• Asian Pacific Journal of Cancer Prevention
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• v.14 no.1
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• pp.329-332
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• 2013

Background: The study aimed to determine the incidence of K-ras and BRAF mutations in colorectal cancers (CRCs) in Thai patients and evaluate association with clinicopathological parameters including treatment outcomes in terms of event free survival (EFS). Materials and Methods: Two-hundred colorectal cancer specimens were collected for studies of K-Ras codon 12, 13 and 61, and BRAF codon 600 by polymerase chain reaction and direct nucleotide sequencing. Results: The overall incidence of K-Ras mutations in our patients was 23%. K-ras mutation frequencies in CRC stages (AJCC) I, II, III and IV were 6.7%, 16.1%, 23.3% and 26.6%, respectively (p-value>0.05). The three most common mutation forms were G12D, G12V and G13D. K-Ras mutation status was associated with poorer EFS in stage I-III CRCs (p-value 0.03). Conclusions: The study found a lower mutation frequency of K-Ras and BRAF compared to reports involving other ethnic groups. However, K-Ras mutations did have a negative prognostic value in early-stage CRCs.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.9
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• pp.5067-5072
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• 2013

Background: The phosphatidylinositol 3-kinase (PI3K) pathway plays a significant role in apoptosis, cellular proliferation and motility. The aim of the present study was to analyze mutations and gene expression profiles of the PI3KCA gene to determine any role in breast carcinomas. Materials and Methods: We analyzed 38 breast cancers for mutations in the two PIK3CA hotspots in exons 9 and 20 by direct sequencing of DNA obtained from biopsy samples. We have also analyzed expression of the PI3KCA gene in 38 breast carcinoma tumor and corresponding control tissue samples at the mRNA level by RT-PCR. The Fisher's exact test ($2{\times}2$ only) was performed using MedCalc software for to examine associations with mRNA levels. Results: In the present study a total of 13 cases demonstrated somatic mutations. In 9/13 cases 1633 G>A (E545K) were found in exon 9, whereas in exon 20, 4/13 cases had 3140A>G mutation. Our combined analysis showed PI3KCA mutations present in 34% of human breast cancer patients. In our study, we have also clearly found significantly higher expression in breast cancer tissues in comparison with control tissues (p=0.001). Conclusions: PIK3CA mutation is an emerging tumor marker that, in the future, might be used in the process of choosing a treatment. The detection of PI3KCA mutation might have important clinical implications for diagnosis, progression and therapy.

• Korean journal of applied entomology
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• v.35 no.4
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• pp.315-320
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• 1996

The effects of 2-arnino-3-methyIimidazo[4,5-fq]u inoline (IQ), 2-amino-6dimethyl-dipyrido[l,2-a;3',2'-d] imidazole (Glu-P-1) and aflatoxin B1 (AFBI) on the mitotic recombinations and somatic chromosome mutations were investigated using the transgenic Drosophila bearing a chimeric gene consisting of a promoter region of Drosophila actin 5C gene and rat DNA polymerase $. For investigating mitotic recombinations and the somatic chromosome mutations, the heterozygous (mwhl+) strain possessing or lacking transgene pol P was used. The spontaneous frequency of small mwh spots, due to deletion or nondisjunction etc., in the non-transgenic w strain and the transgenic plpol $1-130 strain was 0.351 and 0.606, respectively. The spontaneous frequency (0.063) of large mwh spots, arising mostly from somatic recombination between the centromere and the locus mwh, in the transgenic plpol $1-130 strain, was about three times higher than that (0.021) of the non-transgenic w strain. The mutant clone frequencies of two types induced by two heterocyclic mines (IQ and Glu-P-1) and AFBl in the transformant pbol PI-130 were two or three times higher than those in the host strain w. These mean that rat DNA polymerase P participates at least in the somatic chromosome mutations and mitotic recombination processes. And the present results suggest that the transgenic Drosophl!~ used in this study can be used as a hypersensitive, in vivo short-term assaying system for various environmental mutagens.

• Korean Journal of Environmental Biology
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• v.29 no.4
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• pp.373-378
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• 2011

