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Mack SJ, Single RM, Solberg OD, Thomson G, Erlich HA. Population Genetic Dissection of HLA-DPB1 Amino Acid Polymorphism to Infer Selection. Hum Immunol 2024; 85:111151. [PMID: 39413638 DOI: 10.1016/j.humimm.2024.111151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 09/02/2024] [Accepted: 10/01/2024] [Indexed: 10/18/2024]
Abstract
Although allele frequency data for most HLA loci provide strong evidence for balancing selection at the allele level, the DPB1 locus is a notable exception, with allele frequencies compatible with neutral evolution (genetic drift) or directional selection in most populations. This discrepancy is especially interesting as evidence for balancing selection has been seen at the nucleotide and amino acid (AA) sequence levels for DPB1. We describe methods used to examine the global distribution of DPB1 alleles and their constituent AA sequences. These methods allow investigation of the influence of natural selection in shaping DPβ diversity in a hierarchical fashion for DPB1 alleles, all polymorphic DPB1 exon 2-encoded AA positions, as well as all pairs and trios of these AA positions. In addition, we describe how asymmetric linkage disequilibrium for all DPB1 exon 2-encoded AA pairs can be used to complement other methods. Application of these methods provides strong evidence for the operation of balancing selection on AA positions 56, 85-87, 36, 55 and 84 (listed in decreasing order of the strength of selection), but no evidence for balancing selection on DPB1 alleles.
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Affiliation(s)
- Steven J Mack
- Department of Pediatrics, University of California, San Francisco, Oakland, CA, United States.
| | - Richard M Single
- Department of Mathematics and Statistics, University of Vermont, Burlington, VT, United States
| | - Owen D Solberg
- Bioinformatics and Biostatistics, Monogram Biosciences, South San Francisco, CA, United States
| | - Glenys Thomson
- Department of Integrative Biology, University of California, Berkeley, CA, United States
| | - Henry A Erlich
- Center for Genetics, Children's Hospital & Research Center Oakland, Oakland, CA, United States
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2
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Gomes MB, Rodrigues V, Santos DC, Bôas PRV, Silva DA, de Sousa Azulay RS, Dib SA, Pavin EJ, Fernandes VO, Montenegro Junior RM, Felicio JS, Réa R, Negrato CA, Porto LC. Association between HLA Class II Alleles/Haplotypes and Genomic Ancestry in Brazilian Patients with Type 1 Diabetes: A Nationwide Exploratory Study. Genes (Basel) 2023; 14:genes14050991. [PMID: 37239351 DOI: 10.3390/genes14050991] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
We aimed to identify HLA-DRB1, -DQA1, and -DQB1 alleles/haplotypes associated with European, African, or Native American genomic ancestry (GA) in admixed Brazilian patients with type 1 diabetes (T1D). This exploratory nationwide study enrolled 1599 participants. GA percentage was inferred using a panel of 46 ancestry informative marker-insertion/deletion. Receiver operating characteristic curve analysis (ROC) was applied to identify HLA class II alleles related to European, African, or Native American GA, and showed significant (p < 0.05) accuracy for identifying HLA risk alleles related to European GA: for DRB1*03:01, the area under the curve was (AUC) 0.533; for DRB1*04:01 AUC = 0.558, for DRB1*04:02 AUC = 0.545. A better accuracy for identifying African GA was observed for the risk allele DRB1*09:01AUC = 0.679 and for the protective alleles DRB1*03:02 AUC = 0.649, DRB1*11:02 AUC = 0.636, and DRB1*15:03 AUC = 0.690. Higher percentage of European GA was observed in patients with risk haplotypes (p < 0.05). African GA percentage was higher in patients with protective haplotypes (p < 0.05). Risk alleles and haplotypes were related to European GA and protective alleles/haplotypes to African GA. Future studies with other ancestry markers are warranted to fill the gap in knowledge regarding the genetic origin of T1D in highly admixed populations such as that found in Brazil.
