Base-excision repair pathway regulates transcription-replication conflicts in pancreatic ductal adenocarcinoma

• Published in: Cell reports (Cambridge) Vol. 43; no. 10; p. 114820
• Main Authors: Meng, Fan, Li, Tiane, Singh, Anup K., Wang, Yingying, Attiyeh, Marc, Kohram, Fatemeh, Feng, Qianhua, Li, Yun R., Shen, Binghui, Williams, Terence, Liu, Yilun, Raoof, Mustafa
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 04.10.2024; Elsevier
• Subjects: ATR pathway; base excision repair; CP: Cancer; CP: Molecular biology; DNA repair; oncogene-induced replication stress; pancreatic cancer; R-loops; replication stress; transcription replication conflict; oncogene-induced replication stress; pancreatic cancer; replication stress; ATR pathway; CP: Cancer; base excision repair; CP: Molecular biology; transcription replication conflict; R-loops; DNA repair
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2024.114820

Oncogenic mutations (such as in KRAS) can dysregulate transcription and replication, leading to transcription-replication conflicts (TRCs). Here, we demonstrate that TRCs are enriched in human pancreatic ductal adenocarcinoma (PDAC) compared to other common solid tumors or normal cells. Several orthogonal approaches demonstrated that TRCs are oncogene dependent. A small interfering RNA (siRNA) screen identified several factors in the base-excision repair (BER) pathway as main regulators of TRCs in PDAC cells. Inhibitors of BER pathway (methoxyamine and CRT) enhanced TRCs. Mechanistically, BER pathway inhibition severely altered RNA polymerase II (RNAPII) and R-loop dynamics at nascent DNA, causing RNAPII trapping and contributing to enhanced TRCs. The ensuing DNA damage activated the ATR-Chk1 pathway. Co-treatment with ATR inhibitor (VX970) and BER inhibitor (methoxyamine) at clinically relevant doses synergistically enhanced DNA damage and reduced cell proliferation in PDAC cells. The study provides mechanistic insights into the regulation of TRCs in PDAC by the BER pathway, which has biologic and therapeutic implications. [Display omitted] •Human PDAC demonstrates high levels of TRCs driven by oncogenic KRAS•Base-excision repair (BER) pathway regulates TRCs in PDAC cells•BER inhibition causes DNA damage by impacting RNAPII and R-loop dynamics at TRCs•BER and ATR inhibition cause synergistic toxicity in PDAC cells Meng et al. characterize transcription-replication conflicts (TRCs) as a key adaptive dependency of oncogenic KRAS in human PDAC. Their work uncovers the base-excision repair (BER) pathway as a key regulator of TRCs. Inhibition of the BER pathway altered transcription dynamics and activated ATR checkpoint. Co-inhibition of the BER and ATR pathway produced lethal DNA damage.