ctDNA-based mutational landscape following anti-EGFR antibodies in metastatic colorectal cancer (mCRC) to uncover novel resistance mechanisms in the CCTG CO.26 trial.
Authors: Topham James T. , O'Callaghan Christopher J. , Feilotter Harriet , Kennecke Hagen F. , Lee Young S , Li Weimin , Banks Kimberly , Renouf Daniel John , Jonker Derek , Tu Dongsheng , Chen Eric Xueyu , Loree Jonathan M. 
Published: January 2021

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Background: Previous studies have identified MAPK and PIK3CA/AKT/mTOR pathways as common mechanisms of acquired resistance to anti-EGFR antibodies (EGFRab) in mCRC. However, such alterations do not account for all patients that become treatment resistant. Using paired whole-exome (WES; tissue) and circulating tumor DNA (ctDNA; plasma) sequencing, we performed characterization of the EGFRab resistance landscape in patients with mCRC. Methods: Post-treatment (ctDNA; plasma) sequencing was performed for 169 patients with mCRC, with 112 (66%) patients also receiving pre-treatment (WES; primary tumor) sequencing as part of the CO.26 trial. 66 (39%) patients received EGFRab previously at a median of 132.0 days prior to plasma sampling. Using bespoke bioinformatics pipelines (WES) coupled with the GuardantOMNI assay (plasma), we compared somatic mutation (SNV/indel, CNV and fusion) frequencies between pre- and post-EGFRab timepoints, and contrasted results between the two groups. Results: Significant increases in de novo acquisition of EGFR (p = 5.6e-4), KRAS (p = 0.011), ZNF217 (p = 0.0022), MAP2K1 (p = 0.0078) and LRP1B (p = 0.017) SNV/indels were unique to the EGFRab group and often occurred as multiple, low allele frequency events in the same patient. De novo copy number amplification of known resistance genes EGFR/ BRAF/ MET were observed in EGFRab-treated patients (p < 0.05), along with SMO (p = 6.8e-7), PTEN inhibitory gene PREX2 (p = 5.6e-4), FLT3 (p = 2.0e-5), NOTCH4 (p = 6.3e-5), ERBB2 (7.4e-4), KMT2A (p = 3.7e-4) and ARID1B (p = 0.0014). Genes impacted by fusion events in EGFRab-treated patients included BRAF-KIAA1549 (1 patient) and MET-CAV1 (1 patient), and these events were not detected in matched pre-treatment samples. EGFRab-treated patients were found to acquire a combination of multiple (≥5) mutation events (SNV/indel, CNV or fusion) at much higher frequency compared to non-EGFRab-treated patients (67% versus 25% of patients, p = 8.7e-8). Tumor mutation burden (TMB) was not significantly different (p = 0.71) between treatment groups prior to therapy initiation, while post-treatment TMB was significantly higher (p = 1.8e-7) in EGFRab-treated patients (median 25.4 versus 13.1 mut/mb). Conclusions: In addition to previously established resistance pathways, we identified acquired alterations in additional genes such as SMO, PREX2 and epigenetic modifiers KMT2A/ARID1B in EGFRab-treated patients . Moreover, we highlight the phenomenon by which EGFRab-treated tumors acquire multiple concurrent resistance mutations and heightened TMB. Our analysis provides novel insight into the landscape of resistance mechanisms to EGFRab in mCRC while highlighting the potential role for immunotherapy post-EGFRab. Clinical trial information: NCT02870920.