Entinostat Treatment Research Articles

Entinostat treatment causes hypophosphatemia and hypocalcemia by increasing Fgf23 in mice

Entinostat, a class I HDACs-selective inhibitor, is currently in clinical trials for treating cancers. In some of the trials, Entinostat treatment frequently causes hypophosphatemia and/or hypocalcemia. Moreover, the effect of Entinostat treatment on bone remains incompletely understood. In this study, we found that Entinostat treatment mildly increased the trabecular but not cortical bone volume, without compromising the bone strength, the numbers of Runx2-positive cells and TRAP-positive cells, and the serum levels of P1NP and TRAP-5b. Entinostat treatment significantly reduced the level of Runx2 mRNA but not Runx2 protein, and as a trend attenuated Ctsk expression. Furthermore, Entinostat treatment did not enhance MC3T3-E1 cell proliferation in vitro. These findings suggest that Entinostat increases trabecular bone volume not by regulating osteoblastogenesis or osteoclastogenesis, but possibly by attenuating the resorption capacity. Unexpectedly, Entinostat treatment increased the expression of Fgf23, whose protein is a hormone that regulates the serum level of phosphate (Pi). Meanwhile, Entinostat treatment increased the serum level of the active form (intact) Fgf23 and reduced that of Pi and calcium (Ca) as well. This study raised a concern about the anabolic effects of Entinostat in bone, and demonstrated that Entinostat treatment causes hypophosphatemia and hypocalcemia by upregulating Fgf23 mRNA and increasing intact Fgf23 protein in serum.

Combining ERAP1 silencing and entinostat therapy to overcome resistance to cancer immunotherapy in neuroblastoma

BackgroundCheckpoint immunotherapy unleashes tumor control by T cells, but it is undermined in non-immunogenic tumors, e.g. with low MHC class I expression and low neoantigen burden, such as neuroblastoma (NB). Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an enzyme that trims peptides before loading on MHC class I molecules. Inhibition of ERAP1 results in the generation of new antigens able of inducing potent anti-tumor immune responses. Here, we identify a novel non-toxic combinatorial strategy based on genetic inhibition of ERAP1 and administration of the HDAC inhibitor (HDACi) entinostat that increase the immunogenicity of NB, making it responsive to PD-1 therapy.MethodsCRISPR/Cas9-mediated gene editing was used to knockout (KO) the ERAP1 gene in 9464D NB cells derived from spontaneous tumors of TH-MYCN transgenic mice. The expression of MHC class I and PD-L1 was evaluated by flow cytometry (FC). The immunopeptidome of these cells was studied by mass spectrometry. Cocultures of splenocytes derived from 9464D bearing mice and tumor cells allowed the assessment of the effect of ERAP1 inhibition on the secretion of inflammatory cytokines and activation and migration of immune cells towards ERAP1 KO cells by FC. Tumor cell killing was evaluated by Caspase 3/7 assay and flow cytometry analysis. The effect of ERAP1 inhibition on the immune content of tumors was analyzed by FC, immunohistochemistry and multiple immunofluorescence.ResultsWe found that inhibition of ERAP1 makes 9464D cells more susceptible to immune cell-mediated killing by increasing both the recall and activation of CD4+ and CD8+ T cells and NK cells. Treatment with entinostat induces the expression of MHC class I and PD-L1 molecules in 9464D both in vitro and in vivo. This results in pronounced changes in the immunopeptidome induced by ERAP1 inhibition, but also restrains the growth of ERAP1 KO tumors in vivo by remodelling the tumor-infiltrating T-cell compartment. Interestingly, the absence of ERAP1 in combination with entinostat and PD-1 blockade overcomes resistance to PD-1 immunotherapy and increases host survival.ConclusionsThese findings demonstrate that ERAP1 inhibition combined with HDACi entinostat treatment and PD-1 blockade remodels the immune landscape of a non-immunogenic tumor such as NB, making it responsive to checkpoint immunotherapy.

Transcriptional repression by HDAC3 mediates T cell exclusion from Kras mutant lung tumors

Histone Deacetylase 3 (HDAC3) function in vivo is nuanced and directed in a tissue-specific fashion. The importance of HDAC3 in Kras mutant lung tumors has recently been identified, but HDAC3 function in this context remains to be fully elucidated. Here, we identified HDAC3 as a lung tumor cell-intrinsic transcriptional regulator of the tumor immune microenvironment. In Kras mutant lung cancer cells, we found that HDAC3 is a direct transcriptional repressor of a cassette of secreted chemokines, including Cxcl10. Genetic and pharmacological inhibition of HDAC3 robustly up-regulated this gene set in human and mouse Kras, LKB1 (KL) and Kras, p53 (KP) mutant lung cancer cells through an NF-κB/p65-dependent mechanism. Using genetically engineered mouse models, we found that HDAC3 inactivation in vivo induced expression of this gene set selectively in lung tumors and resulted in enhanced T cell recruitment at least in part via Cxcl10. Furthermore, we found that inhibition of HDAC3 in the presence of Kras pathway inhibitors dissociated Cxcl10 expression from that of immunosuppressive chemokines and that combination treatment of entinostat with trametinib enhanced T cell recruitment into lung tumors in vivo. Finally, we showed that T cells contribute to in vivo tumor growth control in the presence of entinostat and trametinib combination treatment. Together, our findings reveal that HDAC3 is a druggable endogenous repressor of T cell recruitment into Kras mutant lung tumors.

