Translating genomic discoveries to improved outcomes for high risk acute leukemia

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ABSTRACT Acute lymphoblastic leukemia (ALL) is a leading cause of cancer death in children. The goal of my research is to use integrated genomic and epigenomic profiling to define the genomic alterations that drive leukemogenesis and treatment failure in ALL, and to use this information to develop mouse models to translate these discoveries to innovative therapeutic approaches. My research program has revised the molecular taxonomy of ALL, identified constellations of genetic mutations that define subtypes of ALL, has dissected the genetic basis of clonal evolution, identified new targets for therapeutic intervention, notably with tyrosine kinase inhibitors, and has established several new engineered models of high-risk B-progenitor ALL. Recent advances include identification of a high frequency of mutations in epigenetic regulators at relapse in ALL, and demonstrating that specific genomic alterations perturb the interaction of leukemic cells with the microenvironment, resulting in resistance to therapy. This research proposal will determine the mechanistic basis by which genetic lesions present at diagnosis, or enriched at relapse, determine resistance to therapy, and exploit these for therapeutic intervention. Research goals are (1) to identify the constellations of genomic and epigenomic alterations that characterize each subtype of ALL across the age spectrum, and identifying those alterations that cause treatment failure. This involves genome and transcriptome sequencing of childhood and adult ALL, and integrated whole genome, whole genome bisulfite, transcriptome and chromatin mark sequencing of a cohort of 100 ALL cases, including matched samples obtained at diagnosis and relapse and corresponding xenografts. This is essential to identify all coding and non-coding mutations driving disease, to systematically examine the effect of genetic alterations on chromatin remodeling, and to guide the development and interpretation of mouse models of ALL. (2) To perform multiplexed loss-of-function screens using expression of founding oncogenic fusions, coupled with RNA interference and genome editing to dissect the interaction of polygenic alterations in leukemogenesis. (3) To use gene-specific and loss-of-function screens to examine the role of epigenomic alterations in ALL relapse. These include detailed characterization of Crebbp knockin models of ALL, and RNAi/CRISPR/Cas9 screens targeting over 700 chromatin modifier genes in B-ALL leukemia models. Enriched hits, and their effects on chromatin modeling and transcriptional regulation will be compared to data from human leukemic cells; and the resulting models used to test the effect of epigenetic modifying agents on modulating drug resistance. (4) To use mouse models of B-ALL to dissect the role of cellular mislocalization and “hijacking” of the bone marrow niche and the role of this phenomenon in drug resistance. Together, these approaches provide a comprehensive strategy to fully define the genomic alterations driving treatment failure in ALL, and to mechanistically validate these in logical experimental systems to guide further drug development approaches.