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Updated: Feb 8, 2026
Quantitative Analysis of Alternative Pre-mRNA Splicing in Mouse Brain Sections Using RNA In Situ Hybridization Assay
Published on: August 26, 2018
Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells
Ksenia S Anufrieva1,2,3, Victoria О Shender4,5, Georgij P Arapidi6,7,8
1Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia. anufrieva@phystech.edu.
Background:
Abnormal pre-mRNA splicing regulation is common in cancer, but the effects of chemotherapy on this process remain unclear.
Methods:
To 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.
Results:
Our 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.
Conclusions:
Decreased 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.
Insights
Chemotherapy causes cancer cells to retain introns, decreasing splicing efficiency. This novel stress response can be targeted by pladienolide B to enhance cancer therapy effectiveness.
Area of Science:
- Molecular Biology
- Cancer Research
- Genomics
Background:
- Abnormal pre-messenger RNA (pre-mRNA) splicing regulation is a hallmark of cancer.
- The impact of chemotherapy on splicing regulation remains largely unknown.
Purpose of the Study:
- To investigate the effects of chemotherapy on pre-mRNA splicing regulation in cancer cells.
- To identify potential therapeutic strategies to overcome chemotherapy resistance.
Main Methods:
- Meta-analyses of transcriptomic, proteomic, phosphoproteomic, and secretome datasets.
- Validation using LC-MS/MS, western blotting, immunofluorescence, and FACS analyses.
- Gene expression analysis in 101 cell lines under various stress conditions.
Main Results:
- Chemotherapy induces similar alternative splicing changes, primarily intron retention, across multiple genes.
- Cell cycle and pre-mRNA splicing genes show coordinated downregulation under various stress stimuli.
- Splicing efficiency decreases due to reduced spliceosomal protein levels and global intron retention.
Conclusions:
- Decreased splicing efficiency and global intron retention represent a novel stress response mechanism promoting cancer cell survival post-therapy.
- Pladienolide B inhibits this mechanism, enhancing cancer cell sensitivity to chemotherapy, particularly cisplatin.
- Pladienolide B is a promising candidate for improving cancer treatment efficacy.
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