Cores
Core A: Administrative Core
Core Lead: Ronald Hoffman, MD
The Administrative Core provides the infrastructure for and coordinates all activities of the Myeloproliferative Neoplasm-Research Consortium (MPN-RC). The goal of the Core is to actively and dynamically maintain a collaborative translational research network that supports and synergizes the laboratory and clinical studies led by MPN-RC investigators. Key functions include organizational management and communication, resource allocation and financial management (personnel, funds, equipment, and supplies), organization of all internal and external advisory boards and committees, scientific and clinical trials oversight to ensure regulatory compliance and procedural implementation, and external liaison to appropriate governmental agencies. The specific aims of the Administrative Core are: (1) Coordinate the activities of all MPN-RC Projects and Cores and monitor their progress and effective use of shared resource Cores; (2) Schedule and provide optimal staff support for all MPN-RC committees and boards; (3) Assure that research involving the use of human subjects and vertebrate animals is pursued in compliance with NIH regulations; (4) Establish all contracts with participating organizations and administer and oversee all budgets and the disperal of funds; (5) Liaison to the NCI and MPN patient advocacy groups for all matters pertaining to the MPN-RC; (6) Develop and negotiate budgets and contracts with pharmaceutical companies to gain access to drugs for clinical trials to be pursued by Project 4; (7) Develop criteria for institutional membership in the MPN-RC and assist in membership applications and site initiation visits. As well as, monitor performance of all members to assure that they are optimally functioning in a fashion that merits their continued participation; (8) Prepare annual progress reports to be submitted to the NCI. Orchestrate the resubmission of this competitive renewal application to the NCI; (9) Maintain and update the MPN-RC website; (10) Raise supplementary funds to assist in funding the MPN-RC activities; (11) Establish and maintain educational activities in MPN research and treatment, and maintain communications with the MPN patient community with the updates on the activities of the MPN-RC.
Core B: MPN-RC Tissue Bank
Core Lead: Bridget Marcellino, MD, PhD
Core B, Tissue Bank provides the infrastructure to transport, receive, process, store, and distribute tissue specimens obtained from patients with myeloproliferative neoplasms (MPN) enrolled on the longitudinal tissue bank as well as patients enrolled on clinical trials (Project 4). These specimens are provided to MPN-RC investigators performing translational research for the purpose of developing innovative therapies (Projects 1-3). They are also provided to the Biomarker and Bioinformatics Core D to perform biomarker analyses to evaluate the effectiveness or causes of resistance of specific therapies being evaluated to deplete MPN hematopoietic stem and progenitor cells. Tissues are also available to members of the scientific community at large for translational research. Translational research is dependent on the ready availability of tissues from a sufficient number of accurately diagnosed patients to generate statistically significant data. Because the MPNs are relatively uncommon and their accurate diagnosis can be difficult, there has been a paucity of tissue, linked to clinical data, available to individual investigators at single institutions. Core B fills this void. With an inventory of specimens from more than 1700 individual patients with MPNs, Core B maintains one of the world’s largest inventories of MPN tissues available for research. In addition, Core B collects specimens from patients participating in MPN-RC sponsored clinical trials (Project 4) for the purpose of performing biomarker studies to demonstrate the effectiveness of specific therapies on the depletion of MPN hematopoietic stem and progenitor cells. The specific aims of Tissue Bank Core B are the following: (1) Receive, process, cryopreserve, and store tissues from MPN patients participating in a longitudinal tissue bank (MPN-RC 106) as well as patients enrolled on clinical trials (Project 4) at MPN-RC clinical sites. (2) Provide a central repository for MPN tissues that are associated with clinical and mutational annotation data stored in the web-based data bank maintained by Biostatistics and Data Management Core C. This annotation, selection and distribution of tissues is tailored for each translational research project. (3) a. Distribute tissues to MPN-RC investigators and the larger scientific community for translational research dedicated to elucidating the mechanisms driving the pathogenesis and progression of MPNs and developing novel therapeutic strategies to target MF stem cells. b. Distribute clinical trial specimens to analyze on-target effects of novel agents and create biomarkers which will determine therapeutic and pharmacodynamic responses to therapy (Core D). Core B is an essential shared resource that enables translational research that will ultimately lead to the development of therapies, which target the MPN stem cell.
