Combination Epigenetic Therapy Research Articles

Overcoming Clinical Resistance to EZH2 Inhibition Using Rational Epigenetic Combination Therapy.

Genomic studies of patient epithelioid sarcomas and rhabdoid tumors identify mutations converging on a common pathway for response to EZH2 inhibition. Resistance mutations decouple drug-induced differentiation from cell-cycle control. We identify an epigenetic combination strategy to overcome resistance and improve durability of response, supporting its investigation in clinical trials. See related commentary by Paolini and Souroullas, p. 903. This article is featured in Selected Articles from This Issue, p. 897.

Abstract 6551: Comprehensive genomic and transcriptomic analyses capture the effects of epigenetic therapy priming on immune checkpoint blockade response in non-small cell lung cancer

Abstract Introduction: Emergence of resistance to immune checkpoint blockade (ICB) mandates the development of strategies for ICB sensitization. Here we employed a multi-omic approach to understand the effects of epigenetic priming in re-shaping the tumor microenvironment, together with genomic drivers of therapeutic response of epigenetic therapy followed by ICB in non-small cell lung cancer (NSCLC). Methods: We performed whole exome sequencing (WES) on 39 baseline tumors and bulk RNA sequencing (RNAseq) on 18 serial tumors across 42 patients with metastatic immunotherapy-naïve NSCLC, who received azacitidine and entinostat followed by nivolumab (NCT01928576). WES was utilized to assess co-mutations, mutation signatures and genome-wide structural changes. RNAseq was utilized for gene and gene set enrichment analysis (GSEA) and repeat element analysis. Response after nivolumab initiation was assessed using RECIST 1.1 criteria. Patients who were progression-free at 6 months or alive at 2 years after initial treatment were defined as exceptional responders. Results: We found an enrichment in inactivating mutations in homologous recombination genes in radiographic responders (Fisher’s exact, p=0.0007). Higher germline and somatic HLA class II diversity (Mann-Whitney U-test, p=0.05 and p=0.03 respectively), and an enrichment of smoking and DNA damage mutational signatures were noted in radiographic responders (Mann-Whitney U-test, p=0.03 and p=0.15 respectively). Radiographically responding tumors harbored a higher number of mutations in genomic regions that were haploid or present in multiple copies (persistent tumor mutation burden; Mann-Whitney U-test, p=0.018). GSEA revealed an upregulation of inflammatory response gene sets post-epigenetic therapy in patients attaining an exceptional response. Antigen presentation, interferon-alpha, and interferon-gamma related gene sets were upregulated in exceptional responders post epigenetic priming (FDR-adjusted p=0.005, p=0.009, and p=0.011 respectively). Additionally, we observed an enrichment in interferon-alpha, cancer testis antigens, and interferon-gamma related gene sets in patients with a longer progression-free survival (FDR-adjusted p=0.007, p=0.011, and p=0.013 respectively). Repeat element analysis showed an increase in long terminal repeats on-therapy in exceptional responders, suggesting induction of repeat element expression with epigenetic therapy. A higher expression of MAGE family tumor associated antigens (MAGEA10, MAGEB1, MAGEB2) was noted post-epigenetic therapy in exceptional responders. Conclusions: Genomic and transcriptomic analyses reveal the potential of epigenetic-priming to re-shape the tumor microenvironment and highlight patients that could benefit from combination epigenetic therapy with immunotherapy. Citation Format: Blair V. Landon, Kristen A. Marrone, Michael J. Topper, Akshaya Annapragada, Hua-Ling Tsai, Archana Balan, Noushin Niknafs, Christopher Cherry, James R. White, Gavin Pereira, Vilmos Adleff, Chen Hu, Joanne Riemer, Margaret Fitzpatrick, Patrick Forde, Christine L. Hann, Ronan J. Kelly, David S. Ettinger, Benjamin Levy, Jorge Nieva, James Herman, Victor E. Velculescu, Stephen Baylin, Julie Brahmer, Valsamo Anagnostou. Comprehensive genomic and transcriptomic analyses capture the effects of epigenetic therapy priming on immune checkpoint blockade response in non-small cell lung 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 6551.

Abstract B016: Targeting the epigenome through combined Facilitates Chromatin Transcription (FACT) and Bromodomain and Extra-Terminal Domain (BET) inhibition in Diffuse Midline Glioma (DMG)

