• Title, Summary, Keyword: tissue microarray

Search Result 181, Processing Time 0.044 seconds

Identification of DNA Methylation Markers for NSCLC Using Hpall-Mspl Methylation Microarray (Hpall-Mspl Methylation Microarray를 이용한 비소세포폐암의 DNA Methylation Marker 발굴)

  • Kwon, Mi Hye;Lee, Go Eun;Kwon, Sun Jung;Choi, Eugene;Na, Moon Jun;Cho, Hyun Min;Kim, Young Jin;Sul, Hye Jung;Cho, Young Jun;Son, Ji Woong
    • Tuberculosis and Respiratory Diseases
    • /
    • v.65 no.6
    • /
    • pp.495-503
    • /
    • 2008
  • Background: Epigenetic alterations in certain genes are now known as at least important as genetic mutation in pathogenesis of cancer. Especially abnormal hypermethylation in or near promoter region of tumor suppressor genes (TSGs) are known to result in gene silencing and loss of gene function eventually. The authors tried to search for new lung cancer-specific TSGs which have CpG islands and HpaII sites, and are thought to be involved in carcinogenesis by epigenetic mechanism. Methods: Tumor tissue and corresponding adjacent normal tissue were obtained from 10 patients who diagnosed with non small cell lung cancer (NSCLC) and underwent surgery in Konyang university hospital in 2005. Methylation profiles of promoter region of 21 genes in tumor tissue & non-tumor tissue were examined with HpaII-MspI methylation microarray (Methyl-Scan DNA chip$^{(R)}$, Genomic tree, Inc, South Korea). The rates of hypermethylation were compared in tumor and non-tumor group, and as a normal control, we obtained lung tissue from two young patients with pneumothorax during bullectomies, methylation profiles were examined in the same way. Results: Among the 21 genes, 10 genes were commonly methylated in tumor, non-tumor, and control group. The 6 genes of APC, AR, RAR-b, HTR1B, EPHA3, and CFTR, among the rest of 11 genes were not methylated in control, and more frequently hypermethylated in tumor tissue than non-tumor tissue. Conclusion: In the present study, HTR1B, EPHA3, and CFTR are suggested as possible novel TSGs of NSCLC by epigenetic mechanism.

Evaluation of c-erbB2/neu Oncogene Status in Canine Mammary Tumors on Tissue Microarray

  • Kang, Jong-il;Cho, Ho-seong;A.W.M. Effendy;Park, Nam-yong
    • Proceedings of the Korean Society of Veterinary Pathology Conference
    • /
    • /
    • pp.40-40
    • /
    • 2003
  • The c-erbB2/neu oncogene (alias HER2, NEU) encoding a tyrosine kinase receptor protein, the overexpression of which correlates with a more rapid progression and a worse prognosis in human breast cancer [1]. Otherwise, this gene is still poorly investigated in veterinary oncology [2,3]. To gain insight into the patterns of c-erbB2/neu status in canine mammary tumor, we constructed one such mammary tumor tissue microarray (TMA) from 60 tumors from our lab. This enabled the amplification of c-erbB2/neu oncogene of all 60 tumors to be simultaneously analyzed by chromogenic in situ hybridization (CISH). The aim of this study was to evaluate status of c-erbB2/neu oncogene in canine mammary tumors and to correlate this status with the differentiation grade of neoplasm. (omitted)

  • PDF

A Method for Microarray Data Analysis based on Bayesian Networks using an Efficient Structural learning Algorithm and Data Dimensionality Reduction (효율적 구조 학습 알고리즘과 데이타 차원축소를 통한 베이지안망 기반의 마이크로어레이 데이타 분석법)

  • 황규백;장정호;장병탁
    • Journal of KIISE:Software and Applications
    • /
    • v.29 no.11
    • /
    • pp.775-784
    • /
    • 2002
  • Microarray data, obtained from DNA chip technologies, is the measurement of the expression level of thousands of genes in cells or tissues. It is used for gene function prediction or cancer diagnosis based on gene expression patterns. Among diverse methods for data analysis, the Bayesian network represents the relationships among data attributes in the form of a graph structure. This property enables us to discover various relations among genes and the characteristics of the tissue (e.g., the cancer type) through microarray data analysis. However, most of the present microarray data sets are so sparse that it is difficult to apply general analysis methods, including Bayesian networks, directly. In this paper, we harness an efficient structural learning algorithm and data dimensionality reduction in order to analyze microarray data using Bayesian networks. The proposed method was applied to the analysis of real microarray data, i.e., the NC160 data set. And its usefulness was evaluated based on the accuracy of the teamed Bayesian networks on representing the known biological facts.

