Functional Interrogation of Non-coding DNA Sequences in leukemia development and drug resistance

ongoing

Functional non-coding regions of the genome play a fundamental role in gene expression and are enriched for disease associated variants. Perturbation of non-coding regions harbouring disease-associated variants is now the rationale of ongoing clinical trials (e.g. NCT03432364), highlighting the translational potential of basic research in the non-coding space. However, our ability to systematically identify disease-associated functional elements in the non-coding genome, understand its grammar, and subsequently develop new therapies is limited. CRISPR-based pooled screens targeting non-coding elements in situ have been successful in uncovering complex gene regulatory architecture in a variety of biological systems. However, these approaches are limited to a few loci, lack of direct genotype-phenotype correlation, and do not target large chromatin structures that determine gene expression programs. To overcome these limitations, I propose a multi-scale approach platform that is generalizable to different cell types and phenotypes. Under this proposal, I will focus on the role of non-coding sequences in the context of blood malignancies. I will investigate non-coding sequences whose change in chromatin state (activation or repression) is associated with drug resistance in Chronic Myelogenous Leukemia (CML). I will study alterations in the chromatin structure (i.e. at chromatin loops or topologically associated domains) that are causal to imatinib resistance in CML. Finally, to learn enhancer grammar and mechanistically link non-coding variants to disease, I will focus on non-coding sequence variation in leukemia and dissect non-coding sequences at base pair resolution using dense mutagenesis coupled with long-reads sequencing. A deeper understanding of the non-coding regulatory architecture in diseases will provide the basis for development of innovative therapies targeting the non-coding genome.