Project description:Primary human gastric cancer-associated fibroblast (CAF) cultures (CAF14 and CAF32) were establised from 2 gastrectomy specimens. Silencing the expression (loss-of-function effect) of Twist1 in CAFs showed candidate target genes regulated by Twist1 and abrogated their tumor-promoting properties. Experiment design: two gastric CAFs (CAF14 adn CAF32, respectively) were establised from two gastric cancer patients and Twist1 knockdown studies were performed using shRNA.
Project description:Primary human gastric normal fibroblast cultures (NL14 and NL32, repectivley) were establised from 2 gastrectomy specimens. Enforced expression (gain-of-function effect) of Twist1 in 2 gastric normal fibroblasts (NL14 and NL32) showed candidate target genes and CAF markers upregulated by Twist1. Experiment design: 2 normal gastric fibroblasts (NL14 and NL32) were establised and studied for Twist1 gain-of-function.
Project description:The miRNA expression profiles in one pair of hTERT-positive gastric cancer tissue and an hTERT-negative para-cancerous tissue. The para-cancerous tissue is at least 5cm away from the cancer tisse. The expression of hTERT of identified by immunohistochemistry before RNA extraction for miRNA assay. One pair of gastric cancer tissue and para-cancerous tissue(Control). Four replicates per array.
Project description:The study was undertaken to identify microRNAs differently expressed by intestinal type of gastric cancer using miRNA microarray. The miRNA expression in the intestinal type of gastric cancer depending on H. pylori infection suggest that different gastric cancer pathogenesis could be exist between H. pylori-positive and -negative gastric cancer. Total RNA was extracted from cancerous region and non-cancerous regions in formalin fixed paraffin embedded tissues of intestinal type gastric cancer patients who were H. pylori-positive (n=8) or -negative (n=8). Corresponding author: Nayoung Kim, M.D., Department of Internal Medicine, Seoul National University Bundang Hospital (Tel., +82-31-787-7008; e-mail, nayoungkim49@empas.com).
Project description:We did the microarray to further compare the changes of gene expression between gastric cancer stem cells with CD44 knockdown by lentivirus and gastric cancer stem cells by scamble short hairpin RNA. Gastric cancer stem cells (Lentivirus) were infected with lentivirus that expressed human CD44-speciï¬c short hairpin RNA (shRNA). Control group of gastric cancer stem cells (Vector group) were only infected with scramble shRNA.
Project description:Copy number alteration (CNA) is a good signpost to identify cancer related genes. CNAs were analyzed using the Agilent 400K array comparative genomic hybridization (aCGH) in fresh-frozen tumor and matched normal tissues from 30 gastric cancer patients. Whole genomic CNAs in 30 human gastric cancers were analyzed using the Agilent aCGH-400K arrays. Matched normal tissues were used as the reference.
Project description:To further investigate of microRNA expression profile of gastric cancer, we have employed whole microRNA gene chip as a discovery platform to identify gene differential expression between gastric cancer tissues with mormal gastric tissues.Expression of four microRNAs (miR-125b,miR-451,miR-192b,miR-200b) from this signature was quantified and verified in the same RNA samples by real-time PCR. A total of 4 consecutive patients with gastric cancer undergoing elective surgery were entered into this study. After obtaining informed consent from the patients and after receiving the approval of the ethics committee, the following tissue samples were collected: tumor (3 × 3 × 5 mm) and adjacent normal tissues (3 × 3 × 5 mm).
Project description:Surgically resected gastric adenocarcinoma samples and their paired disease-free (R0) marginal nonmalignant tissue were obtained from 14 patients with gastric adenocarcinoma. RNA was isolated using the RNAeasy Kit (Qiagen Valencia, CA) from 15 mg of tissue. The quality of total RNA and its integrity was assessed using the Bioanalyzer 2100 (Agilent, Palo Alto, CA) and RIN value (RNA Integrity Number) was recorded for all the samples for intact 18S and 28S rRNA. Total RNA (800 ng) from each sample was reverse transcribed and linear amplified using the low RNA input linear amplification kit (Agilent Technologies). After synthesis of the first and second strand of cDNA, the product was used in an in vitro transcription reaction to generate cRNAs in the presence of cyanine 3-labeled UTP (Cy3) for normal and cyanine 5-labeled UTP (Cy5) for tumor. Fragmented Cy3-labeled cRNA of the control sample were mixed with equal amounts of Cy5-labeled cRNA from the gastric tumor sample, and the mixtures were hybridized onto 44K whole human genome DNA microarrays (Agilent Technologies) for 17 hrs at 65M-BM-0C with constant rotation (10 rpm). Subsequently, the arrays were washed according to manufacturerM-bM-^@M-^Ys instructions. The slides were scanned using an Agilent microarray scanner (G2565AA), and the images were processed using the Agilent feature extraction software AFE 9.5. GeneSpring GX v10.1 (Agilent Technologies) was used to analyze the expression profiles obtained after microarray hybridization. The feature extraction files from all the samples were uploaded to GeneSpring. Following intensity-dependent normalization (Lowess), the data was subjected to statistical analysis. A two tailed studentM-bM-^@M-^Ys t-test was used to determine significance of the differences observed between the normal and tumor samples. Benjamini Hochberg algorithm was used to compute false discovery rates. Genes were filtered based on P value threshold of 0.001 and false discovery rate of less than 1%. Transcriptional profiling of normal vs. tumor tissues from 14 patients with gastric cancer. Two-color experiment.
Project description:Endoplasmic reticulum stress (ERS) regulates the function of immune cells in the tumor microenvironment and suppresses the antitumor immune response. In order to formulate the TME of ERS-GC, we cocultured the human CAFs with the supernatant of human gastric cancer cells stimulated by TM. Mass spectrometry sequencing revealed that ERS state regulated the overexpression of 58 proteins and downregulation of the expression of 56 proteins in CAFs, including m6A-modified proteins and SEMA3A, an immunosuppression-related protein.
Project description:Selected genes within the 1 Mb minimal amplified region on 20q13.3 driven by ADRM1 in gastric cancer cell line AGS were analyzed by Gene expression Microarray. Gene Expression of ADRM1, HRH3, MTG2, LAMA5 and OSBPL2 were then compared in 16 Gastric cancer cell lines to a reference composed of mixed gastric cancer cell lines.