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Ryan JC, Haight C, Niemi EC, Grab JD, Dodge JL, Lanier LL, Monto A. Hepatocellular carcinoma after direct-acting antivirals for hepatitis C is associated with KIR-HLA types predicting weak NK cell-mediated immunity. Eur J Immunol 2024; 54:e2350678. [PMID: 38700055 DOI: 10.1002/eji.202350678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 04/13/2024] [Accepted: 04/18/2024] [Indexed: 05/05/2024]
Abstract
BACKGROUND AND AIMS Second-generation direct-acting antivirals (2G DAA) to cure HCV have led to dramatic clinical improvements. HCV-associated hepatocellular carcinoma (HCC), however, remains common. Impaired immune tumor surveillance may play a role in HCC development. Our cohort evaluated the effects of innate immune types and clinical variables on outcomes including HCC. METHODS Participants underwent full HLA class I/KIR typing and long-term HCV follow-up. RESULTS A total of 353 HCV+ participants were followed for a mean of 7 years. Cirrhosis: 25% at baseline, developed in 12% during follow-up. 158 participants received 2G DAA therapy. HCC developed without HCV therapy in 20 subjects, 24 HCC after HCV therapy, and 10 of these after 2G DAA. Two predictors of HCC among 2G DAA-treated patients: cirrhosis (OR, 10.0, p = 0.002) and HLA/KIR profiles predicting weak natural killer (NK) cell-mediated immunity (NK cell complementation groups 6, 9, 11, 12, OR of 5.1, p = 0.02). Without 2G DAA therapy: cirrhosis was the main clinical predictor of HCC (OR, 30.8, p < 0.0001), and weak NK-cell-mediated immunity did not predict HCC. CONCLUSION Cirrhosis is the main risk state predisposing to HCC, but weak NK-cell-mediated immunity may predispose to post-2G DAA HCC more than intermediate or strong NK-cell-mediated immunity.
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Affiliation(s)
- James C Ryan
- Department of Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
- Division of Gastroenterology, University of California, San Francisco, California, USA
| | - Christina Haight
- Department of Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
| | - Erene C Niemi
- Department of Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
| | - Joshua D Grab
- Department of Medicine, University of California, San Francisco, California, USA
| | - Jennifer L Dodge
- Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Lewis L Lanier
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Alexander Monto
- Department of Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, California, USA
- Division of Gastroenterology, University of California, San Francisco, California, USA
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2
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Sakaue S, Gurajala S, Curtis M, Luo Y, Choi W, Ishigaki K, Kang JB, Rumker L, Deutsch AJ, Schönherr S, Forer L, LeFaive J, Fuchsberger C, Han B, Lenz TL, de Bakker PIW, Okada Y, Smith AV, Raychaudhuri S. Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease. Nat Protoc 2023; 18:2625-2641. [PMID: 37495751 PMCID: PMC10786448 DOI: 10.1038/s41596-023-00853-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 04/27/2023] [Indexed: 07/28/2023]
Abstract
The human leukocyte antigen (HLA) locus is associated with more complex diseases than any other locus in the human genome. In many diseases, HLA explains more heritability than all other known loci combined. In silico HLA imputation methods enable rapid and accurate estimation of HLA alleles in the millions of individuals that are already genotyped on microarrays. HLA imputation has been used to define causal variation in autoimmune diseases, such as type I diabetes, and in human immunodeficiency virus infection control. However, there are few guidelines on performing HLA imputation, association testing, and fine mapping. Here, we present a comprehensive tutorial to impute HLA alleles from genotype data. We provide detailed guidance on performing standard quality control measures for input genotyping data and describe options to impute HLA alleles and amino acids either locally or using the web-based Michigan Imputation Server, which hosts a multi-ancestry HLA imputation reference panel. We also offer best practice recommendations to conduct association tests to define the alleles, amino acids, and haplotypes that affect human traits. Along with the pipeline, we provide a step-by-step online guide with scripts and available software ( https://github.com/immunogenomics/HLA_analyses_tutorial ). This tutorial will be broadly applicable to large-scale genotyping data and will contribute to defining the role of HLA in human diseases across global populations.
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Affiliation(s)
- Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saisriram Gurajala
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle Curtis
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Wanson Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Joyce B Kang
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Laurie Rumker
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Aaron J Deutsch
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Program in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Jonathon LeFaive
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Christian Fuchsberger
- Institute of Genetic Epidemiology, Department of Genetics, Medical University of Innsbruck, Innsbruck, Austria
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Tobias L Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Paul I W de Bakker
- Data and Computational Sciences, Vertex Pharmaceuticals, Boston, MA, USA
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Albert V Smith
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester, Manchester, UK.
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3
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Creary LE, Sacchi N, Mazzocco M, Morris GP, Montero-Martin G, Chong W, Brown CJ, Dinou A, Stavropoulos-Giokas C, Gorodezky C, Narayan S, Periathiruvadi S, Thomas R, De Santis D, Pepperall J, ElGhazali GE, Al Yafei Z, Askar M, Tyagi S, Kanga U, Marino SR, Planelles D, Chang CJ, Fernández-Viña MA. High-resolution HLA allele and haplotype frequencies in several unrelated populations determined by next generation sequencing: 17th International HLA and Immunogenetics Workshop joint report. Hum Immunol 2021; 82:505-522. [PMID: 34030896 PMCID: PMC8315142 DOI: 10.1016/j.humimm.2021.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
The primary goal of the unrelated population HLA diversity (UPHD) component of the 17th International HLA and Immunogenetics Workshop was to characterize HLA alleles at maximum allelic-resolution in worldwide populations and re-evaluate patterns of HLA diversity across populations. The UPHD project included HLA genotype and sequence data, generated by various next-generation sequencing methods, from 4,240 individuals collated from 12 different countries. Population data included well-defined large datasets from the USA and smaller samples from Europe, Australia, and Western Asia. Allele and haplotype frequencies varied across populations from distant geographical regions. HLA genetic diversity estimated at 2- and 4-field allelic resolution revealed that diversity at the majority of loci, particularly for European-descent populations, was lower at the 2-field resolution. Several common alleles with identical protein sequences differing only by intronic substitutions were found in distinct haplotypes, revealing a more detailed characterization of linkage between variants within the HLA region. The examination of coding and non-coding nucleotide variation revealed many examples in which almost complete biunivocal relations between common alleles at different loci were observed resulting in higher linkage disequilibrium. Our reference data of HLA profiles characterized at maximum resolution from many populations is useful for anthropological studies, unrelated donor searches, transplantation, and disease association studies.
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Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA.
| | - Nicoletta Sacchi
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Michela Mazzocco
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Gonzalo Montero-Martin
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA
| | - Winnie Chong
- Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK
| | - Colin J Brown
- Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, London, UK; Faculty of Life Sciences and Medicine, King's College London, University of London, England, UK
| | - Amalia Dinou
- Biomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece
| | | | - Clara Gorodezky
- Laboratory of Immunology and Immunogenetics, Fundación Comparte Vida, A.C. Mexico City, Mexico
| | | | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, USA
| | | | - Jennifer Pepperall
- Welsh Transplant and Immunogenetics Laboratory, Welsh Blood Service, Pontyclun, United Kingdom
| | - Gehad E ElGhazali
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Zain Al Yafei
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical center, Dallas, USA
| | - Shweta Tyagi
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Susana R Marino
- Department of Pathology, The University of Chicago Medicine, Chicago, IL, USA
| | - Dolores Planelles
- Histocompatibility, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain; Grupo Español de Trabajo en Histocompatibilidad e Inmunología del Trasplante (GETHIT), Spanish Society for Immunology, Madrid, Spain
| | | | - Marcelo A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA.
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High-resolution characterization of the structural features and genetic variation of six feline leukocyte antigen class I loci via single molecule, real-time (SMRT) sequencing. Immunogenetics 2021; 73:381-393. [PMID: 34175985 DOI: 10.1007/s00251-021-01221-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/28/2021] [Indexed: 10/21/2022]
Abstract
Of the 12 full-length feline leukocyte antigen class I (FLAI) loci, 3 are presumed to be classical: FLAI-E, FLAI-H, and FLAI-K. As diversity is a class Ia hallmark, multi-allelism is an important surrogate supporting a classical designation, in the absence of direct demonstration of T-cell restriction. Conversely, limited polymorphism at an expressed locus suggests regulation of immune effectors with invariant receptors, and non-classical status. FLAI-A, FLAI-J, FLAI-L, and FLAI-O are putative class Ib genes in cats. For both classes, identifying prevalent variants across outbred populations can illuminate specific genotypes to be prioritized for immune studies, as shared alleles direct shared responses. Since variation is concentrated in exons 2 and 3, which encode the antigen-binding domains, partial-length cloning/sequencing can be used for allele discovery, but is laborious and occasionally ambiguous. Here we develop a targeted approach to FLAI genotyping, using the single-molecule real-time (SMRT) platform, which allows full-length (3.4-kb) reads without assembly. Consensus sequences matched full-length Sanger references. Thirty-one new class Ia genes were found in 17 cats. Alleles segregated strongly by loci, and the origins of formerly difficult-to-assign sequences were resolved. Although not targeted, FLAI-L and FLAI-J, and the pseudogene FLAI-F, were also returned. Eighteen class Ib alleles were identified. Diversity was restricted and outside hypervariable regions. Both class Ib genes were transcriptionally active. Novel alternative splicing of FLAI-L was observed. SMRT sequencing of FLAI amplicons is useful for full-length genotyping at feline class Ia loci. High-throughput sequencing could allow highly accurate allele surveys in large cat cohorts.
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5
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Wang H, Nakajima T, Ito Y, Naito H, Zhao N, Li H, Qiu X, Xia L, Chen J, Wu Q, Li L, Huang H, Yanagiba Y, Qu H, Yatsuya H, Kamijima M. Increased risk of occupational trichloroethylene hypersensitivity syndrome at exposure levels higher than 15 mg/L of urinary trichloroacetic acid, regardless of whether the patients had the HLA-B*13:01 allele. ENVIRONMENTAL RESEARCH 2020; 191:109972. [PMID: 32758551 DOI: 10.1016/j.envres.2020.109972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/18/2020] [Accepted: 07/17/2020] [Indexed: 06/11/2023]
Abstract
Occupational trichloroethylene (TCE) exposure can cause hypersensitivity syndrome (TCE-HS). The human leukocyte antigen (HLA)-B*13:01 is reportedly an important allele involved in TCE-HS onset. However, the threshold exposure level causing TCE-HS in relation to HLA-B*13:01 remains unknown. We conducted a case-control study comprising 37 TCE-HS patients and 97 age- and sex-matched TCE-tolerant controls from the Han Chinese population. Urine and blood of patients were collected on the first day of hospitalization, and those of controls were collected at the end of their shifts. Urinary trichloroacetic acid (TCA) was measured as an exposure marker, and end-of-shift levels in the patients were estimated using the biological half-life of 83.7 h. HLA-B genotype was identified using DNA from blood. Crude odds ratios (ORs) for TCE-HS in the groups with urinary TCA concentration >15 mg/L to ≤50 mg/L and of >50 mg/L were 21.9 [95% confidence interval (CI) 4.2-114.1] and 27.6 (6.1-125.8), respectively, when the group with urinary TCA ≤15 mg/L was used as a reference. The frequency of HLA-B*13:01, the most common allele in the patients, was 62.2% (23/37), which was significantly higher than 17.5% (17/97) in the TCE-tolerant controls, with a crude OR of 8.4 (3.1-22.6). The mutually-adjusted ORs for urinary TCA >15 to ≤50 mg/L, >50 mg/L, and for HLA-B*13:01 were 33.4 (4.1-270.8), 34.0 (5.3-217.1), and 11.0 (2.4-50.7), respectively. In conclusion, reduction of TCE exposure to ≤15 mg/L is required for TCE-HS prevention because urinary TCA concentration >15 mg/L showed increased risk of TCE-HS, regardless of whether the patients had the HLA-B*13:01 allele.
