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An amphiregulin reporter mouse enables transcriptional and clonal expansion analysis of reparative lung Tregs
Lucas F. Loffredo, Katherine A. Kaiser, Adam Kornberg, Samhita Rao, Kenia de los Santos-Alexis, Arnold Han, Nicholas Arpaia
Lucas F. Loffredo, Katherine A. Kaiser, Adam Kornberg, Samhita Rao, Kenia de los Santos-Alexis, Arnold Han, Nicholas Arpaia
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Research Article Cell biology Immunology

An amphiregulin reporter mouse enables transcriptional and clonal expansion analysis of reparative lung Tregs

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Abstract

Regulatory T cells (Tregs) are known to play critical roles in tissue repair via provision of growth factors, such as amphiregulin (Areg). Areg-producing Tregs have previously been difficult to study because of an inability to isolate live Areg-producing cells. In this report, we created a reporter mouse to detect Areg expression in live cells (AregThy1.1). We employed influenza A and bleomycin models of lung damage to sort Areg-producing and non-Areg-producing Tregs for transcriptomic analyses. Single-cell RNA-Seq revealed distinct subpopulations of Tregs and allowed transcriptomic comparisons of damage-induced populations. Single-cell TCR sequencing showed that Treg clonal expansion was biased toward Areg-producing Tregs and largely occurred within damage-induced subgroups. Gene module analysis revealed functional divergence of Tregs into immunosuppression-oriented and tissue repair–oriented groups, leading to identification of candidate receptors for induction of repair activity in Tregs. We tested these using an ex vivo assay for Treg-mediated tissue repair, identifying 4-1BB agonism as a mechanism for reparative activity induction. Overall, we demonstrate that the AregThy1.1 mouse is a promising tool for investigating tissue repair activity in leukocytes.

Authors

Lucas F. Loffredo, Katherine A. Kaiser, Adam Kornberg, Samhita Rao, Kenia de los Santos-Alexis, Arnold Han, Nicholas Arpaia

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Figure 7

4-1BB agonism effects reparative activity induction and immunosuppression reduction in lung Tregs and identifies potential ligand-receptor interactions with structural tissue cells.

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4-1BB agonism effects reparative activity induction and immunosuppressio...
(A) Experimental schematic for bulk RNA-Seq of bleomycin lung Tregs stimulated with 4-1BB agonistic antibody. (B) Volcano plots of DEGs for 4-1BB agonistic antibody–stimulated (3H3) vs. control IgG–treated lung Tregs. Red dots on volcano plots: significant DEGs (FDR adj. P value < 0.05). No fold-change cutoff. Numbers of significantly upregulated and downregulated genes indicated on plot. (C) Pathway analysis using GSEA, in full gene signature depicted in B (from Hallmark curated gene sets). All values displayed are significant at FDR q value < 0.05. (D) ICELLNET ligand/receptor interaction analysis of IgG-treated or 4-1BB agonistic antibody–treated lung Tregs, with lung cell types from the Mouse Cell Atlas scRNA-Seq dataset (National Center for Biotechnology Information Gene Expression Omnibus GSE108097). Arrows indicate composite interaction scores (IS) over all ligand/receptor pairs for a given pairing. Table inset: IS values for each pairing. Endo., endothelium; Mes., mesenchyme; Ep., epithelium; AM, alveolar macrophages; IM/DC, interstitial macrophages/dendritic cells; NK, NK cells; T/ILC, T cells/innate lymphoid cells; Gran., granulocytes; B, B cells. (E) ICELLNET bubble plots identifying all interactions between significantly upregulated genes from B with expressed receptors from mesenchymal cells, epithelial cells, and endothelial cells. IS for a given ligand/receptor pairing are given to the right of each bubble. Inset: Venn diagram comparing ligands found for each structural cell type.

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