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Robinson J, Barker DJ, Marsh SGE. 25 years of the IPD-IMGT/HLA Database. HLA 2024; 103:e15549. [PMID: 38936817 DOI: 10.1111/tan.15549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/03/2024] [Accepted: 05/16/2024] [Indexed: 06/29/2024]
Abstract
Twenty-five years ago, in 1998, the HLA Informatics Group of the Anthony Nolan Research Institute released the IMGT/HLA Database. Since this time, this online resource has acted as the repository for the numerous variant sequences of HLA alleles named by the WHO Nomenclature Committee for Factors of the HLA System. The IPD-IMGT/HLA Database has provided a stable, highly accessible, user-friendly repository for this work. During this time, the technology underlying HLA typing has undergone significant changes. Next generation sequencing (NGS) has superseded previous methodologies of HLA typing and can generate large amounts of high-resolution sequencing data. This has resulted in a drastic increase in the number and complexity of sequences submitted to the database. The challenge for the IPD-IMGT/HLA Database has been to maintain the highest standards of curation, while supporting the core set of tools and functionality to our users with increased numbers of submissions and sequences. Traditional methods of accessing and presenting data have been challenged and new methods utilising new computing technologies have had to be developed to keep pace and support a shifting user demographic.
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Affiliation(s)
- James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London (UCL), London, UK
| | - Dominic J Barker
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London (UCL), London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK
- UCL Cancer Institute, University College London (UCL), London, UK
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Guo W, Peng D, Liao Y, Lou L, Guo M, Li C, Yu W, Tian X, Wang G, Lv P, Zuo J, Shen H, Li Y. Upregulation of HLA-II related to LAG-3 +CD4 + T cell infiltration is associated with patient outcome in human glioblastoma. Cancer Sci 2024; 115:1388-1404. [PMID: 38480275 PMCID: PMC11093187 DOI: 10.1111/cas.16128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/01/2024] [Accepted: 02/17/2024] [Indexed: 05/15/2024] Open
Abstract
Glioblastoma (GBM) is the most common malignant diffuse glioma of the brain. Although immunotherapy with immune checkpoint inhibitors (ICIs), such as programmed cell death protein (PD)-1/PD ligand-1 inhibitors, has revolutionized the treatment of several cancers, the clinical benefit in GBM patients has been limited. Lymphocyte-activation gene 3 (LAG-3) binding to human leukocyte antigen-II (HLA-II) plays an essential role in triggering CD4+ T cell exhaustion and could interfere with the efficiency of anti-PD-1 treatment; however, the value of LAG-3-HLA-II interactions in ICI immunotherapy for GBM patients has not yet been analyzed. Therefore, we aimed to investigate the expression and regulation of HLA-II in human GBM samples and the correlation with LAG-3+CD4+ T cell infiltration. Human leukocyte antigen-II was highly expressed in GBM and correlated with increased LAG-3+CD4+ T cell infiltration in the stroma. Additionally, HLA-IIHighLAG-3High was associated with worse patient survival. Increased interleukin-10 (IL-10) expression was observed in GBM, which was correlated with high levels of HLA-II and LAG-3+ T cell infiltration in stroma. HLA-IIHighIL-10High GBM associated with LAG-3+ T cells infiltration synergistically showed shorter overall survival in patients. Combined anti-LAG-3 and anti-IL-10 treatment inhibited tumor growth in a mouse brain GL261 tumor model. In vitro, CD68+ macrophages upregulated HLA-II expression in GBM cells through tumor necrosis factor-α (TNF-α). Blocking TNF-α-dependent inflammation inhibited tumor growth in a mouse GBM model. In summary, T cell-tumor cell interactions, such as LAG-3-HLA-II, could confer an immunosuppressive environment in human GBM, leading to poor prognosis in patients. Therefore, targeting the LAG-3-HLA-II interaction could be beneficial in ICI immunotherapy to improve the clinical outcome of GBM patients.
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Affiliation(s)
- Wenli Guo
- Department of PathologyThe Second Hospital, Hebei Medical UniversityShijiazhuangChina
- Laboratory of PathologyHebei Medical UniversityShijiazhuangChina
| | - Daijun Peng
- Department of PathologyThe Second Hospital, Hebei Medical UniversityShijiazhuangChina
| | - Yuee Liao
- Department of PathologyThe Second Hospital, Hebei Medical UniversityShijiazhuangChina
| | - Lei Lou
- Department of PathologyThe Second Hospital, Hebei Medical UniversityShijiazhuangChina
| | - Moran Guo
- Department of NeurologySecond Hospital of Hebei Medical UniversityShijiazhuangChina
| | - Chen Li
- Department of NeurosurgerySecond Hospital of Hebei Medical UniversityShijiazhuangChina
| | - Wangyang Yu
- Department of NeurosurgerySecond Hospital of Hebei Medical UniversityShijiazhuangChina
| | - Xiaoxi Tian
- Department of PathologyThe Second Hospital, Hebei Medical UniversityShijiazhuangChina
| | - Guohui Wang
- Department of PathologyThe Second Hospital, Hebei Medical UniversityShijiazhuangChina
| | - Ping Lv
- Department of PharmacologyHebei Medical UniversityShijiazhuangChina
| | - Jing Zuo
- Department of OncologyThe Fourth Hospital of Hebei Medical UniversityShijiazhuangChina
| | - Haitao Shen
- Laboratory of PathologyHebei Medical UniversityShijiazhuangChina
- Hebei Collaborative Innovation Center of Tumor Microecological Metabolism RegulationHebei UniversityBaodingChina
| | - Yuehong Li
- Department of PathologyThe Second Hospital, Hebei Medical UniversityShijiazhuangChina
- Laboratory of PathologyHebei Medical UniversityShijiazhuangChina
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Hartman K, Steiner G, Siegel M, Looney CM, Hickling TP, Bray-French K, Springer S, Marban-Doran C, Ducret A. Expanding the MAPPs Assay to Accommodate MHC-II Pan Receptors for Improved Predictability of Potential T Cell Epitopes. BIOLOGY 2023; 12:1265. [PMID: 37759665 PMCID: PMC10525474 DOI: 10.3390/biology12091265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
A critical step in the immunogenicity cascade is attributed to human leukocyte antigen (HLA) II presentation triggering T cell immune responses. The liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based major histocompatibility complex (MHC) II-associated peptide proteomics (MAPPs) assay is implemented during preclinical risk assessments to identify biotherapeutic-derived T cell epitopes. Although studies indicate that HLA-DP and HLA-DQ alleles are linked to immunogenicity, most MAPPs studies are restricted to using HLA-DR as the dominant HLA II genotype due to the lack of well-characterized immunoprecipitating antibodies. Here, we address this issue by testing various commercially available clones of MHC-II pan (CR3/43, WR18, and Tü39), HLA-DP (B7/21), and HLA-DQ (SPV-L3 and 1a3) antibodies in the MAPPs assay, and characterizing identified peptides according to binding specificity. Our results reveal that HLA II receptor-precipitating reagents with similar reported specificities differ based on clonality and that MHC-II pan antibodies do not entirely exhibit pan-specific tendencies. Since no individual antibody clone is able to recover the complete HLA II peptide repertoire, we recommend a mixed strategy of clones L243, WR18, and SPV-L3 in a single immunoprecipitation step for more robust compound-specific peptide detection. Ultimately, our optimized MAPPs strategy improves the predictability and additional identification of T cell epitopes in immunogenicity risk assessments.
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Affiliation(s)
- Katharina Hartman
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Guido Steiner
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Michel Siegel
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Cary M. Looney
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Timothy P. Hickling
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Katharine Bray-French
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Sebastian Springer
- School of Science, Department of Biochemistry and Cell Biology, Constructor University, Campus Ring 1, 28759 Bremen, Germany
| | - Céline Marban-Doran
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
| | - Axel Ducret
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland (C.M.L.)
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Akarsu M, Ak G, Dündar E, Metintaş M. Genetic analysis of familial predisposition in the pathogenesis of malignant pleural mesothelioma. J Cancer Res Clin Oncol 2023; 149:7767-7778. [PMID: 37027032 DOI: 10.1007/s00432-023-04730-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023]
Abstract
PURPOSE Mesothelioma is the primary tumor of the mesothelial cell membrane. The most important etiology is asbestos exposure. The development of malignant mesothelioma in very few of the population exposed to asbestos and its frequent occurrence in some families may be significant in terms of genetic predisposition. Again, the presence of relatives with mesothelioma who did not have asbestos contact strengthens this argument. This disease, which has limited treatment options and has a poor prognosis, revealing a genetic predisposition, if any, may prolong survival with early diagnosis and effective treatment. METHODS Based on the genetic predisposition idea, we diagnosed and followed a total of ten individuals of relatives with mesothelioma. DNA was isolated from peripheral blood and whole genome sequencing analysis was done. Common gene mutations in ten individuals were filtered using bioinformatics. After this filter, from the remaining variants, very rare in the population and damaging mutations are selected. RESULTS Eight thousand six hundred and twenty-two common variants have been identified in ten individuals with this analysis. In total, 120 variants were found on 37 genes in 15 chromosomes. These genes are PIK3R4, SLC25A5, ITGB6, PLK2, RAD17, HLA-B, HLA-DRB1, HLA-DQB1, GRM, IL20RA, MAP3K7, RIPK2, and MUC16. CONCLUSION Our finding, PIK3R4 gene, is directly associated with mesothelioma development. Twelve genes, which are associated with cancer, were detected in literature. Additional studies, which scan first-degree relatives of individual, are needed to find the specific gene region.
