miRNA expression profiling of Epstein-Barr virus-associated NKTL cell lines by Illumina deep sequencing

The aim of this work was to establish the microRNA profile of SNK6 and SNT16, two Epstein-Barr virus (EBV)-infected cell lines derived from nasal NK/T-cell lymphoma (NKTL). The oncogenic EBV is strongly associated with the pathogenesis of nasal and extranodal NK/T-cell lymphoma and expresses 44 mature microRNAs and two noncoding EBV-encoded RNAs (EBERs). miRNAs are 19-25nt noncoding RNAs that affect host and viral gene expression post-transcriptionally. Deregulated miRNA patterns are frequently linked to a variety of human cancers including lymphomas. miRNA profiling of the two NK/T cell lines vs. primary cells revealed 10 and 4 up-regulated and 10 and 12 down-regulated miRNAs in SNK6 and SNT16 cells respectively. The results were validated by qRT-PCR for selected miRNAs. Target gene analyses confirmed cullin 5 (CUL5) and sphingosin-1-phosphate receptor 1 (S1PR1) as targets for the down-regulated hsa-miR-148a and viral ebv-miR-BART16 respectively. As recently demonstrated for the regulation of IL1-alpha by miR-142-3p, coexpression of the EBERs selectively exerted corepression of S1PR1 by BART16 but not of CUL5 by miR-148a, indicating selective corepression by the EBERs.