Grant: 5468-18 | Career Development Program (CDP):
Location:New York University School of Medicine, Boston, Massachusetts 02241-415026
Project Title: Understanding The Function Of 3D Chromatin Topology In Myeloid DiseaseProject Summary:
Greater understanding of the fundamental mechanisms promoting the development of acute myeloid leukemia (AML) may help researchers develop new treatment approaches targeting these mechanisms. Chromosomes (collections of DNA and their associated proteins) are heritable and dynamic carriers of genetic information. Chromosomes are constantly looping, and these structural changes shape the gene expression pattern of a cell. This 3D genome landscape, known as genome topology, provides the physical structure required to inform the identity and function of a cell. The key players in establishing genome topology include the cohesin complex, a group of proteins that physically wraps around DNA to establish looping events, as well as the CTCF protein, which acts to bind DNA and establish the boundary of genome topological domains. Though genomic topological changes are normal in a healthy cell, alterations in genome topology likely play a role in cancer development.
Interestingly, regulators of genome topology are commonly mutated in various diseases, including cancers such as AML. AML is a common adult leukemia characterized by excessive proliferation of abnormal immature white blood cells. AML patients continue to have a dismal survival rate. Notably, mutations in the cohesin complex are an early step in AML formation, suggesting that controlling DNA looping and overall genome topology is a critical function to prevent cancer. However, there are limited insights into how maintaining the topological integrity of the genome halts AML formation. Our research focuses on understanding how regulators of the genome’s 3D structure protect healthy blood stem cells from forming leukemia. Using cutting edge technology, such as inducible RNA interference and CRISPR/Cas9, we will shed new light into the earliest steps in leukemia formation. Ultimately, mechanistic insights uncovered by these approaches have the potential to inform new treatment strategies targeting the root genetic causes of leukemia development.
Grant: 1351-18 | Career Development Program (CDP):
Location:The Ohio State University, Columbus, Ohio 43210
Project Title: Understanding And Overcoming Resistance To Bruton Tyrosine Kinase Inhibitors In Chronic Lymphocytic LeukemiaProject Summary:
Chronic lymphocytic leukemia (CLL) is the most common adult leukemia and until recently was treated with therapies toxic to the patient. Our clinical and research team at The Ohio State University Comprehensive Cancer Center helped provide critical information which led to the FDA approval of ibrutinib, a less toxic targeted therapy. Ibrutinib inhibits the BTK protein, which is a protein that CLL uses for its own pathological survival. Ibrutinib shows remarkable clinical activity that is more durable than any therapy ever studied in CLL. Unlike some CLL treatments, ibrutinib can be given to all age groups, making it a more widespread therapy. Ibrutinib’s success should form the basis for its inclusion in even more effective combination therapies that may someday lead to a cure. Historical experience indicates that effective new therapeutics for CLL will also have a major role in treatment of non-Hodgkin lymphoma and autoimmune diseases.
While ibrutinib is effective for many patients, some develop resistance to this treatment. My research team seeks to determine predictive genomic factors that result in BTK inhibitor therapy resistance. We discovered that some patients acquire mutations that then confer resistance to ibrutinib. The large group of patients treated with ibrutinib, including our collection of samples from patients with resistance mutations, represents an invaluable resource to pursue pre-clinical and clinical work to identify more effective CLL treatments. Exploring the mutations and their associated signaling pathways (which we will continue to discover) will help us understand ways to overcome treatment-related resistance by either early recognition or, potentially, novel therapeutic approaches.
Our experiments use primary CLL cells from patients whom are seen by our clinical team. We are also using the most appropriate laboratory-based model available for understanding preclinical drug development and CLL biology. Our experimental approach will directly address the Leukemia & Lymphoma Society’s mission to cure blood cancer by discovering new potentially curative treatment strategies for CLL.
Grant: 3374-18 | Career Development Program (CDP):
Location:Brigham and Women’s Hospital, Boston, Massachusetts 02241-3149
Project Title: Functional Characterization Of The Mutant Calreticulin-MPL Interaction In Myeloproliferative NeoplasmsProject Summary:
Myeloproliferative neoplasms (MPN) are a group of rare blood cancers that occur when the body produces too many white blood cells, red blood bloods, or platelets. Though the overall prognosis for MPN tends to be favorable, more advanced forms of these diseases can lead to severe anemia, increased risk of blood clots, and transformation to leukemia. MPN were first described in 1951 by hematologist William Dameshek, but the underlying genetic cause of these diseases remained a mystery for over 50 years. In 2005, four different research groups simultaneously discovered that approximately 63% of MPN patients harbor mutations in the gene JAK2. This was a tremendous breakthrough in the MPN field and led to the development of the FDA-approved drug ruxolitinib (Jakafi), a compound that inhibits JAK2 activity, for the treatment of MPN. Despite this advance however, the causal genetic abnormalities in the remaining 40% of non-mutated JAK2 MPN patients remained unknown for nearly a decade thereafter. In 2013, two different groups performed sequencing experiments on blood cells from non-mutated JAK2 MPN patients, and found that the majority of these patients harbor mutations in the gene calreticulin (CALR). The CALR gene encodes a “housekeeping” protein that resides in the endoplasmic reticulum (ER) and ensures quality control of protein folding in the cell. We currently have an incomplete understanding of the mechanism by which CALR mutations transform normal blood cells to cause MPN.
