An immune epigenetic insight to COVID-19 infection

Cellular and epigenetic perspective of protein stability and its implications in the biological system

Protein stability is a fundamental prerequisite in both experimental and therapeutic applications. Current advancements in high throughput experimental techniques and functional ontology approaches have elucidated that impairment in the structure and stability of proteins is intricately associated with the cause and cure of several diseases. Therefore, it is paramount to deeply understand the physical and molecular confounding factors governing the stability of proteins. In this review article, we comprehensively investigated the evolution of protein stability, examining its emergence over time, its relationship with organizational aspects and the experimental methods used to understand it. Furthermore, we have also emphasized the role of Epigenetics and its interplay with post-translational modifications (PTMs) in regulating the stability of proteins.

Epigenetic repression of antiviral genes by SARS-CoV-2 NSP1

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evades the innate immune machinery through multiple viral proteins, including nonstructural protein 1 (NSP1). While NSP1 is known to suppress translation of host mRNAs, the mechanisms underlying its immune evasion properties remain elusive. By integrating RNA-seq, ribosome footprinting, and ChIP-seq in A549 cells we found that NSP1 predominantly represses transcription of immune-related genes by favoring Histone 3 Lysine 9 dimethylation (H3K9me2). G9a/GLP H3K9 methyltransferase inhibitor UNC0638 restored expression of antiviral genes and restricted SARS-CoV-2 replication. Our multi-omics study unravels an epigenetic mechanism underlying host immune evasion by SARS-CoV-2 NSP1. Elucidating the factors involved in this phenomenon, may have implications for understanding and treating viral infections and other immunomodulatory diseases.

Epigenetic perspectives associated with COVID-19 infection and related cytokine storm: an updated review

PURPOSE

The COVID-19 pandemic caused by the novel Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has put the world in a medical crisis for the past three years; nearly 6.3 million lives have been diminished due to the virus outbreak. This review aims to update the recent findings on COVID-19 infections from an epigenetic scenario and develop future perspectives of epi-drugs to treat the disease.

METHODS

Original research articles and review studies related to COVID-19 were searched and analyzed from the Google Scholar/PubMed/Medline databases mainly between 2019 and 2022 to brief the recent work.

RESULTS

Numerous in-depth studies of the mechanisms used by SARS-CoV-2 have been going on to minimize the consequences of the viral outburst. Angiotensin-Converting Enzyme 2 receptors and Transmembrane serine protease 2 facilitate viral entry to the host cells. Upon internalization, it uses the host machinery to replicate viral copies and alter the downstream regulation of the normal cells, causing infection-related morbidities and mortalities. In addition, several epigenetic regulations such as DNA methylation, acetylation, histone modifications, microRNA, and other factors (age, sex, etc.) are responsible for the regulations of viral entry, its immune evasion, and cytokine responses also play a major modulatory role in COVID-19 severity, which has been discussed in detail in this review.

CONCLUSION

Findings of epigenetic regulation of viral pathogenicity open a new window for epi-drugs as a possible therapeutical approach against COVID-19.

Modulation of various host cellular machinery during COVID-19 infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) emerged in December 2019, causing a range of respiratory infections from mild to severe. This resulted in the ongoing global COVID-19 pandemic, which has had a significant impact on public health. The World Health Organization declared COVID-19 as a global pandemic in March 2020. Viruses are intracellular pathogens that rely on the host's machinery to establish a successful infection. They exploit the gene expression machinery of host cells to facilitate their own replication. Gaining a better understanding of gene expression modulation in SARS-CoV2 is crucial for designing and developing effective antiviral strategies. Efforts are currently underway to understand the molecular-level interaction between the host and the pathogen. In this review, we describe how SARS-CoV2 infection modulates gene expression by interfering with cellular processes, including transcription, post-transcription, translation, post-translation, epigenetic modifications as well as processing and degradation pathways. Additionally, we emphasise the therapeutic implications of these findings in the development of new therapies to treat SARS-CoV2 infection.

