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
|
Chung S, Roh EY, Park B, Lee Y, Shin S, Yoon JH, Song EY. GWAS identifying HLA-DPB1 gene variants associated with responsiveness to hepatitis B virus vaccination in Koreans: Independent association of HLA-DPB1*04:02 possessing rs1042169 G - rs9277355 C - rs9277356 A. J Viral Hepat 2019; 26:1318-1329. [PMID: 31243853 DOI: 10.1111/jvh.13168] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 05/07/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023]
Abstract
Recently, HLA class II loci, including HLA-DPB1, have been reported to be associated with interindividual variance in the hepatitis B (HB) vaccine response. In this study, we investigated significant single nucleotide polymorphisms (SNPs) for anti-HBs antibody levels in 6867 healthy Koreans using a genome-wide association study (GWAS). In GWAS, the top 20 SNPs that showed significant association with anti-HBs levels (P < 1.0 × 10-29 ) all resided in HLA-DPB1. Utilizing PCR sequencing, we verified the relationship of the top 3 most significant SNPs (rs1042169, rs9277355 and rs9277356) from the GWAS and genotypes of HLA-DPB1 with the HB vaccine response in Korean infants who received a scheduled vaccination. The DPB1*04:02 allele has G, C and A nucleotides for the 3SNP sites, and was significantly more frequent in responders than in nonresponders (10.9% vs 1.0%, Pc = 0.018). DPB1*05:01 was significantly more frequent in nonresponders than in responders (49.0% vs 31.1%, Pc = 0.018). In multivariate logistic regression, DPB1*04:02 showed a significant association with both vaccine response (P = 0.037, OR = 8.465) and high-titre response (P = 0.027, OR = 9.860). The haplotypes rs1042169 G - rs9277355 C - rs9277356 A showed a significant association with a high-titre response only (P = 0.002, OR = 2.941). In conclusion, DPB1*04:02 possessing rs1042169 G - rs9277355 C - rs9277356 A is an independent predictor of the HB vaccine response in Koreans.
Collapse
Affiliation(s)
- Soie Chung
- Department of Laboratory Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea.,Seoul Metropolitan Public Cord Blood Bank-ALLCORD, Seoul, Republic of Korea
| | - Boram Park
- Department of Public Health Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yunhwan Lee
- Department of Public Health Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea.,Seoul Metropolitan Public Cord Blood Bank-ALLCORD, Seoul, Republic of Korea
| | - Jong Hyun Yoon
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea.,Seoul Metropolitan Public Cord Blood Bank-ALLCORD, Seoul, Republic of Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
3
|
Voorter CEM, Groeneweg M, Joannis MO, Meertens C, Agis F, Tilanus MGJ. Allele and haplotype frequencies of HLA-DPA1 and -DPB1 in the population of Guadeloupe. ACTA ACUST UNITED AC 2014; 83:147-53. [DOI: 10.1111/tan.12271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 11/15/2013] [Accepted: 11/28/2013] [Indexed: 11/30/2022]
Affiliation(s)
- C. E. M. Voorter
- Transplantation Immunology, Tissue Typing Laboratory; Maastricht University Medical Center; Maastricht the Netherlands
| | - M. Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory; Maastricht University Medical Center; Maastricht the Netherlands
| | - M.-O. Joannis
- Laboratoire d'Hématologie-Immunologie; Centre Hospitalier Universitaire de Point-à-Pitre/Abymes; Point-à-Pitre Guadeloupe
| | - C. Meertens
- Transplantation Immunology, Tissue Typing Laboratory; Maastricht University Medical Center; Maastricht the Netherlands
| | - F. Agis
- Laboratoire d'Hématologie-Immunologie; Centre Hospitalier Universitaire de Point-à-Pitre/Abymes; Point-à-Pitre Guadeloupe
| | - M. G. J. Tilanus
- Transplantation Immunology, Tissue Typing Laboratory; Maastricht University Medical Center; Maastricht the Netherlands
| |
Collapse
|
4
|
Voorter CEM, Amicosante M, Berretta F, Groeneveld L, Drent M, van den Berg-Loonen EM. HLA class II amino acid epitopes as susceptibility markers of sarcoidosis. ACTA ACUST UNITED AC 2007; 70:18-27. [PMID: 17559577 DOI: 10.1111/j.1399-0039.2007.00842.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sarcoidosis is a multisystemic disorder of unknown etiology, affecting primarily the lung and characterized by epithelioid granulomas. Disease association studies showed human leukocyte antigen (HLA) class II to be related to sarcoidosis. Initially, we studied the association of sarcoidosis with DQB1, and in the present study, we evaluated all amino acid variants of the HLA-DPB1, -DQB1, -DRB1, -DRB3, -DRB4 and -DRB5 genes to identify possible polymorphisms associated with the disease. Patients and controls were typed for class II genes to the allele level by sequence-based typing. Multiple logistic regression models showed DRAla71 and DQPhe9 to be independently associated with the disease. Subdivision of patients according to their radiographic stage resulted in identification of DRArg74 as independent associated residue in the RS I group, whereas DRAla71 and DQTyr30 were associated with RS II-IV groups. Polymorphic residues specifically associated with sarcoidosis shed new light on the characteristics of sarcoidosis-triggered peptides. Overall, pocket 9 of DQ and pocket 4 of DR seem to be the most important areas involved in the association with sarcoidosis.
