Transcriptome network analysis implicates CX3CR1-positive type 3 dendritic cells in non-infectious uveitis

Elife. 2023 Apr 12:12:e74913. doi: 10.7554/eLife.74913.

Abstract

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 toward 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.

Conclusions: These results show that CX3CR1+ DC3s are implicated in non-infectious uveitis and can secrete proinflammatory mediators implicated in its pathophysiology.

Funding: The presented work is supported by UitZicht (project number #2014-4, #2019-10, and #2021-4). The funders had no role in the design, execution, interpretation, or writing of the study.

Keywords: CD1c; RNA-seq; autoimmune response/disease; dendritic cells; human; immunology; inflammation; interferons; medicine; uveitis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antigens, CD1 / analysis
  • CX3C Chemokine Receptor 1 / genetics
  • Cytokines
  • Dendritic Cells / physiology
  • Flow Cytometry
  • Humans
  • Transcriptome*
  • Uveitis* / genetics

Substances

  • Antigens, CD1
  • Cytokines
  • CX3CR1 protein, human
  • CX3C Chemokine Receptor 1

Associated data

  • GEO/GSE195501
  • GEO/GSE194060
  • GEO/GSE48590
  • GEO/GSE119242
  • GEO/GSE149619
  • GEO/GSE110577
  • GEO/GSE178833

Grants and funding

The funders had no role in study design, data collection, and interpretation, or the decision to submit the work for publication.