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Lyn Fortier A, Pritchard JK. The Primate Major Histocompatibility Complex: An Illustrative Example of Gene Family Evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.613318. [PMID: 39345418 PMCID: PMC11429698 DOI: 10.1101/2024.09.16.613318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Gene families are groups of evolutionarily-related genes. One large gene family that has experienced rapid evolution is the Major Histocompatibility Complex (MHC), whose proteins serve critical roles in innate and adaptive immunity. Across the ~60 million year history of the primates, some MHC genes have turned over completely, some have changed function, some have converged in function, and others have remained essentially unchanged. Past work has typically focused on identifying MHC alleles within particular species or comparing gene content, but more work is needed to understand the overall evolution of the gene family across species. Thus, despite the immunologic importance of the MHC and its peculiar evolutionary history, we lack a complete picture of MHC evolution in the primates. We readdress this question using sequences from dozens of MHC genes and pseudogenes spanning the entire primate order, building a comprehensive set of gene and allele trees with modern methods. Overall, we find that the Class I gene subfamily is evolving much more quickly than the Class II gene subfamily, with the exception of the Class II MHC-DRB genes. We also pay special attention to the often-ignored pseudogenes, which we use to reconstruct different events in the evolution of the Class I region. We find that despite the shared function of the MHC across species, different species employ different genes, haplotypes, and patterns of variation to achieve a successful immune response. Our trees and extensive literature review represent the most comprehensive look into MHC evolution to date.
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Affiliation(s)
- Alyssa Lyn Fortier
- Department of Biology, Stanford University, Stanford, CA USA
- Department of Genetics, Stanford University, Stanford, CA USA
| | - Jonathan K. Pritchard
- Department of Biology, Stanford University, Stanford, CA USA
- Department of Genetics, Stanford University, Stanford, CA USA
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2
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Zhou Y, Song L, Li H. Full resolution HLA and KIR genes annotation for human genome assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576452. [PMID: 38328160 PMCID: PMC10849470 DOI: 10.1101/2024.01.20.576452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The HLA (Human Leukocyte Antigen) genes and the KIR (Killer cell Immunoglobulin-like Receptor) genes are critical to immune responses and are associated with many immune-related diseases. Located in highly polymorphic regions, they are hard to be studied with traditional short-read alignment-based methods. Although modern long-read assemblers can often assemble these genes, using existing tools to annotate HLA and KIR genes in these assemblies remains a non-trivial task. Here, we describe Immuannot, a new computation tool to annotate the gene structures of HLA and KIR genes and to type the allele of each gene. Applying Immuannot to 56 regional and 212 whole-genome assemblies from previous studies, we annotated 9,931 HLA and KIR genes and found that almost half of these genes, 4,068, had novel sequences compared to the current Immuno Polymorphism Database (IPD). These novel gene sequences were represented by 2,664 distinct alleles, some of which contained non-synonymous variations resulting in 92 novel protein sequences. We demonstrated the complex haplotype structures at the two loci and reported the linkage between HLA/KIR haplotypes and gene alleles. We anticipate that Immuannot will speed up the discovery of new HLA/KIR alleles and enable the association of HLA/KIR haplotype structures with clinical outcomes in the future.
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Affiliation(s)
- Ying Zhou
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Li Song
- Department of Biomedical Data Science, Dartmouth College, Hanover, NH, 03755, USA
| | - Heng Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
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3
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Alizadeh M, Frassati C, Walencik A, Picard C, Pedini P. Characterization of 43 novel HLA-H alleles. HLA 2024; 103:e15203. [PMID: 37632724 DOI: 10.1111/tan.15203] [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: 07/28/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/28/2023]
Abstract
Forty-three novel HLA-H alleles, including 32 identified in cohorts of French donors for Hematopoietic Stem Cell Transplantation, have been characterized by Next-Generation Sequencing (NGS) using a long range PCR approach. A phylogenetic study confirms three main HLA-H clades.
