Stepwise acquisition of unique epigenetic signatures during differentiation of tissue Treg cells

The effector program of human CD8 T cells supports tissue remodeling

CD8 T lymphocytes are classically viewed as cytotoxic T cells. Whether human CD8 T cells can, in parallel, induce a tissue regeneration program is poorly understood. Here, antigen-specific assay systems revealed that human CD8 T cells not only mediated cytotoxicity but also promoted tissue remodeling. Activated CD8 T cells could produce the epidermal growth factor receptor (EGFR)-ligand amphiregulin (AREG) and sensitize epithelial cells for enhanced regeneration potential. Blocking the EGFR or the effector cytokines IFN-γ and TNF could inhibit tissue remodeling. This regenerative program enhanced tumor spheroid and stem cell-mediated organoid growth. Using single-cell gene expression analysis, we identified an AREG+, tissue-resident CD8 T cell population in skin and adipose tissue from patients undergoing abdominal wall or abdominoplasty surgery. These tissue-resident CD8 T cells showed a strong TCR clonal relation to blood PD1+TIGIT+ CD8 T cells with tissue remodeling abilities. These findings may help to understand the complex CD8 biology in tumors and could become relevant for the design of therapeutic T cell products.

Using single-cell chromatin accessibility sequencing to characterize CD4+ T cells from murine tissues

The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a cutting-edge technology that enables researchers to assess genome-wide chromatin accessibility and to characterize cell type specific gene-regulatory programs. Recent technological progress allows for using this technology also on the single-cell level. In this article, we describe the whole value chain from the isolation of T cells from murine tissues to a complete bioinformatic analysis workflow. We start with methods for isolating scATAC-seq-ready CD4+ T cells from murine tissues such as visceral adipose tissue, skin, colon, and secondary lymphoid tissues such as the spleen. We describe the preparation of nuclei and quality control parameters during library preparation. Based on publicly available sequencing data that was generated using these protocols, we describe a step-by-step bioinformatic analysis pipeline for data pre-processing and downstream analysis. Our analysis workflow will follow the R-based bioinformatics framework ArchR, which is currently well established for scATAC-seq datasets. All in all, this work serves as a one-stop shop for generating and analyzing chromatin accessibility landscapes in T cells.