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Vanhee, S.

Publications and source records attributed to Vanhee, S..

2 recordsLinked to original sources

Enhanced protein synthesis is a defining requirement for neonatal B cell development

The LIN28B RNA binding protein exhibits a ontogenically restricted expression pattern and is a key molecular regulator of fetal and neonatal B lymphopoiesis. It enhances the positive selection of CD5+ immature B cells early in life through amplifying the CD19/PI3K/c-MYC pathway and is sufficient to reinitiate self-reactive B-1a cell output when ectopically expressed in the adult. In this study, interactome analysis in primary B cell precursors showed direct binding by LIN28B to numerous ribosomal protein transcripts, consistent with a regulatory role in cellular protein synthesis. Induction of LIN28B expression in the adult setting is sufficient to promote enhanced protein synthesis during the small Pre-B and immature B cell stages, but not during the Pro-B cell stage. This stage dependent effect was dictated by IL-7 mediated signaling, which masked the impact of LIN28B through an overpowering stimulation on the c-MYC / protein synthesis axis in Pro-B cells. Importantly, elevated protein synthesis was a distinguishing feature between neonatal and adult B cell development that was critically supported by endogenous Lin28b expression early in life. Finally, we used a ribosomal hypomorphic mouse model to demonstrate that subdued protein synthesis is specifically detrimental for neonatal B lymphopoiesis and the output of B-1a cells, without affecting B cell development in the adult. Taken together, we identify elevated protein synthesis as a defining requirement for early-life B cell development that critically depends on Lin28b. Our findings offer new mechanistic insights into the layered formation of the complex adult B cell repertoire.

immunology↗

DALI (Diversity AnaLysis Interface): a novel tool for the integrated analysis of multimodal single cell RNAseq data and immune receptor profiling.

Single-cell RNA sequencing is instrumental to unravel the cellular and transcriptomic heterogeneity of T and B cells in health and disease. Recent technological advances add additional layers of information allowing researchers to simultaneously explore the transcriptomic, surface protein and immune receptor diversity during adaptive immune responses. The increasing data complexity poses a burden on the workload for bioinformaticians, who are often not familiar with the specificities and biology of immune receptor profiling. The wet-lab modalities and sequencing capabilities currently have outpaced bioinformatics solutions, which forms an ever-increasing barrier for many biologists to analyze their datasets. Here, we present DALI (Diversity AnaLysis Interface), a software package to identify and analyze T cell and B cell receptor diversity in high-throughput single-cell sequencing data. DALI aims to support bioinformaticians with a functional toolbox, allowing seamless integration of multimodal scRNAseq and immune receptor profiling data generated through 10X Genomics Cell Ranger software. The R-based package builds further on workflows using the Seurat package and other existing tools for BCR/TCR analyses. In addition, DALI is designed to engage immunologists having limited coding experience with their data, using a browser-based interactive graphical user interface. The implementation of DALI can effectively lead to a two-way communication between wet-lab scientists and bioinformaticians to advance the analysis of complex datasets.

bioinformatics↗