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Hosseini E, Sarraf Kazerooni E, Azarkeivan A, Sharifi Z, Shahabi M, Ghasemzadeh M. HLA-E*01:01 allele is associated with better response to anti-HCV therapy while homozygous status for HLA-E*01:03 allele increases the resistance to anti-HCV treatments in frequently transfused thalassemia patients. Hum Immunol 2022; 83:556-563. [PMID: 35570067 DOI: 10.1016/j.humimm.2022.04.010] [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: 12/28/2021] [Revised: 04/23/2022] [Accepted: 04/24/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND HLA-E binding to NKG2A/CD94 induces inhibitory signals that modulate NK cells cytotoxicity against infected targets. HCV-derived peptides stabilize HLA-E molecule that favours its higher expression. However, HLA-E stability and expression vary in different genotypes where the presence of HLA-E*01:03 allele is associated with higher HLA-E expression on targets that enhances NK cells inhibition and increases the chance of virus to escape from innate immune system. Here, we aimed to investigate whether HLA-E polymorphism affects HCV infection status or its treatment in major thalassemia patients who are more vulnerable to hepatitis C. METHODS AND MATERIALS Study included 89 cases of major thalassemia positive for HCV-antibody; of those 17 patients were negative for HCV-PCR (spontaneously cleared) and 72 patients were HCV-PCR positive (persistent hepatitis under different anti-viral treatment). 16 major thalassemia patients without hepatitis, negative for HCV-antibody were also considered as patients control group. Genomic DNAs extracted from whole bloods were genotyped for HLA-E locus using a sequence specific primer-PCR strategy. RESULTS In thalassemia patients, HLA-E*01:03 allele increased susceptibility to HCV infection [p = 0.02; 4.74(1.418-15.85)]. In addition, HLA-E*01:03/*01:03 genotype predicted more resistance to HCV treatment compared to other genotypes [p = 0.037; 3.5(1.1-11.4)]. In other words, we found that the presence of HLA-E*01:01 allele favors better response to anti-HCV therapy [p = 0.037; 3.5(1.1-11.4)]. CONCLUSION From a mechanistic point of view, the associations between HLA-E polymorphisms and susceptibility to HCV infection or its therapeutic resistance in thalassemia patients may suggest potential roles for the innate and adaptive immune responses to this infection, which are manifested by the acts of HLA-E - NKG2A/CD94 axis in the modulation of NK cell inhibitory function as well as HLA-E associated CD8+ T cell cytolytic activity against HCV, respectively. Notably, from a clinical point of view, paying attention to these associations may not only be useful in increasing the effectiveness of current anti-HCV regimens comprising direct acting antivirals (DAAs) in more complicated patients, but may also suggest antiviral prophylaxis for patients more vulnerable to HCV infection.
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Affiliation(s)
- Ehteramolsadat Hosseini
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Ehsan Sarraf Kazerooni
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Azita Azarkeivan
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran; Iranian Blood Transfusion Organization, Thalassemia Clinic, Tehran, Iran
| | - Zohreh Sharifi
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Majid Shahabi
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Mehran Ghasemzadeh
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran.
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Xu YP, Sun LY, Wang SX, Hong WX. Correlation of Human Leukocyte Antigen-E Genomic Polymorphism with Leukemia and Functional Study of Human Leukocyte Antigen-E Different Type Promoters. DNA Cell Biol 2022; 41:235-244. [PMID: 34986028 DOI: 10.1089/dna.2021.0483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human leukocyte antigen (HLA)-E is one of the least polymorphic nonclassical major histocompatibility complex (MHC) I genes; its nucleotide variability can affect immune response. In this study, we assess the correlation between HLA-E polymorphism and leukemia and further study the transcriptional activity of promoter variation at nucleotide position-26. A total of 142 healthy blood donors and 111 leukemia patients were collected. The genomic sequence of HLA-E was amplified by high-fidelity reaction system and identified by Sanger and cloning sequencing. The dual luciferase reporter gene assay was used to detect the transcription activity of promoter variation at nucleotide position-26. In the HLA-E genomic sequence results, a total of 16 alleles and 32 genotypes were detected; the HLA-E*01:01:01:06 allele had a significantly lower frequency in leukemia patients than in healthy participants (p = 0.026 < 0.05). And the HLA-E*01:03:02:01, *01:03:02:01 genotype showed the greatest difference in frequency between the two groups of participants (p = 0.028 < 0.05). Eight HLA-E alleles were first reported worldwide in Chinese individuals. The results of the dual luciferase reporter gene experiment showed that the transcription activity of the mutant-type promoter (HLA-E*01:01:01:06 with "T" allele at nucleotide position-26) was significantly lower compared with the wild-type promoter (HLA-E*01:01:01:01 with "G" allele at nucleotide position-26) (p = 0.0242 < 0.05). HLA-E*01:01:01:06 allele has a protective effect against leukemia through decreasing transcription activity by "T" variation at nucleotide position-26.
