Metabolic dependency mapping identifies Peroxiredoxin 1 as a driver of resistance to ATM inhibition

Metabolic pathways fuel tumor progression and resistance to stress conditions including chemotherapeutic drugs, such as DNA damage response (DDR) inhibitors. Yet, significant gaps persist in how metabolic pathways confer resistance to DDR inhibition in cancer cells. Here, we employed a metabolism-focused CRISPR knockout screen and identified genetic vulnerabilities to DDR inhibitors. We unveiled Peroxiredoxin 1 (PRDX1) as a synthetic lethality partner with Ataxia Telangiectasia Mutated (ATM) kinase. Tumor cells depleted of PRDX1 displayed heightened sensitivity to ATM inhibition in vitro and in mice in a manner dependent on p53 status. Mechanistically, we discovered that the ribosomal protein RPL32 undergoes redox modification on active cysteine residues 91 and 96 upon ATM inhibition, promoting p53 stability and altered cell fitness. Our findings reveal a new pathway whereby RPL32 senses stress and induces p53 activation impairing tumor cell survival. Overall design: To investigate the effect of ATM kinase inhibition on PRDX1 deficient cells, we established A549 cell line in which PRDX1 gene has been knocked out by CRISPR/Cas9 and NCIH1299 cell line in which PRDX1 gene has been knocked down by shRNA. We then performed gene expression profiling analysis using data from RNA-seq of the established cell lines (A549_sgControl, A549_sgPRDX1, NCIH1299_shCT and NCIH1299_shPRDX1) with/without ATM inhibition treatment. Comparative gene expression profiling analysis was done by comparing the RNA-seq data from those four cell lines with/without ATM inhibition treatment.