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

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Sergi Guerrero Llobet, Arkajyoti Bhattacharya, Marieke Everts, Klaas Kok, Bert van der Vegt, Rudolf S. N. Fehrmann & Marcel A. T. M. van Vugt


Oncogene-induced replication stress characterizes many aggressive cancers. Several treatments are being developed that target replication stress, however, identification of tumors with high levels of replication stress remains challenging. We describe a gene expression signature of oncogene-induced replication stress. A panel of triple-negative breast cancer (TNBC) and non-transformed cell lines were engineered to overexpress CDC25ACCNE1 or MYC, which resulted in slower replication kinetics. RNA sequencing analysis revealed a set of 52 commonly upregulated genes. In parallel, mRNA expression analysis of patient-derived tumor samples (TCGA, n = 10,592) also revealed differential gene expression in tumors with amplification of oncogenes that trigger replication stress (CDC25ACCNE1MYCCCND1MYBMOSKRASERBB2, and E2F1). Upon integration, we identified a six-gene signature of oncogene-induced replication stress (NAT10DDX27ZNF48C8ORF33MOCS3, and MPP6). Immunohistochemical analysis of NAT10 in breast cancer samples (n = 330) showed strong correlation with expression of phospho-RPA (R = 0.451, p = 1.82 × 10−20) and γH2AX (R = 0.304, p = 2.95 × 10−9). Finally, we applied our oncogene-induced replication stress signature to patient samples from TCGA (n = 8,862) and GEO (n = 13,912) to define the levels of replication stress across 27 tumor subtypes, identifying diffuse large B cell lymphoma, ovarian cancer, TNBC and colorectal carcinoma as cancer subtypes with high levels of oncogene-induced replication stress.