Fig. 3: Lupus-responsive genes are sensitive to SMC1A levels.

A Comparison of lupus-responsive genes (significantly altered in SLE-like vs. basal CD14⁺ monocytes; triplicates, |log₂FC| ≥ 1, adjusted p < 0.05) with DEGs from RNA-sequencing of CD14⁺ monocytes from SLE patients (n = 10, unselected for sex) versus healthy controls (n = 9, unselected for sex) using the same thresholds (|log₂FC| ≥ 1, adjusted p < 0.05). The y-axis shows log₂FC in SLE-like versus basal monocytes, and the x-axis shows log₂FC in SLE versus healthy monocytes. Each dot represents a gene. Genes commonly downregulated fall in the lower-left quadrant, while commonly upregulated genes fall in the upper-right quadrant. Fisher’s exact test revealed significant overlap between transcriptionally activated lupus-responsive genes and SLE-specific DEGs (p = 2.0e-148). B Functional enrichment analysis (Gene Ontology terms) of lupus-responsive genes. The left panel shows enriched pathways among DEGs in SLE versus healthy CD14⁺ monocytes; the right panel shows enriched pathways among lupus-responsive genes (SLE-like versus basal monocytes). C Dot plot showing log₂FC changes in lupus-responsive genes that were also differentially expressed upon SMC1A silencing versus control silencing in CD14⁺ monocytes (Fig. 2C, D). Results are presented separately for genes up- or down-regulated in SMC1A-silenced versus control-silenced cells under basal (left two panels) or SLE-like (right two panels) conditions. Horizontal lines indicate median log₂FC values. One-way ANOVA was performed, followed by post-hoc comparisons using the Least Squares Means method. All p-values are two-tailed.