associated with host resistance, we investigated 87 individuals older than 90 years who recovered from Covid-19 with mild symptoms or who remained asymptomatic following positive test for SARS-CoV-2 as compared to 55 individuals younger than 60 years who had a severe disease or died due to Covid-19, as well as to the general elderly population from the same city. Whole-exome sequencing and an in-depth analysis of the MHC region was performed. All samples were collected in early 2020 and before the local vaccination programs started. RESULTS We found that the resilient super elderly group displayed a higher frequency of some missense variants in the MUC22 gene (a member of the mucins' family) as one of the strongest signals in the MHC region as compared to the severe Covid-19 group and the general elderly control population. For example, the missense variant rs62399430 at MUC22 is two times more frequent among the resilient super elderly (p = 0.00002, OR = 2.24). CONCLUSION Since the pro-inflammatory basal state in the elderly may enhance the susceptibility to severe Covid-19, we hypothesized that MUC22 might play an important protective role against severe Covid-19, by reducing overactive immune responses in the senior population.
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Affiliation(s)
- Erick C. Castelli
- Department of Pathology, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Mateus V. de Castro
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - 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
| | - Marilia O. Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Nayane S. B. Silva
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Raphaela N. Pereira
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Viviane A. O. Ciriaco
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Camila F. B. Castro
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
- Centro Universitário Sudoeste Paulista, Avaré, Brazil
| | - Celso T. Mendes-Junior
- Departamento de Química, Faculdade de Filosofa, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Etiele de S. Silveira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Iuri M. de Oliveira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Eduardo C. Antonio
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gustavo F. Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório de Saúde Humana In Silico, Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Canoas, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Larissa R. B. Matos
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Monize V. R. Silva
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Jaqueline Y. T. Wang
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Joyce Esposito
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Vivian R. Cória
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Jhosiene Y. Magawa
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Keity S. Santos
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Edecio Cunha-Neto
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Jorge Kalil
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia, Instituto Nacional de Ciências e Tecnologia-iii (INCT), São Paulo, Brazil
| | - Raul H. Bortolin
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mário Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | | | | | - Amaro N. Duarte-Neto
- Department of Pathology, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Marisa Dolhnikoff
- Department of Pathology, School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Paulo H. N. Saldiva
- Department of Pathology, School of Medicine, University of Sao Paulo, Sao 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
| | - 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
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11
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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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12
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de Castro MV, Silva MVR, Soares FB, Cória VR, Naslavsky MS, Scliar MO, Castelli EC, de Oliveira JR, Sasahara GL, Santos KS, Cunha-Neto E, Kalil J, Zatz M. Follow-up of young adult monozygotic twins after simultaneous critical coronavirus disease 2019: A case report. Front Med (Lausanne) 2022; 9:1008585. [PMID: 36250103 PMCID: PMC9558815 DOI: 10.3389/fmed.2022.1008585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/15/2022] [Indexed: 11/18/2022] Open
Abstract
Background The influence of the host genome on coronavirus disease 2019 (COVID-19) susceptibility and severity is supported by reports on monozygotic (MZ) twins where both were infected simultaneously with similar disease outcomes, including several who died due to the SARS-CoV-2 infection within days apart. However, successive exposures to pathogens throughout life along with other environmental factors make the immune response unique for each individual, even among MZ twins. Case presentation and methods Here we report a case of a young adult monozygotic twin pair, who caught attention since both presented simultaneously severe COVID-19 with the need for oxygen support despite age and good health conditions. One of the twins, who spent more time hospitalized, reported symptoms of long-COVID even 7 months after infection. Immune cell profile and specific responses to SARS-CoV-2 were evaluated as well as whole exome sequencing. Conclusion Although the MZ twin brothers shared the same genetic mutations which may be associated with their increased risk of developing severe COVID-19, their clinical progression was different, reinforcing the role of both immune response and genetics in the COVID-19 presentation and course. Besides, post-COVID syndrome was observed in one of them, corroborating an association between the duration of hospitalization and the occurrence of long-COVID symptoms.
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Affiliation(s)
- Mateus V. de Castro
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Monize V. R. Silva
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Flávia B. Soares
- 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
| | - Vivian R. Cória
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - 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
| | - Marilia O. Scliar
- 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
| | - Erick C. Castelli
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (Unipex), School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Jamile R. de Oliveira
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM 19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
| | - Greyce L. Sasahara
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM 19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
| | - Keity S. Santos
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM 19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia—Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
| | - Edecio Cunha-Neto
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM 19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia—Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
| | - Jorge Kalil
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM 19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia—Instituto Nacional de Ciências e Tecnologia-iii-INCT, 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
- *Correspondence: Mayana Zatz,
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13
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Maróstica AS, Nunes K, Castelli EC, Silva NSB, Weir BS, Goudet J, Meyer D. How HLA diversity is apportioned: influence of selection and relevance to transplantation. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200420. [PMID: 35430892 PMCID: PMC9014195 DOI: 10.1098/rstb.2020.0420] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In his 1972 paper ‘The apportionment of human diversity’, Lewontin showed that, when averaged over loci, genetic diversity is predominantly attributable to differences among individuals within populations. However, selection can alter the apportionment of diversity of specific genes or genomic regions. We examine genetic diversity at the human leucocyte antigen (HLA) loci, located within the major histocompatibility complex (MHC) region. HLA genes code for proteins that are critical to adaptive immunity and are well-documented targets of balancing selection. The single-nucleotide polymorphisms (SNPs) within HLA genes show strong signatures of balancing selection on large timescales and are broadly shared among populations, displaying low FST values. However, when we analyse haplotypes defined by these SNPs (which define ‘HLA alleles’), we find marked differences in frequencies between geographic regions. These differences are not reflected in the FST values because of the extreme polymorphism at HLA loci, illustrating challenges in interpreting FST. Differences in the frequency of HLA alleles among geographic regions are relevant to bone-marrow transplantation, which requires genetic identity at HLA loci between patient and donor. We discuss the case of Brazil's bone marrow registry, where a deficit of enrolled volunteers with African ancestry reduces the chance of finding donors for individuals with an MHC region of African ancestry. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- André Silva Maróstica
