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

Andrew Woolston,Matthew N Davies,Louise J Barber,Ian Chau,Romana Ranftl,Kyriakos Kouvelakis,Nikolaos Fotiadis,Anguraj Sadanandam,Teresa Marafioti,Katharina Von Loga,Naureen Starling,Beatrice Griffiths,Annette Bryant,Janet Thomas,Sebastian Guettler,Clare Peckitt,Yatish Patil,Francesco Sclafani,Andrew Furness,Fernando Calvo,Reyes Gonzalez-Exposito,Alice Newey,Mirta Jiménez,Ruwaida Begum,David Watkins,Marco Gerlinger,Stefano Lise,Georgia Spain,Marco Punta,David Cunningham,Sonia Mansukhani,Isma Rana,Nasir Khan,Khurum Khan,Lisa Hornsteiner,Andrew Wotherspoon,Thomas Powles,Sergio A Quezada ,Rao S

doi:10.1016/j.ccell.2019.05.013

Abstract

SummaryDespite 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

Anti-epidermal growth factor receptor (EGFR) antibodies are effective in a subgroup of patients with metastatic colorectal cancer (CRC)
Progressive disease (PD) biopsies were taken after radiological progression from 25/35 cases, and 24 were successfully exome sequenced
All genes were large and we found no evidence of biallelic inactivation, which would be expected for tumor suppressor genes, or for recurrence of mutations in specific functional domains or amino acid positions, which would indicate gain-of-function mutations either in our samples or in the COSMIC mutation database

Summary

Introduction

Anti-epidermal growth factor receptor (EGFR) antibodies (antiEGFR-Ab) are effective in a subgroup of patients (pts) with metastatic colorectal cancer (CRC). Activating KRAS or NRAS mutations in codons 12, 13, 59, 61, 117, and 146 have been associated with primary resistance in randomized trials and anti-EGFR-Ab treatment should only be administered for tumors Significance. The identified associations of NF1, non-canonical KRAS and BRAF aberrations with primary resistance, and of CMS2/TA transcriptomic subtypes with prolonged benefit may enable more effective treatment allocation and avoid toxicities from ineffective therapy. Genetic resistance drivers were not identified in the majority of metastases that had acquired resistance Most of these had switches from the cetuximab-sensitive CMS2/TA subtype to a fibroblast- and growth factor-rich subtype. This challenges the paradigm that genetic drivers predominate at acquired resistance and suggests therapeutic approaches by targeting fibroblasts. Increased T cell infiltration and immune checkpoint upregulation following cetuximab responses warrant trials of checkpoint inhibitors

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Conclusion