1
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Wang Y, Seliger B. Identification of RNA-binding protein hnRNP C targeting the 3'UTR of the TAP-associated glycoprotein tapasin in melanoma. Oncoimmunology 2024; 13:2370928. [PMID: 38948930 PMCID: PMC11212565 DOI: 10.1080/2162402x.2024.2370928] [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: 01/26/2024] [Accepted: 06/18/2024] [Indexed: 07/02/2024] Open
Abstract
Deregulation or loss of the human leukocyte antigen class I (HLA-I) molecules on tumor cells leading to inhibition of CD8+ T cell recognition is an important tumor immune escape strategy, which could be caused by a posttranscriptional control of molecules in the HLA-I pathway mediated by RNA-binding proteins (RBPs). So far, there exists only limited information about the interaction of RBPs with HLA-I-associated molecules, but own work demonstrated a binding of the heterogeneous ribonucleoprotein C (hnRNP C) to the 3' untranslated region (UTR) of the TAP-associated glycoprotein tapasin (tpn). In this study, in silico analysis of pan-cancer TCGA datasets revealed that hnRNP C is higher expressed in tumor specimens compared to corresponding normal tissues, which is negatively correlated to tpn expression, T cell infiltration and the overall survival of tumor patients. Functional analysis demonstrated an upregulation of tpn expression upon siRNA-mediated downregulation of hnRNP C, which is accompanied by an increased HLA-I surface expression. Thus, hnRNP C has been identified to target tpn and its inhibition could improve the HLA-I surface expression on melanoma cells suggesting its use as a possible biomarker for T-cell-based tumor immunotherapies.
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Affiliation(s)
- Yuan Wang
- Institute for Medical Immunology, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Barbara Seliger
- Institute for Medical Immunology, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
- Institute of Translational Immunology, Medical School “Theodor Fontane”, Brandenburg an der Havel, Germany
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2
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Vasoya D, Connelley T, Tzelos T, Todd H, Ballingall KT. Large scale transcriptional analysis of MHC class I haplotype diversity in sheep. HLA 2024; 103:e15356. [PMID: 38304958 DOI: 10.1111/tan.15356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/15/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Domestic sheep (Ovis aries) have been an important component of livestock agricultural production for thousands of years. Preserving genetic diversity within livestock populations maintains a capacity to respond to changing environments and rapidly evolving pathogens. MHC genetic diversity can influence immune functionality at individual and population levels. Here, we focus on defining functional MHC class I haplotype diversity in a large cohort of Scottish Blackface sheep pre-selected for high levels of MHC class II DRB1 diversity. Using high-throughput amplicon sequencing with three independent sets of barcoded primers we identified 134 MHC class I transcripts within 38 haplotypes. Haplotypes were identified with between two and six MHC class I genes, plus variable numbers of conserved sequences with very low read frequencies. One or two highly transcribed transcripts dominate each haplotype indicative of two highly polymorphic, classical MHC class I genes. Additional clusters of medium, low, and very low expressed transcripts are described, indicative of lower transcribed classical, non-classical and genes whose function remains to be determined.
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Affiliation(s)
- Deepali Vasoya
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
| | - Timothy Connelley
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
| | - Thomas Tzelos
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
- Moredun Research Institute, Pentlands Science Park, Scotland, UK
| | - Helen Todd
- Moredun Research Institute, Pentlands Science Park, Scotland, UK
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3
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Aguiar VRC, Castelli EC, Single RM, Bashirova A, Ramsuran V, Kulkarni S, Augusto DG, Martin MP, Gutierrez-Arcelus M, Carrington M, Meyer D. Comparison between qPCR and RNA-seq reveals challenges of quantifying HLA expression. Immunogenetics 2023; 75:249-262. [PMID: 36707444 PMCID: PMC9883133 DOI: 10.1007/s00251-023-01296-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/11/2023] [Indexed: 01/29/2023]
Abstract
Human leukocyte antigen (HLA) class I and II loci are essential elements of innate and acquired immunity. Their functions include antigen presentation to T cells leading to cellular and humoral immune responses, and modulation of NK cells. Their exceptional influence on disease outcome has now been made clear by genome-wide association studies. The exons encoding the peptide-binding groove have been the main focus for determining HLA effects on disease susceptibility/pathogenesis. However, HLA expression levels have also been implicated in disease outcome, adding another dimension to the extreme diversity of HLA that impacts variability in immune responses across individuals. To estimate HLA expression, immunogenetic studies traditionally rely on quantitative PCR (qPCR). Adoption of alternative high-throughput technologies such as RNA-seq has been hampered by technical issues due to the extreme polymorphism at HLA genes. Recently, however, multiple bioinformatic methods have been developed to accurately estimate HLA expression from RNA-seq data. This opens an exciting opportunity to quantify HLA expression in large datasets but also brings questions on whether RNA-seq results are comparable to those by qPCR. In this study, we analyze three classes of expression data for HLA class I genes for a matched set of individuals: (a) RNA-seq, (b) qPCR, and (c) cell surface HLA-C expression. We observed a moderate correlation between expression estimates from qPCR and RNA-seq for HLA-A, -B, and -C (0.2 ≤ rho ≤ 0.53). We discuss technical and biological factors which need to be accounted for when comparing quantifications for different molecular phenotypes or using different techniques.
