• Tuberculosis and Respiratory Diseases
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• v.70 no.1
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• pp.21-27
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• 2011

Background: Although the gold standard method for research trials on epidermal growth factor receptor (EGFR) mutations has been direct sequencing, this approach has the limitations of low sensitivity and of being time-consuming. Peptide nucleic acid (PNA)-mediated polymerase chain reaction (PCR) clamping is known to be a more sensitive detection tool. The aim of this study was to compare the detection rate of $EGFR$ mutation and EGFR-tyrosine kinase inhibitor (TKI) responsiveness according to $EGFR$ mutation status using both methodologies. Methods: Clinical specimens from 112 NSCLC patients were analyzed for $EGFR$ mutations in exons 18, 19, 20, and 21. All clinical data and tumor specimens were obtained from 3 university hospitals in Korea. After genomic DNA was extracted from paraffin-embedded tissue specimens, both PNA-mediated PCR clamping and direct-sequencing were performed. The results and clinical response to $EGFR$-TKIs were compared. Results: Sequencing revealed a total of 35 (22.9%) mutations: 8 missense mutations in exon 21 and 26 deletion mutations in exon 19. PNA-mediated PCR clamping showed the presence of genomic alterations in 45 (28.3%) samples, including the 32 identified by sequencing plus 13 additional samples (6 in exon 19 and 7 in exon 21). Conclusion: PNA-mediated PCR clamping is simple and rapid, as well as a more sensitive method for screening of genomic alterations in $EGFR$ gene compared to direct sequencing. This data suggests that PNA-mediated PCR clamping should be implemented as a useful screening tool for detection of $EGFR$ mutations in clinical setting.

• Tuberculosis and Respiratory Diseases
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• v.58 no.1
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• pp.11-17
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• 2005

Background : Interferon-gamma ($IFN-{\gamma}$) is essential in the immune response to mycobacterial infections, and a complete or partial deficiency in the $IFN-{\gamma}$ receptor 1 ($IFN{\gamma}R1$) or the $IFN-{\gamma}$ receptor 2 ($IFN{\gamma}R2$) have been reported to confer susceptibility to a disseminated infection with nontuberculous mycobacteria. However, similar mutations in the $IFN-{\gamma}$ receptor have not been specifically examined in the patients with clinical tuberculosis. Methods : This study searched for mutations in the $IFN-{\gamma}$ receptor gene that resulted in a partial $IFN-{\gamma}$ receptor deficiency in six patients with disseminated tuberculosis. The previously identified $IFN{\gamma}R1$ and $IFN{\gamma}R2$ coding regions were sequenced after amplification. Results : There was no partial $IFN{\gamma}R1$ deficiency including a homozygous recessive missense mutation causing an amino-acid substitution in the extracellular domain of the receptor (I87T) and a hotspot for small deletions (818delT, 818del4, 818insA) found in any of the patients. In addition, a partial $IFN{\gamma}R2$ deficiency of the homozygous missense mutation (R114C) was not found in any of the patients. Conclusion : Genetic defects causing a partial $IFN-{\gamma}$ receptor deficiency were not identified in our patients with disseminated tuberculosis.

• Pediatric Infection and Vaccine
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• v.16 no.2
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• pp.199-204
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• 2009

Purpose : Various proteins encoded in the early region 3 (E3) of adenoviruses protect cells from being killed by cytotoxic T cells and death-inducing cytokines. We sought to find out whether the genetic heterogeneity of the E3 gene might contribute to the molecular diversity of adenoviruses. Methods : Sequences in the E3 region were analyzed for 14 adenovirus type 3 (Ad3) strains that were isolated from children with lower respiratory tract infections in the Seoul National University Children's Hospital during the period 1991-2000. Full-length adenoviral DNA was purified from the infected A549 cell lysates using a modified Hirt procedure. Results : There was 98% homology between 14 Korean Ad3 strains with a reference strain (M15952). Homology within the Korean Ad3 strains was 98.7%. Variation was found in the region of transcripts 20.1 kDa, 20.6 kDa, truncated 7.7 kDa, 10.3 kDa, 14.9 kDa, and 15.3 kDa. In particular, all 14 Korean strains showed a missense single point mutation at the start codon of the truncated 7.7 kDa. In addition, a deletion was found in the truncated 7.7 kDa region by 58 base pairs in 10 strains and 94 base pairs in 4 strains. Variations in amino acids were observed in the receptor internalization and degradation complex (10.3 kDa/14.9 kDa) which stimulates the clearance from the cell surface and subsequent degradation of the receptors for the Fas ligand and TRAIL, while no variations were observed in another immunoregulatory transcript, 19 kDa. Conclusion : Sequence analysis of the immunoregulatory region of adenovirus E3 shows that genetic heterogeneities are related to genome type patterns.

