Single-cell analysis with childhood and adult systemic lupus erythematosus

Figures & data

Figure 1. Single-cell RNA sequencing reveals the composition and transcriptional characteristics of peripheral blood mononuclear cells (PBMCs) in childhood-onset systemic lupus erythematosus (cSLE) patients. (A-B) Two-dimensional projection of the sample distribution (A) and identification of 34 subclusters (B) across a total of 234,238 PBMCs from 44 individuals, including 33 cSLE patients (case) and 11 healthy donors (control). (C) t-SNE analysis identifies eight distinct PBMC subsets, including B cells, monocytes (CD16^-), monocytes (CD16⁺), natural killer (NK) cells, CD4⁺ T cells, CD8⁺ T cells, pre-B cells (CD34^-), and common myeloid progenitor (CMP). (D) Annotation of the eight clusters identified in C. The dot plot shows the expression values of selected genes (x-axis) across each cluster (y-axis). dot size represents the percentage of cells expressing the marker gene, and colour intensity indicates the mean expression within expressing cells. (E-F) Bar plots illustrating the abundance of cells within each of the eight clusters (B cells: 25,451 cells, monocytes (CD16^-): 30,413 cells, monocytes (CD16⁺): 5,215 cells, NK cells: 14,810 cells, CD4⁺ T cells: 134,874 cells, CD8⁺ T cells: 22,632 cells, pre-B cells (CD34^-): 673 cells, CMP: 170 cells). (G) Differential expression analysis highlights the differentially expressed genes (DEGs) across the eight clusters.

Figure 2. Single-cell RNA sequencing reveals the composition and transcriptional characteristics of peripheral blood mononuclear cells (PBMCs) in adult-onset systemic lupus erythematosus (aSLE) patients. (A-B) Two-dimensional projection of the sample distribution (A) and identification of 30 subclusters (B) across a total of 69,588 PBMCs from 17 individuals, including 10 aSLE patients (case) and 7 adult healthy donors (control). (C) t-SNE analysis identifies seven distinct PBMC subsets, including B cells, monocytes (CD16^-), monocytes (CD16⁺), natural killer (NK) cells, CD4⁺ T cells, CD8⁺ T cells, and neutrophil cells. (D) Annotation of the seven clusters identified in C. The dot plot shows the expression values of selected genes (x-axis) across each cluster (y-axis). dot size represents the percentage of cells expressing the marker gene, and colour intensity indicates the mean expression within expressing cells. (E-F) Bar plots illustrating the abundance of cells within each of the seven clusters (B cells: 3,632 cells, monocytes (CD16^-): 9,356 cells, monocytes (CD16⁺): 2,571 cells, NK cells: 3,981 cells, CD4⁺ T cells: 39,908 cells, CD8⁺ T cells: 8,751 cells, and neutrophil cells: 1,389 cells). (G) Differential expression analysis shows the differentially expressed genes (DEGs) across the seven clusters.

Figure 3. Single-cell RNA sequencing reveals the overlapped differentially expressed genes (DEGs) in peripheral blood mononuclear cells (PBMCs) between childhood-onset (cSLE) and adult-onset (aSLE) systemic lupus erythematosus patients. Venn diagram illustrating the overlapped DEGs between cSLE patients and aSLE patients within the same PBMC cluster.

Figure 4. Functional enrichment analysis was performed on differentially expressed genes (DEGs) in monocyte (CD16⁺) cells between systemic lupus erythematosus (SLE) patients and matched healthy donors. (A-B) Gene Ontology (GO) enrichment analysis of DEGs in monocyte (CD16⁺) cells was conducted separately for adults (A) and children (B). (C-D) the top 5 DEGs in monocyte (CD16⁺) cells for both adults (C) and children (D) were further analysed using the Seurat R package.

Table 1. Functional enrichment results of differentially expressed genes between SLE patients and healthy donors in different cell types

term_name	adjusted_p_value
response to biotic stimulus	3.29E-21
immune system process	2.30E-18
regulation of viral process	5.94E-17
defense response	2.74E-16
innate immune response	3.14E-14
response to type I interferon	2.36E-10
response to interferon-beta	4.38E-08
antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	1.37E-07
response to interferon-alpha	3.63E-07
response to interferon-gamma	5.11E-07
antigen processing and presentation of exogenous peptide antigen via MHC class II	1.80229E-06
mitochondrial ATP synthesis coupled electron transport	6.29785E-06
MHC protein complex assembly	1.18522E-05
peptide antigen assembly with MHC protein complex	1.18522E-05
leukocyte cell-cell adhesion	3.32679E-05
cell death	4.4851E-05
cell killing	5.89823E-05
regulation of lymphocyte activation	0.000189073
leukocyte mediated immunity	0.000193137
regulation of cell death	0.000656868

Figure 5. Functional enrichment analysis was performed on differentially expressed genes (DEGs) in monocyte (CD16^-) cells between SLE patients and matched healthy donors. (A-B) Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) in monocyte (CD16^-) cells was conducted separately for adults (A) and children (B). (C-D) the top 5 DEGs in monocyte (CD16^-) cells for both adults (C) and children (D) were further analysed using the Seurat R package.

Figure 6. Functional enrichment analysis was performed on differentially expressed genes (DEGs) in CD8⁺ T cells between SLE patients and matched healthy donors. (A-B) Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) in CD8⁺ T cells was conducted separately for adults (A) and children (B). (C-D) the top 5 DEGs in CD8⁺ T cells for both adults (C) and children (D) were further analysed using the Seurat R package.

Figure 7. Functional enrichment analysis was performed on differentially expressed genes (DEGs) in NK cells between SLE patients and matched healthy donors. (A-B) Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) in NK cells was conducted separately for adults (A) and children (B). (C-D) the top 5 DEGs in NK cells for both adults (C) and children (D) were further analysed using the Seurat R package.

Figure 8. Functional enrichment analysis was performed on differentially expressed genes (DEGs) in B cells between SLE patients and matched healthy donors. (A-B) Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) in B cells was conducted separately for adults (A) and children (B). (C-D) the top 5 DEGs in B cells for both adults (C) and children (D) were further analysed using the Seurat R package.

Figure 9. Functional enrichment analysis was performed on differentially expressed genes (DEGs) in neutrophil and pre-B (CD34^-) cells between SLE patients and matched healthy donors. (A) Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) in neutrophil between aSLE and matched healthy donors. (B) Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) in pre-B (CD34^-) cells between cSLE and matched healthy donors. (C) Analysis of the top 5 DEGs enrichment in neutrophil between aSLE and matched healthy donors using the Seurat R package. (D) Analysis of the top 5 DEGs enrichment in pre-B (CD34^-) cells between cSLE and matched healthy donors using the Seurat R package.

Availability of data and materials

We downloaded the PBMC’ 10X scRNA-seq matrix data of 43 SLE patients (33 cSLE and 10 aSLE patients) and 18 health donors (11 cHD and 7 aHD) from Gene Expression Omnibus (GEO) database under the accession number GSE135779 and GSE142016 [14,17].