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Lautert-Dutra W, M Melo C, Chaves LP, Crozier C, P Saggioro F, B Dos Reis R, Bayani J, Bonatto SL, Squire JA. Loss of heterozygosity impacts MHC expression on the immune microenvironment in CDK12-mutated prostate cancer. Mol Cytogenet 2024; 17:11. [PMID: 38704603 PMCID: PMC11070094 DOI: 10.1186/s13039-024-00680-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/24/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND In prostate cancer (PCa), well-established biomarkers such as MSI status, TMB high, and PDL1 expression serve as reliable indicators for favorable responses to immunotherapy. Recent studies have suggested a potential association between CDK12 mutations and immunotherapy response; however, the precise mechanisms through which CDK12 mutation may influence immune response remain unclear. A plausible explanation for immune evasion in this subset of CDK12-mutated PCa may be reduced MHC expression. RESULTS Using genomic data of CDK12-mutated PCa from 48 primary and 10 metastatic public domain samples and a retrospective cohort of 53 low-intermediate risk primary PCa, we investigated how variation in the expression of the MHC genes affected associated downstream pathways. We classified the patients based on gene expression quartiles of MHC-related genes and categorized the tumors into "High" and "Low" expression levels. CDK12-mutated tumors with higher MHC-expressed pathways were associated with the immune system and elevated PD-L1, IDO1, and TIM3 expression. Consistent with an inflamed tumor microenvironment (TME) phenotype, digital cytometric analyses identified increased CD8 + T cells, B cells, γδ T cells, and M1 Macrophages in this group. In contrast, CDK12-mutated tumors with lower MHC expression exhibited features consistent with an immune cold TME phenotype and immunoediting. Significantly, low MHC expression was also associated with chromosome 6 loss of heterozygosity (LOH) affecting the entire HLA gene cluster. These LOH events were observed in both major clonal and minor subclonal populations of tumor cells. In our retrospective study of 53 primary PCa cases from this Institute, we found a 4% (2/53) prevalence of CDK12 mutations, with the confirmation of this defect in one tumor through Sanger sequencing. In keeping with our analysis of public domain data this tumor exhibited low MHC expression at the RNA level. More extensive studies will be required to determine whether reduced HLA expression is generally associated with primary tumors or is a specific feature of CDK12 mutated PCa. CONCLUSIONS These data show that analysis of CDK12 alteration, in the context of MHC expression levels, and LOH status may offer improved predictive value for outcomes in this potentially actionable genomic subgroup of PCa. In addition, these findings highlight the need to explore novel therapeutic strategies to enhance MHC expression in CDK12-defective PCa to improve immunotherapy responses.
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Affiliation(s)
- William Lautert-Dutra
- Department of Genetics, Medical School of Ribeirao Preto, University of Sao Paulo - USP, Ribeirão Prêto, SP, 14048-900, Brazil
| | - Camila M Melo
- Department of Genetics, Medical School of Ribeirao Preto, University of Sao Paulo - USP, Ribeirão Prêto, SP, 14048-900, Brazil
| | - Luiz P Chaves
- Department of Genetics, Medical School of Ribeirao Preto, University of Sao Paulo - USP, Ribeirão Prêto, SP, 14048-900, Brazil
| | - Cheryl Crozier
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Fabiano P Saggioro
- Department of Pathology, Ribeirao Preto Medical School, University of Sao Paulo - USP, Ribeirão Prêto, Brazil
| | - Rodolfo B Dos Reis
- Department of Pathology, Ribeirao Preto Medical School, University of Sao Paulo - USP, Ribeirão Prêto, Brazil
- Division of Urology, Department of Surgery and Anatomy, Medical School of Ribeirao Preto, University of Sao Paulo - USP, Ribeirão Prêto, Brazil
| | - Jane Bayani
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Laboratory Medicine and Pathology, University of Toronto, Toronto, ON, Canada
| | - Sandro L Bonatto
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande Do Sul - PUCRS, Av. Ipiranga, 668, Porto Alegre, RS, 90619-900, Brazil
| | - Jeremy A Squire
- Department of Genetics, Medical School of Ribeirao Preto, University of Sao Paulo - USP, Ribeirão Prêto, SP, 14048-900, Brazil.
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, K7L3N6, Canada.
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2
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Martin KE, Hammer Q, Perica K, Sadelain M, Malmberg KJ. Engineering immune-evasive allogeneic cellular immunotherapies. Nat Rev Immunol 2024:10.1038/s41577-024-01022-8. [PMID: 38658708 DOI: 10.1038/s41577-024-01022-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2024] [Indexed: 04/26/2024]
Abstract
Allogeneic cellular immunotherapies hold a great promise for cancer treatment owing to their potential cost-effectiveness, scalability and on-demand availability. However, immune rejection of adoptively transferred allogeneic T and natural killer (NK) cells is a substantial obstacle to achieving clinical responses that are comparable to responses obtained with current autologous chimeric antigen receptor T cell therapies. In this Perspective, we discuss strategies to confer cell-intrinsic, immune-evasive properties to allogeneic T cells and NK cells in order to prevent or delay their immune rejection, thereby widening the therapeutic window. We discuss how common viral and cancer immune escape mechanisms can serve as a blueprint for improving the persistence of off-the-shelf allogeneic cell therapies. The prospects of harnessing genome editing and synthetic biology to design cell-based precision immunotherapies extend beyond programming target specificities and require careful consideration of innate and adaptive responses in the recipient that may curtail the biodistribution, in vivo expansion and persistence of cellular therapeutics.
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Affiliation(s)
- Karen E Martin
- Precision Immunotherapy Alliance, The University of Oslo, Oslo, Norway
- Department of Cancer Immunology, Institute for Cancer Research Oslo, Oslo University Hospital, Oslo, Norway
| | - Quirin Hammer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Karlo Perica
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell Therapy Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karl-Johan Malmberg
- Precision Immunotherapy Alliance, The University of Oslo, Oslo, Norway.
- Department of Cancer Immunology, Institute for Cancer Research Oslo, Oslo University Hospital, Oslo, Norway.
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
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3
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Velastegui E, Vera E, Vanden Berghe W, Muñoz MS, Orellana-Manzano A. "HLA-C: evolution, epigenetics, and pathological implications in the major histocompatibility complex". Front Genet 2023; 14:1206034. [PMID: 37465164 PMCID: PMC10350511 DOI: 10.3389/fgene.2023.1206034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
HLA-C, a gene located within the major histocompatibility complex, has emerged as a prominent target in biomedical research due to its involvement in various diseases, including cancer and autoimmune disorders; even though its recent addition to the MHC, the interaction between HLA-C and KIR is crucial for immune responses, particularly in viral infections. This review provides an overview of the structure, origin, function, and pathological implications of HLA-C in the major histocompatibility complex. In the last decade, we systematically reviewed original publications from Pubmed, ScienceDirect, Scopus, and Google Scholar. Our findings reveal that genetic variations in HLA-C can determine susceptibility or resistance to certain diseases. However, the first four exons of HLA-C are particularly susceptible to epigenetic modifications, which can lead to gene silencing and alterations in immune function. These alterations can manifest in diseases such as alopecia areata and psoriasis and can also impact susceptibility to cancer and the effectiveness of cancer treatments. By comprehending the intricate interplay between genetic and epigenetic factors that regulate HLA-C expression, researchers may develop novel strategies for preventing and treating diseases associated with HLA-C dysregulation.
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Affiliation(s)
- Erick Velastegui
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Edwin Vera
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Wim Vanden Berghe
- Epigenetic Signaling Lab, Faculty Biomedical Sciences, PPES, University of Antwerp, Antwerp, Belgium
| | - Mindy S. Muñoz
- Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Andrea Orellana-Manzano
- Escuela Superior Politécnica del Litoral, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la Vida (FCV), Guayaquil, Ecuador
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4
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Anand S, Littler DR, Mobbs JI, Braun A, Baker DG, Tennant L, Purcell AW, Vivian JP, Rossjohn J. Complimentary electrostatics dominate T Cell Receptor binding to a psoriasis-associated-peptide-antigen presented by Human Leukocyte Antigen (HLA) C*06:02. J Biol Chem 2023:104930. [PMID: 37330172 PMCID: PMC10371836 DOI: 10.1016/j.jbc.2023.104930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
Psoriasis is a chronic skin disease characterised by hyperproliferative epidermal lesions infiltrated by autoreactive T cells. Individuals expressing the Human Leukocyte antigen (HLA) C*06:02 allele are at highest risk for developing psoriasis. An autoreactive T cell clone (termed Vα3S1/Vβ13S1) isolated from psoriatic plaques is selective for HLA-C*06:02-presenting a peptide derived from the melanocyte-specific auto-antigen ADAMTSL5 (VRSRRCLRL). Here we determine the crystal structure of this psoriatic TCR-HLA-C*06:02- ADAMTSL5 complex with a stabilised peptide. Docking of the TCR involves an extensive complementary charge network formed between negatively charged TCR residues interleaving with exposed arginine residues from the self-peptide and the HLA-C*06:02 α1 helix. We probed these interactions through mutagenesis and activation assays. The charged interface spans the polymorphic region of the C1/C2 HLA group. Notably the peptide binding groove of HLA C*06:02 appears exquisitely suited for presenting highly charged Arg-rich epitopes recognised by this acidic psoriatic TCR. Overall, we provide a structural basis for understanding engagement of melanocyte antigen-presenting cells by a TCR implicated in psoriasis, while simultaneously expanding our knowledge of how TCRs engage HLA-C.
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Affiliation(s)
- Sushma Anand
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Dene R Littler
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Jesse I Mobbs
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Asolina Braun
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Daniel G Baker
- Janssen Research & Development, LLC, Horsham, Philadelphia, Pennsylvania, USA
| | - Luke Tennant
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Anthony W Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Julian P Vivian
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia; Institute of Infection and Immunity, Cardiff University, School of Medicine, Cardiff, UK.
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5
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Johansson T, Partanen J, Saavalainen P. HLA allele-specific expression: Methods, disease associations, and relevance in hematopoietic stem cell transplantation. Front Immunol 2022; 13:1007425. [PMID: 36248878 PMCID: PMC9554311 DOI: 10.3389/fimmu.2022.1007425] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/09/2022] [Indexed: 11/27/2022] Open
Abstract
Varying HLA allele-specific expression levels are associated with human diseases, such as graft versus host disease (GvHD) in hematopoietic stem cell transplantation (HSCT), cytotoxic T cell response and viral load in HIV infection, and the risk of Crohn’s disease. Only recently, RNA-based next generation sequencing (NGS) methodologies with accompanying bioinformatics tools have emerged to quantify HLA allele-specific expression replacing the quantitative PCR (qPCR) -based methods. These novel NGS approaches enable the systematic analysis of the HLA allele-specific expression changes between individuals and between normal and disease phenotypes. Additionally, analyzing HLA allele-specific expression and allele-specific expression loss provide important information for predicting efficacies of novel immune cell therapies. Here, we review available RNA sequencing-based approaches and computational tools for NGS to quantify HLA allele-specific expression. Moreover, we explore recent studies reporting disease associations with differential HLA expression. Finally, we discuss the role of allele-specific expression in HSCT and how considering the expression quantification in recipient-donor matching could improve the outcome of HSCT.
