Generation of a single-cell B cell atlas of antibody repertoires and transcriptomes to identify signatures associated with antigen specificity

Andreas Agrafiotis; Daniel Neumeier; Kai-Lin Hong; Tasnia Chowdhury; Roy Ehling; Raphael Kuhn; Ioana Sandu; Victor Kreiner; Tudor-Stefan Cotet; Danielle Shlesinger; Daria Laslo; Stine Anzböck; Dale Starkie; Daniel J Lightwood; Annette Oxenius; Sai T Reddy; Alexander Yermanos

doi:10.1016/j.isci.2023.106055

Generation of a single-cell B cell atlas of antibody repertoires and transcriptomes to identify signatures associated with antigen specificity

iScience. 2023 Jan 25;26(3):106055. doi: 10.1016/j.isci.2023.106055. eCollection 2023 Mar 17.

Authors

Andreas Agrafiotis^{1

2}, Daniel Neumeier¹, Kai-Lin Hong¹, Tasnia Chowdhury³, Roy Ehling¹, Raphael Kuhn¹, Ioana Sandu², Victor Kreiner¹, Tudor-Stefan Cotet¹, Danielle Shlesinger¹, Daria Laslo¹, Stine Anzböck¹, Dale Starkie³, Daniel J Lightwood³, Annette Oxenius², Sai T Reddy¹, Alexander Yermanos^{1

2

4

5}

Affiliations

¹ Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
² Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
³ UCB Pharma, Slough, Berkshire, UK.
⁴ Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland.
⁵ Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands.

Abstract

Although new genomics-based pipelines have potential to augment antibody discovery, these methods remain in their infancy due to an incomplete understanding of the selection process that governs B cell clonal selection, expansion, and antigen specificity. Furthermore, it remains unknown how factors such as aging and reduction of tolerance influence B cell selection. Here we perform single-cell sequencing of antibody repertoires and transcriptomes of murine B cells following immunizations with a model therapeutic antigen target. We determine the relationship between antibody repertoires, gene expression signatures, and antigen specificity across 100,000 B cells. Recombinant expression and characterization of 227 monoclonal antibodies revealed the existence of clonally expanded and class-switched antigen-specific B cells that were more frequent in young mice. Although integrating multiple repertoire features such as germline gene usage and transcriptional signatures failed to distinguish antigen-specific from nonspecific B cells, other features such as immunoglobulin G (IgG) subtype and sequence composition correlated with antigen specificity.

Keywords: Immune response; Immunology; Transcriptomics.