A Novel Transmembrane Glycoprotein Cancer Biomarker Present in the X Chromosome

Background: The uncharacterized proteins of the human proteome offer an untapped potential for cancer biomarker discovery. Numerous predicted open reading frames (ORFs) are present in diverse chromosomes. The mRNA and protein expression data, as well as the mutational and variant information for these ORF proteins are available in the cancer-related bioinformatics databases. Materials and Methods: ORF proteins were mined using bioinformatics and proteomic tools to predict motifs and domains, and cancer relevance was established using cancer genome, transcriptome and proteome analysis tools. Results: A novel testis-restricted ORF protein present in chromosome X called CXorf66 was detected in the serum, plasma and neutrophils. This gene is termed secreted glycoprotein in chromosome X (SGPX). The SGPX gene is up-regulated in cancer of the brain, lung and in leukemia, and down-regulated in liver and prostate cancer. Brain cancer in female patients exhibited elevated copy numbers of the SGPX gene. Conclusion: The SGPX gene is a putative novel cancer biomarker. Our results demonstrate the feasibility of mining the 'dark matter' of the cancer proteome for rapid cancer biomarker discovery. The human genome project is an attractive starting point for cancer gene discovery (1-3). Numerous drug targets and biomarkers have emerged from the Genome Project (3-7). Expression specificity provides a strong rationale for finding targets that can lead to highly selective and less toxic therapeutics (6-8). An attractive area for mining the human genome resides in the uncharacterized proteome (9). Currently, over half of the predicted proteins in the human genome are of unknown nature (10). These proteins and the non-coding RNAs are called the 'dark matter' of the genome (11-13). Whereas in the past most gene discovery has revolved around known genes due to the ease of follow-up studies (14-17), the dark matter of the genome offers an untapped potential (18). Realizing the importance of this area, the US National Cancer Institute has recently announced a major initiative called illuminating the dark matter for druggable targets (http://commonfund.nih.gov/idg/index). Establishing cancer relevance for novel or uncharacterized proteins is a crucial first step in lead discovery. The cancer genomes of patients from around the world can be readily mined using databases such as the cBioPortal (19), canSar (20), the Catalogue of Somatic Mutations in Cancer, COSMIC (21), The Cancer Gene Atlas, TCGA (http://cancergenome.nih.gov) and the International Cancer Genome Consortium, ICGC (https://www.icgc.org). The availability of microarray databases such as Oncomine (22) and ArrayExpress (23), and protein expression analysis tools including the Human Protein Atlas (24), the Human Protein Reference Database, HPRD (25), and the Model Organism Protein Expression database, MOPED (26) can facilitate the cancer target verification. Numerous proteomic analysis tools including Expasy (http://www.expasy.org), PredictProtein (27) and MESSA Meta analysis server (28) are available for predicting the putative motifs and domains of the novel proteins. These tools can be used to mine the dark matter of the proteome to identify motifs with biomarker and druggable potential (signal peptides, receptors, transporters and enzyme) signatures (29-31). In the present report, we demonstrate the feasibility of discovering novel biomarkers from a database of cancer- related uncharacterized proteins we have recently developed (18). An X-chromosome specific ORF, CXorf66, was rapidly validated for secreted nature using the protein expression databases. Detailed bioinformatics and proteomics characterization of the CXorf66 gene confirmed the cancer biomarker potential of this gene. Our results support the potential of the uncharacterized proteome to be tapped for cancer biomarker discovery.