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1.
Front Cell Infect Microbiol ; 12: 905757, 2022.
Article in English | MEDLINE | ID: covidwho-2198697

ABSTRACT

In early 2020, one of the most prevalent symptoms of SARS-CoV-2 infection was the loss of smell (anosmia), found in 60-70% of all cases. Anosmia used to occur early, concomitantly with other symptoms, and often persisted after recovery for an extended period, sometimes for months. In addition to smell disturbance, COVID-19 has also been associated with loss of taste (ageusia). The latest research suggests that SARS-CoV-2 could spread from the respiratory system to the brain through receptors in sustentacular cells localized to the olfactory epithelium. The virus invades human cells via the obligatory receptor, angiotensin-converting enzyme II (ACE2), and a priming protease, TMPRSS2, facilitating viral penetration. There is an abundant expression of both ACE2 and TMPRSS2 in sustentacular cells. In this study, we evaluated 102 COVID-19 hospitalized patients, of which 17.60% presented anosmia and 9.80% ageusia. ACE1, ACE2, and TMPRSS2 gene expression levels in nasopharyngeal tissue were obtained by RT-qPCR and measured using ΔCT analysis. ACE1 Alu287bp association was also evaluated. Logistic regression models were generated to estimate the effects of variables on ageusia and anosmia Association of ACE2 expression levels with ageusia. was observed (OR: 1.35; 95% CI: 1.098-1.775); however, no association was observed between TMPRSS2 and ACE1 expression levels and ageusia. No association was observed among the three genes and anosmia, and the Alu287bp polymorphism was not associated with any of the outcomes. Lastly, we discuss whetherthere is a bridge linking these initial symptoms, including molecular factors, to long-term COVID-19 health consequences such as cognitive dysfunctions.


Subject(s)
Ageusia , Angiotensin-Converting Enzyme 2/genetics , COVID-19 , Olfaction Disorders , Ageusia/etiology , Anosmia , COVID-19/genetics , Cognition , Gene Expression , Humans , Olfaction Disorders/genetics , Receptors, Angiotensin , SARS-CoV-2
2.
Sci Rep ; 12(1): 20167, 2022 Nov 23.
Article in English | MEDLINE | ID: covidwho-2133629

ABSTRACT

To create a scientific resource of expression quantitative trail loci (eQTL), we conducted a genome-wide association study (GWAS) using genotypes obtained from whole genome sequencing (WGS) of DNA and gene expression levels from RNA sequencing (RNA-seq) of whole blood in 2622 participants in Framingham Heart Study. We identified 6,778,286 cis-eQTL variant-gene transcript (eGene) pairs at p < 5 × 10-8 (2,855,111 unique cis-eQTL variants and 15,982 unique eGenes) and 1,469,754 trans-eQTL variant-eGene pairs at p < 1e-12 (526,056 unique trans-eQTL variants and 7233 unique eGenes). In addition, 442,379 cis-eQTL variants were associated with expression of 1518 long non-protein coding RNAs (lncRNAs). Gene Ontology (GO) analyses revealed that the top GO terms for cis-eGenes are enriched for immune functions (FDR < 0.05). The cis-eQTL variants are enriched for SNPs reported to be associated with 815 traits in prior GWAS, including cardiovascular disease risk factors. As proof of concept, we used this eQTL resource in conjunction with genetic variants from public GWAS databases in causal inference testing (e.g., COVID-19 severity). After Bonferroni correction, Mendelian randomization analyses identified putative causal associations of 60 eGenes with systolic blood pressure, 13 genes with coronary artery disease, and seven genes with COVID-19 severity. This study created a comprehensive eQTL resource via BioData Catalyst that will be made available to the scientific community. This will advance understanding of the genetic architecture of gene expression underlying a wide range of diseases.


Subject(s)
Genetic Predisposition to Disease , Genome-Wide Association Study , Quantitative Trait Loci , Humans , DNA , Gene Expression , Quantitative Trait Loci/genetics , Sequence Analysis, RNA
3.
J Neuroinflammation ; 19(1): 267, 2022 Nov 04.
Article in English | MEDLINE | ID: covidwho-2108803