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Affiliation(s)
- Muhittin Akarsu
- Department of Chest Disease, Eskisehir City Hospital, 26080, Eskisehir, Turkey.
| | - Güntülü Ak
- Lung and Pleural Cancers Research and Clinical Center, Eskisehir Osmangazi University, 26040, Eskisehir, Turkey
| | - Emine Dündar
- Department of Pathology, Faculty of Medicine, Eskisehir Osmangazi University, Meselik Kampusu, 26480, Eskisehir, Turkey
| | - Muzaffer Metintaş
- Lung and Pleural Cancers Research and Clinical Center, Eskisehir Osmangazi University, 26040, Eskisehir, Turkey
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Fan J, Shi J, Zhang Y, Liu J, An C, Zhu H, Wu P, Hu W, Qin R, Yao D, Shou X, Xu Y, Tong Z, Wen X, Xu J, Zhang J, Fang W, Lou J, Yin W, Chen W. NKG2D discriminates diverse ligands through selectively mechano-regulated ligand conformational changes. EMBO J 2022; 41:e107739. [PMID: 34913508 PMCID: PMC8762575 DOI: 10.15252/embj.2021107739] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 11/10/2021] [Accepted: 11/18/2021] [Indexed: 11/12/2022] Open
Abstract
Stimulatory immune receptor NKG2D binds diverse ligands to elicit differential anti-tumor and anti-virus immune responses. Two conflicting degeneracy recognition models based on static crystal structures and in-solution binding affinities have been considered for almost two decades. Whether and how NKG2D recognizes and discriminates diverse ligands still remain unclear. Using live-cell-based single-molecule biomechanical assay, we characterized the in situ binding kinetics of NKG2D interacting with different ligands in the absence or presence of mechanical force. We found that mechanical force application selectively prolonged NKG2D interaction lifetimes with the ligands MICA and MICB, but not with ULBPs, and that force-strengthened binding is much more pronounced for MICA than for other ligands. We also integrated steered molecular dynamics simulations and mutagenesis to reveal force-induced rotational conformational changes of MICA, involving formation of additional hydrogen bonds on its binding interface with NKG2D, impeding MICA dissociation under force. We further provided a kinetic triggering model to reveal that force-dependent affinity determines NKG2D ligand discrimination and its downstream NK cell activation. Together, our results demonstrate that NKG2D has a discrimination power to recognize different ligands, which depends on selective mechanical force-induced ligand conformational changes.
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Affiliation(s)
- Juan Fan
- Department of Cell Biology and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Jiawei Shi
- Key Laboratory for Biomedical Engineering of the Ministry of EducationZhejiang UniversityHangzhouChina
| | - Yong Zhang
- Key Laboratory of RNA BiologyCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Junwei Liu
- Key Laboratory for Biomedical Engineering of the Ministry of EducationZhejiang UniversityHangzhouChina
- Department of Hepatobiliary and Pancreatic SurgeryThe Center for Integrated Oncology and Precision MedicineAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhouChina
| | - Chenyi An
- Department of Cell Biology and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Huaying Zhu
- Department of Cell Biology and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Peng Wu
- Department of Cell Biology and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Wei Hu
- Department of Cell Biology and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Rui Qin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Danmei Yao
- Department of Cell Biology and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Xin Shou
- Institute of Translational MedicineSchool of MedicineZhejiang UniversityHangzhouChina
| | - Yibing Xu
- Institute of Translational MedicineSchool of MedicineZhejiang UniversityHangzhouChina
| | - Zhou Tong
- Department of Medical OncologyFirst Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
| | - Xue Wen
- Department of PathologyThe First Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
| | - Jianpo Xu
- Center for Stem Cell and Regenerative MedicineDepartment of Basic Medical SciencesThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Jin Zhang
- Center for Stem Cell and Regenerative MedicineDepartment of Basic Medical SciencesThe First Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Zhejiang Laboratory for Systems and Precision MedicineZhejiang University Medical CenterHangzhouChina
- Institute of HematologyZhejiang UniversityHangzhouChina
| | - Weijia Fang
- Department of Medical OncologyFirst Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
| | - Jizhong Lou
- Key Laboratory of RNA BiologyCAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Weiwei Yin
- Key Laboratory for Biomedical Engineering of the Ministry of EducationZhejiang UniversityHangzhouChina
- Department of Thoracic SurgerySir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
- Zhejiang Provincial Key Laboratory of Cardio‐Cerebral Vascular Detection Technology and Medicinal Effectiveness AppraisalCollege of Biomedical Engineering and Instrument of ScienceZhejiang UniversityHangzhouChina
| | - Wei Chen
- Department of Cell Biology and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Key Laboratory for Biomedical Engineering of the Ministry of EducationZhejiang UniversityHangzhouChina
- Department of Hepatobiliary and Pancreatic SurgeryThe Center for Integrated Oncology and Precision MedicineAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhouChina
- Zhejiang Laboratory for Systems and Precision MedicineZhejiang University Medical CenterHangzhouChina
- The MOE Frontier Science Center for Brain Science & Brain‐machine IntegrationZhejiang UniversityHangzhouChina
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Barker DJ, Maccari G, Georgiou X, Cooper MA, Flicek P, Robinson J, Marsh SGE. The IPD-IMGT/HLA Database. Nucleic Acids Res 2022; 51:D1053-D1060. [PMID: 36350643 PMCID: PMC9825470 DOI: 10.1093/nar/gkac1011] [Citation(s) in RCA: 535] [Impact Index Per Article: 267.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
It is 24 years since the IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The database now contains over 35 000 alleles of the human Major Histocompatibility Complex (MHC) named by the WHO Nomenclature Committee for Factors of the HLA System. This complex contains the most polymorphic genes in the human genome and is now considered hyperpolymorphic. The IPD-IMGT/HLA Database provides a stable and user-friendly repository for this information. Uptake of Next Generation Sequencing technology in recent years has driven an increase in the number of alleles and the length of sequences submitted. As the size of the database has grown the traditional methods of accessing and presenting this data have been challenged, in response, we have developed a suite of tools providing an enhanced user experience to our traditional web-based users while creating new programmatic access for our bioinformatics user base. This suite of tools is powered by the IPD-API, an Application Programming Interface (API), providing scalable and flexible access to the database. The IPD-API provides a stable platform for our future development allowing us to meet the future challenges of the HLA field and needs of the community.
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Affiliation(s)
- Dominic J Barker
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London, NW3 2QG, UK,UCL Cancer Institute, University College London (UCL), Royal Free Campus, Pond Street, London, NW3 2QG, UK
| | - Giuseppe Maccari
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Xenia Georgiou
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London, NW3 2QG, UK
| | - Michael A Cooper
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London, NW3 2QG, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - James Robinson
- To whom correspondence should be addressed. Tel: +44 20 7284 8307;
| | - Steven G E Marsh
- Correspondence may also be addressed to Steven G.E. Marsh. Tel: +44 20 7284 8321;
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Huseby ES, Teixeiro E. The perception and response of T cells to a changing environment are based on the law of initial value. Sci Signal 2022; 15:eabj9842. [PMID: 35639856 PMCID: PMC9290192 DOI: 10.1126/scisignal.abj9842] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
αβ T cells are critical components of the adaptive immune system and are capable of inducing sterilizing immunity after pathogen infection and eliminating transformed tumor cells. The development and function of T cells are controlled through the T cell antigen receptor, which recognizes peptides displayed on major histocompatibility complex (MHC) molecules. Here, we review how T cells generate the ability to recognize self-peptide-bound MHC molecules and use signals derived from these interactions to instruct cellular development, activation thresholds, and functional specialization in the steady state and during immune responses. We argue that the basic tenants of T cell development and function follow Weber-Fetcher's law of just noticeable differences and Wilder's law of initial value. Together, these laws argue that the ability of a system to respond and the quality of that response are scalable to the basal state of that system. Manifestation of these laws in T cells generates clone-specific activation thresholds that are based on perceivable differences between homeostasis and pathogen encounter (self versus nonself discrimination), as well as poised states for subsequent differentiation into specific effector cell lineages.
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Affiliation(s)
- Eric S. Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Emma Teixeiro
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
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Robinson J, Barker DJ, Georgiou X, Cooper MA, Flicek P, Marsh SGE. IPD-IMGT/HLA Database. Nucleic Acids Res 2020; 48:D948-D955. [PMID: 31667505 PMCID: PMC7145640 DOI: 10.1093/nar/gkz950] [Citation(s) in RCA: 315] [Impact Index Per Article: 78.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/03/2019] [Accepted: 10/29/2019] [Indexed: 11/14/2022] Open
Abstract
The IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, currently contains over 25 000 allele sequence for 45 genes, which are located within the Major Histocompatibility Complex (MHC) of the human genome. This region is the most polymorphic region of the human genome, and the levels of polymorphism seen exceed most other genes. Some of the genes have several thousand variants and are now termed hyperpolymorphic, rather than just simply polymorphic. The IPD-IMGT/HLA Database has provided a stable, highly accessible, user-friendly repository for this information, providing the scientific and medical community access to the many variant sequences of this gene system, that are critical for the successful outcome of transplantation. The number of currently known variants, and dramatic increase in the number of new variants being identified has necessitated a dedicated resource with custom tools for curation and publication. The challenge for the database is to continue to provide a highly curated database of sequence variants, while supporting the increased number of submissions and complexity of sequences. In order to do this, traditional methods of accessing and presenting data will be challenged, and new methods will need to be utilized to keep pace with new discoveries.
