Competing gene regulatory networks drive naive and memory B cell differentiation

Demela, P.; Esposito, L.; Marchesan, P.; Bolognini, D.; Giacopuzzi, E.; Ricciardelli, E.; Ferrari, P.; Bombelli, S.; Peano, C.; Prati, D.; Valenti, L.; Soskic, B.

doi:10.1101/2025.06.04.657836

bioRxiv · 10.1101/2025.06.04.657836

Competing gene regulatory networks drive naive and memory B cell differentiation

Demela, P.·Esposito, L.·Marchesan, P.·Bolognini, D.·Giacopuzzi, E.·Ricciardelli, E.·Ferrari, P.·Bombelli, S.·Peano, C.·Prati, D.·Valenti, L.·Soskic, B.

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Abstract

Elucidating the gene regulatory networks (GRNs) that govern human B cell differentiation is essential for understanding immune responses to infection, vaccination and autoantigens. Here, we show that individual naive B cells can give rise to both plasma cells and germinal centre (GC) B cells. In contrast, memory B cells display a progressive increase in IRF4 activity over time, leading to PRDM1 induction and exclusive differentiation into plasma cells. Using CRISPR-based perturbations, we demonstrate that IRF4 is indispensable for both GC and plasma cell development. Notably, IRF4 promotes GC fate independently of PRDM1, as PRDM1 disruption did not impair GC differentiation. We also find that while the abundance of antibody mRNAs is clonally correlated, class switch recombination (CSR) occurs stochastically and is clonally independent. Together, these findings reveal distinct regulatory dynamics during naive and memory B cell activation and offer new insights into the GRNs underlying human B cell fate decisions.

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Demela, P., Esposito, L., Marchesan, P., Bolognini, D., Giacopuzzi, E., Ricciardelli, E., Ferrari, P., Bombelli, S., Peano, C., Prati, D., Valenti, L., Soskic, B.. 2025-06-08. Competing gene regulatory networks drive naive and memory B cell differentiation. https://doi.org/10.1101/2025.06.04.657836

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