title: Quantitative proteomics in resected renal cancer tissue for biomarker discovery and profiling.
abstract: BACKGROUND
  Proteomics-based approaches for biomarker discovery are promising strategies used in cancer research. We present state-of-art label-free quantitative proteomics method to assess proteome of renal cell carcinoma (RCC) compared with noncancer renal tissues.
  
  
  METHODS
  Fresh frozen tissue samples from eight primary RCC lesions and autologous adjacent normal renal tissues were obtained from surgically resected tumour-bearing kidneys. Proteins were extracted by complete solubilisation of tissues using filter-aided sample preparation (FASP) method. Trypsin digested proteins were analysed using quantitative label-free proteomics approach followed by data interpretation and pathways analysis.
  
  
  RESULTS
  A total of 1761 proteins were identified and quantified with high confidence (MASCOT ion score threshold of 35 and P-value <0.05). Of these, 596 proteins were identified as differentially expressed between cancer and noncancer tissues. Two upregulated proteins in tumour samples (adipose differentiation-related protein and Coronin 1A) were further validated by immunohistochemistry. Pathway analysis using IPA, KOBAS 2.0, DAVID functional annotation and FLink tools showed enrichment of many cancer-related biological processes and pathways such as oxidative phosphorylation, glycolysis and amino acid synthetic pathways.
  
  
  CONCLUSIONS
  Our study identified a number of differentially expressed proteins and pathways using label-free proteomics approach in RCC compared with normal tissue samples. Two proteins validated in this study are the focus of on-going research in a large cohort of patients.
authors.affiliation: Fingerprints Proteomics Facility, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
authors.forename: A
authors.initials: A
authors.lastname: Atrih
authors.affiliation: 1] Data Analysis Group, Division of Computational Biology, School of Research, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK [2] Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
authors.forename: M A V
authors.initials: MA
authors.lastname: Mudaliar
authors.affiliation: Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK.
authors.forename: P
authors.initials: P
authors.lastname: Zakikhani
authors.affiliation: Fingerprints Proteomics Facility, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
authors.forename: D J
authors.initials: DJ
authors.lastname: Lamont
authors.affiliation: Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK.
authors.forename: J T-J
authors.initials: JT
authors.lastname: Huang
authors.affiliation: Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK.
authors.forename: S E
authors.initials: SE
authors.lastname: Bray
authors.affiliation: Data Analysis Group, Division of Computational Biology, School of Research, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
authors.forename: G
authors.initials: G
authors.lastname: Barton
authors.affiliation: Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK.
authors.forename: S
authors.initials: S
authors.lastname: Fleming
authors.affiliation: Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK.
authors.forename: G
authors.initials: G
authors.lastname: Nabi
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000032:analysis* / Q000096:biosynthesis / Q000652:urine; D002292:Carcinoma, Renal Cell / Q000737:chemistry* / Q000378:metabolism / Q000473:pathology / Q000652:urine; D005260:Female; D006801:Humans; D007680:Kidney Neoplasms / Q000737:chemistry* / Q000378:metabolism / Q000473:pathology / Q000652:urine; D008297:Male; D013058:Mass Spectrometry; D008875:Middle Aged; D009363:Neoplasm Proteins / Q000032:analysis / Q000096:biosynthesis / Q000652:urine; D040901:Proteomics / Q000379:methods*; D015398:Signal Transduction
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins