Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoire.

Ivy K Brown,James Scott-Browne,Radleigh G Santos,Laura Harmacek,Cydney Rios,R Lee Reinhardt,Nathan Dyjack,Harsha Krovi,Ting-Hui Tu,Thomas Danhorn,Mindy M Miller,Max A Seibold,Clemencia Pinilla,Brian Vestal,Brian P O’Connor,Rachel Woolaver,Laurent Gapin,William C Gause

doi:10.1371/journal.ppat.1009602

Abstract

The CD4+ T cell response is critical to host protection against helminth infection. How this response varies across different hosts and tissues remains an important gap in our understanding. Using IL-4-reporter mice to identify responding CD4+ T cells to Nippostrongylus brasiliensis infection, T cell receptor sequencing paired with novel clustering algorithms revealed a broadly reactive and clonally diverse CD4+ T cell response. While the most prevalent clones and clonotypes exhibited some tissue selectivity, most were observed to reside in both the lung and lung-draining lymph nodes. Antigen-reactivity of the broader repertoires was predicted to be shared across both tissues and individual mice. Transcriptome, trajectory, and chromatin accessibility analysis of lung and lymph-node repertoires revealed three unique but related populations of responding IL-4+ CD4+ T cells consistent with T follicular helper, T helper 2, and a transitional population sharing similarity with both populations. The shared antigen reactivity of lymph node and lung repertoires combined with the adoption of tissue-specific gene programs allows for the pairing of cellular and humoral responses critical to the orchestration of anti-helminth immunity.

Highlights

CD4+ T helper 2 (Th2) cells have been shown to exhibit remarkable heterogeneity in gene expression and cytokine potential in settings of type-2 inflammation in both mice and humans [1,2,3]
Using various “omic” approaches, the CD4+ T cell receptor (TCR) repertoire was explored after primary helminth infection
Tissue-specific programming of responding CD4+ T cells directed the establishment of committed T follicular helper (Tfh) and Th2 cells, both critical for driving distinct hallmarks of type-2 inflammation

Summary

Introduction

CD4+ T helper 2 (Th2) cells have been shown to exhibit remarkable heterogeneity in gene expression and cytokine potential in settings of type-2 inflammation in both mice and humans [1,2,3] Our understanding of this heterogeneity has been greatly advanced using repeated or prolonged exposure to model allergens and antigens [4,5,6]. How the type-2 CD4+ T cell repertoire changes in response to more epitoperich antigenic stimuli, such as that found in parasitic helminth infection, remains poorly understood These large extracellular worms express and secrete a diverse array of stage-specific proteins which influence both the immunogenic epitopes available during infection and the tissue-specific nature of the immune response [7,8]. The presence of public or dominant clonotypes, breadth of antigen specificity, relatedness between TCR repertoires in lymphoid and nonlymphoid tissues of the same mouse or across different mice, and heterogeneity of the IL-4+ T cell compartment in response to helminth infection are not known

Methods

Results

Discussion

Conclusion