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Affiliation(s)
- Hailan Wang
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Tamie Nakajima
- Department of Life and Health Sciences, Chubu University, 487-8501, Kasugai, Japan.
| | - Yuki Ito
- Department of Occupational and Environmental Health, Nagoya City University Graduate School of Medical Sciences, 467-8601, Nagoya, Japan.
| | - Hisao Naito
- Department of Public Health, Fujita Health University School of Medicine, 470-1192, Toyoake, Japan.
| | - Na Zhao
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Hongling Li
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Xinxiang Qiu
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Lihua Xia
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Jiabin Chen
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Qifeng Wu
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Laiyu Li
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Hanlin Huang
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Yukie Yanagiba
- National Institute of Occupational Safety and Health, 214-8585, Kawasaki, Japan.
| | - Hongyung Qu
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Hiroshi Yatsuya
- Department of Public Health, Fujita Health University School of Medicine, 470-1192, Toyoake, Japan.
| | - Michihiro Kamijima
- Department of Occupational and Environmental Health, Nagoya City University Graduate School of Medical Sciences, 467-8601, Nagoya, Japan.
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Benencio P, Fraile Gonzalez SA, Ducasa N, Page K, Berini CA, Biglione MM. HLA-B*35 as a new marker for susceptibility to human T-cell lymphotropic virus type 1 (HTLV-1) Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP) in patients living in Argentina. Retrovirology 2020; 17:29. [PMID: 32883310 PMCID: PMC7469403 DOI: 10.1186/s12977-020-00536-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/19/2020] [Indexed: 11/21/2022] Open
Abstract
Background Human T-cell lymphotropic virus type 1 (HTLV-1) is the etiological agent of HTLV associated myelopathy/ Tropical Spastic Paraparesis (HAM/TSP) and Adult T cell leukemia/lymphoma (ATLL), in around 2–5% of the infected individuals. Host genetic background might play a role in disease progression. Several previous studies across many countries report HLA haplotype to be one such factor. Here, we sequenced HLA-A, -B and -C of 66 individuals by Sequence-Based Typing (SBT), and compared the frequency of different alleles among ATLL patients, HAM/TSP patients, asymptomatic carriers and non-infected individuals living in Argentina. Results The frequency of HLA-A, -B and -C alleles largely matched that of the general population in Argentina. We identified HLA-A*02, HLA-B*35 and HLA-C*07 as associated to protection from ATLL (p = 0.031), susceptibility to HAM/TSP (p < 0.001) and susceptibility to ATLL (p = 0.017), respectively. We also found a strong correlation between high proviral load (PVL) and disease (p = 0.008), but were unable to identify any particular allele associated with high or low PVL. Conclusions We have found HLA-A*02, HLA-B*35 and HLA-C*07 to be associated to protection from ATLL (HLA-A*02) and susceptibility to HAM/TSP (HLA-B*35) or to ATLL (HLA-C*07), respectively. Whereas HLA-A*02 protection from ATLL has already been extensively described in other regions of the world, this is the first report that links HLA-B*35 and an increased susceptibility to HAM/TSP. As for HLA-C*07 it has previously been associated to susceptibility to HAM/TSP in other countries but in our population it has been linked to ATLL.
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Affiliation(s)
- Paula Benencio
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Paraguay 2155, C1121ABG, Ciudad Autónoma de Buenos Aires, Argentina
| | - Sindy A Fraile Gonzalez
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Paraguay 2155, C1121ABG, Ciudad Autónoma de Buenos Aires, Argentina
| | - Nicolás Ducasa
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Paraguay 2155, C1121ABG, Ciudad Autónoma de Buenos Aires, Argentina
| | - Kimberly Page
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,The University of New Mexico, Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Carolina A Berini
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Paraguay 2155, C1121ABG, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Mirna M Biglione
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Paraguay 2155, C1121ABG, Ciudad Autónoma de Buenos Aires, Argentina
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Next-generation sequencing reveals new information about HLA allele and haplotype diversity in a large European American population. Hum Immunol 2019; 80:807-822. [PMID: 31345698 DOI: 10.1016/j.humimm.2019.07.275] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 06/21/2019] [Accepted: 07/06/2019] [Indexed: 12/11/2022]
Abstract
The human leukocyte antigen (HLA) genes are extremely polymorphic and are useful molecular markers to make inferences about human population history. However, the accuracy of the estimation of genetic diversity at HLA loci very much depends on the technology used to characterize HLA alleles; high-resolution genotyping of long-range HLA gene products improves the assessment of HLA population diversity as well as other population parameters compared to lower resolution typing methods. In this study we examined allelic and haplotype HLA diversity in a large healthy European American population sourced from the UCSF-DNA bank. A high-resolution next-generation sequencing method was applied to define non-ambiguous 3- and 4-field alleles at the HLA-A, HLA-C, HLA-B, HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1 loci in samples provided by 2248 unrelated individuals. A number of population parameters were examined including balancing selection and various measurements of linkage disequilibrium were calculated. There were no detectable deviations from Hardy-Weinberg proportions at HLA-A, HLA-DRB1, HLA-DQA1 and HLA-DQB1. For the remaining loci moderate and significant deviations were detected at HLA-C, HLA-B, HLA-DRB3/4/5, HLA-DPA1 and HLA-DPB1 loci mostly from population substructures. Unique 4-field associations were observed among alleles at 2 loci and haplotypes extending large intervals that were not apparent in results obtained using testing methodologies with limited sequence coverage and phasing. The high diversity at HLA-DPA1 results from detection of intron variants of otherwise well conserved protein sequences. It may be speculated that divergence in exon sequences may be negatively selected. Our data provides a valuable reference source for future population studies that may allow for precise fine mapping of coding and non-coding sequences determining disease susceptibility and allo-immunogenicity.
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8
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Creary LE, Guerra SG, Chong W, Brown CJ, Turner TR, Robinson J, Bultitude WP, Mayor NP, Marsh SGE, Saito K, Lam K, Duke JL, Mosbruger TL, Ferriola D, Monos D, Willis A, Askar M, Fischer G, Saw CL, Ragoussis J, Petrek M, Serra-Pagés C, Juan M, Stavropoulos-Giokas C, Dinou A, Ameen R, Al Shemmari S, Spierings E, Gendzekhadze K, Morris GP, Zhang Q, Kashi Z, Hsu S, Gangavarapu S, Mallempati KC, Yamamoto F, Osoegawa K, Vayntrub T, Chang CJ, Hansen JA, Fernández-Viňa MA. Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-lymphoblastoid cell lines: Report from the 17th International HLA and Immunogenetics Workshop. Hum Immunol 2019; 80:449-460. [PMID: 30844424 DOI: 10.1016/j.humimm.2019.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/09/2019] [Accepted: 03/01/2019] [Indexed: 10/27/2022]
Abstract
Extended molecular characterization of HLA genes in the IHWG reference B-lymphoblastoid cell lines (B-LCLs) was one of the major goals for the 17th International HLA and Immunogenetics Workshop (IHIW). Although reference B-LCLs have been examined extensively in previous workshops complete high-resolution typing was not completed for all the classical class I and class II HLA genes. To address this, we conducted a single-blind study where select panels of B-LCL genomic DNA samples were distributed to multiple laboratories for HLA genotyping by next-generation sequencing methods. Identical cell panels comprised of 24 and 346 samples were distributed and typed by at least four laboratories in order to derive accurate consensus HLA genotypes. Overall concordance rates calculated at both 2- and 4-field allele-level resolutions ranged from 90.4% to 100%. Concordance for the class I genes ranged from 91.7 to 100%, whereas concordance for class II genes was variable; the lowest observed at HLA-DRB3 (84.2%). At the maximum allele-resolution 78 B-LCLs were defined as homozygous for all 11 loci. We identified 11 novel exon polymorphisms in the entire cell panel. A comparison of the B-LCLs NGS HLA genotypes with the HLA genotypes catalogued in the IPD-IMGT/HLA Database Cell Repository, revealed an overall allele match at 68.4%. Typing discrepancies between the two datasets were mostly due to the lower-resolution historical typing methods resulting in incomplete HLA genotypes for some samples listed in the IPD-IMGT/HLA Database Cell Repository. Our approach of multiple-laboratory NGS HLA typing of the B-LCLs has provided accurate genotyping data. The data generated by the tremendous collaborative efforts of the 17th IHIW participants is useful for updating the current cell and sequence databases and will be a valuable resource for future studies.
