Abstract 3885: Inactivation of expression of many extremely large genes in oropharyngeal cancers

There are a number of human genes which span very large chromosomal regions. Forty genes span greater than 1 megabase and 200 are 500 Kb or larger. We and others have demonstrated that many of the largest genes are derived from within regions of profound genomic instability known as common fragile sites (CFSs). We have been studying oropharyngeal cancers which are derived from the base of tongue, tonsil and larynx. While the traditional etiologic factors underlying the development of this aggressive cancer is a history of smoking and drinking there are an increasing number of younger patients developing this cancer without these risk factors. The most likely cause of these cancers is the presence of human papillomavirus which we detect in over 90% of oropharyngeal cancers derived from the Mayo Clinic. In an attempt to better understand the molecular alterations that underlie oropharyngeal cancers arising from different risk factors we utilized the power of Next Generation sequencing on the Illumina GA IIx to compare the transcriptomes of 12 oropharyngeal cancers to patient matched normal tissue. We first observe a division of patients into two groups of oropharyngeal cancers: those caused by mutations and other alterations induced by a history of smoking and drinking and those associated with HPV infection caused by viral-induced genomic instability. We then examined the expression of the 200 largest human genes in the oropharyngeal tumors and find that each tumor has inactivated the expression of at least 20 different very large genes. There is a distinct pattern of inactivation of these genes in different oropharyngeal cancers depending upon the underlying etiology. Some of the genes most frequently inactivated include Dlg2 (the human homolog of the large discs tumor suppressor gene from drosophila and a mutation target in a number of other cancers); ERBB4 (Her4 and a member of the EGFR family), BAI3 (a brain specific angiogenesis inhibitor that is also mutated in multiple cancers), and ANK2 (mutated in long QT patients). Each of these genes may be functioning as tumor suppressors as has already been demonstrated for the two large CFS genes, FHIT and WWOX. The inactivation of so many of these genes in each oropharyngeal tumor may have a profound effect upon the phenotype of the resulting tumor. When we examine the expression of the large genes most frequently inactivated in each of the two groups of oropharyngeal cancers in panels of breast or lung cancer samples we find that we do not detect significant loss of expression of these genes. We believe that genomic instability promotes alterations in the unstable CFS regions but that there is selective inactivation of different large CFS genes in different cancers. The signature of which specific genes are inactivated may have phenotypic and clinical significance which we are just beginning to investigate. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3885. doi:10.1158/1538-7445.AM2011-3885