Our aim was to investigate the genotoxicity of ambient air in the Krak$\acute{o}$w area after Fukushima Nuclear Power Plant (NPP) accident and compare with results from Chernobyl fallout. For the detection of ambient air genotoxicity the technique for screening gene mutation frequency in somatic cells of the $Tradescantia$ stamen hairs ($Trad$-SH assay) was used. Since 11th of March 2011 (Fukushima NPP accident), several pots containing at least 15 shoots of bioindicating plants were exposed to ambient air at 2 sites in the Krak$\acute{o}$w surrounding area, one in the city center, and about 100 pots in a control site (in the glasshouse of the Institute of Nuclear Physics) Continuous screening of mutations was performed. Progenies of 371,090 cells exposed were analyzed. Mutation frequency obtained in the first 10 days has shown a mean control level (GMF*100=$0.06{\pm}0.01$). At scoring period related to influence of a potential Fukushima fallout, a significant increase of gene mutation frequencies above the control level was observed at each site in the range, 0.10~0.33 depending on the location, (mean value for all sites GMF*100=$0.19{\pm}0.05$) that was associated with a strong expression of toxic effects. In the reported studies following the Chernobyl NPP accident monitoring $in$ $situ$ of the ambient air genotoxicity was performed in the period since April $29^{th}$ till June $3^{rd}$ 1986 also with Trad-SH bioindicator. In general, mutation frequency increases due to Chernobyl fallout(GMF*100=$0.43{\pm}0.02$) were corresponding to fluctuation of radioactivity in the air reported from physical measures, and to published reports about increase in chromosome aberration levels. Although, recent data obtained from monitoring of the ambient air quality in the Krak$\acute{o}$w and surroundings are lower when compared to results reported after Chernobyl NPP accident, though results express a significant increase above the control level and also are corresponding with increased air radioactivity reported from physical measurements. Statistically significant in comparison to control increase in gene mutation rates and more prolonged than that after Chernobyl fallout increase of GMF was observed during the period following the Fukushima NPP failure.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.20-20
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• 2017

Plant genomes include heterochromatic loci that consist of repetitive sequences and transposable elements. LTR retrotransposon is the major class of transposons in advanced plants in terms of proportion in plant genome. The elements contribute not only to genome size but also to genome stability and gene expression. A number of cases have been reported transposon insertions near genic regions affect crop traits such as fruit pigments, stress tolerance, and yields. Functional LTR retrotransposons produce extrachromosomal DNA from genomic RNA by reverse transcription that takes place within virus-like-particles (VLPs). DECREASED DNA METHYLATION 1 (DDM1) plays important roles in maintaining DNA methylation of heterochromatin affecting all sequence contexts, CG, CHG, and CHH. Previous studies showed that ddm1 mutant exhibits massive transcription of retrotransposons in Arabidopsis, but only few of them were able to create new insertions into the genome. RNA-dependent RNA POLYMERASE 6 (RDR6) is known to function in restricting accumulation of transposon RNA by processing the transcripts into 21-22 nt epigenetically activated small interfering RNA (easiRNA). We purified VLPs and sequence cDNA to identify functional LTR retrotransposons in Arabidopsis ddm1 and ddm1rdr6 plants. Over 20 LTR copia and gypsy families were detected in ddm1 and ddm1rdr6 sequencing libraries and most of them were not reported for mobility. In ddm1rdr6, short fragments of ATHILA gypsy elements were detected. It suggests easiRNAs might regulate reverse transcription steps. The highest enriched element among transposon loci was previously characterized EVADE element. It has been reported that active EVADE element is more efficiently silenced through female germline than male germline. By genetic analyses, we found ddm1 and rdr6 mutation affect maternal silencing of active EVADE elements. DDM1-GFP protein accumulated in megaspore mother cell but was not found in mature egg cell. The fusion protein was also found in early embryo and maternal DDM1-GFP allele was more dominantly expressed in the embryo. We observed localization of DDM1-GFP in Arabidopsis and DDM1-YFP in maize and found the proteins accumulated in dividing zone of root tips. Currently we are looking at cell cycle dependency of DDM1 expression using maize system. Among 10 AGO proteins in Arabidopsis, AGO9 is specifically expressed in egg cell and shoot meristematic cells. In addition, mutation of AGO9 and RDR6 caused failure in maternal silencing, implying 21-22 nt easiRNA pathway is important for retrotransposon silencing in female gametophyte or/and early embryo. On the other hand, canonical 24 nt sRNA-directed DNA methylation (RdDM) pathways did not contribute to maternal silencing as confirmed by this study. Heat-activated LTR retrotransposon, ONSEN, was not silenced by DDM1 but the silencing mechanisms require RdDM pathways in somatic cells. We will propose distinct mechanisms of LTR retrotransposons in germline and somatic stages.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.97-97
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• 2017

