Modulation of Biliary Cancer Chemo-Resistance Through MicroRNA-Mediated Rewiring of the Expansion of CD133+ Cells

BACKGROUND AND AIMS

Changes in single microRNA (miRNA) expression have been associated with chemo-resistance in biliary tract cancers (BTCs). However, a global assessment of the dynamic role of the microRNome has never been performed to identify potential therapeutic targets that are functionally relevant in the BTC cell response to chemotherapy.

APPROACH AND RESULTS

High-throughput screening (HTS) of 997 locked nucleic acid miRNA inhibitors was performed in six cholangiocarcinoma cell lines treated with cisplatin and gemcitabine (CG) seeking changes in cell viability. Validation experiments were performed with mirVana probes. MicroRNA and gene expression was assessed by TaqMan assay, RNA-sequencing, and in situ hybridization in four independent cohorts of human BTCs. Knockout of microRNA was achieved by CRISPR-CAS9 in CCLP cells (MIR1249KO) and tested for effects on chemotherapy sensitivity in vitro and in vivo. HTS revealed that MIR1249 inhibition enhanced chemotherapy sensitivity across all cell lines. MIR1249 expression was increased in 41% of cases in human BTCs. In validation experiments, MIR1249 inhibition did not alter cell viability in untreated or dimethyl sulfoxide-treated cells; however, it did increase the CG effect. MIR1249 expression was increased in CD133+ biliary cancer cells freshly isolated from the stem cell niche of human BTCs as well as in CD133+ chemo-resistant CCLP cells. MIR1249 modulated the chemotherapy-induced enrichment of CD133+ cells by controlling their clonal expansion through the Wnt-regulator FZD8. MIR1249KO cells had impaired expansion of the CD133+ subclone and its enrichment after chemotherapy, reduced expression of cancer stem cell markers, and increased chemosensitivity. MIR1249KO xenograft BTC models showed tumor shrinkage after exposure to weekly CG, whereas wild-type models showed only stable disease over treatment.

CONCLUSIONS

MIR1249 mediates resistance to CG in BTCs and may be tested as a target for therapeutics.

Molecular profiling and combinatorial activity of CCT068127: a potent CDK2 and CDK9 inhibitor

Deregulation of the cyclin-dependent kinases (CDKs) has been implicated in the pathogenesis of multiple cancer types. Consequently, CDKs have garnered intense interest as therapeutic targets for the treatment of cancer. We describe herein the molecular and cellular effects of CCT068127, a novel inhibitor of CDK2 and CDK9. Optimized from the purine template of seliciclib, CCT068127 exhibits greater potency and selectivity against purified CDK2 and CDK9 and superior antiproliferative activity against human colon cancer and melanoma cell lines. X-ray crystallography studies reveal that hydrogen bonding with the DFG motif of CDK2 is the likely mechanism of greater enzymatic potency. Commensurate with inhibition of CDK activity, CCT068127 treatment results in decreased retinoblastoma protein (RB) phosphorylation, reduced phosphorylation of RNA polymerase II, and induction of cell cycle arrest and apoptosis. The transcriptional signature of CCT068127 shows greatest similarity to other small-molecule CDK and also HDAC inhibitors. CCT068127 caused a dramatic loss in expression of DUSP6 phosphatase, alongside elevated ERK phosphorylation and activation of MAPK pathway target genes. MCL1 protein levels are rapidly decreased by CCT068127 treatment and this associates with synergistic antiproliferative activity after combined treatment with CCT068127 and ABT263, a BCL2 family inhibitor. These findings support the rational combination of this series of CDK2/9 inhibitors and BCL2 family inhibitors for the treatment of human cancer.