Abstract CT016: Immunomodulation of the tumor microenvironment of pancreatic ductal adenocarcinoma with histone deacetylase inhibition: Results of a phase 2 clinical trial of entinostat in combination with nivolumab

Abstract Background The tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDA) is characterized by a paucity of cytotoxic tumor-infiltrating lymphocytes, an abundance of immune-suppressive cell populations, and a general resistance to immune checkpoint inhibitor (ICI) therapy. In preclinical models of PDA, the HDAC inhibitor entinostat modulated the transcriptional programming of myeloid cells, reducing their capacity for immunosuppression and sensitizing tumors to ICI therapy. Methods We conducted a single-center, open-label, Simon two-stage, phase II study of entinostat in combination with the PD1 inhibitor nivolumab in patients with advanced PDA. Patients received oral entinostat 5 mg once a week. After a 14-day lead-in with entinostat monotherapy, patients concurrently receive entinostat 5 mg orally once a week plus nivolumab 240 mg intravenously every 2 weeks. After 4 months, therapy was continued with entinostat 5 mg weekly plus nivolumab at a dose of 480 mg fixed dose every 4 weeks until the time of progression or unacceptable toxicities. The primary endpoint was the objective response rate by Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1. Peripheral immune profiles at baseline and on treatment were assessed by high-dimensional mass cytometry by time of flight (CyTOF) and by Luminex of chemokines in the plasma, and changes in the TME were performed on paired baseline and on treatment biopsies by multiplexed immunohistochemistry (mIHC), image cytometry-based quantification, and bulk RNA-seq analysis. Results From November 2017 to November 2020, 27 evaluable patients were enrolled. Three patients had a partial response (PR) by RECIST v1.1 criteria (objective response rate (ORR)) of 11%, 95% CI, 0.024-0.292), with a median duration of response of 10.2 months. Grade ≥3 treatment-related adverse events (TRAEs) were observed in 19 (63%) patients. The most common grade ≥3 TRAEs were decreased lymphocyte count, anemia hypoalbuminemia, and hyponatremia. Dendritic cell (DC) activation, maturation, migration, antigen processing, and presentation were increased in the periphery after entinostat treatment, consistent with HDAC inhibitor mediated myeloid reprogramming. Gene expression analysis of paired baseline and on treatment tumors demonstrated an enrichment in inflammatory response signaling pathways with combination treatment. Conclusions Entinostat and nivolumab demonstrated durable radiological responses in a subset of patients with PDA. Paired tissue and peripheral analysis showed immunomodulation of myeloid cell populations, consistent with the preclinical hypothesis supporting the trial. This study creates a roadmap for this strategy with future combinatorial therapeutic approaches to enhance the clinical benefit in PDA patients further. Citation Format: Marina Baretti, Ludmila Danilova, Jennifer N. Durham, Courtney B. Betts, Leslie Cope, Dimitrios N. Sidiropoulos, Joseph A. Tandurella, Soren Charmsaz, Nicole Gross, Alexei Hernandez, Won J. HO, Chris Thoburn, Rosalind Walker, James Leatherman Leatherman, Sarah Mitchell, Brian Christmas, Daria A. Gaykalova, Srinivasan Yegnasubramanian, Elana J. Fertig, Lisa M. Coussens, Mark Yarchoan, Elizabeth Jaffee, Nilofer S. Azad. Immunomodulation of the tumor microenvironment of pancreatic ductal adenocarcinoma with histone deacetylase inhibition: Results of a phase 2 clinical trial of entinostat in combination with nivolumab [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT016.

Abstract 6522: Epigenetic modulation decreases myeloid suppression to improve response to immune checkpoint inhibition in breast cancer

Abstract Immune checkpoint inhibitors (ICIs) promote a durable anti-tumor immune response. Unfortunately, many patients with breast cancer are thought to be intrinsically resistant. One potential mechanism of resistance is a myeloid suppressed tumor microenvironment (TME). Targeting myeloid suppression is under investigation as a therapeutic strategy to sensitize tumors to ICI. In our trial, NCI-9844, we demonstrated that the combination of the epigenetic modulator, entinostat with ICIs—nivolumab (anti-PD-1) + ipilimumab (anti-CTLA-4), leads to a 25% objective response rate in patients with advanced breast cancer. Work in our preclinical models showed entinostat decreases suppressive function by myeloid derived suppressor cells (MDSCs). We hypothesized that entinostat decreases intra-tumoral MDSC suppression via the STAT3/AP-1 axis and drives cellular shifts within the TME to improve response to ICI. Here, we examined expression of upstream, downstream, and interacting factors within the STAT3 pathway in MDSCs treated with entinostat. Macro-dissected lung metastases from entinostat treated NeuN mice revealed differential gene expression of AP-1 subunits JunB and FOSL1 in MDSCs identified by single cell RNA sequencing (scRNAseq). Western blot of isolated intratumoral MDSCs from lung metastases revealed decreased STAT3 phosphorylation upon entinostat treatment. In an entinostat treated MDSC-like cell line, J774M, JunB phosphorylation and FOSL1 were both decreased. scRNAseq also revealed decreased gene expression of STAT3 upstream receptors IL4RA and IFNGR1 and increased expression of STAT3 negative regulator SOCS3. Chromatin immunoprecipitation sequencing is planned to further narrow the molecular mechanism of action. Cell-cell communication analysis of scRNAseq data was performed to evaluate the contribution of entinostat treated macrophages, dendritic cells (DCs), and natural killer (NK) cells on MDSC function. We observed increased frequency of DC populations (classic DC2s and Ccr7 DCs). Following combined treatment with entinostat + ICIs, we also found increased DC to T cell signaling strength for receptor-ligand pairs involved in T cell activation, including Tnfsf9__Tnfrsf9, Cd70_Cd27, H2-dmb2_Cd4, and Cd80_Cd28. Analysis of macrophage-T cell interactions revealed a synergistic decrease in signaling associated with immunosuppression after combined treatment, such as Cd80_Ctla4, Tnf_Tnfrsf1b, and Entpd1_Adora2a. Suppressive function of treated sub-populations of macrophages is planned to determine functional effect of findings. Finally, we are using imaging mass cytometry and bulk RNA sequencing to evaluate proposed mechanisms in patient specimens (NCI-9844). The goal of this work is to identify the molecular and cellular mechanisms driving myeloid suppression of the TME thereby identifying potential therapeutic targets. Citation Format: Aaron G. Baugh, Edgar Gonzalez, Jesse Kreger, Yingtong Liu, Batul Al-Zubeidy, Ludmila Danilova, Sarah M. Shin, Valerie H. Narumi, Sofi Castanon, Julie Jang, Elana J. Fertig, Ashley Cimino-Mathews, Elizabeth M. Jaffee, Vered Stearns, Roisin M. Connolly, Won Jin Ho, Adam MacLean, Evanthia T. Roussos Torres. Epigenetic modulation decreases myeloid suppression to improve response to immune checkpoint inhibition in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6522.