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Affiliation(s)
- Yun-Ping Xu
- Shenzhen Institution of Transfusion Medicine, Shenzhen Blood Center, Shenzhen, Guangdong, China
| | - Li-Yan Sun
- Shenzhen Institution of Transfusion Medicine, Shenzhen Blood Center, Shenzhen, Guangdong, China.,Department of Transfusion Medicine, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Song-Xing Wang
- Shenzhen Institution of Transfusion Medicine, Shenzhen Blood Center, Shenzhen, Guangdong, China
| | - Wen-Xu Hong
- Shenzhen Institution of Transfusion Medicine, Shenzhen Blood Center, Shenzhen, Guangdong, China
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3
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Duygu B, Olieslagers TI, Groeneweg M, Voorter CEM, Wieten L. HLA Class I Molecules as Immune Checkpoints for NK Cell Alloreactivity and Anti-Viral Immunity in Kidney Transplantation. Front Immunol 2021; 12:680480. [PMID: 34295330 PMCID: PMC8290519 DOI: 10.3389/fimmu.2021.680480] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022] Open
Abstract
Natural killer (NK) cells are innate lymphocytes that can kill diseased- or virally-infected cells, mediate antibody dependent cytotoxicity and produce type I immune-associated cytokines upon activation. NK cells also contribute to the allo-immune response upon kidney transplantation either by promoting allograft rejection through lysis of cells of the transplanted organ or by promoting alloreactive T cells. In addition, they protect against viral infections upon transplantation which may be especially relevant in patients receiving high dose immune suppression. NK cell activation is tightly regulated through the integrated balance of signaling via inhibitory- and activating receptors. HLA class I molecules are critical regulators of NK cell activation through the interaction with inhibitory- as well as activating NK cell receptors, hence, HLA molecules act as critical immune checkpoints for NK cells. In the current review, we evaluate how NK cell alloreactivity and anti-viral immunity are regulated by NK cell receptors belonging to the KIR family and interacting with classical HLA class I molecules, or by NKG2A/C and LILRB1/KIR2DL4 engaging non-classical HLA-E or -G. In addition, we provide an overview of the methods to determine genetic variation in these receptors and their HLA ligands.
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Affiliation(s)
- Burcu Duygu
- Department of Transplantation Immunology, Maastricht University Medical Center, Maastricht, Netherlands.,GROW, School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Timo I Olieslagers
- Department of Transplantation Immunology, Maastricht University Medical Center, Maastricht, Netherlands.,GROW, School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Mathijs Groeneweg
- Department of Transplantation Immunology, Maastricht University Medical Center, Maastricht, Netherlands.,GROW, School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Christina E M Voorter
- Department of Transplantation Immunology, Maastricht University Medical Center, Maastricht, Netherlands.,GROW, School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Lotte Wieten
- Department of Transplantation Immunology, Maastricht University Medical Center, Maastricht, Netherlands.,GROW, School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
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4
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Williams RC, Koroglu C, Knowler WC, Shuldiner AR, Gosalia N, Van Hout C, Hanson RL, Bogardus C, Baier LJ. Next generation sequencing for HLA loci in full heritage Pima Indians of Arizona, Part II: HLA-A, -B, and -C with selected non-classical loci at 4-field resolution from whole genome sequences. Hum Immunol 2021; 82:385-403. [PMID: 33875299 DOI: 10.1016/j.humimm.2021.03.013] [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: 04/16/2019] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 11/19/2022]
Abstract
While the samples and data from the Pima Indians of the Gila River Indian Community have been included in many international HLA workshops and conferences and have been the focus of numerous population reports and the source of novel alleles at the classical HLA loci, they have not been studied for the non-classical loci. In order to expand our HLA-disease association studies, we typed over 300 whole genome sequences from full Pima heritage members, controlled for first degree relationship, and employed recently developed computer algorithms to resolve HLA alleles. Both classical-HLA-A, -B, and -C- and non-classical- HLA-E, -F, -G, -J, -L, -W, -Y, -DPA2, -DPB2, -DMA, -DMB, -DOA, -DRB2, -DRB9, TAP1- loci were typed at the 4-field level of resolution. We present allele and selected haplotype frequencies, test the genotype distributions for population structure, discuss the issues that are created for tests of Hardy-Weinberg equilibrium over the four sample spaces of high resolution HLA typing, and address the implications for the evolution of non-classical pseudogenes that are no longer expressed in a phenotype subject to natural selection.