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Affiliation(s)
- Marília Brito Gomes
- Department of Internal Medicine, Diabetes Unit, Rio de Janeiro State University (UERJ), Rio de Janeiro 20950-003, Brazil
| | - Vandilson Rodrigues
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís 65080-805, Brazil
| | - Deborah Conte Santos
- Department of Internal Medicine, Diabetes Unit, Rio de Janeiro State University (UERJ), Rio de Janeiro 20950-003, Brazil
| | - Paulo Ricardo Villas Bôas
- Histocompatibility and Cryopreservation Laboratory (HLA), Rio de Janeiro State University (UERJ), Rio de Janeiro 20950-003, Brazil
| | - Dayse A Silva
- DNA Diagnostic Laboratory (LDD), Rio de Janeiro State University (UERJ), Rio de Janeiro 20550-900, Brazil
| | - Rossana Santiago de Sousa Azulay
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís 65080-805, Brazil
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), São Luís 65020-070, Brazil
| | - Sergio Atala Dib
- Endocrinology Division, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
| | - Elizabeth João Pavin
- Endocrinology Division, School of Medical Sciences, University of Campinas (UNICAMP), São Paulo 13083-970, Brazil
| | - Virgínia Oliveira Fernandes
- Department of Clinical Medicine, Federal University of Ceará (UFC), Fortaleza 60430-275, Brazil
- Department of Community Health, Federal University of Ceará (UFC), Fortaleza 60430-275, Brazil
- Clinical Research Unit, Walter Cantídio University Hospital, Federal University of Ceará (UFC/EBSERH), Fortaleza 60430-372, Brazil
| | - Renan Magalhães Montenegro Junior
- Department of Clinical Medicine, Federal University of Ceará (UFC), Fortaleza 60430-275, Brazil
- Department of Community Health, Federal University of Ceará (UFC), Fortaleza 60430-275, Brazil
- Clinical Research Unit, Walter Cantídio University Hospital, Federal University of Ceará (UFC/EBSERH), Fortaleza 60430-372, Brazil
| | - João Soares Felicio
- Endocrinology Division, João de Barros Barreto University Hospital, Federal University of Pará (UFPA), Belém 66073-000, Brazil
| | - Rosangela Réa
- Endocrinology Unit, Federal University of Paraná (UFPR), Curitiba 80060-900, Brazil
| | - Carlos Antonio Negrato
- Medical Doctor Program, School of Dentistry, University of São Paulo (USP), Bauru 17012-901, Brazil
| | - Luís Cristóvão Porto
- Histocompatibility and Cryopreservation Laboratory (HLA), Rio de Janeiro State University (UERJ), Rio de Janeiro 20950-003, Brazil
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Pilli D, Zou A, Dawes R, Lopez JA, Tea F, Liyanage G, Lee FX, Merheb V, Houston SD, Pillay A, Jones HF, Ramanathan S, Mohammad S, Kelleher AD, Alexander SI, Dale RC, Brilot F. Pro-inflammatory dopamine-2 receptor-specific T cells in paediatric movement and psychiatric disorders. Clin Transl Immunology 2020; 9:e1229. [PMID: 33425355 PMCID: PMC7780098 DOI: 10.1002/cti2.1229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/09/2020] [Accepted: 11/29/2020] [Indexed: 12/13/2022] Open
Abstract
Objectives A dysregulated inflammatory response against the dopamine‐2 receptor (D2R) has been implicated in movement and psychiatric disorders. D2R antibodies were previously reported in a subset of these patients; however, the role of T cells in these disorders remains unknown. Our objective was to identify and characterise pro‐inflammatory D2R‐specific T cells in movement and psychiatric disorders. Methods Blood from paediatric patients with movement and psychiatric disorders of suspected autoimmune and neurodevelopmental aetiology (n = 24) and controls (n = 16) was cultured in vitro with a human D2R peptide library, and D2R‐specific T cells were identified by flow cytometric quantification of CD4+CD25+CD134+ T cells. Cytokine secretion was analysed using a cytometric bead array and ELISA. HLA genotypes were examined in D2R‐specific T‐cell‐positive patients. D2R antibody seropositivity was determined using a flow cytometry live cell‐based assay. Results Three immunodominant regions of D2R, amino acid (aa)121–131, aa171–181 and aa396–416, specifically activated CD4+ T cells in 8/24 patients. Peptides corresponding to these regions were predicted to bind with high affinity to the HLA of the eight positive patients and had also elicited the secretion of pro‐inflammatory cytokines IL‐2, IFN‐ γ, TNF, IL‐6, IL‐17A and IL‐17F. All eight patients were seronegative for D2R antibodies. Conclusion Autoreactive D2R‐specific T cells and a pro‐inflammatory Th1 and Th17 cytokine profile characterise a subset of paediatric patients with movement and psychiatric disorders, further underpinning the theory of immune dysregulation in these disorders. These findings offer new perspectives into the neuroinflammatory mechanisms of movement and psychiatric disorders and can influence patient diagnosis and treatment.
