A systems mechanism for KRAS mutant allele–specific responses to targeted therapy

Abstract

Cancer treatment decisions are increasingly guided by which specific genes are mutated within each patient’s tumor. For example, agents inhibiting the epidermal growth factor receptor (EGFR) benefit many colorectal cancer (CRC) patients, with the general exception of those whose tumor includes a KRAS mutation. However, among the various KRAS mutations, that which encodes the G13D mutant protein (KRASG13D) behaves differently; for unknown reasons, KRASG13D CRC patients benefit from the EGFR-blocking antibody cetuximab. Controversy surrounds this observation, because it contradicts the well-established mechanisms of EGFR signaling with regard to RAS mutations. Here, we identified a systems-level, mechanistic explanation for why KRASG13D cancers respond to EGFR inhibition. A computational model of RAS signaling revealed that the biophysical differences between the three most common KRAS mutants were sufficient to generate different sensitivities to EGFR inhibition. Integrated computation with experimentation then revealed a nonintuitive, mutant-specific dependency of wild-type RAS activation by EGFR that is determined by the interaction strength between KRAS and the tumor suppressor neurofibromin (NF1). KRAS mutants that strongly interacted with and competitively inhibited NF1 drove wild-type RAS activation in an EGFR-independent manner, whereas KRASG13D weakly interacted with and could not competitively inhibit NF1 and, thus, KRASG13D cells remained dependent on EGFR for wild-type RAS activity. Overall, our work demonstrates how systems approaches enable mechanism-based inference in genomic medicine and can help identify patients for selective therapeutic strategies.

Inhibition of both mutant and wild-type RAS-GTP in KRAS G12C colorectal cancer through cotreatment with G12C and EGFR inhibitors

“…Our previous studies that investigated the response of KRAS G13D CRC cells to EGFR inhibition found that, upon EGFR inhibition, sensitive G13D cells display a reduction in HRAS-GTP and NRAS-GTP (which is all wild-type in these cells), but not in mutant KRAS-GTP. In contrast, we found that KRAS G12D and G12V lines do not display reductions in HRAS-GTP or NRAS-GTP upon treatment with cetuximab (14). We hypothesized that the sensitivity of the G12C line also follows from reductions in wild-type RAS-GTP, but not in mutant KRAS-GTP.…”

“…To investigate whether the EGFR inhibitor cetuximab might have activity on KRAS G12C CRC we first utilized a panel of isogenic CRC cells derived from the SW48 colon cancer cell line. Through homologous recombination, multiple derivative cell lines are available that have one KRAS allele replaced with a KRAS mutant allele (14)(15)(16). We performed cetuximab dose responses on SW48 KRAS WT cells, as well KRAS G12C, KRAS G12V, and KRAS G12D derivative isogenics.…”

“…Strongly interacting, constitutively active RAS mutants cannot be inactivated by NF1, but their non-productive interaction with the NF1 GAP domain effectively results in a competitive inhibition of NF1 and thereby leads to increased wild-type RAS-GTP in an EGFR-independent manner. Mutants like KRAS G13D that weakly interact with NF1 do not strongly drive wild-type RAS-GTP production through NF1 competitive inhibition and therefore can remain dependent upon EGFR for WT RAS-GTP generation (14). We hypothesized that the sensitivity of G12C also follow from reductions in binding to NF1 for the KRAS G12C mutant.…”

“…We have recently solved the problem of why KRAS G13D, in which the Glycine residue at codon 13 is replaced with an Aspartic Acid (D), and is the third most common KRAS mutant in colorectal cancer, is an exception to the rule that KRAS mutations confer resistance to the EGFR inhibitor cetuximab (14). The original clinical observation that patients with this mutation benefitted from cetuximab was published nearly a decade ago (15) and perplexed RAS biologists and clinicians, who struggled to identify a mechanism that could explain why cancers with a KRAS mutant that is constitutively active in an EGFR-independent manner would respond to an EGFR inhibitor.…”

“…The original clinical observation that patients with this mutation benefitted from cetuximab was published nearly a decade ago (15) and perplexed RAS biologists and clinicians, who struggled to identify a mechanism that could explain why cancers with a KRAS mutant that is constitutively active in an EGFR-independent manner would respond to an EGFR inhibitor. Through mathematical modeling that leveraged available biochemical and biophysical data on KRAS mutants and experimental cancer cell biology, we revealed that EGFR inhibitors like cetuximab can inhibit wild-type RAS-GTP (predominantly HRAS and NRAS) in some colorectal cancer cells with KRAS mutations, and that the determinative property is whether or not the KRAS mutant interacts with tumor suppressor NF1 (14).…”