• Asian Pacific Journal of Cancer Prevention
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• v.14 no.11
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• pp.6803-6806
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• 2013

Background: Interferon regulatory factor 6 (IRF6) is a transcription factor with distinct and conserved DNA and protein binding domains. Mutations within the protein binding domain have been significantly observed in subjects with orofacial cleft relative to healthy controls. In addition, recent studies have identified loss of expression of IRF6 due to promoter hypermethylation in cutaneous squamous cell carcinomas. Since mutational events occurring within the conserved domains are likely to affect the function of a protein, we investigated whether regions within the IRF6 gene that encodes for the conserved protein binding domain carried mutations in oral squamous cell carcinoma (OSCC). Materials and Methods: Total chromosomal DNA extracted from 32 post surgical OSCC tissue samples were amplified using intronic primers flanking the exon 7 of IRF6 gene, which encodes for the major region of protein binding domain. The PCR amplicons from all the samples were subsequently resolved in a 1.2% agarose gel, purified and subjected to direct sequencing to screen for mutations. Results: Sequencing analysis resulted in the identification of a mutation within exon 7 of IRF6 that occurred in heterozygous condition in 9% (3/32) of OSCC samples. The wild type codon TTC at position 252 coding for phenylalanine was found to be mutated to TAC that coded for tyrosine (F252Y). Conclusions: The present study identified for the first time a novel mutation within the conserved protein binding domain of IRF6 gene in tissue samples of subjects with OSCC.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.10
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• pp.5113-5117
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• 2012

Prohibitin (PHB) is a chaperone protein which is highly conserved evolutionarily. It shows significant homology with the Drosophila cc gene which is considered important for development and differentiation of Drosophila melanogaster. Investigations have revealed an involvement of PHB in cellular proliferation and development, apoptosis, signal transduction, mitochondrial function and regulation of the estrogen and androgen receptors. Therefore, we conducted the present study to analyze mutations in the highly conserved region in Indian female breast cancer patients. Conventional PCR-SSCP and Automated DNA sequencing were performed with a total of 105 breast cancer samples along with adjacent normal tissue. Of the total, 14.2% (15/105) demonstrated a mutation status of prohibitin observed in our study population. We identified a novel missense mutation (Thr>Ser), a novel deletion of T nucleotide in an intron adjacent to intron-exon boundary and a previously determined missense mutation (Val>Ala). A statistically significant correlation was obtained which suggested that prohibitin may be associated with tumor development and/or progression of at least some proportion of breast cancers.

• Clinical and Experimental Pediatrics
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• v.59 no.sup1
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• pp.5-9
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• 2016

Blau syndrome (BS) is a rare autosomal dominant, inflammatory syndrome that is characterized by the clinical triad of granulomatous dermatitis, symmetric arthritis, and recurrent uveitis. Mutations in the nucleotide oligomerization domain 2 (NOD2 ) gene are responsible for causing BS. To date, up to 30 Blau-associated genetic mutations have been identified within this gene. We report a novel NOD2 genetic mutation that causes BS. A girl, aged 8 years, and her brother, aged 10 years, developed erythematous skin rashes and uveitis. The computed tomography angiogram of the younger sister showed features of midaortic dysplastic syndrome. The brother had more prominent joint involvement than the sister. Their father (38 years) was also affected by uveitis; however, only minimal skin involvement was observed in his case. The paternal aunt (39 years) and her daughter (13 years) were previously diagnosed with sarcoidosis. Mutational analysis revealed a novel c.1439 A>G mutation in the NOD2 gene in both siblings. The novel c.1439 A>G mutation in the NOD2 gene was found in a familial case of BS. Although BS is rare, it should always be considered in patients presenting with sarcoidosis-like features at a young age. Early diagnosis of BS and prompt multisystem workup including the eyes and joints can improve the patient's outcome.

• BMB Reports
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• v.49 no.9
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• pp.514-519
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• 2016

Korean cattle (Hanwoo) are categorized into three breeds based on color: brown, brindle, and black. Among these breeds, brown Hanwoo has been subjected to intensive selection to improve meat traits. To identify genetic traces driven by recent selection in brown Hanwoo, we scanned the genomes of brown and brindle Hanwoo using a bovine SNP chip. We identified 17 candidate selection signatures in brown Hanwoo and sequenced four candidate regions from 10 individuals each of brown and brindle Hanwoo. In particular, non-synonymous SNPs in the ADSL gene (K88M, L189H, and R302Q) might have had mutational effects on protein structure as a result of altering the purine pathway during nucleotide breakdown. The ADSL gene was previously reported to affect meat quality and yield in livestock. Meat quality and yield are main breeding goals for brown Hanwoo, and our results support a potential causal influence of non-synonymous SNPs in the ADSL gene.

