1
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Wassenaar TM, Harville T, Chastain J, Wanchai V, Ussery DW. DNA structural features and variability of complete MHC locus sequences. FRONTIERS IN BIOINFORMATICS 2024; 4:1392613. [PMID: 39022183 PMCID: PMC11251971 DOI: 10.3389/fbinf.2024.1392613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/07/2024] [Indexed: 07/20/2024] Open
Abstract
The major histocompatibility (MHC) locus, also known as the Human Leukocyte Antigen (HLA) genes, is located on the short arm of chromosome 6, and contains three regions (Class I, Class II and Class III). This 5 Mbp locus is one of the most variable regions of the human genome, yet it also encodes a set of highly conserved and important proteins related to immunological response. Genetic variations in this region are responsible for more diseases than in the entire rest of the human genome. However, information on local structural features of the DNA is largely ignored. With recent advances in long-read sequencing technology, it is now becoming possible to sequence the entire 5 Mbp MHC locus, producing complete diploid haplotypes of the whole region. Here, we describe structural maps based on the complete sequences from six different homozygous HLA cell lines. We find long-range structural variability in the different sequences for DNA stacking energy, position preference and curvature, variation in repeats, as well as more local changes in regions forming open chromatin structures, likely to influence gene expression levels. These structural maps can be useful in visualizing large scale structural variation across HLA types, in particular when this can be complemented with epigenetic signals.
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Affiliation(s)
| | - Terry Harville
- Department of Pathology and Laboratory Services, and Department of Internal Medicine, Division of Hematology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Jonathan Chastain
- Department of Pediatrics, The University of Arkansas for Medical Sciences University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Visanu Wanchai
- Myeloma Center, Winthrop P. Rockefeller Institute, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - David W. Ussery
- Department of BioMedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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2
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Jeong IH, Lee JK, Kwon WK, Song EY, Kim KH, Lee J, Jung S, Jeong M, Park JW, Kang ES. Characterization of novel HLA-A*24:608N allele discovered in Koreans. HLA 2024; 103:e15332. [PMID: 38174645 DOI: 10.1111/tan.15332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 11/13/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
A novel null HLA-A*24 allele, HLA-A*24:608N, was identified in five Korean subjects including three from a family and two separate individuals. This study was performed to discern its immunological function in transplantation settings. Because this null variant had deletions of approximately 12 k base pairs from intron 3 to 3' end of the HLA-A gene, low resolution HLA typing and amplicon-based next generation sequencing (NGS) typing methods had failed to assign it. Hybrid capture-based NGS method confirmed that this novel variant had a large deletion. T-lymphocyte crossmatching by complement-dependent lymphocytotoxicity and flow cytometry with a serum consisting anti-HLA-A24 antibody revealed negative results, implying that an individual with this allele would not carry a functioning A24 antigen. These findings highlight the importance of identifying a null HLA allele by employing appropriate molecular method and providing expected crossmatching outcomes in a real-world transplantation setting.
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Affiliation(s)
- In Hwa Jeong
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- Department of Laboratory Medicine, Dong-A University Hospital, Dong-A University College of Medicine, Busan, South Korea
| | - Jong Kwon Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Won Kyung Kwon
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- U2Labs, Jangwon Medical Foundation, Seoul, South Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University, College of Medicine, Seoul, South Korea
| | - Kyeong-Hee Kim
- Department of Laboratory Medicine, Dong-A University Hospital, Dong-A University College of Medicine, Busan, South Korea
| | - Jina Lee
- BioTide Co., Ltd., Seoul, South Korea
| | | | - Mijeong Jeong
- Research Institute for Future Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - June-Woo Park
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Eun Suk Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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3
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Dong L, Zhao S, Wang F, Zhang W, Zhu F. Identification of the novel HLA-A*24:567N allele in a Chinese individual. HLA 2023; 102:611-612. [PMID: 37533370 DOI: 10.1111/tan.15182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
HLA-A*24:567N differs from HLA-A*24:02:01:01 by a single nucleotide deletion at position 149.
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Affiliation(s)
- Lina Dong
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Shuoxian Zhao
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Fang Wang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Wei Zhang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Faming Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
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4
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Detection and characterization of the novel HLA-DPA1*02:66:02N allele, with a premature stop codon in exon 2. Hum Immunol 2023; 84:296-300. [PMID: 36797092 DOI: 10.1016/j.humimm.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
The failure to identify HLA null alleles in bone marrow transplantation could be life-threatening because this could result in an HLA mismatch with the ability to trigger the graft-vs-host disease (GVHD) and to reduce patient's survival. In this report we describe the identification and characterization of the novel HLA-DPA1*02:66:02N allele with a non-sense codon in exon 2. This new allele was discovered in two unrelated bone marrow donors during routine HLA-typing using next-generation sequencing (NGS). DPA1*02:66:02N is homologous to DPA1*02:01:01:03 with a single nucleotide difference in exon 2, codon 50, where the replacement of C located at genomic position 3825 by T, causes the formation of a premature stop codon (TGA), resulting in a null allele. This description illustrates the benefits of HLA typing by NGS since it permits to reduce ambiguities, identify new alleles, analyze multiple HLA loci and improve transplantation outcome.
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5
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Hu Q, Burns C, McKinley C, Christian D, Berka N. Identification of a novel allele with a frameshift mutation, HLA-DRB4*01:165N, using next-generation sequencing. HLA 2022; 101:699-700. [PMID: 36572633 DOI: 10.1111/tan.14954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022]
Abstract
HLA-DRB4*01:165N exhibits deletion of a nucleotide in exon 3, producing a premature stop codon.
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Affiliation(s)
- Qian Hu
- Histocompatibility and Immunogenetics Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Caitlyn Burns
- Histocompatibility and Immunogenetics Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Connie McKinley
- Histocompatibility and Immunogenetics Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Danielle Christian
- Histocompatibility and Immunogenetics Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Noureddine Berka
- Histocompatibility and Immunogenetics Laboratory, Alberta Precision Laboratories, Calgary, Alberta, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
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6
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Kitano Y, Nishimura S, Kato TM, Ueda A, Takigawa K, Umekage M, Nomura M, Kawakami A, Ogawa H, Xu H, Hotta A, Takasu N, Tsukahara M. Generation of hypoimmunogenic induced pluripotent stem cells by CRISPR-Cas9 system and detailed evaluation for clinical application. Mol Ther Methods Clin Dev 2022; 26:15-25. [PMID: 35755947 PMCID: PMC9198376 DOI: 10.1016/j.omtm.2022.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/25/2022] [Indexed: 11/06/2022]
Abstract
In order to expand the promise of regenerative medicine using allogeneic induced pluripotent stem cells (iPSCs), precise and efficient genome editing of human leukocyte antigen (HLA) genes would be advantageous to minimize the immune rejection caused by mismatches of HLA type. However, clinical-grade genome editing of multiple HLA genes in human iPSC lines remains unexplored. Here, we optimized the protocol for good manufacturing practice (GMP)-compatible CRISPR-Cas9 genome editing to deplete the three gene locus (HLA-A, HLA-B, and CIITA genes) simultaneously in HLA homozygous iPSCs. The use of HLA homozygous iPSCs has one main advantage over heterozygous iPSCs for inducing biallelic knockout by a single gRNA. RNA-seq and flow cytometry analyses confirmed the successful depletion of HLAs, and lineage-specific differentiation into cardiomyocytes was verified. We also confirmed that the pluripotency of genome-edited iPSCs was successfully maintained by the three germ layers of differentiation. Moreover, whole-genome sequencing, karyotyping, and optical genome mapping analyses revealed no evident genomic abnormalities detected in some clones, whereas unexpected copy number losses, chromosomal translocations, and complex genomic rearrangements were observed in other clones. Our results indicate the importance of multidimensional analyses to ensure the safety and quality of the genome-edited cells. The manufacturing and assessment pipelines presented here will be the basis for clinical-grade genome editing of iPSCs.
