Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas.
Title | Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas. |
Publication Type | Journal Article |
Year of Publication | 2013 |
Authors | DeBoever, C, Reid, EG, Smith, EN, Wang, X, Dumaop, W, Harismendy, O, Carson, D, Richman, D, Masliah, E, Frazer, KA |
Journal | PLoS One |
Volume | 8 |
Issue | 9 |
Pagination | e73956 |
Date Published | 2013 |
ISSN | 1932-6203 |
Keywords | Acquired 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. |
DOI | 10.1371/journal.pone.0073956 |
Alternate Journal | PLoS ONE |
PubMed ID | 24023918 |
PubMed Central ID | PMC3762708 |
Grant List | 62512 / / 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 |