Grant: 5462-18 | Career Development Program (CDP):
Location:Yale University, New Haven, Connecticut 06520-8327
Project Title: A Protein Degradation Approach For The Treatment Of Acute Myeloid LeukemiaProject Summary:
Many cancers result from a genetic mutation causing an “always on” protein. Current treatments are based on the deactivation of the proteins by blocking that protein’s active site. Herein I propose an alternative approach in which proteins are permanently degraded rather than temporarily deactivated, which may prove to be a more favourable form of therapy. To do this, I will take advantage of the cell’s own natural ability to degrade its own proteins when they are in excess or no longer needed. I will design and prepare compounds which recruit the native protein degradation machinery to the target proteins by creating a bridge between protein degradation components and the target protein. This approaches uses a two-headed molecule called a Proteolysis Targeting Chimera (PROTAC).
The potential advantages of protein degradation over protein inhibition are three fold:
1. Constant and complete deactivation of proteins is necessary for a treatment to be successful. Protein inhibition, as happens with standard targeted drugs, is often a reversible process, allowing previously inhibited proteins to again be functional. Protein degradation, as happens with PROTACs, is irreversible, therefore resulting in complete deactivation.
2. PROTACs have shown the potential to be catalytic, meaning one PROTAC molecule could destroy more than one protein molecule, preventing cells from simply producing more protein to overcome the deactivation of the existing population.
3. An issue arising from current treatments is the development of resistance after treatment for a relatively short period of time. The proposed PROTAC compounds may be able to circumnavigate such resistance mechanisms.
I propose to prepare PROTACs containing recognition elements for target proteins involved in blood cancers. Specifically, I am focusing on FLT3, which is a protein important in about 1/3 of all AMLs. I will assess PROTACs for the ability to degrade target proteins in cell-based models. The resulting compounds will then be optimised before progression into animal models. It is conceivable that by employing protein degradation, it may be possible to completely remove all disease causing protein. The ultimate goal is to produce a drug that may be useful for the treatment of AML containing FLT3 mutations. Importantly, PROTAC technology has applicability in a number of different cancers.
Grant: 1344-18 | Career Development Program (CDP):
Location:Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024
Project Title: The Biological And Therapeutic Consequences Of SF3B1 Mutations In Myelodysplastic SyndromesProject Summary:
Myelodysplastic syndromes (MDS) are a group of blood disorders characterized by impaired differentiation of hematopoietic stem cells into functional blood cells. MDS frequently has a poor prognosis and is associated with a high risk of transformation into acute myeloid leukemia. There are few treatment options for MDS, largely because the underlying molecular changes that drove MDS were not known until recently.
Recent genome sequencing studies revealed that MDS and related diseases are associated with specific mutations (genetic changes) in hematopoietic stem cells. These mutations most commonly affect genes that control a molecular process termed "RNA splicing." RNA splicing is critical to the process by which genetic information in DNA is "read" to make proteins. We now know that MDS-associated mutations that affect RNA splicing cause mistakes during the transfer of genetic information from DNA to protein. However, we do not yet know precisely which mistakes ultimately give rise to MDS.
We plan to use both experimental and computational methods to determine how mutations that affect RNA splicing give rise to MDS. Understanding the specific molecular changes that occur in MDS cells carrying these mutations will enable us to identify potential new therapeutic opportunities for treating MDS. Because the same mutations affecting RNA splicing are found in other blood diseases as well, such as chronic lymphocytic leukemia, we hope that our discoveries will improve the treatment of many different blood diseases.
Grant: 5465-18 | Career Development Program (CDP):
Location:The Regents of the University of California, San Francisco, San Francisco, California 94143
Project Title: Inhibiting The Palmitoylation/Depalmitoylation Cycle As A Selective Therapeutic Strategy In NRAS Mutant Leukemia.Project Summary:
Acute myeloid leukemia (AML) is an aggressive blood cancer that affects children and adults. Recent advances for sequencing the DNA of leukemia cells have greatly advanced our understanding of the genetic causes of AML; however, this new knowledge has not yet resulted in better treatments.