Abstract Aberrant epigenetic regulation is a hallmark of Diffuse Midline Glioma (DMG), an incurable tumor that primarily arises in the brainstem of young children. The H3K27M driver histone mutation and resulting permissive chromatin indicates epigenetic targeting as a key therapeutic strategy against this aggressive cancer. One such epigenetic target is the Facilitates Chromatin Transcription (FACT) histone chaperone. FACT is targeted by the curaxin compound CBL0137 which is currently in phase I/II clinical trial for pediatric cancer patients (NCT04870944). This study aims to decipher the mechanism of CBL0137 to find effective combination therapies for the next round of clinical implementation. To this end, we applied a multi-omics approach by integrating epigenetic profiling with transcriptomic data sets (CUT&RUN, ATAC-seq and RNA-seq) to interrogate the therapeutic mechanism of CBL0137 in DMG. We then employed in vitro cytotoxicity assays and in vivo orthotopic patient-derived xenograft (PDX) pre-clinical models to test a novel, mechanistic-anchored epigenetic combination therapy. We found FACT to be enriched at the promoters of developmental genes, coinciding with regions of open chromatin and binding motifs of the core DMG regulatory transcription factors TCF12 and OLIG2. Furthermore, FACT interacted and co-localized with the Bromodomain and Extra-Terminal Domain (BET) protein BRD4, suggesting cooperation between FACT and BRD4 in DMG. Given that BRD4 is an established therapeutic target in DMG and other cancers, we investigated the combination of the FACT-inhibitor CBL0137 with the BET-inhibitor JQ1. Combination treatment was cytotoxic against DMG in vitro, with enhanced cytotoxicity observed against H3K27M-mutant cells. We demonstrated a significant survival extension in three independent orthotopic PDX mouse models treated with CBL0137 and JQ1 in combination. Mechanistically, CBL0137 and JQ1 decreased chromatin accessibility and transcription of genes involved in RNA regulatory processes, such as RNA methylation and splicing. Consistently, combination treatment led to increased intron retention, highlighting a possible link between chromatin disruption and the splicing machinery in DMG. Future work will investigate whether treatment-induced intron retention acts as a source of neoantigens, with the potential to enhance DMG immunogenicity. In sum, this study has identified a promising new epigenetic combination therapy – FACT + BET inhibition – while uncovering intriguing new insights into DMG epigenetics and pathobiology. Citation Format: Holly Holliday, Aaminah Khan, Nisitha Jayatilleke, Chelsea Mayoh, Samuel E. Ross, Yolanda Colino Sanguino, Anjana Gopalakrishnan, Anahid Ehteda, Benjamin Rayner, Maria Tsoli, David S. Ziegler. Targeting the epigenome through combined Facilitates Chromatin Transcription (FACT) and Bromodomain and Extra-Terminal Domain (BET) inhibition in Diffuse Midline Glioma (DMG) [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr B016.

Combination Epigenetic Therapy Using YF2, a First-in-Class Histone Acetyltransferase Activator, Restores Immunogenicity in Diffuse Large B-Cell Lymphoma

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma. Molecular studies have identified epigenetic dysregulation as a key driver in germinal center (GC)-derived DLBCL. Mutations in CREBBP/p300 and EZH2 often co-occur and lead to transcriptional repression and decreased immunogenicity as demonstrated by reduced major histocompatibility complex (MHC) expression. Our lab previously reported that YF2, a first-in-class histone acetyltransferase activator discovered at Columbia University, induces cytotoxicity in both cell and murine models of DLBCL. Other epigenetic therapies, such as tazemetostat and belinostat, are approved for use in follicular and T-cell lymphoma, respectively, but have limited single agent activity in DLBCL. We hypothesize that treatment with YF2 in combination with tazemetostat or belinostat increases transcriptional activity and restores tumor immunogenicity in CBP/p300- and EZH2-mutated DLBCL. We utilized several DLBCL cell lines to assess YF2 combination therapy: OCI-Ly7 (CBP/p300 WT, EZH2 WT), SU-DHL-4 (CBP/p300 WT, EZH2 GOF), A20 (CBP/p300 -/-, EZH2 WT), and SU-DHL-6 (CBP/p300 -/-, EZH2 GOF). Cells were treated on day 0 with single agents or with YF2 in combination with either tazemetostat (YF2 + taz) or belinostat (YF2 + bel), retreated on day 3, and collected on day 6 for flow cytometry (n = 4) and western blot (n = 2) analyses. MHC class I/II and β₂ microglobulin (B2M) expression were measured as markers of immunogenicity. To preliminarily assess YF2 combination therapy in vivo, immunocompetent BALB/c mice were engrafted with syngeneic A20 cells, immunized, and segregated (n = 2-4) into treatment groups: control (saline), tazemetostat (300 mg/kg twice daily x 28 days), belinostat (40 mg/kg once daily x 7 days), YF2 (50 mg/kg once daily x 28 days), YF2 + taz, and YF2 + bel. Blood and spleen samples were collected on day 29 to measure T- and B-cell activity via flow cytometry. All fold changes are expressed relative to the corresponding control. Combination therapy generally increased MHC-I, -II, and B2M expression across all cell lines as measured via flow cytometry. In double-mutated SU-DHL-6 cells, MHC-I and -II expression increased 2.0- ( P < 0.01) and 3.1-fold ( P = 0.04), respectively, following YF2 + taz treatment, and increased 1.3- ( P = 0.06) and 4.5-fold ( P < 0.01) after YF2 + bel ( Figure 1). Expression of B2M increased 2.3-fold ( P = 0.01) with YF2 + taz and 1.6-fold ( P = 0.07) with YF2 + bel. Interestingly, YF2 combination therapy was similarly effective in non-mutated OCI-Ly7 cells: MHC-I, -II, and B2M expression increased 1.9- ( P < 0.01), 3.0- ( P < 0.01), and 2.4-fold ( P < 0.01), respectively, following YF2 + taz treatment, and increased 1.5- ( P = 0.01), 3.3- ( P < 0.01), and 2.4-fold ( P < 0.01) with YF2 + bel. Similar expression trends were observed via western blots, but to a lesser degree; MHC-I, -II, and B2M protein increased 1.3-, 1.4-, 1.6-fold with YF2 + taz, and increased 1.1-, 1.6-, and 1.2-fold following YF2 + bel treatment in SU-DHL-6 cells. The combination therapies were tolerated by the mice and decreased tumor size. Splenic MHC-I expression increased 1.2-fold with YF2 + taz and 1.4-fold with YF2 + bel, whereas MHC-II increased 1.3-fold for both combination therapies ( Figure 2). Similarly, circulating B cells displayed increased MHC-I and -II expression with combination therapy. Treatment with YF2 + taz increased the number of circulating CD4 + T cells 1.5-fold and the number of CD8 + T cells 3.5-fold, while YF2 + bel increased the number of central memory and effector memory T cells by 1.6- and 1.9-fold, respectively. To understand the effect of combination therapies on B cell development in the GC, splenic B cells were evaluated and exhibited a 1.9-fold increase of cells in the light zone following YF2 + taz treatment, and a 1.2-fold increase after YF2 + bel exposure. The number of splenic plasma cells increased 1.4- and 1.5-fold following YF2 + taz and YF2 + bel treatments, respectively ( Figure 2). These findings suggest that combination epigenetic therapy may restore homeostatic B cell function and promote B cell cycling through the GC. In summary, these data propose YF2 combination epigenetic therapy as a means to increase immunogenicity in CBP/p300- and EZH2-mutated DLBCL. While our preliminary mouse experiment provided promising initial results, an expanded study is underway to statistically confirm the exciting trends that we observed.