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Affiliation(s)
- Deepti Pilli
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia.,Discipline of Child and Adolescent Health Faculty of Medicine and Health The University of Sydney Sydney NSW Australia
| | - Alicia Zou
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia.,Discipline of Child and Adolescent Health Faculty of Medicine and Health The University of Sydney Sydney NSW Australia
| | - Ruebena Dawes
- Discipline of Child and Adolescent Health Faculty of Medicine and Health The University of Sydney Sydney NSW Australia.,Genomic Medicine Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia
| | - Joseph A Lopez
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia.,Discipline of Child and Adolescent Health Faculty of Medicine and Health The University of Sydney Sydney NSW Australia
| | - Fiona Tea
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia.,Discipline of Child and Adolescent Health Faculty of Medicine and Health The University of Sydney Sydney NSW Australia
| | - Ganesha Liyanage
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia.,School of Medical Sciences Discipline of Applied Medical Science Faculty of Medicine and Health The University of Sydney Sydney NSW Australia
| | - Fiona Xz Lee
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia
| | - Vera Merheb
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia
| | - Samuel D Houston
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia.,School of Biomedical Engineering The University of Sydney Sydney NSW Australia
| | - Aleha Pillay
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia
| | - Hannah F Jones
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia.,Discipline of Child and Adolescent Health Faculty of Medicine and Health The University of Sydney Sydney NSW Australia
| | - Sudarshini Ramanathan
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia.,Discipline of Child and Adolescent Health Faculty of Medicine and Health The University of Sydney Sydney NSW Australia
| | - Shekeeb Mohammad
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia.,Discipline of Child and Adolescent Health Faculty of Medicine and Health The University of Sydney Sydney NSW Australia
| | | | - Stephen I Alexander
- Discipline of Child and Adolescent Health Faculty of Medicine and Health The University of Sydney Sydney NSW Australia.,Centre for Kidney Research Children's Hospital at Westmead Sydney NSW Australia
| | - Russell C Dale
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia.,Discipline of Child and Adolescent Health Faculty of Medicine and Health The University of Sydney Sydney NSW Australia.,Brain and Mind Centre The University of Sydney Sydney NSW Australia
| | - Fabienne Brilot
- Brain Autoimmunity Group Kids Neuroscience Centre Kids Research at the Children's Hospital at Westmead Sydney NSW Australia.,Discipline of Child and Adolescent Health Faculty of Medicine and Health The University of Sydney Sydney NSW Australia.,School of Medical Sciences Discipline of Applied Medical Science Faculty of Medicine and Health The University of Sydney Sydney NSW Australia.,Brain and Mind Centre The University of Sydney Sydney NSW Australia
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4
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Nemat-Gorgani N, Edinur HA, Hollenbach JA, Traherne JA, Dunn PPJ, Chambers GK, Parham P, Norman PJ. KIR diversity in Māori and Polynesians: populations in which HLA-B is not a significant KIR ligand. Immunogenetics 2014; 66:597-611. [PMID: 25139336 DOI: 10.1007/s00251-014-0794-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/04/2014] [Indexed: 12/25/2022]
Abstract
HLA class I molecules and killer cell immunoglobulin-like receptors (KIR) form a diverse system of ligands and receptors that individualize human immune systems in ways that improve the survival of individuals and populations. Human settlement of Oceania by island-hopping East and Southeast Asian migrants started ~3,500 years ago. Subsequently, New Zealand was reached ~750 years ago by ancestral Māori. To examine how this history impacted KIR and HLA diversity, and their functional interaction, we defined at high resolution the allelic and haplotype diversity of the 13 expressed KIR genes in 49 Māori and 34 Polynesians. Eighty KIR variants, including four 'new' alleles, were defined, as were 35 centromeric and 22 telomeric KIR region haplotypes, which combine to give >50 full-length KIR haplotypes. Two new and divergent variant KIR form part of a telomeric KIR haplotype, which appears derived from Papua New Guinea and was probably obtained by the Asian migrants en route to Polynesia. Māori and Polynesian KIR are very similar, but differ significantly from African, European, Japanese, and Amerindian KIR. Māori and Polynesians have high KIR haplotype diversity with corresponding allotype diversity being maintained throughout the KIR locus. Within the population, each individual has a unique combination of HLA class I and KIR. Characterizing Māori and Polynesians is a paucity of HLA-B allotypes recognized by KIR. Compensating for this deficiency are high frequencies (>50 %) of HLA-A allotypes recognized by KIR. These HLA-A allotypes are ones that modern humans likely acquired from archaic humans at a much earlier time.
