CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors

Abstract

An increasing number of noncoding RNAs (ncRNAs) have been implicated in various human diseases including cancer; however, the ncRNA transcriptome of hepatocellular carcinoma (HCC) is largely unexplored. We used CAGE to map transcription start sites across various types of human and mouse HCCs with emphasis on ncRNAs distant from protein-coding genes. Here, we report that retroviral LTR promoters, expressed in healthy tissues such as testis and placenta but not liver, are widely activated in liver tumors. 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. ChIP-seq data show that MYC and MAX are associated with ncRNA deregulation. Globally, CAGE enabled us to build a mammalian promoter map for HCC, which uncovers a new layer of complexity in HCC genomics.

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

“…Notably, this qRT-PCR assay captured the expression of both major KHDRBS2 protein-coding splice isoforms at an exon-exon junction upstream of the L1 insertion. Repeated attempts to robustly measure KHDRBS2 expression at an exon-exon junction downstream from the L1 insertion were unsuccessful, and the gene was not detected by a previously published genome-wide survey of promoter usage (Hashimoto et al 2015). Thus, consistent with previous reports, we find that a tumor-specific intronic L1 insertion can coincide with down-regulation of host gene expression Shukla et al 2013;Helman et al 2014;Tubio et al 2014;Carreira et al 2016), but the mechanism for this potential dysregulation remains unresolved.…”

“…S1A; Supplemental Table S2). A meta-analysis of published RNA-seq data for HCC nodules obtained from FVB mice (Hashimoto et al 2015;Kress et al 2016) did not, however, reveal an alternative Fgf1 promoter located in either of the ETn element LTRs, as has been shown to occur previously for LTRs located proximal to genes in Mdr2 −/− liver nodules (Hashimoto et al 2015). More broadly, polymorphic L1 and SINE insertions typically utilized an L1 EN motif, generated TSDs, and incorporated a poly(A) tail (Supplemental Fig.…”

Novel Aberrations Uncovered in Barrett's Esophagus and Esophageal Adenocarcinoma Using Whole Transcriptome Sequencing

“…In hepatocellular carcinoma, LTR promoters show increased activation and tumors with high LTR expression were less differentiated compared with tumors with low LTR expression (51).…”

LTRs activated by Epstein-Barr virus-induced transformation of B cells alter the transcriptome

“…In the early embryo of both humans and mice, specific ERV groups are transcriptionally active and drive expression of many transcripts in the developing cells Peaston et al 2004;Macfarlan et al 2012;Maksakova et al 2013;Göke et al 2015). Likewise, both embryonic stem cells and induced pluripotent stem cells express LTR-driven transcripts, suggesting that they are important for pluripotency (Leung and Lorincz 2012;Fort et al 2014;Lock et al 2014;Lu et al 2014;Ohnuki et al 2014;Hashimoto et al 2015;. In pathways other than development, LTR-driven transcripts have also been found to be expressed in autoimmune diseases and several types of cancer, including lymphoma, hepatocellular carcinoma, and prostate cancer (Prensner et al 2013;Lock et al 2014;Hashimoto et al 2015;.…”

“…Likewise, both embryonic stem cells and induced pluripotent stem cells express LTR-driven transcripts, suggesting that they are important for pluripotency (Leung and Lorincz 2012;Fort et al 2014;Lock et al 2014;Lu et al 2014;Ohnuki et al 2014;Hashimoto et al 2015;. In pathways other than development, LTR-driven transcripts have also been found to be expressed in autoimmune diseases and several types of cancer, including lymphoma, hepatocellular carcinoma, and prostate cancer (Prensner et al 2013;Lock et al 2014;Hashimoto et al 2015;. While this work has led to an appreciation of the degree of aberrant LTR activation in normal and disease cells, the mechanisms that lead to LTR activation have remained unclear.…”