Keywords
COVID-19 - epigenetics - methylation
Key Points
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Genetic and epigenetic profile play a key role during coronavirus disease 2019 (COVID-19)
infection.
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Epigenetic alterations on the host genome are related to COVID-19 susceptibility.
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Genetic and epigenetic alterations in ACE2, TMPRSS2, IFN-related genes, and FURIN genes were an important determinant of severe acute respiratory syndrome coronavirus
2 cell entry of host and severity of the disease.
Introduction
Coronaviruses (CoV) are a major family of pathogens that include severe acute respiratory
syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV)
strain.[1] SARS-CoV-2 is a member of β-genus coronaviruses containing a single-strand enveloped
RNA that is 29 Kb long. The similarity between SARS-CoV-2 and MERS-CoV was 50 and
80% with SARS-CoV.[2] SARS-CoV-2 infection caused coronavirus disease 2019 (COVID-19) in humans. The rapid
spread of SARS-CoV-2 highlights the importance of understanding its nature and biological
function. Studies showed that genetic and epigenetic modifications were important
during the regulation of host response.[2] Epigenetic modifications are posttranslational chemical changes that occur at the
level of histone proteins, RNA and DNA, and regulate gene expression without alterations
of nucleotide sequence.[2] According to the RNA sequencing studies, 41 RNA modifications sites on viral transcripts
were observed throughout the viral genome. These internal modifications contribute
to viral RNA stability and translation efficiency and can be used for the explanation
of escaping from host immune response.[2]
In this article, we discussed genetic and epigenetic alterations that play a role
during the SARS CoV-2 infection and show differences in tissue/cell-, age-, and sex-biased
patterns.[2]
Genetic Alterations and SARS-CoV-2 Infection
Genetic Alterations and SARS-CoV-2 Infection
The virus uses the angiotensin-converting enzyme 2 (ACE2) type I membrane receptor
to enter the host cell. ACE2 receptors were found on different tissues like arterial
and venous endothelial cells, alveolar cells, enterocytes of the small intestine,
and arterial smooth muscle cells in most organs.[2] While the virus enters the host cell, subgenomic RNAs were transcribed from the
genomic RNA that encodes the spike protein (S), an envelope protein (E), membrane
protein (M), and nucleocapsid protein (N).[2] This encoded protein was a functional receptor for the human coronaviruses SARS,
human coronavirus NL63 , and SARS-CoV-2.[3] Transmembrane serine protease 2 (TMPRSS2), cathepsin L (CTSL), and furin, paired
basic amino acid cleaving enzyme (FURIN) were responsible for cleaving of SARS-CoV
proteins.[2] The human ACE2 gene contains hot spots for virus binding and mutations occur near these hot spots
that were important to the host diversity of the virus.[2]
[4]
[5] Studies showed that N501 T mutation at the position significantly enhances the binding
capacity of SARSCoV-2 spike protein receptor-binding domain.[6] Up to date, more than 1,700 variants have been identified on the ACE2 gene, which is nonsense, missense, and intron variants in the 3–UTR of the gene.
The important point of ACE2 variants may affect intermolecular interaction with the SARS-CoV-2 S protein like
interaction-booster between ACE2 and S1 or interaction-inhibitor between ACE2 and
S1.[3]
The TMPRSS2 gene encoded a serine protease family member and is critical for the entry of viruses.
The TMPRSS2 gene encodes a serine protease family member and is critical for the entry
of viruses. Because this protease proteolytically cleaved and activated viral envelope
glycoproteins during the infection. TMPRSS2 polymorphisms were associated with an increased risk of severe COVID-19.[3] There is no published epigenetic study that shows the interaction TMPRSS gene and COVID-19. Methylation studies of the TMPRSS gene were based on prostate
cancer patients.[3]
The FURIN gene was located on chromosome 15q26.1 and plays an important role during the process
of protein trafficking of the secretory pathway. Papa et al demonstrated that SARS-CoV-2
replication promoted by cleavage of furin.[7]
ADAM-17 gene plays a role during viral infection. The virus uses the angiotensin-converting
enzyme 2 (ACE2) type I membrane receptor to enter the host cell.[7]
An increased number of studies demonstrated that variations in TMPRSS2, FURIN, and ADAM-17 may also have a role in the SARS-CoV-2 infectivity, disease severity, the outcome
of the disease, and during the personalization of treatment planning of affected patients.
