A Novel Irreversible TEAD Inhibitor, SWTX-143, Blocks Hippo Pathway Transcriptional Output and Causes Tumor Regression in Preclinical Mesothelioma Models

The Hippo pathway and its downstream effectors, the YAP and TAZ transcriptional coactivators, are deregulated in multiple different types of human cancer and are required for cancer cell phenotypes in vitro and in vivo, while largely dispensable for tissue homeostasis in adult mice. YAP/TAZ and their main partner transcription factors, the TEAD1-4 factors, are therefore promising anticancer targets. Because of frequent YAP/TAZ hyperactivation caused by mutations in the Hippo pathway components NF2 and LATS2, mesothelioma is one of the prime cancer types predicted to be responsive to YAP/TAZ-TEAD inhibitor treatment. Mesothelioma is a devastating disease for which currently no effective treatment options exist. Here, we describe a novel covalent YAP/TAZ-TEAD inhibitor, SWTX-143, that binds to the palmitoylation pocket of all four TEAD isoforms. SWTX-143 caused irreversible and specific inhibition of the transcriptional activity of YAP/TAZ-TEAD in Hippo-mutant tumor cell lines. More importantly, YAP/TAZ-TEAD inhibitor treatment caused strong mesothelioma regression in subcutaneous xenograft models with human cells and in an orthotopic mesothelioma mouse model. Finally, SWTX-143 also selectively impaired the growth of NF2-mutant kidney cancer cell lines, suggesting that the sensitivity of mesothelioma models to these YAP/TAZ-TEAD inhibitors can be extended to other tumor types with aberrations in Hippo signaling. In brief, we describe a novel and specific YAP/TAZ-TEAD inhibitor that has potential to treat multiple Hippo-mutant solid tumor types.

Abstract 4964: SW-682: A novel TEAD inhibitor for the treatment of cancers bearing mutations in the Hippo signaling pathway

Many cancers harbor mutations in the Hippo pathway that lead to constitutive activation of the transcriptional co-activators YAP/TAZ that then bind the transcription factor TEAD and drive aberrant transcription of target genes involved in cell proliferation and tumor progression. Hyperactivation of YAP/TAZ has also been associated with resistance to targeted therapies, including MAPK pathway inhibitors. To target cancers that bear mutations in the Hippo pathway or are resistant to therapies due to YAP/TAZ activation, we developed SW-682, a pan-TEAD small molecule inhibitor that blocks TEAD-dependent transcription by binding to the palmitoylation pocket of all TEAD isoforms. In vitro, SW-682 inhibited the proliferation of human Hippo-mutant mesothelioma cells with nanomolar potency, with little to no effect on Hippo wild-type tumor cells. SW-682 down-regulated TEAD-dependent reporter gene expression in a dose-dependent manner, while having no effect on reporters monitoring other pathways. In vivo, daily oral administration of SW-682 to adult mice resulted in tumor regression in Hippo-mutant mesothelioma models and caused down-regulation of expression of the TEAD-dependent genes CCN1 and CCN2 and a YAP gene signature, as measured by qPCR or RNA-seq analysis. SW-682 has a favorable PK profile with good oral bioavailability in the mouse and was well tolerated with no signs of body weight loss. To test the hypothesis that TEAD inhibition can overcome YAP-driven resistance mechanisms, we explored SW-682 in combination with MEK inhibitors in several in vitro and ex vivo patient-derived tumor models including BRAF and NRAS mutated melanoma. Moreover, to identify new indications that may benefit from TEAD inhibition, we screened patient-derived 3D organoid tumor cells and matching patient-derived xenograft models that have been molecularly profiled. In summary, SW-682 is a potent and selective investigational TEAD inhibitor which demonstrated anti-tumor effects in models harboring aberrant expression of the Hippo pathway, suggesting therapeutic potential in multiple Hippo-mutant solid tumors.

Citation Format: Lei Chen, Paula Milani de Marval, Kendall Powell, Mark Johnson, Greg Falls, Brian Lawhorn, Aurélie Candi, Amuri Kilonda, Bart Vanderhoydonck, Arnaud Marchand, Matthias Versele, Georg Halder, Stephen L. Gwaltney, Adeela Kamal. SW-682: A novel TEAD inhibitor for the treatment of cancers bearing mutations in the Hippo signaling pathway. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4964.

Abstract 3945: Novel antagonists of TEAD palmitoylation inhibit the growth of Hippo-altered cancers in preclinical models

Background: The Hippo pathway is an evolutionarily conserved signaling cascade whose deregulation can promote excessive cell proliferation and tumor development. Pathway output is mediated by the YAP and TAZ transcriptional co-activators, which bind to TEAD family transcription factors to drive target gene expression. Genomic aberrations in Hippo pathway components result in constitutive activation of YAP/TAZ, as seen with NF2 mutations in subsets of mesothelioma and other cancers. Hyperactivation of YAP/TAZ has also been associated with resistance to a variety of targeted agents, including EGFR and CDK4/6 inhibitors, suggesting that targeting the pathway may have utility as part of rationally selected combinations, in addition to genomically-informed monotherapy applications. Activity of the YAP/TAZ-TEAD complex thus represents a compelling pharmacologic target, due to its essential role in the pathway, and the presence of a conserved druggable site in TEAD that is required for transcriptional function.

Results and Discussion: Using biophysical techniques, we identified novel small molecules that bind to the TEAD auto-palmitoylation pocket. Initial hits were optimized for antagonism of TEAD-based transcription and drug-like properties, ultimately producing highly potent and orally bioavailable TEAD inhibitors. These compounds selectively inhibited the proliferation of cancer cell lines harboring genomic alterations in the Hippo pathway with low nM potency. In vivo models of Hippo pathway-altered xenografts showed consistent monotherapy activity, with dose-dependent and durable tumor regressions achieved at well-tolerated doses. Further characterization of these compounds as monotherapies and as part of rationally-designed combination regimens is ongoing.

Citation Format: Adeela Kamal, Aurélie Candi, Matthias Versele, Bart Vanderhoydonck, Arnaud Marchand, Ron de Jong, Thuy Hoang, Georg Halder, Patrick Chaltin, Stephen L. Gwaltney, Mike Burgess. Novel antagonists of TEAD palmitoylation inhibit the growth of Hippo-altered cancers in preclinical models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3945.

Stimulation of the atypical chemokine receptor 3 (ACKR3) by a small-molecule agonist attenuates fibrosis in a preclinical liver but not lung injury model

Atypical chemokine receptor 3 (ACKR3, formerly CXC chemokine receptor 7) is a G protein-coupled receptor that recruits β-arrestins, but is devoid of functional G protein signaling after receptor stimulation. In preclinical models of liver and lung fibrosis, ACKR3 was previously shown to be upregulated after acute injury in liver sinusoidal and pulmonary capillary endothelial cells, respectively. This upregulation was linked with a pro-regenerative and anti-fibrotic role for ACKR3. A recently described ACKR3-targeting small molecule agonist protected mice from isoproterenol-induced cardiac fibrosis. Here, we aimed to evaluate its protective role in preclinical models of liver and lung fibrosis. After confirming its in vitro pharmacological activity (i.e., ACKR3-mediated β-arrestin recruitment and receptor binding), in vivo administration of this ACKR3 agonist led to increased mouse CXCL12 plasma levels, indicating in vivo interaction of the agonist with ACKR3. Whereas twice daily in vivo administration of the ACKR3 agonist lacked inhibitory effect on bleomycin-induced lung fibrosis, it had a modest, but significant anti-fibrotic effect in the carbon tetrachloride (CCl4)-induced liver fibrosis model. In the latter model, ACKR3 stimulation affected the expression of several fibrosis-related genes and led to reduced collagen content as determined by picro-sirius red staining and hydroxyproline quantification. These data confirm that ACKR3 agonism, at least to some extent, attenuates fibrosis, although this effect is rather modest and heterogeneous across various tissue types. Stimulating ACKR3 alone without intervening in other signaling pathways involved in the multicellular crosstalk leading to fibrosis will, therefore, most likely not be sufficient to deliver a satisfactory clinical outcome.

