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Zhang X, Chao P, Zhang L, Xu L, Cui X, Wang S, Wusiman M, Jiang H, Lu C. Single-cell RNA and transcriptome sequencing profiles identify immune-associated key genes in the development of diabetic kidney disease. Front Immunol 2023; 14:1030198. [PMID: 37063851 PMCID: PMC10091903 DOI: 10.3389/fimmu.2023.1030198] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 02/16/2023] [Indexed: 03/31/2023] Open
Abstract
BackgroundThere is a growing public concern about diabetic kidney disease (DKD), which poses a severe threat to human health and life. It is important to discover noninvasive and sensitive immune-associated biomarkers that can be used to predict DKD development. ScRNA-seq and transcriptome sequencing were performed here to identify cell types and key genes associated with DKD.MethodsHere, this study conducted the analysis through five microarray datasets of DKD (GSE131882, GSE1009, GSE30528, GSE96804, and GSE104948) from gene expression omnibus (GEO). We performed single-cell RNA sequencing analysis (GSE131882) by using CellMarker and CellPhoneDB on public datasets to identify the specific cell types and cell-cell interaction networks related to DKD. DEGs were identified from four datasets (GSE1009, GSE30528, GSE96804, and GSE104948). The regulatory relationship between DKD-related characters and genes was evaluated by using WGCNA analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) datasets were applied to define the enrichment of each term. Subsequently, immune cell infiltration between DKD and the control group was identified by using the “pheatmap” package, and the connection Matrix between the core genes and immune cell or function was illuminated through the “corrplot” package. Furthermore, RcisTarget and GSEA were conducted on public datasets for the analysis of the regulation relationship of key genes and it revealed the correlation between 3 key genes and top the 20 genetic factors involved in DKD. Finally, the expression of key genes between patients with 35 DKD and 35 healthy controls were examined by ELISA, and the relationship between the development of DKD rate and hub gene plasma levels was assessed in a cohort of 35 DKD patients. In addition, we carried out immunohistochemistry and western blot to verify the expression of three key genes in the kidney tissue samples we obtained.ResultsThere were 8 cell types between DKD and the control group, and the number of connections between macrophages and other cells was higher than that of the other seven cell groups. We identified 356 different expression genes (DEGs) from the RNA-seq, which are enriched in urogenital system development, kidney development, platelet alpha granule, and glycosaminoglycan binding pathways. And WGCNA was conducted to construct 13 gene modules. The highest correlations module is related to the regulation of cell adhesion, positive regulation of locomotion, PI3K-Akt, gamma response, epithelial-mesenchymal transition, and E2F target signaling pathway. Then we overlapped the DEGs, WGCNA, and scRNA-seq, SLIT3, PDE1A and CFH were screened as the closely related genes to DKD. In addition, the findings of immunological infiltration revealed a remarkable positive link between T cells gamma delta, Macrophages M2, resting mast cells, and the three critical genes SLIT3, PDE1A, and CFH. Neutrophils were considerably negatively connected with the three key genes. Comparatively to healthy controls, DKD patients showed high levels of SLIT3, PDE1A, and CFH. Despite this, higher SLIT3, PDE1A, and CFH were associated with an end point rate based on a median follow-up of 2.6 years. And with the gradual deterioration of DKD, the expression of SLIT3, PDE1A, and CFH gradually increased.ConclusionsThe 3 immune-associated genes could be used as diagnostic markers and therapeutic targets of DKD. Additionally, we found new pathogenic mechanisms associated with immune cells in DKD, which might lead to therapeutic targets against these cells.
