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File includes drug synergy scores for 1 cell line screened against OTX015

File contains information on small molecules included in screening library

File includes AlphaScreening values for activity of the screening library against the BET or p300 bromodomains

Supplemental figures, figure legends, table legends, methods, and references

File includes drug synergy scores for 4 cell lines screened against CPI-637

File includes drug synergy scores for 6 cell lines screened against JQ1

File contains enrichment scores and p-values for gene sets evaluated using GSEA for RNA sequencing data sets

Inhibition of the HER2/ERBB2 receptor is a keystone to treating HER2-positive malignancies, particularly breast cancer, but a significant fraction of HER2-positive (HER2+) breast cancers recur or fail to respond. Anti-HER2 monoclonal antibodies, like trastuzumab or pertuzumab, and ATP active site inhibitors like lapatinib, commonly lack durability because of adaptive changes in the tumor leading to resistance. HER2+ cell line responses to inhibition with lapatinib were analyzed by RNAseq and ChIPseq to characterize transcriptional and epigenetic changes. Motif analysis of lapatinib-responsive genomic regions implicated the pioneer transcription factor FOXA1 as a mediator of adaptive responses. Lapatinib in combination with FOXA1 depletion led to dysregulation of enhancers, impaired adaptive upregulation of HER3, and decreased proliferation. HER2-directed therapy using clinically relevant drugs (trastuzumab with or without lapatinib or pertuzumab) in a 7-day clinical trial designed to examine early pharmacodynamic response to antibody-based anti-HER2 therapy showed reduced FOXA1 expression was coincident with decreased HER2 and HER3 levels, decreased proliferation gene signatures, and increased immune gene signatures. This highlights the importance of the immune response to anti-HER2 antibodies and suggests that inhibiting FOXA1-mediated adaptive responses in combination with HER2 targeting is a potential therapeutic strategy.

PurposexDECIDE is a clinical decision support system, accessed through a web portal and powered by a “Human-AI Team”, that offers oncology healthcare providers a set of treatment options personalized for their cancer patients, and provides outcomes tracking through an observational research protocol. This article describes the xDECIDE process and the AI-assisted technologies that ingest semi-structured electronic medical records to identify and then standardize clinico-genomic features, generate a structured personal health record (PHR), and produce ranked treatment options based on clinical evidence, expert insights, and the real world evidence generated within the system itself.MethodPatients may directly enroll in the IRB-approved pan-cancer XCELSIOR registry (NCT03793088). Patient consent permits data aggregation, continuous learning from clinical outcomes, and sharing of limited datasets within the research team. Assisted by numerous AI-based technologies, the xDECIDE team aggregates and processes patients’ electronic medical records, and applies multiple levels of natural language processing (NLP) and machine learning to generate a structured case summary and a standardized list of patient features. Next a ranked list of treatment options is created by an ensemble of AI-based models, called xCORE. The output of xCORE is reviewed by molecular pharmacologists and expert oncologists in a virtual tumor board (VTB). Finally a report is produced that includes a ranked list of treatment options and supporting scientific and medical rationales. Treating physicians can use an interactive portal to view all aspects of these data and associated reports, and to continuously monitor their patients’ information. The xDECIDE system, including xCORE, is self-improving; feedback improves aspects of the process through machine learning, knowledge ingestion, and outcomes-directed process improvement.ResultsAt the time of writing, over 2,000 patients have enrolled in XCELSIOR, including over 650 with CNS cancers, over 300 with pancreatic cancer, and over 100 each with ovarian, colorectal, and breast cancers. Over 150 VTBs of CNS cancer patients and ∼100 VTBs of pancreatic cancer patients have been performed. In the course of these discussions, ∼450 therapeutic options have been discussed and over 2,000 consensus rationales have been delivered. Further, over 500 treatment rationale statements (“rules”) have been encoded to improve algorithm decision making between similar therapeutics or regimens in the context of individual patient features. We have recently deployed the xCORE AI-based treatment ranking algorithm for validation in real-world patient populations.ConclusionClinical decision support through xDECIDE is available for oncologists to utilize in their standard practice of medicine by enrolling a patient in the XCELSIOR trial and accessing xDECIDE through its web portal. This system can help to identify potentially effective treatment options individualized for each patient, based on sophisticated integration of real world evidence, human expert knowledge and opinion, and scientific and clinical publications and databases.

Mutations in MAPT (microtubule-associated protein tau) cause frontotemporal dementia (FTD). MAPT mutations are associated with abnormal tau phosphorylation levels and accumulation of misfolded tau protein that can propagate between neurons ultimately leading to cell death (tauopathy). Recently, a p.A152T tau variant was identified as a risk factor for FTD, Alzheimer's disease, and synucleinopathies. Here we used induced pluripotent stem cells (iPSC) from a patient carrying this p.A152T variant to create a robust, functional cellular assay system for probing pathophysiological tau accumulation and phosphorylation. Using stably transduced iPSC-derived neural progenitor cells engineered to enable inducible expression of the pro-neural transcription factor Neurogenin 2 (Ngn2), we generated disease-relevant, cortical-like glutamatergic neurons in a scalable, high-throughput screening compatible format. Utilizing automated confocal microscopy, and an advanced image-processing pipeline optimized for analysis of morphologically complex human neuronal cultures, we report quantitative, subcellular localization-specific effects of multiple kinase inhibitors on tau, including ones under clinical investigation not previously reported to affect tau phosphorylation. These results demonstrate the potential for using patient iPSC-derived ex vivo models of tauopathy as genetically accurate, disease-relevant systems to probe tau biochemistry and support the discovery of novel therapeutics for tauopathies.