TMOD-22. DIFFERENTIAL DRUG SENSITIVITY ANALYSIS IN PAIRED PATIENT-DERIVED CELL LINES OF GLIOBLASTOMA

Glioblastoma (GBM) remains the most aggressive adult brain tumour with dismal prognosis. Even when treated by the most optimal standard-of-care modalities, disease progression remains consistently inevitable. Understanding how tumours evolve from a newly diagnosed to a recurrent setting is therefore critical, but research models to functionally test how therapeutic interventions evolve accordingly remain scarce. Here, we describe our efforts to develop paired models including newly diagnosed and recurrent GBM cell lines derived from the same patients. Overall, we collected 50 tumour samples originating from 24 patients at different time points in their treatment scheme. This resulted in the generation of 27 models overall, from which 18 originated from 9 patients at different timepoints. The latter were subsequently investigated extensively. First, using genomic profiling, we consistently observed an increase in mutational burden and chromosomal aberrations in the recurrent samples, while transcriptomic profiling showed that tumour subtypes evolved in a very patient-specific way. A large fraction of the recurrent models showed resistance to temozolomide (TMZ), which coincided with a downregulation of DNA repair (MMR) pathways or mutations. Half of the tested models also acquired resistance to radiation therapy. Next to standard-of-care therapy, we investigated several small molecule inhibitors that are currently in clinical evaluation, which also showed differential sensitivity. Overall, the developed paired cell lines recapitulate the most important features related to tumour recurrence, and offer the opportunity for more elaborate dependency screening efforts.

Combining Cell Envelope Stress Reporter Assays in a Screening Approach to Identify BAM Complex Inhibitors

The development of new antibiotics is particularly problematic in Gram-negative bacteria due to the presence of the outer membrane (OM), which serves as a permeability barrier. Recently, the β-barrel assembly machine (BAM), located in the OM and responsible for β-barrel type OM protein (OMP) assembly, has been validated as a novel target for antibiotics. Here, we identified potential BAM complex inhibitors using a screening approach that reports on cell envelope σE and Rcs stress in Escherichia coli. Screening a library consisting of 316 953 compounds yielded five compounds that induced σE and Rcs stress responses, while not inducing the intracellular heat-shock response. Two of the five compounds (compounds 2 and 14) showed the characteristics of known BAM complex inhibitors: synergy with OMP biogenesis mutants, decrease in the abundance of various OMPs, and loss of OM integrity. Importantly, compound 2 also inhibited BAM-dependent OMP folding in an in vitro refolding assay using purified BAM complex reconstituted in proteoliposomes.

Abstract 53: Discovery of novel potent and orally bioavailable small-molecule inhibitors of ENPP1 to stabilize cGAMP and ATP in the tumor microenvironment and boost anti-tumor immunity

Extracellular 2',3'-cyclic GMP-AMP (cGAMP) has a critical immune-transmitter role in the tumor microenvironment (TME). Tumor cells produce and secrete cGAMP, which primes immune cells for tumor rejection through STING (stimulator of interferon genes) signalling (Marcus et al., Immunity 2018; Carozza et al., Nature Cancer 2020). Ecto-nucleotide pyrophosphatase/phosphodiesterase-1 (ENPP1) is the only enzyme known to hydrolyze extracellular cGAMP. In concert with the ectoATPase CD39 and the 5'-nucleotidase CD73, ENPP1 also contributes to the generation of an immunosuppressive TME by converting extracellular ATP into adenosine. ENPP1 is overexpressed in a number of tumor types, including breast cancer, liver cancer, thyroid cancer and sarcomas, and has been associated with poor outcome. Hence, inhibition of ENPP1 is an emerging strategy to augment anti-tumor immunity by stabilizing extracellular cGAMP and ATP, thereby turning cold tumors into immunologically hot tumors. Here, we report on the identification and characterization of novel chemical series of ENPP1 inhibitors. A drug-like small-molecule library (~160,000 compounds) was screened to identify inhibitors of ENPP1-mediated cGAMP hydrolysis. Hits were confirmed to also inhibit ATP hydrolysis by ENPP1, but not nucleotide hydrolysis mediated by the closely related ENPP2 (autotaxin) enzyme. A selection of hits, chemically distinct from previously reported ENPP1 inhibitors (such as those based on QS1; Carroza et al, Cell Chem Biol, 2020), were subjected to hit-to-lead optimization supported by structure-based guidance. This led to the identification of ENPP1 inhibitors with sub-nM potency on ENPP1 in biochemical assays, which maintained a >1000x selectivity window with respect to ENPP2 and to other phosphodiesterases. These compounds translated well to stabilization of nucleotides in the presence of ENPP1-overexpressing cancer cell lines, with IC50 values in the nM range. A selection of compounds was profiled for DMPK (drug metabolism and pharmacokinetic) parameters, and compounds with a suitable profile were prioritized for in vivo evaluation. Orally bio-available, metabolically stable compounds were assessed in mouse syngeneic tumor models, selected on the basis of high ENPP1 and high cGAS (cGAMP synthase) expression. Stabilization of cGAMP, activation of a STING-mediated cytokine response and immune-cell infiltration/activation in the TME were used as pharmacodynamic endpoints. An update on in vivo efficacy data in a range of ENPP1-positive tumor models will be provided during the presentation. These novel orally bioavailable ENPP1 inhibitors unleash local, TME-restricted, innate immune activation, and hold the promise to overcome the current limitations of direct STING agonists.

Citation Format: Matthias Versele, Javier del Pino Garcia, Ilse Vandecaetsbeek, Karolien Castermans, Ranie Kellens, Wanda Haeck, Hugo Klaassen, Arnaud Bourin, Dries De Clercq, Sara Allasia, Sandro Boland, Arnaud Marchand, Patrick Chaltin, Mathieu Bollen. Discovery of novel potent and orally bioavailable small-molecule inhibitors of ENPP1 to stabilize cGAMP and ATP in the tumor microenvironment and boost anti-tumor immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 53.

Abstract 5229: Discovery of novel potent allosteric inhibitors of YAP/TAZ-TEAD transcription for the treatment of multiple solid tumor types addicted to Hippo signaling

The Hippo pathway is a highly conserved signaling pathway across higher-order vertebrates and a key modulator of developmental biology. Both genetic aberrations as well as non-genetic dysregulation of the pathway lead to constitutive nuclear localization and transcriptional activity of the YAP/TAZ-TEAD complex in multiple solid tumor types, including mesothelioma, uveal melanoma, squamous cell cancer, liver cancer, lung cancer, etc. Genetic aberrations are manifested as gene amplifications and gene fusions of the core transcriptional YAP/TAZ-TEAD complex subunits, and, more commonly, as deletions or loss-of-function mutations in the upstream negative regulators of the Hippo pathway such as NF2, LATS1/2 or FAT1. More recently, constitutive activation of YAP/TAZ-TEAD has been implicated in cancer therapy resistance and in immune evasion. Multiple efforts have been devoted to identify small-molecule inhibitors of the YAP/TAZ-TEAD protein-protein interaction, yet with limited success reported to date. Based on the identification of an auto-palmitoylation pocket centrally located in TEAD, and its reported role to sustain YAP/TAZ-TEAD transcriptional activity, we set up a biophysical assay to detect selective small-molecule binding into the palmitoylation pocket of TEAD1. Based on screening a rationally designed compound collection in this assay and iterations of analoging, we identified several novel chemical series of TEAD-palmitoylation pocket binders. Hits were confirmed as specific allosteric inhibitors of YAP/TAZ-TEAD transcription in cell-based assays (Q-PCR and reporter gene assays). Soaking compounds in TEAD crystals revealed structural information enabling hit-to-lead optimization of two different chemical series. Best allosteric inhibitors in the series display single-digit nM potency in transcriptional assays, and translate to low nM inhibition of Hippo mutant (but not WT, >1000x selectivity window) mesothelioma proliferation. These molecules are well suited to probe for additional Hippo-dependent solid cancer types using in vitro cancer cell panels, selected based on genetics and/or a YAP/TAZ-TEAD gene signature. Furthermore, optimization towards orally bioavailable compounds is in progress and an update on in vivo efficacy in various solid tumor models will be presented.

Citation Format: Matthias Versele, Aurélie Candi, Marnik Nijs, Wanda Haeck, Hugo Klaassen, Wim Smets, Stéphane Spieser, Bart Vanderhoydonck, Arnaud Marchand, Patrick Chaltin, Leticia Sansores, Georg Halder. Discovery of novel potent allosteric inhibitors of YAP/TAZ-TEAD transcription for the treatment of multiple solid tumor types addicted to Hippo signaling [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 5229.

Abstract 3865: Discovery of novel DHODH and OXPHOS inhibitors

Inhibition of mitochondrial metabolism for treatment-resistant tumors has attracted renewed attention. Pharmacologic inhibition of mitochondrial oxidative phosphorylation (OXPHOS) is efficacious in preclinical models of chemo-resistant AML, glycolysis-deficient glioma, and Swi/Snf mutant lung cancer, and is associated with an apparent robust safety index (Molina et al., 2018, Nat Med 24: 1036-1046; Lissanu Deribe et al., 2018, Nat Med 24: 1047-1057). In addition, immune-suppressive cell types in the tumor micro-environment depend on OXPHOS metabolism, including CD4+ regulatory T-cells (Tregs), whereas tumor-infiltrating effector T-cells instead rely on glycolytic metabolism (Angelin et al., 2017, Cell Metab. 25: 1282-1293).

