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Park JS, Kim K. Antigen Coverage Presented by MHC Class I Has a Negative Correlation with SARS-CoV-2-Induced Mortality. Vaccines (Basel) 2022; 10:1917. [PMID: 36423013 PMCID: PMC9698063 DOI: 10.3390/vaccines10111917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/29/2022] [Accepted: 11/09/2022] [Indexed: 11/11/2023] Open
Abstract
The COVID-19 pandemic has caused a health crisis worldwide; therefore, it is necessary to understand the factors related to its prognosis. In this study, we hypothesized that SARS-CoV-2-derived antigens presented by MHC class I may correlate with mortality in COVID-19 because they induce adaptive immune responses. Antigen coverage at the national level was inferred using country-specific HLA allele frequencies and relative predictions of binding antigens. We performed regression analysis between antigen coverage and the death rate due to COVID-19 across countries and found a negative correlation, although it was statistically significant only in HLA-B. This negative correlation was corroborated in multiple regression analysis with known risk factors, such as the prevalence of underlying disease. Furthermore, we analyzed antigen coverage in accordance with SARS-CoV-2 domains and identified a significant negative correlation when it was derived from the spike domain, which is reported to be favorable for COVID-19 prognosis. Taken together, the results indicate that the antigen coverage of SARS-CoV-2 specifically presented by HLA-B may act as a favorable factor when explaining COVID-19-induced mortality.
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Affiliation(s)
- Ji Soo Park
- Department of Biology, Kyung Hee University, Seoul 02447, Korea
| | - Kwoneel Kim
- Department of Biology, Kyung Hee University, Seoul 02447, Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Korea
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2
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Won DI. A novel analysis strategy for HLA typing using a sequence-specific oligonucleotide probe method. HLA 2017; 90:276-283. [PMID: 28796439 DOI: 10.1111/tan.13114] [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: 04/12/2017] [Revised: 07/01/2017] [Accepted: 08/04/2017] [Indexed: 12/01/2022]
Abstract
The technique of reverse sequence-specific oligonucleotide probes (SSOPs) is commonly used in human leukocyte antigen (HLA) typing. In the conventional method for data analysis (exact pattern matching, EPM), the larger is the number of mismatched probes, the longer the time for final typing assignment. A novel strategy, filtering and scoring (FnS), has been developed to easily assign the best-fit allele pair. In the FnS method, candidate alleles and allele pairs were filtered based on (1) subject's ethnicity, and (2) the measured partial reaction pattern with only definitely negative or positive probes. Then, the complete reaction pattern for all probes (CRPoAPs) were compared between the raw sample and expected residual allele pairs to obtain mismatch scores. To compare the FnS and EPM methods, each analysis time (minutes:seconds) for reverse SSOP HLA typing with intermediate resolution (n = 507) was measured. The analysis time with FnS method was shorter than that of the EPM method [00:21 (00:08-01:47) and 01:04 (00:15-23:45), respectively, P < .05]. In addition, the analysis time of the FnS method was relatively constant, regardless of the number of mismatched probes. The alternative approach of filtering based only on definite probes (neglecting ethnicity) took a long time for analysis. However, this approach did not compromise the accuracy. The FnS method showed improved accuracy and efficiency of HLA typing in a comprehensive and quantitative comparison between measured and expected CRPoAPs of candidate allele pairs. Therefore, this analysis strategy might be useful in a clinical setting.