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Affiliation(s)
- Yuko Kitano
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Sayaka Nishimura
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Tomoaki M Kato
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Anna Ueda
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Kaho Takigawa
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Masafumi Umekage
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Masaki Nomura
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Ayane Kawakami
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Haruna Ogawa
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Huaigeng Xu
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Akitsu Hotta
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Naoko Takasu
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
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7
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Hod‐Dvorai R, Schiller JJ, Riddick MC, Gallay B. Identification of a
DRB1*04:07
–
DRB4*01:03:01:02N
haplotype in a native
American
individual. HLA 2022; 100:500-504. [DOI: 10.1111/tan.14762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/26/2022] [Accepted: 08/05/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Reut Hod‐Dvorai
- Department of Pathology SUNY Upstate Medical University Syracuse New York USA
| | | | - Mary C. Riddick
- Department of Pathology SUNY Upstate Medical University Syracuse New York USA
| | - Brian Gallay
- Department of Medicine SUNY Upstate Medical University Syracuse New York USA
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8
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Marin Rubio LA, Aroca-Aguilar JD, Luis-Hidalgo M, Escribano J, Ontañon J. RNA and protein expression analysis of HLA-DQB1*03:01:01:21Q allele: A null allele renamed as HLA-DQB1*03:01:01:21N. HLA 2022; 99:160-166. [PMID: 34997833 DOI: 10.1111/tan.14537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/03/2021] [Accepted: 01/04/2022] [Indexed: 12/15/2022]
Abstract
The characterization of the expression profile of HLA questionable alleles (Q) is clinically relevant in allogeneic hematopoietic stem cell transplantation (HSTC) because an aberrant expression of these alleles could lead to transplantation-related complications. HLA-DQB1*03:01:01:21Q shows a substitution at the donor splice site of intron 3 that potentially could affect the expression of this allele. In order to determine their expression profile at RNA and protein level, we analyzed the presence of the HLA-DQ7 molecule by complement-dependent cytotoxicity test (CDC) and flow cytometry, and their RNA processing by cDNA analyses and sequencing by Sanger methods. Our results reveal that HLA-DQ7 is not detectable by serological methods, this is confirmed by cDNA methods demonstrating the absence of specific HLA-DQB1*03:01:01:21Q mRNA, probably due to an intron 3 retention that creates a premature TGA stop codon, leading to mRNA degradation via nonsense-mediated decay (NMD). These findings demonstrate that the HLA-DQB1*03:01:01:21Q allele is nonexpressed, thus it has been renamed as DQB1*03:01:01:21N.
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Affiliation(s)
- Luis Alberto Marin Rubio
- Immunology Unit, Clinical Analysis Department, Albacete University Hospital Complex, Albacete, Spain
| | - Jose Daniel Aroca-Aguilar
- Área de Genética, Facultad de Medicina de Albacete/Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha, Albacete, Spain
| | - Mar Luis-Hidalgo
- Histocompatibilidad, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
| | - Julio Escribano
- Área de Genética, Facultad de Medicina de Albacete/Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha, Albacete, Spain
| | - Jesus Ontañon
- Immunology Unit, Clinical Analysis Department, Albacete University Hospital Complex, Albacete, Spain
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9
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Liacini A, Peters L, Gravante C, Pfau K, Geier S. A novel allele, HLA-DPA1*01:87Q identified by next generation sequencing. HLA 2021; 99:147-148. [PMID: 34636171 DOI: 10.1111/tan.14457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 11/27/2022]
Abstract
A point mutation in Exon 1, 1-3 (ATG>ACG) causes a non-synonymous change to the start codon, which may affect expression.
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Affiliation(s)
- Abdelhamid Liacini
- Lewis Katz School of Medicine, Temple University Hospital, Philadelphia, Pennsylvania, USA
| | - Lindsey Peters
- Pathology & Laboratory Medicine, Temple University Hospital, Philadelphia, Pennsylvania, USA
| | - Christopher Gravante
- Pathology & Laboratory Medicine, Temple University Hospital, Philadelphia, Pennsylvania, USA
| | - Kimberly Pfau
- Pathology & Laboratory Medicine, Temple University Hospital, Philadelphia, Pennsylvania, USA
| | - Steven Geier
- Lewis Katz School of Medicine, Temple University Hospital, Philadelphia, Pennsylvania, USA
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10
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Ulrich S, Lang J, Bodem O, Posch U, Schlenke P. Identification of the novel HLA-C*03:03:01:52N allele, a splice-site variant at the boundary of intron1 and exon2. HLA 2021; 99:50-51. [PMID: 34632728 PMCID: PMC9542030 DOI: 10.1111/tan.14454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 12/03/2022]
Abstract
HLA‐C*03:03:01:52N differs from HLA‐C*03:03:01:01 by one nucleotide substitution at position gDNA 202 (A>G) in Intron1.
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Affiliation(s)
- Silvia Ulrich
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Graz, Graz, Austria
| | - Johanna Lang
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Graz, Graz, Austria
| | - Oliver Bodem
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Graz, Graz, Austria
| | - Ursula Posch
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Graz, Graz, Austria
| | - Peter Schlenke
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Graz, Graz, Austria
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11
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The HLA System in Transfusion Medicine and Transplantation. Transfus Med 2021. [DOI: 10.1002/9781119599586.ch18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Jekarl DW, Lee GD, Yoo JB, Kim JR, Yu H, Yoo J, Lim J, Kim M, Kim Y. HLA-A, -B, -C, -DRB1 allele and haplotype frequencies of the Korean population and performance characteristics of HLA typing by next-generation sequencing. HLA 2021; 97:188-197. [PMID: 33314756 DOI: 10.1111/tan.14167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/06/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Human leukocyte antigen (HLA) identification at the allelic level is important for haematopoietic stem cell transplantation (HSCT). Next-generation sequencing (NGS) resolves ambiguous alleles by determining the phase of the polymorphisms. The aim of this study was to validate the software for HLA-SBT (sequence-based typing), assess Korean allele frequency, and characterise the performance of NGS-HLA typing. METHODS From the 2009 to 2016 registry, 1293 unrelated healthy donors with a complete dataset of previously characterised HLA-A, -B, -C, and -DRB1 loci were selected and assessed for frequency, haplotype inference, and relative linkage disequilibrium. For performance characteristics of NGS-HLA, alleles included in 1293 cases and ambiguous or alleles assigned as new by SBT-HLA software, or unassigned alleles were included. A total of 91 and 41 quality control samples resulted in 1056 alleles (132 samples × 4 loci × 2 diploid) for analysis. The GenDx NGSgo kit was used for NGS-HLA typing using the Illumina MiSeq platform. RESULTS A panel of 132 samples covered 231 alleles, including 53 HLA-A, 80 HLA-B, 43 HLA-C, and 55 HLA-DRB1 by HLA-SBT typing. Comparison of SBT-HLA and NGS-HLA typing showed 99.7% (1053/1056) concordance and discrepant cases were resolved by manual evaluation. Typing by NGS resulted in 67 HLA-A, 112 HLA-B, 71 HLA-C, and 72 HLA-DRB1 alleles. A total of 132 ambiguous, 4 new, and 1 unassigned alleles by HLA-SBT were resolved by NGS-HLA typing. CONCLUSIONS NGS-HLA typing provided robust and conclusive results without ambiguities, and its implementation could support HSCT in clinical settings.
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Affiliation(s)
- Dong Wook Jekarl
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Gun Dong Lee
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jae Bin Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jung Rok Kim
- Department of Laboratory Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Haein Yu
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jaeeun Yoo
- Department of Laboratory Medicine, College of Medicine, Incheon St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jihyang Lim
- Department of Laboratory Medicine, College of Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
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13
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Cheranev V, Loginova M, Jankevic T, Rebrikov D, Korostin D. HLA-A*11:382N, a novel HLA-A null allele identified by next-generation sequencing. HLA 2021; 97:448-449. [PMID: 33448684 DOI: 10.1111/tan.14185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 12/01/2022]
Abstract
The new allele HLA-A*11:382N showed one nucleotide difference with HLA-A*11:01:01:01 at codon 254 (nonsense mutation).
