This dataset contains the processed RNA sequencing data of purified CD1c-positive conventional type 2 dendritic cells (CD1c+ cDC2s), functional enrichment analysis, manual and automatic gating data of (i.e., flowSOM) flow cytometry, and multiplex cytokine analyses as outlined in Hiddingh et al. 2022 "Transcriptome network analysis implicates CX3CR1-positive type 3 dendritic cells in non-infectious uveitis see preprint on BioRxiv
Data are from two cohorts (cohort I, n=36, and cohort II, n=42) of in total 51 patients with non-infectious uveitis (HLA-B27-positive acute anterior uveitis, idiopathic intermediate uveitis, HLA-A29-positive Birdshot Uveitis (Birdshot chorioretinopathy), and 27 sex/age-matched healthy controls without ocular inflammatory disease).
All raw sequencing data are available at NCBI SRA under the accession number:
GSE195501 (FACS-sorted cohort I).
GSE194060 (MACS-sorted cohort II).
This dataverseNL dataset contains additional raw, processed, and metadata (see readme file and reproducible R notebooks (R script and Image) used for the analysis in the manuscript:
R scripts (markdown + R image) with step-by-step analyses
Figure_1.rmd (see "Figure_1.html")
Figure_2.rmd (see "Figure_2.html")
Figure_3.rmd (see "Figure_3.html")
Figure_4.rmd (see "Figure_4.html")
Figure_5.rmd(see "Figure_5.html")
Processed RNA seq data (including WGCNA) (see folder Uveitis_mDC in files)
Experimental data
Manual gating data of MACS-sorted fractions cohort I (see here)
Manual gating data for CD1c+ cDC2 subsets in PBMCs (see here)
Manual gating CD14+ and CD14- CD1c+ cDC2 fractions from Buffy (see here)
qPCR data for CX3CR1,CCR5,CCR2,IRF8,TLR7,RUNX3 and CD36 in sorted CD14+ and CD14- CD1c+ DCs (see here)
qPCR data (fold change compared to medium) for RUNX3 and CD36 in overnight stimulated cDC2 cultures (see here)
Cell phenotypes identified by flowSOM (7x7 grid) using the cDC2-subset flow cytometry panel (see here)
IL-23 ELISA concentration in supernatant of overnight LTA-stimulated cDC2 subset cultures (see here)
Luminex Multiplex Cytokine analysis of supernatant of overnight LTA-stimulated cDC2 subset cultures (see here)
Other transcriptomic data used in the R scripts (above)
WT Untreated cDC2 versus cDC2 from Runx3-11cKO miceGSE48590 generated by Dicken et al., PLoS One
2013
WT Untreated cDC2 versus cDC2 from Notch2-11cKO miceGSE119242 generated by Briseño et al., Proc Natl Acad Sci U S A 2018
Sorted CD14+CD5-CD163+ and CD14-CD5-CD163+ cDC2s from SLE and Scleroderma patients GSE136731 generated by Dutertre et al., Immunity 2019
Single-cell RNA-seq of aqueous humor from 4 HLA-B27-positive uveitis patients and control GSE178833 generated by Kasper et al., Elife 2021
Inflammatory [inf-]cDC2sGSE149619 generated by Bosteels et al., Immunity 2020
RNA-seq data from cDC2s generated from murine bone marrow cells in co-culture with stromal OP-9 cell line transduced with or without expression of the Notch ligand Delta-like 1GSE110577 generated by Kirkling et al., Cell Rep 2018
Transcriptome network analysis implicates CX3CR1-positive type 3 dendritic cells in non-infectious uveitis
Background:Type I interferons (IFNs) promote the expansion of subsets of CD1c+ conventional dendritic cells (CD1c+ DCs), but the molecular basis of CD1c+ DCs involvement in conditions not associated without elevated type I IFNs remains unclear.
Methods: We analyzed CD1c+ DCs from two cohorts of non-infectious uveitis patients and healthy donors using RNA-sequencing followed by high-dimensional flow cytometry to characterize the CD1c+ DC populations.
Results: We report that the CD1c+ DCs pool from patients with non-infectious uveitis is skewed towards a gene module with the chemokine receptor CX3CR1 as the key hub gene. We confirmed these results in an independent case-control cohort and show that the disease-associated gene module is not mediated by type I IFNs. An analysis of peripheral blood using flow cytometry revealed that CX3CR1+ DC3s were diminished, whereas CX3CR1- DC3s were not. Stimulated CX3CR1+ DC3s secrete high levels of inflammatory cytokines, including TNF-alpha, and CX3CR1+ DC3-like cells can be detected in inflamed eyes of patients. Conclusion: These results show that CX3CR1+ DC3s are implicated in non-infectious uveitis and can secrete proinflammatory mediators implicated in its pathophysiology.
