51
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Malnati MS, Biswas P, Ugolotti E, Di Marco E, Sironi F, Parolini F, Garbarino L, Mazzocco M, Zipeto D, Biassoni R. A fast and reliable method for detecting SNP rs67384697 (Hsa-miR-148a binding site) by a single run of allele-specific real-time PCR. HLA 2020; 96:312-322. [PMID: 32530084 DOI: 10.1111/tan.13971] [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: 03/11/2020] [Revised: 05/22/2020] [Accepted: 06/10/2020] [Indexed: 11/28/2022]
Abstract
Surface expression of human leukocyte antigen (HLA)-class I molecules is critical for modulating T/natural killer lymphocytes' effector functions. Among HLA molecules, HLA-C, the most recently evolved form of class I antigens, is subjected to both transcriptional and multiple post-transcriptional regulation mechanisms affecting its cell surface expression. Among the latter a region placed in the 3' untranslated region of HLA-C transcript contains the single nucleotide polymorphism (SNP) rs67384697 "G-ins/del" that has been found to be strictly associated with surface levels of HLA-C allomorphs because of the effect on the binding site of a microRNA (Hsa-miR-148a). Higher expression of HLA-C has been proved to influence HIV-1 infection via a better control of viremia and a slower disease progression. More importantly, the analysis of SNP rs67384697 "G-ins/del" combined with the evaluation of the HLA-Bw4/-Bw6 C1/C2 supratype, as well as the killer immunoglobulin-like receptor genetic asset, has proved to be pivotal in defining the status of Elite Controllers in the Caucasian population. Here we describe a new reliable and fast method of allele-specific real-time PCR to monitor the integrity/disruption of the binding site of the microRNA Hsa-miR-148a in a high-throughput format that can be easily applied to studies involving large cohorts of individuals.
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Affiliation(s)
- Mauro S Malnati
- Unit of Human Virology, Division of Immunology, Transplantation and Infectious Diseases IRCCS Ospedale San Raffaele, Milan, Italy
| | - Priscilla Biswas
- Unit of Human Virology, Division of Immunology, Transplantation and Infectious Diseases IRCCS Ospedale San Raffaele, Milan, Italy
| | - Elisabetta Ugolotti
- Translational Research Department, Laboratory Medicine, Diagnostics and Services, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Eddi Di Marco
- Translational Research Department, Laboratory Medicine, Diagnostics and Services, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Francesca Sironi
- Unit of Human Virology, Division of Immunology, Transplantation and Infectious Diseases IRCCS Ospedale San Raffaele, Milan, Italy
| | - Francesca Parolini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Lucia Garbarino
- Histocompatibility Laboratory, Galliera Hospital, Genoa, Italy
| | | | - Donato Zipeto
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Roberto Biassoni
- Translational Research Department, Laboratory Medicine, Diagnostics and Services, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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52
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Chitnis NS, Shieh M, Monos D. Regulatory noncoding RNAs and the major histocompatibility complex. Hum Immunol 2020; 82:532-540. [PMID: 32636038 DOI: 10.1016/j.humimm.2020.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/21/2020] [Accepted: 06/09/2020] [Indexed: 12/15/2022]
Abstract
The Major Histocompatibility Complex (MHC) is a 4 Mbp genomic region located on the short arm of chromosome 6. The MHC region contains many key immune-related genes such as Human Leukocyte Antigens (HLAs). There has been a growing realization that, apart from MHC encoded proteins, RNAs derived from noncoding regions of the MHC-specifically microRNAs (miRNAs) and long noncoding RNAs (lncRNAs)-play a significant role in cellular regulation. Furthermore, regulatory noncoding RNAs (ncRNAs) derived from other parts of the genome fine-tune the expression of many immune-related MHC proteins. Although the field of ncRNAs of the MHC is a research area that is still in its infancy, ncRNA regulation of MHC genes has already been shown to be vital for immune function, healthy pregnancy and cellular homeostasis. Dysregulation of this intricate network of ncRNAs can lead to serious perturbations in homeostasis and subsequent disease.
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Affiliation(s)
- Nilesh Sunil Chitnis
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mengkai Shieh
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Dimitri Monos
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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53
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Lazaridou MF, Gonschorek E, Massa C, Friedrich M, Handke D, Mueller A, Jasinski-Bergner S, Dummer R, Koelblinger P, Seliger B. Identification of miR-200a-5p targeting the peptide transporter TAP1 and its association with the clinical outcome of melanoma patients. Oncoimmunology 2020; 9:1774323. [PMID: 32923135 PMCID: PMC7458634 DOI: 10.1080/2162402x.2020.1774323] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/23/2020] [Accepted: 03/29/2020] [Indexed: 12/21/2022] Open
Abstract
Tumor escape is often associated with abnormalities in the surface expression of the human leukocyte antigen class I (HLA-I) antigens thereby limiting CD8+ cytotoxic T cell responses. This impaired HLA-I surface expression can be mediated by deficient expression of components of the antigen processing and presentation machinery (APM) due to epigenetic, transcriptional and/or post-transcriptional processes. Since a discordant mRNA and protein expression pattern of APM components including the peptide transporter associated with antigen processing 1 (TAP1) has been frequently described in tumors of distinct origin, a post-transcriptional control of APM components caused by microRNAs (miR) was suggested. Using an in silico approach, miR-200a-5p has been identified as a candidate miR binding to the 3' untranslated region (UTR) of TAP1. Luciferase reporter assays demonstrated a specific binding of miR-200a-5p to the TAP1 3'-UTR. Furthermore, the miR-200a-5p expression is inversely correlated with the TAP1 protein expression in HEK293T cells and in a panel of melanoma cell lines as well as in primary melanoma lesions. High levels of miR-200a-5p expression were associated with a shorter overall survival of melanoma patients. Overexpression of miR-200a-5p reduced TAP1 levels, which was accompanied by a decreased HLA-I surface expression and an enhanced NK cell sensitivity of melanoma cells. These data show for the first time a miR-mediated control of the peptide transporter subunit TAP1 in melanoma thereby leading to a reduced HLA-I surface expression accompanied by an altered immune recognition and reduced patients' survival. Abbreviations Ab: antibody; ACTB: β-actin; APM: antigen processing and presentation machinery; ATCC: American tissue culture collection; β2-m: β2-microglobulin; BSA: bovine serum albumin; CTL: cytotoxic T lymphocyte; FCS: fetal calf serum; FFL: firefly luciferase; FFPE: formalin-fixed paraffin-embedded; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; HC: heavy chain; HLA: human leukocyte antigen; HLA-I: HLA class I; HRP: horseradish peroxidase; IFN: interferon; im-miR: immune modulatory miRNA; LMP: low molecular weight protein; luc: luciferase; MFI: mean fluorescence intensity; MHC: major histocompatibility complex; miR: microRNA; NC: negative control; NK: natural killer; NSCLC: non-small cell lung carcinoma; OS: overall survival; PBMC: peripheral blood mononuclear cells; RBP: RNA-binding proteins; RL: Renilla; RLU: relative light units; TAP: transporter associated with antigen processing; tpn: tapasin; UTR: untranslated region.
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Affiliation(s)
| | - Evamaria Gonschorek
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chiara Massa
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Michael Friedrich
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Diana Handke
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Anja Mueller
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Simon Jasinski-Bergner
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Reinhard Dummer
- Institute of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Peter Koelblinger
- Department of Dermatology and Allergology, University Hospital Salzburg, Salzburg, Austria
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
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Yamamoto F, Suzuki S, Mizutani A, Shigenari A, Ito S, Kametani Y, Kato S, Fernandez-Viña M, Murata M, Morishima S, Morishima Y, Tanaka M, Kulski JK, Bahram S, Shiina T. Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes by a New Capture RNA-Seq Method. Front Immunol 2020; 11:941. [PMID: 32547543 PMCID: PMC7272581 DOI: 10.3389/fimmu.2020.00941] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/22/2020] [Indexed: 12/19/2022] Open
Abstract
The highly polymorphic human major histocompatibility complex (MHC) also known as the human leukocyte antigen (HLA) encodes class I and II genes that are the cornerstone of the adaptive immune system. Their unique diversity (>25,000 alleles) might affect the outcome of any transplant, infection, and susceptibility to autoimmune diseases. The recent rapid development of new next-generation sequencing (NGS) methods provides the opportunity to study the influence/correlation of this high level of HLA diversity on allele expression levels in health and disease. Here, we describe the NGS capture RNA-Seq method that we developed for genotyping all 12 classical HLA loci (HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, and HLA-DRB5) and assessing their allelic imbalance by quantifying their allele RNA levels. This is a target enrichment method where total RNA is converted to a sequencing-ready complementary DNA (cDNA) library and hybridized to a complex pool of RNA-specific HLA biotinylated oligonucleotide capture probes, prior to NGS. This method was applied to 161 peripheral blood mononuclear cells and 48 umbilical cord blood cells of healthy donors. The differential allelic expression of 10 HLA loci (except for HLA-DRA and HLA-DPA1) showed strong significant differences (P < 2.1 × 10-15). The results were corroborated by independent methods. This newly developed NGS method could be applied to a wide range of biological and medical questions including graft rejections and HLA-related diseases.
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Affiliation(s)
- Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Shingo Suzuki
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Akiko Mizutani
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- Faculty of Health and Medical Science, Teikyo Heisei University, Toshima-ku, Tokyo, Japan
| | - Atsuko Shigenari
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Sayaka Ito
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Yoshie Kametani
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Shunichi Kato
- Division of Hematopoietic Cell Transplantation, Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Marcelo Fernandez-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
- Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Stanford Health Care, Palo Alto, CA, United States
| | - Makoto Murata
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoko Morishima
- Division of Endocrinology, Diabetes and Metabolism, Hematology, Rheumatology, Second Department of Internal Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Yasuo Morishima
- Department of Promotion for Blood and Marrow Transplantation, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Masafumi Tanaka
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Jerzy K Kulski
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- Faculty of Health and Medical Sciences, The University of Western Australia Medical School, Crawley, WA, Australia
| | - Seiamak Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, LabEx TRANSPLANTEX, Fédération Hospitalo-Universitaire OMICARE, Laboratoire International Associé INSERM FJ-HLA-Japan, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Faculté de Médecine, Université de Strasbourg, Service d'Immunologie Biologique, Nouvel Hôpital Civil, Strasbourg, France
| | - Takashi Shiina
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
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Sznarkowska A, Mikac S, Pilch M. MHC Class I Regulation: The Origin Perspective. Cancers (Basel) 2020; 12:cancers12051155. [PMID: 32375397 PMCID: PMC7281430 DOI: 10.3390/cancers12051155] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/27/2020] [Accepted: 05/03/2020] [Indexed: 12/11/2022] Open
Abstract
Viral-derived elements and non-coding RNAs that build up “junk DNA” allow for flexible and context-dependent gene expression. They are extremely dense in the MHC region, accounting for flexible expression of the MHC I, II, and III genes and adjusting the level of immune response to the environmental stimuli. This review brings forward the viral-mediated aspects of the origin and evolution of adaptive immunity and aims to link this perspective with the MHC class I regulation. The complex regulatory network behind MHC expression is largely controlled by virus-derived elements, both as binding sites for immune transcription factors and as sources of regulatory non-coding RNAs. These regulatory RNAs are imbalanced in cancer and associate with different tumor types, making them promising targets for diagnostic and therapeutic interventions.