Non-Hodgkin lymphomas (NHLs) make up the majority of lymphoma diagnoses and represent a very diverse set of malignancies. We sought to identify kinases uniquely up-regulated in different NHL subtypes. Using multiplexed inhibitor bead-mass spectrometry (MIB/MS), we found Tyro3 was uniquely up-regulated and important for cell survival in primary effusion lymphoma (PEL), which is a viral lymphoma infected with Kaposi’s sarcoma-associated herpesvirus (KSHV). Tyro3 was also highly expressed in PEL cell lines as well as in primary PEL exudates. Based on this discovery, we developed an inhibitor against Tyro3 named UNC3810A, which hindered cell growth in PEL, but not in other NHL subtypes where Tyro3 was not highly expressed. UNC3810A also significantly inhibited tumor progression in a PEL xenograft mouse model that was not seen in a non-PEL NHL model. Taken together, our data suggest Tyro3 is a therapeutic target for PEL.

Metastasis suppression by high-dose, multi-drug targeting is largely unsuccessful due to network heterogeneity and compensatory network activation. Here we show that targeting driver network signaling capacity by limited inhibition of its core pathways is a more effective anti-metastatic strategy. This principle underlies the action of a physiological metastasis suppressor, Raf Kinase Inhibitory Protein, which moderately decreases stress-regulated MAP kinase network activity, reducing the output to metastatic transcription factor BACH1 and motility-related target genes. We developed a low-dose four-drug mimic that blocks metastatic colonization in mouse breast cancer models and increases survival. Experiments and network flow modeling show: 1) limited inhibition of multiple pathways is required to overcome variation in MAPK network topology and suppress signaling output across heterogeneous tumor cells, and 2) restricting inhibition of individual kinases dissipates surplus signal, preventing threshold activation of compensatory kinase networks. This low-dose multi-drug approach to decrease signaling capacity of driver networks represents a transformative, clinically-relevant strategy for anti-metastatic treatment.

Metastasis suppression by high-dose, multi-drug targeting is unsuccessful due to network heterogeneity and compensatory network activation. Here, we show that targeting driver network signaling capacity by limited inhibition of core pathways is a more effective anti-metastatic strategy. This principle underlies the action of a physiological metastasis suppressor, Raf Kinase Inhibitory Protein (RKIP), that moderately decreases stress-regulated MAP kinase network activity, reducing output to transcription factors such as pro-metastastic BACH1 and motility-related target genes. We developed a low-dose four-drug mimic that blocks metastatic colonization in mouse breast cancer models and increases survival. Experiments and network flow modeling show limited inhibition of multiple pathways is required to overcome variation in MAPK network topology and suppress signaling output across heterogeneous tumor cells. Restricting inhibition of individual kinases dissipates surplus signal, preventing threshold activation of compensatory kinase networks. This low-dose multi-drug approach to decrease signaling capacity of driver networks represents a transformative, clinically relevant strategy for anti-metastatic treatment.

Background Meningiomas are the most common primary brain tumor in adults, and somatic loss of the neurofibromatosis 2 (NF2) tumor suppressor gene is a frequent genetic event. There is no effective treatment for tumors that recur or continue to grow despite surgery and/or radiation. Therefore, targeted therapies that either delay tumor progression or cause tumor shrinkage are much needed. Our earlier work established mammalian target of rapamycin complex mTORC1/mTORC2 activation in NF2-deficient meningiomas. Methods High-throughput kinome analyses were performed in NF2-null human arachnoidal and meningioma cell lines to identify functional kinome changes upon NF2 loss. Immunoblotting confirmed the activation of kinases and demonstrated effectiveness of drugs to block the activation. Drugs, singly and in combination, were screened in cells for their growth inhibitory activity. Antitumor drug efficacy was tested in an orthotopic meningioma model. Results Erythropoietin-producing hepatocellular receptor tyrosine kinases (EPH RTKs), c-KIT, and Src family kinase (SFK) members, which are biological targets of dasatinib, were among the top candidates activated in NF2-null cells. Dasatinib significantly inhibited phospho-EPH receptor A2 (pEPHA2), pEPHB1, c-KIT, and Src/SFK in NF2-null cells, showing no cross-talk with mTORC1/2 signaling. Posttreatment kinome analyses showed minimal adaptive changes. While dasatinib treatment showed some activity, dual mTORC1/2 inhibitor and its combination with dasatinib elicited stronger growth inhibition in meningiomas. Conclusion Co-targeting mTORC1/2 and EPH RTK/SFK pathways could be a novel effective treatment strategy for NF2-deficient meningiomas.

xCures operates a direct-to-patient, real-world evidence platform for decentralized clinical research. The platform leverages a nationwide observational research protocol (XCELSIOR, NCT03793088) to aggregate, normalize, and analyze N-of-1 clinical outcomes to continuously learn from and inform treatment decisions. Individual data elements are extracted directly from medical documents such as clinic notes, and radiology, genomics, and pathology reports. The data elements are standardized to established biomedical ontologies and stored in a validated and part 11 compliant electronic database, suitable for statistical analyses and regulatory filings. This permits comparison of patient outcomes across institutions and removes the burden of data entry from oncologists and their staff. As an extremely efficient real-world data solution, we have utilized this platform to accelerate both academic- and commercial-sponsored clinical research, prospectively integrating diagnostics and algorithms with interventional treatments. For each patient that participates in XCELSIOR, artificial intelligence-powered clinical decision support algorithms suggest testing and treatment options. These options and supporting treatment rationales are sourced from key opinion leaders, tumor boards, clinical researchers, practicing oncologists, and published literature, and ranked using the real-world outcomes data from the registry. At the conference, we will present an overview of this real-time learning infrastructure and report on clinical case studies for pharma and non-profit groups including over 75 virtual tumor boards and real-world evidence generated from over 150 patients with CNS cancers that we have helped in partnership with Cancer Commons and The Musella Foundation for Brain Tumor Research and Education. Outcomes analyses stratified by therapeutic interventions and biomarkers will be reported, including frequency of adverse events, time to treatment failure, time to disease progression, and overall survival. Interventions include standard-of-care chemotherapies as well as therapies accessed by clinical trial, expanded access, and off-label prescription.

