ABSTRACT: The aim of this study was to determine differences in microRNA expression profiles of gastric cancer and adjacent healthy gastric mucosa. Both types of tissue samples were collected during operative procedures of 20 patients. microRNA expression was determined by miRNA microarrays. Overall design: Twenty pairs of tissue samples collected from patients diagnosed with gastric cancer. Each pair included resected primary tumor and corresponding healthy gastric mucosa. There were no replicates. Comparative expression analysis was carried out to determine microRNAs up-regulated and down-regulated in cancer tissues compared to healthy mucosa. Please note that each sample was labeled with both Cy3 and Cy5, resulting in two raw data files per sample ('1_Exiqon_*_S01.txt' for Cy3; '0_Exiqon_*_S01.txt' is for Cy5 data).
Project description:Comparing to matched normal mucosa, WTX was lost in most of human gastric cancers (Zhang et al., 2016). We analyzed the microRNA expression profiling among WTX low human colorectal cancer tissues and matched adjacent WTX high normal colorectal mucosa. The aimed to identify the unique signature of miRNAs which related to WTX loss in human colorectal cancers. Overall design: We performed microRNA expression profiling on 5 patients who were WTX low in gastric cancers and WTX high in matched normal mucosa samples.
Project description:Background: Intestinal metaplasia (IM) is a gastric precancerous lesion that precedes the development of gastric cancer in up to 3.77 cases/1000 person-years. It consists in a trans-differentiation process of gastric to intestinal tissue. Two histological subtypes exist, complete (CIM) and incomplete (IIM), the latter having higher progression rates to gastric cancer . Our objective was to identify molecular processes responsible for the tumoral transition from intestinal metaplasia to GC and the initial steps of this lesion Methods: We used expression microarray to compare the transcriptome of intestinal metaplasia subtypes that progress to gastric cancer (IIM-GC and CIM-GC) after a follow-up period with respect to those that do not progress (IIM control and CIM control). Also, IM-NoGC (IM control, comprising both IIM and CIM Control) was compared with healthy gastric mucosa. Differentially expressed genes were obtained and functional analyses (GSEA and IPA softwares) were performed. Some deregulated genes were validated by qPCR. Results: Histological subtypes of intestinal metaplasia that progress or not to GC differ less among them than to healthy mucosa. Incomplete intestinal metaplasia has a higher number of over-expressed carcinogenic genes and molecular processes than the complete subtype. Most relevant molecular processes and genes in this group include antigenic processing, inflammation, activation of cell cycle and cell proliferation, oncogenes and tumor suppressors. When IM-NoGC is compared with healthy gastric mucosa new identified transcripts include TRIM, TMEM, homeobox, transporters and nucleolar RNAs SNORDs116. We confirm previously reported processes such us intestinal differentiation, metabolism of lipids and of xenobiotics and identify new ones such as non tumoral Warburg effect and melatonin degradation. Conclusions: Differentially expressed genes and molecular processes have been identified for the first time in intestinal metaplasia that progress to gastric cancer. New genes and molecular processes have also been identified in intestinal metaplasia in comparison with healthy gastric mucosa. Overall design: Using the Almac-Xcel array (Affymetrix) we profiled total RNA of gastric mucosa from: Incomplete Intestinal metaplasia that progress to GC (N=6) vs Incomplete Intestinal metaplasia that not progress to GC (IIM Controls, N=7) Complete Intestinal metaplasia that progress to GC (N=8) vs Complete Intestinal metaplasia that not progress to GC (CIM controls, N=9) Healthy controls (N=15)
Project description:Using the highly sensitive miRCURY LNA™ microRNA array, we screened 3100 microRNAs abundant in the human gastric cancer and Adjacent normal gastric mucosa tissues, and the function of differentially expressed microRNAs were analyzed by bioinformatics. The enrichment results indicated that these microRNAs perhaps participated in the occurrence and development process of gastric cancer. Overall design: In this study, three cases of gastric cancer were used to acquire the microRNA expression profiling, and qPCR was employed to confirm the results of microRNA chip. The function of the differentially expressed microRNA were analyzed by bioinformatic methods. Finally,compared with the adjacent mormal moucosa tissues，the expression of 99 microRNAs were up regulated,and 21 microRNAS were down regulated in gastric cancer.qPCR results showed an expression pattern consistent with that of the chip analysis.