Collapse
Affiliation(s)
- C E M Voorter
- Tissue Typing Laboratory, and Sarcoidosis Management Centre, University Hospital Maastricht, 6202 AZ Maastricht, The Netherlands
| | | | | | | | | | | |
Collapse
|
5
|
Witter K, Gervais T, Dunn PPJ, Voorter C, Muramoto J, Albert ED. Sequence-based typing identifies a novel HLA-DPB1 allele, DPB1*9601. TISSUE ANTIGENS 2003; 62:185-7. [PMID: 12890001 DOI: 10.1034/j.1399-0039.2003.00081.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this report we describe the identification of a novel HLA-DPB1 allele, DPB1*9601, found in a Caucasian individual sample named ucla#356. The new allele was detected in the DNA of ucla#356 during routine HLA sequence-based typing (SBT) of samples participating in the UCLA International HLA DNA Exchange (number 55) for HLA DNA Proficiency Testing. DPB1*9601 was identical to DPB1*3901 except for a single nucleotide substitution 'G'-->'C' in previously constant position 277 (position 177, respectively, counting only exon 2). This nucleotide change causes an amino acid substitution from aspartic acid in DPB1*3901 to histidine at codon 64 in the novel allele. This new allele has been submitted to the EMBL database and has been assigned the accession number AJ514871. The WHO Nomenclature Committee has officially assigned the name DPB1*9601.
Collapse
Affiliation(s)
- K Witter
- Labor of Immunogenetics, University Munich, Munich, Germany.
| | | | | | | | | | | |
Collapse
|
6
|
Weston A, Ensey J, Kreiss K, Keshava C, McCanlies E. Racial differences in prevalence of a supratypic HLA-genetic marker immaterial to pre-employment testing for susceptibility to chronic beryllium disease. Am J Ind Med 2002; 41:457-65. [PMID: 12173370 DOI: 10.1002/ajim.10072] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND A beryllium materials manufacturer is conducting a limited pilot program that offers testing for HLA-DP beta 1E69 with genetic counseling through a third party to applicants for employment. An important consideration in this regard is the prevalence of this marker in the general population, and its consequent positive predictive value of disease susceptibility. METHODS Polymerase chain reaction and restriction fragment length polymorphism analyses were used to determine HLA-DP beta 1E69 population frequencies. Estimation of positive predictive values assumed a disease frequency among beryllium workers of either 5 or 15% and used an odds ratio for disease risk of 35 for the HLA-DP beta 1E69 marker. RESULTS Allelic/carrier frequencies were found to be 0.21/0.33, 0.24/0.40, 0.27/0.47, and 0.38/0.59 for Caucasians, African-Americans, Hispanics, and Chinese, respectively. Ranges of positive predictive values for a genetic test based on HLA-DP beta 1E69 in these populations were calculated to be 8.3-14.3% for carriers with an assumed disease frequency of 5%. For high risk subgroups with disease frequencies of 15%, the range of positive predictive values was found to span between 24.9-43.0%. CONCLUSIONS These estimates suggest that using HLA-DP beta 1E69 genotyping for general pre-employment screening in the beryllium industry has a low positive predictive value, which varies little among racial groups where carrier frequencies differ significantly.
Collapse
Affiliation(s)
- Ainsley Weston
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, CDC, MS-L3014, 1095 Willowdale Road, Morgantown, WV 26505-2888, USA.
| | | | | | | | | |
Collapse
|
7
|
Marsh SG, Bodmer JG, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Hansen JA, MacH B, Mayr WR, Parham P, Petersdorf EW, Sasazuki T, Schreuder GM, Strominger JL, Svejgaard A, Terasaki PI. Nomenclature for factors of the HLA system, 2000. EUROPEAN JOURNAL OF IMMUNOGENETICS : OFFICIAL JOURNAL OF THE BRITISH SOCIETY FOR HISTOCOMPATIBILITY AND IMMUNOGENETICS 2001; 28:377-424. [PMID: 11422419 DOI: 10.1046/j.1365-2370.2001.00268.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- S G Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Marsh SG, Bodmer JG, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Hansen JA, Mach B, Mayr WR, Parham P, Petersdorf EW, Sasazuki T, Schreuder GM, Strominger JL, Svejgaard A, Terasaki PI. Nomenclature for factors of the HLA system, 2000. Hum Immunol 2001; 62:419-68. [PMID: 11295476 DOI: 10.1016/s0198-8859(01)00229-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- S G Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, Hampstead, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Marsh SG, Bodmer JG, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Hansen JA, Mach B, Mayr WR, Parham P, Petersdorf EW, Sasazuki T, Schreuder GM, Strominger JL, Svejgaard A, Terasaki PI. Nomenclature for factors of the HLA system, 2000. TISSUE ANTIGENS 2001; 57:236-83. [PMID: 11285132 DOI: 10.1034/j.1399-0039.2001.057003236.x] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- S G Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|