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Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
| | - Sandra G Guerra
- Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK
| | - Winnie Chong
- Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK
| | - Colin J Brown
- Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, London, UK
| | - Thomas R Turner
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Will P Bultitude
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Neema P Mayor
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK
| | - Katsuyuki Saito
- Molecular Biology Research Department, One Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA
| | - Kevin Lam
- Molecular Biology Research Department, One Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA
| | - Jamie L Duke
- Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Timothy L Mosbruger
- Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Deborah Ferriola
- Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dimitrios Monos
- Immunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Lab Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda Willis
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, USA
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, USA
| | - Gottfried Fischer
- Department for Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria
| | - Chee Loong Saw
- HLA Laboratory, Division of Haematology, McGill University Health Centre, Montreal, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University & McGill University and Genome Quèbec Innovation Centre, Montreal, Canada
| | - Martin Petrek
- Department of Pathological Physiology and Immunogenomics, IMTM, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Carles Serra-Pagés
- Immunology Department, Hospital Clinic de Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Manel Juan
- Immunology Department, Hospital Clinic de Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain
| | | | - Amalia Dinou
- Biomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece
| | - Reem Ameen
- Health Sciences Center, Kuwait University, Kuwait
| | | | - Eric Spierings
- Laboratory of Translational Immunology, UMC Utrecht, Utrecht, Netherlands
| | | | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Qiuheng Zhang
- Department of Pathology and Laboratory Medicine, UCLA Immunogenetics Center, Los Angeles, CA, USA
| | - Zahra Kashi
- HLA Department, Kashi Clinical Laboratories, Inc., Portland, OR, USA
| | - Susan Hsu
- HLA Laboratory, American Red Cross, Philadelphia, PA, USA
| | - Sridevi Gangavarapu
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Kalyan C Mallempati
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Fumiko Yamamoto
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Kazutoyo Osoegawa
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Tamara Vayntrub
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | | | - John A Hansen
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marcelo A Fernández-Viňa
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
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9
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Abduriyim S, Nishita Y, Kosintsev PA, Raichev E, Väinölä R, Kryukov AP, Abramov AV, Kaneko Y, Masuda R. Evolution of MHC class I genes in Eurasian badgers, genus Meles (Carnivora, Mustelidae). Heredity (Edinb) 2019; 122:205-218. [PMID: 29959426 PMCID: PMC6327056 DOI: 10.1038/s41437-018-0100-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 11/09/2022] Open
Abstract
Because of their role in immune defense against pathogens, major histocompatibility complex (MHC) genes are useful in evolutionary studies on how wild vertebrates adapt to their environments. We investigated the molecular evolution of MHC class I (MHCI) genes in four closely related species of Eurasian badgers, genus Meles. All four species of badgers showed similarly high variation in MHCI sequences compared to other Carnivora. We identified 7-21 putatively functional MHCI sequences in each of the badger species, and 2-7 sequences per individual, indicating the existence of 1-4 loci. MHCI exon 2 and 3 sequences encoding domains α1 and α2 exhibited different clade topologies in phylogenetic networks. Non-synonymous nucleotide substitutions at codons for antigen-binding sites exceeded synonymous substitutions for domain α1 but not for domain α2, suggesting that the domains α1 and α2 likely had different evolutionary histories in these species. Positive selection and recombination seem to have shaped the variation in domain α2, whereas positive selection was dominant in shaping the variation in domain α1. In the separate phylogenetic analyses for exon 2, exon 3, and intron 2, each showed three clades of Meles alleles, with rampant trans-species polymorphism, indicative of the long-term maintenance of ancestral MHCI polymorphism by balancing selection.
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Affiliation(s)
- Shamshidin Abduriyim
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yoshinori Nishita
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Pavel A Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Ekaterinburg, 620144, Russia
| | - Evgeniy Raichev
- Agricultural Faculty, Trakia University, 6000, Stara Zagora, Bulgaria
| | - Risto Väinölä
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, FI-00014, Helsinki, Finland
| | - Alexey P Kryukov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, 199034, Russia
| | - Yayoi Kaneko
- Carnivore Ecology and Conservation Research Group, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Ryuichi Masuda
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan.
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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10
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Kone A, Diarra B, Cohen K, Diabate S, Kone B, Diakite MT, Diarra H, Sanogo M, Togo ACG, Sarro YDS, Baya B, Coulibaly N, Kodio O, Achenbach CJ, Murphy RL, Holl JL, Siddiqui S, Doumbia S, Bishai WR, Diallo S, Maiga M. Differential HLA allele frequency in Mycobacterium africanum vs Mycobacterium tuberculosis in Mali. HLA 2019; 93:24-31. [PMID: 30516034 DOI: 10.1111/tan.13448] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 10/22/2018] [Accepted: 11/28/2018] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC), however, the distribution and frequency of MTBC lineages and sublineages vary in different parts of the globe. Mycobacterium africanum, a member of MTBC is responsible for a large percentage of TB cases in West Africa, however, it is rarely identified outside of this part of the World. Whether or not differential HLA polymorphism (an important host factor) is contributing to the geographic restriction of M. africanum to West Africa is unknown. Here, we conducted a cohort study in Mali of newly diagnosed individuals with active pulmonary TB and normal healthy controls. The MTBC isolates were spoligotyped to determine the TB study groups (M. tuberculosis sensu stricto LAM10 and M. africanum), and HLA typing was performed on peripheral blood. Unlike previous reports on other populations, we found that HLA class-I alleles were significantly associated with active TB disease in this population. HLA-B alleles (B*07:02, B*08:01, B*14:02, B*15:03, B*15:10, B*18:01, B*42:01, B*42:02, B*51:01 and B*81:01) were significantly associated with M. africanum (40%-45%) and M. tuberculosis (75%) compared with healthy controls. Many HLA-A alleles (A*02:05, A*34:02, A*66:01 and A*68:02) were also associated with both TB groups (65%-70%). However, many class II HLA-DR variants were found to be associated with M. tuberculosis but not M. africanum with the exception of the DRB1*03:01, which was associated with both groups. The differential HLA distribution observed in this study might be at least partially responsible for the geographical restriction of M. africanum infections to West Africa.
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Affiliation(s)
- Amadou Kone
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bassirou Diarra
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Keira Cohen
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Seydou Diabate
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bourahima Kone
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mahamane T Diakite
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Hawa Diarra
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Moumine Sanogo
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Antieme C G Togo
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Yeya Dit Sadio Sarro
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bocar Baya
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Nadie Coulibaly
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Ousmane Kodio
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | | | | | - Sophia Siddiqui
- National Institute of Allergic and Infectious Diseases, Rockville, Maryland
| | - Seydou Doumbia
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - William R Bishai
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Souleymane Diallo
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mamoudou Maiga
- University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali.,Northwestern University, Chicago, Illinois
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11
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Dello Russo C, Cappoli N, Coletta I, Mezzogori D, Paciello F, Pozzoli G, Navarra P, Battaglia A. The human microglial HMC3 cell line: where do we stand? A systematic literature review. J Neuroinflammation 2018; 15:259. [PMID: 30200996 PMCID: PMC6131758 DOI: 10.1186/s12974-018-1288-0] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/21/2018] [Indexed: 02/08/2023] Open
Abstract
Microglia, unique myeloid cells residing in the brain parenchyma, represent the first line of immune defense within the central nervous system. In addition to their immune functions, microglial cells play an important role in other cerebral processes, including the regulation of synaptic architecture and neurogenesis. Chronic microglial activation is regarded as detrimental, and it is considered a pathogenic mechanism common to several neurological disorders. Microglial activation and function have been extensively studied in rodent experimental models, whereas the characterization of human cells has been limited due to the restricted availability of primary sources of human microglia. To overcome this problem, human immortalized microglial cell lines have been developed. The human microglial clone 3 cell line, HMC3, was established in 1995, through SV40-dependent immortalization of human embryonic microglial cells. It has been recently authenticated by the American Type Culture Collection (ATCC®) and distributed under the name of HMC3 (ATCC®CRL-3304). The HMC3 cells have been used in six research studies, two of which also indicated by ATCC® as reference articles. However, a more accurate literature revision suggests that clone 3 was initially distributed under the name of CHME3. In this regard, several studies have been published, thus contributing to a more extensive characterization of this cell line. Remarkably, the same cell line has been used in different laboratories with other denominations, i.e., CHME-5 cells and C13-NJ cells. In view of the fact that "being now authenticated by ATCC®" may imply a wider distribution of the cells, we aimed at reviewing data obtained with the human microglia cell line clone 3, making the readers aware of this complicated nomenclature. In addition, we also included original data, generated in our laboratory with the HMC3 (ATCC®CRL-3304) cells, providing information on the current state of the culture together with supplementary details on the culturing procedures to obtain and maintain viable cells.
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Affiliation(s)
- Cinzia Dello Russo
- Institute of Pharmacology, Università Cattolica del S. Cuore, L.go F Vito 1, 00168, Rome, Italy. .,Pharmacology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.
| | - Natalia Cappoli
- Institute of Pharmacology, Università Cattolica del S. Cuore, L.go F Vito 1, 00168, Rome, Italy
| | - Isabella Coletta
- Angelini RR&D (Research, Regulatory & Development) - Angelini S.p.A., Rome, Italy
| | - Daniele Mezzogori
- Institute of Human Physiology, Università Cattolica del S. Cuore, Rome, Italy
| | - Fabiola Paciello
- Institute of Otolaryngology, Università Cattolica del S. Cuore, Rome, Italy
| | - Giacomo Pozzoli
- Institute of Pharmacology, Università Cattolica del S. Cuore, L.go F Vito 1, 00168, Rome, Italy.,Pharmacology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Pierluigi Navarra
- Institute of Pharmacology, Università Cattolica del S. Cuore, L.go F Vito 1, 00168, Rome, Italy.,Pharmacology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Alessandra Battaglia
- Immunology Laboratory, Department of Oncological Gynecology, Università Cattolica del S. Cuore, Rome, Italy
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12
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KIR3DL1 alleles and their epistatic interactions with human leukocyte antigen class I influence resistance and susceptibility to HIV-1 acquisition in the Pumwani sex worker cohort. AIDS 2018; 32:841-850. [PMID: 29280757 DOI: 10.1097/qad.0000000000001735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To determine the associations of KIR3DL1/S1(3DL1/S1) and its epistatic interactions with human leukocyte antigen class I (HLA-I) alleles with resistance and susceptibility to HIV-1. DESIGN Despite repeated exposure to HIV-1, a subset of women enrolled in the Pumwani sex worker cohort remain HIV uninfected. Previous studies have shown that specific HLA class I and II alleles were associated with this natural immunity. In this study, we investigated the association of 3DL1/S1 and its epistatic interactions with HLA-I, with resistance or susceptibility to HIV-1 acquisition. METHODS We used a sequence-based typing method to genotype 3DL1/S1 of 641 women in this cohort. The association of 3DL1/S1 and its epistatic interactions with HLA-I were analyzed using SPSS statistics software. RESULTS 3DL1041 is enriched in the HIV-1-resistant women [P = 0.009, Pc = 0.0468, odds ratio (OR): 3.359, 95% confidence interval (CI): 1.39-8.32], whereas, 3DL1020 was associated with susceptibility to HIV-1 infection before correction for multiple comparisons (P = 0.029, Pc = 0.0858, OR: 0.316, 95%CI: 0.10-1.04). Epistatic interactions between several 3DL1 alleles and specific HLA-I alleles were observed. Among them the cocarriage of 3DL1041 with Bw4 (P = 1E - 05, Pc = 0.0015, OR: 13.33, 95%CI: 3.43-51.9), or Bw6 (P = 0.008, Pc = 0.272, OR: 3.92, 95%CI: 1.51-10.17), increased the odds of remaining HIV-1 uninfected. Further, 3DL1041+/Bw4+ women who entered the cohort HIV negative remained uninfected (P = 0.032, Pc = 0.0858). Cocarriage of 3DL101501 with C02 : 10 (P = 2.73E - 07, Pc = 7.0954E - 06), B15 : 03 (P = 3.21E - 04, Pc = 0.0042), A24 supertype (P = 8.89E - 04, Pc = 0.0077), or A23 : 01 (P = 0.0036, Pc = 0.0236) was associated with increased susceptibility to seroconversion. CONCLUSION The effects of interactions between 3DL1 and HLA-I alleles on resistance/susceptibility to HIV-1 infection suggest that innate immunity plays an important role in HIV-1 acquisition and should be studied and explored for HIV prevention.
