Inhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills tumours by inducing readthrough transcription [RNA-seq]

Transcription inhibition has become an attractive strategy for anticancer therapy because many cancers arise from dysregulated transcription programs. Topoisomerase 1 (TOP1) and bromodomain containing protein 4 (BRD4) coordinate each other to regulate transcriptional elongation. Using a collection of patient-derived xenograft mouse models of pancreatic cancer we show that the combined inhibition of TOP1 and BRD4 is synergistic in arresting tumor growth. We link this effect to the ability of TOP1 and BRD4 to control pause-release, a rate-limiting step in early elongation. By comparing nascent transcripts with the recruitment of elongation and termination factors along genes, we found that combined inhibition of TOP1 and BRD4, while globally impairing RNA production, also disturbs the recruitment of proteins involved in termination. Thus, RNA polymerases stay engaged with the DNA downstream of polyadenylation sites for hundreds of kilobases leading to readthrough-transcription. Because this pervasive transcription occurs also during replication, it perturbs replisome progression leading to increased DNA damage and cell cycle arrest. The synergistic effect of TOP1 and BRD4 inhibition is specific for the tumor cells as negligible transcriptional defects are observed in non-tumor cells. This work provides a mechanistic understanding of the benefit of combining TOP1 and BRD4 inhibitors in the treatment of highly transcription- and replication-driven tumors. Overall design: RNA-seq of extracts from patient-derived xenografts of pancreactic tumors (B099, neuroendochrine tumor(panNEC); Bo103, pancreatic ductal adenocarcinoma(PDAC)). Mice with one tumor implanted on either side were either treated for 5 days with the indicated drug combinations (or DMSO for control) or subjected to zero, one or two cycles (C1, C2, C3) of Irinotecan + JQ1 treatment and tumor recovery before harvest at set time points after the last treatment.