Bioinformatics-based discovery of a novel factor with apparent specificity to colon cancer.
In a previous study, a data mining tool called Digital Differential Display (DDD) from the Cancer Genome Anatomy Project (CGAP) was used to predict solid tumor- and organ-specific genes from the expressed sequence tag (EST) database. To validate the use of bioinformatics approaches in gene discovery, one of the ESTs, which was predicted to be colon tumor-specific, was chosen for further study. Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) analysis of matched sets of cDNAs from normal and colon tumor tissues indicated that the EST was specifically expressed in the majority of colon tumors. Expression was also detected in early adenomas. Among other normal tissues, EST expression was detected only in the small intestine. The colon tumor specificity of this EST was inferred from the lack of expression in carcinomas of the breast, lung, ovary, pancreas and prostate. To validate the computational prediction of specificity, a full-length cDNA encompassing the entire open reading frame was cloned and, in view of its apparent specificity to the colon tumors, this gene was termed Colon Carcinoma Related Gene (CCRG). CCRG encodes a novel cysteine-rich motif and a putative signal peptide sequence. Supernatant from COS cells transfected with the CCRG expression vector stimulated proliferation of colon cancer cells. Immunoreactive CCRG was also detected in the paraffin sections of colon tumor samples. CCRG belongs to a new class of growth factors and may be important in the diagnosis and treatment of colon cancers. Identification of CCRG using bioinformatics approaches validates gene discovery using computational approaches.
De Young
Maurice Phil
MP
Department of Biology and Center for Molecular Biology and Biotechnology, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431, USA.
Damania
Hema
H
Scheurle
Daniela
D
Zylberberg
Claudia
C
Narayanan
Ramaswamy
R
D000595:Amino Acid Sequence; D014408:Biomarkers, Tumor / Q000235:genetics*; D003110:Colonic Neoplasms / Q000737:chemistry / Q000235:genetics* / Q000473:pathology*; D019295:Computational Biology; D018076:DNA, Complementary; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins; D008969:Molecular Sequence Data; D009363:Neoplasm Proteins / Q000032:analysis / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics; D021382:Protein Sorting Signals / Q000235:genetics; D012680:Sensitivity and Specificity
D014408:Biomarkers, Tumor; D018076:DNA, Complementary; D036341:Intercellular Signaling Peptides and Proteins; D009363:Neoplasm Proteins; D021382:Protein Sorting Signals; C486574:RETNLB protein, human