Abstract
DNA methylation is an epigenetic process that controls DNA accessibility and serves as a transcriptomic switch when deposited at regulatory regions. The adequate functioning of this process is indispensable for tissue homeostasis and cell fate determination. Conversely, altered DNA methylation patterns result in abnormal gene transcription profiles that contribute to tumor initiation and progression. However, whether the consequence of DNA methylation on gene expression and cell fate is uniform regardless of the cell type or state could so far not been tested due to the lack of technologies to target DNA methylation in-situ. Here, we have taken advantage of CRISPR/dCas9 technology adapted for epigenetic editing through site-specific targeting of DNA methylation to characterize the transcriptional changes of the candidate gene and the functional effects on cell fate in different tumor settings. As a proof-of-concept, we were able to induce de-novo site-specific methylation of the gene promoter of IGFBP2 up to 90% with long-term and bona-fide inheritance by daughter cells. Strikingly, this modification led to opposing expression profiles of the target gene in different cancer cell models and affected the expression of mesenchymal genes CDH1, VIM1, TGFB1 and apoptotic marker BCL2. Moreover, methylation-induced changes in expression profiles was also accompanied by a phenotypic switch in cell migration and cell morphology. We conclude that in different cell types the consequence of DNA methylation on gene expression and cell fate can be completely different.
Highlights
Increasing number of studies report that proteins do not work in isolation but are part of a complex network of biomolecules, that may differ at various settings
We will focus on the insulin-like growth factor binding protein 2 (IGFBP2), a recently discovered multitasked gene regulated by DNA methylation which has been reported to function both as a tumor-promoting and -suppressing gene
In this study we revealed the consequence of DNA methylation on the expression of IGFBP2, and we gain some basic insights into on the process of DNA methylation itself
Summary
Increasing number of studies report that proteins do not work in isolation but are part of a complex network of biomolecules, that may differ at various settings (e.g., different tumor types [1, 2] or stages of tumor progression [3]). We will focus on the insulin-like growth factor binding protein 2 (IGFBP2), a recently discovered multitasked gene regulated by DNA methylation which has been reported to function both as a tumor-promoting and -suppressing gene. IGFBP2 is a secreted protein that competes with IGF-1 and IGF2 ligands for IGF receptor binding, thereby modulating the downstream cascade of IGF signaling that mediates essential cellular processes such as proliferation and migration. On one hand, it has been described as a tumor suppressor by promoting a p53-dependent IGF-1 and ERK inactivation and leading to proliferation attenuation [9]. IGFBP2 has been shown to act as an oncogene since it www.oncotarget.com promotes invasion through interaction with integrin α5 and β1 [11, 12], it activates the NFkβ-Zeb1 [13] and EGFR/ STAT3 axes [14], it promotes vascular mimicry by CD144 and MMP2 [15], and it induces immunosuppression [16]
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