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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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Bernit E, Jean E, Marlot B, Laget L, Izard C, Dettori I, Beley S, Gautier I, Agouti I, Frassati C, Pedini P, Picard C, Paganini J, Chiaroni J, Di Cristofaro J. HLA-F and LILRB1 Genetic Polymorphisms Associated with Alloimmunisation in Sickle Cell Disease. Int J Mol Sci 2023; 24:13591. [PMID: 37686397 PMCID: PMC10487752 DOI: 10.3390/ijms241713591] [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: 07/26/2023] [Revised: 08/25/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Red blood cell (RBC) transfusion remains a critical component in caring for the acute and chronic complications of sickle cell disease (SCD). Patient alloimmunisation is the main limitation of transfusion, which can worsen anaemia and lead to delayed haemolytic transfusion reaction or transfusion deadlock. Although biological risk factors have been identified for immunisation, patient alloimmunisation remains difficult to predict. We aimed to characterise genetic alloimmunisation factors to optimise the management of blood products compatible with extended antigen matching to ensure the self-sufficiency of labile blood products. Considering alloimmunisation in other clinical settings, like pregnancy and transplantation, many studies have shown that HLA Ib molecules (HLA-G, -E, and -F) are involved in tolerance mechanism; these molecules are ligands of immune effector cell receptors (LILRB1, LILRB2, and KIR3DS1). Genetic polymorphisms of these ligands and receptors have been linked to their expression levels and their influence on inflammatory and immune response modulation. Our hypothesis was that polymorphisms of HLA Ib genes and of their receptors are associated with alloimmunisation susceptibility in SCD patients. The alloimmunisation profile of thirty-seven adult SCD patients was analysed according to these genetic polymorphisms and transfusion history. Our results suggest that the alloimmunisation of SCD patients is linked to both HLA-F and LILRB1 genetic polymorphisms located in their regulatory region and associated with their protein expression level.
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Affiliation(s)
- Emmanuelle Bernit
- Unité Transversale de la Drépanocytose, Centre de Référence Antilles-Guyane pour la Drépanocytose, les Thalassémies et les Maladies Constitutives du Globule Rouge et de l’Erythropoïèse, CHU Guadeloupe, 97110 Pointe à Pitre, France
| | - Estelle Jean
- Centre de Référence pour la Drépanocytose, les Thalassémies et les Maladies Constitutives du Globule Rouge et de l’Erythropoïèse, Assistance Publique des Hôpitaux de Marseille, 13005 Marseille, France
| | - Bastien Marlot
- UMR7268, ADES, EFS, CNRS, Aix Marseille University, 13003 Marseille, France
| | - Laurine Laget
- Etablissement Français du Sang PACA Corse, 13001 Marseille, France
| | - Caroline Izard
- Etablissement Français du Sang PACA Corse, 13001 Marseille, France
| | - Isabelle Dettori
- Etablissement Français du Sang PACA Corse, 13001 Marseille, France
| | - Sophie Beley
- UMR7268, ADES, EFS, CNRS, Aix Marseille University, 13003 Marseille, France
| | - Isabelle Gautier
- Centre de Référence pour la Drépanocytose, les Thalassémies et les Maladies Constitutives du Globule Rouge et de l’Erythropoïèse, Assistance Publique des Hôpitaux de Marseille, 13005 Marseille, France
| | - Imane Agouti
- Centre de Référence pour la Drépanocytose, les Thalassémies et les Maladies Constitutives du Globule Rouge et de l’Erythropoïèse, Assistance Publique des Hôpitaux de Marseille, 13005 Marseille, France
| | - Coralie Frassati
- UMR7268, ADES, EFS, CNRS, Aix Marseille University, 13003 Marseille, France
- Etablissement Français du Sang PACA Corse, 13001 Marseille, France
| | - Pascal Pedini
- UMR7268, ADES, EFS, CNRS, Aix Marseille University, 13003 Marseille, France
- Etablissement Français du Sang PACA Corse, 13001 Marseille, France
| | - Christophe Picard
- UMR7268, ADES, EFS, CNRS, Aix Marseille University, 13003 Marseille, France
- Etablissement Français du Sang PACA Corse, 13001 Marseille, France
| | | | - Jacques Chiaroni
- UMR7268, ADES, EFS, CNRS, Aix Marseille University, 13003 Marseille, France
- Etablissement Français du Sang PACA Corse, 13001 Marseille, France
| | - Julie Di Cristofaro
- UMR7268, ADES, EFS, CNRS, Aix Marseille University, 13003 Marseille, France
- Etablissement Français du Sang PACA Corse, 13001 Marseille, France
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Kloch A, Mierzejewska EJ, Welc-Falęciak R, Bajer A, Biedrzycka A. Cytokine gene polymorphism and parasite susceptibility in free-living rodents: Importance of non-coding variants. PLoS One 2023; 18:e0258009. [PMID: 36693052 PMCID: PMC9873194 DOI: 10.1371/journal.pone.0258009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/06/2023] [Indexed: 01/25/2023] Open