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Affiliation(s)
- Mehdi Alizadeh
- National Reagent Production Laboratory, Établissement Français du Sang Bretagne, Rennes, France
| | - Coralie Frassati
- Immunogenetics Laboratory, Établissement Français du Sang PACA Corse, Marseille, France
- ADES UMR, Aix Marseille Univ, Marseille, France
| | - Alexandre Walencik
- Imunogenetics Laboratory, Établissement Français du Sang, Nantes, France
| | - Christophe Picard
- Immunogenetics Laboratory, Établissement Français du Sang PACA Corse, Marseille, France
- ADES UMR, Aix Marseille Univ, Marseille, France
| | - Pascal Pedini
- Immunogenetics Laboratory, Établissement Français du Sang PACA Corse, Marseille, France
- ADES UMR, Aix Marseille Univ, Marseille, France
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4
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Paganini J, Faux P, Beley S, Picard C, Chiaroni J, Di Cristofaro J. HLA-F transcriptional and protein differential expression according to its genetic polymorphisms. HLA 2023; 102:578-589. [PMID: 37166140 DOI: 10.1111/tan.15087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/21/2023] [Accepted: 04/20/2023] [Indexed: 05/12/2023]
Abstract
Many specificities single out HLA-F: its structure, expression regulation at cell membrane and function. HLA-F mRNA is detected in the most cell types and the protein is localized in the ER and Golgi apparatus. When expressed at cell surface, HLA-F may be associated to β2-microglobulin and peptide or expressed as an open-conformer molecule. HLA-F reaches the membrane upon activation of different primary cell types and cell-lines. HLA-F has its highest affinity for the KIR3DS1-activating NK receptor, but also binds inhibitory immune receptors. Some studies reported that HLA-F expression is associated with its genotype. Higher HLA-F mRNA expression associated with F*01:01:02, and 3 noncoding SNPs, rs1362126, rs2523405, and rs2523393, located in HLA-F-AS1 or upstream the HLA-F sequence were associated with HLA-F mRNA expression. Given the implication of HLA-F in many clinical setting, and the undisclosed process of its expression regulation, we aim to confirm the effect of the aforementioned SNPs with HLA-F transcriptional and protein expression. We analyzed the distribution, frequency and linkage disequilibrium of these SNPs at worldwide scale in the 1000 Genomes Project samples. Influence on the genotype of each SNP on HLA-F expression was explored using RNAseq data from the 1000 Genomes Project, and using Q-PCR and intracellular cytometry in PBMC from healthy individuals. Our results show that the SNPs under studied displayed remarkably different allelic proportion according to geography and confirm that rs1362126, rs2523405, and rs2523393 displayed the most concordant results, with the highest effect size and a double-dose effect.
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Affiliation(s)
| | - Pierre Faux
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, Castanet Tolosan, France
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
| | - Sophie Beley
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Christophe Picard
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Jacques Chiaroni
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Julie Di Cristofaro
- Aix Marseille University, CNRS, EFS, ADES, UMR7268, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
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5
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Lucas JAM, Georgiou X, Cooper MA, Robinson J, Marsh SGE, Mayor NP. 86 novel HLA-E alleles discovered through full-gene sequencing of 6227 hematopoietic cell transplant patients and unrelated donors. HLA 2023; 101:34-41. [PMID: 36303277 DOI: 10.1111/tan.14871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 12/13/2022]
Abstract
Until recently the number of alleles of the nonclassical HLA class I gene HLA-E documented in the IPD-IMGT/HLA Database was small and as a result, the gene was often not considered to be notably polymorphic. Here, we describe our work in identifying and submitting 86 novel HLA-E alleles after full-gene single-molecule real-time (SMRT) DNA sequencing of 6227 DNA samples. These samples were comprised of 2468 patients undergoing hematopoietic cell transplantation and 3759 unrelated potential donors. A total of 111 unique HLA-E alleles were detected in this cohort. The majority of novel alleles (79.1%) contained polymorphisms in intronic regions, highlighting the significant undiscovered variation present in the noncoding regions of the HLA-E gene.
