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Restoration of CD56dim NK Cells by Methotrexate Contributes to the Treatment of Juvenile Idiopathic Arthritis

ABSTRACT: Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic disease in childhood. To elucidate the mechanism of methotrexate (MTX) treatment-induced JIA clinical remission, we conducted single-cell RNA sequencing (scRNA-seq) analysis of peripheral blood mononuclear cells (PBMCs) obtained from a female JIA patient before and after MTX treatment. Besides, we integrated our data with public bulk RNA-seq data. We found that the proportion of the CD56dim NK subsets was restored after MTX treatment, suggesting that CD56dim NK subsets are mainly involved in MTX treatment-induced JIA clinical remission. Differential expression analysis showed that the NK cell-mediated cytotoxicity pathway was riched in CD56dim NK subsets. Furthermore, bulk RNA-seq results showed that MTX-treated NK-92 cell lines were also enriched for NK cell-mediated cytotoxicity pathways. Our data highlight the importance of CD56dim NK subsets in MTX treatment-induced JIA clinical remission.

ORGANISM(S): Homo sapiens

PROVIDER: GSE268374 | GEO | 2025/12/31

REPOSITORIES: GEO

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Project description:Human Natural Killer (NK) cells comprise two main subsets, CD56bright and CD56dim cells, that differ in function, phenotype and tissue localization. To further dissect the heterogeneity of CD56dim cells, we have performed transcriptome analysis and functional ex vivo characterization of human NK cell subsets according to the expression of markers related to differentiation, migration or competence. Here, we show for the first time that the ability to respond to cytokines or to activating receptors is mutually exclusive in almost all NK cells with the exception of CD56dim CD62L+ cells. Indeed, only these cells combine the ability to produce interferon (IFN)-gamma after cytokines and proliferate in vivo during viral infection with the capacity to kill and produce cytokines upon engagement of activating receptors. Therefore, CD56dim CD62L+ cells represent a unique subset of polyfunctional NK cells. Ex vivo analysis of their function, phenotype, telomere length, frequencies during ageing as well as transfer experiments of NK cell subsets into immunodeficient mice suggest that CD56dim CD62L+ cells represent an intermediate stage of NK cell maturation, which after restimulation can accomplish multiple tasks and further develop into terminally differentiated effectors. Gene expression profiles of FACSAria sorted CD3- CD56bright CD62L+, CD3- CD56dim CD62L+ and CD3- CD56dim CD62L- NK cells from human peripheral blood of three donors were compared using Affymetrix GeneChip Human Genome HG-U133_Plus_2. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 Âµg cRNA hybridized in triplicates for each of the three groups to the GeneChip arrays. Group1: CD3- CD56bright CD62L+,.Group2: CD3- CD56dim CD62L+, Group3: CD3- CD56dim CD62L-. Lists of differentially regulated genes were created using High Performance Chip Data Analysis (HPCDA) with Bioretis database (http://www.bioretis-analysis.de). Worldwide data sharing is possible via Bioretis, please ask the authors.

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Restoration of CD56dim NK Cells by Methotrexate Contributes to the Treatment of Juvenile Idiopathic Arthritis

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