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We describe the assembly and annotation of a chemogenomic set of protein kinase inhibitors as an open science resource for studying kinase biology. The set only includes inhibitors that show potent kinase inhibition and a narrow spectrum of activity when screened across a large panel of kinase biochemical assays. Currently, the set contains 187 inhibitors that cover 215 human kinases. The kinase chemogenomic set (KCGS), current Version 1.0, is the most highly annotated set of selective kinase inhibitors available to researchers for use in cell-based screens.

Patients with melanoma resistant to RAF/MEK inhibitors (RMi) are frequently resistant to other therapies, such as immune checkpoint inhibitors (ICI), and individuals succumb to their disease. New drugs that control tumor growth and favorably modulate the immune environment are therefore needed. We report that the small-molecule CX-6258 has potent activity against both RMi-sensitive (RMS) and -resistant (RMR) melanoma cell lines. Haspin kinase (HASPIN) was identified as a target of CX-6258. HASPIN inhibition resulted in reduced proliferation, frequent formation of micronuclei, recruitment of cGAS, and activation of the cyclic GMP-AMP synthase (cGAS)–stimulator of interferon genes (STING) pathway. In murine models, CX-6258 induced a potent cGAS-dependent type-I IFN response in tumor cells, increased IFNγ-producing CD8+ T cells, and reduced Treg frequency in vivo. HASPIN was more strongly expressed in malignant compared with healthy tissue and its inhibition by CX-6258 had minimal toxicity in ex vivo–expanded human tumor-infiltrating lymphocytes (TIL), proliferating TILs, and in vitro differentiated neurons, suggesting a potential therapeutic index for anticancer therapy. Furthermore, the activity of CX-6258 was validated in several Ewing sarcoma and multiple myeloma cell lines. Thus, HASPIN inhibition may overcome drug resistance in melanoma, modulate the immune environment, and target a vulnerability in different cancer lineages. Significance: HASPIN inhibition by CX-6258 is a novel and potent strategy for RAF/MEK inhibitor–resistant melanoma and potentially other tumor types. HASPIN inhibition has direct antitumor activity and induces a favorable immune microenvironment.

We describe the assembly and annotation of a chemogenomic set of protein kinase inhibitors as an open science resource for studying kinase biology. The set only includes inhibitors that show potent kinase inhibition and a narrow spectrum of activity when screened across a large panel of kinase biochemical assays. Currently, the set contains 187 inhibitors that cover 215 human kinases. The kinase chemogenomic set (KCGS) is the most highly annotated set of selective kinase inhibitors available to researchers for use in cell-based screens.

Frequent mutation of genes in the PI3K/AKT/mTOR signaling pathway in human cancers has stimulated large investments in therapeutic drugs but clinical successes have been rare. As a result, many cancers with high PI3K pathway activity such as triple-negative breast cancer (TNBC) are still treated primarily with conventional chemotherapy. By systematically analyzing responses of TNBC cells to a diverse collection of PI3K pathway inhibitors, we find that one drug, Torin2, is unusually effective because it inhibits both mTOR and PI3K-like kinases (PIKKs). In contrast to mTOR-selective inhibitors, Torin2 exploits dependencies on several kinases for progression of S-phase and for cell cycle checkpoints, thereby causing accumulation of single-stranded DNA and death by replication catastrophe or mitotic failure. Thus, Torin2 and its analogs represent a mechanistically distinct class of PI3K pathway inhibitors that are uniquely cytotoxic to TNBC cells. This insight could be translated therapeutically by further developing Torin2 analogs or combinations of existing mTOR and PIKK inhibitors.

