Gene expression profiling of drug-persistent breast and prostate cancer cells derived from treatment of organoids or PDX with cytotoxic agents

Cancer treatments often fail to achieve complete and sustained responses due to persistent residual tumor foci with acquired drug refractoriness, the “seed” for eventual relapse. The biological underpinning of this in situ resistance is not clear, while faithful in vitro models of this cancer cell state are lacking. We observed that the in vitro cytotoxic treatment of breast and prostate cancer patient-derived cells and cell lines cultured as 3D organoids generates persistent tumor cell subpopulations that phenotypically and molecularly simulate the in vivo emergence of drug-refractory residual tumors in preclinical and clinical settings. Here we provide RNAseq gene expression profiling data from drug-persistent cancer cells generated after longitudinal treatment of cancer organoids or PDX/xenograft tumors with chemotherapeutic (docetaxel, vinblastine) or targeted (afatinib) agents. These data can be used to identify genes and pathways which are upregulated in residual drug-persistent tumors. RNA profiles of drug-persistent cancer cells in 3D organoid cultures or in vivo tumors treated with chemotherapeutics and/or targeted agents