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Affiliation(s)
- James Robinson
- Anthony Nolan Research Institute, London, UK
- UCL Cancer Institute, University College London (UCL), London, UK
| | | | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, London, UK
- UCL Cancer Institute, University College London (UCL), London, UK
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Ferreira MG, De Vito FB, Ferreira AA, Bub CB, Santos FAVD, Filho AB, Silva SS, Moraes-Souza H. Applicability of an instrument to identify human leukocyte antigen-compatible donors for platelet transfusions. Hematol Transfus Cell Ther 2018; 40:298-304. [PMID: 30370406 PMCID: PMC6200671 DOI: 10.1016/j.htct.2018.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 03/21/2018] [Indexed: 11/19/2022] Open
Abstract
Background The selection of compatible human leukocyte antigen platelets has been associated with improved platelet increments. Therefore, an effective strategy would be the selection of donors who are genetically compatible according to the human leukocyte antigen system. Nonetheless, this is costly as it concerns a highly polymorphic system, which requires a large bank of genotyped donors. Methods This study evaluated the feasibility of virtual crossmatching using EpVix software, which simplifies the identification of compatible donors or donors with acceptable incompatibilities. Results Forty-three oncohematological patients were evaluated, in 96 platelet transfusion episodes with 16.3% of the patients being found to be refractory to platelet transfusions. Eight alloimmunized, multitransfused patients were selected to evaluate human leukocyte antigen compatibility against a bank of 336 platelet donors. At least partially compatible donors were found for all patients. The number of compatible donors was found to be inversely proportional to the human leukocyte antigen-panel reactive antibody score of each patient. It was noted that five patients with scores of 15% or less had at least 190 compatible donors; four fully compatible donors were found for two other patients with scores greater than 80% and only one patient (score of 93%) did not have a fully compatible donor. However, for this last patient, 40 donors were partially compatible according to the software. Conclusion The results showed the effectiveness of the use of the EpVix tool to identify potential platelet donors for multitransfused and/or alloimmunized patients, even with a small number of human leukocyte antigen genotyped donors available.
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Affiliation(s)
| | | | - Aline Aparecida Ferreira
- Universidade Federal do Triângulo Mineiro (UFTM), Uberaba, MG, Brazil.,Hemocentro Regional de Uberaba, Uberaba, MG, Brazil
| | | | | | | | - Sheila Soares Silva
- Universidade Federal do Triângulo Mineiro (UFTM), Uberaba, MG, Brazil.,Hemocentro Regional de Uberaba, Uberaba, MG, Brazil
| | - Helio Moraes-Souza
- Universidade Federal do Triângulo Mineiro (UFTM), Uberaba, MG, Brazil.,Hemococentro Regional de Uberlândia, Uberlandia, MG, Brazil.,Universidade Federal de Uberlândia (UFU), Uberlândia, MG, Brazil
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Rajčáni J, Szathmary S. Peptide Vaccines: New Trends for Avoiding the Autoimmune Response. ACTA ACUST UNITED AC 2018. [DOI: 10.2174/1874279301810010047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Background:Several marketed antiviral vaccines (such as that against hepatitis virus A and/or B, influenza virus, human papillomavirus, yellow fever virus, measles, rubella and mumps viruses) may elicit various autoimmune reactions.Results:The cause of autoimmune response due to vaccination may be: 1. the adjuvant which is regularly added to the vaccine (especially in the case of various oil substrates), 2. the specific viral component itself (a protein or glycoprotein potentially possessing cross-reactive epitopes) and/or 3. contamination of the vaccine with traces of non-viral proteins mostly cellular in origin. Believing that peptide vaccines might represent an optimal solution for avoiding the above-mentioned problems, we discuss the principles of rational design of a typical peptide vaccine which should contain oligopeptides coming either from the selected structural virion components (i.e.capsid proteins and/or envelop glycoproteins or both) or from the virus-coded non-structural polypeptides. The latter should be equally immunogenic as the structural virus proteins. Describing the feasibility of identification and design of immunogenic epitopes, our paper also deals with possible problems of peptide vaccine manufacturing. The presented data are in part based on the experience of our own, in part, they are coming from the results published by others.Conclusion:Any peptide vaccine should be able to elicit relevant and specific antibody formation, as well as an efficient cell-mediated immune response. Consequently, the properly designed peptide vaccine is expected to consist of carefully selected viral peptides, which should stimulate the receptors of helper T/CD4 cells as well as of cytotoxic (T/CD8) lymphocytes.
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Human Leukocyte Antigen-A, B, C, DRB1, and DQB1 Allele and Haplotype Frequencies in a Subset of 237 Donors in the South African Bone Marrow Registry. J Immunol Res 2018; 2018:2031571. [PMID: 29850621 PMCID: PMC5937380 DOI: 10.1155/2018/2031571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/30/2018] [Accepted: 04/11/2018] [Indexed: 12/31/2022] Open
Abstract
Human leukocyte antigen- (HLA-) A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 allele and haplotype frequencies were studied in a subset of 237 volunteer bone marrow donors registered at the South African Bone Marrow Registry (SABMR). Hapl-o-Mat software was used to compute allele and haplotype frequencies from individuals typed at various resolutions, with some alleles in multiple allele code (MAC) format. Four hundred and thirty-eight HLA-A, 235 HLA-B, 234 HLA-DRB1, 41 HLA-DQB1, and 29 HLA-C alleles are reported. The most frequent alleles were A∗02:02g (0.096), B∗07:02g (0.082), C∗07:02g (0.180), DQB1∗06:02 (0.157), and DRB1∗15:01 (0.072). The most common haplotype was A∗03:01g~B∗07:02g~C∗07:02g~DQB1∗06:02~DRB1∗15:01 (0.067), which has also been reported in other populations. Deviations from Hardy-Weinberg equilibrium were observed in A, B, and DRB1 loci, with C~DQB1 being the only locus pair in linkage disequilibrium. This study describes allele and haplotype frequencies from a subset of donors registered at SABMR, the only active bone marrow donor registry in Africa. Although the sample size was small, our results form a key resource for future population studies, disease association studies, and donor recruitment strategies.
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Abstract
The rapidly increasing number of characterized allergens has created huge demands for advanced information storage, retrieval, and analysis. Bioinformatics and machine learning approaches provide useful tools for the study of allergens and epitopes prediction, which greatly complement traditional laboratory techniques. The specific applications mainly include identification of B- and T-cell epitopes, and assessment of allergenicity and cross-reactivity. In order to facilitate the work of clinical and basic researchers who are not familiar with bioinformatics, we review in this chapter the most important databases, bioinformatic tools, and methods with relevance to the study of allergens.
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Leiro-Fernández V, Valverde D, Vázquez-Gallardo R, Constenla-Caramés L, Del Campo-Pérez V, Fernández-Villar A. HLA-DQ B1*0201 and A1*0102 Alleles Are Not Responsible for Antituberculosis Drug-Induced Hepatotoxicity Risk in Spanish Population. Front Med (Lausanne) 2016; 3:34. [PMID: 27597944 PMCID: PMC4992991 DOI: 10.3389/fmed.2016.00034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/29/2016] [Indexed: 12/26/2022] Open
Abstract
Aims To evaluate the role of human leukocyte antigen (HLA) class II DQB1*0201 and DQA1*0102 in the risk of antituberculosis drug (ATD)-induced hepatotoxicity (ATDH) in a cohort of tuberculosis patients of Caucasian origin from Spain. Methods Matched case-control study including active tuberculosis (TB) patients from Spain (Caucasian) treated with first-line ATD (Isoniazid, Rifampin, and Pyrazinamide). Presence or absence of HLA class II DQB1*0201 and DQA1*0102 alleles were compared between cases and controls. Results We included 110 TB patients, 55 ATDH cases, and 55 sex-matched controls. The analysis of the presence of HLA-DQB1*0201 and HLA-DQA*0102 did not show significative differences between both groups [presence of HLA-DQB1*0201 53.6% of the cases vs. 45.4% of the controls, OR: 1.63 95% CI (0.62–4.52) p = 0.38; presence of HLA-DQA*0102 7.5% of cases vs. 20% of controls, OR: 0.36 95% CI (0.08–1.23) p = 0.12]. After multivariate logistic regression analysis including in the model, other potential risk factors of hepatotoxicity HLA class II DQB1*0201 and DQA1*0102 alleles were not found significantly associated with the risk of development ATDH. We could not demonstrate an association between HLA-DQA1*0102 and HLA-DQB1*0201 with the risk of ATDH in this Caucasian population of Spanish origin.
