The role of novel long non-coding RNA TRIDENT in non-small cell lung cancer

Abstract

Non-small cell lung cancer (NSCLC) continues to be the leading cause of cancer mortality. While significant advancements have been made in its treatment and management, it remains incurable due to tumor recurrence. The molecular mechanisms driving NSCLC involving protein-coding genes have been extensively studied. However, systematically identifying and characterizing the regulatory factors involved in NSCLC can also provide invaluable insight into the pathways involved and aid in developing novel therapeutic and diagnostic strategies. Long non-coding RNAs (lncRNAs) are a class of non-coding regulatory RNAs that have been implicated in many human diseases. These RNAs, primarily through their secondary structure, employ diverse mechanisms to regulate most processes important for cell survival. Due to bioinformatic and technical limitations and a nascent understanding of functional RNA domains, most of these RNA molecules remain uncharacterized. During my dissertation, I sought to use existing RNAseq databases to identify and characterize novel lncRNAs that show differential regulation in NSCLC. Through our screen, we identified several lncRNAs that have been previously described and some not. We focused on the novel lncRNAs and utilized online tools to filter out lncRNAs whose expression was significantly associated with patient prognosis. Next, we employed CRISPRi and antisense oligos (ASOs) to knock them down in cellular models of NSCLC to assess the effect on classical cancer phenotypes such as proliferation, invasion, and migration. Our analysis revealed several lncRNAs, yet uncharacterized, that significantly alter cancer phenotypes when their levels are perturbed. We delved deeper into the mechanism of one such lncRNA - RP11-462G12.1 or TRIDENT. We found that TRIDENT expression was significantly induced upon EGFR activation. Perturbing levels of TRIDENT highlighted its role in cell proliferation and drug resistance. Using ChIRP-MS analysis we identified TRIM28 as a protein interactor of TRIDENT. TRIDENT promotes phosphorylation of TRIM28 and knocking down TRIDENT leads to the accumulation of DNA damage in cancer cells via decrease TRIM28 phosphorylation. Altogether, our results reveal a novel molecular pathway in which TRIDENT regulates TRIM28 phosphorylation to promote tumor cell growth and drug resistance. My work highlights the critical roles lncRNAs can play in modulating disease mechanisms and response to treatments. Their effect, though subtle, can have implications for treatment strategies for patients and aid in the development of better therapeutic targets