Class I HDAC inhibition reduces DNA damage repair capacity of MYC-amplified medulloblastoma cells

PurposeMYC-driven Group 3 medulloblastoma (MB) (subtype II) is a highly aggressive childhood brain tumor. Sensitivity of MYC-driven MB to class I histone deacetylase inhibitors (HDACi) has been previously demonstrated in vitro and in vivo. In this study we characterize the transcriptional effects of class I HDACi in MYC-driven MB and explore beneficial drug combinations.MethodsMYC-amplified Group 3 MB cells (HD-MB03) were treated with class I HDACi entinostat. Changes in the gene expression profile were quantified on a microarray. Bioinformatic assessment led to the identification of pathways affected by entinostat treatment. Five drugs interfering with these pathways (olaparib, idasanutlin, ribociclib, selinexor, vinblastine) were tested for synergy with entinostat in WST-8 metabolic activity assays in a 5 × 5 combination matrix design. Synergy was validated in cell count and flow cytometry experiments. The effect of entinostat and olaparib on DNA damage was evaluated by γH2A.X quantification in immunoblotting, fluorescence microscopy and flow cytometry.ResultsEntinostat treatment changed the expression of genes involved in 22 pathways, including downregulation of DNA damage response. The PARP1 inhibitors olaparib and pamiparib showed synergy with entinostat selectively in MYC-amplified MB cells, leading to increased cell death, decreased viability and increased formation of double strand breaks, as well as increased sensitivity to additional induction of DNA damage by doxorubicin. Non-MYC-amplified MB cells and normal human fibroblasts were not susceptible to this triple treatment.ConclusionOur study identifies the combination of entinostat with olaparib as a new potential therapeutic approach for MYC-driven Group 3 MB.

Abstract 5167: Entinostat's modulation of myeloid derived suppressor cells through the STAT3-NFκB-AP-1 axis decreases suppressive signaling

Abstract Metastatic breast cancer remains one of the leading causes of global cancer incidence in women, despite the benefit of immune checkpoint inhibitors (ICIs) in managing various cancers and improving patient quality of life. Metastatic breast cancer is characterized by extensive infiltration of the tumor microenvironment (TME) with immunosuppressive cells, such as myeloid derived suppressor cells (MDSCs), that inhibit anti-tumoral immune cells and prevent effective activation of the adaptive immune system by ICIs. Previously, our group has shown in the breast TME that epigenetic reprogramming of MDSCs by entinostat, a histone deacetylase inhibitor, decreases MDSC immunosuppressive function and enhances response to ICIs, in part mediated by altered signaling within the Signal transducer and activator of transcription 3 (STAT3) and Nuclear factor kappa B (NFκB) axis. Next, we sought to examine the effects of entinostat on MDSC reprogramming in a distant metastatic TME. Using the syngeneic NT2.5LM NeuN mouse model of metastatic breast cancer, we established spontaneous lung metastases and treated with either vehicle or entinostat (5 mg/kg by oral gavage, 5x/week) for 3 weeks. Single cell RNA sequencing (scRNAseq) of macro-dissected lung metastases revealed a large MDSC population, and unsupervised pathways analysis of the MDSC cluster showed differential regulation of the IL6-JAK-STAT3 and TNFα-signaling-via-NFκB pathways upon entinostat treatment. In line with reports of crosstalk among STAT3, NFκB, and AP-1 pathways regulating inflammation in breast cancer, we also found through scRNAseq differential expression of AP-1 subunits JunB and FOSL1 upon entinostat treatment. At the protein level, western blot analysis of isolated intratumoral MDSCs from lung metastases revealed decreased STAT3 phosphorylation upon entinostat treatment. Using J774M cells, an MDSC-like cell line, we found decreased JunB phosphorylation and decreased FOSL1 protein upon entinostat treatment. Furthermore, preliminary evaluation of imaging mass cytometry (IMC) from tumor biopsies in selected patients with metastatic breast cancer treated with entinostat during the clinical trial NCI-9844 confirmed decreased STAT3 phosphorylation in MDSCs. Taken together, we provide new evidence in the metastatic lung TME that implicates a STAT3-NFκB-AP-1 mediated mechanism leading to decreased MDSC suppression. Evaluating this mechanism in MDSCs taken directly from treated lung metastases represents the most biologically relevant mechanistic study to date, and preliminary translation of findings in patients suggests that planned studies will lead to identification of the mechanism driving response. Citation Format: Aaron G. Baugh, Edgar Gonzalez, Valerie H. Narumi, Sofi Castanon, Jesse Kreger, James Leatherman, Won Jin Ho, Ashley Cimino-Mathews, Vered Stearns, Roisin M. Connolly, Elizabeth M. Jaffee, Adam L. MacLean, Evanthia T. Roussos Torres. Entinostat's modulation of myeloid derived suppressor cells through the STAT3-NFκB-AP-1 axis decreases suppressive signaling. [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 5167.

