SPORE in Leukemia
Principal Investigator: Daniel Link, MD
Washington University’s Specialized Programs of Research Excellence (SPORE) in Leukemia aims to develop novel biomarkers and treatments for leukemias and myelodysplastic syndromes. In this SPORE, we leverage our expertise in cancer genomics, immunology, and hematopoiesis to develop innovative translational research in leukemia.
Our SPORE includes five translational research projects:
- Basic Science Co-Leader: Timothy Ley, MD
- Clinical Science Co-Leader: John Welch, MD, PhD
- Basic Science Co-Leader: Daniel Link, MD
- Clinical Science Co-Leader: Geoffrey Uy, MD
- Basic Science Co-Leader: Timothy Graubert, MD
- Clinical Science Co-Leader: Matthew Walter, MD
- Basic Science Co-Leader: John F. DiPersio, MD, PhD
- Clinical Science Co-Leader: Peter Westevelt, MD, PhD
- Basic Science Co-Leader: Todd Fehniger, MD, PhD
- Clinical Science Co-Leader: Amanda Cashen, MD
These projects are supported by three shared resources: Core A. Biospecimen Processing; Core B. Biostatistics; and Core C. Administration. This SPORE also supports a Career Enhancement Program to recruit and mentor new investigators in translational leukemia research and a Developmental Research Program to support innovative translational concepts.
SPORE Shared Resources (Cores)
Core A: Biospecimen Processing
The Biospecimen Processing Core (Core A) is responsible for the identification and enrollment of every patient referred to the Siteman Cancer Center with newly diagnosed and relapsed hematologic malignancy (excluding multiple myeloma). The pathologic material from these patients will be banked using the existing Siteman Cancer Center (SCC) Tissue Processing Core (TPC), and clinical data will be tracked prospectively in a clinical database.
Core B: Biostatistics
Director: J. Philip Miller, PhD
The Biostatistics Core provides resources to assist in the planning, conduct and analysis of the proposed research in such a way that quantitative analyses are appropriate and illuminating. The Core also assists in the dissemination of appropriate information both within and external to the SPORE and the Siteman Cancer Center (SCC). The Core is staffed by a dedicated biostatistician for each of the 4 projects. In addition a designated faculty member is devoted to collaborations concerning specialized bioinformatics issues. The Biostatistics Core will serve as a resource and collaborator for the four main projects proposed in this application, Career Development Program and Developmental Research Program projects and the SPORE Cores.
Core C: Administration
Director: Daniel Link, MD
The Administration Core provides executive oversight and administrative support for all of the projects and cores that comprise the Leukemia SPORE. The goal of the Administration Core is to monitor the activities of all of the program components, to comply with all local and federal guideline for grant administration, and to facilitate communication and collaboration among the program members.
Career Enhancement Program (CEP)
The goal is to recruit and support new independent investigators in the field of translational leukemia research. The research initiatives that will be funded by the CDP are expected to have a major translational component, focusing on leukemia etiology, diagnosis, early detection, treatment, or population science.
Junior faculty (Instructor or Assistant Professor) without RO1 or equivalent grant or senior post-doctoral fellows (PhD, MD, or MD-PhD) who have a written commitment from their department chair indicating promotion to Instructor or Assistant Professor by the time of the award also will be eligible.
One award of $70,000 (direct cost) will be made annually. The second year of funding is contingent upon adequate progress.
The current application cycle is now closed. For additional information please contact Brittni Cannella at firstname.lastname@example.org.
Miriam Kim, MD
Project title: Chimeric antigen receptor T cells targeting KIT for treatment of acute myeloid leukemia
T cells can be genetically engineered to target a specific cell surface marker that is present on cancer cells, and this form of therapy, termed chimeric antigen receptor (CAR) T cells, has been highly successful in the treatment of acute lymphoblastic leukemia. We propose to adapt CAR T cell therapy to meet the unmet needs of patients with acute myeloid leukemia (AML), an aggressive disease with generally poor clinical outcomes. One of the barriers to utilizing CAR T cells for AML has been the concurrent presence of AML surface markers on normal blood stem cells, as targeting these antigens will then lead to bone marrow failure. Prior efforts in the field have concentrated on trying to find strategies to mitigate this toxic side effect; however, we propose to use this to our advantage, by developing CAR T cells as both a therapy for AML and a conditioning regimen prior to allogeneic hematopoietic stem cell transplant (HSCT). We believe that combining CAR T cells with an HSCT will maximize the benefit of both therapeutic approaches and can lead to long-term cures for patients with AML. As proof-of-concept for this strategy we plan to target KIT, a classical marker of HSPCs, with CAR T cells. We will extensively characterize the activity and toxicity of this therapy in different mouse models to ensure its safety and efficacy.
