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Include results from ANY of the following program type(s)
disease
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Investigator Address Date Body Grant Program
Targeting Enhancer Dysfunction in Hematological Malignancy United States -

What is the overall scientific/clinical problem?

Blood cancers such as leukemia, lymphoma and myeloma may be caused by abnormal regulation of genes that control normal cell growth and development. Genes that are normally active can be silenced and/or genes normally not present in a blood cell are abnormally activated. The result can be an uncontrolled signal for continued cell growth or survival. The root cause of this problem may be the presence of an abnormal regulator protein in the cell that was generated in the cancer cell by shuffling of chromosome segments, or the presence of a more subtle but functionally very important mutation in a regulatory protein. These abnormal regulatory proteins bind to a host of other proteins and recruit these proteins to target genes leading to the abnormal switching on or off of the target gene. Our group studies the molecular basis of this gene deregulation using cells cultured in the laboratory, human specimens, and animal models.

What is the overall goal of your SCOR?

We have assembled a group of physician-scientists and basic scientists to mount an attack on abnormal gene regulation in blood cancers. Over the past 11 years the group published numerous joint papers on the underlying mechanisms of leukemia in the highest quality scientific journals. It is our aim to understand the fundamental basis for abnormal gene regulation in blood cancers and to develop strategies to reverse this process. In the coming 5 years we are focusing on a family of proteins that target so called enhancer sequences- sites in the genome that have a role in controlling gene expression. We have found that inactivation of these enhancer active sequences causes a growth advantage to blood cancer cells and this may be in part by blocking the human immune response against the tumor.

What is the specific goal of each project?

Project 1: Ari Melnick, Weill Cornell- Dr. Melnick studies a regulator called KMT2D which is one of the commonest genes mutated in lymphoma. Loss of function of this gene causes enhancer sequences to fail to function and sets of critical genes fail to be activated in lymphoma cells. KMT2D loss causes the lymphoma cells to be hidden from the immune system. Melnick has found that a protein called KDM5 opposes the action of KMT2D and KMT2D inactivation causes a cancer cell dependence on KDM5. Melnick will study how chemical inhibitors of KDM5 may inhibit growth of lymphoma cells and how KDM5 inhibitors can make the lymphoma respond to immune therapy.
Project 2: C. David Allis, PhD (Rockefeller U) and Scott Lowe, PhD (Memorial Sloan Kettering). These scientists study a class of leukemia associated with the shuffling of the protein called MLL (Mixed lineage leukemia). Prior work from our SCOR group found that MLL interacts with a protein called menin and this interaction is critical for the development of leukemia. LLS investigators including our prior collaborator Jay Hess developed an inhibitor of MLL- Menin interaction that has an antileukemia effect. These investigators then screened for genes that made cells resistant to the menin inhibitor and identified the KDM6A protein which can bind to KMT2D and affect gene regulation. Through this work the group has found that menin inhibitors may be useful in other forms of blood cancer.
Project 3: Robert Roeder, PhD, Rockefeller U. Dr. Roeder found a critical role for KDM6A in the development of MLL-associated leukemia and will map the regions of the protein required for the KDM6A action- such identification is followed by biochemical experiments to map critical interactions of KDM6A that may be targeted therapeutically by small molecules in a manner akin to the targeting of menin and MLL. He will identify the key target genes of KDM6A in leukemia and determine if these may represent new therapeutically targetable pathways. He will determine the domains of KMT2D required for tumor suppressor activity and determine if KMT2D-interacting proteins and gene targets differ in leukemia and lymphoma which may necessitate the customizing targeting in different diseases.
Project 4: Jonathan D. Licht, MD- The U of Florida. Dr. Licht studies KMT2C/D and KDM6A tumor suppression in multiple myeloma. He will define the regions of KDM6A required for tumor suppression and map critical areas of protein interaction for targeting. He will create animal models of myeloma with loss of KMT2C/D and KDM6A and determine how these genetic models lead to more aggressive myeloma and determine if these tumors have new susceptibilities to gene regulator inhibitors. He already found that KDM6A loss sensitizes cells to EZH2 inhibitors, which motivates clinical trials of the agent in myeloma.
Project 5: DInshaw Patel, PhD- Memorial Sloan Kettering Cancer Center. Dr. Patel will guide molecular and mechanistic studies of the KMD6A/KMT2C/D complex by use of the latest techniques to solve structures at the atomic level, cryo-EM, which uses electron beams to take a 3 dimensional picture of purified proteins in large complexes. This technology allows higher resolution of larger size proteins than previously available.
What is unique about your SCOR?

The unique aspects include 1) the focus on a specific family of gene regulators recurrently malfunctioning in cancer; the complex of KMT2C/D and KDM6A; 2) A broad approach spanning from structural studies at the atomic level, chemical methods to inhibit gene regulators, genetic models in cell culture and animals to validate the ideas; 3) the study of the complex in all major forms of blood diseases: leukemia, lymphoma and myeloma; 4) The use of advanced gene editing screening and bioinformatics experts.

