1
|
Shiina T, Kulski JK. HLA Genetics for the Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 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] [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.
Collapse
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
| |
Collapse
|
2
|
Lee WP, Wang H, Dombroski B, Cheng PL, Tucci A, Si YQ, Farrell J, Tzeng JY, Leung YY, Malamon J, Wang LS, Vardarajan B, Farrer L, Schellenberg G. Structural Variation Detection and Association Analysis of Whole-Genome-Sequence Data from 16,905 Alzheimer's Diseases Sequencing Project Subjects. RESEARCH SQUARE 2023:rs.3.rs-3353179. [PMID: 37886469 PMCID: PMC10602095 DOI: 10.21203/rs.3.rs-3353179/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Structural variations (SVs) are important contributors to the genetics of human diseases. However, their role in Alzheimer's disease (AD) remains largely unstudied due to challenges in accurately detecting SVs. We analyzed whole-genome sequencing data from the Alzheimer's Disease Sequencing Project (N = 16,905) and identified 400,234 (168,223 high-quality) SVs. Laboratory validation yielded a sensitivity of 82% (85% for high-quality). We found a significant burden of deletions and duplications in AD cases, particularly for singletons and homozygous events. On AD genes, we observed the ultra-rare SVs associated with the disease, including protein-altering SVs in ABCA7, APP, PLCG2, and SORL1. Twenty-one SVs are in linkage disequilibrium (LD) with known AD-risk variants, exemplified by a 5k deletion in complete LD with rs143080277 in NCK2. We also identified 16 SVs associated with AD and 13 SVs linked to AD-related pathological/cognitive endophenotypes. This study highlights the pivotal role of SVs in shaping our understanding of AD genetics.
Collapse
|
3
|
Gaudieri S, Reyburn HT, Vales-Gomez M, Leelayuwat C. Editorial: The interaction of NKG2D and its ligands in health and diseases. Front Immunol 2022; 13:1099580. [PMID: 36569955 PMCID: PMC9774470 DOI: 10.3389/fimmu.2022.1099580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Affiliation(s)
- Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia,Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States,Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia,*Correspondence: Silvana Gaudieri,
| | - Hugh T. Reyburn
- National Center for Biotechnology, Spanish National Research Council, Madrid, Spain
| | - Mar Vales-Gomez
- National Center for Biotechnology, Spanish National Research Council, Madrid, Spain
| | - Chanvit Leelayuwat
- Department of Clinical Immunology and Transfusion Sciences and The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| |
Collapse
|
4
|
Fuertes MB, Domaica CI, Zwirner NW. Leveraging NKG2D Ligands in Immuno-Oncology. Front Immunol 2021; 12:713158. [PMID: 34394116 PMCID: PMC8358801 DOI: 10.3389/fimmu.2021.713158] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/02/2021] [Indexed: 12/14/2022] Open
Abstract
Immune checkpoint inhibitors (ICI) revolutionized the field of immuno-oncology and opened new avenues towards the development of novel assets to achieve durable immune control of cancer. Yet, the presence of tumor immune evasion mechanisms represents a challenge for the development of efficient treatment options. Therefore, combination therapies are taking the center of the stage in immuno-oncology. Such combination therapies should boost anti-tumor immune responses and/or target tumor immune escape mechanisms, especially those created by major players in the tumor microenvironment (TME) such as tumor-associated macrophages (TAM). Natural killer (NK) cells were recently positioned at the forefront of many immunotherapy strategies, and several new approaches are being designed to fully exploit NK cell antitumor potential. One of the most relevant NK cell-activating receptors is NKG2D, a receptor that recognizes 8 different NKG2D ligands (NKG2DL), including MICA and MICB. MICA and MICB are poorly expressed on normal cells but become upregulated on the surface of damaged, transformed or infected cells as a result of post-transcriptional or post-translational mechanisms and intracellular pathways. Their engagement of NKG2D triggers NK cell effector functions. Also, MICA/B are polymorphic and such polymorphism affects functional responses through regulation of their cell-surface expression, intracellular trafficking, shedding of soluble immunosuppressive isoforms, or the affinity of NKG2D interaction. Although immunotherapeutic approaches that target the NKG2D-NKG2DL axis are under investigation, several tumor immune escape mechanisms account for reduced cell surface expression of NKG2DL and contribute to tumor immune escape. Also, NKG2DL polymorphism determines functional NKG2D-dependent responses, thus representing an additional challenge for leveraging NKG2DL in immuno-oncology. In this review, we discuss strategies to boost MICA/B expression and/or inhibit their shedding and propose that combination strategies that target MICA/B with antibodies and strategies aimed at promoting their upregulation on tumor cells or at reprograming TAM into pro-inflammatory macrophages and remodeling of the TME, emerge as frontrunners in immuno-oncology because they may unleash the antitumor effector functions of NK cells and cytotoxic CD8 T cells (CTL). Pursuing several of these pipelines might lead to innovative modalities of immunotherapy for the treatment of a wide range of cancer patients.
Collapse
Affiliation(s)
- Mercedes Beatriz Fuertes
- Laboratorio de Fisiopatología de la Inmunidad Innata, Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina
| | - Carolina Inés Domaica
- Laboratorio de Fisiopatología de la Inmunidad Innata, Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina
| | - Norberto Walter Zwirner
- Laboratorio de Fisiopatología de la Inmunidad Innata, Instituto de Biología y Medicina Experimental (IBYME-CONICET), Buenos Aires, Argentina.,Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|
5
|
Kulski JK. Long Noncoding RNA HCP5, a Hybrid HLA Class I Endogenous Retroviral Gene: Structure, Expression, and Disease Associations. Cells 2019; 8:cells8050480. [PMID: 31137555 PMCID: PMC6562477 DOI: 10.3390/cells8050480] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 02/06/2023] Open
Abstract
The HCP5 RNA gene (NCBI ID: 10866) is located centromeric of the HLA-B gene and between the MICA and MICB genes within the major histocompatibility complex (MHC) class I region. It is a human species-specific gene that codes for a long noncoding RNA (lncRNA), composed mostly of an ancient ancestral endogenous antisense 3′ long terminal repeat (LTR, and part of the internal pol antisense sequence of endogenous retrovirus (ERV) type 16 linked to a human leukocyte antigen (HLA) class I promoter and leader sequence at the 5′-end. Since its discovery in 1993, many disease association and gene expression studies have shown that HCP5 is a regulatory lncRNA involved in adaptive and innate immune responses and associated with the promotion of some autoimmune diseases and cancers. The gene sequence acts as a genomic anchor point for binding transcription factors, enhancers, and chromatin remodeling enzymes in the regulation of transcription and chromatin folding. The HCP5 antisense retroviral transcript also interacts with regulatory microRNA and immune and cellular checkpoints in cancers suggesting its potential as a drug target for novel antitumor therapeutics.
