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Yu L, Li G, Jin S, Su J, Li S. Identification of the core genes in Randall's plaque of kidney stone and immune infiltration with WGCNA network. Front Genet 2023; 14:1048919. [PMID: 36816033 PMCID: PMC9931196 DOI: 10.3389/fgene.2023.1048919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/13/2023] [Indexed: 02/04/2023] Open
Abstract
Background: Randall's plaque is regarded as the precursor lesion of lithiasis. However, traditional bioinformatic analysis is limited and ignores the relationship with immune response. To investigate the underlying calculi formation mechanism, we introduced innovative algorithms to expand our understanding of kidney stone disease. Methods: We downloaded the GSE73680 series matrix from the Gene Expression Omnibus (GEO) related to CaOx formation and excluded one patient, GSE116860. In the RStudio (R version 4.1.1) platform, the differentially expressed genes (DEGs) were identified with the limma package for GO/KEGG/GSEA analysis in the clusterProfiler package. Furthermore, high-correlated gene co-expression modules were confirmed by the WGCNA package to establish a protein-protein interaction (PPI) network. Finally, the CaOx samples were processed by the CIBERSORT algorithm to anchor the key immune cells group and verified in the validation series matrix GSE117518. Results: The study identified 840 upregulated and 1065 downregulated genes. The GO/KEGG results revealed fiber-related or adhesion-related terms and several pathways in addition to various diseases identified from the DO analysis. Moreover, WGCNA selected highly correlated modules to construct a PPI network. Finally, 16 types of immune cells are thought to participate in urolithiasis pathology and are related to hub genes in the PPI network that are proven significant in the validation series matrix GSE117518. Conclusion: Randall's plaque may relate to genes DCN, LUM, and P4HA2 and M2 macrophages and resting mast immune cells. These findings could serve as potential biomarkers and provide new research directions.
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Affiliation(s)
- Lingyun Yu
- Department of Urology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Gefei Li
- Department of Cardiovascular Surgery, Shenzhen, Guangdong, China
| | - Shiyao Jin
- Department of Urology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Jiahong Su
- Department of Urology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Shoulin Li
- Department of Urology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China,*Correspondence: Shoulin Li,
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Zhu Z, Zhang X, Jiang Y, Ruan S, Huang F, Zeng H, Liu M, Xia W, Zeng F, Chen J, Cui Y, Chen H. NEAT1 functions as a key mediator of BMP2 to promote osteogenic differentiation of renal interstitial fibroblasts. Epigenomics 2021; 13:1171-1186. [PMID: 34325517 DOI: 10.2217/epi-2021-0212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Aim: To clarify the mechanism of NEAT1, an aberrantly upregulated lncRNA in Randall's plaques (RP) similar to biomineralization, in mediating osteogenic differentiation of human renal interstitial fibroblasts. Materials & methods: A comprehensive strategy of bioinformatic analysis and experimental verification was performed. Results: BMP2 silence abolished the osteogenic differentiation of human renal interstitial fibroblasts promoted by NEAT1. Mechanically, NEAT1 not only induced the nucleolar translocation of EGR1 binding to BMP2 promotor, but also functioned as a sponge of miR-129-5p in the cytoplasm to promote BMP2 expression. Moreover, there was a positive correlation between NEAT1 and BMP2 expression in RP instead of normal renal papilla. Conclusion: NEAT1 acted as a key mediator of BMP2 to promote human renal interstitial fibroblast osteogenic differentiation, through which NEAT1 might be involved in RP formation.
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Affiliation(s)
- Zewu Zhu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Xiaoqiong Zhang
- Transplantation Center, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yingcheng Jiang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Shuhao Ruan
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Fang Huang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Huimin Zeng
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Minghui Liu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Weiping Xia
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Feng Zeng
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Jinbo Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Yu Cui
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Hequn Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
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Iaquinta MR, Lanzillotti C, Mazziotta C, Bononi I, Frontini F, Mazzoni E, Oton-Gonzalez L, Rotondo JC, Torreggiani E, Tognon M, Martini F. The role of microRNAs in the osteogenic and chondrogenic differentiation of mesenchymal stem cells and bone pathologies. Theranostics 2021; 11:6573-6591. [PMID: 33995677 PMCID: PMC8120225 DOI: 10.7150/thno.55664] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Mesenchymal stem cells (MSCs) have been identified in many adult tissues. MSCs can regenerate through cell division or differentiate into adipocytes, osteoblasts and chondrocytes. As a result, MSCs have become an important source of cells in tissue engineering and regenerative medicine for bone tissue and cartilage. Several epigenetic factors are believed to play a role in MSCs differentiation. Among these, microRNA (miRNA) regulation is involved in the fine modulation of gene expression during osteogenic/chondrogenic differentiation. It has been reported that miRNAs are involved in bone homeostasis by modulating osteoblast gene expression. In addition, countless evidence has demonstrated that miRNAs dysregulation is involved in the development of osteoporosis and bone fractures. The deregulation of miRNAs expression has also been associated with several malignancies including bone cancer. In this context, bone-associated circulating miRNAs may be useful biomarkers for determining the predisposition, onset and development of osteoporosis, as well as in clinical applications to improve the diagnosis, follow-up and treatment of cancer and metastases. Overall, this review will provide an overview of how miRNAs activities participate in osteogenic/chondrogenic differentiation, while addressing the role of miRNA regulatory effects on target genes. Finally, the role of miRNAs in pathologies and therapies will be presented.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Fernanda Martini
- Department of Medical Sciences, Section of Experimental Medicine, School of Medicine, University of Ferrara. Ferrara, Italy
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