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Erick C. Castelli
- Departamento de Patologia, Universidade Estadual Paulista - Unesp, Faculdade de Medicina de Botucatu, Botucatu, SP, Brazil
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University - Unesp, Botucatu, SP, Brazil
| | - Nayane S. B. Silva
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University - Unesp, Botucatu, SP, Brazil
| | - Bruce S. Weir
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Diogo Meyer
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, SP, Brazil
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14
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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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15
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de Castro MV, Santos KS, Apostolico JS, Fernandes ER, Almeida RR, Levin G, Magawa JY, Nunes JPS, Bruni M, Yamamoto MM, Lima AC, Silva MVR, Matos LRB, Coria VR, Castelli EC, Scliar MO, Kuramoto A, Bruno FR, Jacintho LC, Nunes K, Wang JYT, Coelho VP, Neto MM, Maciel RMB, Naslavsky MS, Passos-Bueno MR, Boscardin SB, Rosa DS, Kalil J, Zatz M, Cunha-Neto E. Recurrence of COVID-19 associated with reduced T-cell responses in a monozygotic twin pair. Open Biol 2022; 12:210240. [PMID: 35104433 PMCID: PMC8807054 DOI: 10.1098/rsob.210240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Recurrence of COVID-19 in recovered patients has been increasingly reported. However, the immune mechanisms behind the recurrence have not been thoroughly investigated. The presence of neutralizing antibodies (nAbs) in recurrence/reinfection cases suggests that other types of immune response are involved in protection against recurrence. Here, we investigated the innate type I/III interferon (IFN) response, binding and nAb assays and T-cell responses to severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2) with IFN gamma (IFNγ) enzyme-linked spot assay (ELISPOT) in three pairs of young adult monozygotic (MZ) twins with previous confirmed COVID-19, one of them presenting a severe recurrence four months after the initial infection. Twin studies have been of paramount importance to comprehend the immunogenetics of infectious diseases. Each MZ twin pair was previously exposed to SARS-CoV-2, as seen by clinical reports. The six individuals presented similar overall recovered immune responses except for the recurrence case, who presented a drastically reduced number of recognized SARS-CoV-2 T-cell epitopes on ELISPOT as compared to her twin sister and the other twin pairs. Our results suggest that the lack of a broad T-cell response to initial infection may have led to recurrence, emphasizing that an effective SARS-CoV-2-specific T-cell immune response is key for complete viral control and avoidance of clinical recurrence of COVID-19.
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Affiliation(s)
- Mateus V. de Castro
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Keity S. Santos
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - Juliana S. Apostolico
- Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Department of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Edgar R. Fernandes
- Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Department of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Rafael R. Almeida
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil
| | - Gabriel Levin
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil
| | - Jhosiene Y. Magawa
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - João Paulo S. Nunes
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - Mirian Bruni
- Department of Parasitology, Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Marcio M. Yamamoto
- Department of Parasitology, Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ariane C. Lima
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - Monize V. R. Silva
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Larissa R. B. Matos
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Vivian R. Coria
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Erick C. Castelli
- School of Medicine, Universidade Estadual Paulista (UNESP), Botucatu, SP, Brazil
| | - Marilia O. Scliar
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Andreia Kuramoto
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - Fernanda R. Bruno
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - Lucas C. Jacintho
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | - Kelly Nunes
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jaqueline Y. T. Wang
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Veronica P. Coelho
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil
| | | | | | - Michel S. Naslavsky
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Silvia B. Boscardin
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Division of Clinical Immunology and Allergy, Department of Medicine, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo SP, Brazil,Department of Parasitology, Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Daniela S. Rosa
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Department of Microbiology, Immunology and Parasitology, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Jorge Kalil
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil,Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil,Institute for Investigation in Immunology—Instituto Nacional de Ciência e Tecnologia—iii-INCT, São Paulo, SP, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center (HUG-CELL), Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Edecio Cunha-Neto
- Laboratory of Immunology, Heart Institute (InCor), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, SP, Brazil
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16
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Zaimoku Y, Patel BA, Adams SD, Shalhoub R, Groarke EM, Lee AAC, Kajigaya S, Feng X, Rios OJ, Eager H, Alemu L, Quinones Raffo D, Wu CO, Flegel WA, Young NS. HLA associations, somatic loss of HLA expression, and clinical outcomes in immune aplastic anemia. Blood 2021; 138:2799-2809. [PMID: 34724566 PMCID: PMC8718630 DOI: 10.1182/blood.2021012895] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023] Open
Abstract
Immune aplastic anemia (AA) features somatic loss of HLA class I allele expression on bone marrow cells, consistent with a mechanism of escape from T-cell-mediated destruction of hematopoietic stem and progenitor cells. The clinical significance of HLA abnormalities has not been well characterized. We examined the somatic loss of HLA class I alleles and correlated HLA loss and mutation-associated HLA genotypes with clinical presentation and outcomes after immunosuppressive therapy in 544 AA patients. HLA class I allele loss was detected in 92 (22%) of the 412 patients tested, in whom there were 393 somatic HLA gene mutations and 40 instances of loss of heterozygosity. Most frequently affected was HLA-B*14:02, followed by HLA-A*02:01, HLA-B*40:02, HLA-B*08:01, and HLA-B*07:02. HLA-B*14:02, HLA-B*40:02, and HLA-B*07:02 were also overrepresented in AA. High-risk clonal evolution was correlated with HLA loss, HLA-B*14:02 genotype, and older age, which yielded a valid prediction model. In 2 patients, we traced monosomy 7 clonal evolution from preexisting clones harboring somatic mutations in HLA-A*02:01 and HLA-B*40:02. Loss of HLA-B*40:02 correlated with higher blood counts. HLA-B*07:02 and HLA-B*40:01 genotypes and their loss correlated with late-onset of AA. Our results suggest the presence of specific immune mechanisms of molecular pathogenesis with clinical implications. HLA genotyping and screening for HLA loss may be of value in the management of immune AA. This study was registered at clinicaltrials.gov as NCT00001964, NCT00061360, NCT00195624, NCT00260689, NCT00944749, NCT01193283, and NCT01623167.