Abstract 3256: Entinostat enhances the efficacy of checkpoint inhibition in breast-to-lung metastases and is associated with alterations in the phenotype and function of myeloid cell populations

Abstract Single agent immune checkpoint inhibitors (ICIs) are ineffective against metastatic breast cancer. One mechanism of intrinsic resistance is the presence of immunosuppressive myeloid cells and dysfunctional dendritic cells in the metastatic tumor microenvironment (TME) that impede the activation of anti-tumor T cells. A comparison of single-cell RNA sequencing analyses between breast-to-lung metastases and published data from breast tumors in the syngeneic NeuN mouse model of HER2+ breast cancer revealed that despite the presence of additional immune cell populations in the lungs, myeloid cells represented the predominant immune cell population in both TMEs and demonstrated similar changes in frequency and gene expression following treatment with the histone deacetylase inhibitor, entinostat. Our work highlights for the first time an increase in the frequency of conventional dendritic cells (cDC) with entinostat treatment in breast-to-lung metastases. Gene expression analyses of breast-to-lung metastases showed that entinostat-treated myeloid derived suppressor cells (MDSCs) and tumor associated macrophages (TAMs) downregulated genes associated with immunosuppression such as S100a8, Cd84, Trem2, and Mmp9. In addition, TAMs and cDCs upregulated the expression of genes associated with antigen presentation such as H2-K1, H2-Ab1, B2m, and Cd74 and pro-inflammatory markers such as Ccl3. NeuN mice were treated with the combination of entinostat and the immune checkpoint inhibitors, anti-PD-1 and anti-CTLA-4, and breast-to-lung metastases were analyzed via flow cytometry, demonstrating an increase in the frequency of cDC1s and CD8+ T cells expressing granzyme B. Furthermore, the treatment combination of entinostat + anti-PD-1 + anti-CTLA-4 significantly increased survival in an experimental model of lung metastasis using a newly characterized model derived from the original NT2.5 HER2+ cell line, NT2.5LM. These results confirm those of our breast expansion cohort from the phase I clinical trial NCI-9844 that demonstrate a 30% overall response rate in 20 heavily pretreated patients with metastatic disease treated with entinostat + Nivolumab (anti-PD-1) + Ipilimumab (anti-CTLA-4). We highlight for the first time significant alterations within multiple myeloid derived cell types, cDCs, TAMs and MDSCs, from within a native metastatic niche, that are likely driving an entinostat mediated improved response to ICI treatment. Citation Format: Edgar Gonzalez, Adam L. MacLean, Evanthia T. Roussos Torres, Aaron Baugh, Jesse Kreger, Sofi Castanon, Valerie Narumi, Elizabeth M. Jaffee. Entinostat enhances the efficacy of checkpoint inhibition in breast-to-lung metastases and is associated with alterations in the phenotype and function of myeloid cell populations [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 3256.

HDAC3 is critical in tumor development and therapeutic resistance in Kras-mutant non-small cell lung cancer.

HDAC3 is one of the main targets of histone deacetylase (HDAC) inhibitors in clinical development as cancer therapies, yet the in vivo role of HDAC3 in solid tumors is unknown. We identified a critical role for HDAC3 in Kras-mutant lung cancer. Using genetically engineered mouse models (GEMMs), we found that HDAC3 is required for lung tumor growth in vivo. HDAC3 was found to direct and enhance the transcription effects of the lung cancer lineage transcription factor NKX2-1 to mediate expression of a common set of target genes. We identified FGFR1 as a critical previously unidentified target of HDAC3. Leveraging this, we identified that an HDAC3-dependent transcriptional cassette becomes hyperactivated as Kras/LKB1-mutant cells develop resistance to the MEK inhibitor trametinib, and this can be reversed by treatment with the HDAC1/HDAC3 inhibitor entinostat. We found that the combination of entinostat plus trametinib treatment elicits therapeutic benefit in the Kras/LKB1 GEMM.

Abstract 239: Assessment of immunotherapeutic efficacy of entinostat by using the 3d-explore ex vivo platform utilizing tumoroids of fresh patient tumor samples with intact tumor microenvironment

Abstract Background: Entinostat, a selective histone deacetylase 1/3 inhibitor has been shown to promote a robust anti-tumor response and increased neoantigen expression and antigen-specific T cell activation in preclinical tumor models. Entinostat plays a role in neutralizing myeloid derived suppressor cells (MDSC) to improve anti-tumor immune response. Entinostat is currently being tested in later-stage clinical trials in various types of cancer. Using a novel 3D ex-vivo platform with fresh patient tumor samples we assessed the therapeutic efficacy of Entinostat with intact stromal components and tumor immune microenvironment. Methods: All tumor samples were obtained with patient consent and relevant IRB approval. Unpropagated 3D tumoroids with intact TME measuring 150 µm in size were prepared from fresh tumor samples from renal cell carcinoma (RCC) patients using a proprietary technology developed at Nilogen Oncosystems. Tumoroids prepared from each patient’s tumor sample were pooled to represent the tumor heterogeneity and treated ex vivo with Entinostat for 48h to detect treatment-mediated changes in tumor immune cell composition including lymphoid and myeloid markers and their activation status. Results: Tumoroids treated with Entinostat increased NK, NKT, CD4 and CD8+T cells compared to untreated control. Ex vivo treatment with Entinostat led to an increase in CD69 and Granzyme B expression in tumor resident CD4+ T cells. Immune checkpoint receptors, 41BB and PD-1 expression was increased in CD8+T cells followed by Entinostat treatment. Decreased monocytic MDSC was seen in Entinostat treated tumoroids compared to untreated control and this was associated with decreased GM-CSF, IL-4, IL-6 cytokine levels and increased IFN-γ and IL-2, quantified by multiplex cytokine assay. Interestingly, the tumor cell killing study revealed a higher percentage of death in early stage MDSC (eMDSC) indicating a direct effect of Entinostat on MDSC survival. Conclusions: These results demonstrate that Entinostat treatment leads to a broad range of immune cell activation and MDSC inhibition in RCC. These data provide a mechanistic rationale utilizing our 3D tumoroid platform for discovery of potential biomarkers of drug sensitivity and to identify novel immunotherapeutic approaches. Clinical applications of 3D-EXplore may help to identify RCC patients who may likely benefit from Entinostat treatment. Citation Format: Krithika Nandakumar Kodumudi, Brittany Bunch, Jared Ehrhart, Matt Weitzman, Olivia MacIntosh, Kelly Sussman, Soner Altiok. Assessment of immunotherapeutic efficacy of entinostat by using the 3d-explore ex vivo platform utilizing tumoroids of fresh patient tumor samples with intact tumor microenvironment [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 239.