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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, SP Brazil ,Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA ,Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Erick C. Castelli
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University, Botucatu, SP Brazil
| | - Richard M. Single
- Department of Mathematics and Statistics, University of Vermont, Burlington, VT USA
| | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD USA ,Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD USA
| | - Veron Ramsuran
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD USA ,Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD USA ,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa ,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Smita Kulkarni
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD USA ,Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD USA ,Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX USA
| | - Danillo G. Augusto
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD USA ,Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD USA ,Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC USA ,Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, PR Brazil
| | - Maureen P. Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD USA ,Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD USA
| | - Maria Gutierrez-Arcelus
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA ,Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD USA ,Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD USA ,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP Brazil
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4
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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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5
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Francisco Junior RDS, Temerozo JR, Ferreira CDS, Martins Y, Souza TML, Medina-Acosta E, de Vasconcelos ATR. Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines. Front Immunol 2022; 13:1101526. [PMID: 36818472 PMCID: PMC9929942 DOI: 10.3389/fimmu.2022.1101526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/19/2022] [Indexed: 02/05/2023] Open
Abstract
Introduction Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional profiles of genes and biological pathways involved in the pathogenesis of COVID-19. Expression allelic imbalance is characterized by a deviation from the Mendelian expected 1:1 expression ratio and is an important source of allele-specific heterogeneity. Expression allelic imbalance can be measured by allele-specific expression analysis (ASE) across heterozygous informative expressed single nucleotide variants (eSNVs). ASE reflects many regulatory biological phenomena that can be assessed by combining genome and transcriptome information. ASE contributes to the interindividual variability associated with the disease. We aim to estimate the transcriptome-wide impact of SARS-CoV-2 infection by analyzing eSNVs. Methods We compared ASE profiles in the human lung cell lines Calu-3, A459, and H522 before and after infection with SARS-CoV-2 using RNA-Seq experiments. Results We identified 34 differential ASE (DASE) sites in 13 genes (HLA-A, HLA-B, HLA-C, BRD2, EHD2, GFM2, GSPT1, HAVCR1, MAT2A, NQO2, SUPT6H, TNFRSF11A, UMPS), all of which are enriched in protein binding functions and play a role in COVID-19. Most DASE sites were assigned to the MHC class I locus and were predominantly upregulated upon infection. DASE sites in the MHC class I locus also occur in iPSC-derived airway epithelium basal cells infected with SARS-CoV-2. Using an RNA-Seq haplotype reconstruction approach, we found DASE sites and adjacent eSNVs in phase (i.e., predicted on the same DNA strand), demonstrating differential haplotype expression upon infection. We found a bias towards the expression of the HLA alleles with a higher binding affinity to SARS-CoV-2 epitopes. Discussion Independent of gene expression compensation, SARS-CoV-2 infection of human lung cell lines induces transcriptional allelic switching at the MHC loci. This suggests a response mechanism to SARS-CoV-2 infection that swaps HLA alleles with poor epitope binding affinity, an expectation supported by publicly available proteome data.
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Affiliation(s)
| | - Jairo R Temerozo
- Laboratory on Thymus Research, Oswaldo Cruz Institute (Fiocruz), Rio de Janeiro, Brazil.,National Institute of Science and Technology on Neuroimmunomodulation, Rio de Janeiro, Brazil
| | - Cristina Dos Santos Ferreira
- Bioinformatics Laboratory (LABINFO), National Laboratory of Scientific Computation (LNCC/MCTIC), Petrópolis, Brazil
| | - Yasmmin Martins
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA), Buenos Aires, Argentina
| | - Thiago Moreno L Souza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil.,Center for Technological Development in Health (CDTS), National Institute for Science and Technology on Innovation on Neglected Diseases Neglected Populations (INCT/IDNP), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Enrique Medina-Acosta
- Molecular Identification and Diagnostics Unit (NUDIM), Laboratory of Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Brazil
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6
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Relevance of Polymorphic KIR and HLA Class I Genes in NK-Cell-Based Immunotherapies for Adult Leukemic Patients. Cancers (Basel) 2021; 13:cancers13153767. [PMID: 34359667 PMCID: PMC8345033 DOI: 10.3390/cancers13153767] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Immunotherapies are promising approaches to curing different acute leukemias. Natural killer (NK) cells are lymphocytes that are efficient in the elimination of leukemic cells. NK-cell-based immunotherapies are particularly attractive, but the landscape of the heterogeneity of NK cells must be deciphered. This review provides an overview of the polymorphic KIR and HLA class I genes that modulate the NK cell repertoire and how these markers can improve the outcomes of patients with acute leukemia. A better knowledge of these genetic markers that are linked to NK cell subsets that are efficient against hematological diseases will optimize hematopoietic stem-cell donor selection and NK immunotherapy design. Abstract Since the mid-1990s, the biology and functions of natural killer (NK) cells have been deeply investigated in healthy individuals and in people with diseases. These effector cells play a particularly crucial role after allogeneic hematopoietic stem-cell transplantation (HSCT) through their graft-versus-leukemia (GvL) effect, which is mainly mediated through polymorphic killer-cell immunoglobulin-like receptors (KIRs) and their cognates, HLA class I ligands. In this review, we present how KIRs and HLA class I ligands modulate the structural formation and the functional education of NK cells. In particular, we decipher the current knowledge about the extent of KIR and HLA class I gene polymorphisms, as well as their expression, interaction, and functional impact on the KIR+ NK cell repertoire in a physiological context and in a leukemic context. In addition, we present the impact of NK cell alloreactivity on the outcomes of HSCT in adult patients with acute leukemia, as well as a description of genetic models of KIRs and NK cell reconstitution, with a focus on emergent T-cell-repleted haplo-identical HSCT using cyclosphosphamide post-grafting (haplo-PTCy). Then, we document how the immunogenetics of KIR/HLA and the immunobiology of NK cells could improve the relapse incidence after haplo-PTCy. Ultimately, we review the emerging NK-cell-based immunotherapies for leukemic patients in addition to HSCT.
