Base-excision repair pathway regulates transcription-replication conflicts in pancreatic ductal adenocarcinoma
Fan Meng,
Tiane Li,
Anup K. Singh,
Yingying Wang,
Marc Attiyeh,
Fatemeh Kohram,
Qianhua Feng,
Yun R. Li,
Binghui Shen,
Terence Williams,
Yilun Liu,
Mustafa Raoof
Affiliations
Fan Meng
Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA
Tiane Li
Irell & Manella Graduate School of Biological Sciences, City of Hope National Medical Center, Duarte, CA, USA; Department of Cancer Genetic & Epigenetics, City of Hope National Medical Center, Duarte, CA, USA
Anup K. Singh
Pfizer Oncology, La Jolla, CA, USA
Yingying Wang
Department of Cancer Genetic & Epigenetics, City of Hope National Medical Center, Duarte, CA, USA
Marc Attiyeh
Department of Surgery, Cedars Sinai, Los Angeles, CA, USA
Fatemeh Kohram
Department of Child Health, University of Arizona College of Medicine, Phoenix, AZ, USA
Qianhua Feng
Department of Radiation Oncology, City of Hope National Medical Center, Duarte, CA, USA
Yun R. Li
Department of Radiation Oncology, City of Hope National Medical Center, Duarte, CA, USA
Binghui Shen
Department of Cancer Genetic & Epigenetics, City of Hope National Medical Center, Duarte, CA, USA
Terence Williams
Department of Radiation Oncology, City of Hope National Medical Center, Duarte, CA, USA
Yilun Liu
Department of Cancer Genetic & Epigenetics, City of Hope National Medical Center, Duarte, CA, USA
Mustafa Raoof
Department of Surgery, City of Hope National Medical Center, Duarte, CA, USA; Department of Cancer Genetic & Epigenetics, City of Hope National Medical Center, Duarte, CA, USA; Corresponding author
Summary: 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.
