Cell cycle-coupled transcriptional network regulates human B cell fate bifurcation 2257411
TL;DR
A generalizable framework for assembling and testing GRNs in the context of immune cell fate decisions is established, and previously unreported feedback loops that link cell division to fate specification are revealed.
Abstract
Antibody response quality and durability depend on activated B cells bifurcating into plasmablast (PB) or germinal center B cell (GCBC) fates. PBs are short-lived and secrete low-affinity antibodies, whereas GCBCs undergo somatic hypermutation and selection before potentially generating long-lived plasma cells that produce high-affinity antibodies. The gene regulatory networks (GRNs) governing these trajectories in human B cells remain poorly defined. We profiled in vitro—activated human B cells using time-series single-cell multi-omics (RNA/ATAC-seq) and applied machine learning to predict linkages between transcription factors (TFs), cis-regulatory elements, and target genes, building B cell state-specific GRNs. Using these GRNs, we simulated TF perturbations and tested the predicted effects using CRISPR screening in primary B cells. Simulations and experiments converged with predictions of TF activity at single-nucleotide resolution, revealing dominant and reciprocal actions of IRF4 and partners at IRF-related motifs. Single-cell perturbation analysis uncovered a reciprocal negative feedback loop that modulated B cell fate choice, involving BATF, IRF4 and BLIMP1. Additionally, we found that IRF4 and BLIMP1 co-repressed the cell cycle regulator MYC before PB differentiation. G0 lengthening accelerated the switch to a IRF4hi/BLIMP1hi state and enhanced the probability of PB specification, thereby generating a self-reinforcing regulatory module that couples cell cycle dynamics to B cell fate choice. This work establishes a generalizable framework for assembling and testing GRNs in the context of immune cell fate decisions. Applying this approach to human B cells revealed previously unreported feedback loops that link cell division to fate specification. These findings have implications for strategies to modulate antibody responses in humans. Cancer Research Institute (#4185) ; NIAID (#5T32AI089443) Immune Response Regulation: Molecular Mechanisms (IRM)