Detection of First-Line Anti-Tuberculosis Drug Resistance Mutations by Allele-Specific Primer Extension on a Microsphere-Based Platform

BACKGROUND: Resistance of Mycobacterium tuberculosis to anti-tuberculosis (TB) drugs is almost exclusively due to spontaneous chromosomal mutations in target genes. Rapid detection of drug resistance to both first- and second-line anti-TB drugs has become a key component of TB control programs. Technologies that allow rapid, cost-effective, and high-throughput detection of specific nucleic acid sequences are needed. This study was to develop a high-throughput assay based on allele-specific primer extension (ASPE) and MagPlex-TAG microspheres to detect anti-TB drug resistance mutations. METHODS: DNA samples from 357 M. tuberculosis clinical isolates and H37Rv were amplified by multiplex PCR using four primer sets, followed by multiplex ASPE using 23 TAG-ASPE primers. The products were sorted on the TAG-ASPE array and detected by using the Luminex xMAP system. Genotypes were also determined by sequencing. RESULTS: Genetic drug susceptibility typing by the TAG-ASPE method was 100% concordant with those obtained by sequencing. Compared with phenotypic drug susceptibility testing (DST) as a reference method, the sensitivity and specificity of the TAG-ASPE method were 83% (95% confidence interval [CI], 79-88%) and 97% (95% CI, 90-100%) for isoniazid. For rifampin testing, the sensitivity and specificity were 90% (95% CI, 86-93%) and 100% (95% CI, 99-100%). Also, the sensitivity and specificity were 58% (95% CI, 51-65%) and 86% (95% CI, 79-93%) for ethambutol. CONCLUSIONS: This study demonstrated the TAG-ASPE method is suitable for highly reproducible, cost-effective, and high-throughput clinical genotyping applications.

Frequency of Killer Cell Immunoglobulin-like Receptors (KIRs) in Korean Patients with Chronic HCV Infection

Natural killer (NK) cells play an important role in innate immunity, especially in the response to viral infections, such as hepatitis C virus (HCV). Killer cell immunoglobulin-like receptors (KIRs) are the primary receptors of NK cells that mediate innate immunity. KIRs are also involved in acquired immunity, because some KIRs are expressed on the surface of certain subsets of T cells. In this study, the frequency of KIR genes, HLA-C allotypes, and combinations of KIR genes with their HLA-C ligands were evaluated in two different groups of the Korean population: controls and patients with chronic HCV infection. The study population consisted of 147 Korean patients with chronic HCV infection. The frequency of KIR2DS2 in patients with chronic HCV infection was 9.5% which was significantly lower than 19.5% of the control (P < 0.01). However, there were no significant differences in the frequency of other KIR genes, HLA-C allotypes or different combinations of KIR genes with their HLA-C ligands. This study can contribute to the further prospective study with a larger scale, suggesting the assumption that KIR2DS2 might aid in HCV clearance by enhancing both the innate and acquired immune responses of people in Korea.

Recipient's Killer Cell Immunoglobulin-like Receptor Genotype and Human Leukocyte Antigen C Ligand Influence the Clinical Outcome following Living Donor Liver Transplantation

PURPOSE: The design of this study was to determine the most influential factor(s) on post-transplant immunological consequences, particularly with regard to the role of killer cell immunoglobulin-like receptors (KIRs) and their ligands (type I human leukocyte antigen (HLA)) in unstable liver function. METHODS: Retrospectively collected data from 319 recipients undergoing adult living donor liver transplantation (LDLT) using a right lobe graft between January 2002 and August 2008 were analyzed. Patients were categorized according to the serum alanine transaminase (ALT) pattern; stable ALT pattern was defined as ALT pattern during 3 months post-transplantation, except for initial 2 weeks post-transplantation, in which 2 times or less additional elevation(s) of serum alanine transaminase (ALT) (> or =80 IU/L) were observed. When a serum ALT pattern showed fluctuating and/or unpredictable nature, it was defined as an unstable pattern. In addition, genetic information of KIRs and HLA-C allotypes received from 68 recipients and 59 donors was analyzed by way of polymerase chain reaction using sequence-specific primers (PCR-SSP) to determine the factor(s) influencing a serum ALT pattern. RESULTS: Among 319 LDLT recipients included in this study, the actual incidences of AR and unstable ALT pattern were 13.4% (43/319) and 42.3% (135/319), respectively. Unstable ALT pattern correlated with poorer survival following LDLT than stable pattern (P<0.000). Genetically, unstable ALT pattern was related to recipients carrying KIR2DL2(+)/KIR2DS2(+) combined with the heterogeneous HLA-C allotype (HLA-C1/C2), (relative risks 45.0, 95% confidence interval 2.160~937.321; P=0.013). CONCLUSION: This study indicates that, when performing LDLT, pretransplant determination of recipient's KIRs and HLA-C allotypes may be beneficial in coping with post-transplant immunological circumstances.