Abstract 129: Assessing the mechanism and therapeutic potential of modulators of the human mediator complex-associated protein kinases CDK8 and CDK19

Mediator-associated protein kinases CDK8 and CDK19 are context-dependent drivers or suppressors of tumorigenesis. Their inhibition is predicted to have pleiotropic effects, but it is unclear whether this will impact on the clinical utility of CDK8/19 inhibitors. We identified two structurally differentiated chemical series, suitable for exploring their function. In addition to tools that fulfil the criteria set out for chemical probes, the lead compounds from each series, CCT251921 and MSC2530818, had optimal pharmacological and pharmaceutical properties making them suitable for preclinical studies. Having potent, highly selective, orally bioavailable exemplar compounds from these series in hand, we were well positioned to investigate the therapeutic potential of dual CDK8/19 inhibition. The compounds exhibited modest anti-tumor activity in colorectal cancer cell line xenograft models with modulation of p-STAT1SER727, a target engagement biomarker, and altered gene expression profiles, including super-enhancer regulated gene expression, consistent with the inhibition of CDK8/19. In PDX-derived cell cultures we observed inhibition of soft-agar growth in cells derived from different tumor types. However, we only detected significant antitumour activity in 1 of 6 colorectal PDX models tested in vivo, and one example of sensitization to standard of care chemotherapy, despite showing inhibition of p-STAT1SER727. Acute myeloid leukemia cells were the most sensitive cancer type in the PDX panel with therapeutic potency seen in systemic and sub-cutaneous models. Significantly, the compounds impacted on stem cell biology. In a bone progenitor model we saw dose-responsive activation and inhibition of markers of bone matrix and bone deposition that was distinct from WNT blockade. Treatment of a diverse collection of normal cell co-culture models detected a unique response profile consistent with stimulation of an immune/inflammatory response. In vivo treatment of a genetically engineered mouse model expressing oncogenic beta-catenin shifted cells within hyperplastic intestinal crypts from a stem cell to a transit amplifying phenotype. Finally, in pre-clinical tolerability studies we observed a similar, widespread adverse safety profile at therapeutically relevant exposures for both CCT251921 and MSC2530818. At the concentrations tested we detected >80% inhibition of p-STAT1SER727 and increased IL-12 plasma levels. Since the observed pathological effects were generated with two potent, highly selective, but structurally distinct compounds, we conclude that the adverse consequences of treatment are the direct result of inhibition of CDK8 and/or CDK19. The serious and complex nature of the toxicity observed indicates that the clinical development of either series of CDK8/19 modulators, or other chemotypes with similar profiles, will be extremely challenging.

Citation Format: Paul A. Clarke, Maria-Jesus Ortiz-Ruiz, Robert Te Poele, Olajumoke Adeniji-Popoola, Gary Box, Christina Esdar, Kenneth Ewan, Sharon Gowan, Alexis De Haven Brandon, Phllip Hewitt, Wolfgang Kaufmann, Aurelie Mallinger, Florence Raynaud, Felix Rohdich, Kai Schiemann, Stephanie Simon, Richard Schneider, Melanie Valenti, Julian Blagg, Trevor Dale, Suzanne Eccles, Paul Workman, Dirk Wienke Dirk Wienke. Assessing the mechanism and therapeutic potential of modulators of the human mediator complex-associated protein kinases CDK8 and CDK19 [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 129. doi:10.1158/1538-7445.AM2017-129

Discovery of 4,6-disubstituted pyrimidines as potent inhibitors of the heat shock factor 1 (HSF1) stress pathway and CDK9

Heat shock factor 1 (HSF1) is a transcription factor that plays key roles in cancer, including providing a mechanism for cell survival under proteotoxic stress. Therefore, inhibition of the HSF1-stress pathway represents an exciting new opportunity in cancer treatment. We employed an unbiased phenotypic screen to discover inhibitors of the HSF1-stress pathway. Using this approach we identified an initial hit (1) based on a 4,6-pyrimidine scaffold (2.00 μM). Optimisation of cellular SAR led to an inhibitor with improved potency (25, 15 nM) in the HSF1 phenotypic assay. The 4,6-pyrimidine 25 was also shown to have high potency against the CDK9 enzyme (3 nM).

