RESUMO
BACKGROUND: Middle East respiratory syndrome (MERS) is a lower respiratory tract disease caused by a beta coronavirus (CoV) called MERS-CoV, characterized by a high mortality rate. We aimed to evaluate the association between genetic variation in killer cell immunoglobulin-like receptors (KIRs) and the risk of MERS in South Koreans. METHODS: KIR genes were genotyped by multiplex polymerase chain reaction with sequence-specific primers (PCR-SSP). A case-control study was performed to identify the odds ratios (OR) of KIR genes for MERS and the association of KIR genes and their ligands, human leukocyte antigens (HLA) genes. RESULTS: KIR2DS4D and KIR3DP1F showed higher frequencies in the group of all patients infected with MERS-CoV than in the control group (p = 0.023, OR = 2.4; p = 0.039, OR = 2.7). KIR2DL1, KIR2DP1, and KIR3DP1D were significantly associated with moderate/mild (Mo/Mi) cases. KIR2DL2, KIR2DS1, and KIR3DP1F were affected in severe cases. When we investigated the association between KIR genes and their ligands in MERS patient and control groups, KIR3DL1+/Bw4(80I)+, KIR3DL1+/Bw6+, KIR3DL1+/Bw6-, KIR2DS1+/C2+, and KIR3DS+/Bw4(80I)+ were associated with MERS. KIR3DL1+/Bw6- was found in Mo/Mi cases. KIR2DS1+/C2+ and KIR2DS2+/C1+ were found in severe cases. CONCLUSION: Further investigations are needed to prove the various immune responses of MERS-CoV-infected cells according to variations in the KIR gene and ligand gene. A treatment strategy based on current research on the KIR gene and MERS-CoV will suggest potential treatment targets.
RESUMO
The range of HLA typing for successful hematopoietic stem cell transplantation (HSCT) is gradually expanding with the next-generation sequencing (NGS)-based improvement in its quality. However, it is influenced by the allocation of finances and laboratory conditions. HLA-A, -B, -C, -DRB1/3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 alleles were genotyped at the 3-field level by amplicon-based NGS using MiSeqDx system and compared to our previous study employing long-range PCR and NGS using TruSight HLA v2 kit, in healthy donors from South Korea. Exon 2, exons 2/3, exons 2/3/4 or 5 of 11-loci were amplified by multiplex PCR. The sequence reads of over 53 depth counts were consistently obtained in each sample exon, depending on the target exon determined to match the reference sequence contained in the IPD-IMGT/HLA Database. HLA alleles were investigated by combinations of the determined exons. A total of 18 alleles with a frequency over 10% were found at the 11 HLA loci. Three ambiguities of HLA-A, -C, and -DRB1 were resolved. We observed a total of 26 HLA-A ~ C ~ B and 6 HLA-DRB1 ~ DQA1 ~ DQB1 ~ DPA1 ~ DPB1 haplotypes having significant linkage disequilibrium between alleles at all neighboring HLA loci. This result was compatible with the previous one, using TruSight HLA v2 kit. Advantages are simple and short progress time because one plate is used for each PCR step in one PCR machine and 11-loci HLA typing is possible even if only eight samples. These data suggested that expanded 11-loci HLA typing data by amplicon-based NGS might help perform HSCT.
Assuntos
População do Leste Asiático , Antígenos HLA-B , Humanos , Alelos , Haplótipos , Antígenos HLA-B/genética , Teste de Histocompatibilidade , Reação em Cadeia da Polimerase Multiplex , Antígenos HLA-A/genética , Sequenciamento de Nucleotídeos em Larga Escala , Frequência do GeneRESUMO
HLA-B*07:457 differs from HLA-B*07:02:01:01 in codon 117 in exon 3.
Assuntos
Transplante de Células-Tronco Hematopoéticas , Alelos , Sequência de Bases , Antígeno HLA-B7 , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , Homologia de Sequência , Doadores de Tecidos , VoluntáriosRESUMO
HLA-DRB1*12:97 differs from HLA-DRB1*12:02:01:01 in codon 63 in exon 2.
Assuntos
Transplante de Células-Tronco Hematopoéticas , Alelos , Sequência de Bases , Cadeias HLA-DRB1/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , Doadores de Tecidos , VoluntáriosRESUMO
HLA-B*51:353 differs from HLA-B*51:01:01:01 in codon 95 in exon 3.
