Fig 1: Single-cell analysis reveals expression and functional characteristics of four genes in SLE in the GSE142016 dataset. (A) UMAP visualization showing 11 clusters identified. (B) UMAP plot annotated with 5 immune cell types. (C) Heatmap presenting the top 3 marker genes for each cell type. (D) Cell-cell communication network analysis. (E) Major signal senders and receivers in cellular communication. (F) UMAP plots showing distribution and expression levels of the four genes across 5 cell types. (G) Heatmap demonstrating expression patterns of the four genes among 5 cell types. (H) Reconstructed pseudotime trajectory. Each point denotes a single cell colored by pseudotime progression. (I) Cell state assignment along pseudotime, indicating different branches or differentiation states. (J) Developmental trajectories of PTPN14 and DNASE1L3 across pseudotime (ECRG4 and SELENBP1 excluded due to low expression). Line plots show smoothed expression profiles along pseudotime. (K) Expression dynamics of PTPN14 and DNASE1L3 along pseudotime. (L) Proportional distribution of cell types between DNASE1L3-high and -low expression groups. (M) Volcano plot visualizing differentially expressed genes between the two groups. (N) KEGG pathway enrichment analysis of DEGs. PTPN14, protein tyrosine phosphatase non-receptor type 14; DNASE1L3, deoxyribonuclease 1 like 3.
Fig 2: Low levels of DNASE1L3 impair macrophage phagocytic function. (A) ELISA analysis displaying reduced DNASE1L3 levels in SLE and CRC groups compared to the control group. The efficiency of DNASE1L3 knockdown in THP-1 cells was validated by RT-qPCR (B) and Western blotting (C) analyses. RT-qPCR results indicated that knockdown of DNASE1L3 influenced THP-1 cell differentiation (D) and the expression of cytokines and enzymes (E). (F) Flow cytometry analysis demonstrated the effect of DNASE1L3 knockdown on efferocytosis in THP-1 cells. **p < 0.01; ***p < 0.001; ****p < 0.0001.
Fig 3: Single-cell analysis reveals expression and functional characteristics of four genes in CRC in the E-MTAB-8107 dataset. (A) UMAP plot showing 23 clusters identified. (B) UMAP visualization annotated with 8 major cell types. (C) Heatmap exhibiting the top 3 marker genes for each cell type. (D) Analysis of intercellular communication networks. (E) Bar plot or circle plot identifying major “sender” (signal-emitting) and “receiver” (signal-receiving) cell types based on cumulative outgoing and incoming signaling strengths. (F) UMAP plots displaying the distribution and expression levels of the four genes across 8 cell types. (G) Heatmap illustrating expression patterns of the four genes in the 8 cell types. (H) Violin plots showing expression levels of the four genes across three broad cellular categories: immune cells, stromal cells, and epithelial cells. (I) Pseudotime trajectory reconstruction. Each point represents a single cell; colors indicate pseudotime progression from early to late states along inferred lineages. (J) Cell state distribution along pseudotime. (K) Developmental trajectories of the four genes across pseudotime. (L) Dynamic expression changes of the four genes along pseudotime. (M) Cellular composition analysis comparing DNASE1L3-high and DNASE1L3-low expression groups. (N) Volcano plot displaying 360 DEGs between the two groups. (O) KEGG pathway enrichment analysis of identified DEGs. *p < 0.05; ****p < 0.0001; ns, not significant; UMAP, uniform manifold approximation and projection.
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