Widespread Traces of Lytic Kaposi Sarcoma-Associated Herpesvirus in Primary Effusion Lymphoma at Single-Cell Resolution

Abstract

Cancer cells of primary effusion lymphoma (PEL) often contain both Kaposi sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV). We measured the interplay of human, KSHV, and EBV transcription in a cell culture model of PEL using single-cell RNA sequencing. The data detect widespread trace expression of lytic KSHV genes.

ORF45, a multifunctional immediate early and tegument protein of KSHV

“…29 To evaluate the transcription profile of KSHV viral genes in KS specimens, Dittmer et al expression in a subpopulation of PEL cell lines by single-cell RNA sequencing. 30,31 Interestingly, BKRF4 (ORF45 homolog of EBV) could be detected in oral hairy leukoplakia 32 and antibodies against BKRF45 were common among Nasopharyngeal carcinoma patients. 33 The expressions of ORF45 in KS lesion and PEL cell imply possible roles of ORF45 in KSHV pathogenesis.…”

“…To evaluate the transcription profile of KSHV viral genes in KS specimens, Dittmer et al 13 performed real‐time PCR array analysis and found that ORF45 transcript can be detected in 8 out of 21 KS specimens; Hosseinipour et al 14 used improved quantitative RT‐PCR array and found ORF45 transcript is detectable in 27 out of 35 KS lesions; and Tso et al detected ORF45 expression in 3 out of 4 KS lesions by RNA‐seq 15 . In PEL cells, Rondeau et al and Landis et al detected ORF45 expression in a subpopulation of PEL cell lines by single‐cell RNA sequencing 30,31 . Interestingly, BKRF4 (ORF45 homolog of EBV) could be detected in oral hairy leukoplakia 32 and antibodies against BKRF45 were common among Nasopharyngeal carcinoma patients 33 .…”

Single-Cell Transcriptomics of Epstein-Barr Virus and Human Herpesvirus 6 Coinfection

“…A pipeline optimized for simultaneously measuring viral and human transcripts ( 12 , 13 ) was modified for the analysis of EBV and HHV-6. Cell Ranger (10X Genomics) was used to demultiplex raw base call files, trim template switching oligo and poly(A) sequences, align reads, and count unique molecular identifiers (UMIs).…”

Kaposi's sarcoma-associated herpesvirus at 27

“…Sequencing of the lymphoma cell line BCP-1 showed high expression of a subset of lytic genes, including PAN and a cluster of genes involved in immune regulation (K2, K4, K5) [ 39 ]. Single-cell RNA sequencing of the BC1 PEL line also detected many lytic genes in up to 50% of the cells, but at very low levels per cell [ 40 ].…”