Assuntos
Transplante de Células-Tronco Hematopoéticas , Doadores de Tecidos , Alelos , Sequência de Bases , Antígenos HLA-B/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , VoluntáriosRESUMO
INTRODUCTION: Middle East Respiratory Syndrome (MERS) caused by MERS-coronavirus (CoV) is a lower respiratory tract disease characterized by a high mortality rate. MERS-CoV spread from Saudi Arabia to other countries, including South Korea. Dysfunction of the human leukocyte antigen (HLA) system has many effects due to genetic complexity and its role in the adaptive immune response. We investigated the association of HLA class I and II alleles with MERS-CoV in 32 patients with MERS. METHODS: HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1 were genotyped by polymerase chain reaction sequence-based typing. RESULTS: HLA-DQB1*03:02 are significantly associated with moderate/mild cases of MERS-CoV. Other alleles are no statistical significance. CONCLUSIONS: Treatment strategies based on current research on the HLA gene and MERS-CoV will provide potential therapeutic targets.
Assuntos
Genes MHC da Classe II , Genes MHC Classe I , Coronavírus da Síndrome Respiratória do Oriente Médio , Cadeias beta de HLA-DQ/genética , Humanos , Coronavírus da Síndrome Respiratória do Oriente Médio/genética , República da CoreiaRESUMO
Allele frequencies and haplotype frequencies of HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1, and -DPB1 have been rarely reported in South Koreans using unambiguous, phase-resolved next generation DNA sequencing. In this study, HLA typing of 11 loci in 173 healthy South Koreans were performed using next generation DNA sequencing with long-range PCR, TruSight® HLA v2 kit, Illumina MiSeqDx platform system, and Assign™ for TruSight™ HLA software. Haplotype frequencies were calculated using the PyPop software. Direct counting methods were used to investigate the association with DRB1 for samples with only one copy of a particular secondary DRB locus. We compared these allele types with the ambiguous allele combinations of the IPD-IMGT/HLA database. We identified 20, 40, 26, 31, 19, 16, 4, and 16 alleles of HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, and HLA-DPB1, respectively. The number of HLA-DRB3/4/5 alleles was 4, 5, and 3, respectively. The haplotype frequencies of most common haplotypes were as follows: A*33:03:01-B*44:03:01-C*14:03-DRB1*13:02:01-DQB1*06:04:01-DPB1*04:01:01 (2.89%), A*33:03:01-B*44:03:01-C*14:03 (4.91%), DRB1*08:03:02-DQA1*01:03:01-DQB1*06:01:01-DPA1*02:02:02-DPB1*05:01:01 (5.41%), DRB1*04:05:01-DRB4*01:03:01 (12.72%), DQA1*01:03:01-DQB1*06:01:01 (13.01%), and DPA1*02:02:02-DPB1*05:01:01 (30.83%). In samples with only one copy of a specific secondary DRB locus, we examined its association with DRB1. We, thus, resolved 10 allele ambiguities in HLA-B, -C (each exon 2+3), -DRB1, -DQB1, -DQA1, and -DPB1 (each exon 2) of the IPD-IMGT/HLA database. Korean population was geographically close to Japanese and Han Chinese populations in the genetic distances by multidimensional scaling (MDS) plots. The information obtained by HLA typing of the 11 extended loci by next generation sequencing may be useful for more exact diagnostic tests on various transplantations and the genetic population relationship studies in South Koreans.
Assuntos
Frequência do Gene , Antígenos HLA-A/genética , Antígenos HLA-B/genética , Antígenos HLA-C/genética , Cadeias alfa de HLA-DP/genética , Cadeias beta de HLA-DP/genética , Cadeias alfa de HLA-DQ/genética , Cadeias beta de HLA-DQ/genética , Cadeias HLA-DRB1/genética , Cadeias HLA-DRB3/genética , Cadeias HLA-DRB4/genética , Cadeias HLA-DRB5/genética , Haplótipos , Povo Asiático/genética , Frequência do Gene/genética , Loci Gênicos/genética , Haplótipos/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , República da CoreiaRESUMO
HLA-B*13:144 differs from HLA-B*13:01:01:01 in codon 12 in exon 2.
Assuntos
Transplante de Células-Tronco Hematopoéticas , Alelos , Sequência de Bases , Antígenos HLA-B/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , Homologia de Sequência , Doadores de Tecidos , VoluntáriosRESUMO
HLA-A*24:514N differs from HLA-A*24:02:01:01 in codon 167 in exon 3.
Assuntos
Transplante de Células-Tronco Hematopoéticas , Alelos , Sequência de Bases , Antígenos HLA-A/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , Homologia de Sequência , Doadores de Tecidos , VoluntáriosRESUMO
HLA-DRB1*09:45 differs from HLA-DRB1*09:01:02:01 in codon 19 in exon 2.
Assuntos
Transplante de Células-Tronco Hematopoéticas , Alelos , Sequência de Bases , Cadeias HLA-DRB1/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , Doadores de Tecidos , VoluntáriosRESUMO
HLA-A*11:384 differs from HLA-A*11:01:01:01 in codon 151 in exon 3.
