Grant: 6548-18 | Translational Research Program (TRP):
Location:Dana-Farber Cancer Institute, Boston, Massachusetts 02215
Project Title: Development Of Histone Lysine Demethylase KDM3A Inhibitors For Multiple Myeloma TherapyProject Summary:
Cancer arises from a series of mutations in the DNA sequence that either activate (turn on) genes that allow cells to grow uncontrollably, or silence (turn off) genes that would normally tell a cell to die if it acquires DNA mutations. However, recent evidence suggests that some cancers inappropriately activate or silence genes through a different mechanism, called epigenetics. Epigenetics refers to chemical modifications to DNA and histone proteins that control gene activity without causing mutations in the DNA sequence. Recently, we found that one such epigenetic regulator, KDM3A, is overexpressed in multiple myeloma (MM). Biological investigation into the role of KDM3A in MM reveals that it directly regulates multiple other genes required for cancer cell survival, acting as a master regulator. Knockdown of the KDM3A protein in MM cells induces cell death and reduces tumor size in mouse models of MM. Likewise, knockdown of KDM3A reduces cancer cell interaction with the bone marrow, which is required for MM cell survival. Together, these findings suggest that KDM3A may be a novel therapeutic target for the treatment of MM, a disease that remains incurable.
Here, we propose to develop small molecule inhibitors of KDM3A in order to validate inhibition of KDM3A as a therapeutic opportunity in MM. We have developed an integrated chemical biology approach 1) to chemically synthesize and screen for novel KDM3A inhibitors, 2) to optimize inhibitors for drug activity and selectivity (on target effects) in cells and in animals, and 3) to validate KDM3A as a therapeutic target in cell and animal models of MM. Overall, the goal of this research is to develop small molecule inhibitors of KDM3A and to utilize them to gain a better understanding of how KDM3A drives MM biology, and to fully evaluate the therapeutic potential of KDM3A inhibition in MM. Thus, we have assembled scientists with multi-disciplinary expertise ranged from chemistry, medicinal chemistry, chemical biology and biology to achieve the goal proposed in this research. We envisioned that this research will provide the preclinical rationale to prompt clinical investigation of KDM3A inhibitors for MM which affects ~30,000 new patients a year. The identified small molecule inhibitors developed here will be further optimized for therapeutic use to improve patient outcome in MM.
Grant: R0858-18 | Quest for CURES (QFC):
Location:University of Miami, Atlanta, Georgia 30384-5803
Project Title: The Aging Epigenome: Clues To The Pathogenesis Of MDSProject Summary:
Myelodysplastic syndromes (MDS) are diseases of the blood-producing cells in the bone marrow (BM) with a high risk for progression to an aggressive acute leukemia. While rare before the age of 50, its incidence increases significantly with every decade of age and thus it is likely that age-acquired changes in the BM may predispose to the development of MDS. However, the mechanism behind this increased incidence is not fully understood. We propose that as we age, cells in the bone marrow accumulate changes in the nuclear instructions that govern their behavior. These instructions are encoded not only on their genetic material (known as DNA), but also on a series of chemical modifications of the cell’s genetic material known as epigenetic modifications. These epigenetic modifications are what give cells the ability to “interpret” the information on the genetic code. Therefore, any abnormalities acquired at the epigenetic level can have serious consequences on a cell’s behavior. We hypothesize that cumulative changes in the epigenetic information of BM cells acquired during aging change the cells' behavior and susceptibility to other lesions, laying the foundation for the increased incidence of MDS. We will study the normal changes acquired during aging at both the genetic and epigenetic levels and compare them to the disease-associated patterns seen in MDS in order to identify those epigenetic changes that may predispose for the development of this disorder.
Grant: 3372-18 | Career Development Program (CDP):
Location:The Trustees of Columbia University in the City of New York, Columbia University Medical Center, New York, New York 10027
Project Title: The Role Of Diverse Cytokines Secreted By Myeloid-biased Multipotent Progenitors In Driving LeukemiaProject Summary:
Myelogenous leukemia is a type of blood cancer characterized by the abnormal production of white blood cells in the bone marrow. Abnormally produced white blood cells prevent the proper production of healthy blood cells and eventually lead to failure of the healthy blood system. There are several well-known disease-causing mutations, and many researchers are studying them to find out how the mutations cause disease and to develop treatments based on the targeting of those mutations. However, many cancers are characterized by the accumulation of several mutations, and targeting only one specific mutation is not the most efficient way to treat the disease. Therefore, my study aims to find a treatment that is applicable to a broad range of myelogenous leukemias and is not associated with an individual mutation. In a previous study, we identified a specific immature bone marrow cell population whose expansion is common throughout various myelogenous leukemia mouse models with variant disease-causing mutations. This indicates that expansion of this cell population may reflect the commonalities of the various myelogenous leukemia subgroups and suggests that this cell population is also a critical driver of disease progression in various subgroups. We also discovered ways to experimentally regulate the production of that specific population, which may provide potential therapeutic opportunities. Currently, I study the cellular characteristics of that cell population, with the long-term goal of understanding how expansion of these cells contributes to disease development. More specifically, I will focus on a protein secreted by that population, and I will investigate the function of the secreted protein in driving overproduction of abnormal white blood cells. To achieve my goals, I will use diverse experimental methods using cells isolated from mice as well as several mouse models. My study will provide insight into a mechanism common to the development of various forms of myelogenous leukemia and may contribute to the development broadly applicable therapeutic treatments.