Abstract LB566: Class 1 HDAC inhibition induces antitumor immunity by NF-kB-mediated enhanced metabolic fitness and generation of unique effector function enriched memory CD8 T cell subtype

Abstract Histone/protein deacetylases (HDACs) are a class of enzymes that regulate gene expression and are involved in regulating the transcription process as well as regulating fundamental cellular processes such as proliferation, differentiation and development. Class I HDACs (which includes HDAC1, 2, 3, and 8) contribute in epigenetic regulations of T cell tolerance. Under anergic T cell condition, HDAC1 and HDAC2 are involved in the histone deacetylation. However, the role of HDACs in CD8 T cell function and differentiation is not well understood. Therefore, we aimed to understand the effect of HDAC inhibition (HDACi) on CD8 T cells phenotype and functionality by using Entinostat (ENT), a class I HDAC (HDAC1 and 3) inhibitor. We found that ENT induces strong immune-mediated anti-tumor effects in TC-1 and B16 tumor-bearing mice. Mechanistically, ENT modulated the tumor microenvironment through an increased infiltration of CD8 T cells, enhanced CD8 T cell antigen-specificity and CD8 T cell functionality represented by interferon gamma (IFN-γ) and granzyme B (GrB) secretion. Our in vitro and in vivo data also indicate that ENT enhances central memory phenotype (CD62L+, CD44+) of CD8 T cells. We also found that ENT-treated CD8 T cells have distinct metabolic phenotype compared to activated CD8 T cells. Specifically, these cells relied more on amino acid metabolism while, unexpectedly, they had lower fatty acid uptake with enhanced mitochondrial potential (TMRM). Interestingly, ENT-induced central memory CD8 T cells also showed increased mitochondrial potential as well as reliance on amino acid metabolism. Therefore, ENT treatment induced memory cells with a unique phenotype different from the classical memory CD8 T cells with enhanced effector functions and reliance on distinct metabolic pathways. Furthermore, ENT-treated CD8 T cells have higher peaks at H3K27Ac site compared to the control. Since these peaks are mostly associated with genes such as IFN-γ, GrB, Pim1, EOMES, and IL-2, the known canonical target genes of NF-κB in CD8 T cells, we further dissected the role of NF-κB in these ENT-mediated effects. First, motif analysis showed that NF-κB binding motif is enriched in differential H3K27Ac sites associated with HDACi. Next, flow cytometry and immunofluorescence analysis showed that although ENT does not increase total NF-κB levels in CD8 T cells, it enhances its binding to the chromatin due to enhanced gene accessibility. This research highlights the significance of epigenetic modulation in enhancing the immune-mediated anti-tumor effects and provide fundamental understanding of the mechanism of action of HDAC inhibition in CD8 T cells. Citation Format: Nour Shobaki, Pankaj Gaur, Rahul Nadre, Vivek Verma, Peter Ordentlich, Lei Wang, Nazli Jafarzadeh, Wael Traboulsi, Mikayel Mkrtichyan, Seema Gupta, Samir N. Khleif. Class 1 HDAC inhibition induces antitumor immunity by NF-kB-mediated enhanced metabolic fitness and generation of unique effector function enriched memory CD8 T cell subtype [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 LB566.

Abstract GS1-06: A randomized control phase III trial of entinostat, a once weekly, class I selective histone deacetylase inhibitor, in combination with exemestane in patients with hormone receptor positive advanced breast cancer

Abstract Background Entinostat is a novel, potent, once weekly, orally bioavailable, class I selective histone deacetylase (HDAC) inhibitor. In a previous Phase II study, the combination of entinostat with exemestane showed significant improvement of overall survival in patients with advanced hormone receptor (HR) positive breast cancer. To verify and further confirm the benefit of HDAC inhibitor in combination with exemestane we designed a randomized, controlled trial to assess the efficacy and safety in a larger population of Chinese patients with advanced, HR positive breast cancer. Methods We carried out the randomized, double-blind, placebo-controlled, Phase III trial at 35 sites in China. Eligible patients were women (aged ≥18 years) with HR positive, human epidermal growth factor receptor-2 (HER2) negative breast cancer, whose disease had relapsed or progressed after at least one endocrine therapy (either in advanced or metastatic or adjuvant setting), and who had at least one measurable lesion, adequate organ function, ECOG performance status of 0-1, and adequate haematological and biochemical parameters. Patients were randomly assigned (2:1) via an interactive web-response system to orally take 5 mg entinostat or placebo. Both groups received oral administration of 25 mg exemestane daily. Randomization was stratified according to previous usage of CDK4/6 (yes vs no), fulvestrant (yes vs no), chemotherapy (yes vs no), and the presence of visceral metastases (yes vs no). Patients, investigators, study site staff, and the sponsor were masked to treatment assignment. The primary endpoint was Independent Radiographic Committee (IRC)-assessed progression free survival (PFS). Efficacy and safety analyses were done in all patients who received at least one dose of any study treatment. The study has reached the required number of events for final analysis of the primary endpoint. The trial is no longer enrolling patients, but follow-up for investigation of overall survival is ongoing. This study was registered with ClinicalTrials.gov with the number of NCT03538171. Results From April 16th, 2019 to May 13th, 2020, 354 patients were enrolled and randomly assigned as 235 to the entinostat group and 119 to the placebo group. IRC-assessed median PFS was 6.32 months (95% CI 5.30-9.11) in the entinostat group and 3.72 months (95% CI 1.91-5.49) in the placebo group (HR 0.74 [95% CI 0.57-0.96]; p<0.001). The most common Grade 3 or 4 adverse events in the entinostat group vs placebo group were neutropenia (103 [43.8%] vs 119 [0.8%] ), thrombocytopenia (20 [8.5%] vs 1 [0.8%]), and leucopenia (15 [6.4%] vs 0). Serious adverse events occurred in 28 out of 235 patients (11.9%) in the entinostat group and 11 out of 119 patients (9.2%) in the placebo group. Conclusions Entinostat and exemestane combination treatment significantly improved PFS compared with exemestane alone in patients with advanced, HR positive, HER2 negative breast cancer that progressed after previous endocrine therapy. Entinostat and exemestane combination was generally tolerated and can offer meaningful clinical benefit in these patients with unmet medical need. This phase III trial was sponsored by Taizhou EOC Pharma Co., Ltd. Citation Format: Binghe Xu, Qingyuan Zhang, Xichun Hu, Qing Li, Tao Sun, Wei Li, Quchang Ouyang, Jingfen Wang, Zhongsheng Tong, Min Yan, Huiping Li, Xiaohua Zeng, Changping Shan, Xian Wang, Xi Yan, Jian Zhang, Yue Zhang, Jiani Wang, Liang Zhang, Ying Lin, Jifeng Feng, Qianjun Chen, Jian Huang, Yongkui Lu, Hongsheng Li, Jinsheng Wu, Jing Cheng, Yanrong Hao, Cuizhi Geng, Min Lu, Yanping Li, Xi Chen, Lihua Song, Xueying Wu, Changlu Hu, Xinhong Wu, Xiaojia Wang, Yueyin Pan, Yuehong Cui, Guohua Yu, Sanyuan Sun. A randomized control phase III trial of entinostat, a once weekly, class I selective histone deacetylase inhibitor, in combination with exemestane in patients with hormone receptor positive advanced breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr GS1-06.