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Affiliation(s)
- Robert C Williams
- Phoenix Epidemiology and Clinical Research Branch, NIH, NIDDK, Phoenix 85014, AZ, United States.
| | - Cigdem Koroglu
- Phoenix Epidemiology and Clinical Research Branch, NIH, NIDDK, Phoenix 85014, AZ, United States
| | - William C Knowler
- Phoenix Epidemiology and Clinical Research Branch, NIH, NIDDK, Phoenix 85014, AZ, United States
| | | | - Nehal Gosalia
- Regeneron Genetics Center, Tarrytown 10591, NY, United States
| | | | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, NIH, NIDDK, Phoenix 85014, AZ, United States
| | - Clifton Bogardus
- Phoenix Epidemiology and Clinical Research Branch, NIH, NIDDK, Phoenix 85014, AZ, United States
| | - Leslie J Baier
- Phoenix Epidemiology and Clinical Research Branch, NIH, NIDDK, Phoenix 85014, AZ, United States
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5
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Xu YP, Wieten L, Wang SX, Cai Y, Olieslagers T, Zhang L, He LM, Tilanus MGJ, Hong WX. Clinical significance of HLA-E genotype and surface/soluble expression levels between healthy individuals and patients with acute leukemia. Leuk Lymphoma 2019; 60:208-215. [PMID: 29969046 DOI: 10.1080/10428194.2018.1474521] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 04/03/2018] [Accepted: 04/30/2018] [Indexed: 01/09/2023]
Abstract
Human leukocyte antigen (HLA)-E is a nonclassical HLA molecule with limited polymorphisms. Genotype frequency and expression of HLA-E were examined here for the first time in acute leukemia patients and healthy controls. The frequency of HLA-E*01:03/*01:03 individuals was significantly higher (p = .008, OR = 1.845), while the frequency of HLA-E*01:01/*01:01 individuals was much lower in the patient group (p = .002, OR = .363) than in control group. The surface expression on HLA-E*01:03/*01:03 individuals was found to be significantly higher than on HLA-E*01:01/*01:01 individuals in both of acute leukemia and control groups, but no significant difference was observed between the corresponding genotypes in two groups. However, the level of expression of soluble HLA-E is significantly higher in patients than in the control group, but there was no genotype-specific expression in either group. These findings indicate that soluble HLA-E secretion and HLA-E*01:03/*01:03 genotype that brings higher surface expression might play important roles in the mechanisms underlying tumor escape in acute leukemia.
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Affiliation(s)
- Yun-Ping Xu
- a Immunogenetics Laboratory , Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center , Shenzhen , China
- b Transplantation Immunology, Tissue Typing Laboratory , Maastricht University Medical Center , Maastricht , The Netherlands
| | - Lotte Wieten
- b Transplantation Immunology, Tissue Typing Laboratory , Maastricht University Medical Center , Maastricht , The Netherlands
| | - Song-Xing Wang
- a Immunogenetics Laboratory , Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center , Shenzhen , China
| | - Yun Cai
- c Department of Hematopathology , Shenzhen Second People's Hospital , Shenzhen , China
| | - Timo Olieslagers
- b Transplantation Immunology, Tissue Typing Laboratory , Maastricht University Medical Center , Maastricht , The Netherlands
| | - Li Zhang
- a Immunogenetics Laboratory , Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center , Shenzhen , China
| | - Liu-Mei He
- a Immunogenetics Laboratory , Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center , Shenzhen , China
| | - Marce G J Tilanus
- b Transplantation Immunology, Tissue Typing Laboratory , Maastricht University Medical Center , Maastricht , The Netherlands
| | - Wen-Xu Hong
- a Immunogenetics Laboratory , Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center , Shenzhen , China
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Sonon P, Sadissou I, Tokplonou L, M'po KKG, Glitho SSC, Agniwo P, Ibikounlé M, Massaro JD, Massougbodji A, Moreau P, Sabbagh A, Mendes-Junior CT, Moutairou KA, Castelli EC, Courtin D, Donadi EA. HLA-G, -E and -F regulatory and coding region variability and haplotypes in the Beninese Toffin population sample. Mol Immunol 2018; 104:108-127. [PMID: 30448608 DOI: 10.1016/j.molimm.2018.08.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/16/2018] [Indexed: 12/17/2022]
Abstract
HLA-G/E/F genes exhibit immunomodulatory properties and are expressed in placenta. Little attention has been devoted to the study of these genes in sub-Saharan African populations, which are yet the most diverse. To fill this gap, we evaluated the complete gene variability, approximately 5.1 kb for HLA-G (n = 149), 7.7 kb for HLA-E (n = 150) and 6.2 kb for HLA-F (n = 152) in the remote Beninese Toffin population, using massive parallel sequencing. Overall, 96, 37 and 68 variable sites were detected along the entire HLA-G, -E and -F, respectively, arranged into region-specific haplotypes; i.e., promoter haplotypes (16, 19, and 15 respectively), coding haplotypes (19, 15, and 29 respectively), 3' untranslated region (3'UTR) haplotypes (12, 7 and 2, respectively) and extended haplotypes (33, 31 and 32 respectively). All promoter/coding/3'UTR haplotypes followed the patterns already described in worldwide populations. HLA-E was the most conserved, exhibiting mainly two full-length encoded-molecules (E*01:01 and E*01:03), followed by HLA-F, three full-length proteins (F*01:01, F*01:02 and F*01:03) and HLA-G, four proteins: three full-length (G*01:01, G*01:03 and G*01:04) and one truncated (G*01:05N). Although HLA-G/E/F alleles in the Toffin population were the most frequently observed worldwide, the frequencies of the coding haplotypes were closely similar to those described for other African populations (Guinea-Conakry and Burkina-Faso), when compared to non-African ones (Brazilian), indicating that variable sites along these genes were present in Africa before human dispersion.
