Circulating Tumour DNA Sequencing Identifies a Genetic Resistance-Gap in Colorectal Cancers with Acquired Resistance to EGFR-Antibodies and Chemotherapy

Abstract

Epidermal growth factor receptor antibodies (EGFR-Abs) confer a survival benefit in patients with RAS wild-type metastatic colorectal cancer (mCRC), but resistance invariably occurs. Previous data showed that only a minority of cancer cells harboured known genetic resistance drivers when clinical resistance to single-agent EGFR-Abs had evolved, supporting the activity of non-genetic resistance mechanisms. Here, we used error-corrected ctDNA-sequencing (ctDNA-Seq) of 40 cancer genes to identify drivers of resistance and whether a genetic resistance-gap (a lack of detectable genetic resistance mechanisms in a large fraction of the cancer cell population) also occurs in RAS wild-type mCRCs treated with a combination of EGFR-Abs and chemotherapy. We detected one MAP2K1/MEK1 mutation and one ERBB2 amplification in 2/3 patients with primary resistance and KRAS, NRAS, MAP2K1/MEK1 mutations and ERBB2 aberrations in 6/7 patients with acquired resistance. In vitro testing identified MAP2K1/MEK1 P124S as a novel driver of EGFR-Ab resistance. Mutation subclonality analyses confirmed a genetic resistance-gap in mCRCs treated with EGFR-Abs and chemotherapy, with only 13.42% of cancer cells harboring identifiable resistance drivers. Our results support the utility of ctDNA-Seq to guide treatment allocation for patients with resistance and the importance of investigating further non-canonical EGFR-Ab resistance mechanisms, such as microenvironmentally-mediated resistance. The detection of MAP2K1 mutations could inform trials of MEK-inhibitors in these tumours.

Genetic and immune landscape evolution in MMR‐deficient colorectal cancer

“…Multiregion sequencing is unlikely to be clinically feasible. However, circulating tumour DNA sequencing is effective in CRC and methods to determine driver aberration clonality have been developed [47,48]. Tumours with subclonal IE evolution showed the highest CD8 T-cell densities.…”

Genetic and immune landscape evolution defines subtypes of MMR deficient colorectal cancer

“…ITH analysis of immune evasion drivers and subtype detection requires clonality analyses which are unlikely to be clinically feasible from tissue samples. However, circulating tumor DNA sequencing is effective in CRC and methods to determine driver aberration clonality have been developed (Knebel et al, 2020; Woolston et al, 2019). This can be readily implemented in clinical trials and may eventually allow stratification of patients to either PD1 inhibitors, more toxic CLTA4/PD1 combinations (e.g.…”