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7
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Daniel M, Liang B, Luo M. Assessment of the population coverage of an HIV-1 vaccine targeting sequences surrounding the viral protease cleavage sites in Gag, Pol, or all 12 protease cleavage sites. Vaccine 2021; 39:2676-2683. [PMID: 33863573 DOI: 10.1016/j.vaccine.2021.03.068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/26/2021] [Accepted: 03/19/2021] [Indexed: 01/06/2023]
Abstract
Development of an effective HIV-1 vaccine has been a great challenge faced by the research community. Recently a novel strategy targeting the viral protease cleavage sites (PCSs) has been tested and shown promising results. This T cell-based vaccine strategy depends on individuals expressing certain HLA class I molecules and since each population has unique distributions of HLA class I alleles, population coverage analysis is required to assess feasibility. Utilizing the validated CD8 T cell epitope data from previous studies we conducted coverage analysis of an HIV-1 vaccine targeting the sequences surrounding all 12-PCSs, Gag-PCSs, and Pol-PCSs. The population coverage, average epitope hit, and minimum number of epitopes recognized by 90% of the population (PC90) was compiled for 66 countries and 16 geographical regions using the web tool provided by "Immune Epitope Database and Analysis Resource". Our analysis shows that the coverage for an HIV-1 vaccine targeting sequences surrounding all 12 PCSs, 5 PCSs in Gag or 6 PCSs in Pol can cover ~ 70% to ~ 100% of the populations analyzed. There was no statistical difference in population coverages for the majority of populations examined when comparing the CD8 T cell epitope sets (12-PCSs, Gag-PCSs, and Pol-PCSs). As expected, vaccines targeting more sequences will have more CD8 T cell epitopes, as the mean average epitope hit for the 12-PCSs, Gag-PCSs, and Pol-PCSs across all countries studied was 9.45, 4.76, and 4.74, respectively, and across all geographical regions was 9.76, 4.99, and 4.92, respectively. The average PC90 for the 12-PCSs, Gag-PCSs, and Pol-PCSs across all countries studied was 2.53, 1.31, and 1.41, respectively, and across all geographical regions was 2.24, 1.23, and 1.29, respectively. Thus, vaccines targeting sequences surrounding the HIV-1 PCSs can cover broad populations; however, whether targeting a subset of the PCSs is sufficient to prevent acquisition requires further preclinical investigation.
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Affiliation(s)
- Mathew Daniel
- Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Binhua Liang
- Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada; National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Ma Luo
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada; Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
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8
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Brown NK, Merkens H, Rozemuller EH, Bell D, Bui TM, Kearns J. Reduced PCR-generated errors from a hybrid capture-based NGS assay for HLA typing. Hum Immunol 2021; 82:296-301. [PMID: 33676750 DOI: 10.1016/j.humimm.2021.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/28/2022]
Abstract
Next generation sequencing (NGS) assays are state of the art for HLA genotyping. To sequence on an Illumina sequencer, the DNA of interest must be enriched, fragmented, and bookended with known oligonucleotide sequences, a process known as library construction. Many HLA genotyping assays enrich the target loci by long-range PCR (LR-PCR), prior to fragmentation. This PCR step has been reported to introduce errors in the DNA to be sequenced, including inaccurate replication of repeated sequences, and the in vitro recombination of alleles encoded on separate chromosomes. An alternative library construction method involves fragmentation of genomic DNA, followed by hybrid-capture (HC) enrichment of target HLA loci. This HC-based method involves PCR, but with far fewer cycles. Consequently, the HC method had significantly fewer PCR-induced errors, including more faithful replication of repeated sequences, and the near elimination of recombinant sequences. These improvements likely produce more accurate NGS sequencing data of HLA loci.
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Affiliation(s)
- Nicholas K Brown
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| | | | | | - Derrick Bell
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Thanh-Mai Bui
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jane Kearns
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
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9
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Giuliani C, Verrocchio S, Verginelli F, Bucci I, Grassadonia A, Napolitano G. Hormonal Regulation of the MHC Class I Gene in Thyroid Cells: Role of the Promoter "Tissue-Specific" Region. Front Endocrinol (Lausanne) 2021; 12:749609. [PMID: 34938270 PMCID: PMC8685237 DOI: 10.3389/fendo.2021.749609] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/15/2021] [Indexed: 11/18/2022] Open
Abstract
In previous studies we have demonstrated that the expression of the Major Histocompatibility Complex (MHC) class I gene in thyrocytes is controlled by several hormones, growth factors, and drugs. These substances mainly act on two regions of the MHC class I promoter a "tissue-specific" region (-800 to -676 bp) and a "hormone/cytokines-sensitive" region (-500 to -68 bp). In a previous study, we have shown that the role of the "tissue-specific" region in the MHC class I gene expression is dominant compared to that of the "hormone/cytokines-sensitive" region. In the present report we further investigate the dominant role of the "tissue-specific" region evaluating the effect of thyroid stimulating hormone (TSH), methimazole (MMI), phenylmethimazole (C10), glucose and thymosin-α1. By performing experiments of electrophoretic mobility shift assays (EMSAs) we show that TSH, MMI and C10, which inhibit MHC class I expression, act on the "tissue-specific" region increasing the formation of a silencer complex. Glucose and thymosin-α1, which stimulate MHC class I expression, act decreasing the formation of this complex. We further show that the silencer complex is formed by two distinct members of the transcription factors families activator protein-1 (AP-1) and nuclear factor-kB (NF-kB), c-jun and p65, respectively. These observations are important in order to understand the regulation of MHC class I gene expression in thyroid cells and its involvement in the development of thyroid autoimmunity.