• Clinical and Experimental Pediatrics
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• v.57 no.9
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• pp.410-415
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• 2014

Purpose: Neurofibromatosis 1 (NF1) is an autosomal dominant condition caused by an NF1 gene mutation. NF1 is also a multisystem disorder that primarily affects the skin and nervous system. The goal of this study was to delineate the phenotypic characterization and assess the NF1 mutational spectrum in patients with NF1. Methods: A total of 42 patients, 14 females and 28 males, were enrolled in this study. Clinical manifestations and results of the genetic study were retrospectively reviewed. Results: Age of the patients at the time of NF1 diagnosis was $15.8{\pm}14.6$ years (range, 1-62 years). Twelve patients (28.6%) had a family history of NF1. Among the 42 patients, $Caf\acute{e}$-au-lait spots were shown in 42 (100%), neurofibroma in 31 (73.8%), freckling in 22 (52.4%), and Lisch nodules in seven (16.7%). The most common abnormal finding in the brain was hamartoma (20%). Mental retardation was observed in five patients (11.9%), seizures in one patient (2.4%), and plexiform neurofibromas (PNFs) in four patients (9.5%). One patient with PNFs died due to a malignant peripheral nerve sheath tumor in the chest cavity. Genetic analysis of seven patients identified six single base substitutions (three missense and three nonsense) and one small deletion. Among these mutations, five (71.4%) were novel (two missense mutations: p.Leu1773Pro, p.His1170Leu; two nonsense mutations: $p.Arg2517^*$, $p.Cys2371^*$; one small deletion: $p.Leu1944Phefs^*6$). Conclusion: The clinical characteristics of 42 Korean patients with NF1 were extremely variable and the mutations of the NF1 gene were genetically heterogeneous with a high mutation-detection rate.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.14 no.2
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• pp.156-162
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• 2014

A 25-month-old boy was referred to the hospital due to large head detected on routine physical examination. At visit, dysmorphic facial appearances, including broad nose, prominent forehead, and coarse face, were noted. Nasal obstruction with nasal voice, prominent adenoids, and bilateral middle ear effusions were detected. His abdomen was distended, and liver and spleen were palpated about 3 finger and 2 finger breadths, respectively. He was operated for bilateral inguinal hernias. The motion of both elbow joints was mildly limited on supination and pronation. Urinary level of glycosaminoglycan was elevated and the enzyme activity of iduronate sulfatase in leukocytes was decreased. The mutational analysis of the gene iduronate 2-sulfatase (IDS) revealed c.263G>A (p.Arg88His) mutation. His developmental scale showed delayed development and there was cardiac valvular involvement (tricuspid regurgitation and mitral valve prolapse). After the diagnosis of Hunter syndrome, enzyme replacement therapy started on a weekly basis without progression of any clinical features. Here we report a case of early diagnosed Hunter syndrome detected by large head on routine examination. Thus, it is important to associate Hunter syndrome in the patient with large head especially, if there is the history of bilateral inguinal hernia and prominent adenoids to increase the possibility of early diagnosis and treatment.

• Journal of Applied Biological Chemistry
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• v.50 no.3
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• pp.109-114
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• 2007

Sar1p is a ras-related GTP-binding protein that functions in intracellular protein transport between the endoplasmic reticulum (ER) and the Golgi complex. The effector domain of Ras family proteins is highly conserved and this domain is functionally interchangeable in plant, yeast and mammalian Sar1. Using a recombinant Brassica sar1 protein (Bsar1p) harboring point mutations in its effector domain, we here investigated the ability of Sar1p to bind and hydrolyze GTP and to interact with the two sar1-specific regulators, GTPase activating protein (GAP) and guanine exchange factor (GEF). The T51A and T55A mutations impaired Bsar1p intrinsic GTP-binding and GDP-dissociation activity. In contrast, mutations in the switch domain of Bsar1 did not affect its intrinsic GTPase activity. Moreover, the P50A, P54A, and S56A mutations affected the interaction between Bsar1p and GAP. P54A mutant protein did not interact with two regulating proteins, GEF and GAP, even though the mutation didn't affect the intrinsic GTP-binding, nucleotide exchange or GTPase activity of Bsar1p.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1573-1576
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• 2010

