Dr. Malachi Griffith – Research in Action
Read moreType: Translational
Facilitate the transition of projects from the laboratory to the clinic. Translational researchers seek to apply basic knowledge of cancer and bring the benefits of the new basic-level understandings to patients more quickly and efficiently. These grants are $600,000, three-year commitments
Michael Deininger, M.D., Ph.D., Thomas O’Hare, Ph.D.
Chronic myelomonocytic leukemia (CMML) is a cancer of the bone marrow that is typically observed in patients over 65 years of age and has no known cause. CMML patients have a short survival, with only ~20% of patients alive five years following diagnosis. Dr. Deininger is a leader of a clinical trial testing a CMML drug called 5-azacytidine and we have many samples from the patients enrolled from across the country. The drug was highly effective in a minority of patients but eventually lost effectiveness for most. The first major objective of our project will focus on specimens collected from patients prior to and throughout 5-azacytidine treatment to allow comparisons between those for whom the drug was effective and for those it was not.
Recent work makes it clear that many genes are mutated in CMML and that no single mutation is the source of the disease. Our laboratory utilizes an advanced, highly accurate DNA sequencing technique called whole exome sequencing to sequence every gene in the genome. We have performed this analysis on specimens from 21 CMML patients. Importantly, we conducted the analysis side-by-side on leukemic and healthy cells from each patient. After careful mathematical analysis of the results, we then directed our attention to the mutated genes found only in leukemic cells. We will compare the mutation profile of each patient with the clinical outcomes to understand whether certain mutation profiles correlate with better or worse responses to drug treatment. To further this understanding, we will assemble the mutation patterns in such a way that we can estimate the number of leukemia initiating cells, also called clones, present in each patient. This yields a quantification of the population diversity and complexity and allows us to provide a scheme for predicting patient outcomes. It is critical to understand not only which genes are mutated but also whether the mutations are located in the same or different cells. Such a high resolution visualization of the disease will enable the first thorough understanding of this genetically complex disease and direct us towards the genetic events that initiate CMML. Altogether, this predictive information will aid physicians in understanding which patients are at high risk for transformation to terminal leukemia and who is most vs. least likely to respond to treatment. In the longer term, deciphering the genetic blueprints of CMML will be instructive for design and implementation of safer and more effective drugs.
Our second goal is to uncover new molecular pathways required by CMML cells but not healthy cells and to develop precision drugs that interrupt these critical processes. The most important requirement for drug design is a well-defined molecular target that is essential only in the cancer cells. While the requirement is selfevident, there are a staggering number of possibilities. To contend with this complexity, we use a ‘function-first’ approach, meaning that we impose an experimental condition on CMML cells and ask whether their ability to survive is compromised. For instances in which we observe compromised survival, we then work backward to understand the molecular pathways involved. We rely on a powerful new tool called an shRNA library to interrupt the function of one gene per cell and determine whether the absence of that gene’s function makes that cell more likely to die. The term ‘library’ in the context of our experimental design refers to an inventory of thousands of different gene-interrupting shRNA molecules that allow us to interrogate the function of thousands of genes, one gene at a time, in one study. We also mimic the bone marrow environment in our experimental design, providing a more realistic proving ground for drug discovery. This novel type of analysis, applied to leukemia cells from CMML patients, has the capability to unveil novel molecular pathways in CMML.
The two complementary objectives of our study will vastly improve our understanding of molecular pathways that are uniquely important for the survival of CMML cells. With this knowledge, we can design drugs that precisely interrupt key components of survival pathways specific for CMML cells. The long-term, overarching goal of our work is to discover novel therapeutic targets in CMML, and based on these insights, to develop precision drugs for translation into the clinic.
Andrew Feinberg, M.D., MPH, Philip Cole, M.D., Ph.D.
While genetic mutations, changes in DNA sequence, are central to the development of Cancer, it is increasingly recognized that associated alterations in the chemical structure of the DNA packing material, known as chromatin, are linked to cancer causation. These distinct chromatin states and the molecules that regulate then form the basis of the field of epigenetics. While epigenetics is generally understood to be important in oncology, it is not yet clear how specific epigenetic changes are generated by different environmental conditions such as UV light exposure. Moreover, it is not understood what epigenetic changes are most impactful for the progression of malignancy and what therapeutic approaches can be used to successfully intervene to prevent or cure cancer. Our team will address how UV exposure in patients can induce particular epigenetic changes in skin lesions, whether existing epigenetic therapies can achieve desired effects of preventing epigenetic changes and progression to cancer, and design and develop new epigenetic therapies that could be useful for skin cancer and other malignancies. We hope to illuminate the factors that dictate patiets’ skin cancer’s responsiveness to epigenetic therapies which could ultimately lead to a new standard of care for treatment. We also plan to synthesize at least one new dual action epigenetic modulator compound that can serve as a clinical candidate for patient cancer trials.