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Affiliation(s)
- Cesidio Giuliani
- Unit of Endocrinology, Department of Medicine and Sciences of Aging, University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
- Centre for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
- *Correspondence: Cesidio Giuliani,
| | - Sara Verrocchio
- Unit of Endocrinology, Department of Medicine and Sciences of Aging, University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
- Centre for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
| | - Fabio Verginelli
- Centre for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
| | - Ines Bucci
- Unit of Endocrinology, Department of Medicine and Sciences of Aging, University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
- Centre for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
| | - Antonino Grassadonia
- Centre for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
- Department of Oral, Medical and Biotechnological Science, University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
| | - Giorgio Napolitano
- Unit of Endocrinology, Department of Medicine and Sciences of Aging, University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
- Centre for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, Chieti, Italy
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10
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Camacho-Bydume C, Wang T, Sees JA, Fernandez-Viña M, Abid MB, Askar M, Beitinjaneh A, Brown V, Castillo P, Chhabra S, Gadalla SM, Hsu JM, Kamoun M, Lazaryan A, Nishihori T, Page K, Schetelig J, Fleischhauer K, Marsh SGE, Paczesny S, Spellman SR, Lee SJ, Hsu KC. Specific Class I HLA Supertypes but Not HLA Zygosity or Expression Are Associated with Outcomes following HLA-Matched Allogeneic Hematopoietic Cell Transplant: HLA Supertypes Impact Allogeneic HCT Outcomes. Transplant Cell Ther 2020; 27:142.e1-142.e11. [PMID: 33053450 DOI: 10.1016/j.bbmt.2020.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/30/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022]
Abstract
Maximizing the probability of antigen presentation to T cells through diversity in HLAs can enhance immune responsiveness and translate into improved clinical outcomes, as evidenced by the association of heterozygosity and supertypes at HLA class I loci with improved survival in patients with advanced solid tumors treated with immune checkpoint inhibitors. We investigated the impact of HLA heterozygosity, supertypes, and surface expression on outcomes in adult and pediatric patients with acute myeloid leukemia (AML), myelodysplastic syndrome, acute lymphoblastic leukemia, and non-Hodgkin lymphoma who underwent 8/8 HLA-matched, T cell replete, unrelated, allogeneic hematopoietic cell transplant (HCT) from 2000 to 2015 using patient data reported to the Center for International Blood and Marrow Transplant Research. HLA class I heterozygosity and HLA expression were not associated with overall survival, relapse, transplant-related mortality (TRM), disease-free survival (DFS), and acute graft-versus-host disease following HCT. The HLA-B62 supertype was associated with decreased TRM in the entire patient cohort (hazard ratio [HR], 0.79; 95% CI, 0.69 to 0.90; P = .00053). The HLA-B27 supertype was associated with worse DFS in patients with AML (HR = 1.21; 95% CI, 1.10 to 1.32; P = .00005). These findings suggest that the survival benefit of HLA heterozygosity seen in solid tumor patients receiving immune checkpoint inhibitors does not extend to patients undergoing allogeneic HCT. Certain HLA supertypes, however, are associated with TRM and DFS, suggesting that similarities in peptide presentation between supertype members play a role in these outcomes. Beyond implications for prognosis following HCT, these findings support the further investigation of these HLA supertypes and the specific immune peptides important for transplant outcomes.
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Affiliation(s)
| | - Tao Wang
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI
| | - Jennifer A Sees
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | | | - Muhammad Bilal Abid
- Divisions of Hematology/Oncology and Infectious Diseases, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, Texas
| | - Amer Beitinjaneh
- Department of Medicine, Division of Transplantation and Cellular Therapy, University of Miami, Miami, Florida
| | - Valerie Brown
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Penn State Hershey Children's Hospital and College of Medicine, Hershey, Pennsylvania
| | - Paul Castillo
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Florida Health Shands Children's Hospital, Gainesville, FL
| | - Saurabh Chhabra
- Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Shahinaz M Gadalla
- Division of Cancer Epidemiology & Genetics, NIH-NCI Clinical Genetics Branch, Rockville, Maryland
| | - Jing-Mei Hsu
- Division of Hematology/Oncology, Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine/New York Presbyterian Hospital, New York, NY
| | - Malek Kamoun
- Deparment of Pathology and Laboratory Medicine, Perelman School of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Aleksandr Lazaryan
- Department of Blood and Marrow Transplant and Cellular Immunotherapy (BMT CI), Moffitt Cancer Center, Tampa, Florida
| | - Taiga Nishihori
- Department of Blood and Marrow Transplant and Cellular Immunotherapy (BMT CI), Moffitt Cancer Center, Tampa, Florida
| | - Kristin Page
- Division of Pediatric Blood and Marrow Transplantation, Duke University Medical Center, Durham, North Carolina
| | - Johannes Schetelig
- Department of Internal Medicine I, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | | | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, London, UK
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Stephanie J Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Medicine, University of Washington, Seattle, WA
| | - Katharine C Hsu
- Department of Medicine, Adult Bone Marrow Transplantation Service, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York; Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
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11
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Grimholt U, Fosse JH, Sundaram AYM. Selective Stimulation of Duplicated Atlantic Salmon MHC Pathway Genes by Interferon-Gamma. Front Immunol 2020; 11:571650. [PMID: 33123146 PMCID: PMC7573153 DOI: 10.3389/fimmu.2020.571650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/25/2020] [Indexed: 11/13/2022] Open
Abstract
Induction of cellular immune responses rely on Major histocompatibility complex (MHC) molecules presenting pathogenic peptides to T cells. Peptide processing, transport, loading and editing is a constitutive process in most cell types, but is accelerated upon infection. Recently, an unexpected complexity in the number of functional genes involved in MHC class I peptide cleavage, peptide transport, peptide loading and editing was found in teleosts, originating from the second and third whole genome duplication events. Salmonids have expanded upon this with functional duplicates also from a fourth unique salmonid whole genome duplication. However, little is known about how individual gene duplicates respond in the context of stimulation. Here we set out to investigate how interferon gamma (IFNg) regulates the transcription of immune genes in Atlantic salmon with particular focus on gene duplicates and MHC pathways. We identified a range of response patterns in Atlantic salmon gene duplicates, with upregulation of all duplicates for some genes, like interferon regulatory factor 1 (IRF1) and interferon induced protein 44-like (IFI44.L), but only induction of one or a few duplicates of other genes, such as TAPBP and ERAP2. A master regulator turned out to be the IRF1 and not the enhanceosome as seen in mammals. If IRF1 also collaborates with CIITA and possibly NLRC5 in regulating IFNg induction of MHCI and MHCII expression in Atlantic salmon, as in zebrafish, remains to be established. Altogether, our results show the importance of deciphering between gene duplicates, as they often respond very differently to stimulation and may have different biological functions.
