Abstract A163: Exoribonuclease XRN1 is a therapeutic vulnerability in tumors with intrinsically elevated type I interferon signaling
Authors: Lynes Maureen M , Shen Sophie A , Nayak Sunaina P , Sparling Brian A , Ribich Scott , Blakemore Stephen J , Silver Serena J 
Published: December 2023

Background: 5′→3′ exoribonuclease 1 (XRN1) degrades single stranded mRNA from the 5′→3′ direction and plays a key role in endogenous cellular mRNA turnover. In addition, XRN1 can degrade double-stranded RNA (dsRNA), and as such plays a role in innate immunity by prevention of dsRNA accumulation and pPKR induction in virus-infected cells.  We identified XRN1 as a putative selective vulnerability in tumor cells with intrinsic elevation of a Type I Interferon Stimulated Gene (TISG) signature through analysis of publicly available CRISPR screen data across 483 tumor cell lines.  We further explored the role of XRN1 in a set of lung cancer cell lines with differential TISG expression in order to validate XRN1 as a compelling target for oncology drug development.

Materials and Methods: NCI-H1650, NCI-H1703, NCI-H1944, and NCI-H838 lung adenocarcinoma cell lines were infected with lentiviruses containing Cas9 and sgRNAs targeting XRN1.  Non-targeting sgRNAs were used as negative controls.  XRN1 knockout (KO) cells and controls were evaluated in proliferation, apoptosis, qPCR and western blot assays.

Results: Consistent with a selective dependency on XRN1 in cells with high intrinsic interferon signaling, XRN1 KO via CRISPR leads to robust anti-proliferative effects in TISG high NCI-H1650 and NCI-H1703 cells, but not in TISG low NCI-H838 and NCI-H1944 cells.  Annexin V staining of NCI-H1650 cells upon XRN1 KO demonstrates that apoptosis is induced in TISG high cells.  XRN1 KO in the TISG high setting leads to robust upregulation of Interferon-β mRNA consistent with activation of the MDA5 pathway by elevation of cytoplasmic dsRNA.   Similarly, XRN1 loss induces pPKR activation in TISG high, but not TISG low cells.  As pPKR activation triggers translational shutdown, TISG high selective pPKR elevation is consistent with the cell death observed.  Exogenous treatment with Interferon-β or dsRNA mimetic Poly I:C to induce elevated Type I Interferon expression sensitizes NCI-H838 cells to XRN1 KO, with effects on cell proliferation.  

Conclusions: Taken together, these results demonstrate a critical role of XRN1 in cancer cells with intrinsically elevated Type I Interferon signaling. Cell death is triggered via accumulation of dsRNA and downstream activation of the MDA5 and PKR innate immune pathways.  These data suggest that XRN1, through its regulation of dsRNA burden, is a compelling oncology target for TISG high tumors.

Conflict of Interests: All authors are current or former employees and shareholders of Accent Therapeutics, Inc.

Citation Format: Maureen M Lynes, Sophie A Shen, Sunaina P Nayak, Brian A Sparling, Scott Ribich, Stephen J Blakemore, Serena J Silver. Exoribonuclease XRN1 is a therapeutic vulnerability in tumors with intrinsically elevated type I interferon signaling [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A163.