Viruses are established, causal factors in 15%-20% of human cancers and are widely suspected to be involved in more. The long-range goals of this project are to develop methods to simultaneously screen tumor and other tissue samples for the genomes or partial genomes of many viruses, to use these methods to test for novel virus-cancer associations, and to determine their statistical and clinical significance. In particular, this highly collaborative proposal describes how a new, uniquely flexible, maskless photolithography technology will be used to produce and refine high density oligonucleotide microarrays able to sensitively detect all genes or transcripts of all known human tumor viruses. For comparison, arrays of PCR-amplified viral probes spotted on glass slides will also be tested. Additional experiments will systematically optimize extraction and amplification methods for specific, sensitive, and robust detection of viral RNA and DNA sequences at low copy number in clinical tissue samples. The resulting tools and methodology will be applied to relevant clinical samples to test and resolve the emerging connections of two well- characterized human tumor viruses, human papilloamavirus (HPV) and Epstein- Barr virus (EBV), with oral cancers and breast cancers, respectively, and to compare the microarray results with other state-of-the-art virus detection methods applied to the same tissue samples. These studies will provide proof- of-principle tests of microarray use in detecting and characterizing viral contributions to cancer and address significant, current issues in the viral etiology of specific tumors. Simultaneous microarray screening for many viruses o viral genotypes amplifies the power of etiologic and diagnostic studies on precious tissue samples, offers the potential to discover unsuspected virus-cancer links, and allows profiling expression of viral and selected cell genes to provide the molecular signatures of a tumor and to evaluate the potential contribution of the virus to that tumor. The methods developed also will be applicable to probe for virus involvement in other chronic or acute disorders.
