1
|
Sarri CA, Giannoulis T, Moutou KA, Mamuris Z. HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action. Immunol Lett 2021; 238:75-95. [PMID: 34329645 DOI: 10.1016/j.imlet.2021.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/05/2021] [Accepted: 07/17/2021] [Indexed: 01/24/2023]
Abstract
BACKGROUND HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR). METHODS For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used. RESULTS All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found. CONCLUSIONS Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.
Collapse
Affiliation(s)
- Constantina A Sarri
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Themistoklis Giannoulis
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece; Department of Animal Science, University of Thessaly, Trikallon 224, 43100 Karditsa, Greece
| | - Katerina A Moutou
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Zissis Mamuris
- Department of Biochemistry and Biotechnology, Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece.
| |
Collapse
|
2
|
Lazaro AM, Henry J, Ng J, Hurley CK, Posch PE. Increased HLA class I and II diversity as 72 novel alleles are identified in volunteers for the National Marrow Donor Program Registry in 2010. ACTA ACUST UNITED AC 2011; 79:50-7. [PMID: 21995494 DOI: 10.1111/j.1399-0039.2011.01788.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Seventy-two novel human leukocyte antigen (HLA) class I and class II alleles are described from volunteers for the 'Be The Match Registry®': 17 HLA-A alleles, 12 HLA-C alleles, 31 HLA-B alleles and 12 HLA-DRB1 alleles. Forty-six (≈ 64%) of the 72 novel alleles are single-nucleotide substitution variants when compared with their most homologous allele. Five of these single-nucleotide variants are silent substitutions and one creates a non-expressed allele (B*44:108N). The remaining novel alleles differ from their most similar allele by two to five nucleotide substitutions. One of the novel HLA-C alleles (C*07:150Q) is of questionable expression due to an insertion of 21 nucleotides starting at codon 143 that adds seven amino acids to exon 3. An inter-locus gene conversion may have created the novel allele HLA-A*23:31 that shares its codon differences with HLA-B*07:28. Some of the new alleles encode novel codons and unique amino acid changes at polymorphic positions in the HLA-A (codons 116 and 150), HLA-C (codon 114), HLA-B (codons 11, 21, 35, 42, 48, 73, 98 and 170) and HLA-DRB1 (codon 29) loci.
Collapse
Affiliation(s)
- A M Lazaro
- Department of Pediatrics and C.W. Bill Young Marrow Donor Research and Recruitment Program, Georgetown University Medical Center, Washington, DC 20057, USA
| | | | | | | | | |
Collapse
|
3
|
Kuranov AB, Mukhamedyarov DA, Momynaliev KT. Characterization of new HLA-A and -B alleles from Kazakhstan. TISSUE ANTIGENS 2011; 78:217-218. [PMID: 21732918 DOI: 10.1111/j.1399-0039.2011.01681.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Eight novel alleles, two HLA-A and six HLA-B, are described in Kazakh individuals.
Collapse
Affiliation(s)
- A B Kuranov
- National Center for Biotechnology, Astana, Republic of Kazakhstan
| | | | | |
Collapse
|
4
|
Lazaro AM, Xiao Y, Masaberg C, Hwang WYK, Yeoh AEJ, Weiyan Y, Ng J, Hurley CK, Posch PE. Novel HLA class I and II alleles identified during routine registry typing in 2010. ACTA ACUST UNITED AC 2011; 78:263-6. [DOI: 10.1111/j.1399-0039.2011.01728.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
5
|
Kuranov AB, Mukhamedyarov DA, Momynaliev KT. Identification of new HLA-DRB1 alleles in Kazakh individuals. ACTA ACUST UNITED AC 2011; 77:263-4. [PMID: 21299539 DOI: 10.1111/j.1399-0039.2010.01611.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Seven novel human leukocyte antigen (HLA)-DRB1 alleles were identified during routine sequence-based typing (SBT) of healthy Kazakh individuals.