Virus hijacking of host epigenetic machinery to impair immune response

Epigenetic modifications, such as DNA hypermethylation, histone acetylation/methylation, or nucleosome positioning, result in differential gene expression. These modifications can have an impact on various pathways, including host antiviral immune responses. In this review, we summarize the current understanding of epigenetic modifications induced by viruses to counteract host antiviral immune responses, which are crucial for establishing and maintaining infection of viruses. Finally, we provide insights into the potential use of epigenetic modulators in combating viral infections and virus-induced diseases.

Investigating the association of measures of epigenetic age with COVID-19 severity: evidence from secondary analyses of open access data

BACKGROUND

Epigenetic modifications may contribute to inter-individual variation that is unexplainable by presently known risk factors for COVID-19 severity (e.g., age, excess weight, or other health conditions). Estimates of youth capital (YC) reflect the difference between an individual's epigenetic - or biological - age and chronological age, and may quantify abnormal aging due to lifestyle or other environmental exposures, providing insights that could inform risk-stratification for severe COVID-19 outcomes. This study aims to thereby a) assess the association between YC and epigenetic signatures of lifestyle exposures with COVID-19 severity, and b) to assess whether the inclusion of these signatures in addition to a signature of COVID-19 severity (EPICOVID) improved the prediction of COVID-19 severity.

METHODS

This study uses data from two publicly-available studies accessed via the Gene Expression Omnibus (GEO) platform (accession references: GSE168739 and GSE174818). The GSE168739 is a retrospective, cross-sectional study of 407 individuals with confirmed COVID-19 across 14 hospitals in Spain, while the GSE174818 sample is a single-center observational study of individuals admitted to the hospital for COVID-19 symptoms (n = 102). YC was estimated using the (a) Gonseth-Nusslé, (b) Horvath, (c) Hannum, and (d) PhenoAge estimates of epigenetic age. Study-specific definitions of COVID-19 severity were used, including hospitalization status (yes/no) (GSE168739) or vital status at the end of follow-up (alive/dead) (GSE174818). Logistic regression models were used to assess the association between YC, lifestyle exposures, and COVID-19 severity.

RESULTS

Higher YC as estimated using the Gonseth-Nusslé, Hannum and PhenoAge measures was associated with reduced odds of severe symptoms (OR = 0.95, 95% CI = 0.91-1.00; OR = 0.81, 95% CI = 0.75 - 0.86; and OR = 0.85, 95% CI = 0.81-0.88, respectively) (adjusting for chronological age and sex). In contrast, a one-unit increase in the epigenetic signature for alcohol consumption was associated with 13% increased odds of severe symptoms (OR = 1.13, 95% CI = 1.05-1.23). Compared to the model including only age, sex and the EPICOVID signature, the additional inclusion of PhenoAge and the epigenetic signature for alcohol consumption improved the prediction of COVID-19 severity (AUC = 0.94, 95% CI = 0.91-0.96 versus AUC = 0.95, 95% CI = 0.93-0.97; p = 0.01). In the GSE174818 sample, only PhenoAge was associated with COVID-related mortality (OR = 0.93, 95% CI = 0.87-1.00) (adjusting for age, sex, BMI and Charlson comorbidity index).

CONCLUSIONS

Epigenetic age is a potentially useful tool in primary prevention, particularly as an incentive towards lifestyle changes that target reducing the risk of severe COVID-19 symptoms. However, additional research is needed to establish potential causal pathways and the directionality of this effect.

Involvement of epigenetics in affecting host immunity during SARS-CoV-2 infection

