Jan 11. [Epub ahead of print]
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.
Lin Z <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Lin%20Z%22%5BAuthor%5D>,
Puetter
A <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Puetter%20A%22%5BAuthor%5D>, Coco
J <http://www.ncbi.nlm.nih.gov/pubmed?term=%22Coco%20J%22%5BAuthor%5D>,
Xu G<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Xu%20G%22%5BAuthor%5D>
, Strong MJ<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Strong%20MJ%22%5BAuthor%5D>
, Wang X<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Wang%20X%22%5BAuthor%5D>
, Fewell C<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Fewell%20C%22%5BAuthor%5D>
, Baddoo M<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Baddoo%20M%22%5BAuthor%5D>
, Taylor C<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Taylor%20C%22%5BAuthor%5D>
, Flemington EK<http://www.ncbi.nlm.nih.gov/pubmed?term=%22Flemington%20EK%22%5BAuthor%5D>
.
Source
Tulane University Health Sciences Center and Tulane Cancer Center, 1430
Tulane Avenue, SL79, New Orleans, LA 70112.
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.
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