Dimitrios Galatis
Are early embryo development and cancer development more similar than we had thought before? The three-dimensional genome dictates cell fate through regulating gene expression. Recent discoveries have highlighted the gene expression control and activity (epigenetic control) similarities as well as functional similarities between cancer and early embryo development. In early development, epigenetic modifications direct the formation of a multicellular organism starting from a single totipotent stem cell that undergoes successive divisions and differentiation events. Whereas in cancer, a complex epigenetic landscape leads to cell dedifferentiation; hallmark of malignancy, and likely invasion and metastasis. Dedifferentiation — that is the cellular growth in reverse, from a terminally differentiated stage to a less differentiated stage, enables uncontrolled proliferation, self-renewal and a metabolism similar to that of embryonic stem cells (ESCs). Transposable Elements (TEs) have been well investigated in tumorigenesis, yet their role as developmental regulators has only recently been recognized, thus stirring the interest towards a likely link between TEs expressed in early development and those expressed in tumorigenesis, since both states exhibit functional and molecular similarities.
Transposable Elements
TEs, also referred as transposons, comprise of highly repetitive strands of “junk” DNA and constitute about 45-50% of the human genome. For comparison, it is important to remember that only 3% of the genome accounts for the protein-coding region. TEs are capable of generating new copies in the human germline and certain somatic tissue via two major pathways: transposition of DNA transposons and retrotransposition of retro (RNA) transposons. The main difference between the two is that transposition works in a ‘cut-and-paste’ fashion, whereas retrotransposition works in a ‘copy-and-paste’ fashion involving an RNA intermediate and enabling transfer of retrotransposons in different parts of the genome while the original retrotransposon retains its location. The transposon activity can affect normal gene expression networks and gene function by inserting into the promoter or the coding sequence. Furthermore, the repetitive nature of TEs favors incorrect recombination events that result in translocations, insertions and deletions. In cancer, TEs have been explored in the context of onco-exaptation, the recruitment of TE derived promoters to activate genes that contribute to cancer growth that are called oncogenes, as well as insertional mutagenesis, that is the insertion of DNA base pairs in the chromosomal DNA, acting towards cancer progression. TEs in the human genome do not always act through transposition that could have a negative impact on normal cell function, in fact TEs’ presence in active genes during early embryo development is vital normal cell function (figure 1).
TEs in early Development
Due to TEs’ parasitic nature and potentially deleterious effects, species have developed silencing mechanisms against TEs to prevent transposition and retrotransposition, primarily via DNA methylation and repressive chromatin, yet TEs do not always remain silenced. In humans, after fertilization, epigenetic reprogramming occurs through an extensive demethylation event followed by remethylation, during which some TEs escape remethylation and become transcriptionally active. These are playing an important role in regulating pluripotency and totipotency factors, as well as other functional roles during development in a tissue-specific fashion, hence these TEs are required for normal cellular function. TE expression that is vital is distinguished by the surreptitious TE expression resulting in transposition.
TEs in early development are recruited to function as genes and regulatory elements, including TE-derived enhancers, promoters and non-coding RNAs, in the extra-embryonic (placenta) and embryonic cell lineages. This recruitment is called exaptation. In the embryonic lineage, TEs in the form of long terminal repeat (LTR) retroelements, which are endogenous retro-transposable elements, and non-coding RNA (ncRNA) are recruited as developmental regulators in specific tissues. Notably, 83% of long-intergenic non-coding (linc) RNAs, which are non-coding RNA transcripts with more than 200 nucleotides located in-between genes, contain TEs. Some of these show stem-cell-specific expression, which is in favor of the idea that TEs have high tissue specificity and are active during early embryonic stages. Moreover, 25% of the binding sites for two regulatory factors, OCT4 and NANOG in humans are formed by TEs. OCT4 and NANOG are essential for the maintenance of pluripotency in stem cells. Some TEs have also been found to take part in the establishment of topologically associated domains (TADs) in human pluripotent stem cells. TADs mediate 3D interactions between promoters and enhancers, and thus can be important for cell-specific gene expression, which is why TADs are reconfigured during differentiation events.
TEs in Cancer and Dedifferentiation
In early embryo development, TEs act in multiple ways with one of them being their presence in active genes that provide the placenta with the characteristics of proliferation, invasion, apoptosis and immunosuppression, hence resembling the characteristics of cancerous cells. The same transposon-derived genes present in the placenta have also been recorded in some cancers. Based on similarities between cells in cancer and early development, it has been suggested that TEs active in both states are silenced after early development stages and become reactivated in cancer, where they retain their function and facilitate proliferation, invasion, and immune modulation. This process is essentially dedifferentiation. TE-promoted and TE-derived placental genes have indeed been characterized as oncogenes in differentiated somatic cells; genes which become activated and facilitate cancer progression (figure 2). Recently, interactions between TEs and cancer, specifically in the form of onco-exaptation, have been recorded in a range of different cancers using genome-wide search, including melanoma, colorectal cancer and lymphoma. To date, there are two main models that describe onco-exaptation; the de-depression and the epigenetic evolution models. The first states that molecular changes occurring during oncogenesis activate TEs which in turn trigger the expression of oncogenes. The latter one, on the other hand, predicts that TEs are transcribed regardless of the pathogenic state of the cell so that TE loci will be activated to be enhancers/promoters of oncogenes. When this happens in a cancerous cell, that cell confers a selective advantage over the rest of the tumor population so that its frequency within the population increases. It is still unclear whether TE activation promotes dedifferentiation or vice versa, while it has also been proposed that the two models do not necessarily act in isolation, but rather in combination. Further investigation is required to better understand the intertwining nature of TEs as regulators in early development and cancer, however it is likely that TEs mediate the transcriptional network of pluripotency factors in cancer the same way they do during early development.
Nevertheless, functional and epigenetic similarities between cancer and early development have been identified that are in favor of dedifferentiation occurring in carcinogenesis, and indirectly suggest that TEs play a pivotal role at it, even though no direct evidence have been published so far that support the hypothesis that early developmental TEs become reactivated in cancer to contribute to dedifferentiation. One example that highlights a direct link between ESCs and cancer is the fact that regulatory sequences of both ESCs and cancer cells, called CpG island shores, which highly influence pluripotency and likely include TEs, exhibit an overlap in their differential methylation pattern. Notable is also that cells of the extraembryonic lineage share a DNA methylation landscape more similar to that of cancerous cells than healthy somatic cells.
Summary
TEs contribute substantially to early development, primarily through their action as regulators of key developmental genes, such as those maintaining pluripotency. Some of these genes have been re-identified as oncogenes in healthy somatic cells, as their reactivation likely leads to cancerous cells acquiring characteristics similar to that of ESCs and cells of the placenta. These evidences, along with the fact that cancer cells and cells during early embryo development share a similar epigenetic landscape, support the hypothesis of dedifferentiation of somatic cells in tumorigenesis so that they become cancerous, while they are also in favor of the idea that the activation of similar TEs in both early development and cancer is likely to contribute to dedifferentiation. TEs being studied in the scope of regulators of early development and cancer could change our understanding of carcinogenesis, however more direct evidence is required to support this hypothesis before reaching any conclusions.
References
Lynch-Sutherland, C. F., et al. (2020) ‘Reawakening the Developmental Origins of Cancer Through Transposable Elements’, Frontiers in Oncology 10, doi: 10.3389/fonc.2020.00468
Saleh A., Macia A., Muotri A. R. (2019) ‘Transposable Elements, Inflammation, and Neurological Disease’, Frontiers in Neurology 10, doi: 10.3389/fneur.2019.00894