Plant genomes include heterochromatic loci that consist of repetitive sequences and transposable elements. LTR retrotransposon is the major class of transposons in advanced plants in terms of proportion in plant genome. The elements contribute not only to genome size but also to genome stability and gene expression. A number of cases have been reported transposon insertions near genic regions affect crop traits such as fruit pigments, stress tolerance, and yields. Functional LTR retrotransposons produce extrachromosomal DNA from genomic RNA by reverse transcription that takes place within virus-like-particles (VLPs). DECREASED DNA METHYLATION 1 (DDM1) plays important roles in maintaining DNA methylation of heterochromatin affecting all sequence contexts, CG, CHG, and CHH. Previous studies showed that ddm1 mutant exhibits massive transcription of retrotransposons in Arabidopsis, but only few of them were able to create new insertions into the genome. RNA-dependent RNA POLYMERASE 6 (RDR6) is known to function in restricting accumulation of transposon RNA by processing the transcripts into 21-22 nt epigenetically activated small interfering RNA (easiRNA). We purified VLPs and sequence cDNA to identify functional LTR retrotransposons in Arabidopsis ddm1 and ddm1rdr6 plants. Over 20 LTR copia and gypsy families were detected in ddm1 and ddm1rdr6 sequencing libraries and most of them were not reported for mobility. In ddm1rdr6, short fragments of ATHILA gypsy elements were detected. It suggests easiRNAs might regulate reverse transcription steps. The highest enriched element among transposon loci was previously characterized EVADE element. It has been reported that active EVADE element is more efficiently silenced through female germline than male germline. By genetic analyses, we found ddm1 and rdr6 mutation affect maternal silencing of active EVADE elements. DDM1-GFP protein accumulated in megaspore mother cell but was not found in mature egg cell. The fusion protein was also found in early embryo and maternal DDM1-GFP allele was more dominantly expressed in the embryo. We observed localization of DDM1-GFP in Arabidopsis and DDM1-YFP in maize and found the proteins accumulated in dividing zone of root tips. Currently we are looking at cell cycle dependency of DDM1 expression using maize system. Among 10 AGO proteins in Arabidopsis, AGO9 is specifically expressed in egg cell and shoot meristematic cells. In addition, mutation of AGO9 and RDR6 caused failure in maternal silencing, implying 21-22 nt easiRNA pathway is important for retrotransposon silencing in female gametophyte or/and early embryo. On the other hand, canonical 24 nt sRNA-directed DNA methylation (RdDM) pathways did not contribute to maternal silencing as confirmed by this study. Heat-activated LTR retrotransposon, ONSEN, was not silenced by DDM1 but the silencing mechanisms require RdDM pathways in somatic cells. We will propose distinct mechanisms of LTR retrotransposons in germline and somatic stages.

• Genomics & Informatics
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• v.15 no.4
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• pp.136-141
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• 2017

Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) <1% can be identified, and any mutation with >3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.8
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• pp.4183-4186
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• 2012

Background: Ovarian cancer is the number one killer among all the gynecological cancers. We undertook association study to identify potential alterations in the genomic DNA of a DNA repair gene, DNA polymerase beta ($pol{\beta}$), involved in base excision repair (BER), in ovarian carcinomas of patients from Haldia, India. Mutations, splice variants have been reported earlier in different tumors other than ovarian tumors. Aim: In this study we explored the possibility of association of any mutation of $pol{\beta}$ (Exon 8) with prognosis in 152 ovarian cancer samples. Results: Alteration in the exon 8 region (Exon 8:468, $A{\rightarrow}C$; 15.1%) was noted among fifty seven polymorphism positive samples. Alteration in the intervening sequence 8 (IVS8, -25, $A{\rightarrow}C$; 3.9%) was also noted. All alterations are heterozygous in nature. Conclusions: We found no significant association among the samples from serous type, stage IV, and the $pol{\beta}$ mutations ($P{\leq}0.01$). Only a slight tendency of association was evident between IVS8, -25, A to C; and stage III. Further analysis with a larger number of samples is needed.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 1998.07a
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• pp.50-51
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• 1998

guanidinoacetate methyltransferase (GAMT) catalyzes the last step of creatine biosynthesis in mammals. Creatine plays an important role in cellular energy metabolism in variety of tissues including brain and male reproductive tract. Congenital deficiency of the enzyme leads to a neurologic disorder in humans. We used an interspecific backcross DNA panel to map Gamt to the central region of mouse Chromosome (Chr) 10 near the locus of hesitant mutation affecting male fertility. We assigned the human GAMT gene to Chr 19 by PCR analysis of a human/rodent somatic hybrid cell line DNA panel, and further localized the human gene to Chr 19 at band p13.3 by PCR analysis of a human radiation hybrid DNA panel. Human chr 19p13.3 is homologous to the central part of mouse Chr 10 where mouse Gamt is located. Furthermore, this part of mouse Chr 10 contains mutant loci the phenotype of which is similar to the GAMT deficiency in human.

• Korean Journal of Environmental Biology
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• v.17 no.3
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• pp.331-335
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• 1999

The present study was carried out to investigate the combined effect of radiation and photoperiod (PP) regimes on Tradescantia 4430 somatic cell mutations. Potted plants were irradiated with 0.3, 0.5 and 1.0 Gy of gamma radiation from 60Co source. The plants irradiated only with gamma radiation were used as control group (CT). The somatic cell mutation rate in 0.5 Gy irradiated CT and PP20 group started to increase on the 6th day and reached a maximum value on the l0th day and 9th day after irradiation while the rate in the experimental group under 4 hours of photoperiod a day (PP4) started to increase on the l0th day and reached a maximal value on the 16th day post-irradiation. The slope of dose-response curve in CT was 5.99 ($r^2$=0.99), while it was 6.93 ($r^2$=0.98) in PP20 and 11.74 ($r^2$=0.99) in PP4, respectively. The biological efficacy of radiation in the induction of pink mutation increased by 15.7% in PP20 and 95.9 % in PP4, respectively. It is suggested that photoperiod regimes unfavorable to the plant have an additive effect on radiation-induced mutations and a delaying or inhibiting effect on cell damage repair, as well.