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Affiliation(s)
- Tiira Johansson
- Translational Immunology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
- *Correspondence: Tiira Johansson,
| | - Jukka Partanen
- Research and Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Päivi Saavalainen
- Translational Immunology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
- Genetics Research Program, Folkhälsan Research Center, Helsinki, Finland
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6
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Daull AM, Dubois V, Labussière-Wallet H, Venet F, Barraco F, Ducastelle-Lepretre S, Larcher MV, Balsat M, Gilis L, Fossard G, Ghesquières H, Heiblig M, Ader F, Alcazer V. Class I/Class II HLA Evolutionary Divergence Ratio Is an Independent Marker Associated With Disease-Free and Overall Survival After Allogeneic Hematopoietic Stem Cell Transplantation for Acute Myeloid Leukemia. Front Immunol 2022; 13:841470. [PMID: 35309346 PMCID: PMC8931406 DOI: 10.3389/fimmu.2022.841470] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/15/2022] [Indexed: 12/04/2022] Open
Abstract
Class I Human Leukocyte Antigen (HLA) evolutionary divergence (HED) is a metric which reflects immunopeptidome diversity and has been associated with immune checkpoint inhibitor responses in solid tumors. Its impact and interest in allogeneic hematopoietic stem cell transplantation (HCT) have not yet been thoroughly studied. This study analyzed the clinical and immune impact of class I and II HED in 492 acute myeloid leukemia (AML) recipients undergoing HCT. The overall cohort was divided into a training (n=338) and a testing (n=132) set. Univariate cox screening found a positive impact of a high class I HED and a negative impact of a high class II HED on both disease-free (DFS) and overall survival (OS). These results were combined in a unique marker, class I/class II HED ratio, and assessed in the testing cohort. The final multivariate cox model confirmed the positive impact of a high versus low class I/class II HED ratio on both DFS (Hazard Ratio (HR) 0.41 [95% CI 0.2-0.83]; p=0.01) and OS (HR 0.34 [0.19-0.59]; p<0.001), independently of HLA matching and other HCT parameters. No significant association was found between the ratio and graft-versus-host disease (GvHD) nor with neutrophil and platelet recovery. A high class I HED was associated with a tendency for an increase in NK, CD8 T-cell, and B cell recovery at 12 months. These results introduce HED as an original and independent prognosis marker reflecting immunopeptidome diversity and alloreactivity after HCT.
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Affiliation(s)
- Anne-Marie Daull
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Valérie Dubois
- Laboratory of histocompatibility, Etablissement Français du Sang, Lyon, France
| | - Hélène Labussière-Wallet
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Fabienne Venet
- Hospices Civils de Lyon, Immunology laboratory, Edouard Herriot Hospital, Lyon, France
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard-Lyon 1, Lyon, France
| | - Fiorenza Barraco
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | | | - Marie-Virginie Larcher
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Marie Balsat
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Lila Gilis
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Gaëlle Fossard
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Hervé Ghesquières
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
| | - Maël Heiblig
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
- UR LIB “Lymphoma Immuno-Biology”, Université Claude Bernard Lyon I, Lyon, France
| | - Florence Ader
- Hospices Civils de Lyon, Immunology laboratory, Edouard Herriot Hospital, Lyon, France
- Hospices Civils de Lyon, Department of infectious diseases, Croix-Rousse hospital, Lyon, France
- LegioPath team, CIRI INSERM U1111 CNRS UMR 5308, Lyon, France
| | - Vincent Alcazer
- Hospices Civils de Lyon, Department of clinical Hematology, Lyon Sud hospital, Pierre-Bénite, France
- UR LIB “Lymphoma Immuno-Biology”, Université Claude Bernard Lyon I, Lyon, France
- *Correspondence: Vincent Alcazer,
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7
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Yeung MY. Histocompatibility Assessment in Precision Medicine for Transplantation: Towards a Better Match. Semin Nephrol 2022; 42:44-62. [DOI: 10.1016/j.semnephrol.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Sim MJW, Stotz Z, Lu J, Brennan P, Long EO, Sun PD. T cells discriminate between groups C1 and C2 HLA-C. eLife 2022; 11:75670. [PMID: 35587797 PMCID: PMC9177145 DOI: 10.7554/elife.75670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/15/2022] [Indexed: 01/09/2023] Open
Abstract
Dimorphic amino acids at positions 77 and 80 delineate HLA-C allotypes into two groups, C1 and C2, which associate with disease through interactions with C1 and C2-specific natural killer cell receptors. How the C1/C2 dimorphism affects T cell recognition is unknown. Using HLA-C allotypes that differ only by the C1/C2-defining residues, we found that KRAS-G12D neoantigen-specific T cell receptors (TCRs) discriminated between C1 and C2 presenting the same KRAS-G12D peptides. Structural and functional experiments, and immunopeptidomics analysis revealed that Ser77 in C1 and Asn77 in C2 influence amino acid preference near the peptide C-terminus (pΩ), including the pΩ-1 position, in which C1 favors small and C2 prefers large residues. This resulted in weaker TCR affinity for KRAS-G12D-bound C2-HLA-C despite conserved TCR contacts. Thus, the C1/C2 dimorphism on its own impacts peptide presentation and HLA-C-restricted T cell responses, with implications in disease, including adoptive T cell therapy targeting KRAS-G12D-induced cancers.
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Affiliation(s)
- Malcolm J W Sim
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - Zachary Stotz
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - Jinghua Lu
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - Paul Brennan
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - Eric O Long
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - Peter D Sun
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
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9
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Zeng H, Wang L, Li J, Luo S, Han Q, Su F, Wei J, Wei X, Wu J, Li B, Huang J, Tang P, Cao C, Zhou Y, Yang Q. Single-cell RNA-sequencing reveals distinct immune cell subsets and signaling pathways in IgA nephropathy. Cell Biosci 2021; 11:203. [PMID: 34895340 PMCID: PMC8665497 DOI: 10.1186/s13578-021-00706-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/31/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND IgA nephropathy (IgAN) is the most common primary glomerulonephritis globally. Increasing evidence suggests the importance of host immunity in the development of IgAN, but its dynamics during the early stage of IgAN are still largely unclear. RESULTS Here we successfully resolved the early transcriptomic changes in immune cells of IgAN by conducting single-cell RNA-sequencing (scRNA-seq) with peripheral blood mononuclear cells. The differentially expressed genes (DEGs) between control and IgAN were predominantly enriched in NK cell-mediated cytotoxicity and cell killing pathways. Interestingly, we discovered that the number and cytotoxicity of NK cells are significantly reduced in IgAN patients, where both the number and marker genes of NK cells were negatively associated with the clinical parameters, including the levels of urine protein creatinine ratio (UPCR), serum galactose-deficient IgA1 and IgA. A distinctive B cell subset, which had suppressed NFκB signaling was predominantly in IgAN and positively associated with disease progression. Moreover, the DEGs of B cells were enriched in different viral infection pathways. Classical monocytes also significantly changed in IgAN and a monocyte subset expressing interferon-induced genes was positively associated with the clinical severity of IgAN. Finally, we identified vast dynamics in intercellular communications in IgAN. CONCLUSIONS We dissected the immune landscape of IgAN at the single-cell resolution, which provides new insights in developing novel biomarkers and immunotherapy against glomerulonephritis.
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Affiliation(s)
- Honghui Zeng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Le Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Jiajia Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Siweier Luo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Qianqian Han
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Fang Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Jing Wei
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Xiaona Wei
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Jianping Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Bin Li
- Clinical Trials Unit, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Jingang Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Patrick Tang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chunwei Cao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
| | - Yiming Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
| | - Qiongqiong Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
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10
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Vollmers S, Lobermeyer A, Körner C. The New Kid on the Block: HLA-C, a Key Regulator of Natural Killer Cells in Viral Immunity. Cells 2021; 10:cells10113108. [PMID: 34831331 PMCID: PMC8620871 DOI: 10.3390/cells10113108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 11/01/2022] Open
Abstract
The human leukocyte antigen system (HLA) is a cluster of highly polymorphic genes essential for the proper function of the immune system, and it has been associated with a wide range of diseases. HLA class I molecules present intracellular host- and pathogen-derived peptides to effector cells of the immune system, inducing immune tolerance in healthy conditions or triggering effective immune responses in pathological situations. HLA-C is the most recently evolved HLA class I molecule, only present in humans and great apes. Differentiating from its older siblings, HLA-A and HLA-B, HLA-C exhibits distinctive features in its expression and interaction partners. HLA-C serves as a natural ligand for multiple members of the killer-cell immunoglobulin-like receptor (KIR) family, which are predominately expressed by natural killer (NK) cells. NK cells are crucial for the early control of viral infections and accumulating evidence indicates that interactions between HLA-C and its respective KIR receptors determine the outcome and progression of viral infections. In this review, we focus on the unique role of HLA-C in regulating NK cell functions and its consequences in the setting of viral infections.
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11
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Sheridan MA, Zhao X, Fernando RC, Gardner L, Perez-Garcia V, Li Q, Marsh SGE, Hamilton R, Moffett A, Turco MY. Characterization of primary models of human trophoblast. Development 2021; 148:272500. [PMID: 34651188 PMCID: PMC8602945 DOI: 10.1242/dev.199749] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 10/01/2021] [Indexed: 01/01/2023]
Abstract
Two recently developed models, trophoblast organoids and trophoblast stem cells (TSCs), are useful tools to further the understanding of human placental development. Both differentiate from villous cytotrophoblast (VCT) to either extravillous trophoblast (EVT) or syncytiotrophoblast (SCT). Here, we compare the transcriptomes and miRNA profiles of these models to identify which trophoblast they resemble in vivo. Our findings indicate that TSCs do not readily undergo SCT differentiation and closely resemble cells at the base of the cell columns from where EVT derives. In contrast, organoids are similar to VCT and undergo spontaneous SCT differentiation. A defining feature of human trophoblast is that VCT and SCT are human leukocyte antigen (HLA) null, whereas EVT expresses HLA-C, -G and -E molecules. We find that trophoblast organoids retain these in vivo characteristics. In contrast, TSCs express classical HLA-A and HLA-B molecules, and maintain their expression after EVT differentiation, with upregulation of HLA-G. Furthermore, HLA expression in TSCs differs when grown in 3D rather than in 2D, suggesting that mechanical cues are important. Our results can be used to select the most suitable model for the study of trophoblast development, function and pathology. Summary: Characterization of trophoblast organoids and trophoblast stem cells as exciting models of human placentation enables the selection of the most suitable system to address specific research questions.