Abstract
Associations between genetic variants and susceptibility to infections have long been studied in free-living hosts so as to infer the contemporary evolutionary forces that shape the genetic polymorphisms of immunity genes. Despite extensive studies of proteins interacting with pathogen-derived ligands, such as MHC (major histocompatilbility complex) or TLR (Toll-like receptors), little is known about the efferent arm of the immune system. Cytokines are signalling molecules that trigger and modulate the immune response, acting as a crucial link between innate and adaptive immunity. In the present study we investigated how genetic variation in cytokines in bank voles Myodes glareolus affects their susceptibility to infection by parasites (nematodes: Aspiculuris tianjensis, Heligmosomum mixtum, Heligmosomoides glareoli) and microparasites (Cryptosporidium sp, Babesia microti, Bartonella sp.). We focused on three cytokines: tumour necrosis factor (TNF), lymphotoxin alpha (LTα), and interferon beta (IFNβ1). Overall, we identified four single nucleotide polymorphisms (SNPs) associated with susceptibility to nematodes: two located in LTα and two in IFNβ1. One of those variants was synonymous, another located in an intron. Each SNP associated with parasite load was located in or next to a codon under selection, three codons displayed signatures of positive selection, and one of purifying selection. Our results indicate that cytokines are prone to parasite-driven selection and that non-coding variants, although commonly disregarded in studies of the genetic background of host-parasite co-evolution, may play a role in susceptibility to infections in wild systems.
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Affiliation(s)
- Agnieszka Kloch
- Department of Ecology, Faculty of Biology, University of Warsaw, Warszawa, Poland
- * E-mail:
| | - Ewa J. Mierzejewska
- Wild Urban Evolution and Ecology Laboratory, Centre of New Technologies, University of Warsaw, Warszawa, Poland
| | - Renata Welc-Falęciak
- Department of Parasitology, Faculty of Biology, University of Warsaw, Warszawa, Poland
| | - Anna Bajer
- Department of Eco-epidemiology of Parasitic Diseases, Faculty of Biology, University of Warsaw, Warszawa, Poland
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OUP accepted manuscript. Hum Reprod Update 2022; 28:435-454. [DOI: 10.1093/humupd/dmac007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/15/2021] [Indexed: 11/13/2022] Open
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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: 17] [Impact Index Per Article: 5.7] [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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Sonon P, Collares CVA, Ferreira MLB, Almeida RS, Sadissou I, Cordeiro MT, de Fátima Militão de Albuquerque M, Castelli EC, Lucena-Silva N, Donadi EA. Peripheral spectrum neurological disorder after arbovirus infection is associated with HLA-F variants among Northeastern Brazilians. INFECTION GENETICS AND EVOLUTION 2021; 92:104855. [PMID: 33839310 DOI: 10.1016/j.meegid.2021.104855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Non-classical class I human leukocyte antigens (HLA) molecules are known to modulate the function of cytotoxic cells (NK and T CD8+) during viral infection by interacting with inhibitory/activating receptors. However, little is known about the HLA-E/-F genetic variability on arbovirus infections. METHODS We evaluated by massive parallel sequencing the full HLA-E/-F genetic diversity among patients infected during the arbovirus (ZIKV, DENV, and CHIKV) outbreak leading to a broad range of neurological complications in the Brazilian State of Pernambuco. In parallel, healthy blood donors from the same area were also studied. Plink and R software were used for genetic association study. To limit the false-positive results and enhance the reliability of the results, we adopted P-values <0.01 as significant levels. RESULTS Compared to controls, the HLA-F alleles: -1610 C (rs17875375), +1383 G (rs17178385), and +3537 A (rs17875384), all in complete linkage disequilibrium with each other (r2 = 1), were overrepresented in patients presenting peripheral spectrum disorders (PSD). The HLA-F*Distal-D haplotype that harbored the -1610 C allele exhibited a trend increase in PSD group. No associations were found for HLA-E. CONCLUSIONS Our findings showed that the HLA-F genetic background seems to be more important than HLA-E on the susceptibility to PSD complications.