Assuntos
Transplante de Células-Tronco Hematopoéticas , Alelos , Sequência de Bases , Antígenos HLA-A/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , Homologia de Sequência , Doadores de Tecidos , VoluntáriosRESUMO
HLA-A*02:954 differs from HLA-A*02:06:01:01 in codon 82 in exon 2.
Assuntos
Transplante de Células-Tronco Hematopoéticas , Alelos , Sequência de Bases , Antígenos HLA-A/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , Homologia de Sequência , Doadores de Tecidos , VoluntáriosRESUMO
HLA-B*35:01:64 differs from HLA-B*35:01:01:01 in codon 58 in exon 2.
Assuntos
Antígenos HLA-B , Transplante de Células-Tronco Hematopoéticas , Doadores de Tecidos , Alelos , Sequência de Bases , Antígenos HLA-B/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , Homologia de SequênciaRESUMO
HLA genes play a pivotal role for successful hematopoietic stem cell transplantation (HSCT). There is an increasing need for sophisticated screening of donor HLA genotypes for unrelated HSCT. Next generation sequencing (NGS) has emerged as an alternative for classical Sanger sequence for HLA typing. In this study, HLA-A, -B, and -DRB1 alleles were genotyped at the allelic (6-digit) level using MiSeqDx in 26,202 volunteers from the Korean Network for Organ Sharing. Exon 2 and 3 of HLA-A and -B and exon 2 of HLA-DRB1 were amplified by polymerase chain reaction (PCR) and each allele was determined by matching the targeted exons and the reference sequence consisting of the IPD-IMGT/HLA Database. Seventy alleles of HLA-A, 102 alleles of HLA-B, and 69 alleles of HLA-DRB1 were identified. According to common and well-documented catalogs, 34 alleles in HLA-A, 61 in HLA-B, and 45 in HLA-DRB1 locus were common alleles, and 12, 14, and 11 kinds, were well-documented alleles, respectively. Thirteen novel alleles including 3 alleles in HLA-A, 8 alleles in HLA-B, and 2 alleles in HLA-DRB1 loci were found. Ten haplotypes with a frequency of more than 1.0% accounted for 22.4% of the total haplotype frequencies. Cis/trans ambiguities of HLA-A and -B loci by combination of exons 2 and 3 were analyzed to be 0.17% of 3 and 3.95% of 22 genotypes, respectively. This information on rare and novel alleles found by accurate HLA typing with NGS may be helpful for unrelated HSCT among Koreans.
Assuntos
Antígenos HLA-A , Antígenos HLA-B , Cadeias HLA-DRB1 , Transplante de Células-Tronco Hematopoéticas , Alelos , Frequência do Gene , Antígenos HLA-A/genética , Antígenos HLA-B/genética , Cadeias HLA-DRB1/genética , Haplótipos , Sequenciamento de Nucleotídeos em Larga Escala , Teste de Histocompatibilidade , Humanos , República da Coreia , Doadores de TecidosRESUMO
HLA-DRB1*04:05:21 differs from HLA-DRB1*04:05:01:01 in codon 83 in exon 2.
Assuntos
Transplante de Células-Tronco Hematopoéticas , Alelos , Sequência de Bases , Cadeias HLA-DRB1/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , VoluntáriosRESUMO
HLA-A*33:03:42 differs from HLA-A*33:03:01:01 in codon 90 in exon 2.
Assuntos
Transplante de Células-Tronco Hematopoéticas , Alelos , Sequência de Bases , Antígenos HLA-A/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , Homologia de Sequência , Doadores de Tecidos , VoluntáriosRESUMO
HLA-DRB1*04:277 differs from HLA-DRB1*04:06:01:01 in codon 62 in exon 2.
Assuntos
Cadeias HLA-DRB1 , Transplante de Células-Tronco Hematopoéticas , Alelos , Sequência de Bases , Cadeias HLA-DRB1/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , Doadores de TecidosRESUMO
HLA-A*02:842 differs from HLA-A*02:149 in codon 99 in exon 3.
Assuntos
Antígenos HLA-A , Transplante de Células-Tronco Hematopoéticas , Alelos , Sequência de Bases , Antígenos HLA-A/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , Doadores de TecidosRESUMO
HLA-B*46:01:26 differs from HLA-B*46:01:01:01 in codon 66 in exon 2.
Assuntos
Antígenos HLA-B , Transplante de Células-Tronco Hematopoéticas , Alelos , Sequência de Bases , Antígenos HLA-B/genética , Teste de Histocompatibilidade , Humanos , Análise de Sequência de DNA , Homologia de Sequência , Doadores de TecidosRESUMO
HLA-A*31:154 differs from HLA-A*31:01:02:01 in codon 115 in exon 3.
