Paris forrestii is a unique plant found in Tibet and Yunnan, China, and total saponins from Paris forrestii (PCT3) contain anticancer steroid glycosides. RNA expression plays an important role in various biological processes. However, the cytotoxicity effects and mechanisms of PCT3 in relation to prostate cancer (PCa) cells have not yet been reported. In the present study, the antitumor activity of PCT3 on PCa cells was evaluated. PCT3 displayed potent anticancer effects toward PCa cells that were similar to the effects of pure saponins from P. forrestii, but PCT3 had less activity in suppressing the prostate epithelial cell line RWPE. Furthermore, using CCK-8 assays, Edu incorporation, colony formation assays, Annexin V/PI assays and western blotting, we found that treatment with 4 μg/mL PCT3 significantly decreased proliferation and induced apoptosis in PCa cells. Using wound healing and transwell assays, we demonstrated that treatment with 2 μg/mL PCT3 significantly suppressed the migration and invasion of PCa cells. To explore the molecular mechanisms behind the anticancer effect of PCT3, PCT3 (5 μg/mL) treated and untreated PCa cells (LNCAP and PC3 cell lines) were analyzed using transcriptomics. Taking the commonly differentially expressed genes (log2FC > 0.585) in both cell lines, 41 mRNAs and 5 lncRNAs were eventually identified. Bioinformatics analysis (GO and KEGG analyses) revealed that some genes involved in classical cell proliferation and apoptosis pathways were aberrantly expressed after PCT3 treatment of PCa cells. By using q-PCR, the expression levels of NEAT1, MALAT1, TIPIN, LYAR, IQGAP3, GINS2, and ZGRF1 were validated as consistent with microarray data, suggesting that these genes might participate in the PCT3 anticancer effect. The present study suggests that PCT3 exhibits an anticancer effect on PCa and reveals some crucial lncRNAs and mRNAs that are involved in the anticancer mechanisms of PCT3 on Pca.Copyright © 2019 The Authors. Published by Elsevier Masson SAS.. All rights reserved.