Combination epigenetic therapy activates immune cells in a murine model of ovarian cancer

Abstract Ovarian cancer (OC) is the fifth leading cause of cancer death in women in the United States. Despite novel therapies and significant advances in our understanding of the disease, the five-year survival rate for OC has not changed in decades. The immunosuppressive microenvironment of OC leads to a low response rate to immunotherapies. We have previously shown that in a murine model of OC epigenetic therapies including DNA methyltransferase inhibitors (DNMTis) and histone deacetylase inhibitors (HDACis) activate type I interferon signaling in tumor cells to drive immune infiltration and sensitization to immunotherapy. This indicates a role for immune control of the tumor, but we did not directly investigate the effects of these epigenetic therapies on the immune cells. We hypothesized that T cells could be activated by epigenetic therapy in this model. We isolated T cells from the spleens of healthy C57/Bl6 mice and treated the cells with a DNMTi, 5-azacytidine (Aza) at 500 nmol/L, and an HDACi, ITF-2357 (ITF) at 100 nmol/L, singly and in combination. Cell pellets were isolated, RNA extracted, and analyzed via qRT-PCR. Cell supernatants were analyzed for cytokine and chemokine production using a Legendplex assay. The treated bulk T cells, CD8+ T cells, and CD4+ T cells showed anti-tumor cytokines, including CCL5, TNF-α and IFN-γ, were upregulated while the pro-tumor cytokine IL-10 was downregulated. These changes were evident at the transcript and secreted cytokine level, pointing to transcriptional upregulation of the target genes. This study demonstrates direct activation of T cells by DNMTis and HDACis and provides mechanistic insight into the role of epigenetic therapies in the murine model of OC.

A stem cell epigenome is associated with primary nonresponse to CD19 CAR T cells in pediatric acute lymphoblastic leukemia

AbstractCD19 chimeric antigen receptor T-cell therapy (CD19-CAR) has changed the treatment landscape and outcomes for patients with pre–B-cell acute lymphoblastic leukemia (B-ALL). Unfortunately, primary nonresponse (PNR), sustained CD19+ disease, and concurrent expansion of CD19-CAR occur in 20% of the patients and is associated with adverse outcomes. Although some failures may be attributable to CD19 loss, mechanisms of CD19-independent, leukemia-intrinsic resistance to CD19-CAR remain poorly understood. We hypothesize that PNR leukemias are distinct compared with primary sensitive (PS) leukemias and that these differences are present before treatment. We used a multiomic approach to investigate this in 14 patients (7 with PNR and 7 with PS) enrolled in the PLAT-02 trial at Seattle Children’s Hospital. Long-read PacBio sequencing helped identify 1 PNR in which 47% of CD19 transcripts had exon 2 skipping, but other samples lacked CD19 transcript abnormalities. Epigenetic profiling discovered DNA hypermethylation at genes targeted by polycomb repressive complex 2 (PRC2) in embryonic stem cells. Similarly, assays of transposase-accessible chromatin–sequencing revealed reduced accessibility at these PRC2 target genes, with a gain in accessibility of regions characteristic of hematopoietic stem cells and multilineage progenitors in PNR. Single-cell RNA sequencing and cytometry by time of flight analyses identified leukemic subpopulations expressing multilineage markers and decreased antigen presentation in PNR. We thus describe the association of a stem cell epigenome with primary resistance to CD19-CAR therapy. Future trials incorporating these biomarkers, with the addition of multispecific CAR T cells targeting against leukemic stem cell or myeloid antigens, and/or combined epigenetic therapy to disrupt this distinct stem cell epigenome may improve outcomes of patients with B-ALL.

Abstract B007: Endogenous retrotransposable elements induction in SMARCA4-deficient ovarian cancer is associated with immunomodulatory changes in the tumor microenvironment

