Circulating Tumor DNA Identifies Diverse Landscape of Acquired Resistance to Anti-Epidermal Growth Factor Receptor Therapy in Metastatic Colorectal Cancer.

Abstract

Anti-epidermal growth factor receptor (EGFR) antibodies are effective treatments for metastatic colorectal cancer. Improved understanding of acquired resistance mechanisms may facilitate circulating tumor DNA (ctDNA) monitoring, anti-EGFR rechallenge, and combinatorial strategies to delay resistance. Patients with treatment-refractory metastatic colorectal cancer (n = 169) enrolled on the CO.26 trial had pre-anti-EGFR tissue whole-exome sequencing (WES) compared with baseline and week 8 ctDNA assessments with the GuardantOMNI assay. Acquired alterations were compared between patients with prior anti-EGFR therapy (n = 66) and those without. Anti-EGFR therapy occurred a median of 111 days before ctDNA assessment. ctDNA identified 12 genes with increased mutation frequency after anti-EGFR therapy, including <i>EGFR</i> (<i>P</i> = .0007), <i>KRAS</i> (<i>P</i> = .0017), <i>LRP1B</i> (<i>P</i> = .0046), <i>ZNF217</i> (<i>P</i> = .0086), <i>MAP2K1</i> (<i>P</i> = .018), <i>PIK3CG</i> (<i>P</i> = .018), <i>BRAF</i> (<i>P</i> = .048), and <i>NRAS</i> (<i>P</i> = .048). Acquired mutations appeared as multiple concurrent subclonal alterations, with most showing decay over time. Significant increases in copy-gain frequency were noted in 29 genes after anti-EGFR exposure, with notable alterations including <i>EGFR</i> (<i>P</i> < .0001), <i>SMO</i> (<i>P</i> < .0001), <i>BRAF</i> (<i>P</i> < .0001), <i>MET</i> (<i>P</i> = .0002), <i>FLT3</i> (<i>P</i> = .0002), <i>NOTCH4</i> (<i>P</i> = .0006), <i>ERBB2</i> (<i>P</i> = .004), and <i>FGFR1</i> (<i>P</i> = .006). Copy gains appeared stable without decay 8 weeks later. There were 13 gene fusions noted among 11 patients, all but one of which was associated with prior anti-EGFR therapy. Polyclonal resistance was common with acquisition of ≥ 10 resistance related alterations noted in 21% of patients with previous anti-EGFR therapy compared with 5% in those without (<i>P</i> = .010). Although tumor mutation burden (TMB) did not differ pretreatment (<i>P</i> = .63), anti-EGFR exposure increased TMB (<i>P</i> = .028), whereas lack of anti-EGFR exposure resulted in declining TMB (<i>P</i> = .014). Paired tissue and ctDNA sequencing identified multiple novel mutations, copy gains, and fusions associated with anti-EGFR therapy that frequently co-occur as subclonal alterations in the same patient.