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56
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Goodson-Gregg FJ, Krepel SA, Anderson SK. Tuning of human NK cells by endogenous HLA-C expression. Immunogenetics 2020; 72:205-215. [PMID: 32219494 PMCID: PMC7182622 DOI: 10.1007/s00251-020-01161-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/11/2020] [Indexed: 12/14/2022]
Abstract
NK cells are primarily responsible for detecting malignant or pathogen-infected cells, and their function is influenced both by stress-associated activating signals and opposing inhibitory signals from receptors that recognize self MHC. The receptors that produce this inhibitory signal shift from the NKG2A:HLA-E system to that of KIR:HLA as the NK cells mature. This maturation is associated with an increase in lytic activity, as well as an increase in HLA-C protein levels controlled by the NK-specific HLA-C promoter, NK-Pro. We propose that modulation of the translatability of HLA-C transcripts in NK cells constitutes an evolutionary mechanism to control cis inhibitory signaling by HLA-C, which fine tunes NK cell activity. Furthermore, the high degree of variability in KIR receptor affinity for HLA alleles, as well as the variable expression levels of both KIR and HLA, suggest an evolutionary requirement for the tuning of NK lytic activity. Various data have demonstrated that mature NK cells may gain or lose lytic activity when placed in different environments. This indicates that NK cell activity may be more a function of constant tuning by inhibitory signals, rather than a static, irreversible "license to kill" granted to mature NK cells. Inhibitory signaling controls the filling of the cytolytic granule reservoir, which becomes depleted if there are insufficient inhibitory signals, leading to a hyporesponsive NK cell. We propose a novel model for the tuning of human NK cell activity via cis interactions in the context of recent findings on the mechanism of NK education.
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Affiliation(s)
- Frederick J Goodson-Gregg
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Stacey A Krepel
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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57
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Nahand JS, Bokharaei-Salim F, Karimzadeh M, Moghoofei M, Karampoor S, Mirzaei HR, Tbibzadeh A, Jafari A, Ghaderi A, Asemi Z, Mirzaei H, Hamblin MR. MicroRNAs and exosomes: key players in HIV pathogenesis. HIV Med 2020; 21:246-278. [PMID: 31756034 PMCID: PMC7069804 DOI: 10.1111/hiv.12822] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2019] [Indexed: 12/29/2022]
Abstract
OBJECTIVES HIV infection is well known to cause impairment of the human immune system, and until recently was a leading cause of death. It has been shown that T lymphocytes are the main targets of HIV. The virus inactivates T lymphocytes by interfering with a wide range of cellular and molecular targets, leading to suppression of the immune system. The objective of this review is to investigate to what extent microRNAs (miRNAs) are involved in HIV pathogenesis. METHODS The scientific literature (Pubmed and Google scholar) for the period 1988-2019 was searched. RESULTS Mounting evidence has revealed that miRNAs are involved in viral replication and immune response, whether by direct targeting of viral transcripts or through indirect modulation of virus-related host pathways. In addition, exosomes have been found to act as nanoscale carriers involved in HIV pathogenesis. These nanovehicles target their cargos (i.e. DNA, RNA, viral proteins and miRNAs) leading to alteration of the behaviour of recipient cells. CONCLUSIONS miRNAs and exosomes are important players in HIV pathogenesis. Additionally, there are potential diagnostic applications of miRNAs as biomarkers in HIV infection.
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Affiliation(s)
- Javid Sadri Nahand
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farah Bokharaei-Salim
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Karimzadeh
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Moghoofei
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Karampoor
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Tbibzadeh
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Jafari
- Department of Medical Nanotechnology, Faculty of Advanced Technology in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Ghaderi
- Department of Addiction Studies, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Michael R. Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 40 Blossom Street, Boston, MA, 02114, USA
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58
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Zhang Y, Liu S, Jiang H, Deng H, Dong C, Shen W, Chen H, Gao C, Xiao S, Liu ZF, Wei D. G 2-quadruplex in the 3'UTR of IE180 regulates Pseudorabies virus replication by enhancing gene expression. RNA Biol 2020; 17:816-827. [PMID: 32070191 DOI: 10.1080/15476286.2020.1731664] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
RNA secondary structure elements in the mRNA 3'-untranslated regions (3'UTR) play important roles in post-transcriptional regulation. RNA structure elements in the viral RNA provide valuable model for studying diverse regulation mechanisms. Herpesvirus genomes are double-stranded DNA with GC-rich sequences, which can be transcribed into abundant GC-rich RNAs. It is valuable to explore the structures and function of those GC-rich RNAs. We identified a G2-quadruplex-forming sequence named PQS18-1 in the 3'UTR of the unique immediate early gene of Pseudorabies virus (PRV), an important member of Alphaherpesvirinae subfamily. The RNA PQS18-1 was folded into parallel G-quadruplex structure, enhancing gene expression. Both non-G-quadruplex mutant and G3-quadruplex mutant in the 3'UTR showed lower gene expression level than the wildtype G2-quadruplex. TMPyP4 destroyed PQS18-1 G2-quadruplex and suppressed gene expression, accordingly reducing PRV replication by one titre in the PK15 cells at 24 h post infection. Our findings indicated that the RNA G2-quadruplex in 3'UTR was essential for high expression of IE180 gene, and it could be a specific post-transcription regulation element in response to small molecules or other macromolecules. This study discovers a novel RNA G2-quadruplex in the 3'UTR of an immediate early gene of alphaherpesvirus and provides a new nucleic acid target for anti-virus drug design.
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Affiliation(s)
- Yashu Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Science, Huazhong Agricultural University , Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University , Wuhan, China
| | - Sisi Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Science, Huazhong Agricultural University , Wuhan, China
| | - Hui Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University , Wuhan, China
| | - Hui Deng
- College of Science, Huazhong Agricultural University , Wuhan, China
| | - Chen Dong
- College of Science, Huazhong Agricultural University , Wuhan, China
| | - Wei Shen
- College of Science, Huazhong Agricultural University , Wuhan, China
| | - Haifeng Chen
- College of Science, Huazhong Agricultural University , Wuhan, China
| | - Chao Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Science, Huazhong Agricultural University , Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University , Wuhan, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University , Wuhan, China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University , Wuhan, China
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Science, Huazhong Agricultural University , Wuhan, China
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59
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Carey BS, Poulton KV, Poles A. HLA‐C expression level in both unstimulated and stimulated human umbilical vein endothelial cells is defined by allotype. HLA 2020; 95:532-542. [DOI: 10.1111/tan.13852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 12/25/2022]
Affiliation(s)
- B. Sean Carey
- Histocompatibility and Immunogenetics, Combined LaboratoryDerriford Hospital Plymouth Devon PL6 8DH UK
| | - Kay V. Poulton
- Transplantation Laboratory, Manchester Royal Infirmary Manchester M13 9WL UK
| | - Anthony Poles
- Histocompatibility and Immunogenetics, Combined LaboratoryDerriford Hospital Plymouth Devon PL6 8DH UK
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60
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Mollan KR, Trumble IM, Reifeis SA, Ferrer O, Bay CP, Baldoni PL, Hudgens MG. Precise and accurate power of the rank-sum test for a continuous outcome. J Biopharm Stat 2020; 30:639-648. [PMID: 32126888 DOI: 10.1080/10543406.2020.1730866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Accurate power calculations are essential in small studies containing expensive experimental units or high-stakes exposures. Herein, power of the Wilcoxon Mann-Whitney rank-sum test of a continuous outcome is formulated using a Monte Carlo approach and defining [Formula: see text] as a measure of effect size, where [Formula: see text] and [Formula: see text] denote random observations from two distributions hypothesized to be equal under the null. Effect size [Formula: see text] fosters productive communications because researchers understand [Formula: see text] is analogous to a fair coin toss, and [Formula: see text] near 0 or 1 represents a large effect. This approach is feasible even without background data. Simulations were conducted comparing the empirical power approach to existing approaches by Rosner & Glynn, Shieh and colleagues, Noether, and O'Brien-Castelloe. Approximations by Noether and O'Brien-Castelloe are shown to be inaccurate for small sample sizes. The Rosner & Glynn and Shieh, Jan & Randles approaches performed well in many small sample scenarios, though both are restricted to location-shift alternatives and neither approach is theoretically justified for small samples. The empirical method is recommended and available in the R package wmwpow.
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Affiliation(s)
- Katie R Mollan
- Department of Biostatistics and Center for AIDS Research, The University of North Carolina , Chapel Hill, North Carolina, USA
| | - Ilana M Trumble
- Department of Biostatistics and Center for AIDS Research, The University of North Carolina , Chapel Hill, North Carolina, USA
| | - Sarah A Reifeis
- Department of Biostatistics and Center for AIDS Research, The University of North Carolina , Chapel Hill, North Carolina, USA
| | - Orlando Ferrer
- Department of Biostatistics and Center for AIDS Research, The University of North Carolina , Chapel Hill, North Carolina, USA
| | - Camden P Bay
- Department of Biostatistics and Center for AIDS Research, The University of North Carolina , Chapel Hill, North Carolina, USA
| | - Pedro L Baldoni
- Department of Biostatistics and Center for AIDS Research, The University of North Carolina , Chapel Hill, North Carolina, USA
| | - Michael G Hudgens
- Department of Biostatistics and Center for AIDS Research, The University of North Carolina , Chapel Hill, North Carolina, USA
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61
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Arora J, Pierini F, McLaren PJ, Carrington M, Fellay J, Lenz TL. HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation. Mol Biol Evol 2020; 37:639-650. [PMID: 31651980 PMCID: PMC7038656 DOI: 10.1093/molbev/msz249] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control. However, the actual mechanism of the observed heterozygote advantage is still elusive. HLA heterozygotes may present a broader array of antigenic viral peptides to immune cells, possibly resulting in a more efficient cytotoxic T-cell response. Alternatively, heterozygosity may simply increase the chance to carry the most protective HLA alleles, as individual HLA alleles are known to differ substantially in their association with HIV-1 control. Here, we used data from 6,311 HIV-1-infected individuals to explore the relative contribution of quantitative and qualitative aspects of peptide presentation in HLA heterozygote advantage against HIV. Screening the entire HIV-1 proteome, we observed that heterozygous individuals exhibited a broader array of HIV-1 peptides presented by their HLA class I alleles. In addition, viral load was negatively correlated with the breadth of the HIV-1 peptide repertoire bound by an individual's HLA variants, particularly at HLA-B. This suggests that heterozygote advantage at HLA-B is at least in part mediated by quantitative peptide presentation. We also observed higher HIV-1 sequence diversity among HLA-B heterozygous individuals, suggesting stronger evolutionary pressure from HLA heterozygosity. However, HLA heterozygotes were also more likely to carry certain HLA alleles, including the highly protective HLA-B*57:01 variant, indicating that HLA heterozygote advantage ultimately results from a combination of quantitative and qualitative effects in antigen presentation.
