Chromunities Drive Transcriptional Reprogramming in Humoral Immunity and B-cell Lymphomas

PROJECT SUMMARY/ABSTRACT Diffuse large B-cell lymphomas (DLBCL) arise from B-cells transiting different stages of the germinal center (GC) reaction. It has become clear that these tumors can co-opt regulatory circuits of normal B-cells to drive their own malignant phenotype. Prior studies observe an inverse correlation between the timing of

transcriptional activation during reprogramming and the degree of topological reorganization near the gene locus. This suggests that the reorganization of the 3D genome is critical for B-cell development and highlights its importance in DLBCL. Regulatory hubs are highly interactive regions of enhancers that can form

interactions with multiple genes within topologically associating domains (TADs) to induce gene activation at a higher probability than pairs of non-interacting genes within the same TAD. Hubs are often rewired during cell fate transitions. Recent work also suggests a new level of organization into broadly interactive networks called

chromunities, which putatively allow for transboundary sharing of information and more extensive gene regulatory information critical for cell identity. Critical to understanding the mechanisms driving changes in gene networks is the study of how large-scale chromosomal rearrangements (structural variants, SVs) can co-

opt regulatory elements to form aberrant or de novo chromunities, consequently driving aberrant gene expression. While the interpretation of complex structural variants (SVs) has focused primarily on gene dosage and disruption by aberrant TAD structures, little is known regarding the role of SVs in reprogramming

regulatory hubs and their target genes. To investigate the role of chromunities and its associated hubs in cell fate transitions and oncogenesis, we will leverage chromatin conformation capture interaction maps (pcHiC, Pore-C) to develop a computational framework to nominate chromunities and map networks of enhancer and

promoters driving epigenetic and transcriptional reprogramming. We will also integrate chromatin contact maps with WGS data to investigate the role of complex SVs in reprogramming chromunities in lymphomas. Here, we hypothesize that physiological reprogramming of chromunity regulatory elements creates de novo coordination

between sets of genes required to establish specific cell states and phenotypes during the humoral immune response and that SVs occurring in DLBCL alter these hub structures or create new ones leading to selective advantage of malignant clones. In our first aim, we will integrate transcriptional, epigenetic, and chromatin

conformation capture assays to identify chromunities and their regulatory elements associated with establishing cell identity in the GC reaction. In our second aim, we will characterize the genomic rearrangement landscapes of B-cell lymphomas and how these directly link to hubs and chromunities using

patient-derived xenograft models by generating matched WGS, Pore-C, and RNA-seq data.