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Last Updated: 10/01/21

BWH-DF/HCC SPORE in Myeloid Malignancies

Dana-Farber Harvard Cancer Institute

Principal Investigator(s):

Benjamin Ebert, MD, PhD
Benjamin Ebert, MD, PhD

Richard Stone, MD
Richard Stone, MD

Principal Investigator(s) Contact Information

Benjamin Ebert, MD, PhD
Division of Hematology
Brigham and Women's Hospital
75 Francis Street, Karp 5.211
Boston, MA 02115
Tel: (617) 525-4968
Fax: (617) 525-4986

Richard Stone, MD
Harvard School of Medicine
Dana Farber Cancer Institute
Department of Medicine
44 Binney Street
Boston, MA 02115


The overall goal of this SPORE in Myeloid Malignancies is to take advantage of our increased understanding of the genetic and molecular basis of acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) to develop novel, effective therapeutic strategies for patients with these treatment-resistant neoplasms. The extensive scientific and clinical resources at the Dana-Farber/Harvard Cancer Center (DF/HCC) will be leveraged — marshaling local expertise in cell and molecular biology, genetics, immunology, biostatistics, chemistry, murine models, and clinical trial development — in order to perform innovative pre-clinical studies, to validate novel drug targets in patient cells, and to design and implement clinical trials that will eventually lead to improved outcomes for patients with myeloid malignancies. Each of the four Projects will promote detailed analysis of a promising new target by a combination of pre-clinical studies to optimize therapeutic development and early-stage clinical trials. Project 1 leverages recent exciting data from the laboratory of Dr. Scott Armstrong regarding the efficacy of targeting the MLL-menin interaction, which is essential for maintaining HOXA expression and maintenance of leukemia stem cells. Project 2 is based on the discovery by the Stegmaier laboratory that many cases of AML are dependent on SYK kinase activation, and that SYK activation causes chemotherapy resistance. Project 3 will examine the pre-clinical and clinical efficacy of a novel Sf3b1 inhibitor, using an Sf3b1-mutant model developed by the Ebert laboratory, for the treatment MDS. Project 4 will examine the potential synergy of a highly effective vaccine with a potent immunologic checkpoint inhibitor for the treatment of AML. The Cores have been designed to support all projects in translational research. The laboratory and clinical research components of each project will interface with Core 1 for statistical guidance in both experimental design and the interpretation of results. Core 2 will provide biospecimens banking for the samples produced by all projects in the course of clinical trials; these samples will be used for the generation of primagrafts in immunodeficient mice. Samples from the biospecimens bank as well as xenograft samples will, in turn, be available for use by the PI’s of all projects. Core 3 will work with the clinical trials in each project for correlative studies. Ultimately, the proposed studies promise to improve the therapy of chemotherapy-resistant AML and splicing factor-mutant MDS, as well as developing an improved immunotherapeutic strategy for AML.

Specific Aims:

  • To improve the outcome of patients with myeloid malignancies through innovative therapeutic approaches, including) and testing new agents directed at these pathways in innovative clinical trials.
  • To leverage the resources of the DF/HCC, including local expertise in SPORE administration, biostatistics; preclinical disease modeling; biospecimen acquisition, storage, and processing; and clinical research support, to assist in the translation from promising targets to clinical reality in AML, MDS, and MPN.
  • To foster novel translational initiatives in the myeloid leukemias, and promote the careers of talented young investigators interested in this field, by judiciously awarding career development and developmental research awards.

Project 1: Targeting MLL/Menin in AML

Project Co-leaders:
Scott Armstrong, MD, PhD (Basic Leader)
Richard Stone, MD (Clinical Leader)