How will this benefit patients now or in the future?

All of our studies point to the critical protein interactions required for disease development and have already lead to the development of menin inhibitors for leukemia and EZH2 inhibitors as a strategy for myeloma and KDM5 inhibitors for lymphoma. We expect to identify more pathways that can be targeted in blood cancers.

Specialized Center of Research Program
Identification of therapeutic targets sensitizing acute myeloid leukemia to BCL2 inhibitors United States -

This project aims to improve the effectiveness of ventoclax in a greater number of acute myeloid leukemia (AML) patients by targeting MARCH5 and other cell death sensitizers. AML is characterized by uncontrolled growth of abnormal white blood cells. Though current treatments are effective for some patients, the overall cure rate for AML remains unsatisfactory. Apoptosis is a type of normal cell death used to clear damaged or other unwanted cells. Apoptosis is tightly regulated through the balancing of pro-apoptotic and anti-apoptotic proteins mediated by the mitochondria. The evasion of apoptosis is a hallmark of all cancers and is essential for sustaining cancer growth. Thus, inhibition of these anti-apoptotic proteins provides a therapeutic strategy for treating AML. Venetoclax is an inhibitor of the anti-apoptotic protein BCL2 and shows promise in clinical studies. However, some AML patients develop resistance to venetoclax, sometimes through the compensatory increase of another anti-apoptotic protein, MCL1. This indicates that venetoclax will likely be most effective in combination with other drugs. The goal of my research is to identify cooperating targets that enhance the efficacy of venetoclax and thus to provide a rationale for designing combinational therapy that may benefit AML patients in the future.

We identified the mitochondrial protein MARCH5 as a critical regulator of AML cell growth, and we showed that suppression of MARCH5 facilitates apoptosis in AML cells. Our preliminary data also suggests that suppression of MARCH5 enhances the effect of venetoclax on AML cells. This supports the rationale to study MARCH5 as a mediator of the anti-tumor effects of venetoclax in AML cells. We will define the mechanistic role of MARCH5 in AML by determining the critical targets regulated by MARCH5 and develop an understanding of how they might disrupt the evasion of apoptosis and promote venetoclax’s suppression of BCL2. We will determine if there is a connection between MARCH5 and MCL1, which may explain how MARCH5 counteracts BCL2 suppression. The translational value of targeting MARCH5 as a combined therapy with venetoclax will be evaluated using preclinical models that mimic the human disease. In addition, to expand our arsenal for enhancing the efficacy of venetoclax beyond MARCH5, we will perform a CRISPR-based, genome-scale screen in AML cell lines to systematically identify novel venetoclax sensitizers. Our study will provide valuable insights for understanding apoptosis regulation in AML and facilitating the clinical application of venetoclax for AML treatment.

Career Development Program
Development of therapeutic strategy for the treatment of MDS United States -

Myelodysplastic syndromes (MDS) are a group of blood disorders that occur in the elderly affecting between 20,000 and 45,000 people each year in the US. MDS patients are at an increased risk of developing blood cancer. The clinical outcome of MDS patients is still very poor, despite progress in treatment approaches. Previous studies found mutations in TP53, a gene that protecting cells from cancer, in 10% of MDS cases. As TP53 mutations are associated with short survival and drug failure in patients with MDS, the goal of this study is to understand how TP53 mutations contribute to MDS in order to develop novel treatments for MDS patients. A group of mutated blood stem cells called MDS stem cells that cannot efficiently produce normal blood cells cause MDS. There is a protein complex, called the spliceosome, which is the machinery for messenger RNA splicing. If mRNAs in cells are not properly spliced, people may develop diseases, such as MDS. Recently, mutations in spliceosome genes were found in 60% of MDS patients. We found that a decreased amount of spliceosome genes in MDS stems cells actively expressing mutant p53 and we observed that mRNAs are not properly spliced in MDS stem cells with mutant p53. Based on these findings, we hypothesize that mutant p53 proteins change mRNA splicing in blood stem cells, leading to the formation of MDS stem cells. We will test drugs targeting spliceosome on mouse and human MDS cells with mutant p53. We anticipate that these drugs will kill drug resistant MDS stem cells. Upon completion of this research, we expect to establish the spliceosome as a new target for clinical trials of drugs for MDS patients. The successful completion of these studies would be expected to have an important positive impact on MDS patients and their family members.

Translational Research Program
Dissecting the heterogeneity of leukemic and pre-leukemic clonal expansion to identify genes associated with leukemia relapse and genesis United States -

Our group has developed a novel technology to track individual cells in mice and to identify the rare cells that drive clonal expansion. Clonal expansion is the excessive increase in the descendants of a cell. It is thought to play a crucial role during the early stages of blood cancer formation. Clonal expansion is often initiated by rare molecular events, such as mutations in genes and changes in how genes are regulated. These molecular events can increase the opportunities for accumulating additional molecular events that eventually lead to cancer.