Unlike normal CALR, mutant CALR is found near the cell surface. Our recent research has shown that the mutations enable an interaction with a cell surface receptor protein called MPL. We have further shown that this interaction leads to an activation of the JAK2 pathway. A central hypothesis from this research is that mutant CALR binds to proteins that it does not normally bind to, and some of these proteins may be essential for the oncogenic activity of CALR. Building on this work, we will utilize state-of-the-art technology to determine the proteins mutant CALR binds to in the cell that are not bound by normal, non-mutated CALR. Through this work, we hope to gain a comprehensive understanding of the protein partners with which mutant CALR interacts in the cell to drive disease development, which would ultimately inform new targets for therapeutic intervention. Ultimately, we hope that our work will lead to improved therapeutic strategies for MPN patients, particularly those who do not respond well to ruxolitinib and other existing treatments.
Grant: 5461-18 | 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 NOTCH1 Controlled Micropeptides In T-ALLProject Summary:
Acute lymphoblastic leukemia (ALL) is the most common form of pediatric cancer and a leading cause of disease-driven death in children. Understanding the causes and mechanisms of leukemia is essential in order to develop specific highly active and less toxic treatments. One of the most common drivers of leukemia growth and survival is the NOTCH1 gene. NOTCH1 is frequently mutated in leukemia, and these mutations cause increased NOTCH1 activity, which in turn triggers a cellular program driving uncontrolled cell proliferation. Our understanding of the specifics of how NOTCH1 promotes leukemia transformation remains rudimentary.
Though most of our knowledge of T-ALL comes from the genetic dissection of known protein-coding genes, it is likely that other components of the genome contribute to T-ALL as well. A recently discovered component of the genome gives rise to very small proteins, called micropeptides that likely have profound effects on gene expression. Our research aims to investigate the role of this new family of gene-encoding proteins as potential key drivers of leukemia growth. Our central hypothesis is that among the multiple proteins controlled by NOTCH1, micropeptides are of particular importance for leukemia growth and survival. While large proteins function as molecular machines, micropeptides function as keys or switches that bind to and turn these molecular machines “on” and “off”. We are using the latest genomic technologies and refined computational approaches to identify the complete repertoire of NOTCH1-controlled micropeptides operating in leukemia. We will then evaluate the specific role and mechanisms by which these short proteins contribute to leukemia cell growth. Dissecting the mechanism of action of these key leukemia-driving micropeptides may identify novel targets for the treatment of ALL.
Grant: 6527-18 | Translational Research Program (TRP):
Location:Dana-Farber Cancer Institute, Boston, Massachusetts 02215
Project Title: Assessment Of Epigenetic Reprogramming Of The T Cell Response To CTLA-4 Blockade In AMLProject Summary:
The prognosis for patients with relapsed or refractory acute myeloid leukemia (AML)/myelodysplastic syndrome (MDS) whose disease comes back is poor, and innovative new therapeutic approaches are urgently needed. We conducted and published results from a clinical trial for patients whose blood cancer came back after bone marrow transplantation with ipilimumab, which is an antibody drug that uses the immune system to kill cancer cells. A small number of patients, including those with relapsed AML, had durable clinical responses. This clinical activity prompted us to develop a new proposal to evaluate whether or not we could safely boost response by adding a hypomethylating agent, decitabine, to ipilimumab treatment. Decitabine is a drug commonly used in the treatment of MDS/AML that is well-tolerated with modest clinical activity. Decitabine has the ability to affect the expression of genes. We now have a new approved clinical trial to assess the safety and clinical activity of the novel combination of decitabine plus ipilimumab in patients with relapsed or refractory AML/MDS who are post-transplant and who are transplant naïve. Using peripheral blood and bone marrow samples collected throughout treatment on study, we will evaluate the hypothesis that decitabine treatment might sensitize leukemia cells to ipilimumab by altering the immune response within the sites of leukemia infiltrates. Together with local expert collaborators we will perform a comprehensive analysis using patient samples collected from the clinical trial to evaluate for transcriptional (gene expression) and epigenetic (changes in a chromosome that alters gene activity and expression) changes within the immune cells present at leukemia sites including bone marrow and other tissues. We will then study which immune cells subpopulations are present and whether or not they have functional activity. We will correlate these laboratory findings with clinical activity to decitabine and ipilimumab to help us to understand treatment response or resistance. Knowledge gained from this investigation will help us to improve the design of future immunotherapy-based regimens with curative potential for patients.