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12
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Lazaridou MF, Massa C, Handke D, Mueller A, Friedrich M, Subbarayan K, Tretbar S, Dummer R, Koelblinger P, Seliger B. Identification of microRNAs Targeting the Transporter Associated with Antigen Processing TAP1 in Melanoma. J Clin Med 2020; 9:jcm9092690. [PMID: 32825219 PMCID: PMC7563967 DOI: 10.3390/jcm9092690] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 12/15/2022] Open
Abstract
The underlying molecular mechanisms of the aberrant expression of components of the HLA class I antigen processing and presentation machinery (APM) in tumors leading to evasion from T cell-mediated immune surveillance could be due to posttranscriptional regulation mediated by microRNAs (miRs). So far, some miRs controlling the expression of different APM components have been identified. Using in silico analysis and an miR enrichment protocol in combination with small RNA sequencing, miR-26b-5p and miR-21-3p were postulated to target the 3′ untranslated region (UTR) of the peptide transporter TAP1, which was confirmed by high free binding energy and dual luciferase reporter assays. Overexpression of miR-26b-5p and miR-21-3p in melanoma cells downregulated the TAP1 protein and reduced expression of HLA class I cell surface antigens, which could be reverted by miR inhibitors. Moreover, miR-26b-5p overexpression induced a decreased T cell recognition. Furthermore, an inverse expression of miR-26b-5p and miR-21-3p with TAP1 was found in primary melanoma lesions, which was linked with the frequency of CD8+ T cell infiltration. Thus, miR-26-5p and miR-21-3p are involved in the HLA class I-mediated immune escape and might be used as biomarkers or therapeutic targets for HLA class Ilow melanoma cells.
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Affiliation(s)
- Maria-Filothei Lazaridou
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Chiara Massa
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Diana Handke
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Anja Mueller
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Michael Friedrich
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Karthikeyan Subbarayan
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Sandy Tretbar
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Reinhard Dummer
- Institute of Dermatology, University Hospital Zürich, 8091 Zürich, Switzerland;
| | - Peter Koelblinger
- Department of Dermatology and Allergology, University Hospital Salzburg, 5020 Salzburg, Austria;
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
- Correspondence: ; Tel.: +49-(0)-345-557-4054
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13
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Arens R, Scheeren FA. Genetic Screening for Novel Regulators of Immune Checkpoint Molecules. Trends Immunol 2020; 41:692-705. [PMID: 32605801 DOI: 10.1016/j.it.2020.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 06/11/2020] [Accepted: 06/14/2020] [Indexed: 12/31/2022]
Abstract
Inhibitory and stimulatory immune checkpoint molecules play important roles in regulating immune responses. An increasing number of these immune regulators are currently being evaluated as targets in putative anti-cancer therapies. Recently, sophisticated genetic screens have been performed to increase our understanding of immune checkpoint pathways and their immunomodulatory regulators. Here, we summarize novel insights obtained by these screens and discuss new directions to advance possible strategies to treat malignancies.
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Affiliation(s)
- Ramon Arens
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - Ferenc A Scheeren
- Department of Medical Oncology, Leiden University Medical Centre, Leiden, The Netherlands.
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14
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Burr ML, Sparbier CE, Chan KL, Chan YC, Kersbergen A, Lam EYN, Azidis-Yates E, Vassiliadis D, Bell CC, Gilan O, Jackson S, Tan L, Wong SQ, Hollizeck S, Michalak EM, Siddle HV, McCabe MT, Prinjha RK, Guerra GR, Solomon BJ, Sandhu S, Dawson SJ, Beavis PA, Tothill RW, Cullinane C, Lehner PJ, Sutherland KD, Dawson MA. An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in Cancer. Cancer Cell 2019; 36:385-401.e8. [PMID: 31564637 PMCID: PMC6876280 DOI: 10.1016/j.ccell.2019.08.008] [Citation(s) in RCA: 339] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/26/2019] [Accepted: 08/24/2019] [Indexed: 12/21/2022]
Abstract
Loss of MHC class I (MHC-I) antigen presentation in cancer cells can elicit immunotherapy resistance. A genome-wide CRISPR/Cas9 screen identified an evolutionarily conserved function of polycomb repressive complex 2 (PRC2) that mediates coordinated transcriptional silencing of the MHC-I antigen processing pathway (MHC-I APP), promoting evasion of T cell-mediated immunity. MHC-I APP gene promoters in MHC-I low cancers harbor bivalent activating H3K4me3 and repressive H3K27me3 histone modifications, silencing basal MHC-I expression and restricting cytokine-induced upregulation. Bivalent chromatin at MHC-I APP genes is a normal developmental process active in embryonic stem cells and maintained during neural progenitor differentiation. This physiological MHC-I silencing highlights a conserved mechanism by which cancers arising from these primitive tissues exploit PRC2 activity to enable immune evasion.
