Purpose Tumor genotyping using cell free plasma DNA (cfDNA) has the potential to allow noninvasive assessment of tumor biology, yet many existing assays are cumbersome and vulnerable to false positive results. We sought to determine whether droplet digital PCR (ddPCR) of cfDNA would allow highly specific and quantitative assessment of tumor genotype. Experimental Design ddPCR assays for EGFR, KRAS, and BRAF mutations were developed using plasma collected from patients with advanced lung cancer or melanoma of a known tumor genotype. Sensitivity and specificity were determined using cancers with non-overlapping genotypes as positive and negative controls. Serial assessment of response and resistance was studied in EGFR-mutant lung cancer patients on a prospective trial of erlotinib. Results We identified a reference range for EGFR L858R and exon 19 deletions in specimens from KRAS-mutant lung cancer, allowing identification of candidate thresholds with high sensitivity and 100% specificity. Received operative characteristic (ROC) curve analysis of 4 assays demonstrated an area under the curve in the range of 0.80-0.94. Sensitivity improved in specimens with optimal cfDNA concentrations. Serial plasma genotyping of EGFR-mutant lung cancer on erlotinib demonstrated pretreatment detection of EGFR mutations, complete plasma response in most cases, and increasing levels of EGFR T790M emerging prior to objective progression. Conclusions Noninvasive genotyping of cfDNA using ddPCR demonstrates assay qualities that could allow effective translation into a clinical diagnostic. Serial quantification of plasma genotype allows noninvasive assessment of response and resistance, including detection of resistance mutations up to 16 weeks prior to radiographic progression.

The association of mutant forms of Ras protein with a variety of human cancers has stimulated intense interest in therapies based on inhibiting oncogenic Ras signaling. Attachment of Ras proteins to the plasma membrane is required for effective Ras signaling and is initiated by the enzyme farnesyl protein transferase. We found that in the presence of potent farnesyl protein transferase inhibitors, Ras proteins in the human colon carcinoma cell line DLD-1 were alternatively prenylated by geranylgeranyl transferase-1. When H-Ras, N-Ras, K-Ras4A, and K-Ras4B were expressed individually in COS cells, H-Ras prenylation and membrane association were found to be uniquely sensitive to farnesyl transferase inhibitors; N-and K-Ras proteins incorporated the geranylgeranyl isoprene group and remained associated with the membrane fraction. The alternative prenylation of N-and K-Ras has significant implications for our understanding of the mechanism of action of farnesyl protein transferase inhibitors as anti-cancer chemotherapeutics.Newly synthesized Ras proteins are partitioned to the cytoplasmic face of the plasma membrane by a series of posttranslational modifications. The first step, catalyzed by the enzyme farnesyl protein transferase, is the addition of the 15-carbon isoprenyl group farnesyl to the sulfhydryl group of cysteine in the Ras carboxyl-terminal CAAX box (where C is cysteine, A is aliphatic, and X is typically Met or Ser) (1-3). Farnesylation is followed by proteolytic removal of the AAX amino acids and methylation of the carboxyl group of the farnesylated cysteine (4). Ras proteins at the plasma membrane cycle between an active GTP-bound state and an inactive GDPbound state. Mutations that stabilize the active GTP-bound state have been identified in over 30% of human tumors, with particularly high incidences in pancreatic (ϳ90%) and colon (ϳ50%) cancers. Four oncogenic Ras proteins have been described, H-Ras, N-Ras, K-Ras4A, and K-Ras4B. The majority of mutations associated with human cancer have been found in the K-Ras gene. The two K-Ras proteins are products of a single alternatively spliced transcript, with K-Ras4B the predominant isoform (Ͼ80%) (5, 6).Ras proteins that have been genetically modified so that they lack the isoprenylated cysteine do not associate with the plasma membrane and cannot transform fibroblasts (7). These genetic experiments provided the basis for the development of farnesyl transferase inhibitors (FTIs) 1 as anti-cancer agents. A number of reports have demonstrated that pharmacological inhibition of farnesyl protein transferase by CAAX analogs reduces anchorage-independent growth of Ras-transformed cells in soft agar (8) and slows growth of Ras-transformed cells in nude mice (9, 10). The FTIs appear relatively non-toxic in that they do not interfere with normal cell proliferation (11). This result was somewhat surprising because Ras function was shown to be necessary for normal growth factor signaling and cell proliferation (12). A mechanism through which cells may proliferate in...

The high frequency of activating RAS or BRAF mutations in cancer provides strong rationale for targeting the mitogen-activated protein kinase (MAPK) pathway. Selective BRAF and MAP-ERK kinase (MEK) inhibitors have shown clinical effi cacy in patients with melanoma. However, the majority of responses are transient, and resistance is often associated with pathway reactivation of the extracellular signal-regulated kinase (ERK) signaling pathway. Here, we describe the identifi cation and characterization of SCH772984, a novel and selective inhibitor of ERK1/2 that displays behaviors of both type I and type II kinase inhibitors. SCH772984 has nanomolar cellular potency in tumor cells with mutations in BRAF , NRAS , or KRAS and induces tumor regressions in xenograft models at tolerated doses. Importantly, SCH772984 effectively inhibited MAPK signaling and cell proliferation in BRAF or MEK inhibitor-resistant models as well as in tumor cells resistant to concurrent treatment with BRAF and MEK inhibitors. These data support the clinical development of ERK inhibitors for tumors refractory to MAPK inhibitors. SIGNIFICANCE: BRAF and MEK inhibitors have activity in MAPK-dependent cancers with BRAF or RAS mutations. However, resistance is associated with pathway alterations resulting in phospho-ERK reactivation. Here, we describe a novel ERK1/2 kinase inhibitor that has antitumor activity in MAPK inhibitor-naïve and MAPK inhibitor-resistant cells containing BRAF or RAS mutations. Cancer Discov; 3(7); 742-50.