Abstract Introduction: Ovarian cancer (OC) is the most lethal gynecologic cancer, and there is an urgent need to develop new therapies. Patient responses to immune checkpoint blockade have overall been disappointing, which is likely due to the immunosuppressive tumor microenvironment (TME) of most OCs that may be in part under the influence of epigenetic regulation. There is evidence that OCs that harbor loss-of-function mutations in the SWI/SNF chromatin remodeling complex catalytic subunit, SMARCA4, may be more immunogenic and amenable to immunotherapy, however the mechanisms by which this occurs is unclear. Proposed mechanisms include de-methylation of normally silenced noncoding elements. The aim of our study is to investigate the epigenetic changes of retrotransposable elements (RTEs) induced by SMARCA4 mutations that modulate the TME. Experimental Procedures: Stable isogenic SMARCA4-knockout (KO) murine (ID8) and human (OAW28) OC models were generated using CRISPR-Cas9 lentiviral transduction and clonal selection. Transcriptomic analyses of these cells were performed using RNA sequencing using ribosomal depletion protocol and validated using qRT-PCR. Moreover, differentially expressed coding genes in RNA sequencing were identified according to fold change between KO and control cells of RPKM (Reads Per Kilobase of transcript, per Million mapped reads) values. Gene Ontology enrichment analysis was then performed to identify the most altered pathways. Results: CRISPR-Cas9 KO of SMARCA4 in OC cells led to an increased fraction of reads coming from repetitive elements (repeatome). Within the repeatome, short interspersed nuclear elements (SINEs) have increased fraction of mapped reads in KO compared to wildtype OAW28 cells. Quantification analyses of known repeats demonstrate significant upregulation of endogenous retroviruses (ERVs) in KO compared to control ID8 cells. Certain RTEs known to be associated with viral mimicry and increased immunogenicity were upregulated in KO cells. Top 10 upregulated genes were significantly enriched in pathways related to interferon and viral responses. Further quantification analyses demonstrated that the dsRNA sensing pathway was activated in SMARCA4-deficient OCs leading to downstream increase in interferon-response genes. Knockdown of dsRNA sensor mitochondrial antiviral signaling protein (MAVS) downregulates the SMARCA4 loss-induced interferon-response activation. Conclusion: De-repression of normally silenced RTEs and subsequent increased immunogenicity of SMARCA4-deficient OCs suggest a potential new immunomodulatory biomarker for targeted therapy investigation. A mechanistic understanding of the role of SMARCA4 in OCs enhances our knowledge of the epigenetic processes that govern immune-stimulating responses in the TME. Studies are underway to explore combination epigenetic therapy and immunotherapy in these cancers. Citation Format: Melica N. Brodeur, Siyu Sun, Yingjie Zhu, Benjamin Greenbaum, Britta Weigelt, Dmitriy Zamarin. Endogenous retrotransposable elements induction in SMARCA4-deficient ovarian cancer is associated with immunomodulatory changes in the tumor microenvironment. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr B007.

Abstract 3278: Identification of epigenetic therapy induced tumor antigens to promote proliferation and infiltration of antigen specific T cells in non-small cell lung cancer

Abstract Among the hallmarks of non-small cell lung cancer (NSCLC) is cancer immunoediting. Immunoediting results when cancer cells evade immune recognition via positive selection for cells that do not present immunogenic antigens recognized by CD8+ T cells. An epigenetic therapy-based approach has been developed in our lab to enhance expression of tumor antigens using combinatorial DNA methyltransferase inhibition (DNMTi) paired with histone deacetylase inhibition (HDACi). However, durable responses from the application of epigenetic therapy alone or in combination with other therapies have remained elusive in NSCLC. This may be because enhanced proliferation and infiltration of tumor-associated antigen specific CD8+ T cells are necessary to recognize epigenetically induced antigens to halt disease progression. In the current study, we identified epigenetic therapy inducible self-antigens that can potentially be used to activate and guide the differentiation of CD8+ T cells specific to NSCLC tumor antigens. The identification of these candidates was derived from analyses of paired RNAseq data from NSCLC patients treated with combination epigenetic therapy. From these analyses, differentially expressed transcripts selected from total transcriptome data were filtered to remove non-protein coding genes and genes with detectable expression in normal tissues as indicated by GTEx. HLA binding affinity (HLA-A*0201) of selected targets was defined by NetMHC 4.0 artificial neural network-based prediction to identify strong binding peptide candidates. The combined results of these data filtering facilitated the identification of 34 epigenetic therapy induced genes and associated peptides (9mers) with predicted high binding affinity for HLA-A*0201. The predicted peptides of target genes were selected for single peptide pulsing in allogenic dendritic cells to generate antigen specific CD8+ T cells for TCR sequencing (TCRseq). TCRseq libraries derived from peptide stimulation experiments revealed distinct V and J gene frequencies and emergence of antigen specific clonotypes, which suggest clonal expansion. To validate whether epigenetic therapy could induce target genes expression in an independent experimental model, in vitro human NSCLC cell lines were treated with DNMTi and HDACi to mimic the clinical drug paradigm and transcriptional augmentation was assessed by qRT-PCR. In this orthogonal system, we validated eight target genes that were induced by epigenetic therapy in vitro. Altogether, these data suggest that a conserved subset of genes, whose derived proteins are predicted to be presented in class I MHC and act as T cell epitopes, is induced by combination epigenetic treatment. Our studies provide a basis for the development of novel and personalized strategies to improve outcomes and quality of life for more patients with NSCLC. Citation Format: Julia An, Valsamo Anagnostou, Kristen A. Marrone, Victor E. Velculescu, Julie R. Brahmer, Stephen B. Baylin, Michael J. Topper. Identification of epigenetic therapy induced tumor antigens to promote proliferation and infiltration of antigen specific T cells in non-small cell lung cancer [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 3278.

Phase 2 study of azacitidine (AZA) plus pembrolizumab (pembro) as second-line treatment in patients with advanced pancreatic ductal adenocarcinoma.