Rationale: Cystic fibrosis (CF) lung disease is caused by the loss of function of the cystic fibrosis transmembrane conductance regulator (CFTR) combined with hyperactivation of the epithelial sodium channel (ENaC). In the lung, ENaC is responsible for movement of sodium. Hyperactivation of ENaC, which creates an osmotic gradient that pulls fluid out of the airway, contributes to reduced airway hydration, causing mucus dehydration, decreased mucociliary clearance, and recurrent acute bacterial infections. ENaC represents a therapeutic target to treat all patients with CF independent of their underlying CFTR mutation.Objectives: To investigate the in vitro and in vivo efficacy of SPX-101, a peptide mimetic of the natural regulation of ENaC activity by short palate, lung, and nasal epithelial clone 1, known as SPLUNC1.Methods: ENaC internalization by SPX-101 in primary human bronchial epithelial cells from healthy and CF donors was assessed by surface biotinylation and subsequent Western blot analysis. SPX-...

Background: In healthy lungs, epithelial sodium channel (ENaC) is regulated by short, palate, lung, and nasal clone 1 (SPLUNC1). In cystic fibrosis (CF), ENaC is hyperactivated in part due to a loss of SPLUNC1 function. We have developed SPX-101 to replace the lost function of SPLUNC1 in the CF lung. Methods: Expression of SPLUNC1 was determined in sputum from healthy and CF donors. Stability of SPLUNC1, S18 (the ENaC regulatory domain of SPLUNC1), and SPX-101 was determined in sputum from CF donors and towards neutrophil elastase. Activity of SPX-101 after exposure to CF sputum was determined in airway epithelial cells from CF donors and in the βENaC transgenic mouse model. Results: SPLUNC1 protein expression is significantly reduced in CF as compared to healthy sputum. SPLUNC1 is rapidly degraded in CF sputum as well as by a number of individual proteases known to be found in the sputum. SPX-101, but not S18, is stable in CF sputum. Finally, SPX-101 retains its ability to internalize ENaC, regulate airway surface liquid height, and increase survival of βENaC mice after exposure to CF sputum. Conclusions: Our results demonstrate that SPX-101, but not SPLUNC1 or S18, is stable in CF sputum. These results support the therapeutic development of SPX-101 for the treatment of cystic fibrosis. Fil: Sesma, Juliana. Spyryx Biosciences; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Wu, Bryant. Spyryx Biosciences; Estados Unidos Fil: Stuhlmiller, Timothy J.. Spyryx Biosciences; Estados Unidos Fil: Scott, David W.. Spyryx Biosciences; Estados Unidos

Screening of an inhibitor library targeting kinases and epigenetic regulators identified several molecules having antiproliferative synergy with extraterminal domain (BET) bromodomain (BD) inhibitors (JQ1, OTX015) in triple-negative breast cancer (TNBC). GSK2801, an inhibitor of BAZ2A/B BDs, of the imitation switch chromatin remodeling complexes, and BRD9, of the SWI/SNF complex, demonstrated synergy independent of BRD4 control of P-TEFb–mediated pause-release of RNA polymerase II. GSK2801 or RNAi knockdown of BAZ2A/B with JQ1 selectively displaced BRD2 at promoters/enhancers of ETS-regulated genes. Additional displacement of BRD2 from rDNA in the nucleolus coincided with decreased 45S rRNA, revealing a function of BRD2 in regulating RNA polymerase I transcription. In 2D cultures, enhanced displacement of BRD2 from chromatin by combination drug treatment induced senescence. In spheroid cultures, combination treatment induced cleaved caspase-3 and cleaved PARP characteristic of apoptosis in tumor cells. Thus, GSK2801 blocks BRD2-driven transcription in combination with BET inhibitor and induces apoptosis of TNBC. Implications: Synergistic inhibition of BDs encoded in BAZ2A/B, BRD9, and BET proteins induces apoptosis of TNBC by a combinatorial suppression of ribosomal DNA transcription and ETS-regulated genes.

Meningiomas (MN), the most common adult primary intracranial tumor, arise from the arachnoid/meninges and are non-responsive to chemotherapies with a high recurrence rate despite surgery, necessitating effective non-invasive therapies. Our previous work showed that NF2 loss activates mechanistic target of rapamycin complex 1 (mTORC1) and mTORC2 signaling, which led to past NF2 clinical trials using rapalogs (RAD001/everolimus), and current meningioma clinical trials with dual mTORC1/mTORC2 inhibitor (mTORi) AZD2014. To understand additional dysregulated, potentially druggable pathways, we undertook an ‘omics approach of large-scale kinomics and RNA-sequencing employing CRISPR-modified human arachnoidal cells (ACs), NF2-expressing vs NF2-null. In NF2-null ACs, several kinases were elevated including erythropoietin-producing hepatocellular (EPH)-receptor tyrosine kinase (RTK) family members, Src family kinase (SFK) members, and c-KIT, all targets of dasatinib. In vitro treatment of MN cells using mTORi (AZD2014 or INK128) and dasatinib enhanced growth inhibition upon combination mTORi+dasatinib. In vivo treatment of an orthotopic mouse MN model showed moderate response to dasatinib with stronger response using INK128 or INK128+dasatinib (e-published in Neuro-Oncology). Our transcriptomic data also revealed increased expression of several ligands/growth factors, particularly NRG1/neuregulin. Expanding these results, we have confirmed increased expression of NRG1 in human NF2-null ACs. We also find NF2-null ACs secrete NRG1, and in conditioned-media experiments we observe stimulation of ErbB3, EPHA2 and mTOR pathways, suggesting an autocrine signaling mechanism. NF2-null AC or MN cells, when stimulated with exogenous NRG1, show enhanced activation of mTOR and EPH pathways besides ErbB3 signaling. Further, lapatinib (multi-ErbB inhibitor) but not erlotinib (EGFR inhibitor) attenuates the NRG1-stimulated activation of ErbB3, EPHA2 and mTOR, suggesting that NRG1-induced activation is EGFR-independent. Taken together, our results support a mechanistic link where NF2 loss increases NRG1/ErbB signaling to EPH/SFK and mTOR pathways, which may be a critical driver of tumorigenesis, thus providing a therapeutic opportunity to co-target these pathways in NF2-deficient meningiomas.