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Affiliation(s)
- Yoshitaka Zaimoku
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Bhavisha A Patel
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Sharon D Adams
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD; and
| | - Ruba Shalhoub
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Emma M Groarke
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Audrey Ai Chin Lee
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD; and
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Xingmin Feng
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Olga Julia Rios
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Holly Eager
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Lemlem Alemu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Diego Quinones Raffo
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Colin O Wu
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Willy A Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD; and
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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17
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Douillard V, Castelli EC, Mack SJ, Hollenbach JA, Gourraud PA, Vince N, Limou S. Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research. Front Genet 2021; 12:774916. [PMID: 34925459 PMCID: PMC8677840 DOI: 10.3389/fgene.2021.774916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 01/11/2023] Open
Abstract
The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico, population, and individual data. However, they were conducted with variable scale and success; convincing results were mostly obtained with broader whole-genome association studies. Here, we propose a technical review of HLA analysis, including basic HLA knowledge as well as available tools and advice. We notably describe recent algorithms to infer and call HLA genotypes from GWAS SNPs and NGS data, respectively, which opens the possibility to investigate HLA from large datasets without a specific initial focus on this region. We thus hope this overview will empower geneticists who were unfamiliar with HLA to run MHC-focused analyses following the footsteps of the Covid-19|HLA & Immunogenetics Consortium.
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Affiliation(s)
- Venceslas Douillard
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | | | - Steven J. Mack
- Division of Allergy, Immunology and Bone Marrow Transplantation, Department of Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Pierre-Antoine Gourraud
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, Nantes, France
- Ecole Centrale de Nantes, Department of Computer Sciences and Mathematics in Biology, Nantes, France
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18
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Castelli EC, de Almeida BS, Muniz YCN, Silva NSB, Passos MRS, Souza AS, Page AE, Dyble M, Smith D, Aguileta G, Bertranpetit J, Migliano AB, Duarte YAO, Scliar MO, Wang J, Passos-Bueno MR, Naslavsky MS, Zatz M, Mendes-Junior CT, Donadi EA. HLA-G genetic diversity and evolutive aspects in worldwide populations. Sci Rep 2021; 11:23070. [PMID: 34845256 PMCID: PMC8629979 DOI: 10.1038/s41598-021-02106-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/01/2021] [Indexed: 12/15/2022] Open
Abstract
HLA-G is a promiscuous immune checkpoint molecule. The HLA-G gene presents substantial nucleotide variability in its regulatory regions. However, it encodes a limited number of proteins compared to classical HLA class I genes. We characterized the HLA-G genetic variability in 4640 individuals from 88 different population samples across the globe by using a state-of-the-art method to characterize polymorphisms and haplotypes from high-coverage next-generation sequencing data. We also provide insights regarding the HLA-G genetic diversity and a resource for future studies evaluating HLA-G polymorphisms in different populations and association studies. Despite the great haplotype variability, we demonstrated that: (1) most of the HLA-G polymorphisms are in introns and regulatory sequences, and these are the sites with evidence of balancing selection, (2) linkage disequilibrium is high throughout the gene, extending up to HLA-A, (3) there are few proteins frequently observed in worldwide populations, with lack of variation in residues associated with major HLA-G biological properties (dimer formation, interaction with leukocyte receptors). These observations corroborate the role of HLA-G as an immune checkpoint molecule rather than as an antigen-presenting molecule. Understanding HLA-G variability across populations is relevant for disease association and functional studies.
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Affiliation(s)
- Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, Brazil.
- Department of Pathology, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, CEP: 18618970, Brazil.
| | - Bibiana S de Almeida
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, CEP: 14049-900, Brazil
- Laboratório Multiusuário de Estudos em Biologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil
| | - Yara C N Muniz
- Departamento de Biologia Celular, Embriologia e Genética, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil
| | - Nayane S B Silva
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, Brazil
| | - Marília R S Passos
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, Brazil
| | - Andreia S Souza
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo, Brazil
| | - Abigail E Page
- Department of Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Mark Dyble
- Departament of Anthropology, University College London (UCL), London, UK
| | - Daniel Smith
- Bristol Medical School (PHS), University of Bristol, Bristol, UK
| | - Gabriela Aguileta
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaume Bertranpetit
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Andrea B Migliano
- Departament of Anthropology, Unversity of Zurich, Zurich, Switzerland
| | - Yeda A O Duarte
- Escola de Enfermagem e Faculdade de Saúde Pública, Universidade de São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Marília O Scliar
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Jaqueline Wang
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, State of São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo (USP), São Paulo, State of São Paulo, Brazil
| | - Celso Teixeira Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto, SP, Brazil
| | - Eduardo A Donadi
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP, CEP: 14049-900, Brazil.
