Michael J. Greig

KIT kinase mutants show unique mechanisms of drug resistance to imatinib and sunitinib in gastrointestinal stromal tumor patients.

Most gastrointestinal stromal tumors (GISTs) exhibit aberrant activation of the receptor tyrosine kinase (RTK) KIT. The efficacy of the inhibitors imatinib mesylate and sunitinib malate in GIST patients has been linked to their inhibition of these mutant KIT proteins. However, patients on imatinib can acquire secondary KIT mutations that render the protein insensitive to the inhibitor. Sunitinib has shown efficacy against certain imatinib-resistant mutants, although a subset that resides in the activation loop, including D816H/V, remains resistant. Biochemical and structural studies were undertaken to determine the molecular basis of sunitinib resistance. Our results show that sunitinib targets the autoinhibited conformation of WT KIT and that the D816H mutant undergoes a shift in conformational equilibrium toward the active state. These findings provide a structural and enzymologic explanation for the resistance profile observed with the KIT inhibitors. Prospectively, they have implications for understanding oncogenic kinase mutants and for circumventing drug resistance.

Quantitative phosphoproteomic analysis of the STAT3/IL-6/HIF1α signaling network: An initial study in GSC11 glioblastoma stem cells

Initiation and maintenance of several cancers including glioblastoma (GBM) may be driven by a small subset of cells called cancer stem cells (CSCs). CSCs may provide a repository of cells in tumor cell populations that are refractory to chemotherapeutic agents developed for the treatment of tumors. STAT3 is a key transcription factor associated with regulation of multiple stem cell types. Recently, a novel autocrine loop (IL-6/STAT3/HIF1alpha) has been observed in multiple tumor types (pancreatic, prostate, lung, and colon). The objective of this study was to probe perturbations of this loop in a glioblastoma cancer stem cell line (GSC11) derived from a human tumor by use of a JAK2/STAT3 phosphorylation inhibitor (WP1193), IL-6 stimulation, and hypoxia. A quantitative phosphoproteomic approach that employed phosphoprotein enrichment, chemical tagging with isobaric tags, phosphopeptide enrichment, and tandem mass spectrometry in a high-resolution instrument was applied. A total of 3414 proteins were identified in this study. A rapid Western blotting technique (<1 h) was used to confirm alterations in key protein expression and phosphorylation levels observed in the mass spectrometric experiments. About 10% of the phosphoproteins were linked to the IL-6 pathway, and the majority of remaining proteins could be assigned to other interlinked networks. By multiple comparisons between the sample conditions, we observed expected changes and gained novel insights into the contribution of each factor to the IL6/STAT3/HIF1alpha autocrine loop and the CSC response to perturbations by hypoxia, inhibition of STAT3 phosphorylation, and IL-6 stimulation.

Packed Column Supercritical Fluid Chromatography/Mass Spectrometry for High-Throughput Analysis

A supercritical fluid chromatograph was interfaced to a mass spectrometer, and the system was evaluated for applications requiring high sample throughput. Experiments presented demonstrate the high-speed separation capability of supercritical fluid chromatography (SFC) and the effectiveness of supercritical fluid chromatography/mass spectrometry (SFC/MS) for fast, accurate determinations of multicomponent mixtures. A high-throughput liquid chromatography/mass spectrometry (LC/MS) analysis cycle time is reduced 3-fold using our general SFC/MS high-throughput method, resulting in substantial time saving for large numbers of samples. Unknown mixture characterization is improved due to the increased selectivity of SFC/MS compared to LC/MS. This was demonstrated with sample mixtures from a 96-well combinatorial library plate. In this paper, we report a negative mode atmospheric pressure chemical ionization (APCI) method for SFC/MS suitable for most of the components in library production mixtures. Flow injection analysis (FIA) also benefits from this SFC/MS system. A broader range of solvents is amenable to the SFC mobile phase compared with standard LC/MS solvents, and solutes elute more rapidly from the SFC/MS system, reducing sample carryover and cycle time. Finally, our instrumental setup allows for facile conversion between LC/MS and SFC/MS modes of operation.