Grant: 5466-18 | Career Development Program (CDP):
Location:The Wistar Institute, Philadelphia, Pennsylvania 19104
Project Title: The Role Of EBNA1 In Epigenetic Regulation Of Gene Expression And EBV LatencyProject Summary:
Epstein-Barr virus (EBV) is a human tumor virus responsible for over 200,000 cancers per year, including multiple blood cancers such as Burkitt’s lymphoma, Hodgkin’s lymphoma, and NK/T cell lymphoma. Like all herpesviruses, EBV can develop a long-term, largely dormant phase called latency, with only occasional reactivation (called the lytic phase). Unlike most other viruses,however, EBV-associated pathogenesis depends on viral latency, rather than an active, lytic infection. During latency, only a handful of viral proteins are expressed, and among these only EBV nuclear antigen (EBNA)-1 is expressed across all forms of EBV-associated cancers. Although it is known that EBNA1 plays a central role in regulating both viral and host gene expression, the mechanisms associated with this regulation remain incompletely understood. Interestingly,epigenetic regulation, or mechanisms of altering gene expression beyond changes to the genetic code, has been shown to play a significant role in cancer development and plays a role in maintaining EBV latency. While EBNA1 is vital in establishing EBV latency and maintaining the latent viral genome, the role that EBNA1 plays in regulating host gene expression and cancer cell development remains unclear. To better understand EBNA1, we will use various approaches to investigate the role of EBNA1 in regulating gene expression on an epigenetic level, where the proteins bound to DNA are modified. We have previously demonstrated that EBNA1 is a direct regulator of genes involved in cell proliferation and survival, and our current studies will expand our knowledge of the mechanism of this regulation and the identification of additional direct targets of EBNA1. A better understanding of EBNA1-mediated gene regulation will give us the opportunity to investigate new mechanisms for inhibiting the function of EBNA1 and validate the potential of EBNA1 as a therapeutic target.
Grant: 3377-18 | Career Development Program (CDP):
Location:Sloan Kettering Institute for Cancer Research, New York, New York 10087
Project Title: Understanding The Effects Of Leukemia-Associated Mutations In Spliceosomal Proteins On Chromatin StateProject Summary:
In the past few years, genetic analysis of leukemias has identified frequent mutations in a class of genes that encodes for proteins participating in a process called RNA splicing. Mutations in RNA splicing factors are now known to be the most common type of mutation in patients with myelodysplastic syndromes (MDS) and related myeloid leukemias as well as chronic lymphocytic leukemia (CLL). These discoveries have resulted in intense efforts to understand how mutations in RNA splicing factors promote the development of leukemia.
RNA splicing is the process whereby genetic information is read from DNA and used to make proteins. Currently, most efforts to study RNA splicing factor mutations have focused on the effects these mutations have on the process of RNA splicing itself. RNA splicing factors, however, are known to play additional roles not directly related to splicing. In accordance with this, we have identified a unique effect of RNA splicing factor mutations on the epigenome. The epigenome refers to chemical changes on chromatin, which are structures in the cell made up of DNA and the proteins surrounding DNA. These chemical changes regulate which genes are expressed from DNA and when they can be turned on and turned off. Based on our preliminary results, we believe that one of the main ways that RNA splicing factor mutations cause leukemia is by altering the epigenome. We have shown that one of the most commonly mutated splicing genes, SF3B1, produces a protein that binds to some parts of chromatin. However, the extent of this binding to different chromatin components and the role that this binding plays in altering the epigenome needs clarification. We are now studying this relationship between RNA splicing factor mutations and the epigenome in more precise detail. Our longer term goal is to utilize this information to develop new therapeutic approaches for leukemia cells carrying RNA splicing factor mutations.