4158 Background: Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer-related death with a 5-year survival rate of 10%. Novel strategies for advanced PDAC are a critical need. A DNA hypomethylating agent (HMA) increased tumor-infiltrating effector T cells and significantly prolonged survival in combination with immune checkpoint blockade (ICB) in a PDAC mouse model (Gonda et al 2020). We hypothesized that combining HMA with ICB will lead to therapeutic benefit in pts with advanced PDAC. Methods: This is an open-label, single-arm, single-center, Phase 2 trial of AZA plus pembro in pts with unresectable or metastatic PDAC. Pts were treated with AZA 50 mg/m2 subcutaneous daily for 5 days Q4W beginning week 1 day 1 followed by pembro 200 mg IV Q3W starting week 3 day 1. Key eligibility criteria included documented progression on or following first-line systemic treatment, ECOG PS 0-1, and adequate organ function. The primary objective was progression-free survival (PFS). Thirty-one evaluable pts were required to detect an improvement in PFS from 2 mo to 4 mo with a one-sided p-value of 0.05 and 80% power. Secondary endpoints included safety and tolerability, overall response rate (ORR), disease control rate (DCR), and overall survival (OS). Data cutoff was February 10, 2022. Results: Between Oct 2017 and Sept 2021, 36 pts were enrolled (median age 62.5, 75% white, 72% male). At data cutoff, 34 and 31 pts received at least 1 dose of AZA and pembro, respectively. Median PFS for ≥1 dose of AZA was 1.48 mo (95% CI: 1.35, 1.74) and for ≥1 dose of pembro was 1.51 mo (95% CI, 1.38, 3.42). The median OS was 4.67 months. Among the 34 pts, 3 (8.8%) experienced a partial response (PR) by RECIST with a DCR of 32.4%. Of the 3 pts with PR, 2 received 35 doses of pembro and continued beyond 2 years with an ongoing PR. One pt remains on pembro 20 months after study completion. None of the pts with a PR were microsatellite instability-high or tumor mutation burden high, and next-generation sequencing of the 3 cancers identified a BRCA1 variant and POLE variant. Treatment-related AEs (TRAEs) occurred in 20/34 pts (59%), the most common of which were diarrhea and fatigue. Grade ≥3 occurred in 7/34 (21%) including 1 immune-related grade 5 event (encephalitis). Conclusions: AZA plus pembro demonstrated a tolerable safety profile but no PFS benefit compared to historical controls. Our data suggests combined epigenetic therapy and ICB may expand therapeutic options in a subset of pts with PDAC. Further investigation is needed to identify biomarkers to predict response and elucidate effective timing, sequencing, and combination of epigenetic agents. Follow-up for OS is ongoing. Correlative analysis of epigenetic effects and characterization of the tumor immune microenvironment will be reported. Clinical trial information: NCT03264404.

Management of Acute Myeloid Leukemia: Current Treatment Options and Future Perspectives.

Simple SummaryAML is a genetically heterogeneous disease with a median age of diagnosis between 60 and 70 years. Thus, many AML patients are not eligible for intensive chemotherapy. Often, the disease is accompanied by a poor prognosis due to high-risk genetic features or due to antecedent hematologic disorders (e.g., myelodysplastic syndrome). Therefore, AML treatment remains a challenge; even after intensive chemotherapy and allogeneic stem cell transplantation (alloHSCT), AML relapses are regularly observed. Thus, new concepts of AML therapy, considering tailored treatment approaches after comprehensive molecular diagnostic or implementing new immunotherapeutic strategies, are urgently needed. This review provides a detailed overview of recent developments and current promising concepts to improve the treatment and the outcome of AML patients.Treatment of acute myeloid leukemia (AML) has improved in recent years and several new therapeutic options have been approved. Most of them include mutation-specific approaches (e.g., gilteritinib for AML patients with activating FLT3 mutations), or are restricted to such defined AML subgroups, such as AML-MRC (AML with myeloid-related changes) or therapy-related AML (CPX-351). With this review, we aim to present a comprehensive overview of current AML therapy according to the evolved spectrum of recently approved treatment strategies. We address several aspects of combined epigenetic therapy with the BCL-2 inhibitor venetoclax and provide insight into mechanisms of resistance towards venetoclax-based regimens, and how primary or secondary resistance might be circumvented. Furthermore, a detailed overview on the current status of AML immunotherapy, describing promising concepts, is provided. This review focuses on clinically important aspects of current and future concepts of AML treatment, but will also present the molecular background of distinct targeted therapies, to understand the development and challenges of clinical trials ongoing in AML patients.

Epigenetic therapy to enhance therapeutic effects of PD-1 inhibition in therapy-resistant melanoma.

Targeted therapy and immunotherapy have revolutionized the treatment of metastatic skin melanoma but around half of all patients develop resistance early or late during treatment. The situation is even worse for patients with metastatic uveal melanoma (UM). Here we hypothesized that the immunotherapy of therapy-resistant skin melanoma or UM can be enhanced by epigenetic inhibitors. Cultured B16F10 cells and human UM cells were treated with the histone deacetylase inhibitor (HDACi) entinostat or BETi JQ1. Entinostat-induced HLA expression and PD-L1, but JQ1 did not. A syngeneic mouse model carrying B16-F10 melanoma cells was treated with PD-1 and CTLA4 inhibitors, which was curative. Co-treatment with the bioavailable BETi iBET726 impaired the immunotherapy effect. Monotherapy of a B16-F10 mouse model with anti-PD-1 resulted in a moderate therapeutic effect that could be enhanced by entinostat. Mice carrying PD-L1 knockout B16-F10 cells were also sensitive to entinostat. This suggests HDAC inhibition and immunotherapy could work in concert. Indeed, co-cultures of UM with HLA-matched melanoma-specific tumor-infiltrating lymphocytes (TILs) resulted in higher TIL-mediated melanoma killing when entinostat was added. Further exploration of combined immunotherapy and epigenetic therapy in metastatic melanoma resistant to PD-1 inhibition is warranted.

