Fig. S1 - eIF4E expression and survival data for papillary thyroid. Fig. S2 - Effect of BET inhibitors on genes regulating cytoskeleton Fig. S3 - combination of MNK inhibitors and OTX015 or ARV-825

Effect of JQ1 on cytoskeletal genes

Supplementary Figure S1 - Effect of pancreatitis on mast cell infiltration. Supplementary Figure S2 - Snail expression in CD18 cells. Supplementary Figure S3 - Slug expression in AsPC1 cells.

Coefficient of drug interaction calculations

BACKGROUND:Pancreatic ductal adenocarcinoma (PDAC) is characterized by the presence of dense stroma that is enriched in hyaluronan (HA), with increased HA levels associated with more aggressive disease. Increased levels of the HA-degrading enzymes hyaluronidases (HYALs) are also associated with tumor progression. In this study, we evaluate the regulation of HYALs in PDAC.METHODS:Using siRNA and small molecule inhibitors, we evaluated the regulation of HYALs using quantitative real-time PCR (qRT-PCR), Western blot analysis, and ELISA. The binding of BRD2 protein on the HYAL1 promoter was evaluated by chromatin immunoprecipitation (ChIP) assay. Proliferation was evaluated by WST-1 assay. Mice with xenograft tumors were treated with BET inhibitors. The expression of HYALs in tumors was analyzed by immunohistochemistry and by qRT-PCR.RESULTS:We show that HYAL1, HYAL2, and HYAL3 are expressed in PDAC tumors and in PDAC and pancreatic stellate cell lines. We demonstrate that inhibitors targeting bromodomain and extra-terminal domain (BET) proteins, which are readers of histone acetylation marks, primarily decrease HYAL1 expression. We show that the BET family protein BRD2 regulates HYAL1 expression by binding to its promoter region and that HYAL1 downregulation decreases proliferation and enhances apoptosis of PDAC and stellate cell lines. Notably, BET inhibitors decrease the levels of HYAL1 expression in vivo without affecting the levels of HYAL2 or HYAL3.CONCLUSIONS:Our results demonstrate the pro-tumorigenic role of HYAL1 and identify the role of BRD2 in the regulation of HYAL1 in PDAC. Overall, these data enhance our understanding of the role and regulation of HYAL1 and provide the rationale for targeting HYAL1 in PDAC.

PDF - 1346K, Fig. S1: Effect of I-BET151 on PDAC cells. Figs. S2 and S3: Effect of I-BET on Snail-expressing PDAC cells. Fig. S4: Effect of I-BET151 on chemo-resistant cells. Figs. S5 and S6: Effect of I-BET151 on c-MYC and FOSL1. Fig. S7: ChIP results.

Supplemental data related to Figs. 2 and 5 S1. Collagen-dependent MNK phosphorylation in chemoresistant PDAC cells. S2. Targeting eIF4E increases ZEB1 levels in AsPC1 and Panc1 cells. S3. eIF4E and MNK1/2 do not regulate expression of primary transcript of miR-200 (pri-miR-200) microRNAs A and B. S4. miR-141 and miR-200c regulate ZEB1 levels in CD18-CR cells A. S5. Targeting the MNK effector hnRNPA1 increases ZEB1 protein without increasing ZEB1 mRNA levels.

Metastases from primary breast cancer result in poor survival. βIII-tubulin (TUBB3) has been established as a therapeutic target for breast cancer metastases specifically to the brain. In this study, we conducted a systematic analysis to determine the regulation of TUBB3 expression in breast cancer metastases to the brain and strategically target these metastases using vinorelbine (VRB), a drug approved by the U.S. Food and Drug Administration (FDA). We found that human epidermal growth factor receptor 2 (HER2) signaling regulates TUBB3 expression in both trastuzumab-sensitive and trastuzumab-resistant neoplastic cells. We further discovered that bromodomain and extra-terminal domain (BET) inhibition increases TUBB3 expression, rendering neoplastic cells more susceptible to apoptosis by VRB. Orthotopic xenograft assays using two different breast cancer cell models revealed a reduction in tumor volume with BET inhibition and VRB treatment. In addition, in vivo studies using a model of multiple brain metastasis (BM) showed improved survival with the combination of radiation + BET inhibitor (iBET-762) + VRB (75% long-term survivors, P < 0.05). Using in silico analysis and BET inhibition, we found that the transcription factor myeloid zinc finger-1 (MZF-1) protein binds to the TUBB3 promoter. BET inhibition decreases MZF-1 expression and subsequently increases TUBB3 expression. Overexpression of MZF-1 decreases TUBB3 expression and reduces BM in vivo, whereas its knockdown increases TUBB3 expression in breast cancer cells. In summary, this study demonstrates a regulatory mechanism of TUBB3 and provides support for an application of BET inhibition to sensitize breast cancer metastases to VRB-mediated therapy.