Clonal expansion can be easily monitored by periodically sampling the blood. This approach may indicate the onset of cancer. However, not all instances of clonal expansion lead to blood cancer. For example, clonal expansion is frequently observed in the elderly that are free of any apparent diseases. Recently, studies from our group and others have shown that clonal expansion also commonly occurs after bone marrow transplantation. Little is known about the differences between normal and cancer-associated clonal expansion, particularly with respect to the precise cellular and molecular mechanisms that drive clonal expansion to initiate cancer. This knowledge gap largely results from difficulties in identifying and studying rare cancer-initiating cells.

Our approach overcomes the technical barriers associated with the study of clonal expansion. We use genetic barcodes to tag each cell with a unique identifier that can be tracked at any time. Sequencing these barcodes and all the transcribed genes in each of these cells provides the opportunity to understand which genes are important in the cells that are involved in clonal expansion. From this analysis, we will identify the genes that play key roles in acute lymphoblastic leukemia (ALL) onset and relapse. We will dissect clonal expansion using both mouse models and human patient samples. We will also study leukemia relapse using primary human ALL cells obtained from patients upon initial diagnosis and relapse, and we will use the same approach to identify the molecular events leading to hematopoietic stem cell expansion in otherwise healthy individuals, which may identify those who are more likely to eventually develop cancer.

In contrast to conventional studies that analyze cell mixtures, our research uniquely probes the specific cells that drive the development of leukemia. We expect to identify the key cellular and molecular events that drive leukemia onset and relapse. These findings will help improve cancer diagnosis and can serve as new therapeutic targets for treating leukemia.

Career Development Program
Preclinical Notch inhibition to prevent graft-versus-host disease in mice and non-human primates United States -

Graft-versus-host disease (GVHD) remains one of the most dangerous complications of bone marrow transplantation in patients with leukemia, lymphoma and other blood cancers. GVHD arises because donor immune cells recognize foreign antigens in the recipient, causing damage to multiple target organs. Despite use of preventive treatments, many patients still experience acute GVHD, which can be life-threatening, and/or chronic GVHD, which can trigger long-term complications and decrease the quality of life. Better therapies for the prevention and treatment of GVHD could lower the risks and toxicity of bone marrow transplantation, while allowing more patients to benefit from its life-saving potential. Using mouse models of bone marrow transplantation, we discovered a new therapeutic strategy to prevent acute and chronic GVHD by blocking signals delivered to immune cells early after transplantation by the Notch pathway. Inhibiting Notch signaling prevented GVHD through mechanisms that differed from all other treatments tested so far and preserved beneficial aspects of bone marrow transplantation, including anti-tumor effects. Remarkably, a single dose of an antibody blocking Delta-like Notch ligands, when given immediately prior to transplantation, was sufficient to provide potent long-term protection from GVHD in mice. To evaluate how best to develop this new strategy for patients, we have started studying the effects of Notch ligand blockade in a non-human primate model that mimics many aspects of human bone marrow transplantation. This model provides essential translational information to guide the development of new treatments that can be tested directly in patients. Our preliminary data show that a single dose of an antibody targeting the Notch ligand Delta-like4 (anti-DLL4) markedly increased the GVHD-free survival of transplantation recipients in non-human primates. Anti-DLL4 was particularly potent at controlling intestinal GVHD, the most dangerous manifestation of acute GVHD. Our results show that the function of individual Notch ligands in GVHD is preserved from mice to non-human primates, and thus likely in humans. Building on these results and on our collective expertise, we propose to determine key mechanisms of GVHD protection from Notch inhibition and identify the most promising therapeutic strategies for clinical translation. Specifically, we will study the impact of Notch blockade on immune cells that trigger GVHD in the gut and other target organs in mice and non-human primates. Using newly developed anti-DLL1 antibodies, we will explore whether combined inhibition of DLL1 and DLL4 provides superior GVHD control in non-human primates, as observed in mice. Finally, we will administer Notch ligand blockade with other existing treatments in search of combinations that are well tolerated and have optimal efficacy. Our ultimate goal is to develop new clinical trials to better control GVHD in patients.