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Affiliation(s)
- Paulin Sonon
- Laboratório de Biologia Molecular, Universidade de São Paulo, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Estado de São Paulo, SP, Brazil.
| | - Ibrahim Sadissou
- Laboratório de Biologia Molecular, Universidade de São Paulo, Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Estado de São Paulo, SP, 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, Benin; UMR 216 MERIT, IRD, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Université d'Abomey-Calavi, Cotonou, Benin.
| | - 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, Benin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin.
| | - 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, Benin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin.
| | - 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, Benin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin.
| | - Moudachirou Ibikounlé
- Université d'Abomey-Calavi, Cotonou, Benin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin.
| | - Juliana Doblas Massaro
- Laboratório de Biologia Molecular, Universidade de São Paulo, Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Estado de São Paulo, SP, Brazil.
| | - 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, Benin.
| | - 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-Immunologie, Hôpital Saint-Louis, Paris, France; Université Paris-Diderot, Sorbonne Paris-Cité, UMR_E5, Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France.
| | - Audrey Sabbagh
- UMR 216 MERIT, IRD, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, State of São Paulo, Brazil.
| | - Kabirou A Moutairou
- Laboratoire de Biologie et Physiologie Cellulaire, Université d'Abomey-Calavi, Cotonou, Benin.
| | - Erick C Castelli
- São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (UNIPEX), School of Medicine, Botucatu, State of São Paulo, Brazil; São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, State of São Paulo, Brazil.
| | - David Courtin
- UMR 216 MERIT, IRD, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - Eduardo A Donadi
- Laboratório de Biologia Molecular, Universidade de São Paulo, Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Estado de São Paulo, SP, Brazil.
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Ramalho J, Veiga-Castelli LC, Donadi EA, Mendes-Junior CT, Castelli EC. HLA-E regulatory and coding region variability and haplotypes in a Brazilian population sample. Mol Immunol 2017; 91:173-184. [PMID: 28946074 DOI: 10.1016/j.molimm.2017.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/08/2017] [Accepted: 09/13/2017] [Indexed: 12/30/2022]
Abstract
The HLA-E gene is characterized by low but wide expression on different tissues. HLA-E is considered a conserved gene, being one of the least polymorphic class I HLA genes. The HLA-E molecule interacts with Natural Killer cell receptors and T lymphocytes receptors, and might activate or inhibit immune responses depending on the peptide associated with HLA-E and with which receptors HLA-E interacts to. Variable sites within the HLA-E regulatory and coding segments may influence the gene function by modifying its expression pattern or encoded molecule, thus, influencing its interaction with receptors and the peptide. Here we propose an approach to evaluate the gene structure, haplotype pattern and the complete HLA-E variability, including regulatory (promoter and 3'UTR) and coding segments (with introns), by using massively parallel sequencing. We investigated the variability of 420 samples from a very admixed population such as Brazilians by using this approach. Considering a segment of about 7kb, 63 variable sites were detected, arranged into 75 extended haplotypes. We detected 37 different promoter sequences (but few frequent ones), 27 different coding sequences (15 representing new HLA-E alleles) and 12 haplotypes at the 3'UTR segment, two of them presenting a summed frequency of 90%. Despite the number of coding alleles, they encode mainly two different full-length molecules, known as E*01:01 and E*01:03, which corresponds to about 90% of all. In addition, differently from what has been previously observed for other non classical HLA genes, the relationship among the HLA-E promoter, coding and 3'UTR haplotypes is not straightforward because the same promoter and 3'UTR haplotypes were many times associated with different HLA-E coding haplotypes. This data reinforces the presence of only two main full-length HLA-E molecules encoded by the many HLA-E alleles detected in our population sample. In addition, this data does indicate that the distal HLA-E promoter is by far the most variable segment. Further analyses involving the binding of transcription factors and non-coding RNAs, as well as the HLA-E expression in different tissues, are necessary to evaluate whether these variable sites at regulatory segments (or even at the coding sequence) may influence the gene expression profile.
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Affiliation(s)
- Jaqueline Ramalho
- São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (UNIPEX), School of Medicine, Botucatu, State of São Paulo, Brazil
| | - Luciana C Veiga-Castelli
- School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, State of São Paulo, Brazil
| | - Eduardo A Donadi
- School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, State of São Paulo, Brazil
| | - Celso T Mendes-Junior
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Erick C Castelli
- São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (UNIPEX), School of Medicine, Botucatu, State of São Paulo, Brazil; São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, State of São Paulo, Brazil.
