Targeting Chromosomal Instability in the Evolution of Resistance to Matched Therapies Against Colorectal Cancer to Extend Treatment Response - PROJECT SUMMARY Therapies targeting oncogenic drivers have revolutionized the treatment of metastatic colorectal cancer (CRC) with new agents holding the potential to target most CRCs in the not-too-distant future. However, the impact of these new therapies has been limited by the short duration of response in the clinic; most patients with CRC progress within six months of starting targeted therapy. This proposal aims to address this problem of rapid resistance. Our analysis of acquired resistance to BRAF and KRAS G12C selective inhibitors indicates that gene amplification is a recurrent and often early mechanism of resistance in CRC. In our preliminary data, the development of gene amplifications at progression and the detection of amplifications at baseline prior to targeted therapy are both associated with shorter time on treatment. We hypothesize intrinsic tumor features enable a program of enhanced chromosomal instability that underlie rapid resistance to targeted therapy in CRC and that create a therapeutic vulnerability that can be exploited. Gene amplifications at resistance are often carried as extra-chromosomal DNA (ecDNA), which can be dynamically regulated in response to changes in drug levels. Beyond intrachromosomal amplifications, amplifications on ecDNA allow massive induction of expression of the amplified genes, while maintaining high intratumoral heterogeneity, enabling cancers to maximize their response to changing environments. These amplifications develop through chromothripsis, a process in which multiple rearrangements occur during a one-off cellular crisis, and require intact double- stranded DNA break repair pathways to form. In this proposal, we will evaluate how intrinsic tumor features modulate development of targeted therapy resistance and test a novel combination approach to prevent the development of resistance. Through deep analysis of clinical samples previously collected from patients with CRC who received targeted therapies, cell lines, and patient-derived xenograft (PDX) models, we will evaluate levels of markers of chromosomal instability, including amplifications, ecDNA, micronuclei, and fraction of genome altered. Cell lines will be used to map out the timing of increased chromosomal instability leading to resistance, and PDXs will be used to interrogate the effects of baseline tumor features on the time and nature of resistance that emerges in CRC. Using PDX models of BRAF V600E and KRAS G12C CRC, we will test a novel therapeutic strategy of combined DNA repair inhibition and targeted therapy to prevent resistance. We will specifically test DNA repair inhibitors against ATM, ATR, DNA-PK, and ecDNA given with matched targeted therapy from the start of treatment to prevent resistance. We believe this novel approach has the potential to transform targeted therapy for CRC and improve outcomes for patients.