Coronavirus disease 19 (COVID-19) is caused by a highly contagious RNA virus Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2), originated in December 2019 in Wuhan, China. Since then, it has become a global public health concern and leads the disease table with the highest mortality rate, highlighting the necessity for a thorough understanding of its biological properties. The intricate interaction between the virus and the host immune system gives rise to diverse implications of COVID-19. RNA viruses are known to hijack the host epigenetic mechanisms of immune cells to regulate antiviral defence. Epigenetics involves processes that alter gene expression without changing the DNA sequence, leading to heritable phenotypic changes. The epigenetic landscape consists of reversible modifications like chromatin remodelling, DNA/RNA methylation, and histone methylation/acetylation that regulates gene expression. The epigenetic machinery contributes to many aspects of SARS-CoV-2 pathogenesis, like global DNA methylation and receptor angiotensin-converting enzyme 2 (ACE2) methylation determines the viral entry inside the host, viral replication, and infection efficiency. Further, it is also reported to epigenetically regulate the expression of different host cytokines affecting antiviral response. The viral proteins of SARS-CoV-2 interact with various host epigenetic enzymes like histone deacetylases (HDACs) and bromodomain-containing proteins to antagonize cellular signalling. The central role of epigenetic factors in SARS-CoV-2 pathogenesis is now exploited as promising biomarkers and therapeutic targets against COVID-19. This review article highlights the ability of SARS-CoV-2 in regulating the host epigenetic landscape during infection leading to immune evasion. It also discusses the ongoing therapeutic approaches to curtail and control the viral outbreak.

Bioinformatics analysis based on high-throughput sequencing data to identify hub genes related to different clinical types of COVID-19

This article aims to explore hub genes related to different clinical types of cases with COVID-19 and predict the therapeutic drugs related to severe cases. The expression profile of GSE166424 was divided into four data sets according to different clinical types of COVID-19 and then calculated the differential expression genes (DEGs). The specific genes of four clinical types of COVID-19 were obtained by Venn diagram and conducted enrichment analysis, protein-protein interaction (PPI) networks analysis, screening hub genes, and ROC curve analysis. The hub genes related to severe cases were verified in GSE171110, their RNA-specific expression tissues were obtained from the HPA database, and potential therapeutic drugs were predicted through the DGIdb database. There were 536, 266, 944, and 506 specific genes related to asymptomatic infections, mild, moderate, and severe cases, respectively. The hub genes of severe specific genes were AURKB, BRCA1, BUB1, CCNB1, CCNB2, CDC20, CDC6, KIF11, TOP2A, UBE2C, and RPL11, and also differentially expressed in GSE171110 (P < 0.05), and their AUC values were greater than 0.955. The RNA tissue specificity of AURKB, CDC6, KIF11, UBE2C, CCNB2, CDC20, TOP2A, BUB1, and CCNB1 specifically enhanced on lymphoid tissue; CCNB2, CDC20, TOP2A, and BUB1 specifically expressed on the testis. Finally, 55 drugs related to severe COVID-19 were obtained from the DGIdb database. Summary, AURKB, BRCA1, BUB1, CCNB1, CCNB2, CDC20, CDC6, KIF11, TOP2A, UBE2C, and RPL11 may be potential diagnostic biomarkers for severe COVID-19, which may affect immune and male reproductive systems. 55 drugs may be potential therapeutic drugs for severe COVID-19.

Altered expression of DNA methyltransferases and methylation status of the TLR4 and TNF-α promoters in COVID-19

Epigenetic modifications play a significant role in the host's immune response to viral infection. Two epigenetic events, DNA methylation and histone acetylation, are crucial for modifying the chromatin architecture and the location of regulatory elements such as promoters and enhancers. In this case-control study, we evaluated the expression of genes involved in epigenetic machinery (DNMT1, DNMT3A, DNMT3B, HDAC2, and HDAC3) and the degree of methylation of promoters of immune response genes (IFITM1/2/3, TLR3/4, TNF-α, NF-κB, and MYD88) as well as global methylation (LINE-1 and global 5-mC) in blood samples from 120 COVID-19 patients (30 mild, 30 moderate, 30 severe, and 30 critical) and 30 healthy subjects without COVID-19. In contrast to previous reports, DNMT3A and DNMT3B expression was found to be significantly downregulated in COVID-19 cases, whereas DNMT1, HDAC2, and HDAC3 expression did not change. DNMT1 and DNMT3A were negatively correlated with COVID-19 severity. Critically ill patients had lower HDAC3 expression levels. TLR4 and TNF-α had increased promoter methylation, whereas IFITM1/2/3, TLR3, NF-κB, MYD88, and LINE-1 did not differ between cases and controls. Methylation of the TNF-α promoter increased as disease severity increased. Significantly less methylation of the TLR3 promoter was observed in patients with a positive outcome (recovery). We also found a correlation between the expression of DNMT3B and the methylation level of the TLR4 promoter. In milder cases, the global 5-mC levels were lower than that in more severe cases. Our findings suggest the exclusion of DNMTs inhibitors previously recommended for COVID-19 treatment and the need for additional research in this area.

