Accelerating the functional prioritization of gene regulatory biomarkers in acute myeloid leukemia

Abstract

Acute myeloid leukemia (AML) is a blood malignancy demarcated by skewed hematopoietic differentiation and unregulated cellular proliferation, leading to poor mortality rates among adults. While therapies have been developed to target commonly mutated genes in AML, many of which disrupt normal gene expression and chromatin states, how these mutations contribute to leukemic progression largely remains unclear. Thus, the goal of my doctoral research has been to develop platforms to prioritize functional gene regulatory biomarkers of disease progression and therapeutic resistance in AML. Herein, I provide an overview of genetic and biochemical tools commonly used to assess chromatin states and their regulators in AML (Chapter I). I next outline the development of iDAPT (integrative DNA and Protein Tagging), a new biochemical tool to tag both DNA and protein associated with transposase-accessible chromatin (Chapter II). iDAPT enables the inference of proteins, protein complexes, and relationships between transcription factor activity and binding on open chromatin. With iDAPT, I profiled the dynamics of the chromatin proteome upon retinoid-mediated granulocytic differentiation in acute promyelocytic leukemia (APL) (Chapter III). I include evidence of two previously undescribed oncogenic vulnerabilities, EBF3 and NT5DC2, in APL. Attenuation of the activities of either of these genes may serve as therapeutic opportunities downstream of the pathognomonic PML-RARA fusion oncogene. Subsequently, I delineate my bioinformatic efforts to combine cancer cell line drug response, patient outcomes, and CRISPR activation-based genetic screening datasets of protein-coding and lncRNA genes to identify gene regulatory networks modulating chemotherapy response in AML (Chapter IV). I identified the lncRNA GAS6-AS2, found that it regulates its antisense gene partner GAS6 in cis and the GAS6 ligand receptor AXL in trans, and demonstrated that it can be modulated by antisense oligonucleotide challenge. I conclude by providing a brief summary of key findings and possible future research directions (Chapter V). These roadmaps towards the discovery of functional gene regulatory biomarkers may provide opportunities for new mechanistic insights into biological phenomena and disease.