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Affiliation(s)
- Valery Cheranev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Moscow, Russia
| | - Maria Loginova
- The Research Laboratory of Applied Immunogenetics, Federal State Budget Research Institution: Kirov Hematology and Blood Transfusion Research Institute under the Federal Medicine and Biology Agency, Kirov, Russia
| | - Tatjana Jankevic
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Moscow, Russia
| | - Denis Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Moscow, Russia
| | - Dmitriy Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Moscow, Russia
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14
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Lemieux W, Mohammadhassanzadeh H, Klement W, Daniel C, Sapir-Pichhadze R. Matchmaker, matchmaker make me a match: Opportunities and challenges in optimizing compatibility of HLA eplets in transplantation. Int J Immunogenet 2021; 48:135-144. [PMID: 33426788 DOI: 10.1111/iji.12525] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/12/2020] [Accepted: 12/20/2020] [Indexed: 12/20/2022]
Abstract
The development of donor-specific antibodies (DSAs) is a major complication in transplantation, which is associated with inferior graft survival, impaired quality of life, and increased healthcare costs. DSA develop upon recognition of nonself HLA by the recipient's immune system. HLA molecules contain epitopes, which are the surface regions of HLA molecules recognized by antibodies. HLAMatchmaker is an algorithm for assessing donor:recipient HLA compatibility at the level of structurally defined HLA targets called eplets. The consideration of eplets, rather than the whole HLA molecule, could offer some advantages when classifying the immune risk associated with particular donor:recipient pairs. Assessing compatibility at the level of HLA eplets could decrease misclassification of post-transplant immune risk by improving specificity, when antibodies are confirmed to be directed against donor eplets missing from the recipient's repertoire of eplets. Consideration of eplets may also increase the sensitivity of immune risk assessment, when identifying mismatched eplets that could give rise to new, not previously detected, donor-specific antibodies post-transplant. Eplet matching can serve as a rational strategy for immune risk mitigation. Herein, we review the evolution of HLA (in) compatibility assessment for organ allocation. We outline challenges in the implementation of eplet-based donor:recipient matching, including unavailability of allele-level donor genotypes for 11 HLA loci at the time of organ allocation and difficulty in assessing the hierarchy of immune risk associated with particular HLA eplet mismatches. Opportunities to address some of the current shortcomings of donor genotyping and HLAMatchmaker are also discussed. While there is a demonstrated benefit in the application of HLAMatchmaker for donor: recipient HLA (in)compatibility assessment, evolving long-read genotyping methods, compilation of large data sets with allele-level genotypes, and standardization of methods to verify eplets as determinants of immune-mediated injuries are required before HLA eplet matching is implemented in organ allocation to improve upon transplant outcomes.
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Affiliation(s)
- William Lemieux
- Centre for Outcomes Research and Evaluation (CORE), Research Institute of McGill University Health Centre, Montréal, QC, Canada
| | - Hossein Mohammadhassanzadeh
- Centre for Outcomes Research and Evaluation (CORE), Research Institute of McGill University Health Centre, Montréal, QC, Canada
| | - William Klement
- Centre for Outcomes Research and Evaluation (CORE), Research Institute of McGill University Health Centre, Montréal, QC, Canada.,Canadian Blood Services, Ottawa, Ontario, Canada
| | - Claude Daniel
- Division of Hematology, McGill University Health Centre, Montréal, QC, Canada
| | - Ruth Sapir-Pichhadze
- Centre for Outcomes Research and Evaluation (CORE), Research Institute of McGill University Health Centre, Montréal, QC, Canada.,Division of Nephrology and the Multi-Organ Transplant Program, Royal Victoria Hospital, McGill University Health Centre, Montréal, QC, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
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15
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Alvares M, Al Mahri A, Jannang R, Al Yafei Z, ElGhazali G. Identification of the novel HLA-A*26:206N allele by next generation sequencing in an Emirati bone marrow donor. HLA 2020; 96:717-718. [PMID: 32882096 DOI: 10.1111/tan.14064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 11/30/2022]
Abstract
Nucleotide sequence of HLA-A*26:206N differs from HLA-A*26:01:01 at genomic position g.1183 G>A.
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Affiliation(s)
- Marion Alvares
- Immunology and Histocompatibility Laboratory, Pathology and Laboratory Medicine Department, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Ayeda Al Mahri
- Immunology and Histocompatibility Laboratory, Pathology and Laboratory Medicine Department, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Raysha Jannang
- Immunology and Histocompatibility Laboratory, Pathology and Laboratory Medicine Department, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Zain Al Yafei
- Immunology and Histocompatibility Laboratory, Pathology and Laboratory Medicine Department, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | - Gehad ElGhazali
- Immunology and Histocompatibility Laboratory, Pathology and Laboratory Medicine Department, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
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16
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Shimizu M, Kuroda Y, Uchida M, Takada S, Kamada H, Takahashi D, Nakajima F, Miyata S, Igarashi S, Satake M. A new HLA-C allele with an alternative splice site in exon 3: HLA-C*03:23N. HLA 2020; 95:555-560. [PMID: 32034867 DOI: 10.1111/tan.13832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/25/2019] [Accepted: 02/05/2020] [Indexed: 11/26/2022]
Abstract
We identified a probable new null HLA-C allele, C*03:23N, which originated from C*03:04:01:02, but does not react with Cw3 antibodies. This allele was identified by sequence analysis, which indicated that a single G-to-A substitution at position 406 in exon 3 created a null allele under a new mechanism: the mutation changes the position of the intron 2-exon 3 splice site to be further into exon 3, leading to a frameshift and a premature stop codon. Sequence analysis of cDNA confirmed the existence of the causative alternative acceptor splice site and the resultant deletion of 64 nucleotides in exon 3. Analysis of 220 blood or bone marrow donors in Japan with C*03:23N demonstrated that Japanese HLA-C*03:23N is on the haplotype A*26:01∼C*03:23N∼B*40:02∼DRB1*09:01.
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Affiliation(s)
- Marie Shimizu
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Yukari Kuroda
- Kyushu Block Blood Center, Japanese Red Cross Society, Fukuoka, Japan
| | - Miyuki Uchida
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | | | - Hiromi Kamada
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | | | - Fumiaki Nakajima
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Shigeki Miyata
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Shigeru Igarashi
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
| | - Masahiro Satake
- Central Blood Institute, Japanese Red Cross Society, Tokyo, Japan
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17
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Fusco C, Cervelli C, Dal Mas A, Canossi A, Azzarone R, Valdez O, Auriemma L, Madalese D, Maisto G, Toriello M, Penta de Vera d'Aragona R, Scimitarra M, Scarnecchia MA, Battistoni C, Fracassi D, Papola F. Expression profile of HLA-B*38:55Q allele. HLA 2020; 95:449-456. [PMID: 31891446 DOI: 10.1111/tan.13790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/24/2019] [Accepted: 12/30/2019] [Indexed: 11/29/2022]
Abstract
The identification of null or questionably expressed HLA allelic variants is a major issue in HLA diagnostics, because the mistyping of the aberrant expression of such alleles can have a major impact on the outcome of both hematopoietic stem cell transplantation (HSCT) and solid organ transplants. It is debated how questionable (Q) alleles, because of their unknown expression profile, should be considered in an allogenic HSCT setting. The HLA-B*38:55Q allele was detected as an HLA-B blank specificity; DNA sequencing identified a single polymorphism at position 373 in exon 3 (TGC > CGC), which results in the replacement of cysteine 101 with an arginine in the HLA-B heavy chain, thus, impairing disulfide bridge formation in the alpha-2 domain, essential for the normal expression of the HLA molecules. In order to determine the RNA and protein expression profile of this allelic variant, we analyzed antigenic expression at different levels, transcriptional and transductional, using a combination of cellular methods, such as serological testing and flow cytometric analysis, polymerase chain reaction (PCR) sequence-specific primer (SSP) cDNA group-specific amplification and immunocytochemical assay, demonstrating the prevalent cytoplasmatic distribution of the HLA-B*38:55Q protein. Our findings suggest that in matching process the HLA-B*38:55Q allele needs to be considered as a low expressed allele, able to elicit an allogenic T-cell response in vivo and impair the transplant outcome.