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Affiliation(s)
- Paulin Sonon
- Immunogenetic Laboratory, Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil; Ribeirão Preto Medical School, University of São Paulo, AV Bandeirantes, 3900, HC, Vila Monte Alegre, 14049900 Ribeirão Preto, SP, Brazil
| | - Cristhianna V A Collares
- Ribeirão Preto Medical School, University of São Paulo, AV Bandeirantes, 3900, HC, Vila Monte Alegre, 14049900 Ribeirão Preto, SP, Brazil
| | - Maria Lúcia Brito Ferreira
- Hospital da Restauração Gov. Paulo Guerra, Av. Gov. Agamenon Magalhães, s/n, Derby, 52171011 Recife, PE, Brazil
| | - Renata Santos Almeida
- Immunogenetic Laboratory, Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Ibrahim Sadissou
- Ribeirão Preto Medical School, University of São Paulo, AV Bandeirantes, 3900, HC, Vila Monte Alegre, 14049900 Ribeirão Preto, SP, Brazil
| | - Marli Tenório Cordeiro
- Virology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Maria de Fátima Militão de Albuquerque
- Public Health Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Erick C Castelli
- São Paulo State University (UNESP), School of Medicine, Molecular Genetics and Bioinformatics Laboratory, Prof. Dr. Walter Maurício Correa, s/n Unesp, Campus de Botucatu, Botucatu CEP 18618681, SP, Brazil; São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, SP, Brazil
| | - Norma Lucena-Silva
- Immunogenetic Laboratory, Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Eduardo A Donadi
- Ribeirão Preto Medical School, University of São Paulo, AV Bandeirantes, 3900, HC, Vila Monte Alegre, 14049900 Ribeirão Preto, SP, Brazil.
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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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Mariella E, Marotta F, Grassi E, Gilotto S, Provero P. The Length of the Expressed 3' UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases. Front Genet 2019; 10:714. [PMID: 31475030 PMCID: PMC6707137 DOI: 10.3389/fgene.2019.00714] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/05/2019] [Indexed: 11/13/2022] Open
Abstract
In the last decades, genome-wide association studies (GWAS) have uncovered tens of thousands of associations between common genetic variants and complex diseases. However, these statistical associations can rarely be interpreted functionally and mechanistically. As the majority of the disease-associated variants are located far from coding sequences, even the relevant gene is often unclear. A way to gain insight into the relevant mechanisms is to study the genetic determinants of intermediate molecular phenotypes, such as gene expression and transcript structure. We propose a computational strategy to discover genetic variants affecting the relative expression of alternative 3′ untranslated region (UTR) isoforms, generated through alternative polyadenylation, a widespread posttranscriptional regulatory mechanism known to have relevant functional consequences. When applied to a large dataset in which whole genome and RNA sequencing data are available for 373 European individuals, 2,530 genes with alternative polyadenylation quantitative trait loci (apaQTL) were identified. We analyze and discuss possible mechanisms of action of these variants, and we show that they are significantly enriched in GWAS hits, in particular those concerning immune-related and neurological disorders. Our results point to an important role for genetically determined alternative polyadenylation in affecting predisposition to complex diseases, and suggest new ways to extract functional information from GWAS data.