Here, we have used a phenotypic drug discovery approach to identify selective inhibitors of mitochondrial -but not glycolytic- tumor cell metabolism. Based on initial hits derived from a high-throughput screening campaign, a chemical series was optimized to achieve single digit nM potency (best IC50= 2 nM) in targeting OXPHOS-dependent cancer cells (grown on lactate as sole carbon source) but not glycolytic cells (grown on glucose; IC50 > 10 microM). Target deconvolution within this chemical series revealed 2 distinct mechanisms. One chemical subseries are direct inhibitors of the mitochondrial enzyme, dihydroorotate dehydrogenase (DHODH). Consistent with previous reports on DHODH inhibitors, these compounds potently impair AML cell proliferation (best IC50= 10nM) through induction of myeloid cell differentiation -a trait that can be rescued by providing exogenous uridine to the cell cultures (IC50 > 10 microM). A second chemically distinct subset of compounds inhibit mitochondrial OXPHOS, but does not inhibit DHODH. As expected, these compounds selectively target OXPHOS-dependent cancer cell lines, and display a robust selectivity window (determined in glycolysis-dependent cell lines). Moreover, these inhibitors do not affect a mixed-lymphocyte reaction (MLR) assay. In-depth metabolomic profiling in cancer cells fueled by glucose, lactate or glutamine, the precise molecular target of these compounds, and further in vivo characterization of these compounds will be presented. Finally, the unique opportunity to simultaneously inhibit both DHODH and OXPHOS using dual inhibitors will be evaluated in chemo-resistant AML models.

Citation Format: Matthias Versele, Philippe Selhorst, Kristine Metzger, Marnik Nijs, Hugo Klaassen, Amuri Kilonda, Damien Marchand, Philippe Arzel, Dominique Lambin, Jean-Christophe Vanherck, Arnaud Marchand, Patrick Chaltin, Cyril Corbet, Olivier Feron. Discovery of novel DHODH and OXPHOS inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3865.

Prospective Isolation and Characterization of Genetically and Functionally Distinct AML Subclones

Intra-tumor heterogeneity caused by clonal evolution is a major problem in cancer treatment. To address this problem, we performed label-free quantitative proteomics on primary acute myeloid leukemia (AML) samples. We identified 50 leukemia-enriched plasma membrane proteins enabling the prospective isolation of genetically distinct subclones from individual AML patients. Subclones differed in their regulatory phenotype, drug sensitivity, growth, and engraftment behavior, as determined by RNA sequencing, DNase I hypersensitive site mapping, transcription factor occupancy analysis, in vitro culture, and xenograft transplantation. Finally, we show that these markers can be used to identify and longitudinally track distinct leukemic clones in patients in routine diagnostics. Our study describes a strategy for a major improvement in stratifying cancer diagnosis and treatment.

The effect of Bruton's tyrosine kinase (BTK) inhibitors on collagen-induced platelet aggregation, BTK, and tyrosine kinase expressed in hepatocellular carcinoma (TEC)

OBJECTIVES

Bruton's tyrosine kinase (BTK) and tyrosine kinase expressed in hepatocellular carcinoma (TEC) are expressed by human platelets. These kinases participate in platelet activation through the collagen receptor glycoprotein VI and may perform overlapping functions. In clinical studies, BTK inhibitors (ibrutinib, acalabrutinib, tirabrutinib, zanubrutinib) have been associated with increased bleeding risk, which may result from inhibition of BTK alone or of both BTK and TEC, although the role of TEC in bleeding risk remains unclear.

METHODS

Here, in vitro catalytic and binding activities of ibrutinib and acalabrutinib were determined with four assay systems. Platelet aggregation assays determined inhibitor potency and its relationship to selectivity between BTK and TEC.

RESULTS

Neither inhibitor was substantially more selective for BTK over TEC. The potencies at which BTK inhibitors suppressed platelet aggregation correlated with the potencies in on-target BTK assays, including those in cells. At clinically relevant plasma concentration, ibrutinib, acalabrutinib, and tirabrutinib inhibited collagen-induced platelet aggregation to a similar extent, despite differing in vitro IC50 s.

CONCLUSIONS

Our results suggest BTK inhibition is the primary driver for inhibition of platelet aggregation. The subtle differences between these inhibitors suggest only randomized, double-blind, placebo-controlled clinical studies can fully address the bleeding risks of different BTK inhibitors.

Abstract 4199: Inhibition of NF-kB inducing kinase (NIK) selectively abrogates NIK and TRAF3 mutant multiple myeloma tumor growth

Enhanced NF-kB signaling is a hallmark of aggressive lymphoid malignancies, including multiple myeloma (MM), mantle cell lymphoma (MCL), and diffuse large B-cell lymphoma (DLBCL). Non-canonical NF-kB signaling involves NIK-dependent activation of IKKα, which triggers nuclear accumulation of p52/RelB heterodimers. NIK is a highly unstable protein and degradation is mediated by a ubiquitin ligase complex consisting of TRAF2, TRAF3 and c-IAP1/2 (encoded by BIRC2/3). In a subset of MM, NIK is stabilized by mutations in NIK, TRAF2/3 or BIRC2/3 (Annunziata et al./Keats et al., Canc. Cell 2007). Similar activating mutations in the non-canonical NF-kB signaling pathway were recently found in ibrutinib-refractory MCL cell lines (Rahal et al., Nat. Med. 2014), and in DLBCL (Zhang et al., Cell Rep. 2015). In many other cases of B-cell malignancies, NIK is stabilized by high level expression of the upstream TNF receptors (BAFFR, CD40, LTβR) or high abundance of their ligands in the bone marrow or the lymph nodes. To date, bioavailable NIK inhibitors have not been reported, and it has remained unclear whether NIK inhibitors are effective and tolerated in mouse models of B-cell malignancies associated with activation of NIK. Here, we report for the first time on a potent orally bioavailable NIK kinase inhibitor, TRC694. TRC694 selectively inhibits NIK enzymatic activity, translating into inhibition of phospho-IKKα in NIK and in TRAF3 mutant cell lines with single digit nM IC50. TRC694 prevents nuclear accumulation of p52/RelB (but not canonical NF-kB) and represses the associated NF-kB gene program selectively in MM cell lines with genetic activation of the non-canonical NF-kB pathway. Proliferation of NIK translocated, TRAF3 or BIRC3 mutant MM cell lines is inhibited by low nM concentrations of TRC694, whereas MM cell lines which lack genetic activation of non-canonical NF-kB are much less sensitive to TRC694. Consistently, elevated expression of a previously described 11-gene NFkB signature in MM (Annunziata et al., Canc. Cell 2007) is predictive of sensitivity to TRC694 in a 21-MM cell line panel. A single, oral dose of 10 to 40 mg/kg of TRC694 to mice bearing a NIK-translocated MM tumor (JJN-3), was sufficient to inhibit phospho-IKKα and repress P52-mediated transcription of NFkB regulated genes in the tumors. Consistently, once-daily, oral dosing of TRC694 to mice bearing subcutaneous NIK translocated (JJN-3) or TRAF3 (RPMI-8226, MM.1S) mutant MM tumors, completely inhibits growth of these tumors at doses of 10 to 40 mg/kg, with no signs of toxicities. In conclusion, TRC694 is a first-in-class orally bioavailable NIK kinase inhibitor, and provides the first opportunity to test the clinical relevance of non-canonical NF-kB inhibition in aggressive lymphoid malignancies.

Citation Format: Matthias Versele, Lut Janssen, Tamara Geerts, Wim Floren, Boudewijn Janssens, Hillary Millar, Edgar Jacoby, Gerhard Gross, Yannick Ligny, Yvan Simonnet, Nathalie Amblard, Olivier Querolle, Imre Csoka, Virginie Poncelet, Virginie Tronel, Sophie Nocquet-Thibault, Lieven Meerpoel, James Edwards, Marc Salvati, Sriram Balasubramanian, Laurie Lenox, Charles Theuer, Ricardo Attar, Ian Stansfield. Inhibition of NF-kB inducing kinase (NIK) selectively abrogates NIK and TRAF3 mutant multiple myeloma tumor growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4199. doi:10.1158/1538-7445.AM2017-4199

Combination of Ibrutinib and ABT-199 in Diffuse Large B-Cell Lymphoma and Follicular Lymphoma

Diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma are the most prevalent B-lymphocyte neoplasms in which abnormal activation of the Bruton tyrosine kinase (BTK)-mediated B-cell receptor signaling pathway contributes to pathogenesis. Ibrutinib is an oral covalent BTK inhibitor that has shown some efficacy in both indications. To improve ibrutinib efficacy through combination therapy, we first investigated differential gene expression in parental and ibrutinib-resistant cell lines to better understand the mechanisms of resistance. Ibrutinib-resistant TMD8 cells had higher BCL2 gene expression and increased sensitivity to ABT-199, a BCL-2 inhibitor. Consistently, clinical samples from ABC-DLBCL patients who experienced poorer response to ibrutinib had higher BCL2 gene expression. We further demonstrated synergistic growth suppression by ibrutinib and ABT-199 in multiple ABC-DLBCL, GCB-DLBCL, and follicular lymphoma cell lines. The combination of both drugs also reduced colony formation, increased apoptosis, and inhibited tumor growth in a TMD8 xenograft model. A synergistic combination effect was also found in ibrutinib-resistant cells generated by either genetic mutation or drug treatment. Together, these findings suggest a potential clinical benefit from ibrutinib and ABT-199 combination therapy. Mol Cancer Ther; 16(7); 1246-56. ©2017 AACR.