Mutations that drive leukemia development frequently lead to over expression or rearrangement of genes encoding proteins that control gene expression. As a result, gene expression programs that direct normal hematopoietic development are corrupted leading to leukemia. Reversal of these aberrant gene expression programs and expression of transcription factors such as HOXA9/MEIS1, MYB, and MYC leads to leukemia cell differentiation and apoptosis suggesting that these approaches should be therapeutically beneficial. However, the mutations that drive aberrant expression rarely lead to direct activation of an enzyme, and thus targeting with small molecules has been challenging. Recent studies have shown that disrupting critical interactions of multiprotein complexes that control gene expression frequently through chromatin-based mechanisms can modulate expression of these critical genes. This has prompted a wave of small molecule development. Inhibitors of histone modifying complex components such as BET-Bromodomain inhibitors, DOT1L inhibitors, and LSD1 inhibitors have all entered phase I trials for patients with relapsed leukemia. Furthermore, inhibitors of the MLL1/Menin interaction (which is also critical for the maintenance of HOXA gene expression) are being developed and will likely enter clinical assessment in the next year. We propose studies that will provide a broader understanding of the importance of the MLL-Menin interaction and identify biomarker strategies that will be employed in early phase clinical trials that we will initiate. We will assess which types of leukemia might benefit from these newly developed approaches, and which combinations of small molecules should move forward to clinical assessment.

Specific Aims:

  • To assess MLL1/Menin inhibitors in murine models of AML including those with MLL-rearrangements and NPM1 mutations.
  • To identify mechanisms of resistance to MLL1/Menin inhibitors and potential combination approaches.
  • To perform a phase 1 clinical trial with biomarker assessment of MLL1/Menin inhibitors in relapsed/refractory AML

Project 2: Targeting SYK Kinase in AML

Project Co-Leaders:
Kimberly Stegmaier, MD (Basic Co-Leader)
Daniel J. DeAngelo, MD, PhD (Clinical Co-Leader)

While much progress has been made in understanding the pathogenesis of acute myeloid leukemia (AML) through the application of genetic and genomic approaches, clinical progress in treating this disease has lagged far behind. The backbone of treatment for most patients with AML still relies on the use of cytotoxic drugs that are several decades old. Through the application of integrative chemical and functional genomic approaches, we identified the target spleen tyrosine kinase (SYK) as a new dependency in AML. SYK is a cytoplasmic tyrosine kinase widely expressed in hematopoietic cells and critical in B cell differentiation and signal transduction pathways. We have determined that 1) SYK is a new target for promoting AML differentiation, 2) SYK is a critical regulator of FLT3, and 3) FLT3-ITD, one of the most common genetic abnormalities in AML, is a candidate biomarker of response to SYK inhibition. In this proposal, we will build upon our prior work to now translate SYK inhibitors to the clinic for patients with AMLwith the goals of identifying synergistic combinations of drugs with SYK inhibitors, both chemotherapy and targeted agents, and testing SYK inhibitors alone and in combination in patients with AML.

Specific Aims:

  • Test the hypothesis that SYK activation engenders resistance to chemotherapy.
  • Develop new drug combination strategies with SYK inhibitors in AML through the identification of resistance mechanisms.
  • Perform biomarker studies within the context of clinical trials of SYK inhibitor in patients with AML.

Project 3: Targeting SF3B1 for the treatment of MDS

Project Co-Leaders:
Benjamin Ebert, MD, PhD (Basic Leader Co-Leaders)
Andrew Brunner, MD (Clinical Leader Co-Leaders)

Somatic mutations in the core components of the pre-mRNA splicing complex, the spliceosome, are the most common genetic lesions in patients with myelodsyplastic syndromes (MDS). Specifically, recurrent missense mutations in the SF3B1 gene are present in 10-20% of all MDS cases. Inhibitors of SF3B1 have been developed and represent a promising new frontier for MDS therapy. We propose to develop pre-clinical models of Sf3b1 mutation, to test a novel SF3B1 inhibitor in these models, alone or in combination with azacitidine; and to perform correlative studies on a Phase I/II clinical trial of an SF3B1 inhibitor in collaboration with H3 Biomedicine. H3 Biomedicine has generated a compound, H3B 8800, that shows promising mutant-selective activity in cell lines and that is poised for clinical trials. The Ebert laboratory has developed a conditional knock-in mouse model that expresses the Sf3b1 K700E mutation, the most common mutation in MDS patients. Since SF3B1 mutations commonly co-occur with mutations in DNMT3A in MDS, we will create a model with both conditional Sf3b1 knock-in mutation and conditional Dnmt3a inactivation. We will test H3B 8800 in this model and will test the combination of H3B 8800 with azacitidine, a drug with efficacy in MDS and in TET2-mutated cases in particular. We will identify mechanisms of resistance to H3B 8800 using a genome-wide CRISPR-Cas9 screen. Finally, we will examine the safety and efficacy of H3B 8800 in MDS patients in a phase I/II clinical trial. This first-in-class agent has the potential for major clinical impact in a large fraction of MDS cases with aberrant spliceosome function due to somatic mutations. The studies described in this proposal will define the activity of the drug in different genetic backgrounds, examine the activity of the drug in hematopoietic stem and progenitor cells, identify mechanisms of therapy resistance as well as insights into the mode of action of the drug, and examine therapeutic efficacy in patients.