Collapse
Affiliation(s)
- Jerzy K Kulski
- Faculty of Health and Medical Sciences, UWA Medical School, The University of Western Australia, Crawley, WA 6009, Australia.
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan.
| |
Collapse
|
6
|
Cox ST, Danby R, Hernandez D, Laza-Briviesca R, Pearson H, Madrigal JA, Saudemont A. Functional Characterisation and Analysis of the Soluble NKG2D Ligand Repertoire Detected in Umbilical Cord Blood Plasma. Front Immunol 2018; 9:1282. [PMID: 29963042 PMCID: PMC6013648 DOI: 10.3389/fimmu.2018.01282] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/22/2018] [Indexed: 12/19/2022] Open
Abstract
We previously reported that cord blood plasma (CBP) contains significantly more soluble NKG2D ligands (sNKG2DLs), such as sMICB and sULBP1, than healthy adult plasma. Viral infection or malignant transformation upregulates expression of NKG2D ligand on affected cells, leading to NK group 2, member D (NKG2D)-mediated natural killer (NK) cell lysis. Conversely, sNKG2DL engagement of NKG2D decreases NK cell cytotoxicity leading to viral or tumour immune escape. We hypothesised that sNKG2DLs detected in CBP may represent an additional fetal–maternal tolerance mechanism. To further understand the role of sNKG2DL in pregnancy and individual contributions of the various ligand types, we carried out functional analysis using 181 CBP samples. To test the ability of CBP to suppress the function of NK cells in vitro, we measured expression of NKG2D, CD107a, and IFN-γ in NK cells from control donors after exposure to 181 individual CBP samples and characterised the sMICA, sMICB, and sULBP1 content of each one. Furthermore, to detect possible allelic differences between samples that may also affect function, we carried out umbilical cord blood typing for MHC class I-related chain A (MICA) and MHC class I-related chain B (MICB) coding and promoter allelic types. Strongest functional correlations related to increasing concentration of exosomal sULBP1, which was present in all CBP samples tested. In addition, common MICB alleles, such as MICB*005:02, resulted in increased concentration of sMICB. Interestingly, MICB*005:02 uniquely associated with eight different promoter types. Among promoter polymorphisms, P2 resulted in the highest expression of sMICB and P9 the least and was confirmed using luciferase reporter assays. Higher levels of sMICB associated with lower IFN-γ production, indicating that sMICB also suppressed NK cell function. We also examined the MICA functional dimorphism encoding methionine (met) or valine (val) at residue 129 associated with strong or weak NKG2D binding, respectively. Most sMICA associated with val/val, some with met/val but none with met/met and, counter-intuitively, the presence of sMICA in CBP increased NK cell cytotoxicity. We propose a model for fetal–maternal tolerance, whereby NK cell activity is limited by sULBP1 and sMICB in CBP. The release of 129val sMICA with weak NKG2D signalling may reduce the overall net suppressive signal and break tolerance thus allowing fetal NK cells to overcome immunological threats in utero.
Collapse
Affiliation(s)
- Steven T Cox
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,Cancer Institute, University College London, London, United Kingdom
| | - Robert Danby
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Diana Hernandez
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,Cancer Institute, University College London, London, United Kingdom
| | | | - Hayley Pearson
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
| | - J Alejandro Madrigal
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,Cancer Institute, University College London, London, United Kingdom
| | - Aurore Saudemont
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.,Cancer Institute, University College London, London, United Kingdom
| |
Collapse
|
7
|
Schmiedel D, Mandelboim O. Disarming Cellular Alarm Systems-Manipulation of Stress-Induced NKG2D Ligands by Human Herpesviruses. Front Immunol 2017; 8:390. [PMID: 28443092 PMCID: PMC5387052 DOI: 10.3389/fimmu.2017.00390] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/20/2017] [Indexed: 12/18/2022] Open
Abstract
The coevolution of viruses and their hosts led to the repeated emergence of cellular alert signals and viral strategies to counteract them. The herpesvirus family of viruses displays the most sophisticated repertoire of immune escape mechanisms enabling infected cells to evade immune recognition and thereby maintain infection. The herpesvirus family consists of nine viruses that are capable of infecting humans: herpes simplex virus 1 and 2 (HSV-1, HSV-2), varicella zoster virus (VZV), Epstein–Barr virus (EBV), human cytomegalovirus (HCMV), roseoloviruses (HHV-6A, HHV-6B, and HHV-7), and Kaposi’s-sarcoma-associated herpesvirus (KSHV). Most of these viruses are highly prevalent and infect a vast majority of the human population worldwide. Notably, research over the past 15 years has revealed that cellular ligands for the activating receptor natural-killer group 2, member D (NKG2D)—which is primarily expressed on natural killer (NK) cells—are common targets suppressed during viral infection, i.e., their surface expression is reduced in virtually all lytic herpesvirus infections by diverse mechanisms. Here, we review the viral mechanisms by which all herpesviruses known to date to downmodulate the expression of the NKG2D ligands. Also, in light of recent findings, we speculate about the importance of the emergence of eight different NKG2D ligands in humans and further allelic diversification during host and virus coevolution.
Collapse
Affiliation(s)
- Dominik Schmiedel
- Faculty of Medicine, The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | - Ofer Mandelboim
- Faculty of Medicine, The Lautenberg Center for General and Tumor Immunology, The BioMedical Research Institute Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, Israel
| |
Collapse
|
8
|
Abstract
NKG2D ligands (NKG2DLs) are a group of stress-inducible major histocompatibility complex (MHC) class I-like molecules that act as a danger signal alerting the immune system to the presence of abnormal cells. In mammals, two families of NKG2DL genes have been identified: the MIC gene family encoded in the MHC region and the ULBP gene family encoded outside the MHC region in most species. Some mammals have a third family of NKG2DL-like class I genes which we named MILL (MHC class I-like located near the leukocyte receptor complex). Despite the fact that MILL genes are more closely related to MIC genes than ULBP genes are to MIC genes, MILL molecules do not function as NKG2DLs, and their function remains unknown. With the progress of mammalian genome projects, information on the MIC, ULBP, and MILL gene families became available in many mammalian species. Here, we summarize such information and discuss the origin and evolution of the NKG2DL gene family from the viewpoint of host-pathogen coevolution.
