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Cleavage and polyadenylation machinery as a novel targetable vulnerability for human cancer

Abstract

The role of alternative polyadenylation of mRNA in sustaining aggressive features of tumors is quite well established, as it is responsible for the 3’UTR shortening of oncogenes and subsequent relief from miRNA-mediated repression observed in cancer cells. However, the information regarding the vulnerability of cancer cells to the inhibition of cleavage and polyadenylation (CPA) machinery is very scattered. Only few recent reports show the antitumor activity of pharmacological inhibitors of CPSF3, one among CPA factors. More in general, the fact that deregulated CPA can be seen as a new hallmark of cancer and as a potential reservoir of novel therapeutic targets has never been formalized. Here, to extend our view on the potential of CPA inhibition (CPAi) approaches as anticancer therapies, we systematically tested the fitness of about one thousand cell lines of different cancer types upon depletion of all known CPA factors by interrogating genome-scale CRISPR and RNAi dependency maps of the DepMap project. Our analysis confirmed core and accessory CPA factors as novel vulnerabilities for human cancer, thus highlighting the potential of CPAi as anticancer therapy. Among all, CPSF1 appeared as a promising actionable candidate for drug development, as it showed low dependency scores pancancer and particularly in highly proliferating cells. In a personalized medicine perspective, the observed differential vulnerability of cancer cell lines to selected CPA factors may be used to build up signatures to predict response of individual human tumors to CPAi approaches.

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Fig. 1: Analysis of cancer cell line dependencies on core CPA factors.
Fig. 2: Analysis of cancer cell line dependencies on accessory CPA factors promoting proximal or distal PASs.

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Funding

Funding

The research leading to these results has received funding from AIRC under IG 2020 - ID. 24325 – P.I. Gandellini Paolo.

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Giulia Pagani: Investigation, Formal analysis, Visualization, Writing - Original Draft; Paolo Gandellini: Conceptualization, Writing - Review & Editing, Supervision, Project administration, Funding acquisition.

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Correspondence to Paolo Gandellini.

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Pagani, G., Gandellini, P. Cleavage and polyadenylation machinery as a novel targetable vulnerability for human cancer. Cancer Gene Ther (2024). https://doi.org/10.1038/s41417-024-00770-y

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