Specific Aims:

  • Develop pre-clinical models of Sf3b1 mutant MDS
  • Explore mechanisms of SF3B1 inhibitor sensitivity and resistance
  • Conduct phase I/II trial of an SF3B1 modulator in MDS and related myeloid neoplasms

Project 4: DC AML Fusion Cell Vaccination with Immune Checkpoint Blockade

Project Co-Leaders:
Gordon Freeman, PhD (Basic Leader)
David Avigan, MD (Clinical Leader)

We have developed a promising leukemia vaccine in which patient derived AML cells are fused with autologous dendritic cells (DCs), presenting a broad array of antigens that capture the heterogeneity of the leukemia cell population. We are completing a phase II clinical trial in which patients that achieve remission following chemotherapy undergo vaccination with DC/AML fusions. Remarkably, 71% of patients with a median age of 63 remain in remission with a median of over four years of follow up. Vaccination was associated with the dramatic expansion of T cells targeting both autologous AML cells and previously defined leukemia associated antigens. We hypothesize that DC/AML vaccination post- allogeneic transplant would elicit the durable expansion of leukemia specific T cells within the donor T cell repertoire to effectively protect against disease relapse. We postulated that vaccine response would be enhanced during donor lymphopoietic reconstitution due to the relative depletion of inhibitory cells and recovery of functionally competent donor cells. Hypomethylating agents (HMAs) have been shown to enhance immunogenicity of tumor cells via enhanced antigen presentation. We have demonstrated that exposure to a second generation HMA is associated with upregulation of antigen processing, increased expression of the PR1 leukemia associated antigen, decreased expansion of MDSCs, and downregulation of PDL1 expression. DC/AML fusions express high levels of PDL-1 offering a counter-regulatory signal that blunts vaccine mediated T cell activation. Notably, antibody mediated blockade of PDL1/PD1 has resulted in durable clinical responses in a subset of patients with advanced malignancies. The efficacy of antibodies targeting the PD-1/PDL-1 pathway as single agents is most pronounced in tumors characterized by a dense infiltrate of tumor infiltrating lymphocytes. In contrast, effective immunotherapy for AML likely requires a strategy to expand leukemia specific lymphocytes and reverse tumor mediated tolerance. Recent studies highlight the importance of additional checkpoint molecules including TIM3 and RGMb that act in concert with PD-1 to induce an exhausted phenotype in tumor reactive lymphocytes. Combined immune checkpoint blockade has the potential to act synergistically to overcome tolerance and enhance immune response to vaccination. In the present study, we will conduct a clinical trial in which AML patients with high risk features who undergo allogeneic transplantation in remission will undergo posttransplant vaccination with donor DC/AML fusions alone or in conjunction with HMA. The primary clinical endpoint is to assess vaccine associated toxicity including the impact on incidence of GVHD. The secondary clinical endpoint will be to examine the effect of vaccination on relapse-free survival. Immunologic response following post-transplant vaccination alone or with HMA will be assessed. In a preclinical murine leukemia model, we will assess the capacity of the second generation checkpoint inhibitors, RGMb and TIM3 alone and in combination with PD-1 blockade to augment response to DC/AML fusion vaccine.

Specific Aims:

  • To conduct a clinical trial in which AML patients with high risk features who undergo allogeneic transplantation in remission will undergo post-transplant vaccination with donor DC/AML fusions alone or in conjunction with HMA.
  • To assess the immunologic response following post-transplant vaccination alone or with HMA.
  • In a preclinical murine leukemia model, to assess the capacity of the second generation checkpoint inhibitors, RGMb and TIM3 alone and in combination with PD-1 blockade to augment response to DC/AML fusion vaccine.