Translational Research Program
Clonal Evolution of Pre-Leukemic Hematopoietic Stem Cells in Human Myeloid Malignancies United States -

Acute myeloid leukemia (AML) is an aggressive cancer of the bone marrow affecting more than 20,000 adults annually in the United States. Even with aggressive chemotherapy and/or bone marrow transplantation, five-year overall survival is between 30-40%. Sequencing studies have demonstrated that most cases of AML are associated with mutations in multiple genes. Previous studies demonstrated that these mutations initially occur in blood stem cells (HSCs), identifying pre-leukemic HSCs (pHSCs) bearing pre-leukemic mutations. These pre-leukemic mutations are found in genes that regulate gene expression, and the pre-leukemic cells acquire additional mutations, often in genes involved in cell expansion, leading to AML. Stratification of a cohort of AML patients into high or low pHSC groups demonstrated that the high group had much worse overall and relapse-free survival, indicating that the presence of pHSCs may be critical for patient outcomes. A parallel line of sequencing studies investigated the presence of these mutations in the blood of individuals with no history of blood disease, a condition termed clonal hematopoiesis (CH). CH was found to be associated with an increased risk of development of blood cancer. These studies essentially identified pre-leukemic mutations, and presumably pre-leukemic HSCs, in a large portion of the general population, yet progression to AML occurred infrequently. These studies provide novel and significant insights into the events that occur in the development of AML. However, they also raise a number of new detailed questions with significant implications for disease biology, prevention, and treatment. Are pHSCs and pre-leukemic mutations therapeutic targets in AML? Can these pHSCs be targeted with mutation-specific therapies? Why is there a typical order of events with mutations in gene expression regulators occurring first in pHSCs? Is progression of pHSCs and evolution into AML simply the result of rare co-occurrence of additional mutations? Are there other contributions to pHSC progression? This proposal aims to investigate the progression of pre-leukemic and/or CH-associated HSCs to AML based on the observation that such progression occurs in the minority of individuals. In particular, we hypothesize that both cell intrinsic and bone marrow environmental mechanisms contribute to this progression. This hypothesis will be investigated through specific aims designed to determine the effect of pre-leukemic mutations on HSC therapy responses, to investigate the progression of pHSCs into AML through cell intrinsic mechanisms, and to investigate the contribution of cell extrinsic mechanisms to the progression of pHSCs. Ultimately, we propose that pre-leukemic HSCs contribute significantly to disease and represent a critical cellular target for the development of curative therapies.

Discovery
Development of CAR T Cells Targeting AML Stem Cells United States -

Acute myeloid leukemia (AML) is an aggressive cancer of the blood and bone marrow with poor overall outcomes. Standard of care for the treatment of AML consists of high dose chemotherapy, often including bone marrow transplantation, but has not changed for decades. Novel, less-toxic, and more effective therapies are needed for this devastating disease. Here, we propose to develop and test in pre-clinical models chimeric antigen receptor (CAR)-modified T cells directed against CD93 expressed on human AML stem cells. We recently discovered expression of CD93 on AML cells from a variety of clinical subtypes and determined that this antigen is not expressed on blood stem or progenitor cells, or on most normal tissues, making it a good target for CAR T cells. We have generated a humanized antibody against CD93 that will be used to create CAR constructs that will be tested for activity against human AML. Pre-clinical testing will include both in vitro T cell killing assays and in vivo leukemia models, facilitating selection of a lead clinical CAR T cell candidate. The CAR T cell approach has shown enormous promise and activity for the treatment of acute lymphoblastic leukemia (ALL), but thus far, no CAR has been developed for AML. Our approach in targeting CD93 on human AML cells has the potential to bring major clinical benefit to patients without significant toxicity. Importantly, this proposal seeks to develop a leading CAR T cell candidate that could be directly brought forward into clinical trials.

Translational Research Program
Therapeutic implications of altered epigenetics and DNA damage responses in hematologic disorders Canada -

Acute myeloid leukemia and peripheral T-cell lymphoma are diseases with poor prognosis and limited treatment options. Mutations in three genes with similar functions contribute to the development of both of these diseases, but how they do so is unclear. New therapies targeting the effects of these mutations are being developed, but even the most promising of these are likely to be effective in only a subset of patients. A better understanding of how these mutations contribute to leukemia and lymphoma, and how they affect treatment resistance will lead to new and better therapies. Our program consists of 4 Projects supported by 2 Technology Cores, and will examine the effects of these mutations in patient samples and specifically designed genetically engineered mouse models. New technology will allow us to examine the DNA and proteins of individual cells in order to identify how these mutations cause disease and resistance to therapy. We will determine: 1) how mutations in the TET2, DNMT3A and IDH genes drive malignant disease, and why they cooperate differently in different cancers; 2) how these mutations affect the cell’s ability to repair DNA damage; 3) how variation among malignant cells develops and how this variation affects treatment; 4) how these factors affect treatment and if new approaches can be identified. Our Project brings together research scientists and clinical investigators who are leaders in their fields and are strong collaborators.

