RNA Splicing Variants of the Novel Long Non-coding RNA, CyKILR, Possess Divergent Biological Functions in Non-small Cell Lung Cancer

The CDKN2A gene, responsible for encoding the tumor suppressors p16(INK4A) and p14(ARF), is frequently inactivated in non-small cell lung cancer (NSCLC). Herein, an uncharacterized long non-coding RNA (lncRNA) (ENSG00000267053) on chromosome 19p13.12 was found to be overexpressed in NSCLC cells with an active, wild-type CDKN2A gene. This lncRNA, named cyclin-dependent kinase inhibitor 2A-regulated lncRNA (CyKILR), also correlated with an active WT STK11 gene, which encodes the tumor suppressor, liver kinase B1. CyKILR displayed two splice variants, CyKILRa (exon 3 included) and CyKILRb (exon 3 excluded), which are cooperatively regulated by CDKN2A and STK11 as knockdown of both tumor suppressor genes was required to induce a significant loss of exon 3 inclusion in mature CyKILR RNA. CyKILRa localized to the nucleus, and its downregulation using antisense RNA oligonucleotides enhanced cellular proliferation, migration, clonogenic survival, and tumor incidence. In contrast, CyKILRb localized to the cytoplasm, and its downregulation using small interfering RNA reduced cell proliferation, migration, clonogenic survival, and tumor incidence. Transcriptomics analyses revealed the enhancement of apoptotic pathways with concomitant suppression of key cell-cycle pathways by CyKILRa demonstrating its tumor-suppressive role. CyKILRb inhibited tumor suppressor miRNAs indicating an oncogenic nature. These findings elucidate the intricate roles of lncRNAs in cell signaling and tumorigenesis.