Understanding intrinsic resistance to direct KRAS inhibition in colorectal cancers

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PROJECT SUMMARY/ABSTRACT Metastatic colorectal cancers (CRC) are the second leading cause of cancer death in the US. While advances in targeted therapies have transformed the treatment of many cancers, CRC has proven largely refractory to this approach. Thus, while agents targeting BRAFV600E and the KRASG12C mutation have dramatically improved the treatment of lung cancer and melanoma, they have only shown limited impact in CRC. CTNNB1 transcription is upregulated in >75% of CRC via APC inactivation and other mutations. As CTNNB1 is a common mediator of drug resistance and has been shown to be sufficient to maintain CRC proliferation, we hypothesize that it is a key mediator of intrinsic resistance to KRAS inhibition in CRC. Although multiple agents target CTNNB1 regulation via the WNT pathway, these have proven too toxic for human use to date. Thus, we have used proteomics to map the signaling response to KRASG12C inhibition in CRC cell lines and kinome-wide knockdown to identify kinases whose suppression synergizes with KRASG12C inhibition. By integrating these two approaches, we were able to uncover several kinases that function as signaling links between KRAS and CTNNB1, and whose inhibition synergizes with direct KRAS inhibition to reduce CTNNB1 target gene expression. As KRASG12C inhibitors do not impact normal KRAS signaling, this exciting preliminary data suggests that we may be able to preferentially downregulate CTNNB1 in tumors without systemic toxicity. We will build on this key preliminary data in this project: In Aim 1, we will expand our analysis of the kinase response to KRASG12C inhibition to additional CRC cell lines and the assess the impact of key kinases on CTNNB1 transcription. In Aim 2, we will use CRISPR in patient-derived xenografts (PDX) to circumvent the limitations of available small molecules to validate the role of CTNNB1 in APC-mutant CRC PDX. We will further use CRISPR or small molecules (when available) to test kinases already found to modulate CTNNB1 or emerging from Aim 1 in CRC treatment models and to determine their role in in vivo CRC biology. Finally, in Aim 3 we will develop KRASG12C CRC organoid and cell line models with mutations in PIK3CA, a common CRC mutation that co-occurs with KRAS mutations and is likely to cause resistance to KRASG12C inhibitors, but for which there are no models currently available. These tools will allow us to stratify the impact of PIK3CA mutation on our current treatment strategies and to optimize a regimen engineered specifically for this combination of mutations. This rigorous study of KRAS-driven signaling in CRC leverages new small molecules and robust quantitative approaches to unmask links between KRAS and the mechanisms that support CRC after KRAS inhibition. Uncovering the basis of resistance to direct KRAS inhibition in CRC will yield rational combination strategies primed for translation into clinical trials.