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Affiliation(s)
- Virginia Leiro-Fernández
- NeumoVigol+i Research Group, Pulmonary Department, EOXI Vigo, Biomedical Research Institute Vigo (IBIV), Alvaro Cunqueiro Hospital , Vigo , Spain
| | - Diana Valverde
- Biochemical, Genetics and Immunology Department, Biology Faculty, Vigo University , Vigo , Spain
| | - Rafael Vázquez-Gallardo
- NeumoVigol+i Research Group, Pulmonary Department, EOXI Vigo, Biomedical Research Institute Vigo (IBIV), Alvaro Cunqueiro Hospital , Vigo , Spain
| | | | | | - Alberto Fernández-Villar
- NeumoVigol+i Research Group, Pulmonary Department, EOXI Vigo, Biomedical Research Institute Vigo (IBIV), Alvaro Cunqueiro Hospital , Vigo , Spain
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14
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A Novel Peptide Binding Prediction Approach for HLA-DR Molecule Based on Sequence and Structural Information. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3832176. [PMID: 27340658 PMCID: PMC4906198 DOI: 10.1155/2016/3832176] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/04/2016] [Indexed: 11/18/2022]
Abstract
MHC molecule plays a key role in immunology, and the molecule binding reaction with peptide is an important prerequisite for T cell immunity induced. MHC II molecules do not have conserved residues, so they appear as open grooves. As a consequence, this will increase the difficulty in predicting MHC II molecules binding peptides. In this paper, we aim to propose a novel prediction method for MHC II molecules binding peptides. First, we calculate sequence similarity and structural similarity between different MHC II molecules. Then, we reorder pseudosequences according to descending similarity values and use a weight calculation formula to calculate new pocket profiles. Finally, we use three scoring functions to predict binding cores and evaluate the accuracy of prediction to judge performance of each scoring function. In the experiment, we set a parameter α in the weight formula. By changing α value, we can observe different performances of each scoring function. We compare our method with the best function to some popular prediction methods and ultimately find that our method outperforms them in identifying binding cores of HLA-DR molecules.
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Kongmaroeng C, Romphruk A, Puapairoj C, Leelayuwat C, Kulski JK, Inoko H, Dunn DS, Romphruk AV. HLA alleles and haplotypes in Burmese (Myanmarese) and Karen in Thailand. ACTA ACUST UNITED AC 2016; 86:199-204. [PMID: 26265055 DOI: 10.1111/tan.12637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 06/02/2015] [Accepted: 07/14/2015] [Indexed: 11/28/2022]
Abstract
This is the first report on human leukocyte antigen (HLA) allele and haplotype frequencies at three class I loci and two class II loci in unrelated healthy individuals from two ethnic groups, 170 Burmese and 200 Karen, originally from Burma (Myanmar), but sampled while residing in Thailand. Overall, the HLA allele and haplotype frequencies detected by polymerase chain reaction sequence-specific primer (PCR-SSP) at five loci (A, B, C, DRB1 and DRQB1) at low resolution showed distinct differences between the Burmese and Karen. In Burmese, five HLA-B*15 haplotypes with different HLA-A and HLA-DR/DQ combinations were detected with three of these not previously reported in other Asian populations. The data are important in the fields of anthropology, transplantation and disease-association studies.
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Affiliation(s)
- C Kongmaroeng
- Department of Blood Bank, Faculty of Medical Technology, Huachiew Chalermprakiet University, Samut Prakarn, Thailand
| | - A Romphruk
- Department of Clinical Immunology and Transfusion Sciences, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - C Puapairoj
- Blood Transfusion Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - C Leelayuwat
- Department of Clinical Immunology and Transfusion Sciences, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - J K Kulski
- Centre for Forensic Science, The University of Western Australia, Nedlands, Australia
| | - H Inoko
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Tokyo, Japan
| | - D S Dunn
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - A V Romphruk
- The Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand.,Blood Transfusion Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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16
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Elmas A, Wang X, Samoilov MS. Reconstruction of novel transcription factor regulons through inference of their binding sites. BMC Bioinformatics 2015; 16:299. [PMID: 26388177 PMCID: PMC4576408 DOI: 10.1186/s12859-015-0685-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 07/24/2015] [Indexed: 02/04/2023] Open
Abstract
Background In most sequenced organisms the number of known regulatory genes (e.g., transcription factors (TFs)) vastly exceeds the number of experimentally-verified regulons that could be associated with them. At present, identification of TF regulons is mostly done through comparative genomics approaches. Such methods could miss organism-specific regulatory interactions and often require expensive and time-consuming experimental techniques to generate the underlying data. Results In this work, we present an efficient algorithm that aims to identify a given transcription factor’s regulon through inference of its unknown binding sites, based on the discovery of its binding motif. The proposed approach relies on computational methods that utilize gene expression data sets and knockout fitness data sets which are available or may be straightforwardly obtained for many organisms. We computationally constructed the profiles of putative regulons for the TFs LexA, PurR and Fur in E. coli K12 and identified their binding motifs. Comparisons with an experimentally-verified database showed high recovery rates of the known regulon members, and indicated good predictions for the newly found genes with high biological significance. The proposed approach is also applicable to novel organisms for predicting unknown regulons of the transcriptional regulators. Results for the hypothetical protein Dde0289 in D. alaskensis include the discovery of a Fis-type TF binding motif. Conclusions The proposed motif-based regulon inference approach can discover the organism-specific regulatory interactions on a single genome, which may be missed by current comparative genomics techniques due to their limitations. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0685-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abdulkadir Elmas
- Department of Electrical Engineering, Columbia University, 500W 120th Street, New York, 10027, NY, USA.
| | - Xiaodong Wang
- Department of Electrical Engineering, Columbia University, 500W 120th Street, New York, 10027, NY, USA.
| | - Michael S Samoilov
- Department of Bioengineering, QB3 California Institute for Quantitative Biosciences UC Berkeley, 1700 4th St #214, Berkeley, 94720, California, USA.
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17
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Bub CB, Gonçalez AC, Barjas-Castro ML, Sousa LCDM, do Monte SJH, Castro V. The use of a potential novel tool in virtual crossmatching for platelet transfusion in platelet refractoriness. Vox Sang 2015; 110:70-8. [DOI: 10.1111/vox.12315] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 06/17/2015] [Accepted: 06/22/2015] [Indexed: 12/01/2022]
Affiliation(s)
- C. B. Bub
- Hematology and Hemotherapy Center; University of Campinas - UNICAMP; Instituto Nacional de Ciência e Tecnologia do Sangue (INCTS); Campinas Brazil
| | - A. C. Gonçalez
- Hematology and Hemotherapy Center; University of Campinas - UNICAMP; Instituto Nacional de Ciência e Tecnologia do Sangue (INCTS); Campinas Brazil
| | - M. L. Barjas-Castro
- Hematology and Hemotherapy Center; University of Campinas - UNICAMP; Instituto Nacional de Ciência e Tecnologia do Sangue (INCTS); Campinas Brazil
| | - L. C. D. M. Sousa
- Immunogenetics and Molecular Biology Laboratory; Federal University of Piauí; Teresina Brazil
| | - S. J. H. do Monte
- Immunogenetics and Molecular Biology Laboratory; Federal University of Piauí; Teresina Brazil
| | - V. Castro
- Hematology and Hemotherapy Center; University of Campinas - UNICAMP; Instituto Nacional de Ciência e Tecnologia do Sangue (INCTS); Campinas Brazil
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18
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Zhu X, Yang T, Tan R, Su P, Luo Z, Zhen X. A novel HLA-A allele, HLA-A*02:544. TISSUE ANTIGENS 2015; 85:501-2. [PMID: 25940820 DOI: 10.1111/tan.12560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/26/2015] [Accepted: 03/15/2015] [Indexed: 11/26/2022]
Abstract
The novel allele HLA-A*02:544 has two nucleotide changes from its most closely related allele, HLA-A*02:148. Firstly at nucleotide 255 where C → T (codon 60 GAC → GAT), resulting in a non-coding change as GAC and GAT both code for the same amino acid aspartic acid. Secondly at nucleotide 368 where T → G (codon 98 TTT → TGT) resulting in a coding change, 98 phenylalanine is changed to cysteine.
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Affiliation(s)
- X Zhu
- Department of Obstetrics and Gynecology, Peking University, Third Hospital, Beijing, PR China
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19
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Parham LR, Briley LP, Li L, Shen J, Newcombe PJ, King KS, Slater AJ, Dilthey A, Iqbal Z, McVean G, Cox CJ, Nelson MR, Spraggs CF. Comprehensive genome-wide evaluation of lapatinib-induced liver injury yields a single genetic signal centered on known risk allele HLA-DRB1*07:01. THE PHARMACOGENOMICS JOURNAL 2015; 16:180-5. [PMID: 25987243 PMCID: PMC4819766 DOI: 10.1038/tpj.2015.40] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/13/2015] [Accepted: 03/26/2015] [Indexed: 01/11/2023]
Abstract
Lapatinib is associated with a low incidence of serious liver injury. Previous investigations have identified and confirmed the Class II allele HLA-DRB1*07:01 to be strongly associated with lapatinib-induced liver injury; however, the moderate positive predictive value limits its clinical utility. To assess whether additional genetic variants located within the major histocompatibility complex locus or elsewhere in the genome may influence lapatinib-induced liver injury risk, and potentially lead to a genetic association with improved predictive qualities, we have taken two approaches: a genome-wide association study and a whole-genome sequencing study. This evaluation did not reveal additional associations other than the previously identified association for HLA-DRB1*07:01. The present study represents the most comprehensive genetic evaluation of drug-induced liver injury (DILI) or hypersensitivity, and suggests that investigation of possible human leukocyte antigen associations with DILI and other hypersensitivities represents an important first step in understanding the mechanism of these events.