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13
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Jiao Y, Li R, Wu C, Ding Y, Liu Y, Jia D, Wang L, Xu X, Zhu J, Zheng M, Jia J. High-sensitivity HLA typing by Saturated Tiling Capture Sequencing (STC-Seq). BMC Genomics 2018; 19:50. [PMID: 29334893 PMCID: PMC5769328 DOI: 10.1186/s12864-018-4431-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/03/2018] [Indexed: 12/04/2022] Open
Abstract
Background Highly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious diseases. Additionally, it is routinely performed for identifying matched donors in transplantation medicine. Although many HLA typing approaches have been developed, the complexity, low-efficiency and high-cost of current HLA-typing assays limit their application in population-based high-throughput HLA typing for donors, which is required for creating large-scale databases for transplantation and precision medicine. Results Here, we present a cost-efficient Saturated Tiling Capture Sequencing (STC-Seq) approach to capturing 14 HLA class I and II genes. The highly efficient capture (an approximately 23,000-fold enrichment) of these genes allows for simplified allele calling. Tests on five genes (HLA-A/B/C/DRB1/DQB1) from 31 human samples and 351 datasets using STC-Seq showed results that were 98% consistent with the known two sets of digitals (field1 and field2) genotypes. Additionally, STC can capture genomic DNA fragments longer than 3 kb from HLA loci, making the library compatible with the third-generation sequencing. Conclusions STC-Seq is a highly accurate and cost-efficient method for HLA typing which can be used to facilitate the establishment of population-based HLA databases for the precision and transplantation medicine. Electronic supplementary material The online version of this article (10.1186/s12864-018-4431-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Jiao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Ran Li
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Chao Wu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Yibin Ding
- School of Mathematical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Yanning Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China
| | - Danmei Jia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Lifeng Wang
- Beijing Ming-tian Genetics Ltd, Beijing, 100070, People's Republic of China
| | - Xiang Xu
- School of Mathematical Science, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China
| | - Jing Zhu
- Beijing Ming-tian Genetics Ltd, Beijing, 100070, People's Republic of China.
| | - Min Zheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China. .,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China.
| | - Junling Jia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, Zhejiang, 310058, People's Republic of China. .,Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China.
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14
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Podhorzer A, Dirchwolf M, Machicote A, Belen S, Montal S, Paz S, Fainboim H, Podestá LG, Fainboim L. The Clinical Features of Patients with Chronic Hepatitis C Virus Infections Are Associated with Killer Cell Immunoglobulin-Like Receptor Genes and Their Expression on the Surface of Natural Killer Cells. Front Immunol 2018; 8:1912. [PMID: 29354127 PMCID: PMC5760500 DOI: 10.3389/fimmu.2017.01912] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/14/2017] [Indexed: 12/21/2022] Open
Abstract
Killer cell immunoglobulin-like receptor (KIR) genes are known to play a role in the acute phase of hepatitis C virus (HCV) infection. The present study investigated their roles in chronic HCV (CHCV) infection by analyzing the phenotypes and function of natural killer (NK) and T cells that express KIRs. T cells from CHCV patients showed a more differentiated phenotype, and NK cells exhibited an activated profile. These observations are consistent with the increased expression of the degranulation marker CD107a observed after PMA stimulation. We explored the correlations between the expression of KIR genes and lectin type-C receptors with clinical factors that predict progression to fibrosis and cirrhosis. The expression levels of KIR2DS3 and the functional alleles of KIR2DS4-FL were increased in patients with intermediate and high viral loads. Homozygous KIR2DS4 was also associated with the presence of cirrhosis. In the group of individuals with a shorter infection time who developed cirrhosis, we detected decreased expression of KIR3DL1 in CD56dim NK cells in the presence of its ligand. Similarly, in the group of patients with late CHCV infections complicated with cirrhosis, we detected lower expression of the strong inhibitory receptor NKG2A in CD56bright NK cells. We also detected an increase in NKG2C expression in CD56dim NK cells in CHCV patients who displayed high necroinflammatory activity. Decreased KIR3DL2 expression in CD56dim and CD56bright NK cells was associated with a high body mass index, and KIR3DL2 expression may be one factor associated with the more rapid progression of CHCV to fibrosis in patients.
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Affiliation(s)
- Ariel Podhorzer
- Instituto de Inmunología, Genética y Metabolismo (INIGEM-CONICET), Hospital de Clínicas José de San Martín, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Melisa Dirchwolf
- Hepatopatías Infecciosas, Hospital Francisco J. Muñiz, Buenos Aires, Argentina
| | - Andrés Machicote
- Instituto de Inmunología, Genética y Metabolismo (INIGEM-CONICET), Hospital de Clínicas José de San Martín, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Santiago Belen
- Instituto de Inmunología, Genética y Metabolismo (INIGEM-CONICET), Hospital de Clínicas José de San Martín, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Silvina Montal
- Unidad de Cirugía Hepato-Biliar y Trasplante, Hospital Universitario Austral, Buenos Aires, Argentina
| | - Silvia Paz
- Hepatopatías Infecciosas, Hospital Francisco J. Muñiz, Buenos Aires, Argentina
| | - Hugo Fainboim
- Hepatopatías Infecciosas, Hospital Francisco J. Muñiz, Buenos Aires, Argentina
| | - Luis G Podestá
- Unidad de Cirugía Hepato-Biliar y Trasplante, Hospital Universitario Austral, Buenos Aires, Argentina
| | - Leonardo Fainboim
- Instituto de Inmunología, Genética y Metabolismo (INIGEM-CONICET), Hospital de Clínicas José de San Martín, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina de la Universidad de Buenos Aires, Buenos Aires, Argentina
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15
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Ruiz MJ, Salido J, Abusamra L, Ghiglione Y, Cevallos C, Damilano G, Rodriguez AM, Trifone C, Laufer N, Giavedoni LD, Sued O, Salomón H, Gherardi MM, Turk G. Evaluation of Different Parameters of Humoral and Cellular Immune Responses in HIV Serodiscordant Heterosexual Couples: Humoral Response Potentially Implicated in Modulating Transmission Rates. EBioMedicine 2017; 26:25-37. [PMID: 29129698 PMCID: PMC5832641 DOI: 10.1016/j.ebiom.2017.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/24/2017] [Accepted: 11/01/2017] [Indexed: 02/05/2023] Open
Abstract
As the HIV/AIDS pandemic still progresses, understanding the mechanisms governing viral transmission as well as protection from HIV acquisition is fundamental. In this context, cohorts of HIV serodiscordant heterosexual couples (SDC) represent a unique tool. The present study was aimed to evaluate specific parameters of innate, cellular and humoral immune responses in SDC. Specifically, plasma levels of cytokines and chemokines, HIV-specific T-cell responses, gp120-specific IgG and IgA antibodies, and HIV-specific antibody-dependent cellular cytotoxicity (ADCC) activity were assessed in nine HIV-exposed seronegative individuals (ESN) and their corresponding HIV seropositive partners (HIV+-P), in eighteen chronically infected HIV subjects (C), nine chronically infected subjects known to be HIV transmitters (CT) and ten healthy HIV− donors (HD). Very low magnitude HIV-specific cellular responses were found in two out of six ESN. Interestingly, HIV+-P had the highest ADCC magnitude, the lowest IgA levels and the highest IgG/IgA ratio, all compared to CT. Positive correlations between CD4+ T-cell counts and both IgG/IgA ratios and %ADCC killing uniquely distinguished HIV+-P. Additionally, evidence of IgA interference with ADCC responses from HIV+-P and CT is provided. These data suggest for the first time a potential role of ADCC and/or gp120-specific IgG/IgA balance in modulating heterosexual transmission. In sum, this study provides key information to understand the host factors that influence viral transmission, which should be considered in both the development of prophylactic vaccines and novel immunotherapies for HIV-1 infection. The evaluation of different immune parameters in HIV serodiscordant couples helped identify factors shaping transmission. Innate and cellular immune responses were apparently not involved in this scenario. HIV-specific ADCC, IgA titer and IgG/IgA balance were identified as factors involved in modulating viral transmission.
The existence of individuals that remain HIV negative despite being repeatedly exposed to the virus has long been described. To date, only homozygosis for a 32-base pair deletion in the ccr5 gene has been consistently shown to be a determinant of HIV resistance. Still, subjects bearing the WT ccr5 gene have also been described as resistant or less susceptible to HIV. Thus, other mechanisms must be involved in this phenomenon. The results presented here postulate ADCC and IgG/IgA ratio as potential mechanisms involved in modulating HIV transmission in the context of serodiscordant couples and inspire further investigations.
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Affiliation(s)
- María Julia Ruiz
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina
| | - Jimena Salido
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina
| | | | - Yanina Ghiglione
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina
| | - Cintia Cevallos
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina
| | - Gabriel Damilano
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina
| | - Ana María Rodriguez
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina
| | - César Trifone
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina
| | - Natalia Laufer
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina; Hospital Juan A. Fernández, Unidad Enfermedades Infecciosas, Buenos Aires, Argentina
| | - Luis D Giavedoni
- Department of Virology and Immunology, Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Omar Sued
- Fundación Huésped, Buenos Aires, Argentina; Hospital Juan A. Fernández, Unidad Enfermedades Infecciosas, Buenos Aires, Argentina
| | - Horacio Salomón
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina
| | - María Magdalena Gherardi
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina
| | - Gabriela Turk
- CONICET- Universidad de Buenos Aires, Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Buenos Aires, Argentina.
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16
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Lee HL, Lai SK, Chen PL, Chu CC. Identification of a novel HLA-B allele, HLA-B*40:238, in a Taiwanese individual. HLA 2017; 90:252-253. [PMID: 28715111 DOI: 10.1111/tan.13093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 07/11/2017] [Accepted: 07/11/2017] [Indexed: 11/29/2022]
Abstract
The HLA-B*40:238 allele has one non-synonymous transversion from HLA-B*40:01:01 at nucleotide position 484.
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Affiliation(s)
- H-L Lee
- Department of Medical Research, Mackay Memorial Hospital, New Taipei City, Taiwan
| | - S-K Lai
- Department of Medical Research, Mackay Memorial Hospital, New Taipei City, Taiwan.,Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - P-L Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan
| | - C-C Chu
- Department of Medical Research, Mackay Memorial Hospital, New Taipei City, Taiwan
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17
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Unambiguous high resolution genotyping of human leukocyte antigens. J Immunol Methods 2017; 445:10-14. [PMID: 28238798 DOI: 10.1016/j.jim.2017.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 11/22/2022]
Abstract
We have developed a high resolution sequencing based typing method for genotyping Human Leukocyte Antigens (HLA) over a period of twenty years. The methods are based upon the separation of HLA alleles per locus at the initial amplification to simplify the analysis post-sequencing. The increasing discovery of polymorphism in HLA, manifested in new alleles, has necessitated the continuing development of this method. Here we present methods for the high resolution Sequence Based Typing of HLA-A, B, C (class I) and HLA-DQB1 and DRB1 (class II). The purpose of this article is to provide a valuable resource of methods and primers for other laboratories engaged in HLA typing.