Epigenetic Targets and Pathways Linked to SARS-CoV-2 Infection and Pathology

The scale at which the SARS-CoV-2/COVID-19 pandemic has spread remains enormous. Provided the genetic makeup of the virus and humans is readily available, the quest for knowing the mechanism and epidemiology continues to prevail across the entire scientific community. Several aspects, including immunology, molecular biology, and host-pathogen interaction, are continuously being dug into for preparing the human race for future pandemics. The exact reasons for vast differences in symptoms, pathophysiological implications of COVID-infections, and mortality differences remain elusive. Hence, researchers are also looking beyond traditional genomics, proteomics, and transcriptomics approach, especially entrusting the environmental regulation of the genetic landscape of COVID-human interactions. In line with these questions lies a critical process called epigenetics. The epigenetic perturbations in both host and parasites are a matter of great interest to unravel the disparities in COVID-19 mortalities and pathology. This review provides a deeper insight into current research on the epigenetic landscape of SARS-CoV-2 infection in humans and potential targets for augmenting the ongoing investigation. It also explores the potential targets, pathways, and networks associated with the epigenetic regulation of processes involved in SARS-CoV-2 pathology.

Protein post-translational modification in SARS-CoV-2 and host interaction

SARS-CoV-2 can cause lung diseases, such as pneumonia and acute respiratory distress syndrome, and multi-system dysfunction. Post-translational modifications (PTMs) related to SARS-CoV-2 are conservative and pathogenic, and the common PTMs are glycosylation, phosphorylation, and acylation. The glycosylation of SARS-CoV-2 mainly occurs on spike (S) protein, which mediates the entry of the virus into cells through interaction with angiotensin-converting enzyme 2. SARS-CoV-2 utilizes glycans to cover its epitopes and evade the immune response through glycosylation of S protein. Phosphorylation of SARS-CoV-2 nucleocapsid (N) protein improves its selective binding to viral RNA and promotes viral replication and transcription, thereby increasing the load of the virus in the host. Succinylated N and membrane(M) proteins of SARS-CoV-2 synergistically affect virus particle assembly. N protein regulates its affinity for other proteins and the viral genome through acetylation. The acetylated envelope (E) protein of SARS-CoV-2 interacts with bromodomain-containing protein 2/4 to influence the host immune response. Both palmitoylation and myristoylation sites on S protein can affect the virus infectivity. Papain-like protease is a domain of NSP3 that dysregulates host inflammation by deubiquitination and impinges host IFN-I antiviral immune responses by deISGylation. Ubiquitination of ORF7a inhibits host IFN-α signaling by blocking STAT2 phosphorylation. The methylation of N protein can inhibit the formation of host stress granules and promote the binding of N protein to viral RNA, thereby promoting the production of virus particles. NSP3 macrodomain can reverse the ADP-ribosylation of host proteins, and inhibit the cascade immune response with IFN as the core, thereby promoting the intracellular replication of SARS-CoV-2. On the whole, PTMs have fundamental roles in virus entry, replication, particle assembly, and host immune response. Mutations in various SARS-CoV-2 variants, which lead to changes in PTMs at corresponding sites, cause different biological effects. In this paper, we mainly reviewed the effects of PTMs on SARS-CoV-2 and host cells, whose application is to inform the strategies for inhibiting viral infection and facilitating antiviral treatment and vaccine development for COVID-19.

Thuja occidentalis: An Unexplored Phytomedicine with Therapeutic Applications

BACKGROUND

The recent outbreak of SARS-CoV-2 has received global attention. Due to a lack of recommended treatment regimens, the world faced various limitations resulting in improper management of the disease. Phytomedicines have played a prominent role in the prevention of various epidemics and pandemics in the past.