ABSTRACT

BACKGROUND: Triggering receptor expressed on myeloid cells 2 (Trem2) plays a protective role in neurodegenerative diseases. By contrast, Trem2 functions can exacerbate tissue damage during respiratory viral or liver infections. We, therefore, investigated the role of Trem2 in a viral encephalomyelitis model associated with prominent Th1 mediated antiviral immunity leading to demyelination. METHODS: Wild-type (WT) and Trem2 deficient (Trem2-/-) mice were infected with a sublethal glia tropic murine coronavirus (MHV-JHM) intracranially. Disease progression and survival were monitored daily. Leukocyte accumulation and pathological features including demyelination and axonal damage in spinal cords (SC) were determined by flow cytometry and tissue section immunofluorescence analysis. Expression of select inflammatory cytokines and chemokines was measured by RT-PCR and global myeloid cell gene expression in SC-derived microglia and infiltrated bone-marrow-derived macrophages (BMDM) were determined using the Nanostring nCounter platform. RESULTS: BMDM recruited to SCs in response to infection highly upregulated Trem2 mRNA compared to microglia coincident with viral control. Trem2 deficiency did not alter disease onset or severity, but impaired clinical recovery after onset of demyelination. Disease progression in Trem2-/- mice could not be attributed to altered virus control or an elevated proinflammatory response. A prominent difference was increased degenerated myelin not associated with the myeloid cell markers IBA1 and/or CD68. Gene expression profiles of SC-derived microglia and BMDM further revealed that Trem2 deficiency resulted in impaired upregulation of phagocytosis associated genes Lpl and Cd36 in microglia, but a more complex pattern in BMDM. CONCLUSIONS: Trem2 deficiency during viral-induced demyelination dysregulates expression of other select genes regulating phagocytic pathways and lipid metabolism, with distinct effects on microglia and BMDM. The ultimate failure to remove damaged myelin is reminiscent of toxin or autoimmune cell-induced demyelination models and supports that Trem2 function is regulated by sensing tissue damage including a dysregulated lipid environment in very distinct inflammatory environments.


Subject(s)
Brain , Demyelinating Diseases , Animals , Mice , Brain/metabolism , Phagocytosis/genetics , Microglia/metabolism , Demyelinating Diseases/chemically induced , Disease Progression , Gene Expression , Membrane Glycoproteins/genetics , Membrane Glycoproteins/metabolism , Receptors, Immunologic/genetics , Receptors, Immunologic/metabolism
4.
Sci Rep ; 12(1): 18710, 2022 Nov 04.
Article in English | MEDLINE | ID: covidwho-2106460

ABSTRACT

The purpose of this study is to manually and semi-automatically curate a database and develop an R package that will act as a comprehensive resource to understand how biological processes are dysregulated due to interactions with environmental factors. The initial database search run on the Gene Expression Omnibus and the Molecular Signature Database retrieved a total of 90,018 articles. After title and abstract screening against pre-set criteria, a total of 237 datasets were selected and 522 gene modules were manually annotated. We then curated a database containing four environmental factors, cigarette smoking, diet, infections and toxic chemicals, along with a total of 25,789 genes that had an association with one or more of gene modules. The database and statistical analysis package was then tested with the differentially expressed genes obtained from the published literature related to type 1 diabetes, rheumatoid arthritis, small cell lung cancer, COVID-19, cobalt exposure and smoking. On testing, we uncovered statistically enriched biological processes, which revealed pathways associated with environmental factors and the genes. The curated database and enrichment tool are available as R packages at https://github.com/AhmedMehdiLab/E.PATH and https://github.com/AhmedMehdiLab/E.PAGE respectively.


Subject(s)
COVID-19 , Gene Expression Profiling , Humans , Gene Regulatory Networks , Databases, Factual , Gene Expression
5.
PLoS Pathog ; 18(9): e1010867, 2022 09.
Article in English | MEDLINE | ID: covidwho-2054394

ABSTRACT

How well mouse models recapitulate the transcriptional profiles seen in humans remains debatable, with both conservation and diversity identified in various settings. Herein we use RNA-Seq data and bioinformatics approaches to analyze the transcriptional responses in SARS-CoV-2 infected lungs, comparing 4 human studies with the widely used K18-hACE2 mouse model, a model where hACE2 is expressed from the mouse ACE2 promoter, and a model that uses a mouse adapted virus and wild-type mice. Overlap of single copy orthologue differentially expressed genes (scoDEGs) between human and mouse studies was generally poor (≈15-35%). Rather than being associated with batch, sample treatment, viral load, lung damage or mouse model, the poor overlaps were primarily due to scoDEG expression differences between species. Importantly, analyses of immune signatures and inflammatory pathways illustrated highly significant concordances between species. As immunity and immunopathology are the focus of most studies, these mouse models can thus be viewed as representative and relevant models of COVID-19.