Collapse
Affiliation(s)
- Masanori Kasahara
- Department of Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Yoichi Sutoh
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| |
Collapse
|
9
|
Abstract
Human and mouse NKG2D ligands (NKG2DLs) are absent or only poorly expressed by most normal cells but are upregulated by cell stress, hence, alerting the immune system in case of malignancy or infection. Although these ligands are numerous and highly variable (at genetic, genomic, structural, and biochemical levels), they all belong to the major histocompatibility complex class I gene superfamily and bind to a single, invariant, receptor: NKG2D. NKG2D (CD314) is an activating receptor expressed on NK cells and subsets of T cells that have a key role in the recognition and lysis of infected and tumor cells. Here, we review the molecular diversity of NKG2DLs, discuss the increasing appreciation of their roles in a variety of medical conditions, and propose several explanations for the evolutionary force(s) that seem to drive the multiplicity and diversity of NKG2DLs while maintaining their interaction with a single invariant receptor.
Collapse
Affiliation(s)
- Raphael Carapito
- ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx TRANSPLANTEX, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Laboratoire International Associé (LIA) INSERM, Strasbourg (France) - Nagano (Japan), Strasbourg, France.,Fédération Hospitalo-Universitaire (FHU) OMICARE, Strasbourg, France
| | - Seiamak Bahram
- ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx TRANSPLANTEX, Centre de Recherche d'Immunologie et d'Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.,Laboratoire International Associé (LIA) INSERM, Strasbourg (France) - Nagano (Japan), Strasbourg, France.,Fédération Hospitalo-Universitaire (FHU) OMICARE, Strasbourg, France.,Laboratoire Central d'Immunologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| |
Collapse
|
10
|
Low JSY, Chin YM, Mushiroda T, Kubo M, Govindasamy GK, Pua KC, Yap YY, Yap LF, Subramaniam SK, Ong CA, Tan TY, Khoo ASB, Ng CC. A Genome Wide Study of Copy Number Variation Associated with Nasopharyngeal Carcinoma in Malaysian Chinese Identifies CNVs at 11q14.3 and 6p21.3 as Candidate Loci. PLoS One 2016; 11:e0145774. [PMID: 26730743 PMCID: PMC4701378 DOI: 10.1371/journal.pone.0145774] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 12/08/2015] [Indexed: 11/24/2022] Open
Abstract
Background Nasopharyngeal carcinoma (NPC) is a neoplasm of the epithelial lining of the nasopharynx. Despite various reports linking genomic variants to NPC predisposition, very few reports were done on copy number variations (CNV). CNV is an inherent structural variation that has been found to be involved in cancer predisposition. Methods A discovery cohort of Malaysian Chinese descent (NPC patients, n = 140; Healthy controls, n = 256) were genotyped using Illumina® HumanOmniExpress BeadChip. PennCNV and cnvPartition calling algorithms were applied for CNV calling. Taqman CNV assays and digital PCR were used to validate CNV calls and replicate candidate copy number variant region (CNVR) associations in a follow-up Malaysian Chinese (NPC cases, n = 465; and Healthy controls, n = 677) and Malay cohort (NPC cases, n = 114; Healthy controls, n = 124). Results Six putative CNVRs overlapping GRM5, MICA/HCP5/HCG26, LILRB3/LILRA6, DPY19L2, RNase3/RNase2 and GOLPH3 genes were jointly identified by PennCNV and cnvPartition. CNVs overlapping GRM5 and MICA/HCP5/HCG26 were subjected to further validation by Taqman CNV assays and digital PCR. Combined analysis in Malaysian Chinese cohort revealed a strong association at CNVR on chromosome 11q14.3 (Pcombined = 1.54x10-5; odds ratio (OR) = 7.27; 95% CI = 2.96–17.88) overlapping GRM5 and a suggestive association at CNVR on chromosome 6p21.3 (Pcombined = 1.29x10-3; OR = 4.21; 95% CI = 1.75–10.11) overlapping MICA/HCP5/HCG26 genes. Conclusion Our results demonstrated the association of CNVs towards NPC susceptibility, implicating a possible role of CNVs in NPC development.
Collapse
Affiliation(s)
- Joyce Siew Yong Low
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Translational Genomics Lab, High Impact Research Building (Level 2), University of Malaya, Kuala Lumpur, Malaysia
| | - Yoon Ming Chin
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Translational Genomics Lab, High Impact Research Building (Level 2), University of Malaya, Kuala Lumpur, Malaysia
| | - Taisei Mushiroda
- Laboratory for Pharmacogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Kin Choo Pua
- Department of Otorhinolaryngology, Hospital Pulau Pinang, Penang, Malaysia
| | - Yoke Yeow Yap
- Department of Surgery, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Kuala Lumpur, Malaysia
| | - Lee Fah Yap
- Department of Oral Biology & Biomedical Sciences and Oral Cancer Research & Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Selva Kumar Subramaniam
- Department of Otorhinolaryngology, Head and Neck Surgery, Sarawak General Hospital, Sarawak, Malaysia
| | - Cheng Ai Ong
- ENT Department, Hospital Queen Elizabeth, Karung Berkunci No. 2029, Kota Kinabalu, Sabah, Malaysia
| | - Tee Yong Tan
- Department of Otorhinolaryngology, Sarawak General Hospital, Kuching, Sarawak, Malaysia
| | - Alan Soo Beng Khoo
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - The Malaysian NPC Study Group
- The Malaysian Nasopharyngeal Carcinoma Study Group: Hospital Pulau Pinang, Hospital Kuala Lumpur/Universiti Putra Malaysia, University of Malaya, Institute for Medical Research, Cancer Research Initiatives Foundation, Sarawak General Hospital/Universiti Malaysia Sarawak, Queen Elizabeth Hospital and Hospital Universiti Sains, Malaysia
| | - Ching Ching Ng
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Translational Genomics Lab, High Impact Research Building (Level 2), University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
| |
Collapse
|
11
|
Edinur H, Dunn P, Hammond L, Selwyn C, Brescia P, Askar M, Reville P, Velickovic Z, Lea R, Chambers G. HLA and MICA polymorphism in Polynesians and New Zealand Maori: Implications for ancestry and health. Hum Immunol 2013; 74:1119-29. [DOI: 10.1016/j.humimm.2013.06.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/14/2013] [Accepted: 06/07/2013] [Indexed: 11/27/2022]
|
12
|
Wilming LG, Hart EA, Coggill PC, Horton R, Gilbert JGR, Clee C, Jones M, Lloyd C, Palmer S, Sims S, Whitehead S, Wiley D, Beck S, Harrow JL. Sequencing and comparative analysis of the gorilla MHC genomic sequence. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat011. [PMID: 23589541 PMCID: PMC3626023 DOI: 10.1093/database/bat011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC.
