PBOV1 is a human de novo gene with tumor-specific expression that is associated with a positive clinical outcome of cancer

• Published in: PloS one Vol. 8; no. 2; p. e56162
• Main Authors: Samusik, Nikolay, Krukovskaya, Larisa, Meln, Irina, Shilov, Evgeny, Kozlov, Andrey P
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 13.02.2013; Public Library of Science (PLoS)
• Subjects: Adult; Amino Acid Sequence; Animals; Antigens; Biology; Brain tumors; Breast cancer; Breast Neoplasms - genetics; Breast Neoplasms - pathology; Cancer; Clinical outcomes; Codon; CpG islands; Demethylation; DNA microarrays; Evolution; Evolution, Molecular; Female; Fetuses; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Genes; Genetic aspects; Genetic engineering; Genomes; Genomics; Glioma; Glioma - genetics; Glioma - pathology; Gliomas; Health risks; Hedgehog protein; Hedgehog Proteins - genetics; Human tissues; Humans; Laboratories; Male; Mammals; Medicine; Molecular Sequence Data; Mutation; Negative selection; Neoplasm Proteins - classification; Neoplasm Proteins - genetics; Neoplasms - genetics; Neoplasms - pathology; Oligonucleotide Array Sequence Analysis; Patient outcomes; Phylogeny; Primates; Prognosis; Prostate cancer; Proteins; Sequence Homology, Amino Acid; Signal transduction; Signal Transduction - genetics; Signaling; Single-nucleotide polymorphism; Stop codon; Tissues; Tumors
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0056162

PBOV1 is a known human protein-coding gene with an uncharacterized function. We have previously found that PBOV1 lacks orthologs in non-primate genomes and is expressed in a wide range of tumor types. Here we report that PBOV1 protein-coding sequence is human-specific and has originated de novo in the primate evolution through a series of frame-shift and stop codon mutations. We profiled PBOV1 expression in multiple cancer and normal tissue samples and found that it was expressed in 19 out of 34 tumors of various origins but completely lacked expression in any of the normal adult or fetal human tissues. We found that, unlike the cancer/testis antigens that are typically controlled by CpG island-containing promoters, PBOV1 was expressed from a GC-poor TATA-containing promoter which was not influenced by CpG demethylation and was inactive in testis. Our analysis of public microarray data suggests that PBOV1 activation in tumors could be dependent on the Hedgehog signaling pathway. Despite the recent de novo origin and the lack of identifiable functional signatures, a missense SNP in the PBOV1 coding sequence has been previously associated with an increased risk of breast cancer. Using publicly available microarray datasets, we found that high levels of PBOV1 expression in breast cancer and glioma samples were significantly associated with a positive outcome of the cancer disease. We also found that PBOV1 was highly expressed in primary but not in recurrent high-grade gliomas, suggesting the presence of a negative selection against PBOV1-expressing cancer cells. Our findings could contribute to the understanding of the mechanisms behind de novo gene origin and the possible role of tumors in this process.