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8
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Castelli EC, Gerasimou P, Paz MA, Ramalho J, Porto IO, Lima TH, Souza AS, Veiga-Castelli LC, Collares CV, Donadi EA, Mendes-Junior CT, Costeas P. HLA-G variability and haplotypes detected by massively parallel sequencing procedures in the geographicaly distinct population samples of Brazil and Cyprus. Mol Immunol 2017; 83:115-126. [DOI: 10.1016/j.molimm.2017.01.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/18/2017] [Accepted: 01/20/2017] [Indexed: 12/11/2022]
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9
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Olieslagers TI, Voorter CEM, Groeneweg M, Xu Y, Wieten L, Tilanus MGJ. New insights in HLA-E polymorphism by refined analysis of the full-length gene. HLA 2017; 89:143-149. [PMID: 28127896 DOI: 10.1111/tan.12965] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 12/02/2016] [Accepted: 01/05/2017] [Indexed: 01/25/2023]
Abstract
BACKGROUND Human leukocyte antigen (HLA)-E is a non-classical HLA class I molecule that plays a role in both the innate and the adaptive immune response through interaction with receptors on natural killer- and T-cells. The HLA-E gene is characterized by limited polymorphism compared with the classical HLA loci on chromosome 6. At the start of this study, only 13 variable sites had been identified (IPD-IMGT/HLA Database v3.18.0). While most previous studies focused on polymorphism in exons 2 and 3 or specific gene regions, polymorphism in the other exons and introns could influence protein expression and function as well. Studies that investigate extended HLA-E polymorphism are therefore needed to better understand the functional relevance of HLA-E in health and disease. AIMS The aim of this study was to examine the variability of the full-length HLA-E gene region in individuals originating from different populations. MATERIALS AND METHODS/RESULTS A total of 7 new HLA-E alleles were identified using full-length HLA-E sequencing of 123 individuals from Asian, Dutch or Hunan Han origin. Furthermore, genome variation analysis of the third phase of the 1000 genomes database showed 107 new variable sites in 2504 individuals originating from 26 different populations. DISCUSSION AND CONCLUSION Our study demonstrates that the nucleotide variability of the HLA-E gene is much higher than previously known, albeit in only a limited number of individuals. Overall only 2 variants, HLA-E*01:01 and *01:03, are frequently present worldwide, suggesting that balancing selection is acting on HLA-E.
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Affiliation(s)
- T I Olieslagers
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - C E M Voorter
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - M Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Y Xu
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, China
| | - L Wieten
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - M G J Tilanus
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
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10
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Gelmini GF, Costa CH, Nardi FDS, Wowk PF, Mattar SB, Schuffner A, Bicalho MDG, Roxo VMMS. Is HLA-E a possible genetic marker relevant for natural conception? Am J Reprod Immunol 2016; 76:439-442. [PMID: 27714943 DOI: 10.1111/aji.12587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/13/2016] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND HLA-E products, class Ib human leukocyte antigens, act in the immunology of human reproduction as modulators of the maternal immune system during pregnancy. AIMS To evaluate HLA-E role in the establishment of a viable pregnancy. MATERIALS & METHODS HLA-E was genotyped by sequence-based typing (SBT) and analyzed for specific polymorphisms, comparing couples who underwent assisted reproduction treatment (ART) and fertile control couples. RESULTS There was a significant difference in HLA-E allele and genotype distributions between ART couples and control couples. The allele HLA-E*01:03 was observed in 63.2% of ART men and in 35.1% of fertile men (P = 0.0032). CONCLUSION These results suggest that HLA-E allelic variants may play a role in the modulation of immune responses in the context of the inability of natural conception and establishment of a viable pregnancy.