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19
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Castelli EC, de Castro MV, Naslavsky MS, Scliar MO, Silva NSB, Andrade HS, Souza AS, Pereira RN, Castro CFB, Mendes-Junior CT, Meyer D, Nunes K, Matos LRB, Silva MVR, Wang JYT, Esposito J, Coria VR, Bortolin RH, Hirata MH, Magawa JY, Cunha-Neto E, Coelho V, Santos KS, Marin MLC, Kalil J, Mitne-Neto M, Maciel RMB, Passos-Bueno MR, Zatz M. MHC Variants Associated With Symptomatic Versus Asymptomatic SARS-CoV-2 Infection in Highly Exposed Individuals. Front Immunol 2021; 12:742881. [PMID: 34650566 PMCID: PMC8506217 DOI: 10.3389/fimmu.2021.742881] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/06/2021] [Indexed: 12/11/2022] Open
Abstract
Despite the high number of individuals infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) who develop coronavirus disease 2019 (COVID-19) symptoms worldwide, many exposed individuals remain asymptomatic and/or uninfected and seronegative. This could be explained by a combination of environmental (exposure), immunological (previous infection), epigenetic, and genetic factors. Aiming to identify genetic factors involved in immune response in symptomatic COVID-19 as compared to asymptomatic exposed individuals, we analyzed 83 Brazilian couples where one individual was infected and symptomatic while the partner remained asymptomatic and serum-negative for at least 6 months despite sharing the same bedroom during the infection. We refer to these as "discordant couples". We performed whole-exome sequencing followed by a state-of-the-art method to call genotypes and haplotypes across the highly polymorphic major histocompatibility complex (MHC) region. The discordant partners had comparable ages and genetic ancestry, but women were overrepresented (65%) in the asymptomatic group. In the antigen-presentation pathway, we observed an association between HLA-DRB1 alleles encoding Lys at residue 71 (mostly DRB1*03:01 and DRB1*04:01) and DOB*01:02 with symptomatic infections and HLA-A alleles encoding 144Q/151R with asymptomatic seronegative women. Among the genes related to immune modulation, we detected variants in MICA and MICB associated with symptomatic infections. These variants are related to higher expression of soluble MICA and low expression of MICB. Thus, quantitative differences in these molecules that modulate natural killer (NK) activity could contribute to susceptibility to COVID-19 by downregulating NK cell cytotoxic activity in infected individuals but not in the asymptomatic partners.
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Affiliation(s)
- Erick C. Castelli
- Department of Pathology, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
- Molecular Genetics and Bioinformatics Laboratory–Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Mateus V. de Castro
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - 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
| | - Marilia O. Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Nayane S. B. Silva
- Molecular Genetics and Bioinformatics Laboratory–Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Heloisa S. Andrade
- Molecular Genetics and Bioinformatics Laboratory–Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Andreia S. Souza
- Molecular Genetics and Bioinformatics Laboratory–Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Raphaela N. Pereira
- Molecular Genetics and Bioinformatics Laboratory–Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Camila F. B. Castro
- Molecular Genetics and Bioinformatics Laboratory–Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
- Centro Universitário Sudoeste Paulista, Avaré, Brazil
| | - Celso T. Mendes-Junior
- Departamento de Química, Faculdade de Filosofa, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Larissa R. B. Matos
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Monize V. R. Silva
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Jaqueline Y. T. Wang
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Joyce Esposito
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Vivian R. Coria
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Raul H. Bortolin
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mario H. Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jhosiene Y. Magawa
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Edecio Cunha-Neto
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia - Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
| | - Verônica Coelho
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia - Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
| | - Keity S. Santos
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia - Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
| | - Maria Lucia C. Marin
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia - Instituto Nacional de Ciências e Tecnologia-iii-INCT, São Paulo, Brazil
| | - Jorge Kalil
- Departamento de Clínica Médica, Disciplina de Alergia e Imunologia Clínica, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Imunologia, Instituto do Coração (InCor), LIM19, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, (HCFMUSP), São Paulo, Brazil
- Instituto de Investigação em Imunologia - Instituto Nacional de Ciências e Tecnologia-iii-INCT, 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
| | - 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
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20
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Aguiar VRC, Augusto DG, Castelli EC, Hollenbach JA, Meyer D, Nunes K, Petzl-Erler ML. An immunogenetic view of COVID-19. Genet Mol Biol 2021; 44:e20210036. [PMID: 34436508 PMCID: PMC8388242 DOI: 10.1590/1678-4685-gmb-2021-0036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/12/2021] [Indexed: 02/06/2023] Open
Abstract
Meeting the challenges brought by the COVID-19 pandemic requires an interdisciplinary approach. In this context, integrating knowledge of immune function with an understanding of how genetic variation influences the nature of immunity is a key challenge. Immunogenetics can help explain the heterogeneity of susceptibility and protection to the viral infection and disease progression. Here, we review the knowledge developed so far, discussing fundamental genes for triggering the innate and adaptive immune responses associated with a viral infection, especially with the SARS-CoV-2 mechanisms. We emphasize the role of the HLA and KIR genes, discussing what has been uncovered about their role in COVID-19 and addressing methodological challenges of studying these genes. Finally, we comment on questions that arise when studying admixed populations, highlighting the case of Brazil. We argue that the interplay between immunology and an understanding of genetic associations can provide an important contribution to our knowledge of COVID-19.
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Affiliation(s)
- Vitor R. C. Aguiar
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Danillo G. Augusto
- University of California, UCSF Weill Institute for Neurosciences,
Department of Neurology, San Francisco, CA, USA
- Universidade Federal do Paraná, Departamento de Genética, Curitiba,
PR, Brazil
| | - Erick C. Castelli
- Universidade Estadual Paulista, Faculdade de Medicina de Botucatu,
Departamento de Patologia, Botucatu, SP, Brazil
| | - Jill A. Hollenbach
- University of California, UCSF Weill Institute for Neurosciences,
Department of Neurology, San Francisco, CA, USA
| | - Diogo Meyer
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
| | - Kelly Nunes
- Universidade de São Paulo, Departamento de Genética e Biologia
Evolutiva, São Paulo, SP, Brazil
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21
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Sonon P, Tokplonou L, Sadissou I, M'po KKG, Glitho SSC, Agniwo P, Ibikounlé M, Souza AS, Massaro JD, Gonzalez D, Tchégninougbo T, Ayitchédji A, Massougbodji A, Moreau P, Garcia A, Milet J, Sabbagh A, Mendes-Junior CT, Moutairou KA, Castelli EC, Courtin D, Donadi EA. Human leukocyte antigen (HLA)-F and -G gene polymorphisms and haplotypes are associated with malaria susceptibility in the Beninese Toffin children. INFECTION GENETICS AND EVOLUTION 2021; 92:104828. [PMID: 33781967 DOI: 10.1016/j.meegid.2021.104828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/05/2021] [Accepted: 03/24/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Little attention has been devoted to the role of the immunoregulatory HLA-E/-F/-G genes in malaria. We evaluated the entire HLA-E/-F/-G variability in Beninese children highly exposed to Plasmodium falciparum (P.f.) malaria. METHODS 154 unrelated children were followed-up for six months and evaluated for the presence and number of malaria episodes. HLA-E/-F/-G genes were genotyped using massively parallel sequencing. Anti P.f. antibodies were evaluated using ELISA. RESULTS Children carrying the G allele at HLA-F (-1499,rs183540921) showed increased P.f. asymptomatic/symptomatic ratio, suggesting that these children experienced more asymptomatic P.f. episodes than symptomatic one. Children carrying HLA-G-UTR-03 haplotype exhibited increased risk for symptomatic P.f. episodes and showed lower IgG2 response against P.f. GLURP-R2 when compared to the non-carriers. No associations were observed for the HLA-E gene. CONCLUSION HLA-F associations may be related to the differential expression profiles of the encoded immunomodulatory molecules, and the regulatory sites at the HLA-G 3'UTR may be associated to posttranscriptional regulation of HLA-G and to host humoral response against P.f.