• Molecules and Cells
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• v.22 no.3
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• pp.343-352
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• 2006

Sialic acid is a sugar typically found at the N-glycan termini of glycoproteins in mammalian cells. Lec3 CHO cell mutants are deficient in epimerase activity, due to a defect in the gene that encodes a bifunctional UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE). Sialic acid modification on the cell surface is partially affected in these cells. We have mutagenized Lec3 CHO cells and isolated six mutants (termed C2m) deficient in the cell surface expression of polysialic acid (PSA). Mutant C2m9 was partially defective in expression of cell-surface PSA and wheat germ agglutinin (WGA) binding, while in the other five mutants, both cell-surface PSA and WGA binding were undetectable. PSA expression was restored by complementation with the gene encoding the CMP-sialic acid transporter (CST), indicating that CST mutations were responsible for the phenotypes of the C2m cells. We characterized the CST mutations in these cells by Northern blotting and RT-PCR. C2m9 and C2m45 carried missense mutations resulting in glycine to glutamate substitutions at amino acids 217 (G217E) and 256 (G256E), respectively. C2m13, C2m39 and C2m31 had nonsense mutations that resulted in decreased CST mRNA stability, and C2m34 carried a putative splice site mutation. PSA and CD15s expression in CST-deficient Lec2 cells were partially rescued by G217E CST, but not by G256E CST, although both proteins were expressed at similar levels, and localized to the Golgi. These results indicate that the novel missense mutations isolated in this study affect CST activity.

• Radiation Oncology Journal
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• v.21 no.2
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• pp.149-157
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• 2003

Purpose: The purpose of this study was to determine if there were prognostic differences between BRCA related and BRCA non-related Korean patients with early-onset breast carcinomas. Materials and Methods: Sixty women who had developed breast cancers before the age of 40, and who were treated at the Soonchunhyang University Hospital, were studied independently of their family histories. The age range was 18 to 40 with a median of 34.5 years. Lymphocyte specimens from peripheral blood were studied for the heterozygous mutations of BRCA1 and BRCA2 using direct sequencing methods. Immunohistochemistry was peformed on the paraffin-embedded tissue blocks that were available. Results: Eleven deleterious mutations (18.3%, 6 in BRCA1 and 5 in BRCA2) and 7 missense mutations of unknown significance (11.7%), were found among the 60 patients. More than half of the mutation were novel, and were not reported in the database. Most of the BRCA-associated patients had no history of breast cancer. No treatment related failures were observed in the BRCA carriers, with the exception of one patient that had experienced a new primary tumor of the contralateral breast. The seven year relapse free survival rate were 50 and 79% In the BRCA carrier and BRCA negative patients, respectively. Although the expression of estrogen and progesterone receptors were less common, and histological features more aggressive, in the BRCA associated tumors, the outcome of the patients with BRCA mutations was not poorer than that on the patients without deleterious mutations. Conclusion.: Despite the BRCA mutation carriers having adverse prognostic features, the recurrence rate was relatively lower than that in the BRCA non-carrying Korean patients wi4h early-onset breast carcinomas. In addition, although the prevalence of the BRCA mutation in Korean patients was higher than that in white patients, the penetrance of the cancer seemed to be relatively low in Korean women carrying BRCA mutations. A large population based study of the BRCA mutation, with a long-term follow-up of the study patients will be required to confirm these results.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.8
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• pp.1081-1085
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• 2017

Objective: Previously, we reported quantitative trait loci (QTLs) affecting backfat thickness (BFT) traits on pig chromosome 5 (SW1482-SW963) in an F2 intercross population between Landrace and Korean native pigs. The aim of this study was to evaluate glutamate receptor-interacting protein 1 (GRIP1) as a positional candidate gene underlying the QTL affecting BFT traits. Methods: Genotype and phenotype analyses were performed using the 1,105 $F_2$ progeny. A mixed-effect linear model was used to access association between these single nucleotide polymorphism (SNP) markers and the BFT traits in the $F_2$ intercross population. Results: Highly significant associations of two informative SNPs (c.2442 T>C, c.3316 C>G [R1106G]) in GRIP1 with BFT traits were detected. In addition, the two SNPs were used to construct haplotypes that were also highly associated with the BFT traits. Conclusion: The SNPs and haplotypes of the GRIP1 gene determined in this study can contribute to understand the genetic structure of BFT traits in pigs.

• Journal of Animal Science and Technology
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• v.54 no.6
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• pp.411-418
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• 2012

KIT gene is the major causative gene for coat color variation in diverse animal species. This gene regulates melanocyte migration from the neural crest to target tissues and the mutation of this gene can affect dominant white phenotypes in animals. Because this gene has a major influence for the coat color variation, single nucleotide polymorphisms (SNPs) in 14 Korean cattle (Hanwoo) and 5 Holstein individuals were investigated. The Hanwoo DNA samples included three different colored (5 Black, 5 Yellow and 4 Stripe) animals. Total 126 polymorphisms have been identified and 23 of them are located in the exon region. Also, 5 bp (TTCTC) and 3 bp (TCT) intronic indels in intron 3 and intron 5, respectively, were identified. Out of 23 exonic polymorphisms, 15 SNPs are the missense mutations and the rest of the SNPs are silence mutations. The neighbor-joining phylogenetic tree was constructed for the different colored animals using the obtained KIT gene sequences. Holstein breed showed a clear breed-specific cluster in the phylogenetic tree which is differed from Hanwoo. Also, three colored Hanwoo animals were not discriminated among the breeds. The KIT gene polymorphisms identified in this study will possibly give some solutions for the color variations in cattle with further verifications.

