Journal: Journal of Inflammation Research

Article Title: Integrating Single-Cell and Microarray Data to Explore the Role of Autophagy-Related Gene Atg7 in Osteoporosis

doi: 10.2147/JIR.S579167

Figure Lengend Snippet: Comprehensive analysis of scRNA-seq data. ( A ) UMAP clustering plot depicting ten distinct cell populations identified from single-cell data, including subpopulations within the MSC cluster. ( B ) UMAP GroupPlot illustrating the spatial distribution of cells in the osteoporotic and NC groups. ( C ) Density distribution plot of global autophagy levels at the single-cell level. ( D ) UMAP-based visualization of ATG7 gene expression, with color gradients representing expression levels in individual cells. ( E ) Violin plot showing differential expression of the ATG7 gene across various cell types. ( F ) Violin plot comparing autophagy-related expression levels between MSCs and the other nine cell populations. ( G ) Violin plot (replicated) displaying ATG7 gene expression differences among different cell populations. ( H ) Gene Ontology (GO) analysis results highlighting functional enrichment differences among the ten single-cell populations. ( I ) Cell proportion plots showing the distribution of the ten cell populations across eight single-cell samples. ( J ) Bar plots comparing the proportions of each cell type between the NC and OP groups. ( K ) Heatmap of marker gene expression across the ten identified cell populations. **p < 0.01, ***p < 0.001, ****p < 0.0001.

Article Snippet: Primary antibodies against ATG7 (Proteintech, 67341-LG, 1:200) and EYA1 (Proteintech, 22658-1-AP, 1:100) were applied and incubated overnight at 4 °C.

Techniques: Single Cell, Gene Expression, Expressing, Quantitative Proteomics, Functional Assay, Marker

Journal: Journal of Inflammation Research

Article Title: Integrating Single-Cell and Microarray Data to Explore the Role of Autophagy-Related Gene Atg7 in Osteoporosis

doi: 10.2147/JIR.S579167

Figure Lengend Snippet: DEG validation set. ( A ) GO enrichment analysis of DEGs. ( B ) Volcano plot displaying significantly upregulated and downregulated genes. ( C ) Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs. ( D ) Heatmap illustrating the expression patterns of selected DEGs. ( E ) GSEA plot showing key enriched pathways. ( F ) Violin plot depicting the expression differences of the ATG7 gene in the GSE35958 dataset. *p < 0.05.

Article Snippet: Primary antibodies against ATG7 (Proteintech, 67341-LG, 1:200) and EYA1 (Proteintech, 22658-1-AP, 1:100) were applied and incubated overnight at 4 °C.

Techniques: Biomarker Discovery, Expressing

Journal: Journal of Inflammation Research

Article Title: Integrating Single-Cell and Microarray Data to Explore the Role of Autophagy-Related Gene Atg7 in Osteoporosis

doi: 10.2147/JIR.S579167

Figure Lengend Snippet: Analysis of MSC subgroups. ( A ) UMAP plot illustrating the spatial distribution characteristics of five MSC subsets. ( B ) UMAP comparison showing the distribution differences of MSCs between the osteoporosis group and the NC group. ( C ) t-SNE-based expression density plot displaying the spatial distribution of autophagy levels within the MSC population. ( D ) t-SNE-based expression density plot showing the spatial expression pattern of the ATG7 gene in the MSC population. ( E ) Bar plot depicting the proportion of each MSC subset in the OP and NC groups. ( F ) Violin plots comparing autophagy level expression between the OP and NC groups across five MSC subsets. ( G ) Violin plots comparing ATG7 gene expression between the OP and NC groups across five MSC subsets. ( H ) Heatmap showing the expression profiles of representative marker genes across the five MSC subsets. ( I ) Correlation plot illustrating the expression relationships among ATG7, BECN1, and SPP1 (OPN) in MSCs. ( J ) Violin plot displaying the overall expression differences of the ATG7 gene between the OP and NC groups. ( K ) Violin plot showing overall changes in autophagy levels in MSCs between the OP and NC groups. ( L ) GO enrichment analysis revealing biological process differences among the five MSC subsets. *p < 0.05,**p < 0.01, ***p < 0.001.

Article Snippet: Primary antibodies against ATG7 (Proteintech, 67341-LG, 1:200) and EYA1 (Proteintech, 22658-1-AP, 1:100) were applied and incubated overnight at 4 °C.

Techniques: Comparison, Expressing, Gene Expression, Marker

Journal: Journal of Inflammation Research

Article Title: Integrating Single-Cell and Microarray Data to Explore the Role of Autophagy-Related Gene Atg7 in Osteoporosis

doi: 10.2147/JIR.S579167

Figure Lengend Snippet: Cell communication in MSC subsets. ( A ) Heatmap showing the intensity of cell–cell interactions among the five MSC subsets. ( B ) In the NC group, heatmaps of signaling intensity received by EYA1 cell subsets with high and low ATG7 expression, along with the remaining four MSC subsets. ( C ) In the osteoporosis group, heatmaps of signaling intensity received by EYA1 cell subsets with high and low ATG7 expression, along with the remaining four MSC subsets. ( D ) In the NC group, ligand–receptor interaction pathway changes between EYA1 subsets with high ATG7 expression and osteoblast subsets with low ATG7 expression. ( E ) In the OP group, ligand–receptor pathway changes between EYA1 subsets with high ATG7 expression and osteoblast subsets with low expression. ( F ) Cell–cell interaction network among the five MSC subpopulations. ( G ) Interaction network between the EYA1 subset and the other four MSC subsets. ( H ) In the NC group, interaction patterns between EYA1 subsets (with high and low ATG7 expression) and the other four MSC subsets. ( I ) In the NC group, interaction signal intensity between EYA1 subsets with high and low ATG7 expression. ( J ) In the OP group, interaction patterns between EYA1 subsets (with high and low ATG7 expression) and the other four MSC subsets. ( K ) In the OP group, interaction signal intensity between EYA1 subsets with high and low ATG7 expression.