Grant: 6534-18 | Translational Research Program (TRP):
Location:Yale University, New Haven, Connecticut 06520-8327
Project Title: Exploiting Mutant IDH1/2-induced BRCAness With PARP Inhibitors As A Novel AML/MDS Therapy.Project Summary:
We have identified a novel approach to treat certain types of leukemias that harbor a mutation in key genes that are involved in cellular metabolism. We found that these mutations create an altered chemical in the cell, which blocks the ability of tumor cells to repair broken DNA. This "achilles heel" can be exploited by treating such tumors with DNA damaging agents combined with DNA repair inhibitors. We have already demonstrated that this therapeutic approach is highly effective in brain tumors and other solid cancers which harbor mutations in these genes, and we now seek to determine whether the same is true in leukemias. Current strategies to treat tumors with these mutations are focused on suppressing the production of the altered metabolite. Our data suggest that this approach actually may not be ideal, as the metabolic vulnerability should be exploited rather than suppressed. The studies proposed here represent a highly translational, cross-disciplinary collaboration between researchers in hematology and oncology, radiation oncology, small molecule screening, and DNA repair basic science research. We expect that these studies will directly lead to a novel clinical trial in the future for leukemias with these mutations.
Grant: 6532-18 | Translational Research Program (TRP):
Location:The Regents of the University of California, San Francisco, San Francisco, California 94143
Project Title: Inducing Effective Anti-leukemic Immunity With Novel AML Vaccines Expressing CD80/IL-15/IL-15R-alphaProject Summary:
Patients with high-risk acute myelogenous leukemia (AML) have poor outcomes because current drug regimens fail to eradicate disease. Transplants of bone marrow or peripheral blood stem cells from matched related, or unrelated donors (allo-transplants) improve survival due to elimination of residual AML by immune cells present in donor cell populations. However, many patients are not eligible for allo-transplants, either because they lack suitable donors, or because they have pre-existing conditions making transplant too risky. Other therapies based on stimulating anti-leukemic immune responses have been tested, but achieving reproducible clinical efficacy has been elusive. In one approach, patients’ AML cells are collected before treatment, frozen, and later used as inactivated cell vaccines in order to stimulate immune responses specific to patients’ own tumor. However, to date, anti-leukemic immunity stimulated by unmodified AML cell vaccines has been inadequate.
Our strategy to improve the efficacy of AML cell vaccines is to increase their immune stimulatory activity by viral mediated transfer of a unique combination of three genes. Viral constructs express 1) a protein required to initiate recognition by immune cells, CD80, 2) a hormone shown to stimulate unprecedented levels of anti-tumor immunity, IL-15, and 3) a carrier protein required for efficient production and secretion of IL-15 in leukemic cells, IL-15 receptor alpha (IL-15Ra). For proof of concept studies, vaccines were made by inactivating mouse AML cells with x-ray treatment to prevent introduction of live leukemia cells with skin injections. Serial vaccination with AML cells, in the absence of viral modification, was minimally effective in slowing progression of disease in leukemia-bearing mice. However, injection of mouse leukemia vaccines engineered to express IL-15/IL-15Ra/CD80, induced immune responses that permanently eradicated leukemia in 80% of vaccinated mice.
We now propose to test the effects of engineered, patient-derived AML cell vaccines in stimulating effective anti-leukemic responses. The function of a newly constructed lentivirus expressing human IL-15, IL-15Ra, and CD80, has already been validated in selected patient AML samples. Our aims are to: 1) quantify the level and duration of transferred gene expression in human AML; 2) evaluate the responses of immune cells from normal and leukemic individuals after stimulation with IL-15/IL-15Ra/CD80-expressing human AML cell vaccines. Responses will be evaluated both in cell culture, and by transplanting responding immune cells and human AML cells into immune deficient mouse models; 3) test the specificity of immune responses stimulated by IL-15/IL-15Ra/CD80-expressing AML cell vaccines by comparing effects of stimulated immune cells on AML versus normal bone marrow cells. The additional data provided by these studies will support the design and application for funding of a Phase 1 vaccine trial.
