Targeting ALK, ROS1, and BRAF kinases

Cancer cells demonstrate numerous genetic aberrations. Despite this genetic complexity, it is hypothesized that cancer cells are often addicted to a single oncogenic driver such that inhibition of this single target would lead to cell death.¹ Data collected from patients with adenocarcinoma by the Lung Cancer Mutation Consortium (LCMC) demonstrate a significant number of patients harboring distinct oncogenic drivers, many of which may be amenable to targeted therapies.² Two current areas of intense investigation are to match targeted therapies to a growing list of selected oncogene aberrations in patients with NSCLC and also to understand mechanisms of resistance to these targeted therapies so that resistance can be overcome or potentially delayed with new drugs or drug combinations.

ALK

The recent approval of crizotinib for ALK positive NSCLC patients ushered in the first FDA companion diagnostic for NSCLC, ALK fluorescence in situ hybridization (FISH). ALK break-apart FISH was/is the diagnostic test used for entry into the completed and ongoing crizotinib studies and remains the only prospectively validated test for this drug. Dr. Garcia described other testing methods that are in development including immunohistochemistry (IHC) and bright field in situ hybridization (BISH), both of which might have advantages relating to ease of adoption. Whether either would also have an advantage in terms of cost-effectiveness is more debatable as this will depend on the ultimate cost of a validated assay. IHC takes advantage of the lack of ALK expression in normal lung tissue, or in cancers without an ALK gene rearrangement, by evaluating levels of ALK protein expression. BISH uses a similar strategy to FISH by evaluating the distance between chromagen-labeled probes that are homologous to the 5′ and 3′ ends of the ALK gene to detect evidence of an inversion or translocation involving the ALK gene, but does so without the need for a fluorescent microscope. Although early studies suggest good concordance between these tests and ALK FISH within single centers, the need for both standardized protocols for the multiple different commercially available ALK antibodies for IHC and the need for standardized scoring systems for both BISH and IHC were highlighted.

Drs. Doebele and Shaw presented data on observed mechanisms of resistance to crizotinib in ALK positive NSCLC patients who underwent biopsy at the time of progression.^3,4 Both groups observed a diverse array of ALK kinase domain mutations. The diversity of mutations is reminiscent of those observed in BCR-ABL after resistance to imatinib, rather than the dominant T790M mutation observed in EGFR mutant patients after EGFR kinase inhibitor resistance. ALK resistance mutations were observed in ∼20-40% of patients. Copy number gain through amplification of the ALK gene fusion was observed in ∼5-20% of patients. The University of Colorado series observed 36% percent of patients with the presence of an EGFR or KRAS activating mutation and/or the absence of an ALK gene rearrangement in the resistance biopsy suggesting the emergence of a clonally distinct population of cells that were no longer solely dependent on ALK signaling. The MGH series observed increased phosphorylated EGFR in the absence of an activating mutation in a subset of patients. Previously, some cell lines derived from crizotinib naïve ALK+ patients have also demonstrated increased EGFR and/or HER2 signaling in the absence of activating mutations, with a combination of agents directed against both ALK and EGFR/HER2 signaling required to achieve growth inhibition^4,5. Additionally from the MGH series, KIT gene amplification was observed as a mechanism of resistance in two patients. Collectively, these data suggest that resistance to crizotinib in some patients may emerge through total or partial reliance on other oncogenic drivers and the primary significance of this is that these patients would not be expected to benefit from monotherapy with a more potent ALK inhibitor.