Core C: Biostatistics and Data Management Core
Core Lead: Amylou Dueck, PhD
The Biostatistics and Data Management (BDM) Core is responsible for all statistical and data management activities for each of the Myeloproliferative Neoplasms Research Consortium (MPN-RC) projects and cores including all clinical trials and the tumor bank. Each of the projects presented in this application reflects input from the Director of the BDM Core (Dr. Amylou Dueck, Mayo Clinic) on the design, data management, and biostatistical analysis plan. The BDM Core is constituted to provide state-of-the-art statistical collaboration and data management support to all clinical and translational research projects. The biostatistical and data management components of this Core are integrated at Mayo Clinic under the leadership of Dr. Amylou Dueck. Dr. Dueck and her team are highly published in the MPN field and notable experts in MPN clinical trial design and statistical analysis of patient outcomes. The Core will provide statistical expertise including experimental design for laboratory studies; statistical modeling; statistical analysis of high-dimensional data, patient-reported outcomes, and correlative studies using biospecimens; and state-of-the-art clinical trial design, monitoring, and statistical analysis within an efficient platform protocol. The Core will also provide advanced web-based data management through Mayo Clinic’s data management infrastructure with all clinical trial and tumor bank data captured in REDCap. This web-based system provides ease of use coupled with electronic patient questionnaires, online calendaring/querying/tracking, robust data validation routines, and straightforward integration with SAS/R for seamless overall statistical analysis. Dr. Dueck is an experienced co-investigator on translational and clinical research program grants in hematologic malignancies with extensive collaborations with the MPN-RC investigators. The competencies of the biostatistical and data management components of this Core provide the full spectrum of expertise and operational capacity needed to actively collaborate with the translational and clinical investigators in the formulation of the research protocols, in implementation according to internationally accepted requirements, and in the statistical analysis of the data from clinical, laboratory, and translational studies. The BDM Core is a critical component of the MPN-RC.
Core D: Biomarker and Bio-Informatics Core
Core Lead: Raajit Rampal, MD
The overall aim of Core D is to provide correlative biomarker analyses (including bioinformatics analysis) of primary specimens in the MPN-RC tissue bank, samples arising from all MPN-RC clinical trials, experiments in Projects 1-3, and prospective tissue banking efforts. Core D will carry out assessment of somatic genomic alterations on all MPN-RC samples derived from tissue banking efforts, and from therapeutic trials at baseline and the time of response assessment. The core will also carry out dynamic analyses of other mechanismbased biomarkers (such as serum cytokines, single-cell DNA and RNA sequencing studies, cytogenetics, and histopathology) which pertain to each of the biologic and clinical studies in Projects 1-3. The use of genomic profiling will provide Projects 1-3 with the ability to select genetically annotated samples for biologic studies aimed at investigating the relationship between somatic mutations, biological features of disease pathogenesis, and therapeutic dependencies. The core will also carry out dynamic analyses of mechanism-based biomarkers which pertain to each of the biologic and clinical studies in Projects 1-4. The goal of these assays is to provide comprehensive genetic and biologic correlative studies as well as to help determine the mechanistic impact, and the ability to deplete Myelofibrosis (MF) stem cells, of these hypothesis-driven therapeutic interventions. The proposed analyses will result in integrated genomic, gene expression, and cytokine data of a large number of clinically annotated and homogenously treated patients. As well, the clinical trials proposed in Project 4 are mechanistically based, and stem from work in Projects 1-3. The correlative biomarker assays are directly related to the proposed mechanisms of action of the therapeutic agents which will be investigated in Project 4. These studies will allow for an assessment of the mechanistic impact of specific therapeutic interventions and allow us to credential novel therapeutic targets and pathways. In addition, this will allow biological assessment of treatment responders and non-responders, thus giving insight into mechanisms of resistance. Importantly, we have developed rigorous organizational tools in order to maintain data integrity, traceability and reproducibility standards when dealing with the amount and the variety of data involved in the large-scale biomarker analyses for this core. The integration of state-of-the-art and novel biomarker assays offered by Core D, with robust preclinical and clinical studies will afford a unique opportunity to gain new genomic and biologic insights into MPN pathogenesis.