OBJECTIVE

Here, we attempt to focus on safe and feasible use of Thuja occidentalis to manage and alleviate the panic of viral respiratory infections, including COVID-19, by strengthening an individual's immunity. The relevant information was collected from the web-based databases PubMed, Google Scholar, and MEDLINE, as well as other internet sources to review the applicability of T. occidentalis as a phytomedicine in managing respiratory infections and strengthening immunity.

CONCLUSION

As important phytomedicine, and antipsychotic, T. occidentalis possesses a plethora of immunological properties that can be used effectively in the management of viral respiratory infections and has the potential to prevent further progression of the disease. Importantly, this could be only a part of the approach for treatment during the current outbreak that should be considered along with other measures.

[Molecular basis of biological activity of polysaccharides in COVID-19 associated conditions]

The review considers the main molecular biological features of the COVID-19 causative agent, the SARS-CoV-2 virus: life cycle, viral cell penetration strategies, interactions of viral proteins with human proteins, cytopathic effects. We also analyze pathological conditions that occur both during the course of the COVID-19 disease and after virus elimination. A brief review of the biological activities of polysaccharides isolated from various sources is given, and possible molecular biological mechanisms of these activities are considered. Data analysis shows that polysaccharides are a class of biological molecules with wide potential for use in the treatment of both acute conditions in COVID-19 and post-COVID syndrome.

In silico Analysis of ACE2 Receptor to Find Potential Herbal Drugs in COVID-19 Associated Neurological Dysfunctions

COVID-19 mainly causes the collapse of the pulmonary system thereby causing a dearth of oxygen in the human body. Patients infected with this viral disease have been reported to experience various signs and symptoms associated with brain dysfunction, from the feeling of vagueness to loss of smell and taste to severe strokes. These neurological problems have been reported by younger COVID-19 infected patients mainly in their thirties and forties. Various researchers from around the globe have discerned numerous other brain dysfunctions, such as headache, dizziness, numbness, major depressive disorder, anosmia, encephalitis, febrile seizures, and Guillain-Barre syndrome. The involvement of the CNS by this viral infection has been predicted to be for a longer period of time, even if the patient recovers from COVID-19. The neuronal cell damage caused by COVID-19 is a potent factor responsible for cognitive, behavioral, and psychological problems among its sufferers. The hypoxic conditions can also trigger the formation of beta-amyloid plaques and tau-tangles and thus the virus can even induce Alzheimer’s in patients in the near future. The virus affects the brain directly, thereby causing encephalitis. This pandemic has also been shown to have a negative psychological toll on people. This research aims to highlight the brain dysfunction associated with the ACE2 receptor that is known to be a crucial player in the COVID-19 pandemic using genetic networking approaches. Furthermore, we have identified herbal drug candidates that bind to the ACE2 receptor in order to identify potential treatments for the neurological manifestations of COVID-19.

Leveraging epigenetics to enhance the efficacy of cancer-testis antigen: a potential candidate for immunotherapy

Ovarian cancer is the most lethal gynecological malignancy in women. The phenotype is characterized by delayed diagnosis, recurrence and drug resistance. Inherent immunogenicity potential, oncogenic function and expression of cancer-testis/germline antigen (CTA) in ovarian cancer render them a potential candidate for immunotherapy. Revolutionary clinical findings indicate that tumor antigen-mediated T-cell and dendritic cell-based immunotherapeutic approaches provide an excellent strategy for targeting tumors. Currently, dendritic cell vaccination for the treatment of B-cell lymphoma and CTA-based T-cell receptor transduced T-cell therapy involving MAGE-A4 and NY-ESO-1 are well documented and shown to be effective. This review highlighted the mechanical aspects of epigenetic drugs that can elicit a CTA-based humoral and cellular immune response and implicate T-cell and dendritic cell-based immunotherapeutic approaches.