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Affiliation(s)
- Megan A Sheridan
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Xiaohui Zhao
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK.,Department of Physiology, Neuroscience and Development, University of Cambridge, Cambridge CB2 3EG, UK
| | - Ridma C Fernando
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Lucy Gardner
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Vicente Perez-Garcia
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK.,Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera, Valencia 46012, Spain
| | - Qian Li
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.,Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London NW3 2QG, UK.,UCL Cancer Institute, Royal Free Campus, London WC1E 6DD, UK
| | - Russell Hamilton
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK.,Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Ashley Moffett
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Margherita Y Turco
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
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12
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Gimeno L, González-Lozano I, Soto-Ramírez MF, Martínez-Sánchez MV, López-Cubillana P, Fuster JL, Martínez-García J, Martínez-Escribano J, Campillo JA, Pons-Fuster E, Ferri B, López-Abad A, Muro M, Minguela A. CD8+ T lymphocytes are sensitive to NKG2A/HLA-E licensing interaction: role in the survival of cancer patients. Oncoimmunology 2021; 10:1986943. [PMID: 34676148 PMCID: PMC8525952 DOI: 10.1080/2162402x.2021.1986943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/24/2021] [Indexed: 10/29/2022] Open
Abstract
NK and CD8+ T cells are the main cytolytic effectors involved in innate and adaptive tumor immune surveillance, respectively. Although their educational pathways differ, similarities in their development and function suggest that CD8+ T lymphocytes could be sensitive to NK cell licensing signals, which might influence their antitumor response. To demonstrate this hypothesis, we retrospectively evaluated the impact that NK cell licensing interactions have on the expression of CD226 on CD8+ T lymphocytes and on the survival of patients with different hematopoietic and solid cancers (n = 1,023). Prospectively, we analyzed by multiparametric flow cytometry the anti-CD3/CD28-induced proliferation and immune-receptor expression of purified CD8+ T lymphocytes from healthy donors (n = 17) with different combinations of NK cell licensing ligands. Results show that methionine/threonine (M/T) dimorphism at position -21 of the HLA-B leader peptide, but not other HLA class-I dimorphisms involved in the education of NK cells (HLA-C1/C2 or HLA-Bw4), is associated with greater survival and expression of CD226 in cancer patients, which was proportional to the number of methionines present in their genotype. CD8+ T lymphocytes from healthy donors with -21 M showed higher proliferation rates and lower expression of TIGIT after in vitro stimulation. Therefore, CD8+ T lymphocytes, like NK cells, appear to be sensitive to the -21 M/T dimorphism of HLA-B leader peptide, which results in the modulation of CD226 in vivo and the proliferation and expression of TIGIT after in vitro stimulation, all of which could be related to their immune-surveillance capacity and the survival of cancer patients.
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Affiliation(s)
- Lourdes Gimeno
- Immunology Service, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
- Human Anatomy Department, University of Murcia (Um), Murcia, Spain
| | - Isabel González-Lozano
- Immunology Service, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
| | - María F. Soto-Ramírez
- Immunology Service, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
| | - María V. Martínez-Sánchez
- Immunology Service, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
| | - Pedro López-Cubillana
- Urology Service, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
| | - José L. Fuster
- Pediatric Oncohematology Department, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
| | - Jerónimo Martínez-García
- Oncology Service, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
| | - Jorge Martínez-Escribano
- Dermatology Service, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
| | - José A. Campillo
- Immunology Service, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
| | - Eduardo Pons-Fuster
- Immunology Service, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
| | - Belén Ferri
- Pathology Service, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
| | - Alicia López-Abad
- Urology Service, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
| | - Manuel Muro
- Immunology Service, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
| | - Alfredo Minguela
- Immunology Service, Clinic University Hospital Virgen De La Arrrixaca (Hcuva), Biomedical Research Institute of Murcia (Imib), Murcia, Spain
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13
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Eikmans M, van der Zwan A, Claas FHJ, van der Hoorn ML, Heidt S. Got your mother in a whirl: The role of maternal T cells and myeloid cells in pregnancy. HLA 2020; 96:561-579. [PMID: 32841539 DOI: 10.1111/tan.14055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/09/2020] [Accepted: 07/29/2020] [Indexed: 12/22/2022]
Abstract
Appropriate development of the placenta is required for healthy pregnancy to occur. After implantation of the fertilized blastocyst, fetal trophoblasts invade the endometrium and myometrium of the mother's uterus to establish placentation. In this process, fetal trophoblasts encounter maternal immune cells. In this review, we focus on the role of maternal T cells and myeloid cells (macrophages, dendritic cells) in pregnancy and their interaction with trophoblasts. To retain immunologic tolerization, trophoblasts evade immune recognition by T cells and produce factors that modulate their phenotype and function. On top of that, the local environment at the maternal-fetal interface favors expansion of regulatory T cells. Macrophages and dendritic cells are essential in maintaining a healthy pregnancy. They produce soluble factors and act as antigen-presenting cells, thereby interacting with T cells. Herein, M2 macrophages, immature dendritic cells, CD4+ Th2 cells, and regulatory T cells represent an axis that maintains a local immune tolerant environment. We consider outstanding issues concerning these cell types and their pathways, which need to be addressed in future investigations. Data from recent single-cell sequencing experiments of the placental bed, to study heterogeneity of maternal immune cells and to predict cell-cell interactions, are discussed. Novel ways for long-term culturing of primary trophoblasts allow for cell-cell interaction studies in a functional way. Future directions should include study of the functionality of currently known and newly identified decidual immune cell subsets in healthy and complicated pregnancies, and their interaction with and modulation by trophoblast cells.
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Affiliation(s)
- Michael Eikmans
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anita van der Zwan
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Frans H J Claas
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Sebastiaan Heidt
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
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14
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Suzuki H, Joshita S, Hirayama A, Shinji A, Mukawa K, Sako M, Yoshimura N, Suga T, Umemura T, Ashihara N, Yamazaki T, Ota M. Polymorphism at rs9264942 is associated with HLA-C expression and inflammatory bowel disease in the Japanese. Sci Rep 2020; 10:12424. [PMID: 32709981 PMCID: PMC7381613 DOI: 10.1038/s41598-020-69370-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/08/2020] [Indexed: 11/09/2022] Open
Abstract
An expression quantitative trait locus (eQTL) single-nucleotide polymorphism (SNP) at rs9264942 was earlier associated with human leukocyte antigen (HLA)-C expression in Europeans. HLA-C has also been related to inflammatory bowel disease (IBD) risk in the Japanese. This study examined whether an eQTL SNP at rs9264942 could regulate HLA-C expression and whether four SNP haplotypes, including the eQTL SNP at rs9264942 and three SNPs at rs2270191, rs3132550, and rs6915986 of IBD risk carried in the HLA-C*12:02~B*52:01~DRB1*15:02 allele, were associated with IBD in the Japanese. HLA-C expression on CD3e+CD8a+ lymphocytes was significantly higher for the CC or CT genotype than for the TT genotype of rs9264942. The TACC haplotype of the four SNPs was associated with a strong susceptibility to ulcerative colitis (UC) but protection against Crohn’s disease (CD) as well as with disease clinical outcome. While UC protectivity was significant but CD susceptibility was not for the CGTT haplotype, the significance of UC protectivity disappeared but CD susceptibility reached significance for the CGCT haplotype. In conclusion, our findings support that the eQTL SNP at rs9264942 regulates HLA-C expression in the Japanese and suggest that the four SNPs, which are in strong linkage disequilibrium, may be surrogate marker candidates of a particular HLA haplotype, HLA-C*12:02~B*52:01~DRB1*15:02, related to IBD susceptibility and disease outcome.
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Affiliation(s)
- Hiroshi Suzuki
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Satoru Joshita
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.
| | - Atsuhiro Hirayama
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.,Department of Inflammatory Bowel Disease, Yokohama City University Medical Center, Yokohama, Japan
| | - Akihiro Shinji
- Department of Medical Oncology, Japanese Red Cross Society Suwa Red Cross Hospital, Suwa, Japan
| | - Kenji Mukawa
- Department of Gastroenterology, Japanese Red Cross Society Suwa Red Cross Hospital, Suwa, Japan
| | - Minako Sako
- Center for Inflammatory Bowel Disease, Tokyo Yamate Medical Center, Tokyo, Japan
| | - Naoki Yoshimura
- Center for Inflammatory Bowel Disease, Tokyo Yamate Medical Center, Tokyo, Japan
| | - Tomoaki Suga
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Takeji Umemura
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.,Department of Life Innovation, Institute for Biomedical Sciences, Shinshu University, Matsumoto, Japan
| | - Norihiro Ashihara
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Tomoo Yamazaki
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Masao Ota
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
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15
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A curious case of de novo anti-HLA-C antibody-mediated humoral rejection and Fabry-like zebra bodies in a renal transplant recipient. Clin Nephrol Case Stud 2020; 8:12-16. [PMID: 32038904 PMCID: PMC7003131 DOI: 10.5414/cncs109998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/06/2019] [Indexed: 11/18/2022] Open
Abstract
Detection of donor-specific antibodies (DSA) is an essential part of diagnosing antibody-mediated renal allograft rejection (ABMR). The role of solitary preformed, or post-transplant HLA-C antigens in solid organ transplantation is unclear, due to the less sensitive nature of the historical assays, lack of data, low expression level on the cell surface, and their co-existence with other anti-HLA DSA. Herein, we present the case of a 39-year-old African American man, without prior history of pre-transplant sensitization that was diagnosed with biopsy-proven ABMR due to de novo donor-specific anti-HLA-C antibodies. This case report illustrates the role of HLA-C antibodies in causing ABMR if generated toward immunogenic-shared epitopes and demonstrates the need for their recognition in the pre- and post-transplant period. Another interesting aspect of this case is the incidental finding of Fabry-like zebra bodies, which we eventually determined to be of unclear etiology.
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16
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Using Nanopore Whole-Transcriptome Sequencing for Human Leukocyte Antigen Genotyping and Correlating Donor Human Leukocyte Antigen Expression with Flow Cytometric Crossmatch Results. J Mol Diagn 2020; 22:101-110. [DOI: 10.1016/j.jmoldx.2019.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/27/2019] [Accepted: 09/11/2019] [Indexed: 01/07/2023] Open
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17
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Geneugelijk K, Spierings E. PIRCHE-II: an algorithm to predict indirectly recognizable HLA epitopes in solid organ transplantation. Immunogenetics 2019; 72:119-129. [PMID: 31741009 PMCID: PMC6971131 DOI: 10.1007/s00251-019-01140-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 10/16/2019] [Indexed: 12/14/2022]
Abstract
Human leukocyte antigen (HLA) mismatches between donors and recipients may lead to alloreactivity after solid organ transplantation. Over the last few decades, our knowledge of the complexity of the HLA system has dramatically increased, as numerous new HLA alleles have been identified. As a result, the likelihood of alloreactive responses towards HLA mismatches after solid organ transplantation cannot easily be assessed. Algorithms are promising solutions to estimate the risk for alloreactivity after solid organ transplantation. In this review, we show that the recently developed PIRCHE-II (Predicted Indirectly ReCognizable HLA Epitopes) algorithm can be used to minimize alloreactivity towards HLA mismatches. Together with the use of other algorithms and simulation approaches, the PIRCHE-II algorithm aims for a better estimated alloreactive risk for individual patients and eventually an improved graft survival after solid organ transplantation.