Entinostat Improves Motor Function and Neuronal Damage Via Downregulating NLRP3 Inflammasome Activation After Spinal Cord Injury.

Background: Spinal cord injury (SCI), a major public health problem, has no effective treatment. A large number of studies have confirmed that histone deacetylases (HDACs) are involved in the physiologic processes that occur following SCI. We tried to uncover the potential neuroprotective role of entinostat (a class I HDAC inhibitor) in SCI. Methods: We conducted a study on a preclinical mouse model of SCI and OGD-induced neuronal damage to present the role of entinostat by the analysis of motor function, histopathologic damage, local NLRP3 inflammasome activation, and neuronal damage. Results: The results showed that entinostat suppressed HDAC activation (including HDAC1 and HDAC3 expression), improved the grip strength and BMS score, spinal edema, cell death, and local NLRP3 inflammasome activation in the spinal cord following SCI. Furthermore, entinostat significantly increased OGD-inhibited neuronal activity and decreased PI-positive cells, HDAC activation, caspase-1 activation, IL-1β and IL-18 levels, and NLRP3 expression. Conclusion: In summary, we first documented that entinostat improved the motor function, histopathologic damage, and local inflammatory response and NLRP3 inflammasome activation in the spinal cord following SCI and also presented the neuroprotective role of OGD-induced neuronal damage via the NLRP3 inflammasome. Thus, our study has the potential to reveal the interaction between the HDAC and NLRP3 inflammasome in the pathologic process as well as SCI and further promote the clinical indications of HDACi entinostat and clinical treatment for the inflammatory response after SCI.

Effect of Ketone Body β-Hydroxybutyrate to Attenuate Inflammation-Induced Mitochondrial Oxidative Stress in Vascular Endothelial Cells

To investigate the regulatory function and mechanism of β-hydroxybutyrate (β-OHB), a ketone body, on the mitochondrial oxidative stress of inflammatory human umbilical vein endothelial cells (HUVECs). Lipopolysaccharide (LPS) and adenosine triphosphate (ATP) were used to induce macrophages to release proinflammatory factors, and the culture supernatant was collected as a macrophage-conditioned medium (MCM) to culture HUVECs. A total of 7 groups of cells were used in the study: ①control group, or normal cultured HUVECs; ②MCM group, or the MCM-cultured HUVECs; groups ③ to ⑦ were all HUVECs co-cultured with different reagents, including ③MCM+β-OHB group, ④MCM+N-acetylcysteine (NAC) group, ⑤MCM+β-OHB+NAC group, ⑥MCM+β-OHB+histone deacetylase agonist ITSA1 group, and ⑦MCM+β-OHB+histone deacetylase inhibitor Entinostat group. MitoSOX immunofluorescence staining was conducted to analyzes the mitochondrial superoxide levels, real-time fluorescent quantitative polymerase chain reaction (RT-qPCR) was performed to examine the mRNA expression of antioxidant genes, and Seahorse mitochondrial energy analyzer was used to measure mitochondrial aerobic respiration capacity. Compared with the control group, mitochondrial superoxide production was significantly increased in the MCM cultured HUVECs cells, while β-OHB treatment significantly inhibited mitochondrial superoxide production, which was accompanied by an increase in the mRNA expression of antioxidant genes, and significant increase in the basal mitochondrial oxygen consumption rate and respiratory reserve capacity. NAC treatment did not further enhance the protective effect of β-OHB on mitochondrial functions. In addition, ITSA1 treatment could completely offset the antioxidant and mitochondrial protective effects of β-OHB, and these stated effects were still maintained after Entinostat treatment. The ketone body β-OHB attenuates the mitochondrial oxidative stress of vascular endothelial cells through activating the antioxidant pathway and inhibiting histone deacetylase activity.

