A pan-cancer transcriptome analysis identifies replication fork and innate immunity genes as modifiers of response to the CHK1 inhibitor prexasertib
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Wayne D. Blosser1, Jack A. Dempsey1, Ann M. McNulty1, Xi Rao1, Philip J. Ebert1, Caitlin D. Lowery1, Philip W. Iversen1, Yue Wang Webster1, Gregory P. Donoho1, Xueqian Gong1, Farhana F. Merzoug1, Sean Buchanan1, Karsten Boehnke2, Chunping Yu3, Xin Tian You3, Richard P. Beckmann1, Wenjuan Wu1, Samuel C. McNeely1, Aimee Bence Lin1 and Ricardo Martinez1
1 Eli Lilly and Company, Indianapolis, IN, USA
2 Eli Lilly and Company, New York, NY, USA
3 Eli Lilly and Company, Shanghai, China
Keywords: CHK1; prexasertib; replication stress; replication fork; innate immunity
Received: September 19, 2019 Accepted: December 02, 2019 Published: January 21, 2020
The combined influence of oncogenic drivers, genomic instability, and/or DNA damage repair deficiencies increases replication stress in cancer. Cells with high replication stress rely on the upregulation of checkpoints like those governed by CHK1 for survival. Previous studies of the CHK1 inhibitor prexasertib demonstrated activity across multiple cancer types. Therefore, we sought to (1) identify markers of prexasertib sensitivity and (2) define the molecular mechanism(s) of intrinsic and acquired resistance using preclinical models representing multiple tumor types. Our findings indicate that while cyclin E dysregulation is a driving mechanism of prexasertib response, biomarkers associated with this aberration lack sufficient predictive power to render them clinically actionable for patient selection. Transcriptome analysis of a pan-cancer cell line panel and in vivo models revealed an association between expression of E2F target genes and prexasertib sensitivity and identified innate immunity genes associated with prexasertib resistance. Functional RNAi studies supported a causal role of replication fork components as modulators of prexasertib response. Mechanisms that protect cells from oncogene-induced replication stress may safeguard tumors from such stress induced by a CHK1 inhibitor, resulting in acquired drug resistance. Furthermore, resistance to prexasertib may be shaped by innate immunity.
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