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Affiliation(s)
- Caterina Fusco
- SSD Cryopreservation and Ba.S.C.O, Oncohaematology Department, A.O.R.N. Santobono-Pausilipon of Napoli, Naples, Italy
| | - Carla Cervelli
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Antonella Dal Mas
- UOC Pathological Anatomy, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Angelica Canossi
- CNR Institute of Translational Pharmacology, L'Aquila, L'Aquila, Italy
| | - Raffaella Azzarone
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Olaida Valdez
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Laura Auriemma
- SSD Cryopreservation and Ba.S.C.O, Oncohaematology Department, A.O.R.N. Santobono-Pausilipon of Napoli, Naples, Italy
| | - Donato Madalese
- SSD Cryopreservation and Ba.S.C.O, Oncohaematology Department, A.O.R.N. Santobono-Pausilipon of Napoli, Naples, Italy
| | - Giovanna Maisto
- SSD Cryopreservation and Ba.S.C.O, Oncohaematology Department, A.O.R.N. Santobono-Pausilipon of Napoli, Naples, Italy
| | - Mario Toriello
- SSD Cryopreservation and Ba.S.C.O, Oncohaematology Department, A.O.R.N. Santobono-Pausilipon of Napoli, Naples, Italy
| | | | - Maria Scimitarra
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Maria A Scarnecchia
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Carla Battistoni
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Daniela Fracassi
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Franco Papola
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
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18
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Fuerst D, Tsamadou C, Gowdavally S, Schrezenmeier H, Mytilineos J. HLA‐DRB4*01:14
is a null allele, and renamed
HLA‐DRB4*01:14N. HLA 2019; 95:73-75. [DOI: 10.1111/tan.13701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Daniel Fuerst
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm German Red Cross Blood Transfusion Service, Baden Wuerttemberg – Hessen and University Hospital Ulm Ulm Germany
- Institute of Transfusion Medicine University of Ulm Ulm Germany
| | - Chrysanthi Tsamadou
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm German Red Cross Blood Transfusion Service, Baden Wuerttemberg – Hessen and University Hospital Ulm Ulm Germany
- Institute of Transfusion Medicine University of Ulm Ulm Germany
| | - Sowmya Gowdavally
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm German Red Cross Blood Transfusion Service, Baden Wuerttemberg – Hessen and University Hospital Ulm Ulm Germany
- Institute of Transfusion Medicine University of Ulm Ulm Germany
| | - Hubert Schrezenmeier
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm German Red Cross Blood Transfusion Service, Baden Wuerttemberg – Hessen and University Hospital Ulm Ulm Germany
- Institute of Transfusion Medicine University of Ulm Ulm Germany
| | - Joannis Mytilineos
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm German Red Cross Blood Transfusion Service, Baden Wuerttemberg – Hessen and University Hospital Ulm Ulm Germany
- Institute of Transfusion Medicine University of Ulm Ulm Germany
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19
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Enrich E, Campos E, Martorell L, Herrero MJ, Vidal F, Querol S, Rudilla F. HLA-A, -B, -C, -DRB1, and -DQB1 allele and haplotype frequencies: An analysis of umbilical cord blood units at the Barcelona Cord Blood Bank. HLA 2019; 94:347-359. [PMID: 31353832 DOI: 10.1111/tan.13644] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 07/18/2019] [Accepted: 07/25/2019] [Indexed: 12/16/2022]
Abstract
Allele-level HLA compatibility in cord blood transplantation has been associated with better transplant outcomes and is recommended as a selection criterion. It is also a crucial aspect for other therapeutic applications involving cord blood-derived cells. Determination of high-resolution HLA frequencies is an important step towards improving the quality of cord blood banks. We analyzed HLA-A, -B, -C, -DRB1, and -DQB1 allele frequencies in 5458 high-quality cord blood units from the Barcelona Cord Blood Bank and identified 275 class I and 121 class II HLA alleles. A*02:01, B*44:03, C*07:01, DRB1*07:01 and DQB1*03:01 were the most frequent alleles at each locus. We detected 26 novel alleles and were able to determine the presence or absence of some null alleles, including C*04:09N, in a large number of units. We also analyzed maternal HLA typing information for 1877 units to determine real haplotype frequencies and linkage disequilibrium. A*29:02-B*44:03-C*16:01-DRB1*07:01-DQB1*02:02 was the most frequent HLA haplotype and the DRB1-DQB1 gene pair contained the two-locus haplotypes with the strongest linkage disequilibrium values. Four of the 11 unique haplotypes identified in the HLA-homozygous cord blood units were the top-ranking haplotypes identified and were present in 18% of the cohort. This is the first study to report on HLA allele and haplotype frequencies for umbilical cord blood units from the Barcelona Cord Blood Bank and the largest study to date involving two fields of HLA resolution typing of Spanish registry data.
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Affiliation(s)
- Emma Enrich
- Immunogenetics and Histocompatibility Laboratory, Banc de Sang i Teixits, Barcelona, Spain
- Transfusional Medicine Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
| | - Eva Campos
- Immunogenetics and Histocompatibility Laboratory, Banc de Sang i Teixits, Barcelona, Spain
| | - Lluís Martorell
- Congenital Coagulopathy Laboratory, Banc de Sang i Teixits, Barcelona, Spain
- Cell Therapy Unit, Banc de Sang i Teixits, Barcelona, Spain
| | - María José Herrero
- Immunogenetics and Histocompatibility Laboratory, Banc de Sang i Teixits, Barcelona, Spain
| | - Francisco Vidal
- Transfusional Medicine Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
- Congenital Coagulopathy Laboratory, Banc de Sang i Teixits, Barcelona, Spain
- CIBER of Cardiovascular Diseases (CIBERCV), Madrid, Spain
| | - Sergi Querol
- Transfusional Medicine Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
- Cell Therapy Unit, Banc de Sang i Teixits, Barcelona, Spain
| | - Francesc Rudilla
- Immunogenetics and Histocompatibility Laboratory, Banc de Sang i Teixits, Barcelona, Spain
- Transfusional Medicine Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Barcelona, Spain
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20
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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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21
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Toni Ho GG, Heinen F, Stieglitz F, Blasczyk R, Bade-Döding C. Dynamic Interaction between Immune Escape Mechanism and HLA-Ib Regulation. Immunogenetics 2019. [DOI: 10.5772/intechopen.80731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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22
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Integrate CRISPR/Cas9 for protein expression of HLA-B*38:68Q via precise gene editing. Sci Rep 2019; 9:8067. [PMID: 31147565 PMCID: PMC6542842 DOI: 10.1038/s41598-019-44336-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 05/14/2019] [Indexed: 11/16/2022] Open
Abstract
The determination of null- or low-expressed HLA alleles is clinically relevant in both hematopoietic stem cell transplantation and solid organ transplantation. We studied the expression level of a questionable (Q) HLA-B*38:68Q allele, which carries a 9-nucleotide (nt) deletion at codon 230–232 in exon 4 of HLA-B*38:01:01:01 using CRISPR/Cas9 gene editing technology. CRISPR/Cas9 gene editing of HLA-B*38:01:01:01 homozygous EBV B cell line resulted in one HLA-B*38:68Q/B*38:01:01:01 heterozygous and one HLA-B*38:68Q homozygous clone. Flow cytometric analysis of monoclonal anti-Bw4 antibody showed the protein expression of HLA-B*38:01:01:01 in homozygous cells was 2.2 fold higher than HLA-B*38:68Q/B*38:01:01:01 heterozygous cells, and the expression of HLA-B*38:68Q/B*38:01:01:01 heterozygous cells was over 2.0 fold higher than HLA-B*38:68Q homozygous cells. The HLA-B*38:68Q expression was further confirmed using anti-B38 polyclonal antibody. Similarly, the expression of the HLA-B*38:01:01:01 homozygous cells was 1.5 fold higher than that of HLA-B*38:68Q/B*38:01:01:01 heterozygous cells, and the HLA-B*38:68Q/B*38:01:01:01 heterozygous cells was over 1.6 fold higher than that of HLA-B*38:68Q homozygous cells. The treatment of HLA-B*38:68Q homozygous cells with IFN-γ significantly increased its expression. In conclusion, we demonstrate that HLA-B*38:68Q is a low-expressing HLA allele. The CRISPR/Cas9 technology is a useful tool to induce precise gene editing in HLA genes to enable the characterization of HLA gene variants on expression and function.
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23
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Montero-Martín G, Mallempati KC, Gangavarapu S, Sánchez-Gordo F, Herrero-Mata MJ, Balas A, Vicario JL, Sánchez-García F, González-Escribano MF, Muro M, Moya-Quiles MR, González-Fernández R, Ocejo-Vinyals JG, Marín L, Creary LE, Osoegawa K, Vayntrub T, Caro-Oleas JL, Vilches C, Planelles D, Fernández-Viña MA. High-resolution characterization of allelic and haplotypic HLA frequency distribution in a Spanish population using high-throughput next-generation sequencing. Hum Immunol 2019; 80:429-436. [PMID: 30763600 DOI: 10.1016/j.humimm.2019.02.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 02/07/2019] [Accepted: 02/09/2019] [Indexed: 12/25/2022]
Abstract
Next-generation sequencing (NGS) at the HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1 and -DRB3/4/5 loci was performed on 282 healthy unrelated individuals from different major regions of Spain. High-resolution HLA genotypes defined by full sequencing of class I loci and extended coverage of class II loci were obtained to determine allele frequencies and also to estimate extended haplotype frequencies. HLA alleles were typed at the highest resolution level (4-field level, 4FL); with exception of a minor deviation in HLA-DPA1, no statistically significant deviations from expected Hardy Weinberg Equilibrium (HWE) proportions were observed for all other HLA loci. This study provides new 4FL-allele and -haplotype frequencies estimated for the first time in the Spanish population. Furthermore, our results describe extended haplotypes (including the less frequently typed HLA-DPA1 and HLA-DQA1 loci) and show distinctive haplotype associations found at 4FL-allele definition in this Spanish population study. The distinctive allelic and haplotypic diversity found at the 4FL reveals the high level of heterozygosity and specific haplotypic associations displayed that were not apparent at 2-field level (2FL). Overall, these results may contribute as a useful reference source for future population studies, for HLA-disease association studies as a healthy control group dataset and for improving donor recruitment strategies of bone marrow registries. HLA genotyping data of this Spanish population cohort was also included in the 17th International Histocompatibility and Immunogenetics Workshop (IHIW) as part of the study of HLA diversity in unrelated worldwide populations using NGS.