Subject(s)
COVID-19 , Angiotensin-Converting Enzyme 2/genetics , Animals , COVID-19/genetics , Disease Models, Animal , Gene Expression , Humans , Lung , Mice , Mice, Transgenic , Peptidyl-Dipeptidase A/metabolism , SARS-CoV-2/genetics
6.
Methods Mol Biol ; 2550: 29-32, 2022.
Article in English | MEDLINE | ID: covidwho-2047963

ABSTRACT

Melatonin synthesis by extrapineal sources adjusts physiological and pathophysiological processes in several types of cells and tissues. As measuring locally produced melatonin in fresh tissues might be a challenge due to limited material availability, we created a simple predictive model, the MEL-Index, which infers the content of tissue melatonin using gene expression data. The MEL-Index can be a powerful tool to study the role of melatonin in different contexts. Applying the MEL-Index method to RNA-seq datasets, we have shed light into the clinical relevance of melatonin as a modulator tumor progression and lung infection due to COVID-19. The MEL-Index combines the z-normalized expressions of ASMT (Acetylserotonin O-Methyltransferase), last enzyme of the biosynthetic pathway, and CYP1B1 (cytochrome P450 family enzyme), which encodes the enzyme that metabolizes melatonin in extrahepatic tissues. In this chapter, we describe the steps for calculating the MEL-Index.


Subject(s)
COVID-19 , Melatonin , Acetylserotonin O-Methyltransferase/genetics , Acetylserotonin O-Methyltransferase/metabolism , COVID-19/genetics , Cytochrome P-450 Enzyme System/genetics , Gene Expression , Humans , Melatonin/metabolism
7.
Cells ; 11(19)2022 Sep 21.
Article in English | MEDLINE | ID: covidwho-2043596

ABSTRACT

The coronavirus disease 2019 (COVID-19) is accompanied by a cytokine storm with the release of many proinflammatory factors and development of respiratory syndrome. Several SARS-CoV-2 lineages have been identified, and the Delta variant (B.1.617), linked with high mortality risk, has become dominant in many countries. Understanding the immune responses associated with COVID-19 lineages may therefore aid the development of therapeutic and diagnostic strategies. Multiple single-cell gene expression studies revealed innate and adaptive immunological factors and pathways correlated with COVID-19 severity. Additional investigations covering host-pathogen response characteristics for infection caused by different lineages are required. Here, we performed single-cell transcriptome profiling of blood mononuclear cells from the individuals with different severity of the COVID-19 and virus lineages to uncover variant specific molecular factors associated with immunity. We identified significant changes in lymphoid and myeloid cells. Our study highlights that an abundant population of monocytes with specific gene expression signatures accompanies Delta lineage of SARS-CoV-2 and contributes to COVID-19 pathogenesis inferring immune components for targeted therapy.


Subject(s)
COVID-19 , COVID-19/genetics , Gene Expression , Humans , Immunologic Factors , SARS-CoV-2
8.
Infect Genet Evol ; 104: 105357, 2022 10.
Article in English | MEDLINE | ID: covidwho-2004347

ABSTRACT

BACKGROUND: The ACE2 protein acts as a gateway for SARS-CoV-2 in the host cell, playing an essential role in susceptibility to infection by this virus. Genetics and epigenetic mechanisms related to the ACE2 gene are associated with changes in its expression and, therefore, linked to increased susceptibility to infection. Although some variables such as sex, age, and obesity have been described as risk factors for COVID-19, the molecular causes involved in the disease susceptibility are still unknown. AIM: To evaluate the ACE2 gene expression profiles and their association with epigenetic mechanisms and demographic or clinical variables. METHODS: In 500 adult volunteers, the mRNA expression levels of the ACE2 gene in nasopharyngeal swab samples and its methylation status in peripheral blood samples were quantified by RT-qPCR and qMSP, respectively. The existence of significant differences in the ACE2 gene expression and its determinants were evaluated in different study groups according to several demographic or clinical variables such as sex, age, body mass index (BMI), smoking, SARS-CoV-2 infection, and presence of underlying diseases such as type II diabetes mellitus (DM2), asthma and arterial hypertension (AHT). RESULTS: Our results show that ACE2 gene overexpression, directly involved in susceptibility to SARS-CoV-2 infection, depends on multiple host factors such as male sex, age over 30 years, smoking, the presence of obesity, and DM2. Likewise, it was determined that the ACE2 gene expression is regulated by changes in the DNA methylation patterns in its promoter region. CONCLUSIONS: The ACE2 gene expression is highly variable, and this variability is related to habits such as smoking and demographic or clinical variables, which details the impact of environmental and host factors on our epigenome and, therefore, in susceptibility to SARS-CoV-2 infection.