Abstract 365: High throughput screen to evaluate combinations with ibrutinib in various B-cell malignancies

The primary objective of this study was to discover synergies leading to mechanistic insights and novel combinations for ibrutinib, a small-molecule inhibitor of Bruton's tyrosine kinase (BTK). Ibrutinib has been approved for relapsed/refractory (R/R) and del(17p) chronic lymphocytic leukemia, and R/R mantle-cell lymphoma (MCL). BTK is part of the B-cell receptor (BCR) signaling pathway, so it is of interest to examine synergy between ibrutinib and agents that target other aspects of the BCR pathway. These include PI3K and IRAK inhibitors and apoptosis inhibitors. Combinations were evaluated in a high-throughput, tumor microenvironment-directed format.

Ibrutinib was combined with inhibitors of the BCR pathway and apoptosis, whose targets included MCL-1, BCL2, XPO1, and isoforms of PI3K, IRAK, and BRD. Histologies examined included follicular lymphoma (FL), diffuse large B-cell lymphoma (DLBCL), MCL, acute myeloid leukemia (AML), acute B-lymphoblastic leukemia, and Burkitt's lymphoma. Cell lines were screened in the presence of human marrow stromal-cell-conditioned media and B-cell receptor stimulation via anti-IgG/anti-IgM antibodies in a 72-hour cell viability ATP lite assay (384-well plate, 9×9 optimized matrix, 4 replicates). Dose response matrix screening was used to measure combination effects, which manifest as potency shifts or efficacy boosts. Combination effects can be characterized by comparing each data point to a combination reference model derived from single-agent curves using the Loewe additivity model.

Ibrutinib demonstrated varying activity across cell lines. Combination activity was classified based on synergy score raw values. The best combination among tested compounds was with ABT-199, a BCL2i. This combination showed high or medium synergy in 2/5 DLBCL, 3/4 FL, and 2/5 MCL cell lines; this was also the only agent to show good synergy in AML (3/5 lines). Interestingly, ABT-737, a BCL2i that also targets BCL-XL, has previously been shown to be synergistic with ibrutinib in DLBCL lines. Synergy was also seen with other apoptotic agents such as MCL-1i and the epigenetic BETi JQ-1 across B-NHL, but in fewer lines. Among the PI3Ki, PI3Kα/δi did not show much activity, but the PI3Kδ/γi IPI-145 was synergistic in 2/5 DLBCL, 3/4 FL cell lines, and 1/5 MCL cell lines, a pattern very similar to the PI3Kδi CAL-101 (idelalisib). Ibrutinib also combined well with IRAK1/4i and XPO1i selinexor, with high activity in 1/5 DLBCL cell lines each, and medium activity in 1/5 DLBCL, 1/4 FL, and 2/5 MCL (XPO1i) and 1/5 DLBCL, 2/4 FL, and 1/5 MCL cell lines (IRAK1/4i).

Synergy was mostly observed in B-cell malignancies, but interesting synergy was observed with ABT-199 in AML. In B-NHL, ibrutinib combined with BCL2i and PI3Ki showed the best combination activity. Ibrutinib was also synergistic with other agents in selected B-NHL lines with no observed antagonism, suggesting that further study in specific histologies is warranted.

Citation Format: Shalini Chaturvedi, Michael Schaffer, Cuc Davis, Regina Aquino, Emily Stepanchick, Matthias Versele, Sriram Balasubramanian. High throughput screen to evaluate combinations with ibrutinib in various B-cell malignancies. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 365.

Elongation factor 2 kinase promotes cell survival by inhibiting protein synthesis without inducing autophagy

Eukaryotic elongation factor 2 kinase (eEF2K) inhibits the elongation stage of protein synthesis by phosphorylating its only known substrate, eEF2. eEF2K is tightly regulated by nutrient-sensitive signalling pathways. For example, it is inhibited by signalling through mammalian target of rapamycin complex 1 (mTORC1). It is therefore activated under conditions of nutrient deficiency.

Here we show that inhibiting eEF2K or knocking down its expression renders cancer cells sensitive to death under nutrient-starved conditions, and that this is rescued by compounds that block protein synthesis. This implies that eEF2K protects nutrient-deprived cells by inhibiting protein synthesis. Cells in which signalling through mTORC1 is highly active are very sensitive to nutrient withdrawal. Inhibiting mTORC1 protects them. Our data reveal that eEF2K makes a substantial contribution to the cytoprotective effect of mTORC1 inhibition.

eEF2K is also reported to promote another potentially cytoprotective process, autophagy. We have used several approaches to test whether inhibition or loss of eEF2K affects autophagy under a variety of conditions. We find no evidence that eEF2K is involved in the activation of autophagy in the cell types we have studied.

We conclude that eEF2K protects cancer cells against nutrient starvation by inhibiting protein synthesis rather than by activating autophagy.

•

Eukaryotic elongation factor-2 kinase helps cancer cells survive nutrient starvation and is an attractive anti-cancer target.

•

eEF2K has been reported to promote autophagy; however, our evidence shows eEF2K does not modulate autophagy.

•

eEF2K protects cells by inhibiting protein synthesis.

Abstract 3229: Managing stress: Discovery of inhibitors of the atypical kinase eEF2K and the class III PI3K, VPS34

Adaptation to nutrient deprivation in the tumour microenvironment was recently shown to be dependent on the appropriate regulation of protein elongation rate through activation of the atypical kinase, eukaryotic elongation factor 2 kinase (eEF2K) (Leprivier et al., 2013, Cell 153(5):1064-79). We have solved the crystal structure of the kinase domain of eEF2K, and used structure-based design as well as screening approaches to optimize a chemical series into single-digit nM inhibitors of eEF2K, with remarkable selectivity across the protein kinome (only 5-10 kinases out of 400 tested are inhibited to more than 50% at 1 μM). These compounds inhibit the phosphorylation of eEF2 in nutrient-starved or metabolically stressed cells, and increase protein elongation rates through stabilization of the ribosomal elongation complex under stress. Evotec's Cellular Target Profiling of these compounds in cell lysates, revealed that a subset of the eEF2K inhibitors also bind with low nM affinity to the class III phosphatidylinositol-3-kinase, VPS34, but not to class I or II PI3Ks, and pull down the entire beclin-UVRAG-VPS34 complex. Proteomic and biochemical screening of the compound set enabled deconvolution of potent EF2K versus VPS34 inhibitors. Inhibition of VPS34 results in abrogation of autophagic flux, as indicated by rapid and massive accumulation of p62, and impairs survival in specific subsets of tumor cell lines, consistent with a pro-survival role for autophagy in those models (Cheng et al., 2013, Pharmacol Rev 65(4):1162-97). Interestingly, a whole-genome pooled shRNA screen in a KRAS/PI3KCA mutant colorectal cancer cell line revealed that reduction of beclin levels significantly increased sensitivity to VPS34 inhibition. In contrast, inhibition of eEF2K does not appear to be anti-proliferative across a wide panel of cancer cell lines under standard cell culture conditions.

Our work has provided the first potent inhibitors to unravel the functional relevance of eEF2K and VPS34 in adaptation to cellular stress, and to examine the utility of inhibiting these kinases in nutrient-deprived and/or autophagy-addicted tumours.

Citation Format: Matthias Versele, Claire Moore, Christopher G. Proud, Cindy Rockx, Inez Van de Weyer, Kurt Van Baelen, Stephanie Blencke, Sebastian K. Wanndinger, Gaston Diels, Didier Berthelot, Marcel Viellevoye, Bruno Schoentjes, Berthold Wroblowski, Lieven Meerpoel, William N. Hait. Managing stress: Discovery of inhibitors of the atypical kinase eEF2K and the class III PI3K, VPS34. [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 3229. doi:10.1158/1538-7445.AM2014-3229

Abstract 3228: Characterization of a novel, orally bioavailable, potent and highly selective small molecule inhibitor of PERK: A tool to probe the biphasic concentration-dependent induction of ER stress in models of multiple myeloma and B-cell lymphoma

The unfolded protein response (UPR) is a signal transduction pathway that coordinates cellular adaptation to microenvironmental stress and the accumulation of malfolded proteins in the endoplasmic reticulum (ER). In highly secretory malignancies, such as multiple myeloma (MM), characteristically there is both an extensively developed ER and a markedly elevated UPR to ensure a homeostatic balance between ER burden and ER capacity - thus making components of the UPR attractive targets for therapeutic intervention. One such target is PERK (PKR-like endoplasmic reticulum kinase), a member of the eukaryotic initiation factor (eIF)2α kinase family, that is activated during the UPR to chronic ER stress.