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Affiliation(s)
- Elisa Mariella
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Federico Marotta
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Elena Grassi
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Stefano Gilotto
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Paolo Provero
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.,Center for Tranlational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
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Nilsson LL, Funck T, Kjersgaard ND, Hviid TVF. Next-generation sequencing of HLA-G based on long-range polymerase chain reaction. HLA 2019; 92:144-153. [PMID: 30014615 DOI: 10.1111/tan.13342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/17/2018] [Accepted: 07/12/2018] [Indexed: 12/21/2022]
Abstract
Clarifying the functional roles of HLA-G and the variation in the HLA-G gene that affects the expression are increasingly important in reproduction, cancer, organ transplantation, and autoimmune diseases. The homology between HLA genes and the genetic variability within each gene complicates the design of HLA gene-specific genotyping assays. We have designed a high-throughput, cost-efficient, robust, and specific assay for sequencing the full HLA-G gene including the 5'-upstream regulatory region, introns, and the 3'-untranslated region, using the next-generation sequencing (NGS) platform Ion Torrent PGM (Thermo Fisher Scientific, Waltham, Massachusetts). Conventional sequencing methods require the design of multiple primer pairs in order to cover the entire HLA-G gene. Designing multiple primer pairs specific for the HLA-G gene that also target all known alleles is difficult. Here, we present a setup that by the use of long-range polymerase chain reaction amplifies the whole HLA-G gene in a single reaction, which only requires a single HLA-G-specific primer pair. Enzymatic DNA shearing is used to break the long-range PCR product into shorter fragments ranging from 75 to 200 bp in length that are sequenced by NGS.
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Affiliation(s)
- L L Nilsson
- Centre for Immune Regulation and Reproductive Immunology, The ReproHealth Research Consortium ZUH, Department of Clinical Biochemistry, Zealand University Hospital, University of Copenhagen, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Roskilde, Denmark
| | - T Funck
- Centre for Immune Regulation and Reproductive Immunology, The ReproHealth Research Consortium ZUH, Department of Clinical Biochemistry, Zealand University Hospital, University of Copenhagen, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Roskilde, Denmark
| | - N D Kjersgaard
- Centre for Immune Regulation and Reproductive Immunology, The ReproHealth Research Consortium ZUH, Department of Clinical Biochemistry, Zealand University Hospital, University of Copenhagen, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Roskilde, Denmark
| | - T V F Hviid
- Centre for Immune Regulation and Reproductive Immunology, The ReproHealth Research Consortium ZUH, Department of Clinical Biochemistry, Zealand University Hospital, University of Copenhagen, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Roskilde, Denmark
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10
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HLAIb worldwide genetic diversity: New HLA-H alleles and haplotype structure description. Mol Immunol 2019; 112:40-50. [PMID: 31078115 DOI: 10.1016/j.molimm.2019.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/09/2019] [Accepted: 04/23/2019] [Indexed: 01/01/2023]
Abstract
The classical HLA class I genes (HLA Ia) were extensively studied because of their implication in clinical fields and anthropology. Less is known about worldwide genetic diversity and linkage disequilibrium for non-classical HLA class I genes (HLA Ib) and HLA pseudogenes. Notably, HLA-H, which is deleted in a fraction of the population, remains scarcely explored. The aims of this study were 1/ to get further insight into HLA-H genetic diversity and into how this variability potentially affects its expression and 2/ to define HLA Ib worldwide allelic diversity and linkage. Exome sequence data from the 1000 Genomes Project were used to define second field HLA-A, -E, -F, -G and -H typing using PolyPheMe software. Allelic and two-loci haplotype frequencies were estimated using Gene[Rate] software both at worldwide and continental levels. Eleven novel HLA-H alleles identified in exome data were validated by NGS performed on 25 genomic DNA samples from the same cohort. Phylogenetic analysis and frequency distribution of HLA-H alleles revealed three clades, each predominantly represented in Admixed American, European and East Asian populations, African populations and South Asian populations. Among these eleven novel alleles, two potentially encode complete transmembrane HLA proteins. We confirm the high LD between HLA-H and -A, and between HLA-H and -G, and show the three genes have distinct worldwide allelic distribution. Conversely, HLA-E and HLA-F both showed little LD, displayed restricted allelic diversity and practically no difference in their distribution across the planet. Our work thus reveals an unexpectedly high HLA-H genetic diversity, with alleles highly represented in Asia possibly encoding a functional HLA protein. Functional implication of these results remains to be explored, both in physiological and pathological contexts.
