Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-38467 - Transcriptional perturbations caused by tumor virus proteins

Status
Released on 19 July 2012, last updated on 6 August 2012
Organism
Homo sapiens
Samples (449)
Array (1)
Protocols (7)
Description
Genotypic differences greatly influence susceptibility and resistance to disease. Understanding genotype-phenotype relationships requires that phenotypes be viewed as manifestations of network properties, rather than simply as the result of individual genomic variations. Genome sequencing efforts have identified numerous germline mutations associated with cancer predisposition and large numbers of somatic genomic alterations. However, it remains challenging to distinguish between background, or “passenger” and causal, or “driver” cancer mutations in these datasets. Human viruses intrinsically depend on their host cell during the course of infection and can elicit pathological phenotypes similar to those arising from mutations. To test the hypothesis that genomic variations and tumour viruses may cause cancer via related mechanisms, we systematically examined host interactome and transcriptome network perturbations caused by DNA tumour virus proteins. The resulting integrated viral perturbation data reflects rewiring of the host cell networks, and highlights pathways that go awry in cancer, such as Notch signalling and apoptosis. We show that systematic analyses of host targets of viral proteins can identify cancer genes with a success rate on par with their identification through functional genomics and large-scale cataloguing of tumour mutations. These complementary approaches together result in increased specificity for cancer gene identification. Combining systems-level studies of pathogen-encoded gene products with genomic approaches will facilitate prioritization of cancer-causing driver genes so as to advance understanding of the genetic basis of human cancer. We profiled the transcriptome of human cells expressing tumor virus proteins, in order to trace pathways through which viral proteins could alter cellular states. To examine transcriptome network perturbations directly in human cells, we generated expression constructs fusing each viral ORF (open reading frame) to a tandem epitope tag and introduced each construct into IMR-90 normal human diploid fibroblasts. Total RNA was isolated from IMR-90 cells expressing viORFs and gene expression was assayed on Human Gene 1.0 ST arrays.
Experiment type
transcription profiling by array 
Contacts
Megha Padi <mpadi@jimmy.harvard.edu>, David E Hill, Frederick P Roth, Guillaume Adelmant, James A DeCaprio, Jarrod A Marto, John Quackenbush, Karl Münger, Marc Vidal, Orit Rozenblatt-Rosen, Rahul C Deo
Citation
Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Rozenblatt-Rosen O, Deo RC, Padi M, Adelmant G, Calderwood MA, Rolland T, Grace M, Dricot A, Askenazi M, Tavares M, Pevzner SJ, Abderazzaq F, Byrdsong D, Carvunis AR, Chen AA, Cheng J, Correll M, Duarte M, Fan C, Feltkamp MC, Ficarro SB, Franchi R, Garg BK, Gulbahce N, Hao T, Holthaus AM, James R, Korkhin A, Litovchick L, Mar JC, Pak TR, Rabello S, Rubio R, Shen Y, Singh S, Spangle JM, Tasan M, Wanamaker S, Webber JT, Roecklein-Canfield J, Johannsen E, Barabási AL, Beroukhim R, Kieff E, Cusick ME, Hill DE, Münger K, Marto JA, Quackenbush J, Roth FP, Decaprio JA, Vidal M. , PMID:22810586
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Links