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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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2
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Kaabinejadian S, Barra C, Alvarez B, Yari H, Hildebrand WH, Nielsen M. Accurate MHC Motif Deconvolution of Immunopeptidomics Data Reveals a Significant Contribution of DRB3, 4 and 5 to the Total DR Immunopeptidome. Front Immunol 2022; 13:835454. [PMID: 35154160 PMCID: PMC8826445 DOI: 10.3389/fimmu.2022.835454] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/10/2022] [Indexed: 01/23/2023] Open
Abstract
Mass spectrometry (MS) based immunopeptidomics is used in several biomedical applications including neo-epitope discovery in oncology, next-generation vaccine development and protein-drug immunogenicity assessment. Immunopeptidome data are highly complex given the expression of multiple HLA alleles on the cell membrane and presence of co-immunoprecipitated contaminants. The absence of tools that deal with these challenges effectively and guide the analysis and interpretation of this complex type of data is currently a major bottleneck for the large-scale application of this technique. To resolve this, we here present the MHCMotifDecon that benefits from state-of-the-art HLA class-I and class-II predictions to accurately deconvolute immunopeptidome datasets and assign individual ligands to the most likely HLA molecule, allowing to identify and characterize HLA binding motifs while discarding co-purified contaminants. We have benchmarked the tool against other state-of-the-art methods and illustrated its application on experimental datasets for HLA-DR demonstrating a previously underappreciated role for HLA-DRB3/4/5 molecules in defining HLA class II immune repertoires. With its ease of use, MHCMotifDecon can efficiently guide interpretation of immunopeptidome datasets, serving the discovery of novel T cell targets. MHCMotifDecon is available at https://services.healthtech.dtu.dk/service.php?MHCMotifDecon-1.0.
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Affiliation(s)
- Saghar Kaabinejadian
- Pure MHC, LLC., Oklahoma City, OK, United States.,Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Carolina Barra
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Bruno Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Hooman Yari
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - William H Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
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3
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Zhang Y, Anderson KM, Freed BM, Dai S, Pacheco KA. HLA-DR53 (DRB4∗01) associates with nickel sensitization. Ann Allergy Asthma Immunol 2020; 125:614-616. [PMID: 32693207 DOI: 10.1016/j.anai.2020.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 11/19/2022]
Affiliation(s)
- Yan Zhang
- Department of Pharmaceutical Sciences, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado; Department of Immunology and Microbiology, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Kirsten M Anderson
- Department of Pharmaceutical Sciences, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado; Department of Immunology and Microbiology, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Brian M Freed
- ClinImmune Labs and Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Shaodong Dai
- Department of Pharmaceutical Sciences, University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado; Department of Immunology and Microbiology, University of Colorado School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
| | - Karin A Pacheco
- Department of Medicine, National Jewish Health, Denver, Colorado; Division of Environmental & Occupational Health, Colorado School of Public Health University of Colorado Anschutz Medical Campus, Aurora, Colorado.
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4
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Abad‐Molina C, Vilches‐Moreno M, Cárdaba‐Arranz M, Nieto A, Orduña‐Domingo A. Identification of the
DRB4*01:03:01:02N
null allele with
HLA‐DRB1*04
in a Spanish donor. HLA 2019; 93:471-473. [DOI: 10.1111/tan.13531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/01/2019] [Accepted: 03/18/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Cristina Abad‐Molina
- Servicio de Microbiología e InmunologíaHospital Clínico Universitario de Valladolid Spain
| | - Miriam Vilches‐Moreno
- UGC Hematología, Inmunología y GenéticaHospital Universitario Puerta del Mar Cádiz Spain
| | - Mario Cárdaba‐Arranz
- Servicio de Microbiología e InmunologíaHospital Clínico Universitario de Valladolid Spain
| | - Antonio Nieto
- UGC Hematología, Inmunología y GenéticaHospital Universitario Puerta del Mar Cádiz Spain
| | - Antonio Orduña‐Domingo
- Servicio de Microbiología e InmunologíaHospital Clínico Universitario de Valladolid Spain
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5
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Hurley CK, Ng J. Continue to focus clinical decision-making on the antigen recognition domain for the present. Hum Immunol 2019; 80:79-84. [DOI: 10.1016/j.humimm.2018.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/10/2018] [Accepted: 04/15/2018] [Indexed: 02/04/2023]
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6
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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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7
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Li J, den Hollander N, van Oosterwijk A, Ng CM, Singal DP. Identification of a new HLA-A null allele, A*2436 N. TISSUE ANTIGENS 2002; 60:184-5. [PMID: 12392513 DOI: 10.1034/j.1399-0039.2002.600209.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We describe a new HLA-A null allele in a donor. This null allele resulted from the deletion of two nucleotides in exon 2, which effects a frameshift as well as a premature stop codon. This new null allele has been officially named HLA-A*2436 N.