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Affiliation(s)
- Kirsten Geneugelijk
- Laboratory of Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX, Utrecht, The Netherlands.
| | - Eric Spierings
- Laboratory of Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584, CX, Utrecht, The Netherlands
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18
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Samimi M, Benlalam H, Aumond P, Gaboriaud P, Fradin D, Kervarrec T, Florenceau L, Vignard V, Blom A, Touzé A, Gervois N, Labarriere N. Viral and tumor antigen-specific CD8 T-cell responses in Merkel cell carcinoma. Cell Immunol 2019; 344:103961. [PMID: 31472938 DOI: 10.1016/j.cellimm.2019.103961] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/31/2019] [Indexed: 12/23/2022]
Abstract
Merkel cell carcinoma (MCC) is a rare and aggressive cutaneous cancer, which is immunogenic, regardless of the presence of MCPyV (80% of cases). The identification of MCC-specific epitopes recognized by CD8 T cells is crucial to expand the arsenal of immunotherapeutic treatments. Until now, most efforts focused on the identification of virus-specific epitopes, whereas immune responses directed against shared cellular tumor-specific antigens have not been evidenced. In this study, we measured T-cell responses against viral (n = 3) and tumor antigens (n = 47) from TILs derived from 21 MCC tumors. Virus-specific CD8 T-cell responses dominated MCC-specific immune responses, and we identified two new HLA-peptide complexes derived from the LT antigen, located in a region encompassing 3 previously identified epitopes. Finally, we show that MAGE-A3 antigen, frequently expressed by MCC tumors, was recognized by CD8 TILs from a virus-negative MCC tumor and thus could be a target for immunotherapy in this setting.
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Affiliation(s)
- Mahtab Samimi
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France; Laboratoire "Biologie des infections à polyomavirus", ISP1282 INRA Université de Tours, France; Dermatology Department, University of Tours, CHU Tours, Tours, France
| | - Houssem Benlalam
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.
| | - Pascal Aumond
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Pauline Gaboriaud
- Laboratoire "Biologie des infections à polyomavirus", ISP1282 INRA Université de Tours, France
| | - Delphine Fradin
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France
| | - Thibault Kervarrec
- Laboratoire "Biologie des infections à polyomavirus", ISP1282 INRA Université de Tours, France; Pathology Department, University of Tours, CHU Tours, Tours, France
| | - Laetitia Florenceau
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Virginie Vignard
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France; CHU Nantes, Nantes, France
| | - Astrid Blom
- Dermatology Department, Hôpital Ambroise Paré, Paris, France
| | - Antoine Touzé
- Laboratoire "Biologie des infections à polyomavirus", ISP1282 INRA Université de Tours, France
| | - Nadine Gervois
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Nathalie Labarriere
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France; LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
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19
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Carey BS, Poulton KV, Poles A. Factors affecting HLA expression: A review. Int J Immunogenet 2019; 46:307-320. [PMID: 31183978 DOI: 10.1111/iji.12443] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/26/2019] [Accepted: 05/03/2019] [Indexed: 12/22/2022]
Abstract
The detection and semiquantitative measurement of circulating human leucocyte antigen (HLA)-specific antibodies is essential for the management of patients before and after transplantation. In addition, the pretransplant cross-match to assess the reactivity of recipient HLA antibody against donor lymphocytes has long been the gold standard to prevent hyperacute rejection. Whilst both of these tests assume that recipient HLA-specific antibody is the only variable in the assessment of transplant risk, this is not the case. Transplant immunologists recognize that some HLA antigens are expressed at levels a magnitude lower than others (e.g., HLA-C, HLA-DQ), but within loci, and between different cell types there are many factors that influence HLA expression in both resting and activated cells. HLA is not usually expressed without the specific promoter proteins NLRC5, for HLA class I, and CIITA, for class II. The quantity of HLA protein production is then affected by factors including promoter region polymorphisms, alternative exon splice sites, methylation and microRNA-directed degradation. Different loci are influenced by multiple combinations of these control mechanisms making prediction of HLA regulation difficult, but an ability to measure the cellular expression of each HLA antigen, in conjunction with knowledge of circulating HLA-specific antibody, would lead to a more informed algorithm to assess transplant risk.
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Affiliation(s)
- B Sean Carey
- Histocompatibility and Immunogenetics, Combined Laboratory, University Hospitals Plymouth, Plymouth, UK
| | | | - Anthony Poles
- Histocompatibility and Immunogenetics, Combined Laboratory, University Hospitals Plymouth, Plymouth, UK
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20
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Aguiar VRC, César J, Delaneau O, Dermitzakis ET, Meyer D. Expression estimation and eQTL mapping for HLA genes with a personalized pipeline. PLoS Genet 2019; 15:e1008091. [PMID: 31009447 PMCID: PMC6497317 DOI: 10.1371/journal.pgen.1008091] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 05/02/2019] [Accepted: 03/13/2019] [Indexed: 01/07/2023] Open
Abstract
The HLA (Human Leukocyte Antigens) genes are well-documented targets of balancing selection, and variation at these loci is associated with many disease phenotypes. Variation in expression levels also influences disease susceptibility and resistance, but little information exists about the regulation and population-level patterns of expression. This results from the difficulty in mapping short reads originated from these highly polymorphic loci, and in accounting for the existence of several paralogues. We developed a computational pipeline to accurately estimate expression for HLA genes based on RNA-seq, improving both locus-level and allele-level estimates. First, reads are aligned to all known HLA sequences in order to infer HLA genotypes, then quantification of expression is carried out using a personalized index. We use simulations to show that expression estimates obtained in this way are not biased due to divergence from the reference genome. We applied our pipeline to the GEUVADIS dataset, and compared the quantifications to those obtained with reference transcriptome. Although the personalized pipeline recovers more reads, we found that using the reference transcriptome produces estimates similar to the personalized pipeline (r ≥ 0.87) with the exception of HLA-DQA1. We describe the impact of the HLA-personalized approach on downstream analyses for nine classical HLA loci (HLA-A, HLA-C, HLA-B, HLA-DRA, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1). Although the influence of the HLA-personalized approach is modest for eQTL mapping, the p-values and the causality of the eQTLs obtained are better than when the reference transcriptome is used. We investigate how the eQTLs we identified explain variation in expression among lineages of HLA alleles. Finally, we discuss possible causes underlying differences between expression estimates obtained using RNA-seq, antibody-based approaches and qPCR. The level at which a gene is expressed can have important influence on the phenotype of an organism, including its predisposition to develop diseases. One way to estimate gene expression is by quantifying the abundance of RNA. RNA-seq has become the method of choice to provide such estimates at the genomewide scale. However, the application of RNA-seq to HLA genes —key players in the immune adaptive response— has remained a rarely explored approach. This is due to the problem of mapping bias, which causes deficient read alignment at genes which are very polymorphic and different from the reference genome. This has motivated approaches that replace the single reference genome with personalized sequences, comprised of the individual’s specific HLA genotype. Here we explore the use of computational frameworks to obtain reliable expression levels for HLA genes from RNA-seq datasets. We present a pipeline in which the quantification of HLA expression is carried out using methods which account for HLA diversity, avoiding the biases of standard approaches. We then evaluate the impact of this form of quantifying HLA expression on downstream analyses. The pipeline also allows us to integrate information on eQTLs with expression levels at the HLA allele-level, which can help disentangle different contributions to disease phenotypes and help understand the regulatory architecture at the HLA region.
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Affiliation(s)
- Vitor R. C. Aguiar
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- * E-mail: (VRCA); (DM)
| | - Jônatas César
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Olivier Delaneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- * E-mail: (VRCA); (DM)
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22
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Petersdorf EW, O'hUigin C. The MHC in the era of next-generation sequencing: Implications for bridging structure with function. Hum Immunol 2019; 80:67-78. [PMID: 30321633 PMCID: PMC6542361 DOI: 10.1016/j.humimm.2018.10.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/24/2018] [Accepted: 10/01/2018] [Indexed: 12/19/2022]
Abstract
The MHC continues to have the most disease-associations compared to other regions of the human genome, even in the genome-wide association study (GWAS) and single nucleotide polymorphism (SNP) era. Analysis of non-coding variation and their impact on the level of expression of HLA allotypes has shed new light on the potential mechanisms underlying HLA disease associations and alloreactivity in transplantation. Next-generation sequencing (NGS) technology has the capability of delineating the phase of variants in the HLA antigen-recognition site (ARS) with non-coding regulatory polymorphisms. These relationships are critical for understanding the qualitative and quantitative implications of HLA gene diversity. This article summarizes current understanding of non-coding region variation of HLA loci, the consequences of regulatory variation on HLA expression, the role for evolution in shaping lineage-specific expression, and the impact of HLA expression on disease susceptibility and transplantation outcomes. A role for phased sequencing methods for the MHC, and perspectives for future directions in basic and applied immunogenetic studies of the MHC are presented.
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Affiliation(s)
- Effie W Petersdorf
- University of Washington, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, D4-115, Seattle, WA 98109, United States.
| | - Colm O'hUigin
- Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Microbiome and Genetics Core, Building 37, Room 4140B, Bethesda, MD 20852, United States.
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van der Zwan A, van der Meer-Prins EMW, van Miert PPMC, van den Heuvel H, Anholts JDH, Roelen DL, Claas FHJ, Heidt S. Cross-Reactivity of Virus-Specific CD8+ T Cells Against Allogeneic HLA-C: Possible Implications for Pregnancy Outcome. Front Immunol 2018; 9:2880. [PMID: 30574149 PMCID: PMC6291497 DOI: 10.3389/fimmu.2018.02880] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/23/2018] [Indexed: 01/22/2023] Open
Abstract
Heterologous immunity of virus-specific T cells poses a potential barrier to transplantation tolerance. Cross-reactivity to HLA-A and -B molecules has broadly been described, whereas responses to allo-HLA-C have remained ill defined. In contrast to the transplant setting, HLA-C is the only polymorphic HLA molecule expressed by extravillous trophoblasts at the maternal-fetal interface during pregnancy. Uncontrolled placental viral infections, accompanied by a pro-inflammatory milieu, can alter the activation status and stability of effector T cells. Potential cross-reactivity of maternal decidual virus-specific T cells to fetal allo-HLA-C may thereby have detrimental consequences for the success of pregnancy. To explore the presence of cross-reactivity to HLA-C and the other non-classical HLA antigens expressed by trophoblasts, HLA-A and -B-restricted CD8+ T cells specific for Epstein-Barr virus, Cytomegalovirus, Varicella-Zoster virus, and Influenza virus were tested against target cells expressing HLA-C, -E, and -G molecules. An HLA-B*08:01-restricted EBV-specific T cell clone displayed cross-reactivity against HLA-C*01:02. Furthermore, cross-reactivity of HLA-C-restricted virus-specific CD8+ T cells was observed for HCMV HLA-C*06:02/TRA CD8+ T cell lines and clones against HLA-C*03:02. Collectively, these results demonstrate that cross-reactivity against HLA-C can occur and thereby may affect pregnancy outcome.
