Fate-resolved gene regulatory signatures of individual B lymphocytes in the early stages of Epstein-Barr Virus infection

Abstract

Epstein-Barr Virus (EBV) infection of B lymphocytes elicits diverse host responses via complex, well-adapted transcriptional control dynamics. Consequently, this host-pathogen interaction provides a powerful system to explore fundamental cellular processes that contribute to consensus fate decisions including cell cycle arrest, apoptosis, proliferation, and differentiation. Here we capture these responses and fates with matched single-cell transcriptomics and chromatin accessibility, from which we construct a genome-wide multistate model of early infection dynamics. Notably, our model captures a previously uncharacterized EBV+ analog of a multipotent activated precursor state that can yield early memory B cells. We also find that a marked global reduction in host chromatin accessibility occurs during the first stages of infection in subpopulations of EBV+ cells that display senescent and pre-apoptotic hallmarks induced by innate antiviral sensing and proliferation-linked DNA damage. However, cells in proliferative infection trajectories exhibit greater accessibility at select host sites linked to B cell activation and survival genes as well as key regions within the viral genome. To further investigate such loci, we implement a bioinformatic workflow (crisp-ATAC) to identify phenotype-resolved regulatory signatures. This customizable method applies user-specified logical criteria to produce genome-wide single-cell ATAC- and ChIP-seq range intersections that are used as inputs for cis-linkage prediction and ontology tools. The resulting tri-modal data yield exquisitely detailed hierarchical perspectives of the transforming regulatory landscape during critical stages of an oncogenic viral infection that simulates antigen-induced B cell activation and differentiation. We anticipate these resources will guide investigations of gene regulatory modules controlling EBV-host dynamics, B cell effector fates, and lymphomagenesis.

Time-resolved transcriptomes reveal diverse B cell fate trajectories in the early response to Epstein-Barr virus infection

“…Here we perform an in-depth analysis of the scRNA data, develop a refined germinal center (GC) model of EBV early infection, and detail previously uncharacterized EBV-infected B cell niches. Integration of the scATAC-seq data as well as development, validation, and implementation of a bioinformatic workflow to predict state-resolved regulatory relationships are reported in a companion piece (SoRelle et al, 2022).…”

EBV-associated diseases: Current therapeutics and emerging technologies

“…For example, recent studies have revealed the landscape of both tumor and infiltrating immune cells in NPCs that are associated with prognosis (234,235,408). Additionally, scRNA-seq are now used to delineate rare cell subpopulations such as cancer stem cells, cell-cell interactions via receptor-ligand analyses, cell differentiation via trajectory and time-resolution analyses (409). Additional steps also allow TCR, BCR and cell-surface protein expression (CITE-seq) sequencings at the single cell level to supplement scRNA-seq for the study of the diversity of immune cells.…”

“…It is important to note that most of these assays utilize bulk sample processing and therefore observations in heterogeneous cell populations should be carefully interpreted, as discussed above for bulk RNA-seq. Recently, the limits of some of these technologies have been pushed to the single cell level and integrated into scRNA-seq platforms to enable multiomics based investigation of EBV infection (409).…”