XRN2 Depletion is Synthetic Lethal with PARP1 Inhibition

Abstract

Persistent R‐loops (RNA‐DNA hybrids with a displaced single‐stranded DNA) create DNA damage and lead to genomic instability. The 5’‐3’‐exoribonuclease 2 (XRN2) degrades RNA to resolve R‐loops and promotes transcription termination. Previously, XRN2 was implicated in DNA double strand break (DSB) repair and in resolving replication stress. XRN2 function in DSB repair is not fully understood. We hypothesize that XRN2 plays a critical role in multiple DNA repair pathways. Here, using tandem affinity purification‐mass spectrometry, bioinformatics, and biochemical approaches, we found that XRN2 associates with proteins involved in DNA repair/replication (Ku70‐Ku80, DNA‐PKcs, PARP1, MCM2‐7, PCNA, RPA1), and RNA metabolism (RNA helicases, PRP19, p54(nrb), splicing factors). Novel major pathways linked to XRN2 include cell cycle control of chromosomal replication and DSB repair by non‐homologous end joining. Investigating the biological implications of these interactions led us to discover that XRN2 depletion compromised cell survival after additional knockdown of specific DNA repair proteins, including PARP1. XRN2‐deficient cells also showed enhanced PARP1 activity. Consistent with concurrent depletion of XRN2 and PARP1 promoting cell death, XRN2‐deficient fibroblast and lung cancer cells also demonstrated sensitivity to PARP1 inhibition. The XRN2 alterations (mutations, copy number/expression changes) are frequent in cancers. Thus, PARP1 inhibition could target cancers exhibiting XRN2 functional loss. Collectively, our data suggest XRN2's association with novel protein partners and unravel synthetic lethality between XRN2 loss and PARP1 inhibition.Support or Funding InformationThis work was largely supported by the National Institutes of Health/National Cancer Institute (NCI/NIH) [R01 CA139217] to D.A.B, a minority supplement [R01 CA139217‐05S1] and the Cancer Biology Training Grant T32CA124334‐06 to E.A.M. (PI: Dr. Jerry Shay), Simmons Comprehensive Cancer Center, UT Southwestern. This work was also supported by grant 5P30CA142543, NCI/NIH to the UT Southwestern Proteomics Core. The UT Southwestern Proteomics Core was also supported, in part, by a grant from the Cancer Prevention and Research Institute of Texas [CPRIT, RP1206130] to Dr. Hamid Mirzaei. Funding for open access charges was from NCI/NIH CA139217 to D.A.B. Research reported in this study was also supported by the UT Southwestern CCSG grant 5P30CA142543 from the NCI/NIH.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.