Subject(s)
Angiotensin-Converting Enzyme 2/genetics , COVID-19 , Diabetes Mellitus, Type 2 , Adult , COVID-19/genetics , Epigenesis, Genetic , Gene Expression , Humans , Male , Obesity/genetics , RNA, Messenger/genetics , SARS-CoV-2
9.
Sci Rep ; 12(1): 11763, 2022 08 15.
Article in English | MEDLINE | ID: covidwho-1991656

ABSTRACT

Besides typical respiratory symptoms, COVID-19 patients also have gastrointestinal symptoms. Studies focusing on the gastrointestinal tumors derived from gastrointestinal tissues have raised a question whether these tumors might express higher levels of SARS-CoV-2 associated genes and therefore patients diagnosed with GI cancers may be more susceptible to the infection. In this study, we have analyzed the expression of SARS-CoV-2 associated genes and their co-expressions in gastrointestinal solid tumors, cancer cell lines and patient-derived organoids relative to their normal counterparts. Moreover, we have found increased co-expression of TMPRSS2-TMPRSS4 in gastrointestinal cancers suggesting that SARS-CoV-2 viral infection known to be mediated by this protease pair might facilitate the effects of viral infection in GI cancer patients. Further, our findings also demonstrate that TRIM31 expression is upregulated in gastrointestinal tumors, while the inhibition of TRIM31 significantly altered viral replication and viral processes associated with cellular pathways in gastrointestinal cancer samples. Taken together, these findings indicate that in addition to the co-expression of TMPRSS2-TMPRSS4 protease pair in GI cancers, TRIM31 expression is positively correlated with this pair and TRIM31 may play a role in providing an increased susceptibility in GI cancer patients to be infected with SARS-CoV-2 virus.


Subject(s)
Gastrointestinal Neoplasms , Membrane Proteins , Serine Endopeptidases , Tripartite Motif Proteins , Ubiquitin-Protein Ligases , COVID-19/genetics , Gastrointestinal Neoplasms/genetics , Gene Expression , Humans , Membrane Proteins/genetics , SARS-CoV-2 , Serine Endopeptidases/genetics , Tripartite Motif Proteins/genetics , Ubiquitin-Protein Ligases/genetics
10.
Front Immunol ; 13: 921728, 2022.
Article in English | MEDLINE | ID: covidwho-1987494

ABSTRACT

Fibroblasts of different origins are known to possess stromal memory after inflammatory episodes. However, there are no studies exploring human lung fibroblast memory which may predict a subsequent inflammatory response in chronic respiratory diseases and COVID-19. MRC-5 and HF19 human lung fibroblast cell lines were treated using different primary and secondary stimulus combinations: TNFα-WD-TNFα, Poly (I:C)-WD-TNFα, TNFα-WD-Poly (I:C), or LPS-WD-TNFα with a 24-h rest period (withdrawal period; WD) between the two 24-h stimulations. TLR3 and NF-κB inhibitors were used to determine pathways involved. The effect of SARS-Cov-2 spike protein to inflammatory response of lung fibroblasts was also investigated. mRNA expressions of genes and IL6 release were measured using qRT-PCR and ELISA, respectively. Statistical significance was determined by using one- or two-way ANOVA, followed by Bonferroni's post hoc analysis for comparison of multiple groups. Preexposure with Poly (I:C) significantly increased TNFα-induced IL6 gene expression and IL6 release in both cell lines, while it affected neither gene expressions of IL1B, IL2, IL8, and MMP8 nor fibrosis-related genes: ACTA2, COL1A1, POSTN, and TGFB1. Inhibition of TLR3 or NF-κB during primary stimulation significantly downregulated IL6 release. Simultaneous treatment of MRC-5 cells with SARS-CoV-2 spike protein further increased TNFα-induced IL6 release; however, preexposure to Poly (I:C) did not affect it. Human lung fibroblasts are capable of retaining inflammatory memory and showed an augmented response upon secondary exposure. These results may contribute to the possibility of training human lung fibroblasts to respond suitably on inflammatory episodes after viral infection.


Subject(s)
COVID-19 , Interleukin-6/genetics , Tumor Necrosis Factor-alpha , Fibroblasts/metabolism , Gene Expression , Humans , Inflammation/chemically induced , Inflammation/genetics , Inflammation/metabolism , Interleukin-6/metabolism , Lung/metabolism , NF-kappa B/metabolism , Poly I-C/metabolism , Poly I-C/pharmacology , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Toll-Like Receptor 3/genetics , Toll-Like Receptor 3/metabolism , Tumor Necrosis Factor-alpha/metabolism
11.
J Food Biochem ; 46(10): e14352, 2022 10.
Article in English | MEDLINE | ID: covidwho-1961634