Matthew Christopher, MD, PhD
Project title: Error-Corrected Sequencing for Early Detection of AML Relapse After Stem Cell Transplant
Acute Myeloid Leukemia (AML) is a life-threatening blood disease that affects about 20,000 new patients every year. For many patients, the best chance for a cure is by getting a hematopoietic stem cell transplantation (HSCT) from a donor. Unfortunately, many patients with AML—as many as 40-50%—still relapse even after transplantation, and the chances of curing patients in this setting are low.
Most relapses after HSCT occur within the first two years, and patients undergo surveillance bone marrow biopsies at different time points during this period. If there is evidence that patients are about to relapse, they can get some therapy to try to prevent the recurrence. The methods for trying to predict relapse while the patient is still in remission are relatively insensitive, and it is possible that relapses could be treated more effectively if they are detected earlier. For this reason, many researchers are trying to develop better techniques for predicting relapse. In a preliminary study, our group showed that by using next-generation sequencing with deep coverage, some AML-associated mutations AML can be detected in remission samples up to six months before relapse.
In this proposal, we will go back to a larger group of patient samples and look for AML mutations in patients who ultimately relapsed as well as those who never relapsed. We will test for the presence of mutations in the samples from relapse group and confirm that we can’t find mutations in the patients who didn’t relapse. If successful, we will propose a clinical trial to test whether early prediction of AML relapse by mutation detection can predict and prevent relapse after HSCT.
Grazia Abou-Ezzi, PhD
Project title: TGFB Signaling in Mesenchymal Stromal Cells
Hematopoietic stem/progenitor cells (HSPCs) reside in a specialized microenvironment within the bone marrow called the bone marrow niche. The bone marrow niche is a mix of multiple cell types, including mesenchymal stromal cells. In this study, we focus on understanding how the bone marrow niche is altered in mouse models of myeloproliferative neoplasms (MPNs). Transforming growth factor beta (TGF-β) is known to regulate mesenchymal stromal cell differentiation; interestingly, TGF-β levels are significantly increased in MPN patients. We predict that TGF-β disturbs the bone marrow niche by altering mesenchymal stromal cell homeostasis and, furthermore, that this may lead to the splenomegaly observed in MPN patients. Recent data have shown that TGF-β is a major driver of bone marrow fibrosis. Although the cell of origin of bone marrow fibrosis is largely unknown, we predict that high levels of TGF-β stimulate the secretion of fibronectin and collagen by osteoblastic cells.
To investigate Aim 1, we generated a mouse model in which TGF-β signaling is specifically suppressed in bone marrow mesenchymal cells. Using this model, we will characterize the role that bone marrow mesenchymal cells influenced by TGF-β signaling play in hematopoietic recovery following myelosuppression. In Aim 2, the MPL W515L retroviral transplant model will be used to induce bone marrow fibrosis. Transduced cells will be transplanted into the mouse model described in relation to Aim 1, followed by correlative analysis to assess changes in the bone marrow as fibrosis develops.
The ultimate goal of this study is to translate fundamental observations regarding TGF-β signaling effects on bone marrow mesenchymal cells and the hematopoietic compartment under myelosuppressive and myeloproliferative conditions into advancing care for patients with MPNs. We predict that the results of this study will improve the outcomes of these patients by providing critical insight into optimizing hematopoietic recovery after therapy with myelosuppressive agents. Furthermore, as there are currently no effective treatments for bone marrow fibrosis, our work may provide the foundation for novel therapeutic strategies to treat bone marrow fibrosis in patients with MPNs.