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Affiliation(s)
- Jatin Arora
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul J McLaren
- JC Wilt Infectious Diseases Research Center, National HIV and Retrovirology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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62
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Cubero EM, Ogbe A, Pedroza-Pacheco I, Cohen MS, Haynes BF, Borrow P, Peppa D. Subordinate Effect of -21M HLA-B Dimorphism on NK Cell Repertoire Diversity and Function in HIV-1 Infected Individuals of African Origin. Front Immunol 2020; 11:156. [PMID: 32132995 PMCID: PMC7041644 DOI: 10.3389/fimmu.2020.00156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/21/2020] [Indexed: 02/02/2023] Open
Abstract
Natural Killer (NK) cells play an important role in antiviral defense and their potent effector function identifies them as key candidates for immunotherapeutic interventions in chronic viral infections. Their remarkable functional agility is achieved by virtue of a wide array of germline-encoded inhibitory and activating receptors ensuring a self-tolerant and tunable repertoire. NK cell diversity is generated by a combination of factors including genetic determinants and infections/environmental factors, which together shape the NK cell pool and functional potential. Recently a genetic polymorphism at position -21 of HLA-B, which influences the supply of HLA-E binding peptides and availability of HLA-E for recognition by the inhibitory NK cell receptor NKG2A, was shown to have a marked influence on NK cell functionality in healthy human cytomegalovirus (HCMV) seronegative Caucasian individuals. In this study, -21 methionine (M)-expressing alleles supplying HLA-E binding peptides were largely poor ligands for inhibitory killer immunoglobulin-like receptors (KIRs), and a bias to NKG2A-mediated education of functionally-potent NK cells was observed. Here, we investigated the effect of this polymorphism on the phenotype and functional capacity of peripheral blood NK cells in a cohort of 36 African individuals with human immunodeficiency virus type 1 (HIV-1)/HCMV co-infection. A similarly profound influence of dimorphism at position -21 of HLA-B on NK cells was not evident in these subjects. They predominantly expressed African specific HLA-B and -C alleles that contribute a distinct supply of NKG2A and KIR ligands, and these genetic differences were compounded by the marked effect of HIV-1/HCMV co-infection on NK cell differentiation. Together, these factors resulted in a lack of correlation of the HLA-B -21 polymorphism with surface abundance of HLA-E and loss of the NK cell functional advantage in subjects with -21M HLA-B alleles. Instead, our data suggest that during HIV/HCMV co-infection exposure of NK cells to an environment that displays altered HLA-E ligands drives adaptive NKG2C+ NK cell expansions influencing effector responses. Increased efforts to understand how NK cells are functionally calibrated to self-HLA during chronic viral infections will pave the way to developing targeted therapeutic interventions to overcome the current barriers to enhancing immune-based antiviral control.
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Affiliation(s)
- Elia Moreno Cubero
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Ane Ogbe
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Myron S. Cohen
- University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Barton F. Haynes
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Dimitra Peppa
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Department of HIV, Mortimer Market Centre, Central and North West London NHS Foundation Trust (CNWL),, London, United Kingdom
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63
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Goodson-Gregg FJ, Rothbard B, Zhang A, Wright PW, Li H, Walker-Sperling VE, Carrington M, Anderson SK. Tuning of NK-Specific HLA-C Expression by Alternative mRNA Splicing. Front Immunol 2020; 10:3034. [PMID: 31998314 PMCID: PMC6966967 DOI: 10.3389/fimmu.2019.03034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/11/2019] [Indexed: 01/05/2023] Open
Abstract
A complex system regulating HLA-C expression in NK cells, driven by an NK-specific promoter that produces alternatively spliced variants of the 5'-UTR has been recently identified. Exon content of the NK-specific 5'-UTR varies strikingly across HLA-C alleles, with some exons being allele specific. In order to investigate the possibility that allelic variation in the 5'-UTR modulates HLA-C expression levels, cDNAs containing several distinct classes of 5'-UTR were compared. Subtle changes in 5'-UTR content had a significant effect on the expression of HLA-C * 03 and HLA-C * 12 cDNA clones, suggesting that alternative splicing can fine-tune the level of protein expression. The HLA-C * 06 allele was found to be highly expressed in relation to the other alleles studied. However, its increased expression was primarily associated with differences in the peptide-binding groove. Although the impact of allele-specific alternative splicing of NK-Pro transcripts on protein levels can be modest when compared with the effect of changes in peptide-loading, alternative splicing may represent an additional regulatory mechanism to fine-tune HLA-C levels within NK cells in distinct tissue environments or at different stages of maturation in order to achieve optimal levels of missing-self recognition.
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Affiliation(s)
- Frederick J Goodson-Gregg
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Brian Rothbard
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Amy Zhang
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Paul W Wright
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Hongchuan Li
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Victoria E Walker-Sperling
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
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64
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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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65
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Papúchová H, Meissner TB, Li Q, Strominger JL, Tilburgs T. The Dual Role of HLA-C in Tolerance and Immunity at the Maternal-Fetal Interface. Front Immunol 2019; 10:2730. [PMID: 31921098 PMCID: PMC6913657 DOI: 10.3389/fimmu.2019.02730] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/07/2019] [Indexed: 12/20/2022] Open
Abstract
To establish a healthy pregnancy, maternal immune cells must tolerate fetal allo-antigens and remain competent to respond to infections both systemically and in placental tissues. Extravillous trophoblasts (EVT) are the most invasive cells of extra-embryonic origin to invade uterine tissues and express polymorphic Human Leucocyte Antigen-C (HLA-C) of both maternal and paternal origin. Thus, HLA-C is a key molecule that can elicit allogeneic immune responses by maternal T and NK cells and for which maternal-fetal immune tolerance needs to be established. HLA-C is also the only classical MHC molecule expressed by EVT that can present a wide variety of peptides to maternal memory T cells and establish protective immunity. The expression of paternal HLA-C by EVT provides a target for maternal NK and T cells, whereas HLA-C expression levels may influence how this response is shaped. This dual function of HLA-C requires tight transcriptional regulation of its expression to balance induction of tolerance and immunity. Here, we critically review new insights into: (i) the mechanisms controlling expression of HLA-C by EVT, (ii) the mechanisms by which decidual NK cells, effector T cells and regulatory T cells recognize HLA-C allo-antigens, and (iii) immune recognition of pathogen derived antigens in context of HLA-C.
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Affiliation(s)
- Henrieta Papúchová
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
| | - Torsten B Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States.,Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Qin Li
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
| | - Jack L Strominger
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
| | - Tamara Tilburgs
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States.,Division of Immunobiology, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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66
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Le Clerc S, Limou S, Zagury JF. Large-Scale "OMICS" Studies to Explore the Physiopatholgy of HIV-1 Infection. Front Genet 2019; 10:799. [PMID: 31572435 PMCID: PMC6754074 DOI: 10.3389/fgene.2019.00799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
In this review, we present the main large-scale experimental studies that have been performed in the HIV/AIDS field. These “omics” studies are based on several technologies including genotyping, RNA interference, and transcriptome or epigenome analysis. Due to the direct connection with disease evolution, there has been a large focus on genotyping cohorts of well-characterized patients through genome-wide association studies (GWASs), but there have also been several invitro studies such as small interfering RNA (siRNA) interference or transcriptome analyses of HIV-1–infected cells. After describing the major results obtained with these omics technologies—including some with a high relevance for HIV-1 treatment—we discuss the next steps that the community needs to embrace in order to derive new actionable therapeutic or diagnostic targets. Only integrative approaches that combine all big data results and consider their complex interactions will allow us to capture the global picture of HIV molecular pathogenesis. This novel challenge will require large collaborative efforts and represents a huge open field for innovative bioinformatics approaches.
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Affiliation(s)
- Sigrid Le Clerc
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation en Urologie et Néphrologie (ITUN), CHU de Nantes, Nantes, France.,Computer Sciences and Mathematics Department, Ecole Centrale de Nantes, Nantes, France
| | - Jean-François Zagury
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
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67
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Friedrich M, Jasinski-Bergner S, Lazaridou MF, Subbarayan K, Massa C, Tretbar S, Mueller A, Handke D, Biehl K, Bukur J, Donia M, Mandelboim O, Seliger B. Tumor-induced escape mechanisms and their association with resistance to checkpoint inhibitor therapy. Cancer Immunol Immunother 2019; 68:1689-1700. [PMID: 31375885 DOI: 10.1007/s00262-019-02373-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 07/28/2019] [Indexed: 12/19/2022]
Abstract
Immunotherapy aims to activate the immune system to fight cancer in a very specific and targeted manner. Despite the success of different immunotherapeutic strategies, in particular antibodies directed against checkpoints as well as adoptive T-cell therapy, the response of patients is limited in different types of cancers. This attributes to escape of the tumor from immune surveillance and development of acquired resistances during therapy. In this review, the different evasion and resistance mechanisms that limit the efficacy of immunotherapies targeting tumor-associated antigens presented by major histocompatibility complex molecules on the surface of the malignant cells are summarized. Overcoming these escape mechanisms is a great challenge, but might lead to a better clinical outcome of patients and is therefore currently a major focus of research.
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Affiliation(s)
- Michael Friedrich
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Simon Jasinski-Bergner
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Maria-Filothei Lazaridou
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Karthikeyan Subbarayan
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Chiara Massa
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Sandy Tretbar
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Anja Mueller
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Diana Handke
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Katharina Biehl
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Jürgen Bukur
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany
| | - Marco Donia
- Department of Oncology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Ofer Mandelboim
- Department of Immunology, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Straße 2, 06110, Halle (Saale), Germany.
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68
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Selection of unrelated donors and cord blood units for hematopoietic cell transplantation: guidelines from the NMDP/CIBMTR. Blood 2019; 134:924-934. [PMID: 31292117 PMCID: PMC6753623 DOI: 10.1182/blood.2019001212] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/24/2019] [Indexed: 01/01/2023] Open
Abstract
Allogeneic hematopoietic cell transplantation involves consideration of both donor and recipient characteristics to guide the selection of a suitable graft. Sufficient high-resolution donor-recipient HLA match is of primary importance in transplantation with adult unrelated donors, using conventional graft-versus-host disease prophylaxis. In cord blood transplantation, optimal unit selection requires consideration of unit quality, cell dose and HLA-match. In this summary, the National Marrow Donor Program (NMDP) and the Center for International Blood and Marrow Transplant Research, jointly with the NMDP Histocompatibility Advisory Group, provide evidence-based guidelines for optimal selection of unrelated donors and cord blood units.
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69
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Nguyen DV, Vidal C, Chu HC, van Nunen S. Human leukocyte antigen-associated severe cutaneous adverse drug reactions: from bedside to bench and beyond. Asia Pac Allergy 2019; 9:e20. [PMID: 31384575 PMCID: PMC6676067 DOI: 10.5415/apallergy.2019.9.e20] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 04/22/2019] [Indexed: 12/11/2022] Open
Abstract
Despite their being uncommon, severe cutaneous adverse drug reactions (SCARs) result in a very great burden of disease. These reactions not only carry with them a high mortality (10%-50%) and high morbidity (60%) with severe ocular complications, alopecia, oral and dental complications and development of autoimmune diseases, but also create a substantial economic burden for patients' families and society. SCARs are, therefore, an important medical problem needing a solution in many countries, especially in Asia. The clinical spectrum of SCARs comprises Stevens-Johnson syndrome, toxic epidermal necrolysis, DRESS (drug rash with eosinophilia and systemic symptoms) (also known as drug hypersensitivity syndrome or drug-induced hypersensitivity syndrome) and acute generalised exanthematous pustulosis. Recent crucial advances in determining genetic susceptibility and understanding how T cells recognise certain medications or their metabolites via the major histocompatibility complex and the effects of cofactors, have led to the implementation of cost-effective screening programs enabling prevention in a number of countries, and to further understanding of the patho-mechanisms involved in SCARs and their significance. In this review, we document comprehensively the journey of SCARs from bedside to bench and outline future perspectives in SCARs research.