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Affiliation(s)
| | - Xenia Georgiou
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - Michael A Cooper
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | - Neema P Mayor
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
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Pollock NR, Harrison GF, Norman PJ. Immunogenomics of Killer Cell Immunoglobulin-Like Receptor (KIR) and HLA Class I: Coevolution and Consequences for Human Health. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2022; 10:1763-1775. [PMID: 35561968 PMCID: PMC10038757 DOI: 10.1016/j.jaip.2022.04.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 12/12/2022]
Abstract
Interactions of killer cell immunoglobin-like receptors (KIR) with human leukocyte antigens (HLA) class I regulate effector functions of key cytotoxic cells of innate and adaptive immunity. The extreme diversity of this interaction is genetically determined, having evolved in the ever-changing environment of pathogen exposure. Diversity of KIR and HLA genes is further facilitated by their independent segregation on separate chromosomes. That fetal implantation relies on many of the same types of immune cells as infection control places certain constraints on the evolution of KIR interactions with HLA. Consequently, specific inherited combinations of receptors and ligands may predispose to specific immune-mediated diseases, including autoimmunity. Combinatorial diversity of KIR and HLA class I can also differentiate success rates of immunotherapy directed to these diseases. Progress toward both etiopathology and predicting response to therapy is being achieved through detailed characterization of the extent and consequences of the combinatorial diversity of KIR and HLA. Achieving these goals is more tractable with the development of integrated analyses of molecular evolution, function, and pathology that will establish guidelines for understanding and managing risks. Here, we present what is known about the coevolution of KIR with HLA class I and the impact of their complexity on immune function and homeostasis.
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Affiliation(s)
- Nicholas R Pollock
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo
| | - Genelle F Harrison
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine and Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colo.
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7
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Hubert L, Paganini J, Picard C, Chiaroni J, Abi-Rached L, Pontarotti P, Di Cristofaro J. HLA-H*02:07 Is a Membrane-Bound Ligand of Denisovan Origin That Protects against Lysis by Activated Immune Effectors. THE JOURNAL OF IMMUNOLOGY 2022; 208:49-53. [DOI: 10.4049/jimmunol.2100358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 11/01/2021] [Indexed: 04/08/2023]
Abstract
Abstract
The biological relevance of genes initially categorized as “pseudogenes” is slowly emerging, notably in innate immunity. In the HLA region on chromosome 6, HLA-H is one such pseudogene; yet, it is transcribed, and its variation is associated with immune properties. Furthermore, two HLA-H alleles, H*02:07 and H*02:14, putatively encode a complete, membrane-bound HLA protein. Here we thus hypothesized that HLA-H contributes to immune homeostasis similarly to tolerogenic molecules HLA-G, -E, and -F. We tested if HLA-H*02:07 encodes a membrane-bound protein that can inhibit the cytotoxicity of effector cells. We used an HLA-null human erythroblast cell line transduced with HLA-H*02:07 cDNA to demonstrate that HLA-H*02:07 encodes a membrane-bound protein. Additionally, using a cytotoxicity assay, our results support that K562 HLA-H*02:07 inhibits human effector IL-2–activated PBMCs and human IL-2–independent NK92-MI cell line activity. Finally, through in silico genotyping of the Denisovan genome and haplotypic association with Denisovan-derived HLA-A*11, we also show that H*02:07 is of archaic origin. Hence, admixture with archaic humans brought a functional HLA-H allele into modern European and Asian populations.
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Affiliation(s)
- Lucas Hubert
- *Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins,” Marseille, France
- †Etablissement Français du Sang PACA Corse, Marseille, France
| | | | - Christophe Picard
- *Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins,” Marseille, France
- †Etablissement Français du Sang PACA Corse, Marseille, France
| | - Jacques Chiaroni
- *Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins,” Marseille, France
- †Etablissement Français du Sang PACA Corse, Marseille, France
| | - Laurent Abi-Rached
- §Aix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranée Infection, Marseille, France; and
- ¶CNRS, Marseille, France
| | - Pierre Pontarotti
- §Aix Marseille University, IRD, APHM, MEPHI, IHU-Mediterranée Infection, Marseille, France; and
- ¶CNRS, Marseille, France
| | - Julie Di Cristofaro
- *Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins,” Marseille, France
- †Etablissement Français du Sang PACA Corse, Marseille, France
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8
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Persson G, Picard C, Marin G, Isgaard C, Stæhr CS, Molinari N, Chiaroni J, Lebech M, Hviid TVF, Di Cristofaro J. Maternal HLA Ib Polymorphisms in Pregnancy Allo-Immunization. Front Immunol 2021; 12:657217. [PMID: 33859649 PMCID: PMC8042285 DOI: 10.3389/fimmu.2021.657217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022] Open