EMBR-11. SYNERGISTIC DRUG COMBINATIONS FOR THE TREATMENT OF MYC AMPLIFIED GROUP 3 MEDULLOBLASTOMA

Abstract Background Medulloblastoma (MB) is a highly aggressive brain tumour in children. Patients with Group 3 MB harbouring a MYC-amplification (subtype II) show a particularly poor outcome despite high-intensity multimodal therapy. We and others have previously shown that MYC amplified Group 3 MB cells are highly susceptible towards treatment with class I histone deacetylase (HDAC) inhibitors such as entinostat. However, in clinical trials HDACi as a monotherapy show only modest efficacy in solid tumours. We propose to increase the efficacy of class I HDACi by drug combinations. Methods To identify synergistic drug combinations (entinostat + X) for the treatment of MYC amplified MB we performed a drug screen with a library of n=75 clinically available compounds as single agents and in combination with entinostat in n=3 MYC amplified vs. n=1 MYC-non amplified cell lines. Synergistic behaviour of the six most promising drug combinations was validated by metabolic activity assays, cell count experiments and gene expression profiling. Synergy was assessed by the Loewe additivity model using a combination of ray design and checkerboard matrix. Results The drug screen revealed n=20/75 drugs that were particularly effective (drug sensitivity score ≥10) in combination with entinostat treatment in all three MYC amplified cell lines. Synergy assessment of the top n=6 drugs confirmed strong synergistic activity with entinostat for n=2 drugs (navitoclax, irinotecan). The BCL-2 family inhibitor navitoclax showed the most robust synergy with entinostat in subsequent validation experiments. Conclusion Several drugs either clinically available or currently in clinical trials, including the BCL-2/Xl/w inhibitor navitoclax, show promising effects in a combination therapy with entinostat for the treatment of MYC amplified Group 3 MB.

EMBR-13. NOVEL SYNERGISTIC APPROACHES FOR TARGETED THERAPY OF MYC-DRIVEN MEDULLOBLASTOMA USING CRISPR/CAS9 GENE EDITING

IntroductionResistance to chemotherapy is a common cause of treatment failure in cancer patients and a major problem facing current cancer research. Targeted modulation of oncogenic signaling pathways may be used to systematically characterize drug resistance mechanisms across tumor entities and may help to identify new therapeutic strategies. Since the transcription factor MYC is aberrantly activated in many cancers including pediatric malignant brain tumors, like medulloblastoma (MB), our study focused on MYC-related drug resistance. Methods and ResultsWe performed high-throughput drug screening using our in-house semi-automated platform and identified the HDAC inhibitor Entinostat as a drug that shows promising effects in MYC-driven MB. Investigating genome-wide dCas9-based transcriptional activation screening, potential drug response modulators, mainly TGFB1/Erk/MKNK1 signaling including neural EGFL like 2 (NELL2), were discovered. For further validation, we stably overexpressed NELL2 in MYC-driven MB cells and treated overexpressing cells and the corresponding control cells with Entinostat. Using PI staining, cell cycle status was tracked. Entinostat treatment led to modest induction of cell death in MYC-driven MB control cells but only slightly increased cell death rate in MYC-driven MB cells with NELL2-overexpression. ConclusionWe report that the combination of genetic and pharmacological approaches is a powerful approach to study drug resistance. Our data suggest that activation of the TGFB1/Erk/MKNK1 signaling pathway desensitizes MYC-driven MB cells to Entinostat. Synergistic targeting of TGFB1/Erk/MKNK1 signaling and MYC could therefore provide a novel therapeutic option in this aggressive MB subtype.

Entinostat improves acute neurological outcomes and attenuates hematoma volume after Intracerebral Hemorrhage

Intracerebral hemorrhage (ICH) or hemorrhagic stroke is a major public health problem with no effective treatment. Given the emerging role of epigenetic mechanisms in the pathophysiology of ICH, we tested the hypothesis that a class 1 histone deacetylase inhibitor (HDACi), Entinostat, attenuates neurodegeneration and improves neurobehavioral outcomes after ICH. To address this, we employed a preclinical mouse model of ICH and Entinostat was administered intraperitoneally one-hour post induction of ICH. Entinostat treatment significantly reduced the number of degenerating neurons and TUNEL-positive cells after ICH in comparison to vehicle-treated controls. Moreover, Entinostat treatment significantly reduced hematoma volume, T2-weighted hemorrhagic lesion volume and improved acute neurological outcomes after ICH. Further, Entinostat significantly reduced the hemin-induced release of proinflammatory cytokines in vitro. Consistently, the expression of proinflammatory microglial/macrophage marker, CD16/32, was remarkably reduced in Entinostat treated group after ICH in comparison to control. Altogether, data implicates the potential of class 1 HDACi, Entinostat, in improving acute neurological function after ICH warranting further investigation.

Abstract 1555: Single cell level treatment-specific characterization of HER2+ breast cancers treated with immune checkpoint inhibitors and entinostat

Abstract HER2+ breast cancers are known to be less-immunogenic and associated with low response rates to ICIs such as anti-PD-1, anti-PDL-1 or anti-CTLA-4. A combination of immunosuppressive signals that prevent cytotoxic T cells from infiltrating the tumor microenvironment (TME) and low tumor antigen expression contribute to immunotherapy resistance in this population. Epigenetic modulators can both reexpress tumor antigens and rewire the immunosuppressive environment. We previously used a benzamide histone deacetylase inhibitor, entinostat, in combination with ICIs to reverse the immunosuppressive TME and increase tumor antigen expression in a NeuN HER2+ mouse model of breast cancer. Our results showed that entinostat in combination with anti-PD-1, anti-CTLA-4, or both provided a significant survival benefit compared to either treatment alone. This current study employs single cell RNA-seq on whole tumor samples from mice treated with ICIs and entinostat to investigate the role of epigenetic inhibitors in rewiring the expression of tumor antigens and the cellular landscape of the TME. We generate single cell data of over 54,000 cells from 20 tumors treated with entinostat alone or in combination with anti-PD-1 and anti-CTLA-4 and their combination. Analysis of cells in the TME identifies consistent proportion of monocytes, macrophages, T-cells, Myeloid Derived Suppressor Cells (MDSCs) and Cancer Associated Fibroblasts (CAFs) before and after treatment. Differential expression analysis within the cell types identifies distinct subpopulations and we explore those that are either proportionally higher or lower in each treatment group. Notably, pathway analysis on differentially expressed genes of each cell type identified that combination entinostat and checkpoint treatment increased T cell activation, leukocyte proliferation, myeloid leukocyte and neutrophil migration, and decreased Wnt signaling and histone modifications in tumor cells. Further analysis of the tumor cells from these data and additional ATAC-seq data will enable us to further test the role of antigen reexpression in this TME of activated tumors. We also used the CoGAPS matrix factorization algorithm and RNA velocity analysis to identify transcriptional patterns that are enriched in response to combination treatment. Our current work provides insights into the transcriptional network within a breast tumor after treatment with entinostat. Our follow-up studies in patient samples from a corresponding clinical trial will allow us to map the role of epigenetic modulation in breast tumors. We predict our findings will bring us closer to identifying additional therapeutic targets and ultimately improve survival rates of patients with less-immunogenic tumors. NCT02453620. Citation Format: Dimitrios N. Sidiropoulos, Emily Davis-Marcisak, Christine Rafie, Luciane T. Kagohara, Gaurav Sharma, Roisin M. Connolly, Vered Stearns, Srinivasan Yegnasubramanian, Elizabeth M. Jaffee, Elana J. Fertig, Evanthia T. Roussos Torres. Single cell level treatment-specific characterization of HER2+ breast cancers treated with immune checkpoint inhibitors and entinostat [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 1555.

