title: Bioinformatics analysis of proteomics profiles in senescent human primary proximal tubule epithelial cells.
abstract: BACKGROUND
  Dysfunction of renal tubule epithelial cells is associated with renal tubulointerstitial fibrosis. Exploration of the proteomic profiles of senesced tubule epithelial cells is essential to elucidate the mechanism of tubulointerstitium development.
  
  
  METHODS
  Primary human proximal tubule epithelial cells from passage 3 (P3) and passage 6 (P6) were selected for evaluation. EdU and SA-β-galactosidase staining were used to detect cell senescence. p53, p21, and p16 were detected by Western blot analysis. Liquid chromatography mass spectrometry (LC-MS) was used to examine differentially expressed proteins (DEPs) between P6 and P3 cells. The expression of DEPs was examined by Western blot analysis. Bioinformatics analysis was performed by protein-protein interaction and gene ontology analyses.
  
  
  RESULTS
  The majority of tubule cells from passage 6 (P6) stained positive for SA-β-galactosidase, whereas passage 3 (P3) cells were negative. Senescence biomarkers, including p53, p21, and p16, were upregulated in P6 cells relative to P3 cells. EdU staining results showed a lower rate of EdU positive cells in P6 cells than in P3 cells. LC-MS was used to examine DEPs between P6 and P3 cells. These DEPs are involved in glycolysis, response to stress, cytoskeleton regulation, oxidative reduction, ATP binding, and oxidative stress. Using Western blot analysis, we validated the down-regulation of AKR1B1, EEF2, EEF1A1, and HSP90 and the up-regulation of VIM in P6 cells seen in the LC-MS data. More importantly, we built the molecular network based on biological functions and protein-protein interactions and found that the DEPs are involved in translation elongation, stress, and glycolysis, and that they are all associated with cytoskeleton regulation, which regulates senescent cell activities such as apoptosis and EMT in tubule epithelial cells.
  
  
  CONCLUSIONS
  We explored proteomic profile changes in cell culture-induced senescent cells and built senescence-associated molecular networks, which will help to elucidate the mechanisms of senescence in human proximal tubule epithelial cells.
authors.affiliation: Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, Beijing Key Laboratory of Kidney Disease, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, General Hospital of PLA, Fuxing Road 28, Beijing, 100853, P.R. China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, Beijing Key Laboratory of Kidney Disease, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, General Hospital of PLA, Fuxing Road 28, Beijing, 100853, P.R. China.
authors.forename: Jingchao
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, Beijing Key Laboratory of Kidney Disease, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, General Hospital of PLA, Fuxing Road 28, Beijing, 100853, P.R. China.|Department of Nephrology, China-Japan Friendship Hospital, Beijing, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Dapeng
authors.affiliation: Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, Beijing Key Laboratory of Kidney Disease, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, General Hospital of PLA, Fuxing Road 28, Beijing, 100853, P.R. China.
authors.forename: Di
authors.initials: D
authors.lastname: Wu
authors.affiliation: Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, Beijing Key Laboratory of Kidney Disease, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, General Hospital of PLA, Fuxing Road 28, Beijing, 100853, P.R. China.
authors.forename: Guangyan
authors.initials: G
authors.lastname: Cai
authors.affiliation: Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, Beijing Key Laboratory of Kidney Disease, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, General Hospital of PLA, Fuxing Road 28, Beijing, 100853, P.R. China. xmchen301@126.com.
authors.forename: Xiangmei
authors.initials: X
authors.lastname: Chen
mesh_terms: D000449:Aldehyde Reductase / Q000378:metabolism; D015153:Blotting, Western; D016922:Cellular Senescence; D002853:Chromatography, Liquid; D019295:Computational Biology; D019941:Cyclin-Dependent Kinase Inhibitor p16; D050759:Cyclin-Dependent Kinase Inhibitor p21 / Q000378:metabolism; D004847:Epithelial Cells / Q000378:metabolism*; D018841:HSP90 Heat-Shock Proteins / Q000378:metabolism; D006801:Humans; D007687:Kidney Tubules, Proximal / Q000166:cytology / Q000378:metabolism*; D013058:Mass Spectrometry; D009363:Neoplasm Proteins / Q000378:metabolism; D020648:Peptide Elongation Factor 1 / Q000378:metabolism; D020652:Peptide Elongation Factor 2 / Q000378:metabolism; D040901:Proteomics; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism; D014746:Vimentin / Q000378:metabolism
chemical_list: C493956:CDKN1A protein, human; C000614131:CDKN2A protein, human; D019941:Cyclin-Dependent Kinase Inhibitor p16; D050759:Cyclin-Dependent Kinase Inhibitor p21; C094814:EEF1A1 protein, human; D018841:HSP90 Heat-Shock Proteins; D009363:Neoplasm Proteins; D020648:Peptide Elongation Factor 1; D020652:Peptide Elongation Factor 2; C495901:TP53 protein, human; D016159:Tumor Suppressor Protein p53; D014746:Vimentin; C484670:AKR1B1 protein, human; D000449:Aldehyde Reductase
keywords: Network; Proteomics; Proximal tubule cells; Senescence