Grant: 1347-18 | Career Development Program (CDP):
Location:Sloan Kettering Institute for Cancer Research, New York, New York 10087
Project Title: Uncovering The Dysregulated RNA Binding Protein Network In Normal And Malignant HematopoiesisProject Summary:
Although molecular targeted therapy has dramatically changed how we treat cancer, the treatment for acute myeloid leukemia (AML) remains focused on the use of cytotoxic drugs with many patients eventually relapsing with their disease. One of the major drivers of resistance is the persistence of cells that retain the immature properties of stem cells. Cancer cells are made up of proteins expressed by the genes in the nucleus of the cell. Many RNA molecules comprise the information that is the intermediary between genes and proteins. An emerging focus of study is how these RNA molecules may be involved in disease processes. Our laboratory and others have identified that there are specific RNA binding proteins that regulate gene expression programs that are essential for the survival and immature state of acute myeloid leukemia cells. This network of RNA binding proteins is engaged in the most aggressive leukemias and predicts a poor outcome. We developed a screening strategy to identify other RNA binding proteins that contribute to the leukemic state. Using this novel approach, we identified an RNA binding protein called SYNCRIP that we found to be critical for myeloid leukemia and the response of leukemia patients to therapy. Our studies will further explore SYNCRIP’s role in genetic mouse models,human leukemia cell lines, and primary AML patient samples. We plan to understand the mechanism for the regulation of the dysregulated RNA binding protein network in leukemia and to develop therapeutic strategies for treating this aggressive and devastating disease.
Grant: 6551-18 | Translational Research Program (TRP):
Location:The Board of Regents of the University of Wisconsin System, Madison, Wisconsin 53715-1218
Project Title: Matrix Remodeling In The Myeloma Niche: Implications For Minimal Residual Disease And ImmunotherapyProject Summary:
Despite a revolution in the way we treat myeloma in the last 10-15 years, the disease remains incurable for the vast majority of patients. We have devised powerful novel agents and strategies that kill myeloma cells efficiently, yet not at 100%. Some residual cells remain even after the best of treatments and act as the “seed” from which the disease relapses and ultimately claims human lives. In the last 4-5 years, we have become much better at measuring this “minimal residual disease”. Ultimately however, we should not only recognize and size the enemy, we should eliminate it. The burning question therefore becomes: how are these remaining cells protected and shielded from harm? What is the best way to go after them?
We believe that the best strategy against residual myeloma cells is to mobilize the immune system to attack them. This is called “immunotherapy”. Immunotherapy can be a powerful weapon against cancers because it is endowed with inherent specificity and “memory” (in a manner illustrated by how vaccines work): once the immune system recognizes the tumor as foreign and undesirable, it can keep it in check for long time- hopefully, for ever. However, only a small number of patients have so far benefited from cutting-edge immunotherapies that have seen the front page of the New York Times. Part of the reason is that tumors are very capable at putting up bulwarks that fend off the immune system’s “killer” cells. New immunotherapies, such as drugs called “checkpoint inhibitors” work to remove the “brakes” from the immune killer cells. Still, they do not work for all patients.
Our approach is to “breach the bulwarks” that tumors put up to ward off the immune-killer cells. Once the defenses are gone, immunotherapy-mobilized killer cells have a better chance to work. We recently found that a component of the bone marrow environment in which myeloma cells and immune cells interact with each other is a “double-agent”. The “double-agent” is a bone marrow matrix component called versican. In its intact form, versican helps the myeloma tumor cells by neutering the immune system. However, in many cases, a bit from versican’s end (called “versikine”) gets broken off by specialized enzymes, called ADAMTS proteases. Versikine then stimulates the immune system to fight myeloma cancer cells. In other words, versikine (the “daughter” molecule) antagonizes versican (the “mother” molecule). The current proposal aims to investigate the role of versican and versikine in mobilizing the immune system to attack myeloma cells. Tipping the versican-versikine balance may provide powerful marching orders to anti-myeloma immune fighter cells.
Grant: 6528-18 | Translational Research Program (TRP):
Location:Board of Trustees of the Leland Stanford Junior University, San Francisco, California 94144-4253
Project Title: Identifying Relapse Associated Populations At Diagnosis In LeukemiaProject Summary:
Despite high rates of initial response to frontline treatment in many human cancers, mortality largely results from relapse or metastasis. Diverse clinical outcomes occur because all cells within a given tumor do not possess the same behavior or response to therapy. Although there is debate as to whether resistant populations of cancer cells are present at the time of initial diagnosis or whether these traits develop under the pressure of therapy, many studies have suggested that it is the former. Remission, by definition, is the reduction of cancer cells to undetectable levels. Consequently, if cellular populations predictive of relapse exist at diagnosis, it is reasonable to assume that these cells are a minority of the bulk tumor cells. In order to uncover these key populations, it is required to study cancer at the single cell level. Following this reasoning, we propose to perform analysis of primary leukemia cells at diagnosis by examining over 40 proteins on individual cells from patients with B-cell progenitor acute lymphoblastic leukemia (BCP-ALL), the most common leukemia of childhood. The goal of this research is to identify cells associated with relapse at the time of diagnosis. By identifying such populations, we may begin to understand how these cells survive treatment and cause later relapse. In order to organize diverse single-cell data from many primary patient samples, we will use a tool to match each leukemia cell to it's most similar healthy B-cell population. This allows us to compare leukemia cell subsets across patients.
