Unknown,Transcriptomics,Genomics,Proteomics

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RNA seq from GBM cell lines and primary cultures after irradiation

ABSTRACT: Glioblastoma is the most common, aggressive tumor of CNS, with a 5-year overall survival rate of 5%. The treatment is challenging due to its location and the inevitable recurrence in 80% of the cases. To understand the cause behind this recurrence, we established an in vitro radiation survival model that mimics clinical scenarios. GBM Parent (P) cells, after being given a lethal dose of radiation, undergo tremendous cell death but leave behind a small residual surviving population that shows senescence phenotype. These residual (RS) cells eventually reverse from senescence (End of senescence) and give rise to aggressive relapse (R). To find molecular players behind this reversal of senescence, we carried out RNA sequencing of GBM cell lines U87MG and SF268 at mentioned stages of senescence post-radiation treatment.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Shilpee Dutt

PROVIDER: E-MTAB-13786 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Glioblastoma multiforme (GBM) is the most aggressive form of brain tumors. Despite radical surgery and radiotherapy supported by chemotherapy, the disease still remains incurable with extremely low median survival rate of 12-15 months from the time of initial diagnosis. The main cause of treatment failure is considered to be the presence of cells that are resistant to such treatment. MicroRNAs (miRNAs) as regulators of gene expression are involved in the tumor pathogenesis, including GBM. MiR-338 is a brain specific miRNA which has been described to target pathways involved in proliferation and differentiation. In our study, miR-338-3p and -5p were differentially expressed in GBM tissue in comparison to non-tumor brain tissue. Overexpression of miR-338-3p with miRNA mimic did not show any changes in proliferation rates in GBM cell lines (A172, T98G, U87MG). On the other hand, pre-miR-338-5p notably decreased proliferation and caused cell cycle arrest. Since radiation is currently the main treatment modality in GBM, we combined overexpression of pre-miR-338-5p with radiation, which led to significantly decreased of cell proliferation, and increased cell cycle arrest and apoptosis in comparison to only irradiated cells. To better elucidate the mechanism of action, we performed gene expression profiling analysis that revealed targets of miR-338-5p being Ndfip1, Rheb, ppp2R5a. These genes have been described to be involved in DNA damage response, proliferation and cell cycle regulation. To our knowledge, this is the first study to describe role of miR-338-5p in GBM and its potential to improve sensitivity of GBM to radiation. Study was performed on three glioblastoma multiforme cell lines A172, T98G and U87MG. This experiment was performed on Affymetrix GeneChip Human Gene ST 1.0 to elucidate the targets of miRNA-338-5p. Cell lines were seeded 24 hours prior transfection. After transfection with pre-miR338-5p or negative control cell were cultured for 24 hours and harvested. RNA was isolated using MirVana miRNA Isolation Kit (Ambion, USA) and checked for RNA integrity by Bioanalyzer 2100 and purity by ratios 260/280>1.8 and 260/230>1.8 by Nanodrop2000.

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RNA seq from GBM cell lines and primary cultures after irradiation

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