Susceptibility of Leukemia according to the Genotype of Minor Histocompatibility Antigens in a Korean Population

BACKGROUND: In the search for susceptibility genes responsible for leukemia, genetic studies involving HLA association have been in progress extensively since the first report on its effect on the disease. Here we investigated the genetic associations of different leukemias with 4 autosomal mHags, HA-1, -2, -8 and HB-1. In particular, HB-1 is one of the leukemia-associated minor histocompatibility antigens (mHags) that is significantly expressed by Epstein-Barr virus-transformed- and tumor cells of all B lineage acute lymphoblastic leukemia (ALL). METHODS: A simultaneous genotyping method using PCR sequence-specific primers against HA-1, -2, -8 and HB-1 was developed, and their allelic frequencies in 139 healthy controls and 36 leukemia patients were observed. To compare genotype, phenotype, and gene frequencies of mHags with healthy controls, leukemia patients were classified into sub groups of ALL, acute myeloid leukemia (AML), and chronic myeloid leukemia (CML). RESULTS: The genotype frequencies of HA-1, -2 and -8 were not significantly different from healthy controls in every group of leukemia patients. However, the HB-1 H genotype was significantly increased in leukemia patients (P=0.03, OR=1.82, CI=1.08~3.06), particularly in AML (P=0.01, OR=2.4, CI=1.21~4.76) as compared with healthy controls. CONCLUSION: Our results suggested that the genotype of HB-1 H may be associated with leukemia, particularly with AML. In further study, it is necessary to confirm the association of HB-1 with other leukemias in a larger group of patients, and to identify the underlying mechanism of HB-1 responsible for the occurrence of leukemia.

HLA-restricted and Antigen-specific CD8+ T Cell Responses by K562 Cells Expressing HLA-A*0201

BACKGROUND: Identification of antigen-specific T cells has yielded valuable information on pathologic process and the disease state. Assays for quantification of inflammatory cytokines or lytic-granule molecules have been generally used to evaluate antigen specific T cell response, however their applicability have been hampered due to the limited source of autologous antigen-presenting target cells (APC). METHODS: K562, a leukemic cell line deficient of human leukocyte antigen (HLA), was transfected with a gene encoding HLA-A*02 (K562/A*02) and its function as stimulator cells in inducing activation of HLA-matched T cells was evaluated by IFN-gamma enzyme linked immunospot (ELISPOT) assay. RESULTS: The stable transfectant K562/A*02 pulsed with HLA- A*02 restricted peptide could specifically induce IFN-gamma secretion by CD8+ T cells compared to no detectable secretion by CD4+ T cells. However, CD56+ NK cells secreted IFN-gamma in both K562/A*02 with peptide and without peptide. The number of IFN-gamma secreted CD8+ T cells was increased according to the ratio of T cells to K562 and peptide concentration. Formalin-fixed K562/A*02 showed similar antigen presenting function to live K562/A*02. Moreover, K562/A*02 could present antigenic- peptide to not only A*0201 restricted CD8+ T cells but also CD8+ T cells from A*0206 donor. CONCLUSION: These results suggest that K562/A*02 could be generally used as target having specificity and negligible background for measuring CD8+ T cell responses and selective use of K562 with responsder matched HLA molecules on its surface as APC may circumvent the limitation of providing HLA-matched autologous target cells.