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Affiliation(s)
- J Li
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
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8
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Song EY, Park MH, Kang SJ, Park HJ, Kim BC, Tokunaga K, Akaza T, Juji T. HLA class II allele and haplotype frequencies in Koreans based on 107 families. TISSUE ANTIGENS 2002; 59:475-86. [PMID: 12445317 DOI: 10.1034/j.1399-0039.2002.590604.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have investigated the distribution of HLA class II alleles and haplotypes in 107 Korean families (207 parents and 291 children) for the HLA-DRB1, DRB3/B4/B5, DQA1, DQB1 and DPB1 loci. Numbers of alleles observed for each locus were DRB1: 25, DQA1: 14, DQB1: 15, and DPB1: 13. Only two to three alleles were observed for the DRB3 (*0101, *0202, *0301), DRB4 (*0103, * 0103102 N), and DRB5 (*0101, *0102) loci. These alleles showed strong associations with DRB1 alleles: DRB3*0101 with DRB1*1201, *1301 and *1403; DRB3*0301 with DRB1*1202 and *1302; DRB3*0202 with DRB1*0301, *1101, *1401 and *1405; DRB5*0101 and *0102 were exclusively associated with DRB1*1501 and *1502, respectively. The seven most common DRB1-DQB1 haplotypes of frequencies > 0.06 accounted for 52% of the total haplotypes. These haplotypes were exclusively related with the seven most common DRB1-DRB3/B4/B5-DQA1-DQB1 haplotypes: DRB1*1501-DRB5*0101-DQA1*0102-DQB1*0602 (0.085), DRB1*0405-DRB4*0103-DQA1*0303-DQB1*0401 (0.082), DRB1*09012-DRB4*0103-DQA1*0302-DQB1*03032 (0.082), DRB1*0101-DQA1*0101-DQB1*0501 (0.075), DRB1*0701-DRB4*0103-DQA1*0201-DQB1*0202 (0.065), DRB1*0803-DQA1*0103-DQB1*0601 (0.065), and DRB1*1302-DRB3*0301-DQA1*0102-DQB1*0604 (0.065). When these haplotypes were extended to the DPB1 locus, much diversification of haplotypes was observed and only one haplotype remained with a frequency of > 0.06: DRB1*0405-DRB4*0103-DQA1*0303-DQB1*0401-DPB1*0501 (0.062). Such diversification would have resulted from cumulated events of recombination within the HLA class II region, and the actual recombination rate observed between the HLA-DQB1 and DPB1 loci was 2.3% (10/438 informative meioses, including 2 recombinants informative by analysis of TAP genes). Comparison of the distribution of DRB1-DQB1 haplotypes with other populations revealed that Koreans are closest to Japanese people. However, Koreans share a few haplotypes with white people and Africans, which are rare in Japanese: DRB1*0701-DQB1*0202 and DRB1*1302-DQB1*0609. The results obtained in this study will provide useful information for anthropology, organ transplantation and disease association studies.
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Affiliation(s)
- E Y Song
- Seoul National University College of Medicine, Korea
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9
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denHollander N, Li J, van Oosterwijk A, Ng CM, Singal DP. Identification of a new HLA-B null allele, B*1817 N, in a family. TISSUE ANTIGENS 2002; 59:341-3. [PMID: 12135439 DOI: 10.1034/j.1399-0039.2002.590418.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We describe a new HLA-B null allele found in a daughter and her mother. This null allele was due to a mutation at position 41 of exon 1 which resulted in a premature stop codon. This new null allele was officially named HLA-B*1817N*.
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Affiliation(s)
- N denHollander
- Regional Histocompatibility Laboratory, UHN, Toronto, ON, Canada.
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