• Asian Pacific Journal of Cancer Prevention
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• 제16권6호
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• pp.2231-2235
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• 2015

Genome-wide association studies (GWASs) of the entire genome provide a systematic approach for revealing novel genetic susceptibility loci for breast cancer. However, genetic association studies have hitherto been primarily conducted in women of European ancestry. Therefofre we here performed a pilot GWAS with a single nucleotide polymorphism (SNP) array 5.0 platform from $Affymetrix^{(R)}$ that contains 443,813 SNPs to search for new genetic risk factors in 89 breast cancer cases and 46 healthy women of Indonesian ancestry. The case-control association of the GWAS finding set was evaluated using PLINK. The strengths of allelic and genotypic associations were assessed using logistic regression analysis and reported as odds ratios (ORs) and P values; P values less than $1.00{\times}10^{-8}$ and $5.00{\times}10^{-5}$ were required for significant association and suggestive association, respectively. After analyzing 292,887 SNPs, we recognized 11 chromosome loci that possessed suggestive associations with breast cancer risk. Of these, however, there were only four chromosome loci with identified genes: chromosome 2p.12 with the CTNNA2 gene [Odds ratio (OR)=1.20, 95% confidence interval (CI)=1.13-1.33, $P=1.08{\times}10^{-7}$]; chromosome 18p11.2 with the SOGA2 gene (OR=1.32, 95%CI=1.17-1.44, $P=6.88{\times}10^{-6}$); chromosome 5q14.1 with the SSBP2 gene (OR=1.22, 95%CI=1.11-1.34, $P=4.00{\times}10^{-5}$); and chromosome 9q31.1 with the TEX10 gene (OR=1.24, 95%CI=1.12-1.35, $P=4.68{\times}10^{-5}$). This study identified 11 chromosome loci which exhibited suggestive associations with the risk of breast cancer among Indonesian women.

• Asian Pacific Journal of Cancer Prevention
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• 제13권8호
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• pp.3605-3609
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• 2012

Lung cancer seriously threatens human health, so it is important to investigate gene expression changes in affected individuals in comparison with healthy people. Here we compared the gene expression profiles between smokers with and without lung cancer. We found that the majority of the expressed genes (threshold was set as 0.1 RPKM) were the same in the two samples, with a small portion of the remainder being unique to smokers with and without lung cancer. Expression distribution patterns showed that most of the genes in smokers with and without lung cancer are expressed at low or moderate levels. We also found that the expression levels of the genes in smokers with lung cancer were lower than in smokers without lung cancer in general. Then we detected 27 differentially expressed genes in smokers with versus without lung cancer, and these differentially expressed genes were foudn to be involved in diverse processes. Our study provided detail expression profiles and expression changes between smokers with and without lung cancer.

• 디지털콘텐츠학회 논문지
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• 제19권9호
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• pp.1795-1801
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• 2018

질환의 원인을 규명하기 위해 전장유전체 연관분석 (GWAS; Genome-Wide Association Study) 연구가 활발히 진행되고 유전체 레벨의 단일염기다형성 (SNP; Single-nucleotide polymorphism)이 많이 밝혀지고 있다. 그러나 단일염기다형성의 연관분석을 통해 질환이 발병하는 생물학적 메카니즘을 이해하기 어렵기 때문에 유전자, 생물학적 패스웨이 및 질환 등의 연관성 분석이 이전보다 더욱 중요하다. 본 논문에서는 단일염기다형성과 관련된 유전자와 패스웨이, 질환 정보를 검색하여 통합 분석하는 서비스를 제공하는 PRaDA 웹 시스템을 제안하였다. PRaDA는 사용자로부터 입력받은 유의한 몇몇의 단일염기다형성들과 관련된 유전자 및 패스웨이 뿐만 아니라, 유의하지 않은 다수의 단일염기다형성 집합의 간접적인 영향을 파악하기 위해 기능적으로 근접한 패스웨이를 검색하고 통계적 분석을 실행한다. 사용자들은 PRaDA가 제공하는 통합된 정보를 통해 질병의 전반적인 이해를 할 수 있다.