High-dose, single-drug treatment is unsuccessful at suppressing metastasis due to cellular heterogeneity and feedback activation. Here we demonstrate that targeting driver network signaling capacity by limited inhibition at multiple nodes is a more effective anti-metastatic strategy. A physiological metastasis suppressor, Raf Kinase Inhibitory Protein, decreases the activity of multiple kinases in the stress-regulated MAP kinase (MAPK) network and reduces the output to metastatic transcription factor BACH1 that upregulates motility-related genes. This effect is mimicked by a low-dose four-drug cocktail (4D-MAPKi) that blocks metastatic colonization in mouse breast cancer models and increases survival. Drug treatment and network modeling show that 1) multi-kinase inhibition is required to suppress signaling output across cells with different MAPK network topologies, and 2) restricting inhibition of individual kinases prevents threshold activation of other compensatory kinase networks. This low-dose multi-drug approach to decrease signaling capacity of a driver network represents a transformative, clinically-relevant strategy for anti-metastatic treatment. Citation Format: Ali Ekrem Yesilkanal, Dongbo Yang, Payal Tiwari, Alan U. Sabino, Jiyoung Lee, Xiao-He Xie, Siqi Sun, Christopher Dann, Ethan Steinberg, Timothy Stuhlmiller, Casey Frankenberger, Elizabeth Goldsmith, Gary L. Johnson, Alexandre F. Ramos, Marsha Rosner. Limited inhibition of multiple nodes in a driver network blocks metastasis [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5038.

SummaryTherapeutics that target ERBB2, such as lapatinib, often provide initial clinical benefit, but resistance frequently develops. Adaptive responses leading to lapatinib resistance involve reprogramming of the kinome through reactivation of ERBB2/ERBB3 signaling and transcriptional upregulation and activation of multiple tyrosine kinases. The heterogeneity of induced kinases prevents their targeting by a single kinase inhibitor, underscoring the challenge of predicting effective kinase inhibitor combination therapies. We hypothesized that, to make the tumor response to single kinase inhibitors durable, the adaptive kinome response itself must be inhibited. Genetic and chemical inhibition of BET bromodomain chromatin readers suppresses transcription of many lapatinib-induced kinases involved in resistance, including ERBB3, IGF1R, DDR1, MET, and FGFRs, preventing downstream SRC/FAK signaling and AKT reactivation. Combining inhibitors of kinases and chromatin readers prevents kinome adaptation by blocking transcription, generating a durable response to lapatinib, and overcoming the dilemma of heterogeneity in the adaptive response.

Background Most novel cancer therapeutics target kinases that are essential to tumor survival. Some of these kinase inhibitors are associated with cardiotoxicity, whereas others appear to be cardiosafe. The basis for this distinction is unclear, as are the molecular effects of kinase inhibitors in the heart. Methods and Results We administered clinically relevant doses of sorafenib, sunitinib (cardiotoxic multitargeted kinase inhibitors), or erlotinib (a cardiosafe epidermal growth factor receptor inhibitor) to mice daily for 2 weeks. We then compared the effects of these 3 kinase inhibitors on the cardiac transcriptome using RNA seq and the cardiac kinome using multiplexed inhibitor beads coupled with mass spectrometry. We found unexpectedly broad molecular effects of all 3 kinase inhibitors, suggesting that target kinase selectivity does not define either the molecular response or the potential for cardiotoxicity. Using in vivo drug administration and primary cardiomyocyte culture, we also show that the cardiosafety of erlotinib treatment may result from upregulation of the cardioprotective signal transducer and activator of transcription 3 pathway, as co‐treatment with erlotinib and a signal transducer and activator of transcription inhibitor decreases cardiac contractile function and cardiomyocyte fatty acid oxidation. Conclusions Collectively our findings indicate that preclinical kinome and transcriptome profiling may predict the cardiotoxicity of novel kinase inhibitors, and suggest caution for the proposed therapeutic strategy of combined signal transducer and activator of transcription/epidermal growth factor receptor inhibition for cancer treatment.

// Kyla A.L. Collins 1, * , Timothy J. Stuhlmiller 2, 3, * , Jon S. Zawistowski 2, 3 , Michael P. East 2, 3 , Trang T. Pham 2, 3 , Claire R. Hall 4 , Daniel R. Goulet 2, 3 , Samantha M. Bevill 2, 3 , Steven P. Angus 2, 3 , Sara H. Velarde 2, 3 , Noah Sciaky 2 , Tudor I. Oprea 5, 6 , Lee M. Graves 2, 3 , Gary L. Johnson 2, 3 and Shawn M. Gomez 1, 2, 4 1 Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA 2 Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA 3 Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA 4 Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC 27514, USA 5 Translational Informatics Division, School of Medicine, University of New Mexico, Albuquerque, NM 87106, USA 6 UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA * These authors contributed equally to this work Correspondence to: Gary L. Johnson, email: gary_johnson@med.unc.edu Shawn M. Gomez, email: smgomez@unc.edu Keywords: cancer biology; proteomics; kinase signaling Received: September 27, 2017 Accepted: January 19, 2018 Epub: January 29, 2018 Published: March 20, 2018 ABSTRACT Multiplexed small molecule inhibitors covalently bound to Sepharose beads (MIBs) were used to capture functional kinases in luminal, HER2-enriched and triple negative (basal-like and claudin-low) breast cancer cell lines and tumors. Kinase MIB-binding profiles at baseline without perturbation proteomically distinguished the four breast cancer subtypes. Understudied kinases, whose disease associations and pharmacology are generally unexplored, were highly represented in MIB-binding taxonomies and are integrated into signaling subnetworks with kinases that have been previously well characterized in breast cancer. Computationally it was possible to define subtypes using profiles of less than 50 of the more than 300 kinases bound to MIBs that included understudied as well as metabolic and lipid kinases. Furthermore, analysis of MIB-binding profiles established potential functional annotations for these understudied kinases. Thus, comprehensive MIBs-based capture of kinases provides a unique proteomics-based method for integration of poorly characterized kinases of the understudied kinome into functional subnetworks in breast cancer cells and tumors that is not possible using genomic strategies. The MIB-binding profiles readily defined subtype-selective differential adaptive kinome reprogramming in response to targeted kinase inhibition, demonstrating how MIB profiles can be used in determining dynamic kinome changes that result in subtype selective phenotypic state changes.