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Affiliation(s)
- Georgia Fernanda Gelmini
- Laboratório de Imunogenética e Histocompatibilidade do Departamento de Genética da Universidade Federal do Paraná (UFPR), Curitiba (PR), Brasil
| | - Cynthia Hernandes Costa
- Laboratório de Imunogenética e Histocompatibilidade do Departamento de Genética da Universidade Federal do Paraná (UFPR), Curitiba (PR), Brasil
| | - Fabiola da Silva Nardi
- Laboratório de Imunogenética e Histocompatibilidade do Departamento de Genética da Universidade Federal do Paraná (UFPR), Curitiba (PR), Brasil
| | - Pryscilla Fanini Wowk
- Laboratório de Imunogenética e Histocompatibilidade do Departamento de Genética da Universidade Federal do Paraná (UFPR), Curitiba (PR), Brasil
- Instituto Carlos Chagas, ICC-Fiocruz-PR, Curitiba (PR), Brasil
| | - Sibelle Botogosque Mattar
- Laboratório de Imunogenética e Histocompatibilidade do Departamento de Genética da Universidade Federal do Paraná (UFPR), Curitiba (PR), Brasil
- Instituto Carlos Chagas, ICC-Fiocruz-PR, Curitiba (PR), Brasil
| | | | - Maria da Graça Bicalho
- Laboratório de Imunogenética e Histocompatibilidade do Departamento de Genética da Universidade Federal do Paraná (UFPR), Curitiba (PR), Brasil
| | - Valéria Maria Munhoz Sperandio Roxo
- Laboratório de Imunogenética e Histocompatibilidade do Departamento de Genética da Universidade Federal do Paraná (UFPR), Curitiba (PR), Brasil
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11
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Di Cristofaro J, Pelardy M, Loundou A, Basire A, Gomez C, Chiaroni J, Thomas P, Reynaud-Gaubert M, Picard C. HLA-E(⁎)01:03 Allele in Lung Transplant Recipients Correlates with Higher Chronic Lung Allograft Dysfunction Occurrence. J Immunol Res 2016; 2016:1910852. [PMID: 27493971 PMCID: PMC4967441 DOI: 10.1155/2016/1910852] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/08/2016] [Accepted: 05/19/2016] [Indexed: 11/24/2022] Open
Abstract
Lung transplantation (LTx) is a valid therapeutic option for selected patients with end-stage lung disease. HLA-E seems to play a major role in the immune response to different viral infections and to affect transplantation outcome, in Hematopoietic Stem Cell Transplantation, for example. Two nonsynonymous alleles, HLA-E(⁎)01:01 and HLA-E(⁎)01:03, have functional differences, involving relative peptide affinity, cell surface expression, and potential lytic activity of NK cells. The aim of this retrospective study was to determine the impact of these two alleles for LTx recipients on anti-HLA alloimmunization risk, overall survival, and chronic rejection (CLAD). HLA-E was genotyped in 119 recipients who underwent LTx from 1998 to 2010 in a single transplantation center. In univariate analysis, both HLA-E homozygous states were associated with impaired overall survival compared to heterozygous HLA-E alleles (p = 0.01). In multivariate analysis, HLA-E(⁎)01:03 allele showed increased CLAD occurrence when compared to homozygous HLA-E(⁎)01:01 status (HR: 3.563 (CI 95%, 1.016-12), p = 0.047). HLA-E allele did not affect pathogen infection or the production of de novo DSA. This retrospective study shows an uninvestigated, deleterious association of HLA-E alleles with LTx and requires verification using a larger cohort.
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Affiliation(s)
| | - Mathieu Pelardy
- Immunogenetics Laboratory, EFS-Alpes Méditerranée, 13005 Marseille, France
| | - Anderson Loundou
- Department of Public Health, EA 3279 Research Unit, Marseille University Hospital, Aix-Marseille University, Marseille, France
| | - Agnès Basire
- Immunogenetics Laboratory, EFS-Alpes Méditerranée, 13005 Marseille, France
| | - Carine Gomez
- Service de Pneumologie, Hôpital Nord, 13015 Marseille, France
| | - Jacques Chiaroni
- CNRS, EFS, ADES UMR 7268, Aix-Marseille Université, 13916 Marseille, France
| | - Pascal Thomas
- Service de Chirurgie Thoracique, Hôpital Nord, 13015 Marseille, France
| | | | - Christophe Picard
- CNRS, EFS, ADES UMR 7268, Aix-Marseille Université, 13916 Marseille, France
- Immunogenetics Laboratory, EFS-Alpes Méditerranée, 13005 Marseille, France
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12
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Prasetyo AA, Dharmawan R, Raharjo I, Hudiyono. Human Leukocyte Antigen-E Alleles are Associated with Hepatitis C Virus, Torque Teno Virus, and Toxoplasma Co-infections but are not Associated with Hepatitis B Virus, Hepatitis D Virus, and GB Virus C Co-infections in Human Immunodeficiency Virus Patients. J Glob Infect Dis 2016; 8:75-81. [PMID: 27293362 PMCID: PMC4879794 DOI: 10.4103/0974-777x.182121] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Context: Data regarding the distribution of Human Leukocyte Antigen (HLA)-E alleles and their association with blood-borne pathogen infections/co-infections are limited for many populations, including Indonesia. Aims: The aim of this study was to analyze the association between HLA-E allelic variants and infection with blood-borne pathogens such as hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), torque teno virus (TTV), GB virus C (GBV-C), and Toxoplasma gondii (T. gondii) in Indonesian Javanese human immunodeficiency virus (HIV) patients. Settings and Design: A total of 320 anti-HIV-positive blood samples were analyzed for HBV, HCV, HDV, TTV, GBV-C, and T. gondii infection status and its association with HLA-E allelic variants. Materials and Methods: Nucleic acid was extracted from plasma samples and used for the molecular detection of HBV DNA, HCV RNA, HDV RNA, TTV DNA, and GBV-C RNA, whereas hepatitis B surface antigen, anti-HCV, immunoglobulin M and G (IgM and IgG) anti-T. gondii were detected through serological testing. The blood samples were genotyped for HLA-E loci using a sequence-specific primer-polymerase chain reaction. Statistical Analysis Used: Either the Chi-square or Fisher's exact test was performed to analyze the frequency of HLA-E alleles and blood-borne pathogen infections in the population. Odds ratios (ORs) were calculated to measure the association between the antibodies found and the participants’ possible risk behaviors. A logistic regression analysis was used to assess the associations. Results: HLA-E*101/0101 was associated with HCV/TTV co-infection (adjusted OR [aOR]: 3.5; 95% confidence interval [CI]: 1.156-10.734; P = 0.027) and IgM/IgG anti-Toxo positivity (aOR: 27.0; 95% CI: 3.626-200.472; P = 0.001). HLA-E*103/0103 was associated with TTV co-infection (aOR: 2.7; 95% CI: 1.509-4.796; P = 0.001). Conclusions: HLA-E alleles in Indonesian Javanese HIV patients were found to be associated with HCV, TTV, and toxoplasma co-infections.