ABSTRACT

Dry eye disease (DED) is a complex ocular surface inflammatory disease. Its occurrence varies widely over the world, ranging from 5% to 34%. The use of preservatives, specifically benzalkonium chloride, in the ocular drops worsens the DED conditions. Furthermore, the Covid-19 pandemic increased screen time and the use of face masks and shields. As a result, the number of people suffering from dry eye disease (DED) has increased significantly in recent years. The main objective of our study is to find a solution to manage the dry eye disease (DED) preferably from natural source without any adverse events. In this study, the beneficial effects of capsanthin from Capsicum annum (CCA) were evaluated on benzalkonium chloride (BAC)-induced dry eye disease (DED) in Albino Wistar rats. Oral supplementation of CCA resulted in a statistically significant decrease in intraocular pressure (IOP) (p < .0001), increase in tear break-up time (TBUT) (p < .01), decline in Schirmer test results (p < .01), and decrease in corneal surface inflammation (p < .01). Capsanthin ameliorated in reducing oxidative stress by increasing serum antioxidant levels such as glutathione peroxidase (GPX), nitric oxide (NO), and lactoferrin (LTF) and inhibiting matrix metalloproteinases 2 and 9 (MMP2 and MMP9) (p < .0001). Capsanthin treatment significantly inhibited the expression of inflammatory cytokines, tumor necrosis factor-alpha (TNF-α), interleukins (IL-2, IL-4, IL-6), and pro-inflammatory mediator, matrix metalloproteinase-9 (MMP9). Furthermore, the lacrimal gland expressed vascular cell adhesion molecule (VCAM-1), and prostaglandin-endoperoxide synthase 2 (PTGS2) was suppressed by CCA treatment. PRACTICAL APPLICATIONS: Benzalkonium chloride (BAC), a preservative widely used in the topical ocular drug delivery system (ODDS), causes undesirable effects such as dry eye disease as well as ameliorating intraocular pressure leading to optical nerve damage and irreversible vision loss. Capsanthin from Capsicum annum (CCA) can be used to treat symptoms related to dry eye disease such as inflammation, eye irritation, visual disturbance, ocular discomfort with potential damage to the ocular surface. The CCA may be beneficial in the treatment of glaucoma, an elevated intraocular pressure. Capsanthin from C. annum can be useful in managing DED by increasing tear break-up time (TBUT), declining in Schirmer test results and decreasing in corneal surface inflammation.


Subject(s)
COVID-19 , Capsicum , Dry Eye Syndromes , Animals , Anti-Inflammatory Agents/pharmacology , Antioxidants/therapeutic use , Benzalkonium Compounds , Cyclooxygenase 2/metabolism , Cytokines/genetics , Cytokines/metabolism , Dry Eye Syndromes/chemically induced , Dry Eye Syndromes/drug therapy , Dry Eye Syndromes/genetics , Fruit/metabolism , Gene Expression , Glutathione Peroxidase/metabolism , Humans , Inflammation/chemically induced , Inflammation/drug therapy , Inflammation Mediators , Interleukin-2/metabolism , Interleukin-4 , Interleukin-6/metabolism , Lactoferrin/metabolism , Matrix Metalloproteinase 2/metabolism , Matrix Metalloproteinase 9/metabolism , Nitric Oxide/metabolism , Pandemics , Rats , Tumor Necrosis Factor-alpha/metabolism , Vascular Cell Adhesion Molecule-1/metabolism , Xanthophylls
12.
BMC Res Notes ; 15(1): 252, 2022 Jul 15.
Article in English | MEDLINE | ID: covidwho-1938343

ABSTRACT

OBJECTIVE: SARS CoV-2, the etiologic agent of coronavirus disease-2019 (COVID-19) is well-known to use ACE2 to begin internalization. Some viruses enter the host cell through the endocytosis process and involve some endocytosis proteins, such as the Rab family. However, the relationship between SARS CoV-2 infection with endocytic mRNA RAB5, RAB7, and RAB11B is unknown. This study aims to compare the expression of RAB5, RAB7, and RAB11B between positive and negative COVID-19 patient groups. RESULTS: Both viral and human epithelial RNA Isolation and RT-PCR were performed from 249 samples. The genes expression was analysed using appropriate statistical tests. We found the Median (inter-quartile range/IQR) of RAB5, RAB7, and RAB11B expression among the COVID-19 patient group was 2.99 (1.88), 0.17 (0.47), 0.47 (1.49), and 1.60 (2.88), 1.05 (2.49), 1.10 (3.96) among control group respectively. We proceeded with Mann Whitney U Test and found that RAB5 expression was significantly increased (P < 0.001), and RAB7 and RAB11B expression was significantly decreased (P < 0.001 and P = 0.036) in the COVID-19 patient group compared to the control group. This first report showed significant differences in RAB5, RAB7, and RAB11B exist between COVID-19 positive and negative patients.