Doublecortin-like kinase 1 (DCLK1) is critical for neurogenesis, but overexpression is also observed in multiple cancers and is associated with poor prognosis. Nevertheless, the function of DCLK1 in cancer, especially the context-dependent functions, are poorly understood. We present a "toolkit" that includes the DCLK1 inhibitor DCLK1-IN-1, a complementary DCLK1-IN-1-resistant mutation G532A, and kinase dead mutants D511N and D533N, which can be used to investigate signaling pathways regulated by DCLK1. Using a cancer cell line engineered to be DCLK1 dependent for growth and cell migration, we show that this toolkit can be used to discover associations between DCLK1 kinase activity and biological processes. In particular, we show an association between DCLK1 and RNA processing, including the identification of CDK11 as a potential substrate of DCLK1 using phosphoproteomics.

The target profiles of many drugs are established early in their development and are not systematically revisited at the time of approval, raising the question whether human therapeutics with the same nominal targets but different chemical structures are functionally equivalent. In this paper we use five distinct phenotypic and biochemical assays to compare approved inhibitors of the cyclindependent kinases CDK4/6 (palbociclib, ribociclib, and abemaciclib) that are promising therapies for hormone-receptor positive breast cancer. We find that transcriptional, proteomic and phenotypic changes induced by the three drugs differ significantly and that abemaciclib has activates overlapping those of the older generation CDK inhibitor alvocidib. Abemaciclib’s activities arise from inhibition of kinases other than CDK4/6 including CDK2/Cyclin A/E and CDK1/Cyclin B. Our data suggest the potential for differential use in the clinic and argue that a multi-faceted experimental and computational approach is necessary to obtain a reliable picture of kinase inhibitor target spectrum.

SUMMARYThe target profiles of many drugs are established early in their development and are not systematically revisited at the time of FDA approval. Thus, it is often unclear whether therapeutics with the same nominal targets but different chemical structures are functionally equivalent. In this paper we use five different phenotypic and biochemical assays to compare approved inhibitors of cyclin-dependent kinases 4/6 – collectively regarded as breakthroughs in the treatment of hormone receptor-positive breast cancer. We find that transcriptional, proteomic and phenotypic changes induced by palbociclib, ribociclib, and abemaciclib differ significantly; abemaciclib in particular has advantageous activities partially overlapping those of alvocidib, an older polyselective CDK inhibitor. In cells and mice, abemaciclib inhibits kinases other than CDK4/6 including CDK2/Cyclin A/E – implicated in resistance to CDK4/6 inhibition – and CDK1/Cyclin B. The multi-faceted experimental and computational approaches described here therefore uncover under-appreciated differences in CDK4/6 inhibitor activities with potential importance in treating human patients.

Frequent mutation of PI3K/AKT/mTOR signaling pathway genes in human cancers has stimulated large investments in targeted drugs but clinical successes are rare. As a result, many cancers with high PI3K pathway activity, such as triple-negative breast cancer (TNBC), are treated primarily with chemotherapy. By systematically analyzing responses of TNBC cells to a diverse collection of PI3K pathway inhibitors, we find that one drug, Torin2, is unusually effective because it inhibits both mTOR and other PI3K-like kinases (PIKKs). In contrast to mTOR-selective inhibitors, Torin2 exploits dependencies on several kinases for S-phase progression and cell-cycle checkpoints, thereby causing accumulation of single-stranded DNA and death by replication catastrophe or mitotic failure. Thus, Torin2 and its chemical analogs represent a mechanistically distinct class of PI3K pathway inhibitors that are uniquely cytotoxic to TNBC cells. This insight could be translated therapeutically by further developing Torin2 analogs or combinations of existing mTOR and PIKK inhibitors.