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18
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Falasca F, Russo CD, Mora B, Pirazzoli A, Fantauzzi A, Navarra P, Pizzuti A, De Vito C, Antonelli G, Turriziani O. Comparative Analysis of Real-Time Polymerase Chain Reaction Methods to Typing HLA-B*57:01 in HIV-1-Positive Patients. AIDS Res Hum Retroviruses 2016; 32:654-7. [PMID: 26750774 PMCID: PMC4931735 DOI: 10.1089/aid.2015.0303] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The HLA-B*57:01 allele is strongly associated with the hypersensitivity reaction to Abacavir (ABC). Therefore, treatment guidelines recommend that patients initiating ABC are preventively tested for the presence of this allele. To date, four different commercial assays based on the real-time quantitative polymerase chain reaction (Q-PCR) technique are available for the detection of HLA-B*57:01: Duplicα-RealTime Reagent Set HLA-B*57:01 by Euroclone, HLA-B*57:01 Real-TM by Sacace Biotechnologies, COBAS AmpliPrep/COBAS TaqMan HLA-B*57:01 Screening Test by Roche Diagnostic, and HLA-B*57:01 by Nuclear Laser Medicine. The study was carried out to compare the performance of the first three commercially available Q-PCR kits in a routine clinical setting. A total of 98 samples from Policlinico Umberto I Hospital were tested. Results obtained by the Duplicα-RealTime Genotyping kit and AmpliPrep/TaqMan system were 100% concordant. In contrast, genotyping by the HLA-B*57:01 Real-TM kit showed poor agreement with the other systems, that is, 12 out of 33 positive samples were detected as HLA-B*57:01 negative. To confirm the correct genotype of these discordant samples, two additional methods with rapid turnaround times and already implemented into routine clinical practice were used, that is, a PCR-based microsequence-specific primer DNA typing test and a laboratory-developed screening test in Q-PCR. All 12 discordant samples were genotyped as HLA-B*57:01-positive samples using these two additional methods in a single-blinded manner, thus confirming the low sensitivity of HLA-B*57:01 Real-TM test. These findings underline the need to compare results obtained with commercial assays before choosing a test suitable for use in a routine clinical laboratory.
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Affiliation(s)
- Francesca Falasca
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Cinzia Dello Russo
- Institute of Pharmacology, Catholic University Medical School, Rome, Italy
| | - Barbara Mora
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | | | | | - Pierluigi Navarra
- Institute of Pharmacology, Catholic University Medical School, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Corrado De Vito
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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19
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The early onset of type 1 autoimmune hepatitis has a strong genetic influence: role of HLA and KIR genes. Genes Immun 2016; 17:187-92. [PMID: 26890333 DOI: 10.1038/gene.2016.7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/09/2015] [Accepted: 01/04/2016] [Indexed: 12/19/2022]
Abstract
We have previously reported a strong association between HLA-DRB1*1301 and type 1 pediatric autoimmune hepatitis (PAH) and between HLA-DR*0405 and adult autoimmune hepatitis (AAH). Because human killer cell immunoglobulin-like receptors are known to be associated with susceptibility to autoimmune diseases, we investigated the frequencies of HLA-A, B, C, DRB1 and KIR genes in 144 type 1 PAH and 86 AAH patients, which were compared with 273 healthy controls. We demonstrated in PAH the increased frequency of the functional form of KIR2DS4-Full Length (KIR2DS4-FL), which in combination with HLA-DRB1*1301 revealed a strong synergistic effect (odds ratio=36.5). PAH-KIR2DS4-FL+ subjects have shown an increased frequency of their putative HLA-C*02, 04 and 06 ligands. KIR analysis of PAH also revealed a decreased frequency of KIR2DL2 gene and its ligand. In contrast, AAH cases have shown a weaker increased frequency of KIR2DS4-FL, a lack of synergistic effect with HLA class II antigens and a moderate association with HLA-DRB1*0405. Of note, we demonstrated that liver T cells have a unique pattern of KIR expression. These results show a KIR gene involved in autoimmune hepatitis and suggest a stronger genetic influence for the early onset type I autoimmune hepatitis.
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20
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Brunet L, Mouron D, Villard J, Tiercy JM, Buhler S. Identification of the novel HLA-B*07:261 allele. HLA 2016; 87:102-3. [PMID: 26843514 DOI: 10.1111/tan.12739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 12/18/2015] [Accepted: 01/11/2016] [Indexed: 11/25/2022]
Affiliation(s)
- L Brunet
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland
| | - D Mouron
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland
| | - J Villard
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland
| | - J-M Tiercy
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland
| | - S Buhler
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland.,Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland
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21
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Cereb N, Kim HR, Ryu J, Yang SY. Advances in DNA sequencing technologies for high resolution HLA typing. Hum Immunol 2015; 76:923-7. [PMID: 26423536 DOI: 10.1016/j.humimm.2015.09.015] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 09/24/2015] [Accepted: 09/24/2015] [Indexed: 01/12/2023]
Abstract
This communication describes our experience in large-scale G group-level high resolution HLA typing using three different DNA sequencing platforms - ABI 3730 xl, Illumina MiSeq and PacBio RS II. Recent advances in DNA sequencing technologies, so-called next generation sequencing (NGS), have brought breakthroughs in deciphering the genetic information in all living species at a large scale and at an affordable level. The NGS DNA indexing system allows sequencing multiple genes for large number of individuals in a single run. Our laboratory has adopted and used these technologies for HLA molecular testing services. We found that each sequencing technology has its own strengths and weaknesses, and their sequencing performances complement each other. HLA genes are highly complex and genotyping them is quite challenging. Using these three sequencing platforms, we were able to meet all requirements for G group-level high resolution and high volume HLA typing.
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Affiliation(s)
- Nezih Cereb
- Histogenetics, 300 Executive Blvd, Ossining, NY 10562, USA.
| | - Hwa Ran Kim
- Histogenetics, 300 Executive Blvd, Ossining, NY 10562, USA
| | - Jaejun Ryu
- Histogenetics, 300 Executive Blvd, Ossining, NY 10562, USA
| | - Soo Young Yang
- Histogenetics, 300 Executive Blvd, Ossining, NY 10562, USA
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22
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Biassoni R, Malnati M, Vanni I, Raso A, Sironi F, Broccolo F, Garbarino L, Mazzocco M, Montera M, Larghero P, Di Marco E, Ugolotti E. An improved method for HLA-B and -C supratyping. J Immunol Methods 2015; 426:29-34. [PMID: 26232127 DOI: 10.1016/j.jim.2015.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/16/2015] [Accepted: 07/16/2015] [Indexed: 01/26/2023]
Abstract
A growing body of evidence links the analysis of the KIR genotype and the presence of their HLA-B and -C ligands to a wide repertoire of human diseases. We noticed that, using a panel of 184 Caucasoid donors, a limited number of HLA alleles were incorrectly supratyped by previously described pyrosequence-based assays. Here we describe a simple implementation of the reported methods that corrects all the discrepancies found with HLA-B and -C molecular typing and allows establishing a quick and high-throughput method for the determination of HLA-Bw4 I(80), Bw4T(80), Bw6 and HLA-C1 or -C2 supratype.
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Affiliation(s)
- R Biassoni
- Istituto Giannina Gaslini, Genova, Italy.
| | - M Malnati
- Human Virology Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy
| | - I Vanni
- Istituto Giannina Gaslini, Genova, Italy
| | - A Raso
- Istituto Giannina Gaslini, Genova, Italy
| | - F Sironi
- Human Virology Unit, Division of Immunology, Transplantation and Infectious Disease, San Raffaele Scientific Institute, Milan, Italy
| | - F Broccolo
- Department of Health Sciences, University of Milano-Bicocca, Milano, Italy
| | - L Garbarino
- Histocompatibility Laboratory, Galliera Hospital, Genova, Italy
| | - M Mazzocco
- Histocompatibility Laboratory, Galliera Hospital, Genova, Italy
| | - M Montera
- Istituto Giannina Gaslini, Genova, Italy
| | - P Larghero
- Istituto Giannina Gaslini, Genova, Italy
| | - E Di Marco
- Istituto Giannina Gaslini, Genova, Italy
| | - E Ugolotti
- Istituto Giannina Gaslini, Genova, Italy
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23
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Vanni I, Ugolotti E, Larghero P, Biassoni R. HLA-B and HLA-C Supratyping by Pyrosequencing®. Methods Mol Biol 2015; 1315:133-51. [PMID: 26103897 DOI: 10.1007/978-1-4939-2715-9_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Usually, HLA typing has been performed either by serology-based typing incubating a panel of known anti-HLA antibodies with viable lymphocytes of unknown HLA type or by molecular typing including medium-resolution HLA typing by Sequence Specific Oligonucleotide Probes (SSOP) or high-resolution HLA typing by Sequence Based Typing (SBT). Traditionally, HLA antigens have been defined using serological techniques, but these methods have several disadvantages, such as low resolution, the requirement for viable cells, and cell surface expression of HLA molecules. HLA type screening methods are categorized as low, medium, and high resolution, and only sequencing-based typing methods provide the highest resolution and are considered the gold standard for HLA typing.Among the HLA SBT based-methods, the Pyrosequencing(®) technique is an extremely versatile and accurate real-time sequencing technique with some advantages compared to classic Sanger method.Here, we describe a quick and inexpensive method that allows through the use of Pyrosequencing subtyping of HLA class I molecules, into HLA-Bw6, -Bw4 I80, or -Bw4 T80 and HLA-C1, or -C2 groups. In particular, this analysis is focused on the amino acids around residue 80. This method demonstrated good sensitivity, specificity, and reproducibility. Using a quantitative allele acquisition mode, the method provides accurate sequence information required for the definition of heterozygous and/or homozygous samples.
