CAGE Profiling of ncRNAs in Hepatocellular Carcinoma Reveals a Strong Activation of Retroviral LTR Promoters in Virus-Induced Tumors

Study ID Alternative Stable ID Type
phs000885 Case-Control

Study Description

The ncRNA transcriptome of human hepatocellular carcinoma (HCC) is largely unexplored. We used CAGE to characterize transcription start sites across different etiologies of human HCCs with emphasis on ncRNAs. Here we report that retroviral LTR promoters, expressed in healthy tissues such as testis and placenta but not liver, are widely activated in HCC. Despite HCC heterogeneity, a subset of LTR-derived ncRNAs were more than 10-fold up-regulated in the vast majority of samples. HCCs with a high LTR activity mostly had a viral etiology, were less differentiated and showed higher risk of recurrence. CAGE enabled us to build a promoter map for HCC, which uncovers a new layer of complexity in HCC genomics.

Archive Link Archive Accession
dbGaP phs000885

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