Background Glioblastoma (GBM) is the most common and aggressive primary brain tumor. Prognosis remains poor despite multimodal therapy. Developing alternative treatments is essential. Drugs targeting kinases within the phosphoinositide 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) effectors of receptor tyrosine kinase (RTK) signaling represent promising candidates. Methods We previously developed a non-germline genetically engineered mouse model of GBM in which PI3K and MAPK are activated via Pten deletion and KrasG12D in immortalized astrocytes. Using this model, we examined the influence of drug potency on target inhibition, alternate pathway activation, efficacy, and synergism of single agent and combination therapy with inhibitors of these 2 pathways. Efficacy was then examined in GBM patient-derived xenografts (PDX) in vitro and in vivo. Results PI3K and mitogen-activated protein kinase kinase (MEK) inhibitor potency was directly associated with target inhibition, alternate RTK effector activation, and efficacy in mutant murine astrocytes in vitro. The kinomes of GBM PDX and tumor samples were heterogeneous, with a subset of the latter harboring MAPK hyperactivation. Dual PI3K/MEK inhibitor treatment overcame alternate effector activation, was synergistic in vitro, and was more effective than single agent therapy in subcutaneous murine allografts. However, efficacy in orthotopic allografts was minimal. This was likely due to dose-limiting toxicity and incomplete target inhibition. Conclusion Drug potency influences PI3K/MEK inhibitor-induced target inhibition, adaptive kinome reprogramming, efficacy, and synergy. Our findings suggest that combination therapies with highly potent, brain-penetrant kinase inhibitors will be required to improve patient outcomes.

Targeting the dysregulated BRAF–MEK–ERK pathway in cancer has increasingly emerged in clinical trial design. Despite clinical responses in specific cancers using inhibitors targeting BRAF and MEK, resistance develops often involving nongenomic adaptive bypass mechanisms. Inhibition of MEK1/2 by trametinib in patients with triple-negative breast cancer (TNBC) induced dramatic transcriptional responses, including upregulation of receptor tyrosine kinases (RTK) comparing tumor samples before and after one week of treatment. In preclinical models, MEK inhibition induced genome-wide enhancer formation involving the seeding of BRD4, MED1, H3K27 acetylation, and p300 that drives transcriptional adaptation. Inhibition of the P-TEFb–associated proteins BRD4 and CBP/p300 arrested enhancer seeding and RTK upregulation. BRD4 bromodomain inhibitors overcame trametinib resistance, producing sustained growth inhibition in cells, xenografts, and syngeneic mouse TNBC models. Pharmacologic targeting of P-TEFb members in conjunction with MEK inhibition by trametinib is an effective strategy to durably inhibit epigenomic remodeling required for adaptive resistance. Significance: Widespread transcriptional adaptation to pharmacologic MEK inhibition was observed in TNBC patient tumors. In preclinical models, MEK inhibition induces dramatic genome-wide modulation of chromatin, in the form of de novo enhancer formation and enhancer remodeling. Pharmacologic targeting of P-TEFb complex members at enhancers is an effective strategy to durably inhibit such adaptation. Cancer Discov; 7(3); 302–21. ©2017 AACR. This article is highlighted in the In This Issue feature, p. 235

Regulatory transcription factors of the Pax family play fundamental roles in the function of multipotent cells during vertebrate development, post-natal regeneration, and cancer. Pax7 and its homologue Pax3 are important players in neural crest and muscle development. Both genes are coexpressed in various tissues and are thought to provide similar, but not identical, functions. The mechanisms that allow specific regulation of Pax7 remain largely unknown. Here, we report for the first time that Pax7 is regulated by SUMOylation. We identify the interaction of Pax7 with Ubc9, the SUMO conjugating enzyme, and reveal that SUMOylation machinery is enriched in neural crest precursors and plays a critical role in NC development. We demonstrate that Pax7 becomes SUMOylated and identify an essential role for lysine 85 (K85) in Pax7-SUMOylation. Despite high conservation surrounding K85 amongst Pax genes, we were unable to identify SUMOylation of other Pax proteins tested, including Pax3. Using a non-SUMOylatable Pax7 variant (K85 X R), we demonstrate that SUMOylation is essential for the function of Pax7 in neural crest development, C2C12 myogenic differentiation, and transcriptional transactivation. Our study provides new mechanistic insight into the molecular regulation of Pax7’s function by SUMOylation in neural crest and muscle development.