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Affiliation(s)
- Anita van der Zwan
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | | | - Paula P M C van Miert
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Heleen van den Heuvel
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Jacqueline D H Anholts
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Dave L Roelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Frans H J Claas
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Sebastiaan Heidt
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
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24
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Koefoed-Nielsen P, Møller BK. Donor-specific anti-HLA antibodies by solid phase immunoassays: advantages and technical concerns. Int Rev Immunol 2018; 38:95-105. [DOI: 10.1080/08830185.2018.1525367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Bjarne Kuno Møller
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
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25
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Hilton HG, McMurtrey CP, Han AS, Djaoud Z, Guethlein LA, Blokhuis JH, Pugh JL, Goyos A, Horowitz A, Buchli R, Jackson KW, Bardet W, Bushnell DA, Robinson PJ, Mendoza JL, Birnbaum ME, Nielsen M, Garcia KC, Hildebrand WH, Parham P. The Intergenic Recombinant HLA-B∗46:01 Has a Distinctive Peptidome that Includes KIR2DL3 Ligands. Cell Rep 2018; 19:1394-1405. [PMID: 28514659 PMCID: PMC5510751 DOI: 10.1016/j.celrep.2017.04.059] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/07/2017] [Accepted: 04/20/2017] [Indexed: 01/26/2023] Open
Abstract
HLA-B∗46:01 was formed by an intergenic mini-conversion, between HLA-B∗15:01 and HLA-C∗01:02, in Southeast Asia during the last 50,000 years, and it has since become the most common HLA-B allele in the region. A functional effect of the mini-conversion was introduction of the C1 epitope into HLA-B∗46:01, making it an exceptional HLA-B allotype that is recognized by the C1-specific natural killer (NK) cell receptor KIR2DL3. High-resolution mass spectrometry showed that HLA-B∗46:01 has a low-diversity peptidome that is distinct from those of its parents. A minority (21%) of HLA-B∗46:01 peptides, with common C-terminal characteristics, form ligands for KIR2DL3. The HLA-B∗46:01 peptidome is predicted to be enriched for peptide antigens derived from Mycobacterium leprae. Overall, the results indicate that the distinctive peptidome and functions of HLA-B∗46:01 provide carriers with resistance to leprosy, which drove its rapid rise in frequency in Southeast Asia. The interlocus recombinant HLA-B∗46:01 is found at high frequency in Southeast Asia HLA-B∗46:01 has a low-diversity peptidome that is distinct from both its parents A subset of HLA-B∗46:01 peptides provides ligands for the NK cell receptor KIR2DL3 The unique features of HLA-B∗46:01 correlate with protection against leprosy
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Affiliation(s)
- Hugo G Hilton
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Curtis P McMurtrey
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Alex S Han
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Zakia Djaoud
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lisbeth A Guethlein
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jeroen H Blokhuis
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jason L Pugh
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ana Goyos
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Amir Horowitz
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Rico Buchli
- Pure Protein LLC, Oklahoma City, OK 73104, USA
| | - Ken W Jackson
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Wilfred Bardet
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - David A Bushnell
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Philip J Robinson
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Juan L Mendoza
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michael E Birnbaum
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - K Christopher Garcia
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Molecular & Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - William H Hildebrand
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Peter Parham
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA
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Geneugelijk K, Spierings E. Matching donor and recipient based on predicted indirectly recognizable human leucocyte antigen epitopes. Int J Immunogenet 2018; 45:41-53. [PMID: 29464898 DOI: 10.1111/iji.12359] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/21/2017] [Accepted: 02/01/2018] [Indexed: 12/27/2022]
Abstract
The predicted indirectly recognizable human leucocyte antigen (HLA) epitopes (PIRCHE) algorithm is a novel in silico algorithm to determine donor-recipient compatibility. The PIRCHE algorithm determines donor-recipient compatibility by counting the number of mismatched HLA-derived epitopes that are involved in indirect T-cell alloimmune responses; these epitopes are designated as PIRCHE. Over the last few years, the PIRCHE algorithm has been investigated in both hematopoietic stem cell transplantation and solid organ transplantation. This review describes the theory of the algorithm, its application in transplantation, and highlights the future perspectives on the clinical application of the PIRCHE algorithm.
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Affiliation(s)
- K Geneugelijk
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - E Spierings
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
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27
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Impact of the Polymorphism rs9264942 near the HLA-C Gene on HIV-1 DNA Reservoirs in Asymptomatic Chronically Infected Patients Initiating Antiviral Therapy. J Immunol Res 2017; 2017:8689313. [PMID: 29445759 PMCID: PMC5763112 DOI: 10.1155/2017/8689313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/17/2017] [Indexed: 11/17/2022] Open
Abstract
Several genome-wide association studies have identified a polymorphism located 35 kb upstream of the coding region of HLA-C gene (rs9264942; termed -35 C/T) as a host factor significantly associated with the control of HIV-1 viremia in untreated patients. The potential association of this host genetic polymorphism with the viral reservoirs has never been investigated, nor the association with the viral control in response to the treatment. In this study, we assess the influence of the polymorphism -35 C/T on the outcome of virus burden in 183 antiretroviral-naïve HIV-1-infected individuals who initiated antiviral treatment (study STIR-2102), analyzing HIV-1 RNA viremia and HIV-1 DNA reservoirs. The rs9264942 genotyping was investigated retrospectively, and plasma levels of HIV-1 RNA and peripheral blood mononuclear cell- (PBMC-) associated HIV-1 DNA were compared between carriers and noncarriers of the protective allele -35 C before antiretroviral therapy (ART), one month after ART and at the end of the study (36 months). HIV-1 RNA and HIV-1 DNA levels were both variables significantly different between carriers and noncarriers of the allele -35 C before ART. HIV-1 DNA levels remained also significantly different one month posttherapy. However, this protective effect of the -35 C allele was not maintained after long-term ART.
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Hosie L, Pachnio A, Zuo J, Pearce H, Riddell S, Moss P. Cytomegalovirus-Specific T Cells Restricted by HLA-Cw*0702 Increase Markedly with Age and Dominate the CD8 + T-Cell Repertoire in Older People. Front Immunol 2017; 8:1776. [PMID: 29312307 PMCID: PMC5732243 DOI: 10.3389/fimmu.2017.01776] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/28/2017] [Indexed: 11/18/2022] Open
Abstract
Cytomegalovirus (CMV) infection elicits a strong T-cell immune response, which increases further during aging in a process termed "memory inflation." CMV downregulates the expression of HLA-A and HLA-B on the surface of infected cells to limit presentation of viral peptides to T-cells although HLA-C is relatively spared as it also engages with inhibitory killer immunoglobulin receptor receptors and therefore reduces lysis by natural killer cells. We investigated the magnitude and functional properties of CMV-specific CD8+ T-cells specific for 10 peptides restricted by HLA-C in a cohort of 53 donors between the age of 23 and 91 years. This was achieved via peptide stimulation of PBMCs followed by multicolor flow cytometry. Three peptides, derived from proteins generated in the immediate-early period of viral replication and restricted by HLA-Cw*0702, elicited strong immune responses, which increased substantially with age such that the average aggregate response represented 37% of the CD8+ T-cell pool within donors above 70 years of age. Remarkably, a single response represented 70% of the total CD8+ T-cell pool within a 91-year-old donor. HLA-Cw*0702-restricted CD8+ T-cell responses were immunodominant over HLA-A and HLA-B-restricted CMV-specific responses and did not show features of exhaustion such as PD-1 or CD39 expression. Indeed, such CTL exhibit a polyfunctional cytokine profile with co-expression of IFN-γ and TNF-α and a strong cytotoxic phenotype with intracellular expression of perforin and granzymeB. Functionally, HLA-Cw*0702-restricted CTL show exceptionally high avidity for cognate peptide-HLA and demonstrate very early and efficient recognition of virally infected cells. These observations indicate that CD8+ T-cells restricted by HLA-C play an important role in the control of persistent CMV infection and could represent a novel opportunity for CD8+ T-cell therapy of viral infection within immunosuppressed patients. In addition, the findings provide further evidence for the importance of HLA-C-restricted T-cells in the control of chronic viral infection.
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Affiliation(s)
- Louise Hosie
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
| | - Annette Pachnio
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
| | - Jianmin Zuo
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
| | - Hayden Pearce
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
| | - Stanley Riddell
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Paul Moss
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
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29
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Di Marco M, Schuster H, Backert L, Ghosh M, Rammensee HG, Stevanović S. Unveiling the Peptide Motifs of HLA-C and HLA-G from Naturally Presented Peptides and Generation of Binding Prediction Matrices. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 199:2639-2651. [PMID: 28904123 DOI: 10.4049/jimmunol.1700938] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/12/2017] [Indexed: 12/16/2023]
Abstract
The classical HLA-C and the nonclassical HLA-E and HLA-G molecules play important roles both in the innate and adaptive immune system. Starting already during embryogenesis and continuing throughout our lives, these three Ags exert major functions in immune tolerance, defense against infections, and anticancer immune responses. Despite these important roles, identification and characterization of the peptides presented by these molecules has been lacking behind the more abundant HLA-A and HLA-B gene products. In this study, we elucidated the peptide specificities of these HLA molecules using a comprehensive analysis of naturally presented peptides. To that end, the 15 most frequently expressed HLA-C alleles as well as HLA-E*01:01 and HLA-G*01:01 were transfected into lymphoblastoid C1R cells expressing low endogenous HLA. Identification of naturally presented peptides was performed by immunoprecipitation of HLA and subsequent analysis of HLA-bound peptides by liquid chromatographic tandem mass spectrometry. Peptide motifs of HLA-C unveil anchors in position 2 or 3 with high variances between allotypes, and a less variable anchor at the C-terminal end. The previously reported small ligand repertoire of HLA-E was confirmed within our analysis, and we could show that HLA-G combines a large ligand repertoire with distinct features anchoring peptides at positions 3 and 9, supported by an auxiliary anchor in position 1 and preferred residues in positions 2 and 7. The wealth of HLA ligands resulted in prediction matrices for octa-, nona-, and decamers. Matrices were validated in terms of their binding prediction and compared with the latest NetMHC prediction algorithm NetMHCpan-3.0, which demonstrated their predictive power.
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Affiliation(s)
- Moreno Di Marco
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Heiko Schuster
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
- Immatics Biotechnologies GmbH, 72076 Tübingen, Germany; and
| | - Linus Backert
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Michael Ghosh
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany;
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30
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Mobbs JI, Illing PT, Dudek NL, Brooks AG, Baker DG, Purcell AW, Rossjohn J, Vivian JP. The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule. J Biol Chem 2017; 292:17203-17215. [PMID: 28855257 DOI: 10.1074/jbc.m117.806976] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/18/2017] [Indexed: 12/31/2022] Open
Abstract
Human leukocyte antigen (HLA)-C*06:02 is identified as the allele associated with the highest risk for the development of the autoimmune skin disease psoriasis. However, the diversity and mode of peptide presentation by the HLA-C*06:02 molecule remains unclear. Here, we describe the endogenous peptide repertoire of ∼3,000 sequences for HLA-C*06:02 that defines the peptide-binding motif for this HLA allomorph. We found that HLA-C*06:02 predominantly presents nonamer peptides with dominant arginine anchors at the P2 and P7 positions and a preference for small hydrophobic residues at the C terminus (PΩ). To determine the structural basis of this selectivity, we determined crystal structures of HLA-C*06:02 in complex with two self-peptides (ARTELYRSL and ARFNDLRFV) and an analogue of a melanocyte autoantigen (ADAMTSL5, VRSRR-abu-LRL) implicated in psoriasis. These structures revealed that HLA-C*06:02 possesses a deep peptide-binding groove comprising two electronegative B- and E-pockets that coincide with the preference for P2 and P7 arginine anchors. The ADAMTSL5 autoantigen possessed a P7-Leu instead of the P7-Arg residue, but nevertheless was accommodated within the HLA-C*06:02 antigen-binding cleft. Collectively, our results provide the structural basis for understanding peptide repertoire selection in HLA-C*06:02.
