Genomic and Transcriptomic Determinants of Therapy Resistance and Immune Landscape Evolution during Anti-EGFR Treatment in Colorectal Cancer

Summary

Despite biomarker stratification, the anti-EGFR antibody cetuximab is only effective against a subgroup of colorectal cancers (CRCs). This genomic and transcriptomic analysis of the cetuximab resistance landscape in 35 RAS wild-type CRCs identified associations of NF1 and non-canonical RAS/RAF aberrations with primary resistance and validated transcriptomic CRC subtypes as non-genetic predictors of benefit. Sixty-four percent of biopsies with acquired resistance harbored no genetic resistance drivers. Most of these had switched from a cetuximab-sensitive transcriptomic subtype at baseline to a fibroblast- and growth factor-rich subtype at progression. Fibroblast-supernatant conferred cetuximab resistance in vitro, confirming a major role for non-genetic resistance through stromal remodeling. Cetuximab treatment increased cytotoxic immune infiltrates and PD-L1 and LAG3 immune checkpoint expression, potentially providing opportunities to treat cetuximab-resistant CRCs with immunotherapy.

Highlights

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  NF1 and non-canonical KRAS and BRAF aberrations associate with cetuximab resistance

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  Genetic resistance drivers are absent in most biopsies that acquired resistance

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  Stromal remodeling is an alternative non-genetic mechanism of cetuximab resistance

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  Cetuximab-mediated immune modulation may sensitize CRCs to immunotherapy

Abstract

Woolston et al. show that in metastatic colorectal cancer cetuximab resistance can be conferred by genetic mechanisms, such as NF1 loss or RAS/RAF alterations, or by transcriptomic changes that induce a stroma-rich phenotype. They also provide a rationale for combining cetuximab with immunotherapy.