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Epigenetics of Viruses

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A pathogen is a microorganism that is made up of viruses and bacteria, and cause disease to its host. The National Center for Biotechnology Information (NCBI) states that three new viral pathogen species emerge every year. Viral pathogens contain either DNA or RNA as their genome which can disrupt cell function or kill infected cells; however, this article focuses on DNA viruses and viruses that replicate through a DNA intermediate, such as retroviruses. These infectious particles can be enhanced or repressed through epigenetic changes which alter the organization of DNA. Examples of epigenetic modifications include DNA methylation and histone modifications. Epigenetic research has shown that treatments for certain viral pathogens can be produced through an epigenetic approach.

Epigenetics

Epigenetics is the study of how chemical modifications impact the stable and long-term regulation of gene expression that may affect gene function. In simple terms, different behaviors and environments can cause epigenetic changes that could affect gene expression and/or function. Epigenetic changes do not change the DNA sequence but influence how the DNA sequence is read, alter gene expression patterns, and influence the production of proteins in cells. Specifically, epigenetic changes have an impact on chromatin structure. DNA methylation and histone modification are types of epigenetic changes.

DNA methylation is used to control gene expression and is the process of adding a methyl group at the 5-carbon of the cytosine ring resulting in 5-methylcytosine (5-mC), which inhibits transcription. DNA methylation alters how DNA nucleotides are expressed without changing the actual sequence. The process of detecting and quantifying methylated cytosine nucleotides in DNA is essential because of abnormal methylation patterns. Moreover, DNA methyltransferases are enzymes that add methyl groups to DNA bases which modify the function of genes and gene expression. The methyl group attached to 5mC can be removed through a process called demethylation. Ten-eleven translocation methylcytosine dioxygenases (TET) proteins, which are encoded by the genes TET1, TET2, and TET3, are the enzymes responsible for demethylation. TET proteins cause DNA demethylation by oxidizing 5mC to 5-hydroxymethylcytosine (5-hmC), which contributes to gene activation. Methylation of CpG islands turns genes off while demethylation of CpG islands turns genes on.

Chromosomes are located inside the nucleus of plant and animal cells. The structure of chromosomes tightly warps DNA through histones, a type of protein in chromosomes. Specifically, histones bind to DNA, give chromosomes their shape, and help control the activity of genes. Histones possess long N-terminal tails, which control chromatin compaction and function. Histone modifications regulate chromatin structure and gene transcription. Post-translational modification of histone tails takes the form of methylation, acetylation, phosphorylation, and ubiquitinylation.

Viruses

A virus is an infectious agent that invades a living cell and makes copies of itself within the host cell. It is made out of either DNA or RNA and surrounded by a protein coat. They tend to have a very simple structure and require a microscope to visualize them. Viruses infect a variety of organisms: bacteria, plants, and animals. Even though they replicate and adapt in these environments, they cannot make their own energy or replicate alone. They must infect cells (host cell) and use components from that cell to make copies. Epigenetic research has shown that treatments for certain viral pathogens, like the human immunodeficiency virus and coronavirus, can be produced through an epigenetic approach.

Human Immunodeficiency Virus (HIV)

The human immunodeficiency virus (HIV) is a virus that attacks the body's immune system. It originated from chimpanzees in Central Africa and was passed to humans when they hunted and came in contact with the infected blood of chimpanzees. As the immune system weakens, it becomes harder for one to fight viruses and diseases. There are three stages of HIV: acute HIV infection, chronic HIV infection, and AIDS. Even though HIV does not have a cure, it can be controlled with proper medical care which can elongate one's life. If HIV is not treated, it can lead to the acquired immunodeficiency syndrome (AIDS). Highly active antiretroviral therapy (HAART) is a medication used to manage and treat HIV by stopping the virus from making copies of itself in the body. Overtime, HAART causes drug resistance and unwanted side effects.

Epigenetics Factors

HIV attacks immune system cells; however, some HIV-infected immune cells go into a resting or latent state. The latent HIV reservoir is a group of immune system cells in the body that are infected with HIV but are not actively producing new viruses. Epigenetic research has shown that epigenetic therapy can turn on the silenced HIV proviruses exposing them to detection by the immune system which could lead to the loss of the latent HIV reservoir. For example, BRD4, a transcriptional and epigenetic regulator, has induced HIV transcriptional suppression. On the other hand, epigenetic regulators, like chromatin remodeling enzymes, could potentially aid the drug HAART in minimizing virus replication. Instead of solely using the HAART medication, researchers have found a safer therapy that targets epigenetic repression of HIV.

Long-term stable epigenetic repression of HIV-1 was accomplished by having an HIV-1 promoter-targeting Zinc Finger Protein (ZFP-362) fuse to active domains of DNA methyltransferase 3 A. ZFP-362 play a role in DNA recognition, RNA packaging, transcriptional activation, regulation of apoptosis, protein folding and assembly, and lipid binding. Specific to HIV, ZFP-362 is being used as a DNA-binding protein that recognizes the HIV provirus, and carries fused DNMT3A thereby positioning a cytosine methylase at HIV. Extracellular vesicles known as exosomes were loaded with anti-HIV-1 repressors. These exosomes suppressed HIV virus expression. Current research has mainly focused on the CD4+ T-cells even though HIV proviruses are present in other cell types. Overall, further research on an epigenetic approach toward HIV-infected host cells could result in cell-type-specific epigenetic drugs.

