Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

NP-18 vs. NP-18AR transcriptional profile upon treatment with TK/GCV

ABSTRACT: Pancreatic cancer-derived cells NP-18 underwent four rounds of treatment with increasing doses of an adenoviral vector encoding TK enzyme and GCV. Surviving cells were termed NP-18AR and displayed decreased sensitivity to treatment. This experiment analyses the transcriptomic effect of TK/GCV treatment on NP-18AR as compared to that of NP-18 cells. Two-condition experiment, where response to treatment in naïve cells (NP-18) was compared to response to treatment in previously treated resistant cells (NP-18AR). Biological replicates: samples from 3 independently generated and independently treated NP-18AR lines (NP-18AR1, NP-18AR2 and NP-18AR3) were hibridized with 3 independently treated samples of NP-18 cells. A total of 9 hybridizations were performed, 2 for NP-18AR1 (including 1 dye-swap), 4 for NP-18AR2 (including 2 dye swaps) and 3 for NP-18AR3 (including 1 dye-swap).

ORGANISM(S): Homo sapiens

SUBMITTER: Lauro Sumoy

PROVIDER: E-GEOD-17137 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Cell cycle control pathways act as conditioning factors for TK/GCV sensitivity in pancreatic cancer cells.

Abate-Daga Daniel D Garcia-Rodríguez Laura L Sumoy Lauro L Fillat Cristina C

Biochimica et biophysica acta 20100703 10

The suicide system TK/GCV is an enzyme/prodrug therapy that involves the transfer of the cDNA for the herpes simplex virus thymidine kinase gene (TK) into tumor cells which then sensitizes the cells to the non-toxic antiviral drug ganciclovir. Although extensively characterized, the suicide system TK/GCV conceals the details of its mechanism of action. In order to shed some light on this issue, we conducted experiments designed to identify key features of sensitive cells, as compared to cells th ...[more]

PMID: 20599444

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Project description:Bone mineral density and structure candidate gene analysis in alcohol-non-preferring (NP), alcohol-preferring (P), congenic NP (NP.P) and congenic P (P.NP) rats; Genetic mapping in alcohol-preferring (P) and alcohol-non-preferring (NP) rats has identified a major quantitative trait locus (QTL) in the region between q22 â?? q34 on chromosome (Chr) 4 for alcohol preference. In a separate genome-wide linkage study, using inbred Fischer 344 (F344) and Lewis (LEW) rats, several QTL linked to bone density and structure were identified at the same location suggesting that bone mass and strength genes might co-segregate with genes that regulate the alcohol preference trait. The aim of this study is to identify the genes segregating for skeletal phenotypes and alcohol trait in congenic P/NP rats. We compared bone mineral content (BMC), areal/volumetric bone mineral density (aBMD/vBMD) and biomechanical strength at different skeletal sites from 6-month-old inbred and congenic P/NP rats. Transfer of the NP Chr 4 QTL into P background significantly increased body weight but decreased BMC, aBMD/vBMD in whole body, cranium, femur, and lumbar vertebrae. On the other hand, transfer of P Chr 4 QTL into NP background significantly decreased body weight but increased BMC and aBMD in the same skeletal sites. Microarray analysis was performed from the femurs of 4-week-old rats (n = 5 per strain) using Affymetrix Rat Genome 230 2.0 arrays. A total of 53 genes, including 41 candidate genes and 12 predicted genes, were differentially expressed among all strains of rats with a false discovery rate (FDR) less than 10%. Several candidate genes from microarray analysis were found to be were strongly correlated (r2>0.50) with different skeletal phenotypes. Gene expression of top 3 candidate genes from microarray profiling was validated by quantitative real-time PCR (qRT-PCR). Ingenuity pathway analysis revealed relationships among the candidate genes related to bone metabolism including pathways related to beta-estradiol, tumor necrosis factor and androgen receptor. Experiment Overall Design: Comparison of differentially expressed genes between 4q22-4q34 on chromosome 4 in NP, P, NP.P and P.NP rats.

Dataset Information

NP-18 vs. NP-18AR transcriptional profile upon treatment with TK/GCV

Publications

Cell cycle control pathways act as conditioning factors for TK/GCV sensitivity in pancreatic cancer cells.

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