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: 2318-18 | Career Development Program (CDP):
Location:Charlotte Mecklenburg Hospital Authority d/b/a Carolinas HealthCare System, Charlotte, North Carolina 28203
Project Title: Optimizing Risk And Response Adaptive Strategies Using Immunotherapy In Multiple MyelomaProject Summary:
Despite the more than three-fold improvement in survival outcomes over the last 15 years, multiple myeloma (MM) remains an incurable disease. There is growing recognition that MM disease biology is complex and that personalized treatment strategies need to be developed for different MM patients. However, the current MM treatment paradigm is largely based on a patient’s eligibility for a stem cell transplant. Thus, an incredibly heterogeneous disease is being treated in a ‘one-size-fits-all’ way that translates into broad variability in patient outcomes. As anti-myeloma therapeutics continue to expand, it is becoming more crucial to personalize treatment approaches to provide the most value to each individual patient. In addition, it is imperative to complement clinical trials with development of prognostic and predictive biomarkers. Prognostic biomarkers provide the likely natural course of MM in an untreated patient, while predictive biomarkers identify the subpopulation of patients who have better outcomes with specific treatment strategies. Over the last decade, researchers have explored new prognostic biomarkers, such as imaging (PET-CT) as well as assays that test for minimal residual disease (MRD), which is the small number of tumor cells that may remain after treatment. However, their utility as predictive biomarkers is not well established. The overarching aim of this proposal is to investigate risk- and response-adaptive clinical trial strategies for newly diagnosed MM while exploring the predictive role of these biomarkers.
We will apply this approach in three clinical trials for newly diagnosed MM. The first two trials compare various combinations of immunotherapeutic agents with current regimens. The first trial examines MRD assays and PET-CT as predictive biomarkers. The second trial assesses MRD to determine the need for transplant and maintenance. The third trial examines the effectiveness of the immunotherapeutic antibody Daratumumab in clearing the bone marrow of residual tumor cells before stem cell collection and transplant in MM patients having a less than ideal response to induction chemotherapy. Together, these studies may provide new therapeutic approaches and improve MRD assessment to better understand a patient’s response. These practice-changing strategies will help move the MM field towards personalized care.
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.
Grant: 5460-18 | Career Development Program (CDP):
Location:Sloan Kettering Institute for Cancer Research, New York, New York 10087
Project Title: Defining The Molecular Determinants Of Cysteine Acquisition And Redox Homeostasis In B Cell LymphomaProject Summary:
A key feature of blood cancer cells is the adaptation of their internal cellular metabolism to support nutrient utilization for continuous cell proliferation. Excessive nutrient consumption results in increased levels of reactive oxygen species (ROS). Since increased ROS levels are toxic, there must be countermeasures in place in order for the tumor cell to survive. It is therefore critical for these cancer cells to increase antioxidant capacity in order to overcome the oxidative stress caused by ROS during cancer progression. My research is designed to provide novel insights into the metabolic basis of how cancer cells regulate oxidative stress to maintain an appropriate equilibrium for their own survival. This process of maintaining equilibrium is called “redox homeostasis.”
My preliminary results suggest that two mechanisms function to maintain redox balance in cancer cells and that most cancer cells are committed to one or the other mechanism. It is thought that many blood cancer cells preferentially depend only on the mechanism that creates the amino acid cysteine by modifying another amino acid, which then is converted into the ROS scavenger glutathione. My research will employ metabolic analysis and biochemical approaches to investigate the molecular basis of redox controls and apply various cellular assays to evaluate the functional significance of these controls. My research may reveal critical knowledge of how blood cancer cells maintain redox homeostasis and may also contribute to advances in the clinical treatment of these cancers. Pharmacological inhibitors are currently available to target the metabolic pathway that supports redox balance in blood cancer cells. These chemicals may be adapted and tested for clinical use. Furthermore, the proposed mechanism reveals the metabolic vulnerability of these cancer cells. Therefore, a specific diet may be applied clinically, alone or in combination with standard chemotherapeutics, which may lead to better outcomes for some blood cancer patients.