Projects
Project 1: Molecular Pathogenesis and Therapy of Myeloproliferative Neoplasms
PI: Ross Levine, MD
Primary myelofibrosis (MF) and progression of polycythemia vera (PV) and essential thrombocytosis (ET) to MF represent the most pressing clinical needs of patients with myeloproliferative neoplasms (MPNs), given that MF patients develop progressive cytopenias, splenomegaly, bone marrow fibrosis, disabling systemic symptoms and/or transformation to a treatment refractory form of acute leukemia, termed MPN-blast phase. The identification of somatic activating mutations involving the JAK2, MPL and CALR genes in most MPN/MF patients has underscored the role of constitutive JAK-STAT signaling in MF pathogenesis and has led to the clinical development of JAK2 inhibitors as the standard of care for MF patients. Clinical experience with currently available JAK2 inhibitors has shown that these agents can reduce cytokine production and attenuate MPN symptoms but are not capable of inducing either pathologic or molecular responses in most patients. Our recent work has uncovered a role for key epigenetic and inflammatory pathways in MF pathogenesis, which cooperate with activated JAK-STAT signaling to drive clinical progression and adverse outcomes in MF patients. These newly identified epigenetic and inflammatory pathways provide mechanistic insights into MPN disease pathogenesis and have the potential to serve as targets for the development of novel MF therapeutic approaches. We propose to investigate the role of aberrant epigenetic/inflammatory effector pathways in MF pathogenesis and to identify novel therapeutic targets which cooperate with JAK2 inhibition to increase therapeutic efficacy. The studies in this project will leverage novel, genetically accurate murine models of the most common MPN genotypes, coupled with detailed genomic, epigenomic, and therapeutic studies of primary samples from the MPN-RC Tissue Bank (Core B). Most importantly, the studies in this project are aimed to develop and credential novel therapeutic approaches that can then be transitioned to the clinic for mechanism based clinical trials in collaboration with Project 4 and the entire MPN-RC.
Project 2: Defining the Role of Megakaryocyte Abnormalities in the Progression of Primary Myelofibrosis
PIs: John Crispino, PhD; Anna Rita Migliaccio, PhD
Myelofibrosis (MF), caused by mutations in JAK2, MPL, and CALR, progress from a pre-fibrotic stage where patients have minimal symptoms to a more advanced fibrotic state which is associated with an increasing symptom burden, progressive splenomegaly, cytopenias and marrow fibrosis. MF disease progression is characterized by the accumulation of atypical megakaryocytes that express low levels of the critical transcription factor GATA1 and elevated levels of TGF-β. MF evolves to acute myeloid leukemia (MPN blast phase, MPNBP) in nearly 20% of patients. The goal of project 2 is to understand the events that contribute to disease progression by focusing on megakaryocytes and the factors that they secrete, such as TGF-β and IL-13. Based on our prior research, we hypothesize that changes in the megakaryocytic lineage substantially contribute to key features of MF progression, including bone marrow fibrosis, the predominance of MF hematopoietic stem cells and the impaired function of wild-type hematopoietic stem cells. We further hypothesize that alterations in p53 activity contribute to both the inhibition of normal hematopoiesis and the progression of MF to MPN-BP. In this project, we will: 1) Investigate the changes in the megakaryocyte lineage that contribute to the MF progression; 2) Identify the contributions of IL-13 and TGF-β to MF progression; and 3) Evaluate and target the contributions of HIF-1 alpha pathway activation and p53 inhibition driving MF leukemia progression. Our research interacts with Projects 1 and 3 through our work on cytokines and the role of p53 in MF progression, and with Project 4 through both bench to beside and bedside to bench exchanges of information, with the ultimate goal of bringing new treatments to MF patients. Our work will also require integration with each of the MPN-RC cores. Drs. Crispino and Migliaccio have a longstanding history of collaboration, particularly dealing with the role of GATA1 in megakaryopoiesis, and will leverage their complementary expertise to achieve the goals of this project.
