Divergent Core Transcriptional Regulatory Circuitries to Highlight Context-Specific Vulnerabilities in AML
Background: Acute myeloid leukemia (AML) is one of the deadliest pediatric cancers, responsible for 10% of total cancer mortality in children. AML is caused by mutations in normal bone marrow stem cells that make them grow out of control (i.e. become malignant). There are many AML-causing mutations and they result in many different subtypes of AML with very different responsiveness to treatment and outcomes. We need a better mechanistic understanding of both common and divergent (i.e. subtype-specific) pathways leading to AML.
Project Goal: We propose to systematically identify and characterize the most critical transcription factors (proteins that regulate the function of genes) in various types of AML, called 'core regulatory circuitries' (CRCs). By identifying the common and divergent CRCs in the context of the various AML subtypes, we will gain new insights into the most critical mechanisms of AML survival. Importantly, our preliminary data show that CRCs can accurately predict AML vulnerabilities – they reliably highlight critical genes without which AML cancer cells cannot survive. We propose to extend our data by characterizing AML CRCs in an integrated, unbiased way, in all major subtypes of AML. This will give us a unified understanding of the common and different ways in which AML arises, as well as create an unprecedented way of predicting common and subtype-specific AML vulnerabilities. Our data will create the basis for a new functional classification of AML and identify new targets for drug development.
Project Update 2022: We have successfully created an “encyclopedia” of AML superenhancers – regulatory DNA sequences that regulate key genes responsible for the maintenance of AML cells. We then integrated this dataset with the list of AML vulnerabilities, i.e. genes that encode proteins without which AML cells cannot survive. Integration of these two extensive datasets allowed us to identify the AML core regulatory circuit (CRC) – a set of critical proteins, called transcription factors, that collectively regulate gene function in AML cells. Interestingly, some of these proteins appear to be only important in a subset of AMLs, suggesting a certain divergence of AML-maintaining regulatory circuits. Moreover, these subtype-restricted CRCs correspond to subtype-specific AML vulnerabilities, suggesting suggests a potential “Achilles heel” for leukemia-specific therapy with little or no detrimental effects on normal hematopoiesis. I have also led the development of CORENODE, a novel method for computational transcription network decomposition, able to predict TF combinations that regulate any given target gene. We have applied CORENODE to the problem of AML relapse after allogeneic stem cell transplantation (alloSCT), which has been linked to immune escape due to reduced expression of MHC-II genes. CORENODE identified, and we experimentally validated, the transcription factors IRF8 and MEF2C as positive regulators and MYB and MEIS1 as negative regulators of MHC-II expression in AML cells. We showed that the reduced MHC-II expression at relapse is transcriptionally driven by combinatorial changes in the levels of these TFs. Furthermore, a small number of cells with altered TF levels and silenced MHC-II expression are present at the time of initial leukemia diagnosis and appear to seed the eventual relapse. This work revealed an adaptive transcriptional mechanism of AML evolution and post-alloSCT relapse. This study emphasizes transcriptional plasticity as an important mechanism of non-mutational cancer evolution and the power of computational network decomposition to predict transcriptional regulators of clinically relevant disease phenotypes. In summary, my experiments have allowed us to understand why some TFs are so essential in certain subtypes of AML and revealed general principles of transcriptional regulation that are applicable to all cancers.