Collapse
Affiliation(s)
- Laurens G Wilming
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1HH, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Melis R, Lewis T, Millson A, Lyon E, McMillin GA, Slev PR, Swensen J. Copy number variation and incomplete linkage disequilibrium interfere with the HCP5 genotyping assay for abacavir hypersensitivity. Genet Test Mol Biomarkers 2012; 16:1111-4. [PMID: 22913531 DOI: 10.1089/gtmb.2012.0115] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Carriers of HLA-B*57:01 are at risk for Abacavir hypersensitivity reaction (ABC-HSR). In Caucasians, a SNP (rs2395029) in the HCP5 gene is reported to be in linkage disequilibrium (LD) with HLA-B*57:01. Genotyping the HCP5 SNP has increasingly been adopted as a simple method to screen for susceptibility to ABC-HSR. We genotyped both the HCP5 SNP and HLA-B*57:01 in a set of 1888 samples and found a good correlation; significantly, however, one HLA-B*57:01-positive sample tested negative for the HCP5 SNP. In addition, HCP5 could not be amplified in two samples, both negative for HLA-B*57:01. Further investigation demonstrated both samples were homozygous for deletion of the HCP5 gene. The fact HCP5 occurs within a region of copy number variation and the fact LD is incomplete and may vary between ethnicities should be considered when using the HCP5 SNP as a surrogate marker for HLA-B*57:01.
Collapse
Affiliation(s)
- Roberta Melis
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108, USA.
| | | | | | | | | | | | | |
Collapse
|
14
|
Kasahara M, Yoshida S. Immunogenetics of the NKG2D ligand gene family. Immunogenetics 2012; 64:855-67. [PMID: 22843249 DOI: 10.1007/s00251-012-0638-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 07/18/2012] [Indexed: 12/31/2022]
Abstract
NKG2D ligands (NKG2DLs) are a group of major histocompatibility complex (MHC) class I-like molecules, the expression of which is induced by cellular stresses such as infection, tumorigenesis, heat shock, tissue damage, and DNA damage. They act as a molecular danger signal alerting the immune system for infected or neoplastic cells. Mammals have two families of NKG2DL genes: the MHC-encoded MIC gene family and the ULBP gene family encoded outside the MHC region in most mammals. Rodents such as mice and rats lack the MIC family of ligands. Interestingly, some mammals have NKG2DL-like molecules named MILL that are phylogenetically related to MIC, but do not function as NKG2DLs. In this paper, we review our current knowledge of the MIC, ULBP, and MILL gene families in representative mammalian species and discuss the origin and evolution of the NKG2DL gene family.
Collapse
Affiliation(s)
- Masanori Kasahara
- Department of Pathology, Hokkaido University Graduate School of Medicine, North-15 West-7, Sapporo 060-8638, Japan.
| | | |
Collapse
|
15
|
ULBP4/RAET1E is highly polymorphic in the Old World monkey. Immunogenetics 2011; 63:501-9. [DOI: 10.1007/s00251-011-0531-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 04/21/2011] [Indexed: 01/14/2023]
|
16
|
Vejbaesya S, Luangtrakool P, Luangtrakool K, Kalayanarooj S, Vaughn DW, Endy TP, Mammen MP, Green S, Libraty DH, Ennis FA, Rothman AL, Stephens HAF. TNF and LTA gene, allele, and extended HLA haplotype associations with severe dengue virus infection in ethnic Thais. J Infect Dis 2009; 199:1442-8. [PMID: 19392621 DOI: 10.1086/597422] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Severe dengue virus (DENV) infection is characterized by a cascade of cytokine production, including the production of tumor necrosis factor-alpha (TNF-alpha) and lymphotoxin-alpha (LT-alpha). We have analyzed a variety of polymorphisms in the TNF and LTA genes of 435 ethnic Thais who had subclinical DENV infection, primary or secondary dengue fever (DF), or primary or secondary dengue hemorrhagic fever (DHF). The TNF -238A polymorphism marking the TNF-4,LTA-3 haplotype occurred in a significantly greater number of patients with secondary DHF (20 [15.2%] of 132) than patients with secondary DF (7 [4.1%] of 169) (P < .001; P corrected by use of Bonferroni adjustment, .022; odds ratio, 4.13 [95% confidence interval, 1.59-11.17]). In a subset of patients, the LTA-3 haplotype was associated with in vivo intracellular production of LT-alpha and TNF-alpha during the acute viremic phase of infection. Two extended human major histocompatibility complex (MHC) haplotypes containing TNF-4 and LTA-3, together with HLA-B48, HLA-B57, and HLA-DPB1*0501, were detected only in patients with secondary DHF. These observations indicate that polymorphism in functionally distinct MHC-encoded proteins contributes to the risk of developing severe secondary DENV infection and warrants further investigation.
Collapse
Affiliation(s)
- Sasijit Vejbaesya
- Department of Transfusion Medicine, Siriraj Hospital and Medical School, Mahidol University, Bangkok, Thailand
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Zhu F, Zhao H, He Y, Zhang W, He J, Xu X, Yan L. Distribution ofMICAdiversity in the Chinese Han population by polymerase chain reaction sequence-based typing for exons 2-6. ACTA ACUST UNITED AC 2009; 73:358-63. [DOI: 10.1111/j.1399-0039.2009.01225.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
18
|
Liu H, Lang J, Wang X, Wu S. Comparative proteomic analysis of human adenomyosis using two-dimensional gel electrophoresis and mass spectrometry. Fertil Steril 2007; 89:1625-31. [PMID: 17884045 DOI: 10.1016/j.fertnstert.2007.06.081] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 06/25/2007] [Accepted: 06/25/2007] [Indexed: 11/18/2022]
Abstract
OBJECTIVE To identify the differently expressed proteins in adenomyotic tissue compared with normal uterine muscle. DESIGN Retrospective, case-controlled study. SETTING University-based Department of Obstetrics and Gynecology and Proteomic Research Center. PATIENT(S) Ten patients who underwent transabdominal hysterectomy were included in this study. Five of them were histologically diagnosed with adenomyosis and the other five age-matched patients had cervical carcinoma in situ. INTERVENTION(S) Postoperative adenomyotic tissue and normal uterine muscle samples were collected. MAIN OUTCOME MEASURE(S) The protein extracts from paired sample tissue were separated using two-dimensional gel electrophoresis. The differently expressed protein spots were detected by gel comparison using image analysis software and identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry. RESULT(S) Compared with protein profiling of normal uterine muscle, there were 12 protein spots dysregulated in adenomyotic tissue. Among them, 10 protein spots were successfully identified by mass spectrometry. CONCLUSION(S) Comparative proteomic analysis is a useful approach for the discovery of protein biomarkers for adenomyosis and understanding the pathophysiology of the disease.