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Affiliation(s)
- Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
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5
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Edinur H, Dunn P, Hammond L, Selwyn C, Brescia P, Askar M, Reville P, Velickovic Z, Lea R, Chambers G. HLA and MICA polymorphism in Polynesians and New Zealand Maori: Implications for ancestry and health. Hum Immunol 2013; 74:1119-29. [DOI: 10.1016/j.humimm.2013.06.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/14/2013] [Accepted: 06/07/2013] [Indexed: 11/27/2022]
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6
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Edinur HA, Dunn PPJ, Hammond L, Selwyn C, Velickovic ZM, Lea RA, Chambers GK. Using HLA loci to inform ancestry and health in Polynesian and Maori populations. ACTA ACUST UNITED AC 2012; 80:509-22. [DOI: 10.1111/tan.12026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- H. A. Edinur
- School of Biological Sciences; Victoria University of Wellington; Wellington; New Zealand
| | | | - L. Hammond
- New Zealand Blood Service; Auckland; New Zealand
| | - C. Selwyn
- New Zealand Blood Service; Auckland; New Zealand
| | - Z. M. Velickovic
- Molecular Genetics, Tissue Typing; Australian Red Cross Blood Service; Sydney; Australia
| | - R. A. Lea
- School of Medical Sciences; Griffith University; Gold Coast; Australia
| | - G. K. Chambers
- School of Biological Sciences; Victoria University of Wellington; Wellington; New Zealand
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7
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Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies. Hum Immunol 2008; 69:443-64. [PMID: 18638659 DOI: 10.1016/j.humimm.2008.05.001] [Citation(s) in RCA: 262] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 05/03/2008] [Accepted: 05/07/2008] [Indexed: 12/21/2022]
Abstract
This paper presents a meta-analysis of high-resolution human leukocyte antigen (HLA) allele frequency data describing 497 population samples. Most of the datasets were compiled from studies published in eight journals from 1990 to 2007; additional datasets came from the International Histocompatibility Workshops and from the AlleleFrequencies.net database. In all, these data represent approximately 66,800 individuals from throughout the world, providing an opportunity to observe trends that may not have been evident at the time the data were originally analyzed, especially with regard to the relative importance of balancing selection among the HLA loci. Population genetic measures of allele frequency distributions were summarized across populations by locus and geographic region. A role for balancing selection maintaining much of HLA variation was confirmed. Further, the breadth of this meta-analysis allowed the ranking of the HLA loci, with DQA1 and HLA-C showing the strongest balancing selection and DPB1 being compatible with neutrality. Comparisons of the allelic spectra reported by studies since 1990 indicate that most of the HLA alleles identified since 2000 are very-low-frequency alleles. The literature-based allele-count data, as well as maps summarizing the geographic distributions for each allele, are available online.
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8
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Su X, Bi L, Hai R, Qimuge S, Ying M, Bahring S, Gong M. HLA-DPB1, -DRB1, and -DQB1 polymorphism defined in Ewenki ethnic minority of China Inner Mongolia Autonomous Region. Int J Immunogenet 2007; 34:435-40. [DOI: 10.1111/j.1744-313x.2007.00718.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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