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Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: Insights on the detection and discovery of viral genes

Dresang, LR and Teuton, JR and Feng, H and Jacobs, JM and Camp, DG and Purvine, SO and Gritsenko, MA and Li, Z and Smith, RD and Sugden, B and Moore, PS and Chang, Y (2011) Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: Insights on the detection and discovery of viral genes. BMC Genomics, 12.

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Abstract

Background: 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.Results: 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. Several previously uncharacterized genes were validated at both transcript and protein levels.Conclusions: 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. © 2011 Dresang et al; licensee BioMed Central Ltd.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Dresang, LR
Teuton, JR
Feng, H
Jacobs, JM
Camp, DG
Purvine, SO
Gritsenko, MA
Li, Z
Smith, RD
Sugden, B
Moore, PSpsm9@pitt.eduPSM9
Chang, Yyc70@pitt.eduYC70
Centers: Other Centers, Institutes, Offices, or Units > Hillman Cancer Center
Other Centers, Institutes, Offices, or Units > Pittsburgh Cancer Institute
Date: 20 December 2011
Date Type: Publication
Journal or Publication Title: BMC Genomics
Volume: 12
DOI or Unique Handle: 10.1186/1471-2164-12-625
Refereed: Yes
Date Deposited: 01 Nov 2016 17:05
Last Modified: 13 Oct 2017 22:58
URI: http://d-scholarship.pitt.edu/id/eprint/29977

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