Collapse
Affiliation(s)
- Haiyuan Liu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | | | | | | |
Collapse
|
19
|
Gao X, Single RM, Karacki P, Marti D, O'Brien SJ, Carrington M. Diversity of MICA and linkage disequilibrium with HLA-B in two North American populations. Hum Immunol 2006; 67:152-8. [PMID: 16698437 DOI: 10.1016/j.humimm.2006.02.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Indexed: 10/24/2022]
Abstract
The MICA gene has a high degree of polymorphism. Allelic variation of MICA may influence binding of these ligands to the NK cell receptor NKG2D and may affect organ transplantation and/or disease pathogenesis. Knowledge of the population distribution of MICA alleles and their linkage disequilibrium (LD) with class I human leukocyte antigen (HLA) will enhance our understanding of the potential functional significance of the MICA polymorphism. In the present study, we characterized the MICA and HLA-B polymorphisms in two North American populations: European and African. The individual racial groups showed rather limited variation at the MICA locus, where the same set of three most common alleles, MICA*00201, *004, and *00801, account for 64 and 71% of the allele frequency in European-Americans and African-Americans, respectively. Other common alleles (allele frequency >5% in a population) include MICA*00901 and *010. MICA alleles showed strong linkage disequilibrium with HLA-B. Typically, a common MICA allele has strong LD with several HLA-B alleles, whereas most HLA-B alleles and their related serological groups are associated with a single MICA allele. The lack of evidence for an active diversification of the MICA gene after racial separation indicates an evolutionary history distinct from that of the classical HLA genes.
Collapse
Affiliation(s)
- Xiaojiang Gao
- Laboratory of Genomic Diversity, NCI-Frederick, Basic Research Program, SAIC Frederick, Frederick, MD 21702, USA
| | | | | | | | | | | |
Collapse
|
20
|
González S, Groh V, Spies T. Immunobiology of human NKG2D and its ligands. Curr Top Microbiol Immunol 2006; 298:121-38. [PMID: 16329186 DOI: 10.1007/3-540-27743-9_6] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The NKG2D-DAP10 receptor complex activates natural killer (NK) cells and costimulates effector T cell subsets upon engagement of ligands that can be conditionally expressed under physiologically harmful conditions such as microbial infections and malignancies. These characteristics have given rise to the widely embraced concept of immunorecognition of "induced or damaged self," complementing the "missing self" paradigm that is represented by MHC class I allotypes and their interactions with inhibitory receptors on NK cells. However, this notion may only be partially sustainable, as various patterns of constitutive tissue distributions have become apparent among members of one NKG2D ligand family. This review summarizes the biological properties of NKG2D and its ligands and discusses the interactions and regulation of these molecules with emphasis of their significance in microbial infections, tumor immunology, and autoimmune disease.
Collapse
Affiliation(s)
- S González
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | | | | |
Collapse
|
21
|
Kulski JK, Anzai T, Inoko H. ERVK9, transposons and the evolution of MHC class I duplicons within the alpha-block of the human and chimpanzee. Cytogenet Genome Res 2005; 110:181-92. [PMID: 16093671 DOI: 10.1159/000084951] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2003] [Accepted: 10/21/2003] [Indexed: 11/19/2022] Open
Abstract
The genomic sequences within the alpha-block (approximately 288-310 kb) of the human and chimpanzee MHC class I region contains ten MHC class I genes and three MIC gene fragments grouped together within alternating duplicated genomic segments or duplicons. In this study, the chimpanzee and human genomic sequences were analyzed in order to determine whether the remnants of the ERVK9 and other retrotransposon sequences are useful genomic markers for reconstructing the evolutionary history of the duplicated MHC gene families within the alpha-block. A variety of genes, pseudogenes, autologous DNA transposons and retrotransposons such as Alu and ERVK9 were used to categorize the ten duplicons into four distinct structural groups. The phylogenetic relationship of the ten duplicons was examined by using the neighbour joining method to analyze transposon sequence topologies of selected Alu members, LTR16B and Charlie9. On the basis of these structural groups and the phylogeny of the duplicated transposon sequences, a duplication model was reconstructed involving four multipartite tandem duplication steps to explain the organization and evolution of the ten duplicons within the alpha-block of the chimpanzee and human. The phylogenetic analysis and inferred duplication history suggests that the Patr/HLA-F was the first MHC class I gene to have been fixed and not required as a precursor for further duplication within the alpha-block of the ancestral species.
Collapse
Affiliation(s)
- J K Kulski
- Centre for Bioinformatics and Biological Computing, School of Information Technology, Murdoch University, Murdoch, Western Australia.
| | | | | |
Collapse
|
22
|
Schroeder M, Elsner HA, Kim TD, Blasczyk R. Eight novel MICB alleles, including a null allele, identified in gastric MALT lymphoma patients. ACTA ACUST UNITED AC 2005; 64:276-80. [PMID: 15304008 DOI: 10.1111/j.1399-0039.2004.00286.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MICA and MICB, as members of the major histocompatibility complex (MHC) class I-chain-related genes (MIC), encode stress-inducible glycoproteins that act as activating ligands for NKG2D and gammadelta T-cell receptor-bearing cells. We here describe the identification of eight novel MICB variants, including a null allele, which were identified in peripheral blood leukocytes of gastric MALT lymphoma patients. Only two of the novel alleles are characterized by point mutations, whereas the other variants display a recombination of known exonic MICB sequences that may be best explained by intragenic conversions. The novel MICB null allele is characterized by a Cytosin (C) deletion in a stretch of four Cs beginning from nucleotide 135 of exon 2 that leads to a premature stop codon (TGA) at codon 66.
