Abstract 2644: Therapeutic inhibition of RNA polymerase I reveals vulnerability of mismatch repair defective cancers
Authors: Fan Wenjun , Liu Hester , Begum Asma , Pitts Stephanie , Ford Brittany , Dorado Tony , de Leon Pablo , NV Rajeshkumar , Barrow James C. , Laiho Marikki 
Published: June 2022

RNA polymerase I inhibitors represent a new class of cancer therapeutics with potential application in many cancer types. By curbing the transcription of ribosomal RNAs they block the rate-limiting step in ribosome biogenesis and protein synthesis. We have recently identified specific and selective first-in-class inhibitors of Pol I. This class of Pol I inhibitors, represented by small-molecule BMH-21, blocks transcription initiation and elongation and causes the destruction of the enzyme catalytic subunit. BMH-21 activity is genetically dependent on Pol I in cancer cells and in yeast confirming the targeting specificity. Our earlier mechanistic and efficacy studies with BMH-21 have demonstrated the utility of the approach in targeting colon and prostate cancers and melanoma. The goal of this study was to pinpoint cancer types with specific sensitivity to these inhibitors and to identify markers of this sensitivity. To do so, we undertook unbiased large-scale cancer cell line screens with our Pol I inhibitors and conducted correlative analyses using open source DepMap and Achilles databases to identify cancer types and features that sensitize cancer cells to these inhibitors. The most sensitive lineages were colorectal, endometrial, esophageal, leukemia, myeloma, and ovarian. Comparison of the cancer cell line responses to the Achilles gene essentiality database showed high correlation to genetic knock-out of three Pol I subunits. This unbiased finding strongly supports identification of Pol I as the target. Further, we identified two ribosomal proteins, RPL22 and RPL22L1 as the top genetic and expression markers denoting sensitivity, and MDM4, a p53 transcriptional repressor, as the top protein marker. Together, these three markers conform to a new p53 regulatory pathway. These findings were validated using genetic and mechanistic analyses. We show that Pol I inhibition alters the MDM4 splicing and decreases the expression of MDM4 isoform that represses p53, and that this activity is dependent on the RPL22/RPL22L1 proteins. Notably, perturbation of the biomarkers is strongly associated with mismatch repair defective (MMRd) cancers. We show the efficacy of the Pol I inhibitors in xenograft and patient-derived MMRd models. Our data suggest that RPL22mutation could serve as tumor-agnostic biomarker for targeting cancers with the Pol I inhibitors. Furthermore, this work identifies a new Pol I transcription-dependent ribosomal protein-governed pathway that converges on the regulation of p53.

Citation Format: Wenjun Fan, Hester Liu, Asma Begum, Stephanie Pitts, Brittany Ford, Tony Dorado, Pablo de Leon, Rajeshkumar NV, James C. Barrow, Marikki Laiho. Therapeutic inhibition of RNA polymerase I reveals vulnerability of mismatch repair defective cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2644.