• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.2
• /
• pp.641-646
• /
• 2012

In our recent report on gene expression in gastric cancer we identified the endo-sulfatase Sulf-1 gene to be up-regulated in gastric tumors relative to apparently normal (AN), and paired normal (PN) gastric tissue samples. In the present report we investigate the protein expression levels of Sulf-1 gene in gastric tumors, AN and PN samples using tissue microarray (TMA) and immunohistochemistry. Expression data was collected from two sets of TMA's containing replicate sections of tissue samples. Scoring data from TMA set-1 revealed a significant difference in Sulf-1 immunoreactivity between tumors and "normals" (PN and AN) (p-value = 0.001928). Also, Sulf-1 expression in tumors was also significantly different from either PN (p-value = 0.019) or AN (p-value = 0.006) samples. Similar results were obtained from analysis of scoring data from the second set of arrays. Comparison of mRNA expression and protein expression in gastric tumor tissues revealed that in 6/20 (30%) tumor samples showed up-regulated protein expression concordant with over-expression of mRNA. However, a discord with mRNA being over-expressed relative to down regulated protein expression was observed in majority 14/20 (70%) of tumor samples. Our study indicates down regulation of Sulf-1 protein expression in gastric tumors relative to PN and AN samples which is discordant with mRNA over-expression seen in tumors.

• Molecular & Cellular Toxicology
• /
• v.3 no.4
• /
• pp.320-325
• /
• 2007

Promoter hypermethylation of the $p16^{INK4a}$ gene was investigated in 52 sets of samples of tumor tissue and adjacent normal tissue from Korean patients with colorectal cancer, using the proposed modified the Real-time PCR/SYBR Green detection method presented in this study. In normal tissue, 29 of 52 patients (56%) were methylated and in tumor tissue, 23 of 52 patients (44%) were methylated. The 34 cases (65.4%) showed a concordant DNA methylation pattern in both normal tissue and tumor tissue. Analyzing the association between the clinicopathologic features and DNA methylation status of the $p16^{INK4a}$ gene, the DNA methylation status according to by Duke's stage was different while other clinicopathological characteristics, including the age, sex, tumor stage, and histologic type of the patient were not found to be correlated with $p16^{INK4a}$ methylation. With multivariate logistic regression, it was observed that the DNA methylation status of $p16^{INK4a}$ gene in normal tissue was correlated with the DNA methylation status of the $p16^{INK4a}$ gene in tumor tissue (P=0.026). According to a Kaplan-Meier survival analysis, a difference in the survival rate by DNA methylation status was found, but it was not significant.

• Molecules and Cells
• /
• v.42 no.4
• /
• pp.333-344
• /
• 2019

Various genetic and environmental factors are known to be associated with chronic obstructive pulmonary disease (COPD). We identified COPD-related differentially expressed genes (DEGs) using 189 samples accompanying either adenocarcinoma (AC) or squamous cell carcinoma (SC), comprising 91 normal and 98 COPD samples. DEGs were obtained from the intersection of two DEG sets separately identified for AC and SC to exclude the influence of different cancer backgrounds co-occurring with COPD. We also measured patient samples named group 'I', which were unable to be determined as normal or COPD based on alterations in gene expression. The Gene Ontology (GO) analysis revealed significant alterations in the expression of genes categorized with the 'cell adhesion', 'inflammatory response', and 'mitochondrial functions', i.e., well-known functions related to COPD, in samples from patients with COPD. Multi-omics data were subsequently integrated to decipher the upstream regulatory changes linked to the gene expression alterations in COPD. COPD-associated expression quantitative trait loci (eQTLs) were located at the upstream regulatory regions of 96 DEGs. Additionally, 45 previously identified COPD-related miRNAs were predicted to target 66 of the DEGs. The eQTLs and miRNAs might affect the expression of 'respiratory electron transport chain' genes and 'cell proliferation' genes, respectively, while both eQTLs and miRNAs might affect the expression of 'apoptosis' genes. We think that our present study will contribute to our understanding of the molecular etiology of COPD accompanying lung cancer.

