An mRNA expression-based signature for oncogene-induced replication-stress

Background Oncogene-induced replication stress characterizes many aggressive cancers, including triple-negative breast cancer (TNBC). Several drugs are being developed that target replication stress, although it is unclear how tumors with high levels of replication stress can be identified. We aimed to develop a gene expression signature of oncogene-induced replication stress. Methods TNBC and non-transformed RPE1- TP53 wt and RPE1- TP53 mut cell lines were engineered to overexpress the oncogenes CDC25A , CCNE1 or MYC . DNA fiber analysis was used to measure replication kinetics. Analysis of RNA sequencing data of cell lines and patient-derived tumor samples (TCGA n=10,592) was used to identify differential gene expression. Immunohistochemical validation was conducted on breast cancer samples (n=330). Results RNA sequencing revealed 52 commonly upregulated genes after induction of CDC25A , CCNE1 or MYC in our cell line panel. Integration with gene expression data of TGCA samples with amplification of replication stress-inducing oncogenes ( CDC25A , CCNE1 , MYC , CCND1 , MYB , MOS , KRAS , ERBB2 , and E2F1 ), yielded a six-gene signature of oncogene-induced replication stress ( NAT10 , DDX27 , ZNF48 , C8ORF33 , MOCS3, and MPP6) . Expression of NAT10 in breast cancer samples was correlated with phospho-RPA (R=0.451, p=1.82×10−20) and γH2AX (R=0.304, p=2.95×10−9). Applying the oncogene-induced replication stress signature to patient samples (TCGA n=8,862 and GEO n=13,912) defined the replication stress landscape across 27 tumor subtypes, and identified diffuse large B cell lymphoma, ovarian cancer, TNBC and colorectal carcinoma as cancer subtypes with high levels of oncogene-induced replication stress. Conclusion We developed a gene expression signature of oncogene-induced replication stress, which may facilitate patient selection for agents that target replication stress. ### Competing Interest Statement M.A.T.M.v.V. has acted on the Scientific Advisory Board of Repare Therapeutics, which is unrelated to this work. The other authors declare no conflict of interest.