Identification of Cys255 in HIF‐1α as a novel site for development of covalent inhibitors of HIF‐1α/ARNT PasB domain protein–protein interaction

The heterodimer HIF‐1α (hypoxia inducible factor)/HIF‐β (also known as ARNT‐aryl hydrocarbon nuclear translocator) is a key mediator of cellular response to hypoxia. The interaction between these monomer units can be modified by the action of small molecules in the binding interface between their C‐terminal heterodimerization (PasB) domains. Taking advantage of the presence of several cysteine residues located in the allosteric cavity of HIF‐1α PasB domain, we applied a cysteine‐based reactomics “hotspot identification” strategy to locate regions of HIF‐1α PasB domain critical for its interaction with ARNT. COMPOUND 5 was identified using a mass spectrometry‐based primary screening strategy and was shown to react specifically with Cys255 of the HIF‐1α PasB domain. Biophysical characterization of the interaction between PasB domains of HIF‐1α and ARNT revealed that covalent binding of COMPOUND 5 to Cys255 reduced binding affinity between HIF‐1α and ARNT PasB domains approximately 10‐fold. Detailed NMR structural analysis of HIF‐1α‐PasB‐COMPOUND 5 conjugate showed significant local conformation changes in the HIF‐1α associated with key residues involved in the HIF‐1α/ARNT PasB domain interaction as revealed by the crystal structure of the HIF‐1α/ARNT PasB heterodimer. Our screening strategy could be applied to other targets to identify pockets surrounding reactive cysteines suitable for development of small molecule modulators of protein function.

Drug binding and resistance mechanism of KIT tyrosine kinase revealed by hydrogen/deuterium exchange FTICR mass spectrometry

Mutations of the receptor tyrosine kinase KIT are linked to certain cancers such as gastrointestinal stromal tumors (GISTs). Biophysical, biochemical, and structural studies have provided insight into the molecular basis of resistance to the KIT inhibitors, imatinib and sunitinib. Here, solution‐phase hydrogen/deuterium exchange (HDX) and direct binding mass spectrometry experiments provide a link between static structure models and the dynamic equilibrium of the multiple states of KIT, supporting that sunitinib targets the autoinhibited conformation of WT‐KIT. The D816H mutation shifts the KIT conformational equilibrium toward the activated state. The V560D mutant exhibits two low energy conformations: one is more flexible and resembles the D816H mutant shifted toward the activated conformation, and the other is less flexible and resembles the wild‐type KIT in the autoinhibited conformation. This result correlates with the V560D mutant exhibiting a sensitivity to sunitinib that is less than for WT KIT but greater than for KIT D816H. These findings support the elucidation of the resistance mechanism for the KIT mutants.

Discovery of a Novel B-Raf Fusion Protein Related to c-Met Drug Resistance

In recent years, there have been notable advances with the development of anticancer drugs including those targeting protein tyrosine kinases such as the c-Met receptor, which has been implicated in the development and progression of several cancers. However, despite such progress, drug resistance continues to be the single most important cause of cancer treatment failure, and understanding the mechanisms of drug resistance remains a major hurdle in treating patients with recurrent disease. PF-04217903 is a small-molecule c-Met kinase inhibitor that potently inhibits c-Met-driven processes such as cell growth (proliferation and survival), motility, invasion, and morphology of a variety of tumor cells. Resistance to PF-04217903 was observed in GTL-16, a gastric carcinoma cell line with a constitutively activated c-Met receptor. In this report, mass spectrometry (MS) based quantitative phosphoproteomic analysis was used to determine changes in signaling pathways in the parental cells in response to c-Met inhibition and to investigate the changes in protein levels and related canonical pathways in both parental and PF-04217903 resistant (R3) clones in response to c-Met inhibition. The quantitative MS workflow included phosphoprotein enrichment of cell lysates from six treatment conditions: in-solution digestion, chemical labeling of peptides with a set of 6-plex isobaric tandem mass tags (TMT), HILIC fractionation, phosphopeptide enrichment, and nano LC-MS/MS on a LTQ-Orbitrap mass spectrometer. An investigation of these quantitative datasets using Ingenuity Pathways Analysis (IPA) revealed pathway changes in the various treatments that were consistent with previously observed transcriptomic and phenotypic changes. Proteomic analysis also revealed an increase in B-Raf expression in R3 clones. Expression profiling confirmed that B-Raf gene copy number was up-regulated and also indicated the presence of a mutated form of B-Raf. Using a bottom-up MS approach, SND-1 was identified as the B-Raf fusion partner. The discovery of this novel B-Raf fusion protein presents a novel target with potential clinical implications in the treatment of patients resistant to c-Met inhibitors.

Development of a novel LC/MS method to quantitate cellular stearoyl-CoA desaturase activity.

Stearoyl-CoA desaturase 1 (SCD1) is an enzyme that catalyzes the rate-limiting step in de novo synthesis of monounsaturated fatty acids--mainly oleate and palmitoleate from stearoyl-CoA and palmitoyl-Co A, respectively. These products are the most abundant monounsaturated fatty acids in membrane phospholipids, triglycerides, cholesterol esters. Reports on mice with a targeted disruption of SCD1 gene (SCD1-/-) exhibit improved glucose tolerance and insulin sensitivity compared to wild-type suggesting SCD1 could be a therapeutic target for diabetes and related metabolic diseases. Measurement of SCD1 activity is technically challenging and traditional cell-based SCD1 assay procedure is labor intensive with low throughput. We describe here a novel medium-throughput LC/MS cell-based assay for determining cellular SCD1 activity, facilitating screening of potential SCD1 inhibitor compounds. Confluent HepG2 cells were grown in 24-well plates and incubated with vehicle or an inhibitor followed by incubation with deuterium labeled saturated fatty acid substrates. Total cell lipids were extracted and the conversion of stearate to oleate was measured by liquid chromatography-mass spectrometry. Sterculate, a known inhibitor of SCD1, inhibited the enzyme activity in a dose dependent manner in this assay with a calculated EC(50) of 247 nM. The medium-throughput method described here is an important step towards identifying an inhibitor of SCD1 to treat diabetes and related metabolic diseases.

