ATR Safeguards Epithelial-to-Mesenchymal Transition by Countering R-loops and Enabling Transcription Reprogramming

The epithelial-to-mesenchymal transition (EMT) of cancer cells contributes to tumor plasticity, metastasis, and therapeutic resistance. Here, we show that the transcription reprogramming during EMT induces genomic instability by increasing R-loops and transcription-replication conflicts. The ATR kinase counters R-loops and genomic instability during EMT, and EMT cannot occur without ATR. Notably, ATR inhibition results in R-loop-associated DNA damage at the SNAI1 gene, a key EMT driver, leading to ATM- and Polycomb-mediated local transcription repression. Beyond SNAI1, ATR also prevents R-loops and transcription repression at a group of EMT genes. Importantly, inhibition of ATR in tumors undergoing EMT reduces tumor growth and metastasis, suggesting that ATR inhibition impedes tumor progression by targeting cancer cells in transition. Thus, ATR promotes EMT not only by protecting genome integrity but also by enabling transcription reprogramming, suggesting that ATR is a safeguard of cell state transitions and a potential target to eliminate cancer cells in transition.