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. 2016 Oct 19;11(10):e0164548.
doi: 10.1371/journal.pone.0164548. eCollection 2016.

The Transcriptome of Rhabdomyosarcoma Cells Infected with Cytolytic and Non-Cytolytic Variants of Coxsackievirus B2 Ohio-1

Anna Sävneby  1 , Johannes Luthman  2 , Fabian Nordenskjöld  2 , Björn Andersson  2 , A Michael Lindberg  1
Affiliations

The Transcriptome of Rhabdomyosarcoma Cells Infected with Cytolytic and Non-Cytolytic Variants of Coxsackievirus B2 Ohio-1

Anna Sävneby et al. PLoS One. .

Abstract

The transcriptomes of cells infected with lytic and non-lytic variants of coxsackievirus B2 Ohio-1 (CVB2O) were analyzed using next generation sequencing. This approach was selected with the purpose of elucidating the effects of lytic and non-lytic viruses on host cell transcription. Total RNA was extracted from infected cells and sequenced. The resulting reads were subsequently mapped against the human and CVB2O genomes. The amount of intracellular RNA was measured, indicating lower proportions of human RNA in the cells infected with the lytic virus compared to the non-lytic virus after 48 hours. This may be explained by reduced activity of the cellular transcription/translation machinery in lytic enteroviral replication due to activities of the enteroviral proteases 2A and/or 3C. Furthermore, differential expression in the cells infected with the two virus variants was identified and a number of transcripts were singled out as possible answers to the question of how the viruses interact with the host cells, resulting in lytic or non-lytic infections.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Relative amounts of intracellular RNA.
(A) All sequences were mapped against the CVB2O and human genome to obtain the proportions of viral to human RNA in each sample. Sequences that did not match either genome are denoted other. (B) The intracellular amounts of viral RNA have been normalized against the amount in the first sample of the triplicate of the cells infected with vVP1Q164K and incubated for 24 hours. Error bars indicate 95% confidence interval.
Fig 2
Fig 2. Differentially expressed transcripts at alpha 0.01.
The number of transcripts that are differentially expressed compared to the other conditions.
Fig 3
Fig 3. Comparison of differentially expressed transcribed sequences.
Comparison of the differences in expression between vVP1Q164K, CVB2Owt and mock, at 48 hours post infection. Difference in expression that (only) occurs in: (pink) vVP1Q164K compared to CVB2Owt; (orange) vVP1Q164K compared to both CVB2Owt and mock; (yellow) vVP1Q164K compared to mock; (purple) CVB2Owt compared to both vVP1Q164K and mock; (white) between all conditions; (green) mock compared to both vVP1Q164K and CVB2Owt; (blue) CVB2Owt compared to mock.
Fig 4
Fig 4. The 20 transcripts most differentially expressed between vVP1Q164K (48 h) and CVB2Owt.
The conditions are normalized to mock-cell expression levels.
Fig 5
Fig 5. Gene cloud displaying the 500 most significantly differentially expressed transcripts.
Font size is proportional to the highest change in expression and inversely proportional to the likelihood of the result.
See this image and copyright information in PMC

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