Grant: 6528-18 | Translational Research Program (TRP):
Location:Board of Trustees of the Leland Stanford Junior University, San Francisco, California 94144-4253
Project Title: Identifying Relapse Associated Populations At Diagnosis In LeukemiaProject Summary:
Despite high rates of initial response to frontline treatment in many human cancers, mortality largely results from relapse or metastasis. Diverse clinical outcomes occur because all cells within a given tumor do not possess the same behavior or response to therapy. Although there is debate as to whether resistant populations of cancer cells are present at the time of initial diagnosis or whether these traits develop under the pressure of therapy, many studies have suggested that it is the former. Remission, by definition, is the reduction of cancer cells to undetectable levels. Consequently, if cellular populations predictive of relapse exist at diagnosis, it is reasonable to assume that these cells are a minority of the bulk tumor cells. In order to uncover these key populations, it is required to study cancer at the single cell level. Following this reasoning, we propose to perform analysis of primary leukemia cells at diagnosis by examining over 40 proteins on individual cells from patients with B-cell progenitor acute lymphoblastic leukemia (BCP-ALL), the most common leukemia of childhood. The goal of this research is to identify cells associated with relapse at the time of diagnosis. By identifying such populations, we may begin to understand how these cells survive treatment and cause later relapse. In order to organize diverse single-cell data from many primary patient samples, we will use a tool to match each leukemia cell to it's most similar healthy B-cell population. This allows us to compare leukemia cell subsets across patients.
We have optimized this approach in an early study and have identified specific populations of immature B-cells present at diagnosis which are predictive of relapse by applying advanced computational approaches to this single-cell data. This letter of intent outlines a proposal to extend our initial studies using this approach to validate the proposed cellular population which confers relapse risk and to understand how these cells are treatment resistant. To do so, we propose the following efforts:
1. Validate our relapse prediction model in a large cohort of pediatric patient samples and determine if the same cells exist in adult B-cell progenitor acute lymphoblastic leukemia (BCP-ALL) diagnostic samples
2. Determine if primary treatment-resistant cells, taken from patients early in therapy, are similar to the cells we have identified to be predictive of relapse
3. Determine if treatment resistant cells are better suited to grow in commonly used models of BCP-ALL
This proposal presents a novel approach to bring single-cell studies combined with advanced computational approaches to improve outcomes for patients with BCP-ALL.
Grant: 6533-18 | Translational Research Program (TRP):
Location:Sloan Kettering Institute for Cancer Research, New York, New York 10087
Project Title: Chemotherapy-Free Targeted Therapeutic Approaches For New And Relapsed Hairy Cell LeukemiaProject Summary:
Classic hairy cell leukemia (cHCL) is a relatively rare form of adult blood cancer that causes massive enlargement of spleen and low white blood, red or platelet cell count. It remains incurable despite high initial response rates to DNA-damaging chemotherapy such as cladribine and pentostatin, and 40% of the patients will experience recurrent disease. In order to develop an effective personalized treatment in these patients, our group previously conducted a clinical trial studying the safety and efficacy of the oral drug called vemurafenib specifically targeting the BRAFV600E mutation that is known to occur in almost all patients with cHCL. In that study, we observed a remarkable overall response rate of 96% in cHCL patients who have failed chemotherapy or experienced recurrent disease. However, we also observed key limitations from the study: 1) vemurafenib alone failed to eliminate all leukemic cells from the bone marrow; 2) disease relapsed in over 30% of the patients; and 3) some patients developed resistant disease, no longer responsive to vemurafenib. These limitations were partly addressed by another recent study that showed adding antibody targeting CD20 called rituximab to vemurafenib significantly improved response rates and more effectively eliminated leukemic cells from bone marrow in patients with relapsed cHCL. However, this promising combination has not been studied in untreated patients who would otherwise receive chemotherapy. Furthermore, vemurafenib is not effective in patients with the related disease called HCL variant (HCLv) and high-risk cHCL that does not carry the BRAFV600E mutation. These disease subtypes tends to be more aggressive, respond poorly to standard therapies, and very little is known about the disease biology. While HCLv does not carry the BRAFV600E mutation, it frequently carries MAP2K1 (MEK1) mutations that may be treated by another oral drug inhibiting its downstream target called ERK. Based on the above findings, we believe that (1) the BRAF inhibitor, vemurafenib, plus a potent CD20-specific antibody, obinutuzumab, will be more effective in eliminating leukemic cells from bone marrow, resulting in more durable responses in patients with previously untreated BRAFV600E+ cHCL and (2) ERK inhibition may be a novel and safe targeted therapy for HCLv and cHCL without the BRAF mutation. Therefore, we propose to develop a comprehensive clinical and laboratory program to study rational, chemotherapy-free, targeted therapeutic approaches in all subtypes of HCL for both untreated and relapsed patients. To this end, we will perform a phase 2 clinical trial of vemurafenib plus obinutuzumab in untreated BRAFV600E+ cHCL patients and, in parallel, a phase 1 clinical trial of the ERK inhibitor BVD-523 in patients with HCLv and relapsed cHCL. In addition, we will perform studies involving mouse models and comprehensive genome profiling of patient samples to understand treatment responses and disease biology.
