Fig 1.
Flowchart of this study.
Fig 2.
Identification of DEGs in lupus nephritis.
(A) Normalization of the GSE112943 dataset. Each sample after processing is located at the same baseline. (B) PCA of the GSE112943 dataset. Elimination of different dimensional differences. (C) The volcano plot showing the expression of DEGs between lupus nephritis and normal controls. (D) The heatmap illustrating the top 50 genes with the most significant differences between individuals with lupus nephritis and normal controls.
Fig 3.
Identification of modules and genes most associated with LN based on WGCNA analysis.
(A) The soft threshold power (left) and mean connectivity (right) of the WGCNA. (B) The network topology heatmap for all genes. (C) Cluster dendrogram for WGCNA analysis. (D) The heatmap showing the relationship between the modules and clinical traits, particularly lupus nephritis and normal controls. (E) The scatter plot between gene significance and module membership in the brown module. (F) The scatter plot between gene significance and module membership in the coral 2 module.
Fig 4.
(A) The venn diagram of the intersection of DEGs, WGCNA module genes and ARGs. (B) The PPI network is plotted based on DE-ARGs. (C) The CytoHubba plugin filters to get the most important network clusters. (D) The bubble diagram showing the GO enrichment analysis of DE-ARGs. (E) The bubble plot displaying KEGG enrichment analysis of DE-ARGs.
Fig 5.
Identification of signature genes based on lasso analysis and random forests.
(A) LASSO analysis of cross-validation curves. The optimal λ value was determined using 10-fold cross-validation in the retraining set (left). Penalty score plot of LASSO coefficients for signature genes associated with lupus nephritis in the training set (right). (B) The bubble plot illustrating the relative importance ranking of genes in the random forest model within the training set. (C) The venn diagram of intersection of LASSO analysis and random forest signature genes. (D) The expression levels of five signature genes in individuals with lupus nephritis in the training set compared to normal controls. (E) ROC analysis of five signature genes in the training set.
Fig 6.
Identification of key autophagy-related genes in lupus nephritis.
(A) The expression levels of five signature genes in individuals with lupus nephritis in the validating set compared to normal controls. (B) ROC analysis of five signature genes in the validating set. Inference scores (C) and reference counts (D) between key genes and necrosis, inflammation, kidney disease, memory disorders, acute kidney injury, kidney neoplasms, chronic kidney failure, systemic lupus erythematosus, lupus nephritis, and kidney calculi in the CTD database. MAP1LC3B on the left and TNFSF10 on the right. (E) Other genes that are closely related to the key genes. (F) GO enrichment analysis of key genes and their related genes. (G) KEGG enrichment analysis of key genes and their related genes.
Fig 7.
The results of immunohistochemical staining of key genes in the kidneys of patients with lupus nephritis and normal controls.
(A) MAP1LC3B staining results in lupus nephritis and normal control localized renal tissues. (B) TNFSF10 staining results in lupus nephritis and normal control localized renal tissues.
Fig 8.
The analysis of immune infiltration in lupus nephritis and normal controls.
(A) The heatmap showing the infiltration of 22 immune cells in lupus nephritis and normal control renal tissues. (B) The stacked bar graphs illustrating the composition of each immune cell in lupus nephritis and normal control renal tissues. (C) The heatmap displaying the correlation between the 22 immune cells. (D) The box plots depicting the differences in the expression of 22 immune cells between lupus nephritis and normal controls. (E) The heatmap presenting the correlation between key genes and 22 immune cells. The green color represents a positive correlation and the purple color represents a negative correlation. The darker the color, the stronger the correlation.
Fig 9.
Animal experiments validate the expression of key autophagy genes.
(A-C) The 24h urinary protein level, splenic index, and perirenal lymph node index in lupus mice and C57BL/6 mice. (D) HE staining and glomerular score in lupus and C57BL/6 mice. (E) C3 and IgG immunofluorescence staining in lupus mice and C57BL/6 mice. (F) The pcr results of MAPLC3B and TNFSF10.