Abstract
During pregnancy the formation of alloreactive anti-human leukocyte antigen (HLA) antibodies are a major cause of acute rejection in organ transplantation and of adverse effects in blood transfusion. The purpose of the study was to identify maternal HLA class Ib genetic factors associated with anti-HLA allo-immunization in pregnancy and the degree of tolerance estimated by IgG4 expression. In total, 86 primiparous women with singleton pregnancies were included in the study. Maternal blood samples and umbilical cord samples were collected at delivery. Clinical data were obtained. Maternal blood serum was screened for HLA class I and II antibodies, identification of Donor Specific Antibody (DSA), activation of complement measured by C1q and IgG4 concentrations. Mothers were genotyped for HLA class Ib (HLA-E, -F and -G). Anti-HLA class I and II antibodies were identified in 24% of the women. The maternal HLA-E*01:06 allele was significantly associated with a higher fraction of anti-HLA I immunization (20.0% vs. 4.8%, p = 0.048). The maternal HLA-G 3’-untranslated region UTR4-HLA-G*01:01:01:05 haplotype and the HLA-F*01:03:01 allele were significantly associated with a low anti-HLA I C1q activation (16.7% vs. 57.1%, p = 0.028; 16.7% vs. 50.0%, p = 0.046; respectively). Both HLA‑G and HLA-F*01:03:01 showed significantly higher levels of IgG4 compared with the other haplotypes. The results support an association of certain HLA class Ib alleles with allo-immunization during pregnancy. Further studies are needed to elucidate the roles of HLA-E*01:06, HLA-F*01:03 and HLA‑G UTR4 in reducing the risk for allo-immunization.
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Affiliation(s)
- Gry Persson
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, The ReproHealth Research Consortium ZUH, Zealand University Hospital, Roskilde, Denmark
| | - Christophe Picard
- Aix Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France.,Immunogenetics Laboratory, Etablissement français du Sang PACA Corse, Marseille, France
| | - Gregory Marin
- Unité de Recherche Clinique, Biostatistique et Epidémiologie, Département de l'Information Médicale (DIM) Hôpital La Colombière, Montpellier, France
| | - Cecilie Isgaard
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, The ReproHealth Research Consortium ZUH, Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christina Seefeldt Stæhr
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, The ReproHealth Research Consortium ZUH, Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nicolas Molinari
- Unité de Recherche Clinique, Biostatistique et Epidémiologie, Département de l'Information Médicale (DIM) Hôpital La Colombière, Montpellier, France
| | - Jacques Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
| | - Morten Lebech
- Department of Obstetrics and Gynecology, Zealand University Hospital, Roskilde, Denmark
| | - Thomas Vauvert F Hviid
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, The ReproHealth Research Consortium ZUH, Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Julie Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
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Ashfaq UA, Saleem S, Masoud MS, Ahmad M, Nahid N, Bhatti R, Almatroudi A, Khurshid M. Rational design of multi epitope-based subunit vaccine by exploring MERS-COV proteome: Reverse vaccinology and molecular docking approach. PLoS One 2021; 16:e0245072. [PMID: 33534822 PMCID: PMC7857617 DOI: 10.1371/journal.pone.0245072] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Middle East respiratory syndrome (MERS-COV), first identified in Saudi Arabia, was caused by a novel strain of coronavirus. Outbreaks were recorded from different regions of the world, especially South Korea and the Middle East, and were correlated with a 35% mortality rate. MERS-COV is a single-stranded, positive RNA virus that reaches the host by binding to the receptor of dipeptidyl-peptides. Because of the unavailability of the vaccine available for the protection from MERS-COV infection, the rapid case detection, isolation, infection prevention has been recommended to combat MERS-COV infection. So, vaccines for the treatment of MERS-COV infection need to be developed urgently. A possible antiviral mechanism for preventing MERS-CoV infection has been considered to be MERS-CoV vaccines that elicit unique T-cell responses. In the present study, we incorporated both molecular docking and immunoinformatic approach to introduce a multiepitope vaccine (MEP) against MERS-CoV by selecting 15 conserved epitopes from seven viral proteins such as three structural proteins (envelope, membrane, and nucleoprotein) and four non-structural proteins (ORF1a, ORF8, ORF3, ORF4a). The epitopes, which were examined for non-homologous to host and antigenicity, were selected on the basis of conservation between T-cell, B-cell, and IFN-γ epitopes. The selected epitopes were then connected to the adjuvant (β-defensin) at the N-terminal through an AAY linker to increase the immunogenic potential. Structural modelling and physiochemical characteristic were applied to the vaccine construct developed. Afterwards the structure has been successfully docked with antigenic receptor, Toll-like receptor 3 (TLR-3) and in-silico cloning ensures that its expression efficiency is legitimate. Nonetheless the MEP presented needs tests to verify its safety and immunogenic profile.
