Defective transcription in UPF1-deficient cells safeguards against replication stress induced transcription-replication collisions, driving drug resistance

Accurate DNA replication is essential for the faithful transmission of genetic information to daughter cells. Disruption of this process leads to replication stress, which can trigger mutagenesis, double-stranded DNA breaks, and genomic instability. Transcription is a well-established source of replication stress, contributing through altered chromatin dynamics, DNA structural changes, and direct transcription–replication collisions (TRCs).

Here, we uncover a novel role for the RNA/DNA helicase UPF1 in maintaining replication fidelity and responding to replication stress. We show that cancer cells deficient in UPF1 exhibit elevated levels of spontaneous, transcription-dependent replication fork stalling and double-stranded breaks, along with heightened sensitivity to Rad51 and PARP1 inhibitors. Paradoxically, these cells also display resistance to exogenous replication stress, with reduced replication fork stalling, diminished mitotic delays, and decreased activation of mitotic DNA synthesis (MiDAS), a key salvage pathway under stress conditions.

Low UPF1 expression has been previously linked to drug resistance in renal carcinoma and correlates with poor prognosis across multiple cancer types. Our findings position UPF1 as a critical guardian against transcription-associated replication stress and suggest that UPF1 deficiency may underlie mechanisms of cancer therapy resistance whilst leaving cells vulnerable to the depletion of key DNA repair pathways. Targeting this vulnerability could offer a promising avenue for therapeutic intervention in UPF1-low tumours.