Abstract Peritonitis carcinomatosa (PC) is one of the most devastating states of digestive tract cancers and occurs at a substantial frequency even after curative removal of the primary lesions followed by adjuvant chemotherapy. Tumor cells involved in PC after the adjuvant therapy are considered to have the ability to survive in the presence of anticancer drugs. To clarify the mechanism(s) of cancer relapse after adjuvant chemotherapy, we studied drug-tolerant colonies (DTCs), which are subpopulations of cancer cells that survive in the presence of anticancer drugs. In a dose-dependent fashion, DTC formation was observed in the presence of various drugs, including cisplatin, docetaxel, gefitinib, and sorafenib, in five cell lines: HCT116, HeLa, HT29, MKN45, and MCF7. To characterize DTCs at the protein level, we collected more than 2000 DTCs and drug-free colonies for analysis by means of reverse-phase protein arrays (RPPAs). Profiling of 44 proteins by quantitative RPPA analysis identified two major clusters that were defined by the expression of stem-like (e.g., CD44, Oct-4, and c-Myc) or epithelial proteins (E-cadherin and keratins). However, no distinct DTC subpopulations with defined proteins were found associated with drug type, drug concentration, or cell type. In contrast, the transcriptional product level of some cellular reprograming genes, such as Nanog, seemed to be up-regulated in DTCs. Subsequent functional-level screening of inhibitors for colony suppression indicated that the up-regulation of mRNA synthesis played an important role in emergence of DTCs. In fact, we identified an RNA polymerase inhibitor that effectively inhibits the emergence of DTCs. Intriguingly, DTC inhibition is partially attributed to a gene that encodes for an RNA-binding protein (RBP) that forms a transcriptional complex along with the RNA polymerase. The RNA polymerase inhibitor reduced the gene expression level of the RBP gene. Moreover, knockdown of the RBP gene also reduced the degree of DTC formation comparable to the RNA polymerase inhibitor, suggesting that one of the targets of the RNA polymerase inhibitor is the RBP gene. To validate efficacy of the RNA polymerase inhibitor in terms of DTC suppression in vivo, we established a mouse PC model using the MKN45 gastric cancer cell line. The mouse PC model forms nodules in the mesentery or peritoneum a few weeks after inoculation. Concurrent peritoneal injection of the RNA polymerase inhibitor and cisplatin significantly suppressed the number of nodules. Moreover, overall survival of the mouse PC model was extended in the group treated with the RNA polymerase inhibitor and cisplatin. These results suggest that cancer relapse may occur from rather non-distinct subpopulations that could be suppressed by the RNA polymerase inhibitor via disruption of the transcriptional machinery. Citation Format: Satoshi S. Nishizuka, Kohei Kume, Kei Sato, Takeshi Iwaya, Go Wakabayashi. Prevention of peritonitis carcinomatosa after adjuvant chemotherapy by the inhibition of RNA polymerase in drug-tolerant subpopulations. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5460. doi:10.1158/1538-7445.AM2015-5460