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Affiliation(s)
- Irene Vanni
- Molecular Medicine, Translational Medicine Department, Istituto Giannina Gaslini, Via G. Gaslini 5, Genoa, 16147, Italy
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24
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Host genetic factors associated with symptomatic primary HIV infection and disease progression among Argentinean seroconverters. PLoS One 2014; 9:e113146. [PMID: 25406087 PMCID: PMC4236131 DOI: 10.1371/journal.pone.0113146] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 10/20/2014] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Variants in HIV-coreceptor C-C chemokine receptor type 5 (CCR5) and Human leukocyte antigen (HLA) genes are the most important host genetic factors associated with HIV infection and disease progression. Our aim was to analyze the association of these genetic factors in the presence of clinical symptoms during Primary HIV Infection (PHI) and disease progression within the first year. METHODS Seventy subjects diagnosed during PHI were studied (55 symptomatic and 15 asymptomatic). Viral load (VL) and CD4 T-cell count were evaluated. HIV progression was defined by presence of B or C events and/or CD4 T-cell counts <350 cell/mm3. CCR5 haplotypes were characterized by polymerase chain reaction and SDM-PCR-RFLP. HLA-I characterization was performed by Sequencing. RESULTS Symptoms during PHI were significantly associated with lower frequency of CCR5-CF1 (1.8% vs. 26.7%, p = 0.006). Rapid progression was significantly associated with higher frequency of CCR5-CF2 (16.7% vs. 0%, p = 0.024) and HLA-A*11 (16.7% vs. 1.2%, p = 0.003) and lower frequency of HLA-C*3 (2.8% vs. 17.5%, p = 0.035). Higher baseline VL was significantly associated with presence of HLA-A*11, HLA-A*24, and absence of HLA-A*31 and HLA-B*57. Higher 6-month VL was significantly associated with presence of CCR5-HHE, HLA-A*24, HLA-B*53, and absence of HLA-A*31 and CCR5-CF1. Lower baseline CD4 T-cell count was significantly associated with presence of HLA-A*24/*33, HLA-B*53, CCR5-CF2 and absence of HLA-A*01/*23 and CCR5-HHA. Lower 6-month CD4 T-cell count was associated with presence of HLA-A*24 and HLA-B*53, and absence of HLA-A*01 and HLA-B*07/*39. Moreover, lower 12-month CD4 T-cell count was significantly associated with presence of HLA-A*33, HLA-B*14, HLA-C*08, CCR5-CF2, and absence of HLA-B*07 and HLA-C*07. CONCLUSION Several host factors were significantly associated with disease progression in PHI subjects. Most results agree with previous studies performed in other groups. However, some genetic factor associations are being described for the first time, highlighting the importance of genetic studies at a local level.
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25
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KIR-HLA clase i y tuberculosis pulmonar en población amerindia del Chaco, Argentina. Enferm Infecc Microbiol Clin 2014; 32:565-9. [DOI: 10.1016/j.eimc.2013.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 06/04/2013] [Accepted: 10/07/2013] [Indexed: 11/21/2022]
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26
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Hernández-Frederick CJ, Giani AS, Cereb N, Sauter J, Silva-González R, Pingel J, Schmidt AH, Ehninger G, Yang SY. Identification of 2127 new HLA class I alleles in potential stem cell donors from Germany, the United States and Poland. ACTA ACUST UNITED AC 2014; 83:184-9. [PMID: 24571476 PMCID: PMC4199310 DOI: 10.1111/tan.12304] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/13/2014] [Accepted: 01/13/2014] [Indexed: 11/28/2022]
Abstract
We describe 2127 new human leukocyte antigen (HLA) class I alleles found in registered stem cell donors. These alleles represent 28.9% of the currently known class I alleles. Comparing new allele sequences to homologous sequences, we found 68.1% nonsynonymous nucleotide substitutions, 28.9% silent mutations and 3.0% nonsense mutations. Many substitutions occurred at positions that have not been known to be polymorphic before. A large number of HLA alleles and nucleotide variations underline the extreme diversity of the HLA system. Strikingly, 156 new alleles were found not only multiple times, but also in carriers of various parentage, suggesting that some new alleles are not necessarily rare. Moreover, new alleles were found especially often in minority donors. This emphasizes the benefits of specifically recruiting such groups of individuals.
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27
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Abstract
The hybridization products obtained by PCR using sequence-specific oligonucleotides can be traced either by colorimetric (streptavidin-biotin)-, X-ray (digoxigenin-CSPD)-, or fluorescence (FITC, PE)-based detection systems. To achieve a faster, reliable, automated typing technique microbead and fluorescence detection technology have been combined and introduced to this field (XMAP™ technology). For each locus, a series of microspheres, which are recognizable by their specific color originating from two internal fluorescent dyes, are used. Each microsphere is coupled with a single probe that is capable of hybridizing with the biotin-labeled complementary amplicon. Once hybridization occurs, it can be quantified by measuring the fluorescence signal originating from fluorescently (streptavidin-PE) labeled amplicons captured by the beads. Currently, there are two commercially available systems that differ in the scale of probes and the methods used for amplification and denaturation. One of these is described in detail in this chapter.
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28
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Association of killer cell immunoglobulin-like receptor gene 2DL1 and its HLA-C2 ligand with family history of cancer in oral squamous cell carcinoma. Immunogenetics 2014; 66:439-48. [DOI: 10.1007/s00251-014-0778-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/29/2014] [Indexed: 10/25/2022]
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29
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The role of KIR genes and their cognate HLA class I ligands in childhood acute lymphoblastic leukemia. Blood 2014; 123:2497-503. [PMID: 24518758 DOI: 10.1182/blood-2013-11-540625] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Killer cell immunoglobulin-like receptors (KIRs), via interaction with their cognate HLA class I ligands, play a crucial role in the development and activity of natural killer cells. Following recent reports of KIR gene associations in childhood acute lymphoblastic leukemia (ALL), we present a more in-depth investigation of KIR genes and their cognate HLA ligands on childhood ALL risk. Genotyping of 16 KIR genes, along with HLA class I groups C1/C2 and Bw4 supertype ligands, was carried out in 212 childhood ALL cases and 231 healthy controls. Frequencies of KIR genes, KIR haplotypes, and combinations of KIR-HLA ligands were tested for disease association using logistic regression analyses. KIR A/A genotype frequency was significantly increased in cases (33.5%) compared with controls (24.2%) (odds ratio [OR] = 1.57; 95% confidence interval [CI], 1.04-2.39). Stratifying analysis by ethnicity, a significant difference in KIR genotype frequency was demonstrated in Hispanic cases (34.2%) compared with controls (21.9%) (OR = 1.86; 95% CI, 1.05-3.31). Homozygosity for the HLA-Bw4 allele was strongly associated with increased ALL risk exclusively in non-Hispanic white children (OR = 3.93; 95% CI, 1.44-12.64). Our findings suggest a role for KIR genes and their HLA ligands in childhood ALL etiology that may vary among ethnic groups.
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30
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Russo CD, Lisi L, Fabbiani M, Gagliardi D, Fanti I, Giambenedetto SD, Cauda R, Navarra P. Detection of HLA-B*57:01 by real-time PCR: implementation into routine clinical practice and additional validation data. Pharmacogenomics 2014; 15:319-27. [DOI: 10.2217/pgs.13.242] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim:HLA-B*57:01 status needs to be determined before initiating abacavir therapy. We developed a pharmacogenetic real-time (Q)-PCR screening test using two sets of sequence specific primers. This test has been implemented into routine clinical practice. Materials & methods: HIV-infected patients admitted at our University Hospital were thus genotyped using the above mentioned test. A panel of 80 DNA samples with a known genotype were used to characterize Q-PCR conditions using different master mixes. Results: A total of 353 patients were genotyped, detecting 15 (4.25%) HLA-B*57:01 positive carriers. Among the negative patients, 17.2% were treated with abacavir without any hypersensitivity reaction. Using different Q-PCR master mixes, significantly lower cutoff Ct values were found, thus new analytical settings are provided. Conclusion: The pharmacogenetic test developed in our laboratory for the fast screening of HLA-B*57:01 can be successfully implemented into routine clinical practice. All 16 sequences (including an additional six) currently known for the HLA-B*57:01 allele are detected by sequence specific primers used in this test. The Brilliant II SYBR® Green QPCR MM (Stratagene) can safely replace the master mix originally used to develop the test. Original submitted 2 August 2013; Revision submitted 2 December 2013
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Affiliation(s)
- Cinzia Dello Russo
- Institute of Pharmacology, Catholic University Medical School, L.go F Vito 1, 00168 Rome, Italy
| | - Lucia Lisi
- Institute of Pharmacology, Catholic University Medical School, L.go F Vito 1, 00168 Rome, Italy
| | - Massimiliano Fabbiani
- Institute of Clinical Infectious Diseases, Catholic University Medical School, Rome, Italy
| | - Dimitri Gagliardi
- Manchester Institute of Innovation Research, MBS, the University of Manchester, UK
| | - Iuri Fanti
- Institute of Clinical Infectious Diseases, Catholic University Medical School, Rome, Italy
| | | | - Roberto Cauda
- Institute of Clinical Infectious Diseases, Catholic University Medical School, Rome, Italy
| | - Pierluigi Navarra
- Institute of Pharmacology, Catholic University Medical School, L.go F Vito 1, 00168 Rome, Italy
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Qi J, Li Q, Lin Z, Liao Z, Wei Q, Cao S, Rong J, Hu Z, Yang M, Zhang Y, Lv Q, Huang J, Pan Y, Wu Y, Jin O, Li T, Gu J. Higher risk of uveitis and dactylitis and older age of onset among ankylosing spondylitis patients withHLA-B*2705than patients withHLA-B*2704in the Chinese population. ACTA ACUST UNITED AC 2013; 82:380-6. [PMID: 24498994 DOI: 10.1111/tan.12254] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 10/08/2013] [Accepted: 10/21/2013] [Indexed: 11/28/2022]
Affiliation(s)
- J. Qi
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Q. Li
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Z. Lin
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Z. Liao
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Q. Wei
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - S. Cao
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - J. Rong
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Z. Hu
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - M. Yang
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Y. Zhang
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Q. Lv
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - J. Huang
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Y. Pan
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Y. Wu
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - O. Jin
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - T. Li
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - J. Gu
- Department of Rheumatology; Third Affiliated Hospital of Sun Yat-sen University; Guangzhou China
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32
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Tu B, Cha N, Yang R, Ng J, Hurley CK. A one-step DNA sequencing strategy to HLA type hematopoietic stem cell donors at recruitment - rethinking typing strategies. ACTA ACUST UNITED AC 2013; 81:150-60. [PMID: 23398508 DOI: 10.1111/tan.12072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/27/2012] [Accepted: 01/21/2013] [Indexed: 10/27/2022]
Abstract
In order to reduce the time required to identify a match for unrelated donor hematopoietic stem cell transplantation, a one-step DNA sequencing strategy was employed at the time of recruitment. The impact of this strategy on human leukocyte antigen (HLA) typing resolution and the effect of current registry requirements on resolution and coding of assignments were evaluated. Sanger-based DNA sequencing was used to obtain diploid exons 2 and 3 HLA-A, -B and -C assignments of 2747 unrelated African American and 1822 European American volunteers at recruitment. The results demonstrate the high resolution of the approach and challenge several aspects of the current registry typing strategy. Of the 46% of African American and 74% of European American individuals whose HLA typing resulted in alternative genotypes, the majority (≥93%) was predicted to have only a single 'common' genotype among the alternatives. The common practice of adding secondary assays to resolve alternative genotype assignments that include more than two antigen groups was also evaluated. While the percentage of assignments with greater than two antigen groups reached as high as 21% (HLA-A in European Americans), only 1.8% of individuals at most carried two common genotypes encompassing three antigen groups. The assignment of (National Marrow Donor Program) NMDP-designated allele codes to the one-pass results reduced the resolution substantially and introduced genotypes that were not included in the laboratory's assignments. We suggest the alternative strategy of using the exons 2-3 diploid nucleotide sequence as the assignment submitted to the registry with the added benefit of immortalizing the assignment in time regardless of the introduction of novel alleles. To keep pace with current donor selection criteria and with the increasing number of new alleles, it is time to rethink our recruitment typing strategies.
