SeQuoIA: a single-cell BCR sequencing analysis pipeline for tracking selection mechanisms in germinal centres

Abstract

Germinal centres (GCs) are specialized structures where B cells undergo iterative steps of B-cell receptor (BCR) somatic hypermutation and selection of best antigen binders in a darwinian-like fashion. The accelerated evolutionary process leads to the production of high-affinity antibodies that are crucial for robust and long-term humoral immunity. Within this frame, single-cell BCR sequencing analysis is a method of choice to track GC B cell dynamics as somatic mutations can be utilised as an in vivo molecular tracer. Herein, we present SeQuoIA, a start-to-finish pipeline for the analysis of BCR repertoire sequencing data at the single-cell level, including improved clonotype assignment and phylogeny reconstruction. Most importantly, we introduce a new method for the inference of BCR-driven selection pressure based on somatic mutation patterns, that was validated with biological data. With this pipeline, we explored public datasets and proposed new selection mechanisms in GCs. SignificanceOur pipeline should contribute to a better understanding of the basic biology of GC dynamics, and potentially help in laboratory animal usage reduction. Clinical applications could include assessment of vaccine efficacy, monitoring of B cell anti-tumoral responses, and identification of BCR-mediated processes in B cell lymphomas.