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Affiliation(s)
- L R Parham
- GlaxoSmithKline Research & Development, Research Triangle Park, NC, USA
| | - L P Briley
- GlaxoSmithKline Research & Development, Research Triangle Park, NC, USA
| | - L Li
- GlaxoSmithKline Research & Development, Research Triangle Park, NC, USA
| | - J Shen
- GlaxoSmithKline Research & Development, Research Triangle Park, NC, USA
| | - P J Newcombe
- GlaxoSmithKline Research & Development, Stevenage, UK
| | - K S King
- GlaxoSmithKline Research & Development, Research Triangle Park, NC, USA
| | - A J Slater
- GlaxoSmithKline Research & Development, Research Triangle Park, NC, USA
| | - A Dilthey
- Department of Statistics, University of Oxford, Oxford, UK
| | - Z Iqbal
- Department of Statistics, University of Oxford, Oxford, UK
| | - G McVean
- Department of Statistics, University of Oxford, Oxford, UK
| | - C J Cox
- GlaxoSmithKline Research & Development, Stevenage, UK
| | - M R Nelson
- GlaxoSmithKline Research & Development, Research Triangle Park, NC, USA
| | - C F Spraggs
- GlaxoSmithKline Research & Development, Stevenage, UK
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Song D, Chen J, Chen G, Li N, Li J, Fan J, Bu D, Li SC. Parameterized BLOSUM Matrices for Protein Alignment. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:686-694. [PMID: 26357279 DOI: 10.1109/tcbb.2014.2366126] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein alignment is a basic step for many molecular biology researches. The BLOSUM matrices, especially BLOSUM62, are the de facto standard matrices for protein alignments. However, after widely utilization of the matrices for 15 years, programming errors were surprisingly found in the initial version of source codes for their generation. And amazingly, after bug correction, the "intended" BLOSUM62 matrix performs consistently worse than the "miscalculated" one. In this paper, we find linear relationships among the eigenvalues of the matrices and propose an algorithm to find optimal unified eigenvectors. With them, we can parameterize matrix BLOSUMx for any given variable x that could change continuously. We compare the effectiveness of our parameterized isentropic matrix with BLOSUM62. Furthermore, an iterative alignment and matrix selection process is proposed to adaptively find the best parameter and globally align two sequences. Experiments are conducted on aligning 13,667 families of Pfam database and on clustering MHC II protein sequences, whose improved accuracy demonstrates the effectiveness of our proposed method.
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21
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Testi M, Andreani M, Galluccio T, Guagnano A, Paladini E. HLA-C*07:02:60, a variant of HLA-C*07 found in an unrelated volunteer stem cell donor. ACTA ACUST UNITED AC 2015; 85:77-8. [PMID: 25597904 DOI: 10.1111/tan.12484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/10/2014] [Accepted: 11/06/2014] [Indexed: 11/29/2022]
Abstract
The allele HLA-C*07:02:60 differs from HLA-C*07:02:01:01 by a silent nucleotide substitution in exon 4.
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Affiliation(s)
- M Testi
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation at Polyclinic of Tor Vergata, Rome, 00146, Italy
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22
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Robinson J, Halliwell JA, Hayhurst JD, Flicek P, Parham P, Marsh SGE. The IPD and IMGT/HLA database: allele variant databases. Nucleic Acids Res 2014; 43:D423-31. [PMID: 25414341 PMCID: PMC4383959 DOI: 10.1093/nar/gku1161] [Citation(s) in RCA: 1475] [Impact Index Per Article: 147.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Immuno Polymorphism Database (IPD) was developed to provide a centralized system for the study of polymorphism in genes of the immune system. Through the IPD project we have established a central platform for the curation and publication of locus-specific databases involved either directly or related to the function of the Major Histocompatibility Complex in a number of different species. We have collaborated with specialist groups or nomenclature committees that curate the individual sections before they are submitted to IPD for online publication. IPD consists of five core databases, with the IMGT/HLA Database as the primary database. Through the work of the various nomenclature committees, the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website http://www.ebi.ac.uk/ipd/. The IPD project continues to develop with new tools being added to address scientific developments, such as Next Generation Sequencing, and to address user feedback and requests. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the immunogenetics community, and the wider research and clinical communities.
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Affiliation(s)
- James Robinson
- Anthony Nolan Research Institute, Hampstead, London, NW3 2QG, UK UCL Cancer Institute, University College London, Hampstead, London, NW3 2QG, UK
| | | | - James D Hayhurst
- Anthony Nolan Research Institute, Hampstead, London, NW3 2QG, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5136, USA
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Hampstead, London, NW3 2QG, UK UCL Cancer Institute, University College London, Hampstead, London, NW3 2QG, UK
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Peptide Vaccine: Progress and Challenges. Vaccines (Basel) 2014; 2:515-36. [PMID: 26344743 PMCID: PMC4494216 DOI: 10.3390/vaccines2030515] [Citation(s) in RCA: 451] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/10/2014] [Accepted: 06/13/2014] [Indexed: 12/17/2022] Open
Abstract
Conventional vaccine strategies have been highly efficacious for several decades in reducing mortality and morbidity due to infectious diseases. The bane of conventional vaccines, such as those that include whole organisms or large proteins, appear to be the inclusion of unnecessary antigenic load that, not only contributes little to the protective immune response, but complicates the situation by inducing allergenic and/or reactogenic responses. Peptide vaccines are an attractive alternative strategy that relies on usage of short peptide fragments to engineer the induction of highly targeted immune responses, consequently avoiding allergenic and/or reactogenic sequences. Conversely, peptide vaccines used in isolation are often weakly immunogenic and require particulate carriers for delivery and adjuvanting. In this article, we discuss the specific advantages and considerations in targeted induction of immune responses by peptide vaccines and progresses in the development of such vaccines against various diseases. Additionally, we also discuss the development of particulate carrier strategies and the inherent challenges with regard to safety when combining such technologies with peptide vaccines.
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Abstract
Asparaginase is a therapeutic enzyme used to treat leukemia and lymphoma, with immune responses resulting in suboptimal drug exposure and a greater risk of relapse. To elucidate whether there is a genetic component to the mechanism of asparaginase-induced immune responses, we imputed human leukocyte antigen (HLA) alleles in patients of European ancestry enrolled on leukemia trials at St. Jude Children's Research Hospital (n = 541) and the Children's Oncology Group (n = 1329). We identified a higher incidence of hypersensitivity and anti-asparaginase antibodies in patients with HLA-DRB1*07:01 alleles (P = 7.5 × 10(-5), odds ratio [OR] = 1.64; P = 1.4 × 10(-5), OR = 2.92, respectively). Structural analysis revealed that high-risk amino acids were located within the binding pocket of the HLA protein, possibly affecting the interaction between asparaginase epitopes and the HLA-DRB1 protein. Using a sequence-based consensus approach, we predicted the binding affinity of HLA-DRB1 alleles for asparaginase epitopes, and patients whose HLA genetics predicted high-affinity binding had more allergy (P = 3.3 × 10(-4), OR = 1.38). Our results suggest a mechanism of allergy whereby HLA-DRB1 alleles that confer high-affinity binding to asparaginase epitopes lead to a higher frequency of reactions. These trials were registered at www.clinicaltrials.gov as NCT00137111, NCT00549848, NCT00005603, and NCT00075725.
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25
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Lamaze FC, Pavey SA, Normandeau E, Roy G, Garant D, Bernatchez L. Neutral and selective processes shape MHC gene diversity and expression in stocked brook charr populations (Salvelinus fontinalis). Mol Ecol 2014; 23:1730-48. [PMID: 24795997 DOI: 10.1111/mec.12684] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The capacity of an individual to battle infection is an important fitness determinant in wild vertebrate populations. The major histocompatibility complex (MHC) genes are crucial for a host's adaptive immune system to detect pathogens. However, anthropogenic activities may disrupt natural cycles of co-evolution between hosts and pathogens. In this study, we investigated the dynamic sequence and expression variation of host parasite interactions in brook charr (Salvelinus fontinalis) in a context of past human disturbance via population supplementation from domestic individuals. To do so, we developed a new method to examine selection shaping MHC diversity within and between populations and found a complex interplay between neutral and selective processes that varied between lakes that were investigated. We provided evidence for a lower introgression rate of domestic alleles and found that parasite infection increased with domestic genomic background of individuals. We also documented an association between individual MHC alleles and parasite taxa. Finally, longer cis-regulatory minisatellites were positively correlated with MHC II down-regulation and domestic admixture, suggesting that inadvertent selection during domestication resulted in a lower immune response capacity, through a trade-off between growth and immunity, which explained the negative selection of domestic alleles at least under certain circumstances.
