Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of four glioblastoma (GBM) cell lines treated with irradiation, PARP7i, diABZI alone or in combination with irradiation

ABSTRACT: Glioblastoma (GBM) is the deadliest type of brain cancer, exhibiting resistance not only to traditional treatments like radiation and chemotherapy but also to modern immunotherapy. GBM is classified as an immunologically cold tumor with an immunosuppressive microenvironment. Radio- and chemotherapy have been shown to alter the tumor microenvironment and trigger an anti-tumor immune response in various cancers, including breast, lung, and colorectal cancer, via the cGAS/STING and type I interferon (IFN-I) pathway. Additionally, STING agonists and inhibitors of DNA damage response and cell cycle checkpoints, which promote the accumulation of immunostimulatory cytoplasmic dsDNA, have been found to enhance the effects of radiation. Here we examined the immunogenic response of four different GBM cell lines (U251, T98G, GB-1, KALS-1) exposed to hypofractionated X-ray radiation (3x8 Gy) in combination with a STING agonist or with inhibitors targeting immune signaling (PARP7). We performed RNA-seq analysis of all four GBM cell lines treated with 3x8 Gy, PARP7i, diABZI alone or in combination with 3x8 Gy.

INSTRUMENT(S): Illumina NovaSeq X

ORGANISM(S): Homo sapiens

SUBMITTER: Filip Horvat

PROVIDER: E-MTAB-14858 | 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 of four glioblastoma (GBM) cell lines treated with irradiation, PARP7i, diABZI alone or in combination with irradiation

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