Next‐generation sequencing of miRNAs in clinical samples of Epstein–Barr virus‐associated B‐cell lymphomas

Abstract

Epstein–Barr virus (EBV) encodes 49 microRNAs (miRNAs) in the BART and BHRF1 regions of its genome. Although expression profiles of EBV‐encoded miRNAs have been reported for EBV‐positive cell lines and nasopharyngeal carcinoma, to date there is little information about total miRNA expression, including cellular and viral miRNAs, in the primary tumors of EBV‐associated B‐lymphoproliferative disorders. In this study, next‐generation sequencing and quantitative real‐time reverse transcription‐PCR were used to determine the expression profiles of miRNAs in EBV‐infected cell lines and EBV‐associated B‐cell lymphomas, including AIDS‐related diffuse large B‐cell lymphoma (DLBCL), pyothorax‐associated lymphoma, methotrexate‐associated lymphoproliferative disorder, EBV‐positive DLBCL of the elderly, and Hodgkin lymphoma. Next‐generation sequencing revealed that EBV‐encoded miRNAs accounted for up to 34% of total annotated miRNAs in these cases. Expression of three miR‐BHRF1s was significantly higher in AIDS‐related DLBCL and pyothorax‐associated lymphoma compared with methotrexate‐associated lymphoproliferative disorder and EBV‐positive DLBCL of the elderly, suggesting the association of miR‐BHRF1s expression with latency III EBV infection. Heat map/clustering analysis of expression of all miRNAs, including cellular and EBV miRNAs, by next‐generation sequencing demonstrated that each EBV tumor, except methotrexate‐associated lymphoproliferative disorder, formed an isolated cluster. Principal component analysis based on the EBV‐encoded miRNA expression showed that each EBV tumor formed a distinguished cluster, but AIDS‐related DLBCL and pyothorax‐associated lymphoma formed larger clusters than other tumors. These data suggest that expression of miRNAs, including EBV‐encoded miRNAs, is associated with the tumor type and status of virus infection in these tumors.

High expression of JC polyomavirus-encoded microRNAs in progressive multifocal leukoencephalopathy tissues and its repressive role in virus replication

“…In the NGS results, non-exact mature miRNAs were included in all samples at high frequencies. This phenomenon has been previously observed for other virus and mammalian miRNAs as well [48]. Interestingly, miR-J1-5p contained non-exact mature miRNAs at a higher frequency compared with miR-J1-3p.…”

“…In addition, non-exact mature miRNA is detected more frequently in extracellular vesicles (exosomes) than in intracellular components [49,50]. Although no difference of function between exact and non-exact mature miRNAs has been reported, the detection rate differed between the two PCR systems used (the miScript PCR system and stem-loop real-time RT-PCR) [48]. Further studies will be required to reveal the expression mechanism and function of such non-exact mature miRNAs in virus infection.…”

Epstein barr virus encodes miRNAs to assist host immune escape

“…International Publisher lymphocytic leukemia and EBV-associated gastric cancer are type II latency [18][19][20][21]. The hosts with type III latency express eight latent genes, such as EBERs, EBNA1, EBNA-LP (EBNA-leader protein), EBNA2, EBNA3A, EBNA3B, EBNA3C, LPMs.…”

Plasma EBV miRNA Profiles Reveal Potential Biomarkers for Clinical Prognosis of Acquired Immunodeficiency Syndrome-related Lymphoma

“…EBV was the rst virus found to encode miRNAs [5]. So far, previous studies have found that there were 44 mature miRNAs encoded by EBV : (40 mature miRNAs encoded by 22 miRNA precursors (miR-BART1-22) in BamHI-A region right transcript (BART) encodes and 4 mature miRNAs produced by 3 miRNA precursors(miR-BHRF1-1, -2, -3) expressesed in BamHI fragment H opens to the right Reading frame 1 (BHRF1) [5,6]. EBV miRNAs are expressed differently during different infection periods.…”

“…At present, there are many studies on the occurrence and development of EBV miRNAs in nasopharyngeal carcinoma, but such studies are few in AIDS-related lymphoma patients. Studies have reported that compared with non-HIV-infected patients with EBV-positive Diffuse large B-cell lymphoma (DLBCL), the expression of the three miR-BHRF1s is higher in patients with AIDS and DLBCL [6].…”