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Affiliation(s)
- Dinh Van Nguyen
- Division of Respiratory, Allergy and Clinical Immunology, Vinmec International Hospital, Times City and VinUni Project, Hanoi, Vietnam
- Northern Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Department of Allergy and Clinical Immunology, Hanoi Medical University, Hanoi, Vietnam
| | - Christopher Vidal
- Northern Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Hieu Chi Chu
- Centre of Allergology and Clinical Immunology, Bach Mai Hospital, Hanoi, Vietnam
| | - Sheryl van Nunen
- Northern Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Department of Clinical Immunology and Allergy, Royal North Shore Hospital, Sydney, Australia
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70
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Zhang H, Li W, Gu W, Yan Y, Yao X, Zheng J. MALAT1 accelerates the development and progression of renal cell carcinoma by decreasing the expression of miR-203 and promoting the expression of BIRC5. Cell Prolif 2019; 52:e12640. [PMID: 31250518 PMCID: PMC6797509 DOI: 10.1111/cpr.12640] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 04/30/2019] [Accepted: 05/04/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE We aimed to investigate the roles of the lncRNA MALAT1 in renal cell carcinoma (RCC) progression. METHODS qRT-PCR was used for the assessment of BIRC5, miRNA-203 and MALAT1 expression. Furthermore, the targeted relationships between miR-203 and BIRC5, as well as MALAT1 and miR-203, were predicted by the miRanda/starBase database and verified by dual-luciferase reporter gene assay. The effects of MALAT1, miRNA-203 and BIRC5 on cell proliferation, cell cycle, cell apoptosis, cell invasion and cell migration were studied by using CCK-8, flow cytometry, transwell and wound healing assays, respectively. In addition, the effects of MALAT1 on RCC tumorigenesis were evaluated in vivo by nude mouse tumorigenesis. RESULTS The expression levels of BIRC5 and MALAT1 were higher in RCC tissues and cell lines than in adjacent normal tissues and a normal renal cortex proximal tubule epithelial cell line. In contrast, the expression of miRNA-203 in RCC tissues and cell lines was higher than that in adjacent normal tissues and a normal renal cortex proximal tubule epithelial cell line. BIRC5 and MALAT1 promoted cell proliferation yet decreased the percentage of RCC cells at G0/G1 phase. CONCLUSIONS Our study demonstrated that MALAT1 functions as a miR-203 decoy to increase BIRC5 expression in RCC.
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Affiliation(s)
- Haimin Zhang
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Li
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wenyu Gu
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yang Yan
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xudong Yao
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Junhua Zheng
- Department of Urology, Shanghai General Hospital, The First People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China
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71
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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: 54] [Impact Index Per Article: 10.8] [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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72
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Seshasubramanian V, Venugopal M, D S Kannan A, Naganathan C, Manisekar NK, Kumar YN, Narayan S, Periathiruvadi S. Application of high-throughput next-generation sequencing for HLA typing of DNA extracted from postprocessing cord blood units. HLA 2019; 94:141-146. [PMID: 31056847 DOI: 10.1111/tan.13565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/24/2019] [Accepted: 05/02/2019] [Indexed: 01/05/2023]
Abstract
Cord blood has become an acceptable source of hematopoietic stem cells for transplantation. HLA plays a major role in hematopoietic stem cell transplantation (HSCT). Typing of cord blood samples for HLA alleles has been performed based on the serological and molecular methods. However, with the advent of next-generation sequencing technology, HLA typing becomes more accurate and unambiguous (upto intron level). Contamination of cord blood cells with erythropoietic cells poses a challenge in DNA extraction and downstream application. In the present study, DNA extracted from buffy coat of cord blood samples was typed for HLA-A, -B, -C, DRB1, and DQB1 alleles by Illumina miniseq and the sequences were aligned, phased, and mapped by MIA FORA software algorithms. Most frequent alleles found were HLA A*01:01:01 (17%), A*24:02:01 (15.1%), A*11:01:01 (13.6%), B*40:06:01 (10.7%), C*06:02:01 (17.7%), C*04:01:01 (14.2%), C*15:02:01 (11.4%), C*07:02:01 (10.7%), DRB1*07:01:01 (15.9%), DRB1*10:01:01 (10.2%), DQB1*06:01:01 (17.4%), DQB1*05:01:01 (12.4%), and DQB1*05:03:01 (10.4%). One null allele (A*24:11N), two novel alleles in B loci and three rare alleles (B*40:06:04, B*51:01:05, and C*01:44) were also identified in the present study. This study shows that high-throughput, unambiguous (third-field resolution) HLA typing can be performed on cord blood samples. In order to preserve the precious sample for future use, minimal amount of cord blood samples (postprocessing) could be used for HLA typing purpose.
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73
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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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74
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Mimori T, Yasuda J, Kuroki Y, Shibata TF, Katsuoka F, Saito S, Nariai N, Ono A, Nakai-Inagaki N, Misawa K, Tateno K, Kawai Y, Fuse N, Hozawa A, Kuriyama S, Sugawara J, Minegishi N, Suzuki K, Kinoshita K, Nagasaki M, Yamamoto M. Construction of full-length Japanese reference panel of class I HLA genes with single-molecule, real-time sequencing. THE PHARMACOGENOMICS JOURNAL 2019; 19:136-146. [PMID: 29352165 PMCID: PMC6462828 DOI: 10.1038/s41397-017-0010-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/11/2017] [Accepted: 11/06/2017] [Indexed: 12/30/2022]
Abstract
Human leukocyte antigen (HLA) is a gene complex known for its exceptional diversity across populations, importance in organ and blood stem cell transplantation, and associations of specific alleles with various diseases. We constructed a Japanese reference panel of class I HLA genes (ToMMo HLA panel), comprising a distinct set of HLA-A, HLA-B, HLA-C, and HLA-H alleles, by single-molecule, real-time (SMRT) sequencing of 208 individuals included in the 1070 whole-genome Japanese reference panel (1KJPN). For high-quality allele reconstruction, we developed a novel pipeline, Primer-Separation Assembly and Refinement Pipeline (PSARP), in which the SMRT sequencing and additional short-read data were used. The panel consisted of 139 alleles, which were all extended from known IPD-IMGT/HLA sequences, contained 40 with novel variants, and captured more than 96.5% of allelic diversity in 1KJPN. These newly available sequences would be important resources for research and clinical applications including high-resolution HLA typing, genetic association studies, and analyzes of cis-regulatory elements.
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Affiliation(s)
- Takahiro Mimori
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- Graduate School of Medicine, Tohoku University, Sendai, Japan.
| | - Yoko Kuroki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoko F Shibata
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Sakae Saito
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Naoki Nariai
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, USA
| | - Akira Ono
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | - Kazuharu Misawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Keiko Tateno
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yosuke Kawai
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- Graduate School of Medicine, Tohoku University, Sendai, Japan.
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan.
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
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Abstract
BACKGROUND Autoimmune thrombocytopenia in immune thrombocytopenic purpura (ITP), thrombotic thrombocytopenic purpura (TTP), and heparin-induced thrombocytopenia (HIT) is associated with immunologic degradation of platelets and reduced platelet counts in patients, leading to bleeding risk in patients. Considering the role of human leukocyte antigens (HLA) in the development of immune response, in this review, we examine the relationship between HLA and pathogenesis of the above-mentioned diseases. METHODS Relevant English-language literature was searched and retrieved from Google Scholar search engine and PubMed database (1979 to 2018). The following keywords were used: "Immune Thrombocytopenic purpura," "Thrombotic Thrombocytopenic Purpura," Human Leukocyte Antigen," and "Heparin-induced thrombocytopenia." RESULTS In autoimmune thrombocytopenia, HLA molecule presents self-antigens or foreign antigens similar to self-antigens, provoking an immune response against platelets that results in the degradation of platelets in peripheral blood and possible bleeding in the patient. For example, HLA-DRB1 *11 presents the self-antigen and induces an immune response against ADAMTS13, which is associated with thrombocytopenia in TTP patients. CONCLUSIONS HLA alleles can be used as prognostic biomarkers for immunologic disorders of platelet such as ITP, TTP, and HIT. Different DRB1 alleles enable the assessment of resistance to common ITP treatments as well as disease prognosis. Due to the genetic association between HLA-DR1 and HLA-DQ1 alleles and the role of HLA-DRB1 *11 in TTP, the HLA-DQB1 *02: 02 allele may also play a role in TTP pathogenesis.
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76
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Raghavan M, Yarzabek B, Zaitouna AJ, Krishnakumar S, Ramon DS. Strategies for the measurements of expression levels and half-lives of HLA class I allotypes. Hum Immunol 2019; 80:221-227. [PMID: 30735755 DOI: 10.1016/j.humimm.2019.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 12/05/2018] [Accepted: 02/01/2019] [Indexed: 12/12/2022]
Abstract
HLA class I molecules are highly polymorphic cell surface proteins that trigger immune responses by CD8+ T cells and natural killer (NK) cells. Most humans express six different HLA class I proteins encoded by the HLA-A, HLA-B and HLA-C genes. HLA class I molecules bind to peptide antigens and present these antigens to T cell receptors (TCR) of CD8+ T cells. HLA class I expression levels also regulate NK cell activation. The presence of individual HLA class I genes is linked to many different disease, transplantation and therapy outcomes. An understanding of HLA class I expression and stability patterns is fundamentally important towards a better understanding of the associations of HLA class I genes with disease and treatment outcomes, and towards HLA class I targeting for vaccine development. Quantitative flow cytometry allows for assessments of variations in expression levels of HLA class I molecules in cells from a single blood donor over time, as well as averaged measurements across donors for the same allotype. Since all HLA class I molecules are structurally-related, cellular measurements of the HLA class I expression levels and stabilities of individual variants in human cells require careful choices of donors and antibodies, which are discussed here.
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Affiliation(s)
- Malini Raghavan
- Department of Microbiology and Immunology, Michigan Medicine, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Brogan Yarzabek
- Department of Microbiology and Immunology, Michigan Medicine, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anita J Zaitouna
- Department of Microbiology and Immunology, Michigan Medicine, 1150 W. Medical Center Drive, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sujatha Krishnakumar
- Sirona Genomics, Immucor Inc, Suite A, 1916 Old Middlefield Way Mountain View, CA 94043, USA
| | - Daniel S Ramon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 5777 E. Mayo Blvd, Phoenix, AZ 85054, USA
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77
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The HLA-B -21 dimorphism impacts on NK cell education and clinical outcome of immunotherapy in acute myeloid leukemia. Blood 2019; 133:1479-1488. [PMID: 30647027 DOI: 10.1182/blood-2018-09-874990] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/31/2018] [Indexed: 12/22/2022] Open
Abstract
Natural killer (NK) cell function is regulated by inhibitory receptors, such as the family of killer immunoglobulin-like receptors (KIRs) and the NKG2A/CD94 heterodimer. These receptors recognize cognate HLA class I molecules on potential target cells, and recent studies imply that an HLA-B dimorphism at position -21 in the gene segment encoding the leader peptide dictates whether NK cell regulation primarily relies on the KIRs or the NKG2A/CD94 receptor. The impact of this HLA-B dimorphism on NK cell-mediated destruction of leukemic cells or on the course of leukemia is largely unknown. In a first part of this study, we compared functions of NK cells in subjects carrying HLA-B -21M or 21T using interleukin-2 (IL-2)-activated NK cells and leukemic cells from patients with acute myeloid leukemia (AML). Subjects carrying HLA-B -21M harbored better-educated NKG2A+ NK cells and displayed superior capacity to degranulate lytic granules against KIR ligand-matched primary leukemic blasts. Second, we aimed to define the potential impact of HLA-B -21 variation on the course of AML in a phase 4 trial in which patients received IL-2-based immunotherapy. In keeping with the hypothesis that 21M may be associated with improved NK cell functionality, we observed superior leukemia-free survival and overall survival in -21M patients than in -21T patients during IL-2-based immunotherapy. We propose that genetic variation at HLA-B -21 may determine the antileukemic efficacy of activated NK cells and the clinical benefit of NK cell-activating immunotherapy.
