PMID- 32547543 OWN - NLM STAT- MEDLINE DCOM- 20210406 LR - 20240408 IS - 1664-3224 (Electronic) IS - 1664-3224 (Linking) VI - 11 DP - 2020 TI - Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes by a New Capture RNA-Seq Method. PG - 941 LID - 10.3389/fimmu.2020.00941 [doi] LID - 941 AB - The highly polymorphic human major histocompatibility complex (MHC) also known as the human leukocyte antigen (HLA) encodes class I and II genes that are the cornerstone of the adaptive immune system. Their unique diversity (>25,000 alleles) might affect the outcome of any transplant, infection, and susceptibility to autoimmune diseases. The recent rapid development of new next-generation sequencing (NGS) methods provides the opportunity to study the influence/correlation of this high level of HLA diversity on allele expression levels in health and disease. Here, we describe the NGS capture RNA-Seq method that we developed for genotyping all 12 classical HLA loci (HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, and HLA-DRB5) and assessing their allelic imbalance by quantifying their allele RNA levels. This is a target enrichment method where total RNA is converted to a sequencing-ready complementary DNA (cDNA) library and hybridized to a complex pool of RNA-specific HLA biotinylated oligonucleotide capture probes, prior to NGS. This method was applied to 161 peripheral blood mononuclear cells and 48 umbilical cord blood cells of healthy donors. The differential allelic expression of 10 HLA loci (except for HLA-DRA and HLA-DPA1) showed strong significant differences (P < 2.1 x 10(-15)). The results were corroborated by independent methods. This newly developed NGS method could be applied to a wide range of biological and medical questions including graft rejections and HLA-related diseases. CI - Copyright (c) 2020 Yamamoto, Suzuki, Mizutani, Shigenari, Ito, Kametani, Kato, Fernandez-Vina, Murata, Morishima, Morishima, Tanaka, Kulski, Bahram and Shiina. FAU - Yamamoto, Fumiko AU - Yamamoto F AD - Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States. AD - Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan. FAU - Suzuki, Shingo AU - Suzuki S AD - Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan. FAU - Mizutani, Akiko AU - Mizutani A AD - Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan. AD - Faculty of Health and Medical Science, Teikyo Heisei University, Toshima-ku, Tokyo, Japan. FAU - Shigenari, Atsuko AU - Shigenari A AD - Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan. FAU - Ito, Sayaka AU - Ito S AD - Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan. FAU - Kametani, Yoshie AU - Kametani Y AD - Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan. FAU - Kato, Shunichi AU - Kato S AD - Division of Hematopoietic Cell Transplantation, Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan. FAU - Fernandez-Vina, Marcelo AU - Fernandez-Vina M AD - Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States. AD - Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Stanford Health Care, Palo Alto, CA, United States. FAU - Murata, Makoto AU - Murata M AD - Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan. FAU - Morishima, Satoko AU - Morishima S AD - Division of Endocrinology, Diabetes and Metabolism, Hematology, Rheumatology, Second Department of Internal Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan. FAU - Morishima, Yasuo AU - Morishima Y AD - Department of Promotion for Blood and Marrow Transplantation, Aichi Medical University School of Medicine, Nagakute, Japan. FAU - Tanaka, Masafumi AU - Tanaka M AD - Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan. FAU - Kulski, Jerzy K AU - Kulski JK AD - Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan. AD - Faculty of Health and Medical Sciences, The University of Western Australia Medical School, Crawley, WA, Australia. FAU - Bahram, Seiamak AU - Bahram S AD - Laboratoire d'ImmunoRhumatologie Moleculaire, Plateforme GENOMAX, INSERM UMR_S 1109, LabEx TRANSPLANTEX, Federation Hospitalo-Universitaire OMICARE, Laboratoire International Associe INSERM FJ-HLA-Japan, Federation de Medecine Translationnelle de Strasbourg (FMTS), Faculte de Medecine, Universite de Strasbourg, Service d'Immunologie Biologique, Nouvel Hopital Civil, Strasbourg, France. FAU - Shiina, Takashi AU - Shiina T AD - Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20200529 PL - Switzerland TA - Front Immunol JT - Frontiers in immunology JID - 101560960 RN - 0 (HLA Antigens) SB - IM CIN - Front Immunol. 2024 Jan 24;14:1332636. PMID: 38327766 MH - Gene Frequency MH - *Genetic Loci MH - HLA Antigens/*genetics/immunology MH - *Haplotypes MH - High-Throughput Nucleotide Sequencing MH - Humans MH - Polymorphism, Single Nucleotide MH - Predictive Value of Tests MH - *RNA-Seq MH - Reproducibility of Results PMC - PMC7272581 OTO - NOTNLM OT - HLA allele OT - RNA expression level OT - capture RNA-Seq OT - genotyping OT - human leukocyte antigen OT - next-generation sequencing EDAT- 2020/06/18 06:00 MHDA- 2021/04/07 06:00 PMCR- 2020/01/01 CRDT- 2020/06/18 06:00 PHST- 2019/12/03 00:00 [received] PHST- 2020/04/22 00:00 [accepted] PHST- 2020/06/18 06:00 [entrez] PHST- 2020/06/18 06:00 [pubmed] PHST- 2021/04/07 06:00 [medline] PHST- 2020/01/01 00:00 [pmc-release] AID - 10.3389/fimmu.2020.00941 [doi] PST - epublish SO - Front Immunol. 2020 May 29;11:941. doi: 10.3389/fimmu.2020.00941. eCollection 2020.