Characterization of Epstein-Barr Virus miRNAome in Nasopharyngeal Carcinoma by Deep Sequencing

Abstract

Virus-encoded microRNAs (miRNAs) have been shown to regulate a variety of biological processes involved in viral infection and viral-associated pathogenesis. Epstein-Barr virus (EBV) is a herpesvirus implicated in nasopharyngeal carcinoma (NPC) and other human malignancies. EBV-encoded miRNAs were among the first group of viral miRNAs identified. To understand the roles of EBV miRNAs in the pathogenesis of NPC, we utilized deep sequencing technology to characterize the EBV miRNA transcriptome in clinical NPC tissues. We obtained more than 110,000 sequence reads in NPC samples and identified 44 EBV BART miRNAs, including four new mature miRNAs derived from previously identified BART miRNA precursor hairpins. Further analysis revealed extensive sequence variations (isomiRs) of EBV miRNAs, including terminal isomiRs at both the 5′ and 3′ ends and nucleotide variants. Analysis of EBV genomic sequences indicated that the majority of EBV miRNA nucleotide variants resulted from post-transcriptional modifications. Read counts of individual EBV miRNA in NPC tissue spanned from a few reads to approximately 18,000 reads, confirming the wide expression range of EBV miRNAs. Several EBV miRNAs were expressed at levels similar to highly abundant human miRNAs. Sequence analysis revealed that most of the highly abundant EBV miRNAs share their seed sequences (nucleotides 2–7) with human miRNAs, suggesting that seed sequence content may be an important factor underlying the differential accumulation of BART miRNAs. Interestingly, many of these human miRNAs have been found to be dysregulated in human malignancies, including NPC. These observations not only provide a potential linkage between EBV miRNAs and human malignancy but also suggest a highly coordinated mechanism through which EBV miRNAs may mimic or compete with human miRNAs to affect cellular functions.

Epstein-Barr Virus MicroRNA miR-BART20-5p Suppresses Lytic Induction by Inhibiting BAD -Mediated caspase-3 -Dependent Apoptosis

“…BART miRNAs are expressed at higher levels in epithelial malignancies than in lymphomas (21)(22)(23)(24). Several BART miRNAs have been shown to regulate cellular pathways and EBV latency.…”

Infection of Epstein–Barr virus in a gastric carcinoma cell line induces anchorage independence and global changes in gene expression

“…The miRNAs are ∼22-nt RNAs processed from longer RNA polymerase II transcripts that function much like siRNAs in inhibiting protein translation through base pair interactions with target mRNAs (10). The BART miRNAs can be detected by PCR in all forms of EBV latency, although by far the highest expression is detected in type I and II latency, particularly in epithelial cell infection (e.g., NPC, GC) (7,11,12), in which a large percentage of the total miRNA pool is exclusively BART miRNAs, as evidenced by high-throughput sequencing of small RNA libraries (9,13).…”

Application of Next-Generation Sequencing in the Era of Precision Medicine

“…Applications of NGS in virology diagnostic can be used for analysis of patients with unexplained illness, especially during outbreaks and epidemics [67][68][69][70]. It also includes the identiication of novel pathogens [71][72][73][74], viral community characterization [75][76][77], whole viral genome reconstruction [73,78,79], antiviral drug resistance [80][81][82][83], epidemiology [84][85][86][87] and transcriptomic [88][89][90]. The use of NGS in virology is increasing the knowledge of viral infection dynamics and their correlation with human health and treatment.…”