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

Abstract

Immune-cold tumours such as prostate cancer often resist immune checkpoint therapies (ICT) due to impaired antigen presentation via major histocompatibility complex class I (MHC-I). While MHC-I downregulation is a common immune evasion mechanism, no approved therapies selectively restore MHC-I expression in tumours. We developed a programmable RNA engineering platform, termed the 3′UTR CRISPR/dCas13 Engineering System (3′UTRCES), to precisely manipulate mRNA alternative polyadenylation (APA) in vivo. We identified tumour-specific 3′UTR shortening of the E3 ligase adaptor SPSB1 as a driver of MHC-I degradation via SPSB1-mediated ubiquitination, without affecting PD-L1. Lipid nanoparticle (LNP)-delivered 3′UTRCES reversed SPSB1 3′UTR shortening, restored MHC-I expression and sensitized tumours to ICT in syngeneic mice. These effects were elicited by MHC-I-dependent increases in CD8 T cell infiltration and antitumour cytotoxic activity. Our findings reveal APA-driven MHC-I suppression as a previously unrecognized mechanism of immune escape and establish LNP-3′UTRCES as a versatile platform for post-transcriptional RNA engineering in cancer.