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Affiliation(s)
- Jesse I Mobbs
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Patricia T Illing
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Nadine L Dudek
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Andrew G Brooks
- the Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Daniel G Baker
- Janssen Research & Development, LLC, Horsham, Philadelphia, Pennsylvania 19044
| | - Anthony W Purcell
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia,
| | - Jamie Rossjohn
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia, .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Victoria, Australia, and.,the Institute of Infection and Immunity, Cardiff University, School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Julian P Vivian
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia, .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Victoria, Australia, and
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31
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Crux NB, Elahi S. Human Leukocyte Antigen (HLA) and Immune Regulation: How Do Classical and Non-Classical HLA Alleles Modulate Immune Response to Human Immunodeficiency Virus and Hepatitis C Virus Infections? Front Immunol 2017; 8:832. [PMID: 28769934 PMCID: PMC5513977 DOI: 10.3389/fimmu.2017.00832] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/30/2017] [Indexed: 12/13/2022] Open
Abstract
The genetic factors associated with susceptibility or resistance to viral infections are likely to involve a sophisticated array of immune response. These genetic elements may modulate other biological factors that account for significant influence on the gene expression and/or protein function in the host. Among them, the role of the major histocompatibility complex in viral pathogenesis in particular human immunodeficiency virus (HIV) and hepatitis C virus (HCV), is very well documented. We, recently, added a novel insight into the field by identifying the molecular mechanism associated with the protective role of human leukocyte antigen (HLA)-B27/B57 CD8+ T cells in the context of HIV-1 infection and why these alleles act as a double-edged sword protecting against viral infections but predisposing the host to autoimmune diseases. The focus of this review will be reexamining the role of classical and non-classical HLA alleles, including class Ia (HLA-A, -B, -C), class Ib (HLA-E, -F, -G, -H), and class II (HLA-DR, -DQ, -DM, and -DP) in immune regulation and viral pathogenesis (e.g., HIV and HCV). To our knowledge, this is the very first review of its kind to comprehensively analyze the role of these molecules in immune regulation associated with chronic viral infections.
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Affiliation(s)
- Nicole B Crux
- Faculty of Medicine and Dentistry, Department of Dentistry, University of Alberta, Edmonton, AB, Canada.,Faculty of Medicine and Dentistry, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Shokrollah Elahi
- Faculty of Medicine and Dentistry, Department of Dentistry, University of Alberta, Edmonton, AB, Canada.,Faculty of Medicine and Dentistry, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
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32
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Histocompatibility and management of the highly sensitized kidney transplant candidate. Curr Opin Organ Transplant 2017; 22:415-420. [PMID: 28692441 DOI: 10.1097/mot.0000000000000449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Increasing national participation in kidney paired donation and implementation of new sharing policies via the current kidney allocation system have brought about greater opportunities for the most highly sensitized patients awaiting a kidney transplant. The purpose of this review is to discuss the application of histocompatibility data in the context of the clinical practice of kidney transplantation as pertains to the sensitized candidate. RECENT FINDINGS With desensitization techniques, transplantation across virtually any antibody barrier is technically feasible, but long-term outcomes after transplantation are improved when the immunologic match between donor and recipient is optimized. Solid-phase immunoassays have changed the landscape of histocompatibility testing. These sensitive and specific assays for identifying donor-specific antibody not only help determine feasibility of transplantation but have enabled outcomes studies aimed at understanding the spectrum of risk posed by different antibody profiles. This, in turn, has helped guide decision-making in donor selection, in particular for sensitized patients. SUMMARY Careful evaluation of donor-specific antibody profiles with individualized, patient-specific determination of unacceptable antigens is necessary to ensure that highly sensitized patients receive every opportunity for transplantation.
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33
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Sullivan HC, Gebel HM, Bray RA. Understanding solid-phase HLA antibody assays and the value of MFI. Hum Immunol 2017; 78:471-480. [DOI: 10.1016/j.humimm.2017.05.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 05/26/2017] [Accepted: 05/29/2017] [Indexed: 01/10/2023]
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34
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Dias AL, Hashmi S, Hogan W, Baig N, Wakefield L, Kreuter J, Gandhi MJ. The 'HLA conundrum in bone marrow transplantation': correct interpretation of anti-HLA antibodies in haploidentical donor selection. Bone Marrow Transplant 2017; 52:902-904. [DOI: 10.1038/bmt.2017.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Serena M, Parolini F, Biswas P, Sironi F, Blanco Miranda A, Zoratti E, Scupoli MT, Ziglio S, Valenzuela-Fernandez A, Gibellini D, Romanelli MG, Siccardi A, Malnati M, Beretta A, Zipeto D. HIV-1 Env associates with HLA-C free-chains at the cell membrane modulating viral infectivity. Sci Rep 2017; 7:40037. [PMID: 28051183 PMCID: PMC5209703 DOI: 10.1038/srep40037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/30/2016] [Indexed: 12/13/2022] Open
Abstract
HLA-C has been demonstrated to associate with HIV-1 envelope glycoprotein (Env). Virions lacking HLA-C have reduced infectivity and increased susceptibility to neutralizing antibodies. Like all others MHC-I molecules, HLA-C requires β2-microglobulin (β2m) for appropriate folding and expression on the cell membrane but this association is weaker, thus generating HLA-C free-chains on the cell surface. In this study, we deepen the understanding of HLA-C and Env association by showing that HIV-1 specifically increases the amount of HLA-C free chains, not bound to β2m, on the membrane of infected cells. The association between Env and HLA-C takes place at the cell membrane requiring β2m to occur. We report that the enhanced infectivity conferred to HIV-1 by HLA-C specifically involves HLA-C free chain molecules that have been correctly assembled with β2m. HIV-1 Env-pseudotyped viruses produced in the absence of β2m are less infectious than those produced in the presence of β2m. We hypothesize that the conformation and surface expression of HLA-C molecules could be a discriminant for the association with Env. Binding stability to β2m may confer to HLA-C the ability to preferentially act either as a conventional immune-competent molecule or as an accessory molecule involved in HIV-1 infectivity.
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Affiliation(s)
- Michela Serena
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | - Francesca Parolini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | - Priscilla Biswas
- IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132, Milan, Italy
| | - Francesca Sironi
- IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132, Milan, Italy
| | - Almudena Blanco Miranda
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | - Elisa Zoratti
- University Laboratory of Medical Research, Piazzale L. A. Scuro 10, 37134 Verona, Italy
| | - Maria Teresa Scupoli
- University Laboratory of Medical Research, Piazzale L. A. Scuro 10, 37134 Verona, Italy
| | - Serena Ziglio
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134, Verona, Italy.,Laboratorio de Inmunología Celular y Viral, Unidad de Virología IUETSPC, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, Tenerife, Spain
| | - Agustin Valenzuela-Fernandez
- Laboratorio de Inmunología Celular y Viral, Unidad de Virología IUETSPC, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, Tenerife, Spain
| | - Davide Gibellini
- Department of Diagnostics and Public Health, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | - Maria Grazia Romanelli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | - Antonio Siccardi
- IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132, Milan, Italy
| | - Mauro Malnati
- IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132, Milan, Italy
| | - Alberto Beretta
- IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132, Milan, Italy
| | - Donato Zipeto
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
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36
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HLA-typing analysis following allogeneic bone grafting for sinus lifting. Cell Tissue Bank 2016; 18:75-81. [DOI: 10.1007/s10561-016-9594-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/21/2016] [Indexed: 12/18/2022]
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37
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van Essen TH, van Pelt SI, Bronkhorst IHG, Versluis M, Némati F, Laurent C, Luyten GPM, van Hall T, van den Elsen PJ, van der Velden PA, Decaudin D, Jager MJ. Upregulation of HLA Expression in Primary Uveal Melanoma by Infiltrating Leukocytes. PLoS One 2016; 11:e0164292. [PMID: 27764126 PMCID: PMC5072555 DOI: 10.1371/journal.pone.0164292] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 09/22/2016] [Indexed: 12/22/2022] Open
Abstract
Introduction Uveal melanoma (UM) with an inflammatory phenotype, characterized by infiltrating leukocytes and increased human leukocyte antigen (HLA) expression, carry an increased risk of death due to metastases. These tumors should be ideal for T-cell based therapies, yet it is not clear why prognostically-infaust tumors have a high HLA expression. We set out to determine whether the level of HLA molecules in UM is associated with other genetic factors, HLA transcriptional regulators, or microenvironmental factors. Methods 28 enucleated UM were used to study HLA class I and II expression, and several regulators of HLA by immunohistochemistry, PCR microarray, qPCR and chromosome SNP-array. Fresh tumor samples of eight primary UM and four metastases were compared to their corresponding xenograft in SCID mice, using a PCR microarray and SNP array. Results Increased expression levels of HLA class I and II showed no dosage effect of chromosome 6p, but, as expected, were associated with monosomy of chromosome 3. Increased HLA class I and II protein levels were positively associated with their gene expression and with raised levels of the peptide-loading gene TAP1, and HLA transcriptional regulators IRF1, IRF8, CIITA, and NLRC5, revealing a higher transcriptional activity in prognostically-bad tumors. Implantation of fresh human tumor samples into SCID mice led to a loss of infiltrating leukocytes, and to a decreased expression of HLA class I and II genes, and their regulators. Conclusion Our data provides evidence for a proper functioning HLA regulatory system in UM, offering a target for T-cell based therapies.
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Affiliation(s)
| | - Sake I van Pelt
- Department of Medical Statistics, LUMC, Leiden, the Netherlands
| | | | - Mieke Versluis
- Department of Ophthalmology, LUMC, Leiden, the Netherlands
| | - Fariba Némati
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, Paris, France
| | - Cécile Laurent
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, Paris, France
| | | | | | - Peter J van den Elsen
- Department of Immunohematology and Blood Transfusion, LUMC, Leiden, the Netherlands.,Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Didier Decaudin
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, Paris, France.,Department of Clinical Hematology, Institut Curie, Paris France
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38
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Bardeskar NS, Mania-Pramanik J. HIV and host immunogenetics: unraveling the role of HLA-C. HLA 2016; 88:221-231. [PMID: 27620973 DOI: 10.1111/tan.12882] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 08/19/2016] [Indexed: 01/09/2023]
Abstract
Host genetic factors play a major role in determining the outcome of many infections including human immunodeficiency virus (HIV). Multiple host factors have been studied till date showing their varied role in susceptibility or resistance to HIV infection. HLA-C, however, has been recently started gaining interest in researchers mind revealing its polymorphisms to have an important effect on viral load set-points, disease progression as well as transmission. In this review report, we have compiled these significant findings of HLA-C in HIV infection, in an attempt to highlight the need for further research in the area in different ethnic population to establish its role in the infection.