Subject(s)
COVID-19 , rab5 GTP-Binding Proteins , COVID-19/genetics , Endosomes/metabolism , Gene Expression , Humans , rab GTP-Binding Proteins/genetics , rab GTP-Binding Proteins/metabolism , rab5 GTP-Binding Proteins/genetics , rab5 GTP-Binding Proteins/metabolism , rab7 GTP-Binding Proteins
13.
Microb Pathog ; 169: 105677, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1936991

ABSTRACT

Patients admitted to the hospital with coronavirus disease (COVID-19) are at risk for acquiring mycotic infections in particular Candidemia. Candida albicans (C. albicans) constitutes an important component of the human mycobiome and the most common cause of invasive fungal infections. Invasive yeast infections are gaining interest among the scientific community as a consequence of complications associated with severe COVID-19 infections. Early identification and surveillance for Candida infections is critical for decreasing the COVID-19 mortality. Our current study attempted to understand the molecular-level interactions between the human genes in different organs during systematic candidiasis. Our research findings have shed light on the molecular events that occur during Candidiasis in organs such as the kidney, liver, and spleen. The differentially expressed genes (up and down-regulated) in each organ will aid in designing organ-specific therapeutic protocols for systemic candidiasis. We observed organ-specific immune responses such as the development of the acute phase response in the liver; TGF-pathway and genes involved in lymphocyte activation, and leukocyte proliferation in the kidney. We have also observed that in the kidney, filament production, up-regulation of iron acquisition mechanisms, and metabolic adaptability are aided by the late initiation of innate defense mechanisms, which is likely related to the low number of resident immune cells and the sluggish recruitment of new effector cells. Our findings point to major pathways that play essential roles in specific organs during systemic candidiasis. The hub genes discovered in the study can be used to develop novel drugs for clinical management of Candidiasis.


Subject(s)
COVID-19 , Candidiasis , Candida albicans , Candidiasis/microbiology , Gene Expression , Humans , Systems Biology
14.
Int J Mol Sci ; 23(13)2022 Jun 29.
Article in English | MEDLINE | ID: covidwho-1934130

ABSTRACT

The effect of the antiviral peptide TAT-I24 on viral gene expression in cells infected with murine cytomegalovirus (MCMV) was investigated. The expression of immediate-early, early and late genes was highly induced upon infection with MCMV. In the presence of the peptide, the expression of all tested genes was sustainably reduced to a similar extent, independent of whether they were immediate-early, early or late genes. In contrast, the expression of host genes, such as NF-κB inhibitor alpha (Nfkbia), interferon-induced protein with tetratricopeptide repeats 1 (Ifit1), chemokine (C-X-C motif) ligand 10 (Cxcl10), chemokine (C-C motif) ligand 7 (Ccl7) and chemokine (C-C motif) ligand 5 (Ccl5), which are induced early upon virus infection, was only transiently suppressed in peptide-treated cells. The expression of other host genes which are affected by MCMV infection and play a role in endoplasmic reticulum stress or DNA-damage repair was not inhibited by the peptide. A combination of TAT-I24 with the nucleoside analogue cidofovir showed enhancement of the antiviral effect, demonstrating that viral replication can be more efficiently inhibited with a combination of drugs acting at different stages of the viral life-cycle.


Subject(s)
Muromegalovirus , Animals , Antiviral Agents/pharmacology , Gene Expression , Ligands , Mice , Muromegalovirus/genetics , Peptides/pharmacology , Virus Replication
15.
Front Public Health ; 10: 901602, 2022.
Article in English | MEDLINE | ID: covidwho-1933907

ABSTRACT

Since the first report of SARS-CoV-2 virus in Wuhan, China in December 2019, a global outbreak of Corona Virus Disease 2019 (COVID-19) pandemic has been aroused. In the prevention of this disease, accurate diagnosis of COVID-19 is the center of the problem. However, due to the limitation of detection technology, the test results are impossible to be totally free from pseudo-positive or -negative. Improving the precision of the test results asks for the identification of more biomarkers for COVID-19. On the basis of the expression data of COVID-19 positive and negative samples, we first screened the feature genes through ReliefF, minimal-redundancy-maximum-relevancy, and Boruta_MCFS methods. Thereafter, 36 optimal feature genes were selected through incremental feature selection method based on the random forest classifier, and the enriched biological functions and signaling pathways were revealed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Also, protein-protein interaction network analysis was performed on these feature genes, and the enriched biological functions and signaling pathways of main submodules were analyzed. In addition, whether these 36 feature genes could effectively distinguish positive samples from the negative ones was verified by dimensionality reduction analysis. According to the results, we inferred that the 36 feature genes selected via Boruta_MCFS could be deemed as biomarkers in COVID-19.