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Affiliation(s)
| | - Kalyan C Mallempati
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sridevi Gangavarapu
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | - Antonio Balas
- Histocompatibility, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | - Jose L Vicario
- Histocompatibility, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | | | | | - Manuel Muro
- Immunology, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Maria R Moya-Quiles
- Immunology, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | | | | | - Luis Marín
- Molecular Biology-Hematology, Hospital Clínico Universitario, Salamanca, Spain
| | - Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kazutoyo Osoegawa
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Tamara Vayntrub
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Jose L Caro-Oleas
- Histocompatibility and Immunogenetics, Banc de Sang i Teixits, Barcelona, Spain
| | - Carlos Vilches
- Immunogenetics and Histocompatibility, Instituto de Investigación Sanitaria Puerta de Hierro, Madrid, Spain
| | - Dolores Planelles
- Histocompatibility, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain
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24
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Kaur N, Kransdorf EP, Pando MJ, Maiers M, Ray B, Lee JH, Lalli P, Murphey CL, Bray RA, Gragert L. Mapping molecular HLA typing data to UNOS antigen equivalents. Hum Immunol 2018; 79:781-789. [DOI: 10.1016/j.humimm.2018.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/04/2018] [Accepted: 08/08/2018] [Indexed: 11/27/2022]
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25
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Grubic Z, Maskalan M, Radmanic L, Stingl Jankovic K, Burek Kamenaric M, Zunec R. The distribution of the DRB4*01:03:01:02N null allele in HLA-DRB1~DQB1 haplotypes in the Croatian population. HLA 2017; 91:23-28. [PMID: 29152917 DOI: 10.1111/tan.13178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/06/2017] [Accepted: 11/14/2017] [Indexed: 12/11/2022]
Abstract
The aim of the present study was to investigate frequency and haplotype distribution of DRB4 alleles in the Croatian population. The investigated sample consisted of 288 cadaveric donor samples positive for one of the DR53 alleles. HLA-A, -B, -C, -DRB1, and -DQB1 typing was performed using the polymerase chain reaction-sequence specific primers (PCR-SSP) low resolution method, while HLA-DRB4 and selected HLA class II specificities typing was performed using PCR-SSP at the allelic level. Three different DRB4 alleles were observed among DRB1*04 samples; DRB4*01:02 (2.38%), DRB4*01:03 (91.27%), and DRB4*01:03:01:02N (6.35%). The DRB4*01:03:01:02N allele was predominantly observed among DRB1*04:02-positive samples, while DRB4*01:02 and DRB4*01:03 alleles did not associate preferably with any of the DRB1*04 subtypes. Among DRB1*04~DRB4~DQB1 haplotypes, the predominant DQB1 allele was DQB1*03:02 (69.94%). Seven different DRB4 alleles were found among DRB1*07:01-positive samples. The analysis of DRB1*07~DRB4~DQB1 haplotypes showed that DRB4*01:03 was found in the majority of HLA-DRB1*07:01~DQB1*02:02 (49.09%) haplotypes while DRB1*07:01~DQB1*03:03 haplotypes carried the DRB4*01:03:01:02N allele almost exclusively (98.21%). Among six DRB1*09:01-positive samples, HLA-DRB1*09:01~DRB4*01:03~DQB1*03:03 was the only detected haplotype. The extended haplotype analysis showed a high frequency of HLA-B*15(B62)~C*03(Cw9)~DRB1*04:02~DRB4*01:03:01:02N~DQB1*03:02 and HLA-B*57~C*06~DRB1*07:01~DRB4*01:03:01:02N~DQB1*03:03 haplotypes. In conclusion, the data presented in this study should prompt other population studies focused on DRB3/4/5 genes and be used as a basis for future investigations of the clinical relevance of these genes in transplantation setting.
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Affiliation(s)
- Z Grubic
- Tissue Typing Centre, Clinical Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - M Maskalan
- Tissue Typing Centre, Clinical Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - L Radmanic
- Tissue Typing Centre, Clinical Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - K Stingl Jankovic
- Tissue Typing Centre, Clinical Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - M Burek Kamenaric
- Tissue Typing Centre, Clinical Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - R Zunec
- Tissue Typing Centre, Clinical Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Zagreb, Croatia
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26
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Wenda S, Faé I, Fischer GF. An HLA-B7-specific antibody in an HLA-B*07
positive patient explained by a nonexpressed allele (HLA-B*07:181N
). HLA 2017; 90:32-35. [DOI: 10.1111/tan.13045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/15/2017] [Accepted: 03/22/2017] [Indexed: 11/29/2022]
Affiliation(s)
- S. Wenda
- Department for Blood Group Serology and Transfusion Medicine; Medical University of Vienna; Vienna Austria
| | - I. Faé
- Department for Blood Group Serology and Transfusion Medicine; Medical University of Vienna; Vienna Austria
| | - G. F. Fischer
- Department for Blood Group Serology and Transfusion Medicine; Medical University of Vienna; Vienna Austria
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27
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Balas A, García-Sánchez F, Vicario JL. RNA processing and protein expression of HLA-B*07:44N. HLA 2017; 89:230-234. [PMID: 28205408 DOI: 10.1111/tan.12983] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/17/2017] [Accepted: 01/24/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND The assignment of human leukocyte antigen (HLA) null alleles is clinically relevant in the setting of stem cell transplantation. Cell surface expression profiling and mRNA processing analysis of the HLA-B allele previously designated as B*07:44, have been performed. MATERIALS AND METHODS Cell surface expression of HLA-B*07:44 was determined using flow cytometry. Genomic full-length and HLA-B*07-specific cDNA sequencing were carried out by Sanger procedure. RESULTS Flow cytometric analysis confirmed previous serologic results and demonstrated a lack of cell membrane expression of the HLA-B protein. The mRNA processing, studied using direct HLA-B*07-specific cDNA sequencing, revealed the presence of a unique, aberrantly spliced mRNA, with a deletion of the last 43 bp on the 5'-end of exon 4. The substitution from T to G at genomic position 1799 compared to B*07:02:01 introduced a new and stronger splice donor site at exon 4. This alternative splicing produced an mRNA containing a premature stop codon at position 280, explaining the absence of mature HLA-B7 protein on the cell surface. CONCLUSION These findings led us to consider this HLA-B variant as a HLA null allele. The World Health Organization (WHO) Nomenclature Committee has since renamed this variant B*07:44N .
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Affiliation(s)
- A Balas
- Departamento de Histocompatibilidad, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | - F García-Sánchez
- Departamento de Histocompatibilidad, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | - J L Vicario
- Departamento de Histocompatibilidad, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
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Schöfl G, Lang K, Quenzel P, Böhme I, Sauter J, Hofmann JA, Pingel J, Schmidt AH, Lange V. 2.7 million samples genotyped for HLA by next generation sequencing: lessons learned. BMC Genomics 2017; 18:161. [PMID: 28196473 PMCID: PMC5309984 DOI: 10.1186/s12864-017-3575-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/09/2017] [Indexed: 11/10/2022] Open
Abstract
Background At the DKMS Life Science Lab, Next Generation Sequencing (NGS) has been used for ultra-high-volume high-resolution genotyping of HLA loci for the last three and a half years. Here, we report on our experiences in genotyping the HLA, CCR5, ABO, RHD and KIR genes using a direct amplicon sequencing approach on Illumina MiSeq and HiSeq 2500 instruments. Results Between January 2013 and June 2016, 2,714,110 samples largely from German, Polish and UK-based potential stem cell donors have been processed. 98.9% of all alleles for the targeted HLA loci (HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1) were typed at high resolution or better. Initially a simple three-step workflow based on nanofluidic chips in conjunction with 4-primer amplicon tagging was used. Over time, we found that this setup results in PCR artefacts such as primer dimers and PCR-mediated recombination, which may necessitate repeat typing. Split workflows for low- and high-DNA-concentration samples helped alleviate these problems and reduced average per-locus repeat rates from 3.1 to 1.3%. Further optimisations of the workflow included the use of phosphorothioate oligos to reduce primer degradation and primer dimer formation, and employing statistical models to predict read yield from initial template DNA concentration to avoid intermediate quantification of PCR products. Finally, despite the populations typed at DKMS Life Science Lab being relatively homogenous genetically, an analysis of 1.4 million donors processed between January 2015 and May 2016 led to the discovery of 1,919 distinct novel HLA alleles. Conclusions Amplicon-based NGS HLA genotyping workflows have become the workhorse in high-volume tissue typing of registry donors. The optimisation of workflow practices over multiple years has led to insights and solutions that improve the efficiency and robustness of short amplicon based genotyping workflows. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3575-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gerhard Schöfl
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany.
