Abstract 1218: CDK9 inhibitors modulate the transcriptional landscape of colorectal cancer to suppress MAPK signaling and synergizes with BRAF inhibitors to treat BRAF-mutant colorectal cancer

Abstract Background: Colorectal cancer (CRC) is the second leading cause of cancer deaths in the US, and it remains a significant public health burden. Metastatic CRC (mCRC) is usually treated with combination chemotherapy and targeted therapy regimens, but eventually becomes chemotherapy refractory. Thus, novel and more effective treatments for mCRC are urgently needed. Cyclin-dependent kinase 9 (CDK9) is a key activator of RNA Pol II transcription and promotes the expression of many cancer driver genes, making CDK9 a promising target for cancer therapy. Methods: Human CRC cell lines, patient-derived organoids (PDOs), cell line xenografts, and patient-derived xenografts were used to investigate the efficacy and mechanisms of action of the CDK9 inhibitors AZD4573, enitociclib, and NVP-2, as well as the BRAF inhibitors encorafenib and dabrafenib. In vitro viability was measured by chemical cell proliferation assays and in vivo tumor sizes were measured by calipers. In vitro mechanisms of action were assessed by RNA sequencing, real time polymerase chain reaction, and Western blotting. In vivo mechanisms of action were assessed by immunohistochemistry. Results: CDK9 inhibitors potently inhibited CRC cells and PDOs. In contrast to hematologic malignancies, we did not observe consistent suppression of the oncogenes c-MYC and MCL-1 by CDK9 inhibitor treatment. Instead, CDK9 inhibitors suppressed several other key cancer pathways in CRC, such as MAPK, mTOR, and PI3K signaling pathways. Importantly, multiple targets within the MAPK pathway were strongly suppressed, including EGFR, KRAS, and BRAF. We hypothesized that combination treatment with CKD9 inhibitors and MAPK pathway inhibitors can synergistically treat CRC. As proof-of-concept, we investigated the combination of CDK9 and BRAF inhibitors in models of BRAF-mutant CRC, a particularly aggressive type of CRC. We found this combination to synergistically suppress CRC growth in vitro and in vivo. Compared to single agents, combination treatment led to significantly stronger induction of apoptosis and suppression of MAPK pathway signaling. Our results suggest that concurrent treatment with CDK9 inhibitors plus established MAPK pathway inhibitors, such as BRAF inhibitors, can significantly improve upon single agent treatment. Conclusions: We have found CDK9 inhibitors to potently suppress CRC growth and survival through a unique mechanism of action, by vertical suppression of the MAPK signaling pathway. We demonstrate that CDK9 inhibitors can synergize with BRAF inhibitors in the treatment of BRAF-mutant CRC models. Thus, CDK9 inhibitors are a promising class of drugs warranting further investigation, including early-phase clinical trials, in mCRC. Citation Format: Chaoyuan Kuang, Ning Wei, Mahshid Mohammadi, Muzaffer A. Bhat, Terence Li, Priyanka Patil, Othon Wiltz, Renee Huang, Kohtaro Ooka, Melanie Quintal, Edward Chu. CDK9 inhibitors modulate the transcriptional landscape of colorectal cancer to suppress MAPK signaling and synergizes with BRAF inhibitors to treat BRAF-mutant colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1218.