Biostatistics Core

Core Director:
Donna Neuberg, ScD (Basic)

Biostatistics will provide all manner of statistical support to the four projects in this SPORE, to the Developmental Research Projects, and to the Career Enhancement Program. This will include, but is not limited to, assistance with study design, data collection plans, statistical analysis, interim and final reporting, abstract and paper preparation, and assembly of data for public posting.

Specific Aims:

  • To provide biostatistical collaboration for Projects, Developmental Research Program, and Cores in this SPORE, in order to assure that robust statistical methods support the clinical, correlative, preclinical and basic science of these efforts.
  • To provide biostatistical support and training to junior investigators through the Career Enhancement Program.

Biospecimens and Xenograft Core

Core Directors:
Jerome Ritz, MD (Basic)
David Weinstock, MD (Clinical)

The major goals of Core 2 are to provide the SPORE with the infrastructure and professional expertise needed to bank, characterize and distribute primary specimens and patient-derived xenograft(PDX) models. These will be prospectively collected from patients through established protocols developed by the Administrative Core (Core A), assayed using novel molecular biomarker tests by the Translational Core (Core 3) and serve as essential reagents for each of the Research Projects. Core 2 is jointly directed by Dr. Jerome Ritz and Dr. David Weinstock. Dr. Jerome Ritz has worked in leukemia and transplant research at DFCI for more than 30 years and has extensive experience in cell collection, processing, cryopreservation, flow cytometric analysis and purification, transplant immunology, and database development. Dr. Ritz is currently the Executive Director of the Connell O’Reilly Cell Manipulation Core Facility (CMCF) at DFCI. The Pasquarello Tissue Bank for Hematologic Malignancies was established as a unit of the CMCF in 2001 and will be responsible for processing, banking and distribution of primary myeloid malignancies for this SPORE. This resource has already acquired over 6,400 bone marrow samples from over 1,500 unique patients with myeloid leukemias that are available for use by SPORE investigators. Dr. Weinstock directs the DFCI Hematologic Malignancy PDX repository, which already contains >300 transplantable PDX models that have been viably cryopreserved and are available for SPORE investigators. Nearly 200 have already been fully characterized by whole transcriptome sequencing, DNA sequencing, immunophenotyping and other molecular assays, in collaboration with Core 3. Existing patient samples and PDX lines have already been shared with Project investigators to assay SYK inhibition (Project 2) and spliceosome alterations (Project 3). Experiments to target MLL/Menin (Project 1) are planned for the fall of 2016. The core has extensive experience distributing primary samples and PDXs, including an open-source website ( that has been utilized by >100 different laboratories on 4 continents. Moreover, the Core has extensive experience with utilizing primary patient specimens for in vitro assays and PDX models for in vivo pre-clinical trials of novel therapies.

Specific Aims:

  • To acquire primary samples from patients with myeloid malignancies enrolled in clinical research protocols and to isolate and preserve viable mononuclear cells, DNA and plasma.
  • To establish, characterize, and distribute xenograft models of myeloid malignancies and facilitate pre-clinical trials in collaboration with the Projects.3. To maintain annotated databases containing pathologic, cytogenetic and molecular information for clinical samples and xenografts obtained from patients with myeloid malignancies.

Correlative Science Core

Core Directors:
Jon Aster, MD, PhD (Basic)
David A. Williams, MD (Clinical)

The major goals of Core 3 are to provide the SPORE with the infrastructure and professional expertise needed to develop, validate, and implement molecular biomarker tests on patient samples and xenografted human leukemias. These tests will be used to characterize the response of myeloid neoplasms obtained from patients and preclinical models to targeted therapies being tested in each of the projects. The Core is led by Dr. Jon C. Aster, a senior leukemia investigator and practicing hematopathologist. Tests will be carried out in the Core will include assays that gauge NPM1 and DNMT3A mutational status (Project 1), SYK activation (Project 2), mutational status of genes encoding spliceasome components and SF3B1 inhibition (Project 3), and the expression of immune checkpoint proteins (Project 4). The Core will also perform serial NextGen Sequencing to determine the effect of targeted therapy on clonal dynamics, and develop new tests that assess the sensitivity of tumor cells to apoptosis (BH3 profiling/mitochondrial priming), or that predict and gauge the response of neoplastic cells to SYK inhibitors, Menin/MLL inhibitors, and other targeted therapeutics.