In contrast, patients with ALK kinase domain resistance mutations and copy number gain of the ALK fusion gene are likely to still retain oncogene addiction to ALK signaling. Thus these patients may be much more likely to benefit from a more potent, next generation ALK kinase inhibitor. Drs. Shaw, Gettinger, and Gandhi presented pre-clinical data on three such ALK inhibitors: LDK378 (Novartis), AP26113 (Ariad), and CH5424802 (Chugai), respectively. In xenograft models, all three drugs demonstrated activity against unmutated EML4-ALK and LDK378 and AP26113 also demonstrated activity against xenografts bearing the known C1156Y and L1196M crizotinib resistance mutations, respectively. Interestingly, AP26113 demonstrates activity against mutant EGFR, which could be applicable in patients who demonstrate this mechanism of resistance, although the IC50s associated with EGFR inhibition were significantly higher than for ALK inhibition. Currently, all three compounds are being evaluated in early phase studies in both crizotinib-naïve and crizotinib-resistant patients. AP26113 is also being evaluated in cancers with a ROS1 gene rearrangement (see below). Dr. Camidge described a phase I study combining crizotinib with dacomitinib (PF-299804), Pfizer's irreversible pan-HER inhibitor. This drug combination was initially developed to address the common mechanisms of acquired resistance in EGFR mutant NSCLC (T790M and MET gene amplification), however it may also have a role to explore in crizotinib resistance occurring through increased EGFR and/or HER2 signaling and accrual to a dedicated ALK+ crizotinib resistant cohort is being considered. Given the diversity of resistance mechanisms to crizotinib, and their potential impact on subsequent treatment strategies directly solely against ALK, it will be critical to evaluate the mechanism of crizotinib resistance in the patients treated within all of these studies.

ROS1

ROS1 is a receptor tyrosine kinase that is homologous to ALK. Similar to the ALK FISH break-apart assay, Dr. Garcia described break-apart FISH assays meant to evaluate the deletions, inversions and translocations that can fuse the 3′ region encoding the kinase domain of the ROS1 oncogene to a variety of 5′ fusion partners including CD74, EZR, GOPC (FIG), LRIG3, SL34A2, SDC4, and TPM3.^6,7 The incidence across multiple studies suggests that ROS1 gene fusions occur in slightly greater than 1% of NSCLC. In vitro data suggests that ROS1 can transform cells and that inhibition with the ALK inhibitors, crizotinib or TAE684, blocks cell proliferation and induces cell cycle arrest in G1 via inhibition of downstream signaling cascades through SHP2, AKT, and ERK.^7,8 Treatment with crizotinib in an expanded cohort of the Pfizer phase I trial of PF-02341066 (crizotinib) induced tumor shrinkage in two patients with ROS1 gene rearrangements, one with an SDC4-ROS1 rearrangement and the other unknown, suggesting that these gene rearrangements may be a suitable target for inhibitors such as crizotinib.^6,8

BRAF

BRAF encodes a non-receptor serine/threonine kinase that can activate the MAPK pathway. Activating mutations in BRAF occur in approximately 3% of NSCLC patients, much lower than that observed in melanoma where investigations have recently led to the FDA approval of vemurafenib in this disease.^9,10 The most common mutation, V600E, is seen in approximately 50% of NSCLC patients whereas the other less common non-V600E mutations (G469A and D594G) comprise the other half. Drs. Miller and Riely reported on pre-clinical and clinical activity of dabrafenib (GSK2118436; Glaxo-SmithKline) and vemurafenib (PLX4032; Genentech), respectively. Both drugs are being investigated in a number of BRAF mutant malignancies. One significant safety concern with this class of drug is the induction of squamous cell carcinomas of the skin in less than 20% of patients, which typically occur within weeks to months of initiation of the drug and are treated successfully with curative-intent curettage.¹⁰ One interesting mechanism of intrinsic resistance that has come to light in BRAF mutation positive colorectal cancer is the activation of EGFR via inhibition of BRAF, which inhibits a phosphatase that typically inactivates EGFR.¹¹ This finding highlights a potential pitfall of transferring a targeted therapy from one cancer type to another.

Summary

As the repertoire of targetable genetic abnormalities increase, we will need to develop mechanisms to identify patients with relatively rare oncogenes that are both practical and reliable. The broad range of crizotinib resistance mechanisms observed in ALK+ NSCLC suggests that diversity will re-emerge as a major issue even from initially largely molecular uniform tumors in the acquired resistance setting. Whether therapies directed against resistance mechanisms should be employed only at the time of resistance or earlier, to delay the emergence of resistance, will need to be addressed over the next few years. Factors influencing the choice between these two strategies will include the tolerability of the treatment regimen and whether technology looking, for example, for low levels of resistance mechanisms in treatment naïve patients, will evolve to allow us to accurately predict which patient is more likely to employ a specific mechanism of resistance before it becomes clinically apparent.