Role of chromatin remodeling complex BAF in immunity and lymphoma

PROJECT SUMMARY/ABSTRACT
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.

Grant Number: 5R00CA246080-04
NIH Institute/Center: NIH
Principal Investigator: Darko Barisic