Specialized Center of Research Program
Targeting v-ATPase mutations and activated autophagic flux in follicular lymphoma United States -

Follicular lymphoma (FL) constitutes the second most common non-Hodgkin’s lymphoma (NHL) in the United States, with over 100,000 patients living with the disease. While survival rates at 10 years have been improved, almost all patients with FL need therapy within a few years from diagnosis, and most patients receive multiple chemo- or immunotherapies over their lifetimes. Consequently, the psychological and physical strain on individual patients and the societal burden from this disease are substantial. Unfortunately, the development of targeted therapy in FL lags behind the substantial progress made for other blood cancers, and future advances in this area requires identification and validation of novel drug targets and treatment approaches.
One of the surprising findings from recent research efforts in FL is the discovery of recurrent mutations in genes involved in a self-preserving response pathway to nutrient deprivation called autophagy (self-eating). The autophagy self-eating pathway is activated in times of low nutrient availability and allows cells to self-digest a small portion of their internal organelles to generate novel building material for critically needed biomolecules. Central to this process is a molecular pump called v-ATPase, which creates the correct acidic milieu within cells for digestions of proteins.
We and others have discovered novel mutations in various v-ATPase components and regulators (named ATP6V1B2, APT6AP1, VMA21 and others) in a combined 25-30% of FL cases. Recently, we have made the novel intriguing observation that recurrent mutations in ATP6V1B2 activate autophagy. Physiologically, presence of altered v-ATPase molecules allowed for survival of lymphoma cells under low nutrient conditions, and blocking the self-eating and self-preservation process with drugs killed mutated lymphoma cells. Based on these findings, we wish to clarify the mechanisms of autophagy activation by mutant ATP6V1B2. Further, we wish to define the properties of frequent but unstudied mutations in ATP6AP1 and VMA21 in FL, as we anticipate contributions to activated autophagy as well.
Altogether, we will use knowledge gained from this project to define activated self-eating and self-preservation as new therapeutic vulnerabilities of Follicular Lymphoma. Our work aims at finding a novel way of targeting follicular lymphoma.

Translational Research Program
Rejection-resistant T Cells for the Off-the-shelf Therapy of Hematologic Malignancies United States -

A new wave of therapies for leukemia and lymphoma uses the patient’s own immune system to cure the disease. The immune system is made up of multiple types of cells, including T cells that can target and kill cancer cells. Unfortunately, in cancer patients these T cells often fail to perform their duties. These new therapies therefore take T cells from the patient’s blood, in the lab give them special cancer-targeting properties, and then give them back to the cancer patients where they can effectively fight disease. Indeed, the Food and Drug Administration recently approved the first of these therapies, called CAR T cells, for an aggressive type of leukemia.
Though an exciting new treatment option, the manufacturing process for CAR T cell therapy is time-consuming, labor-intensive and sometimes unsuccessful due to the poor condition of patient’s own T cells after many rounds of chemotherapy. A more efficient approach would be to use pre-made batches of CAR T cells manufactured from healthy donors and stored in a bank, ready for immediate infusion when needed. This alternative approach, however, has two critical problems. First, because these cells come from other people, the cancer patient’s body will treat them as foreign invaders, killing the helpful CAR T cells before they can do their important work. Second, the CAR T cells may themselves recognize the patient’s body as foreign, and mount a toxic reaction against normal, non-cancerous cells. In order to allow for the broader use of this new therapy, we aim to solve both problems in the proposed project.
First, we will educate the healthy donor-derived CAR T cells to recognize and eliminate the patient cells responsible for killing the therapeutic cells. These killer T cells can be distinguished from other cells by the presence of specific markers on their cell surface. We have created two artificial defense receptors (called CDRs) that can instruct the CAR T cells to recognize and destroy the patient’s killer T cells before they can attack, but spare the vast majority of other, non-reactive T cells. This system will enable our off-the-shelf CAR T cells to resist immune rejection by the patient and thus prolong their anti-tumor activity.
Second, we will carefully select the donor T cells used in our off-the-shelf CAR T cell therapy. We will remove all cells with potential reactivity against patient cells, by using only T cells that are specific for viruses, a strategy that has shown to be safe and effective in previous clinical trials. Armed with both the CDR and CAR, we hypothesize these cells will be safe and effective as treatment for lymphoma and leukemia. Further, these cells can be grown to the necessary numbers and stored to be used when needed.
If successful, this approach will dramatically reduce the cost and complexity of T cell therapy, as well as minimize the amount of time patients need to wait before receiving treatment.

Translational Research Program
Abintus Bio United States -

In 2020, LLS made an equity investment in Abintus Bio. Abintus is developing cutting-edge chimeric antigen receptor (CAR) therapies that allow for powerful CAR-T cells to be generated directly in a patient’s body, eliminating the need for time-consuming and costly collection, engineering and re-infusion of patient T-cells. This direct “in situ” approach within the native environment of the immune cells could have scientific advantages.  The innovative Abintus approach aims to reprogram T-cells inside the body to attack and eliminate tumors. This technology is currently in preclinical testing and could, if successful, support immediate patient dosing, a substantial benefit for patients facing advanced forms of cancer with a poor prognosis. Abintus’ platform is versatile and scalable, so they have the potential to meet the needs of a much larger patient population.  

