Date Published: July 17, 2017
Publisher: Public Library of Science
Author(s): Frances E. Lock, Artem Babaian, Ying Zhang, Liane Gagnier, Sabrina Kuah, Antonia Weberling, Mohammad M. Karimi, Dixie L. Mager, Jürgen Schmitz.
Remnants of ancient transposable elements (TEs) are abundant in mammalian genomes. These sequences contain multiple regulatory motifs and hence are capable of influencing expression of host genes. TEs are known to be released from epigenetic repression and can become transcriptionally active in cancer. Such activation could also lead to lineage-inappropriate activation of oncogenes, as previously described in lymphomas. However, there are few reports of this mechanism occurring in non-blood cancers. Here, we re-analyzed whole transcriptome data from a large cohort of patients with colon cancer, compared to matched normal colon control samples, to detect genes or transcripts ectopically expressed through activation of TE promoters. Among many such transcripts, we identified six where the affected gene has described role in cancer and where the TE-driven gene mRNA is expressed in primary colon cancer, but not normal matched tissue, and confirmed expression in colon cancer-derived cell lines. We further characterized a TE-gene chimeric transcript involving the Interleukin 33 (IL-33) gene (termed LTR-IL-33), that is ectopically expressed in a subset of colon cancer samples through the use of an endogenous retroviral long terminal repeat (LTR) promoter of the MSTD family. The LTR-IL-33 chimeric transcript encodes a novel shorter isoform of the protein, which is missing the initial N-terminus (including many conserved residues) of Native IL-33. In vitro studies showed that LTR-IL-33 expression is required for optimal CRC cell line growth as 3D colonospheres. Taken together, these data demonstrate the significance of TEs as regulators of aberrant gene expression in colon cancer.
Gene deregulation is widespread in cancer and can be due to mutations in cis regulatory motifs, disruptions in epigenetic state or dysregulation of other regulatory pathways. One underappreciated mechanism that can cause gene deregulation in cancer is activation of cryptic (or normally dormant) promoters [1–4]. Transposable elements (TEs), including endogenous retroviruses (ERVs) and long interspersed elements (LINEs), comprise nearly half of the human genome [5–7] and represent an abundant source of natural promoters in the genome [8, 9]. In particular, ERV long terminal repeats (LTRs), the termini of integrated retroviruses, naturally harbor promoters and enhancers. Therefore, the >400,000 ERV LTRs in the genome have built-in potential to affect gene expression, as has been shown by many studies [8, 10–18].
All reagents were purchased from Sigma (Ontario, Canada), unless specified. All experiments are representative of at least 3 independent experiments, unless specified. Statistical analysis was performed using T test, unless specified. See S1 Table for all primers used in this study.
We have identified and characterized a novel, shorter isoform of IL-33 driven by an LTR promoter and expressed in a subset of CRC samples. This isoform was also detected in one of five CRC samples by screening RNA-seq from an independent study  (S12 Fig). Because highly conserved N-terminal motifs are lacking in this isoform, it is possible that its function may be altered compared to the normal isoform, although we were unable to demonstrate a clear functional difference in this study. We found that the LTR isoform is still able to be retained in the nucleus, but it is possible that loss of the N-terminus could result in changes in function due to changes in protein folding. However, since the LTR-IL-33 C-terminal sequence is unchanged, and the C-terminal alone is sufficient for IL1R1 receptor binding and is a potent activator of IL1R1 signaling , it is highly likely that the LTR-IL-33 isoform is able to bind and activate IL1R1 signaling as the native isoform does.