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78
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Monos D, Drake J. Perspective: HLA functional elements outside the antigen recognition domains. Hum Immunol 2019; 80:1-4. [DOI: 10.1016/j.humimm.2018.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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79
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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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80
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Ou G, Liu X, Yang L, Yu H, Ji X, Liu F, Xu H, Qian L, Wang J, Liu Z. Relationship between HLA-DPA1 mRNA expression and susceptibility to hepatitis B. J Viral Hepat 2019; 26:155-161. [PMID: 30267609 DOI: 10.1111/jvh.13012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 09/07/2018] [Indexed: 12/12/2022]
Abstract
Chronic hepatitis B virus (HBV) infection is influenced by both viral and host factors. In genome-wide association studies, the human leucocyte antigen HLA-DPA1 and related polymorphism rs3077 were found to be associated with susceptibility to and spontaneous clearance of HBV infection. Here, we evaluated the association between HLA-DPA1 mRNA expression and the risk of HBV infection. HLA-DPA1 and rs3077 polymorphisms were investigated in 169 patients with chronic HBV and 217 healthy controls (HCs) from Sichuan Han blood donors using sequence-based typing and meta-analysis for HLA-DPA1 alleles. HLA-DPA1 mRNA levels were measured by real-time polymerase chain reaction. The results showed that HLA-DPA1 and rs3077 were associated with HBV infection in the Sichuan population. Rs3077T and DPA1*01:03 played protective roles in HBV infection, and rs3077C and DPA1*02:02 increased susceptibility to HBV infection. We found that the HLA-DPA1 mRNA expression was decreased in the CHB group; in particular, the 3077CT, 3077TT, DPA1*01:03 and DPA1*02:01 alleles showed a significant decrease. Our results demonstrated, for the first time, that expression of HLA-DPA1 alleles and rs3077 affected the risk of HBV infection. Genotypes with lower HLA-DPA1 expression had a greater susceptibility to HBV infection. Thus, further independent studies are needed to strengthen the associations of these polymorphisms with susceptibility to and clearance of HBV infection in Chinese populations.
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Affiliation(s)
- Guojin Ou
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, China.,Clinical Blood Transfusion Research Center, Institute of Blood Transfusion, CAMS & PUMC, Chengdu, China.,Key Laboratory of Transfusion Adverse Reactions, CAMS, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, (Sichuan University), Ministry of Education, Chengdu, China
| | - Xiao Liu
- Deyang People's Hospital, Deyang, China
| | - Liu Yang
- Tianfu New District People's Hospital, Chengdu, China
| | - Hao Yu
- Clinical Blood Transfusion Research Center, Institute of Blood Transfusion, CAMS & PUMC, Chengdu, China.,Key Laboratory of Transfusion Adverse Reactions, CAMS, Chengdu, China
| | - Xin Ji
- Clinical Blood Transfusion Research Center, Institute of Blood Transfusion, CAMS & PUMC, Chengdu, China.,Key Laboratory of Transfusion Adverse Reactions, CAMS, Chengdu, China
| | - Fan Liu
- Clinical Blood Transfusion Research Center, Institute of Blood Transfusion, CAMS & PUMC, Chengdu, China.,Key Laboratory of Transfusion Adverse Reactions, CAMS, Chengdu, China
| | - Haixia Xu
- Clinical Blood Transfusion Research Center, Institute of Blood Transfusion, CAMS & PUMC, Chengdu, China.,Key Laboratory of Transfusion Adverse Reactions, CAMS, Chengdu, China
| | | | - Jue Wang
- Clinical Blood Transfusion Research Center, Institute of Blood Transfusion, CAMS & PUMC, Chengdu, China.,Key Laboratory of Transfusion Adverse Reactions, CAMS, Chengdu, China
| | - Zhong Liu
- Clinical Blood Transfusion Research Center, Institute of Blood Transfusion, CAMS & PUMC, Chengdu, China.,Key Laboratory of Transfusion Adverse Reactions, CAMS, Chengdu, China
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81
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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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82
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83
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Li L, Liu Y, Gorny MK. Association of Diverse Genotypes and Phenotypes of Immune Cells and Immunoglobulins With the Course of HIV-1 Infection. Front Immunol 2018; 9:2735. [PMID: 30534128 PMCID: PMC6275200 DOI: 10.3389/fimmu.2018.02735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/06/2018] [Indexed: 12/19/2022] Open
Abstract
Disease progression among HIV-1-infected individuals varies widely, but the mechanisms underlying this variability remains unknown. Distinct disease outcomes are the consequences of many factors working in concert, including innate and adaptive immune responses, cell-mediated and humoral immunity, and both genetic and phenotypic factors. Current data suggest that these multifaceted aspects in infected individuals should be considered as a whole, rather than as separate unique elements, and that analyses must be performed in greater detail in order to meet the requirements of personalized medicine and guide optimal vaccine design. However, the wide adoption of antiretroviral therapy (ART) influences the implementation of systematic analyses of the HIV-1-infected population. Consequently, fewer data will be available for acquisition in the future, preventing the comprehensive investigations required to elucidate the underpinnings of variability in disease outcome. This review seeks to recapitulate the distinct genotypic and phenotypic features of the immune system, focusing in particular on comparing the surface proteins of immune cells among individuals with different HIV infection outcomes.
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Affiliation(s)
- Liuzhe Li
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Yan Liu
- Institute of Pathogenic Biology, Medical College, University of South China, Hengyang, China
| | - Miroslaw K Gorny
- Department of Pathology, New York University School of Medicine, New York, NY, United States
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84
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Anderson SK. Molecular evolution of elements controlling HLA-C expression: Adaptation to a role as a killer-cell immunoglobulin-like receptor ligand regulating natural killer cell function. HLA 2018; 92:271-278. [PMID: 30232844 PMCID: PMC6251751 DOI: 10.1111/tan.13396] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 01/21/2023]
Abstract
The regulatory elements controlling the transcription of the HLA-A, HLA-B, and HLA-C genes have been extensively studied and compared. However, few studies have considered regulatory differences in the HLA genes from the perspective of their role as ligands for the killer-cell immunoglobulin-like receptor (KIR) family of HLA receptors expressed by natural killer (NK) cells. HLA-C is the most recently evolved gene, and there is considerable evidence pointing to its emergence as a specialized KIR ligand playing a major role in the missing-self recognition system of NK cells. Here I evaluate gene-specific differences in regulatory elements of the HLA genes, showing alterations that are consistent with the adaptation of HLA-C to a role in NK cell regulation.
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Affiliation(s)
- Stephen K Anderson
- Basic Science Program, Cancer and Inflammation Program, Frederick National Laboratory sponsored by the National Cancer Institute, Frederick, Maryland
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85
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Suzuki S, Ranade S, Osaki K, Ito S, Shigenari A, Ohnuki Y, Oka A, Masuya A, Harting J, Baybayan P, Kitazume M, Sunaga J, Morishima S, Morishima Y, Inoko H, Kulski JK, Shiina T. Reference Grade Characterization of Polymorphisms in Full-Length HLA Class I and II Genes With Short-Read Sequencing on the ION PGM System and Long-Reads Generated by Single Molecule, Real-Time Sequencing on the PacBio Platform. Front Immunol 2018; 9:2294. [PMID: 30337930 PMCID: PMC6180199 DOI: 10.3389/fimmu.2018.02294] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/17/2018] [Indexed: 01/21/2023] Open
Abstract
Although NGS technologies fuel advances in high-throughput HLA genotyping methods for identification and classification of HLA genes to assist with precision medicine efforts in disease and transplantation, the efficiency of these methods are impeded by the absence of adequately-characterized high-frequency HLA allele reference sequence databases for the highly polymorphic HLA gene system. Here, we report on producing a comprehensive collection of full-length HLA allele sequences for eight classical HLA loci found in the Japanese population. We augmented the second-generation short read data generated by the Ion Torrent technology with long amplicon spanning consensus reads delivered by the third-generation SMRT sequencing method to create reference grade high-quality sequences of HLA class I and II gene alleles resolved at the genomic coding and non-coding level. Forty-six DNAs were obtained from a reference set used previously to establish the HLA allele frequency data in Japanese subjects. The samples included alleles with a collective allele frequency in the Japanese population of more than 99.2%. The HLA loci were independently amplified by long-range PCR using previously designed HLA-locus specific primers and subsequently sequenced using SMRT and Ion PGM sequencers. The mapped long and short-reads were used to produce a reference library of consensus HLA allelic sequences with the help of the reference-aware software tool LAA for SMRT Sequencing. A total of 253 distinct alleles were determined for 46 healthy subjects. Of them, 137 were novel alleles: 101 SNVs and/or indels and 36 extended alleles at a partial or full-length level. Comparing the HLA sequences from the perspective of nucleotide diversity revealed that HLA-DRB1 was the most divergent among the eight HLA genes, and that the HLA-DPB1 gene sequences diverged into two distinct groups, DP2 and DP5, with evidence of independent polymorphisms generated in exon 2. We also identified two specific intronic variations in HLA-DRB1 that might be involved in rheumatoid arthritis. In conclusion, full-length HLA allele sequencing by third-generation and second-generation technologies has provided polymorphic gene reference sequences at a genomic allelic resolution including allelic variations assigned up to the field-4 level for a stronger foundation in precision medicine and HLA-related disease and transplantation studies.