Collapse
Affiliation(s)
- A B Kuranov
- National Center for Biotechnology, Astana, Republic of Kazakhstan
| | | | | |
Collapse
|
6
|
Lazaro AM, Xiao Y, Henry J, Ng J, Hurley CK, Posch PE. Ninety-six novel HLA class I and II alleles identified in volunteers for the National Marrow Donor Program Registry in 2009. ACTA ACUST UNITED AC 2011; 78:195-202. [DOI: 10.1111/j.1399-0039.2011.01704.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
7
|
Chen MJ, Chu CC, Shyr MH, Lin CL, Lin PY, Yang KL. Identification of a novel HLA-DQB1 allele, DQB1*0326, in a College of American Pathologists 2009 survey specimen. Int J Immunogenet 2011; 37:455-7. [PMID: 20618518 DOI: 10.1111/j.1744-313x.2010.00947.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
We identified a novel DQB1*0326 allele from a proficiency test sample provided by the College of American Pathologists (CAP) medical society. This novel DQB1 allele was unexpectedly discovered by sequence-based typing method in an attempt to resolve a discrepant typing result between the CAP survey report and our laboratory report. This novel DQB1 allele is most similar to DQB1*030302 and DQB1*0311. DQB1*0326 has a nucleotide substitution resulting an amino acid change when compared with DQB1*030302 (M to L) and it differs from DQB1*0311 by one nucleotide variation causing an amino acid replacement (A to D).
Collapse
Affiliation(s)
- M J Chen
- Laboratory of Immunogenetics and Cord Blood Bank, Buddhist Tzu Chi Stem Cells Centre and Marrow Donor Registry, Buddhist Tzu Chi General Hospital, Buddhist Compassion Relief Tzu Chi Foundation, Hualien, Taiwan
| | | | | | | | | | | |
Collapse
|
8
|
Lazaro AM, Xiao Y, Masaberg C, Tu B, Ng J, Hurley CK, Posch PE. Seventy-eight novel HLA class I and II alleles identified during routine registry typing in 2008 and 2009. ACTA ACUST UNITED AC 2010; 77:54-61. [DOI: 10.1111/j.1399-0039.2010.01558.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Lazaro AM, Xiao Y, Regenscheid A, Ng J, Hurley CK, Posch PE. Sixty-five novel alleles at the HLA-A, -B, and -DRB1 loci identified from National Marrow Donor Program volunteer donors. ACTA ACUST UNITED AC 2010; 76:319-24. [DOI: 10.1111/j.1399-0039.2010.01524.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
10
|
Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernández-Viña M, Geraghty DE, Holdsworth R, Hurley CK, Lau M, Lee KW, Mach B, Maiers M, Mayr WR, Müller CR, Parham P, Petersdorf EW, Sasazuki T, Strominger JL, Svejgaard A, Terasaki PI, Tiercy JM, Trowsdale J. Nomenclature for factors of the HLA system, 2010. TISSUE ANTIGENS 2010. [PMID: 20356336 DOI: 10.1111/j.1399‐0039.2010.01466.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
11
|
Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernández-Viña M, Geraghty DE, Holdsworth R, Hurley CK, Lau M, Lee KW, Mach B, Maiers M, Mayr WR, Müller CR, Parham P, Petersdorf EW, Sasazuki T, Strominger JL, Svejgaard A, Terasaki PI, Tiercy JM, Trowsdale J. Nomenclature for factors of the HLA system, 2010. TISSUE ANTIGENS 2010; 75:291-455. [PMID: 20356336 PMCID: PMC2848993 DOI: 10.1111/j.1399-0039.2010.01466.x] [Citation(s) in RCA: 2933] [Impact Index Per Article: 209.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
12
|
Klitz W, Gragert L, Maiers M, Tu B, Lazaro A, Yang R, Xu Q, Masaberg C, Ng J, Hurley CK. Four-locus high-resolution HLA typing in a sample of Mexican Americans. ACTA ACUST UNITED AC 2009; 74:508-13. [PMID: 19845916 DOI: 10.1111/j.1399-0039.2009.01374.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Mexicans are the most common minority population of the United States. From a sample of 553 bone marrow donor registrants of self-described Mexican ancestry, human leukocyte antigen (HLA) loci A, C, B and DRB1 were typed by high resolution sequence based typing (SBT) methods. A total of 47, 34, 76 and 46 distinct alleles at A, C, B and DRB1 respectively were identified, including 3 new alleles. The four-locus haplotype frequency distribution was extremely skewed with only 53.9% of 1106 chromosomes present with more than one estimated copy. Haplotypes of Native American origin were identified. These data form an initial basis for determining the requirements for an adequate donor pool for stem cell transplantation in this population.