Grant: R6507-18 | Translational Research Program (TRP):
Location:Dana-Farber Cancer Institute, Boston, Massachusetts 02215
Project Title: MYD88 And CXCR4 WHIM-like Mutations Offer A Targeted Treatment Approach For WMProject Summary:
Ibrutinib is an active drug that is approved by the U.S. FDA and European Medicines Agency for the treatment of WM. WM patients who have a mutation in MYD88 (over 90% do) respond to ibrutinib, while those with mutations in CXCR4 show lower levels of response and delayed responses. Despite the overall high levels of response to ibrutinib among WM patients, the achievement of complete responses is lacking. We discovered as part of the LLS sponsored study that two important pathways exist by which mutated MYD88 can support growth and survival of WM cells. One pathway is mediated by BTK, a protein targeted by ibrutinib. The other pathway involves a family of proteins known as the IRAK proteins. We discovered as part of this work that the IRAK1 protein was particularly important in relaying survival signals, and that it remains turned on in tumor cells taken from patients with WM, whereas BTK is shutoff. This finding encouraged us to develop potent and selective inhibitors that target IRAK1. One compound that we developed (JH-X-119-01) potently blocked IRAK1, and was very selective for IRAK1. We showed that this compound could synergize with ibrutinib and kill more MYD88 mutated tumor cells, including WM cells and those derived from patients with aggressive lymphomas (ABC type), than Ibrutinib alone. While the activity of this compound is excellent in cell models it does not possess all the requisite parameters for evaluating its efficacy in preclinical murine models. We therefore propose to execute a medicinal chemistry campaign to achieve compounds simultaneously optimized for potency and drug like properties such as resistance to being degraded by liver enzymes and being able to be absorbed across the gut for therapy of MYD88 mutated diseases, including WM, ABC DLBCL, and primary brain lymphomas. During the course of our studies, we also pursued identifying other targets that are in the pathway that allow MYD88 mutated cells to grow. One target known as HCK was discovered that plays a master role as a regulator of many growth and survival pathways including BTK. We performed proof-of-concept studies with a toolbox compound, a compound that blocks HCK but is not suitable for use as a drug in humans, and showed this drug was very active in MYD88 mutated diseases. We propose to do medicinal chemistry to optimize this molecule for use in humans. During our studies, we also discovered that CXCR4 mutations found in 30-40% of WM patients cause resistance to ibrutinib. We worked out the signaling responsible for this resistance, and also found that blockers of CXCR4 reverse drug resistance. We developed a clinical trial that will open in the Spring 2017, and combine a CXCR4 blocker (ulocuplumab) with ibrutinib in WM patients who have the CXCR4 mutation. We will use advanced genetic technologies to see how CXCR4 mutated cells behave when a CXCR4 blocking agent is combined with ibrutinib.
Grant: 1346-18 | Career Development Program (CDP):
Location:University of Cincinnati, Cincinnati, Ohio 45221-0222
Project Title: The Oncogenic Role And Underlying Mechanism Of TET1 In Acute Myeloid LeukemiaProject Summary:
Acute myeloid leukemia (AML) is one of the most common and fatal forms of hematopoietic malignancies. Thus, it is urgent to better understand the mechanisms underlying the pathogenesis of AML, and on the basis of such understanding, to develop novel therapies with higher efficacy and minimal side effects to treat AML. The properties of cancer are often determined by the proteins that are expressed from information provided by the genes in the cell. Expression of information from genes is regulated in part by chemical modifications of the DNA in the gene, in a process called “epigenetic regulation.” One such modification is called methylation. A family of proteins involved in epigenetic regulation are the 3 TET proteins, which ultimately affect the methylation status of critical genes. TET proteins are traditionally thought to be negative regulators of tumor growth. However, in contrast to this tumor suppressive role, we recently reported that TET1 is highly expressed in certain subtypes of AML, suggesting an opposite role for TET1, the promotion of tumor growth.
We are currently studying the mechanisms by which TET1 promotes tumorigenesis and how we might use this information to develop a novel approach to treat AML. Some central questions are to understand how tumors develop, how they are maintained after they develop, and how the leukemia stem cells provide a reservoir for continued tumor development in a patient. Therefore, we seek to understand the role of TET1 in both the development and maintenance of the AML types that overexpress TET1, and the role of TET1 in the leukemic stem cells. In addition, we are studying the critical target genes that are affected by TET1, which will provide further insight into the role of TET1 in AML. Lastly, we are examining ways to therapeutically target TET1 using mouse models of AML. The success of our studies will provide novel insights into our understanding of the critical role of TET1 in AML and may also lead to the development of novel and more effective therapeutic approaches to treat the AML.
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.