Epigenetic Therapies SPORE

The Epigenetic Therapies SPORE (or Specialized Program of Research Excellence) seeks to improve on current epigenetic therapies by exploring new targets, new ways of combining epigenetic therapy with other cancer therapies, and by designing and running clinical trials of these new strategies.

Epigenetic therapy aims to treat cancer by blocking enzymes that control regulation of abnormal cellular identity in cancer. In doing so, these therapies also make immunotherapies more effective. This is the first thematic SPORE supported by the National Cancer Institute to focus on epigenetic therapy. 

This SPORE is led by scientists at the Coriell Institute for Medical Research and Van Andel Institute with assistance from several collaborating institutions.

Over the past 20 years, in work led in part by investigators in this project, epigenetic changes were recognized as important drivers of cancer formation, progression and resistance to therapy. This recognition, along with the reversible nature of the biochemical modifications required for epigenetics led to the field of epigenetic therapy, which aims to reprogram gene expression to achieve a therapeutic effect.

This Epigenetic Therapies SPORE encompasses four major themes: Develop and test drugs against new epigenetic targets, mechanistic and translational studies of immunosensitization by epigenetic therapy, studies of drug combinations that enhance the efficacy of known epigenetic drugs, and biomarker studies to define sensitivity and resistance to epigenetic therapy in the clinic.

Research Projects

Jean-Pierre Issa, MD (Clinical Co-Leader)
Yi Zhang, PhD (Applied Co-Leader)

Epigenetic therapy aims to reprogram gene expression in cancer cells to achieve a therapeutic effect. To date, DNA methyltransferase (DNMT) inhibition (DNMTi) is the most effective form of epigenetic therapy, being particularly active in myeloid leukemias. Using a live cell assay to screen for drugs that achieve the same degree of epigenetic reprogramming as DNMTi, we discovered a new class of epigenetic drugs that activate silenced expression through inhibition of CDK9. Cyclin Dependent Kinases (CDKs) are of considerable clinical interest in cancer therapy and fall into two classes – cell cycle regulatory (e.g. CDK1,2,4,6 etc.) and transcriptional regulators (e.g. CDK7,9,12 etc.). Our new data place CDK9 at the heart of a node that regulates both gene silencing and activation. Targeting CDK9 has pleotropic effects on gene expression that appear ideal from an anti-tumor perspective: One observes simultaneous gene activation (of tumor suppressors), repression (of oncogenes), and induction of an interferon immune signature, which may be immunosensitizing for cancer therapy.

This project therefore aims to test the hypothesis that targeting CDKs leads to immunosensitizing epigenetic effects. We will confirm this hypothesis and test mechanisms and clinical/translational implications for cancer therapy in three aims: (i) Immunosensitization by CDK9 inhibition, in which we will study mechanisms and potential ways to enhance the effects; (ii) Epigenetic effects of CDKs, in which we will ask whether targeting CDK4,5,6 and 7 has similar epigenetic and immunosensitizing effects as targeting CDK9; and (iii) Preclinical studies and a clinical trial of combined CDK9 inhibition, DNMT inhibition and Immune checkpoint inhibition in AML and MDS, in which we will complete the necessary studies to bring CDK targeting as epigenetic therapy into the clinic, in combination with DNMT

Scott Rothbart, PhD (Basic Co-Leader)
Stephen Baylin, MD (Applied Co-Leader)

DNA methyltransferase inhibitors (DNMTi), such as the FDA-approved nucleoside analog 5-aza-2'-deoxycytidine (DAC), are currently the only available clinical drugs that can reverse abnormal DNA methylation in cancer cells and have emerged as a potential means to increase the efficacy of immunotherapy in cancer. However, the DNA de-methylation utility of these agents, particularly in solid tumors, does not attain the desired downstream transcriptional consequences seen in preclinical models. As such, novel therapeutic strategies to regulate DNMT activity are urgently needed and are directly addressed in this SPORE project.

Our preliminary data shows that several clinically applied EZH1/2 inhibitors block compensatory repressive activity of PRC2 at select tumor suppressor genes and repeat elements consequent to DNA methylation removal by DAC. Blocking this repressive “epigenetic switch,” which we propose is a key contributor to DNMTi resistance seen in patients treated with these drugs, may underlie an observed synergy of DNMTi+EZH1/2i to de-repress cancer-associated genic and intergenic transcriptional silencing.

Our overall goal is to define mechanisms of transcriptional synergy and immune crosstalk consequent to DNMTi+EZH1/2i and evaluate the clinical potential of this epigenetic therapeutic combination, alone, and as a primer to immunotherapy. To this end, we will (Aim 1) define cancer cell-intrinsic chromatin regulatory mechanisms and cellular pathways involved in the molecular and therapeutic effects of combined EZH1/2 and DNMT inhibition. Concurrently, we will (Aim 2) determine in mouse models of checkpoint therapy resistant disease, the antitumor effects of combined EZH1/2 and DNMT inhibition on cancer vs. immune cells and those dependent on interactions between the two. In addition, a proposed Phase 1 clinical trial, inclusive of extensive correlative science endpoints, will (Aim 3) validate the impact of combination EZH1/2 and DNMT inhibitor therapy on immune-response gene signaling circuits and the tumor microenvironment across multiple solid tumor types.

