Unknown,Transcriptomics,Genomics,Proteomics

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MDA-MB-361 breast adenocarcinoma cells treated in vitro with allosteric AKT inhibitor MK2206 until development of resistance.

ABSTRACT: Whole exome sequencing to determine whether acquisition of resistance to MK2206 in MDA-MB-361 is mediated by a new AKT1 mutation. Cells were exposed in vitro to drug for 12 weeks. Surviving cells were expanded for another 2 weeks in the presence of drug before sequencing.

INSTRUMENT(S): HiSeq X Ten

ORGANISM(S): Homo sapiens

SUBMITTER: NICOLAOS PALASKAS

PROVIDER: E-MTAB-8066 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Formalin-fixed, paraffin-embedded (FFPE) tissues are an underused resource for molecular analyses. This proof of concept study aimed to compare RNAseq results from FFPE biopsies with the corresponding RNAlaterÂ® (Qiagen, Germany) stored samples from clear cell renal cell carcinoma (ccRCC) patients, to enable the decision of whether or not it is feasible to apply RNAseq technology to archival tissue. Core biopsies were obtained with a 16g needle from 16 patients undergoing partial or full nephrectomy. The RNA sequencing libraries were generated applying the new Illumina TruSeqÂ® Access library preparation protocol. Comparative analysis was done using voom/Limma R-package. The analysis of the FFPE and RNAlaterÂ® datasets yielded similar numbers of detected genes, differentially expressed transcripts and affected pathways. The FFPE and RNAlater datasets shared 80% (n=1106) differentially expressed genes. The average expression of these transcripts in both datasets correlated with R2=0.97, and the log2 fold changes of these transcripts, which are significantly altered in both datasets, correlated with R2=0.96. Among transcripts with the highest fold changes in both datasets were carbonic anhydrase 9 (CA9), neuronal pentraxin-2 (NPTX2) and uromodulin (UMOD) that were confirmed by immunohistochemistry. IPA revealed the presence of gene signatures of cancer and nephrotoxicity, renal damage and immune response. To simulate the feasibility of clinical biomarker studies with FFPE samples, a classifier model was developed for the FFPE dataset: expression data for CA9 alone had an accuracy, specificity and sensitivity of 94%, respectively, and achieved similar performance in the RNAlater dataset. Transforming growth factor-Ã1 (TGFB1)-regulated genes, epithelial to mesenchymal transition (EMT) and NOTCH signaling cascade may support novel therapeutic strategies. In conclusion, in this proof of concept study, RNAseq data obtained from FFPE kidney biopsies are comparable to data obtained from fresh stored material, thereby expanding the utility of archival tissue specimens. *** Access to raw data can be requested from submitters ***

Dataset Information

MDA-MB-361 breast adenocarcinoma cells treated in vitro with allosteric AKT inhibitor MK2206 until development of resistance.

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