Bromodomain and extraterminal domain (BET) proteins, which are important epigenetic readers, are often dysregulated in cancer. While a number of BET inhibitors are currently in early phase clinical trials, BET inhibitors show limited single-agent activity. The purpose of this study is to determine if Quercetin, a naturally occurring polyphenolic flavonoid often found abundant in fruits and vegetables, can enhance the anti-tumor effects of BET inhibitors. The efficacy of the combination was evaluated in vitro and in a xenograft model of pancreatic cancer. Co-treatment with BET inhibitors and Quercetin promoted apoptosis, decreased sphere-forming ability by cancer cells, and decreased cell proliferation. We found that hnRNPA1, a nuclear protein known to control mRNA export and mRNA translation of anti-apoptotic proteins, mediates some anti-tumor effects by Quercetin. Additionally, we show that combining BET inhibitors with Quercetin or hnRNPA1 knockdown decreased the anti-apoptotic protein Survivin. Significantly, Quercetin decreased hnRNPA1 in vivo and enhanced the effects of BET inhibitors at suppressing tumor growth. Together, these results demonstrate that Quercetin enhances the efficacy of BET inhibitors by suppressing hnRNPA1, and identify combination therapy with Quercetin and BET inhibitors for the treatment of cancer patients.

Abstract BET inhibitors (BETi), which target transcription of key oncogenic genes, are currently being evaluated in early-phase clinical trials. However, because BETis show limited single-agent activity, there is increasing interest in identifying signaling pathways to enhance the efficacy of BETis. Here, we demonstrate increased MNK kinase–dependent eIF4E phosphorylation following treatment with BETis, indicating activation of a prosurvival feedback mechanism in response to BETis. BET PROTACs, which promote degradation of BET proteins, also induced eIF4E phosphorylation in cancer cells. Mechanistically, we show that the effect of BETis on MNK-eIF4E phosphorylation was mediated by p38 MAPKs. We also show that BETis suppressed RacGAP1 to induce Rac signaling–mediated eIF4E phosphorylation. Significantly, MNK inhibitors and MNK1/2 knockdown enhanced the efficacy of BETis in suppressing proliferation of cancer cells in vitro and in a syngeneic mouse model. Together, these results demonstrate a novel prosurvival feedback signaling induced by BETis, providing a mechanistic rationale for combination therapy with BET and MNK inhibitors for synergistic inhibition of cancer cells.

Bromodomain and extraterminal domain (BET) proteins are epigenetic readers that regulate gene expression and are involved in cancer pathogenesis. While a number of BET inhibitors are currently in preclinical development or in early phase clinical trials, BET inhibitors show limited single-agent activity. Thus, there is increasing interest in identifying combination regimens to enhance the efficacy of BET inhibitors. Since MNK kinases can enhance the efficacy of BET inhibitors in vitro and in vivo, in this report we evaluated whether targeting effectors downstream of MNK kinases can enhance the efficacy of BET inhibitors. We show that there is co-expression of the BET protein BRD4 and the MNK effector hnRNPA1 in human tumors. We show that hnRNPA1 knockdown can potentiate the effects of BET inhibitors, with enhanced apoptosis and suppression of proliferation and sphere-forming ability by cancer cells. We also show that the plant flavonoid Quercetin, which reduces hnRNPA1 protein levels in cancer cells, can enhance the efficacy of BET inhibitors. Co-treatment with BET inhibitors and Quercetin results in enhanced apoptosis, further suppression of proliferation, and decreased sphere-forming ability by cancer cells. Significantly, Quercetin synergizes with BET inhibitors at suppressing tumor growth in vivo. Together, these results demonstrate that targeting the MNK effector hnRNPA1 can enhance the efficacy of BET inhibitors, and we identify combination therapy with BET inhibitors and Quercetin for the treatment of cancer patients. Citation Format: Thao Pham, Sophie Stempel, Mario Shields, Christina Spaulding, Krishan Kumar, David Bentrem, Hidayatullah Munshi. Targeting the MNK effector hnRNPA1 enhances the efficacy of BET inhibitors in cancer cells [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 2086.