Analysis of HLA in Patients with Obstructive Sleep Apnea Syndrome / 결핵및호흡기질환

BACKGROUND: Obstructive sleep apnea syndrome (OSAS) is believed to have multifactorial causes. The major risk factors for OSAS are obesity, narrowed upper airways, and abnormal cranial-facial structures. A genetic basis for OSAS has been also suggested by reports of families with many members affected. This study analyzed the HLA typing in patients with OSAS to determine the possible role of genetics in OSAS. METHODS: Twenty-five Korean patients with OSAS (1 woman and 24 men; age range 30-66 years) were enrolled in this study. A diagnosis of OSAS was made using full-night polysomnography. The control group consisted of 200 healthy Korean people. Serologic typing of the HLA-A and B alleles was performed in all patients using a standard lymphocyte microcytotoxicity test. Analysis of the polymorphic second exons of the HLA-DRB1 gene was performed using a polymerase chain reaction-sequence specific oligonucleotide probe. RESULTS: The allele frequency of HLA-A11 was significantly lower in patients with OSAS compared with the controls (p45) than in the controls (p<0.05). CONCLUSION: This study revealed an association between OSAS and the HLA-A11 and DRB1*09 alleles as well as association between the disease severity and the HLA-DRB1*08 allele in Korean patients. These results suggest that genetics plays an important role in both the development and the disease severity of OSAS.

Association of KIR (Killer Cell Immunoglobulin-like Receptor) Genotype with Psoriasis in Korean Population

BACKGROUND: Psoriasis is a multifactorial autoimmune skin disease with a pathogenesis that has remained obscure. Recently, T cells bearing natural killer receptors (NKRs) were precisely and strongly targeted as new putative pathogenic immunocytes in psoriasis. Among NKRs, killer cell immunoglobulin-like receptor (KIR) is the major molecule recognizing HLA class I allotypes and might be closely related to psoriasis. METHODS: To investigate the association of KIR genotype and patients with psoriasis in Korean, we defined the 14 KIR genotypes in 96 patients with psoriasis and 86 healthy controls using PCR-SSP methods. RESULTS: The frequencies of KIR2DS4 and KIR3DL1 were significantly decreased in psoriasis compared with controls (RR=0.21, p or =30 years) respectively, these phenomena were similarly observed independent of groups divided (type I: RR=0.26, p<0.005; type II: RR=0.14, p<0.0006). When the patients were divided into subgroups according to the age of onset and family history, the frequencies of KIR2DS4, KIR3DL1, and KIR2DS3 were significantly decreased in type I compared with type II psoriasis (3DL1, 2DS4: p<0.004; 2DS3: p<0.04) and were significantly decreased in psoriasis without family history compared to with family history (3DL1, 2DS4: p<0.007; 2DS3: p<0.05). The frequency of haplotype combination BB was significantly increased in psoriasis compared with controls (RR=2.74, p<0.009). CONCLUSION: These results suggest that KIR genotype is a factor for the occurrence and development of psoriasis and in future how combinations of HLA and KIR genes influence psoriasis needs to be defined.

Distribution of HLA-DQA1*01, *03, *05 and DQB1*02 Subtypes and the Associated Haplotypes in the Korean Population

BACKGROUND: As all HLA class II genes, the DQ genes show their polymorphic variation mainly in the second exon, which encodes the first extracellular domain of the molecule. PCR-SSOP (Polymerase chain reaction-Sequence specific oligonucleotide probe) techniques were frequently used for HLA-DQA1 and DQB1 typing but certain alleles, DQA1*0101/0104/0105, *0302/0303, *0501/0505 and DQB1*0201/*0202, which differ from each other in segment other than exon 2, could not be unequivocally assigned. METHODS: To overcome this problem, we applied additional PCR-SSP (PCR-Sequence specific primer) method to analyze DQA1 exons 1, 3 and 4 and DQB1 exon 3. And we investigated the distributions and haplotypes of HLA-DRB1, DQA1 and DQB1 alleles in 406 unrelated Korean healthy individuals. RESULTS: Using this method the indistinguishable alleles of DQA1 and DQB1 in PCR-SSOP were typed definitively. We also found several important associations between DQA1 and DQB1 alleles in the Korean population; DQA1*0101-DQB1*0501, DQA1*0104-DQB1*0502 or -*0503, DQA1 *0105-DQB1*0501, DQA1*0302-DQB1*0303, DQA1*0303-DQB1*0401 or -*0402, DQA1 *0501-DQB1*0201, DQA1*0505-DQB1*0301, and DQA1*0201-DQB1*0202. The haplotypes of DRB1-DQA1-DQB1 associated with DQA1*01, *03, *05, and DQB1*02 subtypes were investigated. Several haplotypes associated with these alleles were observed in the Korean population. CONCLUSION: Our results can be helpful to find potential unrelated donors for bone marrow registries and study the HLA-associated disease and anthropology at high-resolution allelic level.

