Table S1. primers and oligonucleotides. Table S2. Microarray gene expression profiling (shPUS7-33 vs shGFP). Table S3. Functional annotation of PUS7 knockdown-responsive genes. Table S4. 13C-glucose metabolic flux analysis. Table S5. 13C-15N-glutamine metabolic flux analysis. Table S6. Nanopore RNA seq - MCTS1 mRNA Y modification. Table S7. Proteomic analysis of proteins downregulated by PUS7 knockdown in BE(2)-C cells. Table S8. Polysome enrichment of transcripts with higher levels of pseudouridylation. Table S9. Nanopore RNA seq - ATF4 mRNA Y modification
ARTICLE ABSTRACT
Pseudouridylation is a common RNA modification that is catalyzed by the family of pseudouridine synthases (PUS). Pseudouridylation can increase RNA stability and rigidity, thereby impacting RNA splicing, processing, and translation. Given that RNA metabolism is frequently altered in cancer, pseudouridylation may be a functionally important process in tumor biology. Here, we show that the MYC family of oncoproteins transcriptionally upregulates PUS7 expression during cancer development. PUS7 is essential for the growth and survival of MYC-driven cancer cells and xenografts by promoting adaptive stress responses and amino acid biosynthesis and import. ATF4, a master regulator of stress responses and cellular metabolism, was identified as a key downstream mediator of PUS7 functional activity. Induction of ATF4 by MYC oncoproteins and cellular stress required PUS7, and ATF4 overexpression overcame the growth inhibition caused by PUS7 deficiency. Mechanistically, PUS7 induced pseudouridylation of MCTS1 mRNA, which enhanced its translation. MCTS1, a noncanonical translation initiation factor, drove stress-induced ATF4 protein expression. A PUS7 consensus pseudouridylation site in the 3′ untranslated region of ATF4 mRNA was crucial for the induction of ATF4 by cellular stress. These findings unveil an MYC-activated mRNA pseudouridylation program that mitigates cellular stress induced by MYC stimulation of proliferation and biomass production, suggesting that targeting PUS7 could be a therapeutic strategy selectively against MYC-driven cancers.Significance: Oncogene activation of mRNA pseudouridylation is a mechanism that facilitates metabolic reprogramming and adaptive responses to overcome cellular stress during cancer development.
