Abstract 4253: Pan-cancer analysis of XPO1 R749Q mutations across 217,570 patients reveals association with high tumor mutational burden and therapy resistance

Abstract

Background: XPO1 is a nuclear export receptor responsible for exporting >200 proteins out of the nucleus, including many cancer-related proteins. We previously reported recurrent hotspot mutations occurring in XPO1 in cancer and identified XPO1 R749Q variant only in solid tumors. To determine the prevalence of XPO1 mutations across cancer types, we performed a large-scale genomic analysis of 217,570 patients with cancer to identify and characterize XPO1 variants from real-world patient tumors. Methods: Solid tumor samples representing 14 cancer types were submitted to Caris Life Sciences (Phoenix, AZ) for Next-generation sequencing of DNA (592 genes or WES). TMB-High (defined as >10 mt/MB) and dMMR/MSI-H was tested by IHC/NGS. We engineered CRISPR knock-in HCT116 and LS-174T colon cancer isogenic cell lines bearing XPO1 R749Q mutations and Stochastic Optical Reconstruction Microscopy (STORM) analysis was performed. Structural modeling was performed with published XPO1 structures by mapping XPO1 mutations from the MSKCC-IMPACT dataset. Results: A total of 96 patients with XPO1 R749Q mutations were identified (50% occurred in endometrial cancer and 23% occurred in colorectal cancer). TMB-H was observed in 92% of XPO1 R749Q mt tumors (9% were dMMR/MSI-H), while 86% of XPO1 R749Q mt tumors were POLE-mutated within the endonuclease domain. Median variant allele frequency for XPO1 R749Q mt and POLE mt were 25% and 29%, respectively. STORM imaging revealed that XPO1 R749Q mutant cells had significant localization of XPO1 in the cytoplasm compared to XPO1 WT cells, especially at the outside edge of the nuclear pores. Structural modeling predicted that XPO1 R749Q mt affected the regulatory H9-loop of XPO1 favoring increased shuttling and retention in the cytoplasm. Mass spectrometry analysis of nuclear and cytoplasmic fractionated proteomes confirmed that XPO1 R749Q mt cells had increased export of proteins compared to XPO1 WT cells. A library screen of >200 FDA-approved drugs revealed a strong therapeutic resistance of XPO1 R749Q cells, especially to chemotherapies used in the treatment of colon cancer. XPO1 inhibition with selinexor synergized with chemotherapy in XPO1 R749Q mt cells in vitro and overcame resistance to irinotecan in vivo in xenograft mice models. Conclusion: This study sheds novel insights into the role of nuclear export in cancers. Specifically, XPO1 R749Q mutations are enriched in TMB-H endometrial and colon cancers and increase nuclear export of key proteins that confer resistance to therapies using DNA-damaging agents. Our current work aims to identify novel therapies that can overcome resistance to DNA-damaging therapies seen in XPO1 mutant cells, such as immune checkpoint inhibitor (ICI) therapy given the co-occurrence with POLE mutations and recent reports of high level of response to ICI therapy in TMB-H and POLE mt colorectal cancers. Citation Format: Tulasigeri M. Totiger, Yasmine Baca, Wannasiri Chiraphapphaiboon, Sana Chaudhry, Skye Montoya, Monika Chojnacka, Gabriel Gaidosh, Jumana Afaghani, Maurizio Affer, Christopher D. Armstrong, Ryan Notti, Jenna Zabroski, Jacob Jahn, Vindhya Nawaratne, Ramiro Verdun, Hai Dang Nguyen, Chadi Nabhan, Thomas J. Herzog, Phil Walker, Andrew Elliott, Emil Lou, Wafik S. El-Deiry, Edith Mitchell, Jose Antonio Rodriguez, Justin Taylor. Pan-cancer analysis of XPO1 R749Q mutations across 217,570 patients reveals association with high tumor mutational burden and therapy resistance. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4253.