Loss of HMCES is synthetic lethal with APOBEC activity in cancer cells

Abstract

Analysis of cancer mutagenic signatures provides information about the origin of mutations and can inform the use of clinical therapies, including immunotherapy. In particular, APOBEC3A (A3A) has emerged as a major driver of mutagenesis in cancer cells and its expression results in DNA damage and susceptibility to treatment with inhibitors of the ATR and CHK1 checkpoint kinases. Here we report the implementation of CRISPR/Cas9 genetic screening to identify susceptibilities of multiple A3A-expressing lung adenocarcinoma cell lines. We identify HMCES, a protein recently linked to the protection of abasic sites, as a central protein for the tolerance of A3A expression. HMCES depletion results in synthetic lethality with A3A expression specifically in a TP53-mutant background. Analysis of previous screening data reveals a strong association between A3A mutational signatures and sensitivity to HMCES loss and indicates that HMCES is specialized in protecting against a narrow spectrum of DNA damaging agents in addition to A3A. We experimentally show that both HMCES disruption and A3A expression increase susceptibility of cancer cells to ionizing radiation, oxidative stress and ATR inhibition; strategies that are often applied in tumor therapies. Overall, our results suggest that HMCES is an attractive target for selective treatment of A3A expressing tumors.

Mutational signatures are markers of drug sensitivity of cancer cells

“…The ATR inhibitors VE-822, AZD6738 and QL-VIII-58 were associated with SBS-APOBEC in lymphoma and in MSI colon cancer (at FDR<17%) with an additional suggestive result in head-and-neck cancer (p=0.004; Figure 5E). We suggest that, despite APOBEC activity in cell lines being intermittent 22 , the historical record of APOBEC activity captured in the mutational signatures is sufficiently predictive of vulnerabilities associated with APOBEC such as ATR inhibition, oras we have recently shown experimentally and with a mutational signature analysisloss of the abasic site sensor HMCES 67 .…”