Oncogene-targeted therapies are initially effective in most patients with BRAF-mutated melanoma. However, patients frequently develop resistance during therapy. At the time of therapy resistance, they are also less likely to respond to immune checkpoint inhibitors (ICI) with response rates ranging from 0-12%, compared to 40-60% when used in the first line. This may be in part be due to rapid tumor growth that outpaces pharmacodynamics of ICI. New drugs that directly control tumor growth and effectively enhance ICI activity are therefore needed. We report that the small molecule CX-6258 has potent activity against both RAF/MEK inhibitor (RMS) and resistant (RMR) BRAF-mutant melanoma cell lines. CX-6258 is annotated as a pan-PIM kinase inhibitor, with an EC50 corrected for growth rate (GR50) of ~200 nM; in contrast, other PIM inhibitors had no in vitro activity, suggesting that PIMs may not be the true target in melanoma - we therefore sought to systematically study the targets of this compound. Using an unbiased kinase profiling approach, we identified Haspin Kinase (HASPIN) as the key target of CX-6258 with an IC50~10nM. Haspin kinase (Haspin) is a poorly understood mitotic kinase, whose only well-defined function is phosphorylation of Histon H3 at Thr3 (pH3T3). Treatment with CX-6258 resulted in reduced proliferation, reduced phosphorylation of pH3T3, frequent formation of micronuclei (MN), recruitment of cGAS and activation of the cGAS-STING-pathway. By using CRISPR/CAS9 knock outs of PIM kinase we show that these targets are not required for CX-6258 function. Furthermore, siRNA mediated knock-down of HASPIN phenocopied CX-6258. In murine models, CX-6258 induces a potent cGAS dependent type-I-interferon response in tumor cells, increases IFNγ-producing CD8+ T-cells, reduces Tregs, and enhances responses to ICIs in vivo. HASPIN is more strongly expressed in malignant compared to healthy tissue and its inhibition by CX-6258 has minimal toxicity in ex vivo expanded human tumor-infiltrating-lymphocytes (TILs) and in vitro differentiated human neurons, suggesting a potential therapeutic index for anti-cancer therapy. CX-6258 also shows activity in several Ewing sarcoma and multiple myeloma cell lines with. In summary, HASPIN inhibition may overcome drug resistance in melanoma, synergize with ICIs and target a vulnerability in different cancer lineages. Citation Format: Johannes C. Melms, Sreeram Vallabhaneni, Caitlin E. Mills, Kai Wucherpfennig, Peter K. Sorger, Benjamin Izar. Inhibition of Haspin kinase to promote cell-intrinsic and extrinsic anticancer therapy [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B132. doi:10.1158/1535-7163.TARG-19-B132

Intrinsic or acquired resistance to targeted therapies, such as RAF/MEK inhibitors in melanoma, represents a significant clinical challenge. We performed a small molecule screen in isogenic sensitive (S) and RAF/MEK-inhibitor-resistant (RMR) melanoma cell lines and identified a nominal PIM kinase inhibitor (Comp-1) with high activity against A375-S and A375-RMR, with an EC50of ~100 nM. While the phosphorylation of some PIM targets, including 4EBP1 and MYC, were significantly inhibited in a dose-dependent fashion, phosphorylation of BAD was not reduced as one would expect. To determine the on-target activity of this compound, we generated A375 cell lines overexpressing WT PIM isoforms 1-3 or their kinase-dead (KD) forms, followed by treatment with PIMi-1. We found only modest shifts in EC50and hypothesized that the beneficial effects of this compounds were due to inhibition of an alternative target. A screen of Comp-1, along with structurally related compounds, against 468 human kinases revealed exquisite affinity for Haspin kinase (HK). We determined the IC50of Comp-1 against HK to be 14.9 nM. The only described role of HK is phosphorylation of Histone H3 at Thr 3 (H3T3) and thereby regulation of mitotic progression. Quantitative single-cell immunofluorescence (IF) analysis of Comp-1 treated A375 confirmed complete abrogation of p-H3T3, indicating on-target activity in vitro. To understand the temporal effects of HK inhibition with Comp-1, we performed live-cell imaging and single-cell analysis of A375 transduced with a mitotic phase-specific reporter. Cells experienced mitotic stress or mitotic slippage resulting in DNA-damage and an increase gamma-H2AX foci per nuclei. In line with these observation, we observed increased phosphorylation p53 and CHECK2. Furthermore, a portion of cells developed micronuclei in a dose-dependent fashion providing a substrate for the cytosolic DNA-sensing machinery, including the cGAS-STING pathway, and rationale for combining Comp-1 with immunotherapies. Ongoing experiments in tumor-bearing BALB/c mice indicate safety and potentially enhanced efficacy of Comp-1 when combined with either anti-CTLA-4 or anti-PD-1 therapy. Ex vivotreatment of patient-derived tumor-infiltrating lymphocytes (TILs) with Comp-1 revealed no toxic effects. A pan-cancer RNA-seq analysis revealed significant upregulation of HK in 34 of 37 tumor types supporting its role as a potential therapeutic target. Overall, our work identified a highly selective Haspin Kinase inhibitor with activity against RAF/MEK inhibitor resistant melanoma, insights into the underlying mechanisms, and potential in vivo benefit when combined with immune checkpoint inhibitors. Citation Format: Johannes C. Melms, Sreeram Vallabhaneni, Caitlin E. Mills, Peter K. Sorger, Kai Wucherpfennig, Benjamin Izar. A highly selective dual Haspin-kinase and PIM-inhibitor overcomes RAF/MEK-inhibitor resistance in melanoma [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 2068.

