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Giziński S, Preibisch G, Kucharski P, Tyrolski M, Rembalski M, Grzegorczyk P, Gambin A. Enhancing antigenic peptide discovery: Improved MHC-I binding prediction and methodology. Methods 2024; 224:1-9. [PMID: 38295891 DOI: 10.1016/j.ymeth.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/30/2023] [Accepted: 01/16/2024] [Indexed: 02/05/2024] Open
Abstract
The Major Histocompatibility Complex (MHC) is a critical element of the vertebrate cellular immune system, responsible for presenting peptides derived from intracellular proteins. MHC-I presentation is pivotal in the immune response and holds considerable potential in the realms of vaccine development and cancer immunotherapy. This study delves into the limitations of current methods and benchmarks for MHC-I presentation. We introduce a novel benchmark designed to assess generalization properties and the reliability of models on unseen MHC molecules and peptides, with a focus on the Human Leukocyte Antigen (HLA)-a specific subset of MHC genes present in humans. Finally, we introduce HLABERT, a pretrained language model that outperforms previous methods significantly on our benchmark and establishes a new state-of-the-art on existing benchmarks.
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Affiliation(s)
| | - Grzegorz Preibisch
- Deepflare, Warsaw, Poland; University of Warsaw, Department of Mathematics Informatics and Mechanics, Warsaw, Poland.
| | | | | | | | | | - Anna Gambin
- University of Warsaw, Department of Mathematics Informatics and Mechanics, Warsaw, Poland.
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2
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Zhang M, Wang Z, Cui J, Ma X, Qiao Z, Kong X, Xu R, Li S, Du J, Zhao C. Development and characterization of 40 InDel markers from the major histocompatibility complex genes of largemouth bass (Micropterus salmoides). Mol Biol Rep 2024; 51:470. [PMID: 38551799 DOI: 10.1007/s11033-024-09429-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/08/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND The genetic improvement in growth and food habit domestication of largemouth bass (Micropterus salmoides) have made breakthroughs in past decades, while the relevant work on disease resistance were rarely carried out. Major histocompatibility complex (MHC) genes, which are well known as their numbers and high polymorphisms, have been used as candidate genes to mine disease-resistant-related molecular markers in many species. METHODS AND RESULTS In present study, we developed and characterized 40 polymorphic and biallelic InDel markers from the major histocompatibility complex genes of largemouth bass. The minor allele frequency, observed heterozygosity, expected heterozygosity and polymorphic information content of these markers ranged from 0.0556 to 0.5000, 0.1111 to 0.6389, 0.1064 to 0.5070, and 0.0994 to 0.3750, respectively. Three loci deviated significantly from Hardy-Weinberg equilibrium, while linkage disequilibrium existed at none of these loci. CONCLUSION These InDel markers might provide references for the further correlation analysis and molecular assisted selection of disease resistance in largemouth bass.
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Affiliation(s)
- Meng Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
- Hangzhou Xiaoshan Donghai Aquaculture Co., Ltd, Hangzhou, 310012, China.
- Hebei Key Laboratory of Marine Biological Resources and Environment, Hebei Ocean and Fisheries Science Research Institute, Qinhuangdao, 066200, China.
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China.
| | - Zerui Wang
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Jiao Cui
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Xiao Ma
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Zhigang Qiao
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Xianghui Kong
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Ruwei Xu
- Hangzhou Xiaoshan Donghai Aquaculture Co., Ltd, Hangzhou, 310012, China
| | - Shengjie Li
- Pearl River Fisheries Research Institute, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Chinese Academy of Fisheries Sciences, China Ministry of Agriculture, Guangzhou, 510380, China
- College of Fisheries, Henan Normal University, Xinxiang, 453007, China
| | - Jinxing Du
- Pearl River Fisheries Research Institute, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Chinese Academy of Fisheries Sciences, China Ministry of Agriculture, Guangzhou, 510380, China
| | - Chunlong Zhao
- Hebei Key Laboratory of Marine Biological Resources and Environment, Hebei Ocean and Fisheries Science Research Institute, Qinhuangdao, 066200, China.
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3
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Fu M. Evolutionary analysis of major histocompatibility complex variants in chytrid-resistant and susceptible amphibians. Infect Genet Evol 2024; 118:105544. [PMID: 38216106 DOI: 10.1016/j.meegid.2023.105544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/09/2023] [Accepted: 12/17/2023] [Indexed: 01/14/2024]
Abstract
An amphibian emerging infectious disease (EID), chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), originated in Asia but primarily led to declines and extinctions in amphibian populations outside of Asia. Host major histocompatibility complex (MHC) molecules exhibit high polymorphism, and the evolution of MHC can be influenced by recombination and pathogens. Previous studies have indicated that host MHC class II is associated with Bd resistance. In this study, I conducted recombination and selection tests on functional MHC IIß1 alleles from an Asian Bd-resistant anuran species (Bufo gargarizans) and an Australasian Bd-susceptible species (Litoria caerulea). Recombination at the same site was identified in both species, supporting the hypothesis that recombination contributes to MHC IIß1 diversity in amphibians. Positive selection was observed in MHC IIß1 alleles in both species. In L. caerulea, at least four amino acid sites were identified under significant positive selection in the MHC IIß1, whereas these sites were either negatively selected or conserved in B. gargarizans. This suggests these sites might be selected for Bd resistance. Hydrophobicity was detected in certain amino acid sites relating to Bd resistance, suggesting this physicochemical property may be a factor selected to counteract Bd infection. These findings of this study provide an evolutionary basis for understanding how amphibian MHC IIß1 may undergo selection in response to chytrid infection.
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Affiliation(s)
- Minjie Fu
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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4
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Shahbazy M, Ramarathinam SH, Li C, Illing PT, Faridi P, Croft NP, Purcell AW. MHCpLogics: an interactive machine learning-based tool for unsupervised data visualization and cluster analysis of immunopeptidomes. Brief Bioinform 2024; 25:bbae087. [PMID: 38487848 PMCID: PMC10940831 DOI: 10.1093/bib/bbae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/12/2023] [Accepted: 02/15/2024] [Indexed: 03/18/2024] Open
Abstract
The major histocompatibility complex (MHC) encodes a range of immune response genes, including the human leukocyte antigens (HLAs) in humans. These molecules bind peptide antigens and present them on the cell surface for T cell recognition. The repertoires of peptides presented by HLA molecules are termed immunopeptidomes. The highly polymorphic nature of the genres that encode the HLA molecules confers allotype-specific differences in the sequences of bound ligands. Allotype-specific ligand preferences are often defined by peptide-binding motifs. Individuals express up to six classical class I HLA allotypes, which likely present peptides displaying different binding motifs. Such complex datasets make the deconvolution of immunopeptidomic data into allotype-specific contributions and further dissection of binding-specificities challenging. Herein, we developed MHCpLogics as an interactive machine learning-based tool for mining peptide-binding sequence motifs and visualization of immunopeptidome data across complex datasets. We showcase the functionalities of MHCpLogics by analyzing both in-house and published mono- and multi-allelic immunopeptidomics data. The visualization modalities of MHCpLogics allow users to inspect clustered sequences down to individual peptide components and to examine broader sequence patterns within multiple immunopeptidome datasets. MHCpLogics can deconvolute large immunopeptidome datasets enabling the interrogation of clusters for the segregation of allotype-specific peptide sequence motifs, identification of sub-peptidome motifs, and the exportation of clustered peptide sequence lists. The tool facilitates rapid inspection of immunopeptidomes as a resource for the immunology and vaccine communities. MHCpLogics is a standalone application available via an executable installation at: https://github.com/PurcellLab/MHCpLogics.
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Affiliation(s)
- Mohammad Shahbazy
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Chen Li
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Patricia T Illing
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Pouya Faridi
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
- Monash Proteomics and Metabolomics Platform, Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
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Nelke C, Schmid S, Kleefeld F, Schroeter CB, Goebel HH, Hoffmann S, Preuße C, Kölbel H, Meuth SG, Ruck T, Stenzel W. Complement and MHC patterns can provide the diagnostic framework for inflammatory neuromuscular diseases. Acta Neuropathol 2024; 147:15. [PMID: 38214778 PMCID: PMC10786976 DOI: 10.1007/s00401-023-02669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024]
Abstract
Histopathological analysis stands as the gold standard for the identification and differentiation of inflammatory neuromuscular diseases. These disorders continue to constitute a diagnostic challenge due to their clinical heterogeneity, rarity and overlapping features. To establish standardized protocols for the diagnosis of inflammatory neuromuscular diseases, the development of cost-effective and widely applicable tools is crucial, especially in settings constrained by limited resources. The focus of this review is to emphasize the diagnostic value of major histocompatibility complex (MHC) and complement patterns in the immunohistochemical analysis of these diseases. We explore the immunological background of MHC and complement signatures that characterize inflammatory features, with a specific focus on idiopathic inflammatory myopathies. With this approach, we aim to provide a diagnostic algorithm that may improve and simplify the diagnostic workup based on a limited panel of stainings. Our approach acknowledges the current limitations in the field of inflammatory neuromuscular diseases, particularly the scarcity of large-scale, prospective studies that validate the diagnostic potential of these markers. Further efforts are needed to establish a consensus on the diagnostic protocol to effectively distinguish these diseases.
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Affiliation(s)
- Christopher Nelke
- Department of Neurology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Simone Schmid
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health (BIH), Charitéplatz 1, 10117, Berlin, Germany
| | - Felix Kleefeld
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health (BIH), Charitéplatz 1, 10117, Berlin, Germany
| | - Christina B Schroeter
- Department of Neurology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Hans-Hilmar Goebel
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health (BIH), Charitéplatz 1, 10117, Berlin, Germany
| | - Sarah Hoffmann
- Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health (BIH), Charitéplatz 1, 10117, Berlin, Germany
| | - Corinna Preuße
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health (BIH), Charitéplatz 1, 10117, Berlin, Germany
- Department of Neuropediatrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health (BIH), Augustenburger Platz 1, 13353, Berlin, Germany
| | - Heike Kölbel
- Department of Neuropaediatrics, Klinik für Kinderheilkunde I, Universitätsklinikum Essen, Essen, Germany
| | - Sven G Meuth
- Department of Neurology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Tobias Ruck
- Department of Neurology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225, Duesseldorf, Germany
| | - Werner Stenzel
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health (BIH), Charitéplatz 1, 10117, Berlin, Germany.
- Leibniz Science Campus Chronic Inflammation, Berlin, Germany.
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6
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Shiina T, Kulski JK. HLA Genetics for the Human Diseases. Adv Exp Med Biol 2024; 1444:237-258. [PMID: 38467984 DOI: 10.1007/978-981-99-9781-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Highly polymorphic human leukocyte antigen (HLA) molecules (alleles) expressed by different classical HLA class I and class II genes have crucial roles in the regulation of innate and adaptive immune responses, transplant rejection and in the pathogenesis of numerous infectious and autoimmune diseases. To date, over 35,000 HLA alleles have been published from the IPD-IMGT/HLA database, and specific HLA alleles and HLA haplotypes have been reported to be associated with more than 100 different diseases and phenotypes. Next generation sequencing (NGS) technology developed in recent years has provided breakthroughs in various HLA genomic/gene studies and transplant medicine. In this chapter, we review the current information on the HLA genomic structure and polymorphisms, as well as the genetic context in which numerous disease associations have been identified in this region.
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Affiliation(s)
| | - Jerzy K Kulski
- Tokai University School of Medicine, Isehara, Japan
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
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7
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ZHAO JIE, YANG XUANTAO, ZHANG HAIXI, GU XUEZHONG. Identification of TNFRSF1A as a novel regulator of carfilzomib resistance in multiple myeloma. Oncol Res 2023; 32:325-337. [PMID: 38186567 PMCID: PMC10765120 DOI: 10.32604/or.2023.030770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/20/2023] [Indexed: 01/09/2024] Open
Abstract
Multiple myeloma (MM) is a hematological tumor with high mortality and recurrence rate. Carfilzomib is a new-generation proteasome inhibitor that is used as the first-line therapy for MM. However, the development of drug resistance is a pervasive obstacle to treating MM. Therefore, elucidating the drug resistance mechanisms is conducive to the formulation of novel therapeutic therapies. To elucidate the mechanisms of carfilzomib resistance, we retrieved the GSE78069 microarray dataset containing carfilzomib-resistant LP-1 MM cells and parental MM cells. Differential gene expression analyses revealed major alterations in the major histocompatibility complex (MHC) and cell adhesion molecules. The upregulation of the tumor necrosis factor (TNF) receptor superfamily member 1A (TNFRSF1A) gene was accompanied by the downregulation of MHC genes and cell adhesion molecules. Furthermore, to investigate the roles of these genes, we established a carfilzomib-resistant cell model and observed that carfilzomib resistance induced TNFRSF1A overexpression and TNFRSF1A silencing reversed carfilzomib resistance and reactivated the expression of cell adhesion molecules. Furthermore, TNFRSF1A silencing suppressed the tumorigenesis of MM cells in immunocompetent mice, indicating that TNFRSF1A may lead to carfilzomib resistance by dampening antitumor immunity. Furthermore, our results indicated that TNFRSF1A overexpression conferred carfilzomib resistance in MM cells and suppressed the expression of MHC genes and cell adhesion molecules. The suppression of MHC genes and cell adhesion molecules may impair the interaction between immune cells and cancer cells to impair antitumor immunity. Future studies are warranted to further investigate the signaling pathway underlying the regulatory role of TNFRSF1A in MM cells.
