El Soufi, K. | Search bioRxiv

bioRxiv2024

AnalyzAIRR: A user-friendly guided workflow for AIRR data analysis

The analysis of bulk adaptive immune receptor repertoires (AIRR) enables the understanding of immune responses in both normal and pathological conditions. However, the complexity of AIRR calls for advanced, specialized methods to extract meaningful biological insights. These sophisticated approaches often present challenges for researchers with limited bioinformatics expertise, hindering access to comprehensive immune system analysis. To address this challenge, we developed AnalyzAIRR, an AIRR-compliant R package enabling advanced bulk AIRR sequencing data. The tool integrates state-of-the-art statistical and visualization methods applicable at various levels of granularity. It offers a platform for general data exploration, filtering and manipulation, and in-depth cross-comparisons of AIRR datasets, aimed at answering specific biological questions. We illustrate AnalyzAIRR functionalities using of a published murine dataset of 18 T-cell receptor repertoires from three diferrent T cell subsets. We first detected and removed a major contaminant in a group of samples, before proceeding with to the comparative analysis. Subsequent cross-sample analysis revealed differences in repertoire diversity that aligned with the respective cell phenotypes, and in repertoire convergence among the studied subsets. AnalyzAIRRs set of analytical metrics is integrated into a Shiny web application and complemented with a tutorial to help users in their analytical strategy, making it user-friendly for biologists with little or no background in bioinformatics.

bioinformatics↗

bioRxiv2017

High-resolution repertoire analysis of Tfr and Tfh cells reveals unexpectedly high diversities indicating a bystander activation of follicular T cells

T follicular helper (Tfh) and regulatory (Tfr) cells regulate B cell activation and ultimately antibody production. While concordant results show that Tfh cells are specific for the immunizing antigens, limited and even controversial results have been reported regarding the specificity of Tfr cells. Here we used high-throughput T cell receptor (TCR) sequencing to address this issue. We observed that although the Tfh- and Tfr-cell repertoires are less diverse than those of effector (Teff) and regulatory T (Treg) cells, they still represent thousands of clonotypes after immunization with a single antigen. T-cell receptor beta variable (TRBV) gene usage distinguishes both follicular T cells (Tfol) from non-Tfol cells, as well as helper (Teff and Tfh) vs. regulatory (Treg and Tfr) cells. Analysis of the sharing of clonotypes between samples revealed that a specific response to the immunizing antigen can only be detected in Tfh cells immunized with a non-self-antigen and Tfr cells immunized with a self-antigen. Finally, the Tfr TCR repertoire is more similar to that of Tregs than to that of Tfh or Teff cells. Altogether, our results highlight a bystander Tfol-cell activation during antigenic response in the germinal centres and support the Treg cell origin of Tfr cells.\n\nSignificance StatementFollicular helper T (Tfh) cells promote high-affinity antibody production by B cells while follicular regulatory T (Tfr) cells represses it. The question of the specificity of follicular T (Tfol) cells is of utmost importance in the understanding of the antibody response specificity and our work is the first to analysed the global Tfol TCR repertoire in wild type mice. This allowed us not only to portray the overall global structure of these repertoires, but also to substantiate the fact that Tfr cells respond to self-antigen while Tfh cells respond to non self-antigen, a still controversial issue. Importantly, our work revealed an unexpected bystander activation of Tfol cells. We think and discuss that it has a general significance in immune responses and possibly immunopathologies.

immunology↗