Abstract 1775: Identification of small molecule inhibitors of HSF1 stress pathway activation in cancer cells

Heat Shock Factor 1 (HSF1) is a key transcription factor involved in proteostasis and response to stress, as well as being implicated in many diseases including cancer. Up-regulation of its activity by environmental stress or oncogenesis leads to transcriptional induction of genes involved in diverse cellular processes supporting the cancer state, including proteostasis, proliferation, survival and metastasis. Inhibition of HSF1 is therefore potentially beneficial for cancer treatment, but HSF1 is not technically druggable. We developed a high-throughput cell-based reporter gene assay to screen a library of small-molecule kinase inhibitors and identified 3 compound series as validated inhibitors of HSF1 activation by the HSP90 inhibitor 17-AAG. Further characterization of imidazo[1,2-b]pyridazine compounds showed inhibition of HSF1 target gene expression and the ability to mimic other features of the HSF1 knockdown phenotype. Using these tool compounds and by siRNA knockdown of HSF1 expression we demonstrate that HSF1 inhibition leads to cell cycle arrest and enhances the antiproliferative effect of 17-AAG. In addition, we show that HSP90 inhibition induces HSF1 phosphorylation at two serine residues, Ser326 and Ser320, highlighting the importance of Ser320 phosphorylation in HSP72 up-regulation by 17-AAG-induced HSF1 activation, and show that this activation is inhibited by our tool compounds. Our findings support the optimization and development of small-molecule inhibitors of the HSF1 pathway for cancer treatment.

Note: This abstract was not presented at the meeting.

Citation Format: Emmanuel de Billy, Nicola Chessum, Robert Te Poele, Jennifer Smith, Lorenzo Zani, Swee Sharp, Mark Stubbs, Wynne Aherne, Keith Jones, Paul Workman. Identification of small molecule inhibitors of HSF1 stress pathway activation in cancer cells. [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 1775. doi:10.1158/1538-7445.AM2014-1775

Abstract 5440: Study of the mechanism of action and pharmacodynamic response of JNJ-26481585, a potent histone deacetylase inhibitor in the setting of melanoma

Background: JNJ-26481585 is a potent histone deacetylase (HDAC) inhibitor. It is undergoing evaluation in phase I trials in solid tumours. The drug has shown plasma concentrations consistent with activity in preclinical models and target inhibition in surrogate and tumour tissue.

Purpose: To determine the mechanism of action of JNJ-26481585 and to study factors determining sensitivity to the drug in-vitro in the setting of melanoma cell lines.

Experimental Procedures: Array comparative genomic hybridization (array CGH) was carried out to study gene copy number. The growth inhibitory (GI50) concentrations of JNJ-26481585 and 17-allylamino, 17-demethoxygeldanamyin (17-AAG) were determined by sulforhodamine (SRB) assays. A panel of melanoma cell lines was exposed to GI50 and 5 X GI50 for 24hrs and gene expression profiling was performed using gene expression microarrays. Changes in protein expression were studied by western blot analysis.

Results: Cells exposed to GI50 and 5X GI50 of 17-AAG for 24hrs showed a molecular signature of HSP90 inhibition including C-RAF depletion and HSP70 induction while this was not the case in equitoxic concentrations of JNJ-26481585. In addition, JNJ-26481585 did not reproducibly induce acetylation of tubulin which is a surrogate for cytoplasmic acetylation of proteins such as HSP90. JNJ-26481585 however induced robust acetylation of histone H3 suggestive of its mechanism of action predominantly as a class I HDAC inhibitor. The micropthalmia associated transcription factor (MITF) locus was amplified in the SKMEL-28 cells. The GI50 concentrations of JNJ-26481585 in the cell lines SKMEL-28, WM266.4, A2058, SKMEL-2 and SKMEL-5 were 5.4 (SD 0.86) nM, 20 (SD 0.58) nM, 28.1 (SD 0.7) nM, 30.4 (SD 3.6) nM, 33.4 (SD 3.6) nM respectively. The cell line panel was exposed to GI50 and 5 X GI50 of JNJ-26481585 for 24hrs. Protein levels of MITF was depleted in addition to MITF m-RNA levels being significantly reduced; p=0.002 (Welch T test with Benjamini and Hochberg correction for multiple testing; FDR 5%) at the time points studied, suggesting down regulation of MITF gene expression as a possible mechanism of action of JNJ-26481585. All the cell lines studied underwent apoptosis as evidenced by demonstration of cleaved PARP on western blotting.