Effects of Activating Mutations on EGFR Cellular Protein Turnover and Amino Acid Recycling Determined Using SILAC Mass Spectrometry

Rapid mutations of proteins that are targeted in cancer therapy often lead to drug resistance. Often, the mutation directly affects a drugs binding site, effectively blocking binding of the drug, but these mutations can have other effects such as changing the protein turnover half-life. Utilizing SILAC MS, we measured the cellular turnover rates of an important non-small cell lung cancer target, epidermal growth factor receptor (EGFR). Wild-type (WT) EGFR, EGFR with a single activating mutant (Del 746–750 or L858R), and the drug-resistant double mutant (L858R/T790M) EGFR were analyzed. In non-small cell lung cancer cell lines, EGFR turnover rates ranged from 28 hours in A431 cells (WT) to 7.5 hours in the PC-9 cells (Del 746–750 mutant). The measurement of EGFR turnover rate in PC-9 cells dosed with irreversible inhibitors has additional complexity due to inhibitor effects on cell viability and results were reported as a range. Finally, essential amino acid recycling (K and R) was measured in different cell lines. The recycling was different in each cell line, but the overall inclusion of the effect of amino acid recycling on calculating EGFR turnover rates resulted in a 10–20% reduction in rates.

Mass spectrometry in high throughput analysis

Elizabeth Want a,b, Michael Greig c, Bruce Compton d, Ben Bolanos c and Gary Siuzdak a,b,∗ a The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA b Mass Consortium Corporation, 3030 Bunker Hill Street, San Diego, CA 92109, USA c Pfizer Global Research and Development – La Jolla Laboratories, Agouron Pharmaceuticals, Inc., 10770 Science Center Drive, San Diego, CA 92121, USA d Waters Corporation, 34 Maple Street, Milford, MA 01757, USA

Abstract 628: A novel SND1-BRAF fusion confers resistance to the cMet inhibitor PF-04217903 in GTL16 cells

The hepatocyte growth factor receptor (HGFR/cMET) signaling pathway is a driver of tumorigenesis in a variety of tumor types, and a number of agents targeting cMet, including PF-04217903, are under investigation in clinical trials. Tumor types exhibiting an amplified MET gene locus such as gastric, NSCLC, or esophageal cancers are of particular interest for clinical development of c-Met inhibitors. While inhibition of other receptor tyrosine kinases (RTKs) such as ErbB2, EGFR, or KIT have proven to be effective treatments for cancer patients, most tumors become refractory to respective targeted therapies due to the emergence of resistance mechanisms associated with drug targets or upregulation of compensatory pathways. To identify potential mechanisms of resistance to c-Met inhibitors, a gastric carcinoma line (GTL16) was placed under selective pressure by culturing cells in increasing concentrations of PF-0421703 in vitro and resistant clones were isolated. Resistant clones were characterized for changes in signaling, gene expression, and DNA copy number variation as compared to parental GTL16 cells. These studies resulted in the identification of genomic rearrangements at the 7q32 and 7q34 loci which produce a novel SND1-BRAF fusion protein in resistant cells. The fusion protein includes the BRAF kinase domain and is both constitutively active and overexpressed relative to parent cells as determined by gene expression array, immunoblot, and mass spectrometry. In addition, phosphoproteomic analyses demonstrated enrichment of phosphopeptides associated with the MAPK pathway signaling proteins relative to wildtype cells. Cells expressing the fusion protein exhibited resistance to multiple c-Met inhibitors whereas treatment of resistant cells with a combination of c-Met and BRAF inhibitors or a MEK inhibitor (PD325901) reversed the resistance phenotype by reestablishing inhibition of MAPK signaling and restoring growth inhibition. Together, these data provide an unique example of a mechanism where MAPK activation, through BRAF amplification/rearrangement, confers resistance to a RTK/cMET inhibitor. Furthermore, the results suggest the importance of MEK/ERK signaling downstream of c-Met and that a potential combination strategy for c-Met inhibitors with BRAF or MEK inhibitors could be employed to delay onset or circumvent potential resistance mechanisms. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 628.