Multi-level functional genomics reveals molecular and cellular oncogenicity of patient-based 3′ untranslated region mutations

• Published in: Cell reports (Cambridge) Vol. 42; no. 8; p. 112840
• Main Authors: Schuster, Samantha L., Arora, Sonali, Wladyka, Cynthia L., Itagi, Pushpa, Corey, Lukas, Young, Dave, Stackhouse, Bethany L., Kollath, Lori, Wu, Qian V., Corey, Eva, True, Lawrence D., Ha, Gavin, Paddison, Patrick J., Hsieh, Andrew C.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 29.08.2023; Elsevier
• Subjects: 3' Untranslated Regions - genetics; 3' UTR; 5' Untranslated Regions; CP: Cancer; CP: Genomics; CRISPR-Cas9 base editing; Genomics; Humans; IGF1R; massively parallel reporter assay; mRNA stability; mRNA translation; Mutation - genetics; prostate cancer; Regulatory Sequences, Nucleic Acid; RNA, Messenger - genetics; RNA, Messenger - metabolism; somatic mutation; untranslated region; ZWILCH; CRISPR-Cas9 base editing; prostate cancer; mRNA translation; ZWILCH; CP: Cancer; untranslated region; massively parallel reporter assay; CP: Genomics; 3' UTR; somatic mutation; mRNA stability; IGF1R
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2023.112840

3′ untranslated region (3′ UTR) somatic mutations represent a largely unexplored avenue of alternative oncogenic gene dysregulation. To determine the significance of 3′ UTR mutations in disease, we identify 3′ UTR somatic variants across 185 advanced prostate tumors, discovering 14,497 single-nucleotide mutations enriched in oncogenic pathways and 3′ UTR regulatory elements. By developing two complementary massively parallel reporter assays, we measure how thousands of patient-based mutations affect mRNA translation and stability and identify hundreds of functional variants that allow us to define determinants of mutation significance. We demonstrate the clinical relevance of these mutations, observing that CRISPR-Cas9 endogenous editing of distinct variants increases cellular stress resistance and that patients harboring oncogenic 3′ UTR mutations have a particularly poor prognosis. This work represents an expansive view of the extent to which disease-relevant 3′ UTR mutations affect mRNA stability, translation, and cancer progression, uncovering principles of regulatory functionality and potential therapeutic targets in previously unexplored regulatory regions. [Display omitted] •3′ UTR mutations are enriched in cancer-related genes and regulatory elements•High-throughput assays reveal 3′ UTR mutations alter mRNA translation and stability•Endogenous CRISPR-edited 3′ UTR mutations increase cellular stress resistance•Functional oncogenic 3′ UTR mutations correlate with poor patient prognosis Using dual massively parallel reporter assays and CRISPR base editing, Schuster et al. demonstrate that 3′ untranslated region mutations found in advanced prostate cancer tumors significantly affect mRNA translation, mRNA stability, and cellular cancer phenotypes, uncovering alternative pathways of oncogenic dysregulation in 3′ UTR-mediated post-transcriptional gene expression.