One of the most common mutations found in AML alters a type of RAS gene called NRAS. The protein made by NRAS works like an “on” and “off” switch that instructs cells to grow in response to growth factors. RAS gene mutations found in AML and other cancers lock these switches in the “on” position, which drives abnormal growth. Recent studies of AML cells have shown that NRAS gene mutations are absent when patients are in remission and frequently reappear when the leukemia relapses. Therefore, NRAS mutations are likely very important for the growth of AML cells, and inhibiting abnormally active N-Ras proteins (proteins created by the NRAS gene) may be of great benefit for patients. Unfortunately, developing drugs that can directly turn abnormal N-Ras proteins “off” is extremely difficult.
We are testing a new approach for inhibiting mutant N-Ras by exploiting a potential “Achilles heel” in the protein. It is likely that N-Ras must be located at the cell surface to stimulate growth. This localization depends on two chemical modifications that are regulated by different enzymes: the addition of a lipid group (palmitoylation) and its subsequent removal (depalmitoylation). We think that inhibiting this cycle will kill AML cells with NRAS mutations but will not affect normal cells. We will test this using a mouse model in which we engineered a mutation of the NRAS gene so it cannot be palmitoylated. Next, we will investigate chemical inhibitors of the enzyme that depalmitoylate the N-Ras protein as a possible treatment for AMLs with NRAS mutations. Finally, we will try to define the enzymes responsible for N-Ras palmitoylation, with the long-term goal of blocking this reaction as an alternative to inhibiting depalmitoylation. Altogether, I anticipate that my project will advance our understanding of NRAS mutant AML and will identify novel strategies to treat this aggressive blood cancer.
Grant: 3380-18 | Career Development Program (CDP):
Location:Dana-Farber Cancer Institute, Boston, Massachusetts 02215
Project Title: Interrogating The Sf3b1 Mutated/Atm Deleted Mouse As A Novel Faithful Model Of Chronic Lymphocytic LeukemiaProject Summary:
Human genomic analyses have defined the complex genetic heterogeneity of chronic lymphocytic leukemia (CLL) as the most common indolent B-cell malignancy. These studies have revealed that selection of certain genetic alterations occurs throughout disease progression and correlates with therapy failure. Despite the remarkable efficacy of a number of recently introduced therapies, CLL remains incurable, and resistance to these novel drugs is challenging the clinical management of CLL patients.
Genetically engineered mouse models represent a promising approach to studying the functional impact of novel cancer-associated gene alterations and are useful to developing preclinical platforms for testing the efficacy of novel drug combinations. The main challenge with CLL modeling is the lack of animal models that faithfully recapitulate the genetic changes discovered in patients. Through novel genetic engineering strategies, we therefore seek to introduce mutations typical of human CLL in mice and to characterize disease features in these novel models, including, but not limited to, aberrancies in B cells (the cell of origin of this leukemia), and T lymphocytes (the cells which generally control immune responses but are notably dysfunctional in CLL patients, thus favoring disease progression).
We recently observed CLL development in animals bearing two of the most common gene alterations found in patients, that is mutations in the genes Sf3b1 and Atm, whose functionality is critical for CLL survival and responsiveness to therapy. We took advantage of this model to create a transplantable platform, whereby leukemias harvested from a donor animal can be expanded into recipients, which are then treated with different drugs (and/or their combinations). The first class of compounds that we will test is splicing modulators, which are drugs capable of interfering with alternative splicing – the main process regulated by Sf3b1 Alternative splicing is a core cellular process involved in the regulation of gene function. Preliminary studies have already shown efficacy of splicing modulators when tested alone or combined with FDA-approved agents for the treatment of CLL.
The overall goal of my studies is to establish robust preclinical platforms to test new therapies and to facilitate the optimization of treatment strategies tailored to the genetic makeup of individual CLL patients, with the aim of obtaining deeper clinical remissions and potentially allowing treatment discontinuation in these patients.
Grant: 6541-18 | Translational Research Program (TRP):
Location:Baylor College of Medicine, Houston, Texas 77030
Project Title: Testing Targeted Therapy In Langerhans Cell HistiocytosisProject Summary:
Rationale and Background: Children with Langerhans cell histiocytosis (LCH) develop destructive lesions that can arise in virtually any organ including bone, brain, liver and bone marrow. LCH occurs with similar frequency as pediatric Hodgkin lymphoma, but there has historically been fewer opportunities for patients with LCH to participate in cancer research studies due to uncertain identity. LCH was first identified over 100 years ago, but only in the past ~5 years has been recognized as a disease in the family of pediatric cancers. Outcomes for children with LCH remain suboptimal, with over 50% failing to be cured with initial chemotherapy, and the majority of patients who are cured suffer long term consequences including problems with growth, control of hormones, and some develop a devastating progressive neurodegenerative condition. Patients who relapse or do not respond to front-line therapy are typically treated with highly toxic chemotherapy or eventually bone marrow transplant. Improved therapies are clearly needed for children with LCH.