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Affiliation(s)
- Paulin Sonon
- Post-graduate Program in Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, 3900, Monte Alegre, 14049-900 Ribeirão Preto, SP, Brazil; Immunogenetic Laboratory, Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Léonidas Tokplonou
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Bénin; Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Ibrahim Sadissou
- Post-graduate Program in Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, 3900, Monte Alegre, 14049-900 Ribeirão Preto, SP, Brazil; Intertryp, IRD, Cirad, University of Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Kuumaaté K G M'po
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Bénin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Sonya S C Glitho
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Bénin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Privat Agniwo
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Bénin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Moudachirou Ibikounlé
- Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Andréia S Souza
- São Paulo State University (UNESP), School of Medicine, Molecular Genetics and Bioinformatics Laboratory, Av. Prof. Dr. Walter Maurício Correa, s/n, 1861868, Botucatu, SP, Brazil
| | - Juliana Doblas Massaro
- Post-graduate Program in Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, 3900, Monte Alegre, 14049-900 Ribeirão Preto, SP, Brazil
| | - Daniel Gonzalez
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France
| | | | | | - Achille Massougbodji
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Bénin
| | - Philippe Moreau
- CEA, DRF-Institut François Jacob, Service de Recherches en Hémato-Immunologie, Hopital Saint-Louis, 75010 Paris, France; Université de Paris, CEA, U976 HIPI Unit (Human Immunology, Physiopathology, Immunotherapy), Institut de Recherche Saint-Louis, 75010 Paris, France
| | - André Garcia
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France
| | | | - Audrey Sabbagh
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, AV Bandeirantes, 3900, 14040901 Ribeirão Preto, SP, Brazil
| | - Kabirou A Moutairou
- Laboratoire de Biologie et Physiologie Cellulaire, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Erick C Castelli
- São Paulo State University (UNESP), School of Medicine, Molecular Genetics and Bioinformatics Laboratory, Av. Prof. Dr. Walter Maurício Correa, s/n, 1861868, Botucatu, SP, Brazil; São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, State of São Paulo, SP, Brazil
| | - David Courtin
- Université de Paris, UMR 261 MERIT, IRD, F-75006 Paris, France
| | - Eduardo A Donadi
- Post-graduate Program in Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, 3900, Monte Alegre, 14049-900 Ribeirão Preto, SP, Brazil.
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22
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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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23
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Souza LS, Almeida CF, Yamamoto GL, Pavanello RDCM, Gurgel-Giannetti J, da Costa SS, Anequini IP, do Carmo SA, Wang JYT, Scliar MDO, Castelli EC, Otto PA, Zanoteli E, Vainzof M. Manifesting carriers of X-linked myotubular myopathy: Genetic modifiers modulating the phenotype. NEUROLOGY-GENETICS 2020; 6:e513. [PMID: 33062893 PMCID: PMC7524580 DOI: 10.1212/nxg.0000000000000513] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 07/16/2020] [Indexed: 12/18/2022]
Abstract
Objective To analyze the modulation of the phenotype in manifesting carriers of recessive X-linked myotubular myopathy (XLMTM), searching for possible genetic modifiers. Methods Twelve Brazilian families with XLMTM were molecularly and clinically evaluated. In 2 families, 4 of 6 and 2 of 5 manifesting female carriers were identified. These females were studied for X chromosome inactivation. In addition, whole-exome sequencing was performed, looking for possible modifier variants. We also determined the penetrance rate among carriers of the mutations responsible for the condition. Results Mutations in the MTM1 gene were identified in all index patients from the 12 families, being 4 of them novel. In the heterozygotes, X chromosome inactivation was random in 3 of 4 informative manifesting carriers. The disease penetrance rate was estimated to be 30%, compatible with incomplete penetrance. Exome comparative analyses identified variants within a segment of 4.2 Mb on chromosome 19, containing the killer cell immunoglobulin-like receptor cluster of genes that were present in all nonmanifesting carriers and absent in all manifesting carriers. We hypothesized that these killer cell immunoglobulin-like receptor variants may modulate the phenotype, acting as a protective factor in the nonmanifesting carriers. Conclusions Affected XLMTM female carriers have been described with a surprisingly high frequency for a recessive X-linked disease, raising the question about the pattern of inheritance or the role of modifier factors acting on the disease phenotype. We demonstrated the possible existence of genetic mechanisms and variants accountable for the clinical manifestation in these women, which can become future targets for therapies.