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26
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Zhu X, Yang T, Yao F, Che Z, Su P, Luo Z, Tan R. A new human leukocyte antigen-A allele, HLA-A*02:482. ACTA ACUST UNITED AC 2014; 84:238-9. [PMID: 24903058 DOI: 10.1111/tan.12378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 03/26/2014] [Accepted: 04/20/2014] [Indexed: 11/28/2022]
Affiliation(s)
- X Zhu
- Transfusion Medicine Research Department, Yunnan Kunming Blood Center, Kunming, PR China
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27
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Wu Y, Jing R, Jiang L, Jiang Y, Kuang Q, Ye L, Yang L, Li Y, Li M. Combination use of protein–protein interaction network topological features improves the predictive scores of deleterious non-synonymous single-nucleotide polymorphisms. Amino Acids 2014; 46:2025-35. [PMID: 24849655 DOI: 10.1007/s00726-014-1760-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 05/03/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Yiming Wu
- College of Chemistry, Sichuan University, Chengdu, 610064, People's Republic of China
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Stadinski BD, Trenh P, Duke B, Huseby PG, Li G, Stern LJ, Huseby ES. Effect of CDR3 sequences and distal V gene residues in regulating TCR-MHC contacts and ligand specificity. THE JOURNAL OF IMMUNOLOGY 2014; 192:6071-82. [PMID: 24813203 DOI: 10.4049/jimmunol.1303209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mature T cell repertoire has the ability to orchestrate immunity to a wide range of potential pathogen challenges. This ability stems from thymic development producing individual T cell clonotypes that express TCRs with unique patterns of Ag reactivity. The Ag specificity of TCRs is created from the combinatorial pairing of one of a set of germline encoded TCR Vα and Vβ gene segments with randomly created CDR3 sequences. How the amalgamation of germline encoded and randomly created TCR sequences results in Ag receptors with unique patterns of ligand specificity is not fully understood. Using cellular, biophysical, and structural analyses, we show that CDR3α residues can modulate the geometry in which TCRs bind peptide-MHC (pMHC), governing whether and how germline encoded TCR Vα and Vβ residues interact with MHC. In addition, a CDR1α residue that is positioned distal to the TCR-pMHC binding interface is shown to contribute to the peptide specificity of T cells. These findings demonstrate that the specificity of individual T cell clonotypes arises not only from TCR residues that create direct contacts with the pMHC, but also from a collection of indirect effects that modulate how TCR residues are used to bind pMHC.
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Affiliation(s)
- Brian D Stadinski
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Peter Trenh
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Brian Duke
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Priya G Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Guoqi Li
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Eric S Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
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Testi M, Andreani M, Locatelli F, Arcese W, Troiano M, Battarra M, Gaziev J, Lucarelli G. Influence of the HLA characteristics of Italian patients on donor search outcome in unrelated hematopoietic stem cell transplantation. ACTA ACUST UNITED AC 2014; 84:198-205. [DOI: 10.1111/tan.12355] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 03/11/2014] [Accepted: 03/19/2014] [Indexed: 11/28/2022]
Affiliation(s)
- M. Testi
- Laboratory of Immunogenetics and Transplant Biology; IME Foundation at Polyclinic of Tor Vergata; Rome Italy
| | - M. Andreani
- Laboratory of Immunogenetics and Transplant Biology; IME Foundation at Polyclinic of Tor Vergata; Rome Italy
| | - F. Locatelli
- Department of Pediatric Hematology-Oncology, IRCCS Bambino Gesù Children's Hospital; University of Pavia; Rome Italy
| | - W. Arcese
- Rome Transplant Network, Department of Hematology, Stem Cell Transplant Unit; Tor Vergata University; Rome Italy
| | - M. Troiano
- Laboratory of Immunogenetics and Transplant Biology; IME Foundation at Polyclinic of Tor Vergata; Rome Italy
| | - M. Battarra
- Laboratory of Immunogenetics and Transplant Biology; IME Foundation at Polyclinic of Tor Vergata; Rome Italy
| | - J. Gaziev
- Rome Transplant Network, Department of Hematology, Stem Cell Transplant Unit; Tor Vergata University; Rome Italy
| | - G. Lucarelli
- International Center for Transplantation in Thalassemia and Sickle Cell Anemia; IME Foundation at Polyclinic of Tor Vergata; Rome Italy
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30
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Li X, Zou H, Li M, Zuo Y, Chen Q. Characterization of a novelHLA-DQB1*05allele,HLA-DQB1*05:03:09. ACTA ACUST UNITED AC 2014; 83:367-8. [DOI: 10.1111/tan.12327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 02/10/2014] [Indexed: 11/27/2022]
Affiliation(s)
- X. Li
- HLA Typing Laboratory; Sichuan Cord Blood Bank; Chengdu Sichuan China
| | - H. Zou
- HLA Typing Laboratory; Sichuan Cord Blood Bank; Chengdu Sichuan China
| | - M. Li
- HLA Typing Laboratory; Sichuan Cord Blood Bank; Chengdu Sichuan China
| | - Y. Zuo
- HLA Typing Laboratory; Sichuan Cord Blood Bank; Chengdu Sichuan China
| | - Q. Chen
- HLA Typing Laboratory; Sichuan Cord Blood Bank; Chengdu Sichuan China
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31
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Testi M, Battarra M, Troiano M, Testa G, Andreani M. The novel HLA-B*35:240 allele identified by sequence-based typing in an Italian family. TISSUE ANTIGENS 2014; 83:363-4. [PMID: 24646331 DOI: 10.1111/tan.12331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 02/11/2014] [Indexed: 11/27/2022]
Affiliation(s)
- M Testi
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation at Polyclinic of Tor Vergata, Rome, Italy
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32
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Bhati M, Cole DK, McCluskey J, Sewell AK, Rossjohn J. The versatility of the αβ T-cell antigen receptor. Protein Sci 2014; 23:260-72. [PMID: 24375592 DOI: 10.1002/pro.2412] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 02/06/2023]
Abstract
The T-cell antigen receptor is a heterodimeric αβ protein (TCR) expressed on the surface of T-lymphocytes, with each chain of the TCR comprising three complementarity-determining regions (CDRs) that collectively form the antigen-binding site. Unlike antibodies, which are closely related proteins that recognize intact protein antigens, TCRs classically bind, via their CDR loops, to peptides (p) that are presented by molecules of the major histocompatibility complex (MHC). This TCR-pMHC interaction is crucially important in cell-mediated immunity, with the specificity in the cellular immune response being attributable to MHC polymorphism, an extensive TCR repertoire and a variable peptide cargo. The ensuing structural and biophysical studies within the TCR-pMHC axis have been highly informative in understanding the fundamental events that underpin protective immunity and dysfunctional T-cell responses that occur during autoimmunity. In addition, TCRs can recognize the CD1 family, a family of MHC-related molecules that instead of presenting peptides are ideally suited to bind lipid-based antigens. Structural studies within the CD1-lipid antigen system are beginning to inform us how lipid antigens are specifically presented by CD1, and how such CD1-lipid antigen complexes are recognized by the TCR. Moreover, it has recently been shown that certain TCRs can bind to vitamin B based metabolites that are bound to an MHC-like molecule termed MR1. Thus, TCRs can recognize peptides, lipids, and small molecule metabolites, and here we review the basic principles underpinning this versatile and fascinating receptor recognition system that is vital to a host's survival.
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Affiliation(s)
- Mugdha Bhati
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, 3800, Australia
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33
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Croft NP, Purcell AW. Peptidomimetics: modifying peptides in the pursuit of better vaccines. Expert Rev Vaccines 2014; 10:211-26. [DOI: 10.1586/erv.10.161] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
The IMGT/HLA Database (http://www.ebi.ac.uk/ipd/imgt/hla/) was first released over 15 years ago, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and are highly polymorphic, with some genes currently having over 3,000 known allelic variants. The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) expands on this model, with a further set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. IPD currently consists of four databases: IPD-KIR contains the allelic sequences of killer-cell immunoglobulin-like receptors; IPD-MHC is a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website http://www.ebi.ac.uk/ipd/.
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Affiliation(s)
- James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, Hampstead, London, NW3 2QG, UK
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35
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Roark CL, Anderson KM, Simon LJ, Schuyler RP, Aubrey MT, Freed BM. Multiple HLA epitopes contribute to type 1 diabetes susceptibility. Diabetes 2014; 63:323-31. [PMID: 24357703 PMCID: PMC3868045 DOI: 10.2337/db13-1153] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Disease susceptibility for type 1 diabetes is strongly associated with the inheritance of specific HLA alleles. However, conventional allele frequency analysis can miss HLA associations because many alleles are rare. In addition, disparate alleles that have similar peptide-binding sites, or shared epitopes, can be missed. To identify the HLA shared epitopes associated with diabetes, we analyzed high-resolution genotyping for class I and class II loci. The HLA epitopes most strongly associated with susceptibility for disease were DQB1 A(57), DQA1 V(76), DRB1 H(13), and DRB1 K(71), whereas DPB1 YD(9,57), HLA-B C(67), and HLA-C YY(9,116) were more weakly associated. The HLA epitopes strongly associated with resistance were DQB1 D(57), DQA1 Y(80), DRB1 R(13), and DRB1 A(71). A dominant resistance phenotype was observed for individuals bearing a protective HLA epitope, even in the presence of a susceptibility epitope. In addition, an earlier age of disease onset correlated with significantly greater numbers of susceptibility epitopes and fewer resistance epitopes (P < 0.0001). The prevalence of both DQ and DR susceptibility epitopes was higher in patients than in control subjects and was not exclusively a result of linkage disequilibrium, suggesting that multiple HLA epitopes may work together to increase the risk of developing diabetes.
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Affiliation(s)
- Christina L. Roark
- ClinImmune Labs and Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
- Corresponding author: Christina L. Roark,
| | - Kirsten M. Anderson
- Department of Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Lucas J. Simon
- ClinImmune Labs and Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ronald P. Schuyler
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Michael T. Aubrey
- ClinImmune Labs and Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Brian M. Freed
- ClinImmune Labs and Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO
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36
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Fan Y, Lu R, Wang L, Andreatta M, Li SC. Quantifying Significance of MHC II Residues. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014; 11:17-25. [PMID: 26355503 DOI: 10.1109/tcbb.2013.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The major histocompatibility complex (MHC), a cell-surface protein mediating immune recognition, plays important roles in the immune response system of all higher vertebrates. MHC molecules are highly polymorphic and they are grouped into serotypes according to the specificity of the response. It is a common belief that a protein sequence determines its three dimensional structure and function. Hence, the protein sequence determines the serotype. Residues play different levels of importance. In this paper, we quantify the residue significance with the available serotype information. Knowing the significance of the residues will deepen our understanding of the MHC molecules and yield us a concise representation of the molecules. In this paper we propose a linear programming-based approach to find significant residue positions as well as quantifying their significance in MHC II DR molecules. Among all the residues in MHC II DR molecules, 18 positions are of particular significance, which is consistent with the literature on MHC binding sites, and succinct pseudo-sequences appear to be adequate to capture the whole sequence features. When the result is used for classification of MHC molecules with serotype assigned by WHO, a 98.4 percent prediction performance is achieved. The methods have been implemented in java (http://code.google.com/p/quassi/).
