Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas.

TitleWhole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas.
Publication TypeJournal Article
Year of Publication2013
AuthorsDeBoever C, Reid EG, Smith EN, Wang X, Dumaop W, Harismendy O, Carson D, Richman D, Masliah E, Frazer KA
JournalPLoS One
Volume8
Issue9
Paginatione73956
Date Published2013
ISSN1932-6203
KeywordsAcquired Immunodeficiency Syndrome, Aged, Central Nervous System Neoplasms, Female, Gene Expression Profiling, Humans, Lymphoma, Male, Middle Aged, Viruses
Abstract

Primary central nervous system lymphomas (PCNSL) have a dramatically increased prevalence among persons living with AIDS and are known to be associated with human Epstein Barr virus (EBV) infection. Previous work suggests that in some cases, co-infection with other viruses may be important for PCNSL pathogenesis. Viral transcription in tumor samples can be measured using next generation transcriptome sequencing. We demonstrate the ability of transcriptome sequencing to identify viruses, characterize viral expression, and identify viral variants by sequencing four archived AIDS-related PCNSL tissue samples and analyzing raw sequencing reads. EBV was detected in all four PCNSL samples and cytomegalovirus (CMV), JC polyomavirus (JCV), and HIV were also discovered, consistent with clinical diagnoses. CMV was found to express three long non-coding RNAs recently reported as expressed during active infection. Single nucleotide variants were observed in each of the viruses observed and three indels were found in CMV. No viruses were found in several control tumor types including 32 diffuse large B-cell lymphoma samples. This study demonstrates the ability of next generation transcriptome sequencing to accurately identify viruses, including DNA viruses, in solid human cancer tissue samples.

DOI10.1371/journal.pone.0073956
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/24023918?dopt=Abstract
Alternate JournalPLoS ONE
PubMed ID24023918
PubMed Central IDPMC3762708
Grant List62512 / / PHS HHS / United States
AG043384 / AG / NIA NIH HHS / United States
MH59745 / MH / NIMH NIH HHS / United States
MH62962 / MH / NIMH NIH HHS / United States
P30 CA023100 / CA / NCI NIH HHS / United States
P30 MH062512 / MH / NIMH NIH HHS / United States
P30CA23100 / CA / NCI NIH HHS / United States
T32 GM008666 / GM / NIGMS NIH HHS / United States
T32 GM008666 / GM / NIGMS NIH HHS / United States
U01 MH083506 / MH / NIMH NIH HHS / United States
U24 MH100928 / MH / NIMH NIH HHS / United States
Track(s): 
Bioinformatics and Systems Biology