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Affiliation(s)
- Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
- * E-mail:
| | - Saman Saleem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad, Pakistan
| | - Nazia Nahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Rashid Bhatti
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Mohsin Khurshid
- Department of Microbiology, Government College University, Faisalabad, Pakistan
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10
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Kulski JK, Suzuki S, Shiina T. SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction. Front Genet 2021; 11:594318. [PMID: 33537058 PMCID: PMC7848197 DOI: 10.3389/fgene.2020.594318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
The genomic region (~4 Mb) of the human major histocompatibility complex (MHC) on chromosome 6p21 is a prime model for the study and understanding of conserved polymorphic sequences (CPSs) and structural diversity of ancestral haplotypes (AHs)/conserved extended haplotypes (CEHs). The aim of this study was to use a set of 95 MHC genomic sequences downloaded from a publicly available BioProject database at NCBI to identify and characterise polymorphic human leukocyte antigen (HLA) class I genes and pseudogenes, MICA and MICB, and retroelement indels as haplotypic lineage markers, and single-nucleotide polymorphism (SNP) crossover loci in DNA sequence alignments of different haplotypes across the Olfactory Receptor (OR) gene region (~1.2 Mb) and the MHC class I region (~1.8 Mb) from the GPX5 to the MICB gene. Our comparative sequence analyses confirmed the identity of 12 haplotypic retroelement markers and revealed that they partitioned the HLA-A/B/C haplotypes into distinct evolutionary lineages. Crossovers between SNP-poor and SNP-rich regions defined the sequence range of haplotype blocks, and many of these crossover junctions occurred within particular transposable elements, lncRNA, OR12D2, MUC21, MUC22, PSORS1A3, HLA-C, HLA-B, and MICA. In a comparison of more than 250 paired sequence alignments, at least 38 SNP-density crossover sites were mapped across various regions from GPX5 to MICB. In a homology comparison of 16 different haplotypes, seven CEH/AH (7.1, 8.1, 18.2, 51.x, 57.1, 62.x, and 62.1) had no detectable SNP-density crossover junctions and were SNP poor across the entire ~2.8 Mb of sequence alignments. Of the analyses between different recombinant haplotypes, more than half of them had SNP crossovers within 10 kb of LTR16B/ERV3-16A3_I, MLT1, Charlie, and/or THE1 sequences and were in close vicinity to structurally polymorphic Alu and SVA insertion sites. These studies demonstrate that (1) SNP-density crossovers are associated with putative ancestral recombination sites that are widely spread across the MHC class I genomic region from at least the telomeric OR12D2 gene to the centromeric MICB gene and (2) the genomic sequences of MHC homozygous cell lines are useful for analysing haplotype blocks, ancestral haplotypic landscapes and markers, CPSs, and SNP-density crossover junctions.
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Affiliation(s)
- Jerzy K. Kulski
- Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, WA, Australia
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Shingo Suzuki
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Takashi Shiina
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
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11
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Paganini J, Dallas P, Chiaroni J, Sayer D, Di Cristofaro J. Complete genetic sequence of 15 novel HLA‐H alleles. HLA 2020; 96:133-135. [DOI: 10.1111/tan.13846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/11/2020] [Accepted: 02/15/2020] [Indexed: 11/29/2022]
Affiliation(s)
| | - Peter Dallas
- CareDx, Inc Fremantle Western Australia Australia
| | - Jacques Chiaroni
- Biologie des Groupes SanguinsEtablissement Français du Sang PACA Corse Marseille France
- CNRS, EFS, ADES, "Biologie des Groupes Sanguins"Aix Marseille Univ Marseille France
| | - David Sayer
- CareDx, Inc Fremantle Western Australia Australia
| | - Julie Di Cristofaro
- Biologie des Groupes SanguinsEtablissement Français du Sang PACA Corse Marseille France
- CNRS, EFS, ADES, "Biologie des Groupes Sanguins"Aix Marseille Univ Marseille France
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12
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Lucas JAM, Hayhurst JD, Turner TR, Gymer AW, Leen G, Robinson J, Marsh SGE, Mayor NP. Single molecule real-time DNA sequencing of the full HLA-E gene for 212 reference cell lines. HLA 2020; 95:561-572. [PMID: 32227678 DOI: 10.1111/tan.13882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/09/2020] [Accepted: 03/23/2020] [Indexed: 01/19/2023]
Abstract
We have developed a genotyping assay that produces fully phased, unambiguous HLA-E genotyping using Pacific Biosciences' single molecule real-time DNA sequencing. In total 212 cell lines were genotyped, including the panel of 107 established at the 10th International Histocompatibility Workshop. Our results matched the previously known HLA-E genotype in 94 (44.3%) cell lines, in all cases either improving or equalling previous genotyping resolution. Three (1.4%) cells had discrepant HLA-E genotyping data and 115 (54.2%) had no previous HLA-E data. The HLA-E genotypes for four (1.9%) cell lines resulted in a change of zygosity by identifying two distinct haplotypes. We discovered eight novel HLA-E alleles, extended the known reference sequence of seven and confirmed the existence of a further 10.