Epigenetic rewiring of pathways related to odour perception in immune cells exposed to SARS-CoV-2 in vivo and in vitro

A majority of SARS-CoV-2 recoverees develop only mild-to-moderate symptoms, while some remain completely asymptomatic. Although viruses, including SARS-CoV-2, may evade host immune responses by epigenetic mechanisms including DNA methylation, little is known about whether these modifications are important in defence against and healthy recovery from COVID-19 in the host. To this end, epigenome-wide DNA methylation patterns from COVID-19 convalescents were compared to uninfected controls from before and after the pandemic. Peripheral blood mononuclear cell (PBMC) DNA was extracted from uninfected controls, COVID-19 convalescents, and symptom-free individuals with SARS-CoV-2-specific T cell-responses, as well as from PBMCs stimulated in vitro with SARS-CoV-2. Subsequently, the Illumina MethylationEPIC 850K array was performed, and statistical/bioinformatic analyses comprised differential DNA methylation, pathway over-representation, and module identification analyses. Differential DNA methylation patterns distinguished COVID-19 convalescents from uninfected controls, with similar results in an experimental SARS-CoV-2 infection model. A SARS-CoV-2-induced module was identified in vivo, comprising 66 genes of which six (TP53, INS, HSPA4, SP1, ESR1, and FAS) were present in corresponding in vitro analyses. Over-representation analyses revealed involvement in Wnt, muscarinic acetylcholine receptor signalling, and gonadotropin-releasing hormone receptor pathways. Furthermore, numerous differentially methylated and network genes from both settings interacted with the SARS-CoV-2 interactome. Altered DNA methylation patterns of COVID-19 convalescents suggest recovery from mild-to-moderate SARS-CoV-2 infection leaves longstanding epigenetic traces. Both in vitro and in vivo exposure caused epigenetic modulation of pathways thataffect odour perception. Future studies should determine whether this reflects host-induced protective antiviral defense or targeted viral hijacking to evade host defence.

Insights into Cardiovascular Defects and Cardiac Epigenome in the Context of COVID-19

Although few in number, studies on epigenome of the heart of COVID-19 patients show that epigenetic signatures such as DNA methylation are significantly altered, leading to changes in expression of several genes. It contributes to pathogenic cardiac phenotypes of COVID-19, e.g., low heart rate, myocardial edema, and myofibrillar disarray. DNA methylation studies reveal changes which likely contribute to cardiac disease through unknown mechanisms. The incidence of severe COVID-19 disease, including hospitalization, requiring respiratory support, morbidity, and mortality, is disproportionately higher in individuals with co-morbidities. This poses unprecedented strains on the global healthcare system. While their underlying conditions make patients more susceptible to severe COVID-19 disease, strained healthcare systems, lack of adequate support, or sedentary lifestyles from ongoing lockdowns have proved detrimental to their underlying health conditions, thus pushing them to severe risk of congenital heart disease (CHD) itself. Prophylactic vaccines against COVID-19 have ushered new hope for CHD. A common connection between COVID-19 and CHD is SARS-CoV-2’s host receptor ACE2, because ACE2 regulates and protects organs, including the heart, in various ways. ACE2 is a common therapeutic target against cardiovascular disease and COVID-19 which damages organs. Hence, this review explores the above regarding CHDs, cardiovascular damage, and cardiac epigenetics, in COVID-19 patients.

HDAC inhibition as neuroprotection in COVID-19 infection

The SARS-CoV-2 virus is responsible of COVID-19 affecting millions of humans around the world. COVID-19 shows diverse clinical symptoms (fever, cough, fatigue, diarrhea, body aches, headaches, anosmia and hyposmia). Approximately 30% of the patients with COVID-19 showed neurological symptoms, these going from mild to severe manifestations including headache, dizziness, impaired consciousness, encephalopathy, anosmia, hypogeusia, hyposmia, psychology and psychiatry among others. The neurotropism of SARS-CoV-2 virus explains its neuroinvasion provoking neurological damage as acute demyelination, neuroinflammation etc. At molecular level, the COVID-19 patients had higher levels of cytokines and chemokines known as cytokines storms which disrupt the blood brain barrier allowing the entrance of monocytes and lymphocytes causing neuroinflammation, neurodegeneration and demyelination. In addition, ischemic, hemorrhagic strokes, seizures and encephalopathy have been observed due to the proinflammatory cytokines. In this sense, to avoid or decrease neurological damage due to SARS-CoV-2 infection, an early neuroprotective management should be adopted. Several approaches can be used; one of them includes the use of HDAC inhibitors (HDACi) due to their neuroprotective effects. Also, the HDACi down regulates the pro-inflammatory cytokines (IL-6 and TNF- decreasing the neurotoxicity. HDACi can also avoid and prevent the entrance of the virus into the Central nervous System (CNS) as well as decrease the virus replication by downregulating the virus receptors. Here we review the mechanisms that could explain how the SARS-CoV-2 virus could reach the CNS, induce the neurological damage and symptoms, as well as the possibility to use HDACi as neuroprotective therapy.

