Differentially Expressed Genes Analysis in the Human Small Airway Epithelium of Healthy Smokers Shows Potential Risks of Disease Caused by Oxidative Stress and Inflammation and the Potentiality of Astaxanthin as an Anti-Inflammatory Agent.

Cigarette smoke (CS) was known for its effect of increasing oxidative stress that could trigger tissue injury and endothelial dysfunction mediated by free radicals and reactive oxygen species (ROS). ROS itself is a key signaling molecule that plays a role in the development of inflammatory disorders. Nuclear factor erythroid2 related factor2 (Nrf2) is the main regulator of antioxidant cellular response to cell and tissue-destroying components caused by CS. Nrf2 protein that is significantly activated in the smokers' small airway epithelium is followed by a series of gene expression changes in the same cells. This study aims to observe differentially expressed genes (DEGs) in the human small airway epithelium of smokers compared to genes whose expression changes due to astaxanthin (AST) treatment, an antioxidant compound that can modulate Nrf2. Gene expression data that was stored in the GEO browser (GSE 11952) was analyzed using GEO2R to search for DEG among smokers and nonsmokers subject. DEG was further compared to those genes whose expression changes due to astaxanthin treatment (AST) that were obtained from the Comparative Toxicogenomics Database (CTD; https://ctdbase.org/). DEG (p < 0.05) analysis result shows that there are 23 genes whose expression regulation is reversed compared to gene expression due to AST treatment. The gene function annotations of the 23 DEGs showed the involvement of some of these genes in chemical and oxidative stress, reactive oxygen species (ROS), and apoptotic signaling pathways. All of the genes were involved/associated with chronic bronchitis, adenocarcinoma of the lung, non-small-cell lung carcinoma, carcinoma, small cell lung carcinoma, type 2 diabetes mellitus, emphysema, ischemic stroke, lung diseases, and inflammation. Thus, AST treatment for smokers could potentially decrease the development of ROS and oxidative stress that leads to inflammation and health risks associated with smoking.

Differentially Expressed Genes Study Shown Potential for BCG Stimulation in Reducing the Severity of COVID-19.

The incidence of COVID-19 infection and death is known to be lower in tuberculosis (TB) endemic countries than in nonendemic countries. The Bacillus Calmette-Guerin (BCG) vaccination, which is commonly administered in TB endemic countries, was previously reported to have a nonspecific protective effect against several infections, including COVID-19. In this study, we used a differentially expressed genes (DEG) approach to analyze the genes modulated by BCG vaccination and COVID-19 infection. The Gene Expression Omnibus (GEO) database was used to select a COVID-19 gene expression data set with GSE164805, GSE14408, and GSE58636, and DEG in each data set were identified using the GEO2R online tools and selected using the adjusted p value (padj) 0.05 criteria. The protein-protein interaction (PPI) network was constructed from DEGs with the same trend of expression (upregulation or downregulation) using STRING version 11. The PPI network was performed by using the highest confidence number (0.9). DEGs that have a high-trust network were collected and functional cluster analysis of biological processes from Gene Ontology (GO), pathway analysis from the Human KEGG pathway, and COVID-19-related gene analysis was carried out using the Enrichr database. We found that either BCG or tuberculin increased the expression of several genes related to hyperinflammation, such as CCL3, CCL4, CSF2, IL1B, and LTA. In severe COVID-19, these genes were downregulated. This leads to the hypothesis that revaccination may have a protective effect against the severity of COVID-19 by reducing the hyperinflammatory status.

Virtual screening of Indonesian herbal compounds as COVID-19 supportive therapy: machine learning and pharmacophore modeling approaches.