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Affiliation(s)
- Marian L Burr
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
| | - Christina E Sparbier
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Kah Lok Chan
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
| | - Ariena Kersbergen
- ACRF Cancer Biology and Stem Cell Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | | | - Dane Vassiliadis
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Omer Gilan
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Susan Jackson
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
| | - Lavinia Tan
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sebastian Hollizeck
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Ewa M Michalak
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Hannah V Siddle
- Department of Biological Sciences, University of Southampton, Southampton, UK; Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Michael T McCabe
- Epigenetics Research Unit, Oncology R&D, GlaxoSmithKline, Collegeville, PA, USA
| | - Rab K Prinjha
- Epigenetics Research Unit, Oncology R&D, GlaxoSmithKline, Collegeville, PA, USA; Epigenetics Research Unit, GlaxoSmithKline, Stevenage, UK
| | - Glen R Guerra
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Benjamin J Solomon
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; Centre for Cancer Research, University of Melbourne, Parkville, Australia
| | - Paul A Beavis
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Richard W Tothill
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; Centre for Cancer Research, University of Melbourne, Parkville, Australia; Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Carleen Cullinane
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Paul J Lehner
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Kate D Sutherland
- ACRF Cancer Biology and Stem Cell Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; Centre for Cancer Research, University of Melbourne, Parkville, Australia.
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15
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Development of data-driven models for the flow cytometric crossmatch. Hum Immunol 2019; 80:983-989. [PMID: 31530432 DOI: 10.1016/j.humimm.2019.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/13/2019] [Accepted: 09/05/2019] [Indexed: 01/08/2023]
Abstract
HLA laboratories use virtual crossmatching (VXM) to predict recipient and donor compatibility using HLA antibody data and donor HLA type. Increasingly, transplant centers are utilizing VXM as the final compatibility determination prior to transplant. However, the VXM interpretation is based on HLA experience of individual transplant centers. This study developed data-driven algorithms that predicted flow cytometric crossmatch (FCXM) outcomes using HLA antibody mean fluorescent intensity (MFI) data and donor HLA typing without the need for human interpretation.Two algorithms were evaluated; an MFI Optimal-Threshold model and a Least-Squares-Fitting model. The Optimal-Threshold model correctly determined between 81.5% and 85.5% of T or B-cell responses. A class I antibody MFI threshold of 4670 was optimal for predicting T-cell response while an antibody MFI threshold of 6180 was optimal for predicting B-cell responses. HLA class I antibodies had a 1.47-fold greater influence on FCXM outcomes than class II antibodies. HLA-B antibodies influenced T and B-cell responses more than HLA-A or -C (-B > -A > -C). The Least-Squares-Fitting model increased accuracy to 94.1% and 88.8% for T and B-cell responses, respectively. The algorithms described here provide enhanced FCXM prediction and novel insights into the influence of specific HLA antibodies on the crossmatch outcome.
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16
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Angulo JMC, Cuesta TAC, Menezes EP, Pedroso C, Brites C. HLA-B*14 allele predicts HIV-1 mother-to-child-transmission, in Salvador, Brazil. Braz J Infect Dis 2019; 23:71-78. [PMID: 31112676 PMCID: PMC9425689 DOI: 10.1016/j.bjid.2019.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/22/2019] [Accepted: 04/25/2019] [Indexed: 11/29/2022] Open
Abstract
Background Class I human leukocyte antigens, especially the molecules encoded at the B locus (HLA-B), are associated with AIDS progression risk. Different groups of HLA-B alleles have been associated to a protective effect or increasing susceptibility to HIV infection and are expressed from the earliest stages of gestation. Objective The aim of this study was to evaluate which variants of HLA-B are associated with the risk of HIV vertical transmission in infected pregnant women and in their offspring, in a referral center in Salvador Bahia. Methods We performed HLA-B genotyping in 52 HIV-infected mothers and their children exposed to HIV-1 during pregnancy (N = 65) in Salvador, Brazil. We compared the HLA-B alleles frequency in mothers, uninfected and infected children, according to the use of antiretroviral prophylaxis. Results Absence of antiretroviral antenatal and postnatal prophylaxis was significantly associated with vertical transmission of HIV-1 (p = <0.01, and p = <0.01 respectively). Frequency of HLA-B*14 (29.2%, p = 0.002), HLA-B*18 (16.7%, p = 0.04) or HLA-B*14:1 (20.8%, p = 0.01) alleles subgroups were significantly higher in HIV-1 infected children and persisted (HLA-B*14, p = 0.04) even after adjusting for use of antiretroviral prophylaxis. No significant difference in expression of HLA-B alleles was observed among mothers who transmitted the virus compared to those who did not. Conclusions Expression of HLA-B*14 allele in children exposed to HIV-1 is predictive of vertical transmission and reinforces the important role of genetics in mother-to-child transmission.
