Human aneuploid cells depend on the RAF/MEK/ERK pathway for overcoming increased DNA damage

Aneuploidy is a hallmark of human cancer, yet the molecular mechanisms to cope with aneuploidy-induced cellular stresses remain largely unknown. Here, we induced chromosome mis-segregation in non-transformed RPE1-hTERT cells and derived multiple stable clones with various degrees of aneuploidy. We performed a systematic genomic, transcriptomic and proteomic profiling of 6 isogenic clones, using whole-exome DNA, mRNA and miRNA sequencing, as well as proteomics. Concomitantly, we functionally interrogated their cellular vulnerabilities, using genome-wide CRISPR/Cas9 and large-scale drug screens. Aneuploid clones activated the DNA damage response and arewere more resistant to further DNA damage induction. Aneuploid cells also exhibitexhibited elevated RAF/MEK/ERK pathway activity and arewere more sensitive to clinically-relevant drugs targeting this pathway, and in particular to CRAF inhibition. Importantly, CRAF and MEK inhibition sensitized aneuploid cells to DNA damage-inducing chemotherapies and to PARP inhibitors. We validate theseThese results arewere validated in human cancer cell lines. Moreover, resistance of breast cancer patients to olaparib iswas associated with high levels of RAF/MEK/ERK signaling, specifically in highly-aneuploid tumors. Overall, our study provides a comprehensive resource for genetically-matched karyotypically-stable cells of various aneuploidy states, revealing a novel therapeutically-relevant cellular dependency of aneuploid cells.