biostudies-literatureYan BIntramural NIH HHSNIAID NIH HHSNCI NIH HHSNIH HHSNIGMS NIH HHSe28362https://www.ebi.ac.uk/biostudies/studies/S-EPMC10027397biostudies-literatureUnknown95(1)We probed the lifecycle of Epstein-Barr virus (EBV) on a cell-by-cell basis using single cell RNA sequencing (scRNA-seq) data from nine publicly available lymphoblastoid cell lines (LCLs). While the majority of LCLs comprised cells containing EBV in the latent phase, two other clusters of cells were clearly evident and were distinguished by distinct expression of host and viral genes. Notably, both were high expressors of EBV LMP1/BNLF2 and BZLF1 compared to another cluster that expressed neither gene. The two novel clusters differed from each other in their expression of EBV lytic genes, including glycoprotein gene GP350. The first cluster, comprising GP350^- LMP1^hi cells, expressed high levels of HIF1A and was transcriptionally regulated by HIF1-α. Treatment of LCLs Journal of medical virologyA comprehensive single cell data analysis of lymphoblastoid cells reveals the role of super-enhancers in maintaining EBV latency.PMC10027397ZIA/DK075149ZIA DK075149P30 CA023168R01 CA047006R35 GM138283R01 AI136995R01 AI123420R35GM138283; 5R01AI123420 and 5R01CA047006P30CA023168Sahoo SSHu YZhao BWang CShao KBriggs SDAfzali BZhuang YWang LTrujillo-Ochoa JLLiu XChakravorty SAnderson NLZhang ZSirit IOlson MRYan BJung MKazemian MKadadi SDfalseA comprehensive single cell data analysis of lymphoblastoid cells reveals the role of super-enhancers in maintaining EBV latency.We probed the lifecycle of Epstein-Barr virus (EBV) on a cell-by-cell basis using single cell RNA sequencing (scRNA-seq) data from nine publicly available lymphoblastoid cell lines (LCLs). While the majority of LCLs comprised cells containing EBV in the latent phase, two other clusters of cells were clearly evident and were distinguished by distinct expression of host and viral genes. Notably, both were high expressors of EBV LMP1/BNLF2 and BZLF1 compared to another cluster that expressed neither gene. The two novel clusters differed from each other in their expression of EBV lytic genes, including glycoprotein gene GP350. The first cluster, comprising GP350^- LMP1^hi cells, expressed high levels of HIF1A and was transcriptionally regulated by HIF1-α. Treatment of LCLs 2023-01-01T00:00:00Z2023 Jan2026-07-14T20:14:08.952Z2025-04-05T19:40:35.702ZS-EPMC100273973645308810.1002/jmv.28362