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37
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Jakubauskas A, Valatkaite B, Griskevicius L. Identification of a novel HLA-B allele, B*56:43, by sequence-based typing in a Lithuanian bone marrow donor. ACTA ACUST UNITED AC 2013; 83:59-60. [PMID: 24286123 DOI: 10.1111/tan.12250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 10/17/2013] [Indexed: 11/28/2022]
Abstract
A novel class I human leukocyte antigen allele HLA-B*56:43 is described.
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Affiliation(s)
- A Jakubauskas
- Department of Molecular and Regenerative Medicine, Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santariskiu Klinikos, Vilnius, LT-08661, Lithuania
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38
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Tu B, Cha N, Yang R, Ng J, Hurley CK. A one-step DNA sequencing strategy to HLA type hematopoietic stem cell donors at recruitment - rethinking typing strategies. ACTA ACUST UNITED AC 2013; 81:150-60. [PMID: 23398508 DOI: 10.1111/tan.12072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/27/2012] [Accepted: 01/21/2013] [Indexed: 10/27/2022]
Abstract
In order to reduce the time required to identify a match for unrelated donor hematopoietic stem cell transplantation, a one-step DNA sequencing strategy was employed at the time of recruitment. The impact of this strategy on human leukocyte antigen (HLA) typing resolution and the effect of current registry requirements on resolution and coding of assignments were evaluated. Sanger-based DNA sequencing was used to obtain diploid exons 2 and 3 HLA-A, -B and -C assignments of 2747 unrelated African American and 1822 European American volunteers at recruitment. The results demonstrate the high resolution of the approach and challenge several aspects of the current registry typing strategy. Of the 46% of African American and 74% of European American individuals whose HLA typing resulted in alternative genotypes, the majority (≥93%) was predicted to have only a single 'common' genotype among the alternatives. The common practice of adding secondary assays to resolve alternative genotype assignments that include more than two antigen groups was also evaluated. While the percentage of assignments with greater than two antigen groups reached as high as 21% (HLA-A in European Americans), only 1.8% of individuals at most carried two common genotypes encompassing three antigen groups. The assignment of (National Marrow Donor Program) NMDP-designated allele codes to the one-pass results reduced the resolution substantially and introduced genotypes that were not included in the laboratory's assignments. We suggest the alternative strategy of using the exons 2-3 diploid nucleotide sequence as the assignment submitted to the registry with the added benefit of immortalizing the assignment in time regardless of the introduction of novel alleles. To keep pace with current donor selection criteria and with the increasing number of new alleles, it is time to rethink our recruitment typing strategies.
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Affiliation(s)
- B Tu
- Department of Pediatrics, CW Bill Young Marrow Donor Recruitment and Research Program, Georgetown University, Washington, DC, USA
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39
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Testi M, Troiano M, Guagnano A, Testa G, Andreani M. A new allele,HLA-DQB1*04:09. ACTA ACUST UNITED AC 2013; 82:215-6. [DOI: 10.1111/tan.12176] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 06/18/2013] [Accepted: 07/04/2013] [Indexed: 11/30/2022]
Affiliation(s)
- M. Testi
- Laboratory of Immunogenetics and Transplant Biology; IME Foundation at Polyclinic of Tor Vergata; Rome; Italy
| | - M. Troiano
- Laboratory of Immunogenetics and Transplant Biology; IME Foundation at Polyclinic of Tor Vergata; Rome; Italy
| | - A. Guagnano
- Laboratory of Immunogenetics and Transplant Biology; IME Foundation at Polyclinic of Tor Vergata; Rome; Italy
| | - G. Testa
- Laboratory of Immunogenetics and Transplant Biology; IME Foundation at Polyclinic of Tor Vergata; Rome; Italy
| | - M. Andreani
- Laboratory of Immunogenetics and Transplant Biology; IME Foundation at Polyclinic of Tor Vergata; Rome; Italy
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40
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Huang W, Liu X, Li E, Zhao C, Liu Q, Liang Z, Wang Y, Lu F. Identification of a novel DRB1 allele through intergenic recombination between HLA-DRB1 and HLA-DRB3∗02 in a Chinese family. Hum Immunol 2013; 74:1603-9. [PMID: 23911361 DOI: 10.1016/j.humimm.2013.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 07/17/2013] [Accepted: 07/19/2013] [Indexed: 10/26/2022]
Abstract
In this study, a novel DRB1 allele was revealed by routine HLA-SBT typing noted for its extensive mismatches to any known DRB1 alleles within the exon 2. Sequences containing the exons 2, 3 of HLA-DRB1, their surrounding introns, and the full-length cDNA of DRB1 were analyzed to determine a possible recombination event. Interestingly, the sequences of entire exon 2 were characterized as DRB3(∗)02:02:01:01/02; while exon 3 were characterized as DRB1(∗)14 like alleles. Further analysis of the sequences using Simplot software suggested that an intergenic recombinant event (i.e. exchange of sequence between non-allelic genes) may have occurred between DRB3(∗)02 allele and DRB1(∗)14 like allele, and the recombination sites are located at intron 1 and the boundary of exon 2 and intron 2 of DRB1. There are 5 CGGGG sequences flanking each side of exon 2 could serve as potential recombination site. Moreover, the full-length cDNA of the novel allele has been identified. The exon 1 and exon 3 to exon 6 share the same sequence as DRB1(∗)14 like alleles. At the mRNA level, the new allele has no significant difference when compared with the other DRB1 allele. This novel recombinant allele is also found to be paternally inherited. In conclusion, this is the first report of a DRB1 and DRB3 intergenic recombination event involving whole exon 2, which generate a new DRB1(∗)14:141.
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Affiliation(s)
- Weijin Huang
- Department of Microbiology, Peking University Health Science Center, Beijing 100191, China; Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, Division of HIV/AIDS and Sex-transmitted Virus Vaccines, National Institutes for Food and Drug Control, Beijing 100050, China
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41
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Stover AE, Brick DJ, Nethercott HE, Banuelos MG, Sun L, O'Dowd DK, Schwartz PH. Process-based expansion and neural differentiation of human pluripotent stem cells for transplantation and disease modeling. J Neurosci Res 2013; 91:1247-62. [PMID: 23893392 DOI: 10.1002/jnr.23245] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 03/20/2013] [Accepted: 03/20/2013] [Indexed: 02/07/2023]
Abstract
Robust strategies for developing patient-specific, human, induced pluripotent stem cell (iPSC)-based therapies of the brain require an ability to derive large numbers of highly defined neural cells. Recent progress in iPSC culture techniques includes partial-to-complete elimination of feeder layers, use of defined media, and single-cell passaging. However, these techniques still require embryoid body formation or coculture for differentiation into neural stem cells (NSCs). In addition, none of the published methodologies has employed all of the advances in a single culture system. Here we describe a reliable method for long-term, single-cell passaging of PSCs using a feeder-free, defined culture system that produces confluent, adherent PSCs that can be differentiated into NSCs. To provide a basis for robust quality control, we have devised a system of cellular nomenclature that describes an accurate genotype and phenotype of the cells at specific stages in the process. We demonstrate that this protocol allows for the efficient, large-scale, cGMP-compliant production of transplantable NSCs from all lines tested. We also show that NSCs generated from iPSCs produced with the process described are capable of forming both glia defined by their expression of S100β and neurons that fire repetitive action potentials.
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Affiliation(s)
- Alexander E Stover
- National Human Neural Stem Cell Resource, Centers for Neuroscience and Translational Research, Children's Hospital of Orange County Research Institute, Orange, California
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42
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Kim HJ, Pourmand N. HLA typing from RNA-seq data using hierarchical read weighting [corrected]. PLoS One 2013; 8:e67885. [PMID: 23840783 PMCID: PMC3696101 DOI: 10.1371/journal.pone.0067885] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 05/23/2013] [Indexed: 11/18/2022] Open
Abstract
Correctly matching the HLA haplotypes of donor and recipient is essential to the success of allogenic hematopoietic stem cell transplantation. Current HLA typing methods rely on targeted testing of recognized antigens or sequences. Despite advances in Next Generation Sequencing, general high throughput transcriptome sequencing is currently underutilized for HLA haplotyping due to the central difficulty in aligning sequences within this highly variable region. Here we present the method, HLAforest, that can accurately predict HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest correctly predicts >99% of allele group level (2 digit) haplotypes and 93% of peptide-level (4 digit) haplotypes of the most diverse HLA genes in simulations with read lengths and error rates modeling currently available sequencing technology. The method is very robust to sequencing error and can predict 99% of allele-group level haplotypes with substitution rates as high as 8.8%. When applied to data generated from a trio of cell lines, HLAforest corroborated PCR-based HLA haplotyping methods and accurately predicted 16/18 (89%) major class I genes for a daughter-father-mother trio at the peptide level. Major class II genes were predicted with 100% concordance between the daughter-father-mother trio. In fifty HapMap samples with paired end reads just 37 nucleotides long, HLAforest predicted 96.5% of allele group level HLA haplotypes correctly and 83% of peptide level haplotypes correctly. In sixteen RNAseq samples with limited coverage across HLA genes, HLAforest predicted 97.7% of allele group level haplotypes and 85% of peptide level haplotypes correctly.