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Affiliation(s)
- Lucas Santos Souza
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
| | - Camila Freitas Almeida
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
| | - Guilherme Lopes Yamamoto
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
| | - Rita de Cássia Mingroni Pavanello
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
| | - Juliana Gurgel-Giannetti
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
| | - Silvia Souza da Costa
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
| | - Isabela Pessa Anequini
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
| | - Silvana Amanda do Carmo
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
| | - Jaqueline Yu Ting Wang
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
| | - Marília de Oliveira Scliar
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
| | - Erick C Castelli
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
| | - Paulo Alberto Otto
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
| | - Edmar Zanoteli
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
| | - Mariz Vainzof
- Human Genome and Stem Cell Research Center (L.S.S., C.F.A., G.L.Y., R.d.C.M.P., S.S.d.C., I.P.A., S.A.d.C., J.Y.T.W., M.d.O.S., P.A.O., M.V.), University of São Paulo; Department of Pediatrics (J.G.-G.), Medical School of Federal University of Minas Gerais, Belo Horizonte; Pathology Department (E.C.C.), School of Medicine, São Paulo State University (UNESP), Botucatu; and Department of Neurology (E.Z.), Medical School (FMUSP), University of São Paulo, Brazil
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24
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Souza AS, Sonon P, Paz MA, Tokplonou L, Lima THA, Porto IOP, Andrade HS, Silva NDSB, Veiga-Castelli LC, Oliveira MLG, Sadissou IA, Massaro JD, Moutairou KA, Donadi EA, Massougbodji A, Garcia A, Ibikounlé M, Meyer D, Sabbagh A, Mendes-Junior CT, Courtin D, Castelli EC. Hla-C genetic diversity and evolutionary insights in two samples from Brazil and Benin. HLA 2020; 96:468-486. [PMID: 32662221 DOI: 10.1111/tan.13996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/18/2020] [Accepted: 07/09/2020] [Indexed: 12/14/2022]
Abstract
Human leukocyte antigen-C (HLA-C) is a classical HLA class I molecule that binds and presents peptides to cytotoxic T lymphocytes in the cell surface. HLA-C has a dual function because it also interacts with Killer-cell immunoglobulin-like receptors (KIR) receptors expressed in natural killer and T cells, modulating their activity. The structure and diversity of the HLA-C regulatory regions, as well as the relationship among variants along the HLA-C locus, are poorly addressed, and few population-based studies explored the HLA-C variability in the entire gene in different population samples. Here we present a molecular and bioinformatics method to evaluate the entire HLA-C diversity, including regulatory sequences. Then, we applied this method to survey the HLA-C diversity in two population samples with different demographic histories, one highly admixed from Brazil with major European contribution, and one from Benin with major African contribution. The HLA-C promoter and 3'UTR were very polymorphic with the presence of few, but highly divergent haplotypes. These segments also present conserved sequences that are shared among different primate species. Nucleotide diversity was higher in other segments rather than exons 2 and 3, particularly around exon 5 and the second half of the 3'UTR region. We detected evidence of balancing selection on the entire HLA-C locus and positive selection in the HLA-C leader peptide, for both populations. HLA-C motifs previously associated with KIR interaction and expression regulation are similar between both populations. Each allele group is associated with specific regulatory sequences, reflecting the high linkage disequilibrium along the entire HLA-C locus in both populations.
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Affiliation(s)
- Andreia S Souza
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Paulin Sonon
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Michelle A Paz
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Léonidas Tokplonou
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France.,Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance, Cotonou, Benin.,Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Thálitta H A Lima
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Iane O P Porto
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Heloisa S Andrade
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Nayane Dos S B Silva
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Luciana C Veiga-Castelli
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Maria Luiza G Oliveira
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Ibrahim Abiodoun Sadissou
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Juliana Doblas Massaro
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Kabirou A Moutairou
- Laboratoire de Biologie et Physiologie Cellulaire, Université d'Abomey-Calavi, Cotonou, Benin
| | - Eduardo A Donadi
- Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Achille Massougbodji
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance, Cotonou, Benin
| | - André Garcia
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Moudachirou Ibikounlé
- Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo (USP), São Paulo, Brazil
| | - Audrey Sabbagh
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - David Courtin
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
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25
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Cismaru AL, Grimm L, Rudin D, Ibañez L, Liakoni E, Bonadies N, Kreutz R, Hallberg P, Wadelius M, Haschke M, Largiadèr CR, Amstutz U. High-Throughput Sequencing to Investigate Associations Between HLA Genes and Metamizole-Induced Agranulocytosis. Front Genet 2020; 11:951. [PMID: 32973882 PMCID: PMC7473498 DOI: 10.3389/fgene.2020.00951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/29/2020] [Indexed: 12/18/2022] Open
Abstract
Background and Objective: Agranulocytosis is a rare and potentially life-threatening complication of metamizole (dipyrone) intake that is characterized by a loss of circulating neutrophil granulocytes. While the mechanism underlying this adverse drug reaction is not well understood, involvement of the immune system has been suggested. In addition, associations between genetic variants in the Human Leukocyte Antigen (HLA) region and agranulocytosis induced by other drugs have been reported. The aim of the present study was to assess whether genetic variants in classical HLA genes are associated with the susceptibility to metamizole-induced agranulocytosis (MIA) in a European population by targeted resequencing of eight HLA genes. Design: A case-control cohort of Swiss patients with a history of neutropenia or agranulocytosis associated with metamizole exposure (n = 53), metamizole-tolerant (n = 39) and unexposed controls (n = 161) was recruited for this study. A high-throughput resequencing (HTS) and high-resolution typing method was used to sequence and analyze eight HLA loci in a discovery subset of this cohort (n = 31 cases, n = 38 controls). Identified candidate alleles were investigated in the full Swiss cohort as well as in two independent cohorts from Germany and Spain using HLA imputation from genome-wide SNP array data. In addition, variant calling based on HTS data was performed in the discovery subset for the class I genes HLA-A, -B, and -C using the HLA-specific mapper hla-mapper. Results: Eight candidate alleles (p < 0.05) were identified in the discovery subset, of which HLA-C∗04:01 was associated with MIA in the full Swiss cohort (p < 0.01) restricted to agranulocytosis (ANC < 0.5 × 109/L) cases. However, no candidate allele showed a consistent association in the Swiss, German and Spanish cohorts. Analysis of individual sequence variants in class I genes produced consistent results with HLA typing but did not reveal additional small nucleotide variants associated with MIA. Conclusion: Our results do not support an HLA-restricted T cell-mediated immune mechanism for MIA. However, we established an efficient high-resolution (three-field) eight-locus HTS HLA resequencing method to interrogate the HLA region and demonstrated the feasibility of its application to pharmacogenetic studies.