Grant: 3371-18 | Career Development Program (CDP):
Location:The University of Chicago, Chicago, Illinois 60637
Project Title: Single-cell Technologies To Dissect 5hmC And 5mC Heterogeneity In Normal And Malignant HematopoiesisProject Summary:
Blood cells arise from stem cells found in our bone marrow. Through a process called differentiation, stem cells develop into the diverse blood cell types with their various functions. Cells of the same blood subtype are often thought of as homogeneous populations, but this extreme simplification imposes limitations on our ability to understand normal and malignant blood cells. Therefore, it is critical to understand the more complicated reality of blood cell diversity. Our laboratory is devising cutting-edge strategies to map normal and diseased blood stem cells and differentiated cells in both healthy and diseased situations. These approaches will allow a better understanding of the differences among cells types, within subtypes, and in different pathological contexts, which will provide the basis for therapeutic approaches in the future.
DNA is the molecule that codes for proteins that help provide the functional attributes of cells. DNA is often changed by a process called epigenetic modification. One common form of epigenetic modification is DNA methylation, which can come in different forms, such as 5mC and 5hmC, and can occur at a large number of places in the billions of building blocks of DNA. We hypothesize that a critical component of understanding the identity and function of a cell, whether healthy or diseased, is in the precise characterization of the complex DNA methylation pattern within each single cell. However, stem cells and cells of various differentiated blood cell subtypes are often found in limited numbers. Therefore, the ability to measure 5mC and 5hmC in various cell types, and at a single cell-level, is essential for a more complete understanding of normal and diseased blood cells.
Our single-cell 5hmC/5mC profiling approach will allow us to identify leukemia-specific, differential methylated regions that could harbor known and novel disease-specific target genes, providing quantitative information to precisely reveal methylation changes during normal and leukemic blood cell development. Ultimately, this research will bring us closer to understanding how acute myeloid leukemia develops and how dysregulation of methylation contributes to this process. Our approach will identify promising ways of targeting leukemia cells, facilitating the treatment of this deadly disease.
Grant: 5472-18 | Career Development Program (CDP):
Location:British Columbia Cancer Agency Branch, Vancouver, British Columbia V5Z 1L3
Project Title: Roles Of MicroRNA MiR-146a In Hematopoietic Stem Cell FunctionProject Summary:
Myelodysplastic syndrome (MDS) is a cancer of blood stem cells, the blood-forming cells in the bone marrow. In MDS, cancerous blood stem cells lose the ability to make blood cells, and can also block the function of the remaining normal blood cells. Aging and environmental factors are associated with developing MDS, but how these processes affect the function of both cancerous and coexisting normal blood stem cells in MDS remains poorly understood. Few treatments are available for MDS, and treatment resistance develops in most patients; therefore, understanding the molecular mechanisms that disrupt blood stem cell function in MDS is critical for improving patient outcomes.
I aim to study the molecular mechanisms affecting the function of coexisting cancerous and normal blood stem cells in a mouse model of MDS. I will focus in particular on a subtype of MDS that lacks the gene miR-146a, as we have found that miR-146a deletion in a mouse model causes aggressive MDS symptoms with severe defects in blood stem cell function. To better recreate the bone marrow of MDS patients in which normal and mutant cells coexist, I will co-transplant equal amounts of normal bone marrow with miR-146a-deleted bone marrow, and study the function of both cancerous (miR-146a deleted) and normal (miR-146a intact) blood stem cells. Our data suggest that miR-146a deletion activates inflammation, increases cellular aging, and disrupts energy metabolism in blood stem cells. I will use chemical and genetic strategies to manipulate inflammation, aging pathways, and energy metabolism, with the hope of reversing the dysfunctions of cancerous and normal blood stem cells in this mouse model.