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Affiliation(s)
- Afiono Agung Prasetyo
- A-IGIC (A-Infection, Genomic, Immunology & Cancer) Research Group, Sutami 36A, Surakarta, Indonesia; Department of Microbiology, Faculty of Medicine, Sutami 36A, Surakarta, Indonesia; Center of Biotechnology and Biodiversity Research and Development, Sebelas Maret University, Jl. Ir. Sutami 36A, Surakarta, Indonesia
| | - Ruben Dharmawan
- A-IGIC (A-Infection, Genomic, Immunology & Cancer) Research Group, Sutami 36A, Surakarta, Indonesia; Department of Parasitology, Faculty of Medicine, Surakarta, Indonesia
| | - Irvan Raharjo
- A-IGIC (A-Infection, Genomic, Immunology & Cancer) Research Group, Sutami 36A, Surakarta, Indonesia
| | - Hudiyono
- A-IGIC (A-Infection, Genomic, Immunology & Cancer) Research Group, Sutami 36A, Surakarta, Indonesia; Department of Microbiology, Faculty of Medicine, Sutami 36A, Surakarta, Indonesia; Center of Biotechnology and Biodiversity Research and Development, Sebelas Maret University, Jl. Ir. Sutami 36A, Surakarta, Indonesia
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13
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Douik H, Romdhane NA, Guemira F. Are HLA-E*0103 alleles predictive markers for nasopharyngeal cancer risk? Pathol Res Pract 2016; 212:345-9. [PMID: 26896927 DOI: 10.1016/j.prp.2016.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/26/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is a particular entity of head neck cancer, tightly related to Epstein-Barr virus infection and thus to HLA genes. In this study, we aimed to analyze HLA-E polymorphism in NPC advent and prognosis. 130 unrelated patients with CNP and 180 unrelated and healthy controls were included in our study. HLA-E genotyping was performed by PCR/RFLP method; SPSS (13.0) was used for statistical analysis, and survival curbs were established with the "Kaplan-Meier" method (Log Rank<0.05). RESULTS We found a significant difference within HLA-E*103 variants between patients and controls: E*1031 and E*1032 were associated with CNP (OR=1.613, p=0.013 and OR=1.0809, p=0.055), and E*1033 with controls (OR=0.254, p<10(-4)). CONCLUSION Our study reveals that HLA-E polymorphism is associated with nasopharyngeal cancer. HLA-E expression studies could be used to understand the implication of E*103 variants.
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Affiliation(s)
- Hayet Douik
- Clinical Biology Department, Salah Azaiz Institute of Cancer, 1006 Bab Saadoun, Tunis, Tunisia.
| | - Neila Attia Romdhane
- Statistic and Epidemiology Department, Faculty of Medicine, 1007, Djebel Lakhdar, La Rabta, Tunis, Tunisia
| | - Fethi Guemira
- Clinical Biology Department, Salah Azaiz Institute of Cancer, 1006 Bab Saadoun, Tunis, Tunisia
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14
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Castelli EC, Mendes-Junior CT, Sabbagh A, Porto IOP, Garcia A, Ramalho J, Lima THA, Massaro JD, Dias FC, Collares CVA, Jamonneau V, Bucheton B, Camara M, Donadi EA. HLA-E coding and 3' untranslated region variability determined by next-generation sequencing in two West-African population samples. Hum Immunol 2015; 76:945-53. [PMID: 26187162 DOI: 10.1016/j.humimm.2015.06.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 05/26/2015] [Accepted: 06/20/2015] [Indexed: 12/30/2022]
Abstract
HLA-E is a non-classical Human Leucocyte Antigen class I gene with immunomodulatory properties. Whereas HLA-E expression usually occurs at low levels, it is widely distributed amongst human tissues, has the ability to bind self and non-self antigens and to interact with NK cells and T lymphocytes, being important for immunosurveillance and also for fighting against infections. HLA-E is usually the most conserved locus among all class I genes. However, most of the previous studies evaluating HLA-E variability sequenced only a few exons or genotyped known polymorphisms. Here we report a strategy to evaluate HLA-E variability by next-generation sequencing (NGS) that might be used to other HLA loci and present the HLA-E haplotype diversity considering the segment encoding the entire HLA-E mRNA (including 5'UTR, introns and the 3'UTR) in two African population samples, Susu from Guinea-Conakry and Lobi from Burkina Faso. Our results indicate that (a) the HLA-E gene is indeed conserved, encoding mainly two different protein molecules; (b) Africans do present several unknown HLA-E alleles presenting synonymous mutations; (c) the HLA-E 3'UTR is quite polymorphic and (d) haplotypes in the HLA-E 3'UTR are in close association with HLA-E coding alleles. NGS has proved to be an important tool on data generation for future studies evaluating variability in non-classical MHC genes.