Association between HLA Class II Alleles and Response to Steroid Therapy in Sudden Sensorineural Hearing Loss / 대한이비인후과학회지

BACKGROUND AND OBJECTIVES: This research investigated the association between HLA (human leukocyte antigen) class II alleles and the susceptibility to sudden sensorineural hearing loss, and between HLA class Il alleles and the results of treatment with steroid in the Korean population. MATERIALS AND METHOD: We carried out HLA-DRR1, -DQA1, -DQR1 and -DPRl genotyping in 41 patients with sudden sensorineural hearing loss and in 206 healthy controls. We examined the initial hearing levels at the onset of hearing loss and the final hearing levels after the treatment, and then evaluated for the association with HLA class II alleles. HLA-DRB1, DQA1, BQB1 and DPB1 genotypings were performed by employing the sequence specific oligonucleotide probes (SSOP) method. RESULTS: The frequencies of HLA-DRB1, DQA1, DQB1, and DP31 alleles were not significantly different between the patients and controls. When the association between the results of treatment and HLA alleles was increased, the frequencies of HLA-DRB1X14 (RR= 3.5, p<0.02), -DQA1X03 (RR=4.2, p<0.02) and -DQA1X05 (RR=3.1, p(0.03) significantly increased, but the frequencies of HIA-DQA1X01 (RR=0.2, p<0.004) and -DQB1X06 (RR =0.2, p<0.009) significantly decreased in patients who did not respond to the steroid treatment, compared with the controls. The frequencies of HLA-DQA1X01 (p<0.04) and -DQB1X06 (p<0.02) significantly increased while the frequency of HLA- DQA1X03 (p<0.003) significantly decreased in patients who responded well to steroid, compared with patients who did not. CONCLUSION: These results suggest that the presence of HLA-DRB1X14, DQA1X03 and DQA1X05 might be an useful marker that implys poor prognoses whereas the presence of HLA-DQA101 and DQB1X06 might be a marker implying good prognoses in Korean patients with sudden sensorineural hearing loss.

The Distribution of CTLA-4 Alleles in Korean Patients with SLE / 대한면역학회지

No abstract available.

Comparison of infrequent restriction site-polymerase chain reaction and pulsed-field gel electrophoresis for molecular typing of Staphylococcus aureus and Escherichia coli

BACKGROUND: Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) are major pathogens in community and hospital. And they sometimes cause the outbreak in hospital in the immunocompromised patients. Pulsed-field gel electrophoresis (PFGE) has been regarded as a standard method for genotyping in epidemiologic studies, but it is laborious and time-consuming. Infrequent restriction site-polymerase chain reaction (IRS-PCR), a new genotyping methods, was performed to compare the applicability with PFGE. METHODS: We performed PFGE and IRS-PCR on S. aurues (n=120) and E. coli (n=117) which were collected clinically in 4 different hospitals. We assessed each method in terms of discriminatory power, quality, and efficiency. RESULTS: In E. coli, the discriminatory power of IRS-PCR was 46.7apprx86.7%, and that of PFGE was 88.9apprx96.7% according to hospital. But in S. aurues, the discriminatory power of IRS-PCR was 20apprx56.7%, and that of PFGE was 40apprx90% according to hospital. The typicality and reproducibility of IRS-PCR were 100% of each. PFGE needed four days to complete the procedure, but IRS-PCR could be performed within one day, IRS-PCR showed better resolution than PFGE. CONCLUSION: In case of gram negative bacteria (like E. coli), IRS-PCR could be a reliable alternative for epidemiologic typing due to better efficiency and comparable discriminatory power. But in the case of gram positive bacteria (like S. aureus), IRS-PCR does not seem to be suitable for the strain-to-strain differentiation. More trials and changes of restriction enzymes or primers could reveal the efficacy of IRS-PCR in the field of molecular typing.