This research will provide the first evidence as to whether drugs targeting inflammation, aging pathways, or energy metabolism may be useful additions to current treatment regimens for MDS. As few effective long-term treatments are available for MDS, my research may one day improve the prognosis for patients with MDS.
Grant: 2317-18 | Career Development Program (CDP):
Location:Washington University in St. Louis, St. Louis , Missouri 63130
Project Title: Targeting Leukemia Stromal Interactions In T-ALLProject Summary:
T-cell acute lymphoblastic leukemia (T-ALL) is a subtype which comprises about 20% of all cases of acute lymphoblastic leukemia. T-ALL is a particularly rare disease in adults, with only about 600 new cases per year in the United States. Furthermore, the prognosis of adults is poor; only 40% of adults with T-ALL are cured with current treatments.
Our laboratory work has demonstrated that T-ALL cells interact with normal cells present in their local environment (called the “microenvironment”), which provides key signals that regulate tumor growth and survival. Our research has focused on a specific protein, CXCR4, which is present in T-ALL cells. In T-ALL, the tumor microenvironment provides a potent growth and survival signal, which is mediated by CXCR4, to T-ALL.
We hypothesize that it is possible to disrupt this tumor-microenvironmental interaction as a means to treat T-ALL patients. We will disrupt the key survival signal to T-ALL cells using a novel inhibitor of CXCR4 known as BL-8040. We are currently conducting a multicenter study to combine BL-8040 treatment with chemotherapy in patients with T-ALL that has relapsed or is refractory to standard treatments. As part of this study, we will test blood and bone marrow samples from patients after treatment to determine the effects of BL-8040 on leukemia cells. We will also conduct additional preclinical studies to test the effects of new combinations of drugs to improve the effectiveness of BL-8040. The overall goal of this project is to target tumor-microenvironment interactions to improve the outcomes of patients with T-ALL.
Grant: 5464-18 | Career Development Program (CDP):
Location:Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
Project Title: The Impact Of Immunoglobulin Isotype (IgM Vs IgG) On B Cell Lymphomagenesis And Progression.Project Summary:
B-cell lymphomas continuously multiply because growth regulation signaling is altered to stay ‘on’ all the time. This signaling is normally triggered by activation of proteins called receptors on the cell surface. Most lymphomas require signaling from a group of receptors called the B-cell receptor (BCR). Normal B-cells produce a type of BCR, called immunoglobulin (Ig), in a process called the germinal center (GC) reaction. There are several types of Ig subtypes – IgM, IgG, and IgA isotypes—which are produced during the GC in response to stimuli generated by agents foreign to the body. B-cells with different Ig isotypes behave and function differently. Diffuse large B-cell Lymphoma (DLBCL) frequently arises during the GC reaction and express either IgM, IgG or IgA types of BCR. However, the signaling potential and role of Ig isotypes in B-cell lymphoma is poorly understood.
DLBCL can be further sub-categorized into two subgroups: the Germinal Center B-cell type (GCB) DLBCL and Activated B-cell type (ABC) DLBCL. While ABC-DLBCL is a more aggressive disease with a poorer clinical outcome, the GCB-DLBCL is a less aggressive disease with better patient outcomes. Importantly, both subgroups of DLBCL depend on B-cell receptor (BCR) signaling for their survival and proliferation. Interestingly, GCB-DLBCL cells primarily express the IgG isotype of BCR, whereas the majority of ABC-DLBCL cells express IgM. Consistent with these findings, the two subgroups of DLBCL respond differently to BCR signaling inhibition by ibrutinib. In a recent study, there was only a 5% response rate among GCB-DLBCL patients treated with ibrutinib, whereas there was a 38% response rate among ABC-DLBCL patients. These findings, along with the expression of different Ig isotypes, are suggestive of the involvement of differential BCR signaling cascades in the pathogenesis of GCB- versus ABC-DLBCL. To address this idea, we analyzed changes in protein activation between IgM and IgG positive cells in normal B-cells from mice. Remarkably, we observed differential activation of common signaling components among the different Ig isotypes. We are currently seeking to elucidate the molecular mechanisms by which different Ig isotypes impact the survival and proliferation of lymphoma cells. We will also study the effect that these differences may have on regulating the sensitivity of lymphoma cells to approved therapies. Lastly, during these studies we hope to uncover novel therapeutic targets, which may eventually lead to better treatments for DLBCL.
