The fetus is thought to be protected from exposure to foreign antigens, yet CD45RO+ T cells reside in the fetal intestine. Here we combined functional assays with mass cytometry, single-cell RNA sequencing and high-throughput T cell antigen receptor (TCR) sequencing to characterize the CD4+ T cell compartment in the human fetal intestine. We identified 22 CD4+ T cell clusters, including naive-like, regulatory-like and memory-like subpopulations, which were confirmed and further characterized at the transcriptional level. Memory-like CD4+ T cells had high expression of Ki-67, indicative of cell division, and CD5, a surrogate marker of TCR avidity, and produced the cytokines IFN-γ and IL-2. Pathway analysis revealed a differentiation trajectory associated with cellular activation and proinflammatory effector functions, and TCR repertoire analysis indicated clonal expansions, distinct repertoire characteristics and interconnections between subpopulations of memory-like CD4+ T cells. Imaging mass cytometry indicated that memory-like CD4+ T cells colocalized with antigen-presenting cells. Collectively, these results provide evidence for the generation of memory-like CD4+ T cells in the human fetal intestine that is consistent with exposure to foreign antigens.

Central European Institute of Technology Masaryk University Brno Czech Republic

Centre for Data Intensive Biomedicine and Biotechnology Skolkovo Institute of Science and Technology Moscow Russia

Computer Graphics and Visualization Group Delft University of Technology Delft the Netherlands

Department of Anatomy and Embryology Leiden University Medical Center Leiden the Netherlands

Department of Immunohematology and Blood Transfusion Leiden University Medical Center Leiden the Netherlands

Department of Molecular Technologies Pirogov Russian National Research Medical University Moscow Russia

Department of Pathology Leiden University Medical Center Leiden the Netherlands

Department of Pattern Recognition and Bioinformatics Group Delft University of Technology Delft the Netherlands

Department of Radiology Leiden University Medical Center Leiden the Netherlands

Division of Infection and Immunity Cardiff University School of Medicine Cardiff UK

Leiden Computational Biology Center Leiden University Medical Center Leiden the Netherlands

MiLaboratory LLC Skolkovo Innovation Centre Moscow Russia

Privolzhsky Research Medical University Nizhny Novgorod Russia

Shemyakin Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences Moscow Russia

Systems Immunity Research Institute Cardiff University School of Medicine Cardiff UK

Nat Immunol. 2019 Mar;20(3):254-256. doi: 10.1038/s41590-019-0326-0. PubMed

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