Tissue Microarray Immunohistochemical Profiles of p53 and pRB in Hepatocellular Carcinoma and Hepatoblastoma

  • Azlin, Abdul Hadi;Looi, Lai Meng;Cheah, Phaik Leng
    • Asian Pacific Journal of Cancer Prevention
    • /
    • v.15 no.9
    • /
    • pp.3959-3963
    • /
    • 2014
  • The tumour suppressor genes, p53 and pRb, are known to play important roles in neoplastic transformation. While molecular routes to the uncontrolled growth of hepatocytes, leading to primary liver cancer have generated considerable interest, the roles of p53 and pRb mutations in hepatocellular carcinoma (HCC) and hepatoblastoma (HB) remain to be clarified. We examined the immunohistochemical expression of p53 and pRb gene products in 26 HCC and 9 HB, sampled into tissue microarray blocks. 10 (38%) of 26 HCC showed > 10% tumour nuclear staining for p53 protein, 3 of these also being HbsAg positive. Conversely, none of 9 HB expressed nuclear p53 immunopositivity. Some 24 (92%) HCC and 8 (89%) HB showed loss of pRb nuclear expression. Two of the 26 HCC and one of the 9 HB showed >10% tumour nuclear staining for pRb protein. Our results suggest that p53 does not have an important role in the development of HB but may contribute in HCC. There is also loss of pRb expression in the majority of HCC and HB, supporting loss of pRb gene function in the hepatocarcinogenesis pathway. However, a comparison of the staining profiles of p53 and pRb proteins in HCC and HB did not reveal a consistent pattern to differentiate between the two types of tumours immunohistochemically. Hence the use of p53 and pRB protein expression has no contribution in the situation where there is a diagnostic difficulty in deciding between HCC and HB.

Expression Pattern of EphB2 in Gastric Cancer (위암에시 EphB2 단백의 발현 양상)

  • Song, Jae-Hwi;Kim, Chang-Jae;Cho, Young-Gu;Park, Cho-Hyun;Nam, Suk-Woo;Yoo, Nam-Jin;Lee, Jung-Young;Park, Won-Sang
    • Journal of Gastric Cancer
    • /
    • v.6 no.1
    • /
    • pp.25-30
    • /
    • 2006
  • Purpose: The EphB2 receptor, a member of the receptor tyrosine kinase family, is a target gene of the Wnt signaling pathway and may achieve a tumor suppressor function through regulation of cell growth and migration. Our aim was to determine whether an altered expression of EphB2 might be associated with gastric cancer development and, if so, to determine to which pathologic parameter it is linked. Materials and Methods: For the construction of the gastric cancer tissue microarray, 83 paraffin-embedded tissues containing gastric cancer areas were cored 3 times and transferred to the recipient master block. The expression patterns of EphB2 were examined on tissue microarray slides by using immunohistochemistry and were compared using pathologic parameters, including histological type, depth of invasion, lymph node metastatsis, and peritoneal dissemination. Results: The EphB2 protein was expressed in the normal gastric mucosal epithelium, especially in the bottom of the mucosa. We found loss of EphB2 expression in 30 (36.1%) of the 83 gastric cancer tissues. Statistically, loss of EphB2 expression was more common in gastric cancer with lymph-node metastasis. There was no significant correlation between EphB2 expression and depth of invasion, histologic type, or peritoneal dissemination. Conclusion: Our findings suggest that loss of EphB2 expression may represent a critical step in gastric carcinogenesis.