Abstract A53: Synergistic interaction of HDACi and PLK1i in Group 3 MYC-amplified medulloblastoma

Abstract Medulloblastoma (MB) is one of the common malignant brain tumors in children. Patients with MYC-amplified Group 3 MBs exhibit particularly poor survival rates even after intensive therapy. Surviving patients often suffer from long-term side effects. This calls for new therapeutic strategies, such as targeted therapy options. The sensitivity of MYC-amplified MBs to class I histone deacetylase (HDAC) inhibition was previously shown. In order to elucidate potential combination partners, we have identified PLK1 as one of the top regulated genes following treatment of MYC-amplified Group 3 MB cells with class I HDACi entinostat. Our aim here is to investigate possible combination treatments with entinostat and several PLK1i (volasertib, GSK461364, onvansertib). The cell metabolic activity was evaluated using MYC-amplified and nonamplified MB, high-grade glioma (HGG) and neuroblastoma (NB) cell lines after single and combination treatments. The interaction effect was determined by combination index (CI) (Chou-Talalay CI calculation method). Results were validated assessing cell viability, cell cycle profile, and caspase activity upon treatment with single agents or combination. On-target activity was examined using immunoblotting for pTCTP and H3K27ac. We have confirmed our findings in an inducible MYC cell line. The gene expression profile was analyzed in HD-MB03 cell line after entinostat, volasertib, or combination treatment. We demonstrate that the MYC target gene PLK1 is significantly downregulated upon HDACi treatment. Based on this, we hypothesized that inhibition of both class I HDACs and PLK1 could have synergistic effects. MYC-amplified cell lines were more sensitive than nonamplified cell lines to treatment with all PLK1i investigated, showing 3 to 10 times lower IC50. PLK1i and entinostat interacted synergistically (CI below 0.9) at lower concentrations in MYC-amplified compared to non-amplified MB cell lines. Similar results were obtained for MYC or N-MYC-amplified HGG and NB cell lines. We also observed the loss of viability and loss of fraction of cells in G1 phase in MYC-amplified MB cells after treatment with entinostat and PLK1i. MYC target genes were significantly downregulated in the MYC-amplified MB cell line HD-MB03 after treatment with PLK1i and entinostat. Moreover, we demonstrated reduction of MYC levels and faster MYC degradation upon volasertib treatment. Our data suggest that MYC-amplification might serve as a predictive biomarker for PLK1i treatment in MB and other entities. The combination of entinostat and PLKi could be a candidate therapy for future clinical trials for MYC-amplified Group 3 MB, and possibly other tumors harboring MYC amplification. Citation Format: Gintvile Valinciute, Jonas Ecker, Thomas Hielscher, Christin Schmidt, Marc Remke, Gianluca Sigismondo, Jeroen Krijgsveld, Stefan M. Pfister, Olaf Witt, Till Milde. Synergistic interaction of HDACi and PLK1i in Group 3 MYC-amplified medulloblastoma [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A53.

Characterization of the immune tumor microenvironment of HER2-positive breast cancer following treatment with entinostat and immune checkpoint inhibition.

e15061 Background: HER2+ breast cancers are known to be less-immunogenic and associated with low response rates to immune checkpoint inhibitors (ICIs). A combination of immunosuppressive signals that prevent cytotoxic T cells from infiltrating the tumor microenvironment (TME) and, low tumor antigen expression, contribute to immunotherapy resistance in this population. Epigenetic modulators can both reexpress tumor antigens and rewire the immunosuppressive environment. We previously used a histone deacetylase inhibitor, entinostat (ENT), in combination with ICIs to reverse the immunosuppressive TME and increase tumor antigen expression in a NeuN HER2+ mouse model of breast cancer. Our results showed that ENT in combination with anti-PD-1, anti-CTLA-4, provided a significant survival benefit compared to either treatment alone. Methods: This current study employs single cell RNA-sequencing on whole tumor samples from mice treated with ICIs and entinostat to investigate the role of epigenetic inhibitors in rewiring the expression of tumor antigens and the cellular landscape of the TME. We generate single cell data over 54,000 cells from 20 tumors treated with entinostat alone or in combination with anti-PD1 and anti-CTLA4 and their combination. Results: Analysis of cells in the TME identifies consistent proportion of monocytes, macrophages, T-cells, Myeloid Derived Suppressor Cells (MDSCs) and Cancer Associated Fibroblasts (CAFs) before and after treatment. Differential expression analysis within the cell types identifies distinct subpopulations and we explore those that are either proportionally higher or lower in each treatment group. Notably, pathway analysis on differentially expressed genes of each cell type identified that combination entinostat and checkpoint treatment increased T cell activation, leukocyte proliferation, myeloid leukocyte and neutrophil migration, and decreased Wnt signaling and histone modifications in tumor cells. These results are being corroborated in patient samples from a parallel clinical trial to provide translational relevance. Conclusions: Our current work provides insights into the transcriptional network within a breast tumor after treatment with ENT+ICIs. We predict our findings will bring us closer to identifying additional therapeutic targets and ultimately improve survival rates of patients with less-immunogenic tumors.