DDRE-03. IDH1-MUTANT GBM CELLS ARE HIGHLY SENSITIVE TO COMBINATION OF KDM6A/B AND HDAC INHIBITORS

Mutations in IDH1 and IDH2 genes are common in low grade gliomas and secondary GBM and are known to cause a distinct epigenetic landscape in these tumors. To interrogate the epigenetic vulnerabilities of IDH-mutant gliomas, we performed a chemical screen with inhibitors of chromatin modifiers and identified 5-azacytidine, Chaetocin, GSK-J4 and Belinostat as potent agents against primary IDH1-mutant cell lines. Testing the combinatorial efficacy of these agents, we demonstrated GSK-J4 and Belinostat combination as a very effective treatment for the IDH1-mutant glioma cells. Engineering established cell lines to ectopically express IDH1R132H, we showed that IDH1R132H cells adopted a different transcriptome with changes in stress-related pathways that were reversible with the mutant IDH1 inhibitor, GSK864. The combination of GSK-J4 and Belinostat was highly effective on IDH1R132H cells, but not on wt glioma cells or nonmalignant fibroblasts and astrocytes. The cell death induced by GSK-J4 and Belinostat combination involved the induction of cell cycle arrest and apoptosis. RNA sequencing analyses revealed activation of inflammatory and unfolded protein response pathways in IDH1-mutant cells upon treatment with GSK-J4 and Belinostat conferring increased stress to glioma cells. Specifically, GSK-J4 induced ATF4-mediated integrated stress response and Belinostat induced cell cycle arrest in primary IDH1-mutant glioma cells; which were accompanied by DDIT3/CHOP-dependent upregulation of apoptosis. Moreover, to dissect out the responsible target histone demethylase, we undertook genetic approach and demonstrated that CRISPR/Cas9 mediated ablation of both KDM6A and KDM6B genes phenocopied the effects of GSK-J4 in IDH1-mutant cells. Finally, GSK-J4 and Belinostat combination significantly decreased tumor growth and increased survival in an orthotopic model in mice. Together, these results suggest a potential combination epigenetic therapy against IDH1-mutant gliomas.

A feasibility study of combined epigenetic and vaccine therapy in advanced colorectal cancer with pharmacodynamic endpoint

Epigenetic therapies may modulate the tumor microenvironment. We evaluated the safety and optimal sequence of combination DNA methyltransferase inhibitor guadecitabine with a granulocyte macrophage-colony-stimulating-factor (GM-CSF) secreting colon cancer (CRC) vaccine (GVAX) using a primary endpoint of change in CD45RO + T cells. 18 patients with advanced CRC enrolled, 11 underwent paired biopsies and were evaluable for the primary endpoint. No significant increase in CD45RO + cells was noted. Grade 3–4 toxicities were expected and manageable. Guadecitabine + GVAX was tolerable but demonstrated no significant immunologic activity in CRC. We report a novel trial design to efficiently evaluate investigational therapies with a primary pharmacodynamic endpoint.Trial registry Clinicaltrials.gov: NCT01966289. Registered 21 October, 2013.

Synergistic induction of apoptosis in resistant head and neck carcinoma and leukemia by alkoxyamide-based histone deacetylase inhibitors.

Targeting epigenetic dysregulation has emerged as a valuable therapeutic strategy in cancer treatment. Especially epigenetic combination therapy of histone deacetylase inhibitors (HDACi) with established anti-cancer drugs has provided promising results in preclinical and clinical studies. The structural optimization of alkoxyamide-based class I/IIb inhibitors afforded improved analogs with potent efficacy in cisplatin-resistant head and neck carcinoma cells and bortezomib-resistant leukemia cells. The most promising HDACi showed a superior synergistic cytotoxic activity as compared to vorinostat and class I HDACi in combination with cisplatin, leading to a full reversal of the chemoresistant phenotype in head and neck cancer cell lines, as well in combination with the proteasome inhibitors (bortezomib and carfilzomib) in a panel of leukemic cell lines. Furthermore, the most valuable alkoxyamide-based HDACi exhibited strong exvivo anticancer efficacy against primary patient samples obtained from different therapy-resistant leukemic entities.

EXTH-10. COMBINATION OF EPIGENETIC ENZYME INHIBITORS, GSK-J4 AND BELINOSTAT, REVEALS HIGH EFFICACY IN IDH1 MUTANT GLIOMAS

Abstract Mutations in IDH1 and IDH2 genes are common in low grade gliomas and secondary GBM and are known to cause a distinct epigenetic landscape in these tumors. To interrogate the epigenetic vulnerabilities of IDH-mutant gliomas, we performed a chemical screen with inhibitors of chromatin modifiers and identified 5-azacytidine, Chaetocin, GSK-J4 and Belinostat as potent agents against primary IDH1-mutant cell lines. Testing the combinatorial efficacy of these agents, we demonstrated GSK-J4 and Belinostat combination as a very effective treatment for the IDH1-mutant glioma cells. Engineering established cell lines to ectopically express IDH1R132H, we showed that IDH1R132H cells adopted a different transcriptome with changes in stress-related pathways that were reversible with the mutant IDH1 inhibitor, GSK864. The combination of GSK-J4 and Belinostat was highly effective on IDH1R132H cells, but not on wt glioma cells or nonmalignant fibroblasts and astrocytes. The cell death induced by GSK-J4 and Belinostat combination involved the induction of cell cycle arrest and apoptosis. RNA sequencing analyses revealed activation of inflammatory and unfolded protein response pathways in IDH1-mutant cells upon treatment with GSK-J4 and Belinostat conferring increased stress to glioma cells. Specifically, GSK-J4 induced ATF4-mediated integrated stress response and Belinostat induced cell cycle arrest in primary IDH1-mutant glioma cells; which were accompanied by DDIT3/CHOP-dependent upregulation of apoptosis. Moreover, to dissect out the responsible target histone demethylase, we undertook genetic approach and demonstrated that CRISPR/Cas9 mediated ablation of both KDM6A and KDM6B genes phenocopied the effects of GSK-J4 in IDH1-mutant cells. Finally, GSK-J4 and Belinostat combination significantly decreased tumor growth and increased survival in an orthotopic model in mice. Together, these results suggest a potential combination epigenetic therapy against IDH1-mutant gliomas.