Impacts of our studies include: 1) defining exploitable mechanisms of molecular crosstalk associated with DNMTi therapy; 2) enabling effective clinical application of DNMTi+EZH1/2i therapy; 3) revealing correlative biomarkers to assess drug action in patient tumors; and 4) expanding opportunities for checkpoint and targeted immunotherapy combinations.

Kenneth Nephew, PhD (Basic Co-Leader)
Feyruz Rassool, PhD (Basic Co-Leader)
Kathy Miller, MD (Clinical Co-Leader)

PARP inhibitor (PARPi) resistance remains a clinical hurdle, with therapy limited to breast and ovarian cancer (OC) patients with BRCA mutations, and some activity seen in OC patients with intact BRCA. Our preclinical studies demonstrate that combining a hypomethylating agent (DNMT inhibitor) and the novel PARPi talazoparib inhibited tumor growth regardless of BRCA mutation status in both breast and OC by inducing STING-dependent inflammasome signaling that generates a BRCAness phenotype, synergistically causing cancer cell death. This led to a dose finding phase I clinical trial in TNBC funded by Pfizer and Astex.

The overall goal of this proposal is to expand the benefit of PARPi therapy to a larger group of patients and further dissect mechanisms of PARPi cytotoxicity and resistance. Our central hypothesis is epigenetic therapy-inducing inflammasome signaling generates BRCAness that enhances the efficacy of PARPi in BRCA-proficient TNBC and OC. We propose three aims. Aim 1: To test the hypothesis that combining DNMTi + PARPi generates STING-dependent IFN and inflammasome signaling leading to a BRCAness phenotype that increases anti-tumor immunity in the tumor microenvironment. We will conduct mechanistic studies of factors linking immune signaling to BRCAness phenotype, functional analysis of immune subsets in immune-competent mice treated with PARPi-DNMTi combination. Aim 2: To test the hypothesis that DNMTi in combination with PARPi activate reactive oxygen species (ROS)-mediated DNA damage leading to cell death in BRCA-proficient TNBC and OC. We will investigate how ROS generated by DNMTi-PARPi combination enhances DNA damage response (DDR) signaling, induces STING activation and enhances immune responses against TNBC and OC tumors using immune-competent mice. Aim 3: To assess the clinical activity of DNMTi-PARPi combination in TNBC and OC patients in phase I/II clinical trials.

After completing the ongoing phase 1, we propose a phase II study in two patient cohorts (one TNBC, one OC), serial tumor biopsies and circulating correlatives to test mechanistic hypotheses derived from our preclinical studies. Impact: Combining DNMTi-PARPi to induce STING-mediated immune signaling linked to induction of a BRCAness-HRD phenotype represents a potentially important therapeutic option for women diagnosed with TNBC and OC who lack BRCA mutations.

Shared Resource Cores

Led by Jaroslav Jelinek, MD, PhD

The Genomics, Epigenomics, and Bioinformatics Core will provide personnel, equipment, and expertise to support all projects of the Epigenetic Therapy SPORE.

This Core serves as a resource for design and execution of genomic and epigenomic experiments, data acquisition, quality control, bioinformatic analysis, data management, sharing and distribution. It closely cooperates with all SPORE projects and the Pathology/Biospecimen Core.

Project 1 studies immune-sensitization by inhibition of cyclin-dependent kinase CDK9. It will discover whether clinically targetable CDKs are also epigenetic regulators and conduct pre-clinical and clinical studies of combined epigenetic therapy and immunotherapy using CDK inhibitors, DNA methyltransferase (DNMT) inhibitors and immune checkpoint inhibitors. The Core will analyze (i) gene expression and chromatin accessibility in tumor and immune cells in preclinical models of tumors treated with CDK9 inhibitors, (ii) genome-wide effects of CDK4, 6 and 7 inhibition on DNA methylation and gene expression, and (iii) support preclinical studies and a clinical trial combining CDK9, DNMT and immune checkpoints inhibitors by the analysis of collected samples for transcriptomic and epigenetic parameters (gene expression and expression of endogenous retroviruses and repetitive elements by RNA-seq, DNA methylation by RRBS) and immune cell parameters (gene expression and markers of exhaustion in sorted T cells).

The Core will also perform whole exome sequencing (WES) to determine whether baseline DNA mutation and DNA methylation profiles predict response. Project 2 is focused on epigenetic synergy between inhibitors of DNMT and Polycomb repressive complex subunits EZH1/2 for therapy in solid tumors. The Core will analyze and integrate DNA methylation, ChIP-seq, RNA-seq and WES data to assess the combinatory effects of DNMT and EZH1/2 inhibitors and perform single-cell RNA-seq analysis of the tumor tissue to delineate tumor-associated immune populations. Project 3 combines induction of inflammasome signaling by hypomethylating agents with inhibitors of polyADP-ribosylation to induce death of cancer cells. The Core will assess genome-wide and LINE-1 repeat methylation. RNA-seq data will be analyzed for expression of ERVs and other repetitive elements in tumors and sorted immune cells.

