Single-cell chromatin accessibility landscape identifies tissue repair program in human regulatory T cells

Studies over the past decade characterized murine regulatory T cells (Tregs) with the capacity to promote tissue regeneration. In humans, such a population of tissue-repair Treg cells has not been discovered yet. Using single-cell chromatin accessibility profiles of murine and human tissue Treg cells, we defined a species-conserved and microbiota-independent repair Treg signature, with a prevailing footprint of the transcription factor BATF. Combining this signature with gene expression profiling and TCR fate mapping, we identified a population of tissue-like Treg cells in peripheral blood, characterized by the expression of BATF, CCR8 and HLA-DR. Human BATF+CCR8+ Treg cells from normal skin and adipose tissue shared features with tumor-resident Treg and tissue T-follicular helper (Tfh) cells. Inducing a Tfh-like differentiation program in naive Treg cells partially recapitulated human tissue Treg characteristics, including enhanced wound healing potential

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

6 Datasets

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Dataset ID	Description	Technology	Samples
EGAD00001006779	T cells were isolated from human blood and tissues: skin and fat. Subsequently, CD4+ T cells and CD25+ T cells were FACS sorted. scATAC libraries were prepared using the 10x Genomics Kit (CG000168_ChromiumSingleCell_ATAC_ReagentKits_UserGuide_RevD.pdf) and sequenced on an Illumina NextSeq550. In total 15 samples were prepared	NextSeq 500	15
EGAD00001007660	Treg and Tfh cells (8 Samples)from the same donors was subject to ATAC-seq processing. Paired end fastq-files are supplied.	NextSeq 550	8
EGAD00001007661	Regulatory Tcells were FACS sorted and processed with 10x Genomics Chromium Next GEM SingleCell V(D)J Reagents Kits v1.1 sequencing. In total 17 samples were processed. Fastq files are supplied.	NextSeq 550	17
EGAD00001007662	Treg and Tfh cells (8 Samples)from the same donors was subject to RNA-seq (TruSeq Stranded Total RNA) processing. Single end fastq-files are supplied.	NextSeq 550	8
EGAD00001007663	Tcells were isolated fom Tissues and FACS sorted. In total 50 samples were processed in 5 replicates with the Takara SmartSeq Stranded kit. Single end fastq-files are supplied.	NextSeq 550	50
EGAD00001007664	Tcells were isolated fom Tissues and FACS sorted. In total 43 samples were processed in 5 replicates with the Takara SmartSeq Stranded kit. Single end fastq-files are supplied.	NextSeq 550	43