Bacillus subtilis PerR is a metal-dependent peroxide-sensing transcription factor which uses metal-catalyzed histidine oxidation for peroxide-sensing. PerR contains two metal binding sites, one for structural $Zn^{2+}$ and the other for the regulatory/peroxide-sensing metal. Here we investigated the effect of mutations at both the structural and regulatory metal binding sites on the oxidation of either H37 or H91, two of the peroxide-sensing ligands. All four serine substitution mutants at the structural $Zn^{2+}$ site (C96S, C99S, C136S and C139S) exhibited no detectable oxidation at histidine residues. Two of the alanine substitution mutants at regulatory metal site (H37A and D85A) exhibited selective oxidation preferentially at the H91-containing tryptic peptide, whereas no oxidation was detected in the other mutants (H91A, H93A and D104A). Our results suggest that the cysteine residues coordinating structural $Zn^{2+}$ are essential for peroxide sensing by PerR, and that the C-terminal regulatory metal binding site composed of H91, H93 and D104 can bind $Fe^{2+}$, providing a possible explanation for the peroxide sensing mechanisms by PerR.

• Genomics & Informatics
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• v.11 no.4
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• pp.239-244
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• 2013

Somatic mutation is a major cause of cancer progression and varied responses of tumors against anticancer agents. Thus, we must obtain and characterize genome-wide mutational profiles in individual cancer subtypes. The Cancer Genome Atlas database includes large amounts of sequencing and omics data generated from diverse human cancer tissues. In the present study, we integrated and analyzed the exome sequencing data from ~3,000 tissue samples and summarized the major mutant genes in each of the diverse cancer subtypes and stages. Mutations were observed in most human genes (~23,000 genes) with low frequency from an analysis of 11 major cancer subtypes. The majority of tissue samples harbored 20-80 different mutant genes, on average. Lung cancer samples showed a greater number of mutations in diverse genes than other cancer subtypes. Only a few genes were mutated with over 5% frequency in tissue samples. Interestingly, mutation frequency was generally similar between non-metastatic and metastastic samples in most cancer subtypes. Among the 12 major mutations, the TP53, USH2A, TTN, and MUC16 genes were found to be frequent in most cancer types, while BRAF, FRG1B, PBRM1, and VHL showed lineage-specific mutation patterns. The present study provides a useful resource to understand the broad spectrum of mutation frequencies in various cancer types.

• Journal of Microbiology and Biotechnology
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• v.32 no.3
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• pp.287-293
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• 2022

The hydroxylation of methane (CH₄) is crucial to the field of environmental microbiology, owing to the heat capacity of methane, which is much higher than that of carbon dioxide (CO₂). Soluble methane monooxygenase (sMMO), a member of the bacterial multicomponent monooxygenase (BMM) superfamily, is essential for the hydroxylation of specific substrates, including hydroxylase (MMOH), regulatory component (MMOB), and reductase (MMOR). The diiron active site positioned in the MMOH α-subunit is reduced through the interaction of MMOR in the catalytic cycle. The electron transfer pathway, however, is not yet fully understood due to the absence of complex structures with reductases. A type II methanotroph, Methylosinus sporium 5, successfully expressed sMMO and hydroxylase, which were purified for the study of the mechanisms. Studies on the MMOH-MMOB interaction have demonstrated that Tyr76 and Trp78 induce hydrophobic interactions through π-π stacking. Structural analysis and sequencing of the ferredoxin domain in MMOR (MMOR-Fd) suggested that Tyr93 and Tyr95 could be key residues for electron transfer. Mutational studies of these residues have shown that the concentrations of flavin adenine dinucleotide (FAD) and iron ions are changed. The measurements of dissociation constants (K_ds) between hydroxylase and mutated reductases confirmed that the binding affinities were not significantly changed, although the specific enzyme activities were significantly reduced by MMOR-Y93A. This result shows that Tyr93 could be a crucial residue for the electron transfer route at the interface between hydroxylase and reductase.