Specific Aims:

  • To use a clinically validated amplicon-based NextGen sequencing test to identify mutations, define clonal heterogeneity, and follow the clonal evolution of myeloid neoplasms during therapy
  • To develop, validate, and implement tests for phospho-SYK, immune checkpoint proteins, lineage specific host immune cell markers, and other protein biomarkers
  • To develop, validate, and implement RNA profiling-based tests that identify signatures of effective targeting of leukemogenic signaling pathways with novel therapeutic agents, including spliceosome inhibitors, and Menin/MLL inhibitors
  • To develop, validate, and implement a BH3 profiling/mitochondrial priming assay to predict the response of myeloid neoplasms to targeted therapeutics

Administrative Core

Core Directors:
Benjamin Ebert, MD, PhD
Richard Stone, MD

The administrative core will monitor the progress of the entire SPORE. This will include oversight of the projects and cores. The SPORE director will be responsible, in conjunction with the governance committee for promotion of developmental projects into translational projects and/or terminate a translational project if required. The Core will facilitate the interchange of research information between SPOREs within the DF/HCC, guide collaboration and retreats with other leukemia SPOREs, and disseminate information about the Clinical Development Awards and Developmental Research Projects within the SPORE itself.

Specific Aims:

  • To monitor research projects and Cores and plan for the future;
  • To foster collaborative research within the SPORE and between SPOREs;
  • To integrate the SPORE in Myeloid Leukemias into the DF/HCC structure;
  • To provide necessary resources for fiscal oversight; and 5) to promote rapid dissemination of significant research findings.

Developmental Research Program

Program Directors:
Benjamin Ebert, MD, PhD
Richard Stone, MD

The objectives of the Developmental Research Projects Program are to provide a continuous flow of new ideas and projects to stimulate myeloid leukemia research in the context of the DF/HCC SPORE in Myeloid Malignancies. The Developmental Research Program (DRP) will encourage new research directions and help to facilitate collaborations. It will provide initial support to pilot projects, and thus will foster the development of new translational projects, an important goal given the circuitous path to clinical development of agents that might be effective in myeloid malignancies. It will provide the opportunity for the DF/HCC Spore in Myeloid Malignancies to recruit new investigators with a diverse range of backgrounds and institutional affiliations. An important aspect of the DRP will be a wide announcement of access to these funds. The program will solicit applications on the web and by frequent email announcements to quality projects with a high likelihood of translational impact.

Specific Aims:

  • Solicit applications and/or identifying novel research projects in myeloid malignancies
  • Evaluate these projects for funding,
  • Fund the most innovative developmental projects,
  • Re-evaluate projects for possible transition into full project status
  • Evaluate success of the program.

Career Enhancement Program

Program Director:
Timothy A. Graubert, MD

The goal of the Career Enhancement Program (CEP) for the SPORE in Myeloid Leukemia is to increase the number of investigators engaged in translational leukemia research. The CEP will solicit applications from advanced fellows, junior faculty, and established investigators new to translational leukemia research and select the most promising candidates. We will provide funding for mentored translational leukemia research and leverage additional institutional resources to prepare trainees for careers as independent investigators. The CEP will actively seek participation of individuals that are under-represented in medicine. The participating SPORE institutions have a large pool of highly qualified candidates for the CEP and skilled faculty with established track records in mentorship across a diverse range of disciplines in translational leukemia research. The CEP has the following Specific Aims: 1) We will recruit new investigators to the field of translational leukemia research, 2) We will provide support for mentored translational leukemia research, and 3) We will monitor the performance and refine the CEP to optimize the training of new investigators in translational leukemia research.

Specific Aims:

  • We will recruit new investigators to the field of translational leukemia research.
  • We will provide support for mentored translational leukemia research.
  • We will monitor the performance and refine the CEP to optimize the training of new investigators in translational leukemia research.

Institutional SPORE Website