Transcriptome profiling of human FoxP3+ regulatory T cells

• Published in: Human immunology Vol. 77; no. 2; pp. 201 - 213
• Main Authors: Bhairavabhotla, Ravikiran, Kim, Yong C, Glass, Deborah D, Escobar, Thelma M, Patel, Mira C, Zahr, Rami, Nguyen, Cuong K, Kilaru, Gokhul K, Muljo, Stefan A, Shevach, Ethan M
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-02-2016
• Subjects: Allergy and Immunology; Cells, Cultured; Differentially expressed; Forkhead Transcription Factors - metabolism; FoxP3; Gene Regulatory Networks; Gene signature; Humans; Immune Tolerance - genetics; Intracellular Signaling Peptides and Proteins - genetics; Intracellular Signaling Peptides and Proteins - metabolism; LAYN; Lectins, C-Type - genetics; Lectins, C-Type - metabolism; MicroRNAs - genetics; MiR-146a; MiR-146b; MiR-21; MiRNA; nCounter analysis; PNA; RNA sequencing; RNA, Small Interfering - genetics; RTKN2; Suppressive cells; T-Lymphocyte Subsets - immunology; T-Lymphocytes, Regulatory - immunology; Transcriptome; fluorescence activated cell sorter; DE; MiR-146b; PNA; MiR-146a; MiR-21; RTKN2; Suppressive cells; FACS; peripheral blood; T conventional cells; differentially expressed; rIL-2; RNA-seq; micro RNA; Tconvs; recombinant Interleukin-2; miRNA; umbilical cord blood; Rhotekin-2; FoxP3; Gene Ontology; CB; peptide nucleic acid; RNA sequencing; Gene signature; Tregs; GO; LAYN; Log2 Fold Change; nCounter analysis; poly A + RNA sequencing; healthy donor; PB; T regulatory cells; Layilin; Log2FC; HD; dendritic cell; DC; Differentially expressed; MiRNA
• ISSN: 0198-8859; 1879-1166
• DOI: 10.1016/j.humimm.2015.12.004

Abstract The major goal of this study was to perform an in depth characterization of the “gene signature” of human FoxP3+ T regulatory cells (Tregs). Highly purified Tregs and T conventional cells (Tconvs) from multiple healthy donors (HD), either freshly explanted or activated in vitro , were analyzed via RNA sequencing (RNA-seq) and gene expression changes validated using the nCounter system. Additionally, we analyzed microRNA (miRNA) expression using TaqMan low-density arrays. Our results confirm previous studies demonstrating selective gene expression of FoxP3 , IKZF2 , and CTLA4 in Tregs. Notably, a number of yet uncharacterized genes ( RTKN2 , LAYN , UTS2 , CSF2RB , TRIB1 , F5 , CECAM4 , CD70 , ENC1 and NKG7 ) were identified and validated as being differentially expressed in human Tregs. We further characterize the functional roles of RTKN2 and LAYN by analyzing their roles in vitro human Treg suppression assays by knocking them down in Tregs and overexpressing them in Tconvs. In order to facilitate a better understanding of the human Treg gene expression signature, we have generated from our results a hypothetical interactome of genes and miRNAs in Tregs and Tconvs.