Developmental Research Program (DRP)
The goal is to support innovative translational leukemia research. Proposed projects will be reviewed with the intent that they will develop sufficiently, within one-two years, to be submitted for external peer-reviewed funding. For projects with a clinical trial, they must be ready to study activation within six months of award.
All faculty members (instructor level or higher) are eligible. In addition, senior post-doctoral fellows who have a written commitment from their department chair indicating promotion to Instructor or Assistant Professor by the time of the award will be eligible. Preference will be given to junior faculty or established investigators with a new translational leukemia research focus.
Up to three projects will be awarded a maximum of $70,000 (direct costs) on an annual basis. Selected projects may be considered for a second year of funding based on a competitive renewal.
The current application cycle is now closed. For additional information please contact Brittni Cannella at email@example.com.
Melissa Berrien-Elliott, PhD
Project title: Chimeric antigen receptor modified memory-like (CAR-ML) NK cells for leukemia immunotherapy
Here we propose to test the pre-clinical efficacy of novel chimeric antigen receptor expressing, memory-like (CAR-ML) natural killer (NK) cells against acute leukemia. Acute myeloid leukemia (AML) is an aggressive cancer of developing myeloid cells that has poor prognosis, and poor long-term disease-free survival for patients treated with standard therapy. Acute lymphoblastic leukemia is the most common childhood cancer of developing lymphocytes. Recently, CAR-T cells have been approved for treating ALL, but are expensive and associated with severe toxicities, including cytokine-release syndrome.
We have established that human NK cells exhibit innate memory following a brief combined stimulation with interleukins (IL)-12, -15, and -18. Preliminary data demonstrates that memory-like NK cells exhibit significantly enhanced AML recognition, functionality, longevity, and proliferative potential compared to naive or control NK cells. Recent preliminary data also shows that administration of allogeneic memory-like NK cells is safe, feasible, and results in clinical responses in both adult and pediatric AML patients. We hypothesize that approaches that enhance tumor targeting (CAR) will improve the clinical efficacy of memory-like NK cells, while minimizing the toxicities associated with current CAR-based therapies. Here were will functionally characterize CD33 and CD19-scFv expressing CAR-ML NK cells against CD33+ and CD19+ AML/ALL targets in vitro and define their efficacy in vivo using NSG-xenograft mouse models. Ultimately, these studies will provide the pre-clinical rationale for novel CAR-ML NK cell for treating acute leukemia.
Matt Walter, MD, and Zhongsheng You, PhD
Project Title: Targeting Nonsense-Mediated RNA Decay in Spliceosome Mutant Myeloid Malignancies
The goal of this project is to develop new ways to treat patients with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) that have mutations in a set of genes involved in RNA splicing (spliceosome genes). Mutations in spliceosome genes in MDS and AML samples causes abnormal stitching together of RNA (i.e., RNA splicing) in a patient’s blood cells. We know from our prior studies that spliceosome mutant cancer cells are more sensitive to drugs that further perturb RNA splicing, raising the possibility that mutant cells are more reliant on a cells ability to degrade abnormal RNA. Nonsense-mediated RNA decay (NMD) is a pathway in our cells that removes abnormal RNA that harbor premature termination codons, which are generated in spliceosome mutant cells.
Our preliminary data suggest that spliceosome mutant cells are sensitive to a drug that inhibits NMD. The data support the hypothesis that spliceosome mutant cells are dependent on intact nonsense-mediated RNA decay for survival. We will test this possibility using several approaches. We will determine whether expressing a wide-range of spliceosome gene mutations makes blood cells sensitive to NMD inhibition using drugs and genetic approaches. Next, we will determine why spliceosome mutant cells are sensitive to NMD inhibition. Collectively, results from these experiments will be used to plan a clinical trial to treat MDS and AML patients with a new drug that can kill spliceosome mutant cancer cells and improve a patient’s outcome.
