Triggering Aberrant RNA Processing for RCC Therapy

ABSTRACT Renal cell carcinoma (RCC) is one of the most lethal urologic malignancies with approximately 81,800 new cases and 15,000 deaths estimated in 2023. Clear cell RCC (ccRCC) along with melanoma has traditionally been viewed as an immunotherapy responsive disease with a storied history of immunotherapy

treatments including high dose interleukin 2 (IL2), interferon, and allogeneic stem cell transplant. Indeed, RCC was one of the first tumor types to garner FDA approval for PD1 immune checkpoint inhibition (ICI). However, unlike melanoma, most RCC tumors do not have a high tumor mutational burden (TMB) to potentially explain

their immunotherapy responsiveness. We and others have sought to explain this unanswered question and have demonstrated that non-canonical tumor associated antigens like endogenous retroviruses (ERVs) may in part explain ICI response in RCC. Nonetheless, ERV expression is unlikely to fully explain ccRCC ICI response

and only 25% of RCC patients respond to single-agent ICI. Therefore, further enhancing ICI response will be clinically meaningful. A collaboration between the Kim and Dominguez labs has uncovered another potentially robust source of tumor associated antigens - retained introns. We have noted that ccRCC tumors have the highest level of

retained introns (RI) across all TCGA tumors, that RI levels are secondary to suppressed non-sense mediated decay (NMD) activity, and that one can subset ccRCC into RI-high and normal-like tumors. Moreover, we have found that mTOR signaling plays a key role in regulating NMD and intron retention and that mTOR inhibition

can promote intron retention. Finally, our preliminary data demonstrates, in a clinical dataset, that ICI responsive tumors are enriched in a RI-high phenotype. In this proposal we will assess how NMD is regulated in ccRCC (Aim 1), determine the impact of suppressed NMD on ccRCC tumorigenicity (Aim 2), and determine

the impact of NMD suppression and resultant enhanced intron retention on the tumor immune microenvironment and ICI response (Aim 3). Successful completion of our proposal will establish sound scientific premise for combining two FDA approved RCC therapies (mTOR inhibition and ICI) to promote expression of highly foreign neoantigens from retained introns (neo-RI-antigens), which should provoke a

robust, antigen-driven immune response that can be leveraged to enhance immune checkpoint blockade.