Adenovirus

The adeno-associated virus is a single-stranded DNA virus. An AAV vector is a recombinant variant of the wild-type AAV virus (rAAV). rAAV cannot replicate and only infects cells and delivers DNA to their nuclei. An AAV enables the process of bringing extraneous genetic material into neurons. Recombinant AAVs utilize vector technology. To go into more detail, rAAVs are episomal. This means they hang out outside and inside the nucleus because they are enclosed in a plasmid. They express whatever is encoded in them and do not impact the genome. The rAAV vectors have successfully transferred genes to various tissues in adult animals. They can be injected at any time during the lifetime of an animal. rAAVs have been used in mouse models to insert genes into the mature nervous systems of the mice and to study gene function in the CNS. Many mammalian species other than mice are resistant to being made transgenic. In wild-type animals, through rAAV vectors, you can introduce them into the injected area and have them express there for a year or two. This can be done to adult animals and even a subset of cells, and you do not need transgenics for it. Also, rAAV vectors over-express genes and knockdown gene expression, making rAAV vectors valuable tools for creating animal models of diseases through the delivery of genetic material.

Epigenetics Factors

The adeno-associated virus genome holds a significant amount of CpG sequences. CpG islands regulate gene expression and can be methylated. These sequences are capable of methylation in their terminal repeat sequences, which are retained in AAV-based vectors used in gene therapy. Studies have explored host cell methylation on wild-type AAV integration and recombinant AAV transgene expression in HeLa cells. It was determined that the methylation of target cells is significant in long-term transgene expression in AAV gene therapy as they can be altered to enhance site-specific AAV integration and therapeutic transgene expression. Histone modifications, like histone methylation, have a significant role in epigenetic regulation.

Specifically, episomal DNA is subject to epigenetic changes when associated with host histones. Researchers have also focused on epigenetic silencing of rAAVs through the protein NP220, a nuclear double-stranded DNA binding protein, and the Human Silencing Hub (HUSH) complex. HUSH regulates deposition of the epigenetic mark H3K9me3 and represses retroviruses, transposons, and genes to maintain vertebrate genomes. Epigenetic silencing is the process in which the expression of genes is regulated through DNA, RNA, or, in this case, histone protein modifications. It was determined that the AAV capsid serotype significantly influences NP220-mediated silencing of packaged genomes. This indicates that capsid-genomes can regulate the epigenetic silencing of rAAV genomes. Overall, epigenetics is helpful in studies utilizing AAVs and rAAVs as their status can enhance site-specific AAV integration, therapeutic transgene expression, and regulate silencing in rAAV genomes.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

SARS-CoV-2 is a RNA virus (COVID-19) discovered in Wuhan, China in December 2019. SARS-CoV originated from bats and was transmitted to humans in 2003-2004. It is a severe and contagious respiratory disease which enters the body through one's mouth, nose, or eyes and attacks, replicates in, and kills healthy cells. It greatly affects the healthy cells in the lungs since the coronavirus travels down the respiratory tract, as well as the heart, kidneys, brain, skin, and liver. There are numerous symptoms and side-effects associated with being infected with COVID-19. The World Health Organization stated that the COVID-19 pandemic was an international public health emergency. As of April 10, 2022, this virus has caused millions of deaths and hundreds of millions of cases worldwide.

Epigenetic Factors

SARS-CoV-2 is known to induce epigenetic alterations. Specific results of epigenetic alterations include antagonizing host antigen presentation, element of host defense, and activating interferon-response genes, gene is expressed in response to stimulation by interferon (glycoproteins that prevent viral replication in infected cells).

The understanding of viral chromatin modification in lytic viruses through epigenetic research have contributed to the investigation for COVID-19 treatments. For example, the polycomb repressive complex 2 (PRC2) could also be considered a target to fight COVID-19. Experiments targeting parts of the PRC2 complex have shown to play a role in modulating viral replication by inhibiting replication of viruses. Specifically, PCR2 inhibitors increase the activation of natural killer cells, so in regards to SARS-CoV-2, PCR2 inhibitors could aid in counteracting the viral repression of interferon stimulated genes. Moreover, the production of PRC2 inhibitors are currently being investigated to be used as a cancer treatment and could be eventually be repurposed to treat COVID-19.

Moreover, epigenetic modifications play an important role during viral replication and infection in COVID-19. The angiotensin-converting enzyme 2 (ACE2) receptor is used by SARS-CoV-2 to enter host cells. SARS-CoV-2 attached to the ACE2 receptor by using the SARS-CoV-2 spike proteins receptor-binding domain (RBD). Studies showed that the methylation of ACE2 could be regulated by autoimmune, neoplastic, metabolic diseases, and sexual factors. For example, a study showed that there was lower methylation of the 5 CpG dinucleotides in the ACE2 promoter in males than in females, which could lead researchers to associate abnormal methylation of the ACE2 promoter with essential hypertension. In regards to COVID-19, such evidence could provide evidence for the differences in susceptibility and severity between the sexes since approximately 60% of deaths from this virus are men.