  • PDF

Expression Pattern of KLF6 in Korean Gastric Cancers (한국인 위암에서 KLF6 단백 발현 양상)

  • Cho Young Gu;Kim Chang Jae;Park Cho Hyun;Kim Su Young;Nam Suk Woo;Lee Sug Hyung;Yoo Nam Jin;Lee Jung Young;Park Won Sang
    • Journal of Gastric Cancer
    • /
    • v.5 no.1
    • /
    • pp.34-39
    • /
    • 2005
  • Purpose: KLF6, a member of the KLF family, is a ubiquitous zinc finger tumor suppressor protein that is mutated in several human cancers. Our aim was to determine whether the expression pattern of KLF6 might be associated with gastric cancer development and, if so, to determine to which pathologic parameter it is linked. Materials and Methods: For the construction of the gastric cancer tissue microarray, 85 paraffin-embedded tissues containing gastric cancer areas were cored 3 times and transferred to the recipient master block. The expression pattern of KLF6 was examined on tissue microarray slides by using immunohistochemistry and was compared with pathologic parameters, including histologic type, depth of invasion, lymph node metastasis, and peritoneal dissemination. Results: The KLF6 protein was expressed on superficial and foveolar epithelial cells in the gastric mucosa. We found loss of KLF6 expression in 28 ($32.9\%$) of the 85 gastric cancer tissues. There was a significant correlation between loss of KLF6 expression and lymph-node metastasis. However, other pathologic parameters, such as histologic type, depth of invasion, and peritoneal dissemination, were not statistically associated with loss of KLF6 expression. Conclusion: Our findings suggest that loss of KLF6 expression may contribute to abnormal regulation of gastrointestinal epithelial cell growth and differentiation and to the development and/or progression of Korean gastric cancer.

  • PDF

Gene Expression Profiling in Hepatic Tissue of two Pig Breeds

  • Jang, Gul-Won;Lee, Kyung-Tai;Park, Jong Eun;Kim, Heebal;Kim, Tae-Hun;Choi, Bong-Hwan;Kim, Myung Jick;Lim, Dajeong
    • Journal of Animal Science and Technology
    • /
    • v.54 no.6
    • /
    • pp.383-394
    • /
    • 2012
  • Microarray analyses provide information that can be used to enhance the efficiency of livestock production. For example, microarray profiling can potentially identify the biological processes responsible for the phenotypic characteristics of porcine liver. We performed transcriptome profiling to identify differentially expressed genes (DEGs) in liver of pigs from two breeds, the Korean native pigs (KNP) and Yorkshire pigs. We correctly identified expected DEGs using factor analysis for robust microarray summarization (FARMS) and robust multi-array average (RMA) strategies. We identified 366 DEGs in liver (p<0.05, fold-change>2). We also performed functional analyses, including gene ontology and molecular network analyses. In addition, we identified the regulatory relationship between DEGs and their transcription factors using in silico and qRT-PCR analysis. Our findings suggest that DEGs and their transcription factors may have a potential role in adipogenesis and/or lipid deposition in liver tissues of two pig breeds.

Radioprotective Effects of Propolis on the Mouse Testis Exposed to X-ray. (프로폴리스가 X-선에 노출된 마우스 정소에 미치는 방사선 방어 효과)

  • Ji, Tae-Jung;Kim, Jong-Sik;Jeong, Hyung-Jin;Seo, Eul-Won
    • Journal of Life Science
    • /
    • v.17 no.5
    • /
    • pp.664-670
    • /
    • 2007
  • The propolis is natural product produced by honeybees and is known to have many biologically useful properties such as anti-microbial, anti-oxidative and anti-tumorigenic activity. However, its radio-protective property has not been well studied. To investigate radio-protective effect of propolis on mouse testis, mice were supplemented with propolis after 5 Gy irradiation. The histological changes of testis were detected by TEM. The results indicate that propolis may protect tissue deformation which is induced by 5 Gy of ionizing radiation. Furthermore, to elucidate the potential molecular mechanisms involved in radio-protective property of propolis, we performed microarray experiments using oligo DNA microarray. We found 65 up-regulated genes and 224 down-regulated genes, whose expression levels were affected more than 2-fold by propolis treatment in mice irradiated at 5 Gy. We confirmed microarray data with reverse transcription-PCR using gene specific primers. The results of RT-PCR are highly correlated with those of microarray. These results may help understanding molecular mechanisms of radioprotective effects by propolis in mouse model.

