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Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes by a New Capture RNA-Seq Method.
Front Immunol. 2020; 11:941.FI

Abstract

The highly polymorphic human major histocompatibility complex (MHC) also known as the human leukocyte antigen (HLA) encodes class I and II genes that are the cornerstone of the adaptive immune system. Their unique diversity (>25,000 alleles) might affect the outcome of any transplant, infection, and susceptibility to autoimmune diseases. The recent rapid development of new next-generation sequencing (NGS) methods provides the opportunity to study the influence/correlation of this high level of HLA diversity on allele expression levels in health and disease. Here, we describe the NGS capture RNA-Seq method that we developed for genotyping all 12 classical HLA loci (HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, and HLA-DRB5) and assessing their allelic imbalance by quantifying their allele RNA levels. This is a target enrichment method where total RNA is converted to a sequencing-ready complementary DNA (cDNA) library and hybridized to a complex pool of RNA-specific HLA biotinylated oligonucleotide capture probes, prior to NGS. This method was applied to 161 peripheral blood mononuclear cells and 48 umbilical cord blood cells of healthy donors. The differential allelic expression of 10 HLA loci (except for HLA-DRA and HLA-DPA1) showed strong significant differences (P < 2.1 × 10-15). The results were corroborated by independent methods. This newly developed NGS method could be applied to a wide range of biological and medical questions including graft rejections and HLA-related diseases.

Authors+Show Affiliations

Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States. Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan. Faculty of Health and Medical Science, Teikyo Heisei University, Toshima-ku, Tokyo, Japan.Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.Division of Hematopoietic Cell Transplantation, Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan.Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States. Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Stanford Health Care, Palo Alto, CA, United States.Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan.Division of Endocrinology, Diabetes and Metabolism, Hematology, Rheumatology, Second Department of Internal Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan.Department of Promotion for Blood and Marrow Transplantation, Aichi Medical University School of Medicine, Nagakute, Japan.Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan. Faculty of Health and Medical Sciences, The University of Western Australia Medical School, Crawley, WA, Australia.Laboratoire d'ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, LabEx TRANSPLANTEX, Fédération Hospitalo-Universitaire OMICARE, Laboratoire International Associé INSERM FJ-HLA-Japan, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Faculté de Médecine, Université de Strasbourg, Service d'Immunologie Biologique, Nouvel Hôpital Civil, Strasbourg, France.Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32547543

Citation

Yamamoto, Fumiko, et al. "Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes By a New Capture RNA-Seq Method." Frontiers in Immunology, vol. 11, 2020, p. 941.
Yamamoto F, Suzuki S, Mizutani A, et al. Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes by a New Capture RNA-Seq Method. Front Immunol. 2020;11:941.
Yamamoto, F., Suzuki, S., Mizutani, A., Shigenari, A., Ito, S., Kametani, Y., Kato, S., Fernandez-Viña, M., Murata, M., Morishima, S., Morishima, Y., Tanaka, M., Kulski, J. K., Bahram, S., & Shiina, T. (2020). Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes by a New Capture RNA-Seq Method. Frontiers in Immunology, 11, 941. https://doi.org/10.3389/fimmu.2020.00941
Yamamoto F, et al. Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes By a New Capture RNA-Seq Method. Front Immunol. 2020;11:941. PubMed PMID: 32547543.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Capturing Differential Allele-Level Expression and Genotypes of All Classical HLA Loci and Haplotypes by a New Capture RNA-Seq Method. AU - Yamamoto,Fumiko, AU - Suzuki,Shingo, AU - Mizutani,Akiko, AU - Shigenari,Atsuko, AU - Ito,Sayaka, AU - Kametani,Yoshie, AU - Kato,Shunichi, AU - Fernandez-Viña,Marcelo, AU - Murata,Makoto, AU - Morishima,Satoko, AU - Morishima,Yasuo, AU - Tanaka,Masafumi, AU - Kulski,Jerzy K, AU - Bahram,Seiamak, AU - Shiina,Takashi, Y1 - 2020/05/29/ PY - 2019/12/03/received PY - 2020/04/22/accepted PY - 2020/6/18/entrez PY - 2020/6/18/pubmed PY - 2020/6/18/medline KW - HLA allele KW - RNA expression level KW - capture RNA-Seq KW - genotyping KW - human leukocyte antigen KW - next-generation sequencing SP - 941 EP - 941 JF - Frontiers in immunology JO - Front Immunol VL - 11 N2 - The highly polymorphic human major histocompatibility complex (MHC) also known as the human leukocyte antigen (HLA) encodes class I and II genes that are the cornerstone of the adaptive immune system. Their unique diversity (>25,000 alleles) might affect the outcome of any transplant, infection, and susceptibility to autoimmune diseases. The recent rapid development of new next-generation sequencing (NGS) methods provides the opportunity to study the influence/correlation of this high level of HLA diversity on allele expression levels in health and disease. Here, we describe the NGS capture RNA-Seq method that we developed for genotyping all 12 classical HLA loci (HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, and HLA-DRB5) and assessing their allelic imbalance by quantifying their allele RNA levels. This is a target enrichment method where total RNA is converted to a sequencing-ready complementary DNA (cDNA) library and hybridized to a complex pool of RNA-specific HLA biotinylated oligonucleotide capture probes, prior to NGS. This method was applied to 161 peripheral blood mononuclear cells and 48 umbilical cord blood cells of healthy donors. The differential allelic expression of 10 HLA loci (except for HLA-DRA and HLA-DPA1) showed strong significant differences (P < 2.1 × 10-15). The results were corroborated by independent methods. This newly developed NGS method could be applied to a wide range of biological and medical questions including graft rejections and HLA-related diseases. SN - 1664-3224 UR - https://www.unboundmedicine.com/medline/citation/32547543/Capturing_Differential_Allele-Level_Expression_and_Genotypes_of_All_Classical_HLA_Loci_and_Haplotypes_by_a_New_Capture_RNA-Seq_Method L2 - https://doi.org/10.3389/fimmu.2020.00941 DB - PRIME DP - Unbound Medicine ER -
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