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Affiliation(s)
- JIE ZHAO
- Department of Hematology, The First People’s Hospital of Yunnan Province, Yunnan Province Clinical Research Center for Hematologic Disease, Yunnan Province Clinical Center for Hematologic Disease, Kunming, 650032, China
| | - XUANTAO YANG
- Department of Pathology, The First People’s Hospital of Yunnan Province, Kunming, 650032, China
| | - HAIXI ZHANG
- Department of Hematology, The First People’s Hospital of Yunnan Province, Yunnan Province Clinical Research Center for Hematologic Disease, Yunnan Province Clinical Center for Hematologic Disease, Kunming, 650032, China
| | - XUEZHONG GU
- Department of Hematology, The First People’s Hospital of Yunnan Province, Yunnan Province Clinical Research Center for Hematologic Disease, Yunnan Province Clinical Center for Hematologic Disease, Kunming, 650032, China
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8
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Priyamvada P, Ramaiah S. Pan-genome and reverse vaccinology approaches to design multi-epitope vaccine against Epstein-Barr virus associated with colorectal cancer. Immunol Res 2023; 71:887-908. [PMID: 37423939 DOI: 10.1007/s12026-023-09403-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/16/2023] [Indexed: 07/11/2023]
Abstract
Epstein-Barr virus (EBV) is a global lymphotropic virus and has been associated with various malignancies, among which colorectal cancer (CRC) is the prevalent one causing mortality worldwide. In the recent past, numerous research efforts have been made to develop a potential vaccine against this virus; however, none is effective possibly due to their low throughput, laboriousness, and lack of sensitivity. In this study, we designed a multi-epitope subunit vaccine that targets latent membrane protein (LMP-2B) of EBV using pan-genome and reverse vaccinology approaches. Twenty-three major histocompatibility complex (MHC) epitopes (five class-I and eighteen class-II) and eight B-cell epitopes, which have been found to be antigenic, immunogenic, and non-toxic, were selected for the vaccine construction. Furthermore, 24 vaccine constructs (VCs) were designed from the predicted epitopes and out of which VC1 was selected and finalized based on its structural parameters. The functionality of VC1 was validated through molecular docking with different immune receptors (MHC class-I, MHC class-II, and TLRs). The binding affinity, molecular and immune simulation revealed that the VC1 had more stable interaction and is believed to elicit good immune responses against EBV. HIGHLIGHTS: Pan-genome and reverse vaccinology approaches were used to design a multi-epitope subunit vaccine against LMP-2B protein of EBV. Epitopes were selected based on the antigenic, immunogenic, and non-toxic properties. Twenty-four vaccine constructs (VCs) were designed from the predicted epitopes. Designed vaccine VC1 has shown good binding affinity and molecular and immune simulation. VC1 was validated using molecular docking with different immune receptors.
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Affiliation(s)
- P Priyamvada
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India
- Department of Bio-Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India.
- Department of Bio-Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India.
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Nayak SS, Panigrahi M, Kumar H, Rajawat D, Sharma A, Bhushan B, Dutt T. Evidence for selective sweeps in the MHC gene repertoire of various cattle breeds. Anim Biotechnol 2023; 34:4167-4173. [PMID: 37039747 DOI: 10.1080/10495398.2023.2196317] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Major Histocompatibility Complex (MHC) genes are among the immune genes that have been extensively studied in vertebrates and are necessary for adaptive immunity. In the immunological response to infectious diseases, they play several significant roles. This research paper provides the selection signatures in the MHC region of the bovine genome as well as how certain genes related to innate immunity are undergoing a positive selective sweep. Here, we investigated signatures of historical selection on MHC genes in 15 different cattle populations and a total of 427 individuals. To identify the selection signatures, we have used three separate summary statistics. The findings show potential selection signatures in cattle from whom we isolated genes involved in the MHC. The most significant regions related to the bovine MHC are BOLA, non-classical MHC class I antigen (BOLA-NC1), Microneme protein 1 (MIC1) , Cluster of Differentiation 244 (CD244), Gap Junction Alpha-5 Protein (GJA5). It will be possible to gain new insight into immune system evolution by understanding the distinctive characteristics of MHC in cattle.
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Affiliation(s)
- Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
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Garcia AA, Plain KM, Thomson PC, Thomas AJ, Davies CJ, Toribio JALML, Whittington RJ. Association between major histocompatibility complex haplotypes and susceptibility of unvaccinated and vaccinated cattle to paratuberculosis. Vet Immunol Immunopathol 2023; 265:110677. [PMID: 37952345 DOI: 10.1016/j.vetimm.2023.110677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Bovine Johne's disease (BJD) or paratuberculosis is caused by Mycobacterium avium spp. paratuberculosis (MAP) and is a worldwide problem among domestic and wild ruminants. While vaccines are available, natural differences in background immunity between breeds within species and between individuals within herds suggest that genetic differences may be able to be exploited in marker-assisted selection as an aid to disease control. The major histocompatibility complex (MHC) is an important component in immune recognition with considerable genetic variability. In this study, associations between the MHC and resistance to BJD were explored in dairy cattle across two herds in which some of the cattle had been vaccinated with Silirum® (n = 540 cows). A BJD susceptible animal was exposed to MAP and became infected, while a resistant animal was exposed but did not become infected. There are different ways to define both exposure and infection, with different levels of stringency, therefore many classifications of the same set of animals are possible and were included in the analysis. The polymorphic regions of major histocompatibility complex class I (MHC I) and class II (MHC II) genes were amplified from the genomic DNA by PCR and sequenced, targeting exons 2 and 3 of the classical and non-classical MHC I genes and exon 2 from the DRB3, DQA1, DQA2 + 3 and DQB MHC II genes. The frequencies of MHC I and MHC II haplotypes and alleles were determined in susceptible and resistant populations. In unvaccinated animals, seven MHC I haplotypes and seven MHC II haplotypes were associated with susceptibility while two MHC I and six MHC II haplotypes were associated with resistance (P < 0.05). In vaccinated animals, two MHC I and three MHC II haplotypes were associated with susceptibility, while one MHC I and two MHC II haplotypes were associated with resistance (P < 0.05). The alleles in significant haplotypes were also identified. Case definitions with higher stringency resulted in fewer animals being included in the analyses, but the power to detect an association was not reduced and there was an increase in strength and consistency of associations. Consistent use of stringent case definitions is likely to improve agreement in future association studies.
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Affiliation(s)
- Anabel A Garcia
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Karren M Plain
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Peter C Thomson
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Aaron J Thomas
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | - Christopher J Davies
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | - Jenny-Ann L M L Toribio
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW 2570, Australia
| | - Richard J Whittington
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW 2570, Australia.
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Murray JS. Dichotomy in TCR V-domain dynamics binding the opposed inclined planes of pMHC-II and pMHC-I α-helices. Mol Immunol 2023; 162:111-124. [PMID: 37677988 DOI: 10.1016/j.molimm.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/24/2023] [Accepted: 07/09/2023] [Indexed: 09/09/2023]
Abstract
Ligand recognition by the human α/β T-cell antigen receptor (TCR) heterodimer protein, unlike the surface immunoglobulin (sIg) B-cell receptor, is not governed by relative binding affinity. Its interaction with the peptide (p) plus major histocompatibility complex (MHC) protein (abbrev. pMHC) likely involves some different molecular mechanism linking pMHC binding to T-cell functions. Recent analytical geometry of TCR:pMHC-II solved crystallographic structures (n = 40) revealed that each variable (V)-domain is bound in similar, yet mathematically unique orientations to its target pMHC groove. The relative position of the central cysteine of each V-domain was examined by multivariable calculus in spherical coordinates, where a simple volume element (dV) was found to describe clonotypic geometry with pMHC-II. Here, the study was expanded to include TCR:pMHC-I structures, and to model a physical mechanism, specifically involving the two directionally opposed inclined planes (IP) manifest by the two major α-helices prominent in both MHC-I and MHC-II proteins. Calculations for rotational torque of each V-domain, together with acceleration up and down the slopes of both MHC α-helices were used to estimate the time a given V-domain spends sliding down its cognate MHC IP. This V-domain rotation/sliding mechanism appears to be quantitatively unique for each TCR:pMHC V-domain (n = 40). However, there is an apparent and common dichotomy between the mobility of each V-domain with respect to the two classes of MHC proteins. Evolutionary motifs in the MHC helices support that the V-domains negotiate the opposed inclined planes of pMHC ligands in clonotypic fashion. Thus, this model is useful in understanding how mechanical forces are linked to TCR function.
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12
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Minias P, Peng WXVH, Matson KD. Evolutionary trade-off between innate and acquired immune defences in birds. Front Zool 2023; 20:32. [PMID: 37684615 PMCID: PMC10486109 DOI: 10.1186/s12983-023-00511-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND The development, maintenance, and use of immune defences are costly. Therefore, animals face trade-offs in terms of resource allocation within their immune system and between their immune system and other physiological processes. To maximize fitness, evolution may favour investment in one immunological defence or subsystem over another in a way that matches a species broader life history strategy. Here, we used phylogenetically-informed comparative analyses to test for relationships between two immunological components. Natural antibodies and complement were used as proxies for the innate branch; structural complexity of the major histocompatibility complex (MHC) region was used for the acquired branch. RESULTS We found a negative association between the levels of natural antibodies (i.e., haemagglutination titre) and the total MHC gene copy number across the avian phylogeny, both at the species and family level. The family-level analysis indicated that this association was apparent for both MHC-I and MHC-II, when copy numbers within these two MHC regions were analysed separately. The association remained significant after controlling for basic life history components and for ecological traits commonly linked to pathogen exposure. CONCLUSION Our results provide the first phylogenetically robust evidence for an evolutionary trade-off within the avian immune system, with a more developed acquired immune system (i.e., more complex MHC architecture) in more derived bird lineages (e.g., passerines) being accompanied by an apparent downregulation of the innate immune system.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Wei-Xuan V-H Peng
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708PB, Wageningen, Netherlands
| | - Kevin D Matson
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708PB, Wageningen, Netherlands
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13
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Fu M, Eimes JA, Kong S, Lamichhaney S, Waldman B. Identification of major histocompatibility complex genotypes associated with resistance to an amphibian emerging infectious disease. Infect Genet Evol 2023; 113:105470. [PMID: 37336279 DOI: 10.1016/j.meegid.2023.105470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
Amphibian chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), emerged from Asia and spread globally. By comparing functional MHC IIß1 alleles from an Asian Bd-resistant anuran species (Bufo gargarizans) with those of an Australasian Bd-susceptible species (Litoria caerulea), we identified MHC genotypes associated with Bd resistance. These alleles encode a glycine deletion (G90β1) and adjacent motifs in the deepest pathogen-derived peptide-binding groove. Every Bd-resistant individual, but no susceptible individuals, possessed at least one allele encoding the variant. We detected trans-species polymorphism at the end of the MHC IIβ1 sequences. The G90β1 deletion was encoded by different alleles in the two species, suggesting it may have evolved independently in each species rather than having been derived from a common ancestor. These results are consistent with a scenario by which MHC adaptations that confer resistance to the pathogen have evolved by convergent evolution. Immunogenetic studies such as this are critical to ongoing conservation efforts.