Overall, an increased number of molecular profile studies will help us to better understand
the heterogeneity of infection and disease and help us design personalized medicine
tools on COVID-19 infection.
Interaction between Epigenetic Modifications and ACE2
Interaction between Epigenetic Modifications and ACE2
The ACE2 gene is located on chromosome Xp22.2. The X-chromosome is one of the important chromosomes
in the female that is epigenetically regulated. X-chromosome inactivation is an epigenetics
process and regulated by X inactivation center). Because of random X inactivation,
females are mosaic but males are hemizygous.[2]
[8] X inactivation is not complete and nearly 25% of X-chromosomal genes are escaped
from X inactivation. ACE2 was one of the genes that escape from X inactivation.[9] Epigenetic regulation of the ACE2 gene was one of the mechanisms related to COVID-19 infection. Studies showed gender
and age-dependent DNA methylation of the ACE2 gene in airway epithelial cells.[10] DNA methylation level was decreased during aging and led to differential methylation
patterns of several genes including aging and immune response-related genes. Therefore,
DNA methylation is one of the main mechanisms that affects the prognosis of patients
affected by SARS-CoV-2.[2] Under the cell energy stress, NAD-dependent histone deacetylase Sirtuin 1 (SIRT1)
regulates ACE2. Also, upregulation was identified in the lung of patients with severe
COVID-19.[4] In this point of view, we can suggest that increased expression level of ACE2 was
correlated with severe COVID-19 infection.
Corley et al analyzed genome-wide methylation profiles of nine terminally ill COVID-19
patients' peripheral blood. They determined differentiated DNA methylation signature
of severe COVID-19 that showed hypermethylation of IFN-related genes and hypomethylation
of inflammatory genes that includes a regulatory region of the NLRP3 inflammasome and antiviral MX1 genes. The methylation pattern of MX1 was associated with plasma SARS-CoV-2 viral load and platelet count.[11] Inactivation of the IFN gene and increased level of chemokine/cytokine gene expression patterns was observed
during the SARS-CoV-2 infection. Therefore, studies concluded that SARS-CoV-2 suppressed
the innate antiviral response of the host.[1] Alterations of IFN-stimulated genes, antigen presentation genes, and proinflammatory
genes were identified on RNA-Seq studies from patients infected with SARS-CoV-2.[12]
[13]
Corley et al demonstrated epigenetic alterations were changed depending on the cell
type. According to the study, enhancer regions of primary neutrophils from peripheral
blood were hypomethylated, but on the other side transcription start site regions
of primary T cells, primary T helper cells, and primary T regulatory were hypermethylated.[11] Based on Corley's study, aberrant DNA methylation pattern at cell-type-specific
regulatory regions of the host genome was observed on severe COVID-19.
RNA type viruses, like SARS-CoV-2, may also be sensitive to RNA modifications, including
N6-methyladenosine (m6A) and N6,2′-Odimethyladenosine (m6Am) modifications (m6A/m).
Identification of the importance of these RNA modifications will help us to explain
the viral life cycle, host response, and severity of COVID-19. These studies showed
the importance of further studies in the field of epigenetics will help us to understand
the severity of the infection and host defense of SARS-CoV-2. A full understanding
of the epigenetic background of COVID-19 will promote docking studies to discover
possible targets on SARS-CoV-2 as an epigenetic-targeted agent of COVID-19. This will
bring up the combination therapy of epigenetic and antiviral drugs for viral infection.
Conclusion
Epigenetic changes regulate many normal and disease-related processes including cancer,
imprinting disorders, obesity, and viral infections. Epigenetic modifications can
be occurred posttranslationally in different ways that alter interactions with DNA
and nuclear proteins and lead to changes in chromatin architecture and alterations
in gene expression.
In general, hypomethylation of inflammatory genes, hypermethylation of IFN-related
genes, and perturbations to the epigenetic clock and epigenetic inferred mortality
risk were the major epigenetic alterations of severe COVID-19 cases. Studies showed
that SARS-CoV-2 alters host epigenome in various ways. Genetic and epigenetic alterations
in ACE2, TMPRSS2, IFN-related genes, and FURIN genes were an important determinant of SARS-CoV-2 cell entry of host and severity
of the disease. In this point of view, reversible nature of epigenetic modifications
holds promise for future studies that may block the infection activity of the virus.
Our study sheds light on future studies that should focus on the role of these epigenetic
modifications in infection outcome, the severity of the disease, and entrance of host
cell.
