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Autophagy is a widely studied self-renewal pathway that is essential for degrading damaged cellular organelles or recycling biomolecules to maintain cellular homeostasis, particularly under cellular stress. This pathway initiates with formation of an autophagosome, which is a double-membrane structure that envelopes cytosolic components and fuses with a lysosome to facilitate degradation of the contents. The endosomal sorting complexes required for transport (ESCRT) proteins play an integral role in controlling autophagosome fusion events and disruption to this machinery leads to autophagosome accumulation. Given the central role of autophagy in maintaining cellular health, it is unsurprising that dysfunction of this process is associated with many human maladies including cancer and neurodegenerative diseases. The cell can also rapidly respond to cellular stress through alternative pre-mRNA splicing that enables adaptive changes to the cell’s proteome in response to stress. Thus, alternative pre-mRNA splicing of genes that are involved in autophagy adds another layer of complexity to the cell’s stress response. Consequently, the dysregulation of alternative splicing of genes associated with autophagy and ESCRT may also precipitate disease states by either reducing the ability of the cell to respond to stress or triggering a maladaptive response that is pathogenic. In this review, we summarize the diverse roles of the ESCRT machinery and alternative splicing in regulating autophagy and how their dysfunction can have implications for human disease.

Reduced expression of haploinsufficient tumour suppressor genes is sufficient to alter cellular phenotypes towards carcinogenesis without complete loss of gene expression. As an essential gene, complete expression loss of pre-mRNA processing factor 4 kinase (PRP4K, also known as PRPF4B) is lethal. However, we demonstrate here that reduction of PRP4K levels by small interfering RNA in the mammary epithelial cell lines HMLE and MCF10A can induce partial epithelial-to-mesenchymal transition (EMT) marked by the retention of epithelial markers such as Zo-1 and E-cadherin, and upregulation of mesenchymal markers such as fibronectin and Zeb1. This partial EMT phenotype in non-transformed PRP4K-depleted cells is associated with greater invasive potential in 3D transwell assays, but either reduces or has no effect on 2D migration examined by scratch assay. This is in contrast to depletion of PRP4K in transformed triple-negative MDA-MB-231 breast cancer cells, which results in enhanced migration in 2D and invasion in 3D. Induction of EMT, using EMT-inducing media containing WNT-5a and TGF-β1 or depletion of eukaryotic translation initiation factor 3e (eIF3e) by shRNA, results in marked reduction of PRP4K expression. EMT induced by eIF3e depletion does not affect the transcription of PRP4K mRNA or turn-over of PRP4K protein, but rather reduces its protein translation. Finally, reduced PRP4K levels after eIF3e depletion correlated with increased YAP activity and nuclear localization, the latter being reversed by overexpression of exogenous PRP4K. Together, these data indicate that PRP4K is a haploinsufficient tumour suppressor negatively regulated by EMT, and that when depleted can induce partial EMT and increased cell invasion.