The unfavorable clinical outcome of COVID-19 in smokers is mediated by H3K4me3, H3K9me3 and H3K27me3 histone marks

Smoking could predispose individuals to a more severe COVID-19 by upregulating a particular gene known as mdig, which is mediated through a number of well-known histone modifications. Smoking might regulate the transcription-activating H3K4me3 mark, along with the transcription-repressing H3K9me3 and H3K27me3 marks, in a way to favor SARS-CoV-2 entry by enhancing the expression of ACE2, NRP1 and NRP2, AT1R, CTSD and CTSL, PGE2 receptors 2-4, SLC6A20 and IL-6, all of which interact either directly or indirectly with important receptors, facilitating viral entry in COVID-19.

Developmental Aspects of SARS-CoV-2, Potential Role of Exosomes and Their Impact on the Human Transcriptome

With over 4.8 million deaths within 2 years, time is of the essence in combating COVID-19. The infection now shows devastating impacts on the younger population, who were not previously predicted to be vulnerable, such as in the older population. COVID-19-related complications have been reported in neonates whose mothers were infected with SARS-CoV-2 during pregnancy, and in children who get infected. Hence, a deeper understanding of the pathophysiology of COVID-19 during various developmental stages and placental transmission is essential. Although a connection has not yet been established between exosomal trafficking and the placental transmission of COVID-19, reports indicate that SARS-CoV-2 components may be trafficked between cells through exosomes. As the infection spreads, the transcriptome of cells is drastically perturbed, e.g., through the severe upregulation of several immune-related genes. Consequently, a major outcome of COVID-19 is an elevated immune response and the detection of viral RNA transcripts in host tissue. In this direction, this review focuses on SARS-CoV-2 virology, its in utero transmission from infected pregnant mothers to fetuses, SARS-CoV-2 and exosomal cellular trafficking, transcriptomic impacts, and RNA-mediated therapeutics against COVID-19. Future research will establish stronger connections between the above processes to develop diagnostic and therapeutic solutions towards COVID-19 and similar viral outbreaks.

Alveolar Regeneration in COVID-19 Patients: A Network Perspective

A viral infection involves entry and replication of viral nucleic acid in a host organism, subsequently leading to biochemical and structural alterations in the host cell. In the case of SARS-CoV-2 viral infection, over-activation of the host immune system may lead to lung damage. Albeit the regeneration and fibrotic repair processes being the two protective host responses, prolonged injury may lead to excessive fibrosis, a pathological state that can result in lung collapse. In this review, we discuss regeneration and fibrosis processes in response to SARS-CoV-2 and provide our viewpoint on the triggering of alveolar regeneration in coronavirus disease 2019 (COVID-19) patients.

Analysis of the Active Components and Mechanism of Three Prescriptions in the Treatment of COVID-19 Via Network Pharmacology and Molecular Docking