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is associated with an extensive desmoplasia which is composed of multiple extracellular matrix components, including collagen, fibronectin, laminin, and hyaluronan (HA). Inhibitors targeting bromodomain and extra-terminal (BETi) proteins have emerged as potential therapeutic agents and are in clinical trials for a range of malignancies. We have previously shown that BETi attenuate fibrosis in vivo by decreasing collagen expression; however, the effect of BETi on HA has not been previously evaluated. Increased HA, which is synthesized by HA synthases (HAS), is associated with poor outcome in PDAC. Targeting HA has been postulated to provide a potential therapeutic opportunity to overcome PDAC chemo-resistance. Preclinical data have demonstrated that enzymatic degradation of HA with PEGPH20 remodels the tumor microenvironment, decreases the interstitial pressure and enhance the drug entry in tumors. Several ongoing clinical trials are evaluating PEGPH20 in combination with chemotherapies. We now report that BET inhibitors markedly decrease expression of HAS2 and HAS3, which are overexpressed in PDAC. Purpose: The aim of this study is to investigate the role of BET proteins in HA synthesis. Methods: mRNA expression levels HAS2 and HAS3 were determined in a panel of 7 PDAC cell lines by quantitative real-time RT-PCR. Protein expression was determined by western blotting. Results: We found that treatment with BET inhibitors decrease the expression of HAS2 and HAS3 in all cell lines. Furthermore, siRNA mediated knockdown of individual BET proteins demonstrated that HAS2 is primarily regulated by BRD2, while HAS3 is primarily regulated by BRD4. Conclusion: Our results demonstrate that BET proteins play a role in HA synthesis by regulating expression of HAS2 and HAS3 enzymes. Citation Format: Krishan Kumar, Kazumi Ebine, Thao Pham, Meng Shang, Hidayatullah G. Munshi. BET proteins regulate hyaluronan synthases in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4500.

Abstract Patients with recurrent differentiated thyroid cancers (DTCs) have poor prognosis and suffer from multiple complications from progressive symptomatic disease. Here we show that eukaryotic translation initiation factor 4E (eIF4E), an oncogene that is overexpressed in aggressive thyroid cancers, is required for growth of DTC cells in collagen microenvironment. We show that inhibitors targeting bromodomain and extra-terminal domain (BET) family of proteins also decrease growth of DTC cells in the collagen microenvironment. Unexpectedly, we have found that BET inhibitors induce MNK and eIF4E phosphorylation in cancer cells. Mechanistically, BET inhibitors induce Rac1-mediated cytoskeletal changes and targeting Rac1 blocks these changes as well as MNK and eIF4E phosphorylation. Functionally, we show that MNK inhibitors potentiate the effects of BET inhibitors at suppressing cancer cell proliferation and limiting sphere-forming ability. Together, these results demonstrate crosstalk between BET proteins and the MNK-eIF4E pathway, suggesting that combination therapy with BET and MNK inhibitors has the potential for synergistic inhibition of cancer cells. Citation Format: Thao Pham, Brian T. Decant, Krishan Kumar, Meng Shang, Maria Matsangou, Kazumi Ebine, Hidayatullah G. Munshi. BET inhibitors induce Rac1-dependent MNK and eIF4E phosphorylation in cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2989.

The fibrotic reaction is a characteristic feature of human pancreatic ductal adenocarcinoma (PDAC) tumors. It is associated with activation and proliferation of pancreatic stellate cells (PSCs), which are key regulators of fibrosis in vivo. While there is increasing interest in the regulation of PD-L1 expression in cancer and immune cells, the expression and regulation of PD-L1 in other stromal cells, such as PSCs, has not been fully evaluated. Here we show that PSCs in vitro express higher PD-L1 mRNA and protein levels compared to the levels present in PDAC cells. We show that inhibitors targeting bromodomain and extra-terminal (BET) proteins and BRD4 knockdown decrease interferon-γ (IFN-γ)-induced PD-L1 expression in PSCs. We also show that c-MYC, one of the well-established targets of BET inhibitors, does not mediate IFN-γ-regulated PD-L1 expression in PSCs. Instead we show that interferon regulatory factor 1 (IRF1) mediates IFN-γ-induced PD-L1 expression in PSCs. Finally, while we show that BET inhibitors do not regulate IFN-γ-induced IRF1 expression in PSCs, BET inhibitors decrease binding of IRF1 and BRD4 to the PD-L1 promoter. Together, these results demonstrate the interplay between IRF1 and BRD4 in the regulation of PD-L1 in PSCs.