| | - Kathrin Lang
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany
| | - Philipp Quenzel
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany
| | - Irina Böhme
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany
| | | | | | | | - Alexander H Schmidt
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany.,DKMS, Kressbach 1, 72072, Tübingen, Germany
| | - Vinzenz Lange
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany
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The HLA System in Transfusion Medicine and Transplantation. Transfus Med 2016. [DOI: 10.1002/9781119236504.ch16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Tiercy JM. How to select the best available related or unrelated donor of hematopoietic stem cells? Haematologica 2016; 101:680-7. [PMID: 27252513 DOI: 10.3324/haematol.2015.141119] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/09/2016] [Indexed: 11/09/2022] Open
Abstract
Recognition of HLA incompatibilities by the immune system represents a major barrier to allogeneic hematopoietic stem cell transplantation. HLA genotypically identical sibling donors are, therefore, the gold standard for transplantation purposes, but only 30% patients have such a donor. For the remaining 70% patients alternative sources of stem cells are a matched unrelated adult volunteer donor, a haploidentical donor or a cord blood unit. The definition of 'HLA matching' depends on the level of resolution and on which loci are tested. The development of HLA molecular typing technologies and the availability of more than 27 million donors in the international database has greatly facilitated unrelated donor searches. The gold standard is high resolution typing at the HLA-A, -B, -C, -DRB1, and -DQB1 loci (10/10 match). Single disparities for HLA-A, -B, - C, or -DRB1 are associated with increased risk of post-transplant complications, but less so in patients with advanced disease, and in those undergoing T-cell-depleted allografting. HLA-DQB1 mismatches seem to be better tolerated and some HLA-C, -DRB1 and -DPB1 disparities are potentially less immunogenic. HLA typing by next-generation sequencing methods is likely to change matching algorithms by providing full sequence information on all HLA loci in a single step. In most European populations a 10/10 matched donor can be found for at least 50% of patients and an additional 20-30% patients may have a 9/10 matched donor. Genetic factors that help in identifying donors with less immunogenic mismatches are discussed. Haploidentical donors are increasingly used as an alternative source of stem cells for those patients lacking a matched unrelated donor.
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Affiliation(s)
- Jean-Marie Tiercy
- National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, University Hospitals Geneva, Switzerland
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31
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Planelles D, Balas A, Muñoz C, Puig N, Vicario JL. A novel null HLA-B allele, B*15:375N, due to a seven base pair deletion within exon 3. HLA 2016; 87:104-6. [DOI: 10.1111/tan.12729] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 12/02/2015] [Accepted: 12/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- D. Planelles
- Departamento de Histocompatibilidad; Centro de Transfusión de la Comunidad Valenciana; Valencia Spain
| | - A. Balas
- Departamento de Histocompatibilidad; Centro de Transfusión de la Comunidad de Madrid; Madrid Spain
| | - C. Muñoz
- Departamento de Inmunología; Hospital General de Alicante; Alicante Spain
| | - N. Puig
- Departamento de Histocompatibilidad; Centro de Transfusión de la Comunidad Valenciana; Valencia Spain
| | - J. L. Vicario
- Departamento de Histocompatibilidad; Centro de Transfusión de la Comunidad de Madrid; Madrid Spain
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32
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Balas A, Sánchez-Gordo F, García-Sánchez F, Gómez-Zumaquero JM, Vicario JL. Characterization of two novel HLA-A null alleles: A*11:210N and A*26:107N. TISSUE ANTIGENS 2015; 85:502-504. [PMID: 25846346 DOI: 10.1111/tan.12558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/17/2015] [Accepted: 03/15/2015] [Indexed: 06/04/2023]
Abstract
Two new HLA-A null alleles were characterized, A*11:210N and A*26:107N.
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Affiliation(s)
- A Balas
- Histocompatibilidad, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
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33
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Gerritsen K, Voorter C, Joannes M, Senden-Gijsbers B, Agis F, Wieten L, Tilanus M. RNA and protein expression of HLA-A∗23:19Q. Hum Immunol 2015; 76:286-91. [DOI: 10.1016/j.humimm.2015.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 02/03/2015] [Indexed: 11/28/2022]
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34
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Nariai N, Kojima K, Saito S, Mimori T, Sato Y, Kawai Y, Yamaguchi-Kabata Y, Yasuda J, Nagasaki M. HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data. BMC Genomics 2015; 16 Suppl 2:S7. [PMID: 25708870 PMCID: PMC4331721 DOI: 10.1186/1471-2164-16-s2-s7] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Human leucocyte antigen (HLA) genes play an important role in determining the outcome of organ transplantation and are linked to many human diseases. Because of the diversity and polymorphisms of HLA loci, HLA typing at high resolution is challenging even with whole-genome sequencing data. Results We have developed a computational tool, HLA-VBSeq, to estimate the most probable HLA alleles at full (8-digit) resolution from whole-genome sequence data. HLA-VBSeq simultaneously optimizes read alignments to HLA allele sequences and abundance of reads on HLA alleles by variational Bayesian inference. We show the effectiveness of the proposed method over other methods through the analysis of predicting HLA types for HLA class I (HLA-A, -B and -C) and class II (HLA-DQA1,-DQB1 and -DRB1) loci from the simulation data of various depth of coverage, and real sequencing data of human trio samples. Conclusions HLA-VBSeq is an efficient and accurate HLA typing method using high-throughput sequencing data without the need of primer design for HLA loci. Moreover, it does not assume any prior knowledge about HLA allele frequencies, and hence HLA-VBSeq is broadly applicable to human samples obtained from a genetically diverse population.
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Park Y, Yoon CE, Kwon OJ, Kim YS, Kim HS. Resolution of ambiguous HLA genotyping in korean by multi-group-specific sequence-based typing. Yonsei Med J 2014; 55:1005-13. [PMID: 24954331 PMCID: PMC4075361 DOI: 10.3349/ymj.2014.55.4.1005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
PURPOSE To evaluate a multi-group-specific sequence-based typing (SBT) method for resolving ambiguous results from human leukocyte antigen (HLA) genotyping. MATERIALS AND METHODS A total of 50 samples that showed ambiguous genotypes for at least two HLA loci from HLA-A, -B, -C and -DRB1 by the conventional SBT assay were evaluated using a new SBT test, the AVITA plus assay. The most likely HLA genotypes for the respective samples considering allele frequencies in Korean were concordant between the AVITA and conventional SBT assays. RESULTS An average of 3.3 loci among the HLA-A, -B, -C and -DRB1 loci per sample gave results with two or more possible allele combinations with the conventional SBT, and 48 (96.0%) out of 50 showed reduced numbers of possible genotypes for at least one HLA locus with the AVITA. A total of 41, 43, 42, and 38 cases among the 50 samples showed ambiguous results for HLA-A, -B, -C, and -DRB1 typing by the conventional SBT, respectively. The average numbers of possible allele combinations for the respective four HLA loci were 8.2, 6.7, 5.9, and 3.2, and they were reduced to 1.5, 2.2, 4.4, and 1.8, respectively, by the AVITA. Ambiguity was resolved by the AVITA in 33 (80.5%), 31 (72.1%), 17 (40.5%) and 28 (73.7%) samples among the ambiguous cases from the conventional SBT for HLA-A, -B, -C, and -DRB1 typing, respectively. CONCLUSION The multi-group-specific SBT method considerably reduced the number of ambiguous results, and thus may be useful for accurate HLA typing in clinical laboratories.
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Affiliation(s)
- Yongjung Park
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | | | - Oh-Joong Kwon
- College of Animal Bioscience & Technology, Konkuk University, Seoul, Korea
| | - Yu-Seun Kim
- Division of Transplantation Surgery, Department of Surgery,The Research Institute for Transplantation, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Hyon-Suk Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea.