• Asian Pacific Journal of Cancer Prevention
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• 제16권14호
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• pp.6155-6158
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• 2015

Background: The human leukocyte antigen-G (HLA-G) gene is highly expressed in cancer pathologies and is one strategy used by tumor cells to escape immune surveillance. A 14-bp insertion/deletion (InDel) polymorphism of the HLA-G gene has been suggested to be associated with HLA-G mRNA stability and the expression of HLA-G. The aim of present study was to assess any genetic association between this polymorphism and breast cancer among Iranian-Azeri women. Materials and Methods: In this study 227 women affected with breast cancer, in addition to 255 age-sex and ethnically matched healthy individuals as the control group, participated. Genotyping was performed using polymerase chain reaction and electrophoresis assays. The data were compiled according to the genotype and allele frequencies, compared using the Chi-square test. Statistical significance was set at P<0.05. Results: In this case-control study, no significant difference was found between the case and control groups at allelic and genotype levels, although there is a slightly higher allele frequency of HLA-G 14bp deletion in breast cancer affected group. However,when the stage I subgroup was compared with stage II plus stage III subgroup of affected breast cancer, a significant difference was seen with the 14 bp deletion allele frequency. The stage II-III subgroup patients had higher frequency of deletion allele (57.4% vs 45.8%) than stage I cases (${\chi}^2=4.16$, p-value=0.041). Conclusions: Our data support a possible action of HLA-G 14bp InDel polymorphism as a potential genetic risk factor for progression of breast cancer. This finding highlights the necessity of future studies of this gene to establish the exact role of HLA-G in progression steps of breast cancer.

• Asian Pacific Journal of Cancer Prevention
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• 제13권5호
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• pp.2121-2127
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• 2012

Objective: Deoxyribonucleoside kinase of Drosophila melanogaster (Dm-dNK) mutants have been reported to exert suicide gene effects in combined gene/chemotherapy of cancer. Here, we aimed to further evaluate the capacity of the mutanted enzyme and its potential for inhibiting cancer cell growth. Methods: We altered the sequence of the last 10 amino acids of Dm-dNK to perform site-directed mutagenesis and constructed active site mutanted Dm-dNK (Dm-dNKmut), RT-PCR and western bloting studies were used to reveal the expression of lentivirus mediated Dm-dNKmut in a breast cancer cell line (Bcap37), a gastric cancer cell line (SGC7901) and a colorectal cancer cell line (CCL187). [3H]-labeled substrates were used for enzyme activity assays, cell cytotoxicity was assessed by MTT assays, cell proliferation using a hemocytometer and apoptosis induction by thenannexin-V-FITC labeled FACS method. In vivo, an animal study was set out in which BALB/C nude mice bearing tumors were treated with lentivirus mediated expression of Dm-dNKmut with the pyrimidine nucleoside analog brivudine (BVDU, (E)-5-(2-bromovinyl)-(2-deoxyuridine). Results: The Dm-dNKmut could be stably expressed in the cancer cell lines and retained its enzymatic activity. Moreover, the cells expressing Dm-dNKmut exhibited increased sensitivity in combination with BVDU, with induction of apoptosis in vitro and in vivo. Conclusion: These findings underlined the importance of BVDU phosphorylated by Dm-dNKmut in transduced cancer cells and the potential role of Dm-dNKmut as a suicide gene, thus providing the basis for future intensive research for cancer therapy.

• 한국해양바이오학회지
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• 제1권3호
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• pp.163-169
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• 2006

본 연구에서는 비장 내의 비대해진 세포 존재와 조직 괴사라는 병리조직학적 관찰에 의하여 우리 나라의 pearl gourami (Trichogaster leeri)에서 iridovirus에 의한 자연 감염이 나타남을 확인하였다. 이러한 iridovirus 감염을 더욱 정확하게 진단하기 위해서 iridovirus 감염 진단에 주로 사용되는 MCP와 ATPase gene 부위에서 2 primer sets를 제작하여 PCR을 실시한 결과, PCR 생성물은 기대한 size와 부합하게 나타났고, MCP gene 부위의 염기서열은 reference strain인 ISKNV와 매우 높은 유사성 (99.6%)을 보였다. 공격 실험을 통하여 pearl gourami에서 분리된 iridovirus의 병원성을 확인하였고, 무분별한 관상어 관리에 의하여 관상어로부터 양식어류에로의 질병 전이가 나타남으로서 일어날 수 있는 국내 양식 산업에 대한 위험성을 제시하였다.

• Journal of Genetic Medicine
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• 제8권2호
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• pp.130-134
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• 2011

Saethre-Chotzen 증후군은 상염색체 우성의 유전 방식을 보이는 두개골유합증후군(craniosynostosis)의 하나로, 원인 유전자는 TWIST1로 알려져 있다. Saethre-Chotzen 증후군의 임상 증상은 두개골유합증 중에서도 특히 관상봉합(coronal suture)이 편측 혹은 양측으로 조기에 폐쇄되는 것이 특징적이며, 이외에도 안검하수, 낮게 위치한 귀, 청력 소실, 손발가락의 기형 등 다양한 이상이 동반될 수 있다. 저자들은 양측성 관상봉합 두개골유합증과 특징적인 얼굴 모습, 다양한 동반 기형을 보인 두 명의 환자에서 TWIST1 유전자의 원인 돌연변이를 각각 확인하고 Saethre-Chotzen 증후군을 확진하였기에, 국내에서 처음으로 보고하는 바이다. 특히, TWIST1 유전자 분석은 관상봉합 유합증을 보이는 환자에서 질환을 확진하고, 및 환자와 가족에 대한 적절한 유전 상담을 제공하는데 유용한 검사로 생각된다.