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Affiliation(s)
- Minjie Fu
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
| | - John A Eimes
- University College, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Sungsik Kong
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Sangeet Lamichhaney
- Department of Biological Sciences, Kent State University, Kent, OH 44243, USA
| | - Bruce Waldman
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea; Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
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Cuevas MVR, Hardy MP, Larouche JD, Apavaloaei A, Kina E, Vincent K, Gendron P, Laverdure JP, Durette C, Thibault P, Lemieux S, Perreault C, Ehx G. BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens. Genome Biol 2023; 24:188. [PMID: 37582761 PMCID: PMC10426134 DOI: 10.1186/s13059-023-03029-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
MHC-I-associated peptides deriving from non-coding genomic regions and mutations can generate tumor-specific antigens, including neoantigens. Quantifying tumor-specific antigens' RNA expression in malignant and benign tissues is critical for discriminating actionable targets. We present BamQuery, a tool attributing an exhaustive RNA expression to MHC-I-associated peptides of any origin from bulk and single-cell RNA-sequencing data. We show that many cryptic and mutated tumor-specific antigens can derive from multiple discrete genomic regions, abundantly expressed in normal tissues. BamQuery can also be used to predict MHC-I-associated peptides immunogenicity and identify actionable tumor-specific antigens de novo.
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Affiliation(s)
- Maria Virginia Ruiz Cuevas
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Jean-David Larouche
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Anca Apavaloaei
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Eralda Kina
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Chemistry, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, H3C 3J7, Canada
| | - Grégory Ehx
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC, H3C 3J7, Canada.
- Laboratory of Hematology, GIGA-I3, University of Liege, CHU of Liege, Liege, Belgium.
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15
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Dimitrakopoulou D, Khwatenge CN, James-Zorn C, Paiola M, Bellin EW, Tian Y, Sundararaj N, Polak EJ, Grayfer L, Barnard D, Ohta Y, Horb M, Sang Y, Robert J. Advances in the Xenopus immunome: Diversification, expansion, and contraction. Dev Comp Immunol 2023; 145:104734. [PMID: 37172665 PMCID: PMC10230362 DOI: 10.1016/j.dci.2023.104734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 03/18/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
Xenopus is a genus of African clawed frogs including two species, X. tropicalis and X. laevis that are extensively used in experimental biology, immunology, and biomedical studies. The availability of fully sequenced and annotated Xenopus genomes is strengthening genome-wide analyses of gene families and transgenesis to model human diseases. However, inaccuracies in genome annotation for genes involved in the immune system (i.e., immunome) hamper immunogenetic studies. Furthermore, advanced genome technologies (e.g., single-cell and RNA-Seq) rely on well-annotated genomes. The annotation problems of Xenopus immunome include a lack of established orthology across taxa, merged gene models, poor representation in gene pages on Xenbase, misannotated genes and missing gene IDs. The Xenopus Research Resource for Immunobiology in collaboration with Xenbase and a group of investigators are working to resolve these issues in the latest versions of genome browsers. In this review, we summarize the current problems of previously misannotated gene families that we have recently resolved. We also highlight the expansion, contraction, and diversification of previously misannotated gene families.
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Affiliation(s)
- Dionysia Dimitrakopoulou
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Collins N Khwatenge
- Department of Agriculture and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, USA
| | - Christina James-Zorn
- Xenbase, Division of Developmental Biology, Cincinnti Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Matthieu Paiola
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Eleanor Wise Bellin
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Yun Tian
- Department of Agriculture and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, USA
| | - Nivitha Sundararaj
- Xenbase, Division of Developmental Biology, Cincinnti Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Emma J Polak
- Biology Department, Worcester State University, MA, USA
| | - Leon Grayfer
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Daron Barnard
- Biology Department, Worcester State University, MA, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marko Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Yongming Sang
- Department of Agriculture and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, USA.
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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16
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Mellinger S, Stervander M, Lundberg M, Drews A, Westerdahl H. Improved haplotype resolution of highly duplicated MHC genes in a long-read genome assembly using MiSeq amplicons. PeerJ 2023; 11:e15480. [PMID: 37456901 PMCID: PMC10349553 DOI: 10.7717/peerj.15480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/08/2023] [Indexed: 07/18/2023] Open
Abstract
Long-read sequencing offers a great improvement in the assembly of complex genomic regions, such as the major histocompatibility complex (MHC) region, which can contain both tandemly duplicated MHC genes (paralogs) and high repeat content. The MHC genes have expanded in passerine birds, resulting in numerous MHC paralogs, with relatively high sequence similarity, making the assembly of the MHC region challenging even with long-read sequencing. In addition, MHC genes show rather high sequence divergence between alleles, making diploid-aware assemblers incorrectly classify haplotypes from the same locus as sequences originating from different genomic regions. Consequently, the number of MHC paralogs can easily be over- or underestimated in long-read assemblies. We therefore set out to verify the MHC diversity in an original and a haplotype-purged long-read assembly of one great reed warbler Acrocephalus arundinaceus individual (the focal individual) by using Illumina MiSeq amplicon sequencing. Single exons, representing MHC class I (MHC-I) and class IIB (MHC-IIB) alleles, were sequenced in the focal individual and mapped to the annotated MHC alleles in the original long-read genome assembly. Eighty-four percent of the annotated MHC-I alleles in the original long-read genome assembly were detected using 55% of the amplicon alleles and likewise, 78% of the annotated MHC-IIB alleles were detected using 61% of the amplicon alleles, indicating an incomplete annotation of MHC genes. In the haploid genome assembly, each MHC-IIB gene should be represented by one allele. The parental origin of the MHC-IIB amplicon alleles in the focal individual was determined by sequencing MHC-IIB in its parents. Two of five larger scaffolds, containing 6-19 MHC-IIB paralogs, had a maternal and paternal origin, respectively, as well as a high nucleotide similarity, which suggests that these scaffolds had been incorrectly assigned as belonging to different loci in the genome rather than as alternate haplotypes of the same locus. Therefore, the number of MHC-IIB paralogs was overestimated in the haploid genome assembly. Based on our findings we propose amplicon sequencing as a suitable complement to long-read sequencing for independent validation of the number of paralogs in general and for haplotype inference in multigene families in particular.
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Affiliation(s)
- Samantha Mellinger
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Martin Stervander
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
- Department of Biology and Environmental Science, Faculty of Health and Life Sciences, Linnaeus University, Kalmar, Sweden
- Bird Group, Natural History Museum, Tring, Hertfordshire, United Kingdom
| | - Max Lundberg
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Anna Drews
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Helena Westerdahl
- Department of Biology, Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
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17
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Wong-Benito V, de Rijke J, Dixon B. Antigen presentation in vertebrates: Structural and functional aspects. Dev Comp Immunol 2023; 144:104702. [PMID: 37116963 DOI: 10.1016/j.dci.2023.104702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 06/05/2023]
Abstract
Antigen presentation is a key process of the immune system and is responsible for the activation of T cells. The main characters are the major histocompatibility complex class I (MHC-I) and class II (MHC-II) molecules, and accessory proteins that act as chaperones for these glycoproteins. Current knowledge of this process and also the elucidation of the structural features of these proteins, has been extensively reviewed in humans. Unfortunately, this is not the case for non-human species, wherein the function and structural characteristic of the antigen presentation proteins is far from being understood. The majority of previous studies in non-human species, especially in teleost fish and lower vertebrates, are limited to the transcriptomic level, which leads to gaps in the knowledge about the functional process of antigen presentation in these species. This review summarizes what is known so far about antigen presentation pathways in vertebrates from a structural and functional perspective. The focus is not only on the MHC receptors, but also, on the forgotten characters of these pathways such as the proteins of the peptide loading complex, and the MHC-II chaperone invariant chain.
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Affiliation(s)
| | - Jill de Rijke
- Department of Biology, University of Waterloo, Canada
| | - Brian Dixon
- Department of Biology, University of Waterloo, Canada.
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18
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Winternitz J, Chakarov N, Rinaud T, Ottensmann M, Krüger O. High functional allelic diversity and copy number in both MHC classes in the common buzzard. BMC Ecol Evol 2023; 23:24. [PMID: 37355591 PMCID: PMC10290333 DOI: 10.1186/s12862-023-02135-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 06/12/2023] [Indexed: 06/26/2023] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC), which encodes molecules that recognize various pathogens and parasites and initiates the adaptive immune response in vertebrates, is renowned for its exceptional polymorphism and is a model of adaptive gene evolution. In birds, the number of MHC genes and sequence diversity varies greatly among taxa, believed due to evolutionary history and differential selection pressures. Earlier characterization studies and recent comparative studies suggest that non-passerine species have relatively few MHC gene copies compared to passerines. Additionally, comparative studies that have looked at partial MHC sequences have speculated that non-passerines have opposite patterns of selection on MHC class I (MHC-I) and class II (MHC-II) loci than passerines: namely, greater sequence diversity and signals of selection on MHC-II than MHC-I. However, new sequencing technology is revealing much greater MHC variation than previously expected while also facilitating full sequence variant detection directly from genomic data. Our study aims to take advantage of high-throughput sequencing methods to fully characterize both classes and domains of MHC of a non-passerine bird of prey, the common buzzard (Buteo buteo), to test predictions of MHC variation and differential selection on MHC classes. RESULTS Using genetic, genomic, and transcriptomic high-throughput sequencing data, we established common buzzards have at least three loci that produce functional alleles at both MHC classes. In total, we characterize 91 alleles from 113 common buzzard chicks for MHC-I exon 3 and 41 alleles from 125 chicks for MHC-IIB exon 2. Among these alleles, we found greater sequence polymorphism and stronger diversifying selection at MHC-IIB exon 2 than MHC-I exon 3, suggesting differential selection pressures on MHC classes. However, upon further investigation of the entire peptide-binding groove by including genomic data from MHC-I exon 2 and MHC-IIA exon 2, this turned out to be false. MHC-I exon 2 was as polymorphic as MHC-IIB exon 2 and MHC-IIA exon 2 was essentially invariant. Thus, comparisons between MHC-I and MHC-II that included both domains of the peptide-binding groove showed no differences in polymorphism nor diversifying selection between the classes. Nevertheless, selection analysis indicates balancing selection has been acting on common buzzard MHC and phylogenetic inference revealed that trans-species polymorphism is present between common buzzards and species separated for over 33 million years for class I and class II. CONCLUSIONS We characterize and confirm the functionality of unexpectedly high copy number and allelic diversity in both MHC classes of a bird of prey. While balancing selection is acting on both classes, there is no evidence of differential selection pressure on MHC classes in common buzzards and this result may hold more generally once more data for understudied MHC exons becomes available.
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Affiliation(s)
- Jamie Winternitz
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Tony Rinaud
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Meinolf Ottensmann
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615 Bielefeld, Germany
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19
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Goto K, Tamehiro N, Yoshida T, Hanada H, Sakuma T, Adachi R, Kondo K, Takeuchi I. Novel Machine Learning Method AllerStat Identifies Statistically Significant Allergen-Specific Patterns in Protein Sequences. J Biol Chem 2023; 299:104733. [PMID: 37086787 DOI: 10.1016/j.jbc.2023.104733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 04/24/2023] Open
Abstract
Cutting-edge technologies such as genome editing and synthetic biology allow us to produce novel foods and functional proteins. However, their toxicity and allergenicity must be accurately evaluated. It is known that specific amino-acid sequences in proteins make some proteins allergic, but many of these sequences remain uncharacterized. In this study, we introduce a data-driven approach and a machine-learning (ML) method to find undiscovered allergen specific patterns (ASPs) among amino acid sequences. The proposed method enables an exhaustive search for amino-acid subsequences whose frequencies are statistically significantly higher in allergenic proteins. As a proof-of-concept, we created a database containing 21,154 proteins of which the presence or absence of allergic reactions are already known, and applied the proposed method to the database. The detected ASPs in this proof-of-concept study were consistent with known biological findings, and the allergenicity prediction performance using the detected ASPs was higher than extant approaches, indicating this method may be useful in evaluating the utility of synthetic foods and proteins.
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Affiliation(s)
- Kento Goto
- Department of Computer Science, Nagoya Institute of Technology. Gokiso-cho, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Norimasa Tamehiro
- Division of Biochemistry, National Institute of Health Sciences. 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takumi Yoshida
- Department of Computer Science, Nagoya Institute of Technology. Gokiso-cho, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Hiroyuki Hanada
- Center for Advanced Intelligence Project, RIKEN. 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Takuto Sakuma
- Department of Computer Science, Nagoya Institute of Technology. Gokiso-cho, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Reiko Adachi
- Division of Biochemistry, National Institute of Health Sciences. 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Kazunari Kondo
- Division of Biochemistry, National Institute of Health Sciences. 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan.
| | - Ichiro Takeuchi
- Graduate School of Engineering, Nagoya University.Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan; Center for Advanced Intelligence Project, RIKEN. 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan.
