title: Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405.
abstract: As part of the genome-wide and chromosome-centric human proteomic project (C-HPP), we have integrated shotgun proteomics approach and a genome-wide transcriptomic approach (RNA-Seq) of a set of human colon cancer cell lines (LIM1215, LIM1899 and LIM2405) that were selected to represent a wide range of pathological states of colorectal cancer. The combination of a standard proteomics approach (1D-gel electrophoresis coupled to LC/ion trap mass spectrometry) and RNA-Seq allowed us to exploit the greater depth of the transcriptomics measurement (∼ 9800 transcripts per cell line) versus the protein observations (∼ 1900 protein identifications per cell line). Conversely, the proteomics data were helpful in identifying both cancer associated proteins with differential expression patterns as well as protein networks and pathways which appear to be deregulated in these cell lines. Examples of potential markers include mortalin, nucleophosmin, ezrin, LASP1, alpha and beta forms of spectrin, exportin, the carcinoembryonic antigen family, EGFR and MET. Interaction analyses identified the large intermediate filament family, the protein folding network and adapter proteins in focal adhesion networks, which included the CDC42 and RHOA signaling pathways that may have potential for identifying phenotypic states representing poorly and moderately differentiated states of CRC, with or without metastases.
authors: Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, NSW 2109, Australia.
authors: Susan
authors: S
authors: Fanayan
authors: Joshua T
authors: JT
authors: Smith
authors: Ling Y
authors: LY
authors: Lee
authors: Fangfei
authors: F
authors: Yan
authors: Michael
authors: M
authors: Snyder
authors: William S
authors: WS
authors: Hancock
authors: Edouard
authors: E
authors: Nice
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism; D002454:Cell Differentiation; D045744:Cell Line, Tumor; D003110:Colonic Neoplasms / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism; D025941:Protein Interaction Mapping; D020543:Proteome / Q000032:analysis* / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012333:RNA, Messenger / Q000032:analysis; D015398:Signal Transduction; D020764:cdc42 GTP-Binding Protein / Q000378:metabolism; D020742:rhoA GTP-Binding Protein / Q000378:metabolism
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D020543:Proteome; D012333:RNA, Messenger; C066737:RHOA protein, human; D020764:cdc42 GTP-Binding Protein; D020742:rhoA GTP-Binding Protein