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36
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Abad ML, Balas A, Andersen I, Rodríguez-Calvo MI, Eiras A, Vicario JL. A new non-expressed allele HLA-A*03:168N, identified by serological and sequence-based typing in a voluntary Norwegian hematopoietic stem cell donor. ACTA ACUST UNITED AC 2014; 83:195-6. [PMID: 24397317 DOI: 10.1111/tan.12274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/10/2013] [Accepted: 11/28/2013] [Indexed: 11/28/2022]
Abstract
HLA-A*03:168N differs from HLA-A*03:01:01 by a single nucleotide substitution resulting in a coding change Y27X.
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Affiliation(s)
- M L Abad
- Unidad de Biología Molecular e Histocompatibilidad, Centro de Transfusión de Galicia, Santiago de Compostela, Spain
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37
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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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38
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Crivello P, Lauterbach N, Zito L, Sizzano F, Toffalori C, Marcon J, Curci L, Mulder A, Wieten L, Zino E, Voorter CEM, Tilanus MGJ, Fleischhauer K. Effects of transmembrane region variability on cell surface expression and allorecognition of HLA-DP3. Hum Immunol 2013; 74:970-7. [PMID: 23619468 DOI: 10.1016/j.humimm.2013.04.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/06/2013] [Accepted: 04/12/2013] [Indexed: 12/01/2022]
Abstract
The functional relevance of polymorphisms outside the peptide binding groove of HLA molecules is poorly understood. Here we have addressed this issue by studying HLA-DP3, a common antigen relevant for functional matching algorithms of unrelated hematopoietic stem cell transplantation (HSCT) encoded by two transmembrane (TM) region variants, DPB1(*)03:01 and DPB1(*)104:01. The two HLA-DP3 variants were found at a overall allelic frequency of 10.4% in 201 volunteer stem cell donors, at a ratio of 4.2:1. No significant differences were observed in cell surface expression levels of the two variants on B lymphoblastoid cell lines (BLCL), primary B cells or monocytes. Three different alloreactive T cell lines or clones showed similar levels of activation marker CD107a and/or CD137 upregulation in response to HLA-DP3 encoded by DPB1(*)03:01 and DPB1(*)104:01, either endogenously on BLCL or after lentiveral-vector mediated transfer into the same cellular background. These data provide, for the first time, direct evidence for a limited functional role of a TM region polymorphism on expression and allorecognition of HLA-DP3 and are compatible with the notion that the two variants can be considered as a single functional entity for unrelated stem cell donor selection.
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Affiliation(s)
- Pietro Crivello
- Unit of Molecular and Functional Immunogenetics, San Raffaele Scientific Institute, Milan, Italy
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39
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Danzer M, Niklas N, Stabentheiner S, Hofer K, Pröll J, Stückler C, Raml E, Polin H, Gabriel C. Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics. BMC Genomics 2013; 14:221. [PMID: 23557197 PMCID: PMC3639865 DOI: 10.1186/1471-2164-14-221] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 03/22/2013] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Human leukocyte antigen matching at allelic resolution is proven clinically significant in hematopoietic stem cell transplantation, lowering the risk of graft-versus-host disease and mortality. However, due to the ever growing HLA allele database, tissue typing laboratories face substantial challenges. In light of the complexity and the high degree of allelic diversity, it has become increasingly difficult to define the classical transplantation antigens at high-resolution by using well-tried methods. Thus, next-generation sequencing is entering into diagnostic laboratories at the perfect time and serving as a promising tool to overcome intrinsic HLA typing problems. Therefore, we have developed and validated a scalable automated HLA class I and class II typing approach suitable for diagnostic use. RESULTS A validation panel of 173 clinical and proficiency testing samples was analysed, demonstrating 100% concordance to the reference method. From a total of 1,273 loci we were able to generate 1,241 (97.3%) initial successful typings. The mean ambiguity reduction for the analysed loci was 93.5%. Allele assignment including intronic sequences showed an improved resolution (99.2%) of non-expressed HLA alleles. CONCLUSION We provide a powerful HLA typing protocol offering a short turnaround time of only two days, a fully integrated workflow and most importantly a high degree of typing reliability. The presented automated assay is flexible and can be scaled by specific primer compilations and the use of different 454 sequencing systems. The workflow was successfully validated according to the policies of the European Federation for Immunogenetics. Next-generation sequencing seems to become one of the new methods in the field of Histocompatibility.
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Affiliation(s)
- Martin Danzer
- Department of Immunogenetics, Red Cross Transfusion Service for Upper Austria, Krankenhausstrasse 7, Linz 4017, Austria.
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40
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Föll D, Hinrichs J, Tischer S, Battermann A, Schambach A, Figueiredo C, Immenschuh S, Blasczyk R, Eiz-Vesper B. Closing the gap: discrimination of the expression profile of HLA questionable alleles by a cytokine-induced secretion approach using HLA-A*32:11Q. ACTA ACUST UNITED AC 2012; 79:340-50. [PMID: 22489943 DOI: 10.1111/j.1399-0039.2012.01864.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Matching of human leukocyte antigen (HLA) alleles between donors and recipients plays a major role in hematopoietic stem cell transplantation (HSCT). Null or questionably expressed HLA allelic variants are a major issue in HLA matching, because the aberrant expression of such alleles can have a major impact on the outcome of HSCT and/or its complications such as graft-versus-host disease. The goal of this study was to investigate the potential of a recently developed cytokine-induced secretion assay to differentiate the expression levels of HLA-A*32:11Q (questionable) into a null (N) or low (L) expression variant. An amino acid mutation at position 164 of HLA-A*32:11Q disrupts the disulfide bridge in the α2 domain. HLA-A*32:11Q is not detectable by standard microlymphocytotoxicity assay. To this end, we cloned soluble HLA-A*32:11Q and a reference allele (HLA-A*32:01) into expression vectors and transfected/transduced HEK293 and K562 cells. Allele-expressing K562 cells were simultaneously transfected/transduced with a β2-microglobulin (B2M)-encoding vector to ensure the intact HLA structure with B2M. After treatment with proinflammatory cytokines, secreted soluble HLA molecules were determined by enzyme-linked immunosorbent assay in the supernatant and intracellular accumulation of the recombinant proteins by flow cytometry. HLA-A*32:11Q was nearly undetectable in untreated transfectants. Cytokine treatment increased the secretion of HLA-A*32:11Q to detectable levels and resulted in intracellular accumulation of the allele. There was no difference in mRNA transcription between the A*32 alleles. On the basis of these results, we recommend reclassification of HLA-A*32:11Q as a low expression (L) variant.
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Affiliation(s)
- D Föll
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
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41
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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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42
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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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43
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Choo SY. The HLA System in Transfusion Medicine and Transplantation. Transfus Med 2011. [DOI: 10.1002/9781444398748.ch16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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44
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Badrinath S, Blasczyk R, Bade-Doeding C. Non-expression of HLA-C*07:55N is caused by a premature stop codon in exon 3. ACTA ACUST UNITED AC 2011; 79:139. [PMID: 22007928 DOI: 10.1111/j.1399-0039.2011.01786.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Sequencing of HLA-C*07:55N assessed the presence of a premature TAG stop codon at residue 113.
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Affiliation(s)
- S Badrinath
- Institute for Transfusion Medicine, MHH, Hannover Medical School, Hannover, Germany
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45
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Gabriel C, Stabentheiner S, Danzer M, Pröll J. What Next? The Next Transit from Biology to Diagnostics: Next Generation Sequencing for Immunogenetics. ACTA ACUST UNITED AC 2011; 38:308-317. [PMID: 22670120 DOI: 10.1159/000332433] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 09/01/2011] [Indexed: 01/06/2023]
Abstract
The human genome project triggered the introduction of next generation sequencing (NGS) systems. Although originally developed for total genome sequencing, metagenomics and plant genetics, the ultra-deep sequencing feature of NGS was utilized for diagnostic purposes in HIV resistance and tropism as well in detecting new mutations and tumor clones in oncology. Recent publications exploited the feature of clonal sequencing for immunogenetics to dissolve the growing number of ambiguities. This concept is quite reliable if all exons of interest are tested and the amplification region includes flanking introns. Challenging questions on quality control, cost effectiveness, workflow, and management of enormous loads of data remain if NGS is considered as routine method in the immunogenetics laboratory. If solved, NGS has big potential to have a major impact on immunogenetics by way of providing ambiguity-free HLA-typing results faster, but will also have a great influence on how immunogenetics testing and workflows are organized.