Here, we describe the identification and characterization of compound (1) - a novel, orally bioavailable, potent and highly selective small molecule inhibitor of PERK. (1) is a sub-nM inhibitor of PERK, with a >100-fold window against other kinases (including other eIF2α kinases) - targeting only 6 out of a 400 kinase panel with sub-μM IC50's. It inhibits phosphorylation of eIF2α at 10 nM (IC50) in HEK293 cells (incubated with the ER stressor tunicamycin) and proves to be selectively anti-proliferative in an ER-stressed epithelial cancer model (A549 cells with tunicamycin) at nM concentrations, but to a lesser extent in the absence of ER stress. Furthermore, in the absence of an exogenous ER stressor, (1) induced excessive ER stress (eg, as evidenced by induction of the pro-apoptotic CHOP gene), and decreased cell viability selectively in MM cell lines and certain B-cell lymphoma lines at low nM concentrations, but not in normal or malignant epithelial cells. However, despite a sustained impact on eIF2α phosphorylation, interestingly compound (1) elicited a biphasic concentration dependent induction of ER stress (and consequent inhibition of cell viability) - with ER stress induction maximal at inhibitor concentrations corresponding to circa 50-75 % inhibition of PERK, returning progressively to baseline with concentrations rising to > IC90. Whole-genome expression profiling revealed that all significant changes seen at 10-100 nM of (1), returned to baseline levels at 1000 nM, suggesting a compensatory mechanism very proximal to phosphorylation of eIF2α. In summary, the highly selective PERK inhibitor, (1), validated the unique sensitivity of subsets of multiple myeloma and B-cell lymphoma to disruption of the UPR, but unexpectedly revealed a compensatory mechanism associated with potent PERK inhibition.

Citation Format: Ian Stansfield, Yannick Ligny, Yvan Simonnet, Christophe Demestre, Nathalie Amblard, Christophe Meyer, Tamara Geerts, Jeroen Van de Ven, Ilse Van den Wyngaert, Peter Vermeulen, Inge Beerden, Danielle Peeters, Johnny Liebregts, Kurt Van Baelen, Cedric Simillion, Boudewijn Janssen, Tinne Verhulst, Norbert Esser, James Bischoff, Lieven Meerpoel, Matthias Versele. Characterization of a novel, orally bioavailable, potent and highly selective small molecule inhibitor of PERK: A tool to probe the biphasic concentration-dependent induction of ER stress in models of multiple myeloma and B-cell lymphoma. [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 3228. doi:10.1158/1538-7445.AM2014-3228

Resistance mechanisms for the Bruton's tyrosine kinase inhibitor ibrutinib

BACKGROUND

Ibrutinib is an irreversible inhibitor of Bruton's tyrosine kinase (BTK) and is effective in chronic lymphocytic leukemia (CLL). Resistance to irreversible kinase inhibitors and resistance associated with BTK inhibition have not been characterized. Although only a small proportion of patients have had a relapse during ibrutinib therapy, an understanding of resistance mechanisms is important. We evaluated patients with relapsed disease to identify mutations that may mediate ibrutinib resistance.

METHODS

We performed whole-exome sequencing at baseline and the time of relapse on samples from six patients with acquired resistance to ibrutinib therapy. We then performed functional analysis of identified mutations. In addition, we performed Ion Torrent sequencing for identified resistance mutations on samples from nine patients with prolonged lymphocytosis.

RESULTS

We identified a cysteine-to-serine mutation in BTK at the binding site of ibrutinib in five patients and identified three distinct mutations in PLCγ2 in two patients. Functional analysis showed that the C481S mutation of BTK results in a protein that is only reversibly inhibited by ibrutinib. The R665W and L845F mutations in PLCγ2 are both potentially gain-of-function mutations that lead to autonomous B-cell-receptor activity. These mutations were not found in any of the patients with prolonged lymphocytosis who were taking ibrutinib.

CONCLUSIONS

Resistance to the irreversible BTK inhibitor ibrutinib often involves mutation of a cysteine residue where ibrutinib binding occurs. This finding, combined with two additional mutations in PLCγ2 that are immediately downstream of BTK, underscores the importance of the B-cell-receptor pathway in the mechanism of action of ibrutinib in CLL. (Funded by the National Cancer Institute and others.).

Use of tumor genomic profiling to reveal mechanisms of resistance to the BTK inhibitor ibrutinib in chronic lymphocytic leukemia (CLL)

7014

Background: Ibrutinib interacts covalently with cysteine 481 of Bruton tyrosine kinase (BTK), resulting in targeted inhibition of B cell receptor signaling. Early trials of ibrutinib mono- or combination therapy enrolled 246 CLL patients receiving a median of 14 months of ibrutinib. 20 patients (8%) experienced progressive disease (PD), including 8 patients with Richter's transformation. Here we examine changes to the CLL genome in 3 patients that acquired resistance to ibrutinib. Methods: Ibrutinib resistance was defined as patients achieving partial response (PR) or better lasting ≥ 6 months, then developing PD without Richter’s transformation. RNAseq and whole exome sequencing (WES) followed by comparative genome analysis was performed at baseline and after PD and confirmed by Sanger sequencing. RNAseq and WES data were aligned using TopHat and BWA software. Single nucleotide variations (SNVs) were identified using SAMtools mpileup. Results: Compared to patients who relapsed from conventional chemotherapy, minimal genomic changes were acquired in ibrutinib resistant patients, reflecting relative genomic stability. SNVs were discovered in 3 patients specific to the relapse sample (Table). 2 out of 3 patients had distinct SNVs that each encode a cysteine-to-serine substitution at position 481of BTK (C481S). Homologous cysteine residues in BMX, ITK, TEC and BLK were wild-type (WT). Ibrutinib inhibited recombinant C481S 25 fold less potently than WT, and could not covalently bind C481S expressed in cells. The third patient had WT BTK, but acquired a potential gain-of-function mutation encoding a R665W substitution in PLCg2, a substrate of BTK, consistent with constitutive PLCg2 activation. Conclusions: Although rare, the acquisition of C481S BTK and R665W PLCg2 mutations in the setting of resistance confirms BTK as an important pharmacologic target of ibrutinib, and suggests mechanisms of ibrutinib resistance. [Table: see text]

Abstract 2215: Pharmacogenomic investigation of Bruton's tyrosine kinase (BTK) inhibitor ibrutinib (PCI-32765): drug sensitivity in diffuse large B-cell lymphoma (DLBCL) within a tumor microenvironment-aligned high-throughput screen

Ibrutinib (PCI-32765) is an orally administered small molecule that covalently binds to Cys-481 of Bruton's tyrosine kinase (BTK). Ibrutinib has demonstrated promise across several types of B-cell malignancies and is currently in Phase 2/3 clinical testing. Preclinical studies have established three key mechanisms following blunting of proximal B cell receptor (BCR) signaling through BTK inhibition: (1) suppression of pro-survival pathways, (2) diminished integrin activation and (3) attenuation of chemotactic response. Single agent ibrutinib Phase 1/2 clinical trials have revealed high clinical response rates in both naïve and relapsed or refractory chronic lymphocytic leukemia (CLL), as well as, relapsed or refractory mantle cell lymphoma (MCL) patients (Byrd, et al. 2012 ASH; Wang, et al. 2012 ASH; Advani, et al. 2010 JCO). Response rates in a phase 2 diffuse large B cell lymphoma (DLBCL) clinical trial appeared to be more prevalent in “activated B-cell” (ABC) over “germinal center B-cell like” (GCB) DLBCL patients (Staudt et al., ASH 2012). To gain a further understanding of ibrutinib response and inform optimal therapeutic combinations in DLBCL, we established a combination high throughput pharmacology screen (cHTS) with ibrutinib. Ibrutinib was evaluated alone and in combination with 99 targeted compounds, across 17 (12 GCB; 5 ABC) DLBCL cell lines. To better align with human biology, DLBCL cell lines were screened in the presence of human marrow stromal cell conditioned media (hMSC-CM) and B-cell receptor stimulation via anti-IgG/anti-IgM antibodies. Interestingly, 8/17 (47%) DLBCL cell lines were intolerant to any external BCR stimulation, so those lines were screened in hMSC-CM without exogenous BCR stimulation. Under our experimental conditions, 11/17 (65%) cell lines displayed some sensitivity (IC50 < 10 M) to ibrutinib at 72 hours based on ATPliteTM measurements [breakdown: 4/17 (24%) highly sensitive (IC50 < 200 nM), 2/17 (12%) sensitive (IC50 200 nM < x < 1 M), 5/17 (29%) modestly sensitive (IC50 1 M < x < 10 M), and 6/17(35%) resistant (IC50 > 10 M)]. Consistent with DLBCL clinical responses, the highly sensitive (IC50 < 200 nM) DLBCL models, which better reflect clinically attainable drug concentrations, demonstrated approximately a two-fold enrichment in ABC (40%; 2/5) versus GCB (17%; 2/12) response with single agent ibrutinib. However, selective drug combinations were found to drive greater sensitivity across both ABC and GCB subtypes. Ongoing work is focused on mapping pathways that contribute to combination drug sensitivity by comparing pharmacologic synergy of targeted agents against mutational (Exome-Seq) and whole genome gene expression profiling (GEP). Together, these data will help to inform optimal ibrutinib combination strategies in DLBCL.

