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Di Camillo B, Puricelli L, Iori E, Toffolo GM, Tessari P, Arrigoni G. Modeling SILAC Data to Assess Protein Turnover in a Cellular Model of Diabetic Nephropathy. Int J Mol Sci 2023; 24:ijms24032811. [PMID: 36769128 PMCID: PMC9917874 DOI: 10.3390/ijms24032811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Protein turnover rate is finely regulated through intracellular mechanisms and signals that are still incompletely understood but that are essential for the correct function of cellular processes. Indeed, a dysfunctional proteostasis often impacts the cell's ability to remove unfolded, misfolded, degraded, non-functional, or damaged proteins. Thus, altered cellular mechanisms controlling protein turnover impinge on the pathophysiology of many diseases, making the study of protein synthesis and degradation rates an important step for a more comprehensive understanding of these pathologies. In this manuscript, we describe the application of a dynamic-SILAC approach to study the turnover rate and the abundance of proteins in a cellular model of diabetic nephropathy. We estimated protein half-lives and relative abundance for thousands of proteins, several of which are characterized by either an altered turnover rate or altered abundance between diabetic nephropathic subjects and diabetic controls. Many of these proteins were previously shown to be related to diabetic complications and represent therefore, possible biomarkers or therapeutic targets. Beside the aspects strictly related to the pathological condition, our data also represent a consistent compendium of protein half-lives in human fibroblasts and a rich source of important information related to basic cell biology.
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Affiliation(s)
- Barbara Di Camillo
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
- Correspondence: (B.D.C.); (G.A.)
| | - Lucia Puricelli
- Department of Medicine, University of Padova, 35128 Padova, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, 35128 Padova, Italy
| | - Elisabetta Iori
- Department of Medicine, University of Padova, 35128 Padova, Italy
| | - Gianna Maria Toffolo
- Department of Information Engineering, University of Padova, 35131 Padova, Italy
| | - Paolo Tessari
- Department of Medicine, University of Padova, 35128 Padova, Italy
| | - Giorgio Arrigoni
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, 35128 Padova, Italy
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Correspondence: (B.D.C.); (G.A.)
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Zhang F, Jiang N, Gao Y, Fan Z, Li Q, Ke G, Li B, Wu Q, Xu R, Liu S. PPBP as a marker of diabetic nephropathy podocyte injury via Bioinformatics Analysis. Biochem Biophys Res Commun 2021; 577:165-172. [PMID: 34555684 DOI: 10.1016/j.bbrc.2021.08.087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 01/15/2023]
Abstract
Diabetic nephropathy (DN) is a type of kidney injuries associated with diabetes mellitus and the prevalence of DN has increased dramatically. However, DN still pose problems in therapy, and prognosis. Identifying new DN biomarkers would be helpful in reducing morbidity and mortality from DN and developing novel preventive approaches. In the study, from GSE36336 dataset with DN glomeruli samples, we screened for 238 differentially expressed genes. Enrichment analysis were performed to find out biological function and diseases of DEGs. Next, depended on protein-protein interaction network, We identified top 10 hub genes (Serpine1, Cxcl10, Cfd, Ppbp, Retn, Socs2, Ccr5, Mmp8, Pf4, Cxcl9) may played potential roles in DN. Meanwhile, transcriptome sequencing on podocyte were performed to reconfirm the reliability of Ppbp. To verify the efficiency of the selected genes as biomarkers, several experiments like qRT-PCR, renal histologic analysis and immunofluorescence were conducted to validate. Our results showed that PPBP have the potential to become a novel biomarker for DN podocyte injury.
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Affiliation(s)
- Fengxia Zhang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China; Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China; Department of Nephrology, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Nan Jiang
- Department of Nephrology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yan Gao
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Zuyan Fan
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Quhuan Li
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Guibao Ke
- Department of Nephrology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; Department of Nephrology, Affiliated Hospital/Clinical Medical College of Chengdu University, Chengdu, China
| | - Bohou Li
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China; Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qiong Wu
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China; Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ruiquan Xu
- Department of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, China; Department of Organ Transplantation, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
| | - Shuangxin Liu
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China; Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
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