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Affiliation(s)
- Shingo Suzuki
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Swati Ranade
- Molecular Biology Applications, Pacific Biosciences, Inc, Menlo Park, CA, United States
| | - Ken Osaki
- Pacific Biosciences Division, Tomy Digital Biology Co., Ltd, Tokyo, Japan
| | - Sayaka Ito
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Atsuko Shigenari
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Yuko Ohnuki
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Akira Oka
- The Institute of Medical Sciences, Tokai University, Isehara, Japan
| | | | - John Harting
- Molecular Biology Applications, Pacific Biosciences, Inc, Menlo Park, CA, United States
| | - Primo Baybayan
- Molecular Biology Applications, Pacific Biosciences, Inc, Menlo Park, CA, United States
| | - Miwako Kitazume
- Pacific Biosciences Division, Tomy Digital Biology Co., Ltd, Tokyo, Japan
| | - Junichi Sunaga
- Pacific Biosciences Division, Tomy Digital Biology Co., Ltd, Tokyo, Japan
| | - Satoko Morishima
- Division of Endocrinology, Diabetes, and Metabolism, Hematology, Rheumatology (Second Department of Internal Medicine), Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Yasuo Morishima
- Department of Promotion for Blood and Marrow Transplantation, Aichi Medical University School of Medicine, Nagakute, Japan
| | | | - Jerzy K. Kulski
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Perth, WA, Australia
| | - Takashi Shiina
- Division of Basic Medical Science and Molecular Medicine, Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
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Zipeto D, Serena M, Mutascio S, Parolini F, Diani E, Guizzardi E, Muraro V, Lattuada E, Rizzardo S, Malena M, Lanzafame M, Malerba G, Romanelli MG, Tamburin S, Gibellini D. HIV-1-Associated Neurocognitive Disorders: Is HLA-C Binding Stability to β 2-Microglobulin a Missing Piece of the Pathogenetic Puzzle? Front Neurol 2018; 9:791. [PMID: 30298049 PMCID: PMC6160745 DOI: 10.3389/fneur.2018.00791] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/03/2018] [Indexed: 01/09/2023] Open
Abstract
AIDS dementia complex (ADC) and HIV-associated neurocognitive disorders (HAND) are complications of HIV-1 infection. Viral infections are risk factors for the development of neurodegenerative disorders. Aging is associated with low-grade inflammation in the brain, i.e., the inflammaging. The molecular mechanisms linking immunosenescence, inflammaging and the pathogenesis of neurodegenerative disorders, such as Alzheimer's disease (AD) and Parkinson's disease, are largely unknown. ADC and HAND share some pathological features with AD and may offer some hints on the relationship between viral infections, neuroinflammation, and neurodegeneration. β2-microglobulin (β2m) is an important pro-aging factor that interferes with neurogenesis and worsens cognitive functions. Several studies published in the 80-90s reported high levels of β2m in the cerebrospinal fluid of patients with ADC. High levels of β2m have also been detected in AD. Inflammatory diseases in elderly people are associated with polymorphisms of the MHC-I locus encoding HLA molecules that, by associating with β2m, contribute to cellular immunity. We recently reported that HLA-C, no longer associated with β2m, is incorporated into HIV-1 virions, determining an increase in viral infectivity. We also documented the presence of HLA-C variants more or less stably linked to β2m. These observations led us to hypothesize that some variants of HLA-C, in the presence of viral infections, could determine a greater release and accumulation of β2m, which in turn, may be involved in triggering and/or sustaining neuroinflammation. ADC is the most severe form of HAND. To explore the role of HLA-C in ADC pathogenesis, we analyzed the frequency of HLA-C variants with unstable binding to β2m in a group of patients with ADC. We found a higher frequency of unstable HLA-C alleles in ADC patients, and none of them was harboring stable HLA-C alleles in homozygosis. Our data suggest that the role of HLA-C variants in ADC/HAND pathogenesis deserves further studies. If confirmed in a larger number of samples, this finding may have practical implication for a personalized medicine approach and for developing new therapies to prevent HAND. The exploration of HLA-C variants as risk factors for AD and other neurodegenerative disorders may be a promising field of study.
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Affiliation(s)
- Donato Zipeto
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Michela Serena
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Simona Mutascio
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Francesca Parolini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Erica Diani
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | | | | | | | | | - Marina Malena
- U.O.S. Infectious Diseases, AULSS 9 Scaligera, Verona, Italy
| | | | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Maria Grazia Romanelli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Stefano Tamburin
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Davide Gibellini
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
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Kelly A, Trowsdale J. Genetics of antigen processing and presentation. Immunogenetics 2018; 71:161-170. [PMID: 30215098 PMCID: PMC6394470 DOI: 10.1007/s00251-018-1082-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/24/2018] [Indexed: 12/31/2022]
Abstract
Immune response to disease requires coordinated expression of an army of molecules. The highly polymorphic MHC class I and class II molecules are key to control of specificity of antigen presentation. Processing of the antigen, to peptides or other moieties, requires other sets of molecules. For classical class I, this includes TAP peptide transporters, proteasome components and Tapasin, genes which are encoded within the MHC. Similarly, HLA-DO and -DM, which influence presentation by HLA class II molecules, are encoded in the MHC region. Analysis of MHC mutants, including point mutations and large deletions, has been central to understanding the roles of these genes. Mouse genetics has also played a major role. Many other genes have been identified including those controlling expression of HLA class I and class II at the transcriptional level. Another genetic approach that has provided insight has been the analysis of microorganisms, including viruses and bacteria that escape immune recognition by blocking these antigen processing and presentation pathways. Here, we provide a brief history of the genetic approaches, both traditional and modern, that have been used in the quest to understand antigen processing and presentation.
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Affiliation(s)
- Adrian Kelly
- Department of Pathology, University of Cambridge, Cambridge, CB21QP, UK
| | - John Trowsdale
- Department of Pathology, University of Cambridge, Cambridge, CB21QP, UK.
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88
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Ramsuran V, Ewy R, Nguyen H, Kulkarni S. Variation in the Untranslated Genome and Susceptibility to Infections. Front Immunol 2018; 9:2046. [PMID: 30245696 PMCID: PMC6137953 DOI: 10.3389/fimmu.2018.02046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 08/20/2018] [Indexed: 12/11/2022] Open
Abstract
The clinical outcomes of infections are highly variable among individuals and are determined by complex host-pathogen interactions. Genome-wide association studies (GWAS) are powerful tools to unravel common genetic variations that are associated with disease risk and clinical outcomes. However, GWAS has only rarely revealed information on the exact genetic elements and their effects underlying an association because the majority of the hits are within non-coding regions. Some of the variants or the linked polymorphisms are now being discovered to have functional significance, such as regulatory elements in the promoter and enhancer regions or the microRNA binding sites in the 3′untranslated region of the protein-coding genes, which influence transcription, RNA stability, and translation of the protein-coding genes. However, only 3% of the entire transcriptome is protein-coding, signifying that non-coding RNAs represent most of the transcripts. Thus, a large portion of previously identified intergenic GWAS single nucleotide polymorphisms (SNPs) is in the non-coding RNAs. The non-coding RNAs form a large-scale regulatory network across the transcriptome, greatly expanding the complexity of gene regulation. Accumulating evidence also suggests that the “non-coding” genome regions actively regulate the highly dynamic three dimensional (3D) chromatin structures, which are critical for genome function. Epigenetic modulation like DNA methylation and histone modifications further affect chromatin accessibility and gene expression adding another layer of complexity to the functional interpretation of genetic variation associated with disease outcomes. We provide an overview of the current information on the influence of variation in these “untranslated” regions of the human genome on infectious diseases. The focus of this review is infectious disease-associated polymorphisms and gene regulatory mechanisms of pathophysiological relevance.
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Affiliation(s)
- Veron Ramsuran
- Centre for the AIDS Programme of Research in South Africa, KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rodger Ewy
- Genetics Department, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Hoang Nguyen
- Genetics Department, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Smita Kulkarni
- Genetics Department, Texas Biomedical Research Institute, San Antonio, TX, United States
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89
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Mari L, Hoefnagel SJM, Zito D, van de Meent M, van Endert P, Calpe S, Sancho Serra MDC, Heemskerk MHM, van Laarhoven HWM, Hulshof MCCM, Gisbertz SS, Medema JP, van Berge Henegouwen MI, Meijer SL, Bergman JJGHM, Milano F, Krishnadath KK. microRNA 125a Regulates MHC-I Expression on Esophageal Adenocarcinoma Cells, Associated With Suppression of Antitumor Immune Response and Poor Outcomes of Patients. Gastroenterology 2018; 155:784-798. [PMID: 29885883 DOI: 10.1053/j.gastro.2018.06.030] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 05/26/2018] [Accepted: 06/01/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Immune checkpoint inhibition may affect growth or progression of highly aggressive cancers, such as esophageal adenocarcinoma (EAC). We investigated the regulation of expression of major histocompatibility complex, class 1 (MHC-I) proteins (encoded by HLA-A, HLA-B, and HLA-C) and the immune response to EACs in patient samples. METHODS We performed quantitative polymerase chain reaction array analyses of OE33 cells and OE19 cells, which express different levels of the ATP binding cassette subfamily B member 1 (TAP1) and TAP2, required for antigen presentation by MHC-I, to identify microRNAs (miRNAs) that regulate their expression. We performed luciferase assays to validate interactions between miRNAs and potential targets. We overexpressed candidate miRNAs in OE33, FLO-1, and OACP4 C cell lines and performed quantitative polymerase chain reaction, immunoblot, and flow cytometry analyses to identify changes in messenger RNA (mRNA) and protein expression; we studied the effects of cytotoxic T cells. We performed miRNA in situ hybridization, RNA-sequencing, and immunohistochemical analyses of tumor tissues from 51 untreated patients with EAC in the Netherlands. Clinical and survival data were collected for patients, and EAC subtypes were determined. RESULTS We found OE19 cells to have increased levels of 7 miRNAs. Of these, we found binding sites for miRNA 125a (MIR125a)-5p in the 3' untranslated region of the TAP2 mRNA and binding sites for MIR148a-3p in 3' untranslated regions of HLA-A, HLA-B, and HLA-C mRNAs. Overexpression of these miRNAs reduced expression of TAP2 in OE33, FLO-1, and OACP4 C cells, and reduced cell-surface levels of MHC-I. OE33 cells that expressed the viral peptide BZLF1 were killed by cytotoxic T cells, whereas OE33 that overexpressed MIR125a-5p or MIR 148a along with BZLF1 were not. In EAC and nontumor tissues, levels of MIR125a-5p correlated inversely with levels of TAP2 protein. High expression of TAP1 by EAC correlated with significantly shorter overall survival times of patients. EACs that expressed high levels of TAP1 and genes involved in antigen presentation also expressed high levels of genes that regulate the adaptive immune response, PD-L1, PD-L2, and IDO1; these EACs had a poor response to neoadjuvant chemoradiotherapy and associated with shorter overall survival times of patients. CONCLUSIONS In studies of EAC cell lines and tumor tissues, we found increased levels of MIR125a-5p and MIR148a-3p to reduce levels of TAP2 and MHC-I, required for antigen presentation. High expression of MHC-I molecules by EAC correlated with markers of an adaptive immune response and significantly shorter overall survival times of patients.
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Affiliation(s)
- Luigi Mari
- Center for Experimental and Molecular Medicine, Department of Gastroenterology and Hepatology, Cancer Center Amsterdam, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Sanne J M Hoefnagel
- Center for Experimental and Molecular Medicine, Department of Gastroenterology and Hepatology, Cancer Center Amsterdam, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Domenico Zito
- Comprehensive Cancer Center, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio
| | - Marian van de Meent
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter van Endert
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Université Paris Descartes, Centre National de la Recherche Scientifique, UMR 8253, Paris, France
| | - Silvia Calpe
- Center for Experimental and Molecular Medicine, Department of Gastroenterology and Hepatology, Cancer Center Amsterdam, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Maria Del Carmen Sancho Serra
- Center for Experimental and Molecular Medicine, Department of Gastroenterology and Hepatology, Cancer Center Amsterdam, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hanneke W M van Laarhoven
- Cancer Center Amsterdam, Laboratory for Experimental Oncology & Radiobiology (LEXOR), AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Maarten C C M Hulshof
- Department of Radiation Oncology, AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Susanne S Gisbertz
- Department of Surgery, AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Jan Paul Medema
- Cancer Center Amsterdam, Center for Experimental & Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology (LEXOR), AMC, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Sybren L Meijer
- Department of Pathology, AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Jacques J G H M Bergman
- Department of Gastroenterology and Hepatology, AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Francesca Milano
- Section of Hematology and Clinical Immunology, Department of Medicine, Center for Hemato-Oncology Research (CREO), University of Perugia, Perugia, Italy
| | - Kausilia K Krishnadath
- Center for Experimental and Molecular Medicine, Department of Gastroenterology and Hepatology, Cancer Center Amsterdam, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, the Netherlands.