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Affiliation(s)
- Anca Liliana Cismaru
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Livia Grimm
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Deborah Rudin
- Division of Clinical Pharmacology & Toxicology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Luisa Ibañez
- Clinical Pharmacology Service, Hospital Universitari Vall d'Hebron, Department of Pharmacology, Therapeutics and Toxicology, Fundació Institut Català de Farmacologia, Autonomous University of Barcelona, Barcelona, Spain
| | - Evangelia Liakoni
- Clinical Pharmacology and Toxicology, Department of General Internal Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Nicolas Bonadies
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Reinhold Kreutz
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Klinische Pharmakologie und Toxikologie, Berlin, Germany
| | - Pär Hallberg
- Department of Medical Sciences, Clinical Pharmacology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mia Wadelius
- Department of Medical Sciences, Clinical Pharmacology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Manuel Haschke
- Clinical Pharmacology and Toxicology, Department of General Internal Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Carlo R Largiadèr
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ursula Amstutz
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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26
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A large familial cluster and sporadic cases of frontal fibrosing alopecia in Brazil reinforce known human leucocyte antigen (HLA) associations and indicate new HLA susceptibility haplotypes. J Eur Acad Dermatol Venereol 2020; 34:2409-2413. [DOI: 10.1111/jdv.16629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/30/2020] [Indexed: 12/28/2022]
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27
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Goubert C, Zevallos NA, Feschotte C. Contribution of unfixed transposable element insertions to human regulatory variation. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190331. [PMID: 32075552 PMCID: PMC7061991 DOI: 10.1098/rstb.2019.0331] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2019] [Indexed: 12/11/2022] Open
Abstract
Thousands of unfixed transposable element (TE) insertions segregate in the human population, but little is known about their impact on genome function. Recently, a few studies associated unfixed TE insertions to mRNA levels of adjacent genes, but the biological significance of these associations, their replicability across cell types and the mechanisms by which they may regulate genes remain largely unknown. Here, we performed a TE-expression QTL analysis of 444 lymphoblastoid cell lines (LCL) and 289 induced pluripotent stem cells using a newly developed set of genotypes for 2743 polymorphic TE insertions. We identified 211 and 176 TE-eQTL acting in cis in each respective cell type. Approximately 18% were shared across cell types with strongly correlated effects. Furthermore, analysis of chromatin accessibility QTL in a subset of the LCL suggests that unfixed TEs often modulate the activity of enhancers and other distal regulatory DNA elements, which tend to lose accessibility when a TE inserts within them. We also document a case of an unfixed TE likely influencing gene expression at the post-transcriptional level. Our study points to broad and diverse cis-regulatory effects of unfixed TEs in the human population and underscores their plausible contribution to phenotypic variation. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
| | | | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Road, Ithaca, NY 14853, USA
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28
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Jordier F, Gras D, De Grandis M, D'Journo XB, Thomas PA, Chanez P, Picard C, Chiaroni J, Paganini J, Di Cristofaro J. HLA-H: Transcriptional Activity and HLA-E Mobilization. Front Immunol 2020; 10:2986. [PMID: 32010122 PMCID: PMC6978722 DOI: 10.3389/fimmu.2019.02986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/05/2019] [Indexed: 01/25/2023] Open
Abstract
Little attention is paid to pseudogenes from the highly polymorphic HLA genetic region. The pseudogene HLA-H is defined as a non-functional gene because it is deleted at different frequencies in humans and because it encodes a potentially non-functional truncated protein. However, different studies have shown HLA-H transcriptional activity. We formerly identified 13 novel HLA-H alleles, including the H*02:07 allele, which reaches 19.6% in East Asian populations and encodes a full-length HLA protein. The aims of this study were to explore the expression and possible function of the HLA-H molecule. HLA-H may act as a transmembrane molecule and/or indirectly via its signal peptide by mobilizing HLA-E to the cell surface. We analyzed HLA-H RNA expression in Peripheral Blood Mononuclear Cells (PBMC), Human Bronchial Epithelial Cells (HBEC), and available RNA sequencing data from lymphoblastoid cell lines, and we looked to see whether HLA-E was mobilized at the cell surface by the HLA-H signal peptide. Our data confirmed that HLA-H is transcribed at similar levels to HLA-G. We characterized a hemizygous effect in HLA-H expression, and expression differed according to HLA-H alleles; most interestingly, the HLA-H*02:07 allele had the highest level of mRNA expression. We showed that HLA-H signal peptide incubation mobilized HLA-E molecules at the cell surface of T-Lymphocytes, monocytes, B-Lymphocytes, and primary epithelial cells. Our results suggest that HLA-H may be functional but raises many biological issues that need to be addressed.
