Identification of pathogenic microRNAs in Helicobacter pylori-associated gastric cancer
ABSTRACT: To identify dysregulated miRNA(s) upon infection with H. pylori during different pre-malignant and malignant stages of gastric cancer in a mouse model miRNA expression in pre-neoplastic and neoplastic lesions in murine stomachs induced by H. pylori and N-methyl-N-nitrosourea (MNU) after 12 months was profiled by miRNA expression array.
Chromatin remodeling has emerged as a hallmark of gastric cancer, but the regulation of chromatin regulators other than genetic change is unknown. Helicobacter pylori causes epigenetic dysregulation to promote gastric carcinogenesis, but the roles and functions of microRNAs (miRNA) in this multistage cascade are not fully explored. In this study, miRNA expression in preneoplastic and neoplastic lesions in murine stomachs induced by H. pylori and N-methyl-N-nitrosourea (MNU) was profiled by miRNA ...[more]
Project description:The CrdR-ChIP profiling is comparing H. pylori gDNA without crdR interaction as control and CrdR interact with H. pylori gDNA (WT vs crdR). The goal was determine the crdR binding site on H. pylori genome, it provide possible crdR-regulated genes. 2 samples: H. pylori 26695 is control, and CrdR is experiment.
Project description:This SuperSeries is composed of the following subset Series: GSE38926: Patterns of aberrant DNA methylation after toxicant-induced malignant transformation (MeDIP-chip dataset 1) GSE38928: Patterns of aberrant DNA methylation after toxicant-induced malignant transformation (MeDIP-chip dataset 2) GSE38929: Patterns of aberrant DNA methylation after toxicant-induced malignant transformation (miRNA dataset) Refer to individual Series
Project description:Methylated modifications of genome are common events in carcinogenesis and is involved in the tumorigenesis and progression of various cancers including gastric cancer Methylated DNA immunoprecipitation (MeDIP) combined with a human miRNA tiling microarray analysis demonstrated that there are much methylation differention between gastric cancers and adjacent controls microRNA gene methylation comparison of 3 pairs of gastric cancer and controls
Project description:We generated murine fibroblast cybrid cell lines that have identical nuclear genomes and differ only in their mtDNA. We observed increased cellular proliferation and resistance to apoptosis in the mtBALB compared to the mtB6 cybrid cells, phenotypes seen in malignant cells. Based on these observations we investigated whether these phenotypic differences could be caused by a unique spectrum of nuclear gene expression alterations induced by the mtDNA changes. Microarray analysis (Agilent, 44K mouse whole genome chip) was conducted in order to elucidate the expression profile of three independent clones of mtBALB and mtB6 cybrid cells. Two-condition experiment, mtB6 vs. mtBALB cells. Biological replicates: 4 control replicates, 4 mutant replicates.
Project description:RIP-Chip analysis of PCBP2 and identification of preferentially associated mRNAs. T98G cells were transfected transiently with BAP-tagged constructs. BAP-tagged proteins were biotinylated in vivo by the co-transfected hBirA enzyme. RNPs were recovered via precipitation with Steptavidin-sepharose beads. Finally, RNAs were purified and analyzed on microarrays. BAP-GFP as control was used in three independent sets of experiments. Two-condition experiment, BAP-PCBP2 vs. BAP-GFP cells. Biological replicates: 3 BAP-PCBP2 replicates, 3 BAP-GFP (Control) replicates
Project description:This SuperSeries is composed of the following subset Series: GSE40097: DNA methylation analysis of pancreatic cancer and non-malignant pancreas cell lines GSE40098: RNA expression analysis of pancreatic cancer and non-malignant pancreas cell lines GSE41794: DNA copy number profiling of 20 pancreatic cancer cell lines Refer to individual Series
Project description:We investigated the global microRNA expression patterns in normal pancreas, pancreatic endocrine tumours and acinar carcinomas to evaluate their involvement in transformation and malignant progression of these tumour types. A neoplastic cellularity higher than 90% was obtained by cryostat enrichment. RNA was extracted with Trizol (Invitrogen, Carlsbad, CA) from 10 20-μm thick cryostat sections, checking the cell composition of the sample every five sections. RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). microRNA microarray (Ohio State University Comprehensive Cancer Center, version 2.0) contains probes for 460 mature microRNAs spotted in quadruplicate (235 homo sapiens, 222 mus musculus, and three Arabidopsis thaliana) with annotated active sites. Often, more than one probe set exists for a given mature microRNA.
Project description:To understand downstream genes affected by overexpression of OsbHLH148, the Rice 3’-Tiling Microarray analysis (GreenGene Biotech, Yongin, Korea) was carried out to profile gene expression of OsCc1:OsbHLH148 transgenic plants in comparison with wild-type plants under normal growth conditions. RNA samples from these plants were used to generate cyanine-3 (Cy3)-labeled complementary DNA (cDNA) probes, which were then hybridized to the microarray. Each data set was obtained from two biological repeats with independent transgenic lines. Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 °C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in OsCc1:OsbHLH148 transgenic and wild-type rice plants. Cy3-labeled target cDNA fragments were synthesized from two-week old seedlings using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment two times with independent transgenic lines, T-2 and T-9, and analyzed each data set statistically using one-way ANOVA.
Project description:To understand the Abscisic Acid (ABA) signaling in response to dehydration stress, we performed analysis of gene expression using Arabidopsis wild-type plants and the nced3-2 mutant under dehydration stress. The nced3-2 mutant is an Arabidopsis T-DNA tagged knock-out mutant of the NCED3 gene, which has an essential role in dehydration-inducible ABA biosynthesis. Arabidopsis plants were grown in in soil (verdenite 40 mmΦ, Verde Co., Ltd., Kanagawa, Japan) in a cell strainer (Falcon, 40 μm; Corning Inc., NY, USA). Plants were grown at 22°C for 3 weeks under illumination (40–60 μmol m-2s-1; 16 h light/8 h darkness). Three-week-old plants were exposed to dehydration stress by being denied water for 6, 24, 48, or 72 h.
Project description:Candidate genes were successfully screened by Cancer PathwayFinder PCR Array Cancer PathwayFinder PCR Array was applied to compare gene changes in xenograft tumor samples of HCC model. A total of 12 samples were examined with 6 from Sorafenib treated group and 6 from control.