Submitted by Micah Alan Luftig (Duke University, USA) on Jun 03 2019
Platform: ngs – Illumina HiSeq 4000 (Homo sapiens; Human gammaherpesvirus 4)
Pubmed: 31266868
Summary Deciphering the molecular pathogenesis of virally induced cancers is challenging due, in part, to the heterogeneity of both viral and host gene expression. Epstein-Barr Virus (EBV) is a ubiquitous herpesvirus prevalent in B-cell lymphomas of the immune suppressed. EBV infection of primary human B cells leads to their immortalization into lymphoblastoid cell lines (LCLs) serving as a model of these lymphomas. In previous studies, our lab has described a temporal model for immortalization with an initial phase characterized by expression of the Epstein-Barr Nuclear Antigens (EBNAs), high c-Myc activity, and hyper-proliferation in the absence of the Latent Membrane Proteins (LMPs), called latency IIb. This is followed by the long-term outgrowth of LCLs expressing the EBNAs along with the LMPs, particularly the NFkB-activating LMP1, defining latency III. LCLs, however, express a broad distribution of LMP1 such that a subset of these cells expresses LMP1 at levels seen in latency IIb, making it difficult to distinguish these two latency states. In this study, we performed mRNA-Seq on early EBV-infected latency IIb cells and latency III LCLs sorted by NFkB activity. We found that latency IIb transcriptomes clustered independently from latency III independent of NFkB. We identified and validated mRNAs defining these latency states. Indeed, we were able to distinguish latency IIb cells from LCLs expressing low levels of LMP1 using multiplex RNA-FISH targeting EBV EBNA2, LMP1, and human CCR7 or MGST1. This study defines latency IIb as a bona fide latency state independent from latency III and identifies biomarkers for understanding EBV-associated tumor heterogeneity
ID | Title | Cell Type | Timepoint | Reported Virus | Virus Species | Exclusion Reason |
---|---|---|---|---|---|---|
GSM3847121 | day 7 donor 1 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | |
GSM3847122 | ICAM1 lo LCL donor 1 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | Extra interventions ICAM1-low sorted cells |
GSM3847123 | ICAM1 mid LCL donor 1 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | Extra interventions ICAM1-mid sorted cells |
GSM3847124 | ICMA1 hi LCL donor 1 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | Extra interventions ICAM1-high sorted cells |
GSM3847125 | day 7 donor 2 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | |
GSM3847126 | ICAM1 lo LCL donor 2 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | Extra interventions ICAM1-low sorted cells |
GSM3847127 | ICAM1 mid LCL donor2 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | Extra interventions ICAM1-mid sorted cells |
GSM3847128 | ICAM1 hi LCL donor 2 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | Extra interventions ICAM1-high sorted cells |
GSM3847129 | Day 7 donor 3 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | |
GSM3847130 | ICAM1 lo LCL donor 3 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | Extra interventions ICAM1-low sorted cells |
GSM3847131 | ICAM1 mid LCL donor 3 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | Extra interventions ICAM1-mid sorted cells |
GSM3847132 | ICAM1 hi LCL donor 3 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | Extra interventions ICAM1-high sorted cells |
GSM3847133 | day 7 donor 4 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | |
GSM3847134 | ICAM1 lo LCL donor 4 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | Extra interventions ICAM1-low sorted cells |
GSM3847135 | ICAM1 mid LCL donor 4 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | Extra interventions ICAM1-mid sorted cells |
GSM3847136 | ICAM1 hi LCL donor 4 | B-lymphocyte ![]() |
7 days | EBV | Human gammaherpesvirus 4 | Extra interventions ICAM1-high sorted cells |