Project name: Coupled Transcriptome and Proteome Analysis of Human Lymphotropic Tumor Viruses: Insights on the Detection and Discovery of Viral Genes

Description: Kaposi’s sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) are related human tumor viruses that cause primary effusion lymphomas (PEL) and Burkitt’s lymphomas (BL), respectively. Viral genes expressed in naturally-infected cancer cells contribute to disease pathogenesis; knowing which viral genes are expressed is critical in understanding how these viruses cause cancer. To evaluate the expression of viral genes, we used high-resolution separation and mass spectrometry coupled with custom tiling arrays to align the viral proteomes and transcriptomes of three PEL and two BL cell lines under latent and lytic culture conditions. The majority of viral genes were efficiently detected at the transcript and/or protein level on manipulating the viral life cycle. Overall the correlation of expressed viral proteins and transcripts was highly complementary in both validating and providing orthogonal data with latent/lytic viral gene expression. Our approach also identified novel viral genes in both KSHV and EBV, and extends viral genome annotation. The expression of several previously uncharacterized latent genes were validated at both transcript and protein levels. This systems biology approach coupling proteome and transcriptome measurements provides a comprehensive view of viral gene expression that could not have been attained using each methodology independently. Detection of viral proteins in combination with viral transcripts is a potentially powerful method for establishing virus-disease relationships.Overall design: All samples relative to KSHV-negative, EBV-negative reference sample (BJAB). Experimental samples were chosen based on their natural infection with either KSHV, EBV, both, or neither virus. Technical replicates of the cell line BC-1 were prepared for both latent (untreated) and lytic (chemically-treated) conditions.

Data type: Transcriptome or Gene expression

Sample scope: Multispecies

Relevance: Medical

Release date: 2011-12-30

Last updated: 2011-12-19