Polymorphism of Antigen Processing ( TAP, HLA-DM, LMP ) Genes in Korean Population / 대한면역학회지

Antigen processing (TAP, HLA-DM and LMP) genes map within the major histocompatibility complex (MHC) class II region between the HLA-DQB1 and -DPB1 loci, and are involved in the processing of peptides bound to HLA class I or class II molecules. In order to determine the allele frequencies of antigen processing genes and the various linkage disequilibria existing among these genes, we have analyzed TAP1, TAP2, HLA-DMA, and HLA-DMB, LMP2, LMP7 polymorphisms in 184 unrelated healthy Koreans using the rnethod of PCR-SSCP, ARMS-PCR and PCR-RFLP. The frequencies of antigen processing genes were TAP1A (77.7%), TAP1*B (17.1%), TAP1*C (5.2%), TAP2*A (41.6%), TAP2*B (31.3%), TAP2*C (3.3%), TAP2*D (0.8%), TAP2*E (6.5%), TAP2*G (0.8%), HLA-DMA*0101 (81.5%), HLA-DMA*0102 (18.2%), HLA-DMA*0103 (0.3%), HLA-DMB*0101 (42.9%), HLA-DMB*0102 (19.0%), HLA-DMB*0103 (38.0%), LMP2*R (78.8%), LMP2*H (21.2%), LMP7*A (35.3%), LMP7*B (56.0%), LMP7*C (4.9%), and LMP7*D (3.8%). We also analysed two- locus association among each locus. Many significant positive associations were observed between these two loci, such as between HLA-DMB and TAP1, between HLA-DMA and HLA-DMB, between LMP2 and LMP7, and between TAP1 and LMP7. Conversely, any significant linkage disequilibrium was not detected between HLA-DMB and LMP2. These results could be used as control data for disease association and population genetics studies in Korean population.

The Distribution of HLA - A * 02 Subtypes in Koreans / 대한면역학회지

HLA-A2 is present at high frequency in most populations, as identified by serological and biochemical means. The values of these methods are limited by their failures to discriminate the products of the known allelic HLA-A02 variants. The great majority of genetic polymorphism which defines the allelic variants is found in exons 2 and 3 of the HLA-A02 gene. These exons encode the a-1 and a-2 domains of the HLA class I molecules, and the variation within the genes may influence the peptide binding specificity of the gene products of each allele. To determine the 17 known alleles of HLA-A02 an ARMS-PCR was developed. We applied this ARMS-PCR to 10 standard cell lines and we confirmed the specificity and sensitivity of this method. We defined the HLA-A 02 subtypes in 146 healthy Koreans who were serologically identified as HLA-A2. Five subtypes out of the 17 known A02 alleles were detected (A'0201, 0203, 0206, 0207, '0210) and A'0201 was most frequent (53.4%) and A'0206, '0207, '0203, 0210 (37.0%, 18.5%, 2.7%, 2.1%), were followed respectively. By linkage disequilibrium analysis with HLA-B alleles, A*02 subtypes were defined to be associated with many B alleles (B27, 35, 38, 39, 46, 52, 60, and 61). It is suggested that these findings may be helpful for the selection of patients for the specific immunotherapy with HLA-A02 restricted peptide vaccines and for the unrelated bone marrow transplantation in Korean.

Distributions of Alleles and Haplotypes of HLA - DRB1, - DQA1 and - DQB1 in Koreans / 대한면역학회지

The thirteen DRB1, 6 DQA1, and 5 DQB1 alleles were defined in 362 healthy Korean controls using reverse dot blot hybridization method. The twenty-four immobilized SSOs for DRB1, 8 for DQA1, and 6 for DQB1 were used for this study. The frequencies of genotypes were DRB104 (17.1'Yo), '09 (13.1%), and '13 (11.6%); DQA1'01 (46.7%), 03 (30.8%), and '05 (11.7%); DQB1*03 (39.5%), '06 '(29.8%), and 05 (16.0%). ...continue...