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.