Collapse
Affiliation(s)
- M Schroeder
- Department of Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | | | | | | |
Collapse
|
23
|
Feng ML, Guo XJ, Zhang JY, Xie JH, Chen L, Lu Q, Yang JH, Ji Y, Qian KC. Study on the haplotypes of MICA and MICB microsatellite and HLA-B locus in the Guangzhou Han population. ACTA ACUST UNITED AC 2005; 64:281-5. [PMID: 15304009 DOI: 10.1111/j.0001-2815.2004.00293.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The purpose of this study was to investigate the genetic polymorphisms and haplotypes of microsatellite locus in exon 5 of the MICA gene and intron 1 of the MICB gene and human leukocyte antigen-B (HLA-B) gene based on 106 samples of the Guangzhou Han population through means of polymerase chain reaction and the fluorescent technique (6-FAM). The corresponding haplotype frequencies, linkage disequilibrium values and relative linkage disequilibrium values were estimated based on population data. The results show that the genotype distributions of MICA and MICB microsatellite and HLA-B satisfy the Hardy-Weinberg equilibrium. In total, five alleles of MICA microsatellite locus and 14 alleles of MICB microsatellite locus were observed. MICA A5 was the most common allele (0.2877), whereas A4 was the least common (0.1321). MICB CA14 was the most common allele (0.3255), and CA19 and CA28 were the two least common (0.0047). CA27 was not observed at all. Five kinds of MICA-MICB haplotypes, 18 kinds of MICA-HLA-B haplotypes and 12 kinds of MICB-HLA-B haplotypes occurred at frequencies of more than 1%. The common haplotypes of MICA-MICB, MICA-HLA-B and MICB-HLA-B were A5-CA14, A5.1-CA18, A4-CA26, A9-CA15, A5-B*15(62), A5.1-B*1301/1302, A4-B*1301/1302, A6-B*51, A6-B*4403, A9-B*3802, CA14-B*4601, CA18-B*1301/1302 and CA26-B*1301/1302, and these haplotypes showed strong linkage disequilibrium. The polymorphisms and haplotype distributions of MICA and MICB microsatellite and HLA-B locus in the Guangzhou Han population have their own distinct genetic characteristics. The microsatellite locus of exon 5 of the MICA gene and intron 1 of the MICB gene could therefore be used as genetic markers in the studies of anthropology, gene linkage analysis in genetic diseases, individual identification and paternity testing in forensic medicine.
Collapse
Affiliation(s)
- M-L Feng
- Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Marin MLC, Savioli CR, Yamamoto JH, Kalil J, Goldberg AC. MICA polymorphism in a sample of the São Paulo population, Brazil. ACTA ACUST UNITED AC 2005; 31:63-71. [PMID: 15086345 DOI: 10.1111/j.1365-2370.2004.00446.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The major histocompatibility complex (MHC) class I chain-related A (MICA) gene, located near HLA-B, codes for protein products with structural similarities to those of classical MHC class I genes, but which neither bind beta(2)-microglobulin nor present peptide. Expressed predominantly on gastrointestinal and tumour epithelial cells, they are stress-induced and interact with C-type lectin like receptor (NKG2D) on gammadelta, alphabeta CD8+ T cells and natural killer (NK) cells. MICA is highly polymorphic, with 54 extracellular allelic sequences described. We typed 200 healthy subjects in a sample of the São Paulo population by extended polymerase chain reaction-sequence-specific primers (PCR-SSP) to characterize the MICA polymorphism and analysed MICA/HLA-B linkage disequilibrium. The MICA*008 group (g) was predominant (47%), with several HLA-B associations. Rare combinations MICA*008g-HLA-B37, MICA*008g-B72 and MICA*010-HLA-B52 were detected. Given the extent of this polymorphism and its possible relevance for disease association, we determined MICA and HLA-B alleles in 33 Behçet's patients, in an attempt to clarify the associated genetic marker. Our results showed an increase of MICA*006, but not MICA*009, in the patient group (6/33) compared with controls (3/200) (18.2% vs. 1.5%; P(c) = 0.005). Both alleles were always in association with HLA-B51, suggesting that HLA-B is indeed the primary susceptibility locus (P = 0.00008) and that MICA*006 may be an additional risk factor.
Collapse
Affiliation(s)
- M L C Marin
- Laboratory of Immunology, Heart Institute-InCor, School of Medicine, University of São Paulo, São Paulo, Brazil
| | | | | | | | | |
Collapse
|
25
|
Dunn DS, Ota M, Inoko H, Kulski JK. Association of MHC dimorphic Alu insertions with HLA class I and MIC genes in Japanese HLA-B48 haplotypes. TISSUE ANTIGENS 2003; 62:259-62. [PMID: 12956881 DOI: 10.1034/j.1399-0039.2003.00092.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A large proportion of Japanese with the HLA-B48 allele have a MICA gene deletion associated with a MICB null allele within the class I region of the Major Histocompatibility Complex (MHC). Here, we report for the first time a novel positive association between the presence of a polymorphic Alu insertion, AluyMICB, within the first intron of the MICB gene and the MICAdel/MICBnull/HLA-B48 haplotype for five of six well-characterized Japanese cell-lines. The AluyMICB insertion was found to be present at a frequency of 0.242 in 86 Japanese tissue donors and in four of the five individuals with the HLA-B48 allele. The AluyMICB insertion was also associated with at least three different MICB alleles, *0102, *0107N and *0105, and three different HLA-B alleles, B13, B48 and B57, respectively, in the seven Workshop cell-lines (the 4th Asia-Oceania Histocompatibility Workshop, and the 10th International Histocompatibility Workshop) and the six Japanese cell-lines that were selected for this study. Based on the analysis of associations between different polymorphic markers within the beta block, the MICB*0102 allele was inferred to be the ancestral form of the MICB*0105 and MICB*0107N alleles. The AluyMICB polymorphism can now be used to further investigate its relationship with other MICB alleles and consequently their origins. In addition, we have examined the absence and presence of three other polymorphic Alu markers distributed within the alpha block of the class I region of the HLA-B48/AluyMICB haplotype. We conclude that the extended HLA-B haplotypes are best defined by considering multiple genomic sites including the four polymorphic Alu insertions described in this study.