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Affiliation(s)
- D I Won
- Department of Clinical Pathology, Kyungpook National University School of Medicine, Daegu, South Korea
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Kim KM, Han O, Kang MS, Huh JY. HLA-A*33:102, a novel allele identified by sequence-based typing in cord blood from a Korean woman. HLA 2016; 87:391-2. [DOI: 10.1111/tan.12772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 11/30/2022]
Affiliation(s)
- K. M. Kim
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
| | - O.J. Han
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
| | - M. S. Kang
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
| | - J. Y. Huh
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
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Park H, Chung YS, Yoon CH, Lee SH, Kim SS, Kang C, Choi BS. Presentation of available CTL epitopes that induction of cell-mediated immune response against HIV-1 Koran clade B strain using computational technology. HIV Med 2015; 17:460-6. [PMID: 26471354 DOI: 10.1111/hiv.12316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2015] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Theoretical predicting cytotoxic T lymphocyte (CTL) epitopes are an important tool in vaccine design and CTL therapy for enhancing our understanding of the cellular immune system. We would like to identify available CTL epitopes against HIV-1 Korean clade B. CTL activity was assessed in freshly isolated peripheral blood mononuclear cells from Korean HIV patients in order to assess whether these CTL epitopes induce a cell-mediated immune response (CMI). METHODS NetCTLpan1.1 software, which is the most popular prediction computer software package, and full atom-based simulation (FABS), which is a 3D modelling system for binding activity between epitopes and human leucocyte antigen (HLA) molecules, were used to predict the peptide-spanning Env region binding to HLA-A*24:02, HLA-A*02:01 and HLA-B*15:01, which are frequently found in the Korean population. Granzyme B and interferon-γ ELISPOT assays were used to determine whether identified CTL epitopes induce CMI. RESULTS Three HIV-1 Korean clade B-specific Env CTL epitopes were identified: Gp41-RYL and Gp41-RQG are localized within gp41, and Gp120-LLQ within gp120. In in vitro assays using granzyme B ELISPOT, Gp120-LLQ and Gp41-RQG induced epitope-specific CTL responses in HLA-restricted cells. In ex vivo assay using IFN-γ ELISPOT, cell-mediated immune responses to Gp41-RYL were present in 50% of HLA-matched patients, and responses to Gp120-LLQ and Gp41-RQG were found in 33% of HLA-matched patients. CONCLUSION In this study, we found that a prediction pipeline for CTL epitopes might be based on the most popular computer prediction software and FABS methods. Our results suggest that these CTL epitopes may provide useful tools and information for the development of a therapeutic vaccine against HIV-1 Korean clade B.
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Affiliation(s)
- H Park
- Division of AIDS, Korea National Institute of Health, Cheongju, Chungbuk, Korea
| | - Y-S Chung
- Division of AIDS, Korea National Institute of Health, Cheongju, Chungbuk, Korea
| | - C-H Yoon
- Division of AIDS, Korea National Institute of Health, Cheongju, Chungbuk, Korea
| | - S H Lee
- Department of Laboratory Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Korea
| | - S S Kim
- Division of AIDS, Korea National Institute of Health, Cheongju, Chungbuk, Korea
| | - C Kang
- Division of AIDS, Korea National Institute of Health, Cheongju, Chungbuk, Korea
| | - B-S Choi
- Division of AIDS, Korea National Institute of Health, Cheongju, Chungbuk, Korea
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Hong SS, Han OJ, Kang MS, Huh JY. HLA-B*59:09, a novel allele identified by sequence-based typing in a cord blood donated by a Korean woman. ACTA ACUST UNITED AC 2015; 86:146-7. [DOI: 10.1111/tan.12592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 05/12/2015] [Indexed: 11/27/2022]
Affiliation(s)
- S. S. Hong
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
| | - O. J. Han
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
| | - M. S. Kang
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
| | - J. Y. Huh
- Department of Laboratory Medicine, CHA Bundang Medical Center; CHA University; Seongnam South Korea
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Development of rheumatoid arthritis specific HLA-DRB1 genotyping microarray. BIOCHIP JOURNAL 2014. [DOI: 10.1007/s13206-014-8305-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Song JS, Kang ES, Joo EY, Hong SB, Seo DW, Lee SY. Absence of HLA-B*1502 and HLA-A*3101 alleles in 9 Korean patients with antiepileptic drug-induced skin rash: a preliminary study. Ann Lab Med 2014; 34:372-5. [PMID: 25187890 PMCID: PMC4151006 DOI: 10.3343/alm.2014.34.5.372] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/14/2014] [Accepted: 07/23/2014] [Indexed: 11/24/2022] Open
Abstract
There have been a number of studies about correlations between HLA genotypes in various ethnic groups and occurrence of various cutaneous adverse drug reactions, ranging in intensity from mild to severe, caused by antiepileptic drugs (AEDs). This is the first report analyzing the HLA genotypes of 9 Korean patients with skin rashes induced by various AEDs. The AEDs that induced skin rash were lamotrigine (n=3), carbamazepine (n=3), oxcarbazepine (n=1), phenobarbital (n=1), and phenytoin (n=1). None of the patients' HLA genotypes was either HLA-B*1502 or HLA-A*3101. Based on these series of cases, AED-induced skin rash can occur independently of HLA-B*1502 or HLA-A*3101 genotypes in the Korean patients.
