Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-12-20

AUTHORS

Lindsay R Dresang, Jeremy R Teuton, Huichen Feng, Jon M Jacobs, David G Camp, Samuel O Purvine, Marina A Gritsenko, Zhihua Li, Richard D Smith, Bill Sugden, Patrick S Moore, Yuan Chang

ABSTRACT

BackgroundKaposi'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.ResultsThe 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.ConclusionsThis 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. More... »

PAGES

625

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-12-625

DOI

http://dx.doi.org/10.1186/1471-2164-12-625

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1037540884

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22185355


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24 schema:description BackgroundKaposi'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.ResultsThe 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.ConclusionsThis 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.
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30 schema:keywords BL cell lines
31 Burkitt's lymphoma
32 Epstein-Barr virus
33 KSHV
34 analysis
35 annotation
36 approach
37 array
38 cancer
39 cancer cells
40 cell lines
41 cells
42 combination
43 comprehensive view
44 conditions
45 correlation
46 culture conditions
47 custom
48 cycle
49 data
50 detection
51 discovery
52 disease pathogenesis
53 effusion lymphoma
54 expression
55 gene expression
56 genes
57 genome annotation
58 herpesvirus
59 high-resolution separation
60 human tumor virus
61 insights
62 latent
63 levels
64 life cycle
65 lines
66 lymphoma
67 lytic viral gene expression
68 majority
69 mass spectrometry
70 measurements
71 method
72 methodology
73 novel viral gene
74 orthogonal data
75 pathogenesis
76 powerful method
77 primary effusion lymphoma
78 protein
79 protein levels
80 proteome
81 proteome analysis
82 relationship
83 sarcoma-associated herpesvirus
84 separation
85 spectrometry
86 transcriptome
87 transcriptome measurements
88 transcripts
89 tumor virus
90 uncharacterized genes
91 view
92 viral gene expression
93 viral genes
94 viral life cycle
95 viral proteins
96 viral proteome
97 viral transcripts
98 virus
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