Purpose: Prescriptions of Han-Shi-Yu-Fei (HSYF), Han-Shi-Zu-Fei (HSZF), and Yi-Du-Bi-Fei (YDBF) were effective in treating COVID-19. Based on network pharmacology and molecular docking, overlapping Traditional Chinese medicines (TCMs), their active components, and core targets were explored in this study. Methods: First, the overlapping TCMs and their active components were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) by evaluating Oral Bioactivity (OB) and Drug Likeness (DL). The overlapping targets of potential components and COVID-19 were collected by SwissTargetPrediction, Gene Cards, and Venn 2.1.0 databases. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were analyzed via DAVID6.8.1 database. Through comprehensive analysis of the “prescriptions-TCMs-components” (P-T-C), “components-targets-pathways” (C-T-P) and “protein–protein interaction” (PPI) networks constructed by Cytoscape 3.7.1 software, the active components and core targets were obtained. Finally, the binding energies of these components with ACE2 and SARS-CoV-2 3CL were analyzed by AutDockTools-1.5.6 and PyMOL software. Results: In all, five overlapping TCMs, 40 potential active components, and 47 candidate targets were obtained and analyzed in these prescriptions. There were 288 GO entries ( P < 0.05), including 211 biological process (BP), 40 cell composition (CC), and 37 molecular function (MF) entries. Most of the 105 KEGG pathways ( P < 0.05) were involved with viral infection and inflammation. Through “PPI” and “C-T-P” networks, the core targets (EGFR, PTGS2, CDK2, GSK3B, PIK3R1, and MAPK3) and active components (Q27134551, acanthoside B, neohesperidin, and irisolidone) with high degrees were obtained. Molecular docking results showed that the above-mentioned four components could inhibit the binding of ACE2 and SARS-COV-2 3CL to protect against COVID-19. Conclusion: In this study, the active components and core targets of three prescriptions in the treatment of COVID-19 were elaborated by network pharmacology and molecular docking, providing a reference for their applications.

Update Advances on C-Reactive Protein in COVID-19 and Other Viral Infections

Severe coronavirus disease 2019 (COVID-19) can manifest as a viral-induced hyperinflammation with multiorgan dysfunction. It has been documented that severe COVID-19 is associated with higher levels of inflammatory mediators than a mild disease, and tracking these markers may allow early identification or even prediction of disease progression. It is well known that C-reactive protein (CRP) is the acute-phase protein and the active regulator of host innate immunity, which is highly predictive of the need for mechanical ventilation and may guide escalation of treatment of COVID-19-related uncontrolled inflammation. There are numerous causes of an elevated CRP, including acute and chronic responses, and these can be infectious or non-infectious in etiology. CRP are normally lacking in viral infections, while adaptive immunity appears to be essential for COVID-19 virus clearance, and the macrophage activation syndrome may explain the high serum CRP contents and contribute to the disease progression. Nevertheless, for the assessment of host inflammatory status and identification of viral infection in other pathologies, such as bacterial sepsis, the acute-phase proteins, including CRP and procalcitonin, can provide more important information for guiding clinical diagnosis and antibiotic therapy. This review is aimed to highlight the current and most recent studies with regard to the clinical significance of CRP in severe COVID-19 and other viral associated illnesses, including update advances on the implication of CRP and its form specifically on the pathogenesis of these diseases. The progressive understanding in these areas may be translated into promising measures to prevent severe outcomes and mitigate appropriate treatment modalities in critical COVID-19 and other viral infections.

Do Transgenerational Epigenetic Inheritance and Immune System Development Share Common Epigenetic Processes?

Epigenetic modifications regulate gene expression for development, immune response, disease, and other processes. A major role of epigenetics is to control the dynamics of chromatin structure, i.e., the condensed packaging of DNA around histone proteins in eukaryotic nuclei. Key epigenetic factors include enzymes for histone modifications and DNA methylation, non-coding RNAs, and prions. Epigenetic modifications are heritable but during embryonic development, most parental epigenetic marks are erased and reset. Interestingly, some epigenetic modifications, that may be resulting from immune response to stimuli, can escape remodeling and transmit to subsequent generations who are not exposed to those stimuli. This phenomenon is called transgenerational epigenetic inheritance if the epigenetic phenotype persists beyond the third generation in female germlines and second generation in male germlines. Although its primary function is likely immune response for survival, its role in the development and functioning of the immune system is not extensively explored, despite studies reporting transgenerational inheritance of stress-induced epigenetic modifications resulting in immune disorders. Hence, this review draws from studies on transgenerational epigenetic inheritance, immune system development and function, high-throughput epigenetics tools to study those phenomena, and relevant clinical trials, to focus on their significance and deeper understanding for future research, therapeutic developments, and various applications.