Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells

Abstract

BackgroundAbnormal pre-mRNA splicing regulation is common in cancer, but the effects of chemotherapy on this process remain unclear.MethodsTo evaluate the effect of chemotherapy on slicing regulation, we performed meta-analyses of previously published transcriptomic, proteomic, phosphoproteomic, and secretome datasets. Our findings were verified by LC-MS/MS, western blotting, immunofluorescence, and FACS analyses of multiple cancer cell lines treated with cisplatin and pladienolide B.ResultsOur results revealed that different types of chemotherapy lead to similar changes in alternative splicing by inducing intron retention in multiple genes. To determine the mechanism underlying this effect, we analyzed gene expression in 101 cell lines affected by ɣ-irradiation, hypoxia, and 10 various chemotherapeutic drugs. Strikingly, оnly genes involved in the cell cycle and pre-mRNA splicing regulation were changed in a similar manner in all 335 tested samples regardless of stress stimuli. We revealed significant downregulation of gene expression levels in these two pathways, which could be explained by the observed decrease in splicing efficiency and global intron retention. We showed that the levels of active spliceosomal proteins might be further post-translationally decreased by phosphorylation and export into the extracellular space. To further explore these bioinformatics findings, we performed proteomic analysis of cisplatin-treated ovarian cancer cells. Finally, we demonstrated that the splicing inhibitor pladienolide B impairs the cellular response to DNA damage and significantly increases the sensitivity of cancer cells to chemotherapy.ConclusionsDecreased splicing efficiency and global intron retention is a novel stress response mechanism that may promote survival of malignant cells following therapy. We found that this mechanism can be inhibited by pladienolide B, which significantly increases the sensitivity of cancer cells to cisplatin which makes it a good candidate drug for improving the efficiency of cancer therapy.Electronic supplementary materialThe online version of this article (10.1186/s13073-018-0557-y) contains supplementary material, which is available to authorized users.

Gallop Racing Shifts Mature mRNA towards Introns: Does Exercise-Induced Stress Enhance Genome Plasticity?

“…In literature a general increase of intron retention events has been observed in response to some types of stress like thermal stress exposure [47,48], chemotherapy-induced stress in cancer cells [49] and hypoxia [50]. The intron retention phenomenon could be triggered by the transcriptional activation of repeated elements contained within the intron sequence [36,37].…”

Effects of KIF2A on the prognosis of nasopharyngeal carcinoma and nasopharyngeal carcinoma cells

“…Cells were collected and treated with RIPA buffer (Beyotime Institute of Biotechnology) on ice and the extracted protein was quantified by a bicinchoninic acid kit (Beyotime Institute of Biotechnology). A total of 30 µg protein sample was separated by 10% SDS-PAGE and subsequently transferred onto a PVDF membrane (18). Following blocking with 5% BSA in TBS + 0.1% Tween-20 for 1 h, the membrane was incubated with antibodies against KIF2A (1:500; catalog no.…”

Are Small Nucleolar RNAs “CRISPRable”? A Report on Box C/D Small Nucleolar RNA Editing in Human Cells

“…The RNA-Seq data have been deposited in ArrayExpress database under accession number E-MTAB-8269. Differential splicing analysis was performed using rMATS splicing tool as described (Anufrieva et al, 2018).…”