Abstract Single agent treatment with T-cell checkpoint inhibitors has not been effective in pancreatic ductal adenocarcinoma (PDAC) patients. The PDAC stroma, which can account for as much as 80-90% of the tumor mass, can act as a physical and an immunologic barrier to T-cell-mediated therapies. Transgenic mouse models have shown that ablation of pancreatic stellate cells (PSCs), key regulators of fibrosis in vivo, can sensitize PDAC tumors to immune checkpoint therapies. Recently, inhibitors targeting bromodomains and extra-terminal (BET) proteins, a number of which are currently being evaluated in clinical trials for solid tumors, were shown to induce stellate cells to become quiescent and decrease collagen production. The BET family of proteins binds to acetylation motifs present in histones and enables recruitment of transcription factors and other chromatin regulators during RNA transcription. We have found that PSCs express significantly increased PD-L1 levels compared to pancreatic cancer cell lines. We show that BET inhibitors, and in particular specific knockdown of BRD4 protein, decrease basal and IFN-γ-mediated PD-L1 expression in primary stellate cells. We also show that, in contrast to a recent report using cancer cells, c-MYC does not mediate basal or IFN-γ-mediated PD-L1 expression in stellate cells. Instead, we show that the IFN-γ-mediated PD-L1 expression is regulated by IRF1, suggesting cross talk between BRD4 and IRF1 in the regulation of PD-L1 expression. Ongoing in vivo experiments will evaluate the role of BET inhibitors in the regulation of PD-L1 in mouse models of pancreatic cancer. Citation Format: Kazumi Ebine, Brian T. DeCant, Katharine A. Collier, Thao N. Pham, Krishan Kumar, Hidayatullah G. Munshi. BET inhibitors suppress PD-L1 expression in pancreatic stellate cells [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 1679. doi:10.1158/1538-7445.AM2017-1679

Cells in the pancreas that have undergone acinar-ductal metaplasia (ADM) can transform into premalignant cells that can eventually become cancerous. Although the epithelial-mesenchymal transition regulator Snail (Snai1) can cooperate with Kras in acinar cells to enhance ADM development, the contribution of Snail-related protein Slug (Snai2) to ADM development is not known. Thus, transgenic mice expressing Slug and Kras in acinar cells were generated. Surprisingly, Slug attenuated Kras-induced ADM development, ERK1/2 phosphorylation and proliferation. Co-expression of Slug with Kras also attenuated chronic pancreatitis-induced changes in ADM development and fibrosis. In addition, Slug attenuated TGF-α-induced acinar cell metaplasia to ductal structures and TGF-α-induced expression of ductal markers in ex vivo acinar explant cultures. Significantly, blocking the Rho-associated protein kinase ROCK1/2 in the ex vivo cultures induced expression of ductal markers and reversed the effects of Slug by inducing ductal structures. In addition, blocking ROCK1/2 activity in Slug-expressing Kras mice reversed the inhibitory effects of Slug on ADM, ERK1/2 phosphorylation, proliferation and fibrosis. Overall, these results increase our understanding of the role of Slug in ADM, an early event that can eventually lead to pancreatic cancer development.

Cancer cells can invade in three-dimensional collagen as single cells or as a cohesive group of cells that require coordination of cell-cell junctions and the actin cytoskeleton. To examine the role of G alpha(13), a G(12) family heterotrimeric G protein, in regulating cellular invasion in three-dimensional collagen, we established a novel method to track cell invasion by membrane type 1 matrix metalloproteinase-expressing cancer cells. We show that knockdown of G alpha(13) decreased membrane type 1 matrix metalloproteinase-driven proteolytic invasion in three-dimensional collagen and enhanced E-cadherin-mediated cell-cell adhesion. E-cadherin knockdown reversed G alpha(13) siRNA-induced cell-cell adhesion but failed to reverse the effect of G alpha(13) siRNA on proteolytic invasion. Instead, concurrent knockdown of E-cadherin and G alpha(13) led to an increased number of single cells rather than groups of cells. Significantly, knockdown of discoidin domain receptor 1 (DDR1), a collagen-binding protein that also co-localizes to cell-cell junctions, reversed the effects of G alpha(13) knockdown on cell-cell adhesion and proteolytic invasion in three-dimensional collagen. Knockdown of the polarity protein Par3, which can function downstream of DDR1, also reversed the effects of G alpha(13) knockdown on cell-cell adhesion and proteolytic invasion in three-dimensional collagen. Overall, we show that G alpha(13) and DDR1-Par3 differentially regulate cell-cell junctions and the actin cytoskeleton to mediate invasion in three-dimensional collagen.