Collapse
Affiliation(s)
- W Klitz
- Public Health Institute, Oakland, CA, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Lazaro AM, Xiao Y, Regenscheid A, Ng J, Hurley CK, Posch PE. Characterization of 104 novel alleles at the HLA-A, -B, and -DRB1 loci from National Marrow Donor Program volunteer donors. ACTA ACUST UNITED AC 2009; 73:364-72. [PMID: 19317748 DOI: 10.1111/j.1399-0039.2009.01226.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One hundred and four novel human leukocyte antigen (HLA) alleles are described from volunteer donors of the National Marrow Donor Program: 37 HLA-A alleles, 37 HLA-B alleles, and 30 HLA-DRB1 alleles. Seventeen ( approximately 16%) of the novel alleles were found in multiple individuals and likely are relatively common in the population. Seventy-two ( approximately 69%) of the 104 novel alleles are single nucleotide substitution variants when compared with their most homologous allele. Nine of these single nucleotide variants are silent substitutions and three create null alleles. The remaining novel alleles differ from their most similar allele by two to seven nucleotide substitutions. Some of the novel alleles encode amino acid changes at positions not previously reported to be polymorphic, such as codons 6 and 11 in HLA-A alleles and codons 5, 105, and 141 in HLA-B alleles. Interestingly, one of the novel HLA-DRB1 alleles (*1471) has a change that is not the typical glycine/valine dimorphism at codon 86, which plays a key role in peptide binding to DR molecules. This is only the second DRB1 allele described that encodes an amino acid other than glycine or valine at this position.
Collapse
Affiliation(s)
- A M Lazaro
- Department of Pediatrics, C.W. Bill Young Marrow Donor Research and Recruitment Program, Georgetown University Medical Center, 3970 Reservoir Road NW, Washington, DC 20057, USA
| | | | | | | | | | | |
Collapse
|
14
|
Lazaro AM, Hwang WYK, Yeoh AEJ, Ng J, Posch PE. Characterization of new HLA-B and -DRB1 alleles from Singapore. ACTA ACUST UNITED AC 2009; 73:75-6. [PMID: 19140838 DOI: 10.1111/j.1399-0039.2008.01176.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Six novel alleles, three human leukocyte antigen (HLA)-B and three HLA-DRB1 alleles, are described. Five of the variants are single nucleotide substitutions from their most homologous allele, of which three result in amino acid changes (B*3572, *9509 and DRB1*1157) and two are silent substitutions (B*370103 and DRB1*150204). DRB1*0462 differs by three nucleotide substitutions that alter two amino acids.
Collapse
Affiliation(s)
- A M Lazaro
- Department of Oncology, Georgetown University Medical Center, Washington, DC 20057, USA
| | | | | | | | | |
Collapse
|
15
|
Nomenclature for Factors of the HLA System, Update June 2008. Hum Immunol 2008. [DOI: 10.1016/j.humimm.2008.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
16
|
Affiliation(s)
- Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London NW3 2QG, UK.
| | | |
Collapse
|
17
|
Marsh SGE. Nomenclature for factors of the HLA system, June 2008 update*. Int J Immunogenet 2008. [DOI: 10.1111/j.1744-313x.2008.00788.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|