DNMTi plus anti-4-1BB therapy reverses suppressive tumor microenvironment and reduces tumor burden in ovarian cancer

Abstract Novel therapies are urgently needed for ovarian cancer (OC), the fifth deadliest cancer in women. Better OC prognosis is associated with high tumor-infiltrating CD8 T cells, but OC is generally characterized by an immunosuppressive tumor microenvironment (TME), with less than 10% of patients responding to immune checkpoint blockade therapy in clinical trials. DNA methyltransferase inhibitors (DNMTi) activate transcription of repetitive elements to induce a type I interferon response in OC, which recruits and activates host immune cells to fight the tumor. Additionally, changes in DNA methylation in T cells regulate T cell memory. Thus, DNMTi increase anti-tumor immunity through 1) tumor IFN response and 2) reversal of T cell exhaustion. To test the hypothesis that combination epigenetic and immune therapy could increase the anti-tumor response in OC, we treated an immunocompetent mouse model of OC with DNMTi +/− anti-CD137. The ID8 MOSE P53−/− model grows intraperitoneally and produces ascites, mimicking human OC which is 90% P53 mutant. The TME of this model is immunosuppressive and it is not responsive to immune checkpoint blockade therapy. At 9 weeks post tumor injection, we observed the following survival percentages: 50% for the combination group, 30% for the DNMTi group, and 0% survival for the both the anti-CD137 and mock groups. We also observed statistically significant increases in %CD3+IFNg+ T cells in the spleen for the DNMTi + anti-CD137 group compared to the mock group. We hypothesize that anti-CD137 treatment is activating immune cells recruited by DNMTi. Future experiments will manipulate cytokine expression to delineate mechanism. We thus describe a novel immunotherapeutic combination for ovarian cancer.

Deformable liposomal codelivery of vorinostat and simvastatin promotes antitumor responses through remodeling tumor microenvironment.

The tumor microenvironment (TME) and its major component tumor-associated macrophages (TAM) play a pivotal role in the development of non-small cell lung cancer (NSCLC). An epigenetic drug-based combinatory therapeutic strategy was proposed and a deformable liposome system (D-Lipo) was developed for vorinostat and simvastatin codelivery for remodeling the TME. The application of deformable liposomes in systemic cancer drug delivery has been underexplored and its potential in cancer therapy is largely unknown. This work revealed that D-Lipo exhibited an enhanced intratumor infiltration ability. The proposed therapeutic strategy was characterized by a chemo-free regimen and TME remodeling function. D-Lipo efficiently inhibited the growth of the xenografted lung tumor. The anti-tumor mechanisms involved the repolarization of TAM from the M2 to M1 phenotype, anti-angiogenesis, and the consequent TME remodeling. As a result, the amounts of the anti-tumor M1 macrophages and the cytotoxic CD8+ T cells increased, while the amounts of the pro-tumor M2 macrophages and regulatory T cells (Tregs) reduced. It provides a promising avenue for epigenetic drug-based combination therapy for treating solid tumors.

Prophylactic or Preemptive Low-Dose Azacitidine (AZA) and Donor Lymphocyte Infusion (DLI) Prevent Disease Relapse Following Allogeneic Transplantation in High Risk Acute Myeloid Leukemia and Myelodysplastic Syndrome