Project 4: MPN Clinical Consortium
PIs: John Mascarenhas, MD; Ruben Mesa, MD; Marina Kremyanskaya, MD
Myelofibrosis (MF) is a myeloproliferative neoplasm (MPN) with an aggressive clinical course and a high risk for early death. Current therapeutic approaches for patients with Philadelphia chromosome negative MPNs aim to normalize blood counts, reduce splenomegaly and eliminate symptoms, but are incapable of halting disease progression/evolution. MF originates at the level of the hematopoietic stem cell (HSC) and the dysfunctional MF bone marrow and splenic microenvironments promote the predominance of the malignant HSC. Based on these observations, we hypothesize that therapeutic approaches which selectively target and deplete the MF HSC pool and restore the dysregulated MF microenvironment will be required to improve the treatment outcomes of MF patients. Concepts developed by members of the MPN-RC (Projects 1-3) have led to novel therapeutic approaches capable of depleting MF disease-initiating HSC. These strategies will be tested and validated in investigator-initiated clinical trials with accompanying correlative biomarkers to document therapeutic responses. These correlates are designed to assess the degree of MF HSC depletion as well as mechanisms underlying treatment responses and resistance. The trials will be pursued using the established infrastructure of the MPN Clinical Consortium, an effective independent clinical trials group focused on improving the outcomes of MF patients. To achieve these goals, the following specific aims will be pursued: (1) Assess whether mechanism based strategies such as combination of an HDM2 antagonist and a BET inhibitor, are tolerable and clinically active in early phase MF clinical trials (MPN-RC 124). (2) Evaluate the safety and clinical activity of a novel type II JAK2 inhibitor in MF patients in an early phase clinical trial (MPN-RC 126). (3) Utilize biomarker studies from patients enrolled in MPN-RC clinical trials to determine target pathway engagement and association with clinical responses or lack of responses and mechanisms of therapeutic resistance in order to better inform future therapeutic development. (4) Annually obtain peripheral blood and/or bone marrow cells from MF patients (MPNRC-106) which will be stored in Core B in order to provide mutational characterized specimens that will be utilized for the investigations planned in Projects 1-3.
Project 3: Development of Strategies to Deplete Myelofibrosis Stem Cells
PI: Ronald Hoffman, MD
First generation JAK2 inhibitor therapy is currently widely employed to treat myelofibrosis (MF) patients. Its use, however, has not substantially altered the risk for disease progression or interrupted the inevitable evolution to MPN-blast phase (MPN-BP), likely due to an inability to selectively deplete MF stem/progenitor cells (HSPC). MF HSPCs are characterized by upregulation of HDM2 which promotes the proteosomal degradation of wildtype (WT) p53. We have focused on implementing strategies that upregulate WT p53 activity in order to deplete MF HSPCs. We subsequently have shown that treatment with the HDM2 antagonist, nutlin-3 antagonizes the interaction between WT p53 and HDM2 resulting in the upregulation of p53 and the depletion of MF but not normal HSCs. Furthermore, p53 dependent signaling is known to play a role in tumor suppression by acting in a non-cell autonomous manner, such that down regulation of p53 leads to upregulation of NFκB resulting in the increased elaboration of abundant amounts of pro-inflammatory cytokines. Subsequent trials of nutlin therapy in MPN patients have resulted in an improvement not only in clinical parameters and symptom scores but also rapid reductions in the variant allele frequencies of MPN driver mutations and other associated myeloid gene mutations, as well as the reversal of marrow fibrosis. We hypothesize that HDM2 antagonist therapy actually depletes MF HSPCs and downregulates NFκB in MF cells and components of the tumor microenvironment. The long-term administration of HDM2 antagonists has, however, proven problematic due to gastrointestinal toxicity. MPN p53 activity can also be downregulated by activating mutations or overexpression of PPM1D, a phosphatase which dephosphorylates p53. To further optimize the therapeutic upregulation of WT p53 and possibly lessen the gastrointestinal toxicity associated with HDM2 antagonist therapy, we hypothesize that adding drugs that either reduce PPMID activity or antagonize the action of BET proteins (epigenetic regulators which downregulate events downstream of p53) will result in further upregulation of p53 activity, greater depletion of MF HSPCs and additional correction of the MF tumor microenvironment. Since HDM2 can also be recruited to chromatin in a p53 independent manner to increase NFκB, HIF1α, and polycomb repressor complex 2 activity, as well as orchestrate the global metabolic reprogramming of cancer cells, we hypothesize that agents that effectively eliminate both the p53 dependent and independent consequences of increased HDM2 copy number, might result in even greater depletion of MF HSPCs. To test these hypotheses, we will pursue the following Specific Aims (1) Determine the degree of malignant MF HSCs depletion achieved by up-regulating WT p53 activity with single agent HDM2 antagonist treatment; (2) Determine if dual targeting of HDM2 and PPM1D or HDM2 and BRD4 leads to further upregulation of p53 activity and a greater degree of MF HSC depletion than targeting HDM2 alone; and (3) Evaluate if targeting the p53 independent roles, in addition to the p53 dependent roles, of HDM2 leads to further depletion of MF HSCs.