John Byrd, M.D., Ching-Shih Chen, Ph.D., Michael Freitas, Ph.D., Michael Grever, Ph.D., Samual Kulp, Ph.D., David Lucas, Ph.D., Mark R. Parthun, Ph.D., Amy Sklenar, B.S., Xiaodan Su, Ph.D.
Partially funded by Cardinal Health
Michael C. Heinrich, M.D.
Activating mutations of KIT are found in a number of human malignancies, including Gastrointestinal stromal tumors ( GIST, 80%), mast cell neoplasms (95-100%), melanoma (rare overall, but up to 25% of certain subtypes), seminoma (10-25%), and acute myeloid leukemia (<5% overall, but 20-40% of certain subtypes). Although KIT inhibitory drugs such as imatinib (Gleevec) have been effective for treating some of these cancers, the efficacy of these drugs is limited by primary as well as acquired drug resistance. Dr. Heinrich and his team have been leaders in the development of these targeted molecular treatments for KIT-mutant cancers. This proposal seeks to further improve treatment of GIST and other KIT-mutant cancers (e.g. melanoma), using combination therapy to simultaneously target KIT and other critical signaling pathways. Dr. Heinrich’s project will provide critical data that can be readily translated into the design and conduct of future clinical studies of the treatment of advanced KIT-mutant cancers. These studies will be conducted by a multidisciplinary team that includes: Dr. Michael Heinrich (Cancer Biology, Medical Oncology), Dr. Christopher Corless (Cancer Biology, Pathology, Animal Models), Dr. Jeffrey Tyner (Cancer Biology, Animal Models), Dr. Marc Loriaux (Cancer Biology, Pathology), and Dr. Harv Fleming (Animal Models of Cancer, Medical Oncology).
Darrell J. Irvine, Ph.D.
Vaccines that prime a patient’s own immune system to attack cancer are an attractive strategy, with the potential to promote durable regression of cancer that is not subject to rapid treatment resistance. However, to date cancer vaccines have generally failed in two important ways to optimally target cancer: First, cancer vaccines have typically targeted proteins that are over-expressed by tumor cells but not necessarily unique to tumor cells- this can lead to poor potency and the danger of autoimmune reactions. Second, vaccines based on peptides, proteins, or whole cell lysates have generally shown poor immunogenicity in patients, due in part to poor uptake of such vaccines by the immune system. We propose the translational development of a novel vaccine platform that addresses these two key limitations and could further be combined with promising immunomodulators such as checkpoint blockade therapies in patients to promote potent but safe anti-tumor immunity. In collaboration with the Broad Institute and the Dana Farber Cancer Institute (DFCI), we are pursuing cancer vaccines that are generated by sequencing the genome of individual patient tumors, and then forming vaccines that are chemically designed to traffic to lymph nodes following injection. We will carry out preclinical safety and manufacturing studies to enable clinical trials of this concept, which has shown great promise in small animal models of cancer therapy. We hypothesize that combining these two promising cancer vaccine technologies will lead to a highly potent, patient-targeted cancer vaccine strategy that could be broadly applied to diverse tumors.
Daphne Bell, Ph.D., Daniel Haber, M.D., Ph.D., Eunice Kwak, M.D., Ph.D., Thomas Lynch, M.D., Jeffrey E. Settleman, Ph.D., Raffaella Sordella, Ph.D.
In memory of Christopher T. Carroll
Michael B. Major, Ph.D., D. Neil Hayes, M.D., MPH, Gary Johnson, Ph.D.
