Isolation and characterization of a novel cDNA, UBAP1, derived from the tumor suppressor locus in human chromosome 9p21-22

Purpose: To clone the putative tumor suppressor gene(s) in a refined region at 9p21-22 undergoing loss of heterozygosity in nasopharyngeal carcinoma (NPC). Methods: We systematically screened the expression patterns of 25 novel ESTs (expressed sequence tags) in a minimal common deleted region of 9p21-22 in NPC. One of these ESTs was found down-regulated in NPC. Subsequently, the corresponding gene sequence of this EST was established by cDNA cloning and RACE (rapid amplification of cDNA end) procedures. Furthermore, a mouse homologue of this gene was identified. The expression of this gene was examined using Northern blot or reverse transcription-polymerase chain reaction (RT-PCR) in various human and mouse tissues. A limited screen for mutation of coding sequence of this novel human gene was undertaken using RT-PCR and direct sequencing analysis. Results: A novel gene was cloned. This gene is a new member of the UBA domain family, so we named it UBAP1 for ubiquitin-associated protein 1 (HUGO Gene Nomenclature Committee-approved symbol). Northern blot and RT-PCR analysis demonstrate a ubiquitous pattern of gene expression in human and mouse tissues. The direct sequencing analysis of the coding region of hUBAP1 following RT-PCR failed to reveal any mutations in a preliminary screen of NPC cell line HNE1 and primary nasopharyngeal carcinoma samples. Conclusions: We cloned a novel gene UBAP1, which is highly conserved between human and mouse. Clearly, as a novel member of UBA domain protein family and taking its map location into account, a more extensive analysis is essential to establish whether subtle mutations are present in nasopharyngeal carcinomas.