Project description:Aberrant DNA methylation is implicated in the epigenetic field defect seen in gastric cancer (GC). Our aim in this study was to identify predictive biomarkers by screening for DNA methylation in noncancerous background gastric mucosa from GC patients. A total of 46 endoscopically obtained human gastric mucosa, 10 gastric cancer and 5 cell lines were analyzed using MCA microarray. Aberrant DNA methylation was compared with clinicopathological features. Healthy individuals were divided into two groups based on the types of chronic gastritis; A: antrum-predominant gastritis P or C: pangastritis or corpus-predominant gastritis
Project description:Using the highly sensitive miRCURY LNA™ microRNA array, we screened 3100 microRNAs abundant in the human colon cancer and Adjacent normal gastric mucosa tissues, and the function of differentially expressed microRNAs were analyzed by bioinformatics. The enrichment results indicated that these microRNAs perhaps participated in the occurrence and development process of colon cancer. In this study, three cases of colon cancer were used to acquire the microRNA expression profiling, and qPCR was employed to confirm the results of microRNA chip. The function of the differentially expressed microRNA were analyzed by bioinformatic methods.Finally,compared with the adjacent normal mucosa tissues，the expression of 2 microRNAs were up regulated in colon cancer. qPCR results showed an expression pattern consistent with that of the chip analysis. Overall design: In this study, three cases of colon cancer were used to acquire the microRNA expression profiling, and qPCR was employed to confirm the results of microRNA chip. The function of the differentially expressed microRNA were analyzed by bioinformatic methods.Finally,compared with the adjacent normal mucosa tissues，the expression of 2 microRNAs were up regulated in colon cancer. qPCR results showed an expression pattern consistent with that of the chip analysis.
Project description:Gastric cancer is a heterogeneous disease. The molecular mechanism behind the development of gastric cancer and the different histological subtypes, are yet not completely clear. A better understanding of this may result in better prevention, early diagnosis and treatment strategies. In this study we analyzed gene expression in tumor, adjacent non-cancerous mucosa biopsies and in age/sex matched samples from healthy individuals.
Project description:For 30 pairs (n=60) normal and tumor gastric tissues fron 30 gastric cancer patients, Cy3-labeled Normal genomic DNA was co-hybridized with Cy5-labeled Tumor genomic DNA from same patient.
Project description:In this dataset, we include the expression data obtained from gastric cancer tissues and gastric normal tissues to determine the differentially expressed microRNA in gastric cancer tissue.s Overall design: Total RNA obtained from 30 tissues (15 paired of gastric cancer vs.normal tissues) was used for microarray analysis.
Project description:Gastric cancer is one of the most aggressive cancers and is the second leading cause of cancer death worldwide. Approximately 40% of global gastric cancer cases occur in China, with peritoneal metastasis being the prevalent form of recurrence and metastasis in advanced disease (>50%). Currently, there are limited clinical approaches for predicting and treatment of peritoneal metastasis, resulting in a 6- month average survival time. By comprehensive genome analysis will uncover the pathogenesis of peritoneal metastasis. Here we describe a comprehensive whole-genome and transcriptome sequencing analysis of one advanced gastric cancer case, including non-cancerous mucosa, primary cancer and matched peritoneal metastatic cancer. The peripheral blood is used as normal control. Overall design: Gastric carcinoma patients and healthy subjects
Project description:microRNA profiling of gastric cancer vs. normal, pre-/-post CF (cisplatin/fluorouracil) chemotherapy. Biopsy samples were collected prior to chemotherapy from 90 gastric cancer patients treated with CF and from 34 healthy volunteers. At the time of disease progression, post-treatment samples were collected from 8 clinical responders. miRNA expression was determined using a custom-designed Agilent microarray. In order to identify an miRNA signature for chemotherapy resistance, we correlated miRNA expression levels with the time to progression (TTP) after CF. 90 pre-treatment gastric cancer samples, 34 healthy volunteers, 8 post-treatment samples.