title: Bioinformatics approach to mRNA markers discovery for detection of circulating tumor cells in patients with gastrointestinal cancer.
abstract: BACKGROUND
  Detection of tumor cells in the blood, or minimal deposits in distant organs as bone marrow, could be important to identify cancer patients at high risk of relapse or disease progression. Quantitative polymerase chain reaction (PCR) amplification of tissue or tumor selective mRNA is the most powerful tool for the detection of this circulating or occult metastatic cells. Our study aims to identify novel gastrointestinal cancer-specific markers for circulating tumor cell detection.
  
  
  METHODS
  Phase I preclinical study was performed by means of computational tools for expression analysis. In silico data were used to identify and prioritize molecular markers highly expressed in gastrointestinal cancers but absent in hematopoietic-derived libraries. Selected genes were evaluated by means of qRT-PCR in gastrointestinal cancer and hematopoietic cell-lines, normal human bone marrows and bloods, tumor tissue, and blood from cancer patients.
  
  
  RESULTS
  Novel and known mRNA markers for circulating tumor cell detection in gastrointestinal cancer have been identified. Among all the genes assessed, PKP3, AGR2, S100A16, S100A6, LGALS4, and CLDN3 were selected and assays based on blood qRT-PCR were developed. Reliably qRT-PCR assays for the novel targets plakophilin 3 (PKP3) and anterior gradient-2 (AGR2) to identify blood-borne cells in cancer patients were developed.
  
  
  CONCLUSIONS
  Novel and known gastrointestinal-specific mRNA markers for circulating tumor cells have been identified through in silico analysis and validated in clinical material. qRT-PCR assay targeted to PKP3 and AGR2 mRNAs might be helpful to detect circulating tumor cells in patients with gastrointestinal cancer.
authors.affiliation: Medical Oncology and Institute for Biomedical Research (INIBIC), Juan Canalejo University Hospital, Spain. manuel_valladares@canalejo.org
authors.forename: Manuel
authors.initials: M
authors.lastname: Valladares-Ayerbes
authors.forename: Silvia
authors.initials: S
authors.lastname: Díaz-Prado
authors.forename: Marga
authors.initials: M
authors.lastname: Reboredo
authors.forename: Vanessa
authors.initials: V
authors.lastname: Medina
authors.forename: Pilar
authors.initials: P
authors.lastname: Iglesias-Díaz
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Lorenzo-Patiño
authors.forename: Rosario G
authors.initials: RG
authors.lastname: Campelo
authors.forename: Mar
authors.initials: M
authors.lastname: Haz
authors.forename: Isabel
authors.initials: I
authors.lastname: Santamarina
authors.forename: Luis M
authors.initials: LM
authors.lastname: Antón-Aparicio
mesh_terms: D014408:Biomarkers, Tumor / Q000097:blood*; D019295:Computational Biology; D005770:Gastrointestinal Neoplasms / Q000097:blood*; D020869:Gene Expression Profiling; D006801:Humans; D009088:Mucoproteins; D009360:Neoplastic Cells, Circulating; D015513:Oncogene Proteins; D051191:Plakophilins / Q000097:blood; D011506:Proteins / Q000032:analysis / Q000378:metabolism; D012333:RNA, Messenger / Q000097:blood*; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: C502296:AGR2 protein, human; D014408:Biomarkers, Tumor; D009088:Mucoproteins; D015513:Oncogene Proteins; C495339:PKP3 protein, human; D051191:Plakophilins; D011506:Proteins; D012333:RNA, Messenger