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20
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Zhang P, Zhang B, Dunn DW, Song X, Huang K, Dong S, Niu F, Ying M, Zhang Y, Shang Y, Pan R, Li B. Social and paternal female choice for male MHC genes in golden snub-nosed monkeys (Rhinopithecus roxellana). Mol Ecol 2023. [PMID: 36942819 DOI: 10.1111/mec.16932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/12/2023] [Accepted: 03/17/2023] [Indexed: 03/23/2023]
Abstract
Genes of the major histocompatibility complex (MHC) play important roles in vertebrate immunocompetence. MHC genes thus offer females indirect benefits to mate choice through the production of offspring of an optimal MHC genotype. Females may choose males with specific MHC haplotypes, dissimilar MHC genotypes, MHC heterozygous males or MHC-diverse males. We tested these four alternatives for both female social and paternal choice in wild golden snub-nosed monkeys (Rhinopithecus roxellana) by examining overall genetic variability (via microsatellites) and four MHC-genes (DRB1, DRB2, DQA1 and DQB1). Monte Carlo randomization tests showed that MHC dissimilarity was favored for social choice (males to which females were socially affiliated) and intermediate MHC dissimilarity was favored in paternal choice (fathers of offspring). No evidence of inbreeding avoidance was found for either social or paternal mates. We found that MHC heterozygotes, higher microsatellite multi-locus heterozygosity and higher microsatellites diversity were favored for social mates, and higher microsatellite diversity was favored for paternal mates. Independent of male age, we found that the formation of male-female social pairings is significantly predicted by compatibility based on the sharing of MHC haplotypes. However, we found no evidence of independent genetic effects on the duration of male-female social pairings, male social status (achieving OMU leader male status or not), the number of females with which individual leader males paired, the likelihood of potential male-female pairings producing offspring, or whether males fathered offspring or not. Overall, our findings suggest different genetic factors are involved in social and paternal choice in R. roxellana.
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Affiliation(s)
- Pei Zhang
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Bingyi Zhang
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Derek W Dunn
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xiaoyue Song
- Shaanxi Province Engineering & Technology Research Center of Shanbei Cashmere Goats, Yulin University, Yulin, 719000, China
| | - Kang Huang
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Shixuan Dong
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Fei Niu
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Meijing Ying
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yingying Zhang
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yixin Shang
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Ruliang Pan
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Baoguo Li
- Shaanxi Key Laboratory of Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
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21
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Yang Z, Wu Z, Santich BH, Liu J, Liu C, Cheung NKV. Targeting Intracellular Antigens with pMHC-Binding Antibodies: A Phage Display Approach. Methods Mol Biol 2023; 2702:327-345. [PMID: 37679628 DOI: 10.1007/978-1-0716-3381-6_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Antibodies that bind peptide-MHC (pMHC) complex in a manner akin to T cell receptor (TCR) have not only helped in understanding the mechanism of TCR-pMHC interactions in the context of T cell biology but also spurred considerable interest in recent years as potential cancer therapeutics. Traditional methods to generate such antibodies using hybridoma and B cell sorting technologies are sometimes inadequate, possibly due to the small contribution of peptide to the overall B cell epitope space on the surface of the pMHC complex (typical peptide MW = 1 kDa versus MHC MW = 45 kDa) and to the multiple efficiency limiting steps inherent in these methods. In this chapter we describe phage display approaches, including a cell panning strategy, for the rapid generation of such antibodies with high specificity and affinity.
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Affiliation(s)
| | - Zhihao Wu
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian H Santich
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | | | - Cheng Liu
- Eureka Therapeutics, Emeryville, CA, USA
| | - Nai-Kong V Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
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22
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Müller L, Burton AK, Tayler CL, Rowedder JE, Hutchinson JP, Peace S, Quayle JM, Leveridge MV, Annan RS, Trost M, Peltier-Heap RE, Dueñas ME. A high-throughput MALDI-TOF MS biochemical screen for small molecule inhibitors of the antigen aminopeptidase ERAP1. SLAS Discov 2023; 28:3-11. [PMID: 36414185 DOI: 10.1016/j.slasd.2022.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Abstract
MALDI-TOF MS is a powerful analytical technique that provides a fast and label-free readout for in vitro assays in the high-throughput screening (HTS) environment. Here, we describe the development of a novel, HTS compatible, MALDI-TOF MS-based drug discovery assay for the endoplasmic reticulum aminopeptidase 1 (ERAP1), an important target in immuno-oncology and auto-immune diseases. A MALDI-TOF MS assay was developed beginning with an already established ERAP1 RapidFire MS (RF MS) assay, where the peptide YTAFTIPSI is trimmed into the product TAFTIPSI. We noted low ionisation efficiency of these peptides in MALDI-TOF MS and hence incorporated arginine residues into the peptide sequences to improve ionisation. The optimal assay conditions were established with these new basic assay peptides on the MALDI-TOF MS platform and validated with known ERAP1 inhibitors. Assay stability, reproducibility and robustness was demonstrated on the MALDI-TOF MS platform. From a set of 699 confirmed ERAP1 binders, identified in a prior affinity selection mass spectrometry (ASMS) screen, active compounds were determined at single concentration and in a dose-response format with the new MALDI-TOF MS setup. Furthermore, to allow for platform performance comparison, the same compound set was tested on the established RF MS setup, as the new basic peptides showed fragmentation in ESI-MS. The two platforms showed a comparable performance, but the MALDI-TOF MS platform had several advantages, such as shorter sample cycle times, reduced reagent consumption, and a lower tight-binding limit.
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Affiliation(s)
- Leonie Müller
- Newcastle University, Faculty of Medical Sciences, Biosciences Institute, Framlington Place, Newcastle Upon Tyne NE2 4HH, United Kingdom
| | - Amy K Burton
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Chloe L Tayler
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - James E Rowedder
- GSK, Screening, Profiling and Mechanistic Biology, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Jonathan P Hutchinson
- GSK, Screening, Profiling and Mechanistic Biology, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Simon Peace
- GSK, Medicinal Chemistry, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Julie M Quayle
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Melanie V Leveridge
- GSK, Screening, Profiling and Mechanistic Biology, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Roland S Annan
- GSK, Discovery Analytical, Gunnels Wood Rd, Stevenage SG1 2NY, United Kingdom
| | - Matthias Trost
- Newcastle University, Faculty of Medical Sciences, Biosciences Institute, Framlington Place, Newcastle Upon Tyne NE2 4HH, United Kingdom.
| | | | - Maria Emilia Dueñas
- Newcastle University, Faculty of Medical Sciences, Biosciences Institute, Framlington Place, Newcastle Upon Tyne NE2 4HH, United Kingdom.
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23
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Worsley SF, Davies CS, Mannarelli ME, Komdeur J, Dugdale HL, Richardson DS. Assessing the causes and consequences of gut mycobiome variation in a wild population of the Seychelles warbler. Microbiome 2022; 10:242. [PMID: 36575553 PMCID: PMC9795730 DOI: 10.1186/s40168-022-01432-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Considerable research has focussed on the importance of bacterial communities within the vertebrate gut microbiome (GM). However, studies investigating the significance of other microbial kingdoms, such as fungi, are notably lacking, despite their potential to influence host processes. Here, we characterise the fungal GM of individuals living in a natural population of Seychelles warblers (Acrocephalus sechellensis). We evaluate the extent to which fungal GM structure is shaped by environment and host factors, including genome-wide heterozygosity and variation at key immune genes (major histocompatibility complex (MHC) and Toll-like receptor (TLR)). Importantly, we also explore the relationship between fungal GM differences and subsequent host survival. To our knowledge, this is the first time that the genetic drivers and fitness consequences of fungal GM variation have been characterised for a wild vertebrate population. RESULTS Environmental factors, including season and territory quality, explain the largest proportion of variance in the fungal GM. In contrast, neither host age, sex, genome-wide heterozygosity, nor TLR3 genotype was associated with fungal GM differences in Seychelles warblers. However, the presence of four MHC-I alleles and one MHC-II allele was associated with changes in fungal GM alpha diversity. Changes in fungal richness ranged from between 1 and 10 sequencing variants lost or gained; in some cases, this accounted for 20% of the fungal variants carried by an individual. In addition to this, overall MHC-I allelic diversity was associated with small, but potentially important, changes in fungal GM composition. This is evidenced by the fact that fungal GM composition differed between individuals that survived or died within 7 months of being sampled. CONCLUSIONS Our results suggest that environmental factors play a primary role in shaping the fungal GM, but that components of the host immune system-specifically the MHC-may also contribute to the variation in fungal communities across individuals within wild populations. Furthermore, variation in the fungal GM can be associated with differential survival in the wild. Further work is needed to establish the causality of such relationships and, thus, the extent to which components of the GM may impact host evolution. Video Abstract.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
| | - Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Maria-Elena Mannarelli
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
- Nature Seychelles, Roche Caiman, Mahé, Republic of Seychelles.
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24
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Kessler BM. Nilabh Shastri - Towards understanding classical and non-classical MHC-I antigen processing and presentation. Cell Immunol 2022; 382:104638. [PMID: 36371991 DOI: 10.1016/j.cellimm.2022.104638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
Major histocompatibility complex (MHC-I) peptide antigen processing and presentation has experienced a revived interest in the context of immuno oncology, immune surveillance escape by pathogen mutations and technical advances that accelerate vaccine design. This sheds new light on the discoveries made by Nilabh Shastri and colleagues that includes the characterisation of cryptic MHC-I peptide antigen epitopes derived from untranslated regions and the N-terminal trimming of peptide antigen precursors by the aminopeptidase ERAAP (ERAP1/2 / ARTS1/LRAP) in the endoplasmic reticulum (ER) prior to the complete assembly of MHC-I complexes and their subsequent exposure to the cell surface. These scientific findings have important implications for developing novel therapeutic approaches in immunotherapy and modern vaccine design.
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Affiliation(s)
- Benedikt M Kessler
- Chinese Academy of Medical Science Oxford Institute, Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK.
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25
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Hu Q, Huang X, Jin Y, Zhang R, Zhao A, Wang Y, Zhou C, Liu W, Liu X, Li C, Fan G, Zhuo M, Wang X, Ling F, Luo W. Long-read assembly of major histocompatibility complex and killer cell immunoglobulin-like receptor genome regions in cynomolgus macaque. Biol Direct 2022; 17:36. [PMID: 36447238 PMCID: PMC9707422 DOI: 10.1186/s13062-022-00350-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) and the killer cell immunoglobulin-like receptors (KIR) are key regulators of immune responses. The cynomolgus macaque, an Old World monkey species, can be applied as an important preclinical model for studying human diseases, including coronavirus disease 2019 (COVID-19). Several MHC-KIR combinations have been associated with either a poor or good prognosis. Therefore, macaques with a well-characterized immunogenetic profile may improve drug evaluation and speed up vaccine development. At present, a complete overview of the MHC and KIR haplotype organizations in cynomolgus macaques is lacking, and characterization by conventional techniques is hampered by the extensive expansion of the macaque MHC-B region that complicates the discrimination between genes and alleles. METHODS We assembled complete MHC and KIR genomic regions of cynomolgus macaque using third-generation long-read sequencing approach. We identified functional Mafa-B loci at the transcriptome level using locus-specific amplification in a cohort of 33 Vietnamese cynomolgus macaques. RESULTS This is the first physical mapping of complete MHC and KIR gene regions in a Vietnamese cynomolgus macaque. Furthermore, we identified four functional Mafa-B loci (B2, B3, B5, and B6) and showed that alleles of the Mafa-I*01, -B*056, -B*034, and -B*001 functional lineages, respectively, are highly frequent in the Vietnamese cynomolgus macaque population. CONCLUSION The insights into the MHC and KIR haplotype organizations and the level of diversity may refine the selection of animals with specific genetic markers for future medical research.