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.11
• /
• pp.5433-5438
• /
• 2012

Background: Hepatocellular carcinoma (HCC) is a common and aggressive malignancy. Despite of the improvements in its treatment, HCC prognosis remains poor due to its recurrence after resection. This study provides complete genetic profile for Egyptian HCC. Genome-wide analyses were performed to identify the predictive signatures. Patients and Methods: Liver tissue was collected from 31 patients with diagnosis of HCC and gene expression levels in the tumours and their adjacent non-neoplastic tissues samples were studied by analyzing changes by microarray then correlate these with the clinico-pathological parameters. Genes were validated in an independent set by qPCR. The genomic profile was associated with genetic disorders and cancer focused on gene expression, cell cycle and cell death. Molecular profile analysis revealed cell cycle progression and arrest at G2/M, but progression to mitosis; unregulated DNA damage check-points, and apoptosis. Result: Nine hundred fifty eight transcripts out of the 25,000 studied cDNAs were differentially expressed; 503 were up-regulated and 455 were down-regulated. A total of 19 pathways were up-regulated through 27 genes and 13 pathways were down-regulated through 19 genes. Thirty-seven genes showed significant differences in their expression between HCC cases with high and low Alpha Feto Protein ($AFP{\geq}600$ IU/ml). The validation for the microarray was done by real time PCR assay in which PPP3CA, ATG-5, BACE genes showed down-regulation and ABCG2, RXRA, ELOVL2, CXR3 genes showed up-regulation. cDNA microarrays showed that among the major upregulated genes in HCC are sets. Conclusion: The identified genes could provide a panel of new diagnostic and prognostic aids for HCC.

• Journal of the Korean Institute of Intelligent Systems
• /
• v.18 no.4
• /
• pp.471-475
• /
• 2008

Microarray technology in biological science enables molecular level observations and analyses on the biological phenomina by allowing to measure the RNA expression profiles in cells. Microarray data analysis is applied in various purposes such as identifying significant genes which react to drug treatment, understanding the genome scale phenomina. In drug response experiments, the microarray-based gene expression analysis could provide meaningful information. It is sometimes needed to identify the genes which shows different expression behavior for treatment group and normal group each other. When the normal group shows the medium level expression, it is not easy to discriminate the group just by expression level comparison. This paper proposes a method which selects group-wise representative values for each gene and sets the value range of the groups in order to filter out the genes with specific pattern. It also shows some experiment results.

• The Korean Journal of Applied Statistics
• /
• v.26 no.2
• /
• pp.307-319
• /
• 2013

With the rapid accumulation of microarray data, it is a significant challenge to integrate available data sets addressing the same biological questions that can provide more samples and better experimental results. Sometimes, different microarray platforms make it difficult to effectively integrate data from several studies and there is no consensus on which method is the best to produce a single and unified data set. Methods using median rank score, quantile discretization and standardization (which directly combine rescaled gene expression values) and meta-analysis (which combine the results of individual studies at the interpretative level) are reviewed. Real data examples downloaded from GEO are used to compare the performance of these methods and to evaluate if the combined data set detects more reliable information from the separated data sets or not.

• Pediatric Gastroenterology, Hepatology & Nutrition
• /
• v.6 no.2
• /
• pp.112-119
• /
• 2003

Purpose: Helicobacter pylori infection is thought to be correlated with iron-deficiency anemia (IDA) at puberty. The H. pylori feoB gene, a high-affinity ferrous iron transporter, plays a central role in iron acquisition. This study aims to analyze the H. pylori feoB status according to the presence of antral gastritis with or without IDA. Methods: Fourteen H. pylori-positive patients aged from 10~18 years were categorized into subgroups based on the presence or absence of IDA. Eight patients had IDA, and the other six showed normal hematological findings. Genomic DNA was isolated from cultured H. pylori. Five sets of primers were used for PCR amplification of the feoB gene. The feoB region, 1.93 kb, was generated by linking of the PCR products and sequenced. The feoB gene sequences of H. pylori J99 and 26695 were used to compare with the clinical strains. Sequence comparisons of the feoB regions between the IDA (+) and (-) groups were performed. Results: Sequence analysis of the complete coding region of the feoB revealed 16 sites of polymorphism. Among these, 3 polymorphisms-Glu/Thr254Ala, Ile263Val, and Lys511Gln - were indigenous to Korean strains. Although statistically significant differences appear in 4 sites between IDA (+) and (-), the number of specimens are too low to assess the real differences. Conclusion: The 4 polymorphisms in the feoB gene seem to be related with IDA, but it is unclear yet because of small number of study strains. Further studies are required to prove the correlation of IDA and H. pylori infection.