We have optimized this approach in an early study and have identified specific populations of immature B-cells present at diagnosis which are predictive of relapse by applying advanced computational approaches to this single-cell data. This letter of intent outlines a proposal to extend our initial studies using this approach to validate the proposed cellular population which confers relapse risk and to understand how these cells are treatment resistant. To do so, we propose the following efforts:
1. Validate our relapse prediction model in a large cohort of pediatric patient samples and determine if the same cells exist in adult B-cell progenitor acute lymphoblastic leukemia (BCP-ALL) diagnostic samples
2. Determine if primary treatment-resistant cells, taken from patients early in therapy, are similar to the cells we have identified to be predictive of relapse
3. Determine if treatment resistant cells are better suited to grow in commonly used models of BCP-ALL
This proposal presents a novel approach to bring single-cell studies combined with advanced computational approaches to improve outcomes for patients with BCP-ALL.
Grant: 6556-18 | Translational Research Program (TRP):
Location:Dana-Farber Cancer Institute, Boston, Massachusetts 02215
Project Title: Interaction Of RUNX1 And The Cohesin Complex In Megakaryocyte Development And Myeloid DiseaseProject Summary:
Inherited mutations in the RUNX1 gene cause abnormal platelets and a predisposition to the development of acute myeloid leukemia. Similarly, patients with RUNX1 mutations that are acquired during adult life have an analogous platelet abnormality and predisposition to acute myeloid leukemia. In order for patients with RUNX1 mutations to progress to acute leukemia, additional mutations need to be acquired. We have found that mutations in the STAG2 gene can cooperate with RUNX1 mutations, likely leading both to the development of worsening platelet abnormalities and progression to overt malignancy.
Our goals are to answer two questions: (1) Does loss of RUNX1 and STAG2 lead to abnormal platelet precursor cell formation, with resultant platelet dysfunction and increased risk of bleeding? If so, we would like to pro-actively identify these patients so that appropriate measures can be taken to mitigate their risk of bleeding, particularly when undergoing diagnostic procedures. (2) Can we model abnormal platelet precursor cell function and AML disease progression in human and mouse bone marrow stem and progenitor cells? If so, this would provide functional evidence that loss of normal function of STAG2 and RUNX1 leads to abnormal platelet precursor cell formation and/or development of leukemia. In addition, these models would facilitate studies of novel therapeutic agents, which are desperately needed for this patient population.
Treatment options for patients with RUNX1 mutations are limited, and better understanding of the mechanisms by which leukemia causing genes contribute to leukemia development in patients will inform the design of urgently needed new treatments. We propose to develop models and investigate therapeutic approaches that have the potential to benefit individuals with RUNX1 mutations.
Grant: R0859-18 | Quest for CURES (QFC):
Location:Joan & Sanford I. Weill Medical College of Cornell University, New York, New York 10022
Project Title: Targeting Of The Senescent Vascular Niche To Treat Age-related Hematopoietic Malignancies.Project Summary:
Physiological aging directly leads to a multitude of age-related diseases, including cardiovascular disease, arthritis and cancer, that affect nearly all systems of the body. The goal of this proposal is to identify alterations in the aged bone marrow vascular system that initiate and facilitate the progression of hematopoietic malignancies. We have demonstrated that vascular cells are a critical component of the bone marrow microenvironment and support the overall health and fitness of blood stem cells. Preliminary data generated in our laboratory demonstrated that the vascular system is altered during the aging process, resulting in the premature aging and a decrease in functionality of the blood stem cells. In order to address whether the aging process promotes hematopoietic malignancies by dysregulating the bone marrow vascular system, we have developed a means to isolate and transplant bone marrow vascular cells to aid in the rejuvenation of the aged bone marrow microenvironment. Utilizing our protocols, we will be able to screen for altered factors produced by aged vascular cells that promote the aggressiveness and elusiveness of leukemic cells. Overall, our laboratory is aiming to design novel therapeutic strategies to be used as an effective means to reduce the morbidity and mortality associated with chemotherapy and radiological regimens used to treat a wide range of aged-related malignancies.