Collapse
Affiliation(s)
- D S Dunn
- Center for Bioinformatics and Biological Computing, School for Information Technology, Murdoch University, Murdoch, WA, Australia
| | | | | | | |
Collapse
|
26
|
Anzai T, Shiina T, Kimura N, Yanagiya K, Kohara S, Shigenari A, Yamagata T, Kulski JK, Naruse TK, Fujimori Y, Fukuzumi Y, Yamazaki M, Tashiro H, Iwamoto C, Umehara Y, Imanishi T, Meyer A, Ikeo K, Gojobori T, Bahram S, Inoko H. Comparative sequencing of human and chimpanzee MHC class I regions unveils insertions/deletions as the major path to genomic divergence. Proc Natl Acad Sci U S A 2003; 100:7708-13. [PMID: 12799463 PMCID: PMC164652 DOI: 10.1073/pnas.1230533100] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite their high degree of genomic similarity, reminiscent of their relatively recent separation from each other ( approximately 6 million years ago), the molecular basis of traits unique to humans vs. their closest relative, the chimpanzee, is largely unknown. This report describes a large-scale single-contig comparison between human and chimpanzee genomes via the sequence analysis of almost one-half of the immunologically critical MHC. This 1,750,601-bp stretch of DNA, which encompasses the entire class I along with the telomeric part of the MHC class III regions, corresponds to an orthologous 1,870,955 bp of the human HLA region. Sequence analysis confirms the existence of a high degree of sequence similarity between the two species. However, and importantly, this 98.6% sequence identity drops to only 86.7% taking into account the multiple insertions/deletions (indels) dispersed throughout the region. This is functionally exemplified by a large deletion of 95 kb between the virtual locations of human MICA and MICB genes, which results in a single hybrid chimpanzee MIC gene, in a segment of the MHC genetically linked to species-specific handling of several viral infections (HIV/SIV, hepatitis B and C) as well as susceptibility to various autoimmune diseases. Finally, if generalized, these data suggest that evolution may have used the mechanistically more drastic indels instead of the more subtle single-nucleotide substitutions for shaping the recently emerged primate species.
Collapse
Affiliation(s)
- Tatsuya Anzai
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
González S, Rodríguez-Rodero S, Martínez-Borra J, López-Vázquez A, Rodrigo L, López-Larrea C. MICB typing by PCR amplification with sequence specific primers. Immunogenetics 2003; 54:850-5. [PMID: 12671735 DOI: 10.1007/s00251-002-0533-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2002] [Revised: 11/27/2002] [Indexed: 10/25/2022]
Abstract
MICB is a member of the MIC (MHC class I chain-related gene) family. Sixteen MICB alleles have been described; however, the functional relevance and population distribution of MICB alleles or their potential association to disease has not yet been evaluated. In this study, we have developed a PCR system using sequence-specific primers (PCR-SSP) that allows unambiguous amplification of all MICB alleles. This approach has been applied to type 100 healthy unrelated individuals from the Spanish population. The extent of polymorphism in this population is lower than that initially expected, and only nine alleles were detected. The alleles MICB01021 (46%), MICB0103101 (13.5%), MICB0104 (13.5%) and MICB0106 (12.5%) were found to be the most frequent alleles. HLA-B and MICA transmembrane polymorphism typing were also performed in this population. Our data showed that MICB is in linkage disequilibrium with MICA and even with HLA-B. Thus, the linkage disequilibrium with MICA and HLA-B suggests that MICB is a potential candidate for those diseases classically associated with HLA class I alleles.
Collapse
Affiliation(s)
- Segundo González
- Department of Functional Biology, University of Oviedo, Julián Clavería sn, 33006 Oviedo, Spain
| | | | | | | | | | | |
Collapse
|
28
|
Ahmad T, Marshall SE, Mulcahy-Hawes K, Orchard T, Crawshaw J, Armuzzi A, Neville M, van Heel D, Barnardo M, Welsh KI, Jewell DP, Bunce M. High resolution MIC genotyping: design and application to the investigation of inflammatory bowel disease susceptibility. TISSUE ANTIGENS 2002; 60:164-79. [PMID: 12392511 DOI: 10.1034/j.1399-0039.2002.600207.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The highly polymorphic nonclassical MHC class I chain-related (MIC) genes MICA and MICB encode stress inducible glycoproteins expressed on a variety of epithelial cells including intestinal cells. Interaction with the receptor NKG2D is likely to provide an important costimulatory signal for activation and proliferation of NK cells, activated macrophages and CD8 alphabeta and gammadelta T cells. Fifty-four MICA and 17 MICB alleles have been described to date. Although the functional significance of this polymorphism is not known, the high degree of nonconservative substitution, concentration to the putative ligand-binding site and recent observation that different MICA alleles bind to NKG2D with varying affinity has generated much interest. The MIC genes are attractive functional and positional candidate genes for inflammatory bowel disease susceptibility as a consequence of their position in the HLA region and expression on the gastrointestinal epithelium. We developed a robust, high-resolution PCR-SSP genotyping method that can be incorporated into the standard 'Phototyping' system and which effectively identifies 46 of 54 MICA alleles, and all 17 MICB alleles. We applied this system in combination with microsatellite genotyping of the exon 5 variable number of tandem repeats (VNTR) to the investigation of genetic susceptibility to the inflammatory bowel diseases, ulcerative colitis and Crohn's disease. We studied 248 patients with Crohn's disease, 329 with ulcerative colitis and 354 ethnically matched controls. Linkage disequilibrium patterns between HLA-B, MICA and MICB are presented. Analysis by individual allele or by multilocus haplotype failed to identify any significant disease associations.
Collapse
Affiliation(s)
- T Ahmad
- Gastroenterology Unit, University of Oxford, Gibson Laboratories, Radcliffe Infirmary, UK.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Zhang Y, Lázaro AM, Mirbaha F, Lavingia B, Vorhaben R, Stastny P. Characterization of a novel MICA allele, MICA*047. TISSUE ANTIGENS 2002; 59:308-10. [PMID: 12135430 DOI: 10.1034/j.1399-0039.2002.590409.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report the identification of a novel MICA allele, MICA*047. It was initially detected because of an unusual hybridization pattern with sequence-specific oligonucleotides (SSOP) in a normal subject of Caucasian origin. Cloning and sequencing of both strands, and comparison of the sequence with previously defined MICA alleles, revealed that the new allele is similar to MICA*041 except for one nucleotide substitution at position 811 (C-->G). It appears that this new allele could have been generated by an interallelic sequence exchange between MICA*011 and MICA*0411.
