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Silencing the SARS-CoV-2 Receptor With CRISPR and Epigenetic Modifications

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The Hackett Group at EMBL Rome explores epigenetics, genome regulation and cell identity. Recently, the scientists developed a novel CRISPR molecular tool for editing the epigenome, enabling transient modifications that can switch certain genes "on" and "off" temporarily.

The SARS-CoV-2 virus that has caused the COVID-19 global pandemic makes its way into a host cell via a protein known as ACE2, which is involved in a range of physiological functions in the body.

What happens when you transiently turn "off" the gene that encodes this protein? Can SARS-CoV-2 still enter the cell and cause infection? This is what Hackett and colleagues are currently exploring in animal models, to determine whether epigenetic silencing could be a treatment approach for COVID-19 in humans.

Technology Networks
spoke with Dr James (Jamie) Hackett, group leader at EMBL, to learn more about the CRISPR tool, how it can be used to silence ACE2 in the context of SARS-CoV-2 infection and whether there could be any adverse implications from doing so.

Molly Campbell (MC): For our readers that may be unfamiliar, can you please describe what epigenetic modifications are?

Jamie Hackett (JH):
Epigenetic modifications are small chemical tags that are physically grafted onto DNA (or the histones that DNA wraps around) to help control how and when the DNA is used. These epigenetic modifications act as signposts that encourage a specific part of DNA, such as a gene, to be switched on or off. In other words, they help control which genes are "expressed", and which are ignored in each cell. This is important to ensure that genes that are required specifically in liver, for example, are only switched on in the liver, and not say, in the brain.

MC: You are developing a CRISPR-based molecular tool to conduct epigenetic editing. Can you please tell us about this approach? How have you developed the tool and how does it work?

CRISPR systems normally locate a specific section of DNA in the genome and alter its genetic sequence, known as genetic "editing". Epigenetic editing uses the same principle but instead alters the epigenetic modifications at a specific region rather than the genetic sequence. This turns genes on or off in a "programmable" manner. Importantly, unlike genetic editing, epigenetic editing is largely reversible, enabling transient changes in how genes operate without changing the DNA sequence itself.

MC: You plan to test the tool in mice to target airway cells that express the ACE2 protein. Can you talk to us about the rationale behind this?

ACE2 is a protein that sits on the outside of many cells and is normally involved in controlling blood pressure. However, the COVID-19 virus hijacks ACE2 by using it as a docking site that enables entry of the virus into a cell. If the gene ACE2 is switched OFF, this should remove the access point for COVID-19 and restrict infection. To test this possibility, we will use mouse models where we attempt to epigenetically switch off ACE2, which will help inform us whether this could be a viable strategy in humans in the future.

MC: Could there be adverse effects from targeting the ACE2 protein, as it is involved in several physiological processes in humans, for example? How will you explore and monitor this?

Impaired levels of ACE2 over long periods are linked with elevated blood pressure. However, over short-term periods loss of ACE2 appears to be relatively tolerable. This is one reason why a reversible "epigenetic" approach could be appealing since it would only temporality deplete ACE2 from cells, potentially to provide protection during high risk periods, before allowing it to return to its original status at the appropriate time. 

MC: What broader applications might this tool have, beyond SARS-CoV-2?

The same technology can, in principle, be applied to change the expression of genes other than ACE2, that are linked with disease. We are at the very beginning of exploring the potential of this, so it is not clear what realistic expectations are, but there is nonetheless great excitement about such precision strategies. For example, diseases where one of the two gene copies is a "mutant", such as Huntington’s disease, could be targets. Here it is hoped to be possible to epigenetically switch off only the mutant version of the gene, leaving the normal copy on. This scenario is predicted to help mitigate symptoms in a very precise and specific way. Conversely, in the neurological disorder Fragile X syndrome, the FMR1 gene has become inappropriately silenced (switched off). Epigenetic editing can be applied to selectively reactivate this gene to switch it on, with initial indications being that this helps restore neuronal functions.     

Jamie Hackett was speaking to Molly Campbell, Science Writer for Technology Networks.