Target Identification in Small Cell Lung Cancer via Integrated Phenotypic Screening and Activity-Based Protein Profiling

Li, Jiannong; Fang, Bin; Kinose, Fumi; Bai, Yun; Kim, Jae-Young; Chen, Yian Ann; Rix, Uwe; Koomen, John M.; Haura, Eric B.

doi:10.1158/1535-7163.mct-15-0444

Cited by 19 publications

(16 citation statements)

References 32 publications

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“…From these 1925 protein groups, we were able to identify 174 protein kinases or 225 kinases in total (including nine lipid kinases and 42 other generic/small molecule kinases). These results are comparable to previously-reported identifications using this technology (188 protein kinases [22], 136 protein kinases [23], and 41 protein kinases [24]). Although kinases were a primary focus, we were able to identify hundreds of other proteins in a variety of different classes (Figure 2B).…”

Section: Resultssupporting

confidence: 89%

“…The desthiobiotin-ATP probe employed in this study was originally developed for drug target profiling to assess the specificity of kinase inhibitors [15,22], but we employed it here to assess global ATP-binding proteome/kinome response to clinical MEK inhibitors in the biological context of various KRAS mutant lung cancer cell lines. Gygi and his colleagues reported that desthiobiotin-ATP probe did not specifically enrich active forms of kinases [38], thus, the changes are likely to be associated with total protein level, rather than activity, at least in the context of kinases.…”

Section: Resultsmentioning

confidence: 99%

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Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer

et al. 2016

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One way cancer cells can escape from targeted agents is through their ability to evade drug effects by rapidly rewiring signaling networks. Many protein classes, such as kinases and metabolic enzymes, are regulated by ATP binding and hydrolysis. We hypothesized that a system-level profiling of drug-induced alterations in ATP-binding proteomes could offer novel insights into adaptive responses. Here, we mapped global ATP-binding proteomes perturbed by two clinical MEK inhibitors, AZD6244 and MEK162, in KRAS mutant lung cancer cells as a model system harnessing a desthiobiotin-ATP probe coupled with LC-MS/MS. We observed strikingly unique ATP-binding proteome responses to MEK inhibition, which revealed heterogeneous drug-induced pathway signatures in each cell line. We also identified diverse kinome responses, indicating each cell adapts to MEK inhibition in unique ways. Despite the heterogeneity of kinome responses, decreased probe labeling of mitotic kinases and an increase of kinases linked to autophagy were identified to be common responses. Taken together, our study revealed a diversity of adaptive ATP-binding proteome and kinome responses to MEK inhibition in KRAS mutant lung cancer cells, and our study further demonstrated the utility of our approach to identify potential candidates of targetable ATP-binding enzymes involved in adaptive resistance and to develop rational drug combinations.

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Section: Resultssupporting

confidence: 89%

Section: Resultsmentioning

confidence: 99%

Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer

et al. 2016

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“…Growth inhibition by dual aurora A/B inhibitors and with AURKB knockdown has been correlated with cMYC amplification alone (15) and by other investigators with any MYC family amplification or high MYC family gene expression (17). Recently, it has also been shown through activity-based protein profiling that AURKB is a critical kinase in cMYC amplified SCLC cell lines but not in SCLC lines that lack cMYC amplification (31). Amplifications and overexpression of MYC family oncogenes has been reported in 15–30% of SCLCs (18, 19).…”

Section: Discussionmentioning

confidence: 99%

Barasertib (AZD1152), a Small Molecule Aurora B Inhibitor, Inhibits the Growth of SCLC Cell Lines In Vitro and In Vivo

Helfrich

Kim

Gao

et al. 2016

Molecular Cancer Therapeutics

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Small cell lung cancer (SCLC) cells have rapid proliferation, universal Rb inactivation and high rates of MYC family amplification, making aurora kinase inhibition a natural target. Preclinical studies have demonstrated activity for Aurora A and pan Aurora inhibitors with some relationship to MYC family expression. A clinical trial showed activity for an Aurora kinase A inhibitor but no biomarkers were evaluated. We screened a panel of 23 SCLC lines with and without MYC family gene amplification or high MYC family gene expression for growth inhibition by the highly potent, selective aurora kinase B inhibitor barasertib. Nine of the SCLC lines were very sensitive to growth inhibition by barasertib with IC50 values of < 50 nM and > 75% growth inhibition at 100 nM. Growth inhibition correlated with cMYC amplification (p = 0.018) and cMYC gene expression (p = 0.026). Sensitive cell lines were also enriched in a published MYC gene signature (p = 0.042). In vivo the barasertib inhibited the growth of xenografts established from a SCLC line which had high cMYC gene expression, no cMYC amplification and was positive for the core MYC gene signature. Our studies suggest that SCLC tumors with cMYC amplification/high gene expression will frequently respond to Aurora B inhibitors and that clinical studies coupled with predictive biomarkers are indicated.

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“…Similarly, screenings of migration inhibitors have also led to the discovery of potential therapeutic kinase targets [ 45 ]. These large screens of uncharacterized compounds are well complemented by other methods such as activity-based protein profiling (ABPP) [ [87] , [88] , [89] , [90] ], peptide arrays or siRNA arrays that can identify the specific proteins and pathways targeted by the inhibitor.…”

Section: Application and Integration Of Systems Kinomics To Diseasesmentioning

confidence: 99%

Methods and approaches to disease mechanisms using systems kinomics

Berard

Kroeker

McQueen

et al. 2018

Synthetic and Systems Biotechnology

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All cellular functions, ranging from regular cell maintenance and homeostasis, specialized functions specific to cellular types, or generating responses due to external stimulus, are mediated by proteins within the cell. Regulation of these proteins allows the cell to alter its behavior under different circumstances. A major mechanism of protein regulation is utilizing protein kinases and phosphatases; enzymes that catalyze the transfer of phosphates between substrates [1]. Proteins involved in phosphate signaling are well studied and include kinases and phosphatases that catalyze opposing reactions regulating both structure and function of the cell. Kinomics is the study of kinases, phosphatases and their targets, and has been used to study the functional changes in numerous diseases and infectious diseases with aims to delineate the cellular functions affected. Identifying the phosphate signaling pathways changed by certain diseases or infections can lead to novel therapeutic targets. However, a daunting 518 putative protein kinase genes have been identified [2], indicating that this protein family is very large and complex. Identifying which enzymes are specific to a particular disease can be a laborious task. In this review, we will provide information on large-scale systems biology methodologies that allow global screening of the kinome to more efficiently identify which kinase pathways are pertinent for further study.

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Target Identification in Small Cell Lung Cancer via Integrated Phenotypic Screening and Activity-Based Protein Profiling

Cited by 19 publications

References 32 publications

Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer

Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer

Barasertib (AZD1152), a Small Molecule Aurora B Inhibitor, Inhibits the Growth of SCLC Cell Lines In Vitro and In Vivo

Methods and approaches to disease mechanisms using systems kinomics

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