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Wang Z, Deng Q, Gu Y, Li M, Chen Y, Wang J, Zhang Y, Zhang J, Hu Q, Zhang S, Chen W, Chen Z, Li J, Wang X, Liang H. Integrated single-nucleus sequencing and spatial architecture analysis identified distinct injured-proximal tubular types in calculi rats. Cell Biosci 2023; 13:92. [PMID: 37208718 DOI: 10.1186/s13578-023-01041-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/01/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Urolithiasis with high prevalence and recurrence rate, has impacts on kidney injury in patients, becomes a socioeconomic and healthcare problem in worldwide. However, the biology of kidney with crystal formation and proximal tubular injury remains essentially unclear. The present study aims to evaluate the cell biology and immune-communications in urolithiasis mediated kidney injury, to provide new insights in the kidney stone treatment and prevention. RESULTS We identified 3 distinct injured-proximal tubular cell types based on the differentially expression injury markers (Havcr1 and lcn2) and functional solute carriers (slc34a3, slc22a8, slc38a3 and slc7a13), and characterized 4 main immune cell types in kidney and one undefined cell population, where F13a1+/high/CD163+/high monocyte & macrophage and Sirpa/Fcgr1a/Fcgr2a+/high granulocyte were the most enriched. We performed intercellular crosstalk analysis based on the snRNA-seq data and explored the potential immunomodulation of calculi stone formation, and founded that the interaction between ligand Gas6 and its receptors (Gas6-Axl, Gas6-Mertk) was specifically observed in the injured-PT1 cells, but not injured-PT2 and -PT3 cells. The interaction of Ptn-Plxnb2 was only observed between the injured-PT3 cells and its receptor enriched cells. CONCLUSIONS Present study comprehensively characterized the gene expression profile in the calculi rat kidney at single nucleus level, identified novel marker genes for all cell types of rat kidney, and determined 3 distinct sub-population of injured-PT clusters, as well as intercellular communication between injured-PTs and immune cells. Our collection of data provides a reliable resource and reference for studies on renal cell biology and kidney disease.
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Affiliation(s)
- Zhu Wang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Qiong Deng
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Yanli Gu
- Central Laboratory, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Min Li
- Department of Pathology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Yeda Chen
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Jieyan Wang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Ying Zhang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Jianwen Zhang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Qiyi Hu
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Shenping Zhang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China
| | - Wei Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 518109, P.R. China
| | - Zhenhua Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 518109, P.R. China
| | - Jiaying Li
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 518109, P.R. China
| | - Xisheng Wang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China.
- Department of Urology, People's Hospital of Longhua, Southern Medical University, 38 Jinglong Jianshe Road, Shenzhen, Guangdong, 518109, P.R. China.
| | - Hui Liang
- Department of Urology, People's Hospital of Longhua Shenzhen, Southern Medical University, Shenzhen, Guangdong, 518109, P.R. China.
- Department of Urology, People's Hospital of Longhua, Southern Medical University, 38 Jinglong Jianshe Road, Shenzhen, Guangdong, 518109, P.R. China.
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Zhawar VK, Kandpal RP, Athwal RS. Alternative Promoters of GRIK2 (GluR6) Gene in Human Carcinoma Cell Lines Are Regulated by Differential Methylation of CpG Dinucleotides. Genes (Basel) 2022; 13:genes13030490. [PMID: 35328043 PMCID: PMC8954616 DOI: 10.3390/genes13030490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 02/04/2023] Open
Abstract
The ionotropic glutamate receptor 6 (GluR6 or GRIK2) gene is transcribed by two cell-type-specific promoters in neuronal and non-neuronal cells, which results in five different transcript variants. The purpose of this study was to explore cell-type-specific silencing of these promoters by epigenetic mechanisms. The neuronal and non-neuronal promoter sequences were cloned upstream of the luciferase gene in the pGL3 luciferase reporter vector. Promoter susceptibility to methylation was confirmed by 5-azacytidine and trichostatin treatment, and the status of CpG dinucleotides was determined by bisulfite sequencing of the promoter was determined by bisulfite sequences. GluR6A transcript variant was expressed in the brain, and GluR6B was most abundant in tumor cell lines. The neuronal promoter was methylated in non-neuronal cell lines. The treatment with 5-azacytidine and trichostatin upregulated transcription of the GluR6 gene, and methylation of the GluR6 promoter sequence in the luciferase reporter system led to downregulation of the luciferase gene transcription. Bisulfite sequencing revealed methylation of 3 and 41 CpG sites in non-neuronal and neuronal promoters, respectively. The differential activation/silencing of GluR6 promoters suggests that the transcript variants of GluR6 are involved in tissue-specific biological processes and their aberrant regulation in tumor cells may contribute to distinct properties of tumor cells.
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Affiliation(s)
- Vikramjit K. Zhawar
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19067, USA;
| | - Raj P. Kandpal
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
- Correspondence: (R.P.K.); (R.S.A.)
| | - Raghbir S. Athwal
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19067, USA;
- Correspondence: (R.P.K.); (R.S.A.)
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