Citation Format: Cuc Davis, Tineke Casneuf, Willem Lightenberg, Richard Rickles, Winnie Tam, Matthias Versele, Steven McClue, Sriram Balasubramanian, Joseph Buggy, Kate Sasser, Brett Hall. Pharmacogenomic investigation of Bruton's tyrosine kinase (BTK) inhibitor ibrutinib (PCI-32765): drug sensitivity in diffuse large B-cell lymphoma (DLBCL) within a tumor microenvironment-aligned high-throughput screen. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2215. doi:10.1158/1538-7445.AM2013-2215

Glucose-induced posttranslational activation of protein phosphatases PP2A and PP1 in yeast

The protein phosphatases PP2A and PP1 are major regulators of a variety of cellular processes in yeast and other eukaryotes. Here, we reveal that both enzymes are direct targets of glucose sensing. Addition of glucose to glucose-deprived yeast cells triggered rapid posttranslational activation of both PP2A and PP1. Glucose activation of PP2A is controlled by regulatory subunits Rts1, Cdc55, Rrd1 and Rrd2. It is associated with rapid carboxymethylation of the catalytic subunits, which is necessary but not sufficient for activation. Glucose activation of PP1 was fully dependent on regulatory subunits Reg1 and Shp1. Absence of Gac1, Glc8, Reg2 or Red1 partially reduced activation while Pig1 and Pig2 inhibited activation. Full activation of PP2A and PP1 was also dependent on subunits classically considered to belong to the other phosphatase. PP2A activation was dependent on PP1 subunits Reg1 and Shp1 while PP1 activation was dependent on PP2A subunit Rts1. Rts1 interacted with both Pph21 and Glc7 under different conditions and these interactions were Reg1 dependent. Reg1-Glc7 interaction is responsible for PP1 involvement in the main glucose repression pathway and we show that deletion of Shp1 also causes strong derepression of the invertase gene SUC2. Deletion of the PP2A subunits Pph21 and Pph22, Rrd1 and Rrd2, specifically enhanced the derepression level of SUC2, indicating that PP2A counteracts SUC2 derepression. Interestingly, the effect of the regulatory subunit Rts1 was consistent with its role as a subunit of both PP2A and PP1, affecting derepression and repression of SUC2, respectively. We also show that abolished phosphatase activation, except by reg1Δ, does not completely block Snf1 dephosphorylation after addition of glucose. Finally, we show that glucose activation of the cAMP-PKA (protein kinase A) pathway is required for glucose activation of both PP2A and PP1. Our results provide novel insight into the complex regulatory role of these two major protein phosphatases in glucose regulation.

The use of semiparametric mixed models to analyze PamChip(R) peptide array data: an application to an oncology experiment

MOTIVATION

Phosphorylation by protein kinases is a central theme in biological systems. Aberrant protein kinase activity has been implicated in a variety of human diseases (e.g. cancer). Therefore, modulation of kinase activity represents an attractive therapeutic approach for the treatment of human illnesses. Thus, identification of signature peptides is crucial for protein kinase targeting and can be achieved by using PamChip(®) microarray technology. We propose a flexible semiparametric mixed model for analyzing PamChip(®) data. This approach enables the estimation of the phosphorylation rate (Velocity) as a function of time together with pointwise confidence intervals.

RESULTS

Using a publicly available dataset, we show that our model is capable of adequately fitting the kinase activity profiles and provides velocity estimates over time. Moreover, it allows to test for differences in the velocity of kinase inhibition between responding and non-responding cell lines. This can be done at individual time point as well as for the entire velocity profile.

CONTACT

pushpike@med.kuleuven.be

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Yeast 3-phosphoinositide-dependent protein kinase-1 (PDK1) orthologs Pkh1-3 differentially regulate phosphorylation of protein kinase A (PKA) and the protein kinase B (PKB)/S6K ortholog Sch9

Pkh1, -2, and -3 are the yeast orthologs of mammalian 3-phosphoinositide-dependent protein kinase-1 (PDK1). Although essential for viability, their functioning remains poorly understood. Sch9, the yeast protein kinase B and/or S6K ortholog, has been identified as one of their targets. We now have shown that in vitro interaction of Pkh1 and Sch9 depends on the hydrophobic PDK1-interacting fragment pocket in Pkh1 and requires the complementary hydrophobic motif in Sch9. We demonstrated that Pkh1 phosphorylates Sch9 both in vitro and in vivo on its PDK1 site and that this phosphorylation is essential for a wild type cell size. In vivo phosphorylation on this site disappeared during nitrogen deprivation and rapidly increased again upon nitrogen resupplementation. In addition, we have shown here for the first time that the PDK1 site in protein kinase A is phosphorylated by Pkh1 in vitro, that this phosphorylation is Pkh-dependent in vivo and occurs during or shortly after synthesis of the protein kinase A catalytic subunits. Mutagenesis of the PDK1 site in Tpk1 abolished binding of the regulatory subunit and cAMP dependence. As opposed to PDK1 site phosphorylation of Sch9, phosphorylation of the PDK1 site in Tpk1 was not regulated by nitrogen availability. These results bring new insight into the control and prevalence of PDK1 site phosphorylation in yeast by Pkh protein kinases.

Response prediction to a multitargeted kinase inhibitor in cancer cell lines and xenograft tumors using high-content tyrosine peptide arrays with a kinetic readout

Multitargeted kinase inhibitors have shown clinical efficacy in a range of cancer types. However, two major problems associated with these drugs are the low fraction of patients for which these treatments provide initial clinical benefit and the occurrence of resistance during prolonged therapy. Several types of predictive biomarkers have been suggested, such as expression level and phosphorylation status of the major targeted kinase(s), mutational status of the kinases involved and of key components of the downstream signaling cascades, and gene expression signatures. In this work, we describe the development of a response prediction platform that does not require prior knowledge of the relevant kinases targeted by the inhibitor; instead, a phosphotyrosine peptide profile using peptide arrays with a kinetic readout is derived in lysates in the presence and absence of a kinase inhibitor. We show in a range of cell lines and in xenograft tumors that this approach allows for the stratification of responders and nonresponders to a multitargeted kinase inhibitor.

Intrinsic differences between the catalytic properties of the oncogenic NUP214-ABL1 and BCR-ABL1 fusion protein kinases

The NUP214-ABL1 fusion kinase has recently been identified in 6% of patients with T-cell acute lymphoblastic leukemia. In contrast to the more common oncogenic ABL1 fusion BCR-ABL1, NUP214-ABL1 localizes to the nuclear pore complexes and has attenuated transforming properties in hematopoietic cells and in mouse bone marrow transplant models. We have performed a thorough biochemical comparative analysis of NUP214-ABL1 and BCR-ABL1 and show that, despite their common tyrosine kinase domain, the two fusion proteins differ in many critical catalytic properties. NUP214-ABL1 has lower in vitro tyrosine kinase activity, which is in agreement with the absence of phosphorylation on its activation loop. NUP214-ABL1 was more sensitive to imatinib (Glivec) than BCR-ABL1 in vitro and in cells, indicating a different activation state and conformation of the two ABL1 fusion kinases. Using a peptide array, we identified differences in the spectrum and efficiency of substrate peptide phosphorylation and a differential involvement of Src kinases in downstream signaling. These results clearly indicate that different fusion partners of the same kinase can determine not only localization, but also critical functional properties of the enzyme such as inhibitor sensitivity and substrate preference, with subsequent differences in downstream signaling effectors and likely consequences in disease pathogenesis.