Article Snippet: Primary antibodies against ATG7 (Proteintech, 67341-LG, 1:200) and EYA1 (Proteintech, 22658-1-AP, 1:100) were applied and incubated overnight at 4 °C.

Techniques: Expressing

Journal: Journal of Inflammation Research

Article Title: Integrating Single-Cell and Microarray Data to Explore the Role of Autophagy-Related Gene Atg7 in Osteoporosis

doi: 10.2147/JIR.S579167

Figure Lengend Snippet: Pseudotemporal trajectory analysis. ( A ) Pseudo-temporal trajectory of MSCs, illustrating a branched developmental structure with five key nodes; node 1 serves as the major bifurcation point leading toward osteogenic, chondrogenic, or adipogenic lineages. ( B ) Pseudo-temporal trajectory colored by different cellular states, reflecting dynamic transitions during MSC development. ( C ) Spatial distribution and evolutionary trajectories of the five MSC subpopulations along the pseudo-time axis. ( D ) Dynamic changes in ATG7 gene expression across the pseudo-temporal trajectory, indicating its potential involvement in lineage differentiation. ( E ) Comparative distribution of MSCs along the pseudo-time trajectory between the osteoporosis group and the NC group. ( F ) GO and KEGG functional enrichment analyses of the major differentiation branch represented by node 1, highlighting the predominant biological processes and signaling pathways. ( G ) Pseudo-temporal feature gene identification plot, used to screen representative dynamic genes that significantly change along the developmental trajectory. ( H ) Expression patterns of ATG7 across the pseudo-temporal trajectories of the five MSC subpopulations.

Article Snippet: Primary antibodies against ATG7 (Proteintech, 67341-LG, 1:200) and EYA1 (Proteintech, 22658-1-AP, 1:100) were applied and incubated overnight at 4 °C.

Techniques: Gene Expression, Functional Assay, Protein-Protein interactions, Expressing

Journal: Journal of Inflammation Research

Article Title: Integrating Single-Cell and Microarray Data to Explore the Role of Autophagy-Related Gene Atg7 in Osteoporosis

doi: 10.2147/JIR.S579167

Figure Lengend Snippet: Histological, Masson’s trichrome, and immunohistochemical analyses of femurs from Sham and OVX mice. ( A and D ) Hematoxylin and eosin (H&E) staining of the femoral sections. ( B and E ) Masson’s trichrome staining of femoral sections. ( C and F ) Immunohistochemical staining of Atg7 in the femoral sections. ( G and J ) Immunohistochemical staining of Beclin1 in femoral sections. ( H and K ) Immunohistochemical staining of OPN in femoral sections. ( I and L ) Immunohistochemical staining of Sp7 in the femoral sections.

Article Snippet: Primary antibodies against ATG7 (Proteintech, 67341-LG, 1:200) and EYA1 (Proteintech, 22658-1-AP, 1:100) were applied and incubated overnight at 4 °C.

Techniques: Immunohistochemical staining, Staining

Journal: Journal of Inflammation Research

Article Title: Integrating Single-Cell and Microarray Data to Explore the Role of Autophagy-Related Gene Atg7 in Osteoporosis

doi: 10.2147/JIR.S579167

Figure Lengend Snippet: Verification of pseudo-temporal trajectories and autophagy. ( A ) The triple immunofluorescence staining of EYA1, ATG7, and DAPI was performed on MSCs from normal mice and OVX mice, showing the co-localization of EYA1 and ATG7. ( B ) Quantitative comparison of fluorescence signal intensities for EYA1 and ATG7. ( C ) Fluorescence imaging of LC3 autophagy dual-labeled adenoviral infection in MSCs derived from Sham and OVX mice. ( D ) Quantification of red fluorescent puncta (autophagosomes) in merged images and comparison of autophagy levels across different groups. ****p < 0.0001.

Article Snippet: Primary antibodies against ATG7 (Proteintech, 67341-LG, 1:200) and EYA1 (Proteintech, 22658-1-AP, 1:100) were applied and incubated overnight at 4 °C.

Techniques: Immunofluorescence, Staining, Comparison, Fluorescence, Imaging, Labeling, Infection, Derivative Assay

Journal: Journal of Inflammation Research

Article Title: Integrating Single-Cell and Microarray Data to Explore the Role of Autophagy-Related Gene Atg7 in Osteoporosis

doi: 10.2147/JIR.S579167

Figure Lengend Snippet: Validation of key autophagy-related genes. ( A and B ) Western blot analysis of MSCs from Sham and OVX mice. ( C–E ) Quantification of grayscale values for Atg7, Beclin1, and Runx2 proteins. ( F and G ) Western blot analysis of MSCs from the Sham group, OVX group, and OVX mice overexpressing ATG7. ( H–J ) Quantification of grayscale values for Atg7, Beclin1, and Runx2 proteins. ( K and L ) Transmission electron microscopy (TEM) images of MSCs from the Sham and OVX groups, with arrows indicating potential autophagosomes or autolysosomes. ( M ) Relative mRNA expression levels of the ATG7 gene in MSCs from the Sham and OVX mice. *p < 0.05,**p < 0.01, ***p <0.001, ****p < 0.0001.

Article Snippet: Primary antibodies against ATG7 (Proteintech, 67341-LG, 1:200) and EYA1 (Proteintech, 22658-1-AP, 1:100) were applied and incubated overnight at 4 °C.

Techniques: Biomarker Discovery, Western Blot, Transmission Assay, Electron Microscopy, Expressing