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Affiliation(s)
- Hyunsung John Kim
- Biomolecular Engineering Department, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (HJK); (NP)
| | - Nader Pourmand
- Biomolecular Engineering Department, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (HJK); (NP)
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43
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Imputing amino acid polymorphisms in human leukocyte antigens. PLoS One 2013; 8:e64683. [PMID: 23762245 PMCID: PMC3675122 DOI: 10.1371/journal.pone.0064683] [Citation(s) in RCA: 473] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 04/17/2013] [Indexed: 12/14/2022] Open
Abstract
DNA sequence variation within human leukocyte antigen (HLA) genes mediate susceptibility to a wide range of human diseases. The complex genetic structure of the major histocompatibility complex (MHC) makes it difficult, however, to collect genotyping data in large cohorts. Long-range linkage disequilibrium between HLA loci and SNP markers across the major histocompatibility complex (MHC) region offers an alternative approach through imputation to interrogate HLA variation in existing GWAS data sets. Here we describe a computational strategy, SNP2HLA, to impute classical alleles and amino acid polymorphisms at class I (HLA-A, -B, -C) and class II (-DPA1, -DPB1, -DQA1, -DQB1, and -DRB1) loci. To characterize performance of SNP2HLA, we constructed two European ancestry reference panels, one based on data collected in HapMap-CEPH pedigrees (90 individuals) and another based on data collected by the Type 1 Diabetes Genetics Consortium (T1DGC, 5,225 individuals). We imputed HLA alleles in an independent data set from the British 1958 Birth Cohort (N = 918) with gold standard four-digit HLA types and SNPs genotyped using the Affymetrix GeneChip 500 K and Illumina Immunochip microarrays. We demonstrate that the sample size of the reference panel, rather than SNP density of the genotyping platform, is critical to achieve high imputation accuracy. Using the larger T1DGC reference panel, the average accuracy at four-digit resolution is 94.7% using the low-density Affymetrix GeneChip 500 K, and 96.7% using the high-density Illumina Immunochip. For amino acid polymorphisms within HLA genes, we achieve 98.6% and 99.3% accuracy using the Affymetrix GeneChip 500 K and Illumina Immunochip, respectively. Finally, we demonstrate how imputation and association testing at amino acid resolution can facilitate fine-mapping of primary MHC association signals, giving a specific example from type 1 diabetes.
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44
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Cosentini E, Andreani M, Ciardiello G, Di Luzio A, Testi M. Characterization of a novelHLA-DQB1*06allele,HLA-DQB1*06:04:04. ACTA ACUST UNITED AC 2013; 82:73-4. [DOI: 10.1111/tan.12119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 03/21/2013] [Indexed: 11/30/2022]
Affiliation(s)
- E. Cosentini
- Immunohematology and Transfusion Medicine; Federico II University; Naples; Italy
| | - M. Andreani
- Laboratory of Immunogenetics and Transplant Biology; IME Foundation at Polyclinic of Tor Vergata; Rome; Italy
| | - G. Ciardiello
- Immunohematology and Transfusion Medicine; Federico II University; Naples; Italy
| | - A. Di Luzio
- Laboratory of Immunogenetics and Transplant Biology; IME Foundation at Polyclinic of Tor Vergata; Rome; Italy
| | - M. Testi
- Laboratory of Immunogenetics and Transplant Biology; IME Foundation at Polyclinic of Tor Vergata; Rome; Italy
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45
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Testi M, Battarra M, Stellitano C, Condello R, Andreani M. Detection of the newHLA-DRB1*14:129allele in a voluntary stem cell donor. ACTA ACUST UNITED AC 2013; 81:229-30. [DOI: 10.1111/tan.12081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 01/30/2013] [Indexed: 11/29/2022]
Affiliation(s)
- M. Testi
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation; Polyclinic of Tor Vergata University; Rome; Italy
| | - M. Battarra
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation; Polyclinic of Tor Vergata University; Rome; Italy
| | - C. Stellitano
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation; Polyclinic of Tor Vergata University; Rome; Italy
| | - R. Condello
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation; Polyclinic of Tor Vergata University; Rome; Italy
| | - M. Andreani
- Laboratory of Immunogenetics and Transplant Biology, IME Foundation; Polyclinic of Tor Vergata University; Rome; Italy
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46
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Lind C, Ferriola D, Mackiewicz K, Papazoglou A, Sasson A, Monos D. Filling the gaps – The generation of full genomic sequences for 15 common and well-documented HLA class I alleles using next-generation sequencing technology. Hum Immunol 2013; 74:325-9. [DOI: 10.1016/j.humimm.2012.12.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 11/30/2012] [Accepted: 12/04/2012] [Indexed: 11/29/2022]
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47
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Painter CA, Stern LJ. Conformational variation in structures of classical and non-classical MHCII proteins and functional implications. Immunol Rev 2013; 250:144-57. [PMID: 23046127 DOI: 10.1111/imr.12003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recent structural characterizations of classical and non-classical major histocompatibility complex class II (MHCII) proteins have provided a view into the dynamic nature of the MHCII-peptide binding groove and the role that structural changes play in peptide loading processes. Although there have been numerous reports of crystal structures for MHCII-peptide complexes, a detailed analysis comparing all the structures has not been reported, and subtle conformational variations present in these structures may not have been fully appreciated. We compared the 91 MHCII crystal structures reported in the PDB to date, including an HLA-DR mutant particularly susceptible to DM-mediated peptide exchange, and reviewed experimental and computational studies of the effect of peptide binding on MHCII structure. These studies provide evidence for conformational lability in and around the α-subunit 3-10 helix at residues α48-51, a region known to be critical for HLA-DM-mediated peptide exchange. A biophysical study of MHC-peptide hydrogen bond strengths and a recent structure of the non-classical MHCII protein HLA-DO reveal changes in the same region. Conformational variability was observed also in the vicinity of a kink in the β-subunit helical region near residue β66 and in the orientation and loop conformation in the β2 Ig domain. Here, we provide an overview of the regions within classical and non-classical MHCII proteins that display conformational changes and the potential role that these changes may have in the peptide loading/exchange process.
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Affiliation(s)
- Corrie A Painter
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, USA
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48
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Mahdi BM. A glow of HLA typing in organ transplantation. Clin Transl Med 2013; 2:6. [PMID: 23432791 PMCID: PMC3598844 DOI: 10.1186/2001-1326-2-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Accepted: 02/15/2013] [Indexed: 01/03/2023] Open
Abstract
The transplant of organs and tissues is one of the greatest curative achievements of this century. In organ transplantation, the adaptive immunity is considered the main response exerted to the transplanted tissue, since the main goal of the immune response is the MHC (major histocompatibility complex) molecules expressed on the surface of donor cells. Cell surface molecules that induce an antigenic stimulus cause the rejection immune response to grafted tissue or organ. A wide variety of transplantation antigens have been described, including the major histocompatibility molecules, minor histocompatibility antigens, ABO blood group antigens and endothelial cell antigens. The sensitization to MHC antigens may be caused by transfusions, pregnancy, or failed previous grafts leading to development of anti-human leukocyte antigen (HLA) antibodies that are important factor responsible for graft rejection in solid organ transplantation and play a role in post-transfusion complication Anti-HLA Abs may be present in healthy individuals. Methods for HLA typing are described, including serological methods, molecular techniques of sequence-specific priming (SSP), sequence-specific oligonucleotide probing (SSOP), Sequence based typing (SBT) and reference strand-based conformation analysis (RSCA) method. Problems with organ transplantation are reservoir of organs and immune suppressive treatments that used to decrease rate of rejection with less side effect and complications.
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Affiliation(s)
- Batool Mutar Mahdi
- Department of Microbiology, Director of HLA Typing research Unit, Al-Kindy College of Medicine, Baghdad University, AL-Nahda Square, Baghdad, Iraq.
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Gong Z, Zhang Z, Shan X, Mei W, Li D. HLA-B*27:44, a novel allele identified by sequence-based typing, is a well-documented allele in China. ACTA ACUST UNITED AC 2013; 81:175-6. [PMID: 23398512 DOI: 10.1111/tan.12062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 12/05/2012] [Accepted: 01/08/2013] [Indexed: 11/26/2022]
Abstract
The sequence of HLA-B*27:44 differs in exon 2 from the sequence of B*27:08 by one amino acid change at codon 74.
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Affiliation(s)
- Z Gong
- HLA Laboratory, Beijing Red Cross Blood Center, Beijing, China
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50
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Gong Z, Zhang Z, Shan X, Li W, Liu N. A novel HLA-B allele, B*40:01:06, identified by sequence-based typing in a Chinese individual. ACTA ACUST UNITED AC 2013; 81:176-7. [PMID: 23398513 DOI: 10.1111/tan.12063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The sequence of HLA-B*40:01:06 differs in exon 3 from the sequence of B*40:01:01 by one nucleotide 435 (codon121) G to A.
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Affiliation(s)
- Z Gong
- HLA Laboratory, Beijing red cross blood center, Beijing, China
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