1027 Background: HER2 targeting is challenging due to heterogeneity in response and resistance. Adaptive kinome reprogramming (AKRP) is a resistance mechanism to kinase-targeted therapy (Rx) in TNBC ( Cancer Discovery2017). We studied AKRP in HER2+ BrCa by comparing transcriptome and kinome profiles before and after Rx with FDA-approved anti-HER2 drugs and combinations: trastuzumab (T), pertuzumab (P), T+P, or T+ lapatinib (T+L). Profiling was by RNA sequencing (RNAseq) and multiplexed inhibitor beads coupled with mass spectrometry (MIB/MS). MIB affinity-purification selectively enriches the functional kinome ( > 250 kinases per sample) for identification/quantification by MS. Methods: Eligible patients (pts) had biopsy then randomization to: T (8 mg/kg iv), P (840 mg iv), T+P (same doses), or T+L (8mg/kg iv x1, 1000 mg po/d) 7 days before breast surgery. RNAseq and MIB/MS on paired pre- and post-Rx samples were analyzed using DESeq2 (comparison of mean difference in log2fold change (post/pre)) and MaxQuant (kinome response profiling) software. Results: Of 23 evaluable pts, we obtained informative paired RNAseq data in 13 (5 T, 3 P, 3 T+P, 2 T+L), and identified distinct expression responses (padj≤0.05) between Rx arms, such as FGFR4 increase in P vs T or T+P. All samples had HER2 enrichment by RNAseq. Kinome response profiling from 11 pts (3 T, 3 P, 4 T+P, 2 T+L) revealed consistent increases in MIB binding (abundance a/o activity) of several tyrosine kinases regardless of Rx, including immune-related kinases SYK, IRAK4, FGR, and FES. Other kinases, such as p90Rsk and GSK3B, exhibited increased binding in response to T and T+P, but not P alone. While not quantifiable in every sample due to detection limits, HER2 inhibition was observed by loss of MIB binding in select post-Rx versus pre-Rx comparisons. Conclusions: HER2 inhibition upregulates and activates specific receptor tyrosine kinases in tumor cells as well as alterations that may reflect changes in the immune compartment. HER2+ BrCa exhibit plasticity, characterized by distinct expression and kinome profile changes within 1 week of initiating Rx, and reprogramming in both immune responses and BrCa cells. Clinical trial information: NCT01875666.

The central role of the BRAF–MEK–ERK pathway in controlling cell fate has made this pathway a primary target for deregulated activation in cancer. BRaf is activated by Ras proteins allowing Ras oncogenes to constitutively activate the pathway. Activating BRaf mutations are also frequent in several cancers, being the most common oncogenic mutation in thyroid carcinoma and melanoma. There are currently two inhibitors, vemurafenib and dabrafenib, approved for treatment of malignant melanoma having activating BRaf mutations. Concurrent administration of BRAF and MAP–ERK kinase (MEK) inhibitor (trametinib) is significantly more active in patients with BRAF-mutant melanoma than either single agent alone, but progression to resistance ultimately occurs by different mechanisms that increase the activation of extracellular signal–regulated kinase (ERK). Such adaptive changes in tumor cell signaling networks allow bypass of targeted oncoprotein inhibition. This is true with targeted inhibitors for BRaf and MEK as well as specific inhibitors for AKT, mTOR, and many receptor tyrosine kinases such as EGF receptor (EGFR) and HER2. It is this adaptive response to targeted kinase inhibitors that contributes to the failure of single-agent kinase inhibitors to have durable responses. This failure is seen in virtually all cancers treated with single-agent kinase inhibitors, most of which are not as dependent on a single signaling pathway such as BRaf–MEK–ERK in melanoma. Thus, understanding the breadth of adaptive reprogramming responses to specific targeted kinase inhibition will be critical to develop appropriate combination therapies for durable clinical responses. Clin Cancer Res; 20(10); 2516–22. ©2014 AACR.

The RAF-MEK-ERK signaling pathway regulates the proliferation of Triple Negative Breast Cancer (TNBC). Although MEK inhibition by trametinib in TNBC cell lines and mouse models inhibits growth, the response is not durable and the tumor develops resistance. The lack of durability of targeted kinase inhibitors is a common problem in many tumor types due to induction of alternative bypass signaling pathways that lead to resistance. We have profiled the response of TNBC to MEK inhibition using trametinib in order to identify adaptive signaling pathways which drive resistance. We used a chemical proteomics method [multiplexed inhibitor beads coupled to mass spectrometry (MIB/MS)], to quantify global changes in kinase activity coupled with transcriptional changes in response to trametinib using RNAseq. Our studies revealed that adaptive resistance to trametinib occurs through increased expression and activation of multiple receptor tyrosine kinases, leading to reactivation of ERK. These adaptive kinases are heterogeneous across TNBC including PDGFRβ, VEGFR2, DDR1, AXL, KIT and FGFR2. There is no single targeted kinase inhibitor able to block all the adaptive kinases induced and activated, making the design of combination targeted kinase inhibitor therapies impractical. We therefore hypothesized an alternative therapeutic approach was required to inhibit adaptive reprogramming. Our goal was to block the initial transcriptional response to trametinib which upregulates adaptive kinase expression. Several studies in the lab determined that we could block adaptive kinase expression by inhibiting BET family bromodomain proteins that interact with acetylated histones and facilitate the formation of transcriptional regulatory complexes. Our work demonstrated that BET family bromodomain inhibitors (JQ1 and iBET151), synergize with trametinib to prevent TNBC growth in short-term (4 days) and long-term (4 weeks) growth assays. Using MIB/MS we found that combination trametinib/BET bromodomain inhibitor treatment blocks upregulation of adaptive kinase expression and activation. RNAseq demonstrated that BET bromodomain inhibitors synergize with trametinib to block the induction of kinases expressed as part of the adaptive bypass response. ChIP-seq of the BET bromodomain protein BRD4 and H3K27ac, a marker of active enhancers, showed BRD4 is recruited to super-enhancer regions proximal to adaptive response kinases as early as 4hr following trametinib treatment. Furthermore, the recruitment of BRD4 to enhancer regions is maintained in cells made resistant to trametinib by constant culture in low-dose drug. In sum, these results suggest that BRD4 recruitment to enhancer regions, following trametinib treatment, leads to the formation of transcriptional complexes which maintain adaptive gene expression. Ongoing studies seek to understand the mechanism by which BRD4 is recruited to super-enhancers following trametinib treatment in TNBC. Mouse xenograft studies also show promising evidence of enhanced tumor growth suppression in vivo using combination trametinib/iBET151 treatment. The results presented provide a novel treatment strategy to block adaptive resistance and have the potential to lead to durable clinical responses of TNBC. Citation Format: Samantha M. Miller, Jon S. Zawistowski, Timothy J. Stuhlmiller, Noah Sciaky, Charlene M. Santos, David B. Darr, Gary L. Johnson. Suppression of adaptive resistance mechanisms to trametinib by inhibition of BET bromodomains in TNBC. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr B21.