• 한방재활의학과학회지
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• 제31권1호
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• pp.1-16
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• 2021

Objectives This study was designed to evaluate the effects of Danggwisu-san (Dangguixu-san, DG) on bone repair from femur fracture in mice. Methods Mice were randomly divided into 4 groups (normal, control, positive control and DG 300 mg/kg-treated group). In order to investigate the effects of DG on gene expressions in experimental animals with fracture, we measured the levels of bone morphogenetic protein-2 (BMP2), cyclooxygenase-2 (COX2), Sox9, collagen type II alpha 1 chain (Col2a1), runt-related transcription factor 2 (Runx2), osterix genes. After the cytotoxicity test, we analyzed the levels of expression of osteocalcin and Runx2, and tumor necrosis factor-α (TNF-α), a pro-inflammatory cytokine. The process of fusion in the fracture was also investigated by gross examination. Results Through in vivo BMP2, COX2 gene expression significantly decreased. Sox9 significantly increased. Col2a1, Runx2, osterix gene expression also increased as well, but there was no statistical significance. The degree of unilateral fracture fusion investigated by gross examination was significantly faster than those of the other groups. Through in vitro the level of TNF-α in macrophages was increased by DG in a dose-dependent mannerand and 250 and 500 ㎍/mL showed statistical significance. Osteocalcin and Runx2 genes expressions increased when DG was treated in osteoblasts. Conclusions DG promotes the healing of the fracture through the expression of bone repair-related genes and TNF-α production. This study may set the foundation for the clinical application of DG to the patients with bone fractures.

• Parasites, Hosts and Diseases
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• 제58권5호
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• pp.513-525
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• 2020

Clonorchis sinensis is a food-borne trematode that infects more than 15 million people. The liver fluke causes clonorchiasis and chronical cholangitis, and promotes cholangiocarcinoma. The underlying molecular pathogenesis occurring in the bile duct by the infection is little known. In this study, transcriptome profile in the bile ducts infected with C. sinensis were analyzed using microarray methods. Differentially expressed genes (DEGs) were 1,563 and 1,457 at 2 and 4 weeks after infection. Majority of the DEGs were temporally dysregulated at 2 weeks, but 519 DEGs showed monotonically changing expression patterns that formed seven distinct expression profiles. Protein-protein interaction (PPI) analysis of the DEG products revealed 5 sub-networks and 10 key hub proteins while weighted co-expression network analysis (WGCNA)-derived gene-gene interaction exhibited 16 co-expression modules and 13 key hub genes. The DEGs were significantly enriched in 16 Kyoto Encyclopedia of Genes and Genomes pathways, which were related to original systems, cellular process, environmental information processing, and human diseases. This study uncovered a global picture of gene expression profiles in the bile ducts infected with C. sinensis, and provided a set of potent predictive biomarkers for early diagnosis of clonorchiasis.

• Genomics & Informatics
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• 제19권1호
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• pp.10.1-10.7
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• 2021

Although many models have been proposed to accurately predict the response of drugs in cell lines recent years, understanding the genome related to drug response is also the key for completing oncology precision medicine. In this paper, based on the cancer cell line gene expression and the drug response data, we established a reliable and accurate drug response prediction model and found predictor genes for some drugs of interest. To this end, we first performed pre-selection of genes based on the Pearson correlation coefficient and then used ElasticNet regression model for drug response prediction and fine gene selection. To find more reliable set of predictor genes, we performed regression twice for each drug, one with IC₅₀ and the other with area under the curve (AUC) (or activity area). For the 12 drugs we tested, the predictive performance in terms of Pearson correlation coefficient exceeded 0.6 and the highest one was 17-AAG for which Pearson correlation coefficient was 0.811 for IC₅₀ and 0.81 for AUC. We identify common predictor genes for IC₅₀ and AUC, with which the performance was similar to those with genes separately found for IC₅₀ and AUC, but with much smaller number of predictor genes. By using only common predictor genes, the highest performance was AZD6244 (0.8016 for IC₅₀, 0.7945 for AUC) with 321 predictor genes.