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90
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Zhao W, Erle DJ. Widespread Effects of Chemokine 3' Untranslated Regions on mRNA Degradation and Protein Production in Human Cells. THE JOURNAL OF IMMUNOLOGY 2018; 201:1053-1061. [PMID: 29907706 DOI: 10.4049/jimmunol.1800114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/21/2018] [Indexed: 12/16/2022]
Abstract
Chemokines are a large family of chemotactic cytokines that play critical roles in inflammation, development, and diseases. Chemokine expression is highly regulated during development and in response to environmental stimuli. The 3' untranslated regions (3'-UTRs) of mRNA are believed to be important in the control of chemokine gene expression. However, the regulatory effects of most chemokine 3'-UTRs have not been characterized previously. In this work, we systematically studied the effects of 43 CC and CXC chemokine 3'-UTRs on gene expression in eight human cell lines and two types of human primary cells. We found that chemokine 3'-UTRs had a wide spectrum of regulatory effects on mRNA abundance and protein production that were tightly correlated with the effects on mRNA stability. In general, 3'-UTRs had remarkably similar effects across all cell types studied. The presence of AU-rich elements, microRNA targets, and Pumilio binding sites were associated with chemokine 3'-UTR activity but did not fully account for all 3'-UTR activity detected using the reporter assay. Mutational analysis illustrated how specific cis-regulatory elements contributed to the regulatory effect of chemokine 3'-UTRs. These findings bring new insights into the mechanisms by which chemokine expression is regulated by 3'-UTRs.
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Affiliation(s)
- Wenxue Zhao
- Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA 94158; and .,School of Basic Medicine (Shenzhen), Sun Yat-Sen University, Guangzhou 510080, People's Republic of China
| | - David J Erle
- Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA 94158; and
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91
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Ellwanger JH, Zambra FMB, Guimarães RL, Chies JAB. MicroRNA-Related Polymorphisms in Infectious Diseases-Tiny Changes With a Huge Impact on Viral Infections and Potential Clinical Applications. Front Immunol 2018; 9:1316. [PMID: 29963045 PMCID: PMC6010531 DOI: 10.3389/fimmu.2018.01316] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/28/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are single-stranded sequences of non-coding RNA with approximately 22 nucleotides that act posttranscriptionally on gene expression. miRNAs are important gene regulators in physiological contexts, but they also impact the pathogenesis of various diseases. The role of miRNAs in viral infections has been explored by different authors in both population-based as well as in functional studies. However, the effect of miRNA polymorphisms on the susceptibility to viral infections and on the clinical course of these diseases is still an emerging topic. Thus, this review will compile and organize the findings described in studies that evaluated the effects of genetic variations on miRNA genes and on their binding sites, in the context of human viral diseases. In addition to discussing the basic aspects of miRNAs biology, we will cover the studies that investigated miRNA polymorphisms in infections caused by hepatitis B virus, hepatitis C virus, human immunodeficiency virus, Epstein–Barr virus, and human papillomavirus. Finally, emerging topics concerning the importance of miRNA genetic variants will be presented, focusing on the context of viral infectious diseases.
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Affiliation(s)
- Joel Henrique Ellwanger
- Laboratório de Imunobiologia e Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Francis Maria Báo Zambra
- Laboratório de Imunobiologia e Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Rafael Lima Guimarães
- Departamento de Genética, Universidade Federal do Pernambuco (UFPE), Recife, Brazil.,Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco (UFPE), Recife, Brazil
| | - José Artur Bogo Chies
- Laboratório de Imunobiologia e Imunogenética, Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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92
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Misra MK, Damotte V, Hollenbach JA. The immunogenetics of neurological disease. Immunology 2018; 153:399-414. [PMID: 29159928 PMCID: PMC5838423 DOI: 10.1111/imm.12869] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/09/2017] [Accepted: 11/14/2017] [Indexed: 12/18/2022] Open
Abstract
Genes encoding antigen-presenting molecules within the human major histocompatibility complex (MHC) account for the highest component of genetic risk for many neurological diseases, such as multiple sclerosis, neuromyelitis optica, Parkinson's disease, Alzheimer's disease, schizophrenia, myasthenia gravis and amyotrophic lateral sclerosis. Myriad genetic, immunological and environmental factors may contribute to an individual's susceptibility to neurological disease. Here, we review and discuss the decades long research on the influence of genetic variation at the MHC locus and the role of immunogenetic killer cell immunoglobulin-like receptor (KIR) loci in neurological diseases, including multiple sclerosis, neuromyelitis optica, Parkinson's disease, Alzheimer's disease, schizophrenia, myasthenia gravis and amyotrophic lateral sclerosis. The findings of immunogenetic association studies are consistent with a polygenic model of inheritance in the heterogeneous and multifactorial nature of complex traits in various neurological diseases. Future investigation is highly recommended to evaluate both coding and non-coding variation in immunogenetic loci using high-throughput high-resolution next-generation sequencing technologies in diverse ethnic groups to fully appreciate their role in neurological diseases.
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Affiliation(s)
- Maneesh K. Misra
- Department of NeurologySan Francisco School of MedicineUniversity of CaliforniaSan FranciscoCAUSA
| | - Vincent Damotte
- Department of NeurologySan Francisco School of MedicineUniversity of CaliforniaSan FranciscoCAUSA
| | - Jill A. Hollenbach
- Department of NeurologySan Francisco School of MedicineUniversity of CaliforniaSan FranciscoCAUSA
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93
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Boegel S, Löwer M, Bukur T, Sorn P, Castle JC, Sahin U. HLA and proteasome expression body map. BMC Med Genomics 2018; 11:36. [PMID: 29587858 PMCID: PMC5872580 DOI: 10.1186/s12920-018-0354-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 03/19/2018] [Indexed: 12/21/2022] Open
Abstract
Background The presentation of HLA peptide complexes to T cells is a highly regulated and tissue specific process involving multiple transcriptionally controlled cellular components. The extensive polymorphism of HLA genes and the complex composition of the proteasome make it difficult to map their expression profiles across tissues. Methods Here we applied a tailored gene quantification pipeline to 4323 publicly available RNA-Seq datasets representing 55 normal tissues and cell types to examine expression profiles of (classical and non-classical) HLA class I, class II and proteasomal genes. Results We generated the first comprehensive expression atlas of antigen presenting-related genes across 56 normal tissues and cell types, including immune cells, pancreatic islets, platelets and hematopoietic stem cells. We found a surprisingly heterogeneous HLA expression pattern with up to 100-fold difference in intra-tissue median HLA abundances. Cells of the immune system and lymphatic organs expressed the highest levels of classical HLA class I (HLA-A,-B,-C), class II (HLA-DQA1,-DQB1,-DPA1,-DPB1,-DRA,-DRB1) and non-classical HLA class I (HLA-E,-F) molecules, whereas retina, brain, muscle, megakaryocytes and erythroblasts showed the lowest abundance. In contrast, we identified a distinct and highly tissue-restricted expression pattern of the non-classical class I gene HLA-G in placenta, pancreatic islets, pituitary gland and testis. While the constitutive proteasome showed relatively constant expression across all tissues, we found the immunoproteasome to be enriched in lymphatic organs and almost absent in immune privileged tissues. Conclusions Here, we not only provide a reference catalog of tissue and cell type specific HLA expression, but also highlight extremely variable expression of the basic components of antigen processing and presentation in different cell types. Our findings indicate that low expression of classical HLA class I molecules together with lack of immunoproteasome components as well as upregulation of HLA-G may be of key relevance to maintain tolerance in immune privileged tissues. Electronic supplementary material The online version of this article (10.1186/s12920-018-0354-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian Boegel
- TRON gGmbH - Translational Oncology at Johannes Gutenberg, University Medical Center gGmbH, Freiligrathstr 12, Mainz, Germany.
| | - Martin Löwer
- TRON gGmbH - Translational Oncology at Johannes Gutenberg, University Medical Center gGmbH, Freiligrathstr 12, Mainz, Germany
| | - Thomas Bukur
- TRON gGmbH - Translational Oncology at Johannes Gutenberg, University Medical Center gGmbH, Freiligrathstr 12, Mainz, Germany
| | - Patrick Sorn
- TRON gGmbH - Translational Oncology at Johannes Gutenberg, University Medical Center gGmbH, Freiligrathstr 12, Mainz, Germany
| | - John C Castle
- TRON gGmbH - Translational Oncology at Johannes Gutenberg, University Medical Center gGmbH, Freiligrathstr 12, Mainz, Germany.,Present address: Agenus Inc, Lexington MA, 02421, USA
| | - Ugur Sahin
- TRON gGmbH - Translational Oncology at Johannes Gutenberg, University Medical Center gGmbH, Freiligrathstr 12, Mainz, Germany
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Nemat-Gorgani N, Hilton HG, Henn BM, Lin M, Gignoux CR, Myrick JW, Werely CJ, Granka JM, Möller M, Hoal EG, Yawata M, Yawata N, Boelen L, Asquith B, Parham P, Norman PJ. Different Selected Mechanisms Attenuated the Inhibitory Interaction of KIR2DL1 with C2 + HLA-C in Two Indigenous Human Populations in Southern Africa. THE JOURNAL OF IMMUNOLOGY 2018; 200:2640-2655. [PMID: 29549179 DOI: 10.4049/jimmunol.1701780] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 02/21/2018] [Indexed: 01/03/2023]
Abstract
The functions of human NK cells in defense against pathogens and placental development during reproduction are modulated by interactions of killer cell Ig-like receptors (KIRs) with HLA-A, -B and -C class I ligands. Both receptors and ligands are highly polymorphic and exhibit extensive differences between human populations. Indigenous to southern Africa are the KhoeSan, the most ancient group of modern human populations, who have highest genomic diversity worldwide. We studied two KhoeSan populations, the Nama pastoralists and the ≠Khomani San hunter-gatherers. Comprehensive next-generation sequence analysis of HLA-A, -B, and -C and all KIR genes identified 248 different KIR and 137 HLA class I, which assort into ∼200 haplotypes for each gene family. All 74 Nama and 78 ≠Khomani San studied have different genotypes. Numerous novel KIR alleles were identified, including three arising by intergenic recombination. On average, KhoeSan individuals have seven to eight pairs of interacting KIR and HLA class I ligands, the highest diversity and divergence of polymorphic NK cell receptors and ligands observed to date. In this context of high genetic diversity, both the Nama and the ≠Khomani San have an unusually conserved, centromeric KIR haplotype that has arisen to high frequency and is different in the two KhoeSan populations. Distinguishing these haplotypes are independent mutations in KIR2DL1, which both prevent KIR2DL1 from functioning as an inhibitory receptor for C2+ HLA-C. The relatively high frequency of C2+ HLA-C in the Nama and the ≠Khomani San appears to have led to natural selection against strong inhibitory C2-specific KIR.