• Journal of Microbiology and Biotechnology
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• v.24 no.8
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• pp.1081-1087
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• 2014

Aspergillus oryzae is generally recognized as safe, but it is closely related to A. flavus in morphology and genetic characteristics. In this study, we tested the aflatoxigenicity and genetic analysis of nine commercial A. oryzae strains that were used in Korean soybean fermented products. Cultural and HPLC analyses showed that none of the commercial strains produced detectable amount of aflatoxins. According to the molecular analysis of 17 genes in the aflatoxin (AF) biosynthetic pathway, the commercial strains could be classified into three groups. The group I strains contained all the 17 AF biosynthetic genes tested in this study; the group II strains deleted nine AF biosynthetic genes and possessed eight genes, including aflG, aflI, aflK, aflL, aflM, aflO, aflP, and aflQ; the group III strains only had six AF biosynthetic genes, including aflG, aflI, aflK, aflO, aflP, and aflQ. With the reverse transcription polymerase chain reaction, the group I A. oryzae strains showed no expression of aflG, aflQ and/or aflM genes, which resulted in the lack of AF-producing ability. Group II and group III strains could not produce AF owing to the deletion of more than half of the AF biosynthetic genes. In addition, the sequence data of polyketide synthase A (pksA) of group I strains of A. oryzae showed that there were three point mutations (two silent mutations and one missense mutation) compared with aflatoxigenic A. flavus used as the positive control in this study.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.3
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• pp.1247-1253
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• 2014

Mutations in the DNMT3A and IDH genes represent the most common genetic alteration after FLT3/NPM1 in acute myeloid leukemia (AML). We here analyzed the frequency and distribution pattern of DNMT3A and IDH mutations and their associations with other molecular markers in normal karyotype AML patients. Fortyfive patients were screened for mutations in DNMT3A (R882), IDH1 (R132) and IDH2 (R140 and R172) genes by direct sequencing. Of the 45 patients screened, DNMT3A and IDH mutations were observed in 6 (13.3%) and 7 (15.4%), respectively. Patients with isolated DNMT3A mutations were seen in 4 cases (9%), isolated IDH mutations in 5 (11.1%), while interestingly, two cases showed both DNMT3A and IDH mutations (4.3%). Nucleotide sequencing of DNMT3A revealed missense mutations (R882H and R882C), while that of IDH revealed R172K, R140Q, R132H and R132S. Both DNMT3A and IDH mutations were observed only in adults, with a higher frequency in males. DNMT3A and IDH mutations were significantly associated with NPM1, while trends towards higher coexistence with FLT3 mutations were observed. This is the first study to evaluate DNMT3A/IDH mutations in Indian patients. Significant associations among the various molecular markers was observed, that highlights cooperation between them and possible roles in improved risk stratification.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.35 no.5
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• pp.304-309
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• 2009

Purpose: Fibrous dysplasia (FD) is a fibro-osseous disease associated with activating missense mutations of the gene encoding the $\alpha$-subunit of stimulatory G protein. FD may affect a single bone (called monostotic form) or multiple bones (called polyostotic form). The extent of lesions reflects the onset time of mutation. In this study, cells from monostotic FD in maxilla of a patient were isolated and cultured in vitro for characterization. Materials and Methods: The single cells were released from FD lesion which was surgical specimen from 15 years-old boy. These isolated cells were cultured in vitro and tested their proliferation activity with MTT assay. In osteogenic media, these cells underwent differentiation process comparing with its normal counterpart i.e. bone marrow stromal cells. The proliferated FD cells were detached and transplanted into the dordsal pocket of nude mouse and harvested in 6 weeks and 12 weeks. Results and Summary: FD cells have an increased proliferation rate and poor differentiation. As a result, cells isolated from FD lesion decreased differentiation into osteoblast and increased proliferation capacity. MTT assay presented that proliferation rate of FD cells were higher than control. However, the mineral induction capacity of FD was lesser than that of control. Monostotic FD cells make fewer amounts of bone ossicles and most of them are woven bone rather than lamellar bone in vivo transplantation. In transplanted FD cells, hematopoietic marrow were not seen in the marrow space and filled with the organized fibrous tissue. Therefore, they were recapitulated to the original histological features of FD lesion. Collectively, these results indicated that the FD cells were shown that the increased proliferation and decreased differentiation potential. These in vitro and in vivo system can be useful to test FD cell's fate and possible.