Identification of key transcriptomic and epigenomic factors influencing conventional and metronomic dosing in aggressive and non-aggressive prostate cancer

Repetitive, low-dose drug administration (metronomic; METRO) shows ability to overcome drug resistance and increased drug efficacy in many cancers, but the mechanisms are not understood fully. Previously we showed topotecan (TOPO) METRO dosing was more effective than conventional (CONV) dosing in aggressive prostate cancer cell lines and xenograft mouse models. To explore possible mechanisms by which METRO dosing alters tumor growth and metastases, we performed targeted mRNA and miRNA expression studies and identified potential candidate cancer pathway genes and miRNA-mRNA pairs as unique treatment-related biomarkers for alternative TOPO-METRO therapy. To determine drug response, Androgen-independent human prostate cancer cells (PC3), androgen-dependent (LNCaP) cell lines were treated with TOPO following CONV and METRO dosing schedules. Cancer pathway gene and micro-RNA expression profiles were assessed at the calculated IC50 of TOPO after each treatment. Expression signatures were identified using differential expression (DE) analysis software and a Spearman’s rank-based correlation was used to assess the association of drug response, mRNA and miRNA expression. Gene signatures associated with TOPO-METRO therapy were validated against patient profiles in The Cancer Genome Atlas (TCGA) and Genomic Data Commons (GDC) and protein expression of most significant genes by immunoblotting. We identified disparate treatment-related mRNA and miRNA expression signatures for TOPO-METRO vs CONV treatment. We also identified a gene signature (top five gene: SERPINB5, CDKN1A, TNF, FOS, & ANGPT1) for both PC-3 and LNCaP following TOPO-METRO dosing. Ingenuity Pathway Analysis identified that upregulation of tumor suppressor, anti-proliferative genes (eg, SERPINB5), genes involved in activation of the immune system (RPL13A) and down regulation of genes involved in apoptosis, invasion, metastasis, and inflammation (TNF, FOS, and MMP1) are likely vital to the observed treatment response. Epigenetic analysis showed distinct miRNA expression changes may influence differential gene expression (miRNA-mRNA pairs) for TOPO-METRO dosing. 20 miRNAs genes (including miR-30c, miR-19a, mir-20a, mir-17, let7i & let7b) were associated with TOPO cytotoxicity (p Citation Format: Taraswi Mitra Ghosh, Joshua Davis, Grafton S. Barnett, Elena Skarupa, Jeff D. Warner, Brian S. Cummings, Robert D. Arnold. Identification of key transcriptomic and epigenomic factors influencing conventional and metronomic dosing in aggressive and non-aggressive prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2944.