Abstract B030: Programmable mRNA 3′UTR engineering restores MHC-I and overcomes immune evasion in prostate cancer

Abstract Background: “Immune-cold” tumors, such as prostate cancer, often resist immune checkpoint therapies (ICT) due to impaired antigen presentation via major histocompatibility complex class I (MHC-I). Although genetic, epigenetic, and transcriptional alterations intrinsic to cancer cells have been linked to MHC-I downregulation as a common immune evasion mechanism, no approved therapies selectively restore MHC-I expression in tumors and thereby overcome ICT resistance in these malignancies. We hypothesize that 3′UTR alternative polyadenylation (APA) is an overlooked tumor-intrinsic mechanism that causally drives immune evasion and ICT resistance. Methods: We developed a programmable RNA engineering system termed 3′UTRCES (3′UTR CRISPR/dCas13 Engineering System) to precisely reverse clinically relevant APA events in prostate cancer. The editing efficiency and specificity of 3′UTRCES was validated by RNase H alternative polyadenylation assay (RHAPA), RNA-sequencing and Northern blotting assays. Quantitative proteomics and immunoprecipitation assays were performed to dissect the mechanisms of SPSB1 3′UTR shortening as a “driver APA” in promoting oncogenic signaling and immune evasion. TT3 lipid nanoparticles (LNPs) were applied for intratumoral delivery of 3′UTRCES RNA to achieve targeted 3′UTR therapy and enhance responses to ICT. Flow cytometry were used to examine the MHC-I-mediated antigen presentation and cytotoxic activity of tumor infiltrating CD8+ T cells. Results: 3′UTR globally shortens during prostate cancer progression to castration-resistance. Through blocking the proximal PASs, 3′UTRCES efficiently and specifically reverses the 3′UTR shortening of novel APA-linked prostate cancer oncogenic mRNAs, such as SPSB1, leading to reduced SPSB1 mRNA translation and cancer cell-autonomous growth. Notably, elevated SPSB1 protein, driven by 3′UTR shortening, was associated with impaired IFNγ signaling, reduced MHC-I expression, and decreased CD8 T cell infiltration in patients with castration resistant prostate cancer. Mechanistic studies revealed that SPSB1 recruits an E3 ligase complex to promote MHC-I degradation. Lipid nanoparticle (LNP)–delivered 3′UTRCES RNA reversed SPSB1 3′UTR shortening, restored MHC-I expression, and sensitized tumors to anti–PD-1 and anti–CTLA-4 therapies in syngeneic mouse models. These therapeutic effects were elicited by MHC-I-dependent increases in antigen presentation, CD8+ T-cell infiltration, and enhanced cytotoxic anti-tumor immunity. Conclusions: Our findings reveal APA-mediated MHC-I suppression as a previously unrecognized mechanism of immune escape in immune-cold tumors and establish LNP-3′UTRCES as a versatile platform for post-transcriptional RNA engineering in cancer and other APA-associated diseases.: Citation Format: Furong Huang, Fuwen Yuan, Kexin Li, Ya Cui, Lei Li, Wenbin Ye, Zhifen Cui, Jingyue Yan, Qiang Chen, Christopher Nicchitta, Yuebao Zhang, William Hankey, Jeffrey Everitt, Kai-Lieh Huang, Mu-En Wang, Ming Chen, Jiaoti Huang, Hongyan Wang, Eric J. Wagner, Xin Lu, Yizhou Dong, Wei Li, Qianben Wang. Programmable mRNA 3′UTR engineering restores MHC-I and overcomes immune evasion in prostate cancer [abstract]. In: Proceedings of the AACR Immuno-Oncology Conference (AACR IO): Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2026 Feb 18-21; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2026;14(2 Suppl):Abstract nr B030.