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

Figure 1. A CX3CR1 gene module in CD1c+ dendritic cells (CD1c+ DC) is associated with non-infectious uveitis.

(A) Study design. CD1c+ DCs were purified from blood and subjected to RNA-sequencing. Co-expression network analysis was used to identify gene modules associated with uveitis. (B) Principal component analysis (PCA) of the 2016 uveitis-associated genes (p < 0.05) in 36 patients and control samples of cohort I. (C) Gene significance for uveitis for the gene modules identified by WGCNA. (D) Module membership and Gene Significance for uveitis for the blue module of cohort I. (E) PCA of the 6794 uveitis-associated genes (p < 0.05) in 42 samples of cohort II. (F) Cross-tabulation of the preservation of co-expressed genes between gene modules from cohort I and the black module from cohort II. p value is from Fisher’s exact test. (G) Same as in D, but for the black module of cohort II. (H) Heatmaps of the 147 replicated co-expressed genes (rows) for samples (columns) from cohorts I and II. The venn diagram shows the up- and downregulated genes (clusters shown in H). (I) The (log2) fold change in gene expression compared to healthy controls (x-axis) for all 147 replicated genes in patients with AU, IU, and BU. Genes encoding surface proteins are indicated in black/gray. Key transcription factors are indicated in blue. AU: anterior uveitis, IU: intermediate uveitis, BU: birdshot uveitis.

Figure 1.

Figure 1—figure supplement 1. Purity check of cell fractions for RNA-sequencing in cohort II.

Figure 1—figure supplement 1.

Representative sample of flow-cytometry gating of CD14+, CD19+, CD3+, and CD1c+ cell fractions in CD304-depleted, CD19-depleted and CD1c+ enriched magnetic-activated cell sorting (MACS) fractions from fresh peripheral blood mononuclear cells. Manual gating data for each individual sample are available via: https://doi.org/10.34894/9Q0FVO. The percentage of cells positive for each marker on the group levels between the disease groups is indicated in the bottom.
Figure 1—figure supplement 2. Clinical parameters of disease activity in non-infectious uveitis in cohort II.

Figure 1—figure supplement 2.

A principal component analysis (PCA) plot based on the 678 differentially expressed genes (padj < 0.05) (A), the anterior chamber cell grade (B), vitreous fluid cell grade (C), macular thickness in the left (OS) eye as determined by optical coherence tomography (OCT) (D), and macular thickness in the right eye (OD) as determined by OCT (E) are shown.
Figure 1—figure supplement 3. Correlation plot of the mean normalized count (baseMean from DESeq2) of the black module genes from cohort II and the 147 overlapping genes in the blue, yellow, and green module in cohort I.

Figure 1—figure supplement 3.