Stephen Oh, MD, PhD
Project title: Single Cell Spatial Characterization of Leukemic Transformation
The goal of this project is to identify and characterize specific cell types in the bone marrow of patients with myeloproliferative neoplasms (MPNs) that transform to acute leukemia. Utilizing a novel technology called imaging mass cytometry (IMC), we aim to determine where these cells reside in the bone marrow, and to thereby understand how they interact with neighboring cells to promote evolution to leukemia. By understanding how these cells behave in their resident locations, we seek to identify novel avenues for therapeutic intervention. In the long-term, we aim to devise strategies to broadly prevent the development of leukemia.
Karolyn Oetjen, MD, PhD
Project Title: Stromal interactions in myelodysplastic syndromes characterized by imaging mass cytometry
Myeloid neoplasms, including myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), have complex interactions with the bone marrow environment. Normal blood development originates from hematopoietic stem cells, which are supported within a niche of bone marrow stromal cells. Many growth signals from cytokines in the hematopoietic stem cell niche may support malignant cell proliferation. Particularly in MDS, increased cytokines in the bone marrow environment are implicated in disease development.
Much of this understanding is from mouse models of disease, but characterizing MDS in patients has been more challenging due to limitations in technology and patient samples. Improvements in imaging now allow simultaneous visualization of up to 40 cell markers simultaneously. We propose to apply this innovative technology to biopsy specimens from patients with MDS in order to examine interactions of malignant cells with stromal cells in the bone marrow environment. Quantifying interactions in the hematopoietic niche will provide an understanding of the inflammatory milieu that drives MDS pathogenesis at an unprecedented scale.
Jaebok Choi, PhD, MA
Title: Enhancing Anti-Leukemia Effects of Hematopoietic Cell Transplantation
Bone marrow transplantation (BMT) remains the most effective treatment for patients with high risk and relapsed leukemia and other blood cancers. The therapeutic benefit of BMT for these hematologic malignancies is primarily derived from the donor’s tumor-fighting T cells also known as a graft-versus leukemia (GvL) effect. However, BMT also comes with the risk that the donor T cells in the transplant (graft) will become overzealous and begin to attack not only the leukemia, but also the patient’s skin, intestines, lung, and liver resulting in graft-versus-host disease (GvHD). These two effects of BMT are difficult to separate. As a result, immunosuppressive therapeutic strategies that are often used to prevent and treat GvHD may adversely affect a patient’s survival by reducing the beneficial GvL effect and consequently increasing malignancy relapse. Therefore, finding a means to enhance the GvL activity of T cells while eliminating their tendency to cause GvHD is a major clinical goal in the BMT field. However, the mechanisms by which allogeneic donor T cells differentially modulate GvHD and GvL remain largely unknown. This gap in our mechanistic understanding hinders our ability to treat GvHD while preserving GvL. Accordingly, we will, for the first time, identify novel GvL- vs GvHD associated molecular targets using an unbiased genome-wide CRISPR/Cas9 library. Our study will mechanistically dissect GvHD vs. GvL and provide insights into novel therapeutic strategies to enhance GvL while eliminating GvHD.
John Welch, PhD
Title: Optimizing retinoids for acute myeloid leukemia
Current therapy for acute myeloid leukemia (AML) is toxic and only cures about 30% of patients. We need better drugs with fewer side-effects. In this project, we will explore the potential of two drugs in AML, all-trans retinoic acid (ATRA) and bexarotene. These are both pills, they are FDA approved, and they have very tolerable side-effects. We found that the combination has striking synergy and leads to cell death in aggressive leukemia models in vitro, which contrasts with the modest outcomes we observe when they are used as singleagents in AML patients. In this study, we seek to better understand the molecular mechanisms that facilitate synergy and to chemically optimize bexarotene to treat AML patients. ATRA and bexarotene bind to two respective proteins, RARA and RXRA, which form a single complex. We think synergy occurs because inhibitory proteins can only be displaced from this complex when both ATRA and bexarotene bind. Many derivatives of bexarotene have been synthesized by other groups. We will combine the best chemical features of these compounds to see if we can develop a single drug with better activity and fewer side effects. Mechanistic discoveries will be used to determine the optimal characteristics of retinoids for AML treatment and to refine our drug development. In parallel, we are working to develop a clinical trial of combination ATRA and bexarotene. We hope to learn from this initial trial and then develop future trials with more optimized and AML-specific compounds.