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Affiliation(s)
- Juan Manuel Cubillos Angulo
- Laboratório de Pesquisa em Infectologia, Salvador, BA, Brazil; Universidade Federal da Bahia, Escola de Medicina Salvador, Complexo Hospitalar Prof. Edgard Santos, Salvador, BA, Brazil
| | - Taryn Ariadna Castro Cuesta
- Universidade Federal da Bahia, Escola de Medicina Salvador, Complexo Hospitalar Prof. Edgard Santos, Salvador, BA, Brazil
| | - Eliane Pereira Menezes
- Universidade Federal da Bahia, Escola de Medicina Salvador, Complexo Hospitalar Prof. Edgard Santos, Salvador, BA, Brazil
| | - Celia Pedroso
- Laboratório de Pesquisa em Infectologia, Salvador, BA, Brazil
| | - Carlos Brites
- Laboratório de Pesquisa em Infectologia, Salvador, BA, Brazil.
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17
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Abstract
The HLA region is the most polymorphic genes in the human genome and is associated with an increasing number of disease states. Historically, HLA typing methodology has been governed by phenotypic determination. This practice has evolved into the use of molecular methods such as real-time PCR, sequence-specific oligonucleotides, and sequencing-based methods. Numerous studies have identified HLA matching as a key determinate to improve patient outcomes from transplantation. Solid-organ transplants focus on HLA-DRB1 in renal organ allocation while hematopoietic cell transplants focus on HLA-A, -B, -C, -DRB1 matching. The role of HLA typing in the future will be driven by HLA expression, understanding of HLA haplotypes, and rapid HLA typing.
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Affiliation(s)
- Claire H Edgerly
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eric T Weimer
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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18
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Giuliani C, Bucci I, Napolitano G. The Role of the Transcription Factor Nuclear Factor-kappa B in Thyroid Autoimmunity and Cancer. Front Endocrinol (Lausanne) 2018; 9:471. [PMID: 30186235 PMCID: PMC6110821 DOI: 10.3389/fendo.2018.00471] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/31/2018] [Indexed: 12/30/2022] Open
Abstract
Nuclear factor-kappa B (NF-κB) is a ubiquitous transcription factor that is involved in inflammatory and immune responses, as well as in regulation of expression of many other genes related to cell survival, proliferation, and differentiation. In mammals, NF-κB comprises five subunits that can bind to promoter regions of target genes as homodimers or heterodimers. The most common dimer is the p50/p65 heterodimer. The several combinations of dimers that can be formed contribute to the heterogeneous regulation of NF-κB target genes, and this heterogeneity is further increased by interactions of the NF-κB dimers with other transcription factors, such as steroid hormone receptors, activator protein-1 (AP-1), and cAMP response element binding protein (CREB). In the thyroid, several studies have demonstrated the involvement of NF-κB in thyroid autoimmunity, thyroid cancer, and thyroid-specific gene regulation. The role of NF-κB in thyroid autoimmunity was hypothesized more than 20 years ago, after the finding that the binding of distinct NF-κB heterodimers to the major histocompatibility complex class I gene is hormonally regulated. Further studies have shown increased activity of NF-κB in thyroid autoimmune diseases and in thyroid orbitopathy. Increased activity of NF-κB has also been observed in thyroid cancer, where it correlates with a more aggressive pattern. Of particular interest, mutation of some oncogenes or tumor suppressor genes involved in thyroid carcinogenesis results in constitutive activation of the NF-κB pathway. More recently, it has been shown that NF-κB also has a role in thyroid physiology, as it is fundamental for the expression of the main thyroid-specific genes, such as sodium iodide symporter, thyroid peroxidase, thyroglobulin, Pax8, and TTF-1 (NKX2-1).
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19
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Pan N, Lu S, Wang W, Miao F, Sun H, Wu S, Nan D, Qiu J, Xu J, Zhang J. Quantification of classical HLA class I mRNA by allele-specific, real-time polymerase chain reaction for most Han individuals. HLA 2017; 91:112-123. [PMID: 29178661 DOI: 10.1111/tan.13186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 12/29/2022]
Abstract
Recent studies have shown that expression levels of different alleles at the same HLA class I locus can vary dramatically, which might have a broad influence on human disease. However, precise quantification of the relative expression level of each HLA allele is challenging, because distinguishing different alleles on the same locus is difficult. Here, we developed a series of allele-specific, real-time polymerase chain reaction assays for quantifying HLA class I allele mRNA in most Han individuals. The alleles of almost all heterozygous genotypes with a frequency higher than 0.5% in our population (78 alleles on HLA-A locus, 124 alleles on HLA-B locus, and 74 alleles on HLA-C locus) were specifically amplified. The specificity of the amplification was strictly validated by setting the corresponding negative control for each allele of each genotype. The amplification efficiency of each reaction was determined, and the slopes of the reactions were compared. This study provides a tool for detecting the comprehensive expression profile of HLA class I alleles and will be useful not only for the investigation of the molecular mechanism underlying HLA allele expression regulation but also for exploration of immunological mechanisms involving HLA expression in the fields of tumour immune evasion, viral infection, auto-immune disorders, and graft vs host disease after haematopoietic stem cell transplantation.