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Affiliation(s)
- Qingxiu Hu
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Xiaoqi Huang
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Yabin Jin
- grid.12981.330000 0001 2360 039XThe First People’s Hospital of Foshan, Sun Yat-sen University, Foshan, 528000 China
| | - Rui Zhang
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Aimin Zhao
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Yiping Wang
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Chenyun Zhou
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Weixin Liu
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Xunwei Liu
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Chunhua Li
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Guangyi Fan
- grid.21155.320000 0001 2034 1839BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555 China
| | - Min Zhuo
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Xiaoning Wang
- grid.414252.40000 0004 1761 8894National Clinic Center of Geriatric, The Chinese PLA General Hospital, Beijing, 100853 China
| | - Fei Ling
- grid.79703.3a0000 0004 1764 3838Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Wei Luo
- grid.12981.330000 0001 2360 039XThe First People’s Hospital of Foshan, Sun Yat-sen University, Foshan, 528000 China
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26
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Yaku A, Ishikawa Y, Iwasaki T, Hiwa R, Matsuo K, Saji H, Yurugi K, Miura Y, Furu M, Ito H, Fujii T, Maekawa T, Hashimoto M, Ohmura K, Mimori T, Terao C. Genetic architecture underlying IgG-RF production is distinct from that of IgM-RF. Rheumatology (Oxford) 2022; 62:2015-2020. [PMID: 36250908 DOI: 10.1093/rheumatology/keac593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/05/2022] [Accepted: 09/28/2022] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVE HLA-DRB1 alleles, particularly the shared epitope (SE) alleles, are strongly associated with RA. Different genetic structures underlie the production of different autoantibodies in RA. While extensive genetic analyses were conducted for detailed profiles of ACPA, a representative autoantibody in RA, the genetic architecture underlying subfractions of RF other than IgM-RF, namely IgG-RF, known to be associated with rheumatoid vasculitis, is not well understood. METHODS We enrolled a total of 743 RA subjects whose detailed autoantibody (IgG-RF, IgM-RF, and ACPA) data were available. We evaluated co-presence and correlations of the levels of these autoantibodies. We analyzed associations between the presence or levels of the autoantibodies and HLA-DRB1 alleles for the 743 RA patients and 2,008 healthy controls. RESULTS We found both IgG-RF(+) and IgG-RF(-) RA subjects showed comparable associations with SE, which was not observed for the other autoantibodies. Furthermore, there was a clear difference in SE associations between IgG-RF(+) and (-) subsets; the association with the IgG-RF(+) subsets was solely driven by HLA-DRB1*04:05, the most frequent SE allele in the Japanese, while not only HLA-DRB1*04:05 but HLA-DRB1*04:01, less frequent in the Japanese but the most frequent SE in Europeans, were main drivers in IgG-RF(-) subset. We confirmed that these associations were irrespective of ACPA presence. CONCLUSION We found a unique genetic architecture of IgG-RF(-) RA, which showed a strong association with the SE allele less frequent among Japanese but the most frequent in Europeans. The findings could shed light on uncovered RA pathology.
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Affiliation(s)
- Ai Yaku
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuki Ishikawa
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Laboratory for statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Takeshi Iwasaki
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryosuke Hiwa
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keitaro Matsuo
- Aichi Cancer Center Hospital and Research Institute, Aichi, Japan
| | | | - Kimiko Yurugi
- Department of Transfusion Medicine and Cell Therapy, Kyoto University Hospital, Kyoto, Japan
| | - Yasuo Miura
- Department of Transfusion Medicine and Cell Therapy, Kyoto University Hospital, Kyoto, Japan
| | - Moritoshi Furu
- Department of the Control for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiromu Ito
- Department of the Control for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takao Fujii
- Department of the Control for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Taira Maekawa
- Department of Transfusion Medicine and Cell Therapy, Kyoto University Hospital, Kyoto, Japan
| | - Motomu Hashimoto
- Department of the Control for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tsuneyo Mimori
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Chikashi Terao
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Laboratory for statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan.,Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan.,The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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27
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Song IH, Kim YA, Heo SH, Bang WS, Park HS, Choi YH, Lee H, Seo JH, Cho Y, Jung SW, Kim HJ, Ahn SH, Lee HJ, Gong G. The Association of Estrogen Receptor Activity, Interferon Signaling, and MHC Class I Expression in Breast Cancer. Cancer Res Treat 2022; 54:1111-1120. [PMID: 34942685 PMCID: PMC9582481 DOI: 10.4143/crt.2021.1017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 12/20/2021] [Indexed: 11/30/2022] Open
Abstract
PURPOSE The expression of major histocompatibility complex class I (MHC I) has previously been reported to be negatively associated with estrogen receptor (ER) expression. Furthermore, MHC I expression, level of tumor-infiltrating lymphocytes (TILs), and expression of interferon (IFN) mediator MxA are positively associated with one another in human breast cancers. This study aimed to investigate the mechanisms of association of MHC I with ER and IFN signaling. MATERIALS AND METHODS The human leukocyte antigen (HLA)-ABC protein expression was analyzed in breast cancer cell lines. The expressions of HLA-A and MxA mRNAs were analyzed in MCF-7 cells in Gene Expression Omnibus (GEO) data. ER and HLA-ABC expressions, Ki-67 labeling index and TIL levels in tumor tissue were also analyzed in ER+/ human epidermal growth factor receptor 2 (HER2)- breast cancer patients who randomly received either neoadjuvant chemotherapy or estrogen modulator treatment followed by resection. RESULTS HLA-ABC protein expression was decreased after β-estradiol treatment or hESR-GFP transfection and increased after fulvestrant or IFN-γ treatment in cell lines. In GEO data, HLA-A and MxA expression was increased after ESR1 shRNA transfection. In patients, ER Allred score was significantly lower and the HLA-ABC expression, TIL levels, and Ki-67 were significantly higher in the estrogen modulator treated group than the chemotherapy treated group. CONCLUSION MHC I expression and TIL levels might be affected by ER pathway modulation and IFN treatment. Further studies elucidating the mechanism of MHC I regulation could suggest a way to boost TIL influx in cancer in a clinical setting.
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Affiliation(s)
- In Hye Song
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
| | | | - Sun-Hee Heo
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
| | - Won Seon Bang
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
| | | | | | | | | | - Youngjin Cho
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
| | - Sung Wook Jung
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
| | - Hee Jeong Kim
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
| | - Sei Hyun Ahn
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
| | - Hee Jin Lee
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
- NeogenTC Corp., Seoul,
Korea
| | - Gyungyub Gong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul,
Korea
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28
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Tomasiak L, Karch R, Schreiner W. Conformational flexibility of a free and TCR-bound pMHC-I protein investigated by long-term molecular dynamics simulations. BMC Immunol 2022; 23:36. [PMID: 35902791 PMCID: PMC9335952 DOI: 10.1186/s12865-022-00510-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background Major histocompatibility complexes (MHCs) play a crucial role in the cell-mediated adaptive immune response as they present antigenic peptides (p) which are recognized by host T cells through a complex formation of the T cell receptor (TCR) with pMHC. In the present study, we report on changes in conformational flexibility within a pMHC molecule upon TCR binding by looking at molecular dynamics (MD) simulations of the free and the TCR-bound pMHC-I protein of the LC13-HLA-B*44:05-pEEYLQAFTY complex. Results We performed long-term MD simulations with a total simulation time of 8 µs, employing 10 independent 400 ns replicas for the free and the TCR-bound pMHC system. Upon TCR ligation, we observed a reduced dynamic flexibility in the central residues of the peptide and the MHC α1-helix, altered occurrences of hydrogen bonds between the peptide and the MHC, a reduced conformational entropy of the peptide-binding groove, as well as a decreased solvent accessible surface area. Conclusions In summary, our results from 8 µs MD simulations indicate a restricted conformational space of the MHC peptide-binding groove upon TCR ligation and suggest a minimum simulation time of approximately 100 ns for biomolecules of comparable complexity to draw meaningful conclusions. Given the relatively long total simulation time, our results contribute to a more detailed view on conformational flexibility properties of the investigated free and TCR-bound pMHC-I system. Supplementary Information The online version contains supplementary material available at 10.1186/s12865-022-00510-7.
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Affiliation(s)
- Lisa Tomasiak
- Institute of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - Rudolf Karch
- Institute of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
| | - Wolfgang Schreiner
- Institute of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
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29
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Wong ATC, Lam DK, Poon ESK, Chan DTC, Sin SYW. Intra-specific copy number variation of MHC class II genes in the Siamese fighting fish. Immunogenetics 2022; 74:327-346. [PMID: 35229174 DOI: 10.1007/s00251-022-01255-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 02/04/2022] [Indexed: 11/28/2022]
Abstract
Duplicates of genes for major histocompatibility complex (MHC) molecules can be subjected to selection independently and vary markedly in their evolutionary rates, sequence polymorphism, and functional roles. Therefore, without a thorough understanding of their copy number variation (CNV) in the genome, the MHC-dependent fitness consequences within a species could be misinterpreted. Studying the intra-specific CNV of this highly polymorphic gene, however, has long been hindered by the difficulties in assigning alleles to loci and the lack of high-quality genomic data. Here, using the high-quality genome of the Siamese fighting fish (Betta splendens), a model for mate choice studies, and the whole-genome sequencing (WGS) data of 17 Betta species, we achieved locus-specific amplification of their three classical MHC class II genes - DAB1, DAB2, and DAB3. By performing quantitative PCR and depth-of-coverage analysis using the WGS data, we revealed intra-specific CNV at the DAB3 locus. We identified individuals that had two allelic copies (i.e., heterozygous or homozygous) or one allele (i.e., hemizygous) and individuals without this gene. The CNV was due to the deletion of a 20-kb-long genomic region harboring both the DAA3 and DAB3 genes. We further showed that the three DAB genes were under different modes of selection, which also applies to their corresponding DAA genes that share similar pattern of polymorphism. Our study demonstrates a combined approach to study CNV within a species, which is crucial for the understanding of multigene family evolution and the fitness consequences of CNV.
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Affiliation(s)
- Anson Tsz Chun Wong
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Derek Kong Lam
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Emily Shui Kei Poon
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - David Tsz Chung Chan
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China.
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Cook RM, Suttner B, Giglio RM, Haines ML, Latch EK. Selection and demography drive range-wide patterns of MHC-DRB variation in mule deer. BMC Ecol Evol 2022; 22:42. [PMID: 35387584 DOI: 10.1186/s12862-022-01998-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 03/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Standing genetic variation is important especially in immune response-related genes because of threats to wild populations like the emergence of novel pathogens. Genetic variation at the major histocompatibility complex (MHC), which is crucial in activating the adaptive immune response, is influenced by both natural selection and historical population demography, and their relative roles can be difficult to disentangle. To provide insight into the influences of natural selection and demography on MHC evolution in large populations, we analyzed geographic patterns of variation at the MHC class II DRB exon 2 locus in mule deer (Odocoileus hemionus) using sequence data collected across their entire broad range. RESULTS We identified 31 new MHC-DRB alleles which were phylogenetically similar to other cervid MHC alleles, and one allele that was shared with white-tailed deer (Odocoileus virginianus). We found evidence for selection on the MHC including high dN/dS ratios, positive neutrality tests, deviations from Hardy-Weinberg Equilibrium (HWE) and a stronger pattern of isolation-by-distance (IBD) than expected under neutrality. Historical demography also shaped variation at the MHC, as indicated by similar spatial patterns of variation between MHC and microsatellite loci and a lack of association between genetic variation at either locus type and environmental variables. CONCLUSIONS Our results show that both natural selection and historical demography are important drivers in the evolution of the MHC in mule deer and work together to shape functional variation and the evolution of the adaptive immune response in large, well-connected populations.
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Bracamonte SE, Hofmann MJ, Lozano-Martín C, Eizaguirre C, Barluenga M. Divergent and non-parallel evolution of MHC IIB in the Neotropical Midas cichlid species complex. BMC Ecol Evol 2022; 22:41. [PMID: 35365100 PMCID: PMC8974093 DOI: 10.1186/s12862-022-01997-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/21/2022] [Indexed: 01/09/2023] Open
Abstract
Background Ecological diversification is the result of divergent natural selection by contrasting habitat characteristics that favours the evolution of distinct phenotypes. This process can happen in sympatry and in allopatry. Habitat-specific parasite communities have the potential to drive diversification among host populations by imposing selective pressures on their host's immune system. In particular, the hyperdiverse genes of the major histocompatibility complex (MHC) are implicated in parasite-mediated host divergence. Here, we studied the extent of divergence at MHC, and discuss how it may have contributed to the Nicaraguan Midas cichlid species complex diversification, one of the most convincing examples of rapid sympatric parallel speciation. Results We genotyped the MHC IIB for individuals from six sympatric Midas cichlid assemblages, each containing species that have adapted to exploit similar habitats. We recovered large allelic and functional diversity within the species complex. While most alleles were rare, functional groups of alleles (supertypes) were common, suggesting that they are key to survival and that they were maintained during colonization and subsequent radiations. We identified lake-specific and habitat-specific signatures for both allelic and functional diversity, but no clear pattern of parallel divergence among ecomorphologically similar phenotypes. Conclusions Colonization and demographic effects of the fish could have contributed to MHC evolution in the Midas cichlid in conjunction with habitat-specific selective pressures, such as parasites associated to alternative preys or environmental features. Additional ecological data will help evaluating the role of host–parasite interactions in the Midas cichlid radiations and aid in elucidating the potential role of non-parallel features differentiating crater lake species assemblages. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01997-9.