Collapse
Affiliation(s)
- Y Zhang
- Department of Internal Medicine, UT South-western Medical Center, Dallas 75390-8886, USA
| | | | | | | | | | | |
Collapse
|
30
|
Radosavljevic M, Cuillerier B, Wilson MJ, Clément O, Wicker S, Gilfillan S, Beck S, Trowsdale J, Bahram S. A cluster of ten novel MHC class I related genes on human chromosome 6q24.2-q25.3. Genomics 2002; 79:114-23. [PMID: 11827464 DOI: 10.1006/geno.2001.6673] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We have identified a novel family of human major histocompatibility complex (MHC) class I genes. This MHC class I related gene family is defined by 10 members, among which 6 encode potentially functional glycoproteins. The 180-kb cluster containing them has been generated by serial duplication and minimal diversification of an ancestral prototype. They are not located within the MHC on 6p21.3, but near the tip of its long arm at q24.2-q25.3, close to the human equivalent of the mouse H2-linked t-complex, a subchromosomal region syntenic to a segment of mouse chromosome 10 harboring the orthologous MHC class I related retinoic acid early transcript loci, Raet1a-d. Hence we have named the identified loci RAET1E-N. Human RAET1 products are all devoid of the membrane-proximal immunoglobulin-like alpha3 domain and most, but not all, are predicted to remain membrane-anchored via glycosylphosphatidylinositol linkage and are shown to display an atypical pattern of polymorphism. RAET1 transcripts are absent from hematopoietic tissues, but largely expressed in tumors. The involvement of orthologous mouse RAET1A-D/H60 in natural killer and T-cell activation through NKG2D engagement augurs a similar function for the human RAET1 proteins.
Collapse
Affiliation(s)
- Mirjana Radosavljevic
- INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 4 rue Kirschleger, 67085 Strasbourg Cedex, France
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Romphruk AV, Naruse TK, Romphruk A, Kawata H, Puapairoj C, Kulski JK, Leelayuwat C, Inoko H. Diversity of MICA (PERB11.1) and HLA haplotypes in Northeastern Thais. TISSUE ANTIGENS 2001; 58:83-9. [PMID: 11696220 DOI: 10.1034/j.1399-0039.2001.580203.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
MICA or PERB11.1 is a polymorphic major histocompatibility complex (MHC) class I-related gene located 46 kb centromeric of the HLA-B gene in the HLA class I region. It is expressed mainly in gut epithelial cells, keratinocytes, endothelial cells, fibroblasts and monocytes, and is upregulated by heat stress. MICA has been found to interact with gamma delta T cells, alpha beta CD8(+) and natural killer (NK) cells bearing the NKG2D/DAP10 receptor. The MICA gene displays a high degree of polymorphism with at least 54 alleles. In the present study, polymorphic exons 2, 3 and 4 of the MICA gene were analyzed using sequencing based typing (SBT) in 255 unrelated healthy northeastern Thais. Thirteen previously reported MICA alleles were detected. MICA*008, *010, *002 and *019 were highly predominant with the allele frequencies of 21.4%, 18.2%, 17.6% and 15.3%, respectively. Five of these 13 MICA alleles show significantly different frequencies from those of the Japanese and Caucasian populations. Interestingly, MICA052, which is a very rare allele in other populations, was prevalent with the allele frequency of 8.2%, mainly on the HLA haplotype carrying HLA-B*13 in this population. Strong linkage disequilibria were observed between MICA and HLA-B, as similarly observed in other populations, namely MICA*010-B*4601, MICA052-B*13, MICA*002-B*5801, and MICA*019-B*15 (1502, 1508, 1511, 1515, 1528, 1530). A large variety of three-locus (MICA - HLA-B - HLA-Cw) and six-locus (HLA-DQB1 - HLA-DRB1 - MICA - HLA-B - HLA-Cw - HLA-A) haplotypes were recognized in the northeastern Thai population. This is the first report on MICA allelic distribution in Southeast Asian populations. These data will provide the important basis for future analyses on the potential role of the MICA gene in disease susceptibility and transplantation matching in Southeast Asian populations.
Collapse
Affiliation(s)
- A V Romphruk
- Blood Transfusion Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Abstract
The human MHC class I chain-related genes (MICA and MICB) are located within the HLA class I region of chromosome 6. Their organization, expression and products differ considerably from classical HLA class I genes. MIC proteins are considered to be markers of "stress" in the epithelia, and act as ligands for cells expressing a common activatory natural killer-cell receptor (NKG2D). Molecular models are now available for the MICA protein, both bound and complexed with NKG2D. MICA molecules appear to be highly flexible and polymorphic, although the functional relevance and implications of their polymorphism have yet to be fully discerned.
Collapse
Affiliation(s)
- H A Stephens
- Institute of Urology and Nephrology, University College London, The Middlesex Hospital, 48 Riding House Street, London, UK, W1W 7EY.
| |
Collapse
|
33
|
Affiliation(s)
- S Bahram
- Centre de Recherche d'Immunologie et d'Hématologie, Strasbourg, France
| |
Collapse
|
34
|
Komatsu-Wakui M, Tokunaga K, Ishikawa Y, Leelayuwat C, Kashiwase K, Tanaka H, Moriyama S, Nakajima F, Park MH, Jia GJ, Chimge NO, Sideltseva EW, Juji T. Wide distribution of the MICA-MICB null haplotype in East Asians. TISSUE ANTIGENS 2001; 57:1-8. [PMID: 11169252 DOI: 10.1034/j.1399-0039.2001.057001001.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Stress-inducible MICA (MHC class I chain-related A) is known to bind to NKG2D, which is one of the natural killer (NK) cell receptors, and plays a role in immune surveillance. We have reported that a MICA-MICB null haplotype is in linkage disequilibrium with HLA-B*4801 in the Japanese population. In the haplotype, an approximately 100-kb deletion, including the entire MICA gene, was observed and MICB possessed a premature stop codon. In this study, a multiplex polymerase chain reaction (PCR) method was developed for detecting the MICA deletion. MICB alleles were typed by PCR-single-strand conformation polymorphism (SSCP) method and direct sequencing. The frequency of the MICA-MICB null haplotype was 3.7% on the average, and was strongly associated with HLA-B48 in seven East Asian populations. It was presumed that the stop codon of MICB gene generated after the large-scale deletion. The wide distribution of the null haplotype at polymorphic frequencies suggests that the haplotype has been conservatively maintained because of some selective advantage.
Collapse
Affiliation(s)
- M Komatsu-Wakui
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|