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Affiliation(s)
- B Tu
- Department of Pediatrics, CW Bill Young Marrow Donor Recruitment and Research Program, Georgetown University, Washington, DC, USA
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33
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Holmes JC, Holmer SG, Ross P, Buntzman AS, Frelinger JA, Hess PR. Polymorphisms and tissue expression of the feline leukocyte antigen class I loci FLAI-E, FLAI-H, and FLAI-K. Immunogenetics 2013; 65:675-89. [PMID: 23812210 PMCID: PMC3777221 DOI: 10.1007/s00251-013-0711-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 05/18/2013] [Indexed: 01/14/2023]
Abstract
Cytotoxic CD8+ T-cell immunosurveillance for intracellular pathogens, such as viruses, is controlled by classical major histocompatibility complex (MHC) class Ia molecules, and ideally, these antiviral T-cell populations are defined by the specific peptide and restricting MHC allele. Surprisingly, despite the utility of the cat in modeling human viral immunity, little is known about the feline leukocyte antigen class I complex (FLAI). Only a few coding sequences with uncertain locus origin and expression patterns have been reported. Of 19 class I genes, three loci--FLAI-E, FLAI-H, and FLAI-K--are predicted to encode classical molecules, and our objective was to evaluate their status by analyzing polymorphisms and tissue expression. Using locus-specific, PCR-based genotyping, we amplified 33 FLAI-E, FLAI-H, and FLAI-K alleles from 12 cats of various breeds, identifying, for the first time, alleles across three distinct loci in a feline species. Alleles shared the expected polymorphic and invariant sites in the α1/α2 domains, and full-length cDNA clones possessed all characteristic class Ia exons. Alleles could be assigned to a specific locus with reasonable confidence, although there was evidence of potentially confounding interlocus recombination between FLAI-E and FLAI-K. Only FLAI-E, FLAI-H, and FLAI-K origin alleles were amplified from cDNAs of multiple tissue types. We also defined hypervariable regions across these genes, which permitted the assignment of names to both novel and established alleles. As predicted, FLAI-E, FLAI-H, and FLAI-K fulfill the major criteria of class Ia genes. These data represent a necessary prerequisite for studying epitope-specific antiviral CD8+ T-cell responses in cats.
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Affiliation(s)
- Jennifer C. Holmes
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Savannah G. Holmer
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Peter Ross
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Adam S. Buntzman
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Jeffrey A. Frelinger
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Paul R. Hess
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
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34
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Song S, Han M, Zhang H, Wang Y, Jiang H. Full screening and accurate subtyping of HLA-A*02 alleles through group-specific amplification and mono-allelic sequencing. Cell Mol Immunol 2013; 10:490-6. [PMID: 23954948 DOI: 10.1038/cmi.2013.33] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 06/13/2013] [Indexed: 11/09/2022] Open
Abstract
HLA-A*02 is the most prevalent and polymorphic major histocompatibility complex (MHC) allele family in humans. Functional differences have been revealed among subtypes, demanding further subtyping of HLA-A*02 in basic and clinical settings. However, the fast growing polymorphisms render traditional primer- or probe-based typing methods impractical and result in increasing ambiguities in direct sequence-based typing. In this study, we combined group-specific amplification and mono-allelic sequencing to design and validate a simple scheme for the complete screening and accurate subtyping of all 540 reported HLA-A*02 alleles. This scheme could be performed in routine labs to facilitate studies with an interest in HLA-A*02.
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35
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Foster L, Tate D, Poulton K. A group-specific sequencing approach to investigate the presence of atypical human leucocyte antigen alleles. Int J Immunogenet 2013; 40:453-9. [PMID: 23724946 DOI: 10.1111/iji.12070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/26/2013] [Accepted: 05/15/2013] [Indexed: 11/29/2022]
Abstract
Accurate human leucocyte antigen (HLA) typing results are essential in determining the degree of compatibility between donor and recipient in both solid organ (SO) and hematopoietic stem cell (HSC) transplantation. Current HLA typing methodologies can generate ambiguous results which may need resolving. This group-specific sequencing approach allowed investigation into the presence of the low expressor HLA-A*24:02:01:02L allele and the rare HLA-A*02:64 allele in a SO transplant recipient and a HSC transplant recipient, respectively. Locus-specific amplification of HLA-A was performed. Exons 2 and 3 were sequenced in both directions followed by group-specific sequencing to resolve ambiguities. Hemizygous sequence data of intron 2 generated from the HLA-A*24 allele indicated the presence of the HLA-A*24:02:01:01 allele. HLA-A*02:64 was identified by sequencing the allele in isolation over exons 2 and 3 and allowed confirmation of this allele sequence with the IMGT/HLA database (Accession number AY297166). This approach is cost efficient and can be modified to sequence alleles at other HLA loci. It has also been adapted to characterize the novel HLA-DQB1*06:48 allele (Accession number HE647646) as well as the non-HLA gene, UGT2B17, making it a useful tool to augment existing typing methodologies.
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Affiliation(s)
- L Foster
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester, UK
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36
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Yao Y, Shi L, Tao Y, Kulski JK, Lin K, Huang X, Xiang H, Chu J, Shi L. Distinct HLA allele and haplotype distributions in four ethnic groups of China. ACTA ACUST UNITED AC 2013; 80:452-61. [PMID: 23020309 DOI: 10.1111/tan.12007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Distinct human leukocyte antigen (HLA) allele and haplotype distributions occur in the northern and southern Han populations of China. However, different ethnic groups in China show limited regional distributions for many HLA alleles and haplotypes. Therefore, it is necessary and meaningful to study the differences in HLA allele and haplotype distribution for northern and southern ethnic groups of China. A total of 428 unrelated individuals from the Lisu, Nu, Tu and Yugur ethnic populations were genotyped for HLA-A, -B, -C and -DRB1 alleles using the PCR-Luminex typing method. The frequencies of HLA alleles and statistically inferred haplotypes were calculated. A total of 29 HLA-A, 54 HLA-B, 27 HLA-C and 41 HLA-DRB1 alleles were spread throughout these four populations with distinct allele and deduced haplotype frequencies between populations. Some alleles and deduced haplotypes exhibited significantly different distributions between northern (Tu and Yugur) and southern groups (Lisu and Nu). A phylogenetic tree and principal component analysis were used to compare the HLA polymorphism between our dataset and 19 other eastern and southeastern Asian populations. This analysis showed that Lisu and Nu belong to a cluster of southern ethnic groups, while Tu and Yugur are most closely related to other northern groups. Thus, distinct ethnic population histories were revealed by analyzing HLA allelic polymorphisms with the HLA profiles of the Lisu and Nu southern Chinese ethnic groups clearly different from the Tu and Yugur northern ethnic groups. The results will be useful for future association studies of infectious disease and contribute toward a more efficient search of organ/tissue matches for transplantation.
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Affiliation(s)
- Y Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, 650118, China
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37
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Anti–IFN-γ autoantibodies in adults with disseminated nontuberculous mycobacterial infections are associated with HLA-DRB1*16:02 and HLA-DQB1*05:02 and the reactivation of latent varicella-zoster virus infection. Blood 2013; 121:1357-66. [PMID: 23243276 DOI: 10.1182/blood-2012-08-452482] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Key Points
Anti–IFN-γ autoantibodies are associated with HLA-DRB1*16:02 and DQB1*05:02.
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38
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Peterson TA, Kimani J, Wachihi C, Bielawny T, Mendoza L, Thavaneswaran S, Narayansingh MJ, Kariri T, Liang B, Ball TB, Ngugi EN, Plummer FA, Luo M. HLA class I associations with rates of HIV-1 seroconversion and disease progression in the Pumwani Sex Worker Cohort. ACTA ACUST UNITED AC 2013; 81:93-107. [DOI: 10.1111/tan.12051] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 11/20/2012] [Accepted: 12/16/2012] [Indexed: 12/01/2022]
Affiliation(s)
- T. A. Peterson
- HIV and Human Genetics, National Microbiology Laboratory; Winnipeg; MB; Canada
| | | | - C. Wachihi
- Department of Medical Microbiology; University of Nairobi; Nairobi; Kenya
| | - T. Bielawny
- HIV and Human Genetics, National Microbiology Laboratory; Winnipeg; MB; Canada
| | - L. Mendoza
- HIV and Human Genetics, National Microbiology Laboratory; Winnipeg; MB; Canada
| | - S. Thavaneswaran
- Department of Medical Microbiology; University of Manitoba; Winnipeg; MB; Canada
| | - M. J. Narayansingh
- Department of Medical Microbiology; University of Manitoba; Winnipeg; MB; Canada
| | - T. Kariri
- Department of Medical Microbiology; University of Nairobi; Nairobi; Kenya
| | - B. Liang
- Department of Medical Microbiology; University of Manitoba; Winnipeg; MB; Canada
| | | | - E. N. Ngugi
- Department of Community Health; University of Nairobi; Nairobi; Kenya
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39
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Lazaro A, Tu B, Yang R, Xiao Y, Kariyawasam K, Ng J, Hurley CK. Human leukocyte antigen (HLA) typing by DNA sequencing. Methods Mol Biol 2013; 1034:161-95. [PMID: 23775737 DOI: 10.1007/978-1-62703-493-7_9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
DNA sequencing is a powerful technique for identifying allelic variation within the human leukocyte antigen (HLA) genes. Sequencing is usually focused on the most polymorphic exons of the class I (HLA-A, -B, -C) and class II (HLA-DR, -DQ, and -DP) genes. These exons encode the antigen recognition site, the region of the HLA molecule that binds peptides and interacts with the T cell receptor for antigen and natural killer cell immunoglobulin-like receptors (KIR). Sanger sequencing of amplified DNA from each HLA gene from a preparation containing one or two alleles yields a sequence that is used to identify the alleles by comparison with a reference database.
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Affiliation(s)
- Ana Lazaro
- CW Bill Young Marrow Donor Recruitment and Research Program, Department of Pediatrics, Georgetown University Medical Center, Rockville, MD, USA
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40
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Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, Holt RA. Derivation of HLA types from shotgun sequence datasets. Genome Med 2012; 4:95. [PMID: 23228053 PMCID: PMC3580435 DOI: 10.1186/gm396] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 10/12/2012] [Accepted: 12/10/2012] [Indexed: 12/19/2022] Open
Abstract
The human leukocyte antigen (HLA) is key to many aspects of human physiology and medicine. All current sequence-based HLA typing methodologies are targeted approaches requiring the amplification of specific HLA gene segments. Whole genome, exome and transcriptome shotgun sequencing can generate prodigious data but due to the complexity of HLA loci these data have not been immediately informative regarding HLA genotype. We describe HLAminer, a computational method for identifying HLA alleles directly from shotgun sequence datasets (http://www.bcgsc.ca/platform/bioinfo/software/hlaminer). This approach circumvents the additional time and cost of generating HLA-specific data and capitalizes on the increasing accessibility and affordability of massively parallel sequencing.