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Affiliation(s)
- Seraina E Bracamonte
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Melinda J Hofmann
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Carlos Lozano-Martín
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Marta Barluenga
- Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006, Madrid, Spain.
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Abstract
The notion that autoimmune responses to α-synuclein may be involved in the pathogenesis of this disorder stems from reports that mutations in α-synuclein or certain alleles of the major histocompatibility complex (MHC) are associated with the disease and that dopaminergic and norepinephrinergic neurons in the midbrain can present antigenic epitopes. Here, we discuss recent evidence that a defined set of peptides derived from α-synuclein act as antigenic epitopes displayed by specific MHC alleles and drive helper and cytotoxic T cell responses in patients with PD. Moreover, phosphorylated α-synuclein may activate T cell responses in a less restricted manner in PD. While the roles for the acquired immune system in disease pathogenesis remain unknown, preclinical animal models and in vitro studies indicate that T cells may interact with neurons and exert effects related to neuronal death and neuroprotection. These findings suggest that therapeutics that target T cells and ameliorate the incidence or disease severity of inflammatory bowel disorders or CNS autoimmune diseases such as multiple sclerosis may be useful in PD.
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Abstract
The immune system is constantly protecting its host from the invasion of pathogens and the development of cancer cells. The specific CD8+ T-cell immune response against virus-infected cells and tumor cells is based on the T-cell receptor recognition of antigenic peptides bound to class I major histocompatibility complexes (MHC) at the surface of antigen presenting cells. Consequently, the peptide binding specificities of the highly polymorphic MHC have important implications for the design of vaccines, for the treatment of autoimmune diseases, and for personalized cancer immunotherapy. Evidence-based machine-learning approaches have been successfully used for the prediction of peptide binders and are currently being developed for the prediction of peptide immunogenicity. However, understanding and modeling the structural details of peptide/MHC binding is crucial for a better understanding of the molecular mechanisms triggering the immunological processes, estimating peptide/MHC affinity using universal physics-based approaches, and driving the design of novel peptide ligands. Unfortunately, due to the large diversity of MHC allotypes and possible peptides, the growing number of 3D structures of peptide/MHC (pMHC) complexes in the Protein Data Bank only covers a small fraction of the possibilities. Consequently, there is a growing need for rapid and efficient approaches to predict 3D structures of pMHC complexes. Here, we review the key characteristics of the 3D structure of pMHC complexes before listing databases and other sources of information on pMHC structures and MHC specificities. Finally, we discuss some of the most prominent pMHC docking software.
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Affiliation(s)
- Marta A S Perez
- Computer-aided Molecular Engineering Group, Department of Oncology UNIL-CHUV, Lausanne University, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michel A Cuendet
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Oncology Department, Centre Hospitalier Universitaire Vaudois (CHUV), Precision Oncology Center, Lausanne, Switzerland
| | - Ute F Röhrig
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Oncology Department, Centre Hospitalier Universitaire Vaudois (CHUV), Precision Oncology Center, Lausanne, Switzerland.
| | - Vincent Zoete
- Computer-aided Molecular Engineering Group, Department of Oncology UNIL-CHUV, Lausanne University, Lausanne, Switzerland.
- Ludwig Institute for Cancer Research, Lausanne, Switzerland.
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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Strand A, Shen ST, Tomchick D, Wang J, Wang CR, Deisenhofer J. Structure and dynamics of major histocompatibility class Ib molecule H2-M3 complexed with mitochondrial-derived peptides. J Biomol Struct Dyn 2022; 40:10300-10312. [PMID: 34176438 PMCID: PMC8722451 DOI: 10.1080/07391102.2021.1942214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Presentation of antigenic peptides to T-cell receptors is an essential step in the adaptive immune response. In the mouse the class Ib major histocompatibility complex molecule, H2-M3, presents bacterial- and mitochondrial-derived peptides to T-cell receptors on cytotoxic T cells. Four mitochondrial heptapeptides, differing only at residue 6, form complexes with H2-M3 which can be distinguished by T cells. No structures of relevant receptors are available. To investigate the structural basis for this distinction, crystal structures were determined and molecular dynamics simulations over one microsecond were done for each complex. In the crystal structures of the heptapeptide complexes with H2-M3, presented here, the side chains of the peptide residues at position 6 all point into the H2-M3 binding groove, and are thus inaccessible, so that the very similar structures do not suggest how recognition and initiation of responses by the T cells may occur. However, conformational differences, which could be crucial to T-cell discrimination, appear within one microsecond during molecular dynamics simulations of the four complexes. Specifically, the three C-terminal residues of peptide ligands with alanine or threonine at position 6 partially exit the binding groove; this does not occur in peptide ligands with isoleucine or valine at position 6. Structural changes associated with partial peptide exit from the binding groove, along with relevant peptide binding energetics and immunological results are discussed. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arne Strand
- Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - San-Tai Shen
- AnTaimmu Biomed Co., Ltd., Zhubei City, Hsinchu County, Taiwan
| | - Diana Tomchick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas, United States of America,Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Junmei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chyung-Ru Wang
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Johann Deisenhofer
- Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, Texas, United States of America,Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas, United States of America,Corresponding author
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Gupta S, Li D, Ostrov DA, Nguyen CQ. Blocking IAg 7 class II major histocompatibility complex by drug-like small molecules alleviated Sjögren's syndrome in NOD mice. Life Sci 2022; 288:120182. [PMID: 34843735 DOI: 10.1016/j.lfs.2021.120182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 10/25/2022]
Abstract
BACKGROUND Sjögren's syndrome (SjS) is an autoimmune disease with a strong genetic association. To date, no vaccine or therapeutic agent exists to cure SjS, and patients must rely on lifelong therapies to treat symptoms. Human leukocyte antigens (HLA) are primary susceptibility loci that form the genetic basis for many autoimmune diseases, including SjS. In this study, we sought to determine whether blocking MHC class II IAg7 antigen presentation in the NOD mouse would alleviate SjS by preventing the recognition of autoantigens by pathogenic T cells. METHODS Mapping of the antigenic epitopes of Ro60 autoantigen to IAg7 of the NOD mice was performed using structural modeling and in-vitro stimulation. Tetraazatricyclo-dodecane (TATD) and 8-Azaguanine (8-Aza) were previously identified as potential binders to IAg7 of the NOD mice using in silico drug screening. Mice were treated with 20mgs/kg via IP every day five days/week for 23 weeks. Disease profiling was conducted. FINDINGS Specific peptides of Ro60 autoantigen were identified to bind to IAg7 and stimulated splenocytes of the NOD mice. Treating NOD mice with TATD or 8-Azaguanine alleviated SjS symptoms by improving salivary and lacrimal gland secretory function, decreasing the levels of autoantibodies, and reducing the severity of lymphocytic infiltration in the salivary and lacrimal glands. INTERPRETATION This study presents a novel therapeutic approach for SjS by identifying small molecules capable of inhibiting T cell response via antigen-specific presentation. FUNDING CQN is supported financially in part by PHS grants AI130561, DE026450, and DE028544 from the National Institutes of Health.
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Affiliation(s)
- Shivai Gupta
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Danmeng Li
- Department of Pathology, Immunology & Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - David A Ostrov
- Department of Pathology, Immunology & Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Cuong Q Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA; Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA; Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, USA.
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Alnaqbi H, Tay GK, Jelinek HF, Francis A, Alefishat E, El Haj Chehadeh S, Tahir Saeed A, Hussein M, Laila Salameh, Mahboub BH, Uddin M, Alkaabi N, Alsafar HS. HLA repertoire of 115 UAE nationals infected with SARS-CoV-2. Hum Immunol 2022; 83:1-9. [PMID: 34462158 PMCID: PMC8391094 DOI: 10.1016/j.humimm.2021.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/11/2022]
Abstract
The class I and class II Human Leucocyte Antigens (HLA) are an integral part of the host adaptive immune system against viral infections. The characterization of HLA allele frequency in the population can play an important role in determining whether HLA antigens contribute to viral susceptibility. In this regard, global efforts are currently underway to study possible correlations between HLA alleles with the occurrence and severity of SARS-CoV-2 infection. Specifically, this study examined the possible association between specific HLA alleles and susceptibility to SARS-CoV-2 in a population from the United Arab Emirates (UAE). The frequencies of HLA class I (HLA-A, -B, and -C) and HLA class II alleles (HLA-DRB1 and -DQB1); defined using Next Generation Sequencing (NGS); from 115 UAE nationals with mild, moderate, and severe SARS-CoV-2 infection are presented here. HLA alleles and supertypes were compared between hospitalized and non-hospitalized subjects. Statistical significance was observed between certain HLA alleles and supertypes and the severity of the infection. Specifically, alleles HLA-B*51:01 and HLA-A*26:01 showed a negative association (suggestive of protection), whilst genotypes HLA-A*03:01, HLA-DRB1*15:01, and supertype B44 showed a positive association (suggestive of predisposition) to COVID-19 severity. The results support the potential use of HLA testing to differentiate between patients who require specific clinical management strategies.
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Affiliation(s)
- Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan K Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Division of Psychiatry, Faculty of Health and Medical Sciences, the University of Western Australia, Crawley, Western Australia, Australia; School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Herbert F Jelinek
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Heath Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Amirtharaj Francis
- Clinical Services, Medical Affairs, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Eman Alefishat
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Department of Biopharmaceutics & Clinical Pharmacy, University of Jordan, Amman, Jordan
| | - Sarah El Haj Chehadeh
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Amna Tahir Saeed
- Dubai Health Authority, Rashid Hospital, Dubai, United Arab Emirates
| | - Mawada Hussein
- Dubai Health Authority, Rashid Hospital, Dubai, United Arab Emirates
| | - Laila Salameh
- Dubai Health Authority, Rashid Hospital, Dubai, United Arab Emirates
| | - Bassam H Mahboub
- Dubai Health Authority, Rashid Hospital, Dubai, United Arab Emirates
| | - Maimunah Uddin
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Nawal Alkaabi
- Department of Pediatric Infectious Disease, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Habiba S Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates; Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
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37
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Ch'ng ACW, Lam P, Alassiri M, Lim TS. Application of phage display for T-cell receptor discovery. Biotechnol Adv 2021; 54:107870. [PMID: 34801662 DOI: 10.1016/j.biotechadv.2021.107870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/23/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022]
Abstract
The immune system is tasked to keep our body unharmed and healthy. In the immune system, B- and T-lymphocytes are the two main components working together to stop and eliminate invading threats like virus particles, bacteria, fungi and parasite from attacking our healthy cells. The function of antibodies is relatively more direct in target recognition as compared to T-cell receptors (TCR) which recognizes antigenic peptides being presented on the major histocompatibility complex (MHC). Although phage display has been widely applied for antibody presentation, this is the opposite in the case of TCR. The cell surface TCR is a relatively large and complex molecule, making presentation on phage surfaces challenging. Even so, recombinant versions and modifications have been introduced to allow the growing development of TCR in phage display. In addition, the increasing application of TCR for immunotherapy has made it an important binding motif to be developed by phage display. This review will emphasize on the application of phage display for TCR discovery as well as the engineering aspect of TCR for improved characteristics.
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Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Paula Lam
- CellVec Private Limited, 118518, Singapore; National University of Singapore, Department of Physiology, 117597, Singapore; Duke-NUS Graduate Medical School, Cancer and Stem Cells Biology Program, 169857, Singapore
| | - Mohammed Alassiri
- Department of Basic Sciences, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia; King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800 Penang, Malaysia.
