Abstract LT10: Targeting post-transcriptional mechanisms of tumour persistence

Abstract

Quiescent (G0) cancer cells are a sub-population of reversible, non-proliferating cells that survive aggressive clinical therapies and cause cancer persistence. While transcriptional changes have been extensively studied in cancers, we find that 50% of gene expression changes in chemoresistant G0 acute myeloid leukaemia (AML), glioblastoma, and breast cancer cells, are at the translation level, without concurrent RNA level changes. Thus, our data revealed that post-transcriptional mechanisms are altered by stress signals, to rapidly adapt such resistant tumour cells for survival. We find that canonical translation is inhibited by low mTOR activity and induction of integrated stress response, in response to G0 cell state and therapy stress signals (Science Adv 2022, Science 2020, Genome Biol. 2020). These block both rate limiting steps of canonical translation in G0, and along with ribosome changes, enable non-canonical translation to express distinct genes for survival. These post-transcriptional survival adaptations are required for tumour cell persistence and provide unique dependencies that can be therapeutically targeted. Specifically, changes in the P-stalk protein, RPLP0/uL10, activate the eIF2α kinase, GCN2. eIF2α phosphorylation increases non-canonical translation of mRNAs with specific 5’UTRs, which promote AML immune evasion. Reduced canonical translation also enables translation of RNAs lacking canonical translation features of cap complex or canonical start sites, such as circular RNAs (circRNAs), translating unannotated atypical start site peptides to persist G0 tumour cells. Due to increased alternative splicing, we find changes in circRNAs that emerge from an alternative splicing called back-splicing. We find that these immune evasion genes and circRNAs are required for the survival of such G0 cancer cells. Overriding non-canonical translation or eIF2α phosphorylation, or suppressing such circRNAs and survival genes, reduces chemoresistance. Together, our data reveal that therapy- and G0-induced stress signals alter conventional post-transcriptional mechanisms, to mediate specialized, non-canonical translation of specific RNAs that elicit tumour persistence.