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Affiliation(s)
- François Jordier
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Delphine Gras
- Aix-Marseille University, INSERM, INRA, C2VN, Marseille, France
| | - Maria De Grandis
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Xavier-Benoît D'Journo
- Department of Thoracic Surgery, North Hospital, Aix-Marseille University & Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pascal-Alexandre Thomas
- Department of Thoracic Surgery, North Hospital, Aix-Marseille University & Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pascal Chanez
- Aix-Marseille University, INSERM, INRA, C2VN, Marseille, France
- Clinique des Bronches, Allergie et Sommeil, North Hospital, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Christophe Picard
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Jacques Chiaroni
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | | | - Julie Di Cristofaro
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
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29
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Veiga-Castelli L, de Oliveira ML, Pereira A, Debortoli G, Marcorin L, Fracasso N, Silva G, Souza A, Massaro J, Simões AL, Sabbagh A, Cardili R, Donadi E, Castelli E, Mendes-Junior C. HLA-G Polymorphisms Are Associated with Non-segmental Vitiligo among Brazilians. Biomolecules 2019; 9:biom9090463. [PMID: 31505868 PMCID: PMC6769860 DOI: 10.3390/biom9090463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 12/31/2022] Open
Abstract
(1) Background: Vitiligo is characterized by white patches on the skin caused by loss of melanocyte activity or the absence of these cells. The available treatments minimize the symptoms by retarding the process of skin depigmentation or re-pigmenting the affected regions. New studies are required for a better comprehension of the mechanisms that trigger the disease and for the development of more efficient treatments. Studies have suggested an autoimmune feature for vitiligo, based on the occurrence of other autoimmune diseases in vitiligo patients and their relatives, and on the involvement of genes related to the immune response. (2) Methods: We evaluated, by massive parallel sequencing, polymorphisms of the HLA-G gene in vitiligo patients and control samples, to verify if variants of this gene could influence the susceptibility to vitiligo. (3) Results: We detected an association with non-segmental vitiligo regarding the haplotype Distal-010101a/G*01:01:01:01/UTR-1, adjusting for population stratification by using ancestry-informative markers (AIMs). (4) Conclusions: It remains unclear whether the HLA-G variants associated with vitiligo were detected because of the high linkage disequilibrium (LD) with HLA-A*02, or if the HLA-A variants previously reported as associated with vitiligo were detected because of the high LD with HLA-G*01:01:01:01/UTR-1, or if both genes jointly contribute to vitiligo susceptibility.
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Affiliation(s)
- Luciana Veiga-Castelli
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
- Correspondence: ; Tel.: +55-16-3315-0417; Fax: +55-16-3315-4838
| | - Maria Luiza de Oliveira
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
| | - Alison Pereira
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
| | - Guilherme Debortoli
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
| | - Letícia Marcorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
| | - Nádia Fracasso
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
| | - Guilherme Silva
- 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 14040-901, Brazil; (G.S.); (C.M.-J.)
| | - Andreia Souza
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (UNIPEX), School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo 18618-687, Brazil; (A.S.); (E.C.)
| | - Juliana Massaro
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (J.M.); (R.C.); (E.D.)
| | - Aguinaldo Luiz Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (M.L.d.O.); (A.P.); (G.D.); (L.M.); (N.F.); (A.L.S.)
| | - Audrey Sabbagh
- UMR 216 MERIT IRD, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France;
| | - Renata Cardili
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (J.M.); (R.C.); (E.D.)
| | - Eduardo Donadi
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto-SP 14049-900, Brazil; (J.M.); (R.C.); (E.D.)
| | - Erick Castelli
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (UNIPEX), School of Medicine, São Paulo State University (UNESP), Botucatu, State of São Paulo 18618-687, Brazil; (A.S.); (E.C.)
| | - Celso 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 14040-901, Brazil; (G.S.); (C.M.-J.)
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30
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Lima THA, Souza AS, Porto IOP, Paz MA, Veiga-Castelli LC, Oliveira MLG, Donadi EA, Meyer D, Sabbagh A, Mendes-Junior CT, Castelli EC. HLA-A promoter, coding, and 3'UTR sequences in a Brazilian cohort, and their evolutionary aspects. HLA 2019; 93:65-79. [PMID: 30666817 DOI: 10.1111/tan.13474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 01/10/2019] [Accepted: 01/18/2019] [Indexed: 12/17/2022]
Abstract
HLA-A is the second most polymorphic locus of the human leucocyte antigen (HLA) complex encoding a key molecule for antigen presentation and NK cell modulation. Many studies have evaluated HLA-A variability in worldwide populations, focusing mainly on exons, but the regulatory segments have been poorly characterized. HLA-A variability is particularly high in the segment encoding the peptide-binding groove (exons 2 and 3), which is related to the antigen presentation function and the balancing selection in these segments. Here we evaluate the genetic diversity of the HLA-A gene considering a continuous segment encompassing the extended promoter (1.5 kb upstream of the first translated ATG), all exons and introns, and the entire 3' untranslated region, by using massively parallel sequencing. To achieve this goal, we used a freely available bioinformatics workflow that optimizes read mapping for HLA genes and defines complete sequences using either the phase among variable sites directly observed in sequencing data and probabilistic models. The HLA-A variability detected in a highly admixed population sample from Brazil shows that the HLA-A regulatory segments present few, but divergent sequences. The regulatory segments are in close association with the coding alleles. Both exons and introns are highly variable. Moreover, patterns of molecular diversity suggest that the promoter, in addition to the coding region, might be under the same selective pressure, but a different scenario arises when it comes to exon 4 and the 3'UTR segment.
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Affiliation(s)
- Thálitta H A Lima
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,São Paulo State University (UNESP), Genetics Program, Institute of Biosciences of Botucatu, Botucatu, Brazil
| | - Andreia S Souza
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,São Paulo State University (UNESP), Genetics Program, Institute of Biosciences of Botucatu, Botucatu, Brazil
| | - Iane O P Porto
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Michelle A Paz
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Luciana C Veiga-Castelli
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Maria Luiza G Oliveira
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Eduardo A Donadi
- Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Audrey Sabbagh
- UMR 216 MERIT, IRD, Université Paris Descartes, Faculté de Pharmacie, Paris, France
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil.,São Paulo State University (UNESP), Genetics Program, Institute of Biosciences of Botucatu, Botucatu, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
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Buttura RV, Ramalho J, Lima TH, Donadi EA, Veiga-Castelli LC, Mendes-Junior CT, Castelli EC. HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels. Hum Immunol 2019; 80:112-119. [DOI: 10.1016/j.humimm.2018.10.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 10/10/2018] [Accepted: 10/26/2018] [Indexed: 12/30/2022]
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