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Pikus E, Włodarczyk R, Jedlikowski J, Minias P. Urbanization processes drive divergence at the major histocompatibility complex in a common waterbird. PeerJ 2021; 9:e12264. [PMID: 34707940 PMCID: PMC8500109 DOI: 10.7717/peerj.12264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/16/2021] [Indexed: 11/20/2022] Open
Abstract
Urban sprawl is one of the most common landscape alterations occurring worldwide, and there is a growing list of species that are recognised to have adapted to urban life. To be successful, processes of urban colonization by wildlife require a broad spectrum of phenotypic (e.g., behavioural or physiological) adjustments, but evidence for genetic adaptations is much scarcer. One hypothesis proposes that different pathogen-driven selective pressures between urban and non-urban landscapes leads to adaptations in host immune genes. Here, we examined urbanization-related differentiation at the key pathogen-recognition genes of vertebrate adaptive immunity-the major histocompatibility complex (MHC)-in a common waterbird, the Eurasian coot (Fulica atra). Samples were collected from an old urban population (established before the 1950s), a new urban population (established in the 2000s), and two rural populations from central Poland. We found strong significant divergence (as measured with Jost's D) at the MHC class II between the old urban population and the remaining (new urban and rural) populations. Also, there was a moderate, but significant divergence at the MHC between the new urban population and two rural populations, while no divergence was found between the two rural populations. The total number of MHC alleles and the number of private (population-specific) MHC alleles was lower in old urban populations, as compared to the rural ones. These patterns of differentiation at the MHC were not consistent with patterns found for neutral genetic markers (microsatellites), which showed few differences between the populations. Our results indicate that MHC allele composition depended on the level of anthropogenic disturbance and the time which passed since urban colonization, possibly due to the processes of genotype sorting and local adaptation. As such, our study contributes to the understanding of genetic mechanisms associated with urbanization processes in wildlife.
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Affiliation(s)
- Ewa Pikus
- Department of Biodiversity Studies and Bioeducation, University of Łódź, Łódź, Poland
| | - Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, University of Łódź, Łódź, Poland
| | - Jan Jedlikowski
- Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, University of Łódź, Łódź, Poland
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Mompart F, Kamgoué A, Lahbib-Mansais Y, Robelin D, Bonnet A, Rogel-Gaillard C, Kocanova S, Yerle-Bouissou M. The 3D nuclear conformation of the major histocompatibility complex changes upon cell activation both in porcine and human macrophages. BMC Mol Cell Biol 2021; 22:45. [PMID: 34521351 PMCID: PMC8442435 DOI: 10.1186/s12860-021-00384-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/30/2021] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The crucial role of the major histocompatibility complex (MHC) for the immune response to infectious diseases is well-known, but no information is available on the 3D nuclear organization of this gene-dense region in immune cells, whereas nuclear architecture is known to play an essential role on genome function regulation. We analyzed the spatial arrangement of the three MHC regions (class I, III and II) in macrophages using 3D-FISH. Since this complex presents major differences in humans and pigs with, notably, the presence of the centromere between class III and class II regions in pigs, the analysis was implemented in both species to determine the impact of this organization on the 3D conformation of the MHC. The expression level of the three genes selected to represent each MHC region was assessed by quantitative real-time PCR. Resting and lipopolysaccharide (LPS)-activated states were investigated to ascertain whether a response to a pathogen modifies their expression level and their 3D organization. RESULTS While the three MHC regions occupy an intermediate radial position in porcine macrophages, the class I region was clearly more peripheral in humans. The BAC center-to-center distances allowed us to propose a 3D nuclear organization of the MHC in each species. LPS/IFNγ activation induces a significant decompaction of the chromatin between class I and class III regions in pigs and between class I and class II regions in humans. We detected a strong overexpression of TNFα (class III region) in both species. Moreover, a single nucleus analysis revealed that the two alleles can have either the same or a different compaction pattern. In addition, macrophage activation leads to an increase in alleles that present a decompacted pattern in humans and pigs. CONCLUSIONS The data presented demonstrate that: (i) the MHC harbors a different 3D organization in humans and pigs; (ii) LPS/IFNγ activation induces chromatin decompaction, but it is not the same area affected in the two species. These findings were supported by the application of an original computation method based on the geometrical distribution of the three target genes. Finally, the position of the centromere inside the swine MHC could influence chromatin reorganization during the activation process.
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Affiliation(s)
- Florence Mompart
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France
| | - Alain Kamgoué
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Yvette Lahbib-Mansais
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France
| | - David Robelin
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France
| | - Agnès Bonnet
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France
| | | | - Silvia Kocanova
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Martine Yerle-Bouissou
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France.
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40
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Minias P, Drzewińska-Chańko J, Włodarczyk R. Evolution of innate and adaptive immune genes in a non-model waterbird, the common tern. Infect Genet Evol 2021; 95:105069. [PMID: 34487864 DOI: 10.1016/j.meegid.2021.105069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Toll-like receptors (TLRs) and the Major Histocompatibility Complex (MHC) are the key pathogen-recognition genes of vertebrate immune system and they have a crucial role in the initiation of innate and adaptive immune response, respectively. Recent advancements in sequencing technology sparked research on highly duplicated MHC genes in non-model species, but TLR variation in natural vertebrate populations has remained little studied and comparisons of polymorphism across both TLRs and MHC are scarce. Here, we aimed to compare variation across innate (four TLR loci) and adaptive (MHC class I and class II) immune genes in a non-model avian species, the common tern Sterna hirundo. We detected relatively high allelic richness at TLR genes (9-48 alleles per locus), which was similar to or even higher than the estimated per locus allelic richness at the MHC (24-30 alleles at class I and 13-16 alleles at class II under uniform sample sizes). Despite this, the total number of MHC alleles across all duplicated loci (four class I and three class II) was much higher and MHC alleles showed greater sequence divergence than TLRs. Positive selection targeted relatively more sites at the MHC than TLRs, but the strength of selection (dN/dS ratios) at TLRs was higher when compared to MHC class I. There were also differences in the signature of positive selection and recombination (gene conversion) between MHC class I and II (stronger signature at class II), suggesting that mechanisms maintaining variation at the MHC may vary between both classes. Our study indicates that allelic richness of both innate and adaptive immune receptors may be maintained at relatively high levels in viable avian populations and we recommend a transition from the traditional gene-specific to multi-gene approach in studying molecular evolution of vertebrate immune system.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland.
| | - Joanna Drzewińska-Chańko
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland
| | - Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland
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41
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Zhou Z, Wu J, Ren J, Chen W, Zhao W, Gu X, Chi Y, He Q, Yang B, Wu J, Chen S. TSNAD v2.0: A one-stop software solution for tumor-specific neoantigen detection. Comput Struct Biotechnol J 2021; 19:4510-4516. [PMID: 34471496 PMCID: PMC8385119 DOI: 10.1016/j.csbj.2021.08.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 12/30/2022] Open
Abstract
TSNAD is a one-stop software solution for predicting neoantigens from the whole genome/exome sequencing data of tumor-normal pairs. Here we present TSNAD v2.0 which provides several new features such as the function of RNA-Seq analysis including gene expression and gene fusion analysis, the support of different versions of the reference genome. Most importantly, we replace the NetMHCpan with DeepHLApan we developed previously, which considers both the binding between peptide and major histocompatibility complex (MHC) and the immunogenicity of the presented peptide-MHC complex (pMHC). TSNAD v2.0 achieves good performamce on a standard dataset. For better usage, we provide the Docker version and the web service of TSNAD v2.0. The source code of TSNAD v2.0 is freely available at https://github.com/jiujiezz/tsnad. And the web service of TSNAD v2.0 is available at http://biopharm.zju.edu.cn/tsnad/.
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Affiliation(s)
- Zhan Zhou
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China
| | - Jingcheng Wu
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Collaborative Innovation Center of Artificial Intelligence by MOE and Zhejiang Provincial Government, College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, China
| | - Jianan Ren
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenfan Chen
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Polytechnic Institute, Zhejiang University, Hangzhou 310015, China
| | - Wenyi Zhao
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Collaborative Innovation Center of Artificial Intelligence by MOE and Zhejiang Provincial Government, College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, China
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Ying Chi
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Alibaba DAMO Academy, Hangzhou 311121, China
| | - Qiaojun He
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China
| | - Bo Yang
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China
| | - Jian Wu
- Collaborative Innovation Center of Artificial Intelligence by MOE and Zhejiang Provincial Government, College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, China.,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China.,Real Doctor AI Research Centre, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shuqing Chen
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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Ladowski JM, Houp J, Hauptfeld-Dolejsek V, Javed M, Hara H, Cooper DKC. Aspects of histocompatibility testing in xenotransplantation. Transpl Immunol 2021; 67:101409. [PMID: 34015463 PMCID: PMC8197754 DOI: 10.1016/j.trim.2021.101409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/14/2021] [Indexed: 12/16/2022]
Abstract
Xenotransplantation, using genetically-modified pigs for clinical organ transplantation, is a solution to the organ shortage. The biggest barrier to clinical implementation is the antigenicity of pig cells. Humans possess preformed antibody to pig cells that initiate antibody-mediated rejection of pig organs in primates. Advances in genetic engineering have led to the development of a pig lacking the three known glycan xenoantigens (triple-knockout [TKO] pigs). A significant number of human sera demonstrate no antibody binding to TKO pig cells. As a result of the TKO pig's low antigen expression, survival of life-supporting pig organs in immunosuppressed nonhuman primates has significantly increased, and hope has been renewed for clinical trials of xenotransplantation. It is important to understand the context in which xenotransplantation's predecessor, allotransplantation, has been successful, and the steps needed for the success of xenotransplantation. Successful allotransplantation has been based on two main immunological approaches - (i) adequate immunosuppressive therapy, and (ii) careful histocompatibility matching. In vivo studies suggest that the available immunosuppressive regimens are adequate to suppress the human anti-pig cellular response. Methods to evaluate and screen patients for the first clinical xenotransplantation trial are the next challenge. The goal of this review is to summarize the history of histocompatibility testing, and the available tools that can be utilized to determine xenograft histocompatibility.
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Affiliation(s)
- Joseph M Ladowski
- Xenotransplantation Program, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Julie Houp
- Histocompatibility Laboratory, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Mariyam Javed
- Xenotransplantation Program, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hidetaka Hara
- Xenotransplantation Program, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - David K C Cooper
- Xenotransplantation Program, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, USA
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43
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Kundu S. Mathematical modeling and stochastic simulations suggest that low-affinity peptides can bisect MHC1-mediated export of high-affinity peptides into "early"- and "late"-phases. Heliyon 2021; 7:e07466. [PMID: 34286133 DOI: 10.1016/j.heliyon.2021.e07466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/23/2021] [Accepted: 06/29/2021] [Indexed: 02/01/2023] Open
Abstract
The peptide loading complex (PLC) is a multi-protein complex of the endoplasmic reticulum (ER) which optimizes major histocompatibility I (MHC1)-mediated export of intracellular high-affinity peptides. Whilst, the molecular biology of MHC1-mediated export is well supported by empirical data, the stoichiometry, kinetics and spatio-temporal profile of the participating molecular entities are a matter of considerable debate. Here, a low-affinity peptide-driven (LAPD)-model of MHC1-mediated high-affinity peptide export is formulated, implemented, analyzed and simulated. The model is parameterized in terms of the contribution of the shunt reaction to the concentration of exportable MHC1. Theoretical analyses and simulation studies of the model suggest that low-affinity peptides can bisect MHC1-mediated export of high-affinity peptides into time-dependent distinct “early”- and “late”-phases. The net exportable MHC1 (eM1β(t)) is a function of the retrograde (rM1β(t))- and anterograde (aM1β(t))-derived fractions. The “early”-phase is dominated by the contribution of the retrograde/recyclable (rM1β≈61%,aM1β≈39%) pathway to exportable MHC1, is characterized by Tapasin-mediated peptide-editing and is ATP-independent. The “late”-phase on the other hand, is characterized by de novo PLC-assembly, rapid disassembly and a significant contribution of the anterograde pathway to exportable MHC1 (rM1β≈21%,aM1β≈79%). The shunt reaction is rate limiting and may integrate peptide translocation with PLC-assembly/disassembly thereby, regulating peptide export under physiological and pathological (viral infections, dysplastic alterations) conditions.