Preliminary Studies: In 2010, a mutation in the BRAF gene (called BRAF-V600E), was discovered in over half of LCH tumor samples tested. Over the past 5 years, more mutations in the same cell growth pathway as BRAF (the MAPK pathway) have been discovered, accounting for over 85% of all cases of LCH. In the MAPK pathway, a series of proteins transmit messages from the cell surface to the nucleus of the cell, where that message is translated by turning on or off certain genes. In LCH, this MAPK pathway is overactive and never turns off, resulting in uncontrolled cell growth, resistance to cell death, and formation of destructive LCH lesions. Studies in blood cells from patients with LCH and in mice demonstrated that LCH is caused by activation of the MAPK pathway at specific stages of blood cell development. In early clinical trials with adult patients, LCH lesions responded to vemurafenib, a drug that blocks BRAF-V600E activation. Studies with cells from patients with LCH and experimental mice suggest that blocking MAPK pathway activation with drugs that inhibit MEK activation may be an effective therapeutic strategy for patients with LCH.
Hypothesis and Aims: We proposed to test the hypothesis that cobimetinib, which targets MEK activation, will be a safe and effective treatment for patients with refractory LCH, LCH-neurodegenerative disease, and disorders related to LCH that are also driven by MAPK activation. Additionally, we propose to study the responses associated with certain mutations, determine if cells in blood carrying LCH mutations can be used to follow disease activity, and study new mutations in patients who relapse despite cobimetinib therapy. This study will be carried out through a consortium of LCH disease experts at 11 different institutions through the North American Consortium for Histiocytosis Research.
Grant: 6552-18 | Translational Research Program (TRP):
Location:Walter & Eliza Hall Institute of Medical Research, Parkville 3050, Victoria
Project Title: Long-term In Vivo Imaging Of Bone Marrow Microenvironments In Multiple Myeloma.Project Summary:
White blood cells are soldiers of the immune system. These cells are responsible for surveillance of the body and protection from invading pathogens. When the machinery that controls growth and death of these cells is disrupted by genetic mutations, these cells can undergo massive unregulated expansion. This leads to the development of blood cancers such as leukemia and multiple myeloma (MM).
Blood cancer cells move uncontrolled throughout the body and expand to enormous numbers not normally present in healthy individuals. In addition, the cancer cells can secrete huge amounts of proteins that upset the equilibrium of healthy tissue in the body. In the case of MM, the leukemic cells infiltrate bones. This has dramatic consequences for the health of patients with MM. Cells that normally inhabit the bone are affected by overcrowding caused by expansion of cancer cells. This prevents them from performing their normal daily functions. For example, stem cells responsible for production of red blood cells that circulate throughout the body each day shut down and cannot make more cells leading to shortage of blood. MM cells can also damage the structure of the bones themselves leading to fractures and significant pain in over 80% of MM patients. Currently, this process is poorly understood. Unfortunately, there is no cure for MM and this is at least in part because MM can cells hide in the bone, protected from drugs used as treatment. Thus, considerable effort is needed to develop new treatments to overcome this resistance to treatment and manage the long-term effects of this disease on bone health.
We will solve this problem by watching how MM cells damage bone tissue using cutting edge microcopy. Using 3-dimensional printing technology, we produce custom optical windows that we surgically attach to living bone tissue. Through these optical windows we can view bone tissue for either short periods of time (hours) or throughout the entire disease process (weeks). Therefore, using this technology we will be able to see inside living organisms while MM cells grow, take over and then destroy bone tissue. Using our revolutionary approach, we are able to watch the same cells in the same bone tissue over hours and weeks. This will give us fundamental knowledge about the life cycle of MM and how it responds to treatment that have never been possible before. Once we can directly watch this process in action, we will be able to start to understand how MM cells live, destroy bone and evade therapy. Therefore, we will be able to develop new ways of targeting MM cells so that we can prevent bone damage, and even potentially stop the growth of MM cells leading to a cure.
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.