The Abintus approach leverages a substantial body of clinical safety data that support the safety of their approach. As with any novel therapy, safety will continue to be carefully characterized and investigated. This project is in preclinical development with a target to explore the first product in lymphoma using this novel technology platform being developed by Abintus.

For more information about Abintus, visit www.abintusbio.com

Therapy Acceleration Program
Improving hematopoietic stem cell transplantation by defining novel regulators of engraftment United States -

Each year in the United States about 3,000 leukemia patients will be treated with a hematopoietic stem cell (HSC) transplant. For many of these patients, HSC transplantation (HSCT) is the only available curative therapy. Stem cells are specialized cells that maintain and repair the tissue in which they reside. HSCs are the stem cell population that maintain blood production in healthy individuals and restore a healthy blood system when transplanted into patients whose own blood system is compromised by leukemia or chemotherapy. Most transplanted HSCs are collected from the blood of donors that have been treated with G-CSF, a drug that coaxes HSC to leave the bone marrow and enter the blood. Unfortunately, G-CSF treatment is a multi-day protocol that comes with high rates of debilitating side-effects, such as fever and bone pain. According to the National Bone Marrow Registry, >50% of potential donors decline donation, many due to fear of these side effects and the inconvenience of current G-CSF treatment protocols. This reality severely limits the donor options of leukemia patients in need of HSCT. Improving the collection of HSC from the blood of donors requires a deep understanding of the mechanisms that regulate how HSCs interact with their bone marrow homes or ‘niches’. Indeed, these same gains in knowledge can also be applied to improve the efficiency of HSC engraftment during transplant, which would allow for reduced pre-transplant conditioning regimens, lowering the long-term risks that plague survivors of leukemia, especially children, such as secondary malignancies, immune dysfunction, growth failure, gonadal dysfunction, and thyroid dysfunction. The major goal of our laboratory is to understand the key mechanisms that control the ability of HSCs to engraft a patient and regenerate the entire blood system. We recently discovered that a family of proteins, known as GPRASP proteins, inhibits the ability of HSC to efficiently replenish the blood system after transplantation. Here, we will determine exactly how these proteins block this critical function. Our hypothesis is that GPRASP proteins degrade critical factors that are required to both attract HSCs to the bone marrow after transplantation and anchor them securely in their niche once they arrive in the bone marrow. This work will illuminate a novel molecular pathway that can be targeted therapeutically, possibly by directly reducing GPRASP function during transplantation, to improve outcomes for leukemia patients in need of HSCT as well as for their donors.

Career Development Program
SIRT3 Targeted Therapy for B-Cell Lymphomas United States - Special Grants
Targeting Unmet Clinical Needs for B-Cell Lymphomas United States -

Approximately half of lymphoma patients cannot be cured and even those who are cured must endure significant toxic chemotherapy effects. We lack a full understanding of what makes certain lymphomas resistant. Hundreds of new drugs becoming available are supposed to hit specific molecular targets in lymphomas. However the task of comparing and contrasting their activity in human lymphomas or models relevant to human lymphomas is daunting since there are thousands of possible dose schedules and combinations. Moreover we have no way to monitor the activity of most drugs in humans. The goal of this SCOR is to remedy this situation. Specifically we will identify molecular features that distinguish refractory from sensitive lymphomas and develop treatments that overcome chemoresistance or eradicate lymphomas without chemotherapy. We will develop biomarkers to accurately monitor these treatments. To achieve this we established a unique suite of technologies called “PATh”. PATh allows us to screen thousands of treatments in perfectly characterized human primary lymphoma specimens and select only the best of these for testing in more advanced systems that we developed in mice, and pet dogs with spontaneous lymphomas. The most potent of these hundreds of tested therapies and biomarkers will be evaluated in clinical trials specifically for those patients with suitable molecular profiles. Hence this SCOR is poised to transform the care of patients who currently have no hope of cure.

Specialized Center of Research Program
Precision medicine deployment of mechanism based Epigenetic – Immune therapy for B-cell lymphoma United States -