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Holmes JC, Scholl EH, Dickey AN, Hess PR. High-resolution characterization of the structural features and genetic variation of six feline leukocyte antigen class I loci via single molecule, real-time (SMRT) sequencing. Immunogenetics 2021. [PMID: 34175985 DOI: 10.1007/s00251-021-01221-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/28/2021] [Indexed: 10/21/2022]
Abstract
Of the 12 full-length feline leukocyte antigen class I (FLAI) loci, 3 are presumed to be classical: FLAI-E, FLAI-H, and FLAI-K. As diversity is a class Ia hallmark, multi-allelism is an important surrogate supporting a classical designation, in the absence of direct demonstration of T-cell restriction. Conversely, limited polymorphism at an expressed locus suggests regulation of immune effectors with invariant receptors, and non-classical status. FLAI-A, FLAI-J, FLAI-L, and FLAI-O are putative class Ib genes in cats. For both classes, identifying prevalent variants across outbred populations can illuminate specific genotypes to be prioritized for immune studies, as shared alleles direct shared responses. Since variation is concentrated in exons 2 and 3, which encode the antigen-binding domains, partial-length cloning/sequencing can be used for allele discovery, but is laborious and occasionally ambiguous. Here we develop a targeted approach to FLAI genotyping, using the single-molecule real-time (SMRT) platform, which allows full-length (3.4-kb) reads without assembly. Consensus sequences matched full-length Sanger references. Thirty-one new class Ia genes were found in 17 cats. Alleles segregated strongly by loci, and the origins of formerly difficult-to-assign sequences were resolved. Although not targeted, FLAI-L and FLAI-J, and the pseudogene FLAI-F, were also returned. Eighteen class Ib alleles were identified. Diversity was restricted and outside hypervariable regions. Both class Ib genes were transcriptionally active. Novel alternative splicing of FLAI-L was observed. SMRT sequencing of FLAI amplicons is useful for full-length genotyping at feline class Ia loci. High-throughput sequencing could allow highly accurate allele surveys in large cat cohorts.
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Bartocillo AMF, Nishita Y, Abramov AV, Masuda R. Evolution of MHC class I genes in Japanese and Russian raccoon dogs, Nyctereutes procyonoides (Carnivora: Canidae). MAMMAL RES 2021;:1-13. [PMID: 33747753 DOI: 10.1007/s13364-021-00561-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/03/2021] [Indexed: 10/27/2022]
Abstract
Major histocompatibility complex (MHC) genes have been widely studied to assess the immunological fitness and evolutionary adaptation of animal populations. Among the Canidae, the raccoon dog's adventurous nature, omnivorous behavior, and high variability of intracellular pathogens make it ideal to study selection on MHC class I in a non-model canid species. Here, we examined allelic diversity and evolutionary patterns of MHC class I genes in the raccoon dog (Nyctereutes procyonoides). We identified 48 novel MHC class I alleles from 31 raccoon dogs from Japan and Russia. Some alleles were geographically restricted, whereas others were widely distributed across the species' range. The rate of non-synonymous substitutions was greater than that of synonymous substitutions for both exon 2 and exon 3 encoding α1 and α2 domains, respectively, in the α chain of the MHC class I protein. Positively selected sites at the amino acid level were evident in both the α1 and α2 domains, and a recombination breakpoint was found in exon 3. Bayesian phylogenetic trees showed no evidence of trans-species polymorphism (TSP) with alleles from carnivoran species in other families but did detect TSP between raccoon dogs and the domestic dog, Canis familiaris, indicative of long-term balancing selection in canids. Our results indicate that the extensive allelic diversity of MHC class I in Japanese and Russian raccoon dogs has been influenced and maintained by pathogen-driven positive selection, recombination, and long-term balancing selection. Supplementary Information The online version contains supplementary material available at 10.1007/s13364-021-00561-y.
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Usureau C, Lefèvre E, Top I, Nikolski M, Varlet P, Choukroun G, Desoutter J, Guillaume N. Antibodies against HLA cross-reactivity groups: From single antigen bead assay to immunoinformatics interpretation of epitopes. Mol Immunol 2021; 133:154-162. [PMID: 33667985 DOI: 10.1016/j.molimm.2021.02.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 01/26/2021] [Accepted: 02/23/2021] [Indexed: 11/30/2022]
Abstract
Identification of anti-human leukocyte antigen (HLA) antibodies (Abs) is based on Luminex™ technology. We used bioinformatics to (i) study the correlations of mean fluorescence intensities (MFIs) for all the possible allele pairs, and (ii) determine the degree of epitope homology between HLA antigens. Using MFI data on anti-HLA Abs from 6000 Luminex™ assays, we provide an updated overview of class I and II HLA antigen cross-reactivity in which each node corresponded to an allele and each link corresponded to a strong correlation between two alleles (Spearman's ρ > 0.8). We compared these correlations with the serological groups and the results of an epitope analysis. The strongest correlations concerned allele-specific Abs directed against the same antigen. For the HLA-A locus, the highest values of Spearman's ρ reflected broad specificity. For the HLA-B locus, graphs defined the HLA-Bw4 public epitope, and correlations between HLA-A and -B alleles were only present for beads with the same Bw4 public epitope. For the HLA-C locus, we identified two groups that differed with regard to their KIR ligand subclassification. Lastly, the HLA-DRB1 subgroups were part of a network. In the epitope analysis, Spearman's ρ was related to the number of matched epitopes within pairs of alleles. The combination of Spearman's ρ with simple, undirected graphing constitutes an effective tool for understanding routinely encountered cross-reactivity profiles. Based on this model, we have implemented an online data visualization tool available at http://cusureau.pythonanywhere.com/.
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Affiliation(s)
- Cédric Usureau
- Department of Hematology and Histocompatibility, Amiens University Medical Center, Amiens, France; EA 4666 Hematim, Jules Verne University of Picardie, Amiens, France; French Speaking Society of Histocompatibility and Immunogenetic (SFHI), France
| | - Edgar Lefèvre
- Bordeaux Bioinformatics Center, CNRS, IBGC CNRS UMR 5095, Bordeaux University, Bordeaux, France
| | - Isabelle Top
- French Speaking Society of Histocompatibility and Immunogenetic (SFHI), France; Department of Immunology and Histocompatibility, Lille University Hospital, Lille, France
| | - Macha Nikolski
- Bordeaux Bioinformatics Center, CNRS, IBGC CNRS UMR 5095, Bordeaux University, Bordeaux, France
| | - Pauline Varlet
- French Speaking Society of Histocompatibility and Immunogenetic (SFHI), France; Department of Immunology and Histocompatibility, Lille University Hospital, Lille, France
| | - Gabriel Choukroun
- Department of Nephrology and Transplantation, Amiens University Hospital, Amiens, France
| | - Judith Desoutter
- Department of Hematology and Histocompatibility, Amiens University Medical Center, Amiens, France; EA 4666 Hematim, Jules Verne University of Picardie, Amiens, France; French Speaking Society of Histocompatibility and Immunogenetic (SFHI), France
| | - Nicolas Guillaume
- Department of Hematology and Histocompatibility, Amiens University Medical Center, Amiens, France; EA 4666 Hematim, Jules Verne University of Picardie, Amiens, France; French Speaking Society of Histocompatibility and Immunogenetic (SFHI), France.
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Honjo Y, Takano K, Ichinohe T. Characterization of novel zebrafish MHC class I U lineage genes and their haplotype. Dev Comp Immunol 2021; 116:103952. [PMID: 33279476 DOI: 10.1016/j.dci.2020.103952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/27/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
Major histocompatibility complex (MHC) genes are essential for distinguishing between individuals in all jawed vertebrates. Although MHC class I (mhc1) genes in zebrafish comprise distinct haplotypes, not all members of the mhc1 gene family have been fully characterized. In this study, we report the identification of two novel U lineage genes isolated from the WIK strain of zebrafish. These new mhc1 genes, named una and uoa, are located in tandem on chromosome 19 with >70% homology to previously isolated U genes. Sequencing of their neighboring genes revealed that una and uoa form a unique haplotype different from the previously known U lineage haplotypes. Additionally, we determined the expression profiles of U, Z, and L genes in three different tissues. These findings collectively suggest that mhc1 U lineage genes and their haplotypes in zebrafish are more divergent than previously considered, and their expression patterns vary significantly among different tissues.
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Affiliation(s)
- Yasuko Honjo
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan.
| | - Kosuke Takano
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan; Division of Hematology, National Defence Medical College, Tokorozawa, Saitama, Japan
| | - Tatsuo Ichinohe
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan.
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Abstract
The human leukocyte antigen (HLA) complex is necessary for antigen presentation and regulates both innate and adaptive immune responses. In the context of cancer and treatment therapies, the HLA locus plays a critical role in tumor recognition and tolerance mechanisms. In silico HLA class I and class II typing, as well as expression quantification from next-generation RNA sequencing, can therefore have great potential clinical applications. However, HLA typing from short-read data is a challenging task given the high polymorphism and homology at the HLA locus. In this chapter, we present our highly accurate HLA typing solution, arcasHLA. We provide a detailed outline for practitioners using our protocol to perform HLA typing and demonstrate the applicability of arcasHLA in several clinical samples from tumors.
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Abstract
The Major Histocompatibility Complex (MHC) on the short arm of chromosome 6 is associated with more diseases than any other region of the genome; it encodes the antigen-presenting Human Leukocyte Antigen (HLA) proteins and is one of the key immunogenetic regions of the genome. Accurate genome inference and interpretation of MHC association signals have traditionally been hampered by the region's uniquely complex features, such as high levels of polymorphism; inter-gene sequence homologies; structural variation; and long-range haplotype structures. Recent algorithmic and technological advances have, however, significantly increased the accessibility of genetic variation in the MHC; these developments include (i) accurate SNP-based HLA type imputation; (ii) genome graph approaches for variation-aware genome inference from next-generation sequencing data; (iii) long-read-based diploid de novo assembly of the MHC; (iv) cost-effective targeted MHC sequencing methods. Applied to hundreds of thousands of samples over the last years, these technologies have already enabled significant biological discoveries, for example in the field of autoimmune disease genetics. Remaining challenges concern the development of integrated methods that leverage haplotype-resolved de novo assembly of the MHC for the development of improved MHC genotyping methods for short reads and the construction of improved reference panels for SNP-based imputation. Improved genome inference in the MHC can crucially contribute to an improved genetic and functional understanding of many immune-related phenotypes and diseases.
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Affiliation(s)
- Alexander T Dilthey
- Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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50
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Katkam SK, Rajasekhar L, Tasneem FSD, Kutala VK. Synergetic Interaction of HLA-DRB1*07 Allele and TNF-Alpha - 863 C/A Single Nucleotide Polymorphism in the Susceptibility to Systemic Lupus Erythematosus. Indian J Clin Biochem 2021; 36:59-66. [PMID: 33505128 DOI: 10.1007/s12291-019-00854-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/09/2019] [Indexed: 10/25/2022]
Abstract
Systemic lupus erythematosus (SLE) is an inflammatory autoimmune disease which is characterized by dysregulation of various cytokines propagating the inflammatory processes that is responsible for tissue damage. Tumor necrosis factor alpha (TNF-α) is one of the most important immunoregulatory cytokines that has been implicated in the different autoimmune diseases including SLE. Two hundred and two patients with SLE and 318 controls were included in the study. The TNF-α gene promoter region (from - 250 to - 1000 base pairs) was analyzed by direct Sanger's DNA sequencing method to find promoter variants associated with South Indian SLE patients. We have analyzed six TNF-α genetic polymorphisms including, - 863C/A (rs1800630), - 857C/T (rs1799724), - 806C/T (rs4248158), - 646G/A (rs4248160), - 572A/C (rs4248161) and - 308G/A (rs1800629) in both SLE patients and controls. We did not find association of TNF-α gene promoter SNPs with SLE patients. However, the - 863A (rs1800630) allele showed association with lupus nephritis phenotype in patients with SLE (OR: 1.62, 95%CI 1.04-2.53, P = 0.034). We found serum TNF-α level was significantly elevated in SLE cases as compared to control and found no association with any of the polymorphisms. The haplotype analysis revealed a significant protective association between the wild TNF-α alleles at positions - 863C, - 857C, - 806C, - 646G, - 572A and - 308G (CCCGAG) haplotype with lupus nephritis phenotype (OR 0.53, 95% CI 0.35-0.82, P = 0.004). Additionally, the TNF-α - 863 C/A (rs1800630) polymorphism and HLA-DRB1*07 haplotype showed significant differences between SLE patients and controls (OR 4.79, 95% CI 1.73-13.29, P = 0.0009). In conclusion, TNF-α - 863A allele (rs1800630) polymorphism is associated with increased risk of nephritis in South Indian SLE patients. We also found an interaction between HLA-DRB1*07 allele with TNF-α - 863 C/A promoter polymorphism giving supportive evidence for the tight linkage disequilibrium between TNF-α promoter SNPs and MHC class II DRB1 alleles.
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