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11
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Würfel FM, Winterhalter C, Trenkwalder P, Wirtz RM, Würfel W. European Patent in Immunoncology: From Immunological Principles of Implantation to Cancer Treatment. Int J Mol Sci 2019; 20:ijms20081830. [PMID: 31013867 PMCID: PMC6514949 DOI: 10.3390/ijms20081830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 12/19/2022] Open
Abstract
The granted European patent EP 2 561 890 describes a procedure for an immunological treatment of cancer. It is based on the principles of the HLA-supported communication of implantation and pregnancy. These principles ensure that the embryo is not rejected by the mother. In pregnancy, the placenta, more specifically the trophoblast, creates an “interface” between the embryo/fetus and the maternal immune system. Trophoblasts do not express the “original” HLA identification of the embryo/fetus (HLA-A to -DQ), but instead show the non-classical HLA groups E, F, and G. During interaction with specific receptors of NK cells (e.g., killer-immunoglobulin-like receptors (KIR)) and lymphocytes (lymphocyte-immunoglobulin-like receptors (LIL-R)), the non-classical HLA groups inhibit these immunocompetent cells outside pregnancy. However, tumors are known to be able to express these non-classical HLA groups and thus make use of an immuno-communication as in pregnancies. If this occurs, the prognosis usually worsens. This patent describes, in a first step, the profiling of the non-classical HLA groups in primary tumor tissue as well as metastases and recurrent tumors. The second step comprises tailored antibody therapies, which is the subject of this patent. In this review, we analyze the underlying mechanisms and describe the currently known differences between HLA-supported communication of implantation and that of tumors.
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Affiliation(s)
- Franziska M Würfel
- STRATIFYER Molecular Pathology GmbH, D-50935 Cologne, Werthmannstrasse 1c, 50935 Cologne, Germany.
| | | | | | - Ralph M Wirtz
- STRATIFYER Molecular Pathology GmbH, D-50935 Cologne, Werthmannstrasse 1c, 50935 Cologne, Germany.
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12
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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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13
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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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14
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Paganini J, Ramdane A, Gouret P, Chiaroni J, Di Cristofaro J. Validation of new HLA-F alleles assigned by next-generation sequencing. HLA 2019; 93:131-132. [PMID: 30556320 DOI: 10.1111/tan.13455] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/12/2022]
Affiliation(s)
| | - Anissa Ramdane
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | | | - Jacques Chiaroni
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France.,Aix Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
| | - Julie Di Cristofaro
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France.,Aix Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
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15
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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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16
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Extended HLA-G genetic diversity and ancestry composition in a Brazilian admixed population sample: Implications for HLA-G transcriptional control and for case-control association studies. Hum Immunol 2018; 79:790-799. [DOI: 10.1016/j.humimm.2018.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/04/2018] [Accepted: 08/09/2018] [Indexed: 12/30/2022]
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17
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Castelli EC, Paz MA, Souza AS, Ramalho J, Mendes-Junior CT. Hla-mapper: An application to optimize the mapping of HLA sequences produced by massively parallel sequencing procedures. Hum Immunol 2018; 79:678-684. [PMID: 30122171 DOI: 10.1016/j.humimm.2018.06.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 06/15/2018] [Accepted: 06/29/2018] [Indexed: 12/30/2022]
Abstract
A challenging task when more than one HLA gene is evaluated together by second-generation sequencing is to achieve a reliable read mapping. The polymorphic and repetitive nature of HLA genes might bias the read mapping process, usually underestimating variability at very polymorphic segments, or overestimating variability at some segments. To overcome this issue we developed hla-mapper, which takes into account HLA sequences derived from the IPD-IMGT/HLA database and unpublished HLA sequences to apply a scoring system. This comprehends the evaluation of each read pair, addressing them to the most likely HLA gene they were derived from. Hla-mapper provides a reliable map of HLA sequences, allowing accurate downstream analysis such as variant calling, haplotype inference, and allele typing. Moreover, hla-mapper supports whole genome, exome, and targeted sequencing data. To assess the software performance in comparison with traditional mapping algorithms, we used three different simulated datasets to compare the results obtained with hla-mapper, BWA MEM, and Bowtie2. Overall, hla-mapper presented a superior performance, mainly for the classical HLA class I genes, minimizing wrong mapping and cross-mapping that are typically observed when using BWA MEM or Bowtie2 with a single reference genome.
