SK4 potentially modulates the alternative splicing profile associated with papillary thyroid cancer development in BHT101 cells

Papillary thyroid cancer (PTC) is an ever-increasing cancer type worldwide, and greatly decreases the life quality and affects survival time of patients during its development and progression, but the underlying mechanisms and key factors for PTC progression are not clear. Recent studies demonstrated the potassium channel protein SK4, also named as KCNN4, participates in the progression of many cancers, while it lacks the molecular mechanism study for SK4 function. In this study, we performed functional and molecular explorations for SK4 by overexpressing its level in thyroid cancer BHT101 cells. Cellular proliferation and invasion experiments were performed to assess the influences of SK4 on cell behaviors. Further, whole transcriptome sequencing (RNA-seq) analysis helped us systematically investigated the down stream targets of SK4, including differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs). We finally validated several DEGs and RASEs associated with the functions of SK4 by RT-qPCR experiment. In thyroid cancer patients, SK4 expression was completely lost in normal tissues and significantly increased in every stage of tumor tissues compared with normal tissues, the reason of which probably results from the low DNA methylation level at its promoter region. Consistent with previous study, SK4 overexpression (SK4-OE) promoted proliferation level and invasion ability of BHT10 cells compared with negative control (NC). By analyzing the RNA-seq data, we detected dozens of DEGs and found that up DEGs were enriched in negative regulation of apoptotic progress, including VTCN1, MSX1, FATE1, TEK, and PRAMEF2. More importantly, we found SK4-OE globally changed the alternative splicing pattern and identified 1639 RASEs. The genes of RASEs were enriched in DNA damage/repair, viral process, translation, and mRNA splicing pathways, which were tightly associated with the pathogenesis and progression of cancers. The splicing regulatory genes from RASGs could partly explain the reason of global AS dysregulation by SK4-OE in BHT101 cells. Finally, we validated several DEGs and RASEs associated with PTC progression by RT-qPCR. We found the expression of VTCN1, EDN1, SLC29A4, RP11-473M20.16, and CH507-513H4.4 were validated by RT-qPCR, as well as the AS pattern of TMEM116, RBM39, and RBM6. In summary, our results deeply explored the molecular targets of SK4 associated them with SK4-induced progression of PTC. We highlight that SE4-regulated AS pattern probably is a novel regulatory mechanism for SK4 in PTC. The identified DEGs and RASEs, as well as SK4 itself, could be used as potential therapeutic targets for PTC treatment in future.