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Marianne Rots, Professor of Molecular Epigenetics at the University Medical Center, Groningen, discusses her exciting research on epigenetic editing.
Marianne Rots did her undergraduate studies at the Faculty of Biology, University of Amsterdam in the Netherlands, and obtained her PhD from the VU University Medical Center, Amsterdam in 2000. She was a postdoctoral fellow at the Gene Therapy Center, University of Birmingham Alabama, before moving to Groningen in the Netherlands.
Since 2010, Marianne has been the Professor of Molecular Epigenetics at the University Medical Center Groningen. She leads a multidisciplinary team in understanding and exploiting epigenetic regulation mechanisms to further develop epigenetic editing as an exciting approach to permanently modulate a gene's expression profile.
The realization at college that "facts" written in textbooks (which students are forced to memorize by heart) might turn out not to be true after all, because of ongoing scientific research. It seemed to me that to challenge the known, while exploring the unknown can never be boring.
We started to work on epigenetic editing (locus-targeted rewriting of epigenetic marks; de Groote et al., 2012) when only a few labs worldwide were engineering DNA binding domains for the binding of any genomic locus at will. The field grew quickly with a strong focus towards genome editing: the fusion of nucleases to such engineered DNA binding domains to introduce local DNA damage.
To me, however, it seemed risky and I reasoned that many diseases would benefit from gene expression modulation (which can be bidirectional: upregulation as well as silencing of expression), leaving the DNA sequence intact.
Together with international collaborators, I started off by engineering artificial transcription factors (ATFs) and epigenetic editors to challenge two persistent dogmas in the field: 1) "heterochromatin is INaccessible" and 2) "epigenetic marks are NOT instructive for gene expression modulation". For both considerations, enough data had been gathered to indicate that epigenetic editing of artificial loci is feasible in human cells.
We and others have certainly challenged such dogmas. For example, see our Chen et al. (2014) paper in Nucleic Acids Research where we targeted a quite large TET-domain to a silenced gene in the heterochromatin context: we induced DNA demethylation, which was associated with gene re-expression.
The next challenge is to identify contexts in which edited epigenetic marks are mitotically stable, as indicated in our Rivenbark et al. (2012) paper. Towards such robust epigenetic editing we need to understand underlying chromatin reinforcing (or counteracting) parameters. So, the focus of my team now is to effectively induce epigenetic reprogramming for any locus in any given context by distilling choices on which effector domain to use for any given microchromatin environment.
During my postdoc training in the US, I aimed to construct efficient and specific gene therapy vectors. I realized then that many diseases are associated with disturbed gene expression profiles, and not so much with genetic mutations requiring compensation gene therapy. I reasoned that re-expressing a gene directly from its genomic locus might be more effective than introducing one isoform.
The choice of transgene is a largely overlooked aspect of gene therapy design: which of the several cDNA isoforms per gene to transfer and also the size of the transgene is not trivial. Moreover, which promoter to choose to control its expression?
By reprogramming the epigenetic landscape, the normal cellular signaling pathway is used to control gene expression, while the different isoforms in their natural rations are expected to be expressed. I reasoned that understanding epigenetics would be helpful in two ways: 1) predicting accessibility of (large) DNA binding domain-fusions, while 2) identifying writers or erasers to permanently reprogram epigenetic landscapes.
Apart from providing an overview of the upcoming field of epigenetic editing (see Nature Method 2014: Method to Watch), I also touch upon the sustainability of epigenetic editing and show some examples of short-term exposure resulting in longer-term effects.
Excitingly, towards the ultimate goal of inducing (permanent) gene expression changes, the epigenetic editing technology provides a unique approach to address cause-versus-consequence of epigenetics versus transcription regulation by transcription factors.
Although ATFs are generally assumed to be transient, we have identified situations in which short-term exposure to ATFs can result in long-term expression changes. Such conditions allow us to explore underlying chromatin changes and to identify instructive dominant epigenetic signatures. Such landscapes are currently being mimicked by epigenetic editing to eventually tip the balance from euchromatin to heterochromatin and vice versa.
In this post-genomics era, huge efforts are devoted to epigenome-wide association studies. This will yield new insights in clinical epigenetics research (for example diagnostics) but such studies are merely associative in nature: few studies actually address the functional effects of epigenetic mutations.
The CRISPR-Cas approach will prove instrumental in validating the involvement of genomic loci in diseases. The approach is currently being repurposed for epigenetic editing, as catalytically inactive Cas proteins can be fused to epigenetic writers and erasers. If we can further optimize CRISPR-Cas epigenetic editing into a robust technology, this will provide a cheap and flexible way to validate functional epigenetic mutations allowing accurate diagnostics and maybe—in the future—open new avenues for therapeutic approaches.
Initially, I faced much disbelief due to dogmas in the field (for instance, epigenetically silenced genes cannot be accessed; epigenetic marks are not instructive of gene expression). Despite this, my team and others were able to show that it is feasible to re-express any given epigenetically silenced gene. So far, in my lab, we have not encountered a gene which could not be re-expressed (out of a list of approximately 20 targets).
Next, we confirmed the overlooked Snowdon et al. (2002) paper by targeting H3K9 methylation to repress an endogenous gene (VEGF-A). Our target gene was a highly overexpressed oncogene (HER2/neu) indicating the relevance of the approach (Falahi et al., 2013). Excitingly, we were able to actually remove local DNA methylation, which did result in gene activation (Chen et al., 2014). Now, we have established a large collection of genes and relevant cell lines to exploit our validated engineered zinc finger proteins and/or sgRNAs, and a wide variety of fused epigenetic effector domains: the stage is set for systematic interrogation of microchromatin restrictions.
Apart from lab work, I am proud to be an associate editor of Clinical Epigenetics, which obtained its first impact factor of 6.2! As a vice-chair of a newly granted EU-COST (European Cooperation in Science and Technology) action (EpiCHEM), I am excited to collaborate with experts within a broad network to, among others, unravel the actual contribution of epigenetic drugs on epigenetic targets.
If dogmas prevent you from achieving wide-spread support: be persistent and keep on trying to realize the "impossible".
Apart from the absolute essentials: sunshine.