Matthew Cooper, PhD
Title: “Off the shelf” fratricide resistant CAR-T for the treatment of T Cell malignancies
T cell malignancies represent a class of devastating hematologic cancers with high rates of relapse and mortality in both children and adults for which there are currently no effective or targeted therapies. Despite intensive multi-agent chemotherapy regimens, fewer than 50% of adults and 75% of children with T-ALL survive beyond five years. For those who relapse after initial therapy, salvage chemotherapy regimens induce remissions in 20-40% of cases. Thus, a targeted therapy against T cell malignancies represents a significant unmet medical need.
T cells engineered to express a chimeric antigen receptor (CAR) are a promising cancer immunotherapy. Such targeted therapies have shown great potential for inducing both remissions and even long-term, relapse-free survival in patients with B cell leukemia and lymphoma. However, shared expression of target antigens between T effector cells and T cell malignancies has limited development of CAR-T targeting T cell neoplasms due to unintended self-killing of CAR-T (fratricide) and an inability to collect sufficient T cell for CAR-T generation from the patient. Using CRISPR/Cas9 gene editing techniques, we have overcome these obstacles to generate CAR-T effective at killing T cell cancers. The goal of this project is to further develop gene edited CAR-T against T cell malignancies, the first clinically feasible adoptive T cell therapy for T cell leukemia and T cell non-Hodgkin’s lymphoma.
Qiang Zhang, PhD
Project title: Stabilizing AML Cells for Comprehensive Global Proteomic Analysis
In studying the causes of leukemia, researchers have discovered multiple genomic faults that are associated with disease progression and recurrence. DNA testing overlooks another potential contributor to disease, proteins that may be driving leukemic cells and also could be targeted with existing and new treatments. If DNA can be described as the body’s genetic blueprint, proteins may be thought of as the construction workers who carry out the plan.
Studying the blueprint can be vital to understanding genetic diseases, including leukemia, but that focus also means that some problems arising with the workers may be missed. Proteogenomics is emerging as a science to integrate these two streams of patient information. This work will assess the potential and develop the facility to use genomically well-characterized banked leukemia cells for next-generation proteomics. Success will make possible the study of large numbers of patients using proteogenomics to discover new biomarkers and drug targets for leukemia.
Project title: Enhancing MHC-haploidentical HCT with donor memory-like NK cell adoptive immunotherapy
This project develops a new strategy to harness the immune system to fight leukemia, and pilots this idea an early phase clinical trial for patients with relapsed or refractory (rel/ref) acute myeloid leukemia (AML). The study harnesses natural killer (NK) cells, which are immune cells that a naturally able to recognize and eliminate cancerous cells. Recent work has shown that activating donor NK cells with three cytokines (IL-12, IL-15 and IL-18), hormone signals used by immune cells to communicate, resulted in a long-lived, highly potent NK cell type called memory-like NK cells. This project combines memory-like NK cell therapy and a standard “mini” hematopoietic cell transplant from the same donor, and will test the ability of memory-like NK cells to expand, proliferate, persist, and fight leukemia in patients with leukemia. This developmental project will lead a larger phase 2 study using this same strategy for patient with relapsed or refractory AML.
Grant Challen, PhD
Project title: Identifying novel dependencies in pre-leukemic HSCs
Epigenetics is a term used to refer to modifications to the genome which change the properties of cells, without changing the sequence of the DNA itself. Epigenetic modifications such as DNA methylation act like a blueprint to maintain cell identity by informing each specific cell type which genes should be switched on or off. Abnormal distribution of epigenetic marks is associated with a variety of human cancers, most notably blood cancer such as acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). Furthermore, genome sequencing studies have revealed that almost half of all patients with AML and MDS have genetic mutations in some component of the molecular machinery that is responsible for regulating these DNA methylation marks. Two of the most commonly mutated genes in these diseases are DNMT3A and TET2, which respectively function to add and remove DNA methylation from the genome. However, analysis of these patients has not revealed consistent DNA methylation differences that explain how the mutations cause cancer. As these mutations often make the cancers resistant to conventional chemotherapy, there is an urgent need to better understand how these mutations contribute to cancer to develop more optimal therapies.