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Affiliation(s)
- N S Bardeskar
- Infectious Diseases Biology Department, National Institute for Research in Reproductive Health, Mumbai, 400012, India
| | - J Mania-Pramanik
- Infectious Diseases Biology Department, National Institute for Research in Reproductive Health, Mumbai, 400012, India.
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39
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Chan WF, Parks-Dely JA, Magor BG, Magor KE. The Minor MHC Class I Gene UDA of Ducks Is Regulated by Let-7 MicroRNA. THE JOURNAL OF IMMUNOLOGY 2016; 197:1212-20. [DOI: 10.4049/jimmunol.1600332] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/08/2016] [Indexed: 01/10/2023]
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40
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Buhler S, Nunes JM, Sanchez-Mazas A. HLA class I molecular variation and peptide-binding properties suggest a model of joint divergent asymmetric selection. Immunogenetics 2016; 68:401-416. [PMID: 27233953 PMCID: PMC4911380 DOI: 10.1007/s00251-016-0918-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/17/2016] [Indexed: 01/20/2023]
Abstract
The main function of HLA class I molecules is to present pathogen-derived peptides to cytotoxic T lymphocytes. This function is assumed to drive the maintenance of an extraordinary amount of polymorphism at each HLA locus, providing an immune advantage to heterozygote individuals capable to present larger repertories of peptides than homozygotes. This seems contradictory, however, with a reduced diversity at individual HLA loci exhibited by some isolated populations. This study shows that the level of functional diversity predicted for the two HLA-A and HLA-B genes considered simultaneously is similar (almost invariant) between 46 human populations, even when a reduced diversity exists at each locus. We thus propose that HLA-A and HLA-B evolved through a model of joint divergent asymmetric selection conferring all populations an equivalent immune potential. The distinct pattern observed for HLA-C is explained by its functional evolution towards killer cell immunoglobulin-like receptor (KIR) activity regulation rather than peptide presentation.
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Affiliation(s)
- Stéphane Buhler
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland. .,Transplantation Immunology Unit & National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland.
| | - José Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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41
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René C, Lozano C, Eliaou JF. Expression of classical HLA class I molecules: regulation and clinical impacts: Julia Bodmer Award Review 2015. HLA 2016; 87:338-49. [PMID: 27060357 DOI: 10.1111/tan.12787] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 03/04/2016] [Indexed: 12/19/2022]
Abstract
Human leukocyte antigen (HLA) class I genes are ubiquitously expressed, but in a tissue specific-manner. Their expression is primarily regulated at the transcriptional level and can be modulated both positively and negatively by different stimuli. Advances in sequencing technologies led to the identification of new regulatory variants located in the untranslated regions (UTRs), which could influence the expression. After a brief description of the mechanisms underlying the transcriptional regulation of HLA class I genes expression, we will review how the expression levels of HLA class I genes could affect biological and pathological processes. Then, we will discuss on the differential expression of HLA class I genes according to the locus, allele and UTR polymorphisms and its clinical impact. This interesting field of study led to a new dimension of HLA typing, going beyond a qualitative aspect.
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Affiliation(s)
- C René
- Department of Immunology, CHRU de Montpellier, University Hospital Saint-Eloi, Montpellier, France.,Faculté de Médecine, University of Montpellier, Montpellier, France.,INSERM U1183, Institute for Regenerative Medicine and Biotherapy (IRMB), CHU Montpellier, Montpellier, France
| | - C Lozano
- Department of Immunology, CHRU de Montpellier, University Hospital Saint-Eloi, Montpellier, France
| | - J-F Eliaou
- Department of Immunology, CHRU de Montpellier, University Hospital Saint-Eloi, Montpellier, France.,Faculté de Médecine, University of Montpellier, Montpellier, France.,INSERM U1194, IRCM, University of Montpellier, Montpellier, France
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42
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Hickey MJ, Valenzuela NM, Reed EF. Alloantibody Generation and Effector Function Following Sensitization to Human Leukocyte Antigen. Front Immunol 2016; 7:30. [PMID: 26870045 PMCID: PMC4740371 DOI: 10.3389/fimmu.2016.00030] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/20/2016] [Indexed: 02/06/2023] Open
Abstract
Allorecognition is the activation of the adaptive immune system to foreign human leukocyte antigen (HLA) resulting in the generation of alloantibodies. Due to a high polymorphism, foreign HLA is recognized by the immune system following transplant, transfusion, or pregnancy resulting in the formation of the germinal center and the generation of long-lived alloantibody-producing memory B cells. Alloantibodies recognize antigenic epitopes displayed by the HLA molecule on the transplanted allograft and contribute to graft damage through multiple mechanisms, including (1) activation of the complement cascade resulting in the formation of the MAC complex and inflammatory anaphylatoxins, (2) transduction of intracellular signals leading to cytoskeletal rearrangement, growth, and proliferation of graft vasculature, and (3) immune cell infiltration into the allograft via FcγR interactions with the FC portion of the antibody. This review focuses on the generation of HLA alloantibody, routes of sensitization, alloantibody specificity, and mechanisms of antibody-mediated graft damage.
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Affiliation(s)
- Michelle J Hickey
- Department of Pathology and Laboratory Medicine, UCLA Immunogenetics Center, University of California Los Angeles , Los Angeles, CA , USA
| | - Nicole M Valenzuela
- Department of Pathology and Laboratory Medicine, UCLA Immunogenetics Center, University of California Los Angeles , Los Angeles, CA , USA
| | - Elaine F Reed
- Department of Pathology and Laboratory Medicine, UCLA Immunogenetics Center, University of California Los Angeles , Los Angeles, CA , USA
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43
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Mack SJ. A gene feature enumeration approach for describing HLA allele polymorphism. Hum Immunol 2015; 76:975-81. [PMID: 26416087 PMCID: PMC4674356 DOI: 10.1016/j.humimm.2015.09.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 09/24/2015] [Accepted: 09/24/2015] [Indexed: 11/25/2022]
Abstract
HLA genotyping via next generation sequencing (NGS) poses challenges for the use of HLA allele names to analyze and discuss sequence polymorphism. NGS will identify many new synonymous and non-coding HLA sequence variants. Allele names identify the types of nucleotide polymorphism that define an allele (non-synonymous, synonymous and non-coding changes), but do not describe how polymorphism is distributed among the individual features (the flanking untranslated regions, exons and introns) of a gene. Further, HLA alleles cannot be named in the absence of antigen-recognition domain (ARD) encoding exons. Here, a system for describing HLA polymorphism in terms of HLA gene features (GFs) is proposed. This system enumerates the unique nucleotide sequences for each GF in an HLA gene, and records these in a GF enumeration notation that allows both more granular dissection of allele-level HLA polymorphism and the discussion and analysis of GFs in the absence of ARD-encoding exon sequences.
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Affiliation(s)
- Steven J Mack
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA.
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44
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Arakawa A, Siewert K, Stöhr J, Besgen P, Kim SM, Rühl G, Nickel J, Vollmer S, Thomas P, Krebs S, Pinkert S, Spannagl M, Held K, Kammerbauer C, Besch R, Dornmair K, Prinz JC. Melanocyte antigen triggers autoimmunity in human psoriasis. J Exp Med 2015; 212:2203-12. [PMID: 26621454 PMCID: PMC4689169 DOI: 10.1084/jem.20151093] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/04/2015] [Indexed: 12/21/2022] Open
Abstract
Psoriasis vulgaris is a common T cell-mediated inflammatory skin disease with a suspected autoimmune pathogenesis. The human leukocyte antigen (HLA) class I allele, HLA-C*06:02, is the main psoriasis risk gene. Epidermal CD8(+) T cells are essential for psoriasis development. Functional implications of HLA-C*06:02 and mechanisms of lesional T cell activation in psoriasis, however, remained elusive. Here we identify melanocytes as skin-specific target cells of an HLA-C*06:02-restricted psoriatic T cell response. We found that a Vα3S1/Vβ13S1 T cell receptor (TCR), which we had reconstituted from an epidermal CD8(+) T cell clone of an HLA-C*06:02-positive psoriasis patient specifically recognizes HLA-C*06:02-positive melanocytes. Through peptide library screening, we identified ADAMTS-like protein 5 (ADAMTSL5) as an HLA-C*06:02-presented melanocytic autoantigen of the Vα3S1/Vβ13S1 TCR. Consistent with the Vα3S1/Vβ13S1-TCR reactivity, we observed numerous CD8(+) T cells in psoriasis lesions attacking melanocytes, the only epidermal cells expressing ADAMTSL5. Furthermore, ADAMTSL5 stimulation induced the psoriasis signature cytokine, IL-17A, in CD8(+) T cells from psoriasis patients only, supporting a role as psoriatic autoantigen. This unbiased analysis of a TCR obtained directly from tissue-infiltrating CD8(+) T cells reveals that in psoriasis HLA-C*06:02 directs an autoimmune response against melanocytes through autoantigen presentation. We propose that HLA-C*06:02 may predispose to psoriasis via this newly identified autoimmune pathway.
