Epigenetics in the Fight against COVID-19

The COVID-19 pandemic and the SARS-CoV-2 virus responsible for it don’t seem to be going away anytime soon. Much of the world is seeing surges in cases, hospitalizations, and deaths, despite highly effective vaccines, antivirals, and other treatments aimed at preventing the infection and ameliorating its sequelae. Some of this is driven by constant and worrisome mutations in the virus, some by human biology and behavior.

Many efforts to counter the disease focus on preventing or fighting the infection, or mitigating its effects, and have been quite successful. Yet these efforts—most of which try to directly block the actions or prevent the expression of viral proteins—don’t always work. There is a need for more weapons in arsenal, with both new and borrowed epigenetic approaches among those being pursued.

What is epigenetics?

Epigenetics looks at heritable changes in phenotype that are not reliant on an alteration of the underlying genetic sequence itself. The most studied of these changes result from the addition/removal of methyl side groups to/from cytosine DNA residues and alteration of chromatin structural components by post-translationally-modifying histone proteins. These may result in altered expression of proteins including transcription factors, for example, or of certain non-coding RNA species, which can then have epigenetic effects. Modifications of the latter are regarded by many researchers as themselves a part of the epigenetic machinery.

Hundreds of enzymes are involved in that machinery. Among these are what are termed “readers,” “writers,” and “erasers” of epigenetic marks. Histone acetyltransferases (HACs) and deacetylases (HDACs), and kinases and phosphatases, for example, act to restructure chromatin, while DNA methyltransferases (DNMTs) change DNA’s methylation status. Many of these and others are, or are actively being pursued as, drug targets.

Patients infected with SARS-CoV-2 may experience acute respiratory distress syndrome (ARDS). This is brought on by an uncontrolled surge of pro-inflammatory cytokines and chemokines—known as a cytokine storm—combined with an impaired interferon (IFN) response. The interferon response is one of the principle early antiviral defenses. Regulatory regions of IFN response genes were found to be hypermethylated in immune cells of severe COVID-19 patients, indicating that these genes were being repressed, while regulatory regions of genes involved in inflammation were hypomethylated.

Commandeering the processes that control these marks could potentially nip the cytokine storm, and thus ARDS, in the bud. Similarly, expression of ACE2, which SARS-CoV-2 uses to gain entry to cells, is known to be regulated by DNA methylation and histone modifications.

Anti-virus or anti-host?

Coronaviruses are positive-stranded RNA viruses that are found in the cytoplasm and do not go through a DNA phase (like HIV does, for example). “It’s mostly the host machinery or the host enzymes that are putting epigenetic marks and manipulating transcription machinery” at the epigenetic level, notes Melanie Ott, Director of the Gladstone Institute of Virology.

“We’ve done a lot of systematic [protein-protein interaction (PPI)] screens, and not a lot of chromatin factors came out,” points out Nevan Krogan, Professor of Cellular and Molecular Pharmacology at the University of California—San Francisco. “That probably makes sense because most of the proteins are not in the nucleus.”

Thus traditional epigenetic interventions targeting DNA methylation or chromatin structure, for example, would be directed at changing host gene expression. Many of these have been pioneered in the field of oncology, with some, such as HDAC and DNMT inhibitors, already having been approved. “Cancer is way ahead of us in terms of … putting these in clinical trials,” Ott says. That is very important in order to learn about toxicities, side effects, and treatment duration. It’s also important to measure these against the new direct-acting antivirals to see which most benefit the patient. Ott thinks perhaps the best use of these host-targeted treatments might be “as a potential combination with direct-acting antivirals to suppress resistance development.”

E protein and BET proteins

“The question is,” Krogan asks, “is there an indirect effect of SARS-CoV-2 infection with chromatin and chromatin remodeling?”

The PPI screen found that the host proteins BRD2 and BRD4 (members of the bromodomain and extra-terminal domain (BET) family of proteins) bind to the SARS-CoV-2 E protein. Bromodomains are reader motifs that recognize acetylated lysines on histones and other proteins, while extra-terminal domains mediate other protein-protein interactions.

The E protein contains a histone-like motif mimicking the histone tail and, Ott and her colleagues have shown in a preprint, interacts with the bromodomains when it is acetylated. That modification on this “histone mimetic” can act like a sponge by siphoning BETs “away from the gene so that certain genes are not regulated in a normal manner anymore,” she explains. “Or it also can serve the virus itself in making it a bit better protein by being modified, or by recruiting other reader proteins.”

BRD4 is a coactivator of proinflammatory and antiviral genes. BRD2 acts as a transcriptional regulator of ACE2. The authors propose a model in which SARS-CoV-2’s E protein has evolved to antagonize BET proteins. Prophylactically treating with bromodomain inhibitors (which have been used for cancer therapy) will cause a downregulation of the ACE2 receptor, making cells more resistant to viral infection. But treating an already infected patient with BET inhibitors will serve to lessen production of antivirals, exacerbating the infection.

“I think that that shows you how viruses that are strictly cytoplasmic, or replicate strictly in the cytoplasm, still have a very good inroad into our nucleus to manipulate our gene expression to their benefit,” concludes Ott.

“And on the other side, it also shows you that manipulating the epigenome requires a lot of knowledge and dissection” to successfully thwart a virus.