Genome-Wide CRISPRi Screening Identifies XPO5 as a Regulator of B Cell Mutation and Fitness

Abstract

The B cell receptor (BCR) is the defining factor of B lymphocyte identity and function, allowing for a robust adaptive immune response through antigen recognition. Strict regulation of BCR surface density dictates proper B cell signaling, immune regulation, and the prevention of malignancy, yet the factors regulating this density remain undefined. Here, we performed a genome-wide CRISPR interference (CRISPRi) screen in Ramos B cells, which undergo constitutive somatic hypermutation (SHM) and identified Exportin-5 (XPO5) as a central regulator of BCR surface expression. XPO5 depleted cells exhibited an accelerated loss of surface BCR with no change in transcript levels, suggesting a potential post-transcriptional regulatory mechanism. Further analysis revealed XPO5 depletion led to an accumulation of non-functional BCR light chain sequences driven by an increase in AID signature mutations, implicating XPO5 in balancing mutagenesis and repair during somatic hypermutation (SHM). Transcriptomic and small RNA sequencing revealed a global reduction in miRNA levels and enrichment of target gene sets indicative of cell cycle arrest and increased DNA damage response. These data suggest that XPO5 plays a multi-faceted regulatory role in B cells via a miRNA-mediated control, supporting both proliferation and regulating DNA repair thresholds to maintain B cell receptor expression and functionality. SignificancePrecise regulation of B cell receptor (BCR) density is essential for immune function and preventing malignancy. Through a genome-wide CRISPR interference (CRISPRi) screen, we identified Exportin-5 (XPO5) as a critical regulator of BCR surface expression. We show that XPO5 is essential to maintain the miRNA landscape that supports DNA repair during somatic hypermutation. Loss of XPO5 destabilizes this mutational balance, driving the accumulation of non-functional BCR sequences. This study uncovers a novel connection between miRNA nuclear export and the preservation of B cell identity and genomic fidelity, highlighting the multi-faceted regulatory role of XPO5.