Led by Scott Jewell, PhD

The Pathology/Biospecimen Core manages the collection of patient-derived biospecimens from blood, bone marrow and tissue (cancer and normal) as determined by the trial parameters often with collections occurring at pre- and post-treatment time points to meet the research aims of the Epigenetic Therapies SPORE projects.

The PBC Core provides collection materials, specimen labels, and manages shipments of biospecimens to VAI. The specimen derivatives are distributed to the locations for assay performance site including the SPORE’s Genomics, Epigenomics, and Bioinformatics Core and other collaborating project investigators.

Pathology-based histology assessment, DNA methylation EPIC BeadChip arrays and immunophenotype monitoring will be provided by the PBC Core. It also assesses and maintains excellent quality in the collection of biospecimens for use in the correlative science research that are used to determine efficacy, biological function and mechanistic details for the evaluation of the therapeutic treatments and scientific goals of the SPORE projects.

For Project 1, the Core will collect process and store peripheral blood and bone marrow samples related to a randomized study of MC180295+Atezolizumab, MC180295+DAC and MC180295+DAC+Atezolizumab in relapsed or refractory AML/MDS. Biospecimens collected will be managed by the PBC Core with nucleic acids being sent to the Genomics Core for assessment of epigenetic parameters. Immune cell parameters (cell numbers, gene expression in T-cells, T-cell exhaustion parameters) will be measured in the PBC Flow Cytometry Core. Approximately 600 data points will be assayed from this cohort.

For Project 2, the Core will collect samples from the clinical trial of combined DNMT and EZH1/2 inhibition that is planned to begin in year 2 with collection and management of peripheral blood and tumor biopsies pre and post therapy to assess epigenetic modulation and biomarkers (done in the Genomics Core) and Immune biomarkers (done in the PBC Core). Approximately 1,400 data points are expected from this cohort.

Project 3 will use the PBC Core resources to collect and manage pre and post therapy biospecimens and to provide specimen DNA and RNA derivatives to the Genomic Core for BRCAness gene expression, DNA methylation and global gene expression including ERVs. The PBC Core’s access to the VAI Flow Cytometry Core will provide immune monitoring and the PBC Core’s access to the VAI Genomics Core will provide the Methylation EPIC BeadChip array for evaluation. Approximately 640 to 800 specimens will be tested to meet the aims of this project. The Pathology and Biospecimen Core will provide access and distribution of project specimens to downstream assay sites, whether they are within the Core Technologies at VAI, the Genomics Core at Coriell, principal investigators laboratories or other approve investigators beyond the principal SPORE investigators.

Supported Programs

Jean-Pierre Issa, MD
Peter Jones, PhD

The goal of the Career Enhancement Program (CEP) is to provide training and guidance for academic physician scientists, clinician-investigators, and laboratory-based scientists who wish to dedicate their career and research efforts to translational cancer epigenetics research. To achieve this goal, the CEP will pursue the following specific aims:

  • Recruit, train, and mentor physicians, scientists, and senior postdoctoral fellows to become excellent investigators focused on cancer epigenetics translational research.
  • Educate awardees in all the basic principles of cancer epigenetics biology, including molecular, cellular and systems biology, drug development, pharmacokinetic and pharmacodynamics studies, and basic principles of biostatistics and bioinformatics.
  • Provide a firm foundation for awardees in the specific area of cancer epigenetics translational and early clinical research.

These objectives will be achieved through strong mentorship in which awardees will be instructed in the principles of clinical, basic, and translational cancer epigenetics research. Specific areas of education may include scientific and clinical methods, biomedical ethics, statistical design and analysis, bioinformatics, biology, biochemistry, genetics, epidemiology, and other areas relevant to individual projects. Mentorship will include laboratory-based investigators, clinical-translational investigators, biostatisticians, bioinformaticians and epidemiologists.

Jean-Pierre Issa, MD
Peter Jones, PhD

The specific objectives of the Developmental Research Program are to:

  • Publicize the availability of funds for pilot translational research studies in the field of Epigenetic Therapy for cancers.
  • Identify through this mechanism innovative projects with significant potential for developing and improving Epigenetic Therapies for cancers.
  • Encourage collaborations of projects with scientists within the SPORE and outside the SPORE, specifically the Van Andel Institute-Stand Up To Cancer Epigenetics Dream Team (VAI-SU2C).
  • Enhance the communication between the SPORE leaders and VAI-SU2C Investigators to encourage the development of innovative epigenetics therapies for cancer.
  • Ensure program flexibility so that developmental projects that show promise can be: 1) funded for a second year; 2) encouraged to apply for peer-reviewed funding (i.e. R01); or 3) expanded to become full SPORE projects.

To achieve our aims, we will establish specific criteria for selection and funding through a peer review mechanism, and mechanisms for close monitoring of, and collaboration between the SPORE leaders and program awardees to enhance the quality of the translational research goals.

Investigators & Staff