Small molecule kinase inhibitors that target oncogene-driven cancers often elicit dramatic initial clinical responses, but adaptive responses from the kinome and transcriptome limit their efficacy and generate resistance. Such adaptive bypass responses are driven by the disruption of regulatory feedback and feedforward loops that govern many signaling networks. To understand these responses in the context of HER2-addicted cancer, we used a chemical proteomics method to assay whole-kinome activation dynamics in cells treated with the small molecule HER2/EGFR tyrosine kinase inhibitor lapatinib. We observed a rapid reactivation of oncogenic signaling and a global re-wiring of kinase signaling networks including activation of receptor tyrosine kinases (RTKs) HER3, DDR1, FGFRs, IGF1R, INSR, and multiple Ephrin receptors, as well as intracellular nodes PKC, SRC family kinases and FAK. Targeting compensatory kinases with a series of kinase inhibitors provided variable and incremental enhancement of growth inhibition but could not prevent resistant colony formation. Cell line heterogeneity and functional redundancy among compensatory kinases added further difficulty to effectively predict the best combination therapy. This presents a dilemma where combinations of two or even three kinase inhibitors would be insufficient to suppress all the bypass tracks that were rapidly induced by HER2 inhibition. RNAseq revealed a 2-fold dysregulation of approximately 20% of expressed genes within 2 days of lapatinib treatment, with many responsive kinases being transcriptionally upregulated. We argued that in order for lapatinib to have a durable effect, the adaptive response itself must be inhibited. We found that by targeting the BET bromodomain family of chromatin readers, we could suppress the transcriptional upregulation of RTKs that reactivate MAPK/AKT and drive the bypass survival tracks through SRC family kinase and FAK signaling. Treatment of HER2-positive cells with three different small molecule BET bromodomain inhibitors (JQ1, I-BET151, and I-BE762) had little effect on HER2 and downstream signaling pathways in the absence of lapatinib and accordingly allowed resistant colony formation in long-term growth assays. Combining BET bromodomain inhibitors with lapatinib caused a loss of signature RTK expression, prevented MAPK/AKT reactivation, and suppressed resistant colonies from forming. BET bromodomain inhibitors also downregulated responsive RTKs in cells made resistant to lapatinib and thus re-sensitized the cells to lapatinib. Transcriptional profiling defined the effects of BET bromodomain inhibition to be less pronounced than lapatinib, with only 8% of expressed genes being downregulated 2-fold or greater. However, more than 25% of lapatinib-induced genes were downregulated 2-fold, indicating BET bromodomains preferentially modulated the induced gene expression. Current literature describes a crucial role for the BET bromodomain protein BRD4 in the regulation and stability of large enhancer regions (super-enhancers) responsible for oncogene regulation and defining cell fate. ChIPseq analysis of enhancer dynamics in response to lapatinib and JQ1 identified a reorganization of the chromatin landscape within 24 hours of drug treatment, with multiple super-enhancers formed and decommissioned. Importantly, the combination of lapatinib and JQ1 caused a loss of the majority of super-enhancers observed in untreated cells. Together, these results demonstrate epigenetic targeting of adaptive response mechanisms can prevent resistance to small molecule kinase inhibitors and provide a more durable effect for oncogene targeting in the treatment of cancer. Citation Format: Timothy J. Stuhlmiller, Samantha M. Miller, Jon S. Zawistowski, James S. Duncan, Steven P. Angus, Deborah A. Granger, Rachel A. Reuther, Kyla A.L. Collins, Gomez M. Shawn, Pei-Fen Kuan, Xin Chen, Noah Sciaky, Gary L. Johnson. BET bromodomain inhibition targets adaptive responses to lapatinib in HER2-positive breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr B25.

