Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory Circuits During Response to MAPK Inhibition in BRAF-mutant Colorectal Cancer

Lee, H. M.; Zheng, Z.; Sorokin, A.; Wong, C. W.; Napolitano, S.; Chowdhury, S.; Kanikarla, P. M.; Singh, A. K.; Kochat, V.; Bristow, C. A.; Srinivasan, S.; Peoples, M.; Arslan, E.; Alshenaifi, J. Y.; Villarreal, O. E.; Morris, V. K.; Shen, J. P.; Meric-Bernstam, F.; Jain, A. K.; Fowlkes, N. W.; Anderson, A.; Menter, D. G.; Saw, A. K.; Rai, K.; Kopetz, S.

doi:10.1101/2025.06.15.659716

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bioRxiv · 10.1101/2025.06.15.659716

Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory Circuits During Response to MAPK Inhibition in BRAF-mutant Colorectal Cancer

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Abstract

BackgroundAberrant enhancer dynamics play a critical role in the initiation and progression of colorectal cancer (CRC). BRAFV600E-mutated metastatic CRC may be a unique subtype, exhibiting a strong epigenetic phenotype. Interestingly, bromodomain 2, a reader protein for H3K27ac-marked enhancers, was found to be synthetically lethal in CRC with BRAF + EGFR inhibition. DesignWe evaluated the effectiveness of targeting aberrant enhancers with bromodomain and extraterminal (BET) + MAPK pathway inhibitors in patient-derived xenograft models of metastatic CRC, followed by comprehensive profiling of transcriptomic and chromatin dynamics upon BET inhibitor combination treatment. ResultsThe combination of BET and standard MAPK inhibitors has demonstrated improved efficacy against BRAFV600E CRC and selective improvements against RAS-mutant CRC in vivo. We showed that BET + MAPK inhibition induced a profound downregulation of the MAPK signaling pathway compared to MAPK inhibition alone. The loss of activation signal on enhancers, as determined by H3K27ac, led to dysregulation of core-regulatory circuitries of CRC, especially loss of the auto-regulatory mechanism of the MAPK downstream E26 transformation-specific transcription factor family. Single nucleus multiome (RNA + ATAC) sequencing further distinguished differential transcriptomic and chromatin dynamics at cell type levels. Profound downregulation of well-differentiated cell types confirmed deep inhibition of MAPK signaling and downstream transcription factors. On the other hand, dedifferentiated cell populations were abundant after MAPK or combination inhibition, suggesting therapy-induced cell state switching and adaptation. ConclusionWe are evaluating BET + BRAF + EGFR inhibition in patients with treatment-refractory BRAFV600E metastatic CRC. ClinicalTrial.gov identifier: NCT06102902. What is already known on this topicEnhancer aberrations emerge as critical epigenetic features in the progression of colorectal cancer (CRC). However, the dynamics of active enhancer and the therapeutic potential of enhancer blockade, particularly in CRC tumors with BRAFV600E mutation, is not well understood. What this study addsThis study demonstrates improved efficacy of BET inhibitor combination therapies in diverse patient-derived models and reveals epigenetic reprogramming driven cellular plasticity in BRAFV600E-mutated CRC. How this study might affect research, practice or policyOur findings support treatment with BET + BRAF + EGFR inhibitors for patients with BRAFV600E-mutant mCRC [NCT06102902]. This study also highlights the potential of combining epigenetic agents to standard targeted therapy, offering a novel treatment option for this subset of patients.

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Lee, H. M., Zheng, Z., Sorokin, A., Wong, C. W., Napolitano, S., Chowdhury, S., Kanikarla, P. M., Singh, A. K., Kochat, V., Bristow, C. A., Srinivasan, S., Peoples, M., Arslan, E., Alshenaifi, J. Y., Villarreal, O. E., Morris, V. K., Shen, J. P., Meric-Bernstam, F., Jain, A. K., Fowlkes, N. W., Anderson, A., Menter, D. G., Saw, A. K., Rai, K., Kopetz, S.. 2025-06-20. Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory Circuits During Response to MAPK Inhibition in BRAF-mutant Colorectal Cancer. https://doi.org/10.1101/2025.06.15.659716

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