Detection of MuLV in the EBV-positive human B-cell line JY

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American Society For Microbiology

Journal of Virology

J. Virol. JVI.06717-11;

published ahead of print 11 January 2012,

Detection of Murine Leukemia Virus in the

Epstein-Barr virus-positive human B-cell line

JY using a computational RNA-seq based

exogenous agent detection pipeline,

PARSES.

Zhen Lin1, e Puetter1, ph Coco2,

Guorong Xu2, J. Strong1, Xia Wang1,

Fewell1, Melody Baddoo1,

2 and K. Flemington1,*

Author Affiliations

1Tulane University Health Sciences Center and Tulane

Cancer Center, 1430 Tulane Avenue, SL79, New Orleans,

LA 70112

2University of New Orleans, 2000 Lakeshore Drive, New

Orleans LA 70148

ABSTRACT

Many cell lines commonly used for biological studies have

been found to harbor exogenous agents such as the human

tumor viruses, Epstein-Barr virus (EBV) and human

papillomavirus.

Nevertheless, broad-based, unbiased approaches to globally

assess the presence of ectopic organisms within cell model

systems has not previously been available.

We reasoned that high-throughput sequencing should

provide unparalleled insights into the microbiomes of tissue

culture cell systems.

Here we have used our RNA-seq analysis pipeline, PARSES

(Pipeline for Analysis of RNA-Seq Exogenous Sequences),

to investigate the presence of ectopic organisms within two

EBV-positive B-cell lines commonly used by EBV

researchers.

Sequencing datasets from both the Akata and JY B-cell

lines were found to contain reads for EBV, and the JY

dataset was found to also contain reads from the murine

leukemia virus (MuLV).

Further investigation revealed that MuLV transcription in JY

cells is highly active.

We also identified a number of MuLV alternative splicing

events and we uncovered evidence of

APOBEC3G-dependent DNA-editing.

Finally, RT-PCR analysis showed the presence of MuLV in

three other human B-cell lines (DG75, Ramos, and P3HR1

Cl. 13) commonly used by investigators in the Epstein-Barr

virus field.

We believe that a thorough examination of tissue culture

microbiomes using RNA-seq/PARSES-like approaches is

critical for the appropriate utilization of these systems in

biological studies.

FOOTNOTES

*Corresponding author: Tel: , email:

eflemin@...

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