Novel mechanisms in nutrient activation of the yeast protein kinase A pathway

In yeast the Protein Kinase A (PKA) pathway can be activated by a variety of nutrients. Fermentable sugars, like glucose and sucrose, trigger a spike in the cAMP level, followed by activation of PKA and phosphorylation of target proteins causing a.o. mobilization of reserve carbohydrates, repression of stress-related genes and induction of growth-related genes. Glucose and sucrose are sensed by a G-protein coupled receptor system that activates adenylate cyclase and also activates a bypass pathway causing direct activation of PKA. Addition of other essential nutrients, like nitrogen sources or phosphate, to glucose-repressed nitrogen- or phosphate-starved cells, also triggers rapid activation of the PKA pathway. In these cases cAMP is not involved as a second messenger. Amino acids are sensed by the Gap1 transceptor, previously considered only as an amino acid transporter. Recent results indicate that the amino acid ligand has to induce a specific conformational change for signaling. The same amino acid binding site is involved in transport and signaling. Similar results have been obtained for Pho84 which acts as a transceptor for phosphate activation of the PKA pathway. Ammonium activation of the PKA pathway in nitrogen-starved cells is mediated mainly by the Mep2 transceptor, which belongs to a different class of transporter proteins. Hence, different types of sensing systems are involved in control of the yeast PKA pathway by nutrients.

Directly from Galpha to protein kinase A: the kelch repeat protein bypass of adenylate cyclase

One major class of G proteins typically functions as heterotrimeric complexes consisting of Galpha, Gbeta and Ggamma subunits. However, recent work in yeast has identified an atypical Galpha protein, Gpa2p, which functions without cognate Gbetagamma subunits. Two novel kelch repeat protein binding partners of Gpa2p, Krh1p and Krh2p, do not function as alternative Gbeta subunits, as initially thought, but rather as Gpa2p effectors. They directly link Gpa2p to protein kinase A, thus forming an adenylate cyclase bypass pathway that enables inputs other than cellular cAMP concentration to affect protein kinase A activity. Because mammalian protein kinase A expressed in yeast is also subject to control by the same bypass pathway, it is exciting to postulate that a functionally similar mechanism might exist in mammalian cells, and that other Galpha proteins could exhibit similar characteristics to Gpa2p.

Kelch-repeat proteins interacting with the Galpha protein Gpa2 bypass adenylate cyclase for direct regulation of protein kinase A in yeast

The cAMP-PKA pathway consists of an extracellular ligand-sensitive G protein-coupled receptor, a G protein signal transmitter, and the effector, adenylate cyclase, of which the product, cAMP, acts as an intracellular second messenger. cAMP activates PKA by dissociating the regulatory subunit from the catalytic subunit. Yeast cells (Saccharomyces cerevisiae) contain a glucose/sucrose-sensitive seven-transmembrane domain receptor, Gpr1, that was proposed to activate adenylate cyclase through the G(alpha) protein Gpa2. Consistently, we show here that adenylate cyclase binds only to active, GTP-bound Gpa2. Two related kelch-repeat proteins, Krh1/Gpb2 and Krh2/Gpb1, are associated with Gpa2 and were suggested to act as G(beta) mimics for Gpa2, based on their predicted seven-bladed beta-propeller structure. However, we find that although Krh1 associates with both GDP and GTP-bound Gpa2, it displays a preference for GTP-Gpa2. The strong down-regulation of PKA targets by Krh1 and Krh2 does not require Gpa2 but is strictly dependent on both the catalytic and the regulatory subunits of PKA. Krh1 directly interacts with PKA by means of the catalytic subunits, and Krh1/2 stimulate the association between the catalytic and regulatory subunits in vivo. Indeed, both a constitutively active GPA2 allele and deletion of KRH1/2 lower the cAMP requirement of PKA for growth. We propose that active Gpa2 relieves the inhibition imposed by the kelch-repeat proteins on PKA, thereby bypassing adenylate cyclase for direct regulation of PKA. Importantly, we show that Krh1/2 also enhance the association between mouse R and C subunits, suggesting that Krh control of PKA has been evolutionarily conserved.

Ammonium permease-based sensing mechanism for rapid ammonium activation of the protein kinase A pathway in yeast

In the yeast Saccharomyces cerevisiae starvation for nitrogen on a glucose-containing medium causes entrance into G0 and downregulation of all targets of the PKA pathway. Re-addition of a nitrogen source in the presence of glucose causes rapid activation of trehalase and other PKA targets. Trehalase activation upon ammonium re-supplementation is dependent on PKA activity, but not on its regulatory subunit nor is it associated with an increase in cAMP. In nitrogen-starved cells, ammonium transport and activation of trehalase are most active in strains expressing either the Mep2 or Mep1 ammonium permease, as opposed to Mep3. The non-metabolizable ammonium analogue, methylamine, also triggers activation of trehalase when transported by Mep2 but not when taken up by diffusion. Inhibition of ammonium incorporation into metabolism did not prevent signalling. Extensive site-directed mutagenesis of Mep2 showed that transport and signalling were generally affected in a similar way, although they could be separated partially by specific mutations. Our results suggest an ammonium permease-based sensing mechanism for rapid activation of the PKA pathway. Mutagenesis of Asn246 to Ala in Mep2 abolished transport and signalling with methylamine but had no effect with ammonium. The plant AtAmt1;1, AtAmt1;2, AtAmt1;3 and AtAmt2 ammonium transporters sustained transport and trehalase activation to different extents. Specific mutations in Mep2 affected the activation of trehalase differently from induction of pseudohyphal differentiation. We also show that Mep permease involvement in PKA control is different from their role in haploid invasive growth, in which Mep1 sustains and Mep2 inhibits, in a way independent of the ammonium level in the medium.

Some assembly required: yeast septins provide the instruction manual

Septins are a family of conserved proteins that form hetero-oligomeric complexes that assemble into filaments. The filaments can be organized into linear arrays, coils, rings and gauzes. They serve as membrane-associated scaffolds and as barriers to demarcate local compartments, especially for the establishment of the septation site for cytokinesis. Studies in budding and fission yeast have revealed many of the protein-protein interactions that govern the formation of multi-septin complexes. GTP binding and phosphorylation direct the polymerization of filaments that is required for septin-collar assembly in budding yeast, whereas a homolog of anillin instructs timely formation of the ring of septin filaments at the medial cortex in fission yeast. These insights should aid understanding of the organization and function of the diverse septin structures in animal cells.

Septin collar formation in budding yeast requires GTP binding and direct phosphorylation by the PAK, Cla4

Assembly at the mother–bud neck of a filamentous collar containing five septins (Cdc3, Cdc10, Cdc11, Cdc12, and Shs1) is necessary for proper morphogenesis and cytokinesis. We show that Cdc10 and Cdc12 possess GTPase activity and appropriate mutations in conserved nucleotide-binding residues abrogate GTP binding and/or hydrolysis in vitro. In vivo, mutants unable to bind GTP prevent septin collar formation, whereas mutants that block GTP hydrolysis do not. GTP binding-defective Cdc10 and Cdc12 form soluble heteromeric complexes with other septins both in yeast and in bacteria; yet, unlike wild-type, mutant complexes do not bind GTP and do not assemble into filaments in vitro. Absence of a p21-activated protein kinase (Cla4) perturbs septin collar formation. This defect is greatly exacerbated when combined with GTP binding-defective septins; conversely, the septin collar assembly defect of such mutants is suppressed efficiently by CLA4 overexpression. Cla4 interacts directly with and phosphorylates certain septins in vitro and in vivo. Thus, septin collar formation may correspond to septin filament assembly, and requires both GTP binding and Cla4-mediated phosphorylation of septins.

Protein-protein interactions governing septin heteropentamer assembly and septin filament organization in Saccharomyces cerevisiae

Mitotic yeast (Saccharomyces cerevisiae) cells express five related septins (Cdc3, Cdc10, Cdc11, Cdc12, and Shs1) that form a cortical filamentous collar at the mother-bud neck necessary for normal morphogenesis and cytokinesis. All five possess an N-terminal GTPase domain and, except for Cdc10, a C-terminal extension (CTE) containing a predicted coiled coil. Here, we show that the CTEs of Cdc3 and Cdc12 are essential for their association and for the function of both septins in vivo. Cdc10 interacts with a Cdc3-Cdc12 complex independently of the CTE of either protein. In contrast to Cdc3 and Cdc12, the Cdc11 CTE, which recruits the nonessential septin Shs1, is dispensable for its function in vivo. In addition, Cdc11 forms a stoichiometric complex with Cdc12, independent of its CTE. Reconstitution of various multiseptin complexes and electron microscopic analysis reveal that Cdc3, Cdc11, and Cdc12 are all necessary and sufficient for septin filament formation, and presence of Cdc10 causes filament pairing. These data provide novel insights about the connectivity among the five individual septins in functional septin heteropentamers and the organization of septin filaments.