Several publications have addressed concerns surrounding drug response screens by pointing out sources of variability and by presenting recommendations for better experimental methods and more robust analytical approaches. In the presented profiling effort, we integrated the latest advances in drug response measurement and focused on data diversity and quality rather than on breadth. We selected 32 breast cancer cell lines with a strong bias towards triple negative lines as well as 4 cell lines established from relevant patient-derived xenografts. We evaluated a panel of clinically relevant kinase inhibitors using a microscopy-based drug response assay to measure drug potency, and to quantify drug efficacy in terms of growth inhibition (GR metrics) and cell death. The use of the GR metrics to quantify drug sensitivity enabled us to identify and study differences between cytostatic and cytotoxic responses. This systematic dose response dataset is complemented by measurements of baseline mRNA expression levels by RNAseq and endogenous protein levels by shotgun mass spectrometry across all cell lines. The completeness and controlled conditions under which these data sets were collected provide confidence in their integration. The baseline RNA and protein expression levels were used to build predictors of the measured drug responses with the goal of identifying the biological processes responsible for the differences in sensitivity across drugs and cell lines. Differences in the phenotypic responses of cell lines to kinase inhibitors with the same nominal targets have been investigated, and associated with variable inhibitor polypharmacology. Citation Format: Caitlin E. Mills, Marc Hafner, Dejan Juric, Peter K. Sorger. Systematic characterization of kinase inhibitors reveals heterogeneity in responses by class and cell line [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 2385. doi:10.1158/1538-7445.AM2017-2385

There is need for improved targeted therapies for the treatment of breast cancer. Kinase inhibitors are candidates to be used in this context. With the goal of uncovering specific vulnerabilities in differing cell lines, we treated five breast cancer cell lines representing triple negative (BT20, MDAMB231, and Hs578T), hormone receptor positive (MCF7), and Her2 amplified (SKBR3) disease and the non-malignant MCF10A line with a panel of 105 kinase inhibitors covering a broad range of targets. Cells were treated with doses between 0.1 and 10 μM for 24 hours, at which time they were stained with DRAQ5 (DNA) and TMRE (mitochondrial membrane potential). Live-cell images were acquired using a high throughput, confocal Opera microscope. Cell segmentation, based on the DRAQ5 staining, and feature extraction (intensity, morphology, and texture) were performed with Acapella software. Over 300 features were extracted for ∼1.5 million cells. Analytical methods have been applied to identify those treatments that induced significant changes to the cells. Over half of the kinase inhibitors queried had a significant effect within 24 hours in all cell lines at 10 μM. Cell cycle inhibitors had the most common effects across cell lines. Cell line specific effects were also uncovered, for example, MDAMB231 cells were the most sensitive to MAPK inhibitors. These, early time point, results have been compared with the effects of the same inhibitors on cell growth to better understand the mechanisms leading to cell line and pathway specific effects. Citation Format: Caitlin Mills, David Andrews, Peter Sorger. Single cell imaging of kinase inhibitor-induced effects in breast cancer cell lines. [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 203.