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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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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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Osoegawa K, Mallempati KC, Gangavarapu S, Oki A, Gendzekhadze K, Marino SR, Brown NK, Bettinotti MP, Weimer ET, Montero-Martín G, Creary LE, Vayntrub TA, Chang CJ, Askar M, Mack SJ, Fernández-Viña MA. HLA alleles and haplotypes observed in 263 US families. Hum Immunol 2019; 80:644-660. [PMID: 31256909 DOI: 10.1016/j.humimm.2019.05.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 11/17/2022]
Abstract
The 17th International HLA and Immunogenetics Workshop (IHIW) conducted a project entitled "The Study of Haplotypes in Families by NGS HLA". We investigated the HLA haplotypes of 1017 subjects in 263 nuclear families sourced from five US clinical immunogenetics laboratories, primarily as part of the evaluation of related donor candidates for hematopoietic stem cell and solid organ transplantation. The parents in these families belonged to five broad groups - African (72 parents), Asian (115), European (210), Hispanic (118) and "Other" (11). High-resolution HLA genotypes were generated for each subject using next-generation sequencing (NGS) HLA typing systems. We identified the HLA haplotypes in each family using HaplObserve, software that builds haplotypes in families by reviewing HLA allele segregation from parents to children. We calculated haplotype frequencies within each broad group, by treating the parents in each family as unrelated individuals. We also calculated standard measures of global linkage disequilibrium (LD) and conditional asymmetric LD for each ethnic group, and used untruncated and two-field allele names to investigate LD patterns. Finally we demonstrated the utility of consensus DNA sequences in identifying novel variants, confirming them using HLA allele segregation at the DNA sequence level.
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Affiliation(s)
- Kazutoyo Osoegawa
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
| | - Kalyan C Mallempati
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Sridevi Gangavarapu
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Arisa Oki
- HLA Laboratory, City of Hope, Duarte, CA, USA
| | | | - Susana R Marino
- Transplant Immunology Laboratory, The University of Chicago Medicine, Chicago, IL, USA
| | - Nicholas K Brown
- Transplant Immunology Laboratory, The University of Chicago Medicine, Chicago, IL, USA
| | | | - Eric T Weimer
- Department of Pathology & Laboratory Medicine, UNC Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Gonzalo Montero-Martín
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Lisa E Creary
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Tamara A Vayntrub
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | | | - Medhat Askar
- Baylor University Medical Center, Dallas, TX, USA
| | - Steven J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Marcelo A Fernández-Viña
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
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6
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Marsh SGE. Nomenclature for factors of the HLA system, update July 2018. Hum Immunol 2018; 79:883-892. [PMID: 30316969 DOI: 10.1016/j.humimm.2018.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London NW3 2QG, United Kingdom. http://www.hla.alleles.org
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- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London NW3 2QG, United Kingdom
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