B-cell lymphomas, especially those that are incurable, remain an important and urgent clinical challenge. One of the salient features of these most malignant and incurable lymphomas is their ability to hide from the immune system by shutting off the production of genes that produce the so-called “major histocompatibility (MHC) class II” proteins. These “cloaked” lymphoma cells are able to spread throughout the body without being noticed by T-cells. Interestingly, in the normal immune system B-cells produce plenty of MHC class II so that our T-cells can see them and make sure that no aberrant B-cells survive in the body. However, we discovered that lymphomas are able to shut off production of MHC class II by chemically modifying these genes through an enzyme called HDAC3 (histone deacetylase 3). In addition to silencing MHC class II, HDAC3 also turns of genes that control cell growth. Hence HDAC3 has the pernicious dual effect of causing lymphoma cells to grow out of control while at the same time hiding them from the immune system. Drugs that target histone deacetylase enzymes in general can reverse the effect of HDAC3. However, these drugs by blocking many different histone deacetylases simultaneously, cause toxic and counterproductive effects that limit their utility. Fortunately, we have a new drug that only blocks HDAC3 without affecting the other enzymes. For the first time, we can now specifically block this critical HDAC3 disease mechanism without the undesirable effects of the older, less specific drugs. Importantly, we also find that targeting molecules that B-cells use to suppress T-cell response (the so-called “Immune Checkpoint”) results in even greater induction of an immune response against lymphomas. We think we can combine HDAC3 inhibitors and checkpoint inhibitors in patients to completely “de-cloak” lymphoma cells and allow the patient’s immune system to destroy them. One of the great challenges in bringing very specific new therapies like this to the clinic is predicting which patients will benefit. Our scientific research suggests that patients with a particular and very common lymphoma mutation affecting a gene called CREBBP, are especially responsive to this therapy. Taken together, our research proposal characterizes a novel molecular mechanism in lymphoma that will yield a completely novel and potent targeted therapy combining effects against the tumor cells themselves while simultaneously causing the immune system to clear any remaining lymphoma cells. Moreover, we will be able to deliver this therapy to the right patients by using genetic, precision medicine biomarkers that can be readily used in the clinical setting.

Translational Research Program
The structural functions of ATR kinase in development, oncogenesis and cancer therapy United States -

Lymphomas are a group of blood cancers that develop from a type of white blood cells called lymphocytes. One common feature of lymphomas, and of many types of cancers, is genome instability, defined as the inability of cells to repair damaged DNA. This leads to the accumulation of mutations and in some cases, larger changes in the chromosomes, all of which can make a more aggressive cancer and can lead to the development of therapeutic resistance. Cells normally have DNA repair mechanisms for correcting mistakes made during ordinary DNA replication. Certain types of developing lymphocytes are particularly dependent on DNA repair mechanisms. These lymphocytes require substantial DNA modifications to produce the diverse array of antibodies the body needs for a properly functioning immune system. In fact, some lymphomas develop mutations in DNA repair genes, and this leads to increased genomic instability, which contributes to the cancer’s survival and proliferation. My research focuses on ATR, a protein that senses the integrity of DNA and chromosomes and alerts the rest of the cell when the DNA needs to be repaired. Research from our group and others suggests that lymphoma-associated mutations in ATR produce a protein that is functionally different from the ATR protein in healthy cells. We therefore hypothesize that the lymphomas with these mutations not only use mutant ATR to enhance their tumor activities but also grow to depend on these mutations for their own survival. This likely explains the killing effect that ATR inhibitors have on lymphoma cells. My research is investigating how the lymphoma-causing changes activate ATR and how ATR inhibitors are able to selectively kill lymphoma cells. Using cutting-edge genetic and cell biology approaches, we aim to understand mechanistically how inhibiting ATR affects lymphoma development. Furthermore, cells derived from lymphomas will be treated with these ATR inhibitors, alone and in combination with classical chemotherapeutic agents, and the responses will be analyzed. These studies will allow us to determine what other treatments, already available in the clinic, could be combined with ATR inhibitors to treat lymphomas. These experiments will provide a greater understanding of ATR in lymphoma and may suggest combination strategies to be tested in lymphoma patients in the future. Ultimately, these experiments lead to an improvement in the lives of lymphoma patients.

Career Development Program
Therapeutic Development of Mesothelin Antibody-Drug Conjugate
Anetumab Ravtansine in Mesothelin Expressing Childhood AML
United States - Special Grants
Novel immunotherapeutic strategies in infants with high risk AML United States -

Acute Myeloid Leukemia (AML) is a particularly devastating disease in infants, where therapies that are intended to cure leukemia frequently fail to cure the disease as well as lead to significant life limiting or life ending complications. Leukemia-specific, targeted therapies are critical, especially in these most vulnerable patients in order to cure the disease without causing irreversible damage to the growing body. Through the largest and most detailed genetic sequencing studies, we have identified two genetic abnormalities (chromosome translocations) that are only seen in babies younger than 5 years of age, and cause lack of response to all available therapies, and more than 80% of babies with these abnormalities die of leukemia despite intensive chemotherapy. In our initial analysis of this sequencing data we discovered that leukemic cells in the babies with one of these abnormalities (CBF/GLIS) express a protein called CD56 at high levels. Expression of this protein on the leukemia provides an opportunity for targeting the leukemic cells with immunotherapy. Our initial studies have shown great promise that targeting CD56 with available drugs bound to CD56 antibody allowed killing of leukemic cells that express CD56. In collaboration with Dr. Correnti (director of protein science lab, FHCRC) and Dr. Fry (Denver Children’s Hospital), we will make new immunotherapies directed at CD56. In addition, we intend to use the genomic sequencing data we have generated from 2000 children with AML to discover novel immunotherapeutic targets and generate new antibodies to generate three different immunotherapies including antibody-drug conjugates (ADCs), Bispecific T-cell engagers (BiTEs), and chimeric antibody T-cells (CARTs). Our initial interrogation of the sequencing data has identified a large number of potential targets and made us highly optimistic that we will be able to identify and validate potential targets and rapidly move into therapeutic development in the first two years of this grant, followed by testing of these immunotherapies for their efficacy in the laboratory.