The high general stress resistance of the Saccharomyces cerevisiae fil1 adenylate cyclase mutant (Cyr1Lys1682) is only partially dependent on trehalose, Hsp104 and overexpression of Msn2/4-regulated genes

The initiation of fermentation in the yeast Saccharomyces cerevisiae is associated with a rapid drop in general stress resistance. Previously we identified a mutant which is deficient in fermentation-induced loss of stress resistance (fil1), as a partially inactivating mutant in adenylate cyclase. We have now investigated possible causes of its high stress resistance. Deletion of the TPS1 gene, encoding the first enzyme in the biosynthesis of trehalose, or the heat shock protein gene HSP104 only resulted in a minor effect on heat stress resistance compared with deletion of these genes in a wild-type background. A strain with a deletion of both genes still showed a higher stress resistance in the fil1 background compared to the corresponding wild-type background. Deletion of the transcription factor genes MSN2 and MSN4, which are required for the expression of STRE-regulated genes, resulted in a dramatic drop in heat resistance in the wild-type background but had much less effect in the fil1 mutant. The fil1 msn2Deltamsn4Delta strain remained more heat-resistant than a wild-type strain. A strain in which all four genes, TPS1, HSP104, MSN2 and MSN4, are deleted was very sensitive to heat stress and also to oxidative and salt stress. Presence of the fil1 mutation in such a strain, however, still clearly enhanced heat, oxidative and salt stress resistance. These results indicate that, in addition to trehalose, Hsp104 and the Msn2/4-controlled genes, other factors exist in S. cerevisiae that can, significantly and independently of the known factors, enhance general stress resistance. The mutants described in this work provide a tool to identify these novel components.

Lre1 affects chitinase expression, trehalose accumulation and heat resistance through inhibition of the Cbk1 protein kinase in Saccharomyces cerevisiae

The addition of glucose to derepressed cells of the yeast Saccharomyces cerevisiae triggers activation of the cAMP pathway with a rapid drop in stress resistance as a consequence. We have isolated the LRE1 gene as a multicopy suppressor of glucose-induced loss of heat resistance. Overexpression of LRE1 in a wild-type strain causes the same phenotype as observed in strains with reduced activity of the cAMP-PKA pathway: higher heat resistance and enhanced trehalose levels. Deletion of LRE1 results in the opposite phenotypes. Epistasis analysis indicates that these effects are independent of cAMP and PKA, of the protein kinases Yak1, Sch9 and Rim15 and of the transcription factors Msn2 and Msn4. Lre1 has recently been isolated in a two-hybrid screen using the conserved protein kinase Cbk1 as a bait. Cbk1 controls the expression of CTS1 (encoding chitinase) through the transcription factor Ace2. We demonstrate here that overexpression of LRE1 represses CTS1 whereas deletion of LRE1 induces the expression of CTS1. Repression of CTS1 results in deficient cell separation as a result of inefficient degradation of the chitin ring after cytokinesis. Neither deletion nor overexpression of LRE1 has any effect on CTS1 expression in a cbk1Delta mutant, indicating that Lre1 inhibits Cbk1. In addition, we show that increased trehalose accumulation and increased heat resistance caused by overexpression of LRE1 are also the result of inhibition of Cbk1, revealing a novel control pathway for certain targets affected by PKA. The yeast genome contains a homologue of LRE1, YDR528w, which we have called HLR1 (for homologue of Lre1). Deletion and overexpression of HLR1 causes similar but less pronounced effects compared with LRE1.

Sex and sugar in yeast: two distinct GPCR systems

Although eukaryotic G-protein coupled receptor (GPCR) systems are well known for their ability to detect and mediate rapid responses to extracellular signals, the full range of stimuli to which they respond may not yet have been identified. Activation of GPCRs by hormones, pheromones, odorants, neurotransmitters, light and different taste compounds is well established. However, the recent discovery of a glucose-sensing GPCR system in Saccharomyces cerevisiae has unexpectedly added common nutrients to this list of stimuli. This GPCR system mediates glucose activation of adenylate cyclase during the switch from respirative/gluconeogenic metabolism to fermentation. The GPCR system involved in pheromone signalling in S. cerevisiae has already served as an important model and tool for the study of GPCR systems in higher eukaryotic cell types. Here, we highlight the similarities and differences between these two signalling systems. We also indicate how the new glucose-sensing system can serve as a model for GPCR function and as a tool with which to screen for heterologous components of signalling pathways as well as for novel ligands in high-throughput assays.

A baker's yeast mutant (fil1) with a specific, partially inactivating mutation in adenylate cyclase maintains a high stress resistance during active fermentation and growth

The initiation of fermentation in the yeast Saccharomyces cerevisiae is associated with a rapid drop in stress resistance. This is disadvantageous for several biotechnological applications, e.g. the preparation of freeze doughs. We have isolated mutants in a laboratory strain which are deficient in fermentation-induced loss of stress resistance ('fil' mutants) using a heat shock selection protocol. We show that the fil1 mutant contains a mutation in the CYR1 gene which encodes adenylate cyclase. It causes a change at position 1682 of glutamate into lysine and results in a tenfold drop in adenylate cyclase activity. The fil1 mutant displays a reduction in the glucose-induced cAMP increase, trehalase activation and loss of heat resistance. Interestingly, the fil1 mutant shows the same growth and fermentation rate as the wild type strain, as opposed to other mutants with reduced activity of the cAMP pathway. Introduction of the fil1 mutation in the vigorous Y55 strain and cultivation of the mutant under pilot scale conditions resulted in a yeast that displayed a higher freeze and drought resistance during active fermentation compared to the wild type Y55 strain. These results show that high stress resistance and high fermentation activity are compatible biological properties. Isolation of fil-type mutations appears a promising avenue for development of industrial yeast strains with improved stress resistance during active fermentation.

Characterization of a new set of mutants deficient in fermentation-induced loss of stress resistance for use in frozen dough applications

In frozen dough applications a prefermentation period during the preparation of the dough is unavoidable and might also be important to obtain bread with a good texture. A major disadvantage of the prefermentation period is that it is associated with a rapid loss of the freeze resistance of the yeast cells. A major goal for the development of new baker's yeast strains for use in frozen dough applications is the availability of strains that maintain a better freeze resistance during the prefermentation period. We have isolated mutants that retain a better stress resistance during the initiation of fermentation. Some of these showed the same growth rate and fermentation capacity as the wild type cells. These mutants are called 'fil', for deficient infermentation induced loss of stress resistance. First we used laboratory strains and heat stress treatment, given shortly after the initiation of fermentation, as the selection protocol. The first two mutants isolated in this way were affected in the glucose-activation mechanism of the Ras-cAMP pathway. The fil1 mutant had a partially inactivating point mutation in CYR1, the gene encoding adenylate cyclase, while fil2 contained a nonsense mutation in GPR1. GPR1 encodes a member of the G-protein coupled receptor family which acts as a putative glucose receptor for activation of the Ras-cAMP pathway. In a next step we isolated fil mutants directly in industrial strains using repetitive freeze treatment of doughs as selection protocol. Surviving yeast strains were tested individually for maintenance of fermentation capacity after freeze treatment in laboratory conditions and also for the best performing strains in frozen doughs prepared with yeast cultivated on a pilot scale. The most promising mutant, AT25, displayed under all conditions a better maintenance of gassing power during freeze-storage. It was not affected in other commercially important properties and will now be characterised extensively at the biochemical and molecular level.

A novel regulator of G protein signalling in yeast, Rgs2, downregulates glucose-activation of the cAMP pathway through direct inhibition of Gpa2

We have characterized a novel member of the recently identified family of regulators of heterotrimeric G protein signalling (RGS) in the yeast Saccharomyces cerevisiae. The YOR107w/RGS2 gene was isolated as a multi-copy suppressor of glucose-induced loss of heat resistance in stationary phase cells. The N-terminal half of the Rgs2 protein consists of a typical RGS domain. Deletion and overexpression of Rgs2, respectively, enhances and reduces glucose-induced accumulation of cAMP. Overexpression of RGS2 generates phenotypes consistent with low activity of cAMP-dependent protein kinase A (PKA), such as enhanced accumulation of trehalose and glycogen, enhanced heat resistance and elevated expression of STRE-controlled genes. Deletion of RGS2 causes opposite phenotypes. We demonstrate that Rgs2 functions as a negative regulator of glucose-induced cAMP signalling through direct GTPase activation of the Gs-alpha protein Gpa2. Rgs2 and Gpa2 constitute the second cognate RGS-G-alpha protein pair identified in yeast, in addition to the mating pheromone pathway regulators Sst2 and Gpa1. Moreover, Rgs2 and Sst2 exert specific, non-overlapping functions, and deletion mutants in Rgs2 and Sst2 are complemented to some extent by different mammalian RGS proteins.