Subject(s)
COVID-19 , Biomarkers , COVID-19/diagnosis , Gene Expression , Gene Ontology , Humans , SARS-CoV-2/genetics
16.
J Neuropathol Exp Neurol ; 81(9): 666-695, 2022 08 16.
Article in English | MEDLINE | ID: covidwho-1931851

ABSTRACT

Brains of 42 COVID-19 decedents and 107 non-COVID-19 controls were studied. RT-PCR screening of 16 regions from 20 COVID-19 autopsies found SARS-CoV-2 E gene viral sequences in 7 regions (2.5% of 320 samples), concentrated in 4/20 subjects (20%). Additional screening of olfactory bulb (OB), amygdala (AMY) and entorhinal area for E, N1, N2, RNA-dependent RNA polymerase, and S gene sequences detected one or more of these in OB in 8/21 subjects (38%). It is uncertain whether these RNA sequences represent viable virus. Significant histopathology was limited to 2/42 cases (4.8%), one with a large acute cerebral infarct and one with hemorrhagic encephalitis. Case-control RNAseq in OB and AMY found more than 5000 and 700 differentially expressed genes, respectively, unrelated to RT-PCR results; these involved immune response, neuronal constituents, and olfactory/taste receptor genes. Olfactory marker protein-1 reduction indicated COVID-19-related loss of OB olfactory mucosa afferents. Iba-1-immunoreactive microglia had reduced area fractions in cerebellar cortex and AMY, and cytokine arrays showed generalized downregulation in AMY and upregulation in blood serum in COVID-19 cases. Although OB is a major brain portal for SARS-CoV-2, COVID-19 brain changes are more likely due to blood-borne immune mediators and trans-synaptic gene expression changes arising from OB deafferentation.


Subject(s)
COVID-19 , SARS-CoV-2 , Brain , Gene Expression , Humans , Immunity
17.
Nat Commun ; 13(1): 3937, 2022 07 08.
Article in English | MEDLINE | ID: covidwho-1927085

ABSTRACT

Unlike other respiratory viruses, SARS-CoV-2 disproportionately causes severe disease in older adults whereas disease burden in children is lower. To investigate whether differences in the upper airway immune response may contribute to this disparity, we compare nasopharyngeal gene expression in 83 children (<19-years-old; 38 with SARS-CoV-2, 11 with other respiratory viruses, 34 with no virus) and 154 older adults (>40-years-old; 45 with SARS-CoV-2, 28 with other respiratory viruses, 81 with no virus). Expression of interferon-stimulated genes is robustly activated in both children and adults with SARS-CoV-2 infection compared to the respective non-viral groups, with only subtle distinctions. Children, however, demonstrate markedly greater upregulation of pathways related to B cell and T cell activation and proinflammatory cytokine signaling, including response to TNF and production of IFNγ, IL-2 and IL-4. Cell type deconvolution confirms greater recruitment of B cells, and to a lesser degree macrophages, to the upper airway of children. Only children exhibit a decrease in proportions of ciliated cells, among the primary targets of SARS-CoV-2, upon infection. These findings demonstrate that children elicit a more robust innate and especially adaptive immune response to SARS-CoV-2 in the upper airway that likely contributes to their protection from severe disease in the lower airway.


Subject(s)
COVID-19 , SARS-CoV-2 , Adaptive Immunity/genetics , Adult , Aged , COVID-19/genetics , Child , Gene Expression , Humans , Nasopharynx , Young Adult
18.
Iran J Allergy Asthma Immunol ; 21(3): 254-262, 2022 Jun 18.
Article in English | MEDLINE | ID: covidwho-1924808

ABSTRACT

The role of microRNA (miR)200c-3p in regulating ACE2 gene expression in viral and bacterial respiratory diseases has been established. Since ACE2 reduces the acute inflammatory effects in lung diseases and acts as a coronavirus receptor to invade the lung cells, this study investigates the relationship between miR-200c-3p and ACE2 expression in COVID -19 patients. In this study, COVID-19 patients were divided into two groups: mild phase (PCR-positive and mild symptoms) and severe phase (PCR-positive with acute pulmonary symptoms and inflammation). Then, the subjects' demographic, clinical, and paraclinical characteristics were recorded using a prepared checklist. Total RNA was isolated from all samples according to the Trizol kit protocol to evaluate gene expression. Subsequently, the extracted product was analysed for miR-200c expression and ACE2 target gene expression by real-time PCR. The results of the checklist data showed that smoking, cough, and the factors ESR and HCT were statistically significant between the two groups of patients in the mild and acute phases. Also, the mean expression of the miR-200c gene in the mild and acute patients was 1.87±0.70 and 1.87±0.62, respectively, which was not statistically significant. Still, the mean expression of the ACE2 gene, which was 3.96±0.76 and 3.28±0.52 in the mild and acute disease groups, respectively, showed a significant difference between the two groups. This study showed that the expression levels of ACE2 were significantly reduced in people with severe inflammation compared to people with mild inflammation.


