Silencing core spliceosome Sm gene expression induces a cytotoxic splicing switch in the proteasome subunit beta 3 mRNA in non-small cell lung cancer cells
The core spliceosomal Sm proteins were recently proposed as cancer-selective lethal targets in non-small cell lung cancer (NSCLC). In contrast, loss of commonly mutated cancer target SF3B1 appeared to be toxic to non-malignant cells as well. In the current study, the transcriptomes of A549 NSCLC cells in which SF3B1 or SNRPD3 was silenced were compared using RNA sequencing. Skipping of exon 4 of the proteasomal subunit beta type-3 (PSMB3) mRNA, resulting in a shorter PSMB3-S variant, occurred only after silencing SNRPD3. This observation was extended to the other six Sm genes. Remarkably, alternative splicing of PSMB3 mRNA upon Sm gene silencing was not observed in non-malignant IMR-90 lung fibroblasts. Furthermore, PSMB3 was found overexpressed in NSCLC clinical samples and PSMB3 expression correlated with Sm gene expression. Moreover, high PSMB3 expression corresponds to worse survival in patients with lung adenocarcinomas. Finally, silencing the canonical full-length PSMB3-L but not the shorter PSMB3-S variant was cytotoxic and was accompanied by a decrease in proteasomal activity. Together, silencing Sm genes, but not SF3B1, causes a cytotoxic alternative splicing switch in the PSMB3 mRNA in NSCLC cells only. Overall design: Examination of the transcriptome of A549 NSCLC cells transfected with a non-targeting negative control siRNA or siRNAs targeting either SF3B1 or SNRPD3