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Affiliation(s)
- Akiko Arakawa
- Department of Dermatology, Ludwig-Maximilian-University, D-80337 Munich, Germany
| | - Katherina Siewert
- Institute of Clinical Neuroimmunology, Ludwig-Maximilian-University, D-82152 Planegg-Martinsried, Germany
| | - Julia Stöhr
- Department of Dermatology, Ludwig-Maximilian-University, D-80337 Munich, Germany
| | - Petra Besgen
- Department of Dermatology, Ludwig-Maximilian-University, D-80337 Munich, Germany
| | - Song-Min Kim
- Department of Dermatology, Ludwig-Maximilian-University, D-80337 Munich, Germany
| | - Geraldine Rühl
- Institute of Clinical Neuroimmunology, Ludwig-Maximilian-University, D-82152 Planegg-Martinsried, Germany
| | - Jens Nickel
- Department of Dermatology, Ludwig-Maximilian-University, D-80337 Munich, Germany
| | - Sigrid Vollmer
- Department of Dermatology, Ludwig-Maximilian-University, D-80337 Munich, Germany
| | - Peter Thomas
- Department of Dermatology, Ludwig-Maximilian-University, D-80337 Munich, Germany
| | - Stefan Krebs
- Gene Center Munich, Ludwig-Maximilian-University, D-81377 Munich, Germany
| | - Stefan Pinkert
- German Cancer Research Center, D-69120 Heidelberg, Germany
| | - Michael Spannagl
- Laboratory of Immunogenetics and Molecular Diagnostics, Ludwig-Maximilian-University, D-81377 Munich, Germany
| | - Kathrin Held
- Institute of Clinical Neuroimmunology, Ludwig-Maximilian-University, D-82152 Planegg-Martinsried, Germany
| | - Claudia Kammerbauer
- Department of Dermatology, Ludwig-Maximilian-University, D-80337 Munich, Germany
| | - Robert Besch
- Department of Dermatology, Ludwig-Maximilian-University, D-80337 Munich, Germany
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, Ludwig-Maximilian-University, D-82152 Planegg-Martinsried, Germany
| | - Jörg C Prinz
- Department of Dermatology, Ludwig-Maximilian-University, D-80337 Munich, Germany
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45
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Filippone EJ, Farber JL. Humoral immunity in renal transplantation: epitopes, Cw and DP, and complement-activating capability - an update. Clin Transplant 2015; 29:279-87. [DOI: 10.1111/ctr.12524] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2015] [Indexed: 01/10/2023]
Affiliation(s)
- Edward J. Filippone
- Division of Nephrology; Department of Medicine; Thomas Jefferson University Hospital; Philadelphia PA USA
| | - John L. Farber
- Department of Pathology; Thomas Jefferson University Hospital; Philadelphia PA USA
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46
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Stoll A, Bergmann S, Mummert C, Mueller-Schmucker SM, Spriewald BM, Harrer EG, Harrer T. Identification of HLA-C restricted, HIV-1-specific CTL epitopes by peptide induced upregulation of HLA-C expression. J Immunol Methods 2015; 418:9-18. [PMID: 25633660 DOI: 10.1016/j.jim.2015.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/19/2015] [Accepted: 01/20/2015] [Indexed: 11/17/2022]
Abstract
HIV-1 negative regulatory factor (Nef) can inhibit CTL recognition by downregulation of HLA-A and HLA-B on the cell surface. In contrast, HLA-C is not affected by Nef and a growing number of studies demonstrate an important role of HLA-C for the control of HIV-1. So far, only a limited number of HLA-C restricted CTL epitopes are known. As the mapping of new CTL epitopes is time and labor intensive, we investigated a novel method for the identification of HLA-C restricted CTL epitopes. B-lymphoblastoid cell lines (B-LCLs) and T2-cells were incubated with HIV-1 specific peptides and subsequently stained for HLA-C surface expression using the HLA-C specific antibody DT9. Peptides that led to increased HLA-C surface expression were used for stimulation of PBMC from HIV-1-infected patients. Subsequently, outgrowing cells were tested for peptide recognition in IFN-γ ELISPOT assays and HLA restriction of the recognized peptides was analyzed in ELISPOT assays using HLA-matched B-LCL. We observed that known HLA-C binding peptides increase HLA-C surface expression on T2-cells and on HLA-C*0102 and HLA-C*0702 homozygous B-LCL. Moreover, screening of HIV-1 Nef with overlapping peptides for potential C*0702 restricted epitopes using this method revealed a total of 8 peptides which considerably increased cell surface expression of HLA-C. By epitope mapping and functional analysis of peptide-stimulated T-cell lines we were able to define the peptide YPLTFGWCY as a new C*0702-restricted CTL epitope. These results show that the analysis of peptide induced HLA-C upregulation on B-LCL and T2-cells enables the efficient identification of new HLA-C restricted CTL epitopes.
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Affiliation(s)
- Andrej Stoll
- Infectious Diseases Unit, Department of Internal Medicine 3, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Silke Bergmann
- Infectious Diseases Unit, Department of Internal Medicine 3, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Christiane Mummert
- Infectious Diseases Unit, Department of Internal Medicine 3, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Sandra M Mueller-Schmucker
- Infectious Diseases Unit, Department of Internal Medicine 3, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Bernd M Spriewald
- Department of Internal Medicine 5, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Ellen G Harrer
- Infectious Diseases Unit, Department of Internal Medicine 3, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Harrer
- Infectious Diseases Unit, Department of Internal Medicine 3, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany.
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47
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van Essen TH, Roelen DL, Williams KA, Jager MJ. Matching for Human Leukocyte Antigens (HLA) in corneal transplantation - to do or not to do. Prog Retin Eye Res 2015; 46:84-110. [PMID: 25601193 DOI: 10.1016/j.preteyeres.2015.01.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 01/05/2015] [Accepted: 01/07/2015] [Indexed: 12/15/2022]
Abstract
As many patients with severe corneal disease are not even considered as candidates for a human graft due to their high risk of rejection, it is essential to find ways to reduce the chance of rejection. One of the options is proper matching of the cornea donor and recipient for the Human Leukocyte Antigens (HLA), a subject of much debate. Currently, patients receiving their first corneal allograft are hardly ever matched for HLA and even patients undergoing a regraft usually do not receive an HLA-matched graft. While anterior and posterior lamellar grafts are not immune to rejection, they are usually performed in low risk, non-vascularized cases. These are the cases in which the immune privilege due to the avascular status and active immune inhibition is still intact. Once broken due to infection, sensitization or trauma, rejection will occur. There is enough data to show that when proper DNA-based typing techniques are being used, even low risk perforating corneal transplantations benefit from matching for HLA Class I, and high risk cases from HLA Class I and probably Class II matching. Combining HLA class I and class II matching, or using the HLAMatchmaker could further improve the effect of HLA matching. However, new techniques could be applied to reduce the chance of rejection. Options are the local or systemic use of biologics, or gene therapy, aiming at preventing or suppressing immune responses. The goal of all these approaches should be to prevent a first rejection, as secondary grafts are usually at higher risk of complications including rejections than first grafts.
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Affiliation(s)
- T H van Essen
- Department of Ophthalmology, J3-S, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
| | - D L Roelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - K A Williams
- Department of Ophthalmology, Flinders University, Adelaide, Australia
| | - M J Jager
- Department of Ophthalmology, J3-S, Leiden University Medical Center (LUMC), Leiden, The Netherlands; Schepens Eye Research Institute, Massachusetts Eye & Ear Infirmary and Harvard Medical School, Boston, USA; Peking University Eye Center, Peking University Health Science Center, Beijing, China.
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48
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Thus KA, Te Boome L, Kuball J, Spierings E. Indirectly Recognized HLA-C Mismatches and Their Potential Role in Transplant Outcome. Front Immunol 2014; 5:210. [PMID: 24860572 PMCID: PMC4026718 DOI: 10.3389/fimmu.2014.00210] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 04/27/2014] [Indexed: 01/02/2023] Open
Abstract
HLA-C mismatches are clearly associated to alloreactivity after hematopoietic stem-cell transplantation; in a number of large cohorts, HLA-C mismatches are correlated to an increased risk of acute graft-versus-host disease (GVHD) or even impaired survival. While for HLA-A and -B, both antigenic as well as allelic mismatches are associated with an increased risk of acute GVHD, such an increased risk is only observed for antigenic HLA-C mismatches and not for allelic mismatches. These observations raise the question what sets HLA-C apart from HLA-A and -B. The difference may well be related to the reduced levels of cell-surface expression of HLA-C as compared to HLA-A and -B, possibly due to, among other factors, a limited peptide-binding capacity. This limited peptide-binding capacity may retain HLA-C in the ER and enhance degradation of the HLA-C protein. Once degraded, HLA-C-derived peptides can be presented to the immune system via other HLA alleles and are thus available for indirect recognition. Indeed, such HLA-C-derived peptides have previously been eluted from other HLA alleles. We have recently developed an approach to predict indirect recognition of HLA molecules, by establishing the numbers of predicted indirectly recognizable HLA epitopes (PIRCHES). The number of PIRCHES presented on HLA class I and II (PIRCHE-I and -II, respectively), are highly correlated to clinical measures of alloreactivity, such as acute GVHD. In the present “Hypothesis & Theory,” we reviewed the current knowledge on HLA-C mismatches and alloreactivity. Moreover, we speculate about the role of direct and indirect recognition of HLA-C and the consequences for donor selection in HLA-C mismatched stem-cell transplantation.
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Affiliation(s)
- Kirsten A Thus
- Laboratory for Translational Immunology, University Medical Center Utrecht , Utrecht , Netherlands
| | - Liane Te Boome
- Department of Hematology, University Medical Center Utrecht , Utrecht , Netherlands
| | - Jürgen Kuball
- Laboratory for Translational Immunology, University Medical Center Utrecht , Utrecht , Netherlands ; Department of Hematology, University Medical Center Utrecht , Utrecht , Netherlands
| | - Eric Spierings
- Laboratory for Translational Immunology, University Medical Center Utrecht , Utrecht , Netherlands
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High-allelic variability in HLA-C mRNA expression: association with HLA-extended haplotypes. Genes Immun 2014; 15:176-81. [DOI: 10.1038/gene.2014.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/06/2013] [Accepted: 12/13/2013] [Indexed: 12/11/2022]
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50
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Kulkarni S, Qi Y, O’hUigin C, Pereyra F, Ramsuran V, McLaren P, Fellay J, Nelson G, Chen H, Liao W, Bass S, Apps R, Gao X, Yuki Y, Lied A, Ganesan A, Hunt PW, Deeks SG, Wolinsky S, Walker BD, Carrington M. Genetic interplay between HLA-C and MIR148A in HIV control and Crohn disease. Proc Natl Acad Sci U S A 2013; 110:20705-10. [PMID: 24248364 PMCID: PMC3870724 DOI: 10.1073/pnas.1312237110] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Variation in the 3' untranslated region (3'UTR) of the HLA-C locus determines binding of the microRNA Hsa-miR-148a, resulting in lower cell surface expression of alleles that bind miR-148a relative to those alleles that escape its binding. The HLA-C 3'UTR variant was shown to associate with HIV control, but like the vast majority of disease associations in a region dense with causal candidates, a direct effect of HLA-C expression level on HIV control was not proven. We demonstrate that a MIR148A insertion/deletion polymorphism associates with its own expression levels, affecting the extent to which HLA-C is down-regulated, the level of HIV control, and the risk of Crohn disease only among those carrying an intact miR-148a binding site in the HLA-C 3'UTR. These data illustrate a direct effect of HLA-C expression level on HIV control that cannot be attributed to other HLA loci in linkage disequilibrium with HLA-C and highlight the rich complexity of genetic interactions in human disease.
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Affiliation(s)
- Smita Kulkarni
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Ying Qi
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Colm O’hUigin
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
| | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Veron Ramsuran
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Paul McLaren
- School of Life Sciences, École Polytechnique Fédérale de Lausanne and Institute of Microbiology, University of Lausanne, 1011 Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne and Institute of Microbiology, University of Lausanne, 1011 Lausanne, Switzerland
| | - George Nelson
- Basic Research Program, Center for Cancer Research Genetics Core, Science Applications International Corporation-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Haoyan Chen
- Department of Dermatology, University of California, San Francisco, CA 94115
- Department of Gastroenterology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute of Digestive Diseases, Shanghai 200001, China
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, CA 94115
| | - Sara Bass
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
| | - Richard Apps
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Yuko Yuki
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Alexandra Lied
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Anuradha Ganesan
- Infectious Disease Clinical Research Program, Uniformed Services University, Bethesda, MD 20817
| | - Peter W. Hunt
- San Francisco General Hospital AIDS Division, University of California, San Francisco, CA 94110; and
| | - Steven G. Deeks
- San Francisco General Hospital AIDS Division, University of California, San Francisco, CA 94110; and
| | - Steven Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology and
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139
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