Transcriptional And Epigenetic Networks Governing B Cell Development And Transformation

Abstract

The formation of the adaptive B cell response is dependent on the production of a diverse repertoire of mature B cells. To ensure sufficient quantity and quality of B cells are generated, developing B cells undergo alternative cycles of proliferation and differentiation, which are biological processes that are heavily regulated via the integration of external signals and B-lymphoid transcription factor activities. Perturbations that disrupt the balance between proliferation and differentiation during development result in transformation of B cells into B-cell acute lymphoblastic leukemia (B-ALL). Therefore, understanding the regulation of B cell proliferation and differentiation during development is critical for garnering insights into the process of B cell leukemic transformation. The characterization of various B cell developmental stages has been made possible through the advent of flow cytometry. Variable expression of surface markers across the B cell development trajectory has allowed for elucidating signaling modules and the importance of B-lymphoid transcription factors. Nonetheless, surface marker-based characterization is insufficient to fully demarcate distinct subsets, resulting in the analysis of mixed populations. These limitations have led to an incomplete understanding of B cell transcription factor kinetics and the diversity of transcriptional networks orchestrating proliferation and differentiation. B-lymphoid transcription factors govern the epigenetic and transcriptional landscape of developing B cells via the recruitment of transcriptional cofactors. In particular, corepressors are critical for target gene repression. However, the types of corepressors that are important in modulating development and the mechanism by which they maintain stage-specific integrity remains largely unknown. The overarching goal of this thesis is to elucidate the transcriptional gene networks underlying B cell development, characterize the role of gene repression and understand the linkage between developmental nodes and leukemic transformation. First, we used single-cell transcriptomics and proteomics to reveal unique transcriptional signatures that refine the pre-B cell expansion stages into pre-BCR-dependent and pre-BCR-independent proliferative phases. This study also revealed unexpected expression kinetics of different biological modalities across normal B cell development, including transcription factors, cytokines, chemokines, and their associated receptors. Secondly, we investigated the role of nuclear corepressors NCOR1 and NCOR2. The deletion of NCOR1 and NCOR2 led to a strong block in B cell development due to decreased proliferation and defective recombination. Single-cell transcriptomic studies on NCOR1/2-deficient B cells revealed diminished pre-BCR signaling, increased STAT5 target gene expression and aberrant RAG expression. Whole-genome sequencing studies suggested genomic instability in the absence of nuclear corepressors. Finally, we studied how key B cell developmental nodes are linked to human B-ALL subtypes and assessed the role of nuclear corepressors in regulating leukemic transformation.