Broad Detection of Alterations Predicted to Confer Lack of Benefit From EGFR Antibodies or Sensitivity to Targeted Therapy in Advanced Colorectal Cancer

Abstract

Introduction: A KRAS mutation represented the first genomic biomarker to predict lack of benefit from anti-epidermal growth factor receptor (EGFR) antibody therapy in advanced colorectal cancer (CRC). Expanded RAS testing has further refined the treatment approach, but understanding of genomic alterations underlying primary and acquired resistance is limited and further study is needed.

Materials and methods: We prospectively analyzed 4,422 clinical samples from patients with advanced CRC, using hybrid-capture based comprehensive genomic profiling (CGP) at the request of the individual treating physicians. Comparison with prior molecular testing results, when available, was performed to assess concordance.

Results: We identified a RAS/RAF pathway mutation or amplification in 62% of cases, including samples harboring KRAS mutations outside of the codon 12/13 hotspot region in 6.4% of cases. Among cases with KRAS non-codon 12/13 alterations for which prior test results were available, 79 of 90 (88%) were not identified by focused testing. Of 1,644 RAS/RAF wild-type cases analyzed by CGP, 31% harbored a genomic alteration (GA) associated with resistance to anti-EGFR therapy in advanced CRC including mutations in PIK3CA, PTEN, EGFR, and ERBB2. We also identified other targetable GA, including novel kinase fusions, receptor tyrosine kinase amplification, activating point mutations, as well as microsatellite instability.

Conclusion: Extended genomic profiling reliably detects alterations associated with lack of benefit to anti-EGFR therapy in advanced CRC, while simultaneously identifying alterations potentially important in guiding treatment. The use of CGP during the course of clinical care allows for the refined selection of appropriate targeted therapies and clinical trials, increasing the chance of clinical benefit and avoiding therapeutic futility.

Implications for practice: Comprehensive genomic profiling (CGP) detects diverse genomic alterations associated with lack of benefit to anti-epidermal growth factor receptor therapy in advanced colorectal cancer (CRC), as well as targetable alterations in many other genes. This includes detection of a broad spectrum of activating KRAS alterations frequently missed by focused molecular hotspot testing, as well as other RAS/RAF pathway alterations, mutations shown to disrupt antibody binding, RTK activating point mutations, amplifications, and rearrangements, and activating alterations in downstream effectors including PI3K and MEK1. The use of CGP in clinical practice is critical to guide appropriate selection of targeted therapies for patients with advanced CRC.

Keywords: Biomarker; Cetuximab; Colon cancer; Epidermal growth factor receptor; Genomic profiling; KRAS.

Figure 1.

Missed detection of KRAS non-G12/13 mutations by prior focused molecular testing. KRAS mutations detected by comprehensive genomic profiling and missed by prior focused molecular testing (red bars), detected by prior focused molecular testing (blue bars), or with no record of prior molecular testing in provided pathology report (green bars).

Figure 2.

Overlap of RAS/RAF alterations and other potential drivers in colorectal cancer. Diagram represents overlap of colorectal patient cases with the indicated classes of genomic alterations detected by comprehensive genomic profiling. (A): Overlap of cases with subtypes of RAS/RAF alterations. (B): Overlap of all cases with RAF/RAS alterations with cases with subtypes of activating alterations in other potential drivers. Abbreviations: amp, amplification; mut, mutation; RTK, receptor tyrosine kinase.

Figure 3.

Quantitation of CRC cases with potential driver alterations and co-occurrence of KRAS mutations. Breakdown of specific subtypes of RTK, MEK1, PIK3CA, and PTEN alteration classes and overlap with RAS/RAF alterations. Dark blue bars specify the subset of cases that overlap specifically with KRAS point mutations. Abbreviations: CRC, colorectal cancer; EC, extracellular domain; KD, kinase domain; RTK, receptor tyrosine kinase.