BACKGROUND: The number of COVID-19 cases continues to grow in Indonesia. This phenomenon motivates researchers to find alternative drugs that function for prevention or treatment. Due to the rich biodiversity of Indonesian medicinal plants, one alternative is to examine the potential of herbal medicines to support COVID therapy. This study aims to identify potential compound candidates in Indonesian herbal using a machine learning and pharmacophore modeling approaches. METHODS: We used three classification methods that had different decision-making processes: support vector machine (SVM), multilayer perceptron (MLP), and random forest (RF). For the pharmacophore modeling approach, we performed a structure-based analysis on the 3D structure of the main protease SARS-CoV-2 (3CLPro) and repurposed SARS, MERS, and SARS-CoV-2 drugs identified from the literature as datasets in the ligand-based method. Lastly, we used molecular docking to analyze the interactions between the 3CLpro and 14 hit compounds from the Indonesian Herbal Database (HerbalDB), with lopinavir as a positive control. RESULTS: From the molecular docking analysis, we found six potential compounds that may act as the main proteases of the SARS-CoV-2 inhibitor: hesperidin, kaempferol-3,4'-di-O-methyl ether (Ermanin); myricetin-3-glucoside, peonidin 3-(4'-arabinosylglucoside); quercetin 3-(2G-rhamnosylrutinoside); and rhamnetin 3-mannosyl-(1-2)-alloside. CONCLUSIONS: Our layered virtual screening with machine learning and pharmacophore modeling approaches provided a more objective and optimal virtual screening and avoided subjective decision making of the results. Herbal compounds from the screening, i.e. hesperidin, kaempferol-3,4'-di-O-methyl ether (Ermanin); myricetin-3-glucoside, peonidin 3-(4'-arabinosylglucoside); quercetin 3-(2G-rhamnosylrutinoside); and rhamnetin 3-mannosyl-(1-2)-alloside are potential antiviral candidates for SARS-CoV-2. Moringa oleifera and Psidium guajava that consist of those compounds, could be an alternative option as COVID-19 herbal preventions.

Combination of Enrichment Using Gene Ontology and Transcriptomic Analysis Revealed Contribution of Interferon Signaling to Severity of COVID-19.

Introduction: The severity of coronavirus disease 2019 (COVID-19) was known to be affected by hyperinflammation. Identification of important proteins associated with hyperinflammation is critical. These proteins can be a potential target either as biomarkers or targets in drug discovery. Therefore, we combined enrichment analysis of these proteins to identify biological knowledge related to hyperinflammation. Moreover, we conducted transcriptomic data analysis to reveal genes contributing to disease severity. Methods: We performed large-scale gene function analyses using gene ontology to identify significantly enriched biological processes, molecular functions, and cellular components associated with our proteins. One of the appropriate methods to functionally group large-scale protein-protein interaction (PPI) data into small-scale clusters is fuzzy K-partite clustering. We collected the transcriptomics data from GEO Database (GSE 164805 and GPL26963 platform). Moreover, we created a data set and analyzed gene expression using Orange Data-mining version 3.30. PPI analysis was performed using the STRING database with a confidence score >0.9. Results: This study indicated that four proteins were associated with 25 molecular functions, three were associated with 22 cellular components, and one was associated with ten biological processes. All GOs of molecular function, cellular components, and 9 of 14 biological processes were associated with important cytokines related to the COVID-19 cytokine storm present in the resulting cluster. The expression analysis showed the interferon-related genes IFNAR1, IFI6, IFIT1, and IFIT3 were significant genes, whereas PPIs showed their interactions were closely related. Conclusion: A combination of enrichment using GOs and transcriptomic analysis showed that hyperinflammation and severity of COVID-19 may be caused by interferon signaling.

Ethanol Extract of Pomegranate (Punica granatum) Peel in Increasing the Expression of Caspase-3 in DSS-Induced Mice.