Subject(s)
Angiotensin-Converting Enzyme 2 , COVID-19 , MicroRNAs , Angiotensin-Converting Enzyme 2/biosynthesis , Angiotensin-Converting Enzyme 2/genetics , COVID-19/blood , COVID-19/enzymology , COVID-19/genetics , Gene Expression , Humans , MicroRNAs/blood , MicroRNAs/genetics
19.
Mol Biol Rep ; 49(9): 8693-8699, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-1919888

ABSTRACT

BACKGROUND: Coronavirus-19 is still considered a pandemic that influences the world. Other molecular alterations should be clearer besides the increasing cytokine storm and pro-inflammatory molecules. Hypoxic conditions that induce HIF-1α lead to stimulate gene expression of STC-2 that targets PAPP-A expression. This study aimed to determine gene expression levels of PAPP-A, STC-2, and HIF-1α in COVID-19 infection. We also aimed to reveal the relationship of these genes with laboratory and clinical data of COVID-19 patients. MATERIALS AND RESULTS: We extracted RNA from peripheral blood samples of COVID-19(+) and COVID-19(-) individuals. The real-time PCR method was used to measure mRNA expression of PAPP-A, STC-2, and HIF-1α. Gene expression analysis was evaluated by the 2-ΔΔCt method. PAPP-A, STC-2, and HIF-1α mRNA expressions of severe patients were higher than healthy individuals (p = 0.0451, p = 0.4466, p < 0.0001, respectively). Correlation analysis of gene expression patterns of severe patients demonstrated a positive correlation between PAPP-A and STC-2 (p < 0.0001, r = 0.8638). CONCLUSION: This is the first study that investigates the relation of PAPP-A, STC-2, and HIF-1α gene expression in patients with COVID-19 infection. Besides the routine laboratory findings, PAPP-A, STC-2, and HIF-1α mRNA expressions may be considered to patients' prognosis as a sign of increased cytokines and pro-inflammatory molecules.


Subject(s)
COVID-19 , Glycoproteins , Hypoxia-Inducible Factor 1, alpha Subunit , Intercellular Signaling Peptides and Proteins , Pregnancy-Associated Plasma Protein-A , COVID-19/genetics , Gene Expression , Glycoproteins/genetics , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , Intercellular Signaling Peptides and Proteins/genetics , Pregnancy-Associated Plasma Protein-A/genetics , RNA, Messenger/genetics , SARS-CoV-2
20.
Viruses ; 14(7)2022 Jun 22.
Article in English | MEDLINE | ID: covidwho-1911644

ABSTRACT

Feline infectious peritonitis (FIP) is a disease of domestic cats caused by the genetic variant of the feline coronavirus (FCoV) and feline infectious peritonitis virus (FIPV), currently grouped into two serotypes, I and II. Although serotype I FIPV is more prevalent in cats with FIP, serotype II has been more extensively studied in vitro due to the relative ease in propagating this viral serotype in culture systems. As a result, more is known about serotype II FIPV than the more biologically prevalent serotype I. The primary cell receptor for serotype II has been determined, while it remains unknown for serotype I. The recent development of a culture-adapted feline cell line that more effectively propagates serotype I FIPV, FCWF-4 CU, derived from FCWF-4 cells available through the ATCC, offers the potential for an improved understanding of serotype I FIPV biology. To learn more about FIPV receptor biology, we determined targeted gene expression patterns in feline cells variably permissive to replication of serotype I or II FIPV. We utilized normal feline tissues to determine the immunohistochemical expression patterns of two known coronavirus receptors, ACE2 and DC-SIGN. Lastly, we compared the global transcriptomes of the two closely related FCWF-4 cell lines and identified viral transcripts with potential importance for the differential replication kinetics of serotype I FIPV.


Subject(s)
Coronavirus, Feline , Feline Infectious Peritonitis , Animals , Biology , Cats , Coronavirus, Feline/genetics , Gene Expression , Serogroup
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