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Affiliation(s)
- N Pan
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China
| | - S Lu
- Center of Liver Transplantation, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - W Wang
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China
| | - F Miao
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China
| | - H Sun
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China
| | - S Wu
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China.,Stem Cells and Regenerative Medicine Key Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - D Nan
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China
| | - J Qiu
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China.,The Second Affiliated Hospital of Southeast University, Nanjing, China
| | - J Xu
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China.,Huai'an First People's Hospital, Nanjing Medical University, Huai'an, China
| | - J Zhang
- Department of Immunology and Pathogen Biology, Medical School, Southeast University, Nanjing, China
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20
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Nitta D, Kinugawa K, Imamura T, Iino J, Endo M, Amiya E, Hatano M, Kinoshita O, Nawata K, Ono M, Komuro I. Association of the Number of HLA-DR Mismatches With Early Post-transplant Acute Cellular Rejection Among Heart Transplantation Recipients: A Cohort Study in Japanese Population. Transplant Proc 2017; 49:125-129. [PMID: 28104119 DOI: 10.1016/j.transproceed.2016.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Although many risk factors are reported about graft rejection after heart transplantation (HTx), the effect of HLA mismatch (MM) still remains unknown, especially in the Japanese population. The aim of the present study was to investigate the influence of HLA MM on graft rejection among HTx recipients in Japan. METHODS We retrospectively investigated the association of the number of HLA MM including class I (A, B) and class II (DR) (for each locus MM: 0 to 2, total MM: 0 to 6) and the incidence of moderate to severe acute cellular rejection (ACR) confirmed by endomyocardial biopsy (International Society for Heart and Lung Transplantation grade ≥ 3A/2R) within 1 year after HTx. RESULTS Between 2007 and 2014, we had 49 HTx cases in our institute. After excluding those with insufficient data and positive donor-specific antigen, finally 35 patients were enrolled. Moderate to severe ACR was observed in 16 (45.7%) patients. The number of HLA-DR MM was significantly associated with the development of ACR (ACR+: 1.50 ± 0.63, ACR-: 1.11 ± 0.46, P = .029). From univariate analysis, DR MM = 2 was the only independent risk factor for ACR episodes (P = .017). The frequency of ACR within 1 year was significantly higher in those with DR MM = 2 (DR MM = 0 to 1: 0.3 ± 0.47, DR MM = 2: 1.17 ± 1.34 times, P = .007). CONCLUSIONS The number of HLA-DR MMs was associated with the development and recurrence of ACR episodes among HTx recipients within 1 year after transplantation in Japanese population.
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Affiliation(s)
- D Nitta
- Department of Cardiovascular Medicine, The University of Tokyo, Tokyo, Japan
| | - K Kinugawa
- Department of Internal Medicine 2, The University of Toyama, Toyama, Japan.
| | - T Imamura
- Department of Cardiovascular Medicine, The University of Tokyo, Tokyo, Japan
| | - J Iino
- Department of Blood Transfusion, The University of Tokyo, Tokyo, Japan
| | - M Endo
- Department of Organ Transplantation, The University of Tokyo, Tokyo, Japan
| | - E Amiya
- Department of Cardiovascular Medicine, The University of Tokyo, Tokyo, Japan
| | - M Hatano
- Department of Therapeutic Strategy for Heart Failure, The University of Tokyo, Tokyo, Japan
| | - O Kinoshita
- Department of Cardiac Surgery, The University of Tokyo, Tokyo, Japan
| | - K Nawata
- Department of Cardiac Surgery, The University of Tokyo, Tokyo, Japan
| | - M Ono
- Department of Cardiac Surgery, The University of Tokyo, Tokyo, Japan
| | - I Komuro
- Department of Cardiovascular Medicine, The University of Tokyo, Tokyo, Japan
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21
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Hou L, Vierra-Green C, Lazaro A, Brady C, Haagenson M, Spellman S, Hurley CK. Limited HLA sequence variation outside of antigen recognition domain exons of 360 10 of 10 matched unrelated hematopoietic stem cell transplant donor-recipient pairs. HLA 2016; 89:39-46. [PMID: 27976839 DOI: 10.1111/tan.12942] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/24/2016] [Accepted: 11/17/2016] [Indexed: 12/27/2022]
Abstract
Traditional DNA-based typing focuses primarily on interrogating the exons of human leukocyte antigen (HLA) genes that form the antigen recognition domain (ARD). The relevance of mismatching donor and recipient for HLA variation outside the ARD on hematopoietic stem cell transplantation (HSCT) outcomes is unknown. This study was designed to evaluate the frequency of variation outside the ARD in 10 of 10 (HLA-A, -B, -C, -DRB1, -DQB1) matched unrelated donor transplant pairs (n = 360). Next-generation DNA sequencing was used to characterize both HLA exons and introns for HLA-A, -B, -C alleles; exons 2, 3 and the intervening intron for HLA-DRB1 and exons only for HLA-DQA1 and -DQB1. Over 97% of alleles at each locus were matched for their nucleotide sequence outside of the ARD exons. Of the 4320 allele comparisons overall, only 17 allele pairs were mismatched for non-ARD exons, 41 for noncoding regions and 9 for ARD exons. The observed variation between donor and recipient usually involved a single nucleotide difference (88% of mismatches); 88% of the non-ARD exon variants impacted the amino acid sequence. The impact of amino acid sequence variation caused by substitutions in exons outside ARD regions in D-R pairs will be difficult to assess in HSCT outcome studies because these mismatches do not occur very frequently.
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Affiliation(s)
- L Hou
- Department of Pediatrics, Georgetown University, Washington, DC, USA
| | - C Vierra-Green
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - A Lazaro
- Department of Pediatrics, Georgetown University, Washington, DC, USA
| | - C Brady
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - M Haagenson
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - S Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - C K Hurley
- Department of Pediatrics, Georgetown University, Washington, DC, USA.,Department of Oncology, Georgetown University, Washington, DC, USA
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