In order to maintain the compact structure of chromatin yet ensure access and functionality when required, eukaryotic genomes utilize multiunit chromatin remodeling complexes such as BAF, to enable dynamic binding of transcription factors to DNA. Being so instrumental in genome regulation, it is not surprising that BAF-complex genes are the most frequently affected by somatic mutations in cancer, in 20% of all patients and in 23% of diffuse large B cell lymphoma (DLBCL). However, the mechanism by which BAF promotes malignant transformation and lymphomagenesis is unclear. Based on our initial analysis, the BAF complex seems to be an important regulator of germinal center B cells, DLBCL cell-of-origin. We hypothesize that BAF enables chromatin accessibility for factors involved in germinal center B cell differentiation and prevents activated B cells from staying in the tumorigenic state of rapid cycling. To investigate the underlying mechanism, we will (Aim 1) define the biological role and mechanism of action of BAF in the normal humoral immune response. To this aim, we will use computational and experimental methods in genomics to determine BAF-complex composition, BAF genomic binding and BAF-dependent changes in chromatin accessibility in primary germinal center B cells with inactivating BAF mutations found in lymphoma patients. Furthermore, we will determine the role of BAF in nucleosome mobility and positioning in germinal center cells using a novel computational approach. The Melnick lab has discovered that regulation of nuclear architecture plays a critical role in germinal center B cell biology and that perturbation of factors involved in nuclear topology leads to lymphoma. However, these factors, such as the cohesin complex, are rarely mutated in lymphoma. By investigating changes in nuclear topology associated with binding of the BAF-complex, we will test if this discrepancy is explained by BAF mutations that might carry out these architectural functions. Furthermore, we will (Aim 2) determine the role of BAF in the initiation and clonal evolution of lymphoma and other tumors through effects on chromatin plasticity. We hypothesize that BAF complex exerts its function by globally inducing nucleosome mobility and exposing transcription factor motifs. Once a mutation in a BAF subunit occurs and the general fluidity of nucleosomes is lost, nucleosomes might be preferentially locked in an unfavorable chromatin position. This might lead to stochastic activation of malignant programs. To address this question, we plan to expand our computational approach to model changes in chromatin stiffness within cancers affected by BAF mutations using publicly available data. Furthermore, we will establish a simple-to-use parallel single-cell transcriptome and chromatin accessibility assay and apply it to lymphoma tumors from our BAF mutant mouse models. Taken together, the proposed project will provide insights into the mechanism of BAF-mediated formation of lymphoma. In case our findings support the hypothesis of BAF being the master regulator of tumor suppression in B cells, we will be able to identify novel therapeutic targets for patients with BAF mutations and further classify those tumors.
Forty-percent of lymphoma patients relapse and face poor prognosis highlighting the inefficiency of current treatment options and the demand for targeted therapies. BAF-complex genes are one of the most mutated in cancer, with 20% of cases overall and 23% in lymphoma, yet, the mechanism by which BAF promotes malignant transformation is poorly understood. This proposal aims to decipher the biological role of BAF in the initiation, propagation and clonal evolution of lymphoma through effects on chromatin structure.