Grant: 1352-18 | Career Development Program (CDP):
Location:New York University School of Medicine, Boston, Massachusetts 02241-415026
Project Title: MicroRNA Regulation Of Leukemia Stem CellsProject Summary:
Acute myeloid leukemia (AML) is composed of two populations of cells with differing characteristics. The bulk population directly gives rise to the disease symptoms. The second population is very small and is composed of leukemia stem cells (LSCs), whose role is to initiate disease and generate the AML bulk population. These self-renewing LSCs are therapy resistant and mediate disease relapse; therefore, it is critical to understand the mechanisms that regulate LSCs in order to develop strategies designed with the intent to cure.
The characteristics of all cells are determined by DNA contained in the nucleus of the cell. The information DNA provides is converted to RNA, which is exported out of the nucleus into the cytoplasm of the cell, where the cell’s proteins are produced. Small RNA molecules, called microRNAs (miRNAs) regulate the expression of protein-encoding genes in cells.
My laboratory has shown that miRNAs can regulate normal blood stem cell function, promote the development of AML, and regulate LSCs. We have shown that two nearly identical microRNAs are frequently overexpressed in LSCs, but it is unclear what their relative contributions are to regulating leukemia cell survival and LSC function. We hypothesize that these two microRNAs can serve overlapping but non-redundant functions due to differences in their location within the cell. Indeed, while most miRNAs are thought to function in the cytoplasm of the cell, some microRNAs enter the nucleus, and we predict that such a nuclear distribution will affect their ability to regulate genes critical for LSC function. Leveraging our expertise in LSC biology, as well as novel technologies that we have either developed or optimized, we seek to better understand the role of these critical miRNAs in AML disease initiation and maintenance. Thus, we propose to: 1) Determine whether structurally similar microRNAs play similar or unique roles in LSCs; 2) Determine whether the subcellular location of microRNAs dictates their ability to regulate LSC function; and 3) Identify the genes that these microRNAs regulate, specifically in LSCs. Overall, we expect to not only reveal how microRNAs regulate LSCs but also to provide general insights into how microRNAs can differentially regulate gene expression based on their position within a cell. These investigations may lead to a better understanding of AML and may provide avenues for novel therapeutic approaches.
Grant: 6543-18 | Translational Research Program (TRP):
Location:Children's Research Institute, Washington, District of Columbia 20010
Project Title: Novel Combination Immunotherapies For High Risk Hodgkin's LymphomaProject Summary:
Hodgkin’s lymphoma (HL), a type of blood cancer is largely curable but with significant long-term side effects. Moreover 10-20% of patients are resistant to treatment and difficult to cure. HL is unique that the tumor cells are surrounded by an inhibitory environment that makes the immune system dysfunctional and allows evasion from an effective anti-tumor response. Understanding this environment may provide insight into how we can spur the immune system to attack HL cells effectively. Like many cancer cells, HL cells escape the immune attack by expressing a protein called PD1 or PDL-1, which is is normally expressed by healthy T cells to prevent them from attacking healthy cells. PD1-inhbitors are drugs that can bind to the PD-1/PDL-1 on lymphoma cells thereby releasing the “brakes” on the immune system to mount a strong attack on the HL cells. The lymphoma cells also secrete certain chemicals like TGFβ which incapacitates the immune cells to kill the lymphoma cells effectively. The goal of this project is to understand how we can change the tumor microenvironment sufficiently to unleash pre-existing anti-tumor immune responses and allow more successful incorporation of killer- T cells. We will determine if PD1 inhibitors when given in combination with the administration of a novel cancer killing T-cell therapy will produce long-lasting cures in patients with high risk HL with less side effects than conventional chemotherapy. Finally, we will continue to improve the efficacy of our combination immunotherapy approach by also engineering the cancer killing T cells to become resistant to the inhibitory chemical TGFβ which is released by the HL tumor cells and has devastating effects on T cell function in vivo. In the laboratory we will determine if these engineered T cells have enhanced killing ability compared to the non engineered T cells.