Protein kinases are a family of 518 human proteins which receive and transmit information within the cell, often from one kinase to another. The information flow within the network governs all aspects of cell biology, including cell growth, movement and survival. Not surprisingly, cancer very often re-wires kinase activity and connectivity to support its uncontrolled growth and metastasis. Indeed, protein kinases are the most commonly mutated protein family in human cancer. Protein kinases are also exceptionally ‘druggable’ and constitute the most tractable class of new therapeutic targets. Two significant challenges exist. First, we know a great deal about very few protein kinases. There is no doubt that targeting understudied kinases in cancer will benefit patients, but what kinases and for which patients? Second, several kinase inhibitors have proven immensely effective in certain cancers, however not all patients respond and for those that do respond, resistance inevitably emerges. We now know that cancer reprograms the kinase network to bypass chemotherapy. To tackle these challenges, we have developed a new technology that allows us to identify and quantify the activity of nearly all kinases in a single experiment. This allows us to comparatively study kinase activity in normal cells and in cancer cells, in chemotherapy-sensitive and resistant cancers, and in tumors before and after relapse. We hypothesize that the responsiveness of cancer to targeted therapy is determined by the baseline activity of specific kinases and the nature by which these activities adapt to therapeutic challenge. We will test this hypothesis in tumors of the lungs and head and neck. Together, our experiments may lead to the identification of specific kinase activities which: 1) predict cancer disease progression, 2) predict response to therapy, and 3) suggest new and rationally designed therapeutic strategies for patients with naïve and relapsed cancer.
Kellie Archer, Ph.D., Harry D. Bear, M.D., Ph.D., Catherine Isabelle Dumur, Ph.D., Carleton T. Garrett, M.D., Ph.D., Peter O’Connell, Ph.D.
Wendy Stock, M.A., M.D., Yusuke Nakamura, M.D., Ph.D., Olatoyosi Odenike, M.D.
In the era of Precision Medicine, the treatment of Acute Myeloid Leukemia (AML) remains a significant challenge with fewer than 50% of patients having long term disease-free survival. Yet, the explosion of genomic information has allowed us to refine our knowledge of the genetic changes that result in the development of the many subsets of AML and has provided us insights into new and potentially groundbreaking clinical advances. One of the most common subsets of AML that affects both children and adults is characterized by mutations in a gene important for normal blood cell growth and development known as FLT3. The FLT3 gene is mutated or abnormally expressed in up to 25% of cases of AML and this abnormal expression results in an aberrantly active FLT3 kinase that results in a rapidly proliferating AML with a poor treatment outcome in all patient age groups. Therefore, specific therapies for FLT3 mutant leukemias are needed urgently. Attempts to target the mutant FLT3 with targeted FLT3 kinase inhibitors is an area of active research but a major breakthrough has not yet been made; in part, this is due to the rapid emergence of resistance to the targeted FLT3 kinase inhibitors that have thus far been tested. In this application, we propose the development of a new agent to treat leukemias with mutation or over-expression of FLT3. Recently, our group identified that a protein kinase, known as TOPK, which is abnormally expressed in many cancers (but not in normal tissues) is also expressed in high levels in AML, particularly in AML cells with mutations of FLT3. The laboratory of Dr. Yusuke Nakamura, one of the principal investigators of this grant identified a specific inhibitor of TOPK which is now being developed in partnership with a Japanese company, OncoTherapy Science. They are now completing toxicity and large animal model feasibility testing. Importantly, Dr. Nakamura’s laboratory has developed other successful new protein kinase inhibitors in collaboration with OncoTherapy Science, including a MELK protein kinase inhibitor that is currently being tested for the first time in patients with a variety of solid tumor malignancies here at the University of Chicago. We have tested the TOPK inhibitor OTS514 in many AML cell lines and in cells from patients with AML. Interestingly, this TOPK inhibitor has tremendous activity against AML cells, particularly in those with FLT3 mutations, resulting in their cell death using clinically achievable concentrations of the drug. Importantly, the TOPK inhibitor, OTS514, does not impair the survival of normal early blood cells. The goal of our grant is to understand how it is that the TOPK inhibitor kills FLT3 driven leukemias, to perform pre-clinical testing of OTS514 in mouse models of FLT3 leukemias and, using these insights, to design and perform a first in human trial of this TOPK inhibitor in patients with AML, focusing on those with mutations in FLT3. Our proposal is a comprehensive bench to bedside approach! The ability to shut down FLT3 expression with TOPK inhibition also provides the potential for circumventing the resistance that occurs with targeted FLT3 kinase inhibitors. Thus, we are optimistic that understanding of the mechanism by which TOPK impairs FLT3 driven leukemia cell growth and survival and the performance of a phase I “first in human” trial will provide us with the insights needed for future successful development of this TOPK inhibitor, with the ultimate goal of using a Precision Medicine approach to improving the survival of patients with FLT3 mutated AML.
