# The role of RNA splicing in non-small cell lung cancer

> **NIH VA I01** · JAMES A. HALEY VA MEDICAL CENTER · 2021 · —

## Abstract

Lung cancer is the leading cause of cancer death for veterans and in the world, for both men and women in
industrialized countries, accounting for an estimated 28% of all cancer deaths in the United States. Non-small
cell lung cancer (NSCLC) represents the majority of these cancers,, and NSCLC has a 5-year survival rate of
~23% with current treatment options palliative. Hence, new therapeutic strategies are needed to impact this
disease, and elucidation of new mechanisms controlling the tumorigenicity of NSCLC cells will provide the
foundation upon which to build. In this regard, the gene, cyclin dependent kinase inhibitor 2A (CDKN2A), that
encodes the tumor suppressors, p16(INK4A) and p14(ARF), is found inactivated or deleted in NSCLC at a high
percentage (e.g., ~53% deletion rate). Importantly, our laboratory linked CDKN2A inactivation to dysregulation
of the RNA splicing of an uncharacterized, long non-coding RNA (lncRNA) located on Chromosome 19p13.12
(ENSG00000267053). Specifically, exon 3 inclusion/exclusion into the mature RNA transcript was
dysregulated in NSCLC cell lines with CDKN2A mutated/deleted, and thus, we now term this lncRNA, Cyclin
Dependent Kinase Inhibitor 2A-regulated lncRNA 1 (CyKILR-1). Initial cell signaling studies using small
molecule inhibitors also identified the AKT/CDK4 axis as a regulatory pathway upstream of CyKILR-1 RNA
splicing linked to CDKN2A inactivation. In human NSCLC, CyKILR-1 splice variant expression correlated with
lower patient survival. These findings are congruent with studies showing the linkage of the aberrant
expression of non-coding RNAs located at Chromosome 19p13.12 to cancer development. In preliminary
studies, specific downregulation of CyKILR-1 splice variants in NSCLC cells induced dramatic decreases in cell
survival and anchorage-independent growth. Initial mechanistic studies examining CyKILR-1 Exon 3 revealed
a consensus sequence for nuclear localization (TCTAGCTCAGCCC). Fractionation experiments then
demonstrated differential localization between the two splice variants with CyKILR-1B (exon 3 excluded)
localized to the cytoplasm in contrast to the nuclear localization of CyKILR-1A (exon 3 included). The
culmination of these data forms the hypothesis that inactivation of the tumor suppressor encoding gene,
CDKN2A, in NSCLC regulates the inclusion of exon 3 producing the CyKILR-1 splice variants, which localize to
the cytoplasm and imparts pro-survival phenotypes to NSCLC cells and tumors. To examine this hypothesis in
depth, we propose in this application the following independent, but synergistic specific aims (SAs): SA1: To
determine the biological relevance of CyKILR-1 RNA splicing in NSCLC; SA2: To determine the regulating
mechanism of CyKILR-1 RNA splicing; and SA3: To determine the cell signaling pathways regulated by
CyKILR-1 splice variants. These specific aims are focused on scientific lines of investigation to address the
need for new and precise therapies for treating NSCLC, w...

## Key facts

- **NIH application ID:** 10118835
- **Project number:** 2I01BX001792-09
- **Recipient organization:** JAMES A. HALEY VA MEDICAL CENTER
- **Principal Investigator:** CHARLES E. CHALFANT
- **Activity code:** I01 (R01, R21, SBIR, etc.)
- **Funding institute:** VA
- **Fiscal year:** 2021
- **Award amount:** —
- **Award type:** 2
- **Project period:** 2012-10-01 → 2024-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10118835

## Citation

> US National Institutes of Health, RePORTER application 10118835, The role of RNA splicing in non-small cell lung cancer (2I01BX001792-09). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10118835. Licensed CC0.

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