title: Label-free LC-MSe in tissue and serum reveals protein networks underlying differences between benign and malignant serous ovarian tumors.
abstract: OBJECTIVE
  To identify proteins and (molecular/biological) pathways associated with differences between benign and malignant epithelial ovarian tumors.
  
  
  METHODS
  Serum of six patients with a serous adenocarcinoma of the ovary was collected before treatment, with a control group consisting of six matched patients with a serous cystadenoma. In addition to the serum, homogeneous regions of cells exhibiting uniform histology were isolated from benign and cancerous tissue by laser microdissection. We subsequently employed label-free liquid chromatography tandem mass spectrometry (LC-MSe) to identify proteins in these serum and tissues samples. Analyses of differential expression between samples were performed using Bioconductor packages and in-house scripts in the statistical software package R. Hierarchical clustering and pathway enrichment analyses were performed, as well as network enrichment and interactome analysis using MetaCore.
  
  
  RESULTS
  In total, we identified 20 and 71 proteins that were significantly differentially expressed between benign and malignant serum and tissue samples, respectively. The differentially expressed protein sets in serum and tissue largely differed with only 2 proteins in common. MetaCore network analysis, however inferred GCR-alpha and Sp1 as common transcriptional regulators. Interactome analysis highlighted 14-3-3 zeta/delta, 14-3-3 beta/alpha, Alpha-actinin 4, HSP60, and PCBP1 as critical proteins in the tumor proteome signature based on their relative overconnectivity. The data have been deposited to the ProteomeXchange with identifier PXD001084.
  
  
  CONCLUSIONS
  Our analysis identified proteins with both novel and previously known associations to ovarian cancer biology. Despite the small overlap between differentially expressed protein sets in serum and tissue, APOA1 and Serotransferrin were significantly lower expressed in both serum and cancer tissue samples, suggesting a tissue-derived effect in serum. Pathway and subsequent interactome analysis also highlighted common regulators in serum and tissue samples, suggesting a yet unknown role for PCBP1 in ovarian cancer pathophysiology.
authors.affiliation: Department of Gynecology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Wouter
authors.initials: W
authors.lastname: Wegdam
authors.affiliation: Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
authors.forename: Carmen A
authors.initials: CA
authors.lastname: Argmann
authors.affiliation: Clinical Proteomics Group, Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Gertjan
authors.initials: G
authors.lastname: Kramer
authors.affiliation: Waters Corporation MS Technologies Center, Manchester, United Kingdom.
authors.forename: Johannes P
authors.initials: JP
authors.lastname: Vissers
authors.affiliation: Department of Gynecology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Marrije R
authors.initials: MR
authors.lastname: Buist
authors.affiliation: Department of Gynecology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Gemma G
authors.initials: GG
authors.lastname: Kenter
authors.affiliation: Clinical Proteomics Group, Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Johannes M F G
authors.initials: JM
authors.lastname: Aerts
authors.affiliation: Department of Gynecology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Danielle
authors.initials: D
authors.lastname: Meijer
authors.affiliation: Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Perry D
authors.initials: PD
authors.lastname: Moerland
mesh_terms: D000328:Adult; D000368:Aged; D002853:Chromatography, Liquid / Q000379:methods*; D016000:Cluster Analysis; D005260:Female; D053263:Gene Regulatory Networks; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D008875:Middle Aged; D009363:Neoplasm Proteins / Q000097:blood / Q000235:genetics / Q000378:metabolism*; D010051:Ovarian Neoplasms / Q000378:metabolism* / Q000473:pathology; D020543:Proteome
chemical_list: D009363:Neoplasm Proteins; D020543:Proteome