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Affiliation(s)
- 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), Pathology Department, School of Medicine, Botucatu, State of São Paulo, Brazil.
| | - Michelle A Paz
- São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (UNIPEX), School of Medicine, Botucatu, State of São Paulo, Brazil
| | - Andréia S Souza
- São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (UNIPEX), School of Medicine, Botucatu, State of São Paulo, Brazil
| | - 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
| | - 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
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18
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Meyer D, C Aguiar VR, Bitarello BD, C Brandt DY, Nunes K. A genomic perspective on HLA evolution. Immunogenetics 2018; 70:5-27. [PMID: 28687858 PMCID: PMC5748415 DOI: 10.1007/s00251-017-1017-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/16/2017] [Indexed: 12/20/2022]
Abstract
Several decades of research have convincingly shown that classical human leukocyte antigen (HLA) loci bear signatures of natural selection. Despite this conclusion, many questions remain regarding the type of selective regime acting on these loci, the time frame at which selection acts, and the functional connections between genetic variability and natural selection. In this review, we argue that genomic datasets, in particular those generated by next-generation sequencing (NGS) at the population scale, are transforming our understanding of HLA evolution. We show that genomewide data can be used to perform robust and powerful tests for selection, capable of identifying both positive and balancing selection at HLA genes. Importantly, these tests have shown that natural selection can be identified at both recent and ancient timescales. We discuss how findings from genomewide association studies impact the evolutionary study of HLA genes, and how genomic data can be used to survey adaptive change involving interaction at multiple loci. We discuss the methodological developments which are necessary to correctly interpret genomic analyses involving the HLA region. These developments include adapting the NGS analysis framework so as to deal with the highly polymorphic HLA data, as well as developing tools and theory to search for signatures of selection, quantify differentiation, and measure admixture within the HLA region. Finally, we show that high throughput analysis of molecular phenotypes for HLA genes-namely transcription levels-is now a feasible approach and can add another dimension to the study of genetic variation.
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Affiliation(s)
- Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil.
| | - Vitor R C Aguiar
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Bárbara D Bitarello
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Débora Y C Brandt
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
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19
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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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Crux NB, Elahi S. Human Leukocyte Antigen (HLA) and Immune Regulation: How Do Classical and Non-Classical HLA Alleles Modulate Immune Response to Human Immunodeficiency Virus and Hepatitis C Virus Infections? Front Immunol 2017; 8:832. [PMID: 28769934 PMCID: PMC5513977 DOI: 10.3389/fimmu.2017.00832] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/30/2017] [Indexed: 12/13/2022] Open
Abstract
The genetic factors associated with susceptibility or resistance to viral infections are likely to involve a sophisticated array of immune response. These genetic elements may modulate other biological factors that account for significant influence on the gene expression and/or protein function in the host. Among them, the role of the major histocompatibility complex in viral pathogenesis in particular human immunodeficiency virus (HIV) and hepatitis C virus (HCV), is very well documented. We, recently, added a novel insight into the field by identifying the molecular mechanism associated with the protective role of human leukocyte antigen (HLA)-B27/B57 CD8+ T cells in the context of HIV-1 infection and why these alleles act as a double-edged sword protecting against viral infections but predisposing the host to autoimmune diseases. The focus of this review will be reexamining the role of classical and non-classical HLA alleles, including class Ia (HLA-A, -B, -C), class Ib (HLA-E, -F, -G, -H), and class II (HLA-DR, -DQ, -DM, and -DP) in immune regulation and viral pathogenesis (e.g., HIV and HCV). To our knowledge, this is the very first review of its kind to comprehensively analyze the role of these molecules in immune regulation associated with chronic viral infections.
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Affiliation(s)
- Nicole B Crux
- Faculty of Medicine and Dentistry, Department of Dentistry, University of Alberta, Edmonton, AB, Canada.,Faculty of Medicine and Dentistry, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Shokrollah Elahi
- Faculty of Medicine and Dentistry, Department of Dentistry, University of Alberta, Edmonton, AB, Canada.,Faculty of Medicine and Dentistry, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
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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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