Translational Research Program
Cobomarsen clinical development for CTCL, mycosis fungoides sub-type United States - Therapy Acceleration Program
Overcoming resistance to targeted therapies in multiple myeloma United States -

Multiple myeloma (MM) is this second most commonly diagnosed blood cancer in the Western world and, during the last 15 years, substantial progress in its clinical management was achieved through the development of novel therapies for this plasma cell malignancy. However, MM is still considered an incurable neoplasia because its tumor cells eventually become resistant to any individual therapies or combinations thereof. The mechanisms that cause treatment resistance in MM can differ substantially, both across patients and within each individual one, and depend on the characteristics of each individual treatment and on the support provided to MM cells by nonmalignant cells of the local microenvironment. The goal of this research program is to systematically characterize the complex mechanisms through which MM cells develop resistance to the main classes of anti-MM therapies and their combinations, with the intent to distill this complexity to a small set of molecular networks that can account for the resistance of most MM patients to currently available treatments or promising investigational agents. Importantly, we seek to develop specific therapies to target these networks in order to improve the clinical outcome of patients, towards the ultimate goal for a cure. We envision that this research will develop a new framework which can be applied not only in MM, but also other blood cancers.

Career Development Program
CRISPR-based functional characterization of WM cells: insights into therapeutic vulnerabilities and strategies to overcome resistance United States - Special Grants
Targeting Thrombopoietin Signaling in the MPN United States - Special Grants
STRUCTURAL CHROMOSOMAL REARRANGEMENTS AND THE MULTI-STEP PROGRESSION OF MULTIPLE MYELOMA United States -

In multiple myeloma (MM) chromosomal structural variants deregulate oncogene function by complex rearrangements termed chromoplexy and chromothripsis that place strong gene control element, a super-enhancer, next to a critical target gene or combination of genes. Using next generation sequencing as a tool to screen the non-coding regions of the MM genome, we will identify these events, determine their molecular associations, contribution to clinical outcome, and the mechanisms by which multiple target genes are deregulated. This work will inform a generalizable mechanism that can be therapeutically targeted in both MM and other cancers.

Translational Research Program
JAK/STAT inhibition as a therapeutic strategy in T-cell lymphoma United States -

This project aims to develop new personalized therapies to work in combination with ruxolitinib for the treatment of T-cell lymphomas. The T-cell lymphomas are rare diseases that are typically associated with poor prognosis. Developing new agents for T-cell lymphomas is particularly challenging due to the marked heterogeneity among these diseases. Despite their heterogeneity, we currently use the same treatment approach for the most common entities; however the treatment should be as varied as the diseases themselves. There are limited numbers of effective treatment options for patients with T-cell lymphoma, and the selection of treatment has been largely based on observation rather than driven by biomarkers or disease biology.

Recent studies have revealed new insight into the biology of T-cell lymphomas, leading to identification of potential therapeutic targets in these diseases. One such target is the JAK and STAT pathway, which is activated in a significant subset of T-cell lymphomas. Ruxolitinib is a JAK inhibitor that is FDA-approved for the treatment of other blood disorders. Based on the biological characteristics of T-cell lymphomas, I am leading a phase II clinical trial to evaluate the efficacy of ruxolitinib in patients with various T-cell lymphoma subtypes, with particular focus on identifying biomarkers that predict sensitivity and resistance to this agent. Identification of biomarkers may be useful in the future to identify patients who are most likely to respond to this therapy as well the earlier identification of patients who are bound to develop resistance. Enrollment in this study is about 80% complete, and we have observed efficacy, particularly in patients with T-cell lymphoma characterized by JAK/STAT pathway activation.

Most responses to ruxolitinib are partial and transient, indicating that T-cell lymphomas treated with ruxolitinib eventually acquire resistance to JAK inhibition. It is likely that activation of alternative pathways are at least in part responsible for acquired resistance. Targeting JAK and one or more such alternative pathways could improve the patient’s response. Through biomarker analyses of tissue and blood samples from patients treated with ruxolitinib, we are working to identify pathways that become activated following exposure to JAK inhibition. These analyses will inform the design of the next studies evaluating ruxolitinib in combination with alternative pathway inhibitors and ultimately lead to the development of promising treatment strategies for these diseases.

Career Development Program
Enhancing the clonal selectivity of current drug therapies in myeloproliferative neoplasms United States -

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.

Career Development Program