Oncotarget

Research Papers:

Diverse transcriptional regulation and functional effects revealed by CRISPR/Cas9-directed epigenetic editing

Miguel Vizoso _ and Jacco van Rheenen _

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Oncotarget. 2021; 12:1651-1662. https://doi.org/10.18632/oncotarget.28037

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Abstract

Miguel Vizoso1 and Jacco van Rheenen1

1 Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands

Correspondence to:

Miguel Vizoso, ORCID: orcid.org/0000-0002-9992-2851
Jacco van Rheenen, email: j.v.rheenen@nki.nl

Keywords: targeted DNA methylation; CRISPR/Cas9-based system; IGFBP2; epithelial-to-mesenchymal transition

Received: November 20, 2020     Accepted: July 27, 2021     Published: August 17, 2021

Copyright: © 2021 Vizoso and Rheenen. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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.


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