Introduction: Despite therapeutic advances in recent years, disease relapse is still observed in up to 50-60% of the patients (pts) receiving allogeneic transplantation for high risk AML and MDS. In an initial Phase II trial of 30 pts treated with prophylactic low-dose AZA and escalated doses of DLI to prevent relapse, we reported that such prophylactic treatment can be safely administered and compared favorably to patients receiving no post-transplant maintenance. We here update 16 pts from our center, included in that protocol, as well as a larger cohort of additional patients treated with combined epigenetic and cellular therapy and the resultant effect on their event-free survival and their overall survival. Patients and methods: Fifty-nine pts (median age 59 yrs (range, 37-70); 30 M/29 F), comprising 40 pts with AML and 19 pts with MDS, were treated. Among the AML pts (ELN classification FAV n=2, INT n=17, ADV n=21), high risk criteria were as follows: 15 had complex karyotypes, 7 Flt3-ITD, 1 MECOM (EVI1) rearr., 3 monosomies, 2 t(9;11), and 1 t(11;19)); 9 were in CR≥2, 4 were refractory, and 13 had 2ary AML to MDS/chemotherapy/or MPS. Among the MDS pts, high risk criteria included 6 pts with complex caryotypes, 2 monosomies, 1 MECOM (EVI1) rearr., and 4 had 2ary MDS. IPSS-R median was 5.5 (3 - 7.5). MDS pre-transplant status included 7 CR1, 1 CR2, 5 PR, 1 relapse, 4 upfront, and 1 refractory. The therapeutic protocol administered to the initial 16 pts consisted of AZA, starting between d56 and d100 post-transplant, at a dose of 32 mg/m²/d SC, for 5 consecutive days, every 28 days, for up to a total of 12 cycles followed by DLI commencing after 3 cycles of AZA and 4 weeks following discontinuation of immunosuppressive prophylaxis. Two additional DLI were scheduled every 8 weeks following the 1st DLI. The doses of DLI 1, 2 and 3 were, respectively, 5x106, 1x107, and 5x107 CD3+ cells/kg for matched related donor (MRD), and 1x106, 5x106, and 1x107 CD3+ cells/kg for unrelated donor (UD). In the extended patient cohort, presented here, we slightly modified the schedule: DLI could be given earlier (after one or two cycles of AZA) and haploidentical pts could receive AZA/DLI as well, with DLI at the escalated doses of 1x105, 5x105, and 1x106 CD3+ cells/kg. Immunosuppression included cyclosporine A (CsA) in case of MRD, CsA and mycophenolate mofetil (MMF) in case of UD or haplo. MMF was progressively reduced during the first 2 months. CsA was tapered starting at day 60-100 post-transplant. Patients could start AZA while they were still receiving CsA. The conditioning regimens consisted of MAC for 5 pts, RIC for 46 pts and sequential for 8 pts. Donors were MRD, MUD, UD 9/10, and haplo for 20, 30, 1 and 8 pts respectively. Results: The median number of cycles AZA was 7 (range 1-12), 17 pts received 12 cycles of AZA, while 42 pts (71%) received at least one DLI. The median number of DLI was 1 (range 0-4), 15 pts received ≥ 3 DLI. The median time for the first post-transplant AZA injection was 83 days (range 56-145 d) and the median time post-transplant for those pts who received a first DLI was 148 days (range 78-245 d). The median pt-follow-up was 17 months (range 2-83). Eight pts (13%) relapsed (7 AML and 1 MDS). The cumulative incidence of relapse and NRM at 1 year was 12% and 11.5% respectively. Fifteen pts (25%) died. Causes of death included relapse in 6 pts, infection in 7 pts, myocardial infarction in 1 pt, and GvHD in 1 pt. Overall survival and event free survival for the entire group at 2 years was 71% (95% CI 54-82%) and 67% (95% CI 50-80%) respectively. The cumulative incidence of acute GvHD grade 1-4 and chronic GvHD were 32% (95% CI 16-49%) and 39% (95% CI 20-58%). Among the 8 pts who developed grade 3 acute GvHD, 4 occurred in pts who had received DLI. One pt died from grade 4 digestive GvHD post-AZA alone. Conclusion: We conclude that, despite their very high risk disease, prophylactic/preemptive low-dose AZA and DLI can be readily and safely administered with an acceptable incidence of subsequent GvHD to the AML and MDS pts described here. Significantly, in the poor-prognosis pts under study, the incidence of relapse is lower than expected. Furthermore, considering the immune escape mechanisms prophylactic or pre-emptive either AZA or DLI might be associated to additive non-cross reactive interventions, such as checkpoint inhibitors, in order to further decrease disease relapse and increase overall survival. Disclosures Peterlin: Jazz Pharma: Consultancy; Astellas: Consultancy; Daiichi-Sankyo: Consultancy; AbbVie Inc: Consultancy. Orvain:Novartis: Honoraria; Incyte: Honoraria. Chevallier:Jazz Pharmaceuticals: Honoraria; Daiichi Sankyo: Honoraria; Incyte: Consultancy, Honoraria.

The emerging role of epigenetic therapeutics in immuno-oncology.

The past decade has seen the emergence of immunotherapy as a prime approach to cancer treatment, revolutionizing the management of many types of cancer. Despite the promise of immunotherapy, most patients do not have a response or become resistant to treatment. Thus, identifying combinations that potentiate current immunotherapeutic approaches will be crucial. The combination of immune-checkpoint inhibition with epigenetic therapy is one such strategy that is being tested in clinical trials, encompassing a variety of cancer types. Studies have revealed key roles of epigenetic processes in regulating immune cell function and mediating antitumour immunity. These interactions make combined epigenetic therapy and immunotherapy an attractive approach to circumvent the limitations of immunotherapy alone. In this Review, we highlight the basic dynamic mechanisms underlying the synergy between immunotherapy and epigenetic therapies and detail current efforts to translate this knowledge into clinical benefit for patients.

The roles of DNA, RNA and histone methylation in ageing and cancer.

Chromatin is a macromolecular complex predominantly comprising DNA, histone proteins and RNA. The methylation of chromatin components is highly conserved as it helps coordinate the regulation of gene expression, DNA repair and DNA replication. Dynamic changes in chromatin methylation are essential for cell-fate determination and development. Consequently, inherited or acquired mutations in the major factors that regulate the methylation of DNA, RNA and/or histones are commonly observed in developmental disorders, ageing and cancer. This has provided the impetus for the clinical development of epigenetic therapies aimed at resetting the methylation imbalance observed in these disorders. In this Review, we discuss the cellular functions of chromatin methylation and focus on how this fundamental biological process is corrupted in cancer. We discuss methylation-based cancer therapies and provide a perspective on the emerging data from early-phase clinical trial therapies that target regulators of DNA and histone methylation. We also highlight promising therapeutic strategies, including monitoring chromatin methylation for diagnostic purposes and combination epigenetic therapy strategies that may improve immune surveillance in cancer and increase the efficacy of conventional and targeted anticancer drugs.