Nonsense-mediated RNA decay is a unique vulnerability of cancer cells harboring sf3b1 or u2af1 mutations

Abigael Cheruiyot, Shan Li, Sridhar Nonavinkere Srivatsan, Tanzir Ahmed, Yuhao Chen, Delphine S. Lemacon, Ying Li, Zheng Yang, Brian A. Wadugu, Wayne A. Warner, Shondra M. Pruett-Miller, Esther A. Obeng, Daniel C. Link, Dalin He, Fei Xiao, Xiaowei Wang, Julie M. Bailis, Matthew J. Walter, Zhongsheng You

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

Nonsense-mediated RNA decay (NMD) is recognized as an RNA surveillance pathway that targets aberrant mRNAs with premature translation termination codons (PTC) for degradation, however, its molecular mechanisms and roles in health and disease remain incompletely understood. In this study, we developed a novel reporter system to accurately measure NMD activity in individual cells. A genome-wide CRISPR-Cas9 knockout screen using this reporter system identified novel NMDpromoting factors, including multiple components of the SF3B complex and other U2 spliceosome factors. Interestingly, cells with mutations in the spliceosome genes SF3B1 and U2AF1, which are commonly found in myelodysplastic syndrome (MDS) and cancers, have overall attenuated NMD activity. Compared with wild-type (WT) cells, SF3B1- A nd U2AF1-mutant cells were more sensitive to NMD inhibition, a phenotype that is accompanied by elevated DNA replication obstruction, DNA damage, and chromosomal instability. Remarkably, the sensitivity of spliceosome mutant cells to NMD inhibition was rescued by overexpression of RNase H1, which removes R-loops in the genome. Together, these findings shed new light on the functional interplay between NMD and RNA splicing and suggest a novel synthetic lethal strategy for the treatment of MDS and cancers with spliceosome mutations.

Original languageEnglish
Pages (from-to)4499-4513
Number of pages15
JournalCancer research
Volume81
Issue number17
DOIs
StatePublished - Sep 1 2021

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