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Affiliation(s)
- Jonathan A M Lucas
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
| | - James D Hayhurst
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
| | - Thomas R Turner
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,UCL Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Arthur W Gymer
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
| | - Gayle Leen
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,UCL Cancer Institute, Royal Free Campus, London, United Kingdom
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,UCL Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,UCL Cancer Institute, Royal Free Campus, London, United Kingdom
| | - Neema P Mayor
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,UCL Cancer Institute, Royal Free Campus, London, United Kingdom
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Jordier F, Gras D, De Grandis M, D'Journo XB, Thomas PA, Chanez P, Picard C, Chiaroni J, Paganini J, Di Cristofaro J. HLA-H: Transcriptional Activity and HLA-E Mobilization. Front Immunol 2020; 10:2986. [PMID: 32010122 PMCID: PMC6978722 DOI: 10.3389/fimmu.2019.02986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/05/2019] [Indexed: 01/25/2023] Open
Abstract
Little attention is paid to pseudogenes from the highly polymorphic HLA genetic region. The pseudogene HLA-H is defined as a non-functional gene because it is deleted at different frequencies in humans and because it encodes a potentially non-functional truncated protein. However, different studies have shown HLA-H transcriptional activity. We formerly identified 13 novel HLA-H alleles, including the H*02:07 allele, which reaches 19.6% in East Asian populations and encodes a full-length HLA protein. The aims of this study were to explore the expression and possible function of the HLA-H molecule. HLA-H may act as a transmembrane molecule and/or indirectly via its signal peptide by mobilizing HLA-E to the cell surface. We analyzed HLA-H RNA expression in Peripheral Blood Mononuclear Cells (PBMC), Human Bronchial Epithelial Cells (HBEC), and available RNA sequencing data from lymphoblastoid cell lines, and we looked to see whether HLA-E was mobilized at the cell surface by the HLA-H signal peptide. Our data confirmed that HLA-H is transcribed at similar levels to HLA-G. We characterized a hemizygous effect in HLA-H expression, and expression differed according to HLA-H alleles; most interestingly, the HLA-H*02:07 allele had the highest level of mRNA expression. We showed that HLA-H signal peptide incubation mobilized HLA-E molecules at the cell surface of T-Lymphocytes, monocytes, B-Lymphocytes, and primary epithelial cells. Our results suggest that HLA-H may be functional but raises many biological issues that need to be addressed.
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Affiliation(s)
- François Jordier
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Delphine Gras
- Aix-Marseille University, INSERM, INRA, C2VN, Marseille, France
| | - Maria De Grandis
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Xavier-Benoît D'Journo
- Department of Thoracic Surgery, North Hospital, Aix-Marseille University & Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pascal-Alexandre Thomas
- Department of Thoracic Surgery, North Hospital, Aix-Marseille University & Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pascal Chanez
- Aix-Marseille University, INSERM, INRA, C2VN, Marseille, France
- Clinique des Bronches, Allergie et Sommeil, North Hospital, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Christophe Picard
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | - Jacques Chiaroni
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
| | | | - Julie Di Cristofaro
- Aix-Marseille University, CNRS, EFS, ADES, “Biologie des Groupes Sanguins”, Marseille, France
- Etablissement Français du Sang PACA Corse, Marseille, France
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