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

Kirch, T. G.; Miller, Z. D.; Dearborn, J. S.; Dowell, W. G.; Languon, S.; Paculova, H.; Cleary, J. H.; Frietze, S.; Freeman, K.; MAJUMDAR, D.

doi:10.64898/2026.04.22.720139

bioRxiv · 10.64898/2026.04.22.720139

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

Kirch, T. G.·Miller, Z. D.·Dearborn, J. S.·Dowell, W. G.·Languon, S.·Paculova, H.·Cleary, J. H.·Frietze, S.·Freeman, K.·MAJUMDAR, D.

View original source ↗Export metadata ↓

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.

Explore related subjects

cell biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Kirch, T. G., Miller, Z. D., Dearborn, J. S., Dowell, W. G., Languon, S., Paculova, H., Cleary, J. H., Frietze, S., Freeman, K., MAJUMDAR, D.. 2026-04-24. Genome-Wide CRISPRi Screening Identifies XPO5 as a Regulator of B Cell Mutation and Fitness. https://doi.org/10.64898/2026.04.22.720139

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Differential requirement for the Ire1 luminal domain in Candida albicans drug susceptibility and pathogenicity

The opportunistic human pathogen Candida albicans depends on the unfolded protein response (UPR) for cell wall integrity, antifungal tolerance, filamentous growth, and virulence. The UPR is driven by the conserved transmembrane sensor Ire1, which is activated either by misfolded proteins through its luminal domain or by lipid bilayer stress (LBS) through its transmembrane domain. In budding yeast, these two activation modes deploy divergent transcriptional programs. Whether the requirement for these two input domains is separable in C. albicans, where the cell membrane and cell wall are themselves the targets of major antifungal drug classes, remains unknown. Here, we engineered a C. albicans strain expressing Ire1 lacking an intact luminal domain (ire1{Delta}LD), which no longer detects proteotoxic stress. The ire1{Delta}LD strain grew in the presence of the azole antifungals fluconazole and miconazole but was highly sensitive to heat shock, cell wall stress, and the echinocandin caspofungin. It was also unable to sustain filamentous growth and showed reduced virulence in a Caenorhabditis elegans infection model. RNA sequencing revealed only modest changes to the steady-state transcriptome of ire1{Delta}LD cells. Together, these findings define a differential requirement for the input domains of C. albicans Ire1, uncoupling growth under azole-induced membrane stress from the cell wall, thermal, and virulence-associated outputs that depend on proteotoxic sensing, a distinction that could inform antifungal strategies targeting the UPR.

cell biology↗

bioRxiv2026

Nucleosome Core Allostery Governs Chromatin Recognition and Cell Fate

Nucleosomes regulate chromatin folding, accessibility, and factor recruitment. Current models primarily attribute these functions to histone tail modifications, while the core is largely viewed as a structural scaffold. Yet subtle changes within the nucleosome core can produce profound functional consequences, and the mechanisms underlying these effects remain unclear. Here, we describe nucleosome core allostery as a fundamental principle of chromatin regulation that amplifies the impact of minimal nucleosome variations. Leveraging natural differences between H2A.Z variants, we show that the nucleosome core encodes distinct conformational dynamics that propagate allosterically, thereby controlling nucleosome accessibility and recognition by chromatin factors. As a result, a single buried amino acid substitution alone is sufficient to reprogram nucleosome dynamics and bias cell identity. Our findings establish the nucleosome core as an allosteric regulatory module and provide a generalizable framework for how subtle variation within nucleosomes is amplified into diverse biological outcomes in development and disease.

cell biology↗

bioRxiv2026

A Novel Open-Source CellProfiler Pipeline for Automated, User-Friendly Hierarchical and K-Means Clustering of Microglial Morphology

Microglia represent a highly dynamic and heterogeneous cell type that is critically implicated in states of health and pathology. Microglial morphological subgroups have been identified that correspond to functional characteristics determining health-related outcomes. The identification of states based on morphological characteristics will therefore provide invaluable insights into the microglia-specific functional mechanisms driving treatment effects. The application of clustering analyses enables the detection of groupings within samples reflecting differences in morphological features. Here we propose the application of three custom-created modules to be used within the open-source software CellProfiler. These modules enable the automated detection of clusters present within the sample of microglia, as well as the assessment of the abundance of these clusters across conditions. The application of the analysis is conducted in a highly user-friendly manner, with a user interface integrated into the pipeline, enabling the performance of the analysis with only minimal user input. The workflow thereby includes the conduction of an outlier assessment, followed by hierarchical clustering and k-means clustering and the generation of interactive graphs to determine the number of microglia states present in the sample. Bar plots displaying the abundance of the microglia states across conditions included in the sample will be created. This approach will facilitate faster and more comparable detection of microglial morphological clusters across studies.

cell biology↗