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Affiliation(s)
- Xueqin Zhang
- Department of Nephropathy, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Peng Chao
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Lei Zhang
- Department of Endocrine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Lin Xu
- Department of Rheumatology Immunology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Xinyue Cui
- Department of Nephropathy, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Shanshan Wang
- Department of Nephropathy, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Miiriban Wusiman
- Department of Nephropathy, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
| | - Hong Jiang
- Department of Nephropathy, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
- Nephrology Clinical Research Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
- *Correspondence: Chen Lu, ; Hong Jiang,
| | - Chen Lu
- Nephrology Clinical Research Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumuqi, Xinjiang Uygur Autonomous Region, China
- Department of Nephropathy, The First Affiliated Hospital of Xinjiang Medical University, Urumuqi, Xinjiang Uygur Autonomous Region, China
- *Correspondence: Chen Lu, ; Hong Jiang,
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Yao X, Shen H, Cao F, He H, Li B, Zhang H, Zhang X, Li Z. Bioinformatics Analysis Reveals Crosstalk Among Platelets, Immune Cells, and the Glomerulus That May Play an Important Role in the Development of Diabetic Nephropathy. Front Med (Lausanne) 2021; 8:657918. [PMID: 34249963 PMCID: PMC8264258 DOI: 10.3389/fmed.2021.657918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/28/2021] [Indexed: 01/15/2023] Open
Abstract
Diabetic nephropathy (DN) is the main cause of end stage renal disease (ESRD). Glomerulus damage is one of the primary pathological changes in DN. To reveal the gene expression alteration in the glomerulus involved in DN development, we screened the Gene Expression Omnibus (GEO) database up to December 2020. Eleven gene expression datasets about gene expression of the human DN glomerulus and its control were downloaded for further bioinformatics analysis. By using R language, all expression data were extracted and were further cross-platform normalized by Shambhala. Differentially expressed genes (DEGs) were identified by Student's t-test coupled with false discovery rate (FDR) (P < 0.05) and fold change (FC) ≥1.5. DEGs were further analyzed by the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to enrich the Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. We further constructed a protein-protein interaction (PPI) network of DEGs to identify the core genes. We used digital cytometry software CIBERSORTx to analyze the infiltration of immune cells in DN. A total of 578 genes were identified as DEGs in this study. Thirteen were identified as core genes, in which LYZ, LUM, and THBS2 were seldom linked with DN. Based on the result of GO, KEGG enrichment, and CIBERSORTx immune cells infiltration analysis, we hypothesize that positive feedback may form among the glomerulus, platelets, and immune cells. This vicious cycle may damage the glomerulus persistently even after the initial high glucose damage was removed. Studying the genes and pathway reported in this study may shed light on new knowledge of DN pathogenesis.
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Affiliation(s)
- Xinyue Yao
- The Hebei Key Lab for Organ Fibrosis, The Hebei Key Lab for Chronic Disease, School of Public Health, International Science and Technology Cooperation Base of Geriatric Medicine, North China University of Science and Technology, Tangshan, China
| | - Hong Shen
- Department of Modern Technology and Education Center, North China University of Science and Technology, Tangshan, China
| | - Fukai Cao
- Department of Jitang College, North China University of Science and Technology, Tangshan, China
| | - Hailan He
- The Hebei Key Lab for Organ Fibrosis, The Hebei Key Lab for Chronic Disease, School of Public Health, International Science and Technology Cooperation Base of Geriatric Medicine, North China University of Science and Technology, Tangshan, China
| | - Boyu Li
- The Hebei Key Lab for Organ Fibrosis, The Hebei Key Lab for Chronic Disease, School of Public Health, International Science and Technology Cooperation Base of Geriatric Medicine, North China University of Science and Technology, Tangshan, China
| | - Haojun Zhang
- Beijing Key Lab for Immune-Mediated Inflammatory Diseases, Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, China
| | - Xinduo Zhang
- The Hebei Key Lab for Organ Fibrosis, The Hebei Key Lab for Chronic Disease, School of Public Health, International Science and Technology Cooperation Base of Geriatric Medicine, North China University of Science and Technology, Tangshan, China
| | - Zhiguo Li
- The Hebei Key Lab for Organ Fibrosis, The Hebei Key Lab for Chronic Disease, School of Public Health, International Science and Technology Cooperation Base of Geriatric Medicine, North China University of Science and Technology, Tangshan, China
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