Redefining mechanisms of transcriptional dysregulation in Diffuse Large B cell Lymphoma with chemical-genetics

Abstract

Transcription is dysregulated in the majority of human cancers. Understanding how normal transcriptional programs are dysregulated in cancers is crucial to understanding how cancers develop and successfully treating them. However, our understanding of the mechanisms controlling transcriptional activation and repression have been hindered by a lack of techniques that can capture transcriptional changes on the appropriate timescale to identify direct mechanisms. Here, I combine cell line models of inducible targeted protein degradation and time-resolved genomic methodologies to study transcriptional dysregulation in the context of diffuse large B-cell lymphomas. Using this approach, I determined that mutant FOXO1 controls the activation of a small gene network that includes known oncogenes and inducers of DNA damage by controlling enhancer activation and accessibility. Under normal conditions, wild type FOXO1 does not exert the same level of transcriptional control. However, if AKT activity is inhibited by a small-molecule, wild type FOXO1 can activate gene targets to the same extent as mutant FOXO1. I also applied this system to study the function of the histone deacetylase, HDAC3. HDAC3 has been implicated to have roles in transcription, chromatin structure, and replication. However, acute degradation of HDAC3 showed very few changes in transcription or global chromatin structure and only modest defects in replication. Unlike chemical inhibition, acute degradation of HDAC3 did not change global levels of histone acetylation suggesting that the characterized effects of HDAC3 inhibition are actually due to off-target inhibition of HDAC1 or HDAC2. Therefore, by combining inducible targeted protein degradation with time resolved genomic techniques, I have been able to identify the direct mechanisms through which FOXO1 controls gene expression and laid the ground work for the identification of the direct mechanisms by which HDAC3 controls DNA-templated processes.