Conclusions: In this model, the mechanism of action of JNJ-26481585 is not predominantly due to HSP90 inhibition caused by acetylation of HSP90 in melanoma cells. Melanoma cell lines which have an amplification of MITF are sensitive to the HDAC inhibitor JNJ-26481585. Further exploration of MITF protein to evaluate pharmacodynamic response of JNJ-26481585 is warranted.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5440.

Molecular pharmacology of phosphatidylinositol 3-kinase inhibition in human glioma

Gliomas are primary brain tumors with poor prognosis that exhibit frequent abnormalities in phosphatidylinositol 3-kinase (PI3 kinase) signaling. We investigated the molecular mechanism of action of the isoform-selective class I PI3 kinase and mTOR inhibitor PI-103 in human glioma cells. The potent inhibitory effects of PI-103 on the PI3 kinase pathway were quantified. PI-103 and the mTOR inhibitor rapamycin both inhibited ribosomal protein S6 phosphorylation but there were clear differences in the response of upstream components of the PI3 kinase pathway, such as phosphorylation of Thr(308)-AKT, that were inhibited by PI-103 but not rapamycin. Gene expression profiling identified altered expression of genes encoding regulators of the cell cycle and cholesterol metabolism, and genes modulated by insulin or IGF1 signaling, rapamycin treatment or nutrient starvation. PI-103 decreased expression of positive regulators of G(1)/S phase progression and increased expression of the negative cell cycle regulator p27(kip1). A reversible PI-103-mediated G(1) cell cycle arrest occurred without significant apoptosis, consistent with the altered gene expression detected. PI-103 induced vacuolation and processing of LC-3i to LC-3ii, which are features of an autophagic response. In contrast to PI-103, LY294002 and PI-387 induced apoptosis, indicative of likely off-target effects. PI-103 interacted synergistically or additively with cytotoxic agents used in the treatment of glioma, namely vincristine, BCNU and temozolomide. Compared to individual treatments, the combination of PI-103 with temozolomide significantly improved the response of U87MG human glioma xenografts. Our results support the therapeutic potential for PI3 kinase inhibitors with a PI-103-like profile as therapeutic agents for the treatment of glioma.

Disruption of WT1 gene expression and exon 5 splicing following cytotoxic drug treatment: antisense down-regulation of exon 5 alters target gene expression and inhibits cell survival

Deregulated expression of the Wilms' tumor gene (WT1) has been implicated in the maintenance of a malignant phenotype in leukemias and a wide range of solid tumors through interference with normal signaling in differentiation and apoptotic pathways. Expression of high levels of WT1 is associated with poor prognosis in leukemias and breast cancer. Using real-time (Taqman) reverse transcription-PCR and RNase protection assay, we have shown up-regulation of WT1 expression following cytotoxic treatment of cells exhibiting drug resistance, a phenomenon not seen in sensitive cells. WT1 is subject to alternative splicing involving exon 5 and three amino acids (KTS) at the end of exon 9, producing four major isoforms. Exon 5 splicing was disrupted in all cell lines studied following a cytotoxic insult probably due to increased exon 5 skipping. Disruption of exon 5 splicing may be a proapoptotic signal because specific targeting of WT1 exon 5-containing transcripts using a nuclease-resistant antisense oligonucleotide (ASO) killed HL60 leukemia cells, which were resistant to an ASO targeting all four alternatively spliced transcripts simultaneously. K562 cells were sensitive to both target-specific ASOs. Gene expression profiling following treatment with WT1 exon 5-targeted antisense showed up-regulation of the known WT1 target gene, thrombospondin 1, in HL60 cells, which correlated with cell death. In addition, novel potential WT1 target genes were identified in each cell line. These studies highlight a new layer of complexity in the regulation and function of the WT1 gene product and suggest that antisense directed to WT1 exon 5 might have therapeutic potential.