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Zhu F, He Y, Tao S, Zhang W, He J, He J, Xu X, Lv H, Yan L. Analysis of the complete cDNA sequences of HLA-DRB1 alleles with group-specific amplification primers in the Chinese Han population. ACTA ACUST UNITED AC 2011; 77:329-32. [PMID: 21388356 DOI: 10.1111/j.1399-0039.2010.01626.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Currently for the majority of HLA-DRB1 alleles the focus has been mainly on exon 2 and complete cDNA sequences of HLA-DRB1 alleles are rare. In this study, we analyzed the complete coding sequences of partial alleles of HLA-DRB1 locus. The cDNA was amplified by polymerase chain reaction using the group-specific primers located in the 5'- and 3'-untranslated regions to obtain the complete coding sequences. The amplification products were sequenced using an ABI BigDye® Terminator Cycle Sequencing kit. The HLA-DRB1 allele phylogenetic tree was analyzed by dnaman software. Full-length cDNA sequences of 22 HLA-DRB1 alleles were obtained in this study. HLA-DRB1*08:09, DRB1 *12:02:01, and DRB1*13:12 alleles were first reported for complete coding sequences. The sequences of exon 1 of HLA-DRB1*04:06:01, DRB1*08:03:02, and DRB1 *14:07:01 were newly presented. The complete coding sequences of HLA-DRB1 *01:01:01, DRB1*03:01:01:01, DRB1*04:01:01, DRB1*04:05:01, DRB1*07:01:01: 01, DRB1*09:01:02, DRB1*10:01:01, DRB1*11:01:01, DRB1*12:01:01, DRB1*13: 01:01, DRB1*13:02:01, DRB1*14:04, DRB1*14:54, DRB1*15:01:01:01, DRB1*15: 02:01, and DRB1*16:02:01 were identical to those previously reported. Forty polymorphic positions in complete coding sequences outside exon 2 of these HLA-DRB1 alleles were confirmed. According to the phylogenetic tree of full-length coding sequence, the HLA-DRB1 allele was classified into seven major allelic lineages. In conclusion, a protocol for HLA-DRB1 cDNA amplification and sequencing was improved and the data may help to determine the polymorphism of coding sequences outside exon 2.
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Affiliation(s)
- F Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang Province, China
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Dunn PPJ, Hammond L, Coates E, Street J, Griner L, Darke C. A "silent" nucleotide substitution in exon 4 is responsible for the "alternative expression" of HLA-A*01:01:38L through aberrant splicing. Hum Immunol 2011; 72:717-22. [PMID: 21741421 DOI: 10.1016/j.humimm.2011.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 04/15/2011] [Accepted: 05/13/2011] [Indexed: 10/18/2022]
Abstract
A Welsh Bone Marrow Donor Registry donor was serologically typed, using both alloantisera and monoclonal antibodies, as human leukocyte antigen (HLA)-A2, A-, but typed by polymerase chain reaction sequence-specific priming as HLA-A*01, A*02. Full gene sequencing of the A*01 separated allele indicated an apparently normal A*01:01:01:01 apart from a silent change at nucleotide 705 in exon 4, codon 211 (alanine: normally GCG but GCA in this donor). Sequence analysis of the amplified A*01 allele in cDNA synthesized from RNA indicated that exons 1, 2, 3, and 5 had typical A*01:01 sequences. However, exon 4 was truncated in this allele (87 nucleotides shorter), beginning just after the single nucleotide polymorphism (SNP) identified in genomic DNA sequencing. The nucleotide sequence up to, and 1 nucleotide after, the SNP is homologous with the 3' end of human leukocyte antigen (HLA)-A intron 3 and thus resembles a splice site. However, a small amount of "normal" HLA-A1 was detected on the surface of cells from an Epstein-Barr virus transformed B-cell line (BCL), but not on peripheral blood mononuclear cells, by flow cytometry. Additionally, a trace amount of "normal sized" A*01 was amplified from cDNA. We suggest that in this A*01 variant allele (A*01:01:38L) intron 3 is largely spliced out with a part of exon 4; exon 4 is still in-frame but the protein is smaller than the wild type. This is likely to affect folding and assembly of the "wild type" mature protein on the cell surface, thus explaining the apparent null phenotype when assayed by conventional serology. However, a small amount of A1 protein is made from correctly spliced A*01 mRNA and is detectable on BCLs using flow cytometry.
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Affiliation(s)
- Paul P J Dunn
- Tissue Typing Laboratory, New Zealand Blood Service, Auckland, New Zealand.
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Voorter CEM, Lauterbach N, Tilanus MGJ. Inactivation of a functional HLA-A gene: a 4-kb deletion turns HLA-A*24 into a pseudogene. Hum Immunol 2010; 71:1197-202. [PMID: 20858522 DOI: 10.1016/j.humimm.2010.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 09/09/2010] [Accepted: 09/16/2010] [Indexed: 10/19/2022]
Abstract
An unusual haplotype without a detectable human leukocyte antigen (HLA)-A allele by serologic or molecular typing methods segregates in a Caucasian family. Microsatellite analysis and fluorescence in situ hybridization implicated that the deletion encompasses a narrow region. To identify the deleted region, five different fragments in close proximity to HLA-A, known to be highly polymorphic, were amplified and sequenced. The presence of heterozygous sequences in all five fragments of the individuals carrying the haplotype with the HLA-A deletion, indicates that the fragments are not involved in the deletion. Therefore, the 5' primer from the fragment closest to the centromeric side of HLA-A was combined with the 3' primer closest to the telomeric side encompassing an 11-kb region. Sequencing revealed that a deletion of 4089 bp was present, located upstream of HLA-A, including exons and introns 1-3 of the HLA gene. Sequence information of the 3' part of HLA-A, downstream the deletion, identified that the deleted allele originates from an A*24 allele. Although different repeat sequences are present in the region both inside and outside the deletion, no evidence points to a retrotransposon mechanism. The detected partial deletion of HLA-A turns this functional gene into a pseudogene.
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Affiliation(s)
- Christina E M Voorter
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University, Medical Centre, Maastricht, the Netherlands.
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Howell WM, Carter V, Clark B. The HLA system: immunobiology, HLA typing, antibody screening and crossmatching techniques. J Clin Pathol 2010; 63:387-90. [PMID: 20418230 DOI: 10.1136/jcp.2009.072371] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Human Leukocyte Antigen (HLA) system plays a critical role in regulating the immune response. As a consequence of its role in immune regulation and exquisite polymorphism, the HLA system also constitutes an immunological barrier which must be avoided or otherwise overcome in clinical transplantation. This introductory review provides a brief summary of the immunobiology of the HLA system and methodology for HLA typing, antibody screening and patient-donor cross-matching. This constitutes a basis for consideration of the importance of these procedures in the system-specific reviews which follow.
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Affiliation(s)
- W M Howell
- Department of Histocompatibility & Immunogenetics, NHS Blood and Transplant, Newcastle upon Tyne NE2 4NQ, UK.
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Development of a DNA microarray for detection of expressed equine classical MHC class I sequences in a defined population. Immunogenetics 2010; 62:633-9. [PMID: 20683590 DOI: 10.1007/s00251-010-0463-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 06/28/2010] [Indexed: 10/19/2022]
Abstract
Development of an accurate and efficient molecular-based equine MHC class I typing method would facilitate the study of T lymphocyte immune responses in horses. Here, a DNA microarray was designed to detect expressed classical MHC class I genes comprising serologically defined equine leukocyte antigen (ELA)-A haplotypes represented in a closed Arabian horse breeding herd. Initially, cloning and sequencing of RT-PCR products were used to identify sequences associated with the ELA-A1, A4, and W11 haplotypes, and one undefined haplotype, in six horses. Subsequently, sequence-specific, conserved (positive control), and random nucleotide (negative control) 23- to 27-mer oligonucleotide microarray probes were designed and spotted onto an epoxy-coated masked slide using a robotic arrayer. Bulk RT-PCR products from each horse were biotinylated by nick translation, hybridized to the array, and detected using tyramide signal amplification. The microarray consistently detected eight of nine classical MHC class I transcripts and allowed ELA haplotypic associations to be made. Cloning and sequencing of RT-PCR products were then performed in a group of ELA disparate horses and ponies, in which six novel sequences were identified. This group was used to determine the specificity of the array. Overall, the microarray was more efficient than cloning and sequencing for detecting expressed classical MHC class I sequences in this defined population of horses, and was significantly more specific than serology. These results confirmed the utility of a microarray-based method for high-resolution MHC class I typing in the horse. With additional probes the array could be useful in a broader population.
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