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Affiliation(s)
- Erick C Castelli
- School of Medicine of Botucatu, UNESP - Univ Estadual Paulista, Department of Pathology, Botucatu, State of São Paulo, Brazil.
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, Brazil
| | - Audrey Sabbagh
- Institute of Research for Development, Mixed Research Unit 216 MERIT, Paris, France; Faculté de Pharmacie, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Iane O P Porto
- School of Medicine of Botucatu, UNESP - Univ Estadual Paulista, Department of Pathology, Botucatu, State of São Paulo, Brazil
| | - André Garcia
- Institute of Research for Development, Mixed Research Unit 216 MERIT, Paris, France; Faculté de Pharmacie, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Jaqueline Ramalho
- School of Medicine of Botucatu, UNESP - Univ Estadual Paulista, Department of Pathology, Botucatu, State of São Paulo, Brazil
| | - Thálitta H A Lima
- School of Medicine of Botucatu, UNESP - Univ Estadual Paulista, Department of Pathology, Botucatu, State of São Paulo, Brazil
| | - Juliana D Massaro
- Division of Clinical Immunology, Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo - USP, Ribeirão Preto, SP, Brazil
| | - Fabrício C Dias
- Division of Clinical Immunology, Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo - USP, Ribeirão Preto, SP, Brazil
| | - Cristhianna V A Collares
- Division of Clinical Immunology, Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo - USP, Ribeirão Preto, SP, Brazil
| | - Vincent Jamonneau
- International Center for Development Research on Aging in Sub-Humid Areas (CIRDES), Bobo-Dioulasso, Burkina Faso; Institute of Research for Development, Mixed Research Unit IRD-CIRAD 177, Montpellier, France
| | - Bruno Bucheton
- Institute of Research for Development, Mixed Research Unit IRD-CIRAD 177, Montpellier, France; National Sleeping Sickness Control Program, Ministry of Health and Public Hygiene, Conakry, Guinea
| | - Mamadou Camara
- National Sleeping Sickness Control Program, Ministry of Health and Public Hygiene, Conakry, Guinea
| | - Eduardo A Donadi
- Division of Clinical Immunology, Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo - USP, Ribeirão Preto, SP, Brazil
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15
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Felício LP, Porto IOP, Mendes-Junior CT, Veiga-Castelli LC, Santos KE, Vianello-Brondani RP, Sabbagh A, Moreau P, Donadi EA, Castelli EC. Worldwide HLA-E nucleotide and haplotype variability reveals a conserved gene for coding and 3' untranslated regions. TISSUE ANTIGENS 2014; 83:82-93. [PMID: 24400773 DOI: 10.1111/tan.12283] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 11/05/2013] [Accepted: 12/03/2013] [Indexed: 11/29/2022]
Abstract
The human leukocyte antigen-E (HLA-E) locus is a human major histocompatibility complex (MHC) gene associated with immune-modulation and suppression of the immune response by the interaction with specific natural killer (NK) and T cell receptors (TCRs). It is considered one of the most conserved genes of the human MHC; however, this low nucleotide variability seems to be a consequence of the scarce number of studies focusing on this subject. In this manuscript we assessed the nucleotide variability at the HLA-E coding and 3' untranslated regions (3'UTRs) in Brazil and in the populations from the 1000Genomes Consortium. Twenty-eight variable sites arranged into 33 haplotypes were detected and most of these haplotypes (98.2%) are encoding one of the two HLA-E molecules found worldwide, E*01:01 and E*01:03. Moreover, three worldwide spread haplotypes, associated with the coding alleles E*01:01:01, E*01:03:01 and E*01:03:02, account for 85% of all HLA-E haplotypes, suggesting that they arose early before human speciation. In addition, the low nucleotide diversity found for the HLA-E coding and 3'UTR in worldwide populations suggests that the HLA-E gene is in fact a conserved gene, which might be a consequence of its key role in the modulation of the immune system.
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Affiliation(s)
- L P Felício
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
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