Quality Control Usage in High-Density Microarrays Reveals Differential Gene Expression Profiles in Ovarian Cancer

  • Villegas-Ruiz, Vanessa;Moreno, Jose;Jacome-Lopez, Karina;Zentella-Dehesa, Alejandro;Juarez-Mendez, Sergio
    • Asian Pacific Journal of Cancer Prevention
    • /
    • v.17 no.5
    • /
    • pp.2519-2525
    • /
    • 2016
  • There are several existing reports of microarray chip use for assessment of altered gene expression in different diseases. In fact, there have been over 1.5 million assays of this kind performed over the last twenty years, which have influenced clinical and translational research studies. The most commonly used DNA microarray platforms are Affymetrix GeneChip and Quality Control Software along with their GeneChip Probe Arrays. These chips are created using several quality controls to confirm the success of each assay, but their actual impact on gene expression profiles had not been previously analyzed until the appearance of several bioinformatics tools for this purpose. We here performed a data mining analysis, in this case specifically focused on ovarian cancer, as well as healthy ovarian tissue and ovarian cell lines, in order to confirm quality control results and associated variation in gene expression profiles. The microarray data used in our research were downloaded from ArrayExpress and Gene Expression Omnibus (GEO) and analyzed with Expression Console Software using RMA, MAS5 and Plier algorithms. The gene expression profiles were obtained using Partek Genomics Suite v6.6 and data were visualized using principal component analysis, heat map, and Venn diagrams. Microarray quality control analysis showed that roughly 40% of the microarray files were false negative, demonstrating over- and under-estimation of expressed genes. Additionally, we confirmed the results performing second analysis using independent samples. About 70% of the significant expressed genes were correlated in both analyses. These results demonstrate the importance of appropriate microarray processing to obtain a reliable gene expression profile.

Differential MicroRNA Expression Between Gastric Cancer Tissue and Non-cancerous Gastric Mucosa According to Helicobacter pylori Status

  • Lee, Jung Won;Kim, Nayoung;Park, Ji Hyun;Kim, Hee Jin;Chang, Hyun;Kim, Jung Min;Kim, Jin-Wook;Lee, Dong Ho
    • Journal of Cancer Prevention
    • /
    • v.22 no.1
    • /
    • pp.33-39
    • /
    • 2017
  • Background: MicroRNAs (miRNAs) are key post-translational mechanisms which can regulate gene expression in gastric carcinogenesis. To identify miRNAs responsible for gastric carcinogenesis, we compared expression levels of miRNAs between gastric cancer tissue and non-cancerous gastric mucosa according to Helicobacter pylori status. Methods: Total RNA was extracted from the cancerous regions of formalin-fixed, paraffin-embedded tissues of H. pylori-positive (n = 8) or H. pylori-negative (n = 8) patients with an intestinal type of gastric cancer. RNA expression was analyzed using a 3,523 miRNA profiling microarray based on the Sanger miRBase. Validation analysis was performed using TaqMan miRNA assays for biopsy samples from 107 patients consisted of control and gastric cancer with or without H. pylori. And then, expression levels of miRNAs were compared according to subgroups. Results: A total of 156 miRNAs in the aberrant miRNA profiles across the miRNA microarray showed differential expression (at least a 2-fold change, P < 0.05) in cancer tissue, compared to noncancerous mucosa in both of H. pylori-negative and -positive samples. After 10 promising miRNAs were selected, validations by TaqMan miRNA assays confirmed that two miRNAs (hsa-miR-135b-5p and hsa-miR-196a-5p) were significantly increased and one miRNA (hsa-miR-145-5p) decreased in cancer tissue compared to non-cancerous gastric mucosa at H. pylori-negative group. For H. pylori-positive group, three miRNAs (hsa-miR-18a-5p, hsa-miR-135b-5p, and hsa-miR-196a-5p) were increased in cancer tissue. hsa-miR-135b-5p and hsa-miR-196a-5p were increased in gastric cancer in both of H. pylori-negative and -positive. Conclusions: miRNA expression of the gastric cancer implies that different but partially common gastric cancer carcinogenic mechanisms might exist according to H. pylori status.