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Affiliation(s)
- Ju Sun Song
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Eun-Suk Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Eun Yeon Joo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung Bong Hong
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea. ; Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Dae-Won Seo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Soo-Youn Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea. ; Department of Clinical Pharmacology and Therapeutics, Samsung Medical Center, Seoul, Korea
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Lim AH, Song SN, Lee JY, Cho NS, Kwon SY. A novel HLA-A*31 allele, A*31:57, identified by sequence-based typing. ACTA ACUST UNITED AC 2012; 79:386-7. [PMID: 22489948 DOI: 10.1111/j.1399-0039.2012.01855.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
The novel allele A*31:57 allele showed a single nucleotide difference with A*31:01:02 at nt 235 G>C in exon 2.
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Affiliation(s)
- A H Lim
- Blood Transfusion Research Institute, Korean Red Cross, Seoul, Korea
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Lim AH, Song SN, Shin GS, Lee SA, Kim MH. A novel HLA-DRB1*12 allele, DRB1*12:16:02, identified by sequence-based typing. ACTA ACUST UNITED AC 2012; 80:278-9. [PMID: 22762239 DOI: 10.1111/j.1399-0039.2012.01919.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 05/21/2012] [Accepted: 06/04/2012] [Indexed: 11/29/2022]
Abstract
The novel allele DRB1*12:16:02 allele showed two single nucleotide differences with HLA-DRB1*12:16:01 at nucleotides 303 G>C and 321 C>T in exon 2.
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Affiliation(s)
- A H Lim
- Blood Transfusion Research Institute, Korean Red Cross, Seoul, Korea
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Kim KM, Sung HY, Jung B, Kang MS, Huh JY. HLA-B*40:179, a novel allele identified by sequence-based typing in cord blood from a Korean woman. ACTA ACUST UNITED AC 2012; 80:194-5. [PMID: 22607317 DOI: 10.1111/j.1399-0039.2012.01894.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The novel allele B*40:179 showed one nucleotide difference with B*40:01:01 in exon 4.
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Affiliation(s)
- K M Kim
- Department of Laboratory Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Gyeonggi-do, Korea
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Hong SS, Sung HY, Kang MS, Huh JY. HLA-A*02:328, a novel allele identified by sequence-based typing in cord blood from a Korean woman. ACTA ACUST UNITED AC 2011; 79:308. [DOI: 10.1111/j.1399-0039.2011.01825.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chung HY, Yoon JA, Han BY, Song EY, Park MH. [Allelic and haplotypic diversity of HLA-A, -B, -C, and -DRB1 genes in Koreans defined by high-resolution DNA typing]. Korean J Lab Med 2011; 30:685-96. [PMID: 21157157 DOI: 10.3343/kjlm.2010.30.6.685] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In this study, we used high-resolution DNA typing to investigate the distribution of HLA alleles and haplotypes in Koreans. METHODS HLA-A, -B, -C, and -DRB1 alleles were genotyped at the allelic (4-digit) level in 474 healthy Koreans. HLA genotyping was performed in two steps. Initially, serologic typing or generic-level DNA typing was performed using the PCR-sequence-specific oligonucleotide method, and then allelic DNA typing (exons 2 and 3 for class I, and exon 2 for DRB1) was carried out using the PCR-single-strand conformation polymorphism method or sequence-based typing. HLA allele and haplotype frequencies and linkage disequilibrium values were calculated by the maximum likelihood method using a computer program developed for the 11th International Histocompatibility Workshop. RESULTS A total of 21 HLA-A, 40 HLA-B, 22 HLA-C, and 29 HLA-DRB1 alleles were found in Koreans. The most frequent alleles in each locus with frequencies of ≥ 10% were, in decreasing order of frequency, as follows: A*24:02, A*02:01, A*33:03; B*51:01; C*01:02, C*03:03; and DRB1*09:01. The numbers of two- and three-locus haplotypes with frequencies of >0.5% were as follows: 44 A-C, 42 B-C, 51 A-B, 52 B-DRB1, 42 A-C-B, and 34 A-B-DRB1. Thirteen A-B-DRB1 haplotypes with frequencies of ≥ 1.0% comprised 26.0% of the total haplotypes. The six most common haplotypes were as follows: A*33:03-B*44:03-DRB1*13:02 (3.7%), A*33:03-B*44:03-DRB1*07:01 (3.0%), A*33:03-B*58:01-DRB1*13:02 (3.0%), A*24:02-B*07:02-DRB1*01:01 (2.8%), A*30:01-B*13:02-DRB1*07:01 (2.3%), and A*11:01-B*15:01-DRB1*04:06 (2.2%). CONCLUSIONS The information obtained in this study can be used as basic data for Koreans in the fields of organ transplantation, disease association, and anthropologic studies.
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Affiliation(s)
- Hye Yoon Chung
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
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