A predominant mechanism by which cancer cells circumvent the action of targeted kinase inhibitors is the activation of bypass signaling networks that reactivate cellular proliferation. In triple negative breast cancer (TNBC), a chief component of the adaptive response to MEK inhibition is the transcriptional upregulation and activation of receptor tyrosine kinases (RTKs), which contributes to drug resistance by reactivating ERK signaling as well as by initiating growth signaling through other kinase nodes. The cohort of RTKs activated differs between TNBC molecular subtypes and is heterogeneous even among cell lines of the same subtype; thus designing effective inhibitor combinations is challenging. Targeting the chromatin reader protein BRD4 via BET bromodomain inhibition attenuates the transcriptional adaptive response to MEK inhibition, yielding a more durable growth suppression than kinase inhibitor combinations. Yet, a detailed understanding of molecular mechanisms underlying BET bromodomain inhibitor synergy with MEK inhibitor remain unclear. We show by ChIP-seq the dynamic formation of BRD4-dense super-enhancers in response to 24 h MEK inhibition. In SUM159PT claudin-low breast cancer cells, de novo super-enhancers, whose identity were validated by histone H3 lysine 27 acetylation and MED1 co-occupancy with BRD4, were found proximal to genomic loci of DDR1, KDR, and MYLK kinases previously implicated in the adaptive MEK inhibitor response. In sum we identified 110 putative MEK inhibitor-induced SUM159PT super-enhancers, 40% of which reside within 100 kilobases 5' or 3' of a gene whose transcript is upregulated 2 fold or greater by MEK inhibition as assessed by RNA-seq, suggesting that de novo superenhancer formation is a general mode of transcriptional regulation of the adaptive response. Importantly, the MEK inhibitor-induced super-enhancers are disrupted by the BET bromodomain inhibitor JQ1, providing one potential mechanism for the growth suppression synergism obtained by combining MEK + BET bromodomain inhibition. To identify candidate direct DNA binding factors that may be seeding the observed super-enhancer formation, Multiple EM for Motif Elicitation (MEME) analysis identified an enrichment of consensus DNA binding motifs for the enhancer factors CEBPB/D in de novo super-enhancer regions, and the presence of CEBPB was confirmed to be a component of these regions by ChIP-seq. Additionally, we have achieved MEK inhibitor growth suppression synergy with inhibitors of the lysine acetyl transferases CBP/p300, known super-enhancer components. These data provide a new mechanism underlying the transcriptional control of the adaptive response to MEK inhibitor and suggest that targeting drug-induced super-enhancer elements may be a potential therapeutic avenue for TNBC. Citation Format: Jon S. Zawistowski, Samantha M. Miller, Daniel R. Goulet, Timothy J. Stuhlmiller, Darshan Singh, Noah Sciaky, Sara H. Velarde, Steven P. Angus, Gary L. Johnson. Triple-negative breast cancer adaptive response to MEK inhibition is regulated by the induction of super-enhancers. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr B24.

Neural crest induction involves the combinatorial inputs of the FGF, BMP and Wnt signaling pathways. Recently, a two-step model has emerged where BMP attenuation and Wnt activation induces the neural crest during gastrulation, whereas activation of both pathways maintains the population during neurulation. FGF is proposed to act indirectly during the inductive phase by activating Wnt ligand expression in the mesoderm. Here, we use the chick model to investigate the role of FGF signaling in the amniote neural crest for the first time and uncover a novel requirement for FGF/MAPK signaling. Contrary to current models, we demonstrate that FGF is required within the prospective neural crest epiblast during gastrulation and is unlikely to operate through mesodermal tissues. Additionally, we show that FGF/MAPK activity in the prospective neural plate prevents the ectopic expression of lateral ectoderm markers, independently of its role in neural specification. We then investigate the temporal participation of BMP/Smad signaling and suggest a later involvement in neural plate border development, likely due to widespread FGF/MAPK activity in the gastrula epiblast. Our results identify an early requirement for FGF/MAPK signaling in amniote neural crest induction and suggest an intriguing role for FGF-mediated Smad inhibition in ectodermal development.

The characterization of kinases as oncogenic drivers has led to more than 30 FDA-approved targeted kinase inhibitors for cancer treatment. Unfortunately, these therapeutics fail to have clinical durability because of adaptive responses from the kinome and transcriptome that bypass inhibition of the targeted pathway. In our recent work, we describe a method to prevent these adaptive responses at an epigenetic level, generating a durable response to kinase inhibition.

Early clinical studies have shown that concurrent administration of BRAF and MEK inhibitors, dabrafenib and trametinib, is more active in patients with BRAFV600E/K melanoma than either single agent alone. Even though the combination of BRAF/MEK inhibitors is initially highly effective in treating melanoma in a subset of patients, progression to resistance ultimately occurs–commonly via reactivation of the BRAF/MEK/ERK pathway. Therefore, therapeutic strategies to counter primary resistance and prevent the emergence of secondary resistance are needed. Following pharmacological or progressive genetic perturbations, dynamic and system-wide adaptive changes (“reprogramming”) in the expression and activity of multiple kinases (collectively termed the kinome) clearly occur in tumor cells. Rich networks of serine/threonine and tyrosine kinases, many of which are understudied, are integrated into the signaling systems controlled by oncogenes known to drive melanoma. Thus, a comprehensive understanding of the kinome at baseline, during the adaptive response to kinase inhibitor treatment, and in the context of acquired resistance is critical. We use Multiplexed Inhibitor Beads (MIBs), mixtures of covalently immobilized, linker-adapted kinase inhibitors coupled with mass spectrometry (MS), to assess changes in activation of kinases in untreated samples, during acute inhibition of BRAF and/or MEK and in the context of acquired resistance. Our enhanced MIB/MS technology allows us to study over 75-80% of the expressed kinome (and numerous lipid and metabolic kinases) simultaneously using lysates from cell lines, genetically engineered mouse model (GEMM) tumors, patient-derived xenografts or human melanoma. We have identified several kinases (e.g. PDGFRβ, DDR1, MAP3K1) that are activated upon acute treatment with dabrafenib, trametinib, or dabrafenib/trametinib as well as in drug-resistant human melanoma cells and BRAFV600E/PTEN-/- GEMM-derived tumors and cell lines. Thus, studies using MIB/MS to measure dynamic kinome responses have identified kinases that have not been previously shown to be involved in the adaptive response to BRAF and/or MEK inhibition. We are currently targeting kinases involved in adaptive kiome reprogramming, pharmacologically or by RNAi, to determine whether their activation leads to vulnerability. This work will lead to the identification of novel and rationally predicted therapies for patients with advanced melanoma. Citation Format: Steven P. Angus, Timothy J. Stuhlmiller, Rachel Reuther, Trang T. Pham, Deborah A. Granger, David B. Darr, Jamie L. Jordan, Stergios J. Moschos, Gary L. Johnson, Norman E. Sharpless. Defining the adaptive kinome response to BRAF and MEK inhibition in melanoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4761. doi:10.1158/1538-7445.AM2014-4761