The fibrotic reaction, which can account for over 70%-80% of the tumor mass, is a characteristic feature of human pancreatic ductal adenocarcinoma (PDAC) tumors. It is associated with activation and proliferation of pancreatic stellate cells (PSCs), which are key regulators of collagen I production and fibrosis in vivo. In this report, we show that members of the bromodomain and extraterminal (BET) family of proteins are expressed in primary PSCs isolated from human PDAC tumors, with BRD4 positively regulating, and BRD2 and BRD3 negatively regulating, collagen I expression in primary cancer-associated PSCs. We show that the inhibitory effect of pan-BET inhibitors on collagen I expression in primary cancer-associated PSCs is through blocking of BRD4 function. Importantly, we show that FOSL1 is repressed by BRD4 in primary cancer-associated PSCs and negatively regulates collagen I expression. While BET inhibitors do not affect viability or induce PSC apoptosis or senescence, BET inhibitors induce primary cancer-associated PSCs to become quiescent. Finally, we show that BET inhibitors attenuate stellate cell activation, fibrosis, and collagen I production in the EL-KrasG12D transgenic mouse model of pancreatic tumorigenesis. Our results demonstrate that BET inhibitors regulate fibrosis by modulating the activation and function of cancer-associated PSCs.

Abstract Human pancreatic ductal adenocarcinoma (PDAC) tumors are associated with dysregulation of mRNA translation. In this report, it is demonstrated that PDAC cells grown in collagen exhibit increased activation of the MAPK-interacting protein kinases (MNK) that mediate eIF4E phosphorylation. Pharmacologic and genetic targeting of MNKs reverse epithelial–mesenchymal transition (EMT), decrease cell migration, and reduce protein expression of the EMT-regulator ZEB1 without affecting ZEB1 mRNA levels. Paradoxically, targeting eIF4E, the best-characterized effector of MNKs, increases ZEB1 mRNA expression through repression of ZEB1-targeting miRNAs, miR-200c and miR-141. In contrast, targeting the MNK effector hnRNPA1, which can function as a translational repressor, increases ZEB1 protein without increasing ZEB1 mRNA levels. Importantly, treatment with MNK inhibitors blocks growth of chemoresistant PDAC cells in collagen and decreases the number of aldehyde dehydrogenase activity–positive (Aldefluor+) cells. Significantly, MNK inhibitors increase E-cadherin mRNA levels and decrease vimentin mRNA levels in human PDAC organoids without affecting ZEB1 mRNA levels. Importantly, MNK inhibitors also decrease growth of human PDAC organoids. Implications: These results demonstrate differential regulation of ZEB1 and EMT by MNKs and eIF4E, and identify MNKs as potential targets in pancreatic cancer. Mol Cancer Res; 14(2); 216–27. ©2015 AACR.

JQ1 and I-BET151 are selective inhibitors of BET bromodomain proteins that have efficacy against a number of different cancers. Since the effectiveness of targeted therapies is often limited by development of resistance, we examined whether it was possible for cancer cells to develop resistance to the BET inhibitor JQ1. Here we show that pancreatic cancer cells developing resistance to JQ1 demonstrate cross-resistance to I-BET151 and insensitivity to BRD4 downregulation. The resistant cells maintain expression of c-MYC, increase expression of JQ1-target genes FOSL1 and HMGA2, and demonstrate evidence of epithelial-mesenchymal transition (EMT). However, reverting EMT fails to sensitize the resistant cells to JQ1 treatment. Importantly, the JQ1-resistant cells remain dependent on c-MYC that now becomes co-regulated by high levels of GLI2. Furthermore, downregulating GLI2 re-sensitizes the resistant cells to JQ1. Overall, these results identify a mechanism by which cancer cells develop resistance to BET inhibitors.