Grant: 6537-18 | Translational Research Program (TRP):
Location:Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
Project Title: Attenuating Oncogenic Myc-driven Transcription Via Modulation Of The Max Heterodimer PartnerProject Summary:
An emerging therapeutic strategy involves controlling the function of overactive transcription factors that regulate the expression of established disease genes in cancer. As transcription factors have historically proven recalcitrant to drug discovery, several labs are pursuing this opportunity by developing indirect inhibitors of transcription that target various chromatin binding factors as well as kinases that play a role in transcriptional initiation. Our lab is focused on discovering and developing small molecules that perturb the function of oncogenic transcription factors by targeting the protein itself or close interacting partners in relevant complexes. We use unbiased binding assays involving small-molecule microrrays to search for compounds that bind to either purified transcription factor, presumably in a highly disordered state, or to protein complexes containing the transcription factor from cell lysates corresponding to various tumors of origin. While our lab is using this approach to identify chemical probes for several transcription factors, roughly half of our group is focused on developing targeted strategies to modulate MYC-driven transcriptional programs. Activation of MYC is one of the most frequent oncogenic events in human malignancies and inactivation of MYC using small molecules may provide a general and effective approach to treating cancer, as MYC is one of the most common drivers of malignancy. Using our screening approach, we identified compounds that bind to c-MYC or its interacting partners such as MAX and found a subset of compounds that modulate a variety of MYC functions in cells, including MYC-mediated transcription. This preliminary data forms the foundation of the studies proposed herein that emphasize advancing the compounds to develop bona fide chemical probes by precisely characterizing their molecular and cellular mechanisms of action as well as synthetically optimizing the compounds with emphasis on improving physicochemical characteristics. Moreover, we propose translational studies involving a lead compound that preliminarily impacts tumor volume in an aggressive murine model of MYC-driven lymphoma. Pursuant to these aims, our lab is comprised of a collaborative, multi-disciplinary team with expertise in methods related to transcriptional profiling, chromatin profiling, quantitative proteomics, computational biology, synthetic chemistry, molecular recognition, and pharmacology. Through these efforts, we hope to build a toolbox of chemical probes that modulate MYC function via different molecular mechanisms and to evaluate these mechanisms as candidates for therapeutic intervention. A key goal for our lab is to make chemical probes and structurally related inactive analogs for MYC and other transcription factors available to the wider research community without encumbrance.
Grant: 6546-18 | Translational Research Program (TRP):
Location:Boston Children's Hospital, Boston, Massachusetts 02241-4413
Project Title: Deciphering Epigenetic Cross-talk In Diffuse Large B-cell LymphomaProject Summary:
With an estimated 73,000 new cases of non-Hodgkin lymphoma (NHL) and 20,000 deaths in the year 2016 alone from NHL, novel therapeutic strategies are urgently required. Specifically, the diffuse large B-cell lymphoma (DLBCL) is the most common form of NHL, and contributes about 30% of new NHL diagnosis every year. Our interest in blood biology, and its mis-regulation is several blood disorders including blood cancers, led us to investigate the role of chemical modifications on one of the most fundamental proteins of like- the histone proteins. We investigated if various histone modifications would be critical for the survival of DLBCL cells. Interestingly, we discovered a unique chemical that specifically abrogates the survival of DLBCL cells but not of any other type of blood cancer cells. We have found that cells commit ‘suicide’ after treatment with our chemical, using a very specific pathway. Furthermore, we have identified a key protein responsible for gene regulation as a likely target of our chemical. This novel target is highly expressed in DLBCL patients, who fare worse after the standard-of-care therapy for DLBCL. Additionally, by performing high throughput gene expression studies, we have identified a completely unique mechanism that bypasses three very frequent mutations found in DLBCL patients, and also explains why our chemical is not very effective against cells that are not coming from DLBCL patients. In essence, we have identified a histone modification pathway that when manipulated kills multiple types of DLBCL cells, but not other types of hematological cancers. We will employ cutting-edge molecular and cell biology, biochemistry, and mouse genetics to carry out specific aims that will a) establish the novel mechanism that allows DLBCL cells to survive. b) Establishes our chemical as a potent strategy against DLBCL through experiments conducted in mouse and c) reveal new details about how histone modifications regulate the formation, and development of B and T cells in humans.