BACKGROUND: Colorectal cancer (CRC) is a malignancy derived from the glandular epithelial cells in the colon. Patients with inflammatory bowel disease (IBD) are more likely to develop CRC. Cancer proliferation is characterized by the loss of inhibition of apoptosis, which involves caspase-3 activation. This study examined the effects of the pomegranate peel extract on the expression of caspase-3 in mice crypt cells induced by dextran sodium sulfate (DSS) 2%. METHODS: The experimental study was done in six groups. All treatments were done in 42 days. The groups were all induced by DSS through water drinking, except for the normal group, which was only given water. The treatments given included the pomegranate extract in two doses (240 mg and 480 mg/kg bw/day), aspirin, and ellagic acid. The specimens were then fixated and stained for the immunohistochemistry scoring for the expression of caspase-3, which was then analyzed statistically. RESULTS: The H-scores of each treatment group were 213.23 ± 8.32 (DSS group), 243.81 ± 18.69 (normal group), 226.10 ± 12.38 (pomegranate peel extract of 240 mg/kg/d), 238.84 ± 15.81 (pomegranate peel extract of 480 mg/kg/d), 227.47 ± 12.15 (aspirin), and 224.01 ± 18.39 (ellagic acid). Statistical differences were found in one-way analysis of variance (ANOVA) and post hoc analysis among the DSS group, normal group, and dose 2 group (pomegranate peel extract of 480 mg/kg/day). CONCLUSIONS: The ethanol extract of pomegranate was able to induce apoptosis, which was demonstrated by the increase of caspase-3 expression.

Xanthine Oxidase-Induced Inflammatory Responses in Respiratory Epithelial Cells: A Review in Immunopathology of COVID-19.

Xanthine oxidase (XO) is an enzyme that catalyzes the production of uric acid and superoxide radicals from purine bases: hypoxanthine and xanthine and is also expressed in respiratory epithelial cells. Uric acid, which is also considered a danger associated molecule pattern (DAMP), could trigger a series of inflammatory responses by activating the inflammasome complex path and NF-κB within the endothelial cells and by inducing proinflammatory cytokine release. Concurrently, XO also converts the superoxide radicals into hydroxyl radicals that further induce inflammatory responses. These conditions will ultimately sum up a hyperinflammation condition commonly dubbed as cytokine storm syndrome (CSS). The expression of proinflammatory cytokines and neutrophil chemokines may be reduced by XO inhibitor, as observed in human respiratory syncytial virus (HRSV)-infected A549 cells. Our review emphasizes that XO may have an essential role as an anti-inflammation therapy for respiratory viral infection, including coronavirus disease 2019 (COVID-19).

The effect of lunasin from Indonesian soybean extract on histopatologic examination and cox-2 expression in dextran sodium sulfate-induced mice colon.

Inflammatory bowel disease (IBD) is a condition describing chronic gastrointestinal inflammation. Chronic inflammation in colon can develop into colon cancer. Lunasin has been known to inhibit inflammatory reactions induced by lipopolysaccharide in vitro. The effect of lunasin to inhibit inflammation in vivo is not widely known. In this study, we analyzed the effect of lunasin from soybean to decrease the risk of inflammation by analyzing histopathologic feature and the expression of COX-2. 30 mice are divided into 6 groups. Normal group was not induced by dextran sodium sulfate (DSS). The other groups were induced by 2% DSS through drinking water for 9 days. After 9 days, negative control group did not receive any treatment. The other groups received treatment given lunasin dose 20 mg/kg body weight (BW) and 40 mg/kg BW, commercial lunasin and positive control given aspirin. Treatment was performed for 5 weeks. Inflammatory colon histopathologic examination and immunohistochemical score of COX-2 proteins were analyzed using statistical tests. Lunasin dose 20 mg/kg BW and 40 mg/kg BW were able to significantly reduce inflammation (P<0.05) performed by histopathologic feature with an average score of 2.52 and 2.16 COX-2 expression decreased significantly (P<0.05) with an average score of 43.674 and 33.349. Lunasin dose 20 mg/kg BW and 40 mg/kg BW were able to inhibit inflammation and decrease the expression of COX-2 in colon induced by DSS.