Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression Data from pancreatic cancer cell lines and orthotopic tumors grown with and without MEK inhibitor

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Stephan Gysin

PROVIDER: E-GEOD-45765 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Analysis of mRNA profiles after MEK1/2 inhibition in human pancreatic cancer cell lines reveals pathways involved in drug sensitivity.

Gysin Stephan S Paquette Jesse J McMahon Martin M

Molecular cancer research : MCR 20120725 12

Mutationally activated KRAS, detected in approximately 90% of pancreatic ductal adenocarcinomas (PDA), has proven an intractable pharmacologic target to date. Consequently, efforts to treat KRAS-mutated cancers are focused on targeting RAS-regulated signaling pathways. In mouse models, expression of BRAF(V600E) combined with dominant-negative TP53 elicits PDA, and pharmacologic blockade of mitogen-activated protein/extracellular signal-regulated kinase (MEK) inhibits proliferation of human PDA-d ...[more]

PMID: 22833572

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Project description:All-trans retinoic acid (ATRA) is used in the treatment of Acute Promyelocytic Leukemia (APL) with exceptional results, inducing long-lasting remissions in 78% of the patients. In previous studies (Bolis M et al., Ann Oncol. 2017, 28:611; Centritto F et al., EMBO Mol Med. 2015, 7:950) we demonstrated the therapeutic potential of ATRA in the personalized treatment of breast cancer. The present study is aimed at providing pre-clinical evidence supporting the use of pharmacological strategies based on ATRA in the management of stomach cancer, a very heterogeneous type of tumor, which lacks effective therapeutic options other than surgery. To define the sensitivity of gastric cancer to the anti-proliferative action of ATRA, we used 27 cell-lines, recapitulating the heterogeneity of the tumor. Fourteen of these cell-lines are characterized by a G-DIF phenotype, while the remainders present with a G-INT phenotype. Each cell-line was exposed to increasing concentrations of ATRA and the growth-inhibitory effects of the retinoid were evaluated at 3, 6, and 9 days. The 27 cell-lines were ranked for their sensitivity to the retinoid with the “ATRA-score”, a continuous/quantitative index, which we developed. The results indicate that the cell-lines can be divided into 3 separate groups characterized by high, intermediate and low sensitivity to ATRA. No significant correlation between ATRA-sensitivity and the G-DIF or G-INT phenotype is observed in our panel of cell-lines. To support the results obtained with the cell-lines, we evaluated the anti-proliferative effects exerted by ATRA on short-term tissue slice cultures of primary tumors derived from 13 cases of stomach cancer, which we classified as G-DIF or G-INT following determination of the basal gene-expression profiles with the use of RNA-sequencing studies. The results obtained with the short-term tissue culture model confirm the data generated with the cell-lines. The whole genome RNA-sequencing studies performed in the cell-lines and short-term tissue cultures in basal conditions allowed us to define a model consisting of 42 genes whose expression is quantitatively correlated with ATRA-sensitivity. The model was used to predict the sensitivity of gastric cancer cases to ATRA using the TCGA dataset. The results obtained indicate that approximately 60% of the gastric cancer cases are predicted to be characterized by high/intermediate sensitivity to ATRA, regardless of the G-DIF or G-INT phenotype. In conclusion, our results support the concept that ATRA-based therapeutic strategies are likely to be beneficial in the majority of stomach cancer cases. In addition, we generate a gene-expression tool that may be used for the selection of ATRA-sensitive patients in the clinics.

Project description:(R,R’)-4-methoxy-1-naphthylfenoterol (MNF) inhibits in vitro proliferation of several types of cancer cell lines. In this study, the in vivo antitumor effects of MNF were evaluated using rat C6 glioma cells implanted subcutaneously into the lower flank of 5 week-old NMRI/Nude female Swiss mice. Three days after the inoculation, the mice were subjected to intraperitoneal injections of saline or MNF (2mg/kg) for five days per week for16 days. Tumor volumes were measured everyday using slide calipers. Significant reductions in mean tumor volumes were observed in mice receiving MNF when compared with the saline-treated group (p<0.001, n=17-19). At the end of the study, animals were sacrificed and tumors were collected for cDNA microarray, quantitative RT-PCR and immunoblot analyses. Significant decrease in expression of genes involved in cellular proliferation, including mitotic checkpoint kinase MAD3L (Bub1b), cyclin-dependent kinase inhibitor 3 (Cdkn3) and cyclin A2 (Ccna2), as well as molecular markers for glioblastoma, such as oligodendrocyte transcription factor 1 (Olig1) and SRY-box 4 (Sox4) was observed in tumors of MNF-treated mice as compared to saline-injected controls. The efficacy of MNF against C6 glioma cancer in vivo was accompanied by marked reduction in the expression of cell cycle regulator proteins, including cyclin A and cyclin D1, in tumor extracts. This study is the first demonstration of MNF-dependent chemoprevention in a glioblastoma xenograft model in the mouse and may offer a potential mechanism for its anticancer action in vivo. Keywords: fenoterol derivative; C6 glioma; tumor xenografts; microarray analysis; Total RNA was isolated from rat C6 glioma xenografts harvested from vehicle and MNF-treated nude mice (n = 3 per group, cohort 1). This analysis was repeated in a second cohort of animals (n = 3 per group, cohort 2). Total cellular RNA was extracted using an RNeasy plus mini kit (QIAGEN, Valencia, CA), and its quality was assessed using an Agilent BioAnalyzer using RNA 6000 Nano Chips (Agilent Technologies, Santa Clara, CA). Transcriptional profiling was determined using Illumina Sentrix BeadChips (Illumina, San Diego, CA). Total RNA was used to generate biotin-labeled cRNA with the Illumina TotalPrep RNA Amplification Kit. In short, 0.5ug of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double-stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated incorporating biotin-16-UTP. A total of 0.75µg of biotin-labeled cRNA was hybridized at 58 °C for 16 h to Illumina's Sentrix Rat Ref-12 Expression BeadChips. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3. Hybridized arrays were scanned using an Illumina BeadStation 500X Genetic Analysis Systems scanner and the image data extracted using Illumina’s GenomeStudio software, version 1.6.1. For statistical analysis, the expression data were filtered to include only probes with a consistent signal on each chip and an Illumina detection p value < 0.02.

Dataset Information

Expression Data from pancreatic cancer cell lines and orthotopic tumors grown with and without MEK inhibitor

Publications

Analysis of mRNA profiles after MEK1/2 inhibition in human pancreatic cancer cell lines reveals pathways involved in drug sensitivity.

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