Grant: 1350-18 | Career Development Program (CDP):
Location:Brigham and Women’s Hospital, Boston, Massachusetts 02241-3149
Project Title: Enhancing The Clonal Selectivity Of Current Drug Therapies In Myeloproliferative NeoplasmsProject Summary:
The objective of my proposal is to develop better treatments for patients with a group of blood cancers called myeloproliferative neoplasms (MPN). There are currently no curative treatment options for MPN apart from stem cell transplantation, which is a high-risk and sometimes life-threatening procedure.
None of the currently available drug treatments for MPN can cure the disease. They can only improve the symptoms. In 2011, the Food and Drug Administration approved a new type of drug treatment for MPN, called JAK2 inhibitors. With the approval of JAK2 inhibitors, MPN patients and their doctors had high hopes that these drugs would have the ability to change the course of MPN, rather than just control symptoms. Unfortunately, JAK2 inhibitors have disappointed in this regard, and although useful at controlling MPN-related symptoms, they cannot eradicate the disease or prevent it from turning into leukemia. In view of this, we are asking the following questions: (1) Why are JAK2 inhibitors not as effective in the treatment of MPN as was initially hoped? (2) What are the mechanisms by which MPN patients are resistant to JAK2 inhibitors? (3) What novel drug targets, if also inhibited, could make JAK2 inhibitors more effective?
We propose to identify (i) the genes that confer resistance to JAK2 inhibitors and (ii) the genes that when inhibited increase the efficacy of JAK2 inhibitors. We plan to do this using a new technology called CRISPR gene editing. With this powerful technique we can target every gene in the human genome in a completely unbiased fashion to identify the genes that underlie JAK2 inhibitor treatment failure. The goal of this work is to identify the “Achilles heel” in MPN cells treated with JAK2 inhibitors and to target this to eradicate MPN. The benefits are the development of potentially curative treatments for MPN. This study will significantly advance the field of blood cancer research through the development of personalized anti-cancer treatment approaches (i.e. precision medicine) and improve the treatment options for MPN patients.
Grant: 3370-18 | Career Development Program (CDP):
Location:Boston Children's Hospital, Boston, Massachusetts 02241-4413
Project Title: Mechanisms Of Orientation-specific RAG Activity In Mediating V(D)J Recombination And Promoting B Cell LymphomaProject Summary:
A properly functioning human immune system recognizes disease-causing pathogens via a diverse set of antibodies and T cell receptors (TCRs). These molecules, expressed in a subset of white blood cells termed B and T lymphocytes, can bind pathogens and initiate an immune response. The enormous diversity of antibodies and TCRs is generated by the development of lymphoid cells through a DNA “cut-and-paste” process termed V(D)J recombination. The genes encoding the components of the antibodies and TCRs are diversified by the “cutting” and “pasting” of different segments (V, D, and J). The cutting of these gene segments is executed by an enzyme called RAG. Though DNA breaks are required for normal immune development, they can be improperly joined to other DNA breaks across the genome to create mutagenic events that contribute to the development of cancer.
Restricting V(D)J recombination to specific chromosomal loops is critical to prevent RAG from escaping and breaking non-intended targets. Genes are contained in larger structures called chromosomes, which are organized within the cell in a series of large chromosomal loops. Chromosome-bound RAG moves directionally, like a train on a track, to locate its target gene cassettes and only stops when it encounters the roadblocks formed by the loop boundaries. We are studying the nature of the engine that moves RAG along the tracks and how normal RAG "tracking" generates diverse antibody repertoires and minimizes potential collateral damage that could lead to blood cancers. We will use genetically engineered cell lines and mouse models to investigate this process. Our research may provide insights into mechanisms that promote normal immune development and the mechanisms that prevent the potent mutagenic activity of RAG, causing unwanted chromosomal lesions underlying some blood cancers. Our over-arching goal is to identify mechanisms and pathways that suppress tumorigenic lesions in developing lymphocytes and to generate information that can potentially serve the development of new therapeutic targets for lymphoid cancers.