• Asian-Australasian Journal of Animal Sciences
• /
• v.30 no.11
• /
• pp.1529-1539
• /
• 2017

Objective: The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper${\times}$Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production. Methods: Six samples (three in each group) were subjected to the methylated DNA immunoprecipitation sequencing (MeDIP-seq) and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs) between the two groups. Results: 23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions. Compared with Small Tailed Han sheep, we observed a tendency toward a global loss of DNA methylation in these DMRs in the crossbred group. Gene ontology enrichment analysis found several gene sets which were hypomethylated in gene-body region, including nucleoside binding, motor activity, phospholipid binding and cell junction. Numerous genes were found to be differentially methylated between the two groups with several genes significantly differentially methylated, including transforming growth factor beta 3 (TGFB3), acyl-CoA synthetase long chain family member 1 (ACSL1), ryanodine receptor 1 (RYR1), acyl-CoA oxidase 2 (ACOX2), peroxisome proliferator activated receptor-gamma2 (PPARG2), netrin 1 (NTN1), ras and rab interactor 2 (RIN2), microtubule associated protein RP/EB family member 1 (MAPRE1), ADAM metallopeptidase with thrombospondin type 1 motif 2 (ADAMTS2), myomesin 1 (MYOM1), zinc finger, DHHC type containing 13 (ZDHHC13), and SH3 and PX domains 2B (SH3PXD2B). The real-time quantitative polymerase chain reaction validation showed that the 12 genes are differentially expressed between the two groups. Conclusion: In the current study, a tendency to a global loss of DNA methylation in these DMRs in the crossbred group was found. Twelve genes, TGFB3, ACSL1, RYR1, ACOX2, PPARG2, NTN1, RIN2, MAPRE1, ADAMTS2, MYOM1, ZDHHC13, and SH3PXD2B, were found to be differentially methylated between the two groups by gene ontology enrichment analysis. There are differences in the expression of 12 genes, of which ACSL1, RIN2, and ADAMTS2 have a negative correlation with methylation levels and the data suggest that DNA methylation levels in DMRs of the 3 genes may have an influence on the expression. These results will serve as a valuable resource for DNA methylation investigations on screening candidate genes which might be related to meat production in sheep.

• Asian-Australasian Journal of Animal Sciences
• /
• v.19 no.10
• /
• pp.1409-1414
• /
• 2006

The objective of this study was to screen single nucleotide polymorphisms (SNPs) of the chicken lipoprotein lipase gene (LPL), using 545 F1 hybrids developed from $4{\times}4$ diallel crossing of four chicken breeds, and to analyze the associations between polymorphisms of the LPL and chicken fat deposition traits. PCR-SSCP was used to detect SNPs in LPL. Fifteen sets of primers were designed to amplify DNA fragments covering the 5'flanking and coding regions of LPL. It showed that there existed 5 polymorphic loci in the 5'flanking region and coding region, respectively. Association analysis was carried out between 10 polymorphic loci and intermuscular fat width, abdominal fat weight, and thickness of subcutaneous fat using ANCOVA, respectively. The results indicated that, in the 5'flanking region, the loci d and e significantly affected thickness of subcutaneous fat (p<0.05), abdominal fat weight (p<0.01) and subcutaneous fat (p<0.05), while in the coding region, synonymous mutation in exon 8 was significantly associated with intermuscular fat width (p<0.05), however, the non-synonymous mutations in exon 7 and exon 9 did not show statistically significant effects on fat deposition traits in this study.

• Journal of Korean Society of Water and Wastewater
• /
• v.26 no.4
• /
• pp.591-598
• /
• 2012

Denitrification is an important biological mechanism in wastewater treatment process because this process is technically to remove nitrogen from water to air. There have been lots of study about denitrification engineering and molecular biological research about denitrifying bacteria, respectively. However, combination of these researches was unusual and rare. This study is about the correlation between quantity of denitrifying bacteria and denitrification potential, and consists of NUR batch test as analysis method of denitrification potential and quantitative molecular analysis for denitrifying bacteria. Three reactors (A/O, MLE and A/O of nitrogen deficiency) are operated to get activated sludge with various denitrification potential. All samples which were acquired from reactors were measured denitrification potential by NUR test and NUiR test. Also, Real-time PCR was conducted for quantification of denitrifying bacteria composition in activated sludge. The various denitrification potentials were measured in the reactors. The denitrifiaction potential was the highest in MLE process and the reactor of the nitrogen deficiency showed the lowest. Genomic DNA of activated sludge was obtained and consequently, real-time PCRuse the primer sets of nirK and nirS　were conducted to quantify genes involving denitrification reductase production. As the result of real-time PCR, nirK gene showed more significant influence on denitrification potential comapred with nirS gene.