Our hypothesis is that epigenetic changes other than DNA methylation are key contributors to the disease in patients with these mutations. In this project, we will identify epigenetic pathways which are crucial to the survival of cells with DNMT3A and TET2 mutations with the goal of identifying new avenues for therapy in these patients. Our primary tools to study this are mouse models we have in the lab which carry genetic mutations in the genes DNMT3A and TET2, which we have shown develop a disease resembling human MDS. We will use the bone marrow stem cells from these mice to identify what other factors are important for cancer initiation by “knocking out” specific epigenetic regulators using a genome editing tool called CRISPR/Cas9. This technology allows us to very rapidly and specifically remove other epigenetic modifying genes from the cells with pre-existing DNMT3A and TET2 mutations. We then track all the mutant cells, and identify which genes are necessary for cancer by identifying which cells “disappear” from the mice over time using high-throughput genome sequencing. Any mutations which disappear means that a particular gene was required for the survival of the cancer cells, as without that gene the cancer cells die and are lost. Thus, any mutations which disappear represent new drug targets for patients with DNMT3A and TET2 mutations.
Human T-cell leukemia virus type 1 (HTLV-1) is the cause of a T cell malignancy, adult T-cell leukemia lymphoma (ATL). This is a highly refractory malignancy, lacking effective treatment approaches, with a long-term survival rate of less than four percent. The current project is based on exciting new data that mutations are common in genes that code for components of a pathway that allows the T cell receptor to induce T cell growth. Notably, we found that one of these components, protein kinase C beta appears to be activated in about one third of cases through mutation, and an additional third of cases through alteration of proteins that turn-on protein kinase c. We will determine if the most common protein kinase c mutation is important for the growth of T cells in mice, and the genes that are turned on by this mutant protein. We will also determine if the protein kinase c mutation is important for growth of human ATL cells in immunodeficient mice. In both murine models, we will determine what genes are activated by this mutant form of protein kinase c. In addition, we will determine if a protein kinase c inhibitor, enzastaurin blocks T cell proliferation. Overall, these studies have the potential to lead to an important clinical advance in ATL treatment, which could have applications in other leukemias or lymphomas.
The Siteman Cancer Center offers many types of clinical trials, also called clinical studies or research protocols. At any given time, Siteman has more than 350 therapeutic trials under way.
For more information about any of the clinical trials listed on this site, call 314-747-7222 or 800-600-3606 toll free or e-mail firstname.lastname@example.org.
SPORE In Touch Patient E-Newsletter
As part of its commitment to patient care, The Washington University SPORE in Leukemia team at Siteman Cancer Center publishes its e-newsletter, SPORE In Touch, for leukemia patients and their families. The goal of this newsletter is to provide valuable information as an extension of our mission to offer world-class care, research and resources within the clinical and medical research communities.
SPORE In Touch is a digital publication that is distributed via email three times a year, and focuses on issues related to leukemia, myelodysplastic syndromes or stem cell transplantation. It features patient stories, physician interviews, clinical trial information, events and other milestones.
To learn more about the publication, please email InTouch@wustl.edu or call 314-273-2607.
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Information for Patients
To Make an Appointment:
- What Are Leukemia and Myelodysplastic Syndromes?
- What’s New in Leukemia Research at Siteman
- Leukemia Patient Stories
- Bone Marrow and Stem Cell Transplantation
Siteman Cancer Center SPORE in Leukemia
Investigators and Staff
John DiPersio, MD, PhD
Leader, Project 4
Timothy Graubert, MD
Co-Leader, Project 3
Timothy Ley, MD
Co-Leader, Project 1
Daniel Link, MD
Principal Investigator; Leader, Project 2; Director, Core C; Co-Chair, DRP
Graham Colditz, MD, DrPH
Director, Core B
Laura Schuettpelz, MD
Geoff Uy, MD
Co-Chair, CEP; Co-Leader, Project 2
Matthew Walter, MD
Co-Chair, CEP; Co-Leader, Project 3
Mark Watson, MD
Co-Director, Core A
John Welch, MD, PhD
Leader, Project 1
Peter Westervelt, MD, PhD
Director, Core A; Co-Leader, Project 4