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Affiliation(s)
- René L Warren
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Gina Choe
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Douglas J Freeman
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Mauro Castellarin
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Sarah Munro
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Richard Moore
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Robert A Holt
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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41
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Cotton LA, Abdur Rahman M, Ng C, Le AQ, Milloy MJ, Mo T, Brumme ZL. HLA class I sequence-based typing using DNA recovered from frozen plasma. J Immunol Methods 2012; 382:40-7. [PMID: 22584155 DOI: 10.1016/j.jim.2012.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 03/26/2012] [Accepted: 05/01/2012] [Indexed: 11/28/2022]
Abstract
We describe a rapid, reliable and cost-effective method for intermediate-to-high-resolution sequence-based HLA class I typing using frozen plasma as a source of genomic DNA. The plasma samples investigated had a median age of 8.5 years. Total nucleic acids were isolated from matched frozen PBMC (~2.5 million) and plasma (500 μl) samples from a panel of 25 individuals using commercial silica-based kits. Extractions yielded median [IQR] nucleic acid concentrations of 85.7 [47.0-130.0]ng/μl and 2.2 [1.7-2.6]ng/μl from PBMC and plasma, respectively. Following extraction, ~1000 base pair regions spanning exons 2 and 3 of HLA-A, -B and -C were amplified independently via nested PCR using universal, locus-specific primers and sequenced directly. Chromatogram analysis was performed using commercial DNA sequence analysis software and allele interpretation was performed using a free web-based tool. HLA-A, -B and -C amplification rates were 100% and chromatograms were of uniformly high quality with clearly distinguishable mixed bases regardless of DNA source. Concordance between PBMC and plasma-derived HLA types was 100% at the allele and protein levels. At the nucleotide level, a single partially discordant base (resulting from a failure to call both peaks in a mixed base) was observed out of >46,975 bases sequenced (>99.9% concordance). This protocol has previously been used to perform HLA class I typing from a variety of genomic DNA sources including PBMC, whole blood, granulocyte pellets and serum, from specimens up to 30 years old. This method provides comparable specificity to conventional sequence-based approaches and could be applied in situations where cell samples are unavailable or DNA quantities are limiting.
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Affiliation(s)
- Laura A Cotton
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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42
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Dunn PPJ. Human leucocyte antigen typing: techniques and technology, a critical appraisal. Int J Immunogenet 2012; 38:463-73. [PMID: 22059555 DOI: 10.1111/j.1744-313x.2011.01040.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Methods for the identification of Human Leukocyte Antigens (HLA) have changed significantly since this group of polymorphic proteins were first characterized by serological reagents in the 1960s and 1970s. The invention and development of the Polymerase Chain Reaction (PCR) has been key in the progress of methods for HLA genotyping. As the complexity of HLA polymorphism has unravelled so it has exposed the weaknesses in techniques such as PCR - Restriction Fragment Length Polymorphism (RFLP) and Reference Strand Mediated Conformation Analysis (RSCA), which are no longer in use today. Methods which have been considered routine laboratory tools in recent years, such as Sequence-Specific Primer - PCR and Sequencing Based Typing (SBT) are now also threatened with extinction, not only because of the depth of HLA variation but also because of the rapid development of Next Generation Sequencing and technologies which will follow this. This review describes the merits and disadvantages of current technologies available to HLA Typing laboratories, future trends and the problems posed by new alleles.
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Affiliation(s)
- P P J Dunn
- Tissue Typing Laboratory, New Zealand Blood Service, Auckland, New Zealand.
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43
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Abstract
Sequencing-based typing is a high resolution method for the identification of HLA polymorphisms. The majority of HLA Class I alleles can be discriminated by their exon 2 and 3 sequence, and for Class II alleles, exon 2 is generally sufficient. There are polymorphic positions in other exons which may require additional sequencing to exclude certain alleles with differences outside exon 2 and 3, depending on the clinical requirement and relevant accredition guidelines. The process involves selective amplification of target alleles by PCR, agarose gel electrophoresis of the PCR products to assess the quantity and quality, followed by purification of PCR amplicons to remove excess primer and dNTPs. Cycle sequencing reactions using Applied Biosystems™ BigDye(®) Terminator Ready Reaction v1.1 or v3.1 Kit are performed, then purification of sequence reactions before electrophoresing using Applied Biosystems™ 3730 or 3730XL Genetic Analyser (or similar). Data is processed by specialised software packages, which compare the sample sequence to the sequences of all possible theoretical allele combinations to assign an accurate genotype. Examination of all nucleotides, both at conserved and polymorphic positions enables the direct identification of new alleles, which may not be possible with techniques such as SSP and SSO typing.
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Affiliation(s)
- Linda K Smith
- Department of Clinical Immunology, PathWest Laboratory Medicine, Royal Perth Hospital, Perth, WA, Australia.
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44
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Agrawal S, Sharma RK. The past, present, and future of human leukocyte antigen techniques. INDIAN JOURNAL OF TRANSPLANTATION 2012. [DOI: 10.1016/s2212-0017(12)60074-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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45
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Isabey EP, Pham HM, Peterson TA, Brunham RC, Luo M, Plummer FA. Identification of a novel HLA-A allele, A*29:28, in an East African population. TISSUE ANTIGENS 2011; 78:451-452. [PMID: 21790513 DOI: 10.1111/j.1399-0039.2011.01741.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The new allele is identical to A*29:01:01:01 in exons 2 and 3, except for a single-nucleotide substitution (TTG to TGG) at codon 156.
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Affiliation(s)
- E P Isabey
- Department of HIV and Human Genetics, National Microbiology Laboratory, Winnipeg, MB, Canada
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46
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Abstract
A novel HLA allele, HLA-A*30:36, is found in a donor from the Central German Bone Marrow Donor Registry.
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Affiliation(s)
- L Jennings
- Children's Memorial Hospital, HLA and Molecular Diagnostics Laboratories, Chicago, IL, USA
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47
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Ugolotti E, Vanni I, Raso A, Benzi F, Malnati M, Biassoni R. Human leukocyte antigen–B (-Bw6/-Bw4 I80, T80) and human leukocyte antigen–C (-C1/-C2) subgrouping using pyrosequence analysis. Hum Immunol 2011; 72:859-68. [DOI: 10.1016/j.humimm.2011.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 05/03/2011] [Accepted: 05/13/2011] [Indexed: 10/18/2022]
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48
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Dello Russo C, Lisi L, Lofaro A, Di Giambenedetto S, Federico B, Madeddu G, Salerno M, Mura MS, Pirazzoli A, de Luca A, Cauda R, Navarra P. Novel sensitive, specific and rapid pharmacogenomic test for the prediction of abacavir hypersensitivity reaction: HLA-B*57:01 detection by real-time PCR. Pharmacogenomics 2011; 12:567-76. [PMID: 21521028 DOI: 10.2217/pgs.10.208] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM International HIV treatment guidelines recommend HLA-B*57:01 typing before abacavir administration, in order to reduce the incidence of abacavir hypersensitivity reactions, the major cause of early therapy discontinuation. A fast, sensitive and specific test for HLA-B*57:01 detection has been developed in the present study. MATERIALS & METHODS Two sets of sequence-specific primers were designed, and amplification rapidly detected by real-time PCR. RESULTS A total of 108 samples were analyzed in a single-blind fashion, and 41 samples were identified as positive. Complete agreement, with κ = 1 (standard error = 0.0962, p < 0.0001), was found, with a validated methodology used in the EPI109367 clinical trial funded by GlaxoSmithKline, and consisting of low-resolution sequence-specific oligonucleotide PCR, followed by high-resolution sequence-specific oligonucleotide PCR carried out on the HLA-B*57-positive samples. CONCLUSION We provided a detailed characterization of a novel HLA-B*57:01 screening test, which can be easily implemented by those laboratories already involved in the detection of viral load and virus genotyping. Original submitted 26 October 2010; Revision submitted 13 December 2010.
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Affiliation(s)
- Cinzia Dello Russo
- Institute of Pharmacology, Catholic University Medical School, Rome, Italy
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Tiemessen CT, Paximadis M, Minevich G, Winchester R, Shalekoff S, Gray GE, Sherman GG, Coovadia AH, Kuhn L. Natural killer cell responses to HIV-1 peptides are associated with more activating KIR genes and HLA-C genes of the C1 allotype. J Acquir Immune Defic Syndr 2011; 57:181-9. [PMID: 21407082 PMCID: PMC3280081 DOI: 10.1097/qai.0b013e3182174a76] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND What characterizes individuals whose natural killer (NK) cells are able to respond to HIV-1 peptides is not known. METHODS The association between NK cell responses and KIR gene profiles and HLA-B and HLA-C alleles was investigated among 76 HIV-1-infected women in South Africa previously categorized as responders (n = 39) or nonresponders (n = 37) to HIV-1 peptide pools in a whole blood intracellular cytokine assay. Viral load was significantly lower and CD4 T-cell counts higher among responders compared with nonresponders (P = 0.023 and P = 0.030, respectively). RESULTS Possession of one HLA-C1 allele associated with increased magnitude of NK cell responses to Env (P = 0.031) and significantly decreased viral load (P = 0.027) compared with its absence. There was a trend to increased possession of KIR2DL3+HLA-C1 in responders (71.8% vs 51.4%, P = 0.098) and decreased possession of KIR2DL3/2DL3+C2C2 (2.6% vs 16.2%, P = 0.053). A total of 64.1% of responders versus 32.4% of nonresponders had 13 or more KIR genes (P = 0.0067). Notably, the 13-KIR gene containing the Bx21 genotype (has eight inhibitory and three activating genes KIR2DS2, 2DS4, 2DS5) showed substantially higher representation among the responders (28.2% vs 2.6%, P = 0.001). A significantly higher proportion of responders had both KIR2DS2 and KIR2DS5 compared with either gene alone (72.4% vs 37%; P = 0.015). At least one HLA-C1 allele together with 13 or more KIR genes was associated with NK cell responsiveness (48.7% vs 13.5%; P = 0.001). CONCLUSION NK cell responses to HIV-1 peptides are more likely to occur among individuals with a genotype supporting a more activating NK cell phenotype and who possess at least one HLA-C1 allele.
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Miao F, Sun H, Pan N, Shen Y, Xie W, Zhang J. Two novel HLA class I alleles, HLA-B*40:122 and HLA-B*40:127. ACTA ACUST UNITED AC 2011; 77:156-7. [PMID: 21214529 DOI: 10.1111/j.1399-0039.2010.01586.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The new alleles human leukocyte antigen (HLA)-B*40:122 and HLA-B*40:127 differs from B*40:02:01 and B*40:06:01:01 by a single nucleotide, respectively.
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Affiliation(s)
- F Miao
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University Medical School, Nanjing, Jiangsu, China
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