title: Quantitative proteomic profiling of paired cancerous and normal colon epithelial cells isolated freshly from colorectal cancer patients.
abstract: The heterogeneous structure in tumor tissues from colorectal cancer (CRC) patients excludes an informative comparison between tumors and adjacent normal tissues. Here, we develop and apply a strategy to compare paired cancerous (CEC) versus normal (NEC) epithelial cells enriched from patients and discover potential biomarkers and therapeutic targets for CRC.
  
  
  
  CEC and NEC cells are respectively isolated from five different tumor and normal locations in the resected colon tissue from each patient (N = 12 patients) using an optimized epithelial cell adhesion molecule (EpCAM)-based enrichment approach. An ion current-based quantitative method is employed to perform comparative proteomic analysis for each patient.
  
  
  
  A total of 458 altered proteins that are common among >75% of patients are observed and selected for further investigation. Besides known findings such as deregulation of mitochondrial function, tricarboxylic acid cycle, and RNA post-transcriptional modification, functional analysis further revealed RAN signaling pathway, small nucleolar ribonucleoproteins (snoRNPs), and infection by RNA viruses are altered in CEC cells. A selection of the altered proteins of interest is validated by immunohistochemistry analyses.
  
  
  
  The informative comparison between matched CEC and NEC enhances our understanding of molecular mechanisms of CRC development and provides biomarker candidates and new pathways for therapeutic intervention.
authors.affiliation: Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA.|New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA.
authors.forename: Chengjian
authors.initials: C
authors.lastname: Tu
authors.affiliation: Department of Pathology, State University of New York at Buffalo-State, University of New York, Buffalo, NY, USA.
authors.forename: Wilfrido
authors.initials: W
authors.lastname: Mojica
authors.affiliation: Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA.|New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Straubinger
authors.affiliation: Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA.|New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA.|New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA.
authors.forename: Shichen
authors.initials: S
authors.lastname: Shen
authors.affiliation: Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA.|Beijing University of Chinese Medicine, Beijing, China.
authors.forename: Miao
authors.initials: M
authors.lastname: Qu
authors.affiliation: School of Pharmaceutical Sciences, Shandong University, Jinan, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Nie
authors.affiliation: Department of Structural Biology, State University of New York at Buffalo, , State University of New York, Buffalo, NY, USA.
authors.forename: Rick
authors.initials: R
authors.lastname: Roberts
authors.affiliation: Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA.|New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA.
authors.forename: Bo
authors.initials: B
authors.lastname: An
authors.affiliation: Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA.|New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Qu
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D003106:Colon / Q000166:cytology* / Q000473:pathology*; D015179:Colorectal Neoplasms / Q000235:genetics / Q000378:metabolism* / Q000473:pathology*; D004847:Epithelial Cells / Q000378:metabolism*; D005189:False Positive Reactions; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D008297:Male; D008875:Middle Aged; D058977:Molecular Sequence Annotation; D040901:Proteomics
keywords: Biomarker discovery; Colorectal cancer; Ion current-based analysis; Tumor cell enrichment