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Affiliation(s)
- Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Hugo G Hilton
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
| | - Meng Lin
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado, Denver, CO 80045.,Department of Biostatistics, University of Colorado, Denver, CO 80045
| | - Justin W Myrick
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
| | - Cedric J Werely
- South African Medical Research Council Centre for Tuberculosis Research, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Julie M Granka
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Marlo Möller
- South African Medical Research Council Centre for Tuberculosis Research, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Eileen G Hoal
- South African Medical Research Council Centre for Tuberculosis Research, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
| | - Makoto Yawata
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, National University of Singapore, Singapore 119077, Singapore.,Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore 117609, Singapore
| | - Nobuyo Yawata
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305.,Section of Ophthalmology, Department of Medicine, Fukuoka Dental College, Fukuoka 814-0193, Japan; and
| | - Lies Boelen
- Section of Immunology, Imperial College London, London SW7 2BX, United Kingdom
| | - Becca Asquith
- Section of Immunology, Imperial College London, London SW7 2BX, United Kingdom
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
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95
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Haidar M, Rchiad Z, Ansari HR, Ben-Rached F, Tajeri S, Latre De Late P, Langsley G, Pain A. miR-126-5p by direct targeting of JNK-interacting protein-2 (JIP-2) plays a key role in Theileria-infected macrophage virulence. PLoS Pathog 2018; 14:e1006942. [PMID: 29570727 PMCID: PMC5892942 DOI: 10.1371/journal.ppat.1006942] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/10/2018] [Accepted: 02/14/2018] [Indexed: 12/12/2022] Open
Abstract
Theileria annulata is an apicomplexan parasite that infects and transforms bovine macrophages that disseminate throughout the animal causing a leukaemia-like disease called tropical theileriosis. Using deep RNAseq of T. annulata-infected B cells and macrophages we identify a set of microRNAs induced by infection, whose expression diminishes upon loss of the hyper-disseminating phenotype of virulent transformed macrophages. We describe how infection-induced upregulation of miR-126-5p ablates JIP-2 expression to release cytosolic JNK to translocate to the nucleus and trans-activate AP-1-driven transcription of mmp9 to promote tumour dissemination. In non-disseminating attenuated macrophages miR-126-5p levels drop, JIP-2 levels increase, JNK1 is retained in the cytosol leading to decreased c-Jun phosphorylation and dampened AP-1-driven mmp9 transcription. We show that variation in miR-126-5p levels depends on the tyrosine phosphorylation status of AGO2 that is regulated by Grb2-recruitment of PTP1B. In attenuated macrophages Grb2 levels drop resulting in less PTP1B recruitment, greater AGO2 phosphorylation, less miR-126-5p associated with AGO2 and a consequent rise in JIP-2 levels. Changes in miR-126-5p levels therefore, underpin both the virulent hyper-dissemination and the attenuated dissemination of T. annulata-infected macrophages.
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Affiliation(s)
- Malak Haidar
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- Inserm U1016, Cnrs UMR8104, Cochin Institute, Paris, France
- Laboratoire de Biologie Cellulaire Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France
| | - Zineb Rchiad
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- Inserm U1016, Cnrs UMR8104, Cochin Institute, Paris, France
- Laboratoire de Biologie Cellulaire Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France
| | - Hifzur Rahman Ansari
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Fathia Ben-Rached
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Shahin Tajeri
- Inserm U1016, Cnrs UMR8104, Cochin Institute, Paris, France
- Laboratoire de Biologie Cellulaire Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France
| | - Perle Latre De Late
- Inserm U1016, Cnrs UMR8104, Cochin Institute, Paris, France
- Laboratoire de Biologie Cellulaire Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France
| | - Gordon Langsley
- Inserm U1016, Cnrs UMR8104, Cochin Institute, Paris, France
- Laboratoire de Biologie Cellulaire Comparative des Apicomplexes, Faculté de Médecine, Université Paris Descartes - Sorbonne Paris Cité, Paris, France
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20 W10 Kita-ku, Sapporo, Japan
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96
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Parham P, Guethlein LA. Genetics of Natural Killer Cells in Human Health, Disease, and Survival. Annu Rev Immunol 2018; 36:519-548. [PMID: 29394121 DOI: 10.1146/annurev-immunol-042617-053149] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Natural killer (NK) cells have vital functions in human immunity and reproduction. In the innate and adaptive immune responses to infection, particularly by viruses, NK cells respond by secreting inflammatory cytokines and killing infected cells. In reproduction, NK cells are critical for genesis of the placenta, the organ that controls the supply of oxygen and nutrients to the growing fetus. Controlling NK cell functions are interactions of HLA class I with inhibitory NK cell receptors. First evolved was the conserved interaction of HLA-E with CD94:NKG2A; later established were diverse interactions of HLA-A, -B, and -C with killer cell immunoglobulin-like receptors. Characterizing the latter interactions is rapid evolution, which distinguishes human populations and all species of higher primate. Driving this evolution are the different and competing selections imposed by pathogens on NK cell-mediated immunity and by the constraints of human reproduction on NK cell-mediated placentation. Promoting rapid evolution is independent segregation of polymorphic receptors and ligands throughout human populations.
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Affiliation(s)
- Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, California 94305, USA; ,
| | - Lisbeth A Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, California 94305, USA; ,
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97
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Kaufman J. Generalists and Specialists: A New View of How MHC Class I Molecules Fight Infectious Pathogens. Trends Immunol 2018; 39:367-379. [PMID: 29396014 PMCID: PMC5929564 DOI: 10.1016/j.it.2018.01.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 12/24/2022]
Abstract
In comparison with the major histocompatibility complexes (MHCs) of typical mammals, the chicken MHC is simple and compact with a single dominantly expressed class I molecule that can determine the immune response. In addition to providing useful information for the poultry industry and allowing insights into the evolution of the adaptive immune system, the simplicity of the chicken MHC has allowed the discovery of phenomena that are more difficult to discern in the more complicated mammalian systems. This review discusses the new concept that poorly expressed promiscuous class I alleles act as generalists to protect against a wide variety of infectious pathogens, while highly expressed fastidious class I alleles can act as specialists to protect against new and dangerous pathogens. A broad overview of classical MHC I expression and bound peptides reveals an inverse correlation between repertoire breadth and cell-surface expression in some chicken and human alleles. Several chicken class I alleles with wide peptide-binding repertoires (promiscuity) are associated with resistance to a variety of common diseases. Conversely, a narrow peptide-binding repertoire (fastidiousness) in some human HLA-B alleles is associated with resistance to HIV progression. Cell-surface expression of some classical class I alleles depends on the regulation of translocation to the cell surface rather than of transcription or translation. MHC translocation is influenced by peptide translocation in chickens and by tapasin interaction in humans.
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Affiliation(s)
- Jim Kaufman
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK; University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge CB2 0ES, UK.
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98
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Ramsuran V, Naranbhai V, Horowitz A, Qi Y, Martin MP, Yuki Y, Gao X, Walker-Sperling V, Del Prete GQ, Schneider DK, Lifson JD, Fellay J, Deeks SG, Martin JN, Goedert JJ, Wolinsky SM, Michael NL, Kirk GD, Buchbinder S, Haas D, Ndung'u T, Goulder P, Parham P, Walker BD, Carlson JM, Carrington M. Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells. Science 2018; 359:86-90. [PMID: 29302013 PMCID: PMC5933048 DOI: 10.1126/science.aam8825] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 10/16/2017] [Accepted: 12/04/2017] [Indexed: 12/12/2022]
Abstract
The highly polymorphic human leukocyte antigen (HLA) locus encodes cell surface proteins that are critical for immunity. HLA-A expression levels vary in an allele-dependent manner, diversifying allele-specific effects beyond peptide-binding preference. Analysis of 9763 HIV-infected individuals from 21 cohorts shows that higher HLA-A levels confer poorer control of HIV. Elevated HLA-A expression provides enhanced levels of an HLA-A-derived signal peptide that specifically binds and determines expression levels of HLA-E, the ligand for the inhibitory NKG2A natural killer (NK) cell receptor. HLA-B haplotypes that favor NKG2A-mediated NK cell licensing (i.e., education) exacerbate the deleterious effect of high HLA-A on HIV control, consistent with NKG2A-mediated inhibition impairing NK cell clearance of HIV-infected targets. Therapeutic blockade of HLA-E:NKG2A interaction may yield benefit in HIV disease.
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Affiliation(s)
- Veron Ramsuran
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Vivek Naranbhai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amir Horowitz
- Department of Oncological Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ying Qi
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Maureen P Martin
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Yuko Yuki
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Victoria Walker-Sperling
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Gregory Q Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Douglas K Schneider
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Steven G Deeks
- Department of Medicine University of California, San Francisco, CA 94143, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143, USA
| | - James J Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Susan Buchbinder
- Department of Medicine University of California, San Francisco, CA 94143, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143, USA
- San Francisco Department of Public Health, HIV Research Section, San Francisco, CA 94102, USA
| | - David Haas
- Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Thumbi Ndung'u
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
- African Health Research Institute, Durban, South Africa
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
| | - Philip Goulder
- African Health Research Institute, Durban, South Africa
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Peter Parham
- Departments of Structural Biology and Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
- African Health Research Institute, Durban, South Africa
- Institute for Medical and Engineering Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
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99
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Regis S, Caliendo F, Dondero A, Bellora F, Casu B, Bottino C, Castriconi R. Main NK cell receptors and their ligands: regulation by microRNAs. AIMS ALLERGY AND IMMUNOLOGY 2018. [DOI: 10.3934/allergy.2018.2.98] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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100
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Meyer D, C Aguiar VR, Bitarello BD, C Brandt DY, Nunes K. A genomic perspective on HLA evolution. Immunogenetics 2018; 70:5-27. [PMID: 28687858 PMCID: PMC5748415 DOI: 10.1007/s00251-017-1017-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/16/2017] [Indexed: 12/20/2022]
Abstract
Several decades of research have convincingly shown that classical human leukocyte antigen (HLA) loci bear signatures of natural selection. Despite this conclusion, many questions remain regarding the type of selective regime acting on these loci, the time frame at which selection acts, and the functional connections between genetic variability and natural selection. In this review, we argue that genomic datasets, in particular those generated by next-generation sequencing (NGS) at the population scale, are transforming our understanding of HLA evolution. We show that genomewide data can be used to perform robust and powerful tests for selection, capable of identifying both positive and balancing selection at HLA genes. Importantly, these tests have shown that natural selection can be identified at both recent and ancient timescales. We discuss how findings from genomewide association studies impact the evolutionary study of HLA genes, and how genomic data can be used to survey adaptive change involving interaction at multiple loci. We discuss the methodological developments which are necessary to correctly interpret genomic analyses involving the HLA region. These developments include adapting the NGS analysis framework so as to deal with the highly polymorphic HLA data, as well as developing tools and theory to search for signatures of selection, quantify differentiation, and measure admixture within the HLA region. Finally, we show that high throughput analysis of molecular phenotypes for HLA genes-namely transcription levels-is now a feasible approach and can add another dimension to the study of genetic variation.
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Affiliation(s)
- Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil.
| | - Vitor R C Aguiar
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Bárbara D Bitarello
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Débora Y C Brandt
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
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