Bioinformatics approach to mRNA markers discovery for detection of circulating tumor cells in patients with gastrointestinal cancer.
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.
Valladares-Ayerbes
Manuel
M
Medical Oncology and Institute for Biomedical Research (INIBIC), Juan Canalejo University Hospital, Spain. manuel_valladares@canalejo.org
Díaz-Prado
Silvia
S
Reboredo
Marga
M
Medina
Vanessa
V
Iglesias-Díaz
Pilar
P
Lorenzo-Patiño
Maria J
MJ
Campelo
Rosario G
RG
Haz
Mar
M
Santamarina
Isabel
I
Antón-Aparicio
Luis M
LM
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
C502296:AGR2 protein, human; D014408:Biomarkers, Tumor; D009088:Mucoproteins; D015513:Oncogene Proteins; C495339:PKP3 protein, human; D051191:Plakophilins; D011506:Proteins; D012333:RNA, Messenger