Machine learning-driven blood transcriptome-based discovery of SARS-CoV-2 specific severity biomarkers

The Coronavirus disease 2019 (COVID-19) pandemic, caused by rapidly evolving variants of severe acute respiratory syndrome coronavirus (SARS-CoV-2), continues to be a global health threat. SARS-CoV-2 infection symptoms often intersect with other nonsevere respiratory infections, making early diagnosis challenging. There is an urgent need for early diagnostic and prognostic biomarkers to predict severity and reduce mortality when a sudden outbreak occurs. This study implemented a novel approach of integrating bioinformatics and machine learning algorithms over publicly available clinical COVID-19 transcriptome data sets. The robust 7-gene biomarker identified through this analysis can not only discriminate SARS-CoV-2 associated acute respiratory illness (ARI) from other types of ARIs but also can discriminate severe COVID-19 patients from nonsevere COVID-19 patients. Validation of the 7-gene biomarker in an independent blood transcriptome data set of longitudinal analysis of COVID-19 patients across various stages of the disease showed that the dysregulation of the identified biomarkers during severe disease is restored during recovery, showing their prognostic potential. The blood biomarkers identified in this study can serve as potential diagnostic candidates and help reduce COVID-19-associated mortality.

Host and viral non-coding RNAs in dengue pathogenesis

Dengue virus (DENV) is a mosquito-borne flavivirus that causes frequent outbreaks in tropical countries. Due to the four different serotypes and ever-mutating RNA genome, it is challenging to develop efficient therapeutics. Early diagnosis is crucial to prevent the severe form of dengue, leading to mortality. In the past decade, rapid advancement in the high throughput sequencing technologies has shed light on the crucial regulating role of non-coding RNAs (ncRNAs), also known as the "dark matter" of the genome, in various pathological processes. In addition to the human host ncRNAs like microRNAs and circular RNAs, DENV also produces ncRNAs such as subgenomic flaviviral RNAs that can modulate the virus life cycle and regulate disease outcomes. This review outlines the advances in understanding the interplay between the human host and DENV ncRNAs, their regulation of the innate immune system of the host, and the prospects of the ncRNAs in clinical applications such as dengue diagnosis and promising therapeutics.

Comparative transcriptome analysis of SARS-CoV, MERS-CoV, and SARS-CoV-2 to identify potential pathways for drug repurposing

The ongoing COVID-19 pandemic caused by the coronavirus, SARS-CoV-2, has already caused in excess of 1.25 million deaths worldwide, and the number is increasing. Knowledge of the host transcriptional response against this virus and how the pathways are activated or suppressed compared to other human coronaviruses (SARS-CoV, MERS-CoV) that caused outbreaks previously can help in the identification of potential drugs for the treatment of COVID-19. Hence, we used time point meta-analysis to investigate available SARS-CoV and MERS-CoV in-vitro transcriptome datasets in order to identify the significant genes and pathways that are dysregulated at each time point. The subsequent over-representation analysis (ORA) revealed that several pathways are significantly dysregulated at each time point after both SARS-CoV and MERS-CoV infection. We also performed gene set enrichment analyses of SARS-CoV and MERS-CoV with that of SARS-CoV-2 at the same time point and cell line, the results of which revealed that common pathways are activated and suppressed in all three coronaviruses. Furthermore, an analysis of an in-vivo transcriptomic dataset of COVID-19 patients showed that similar pathways are enriched to those identified in the earlier analyses. Based on these findings, a drug repurposing analysis was performed to identify potential drug candidates for combating COVID-19.

Liver-related mortality in countries of the developed world: an ecological study approach to explain the variability

BACKGROUND

Liver-related mortality varies across developed nations.

AIM

To assess the relative role of various risk factors in relation to liver-related mortality in an ecological study approach.

METHODS

Data for liver-related mortality, prevalence data for hepatitis B and C, human immunodeficiency virus (HIV), alcohol consumption per capita, Type 2 Diabetes mellitus (T2DM), overweight and obesity were extracted from peer-reviewed publications or WHO databases for different developed countries. As potential other risk-modifying factors, purchase power parity (PPP)-adjusted gross domestic product (GDP) per capita and health expenditure per capita were assessed. As an environmental 'hygiene factor', we also assessed the effect of the prevalence of Helicobacter pylori. Only countries with a PPP-adjusted GDP greater than $20 000 and valid information for at least 8 risk modifiers were included. Univariate and multivariate analyses were utilised to quantify the contribution to the variability in liver-related mortality.

RESULTS

The proportion of chronic liver diseases (CLD)-related mortality ranged from 0.73-2.40% [mean 1.56%, 95% CI (1.43-1.69)] of all deaths. Univariately, CLD-related mortality was significantly associated with Hepatitis B prevalence, alcohol consumption, PPP-adjusted GDP (all P < 0.05) and potentially H. pylori prevalence (P = 0.055). Other investigated factors, including hepatitis C, did not yield significance. Backward elimination suggested hepatitis B, alcohol consumption and PPP-adjusted GDP as risk factors (explaining 66.3% of the variability).

CONCLUSION

Hepatitis B infection, alcohol consumption and GDP, but not hepatitis C or other factors, explain most of the variance of liver-related mortality.

Electronic considerations in the mutagenesis of some 4,5-bridged chrysenes

The mutagenic activity of four 4,5-bridged chrysene derivatives, benz(a)aceanthrylene, and 5-methylchrysene was examined using histidine auxotrophic strains TA98 and TA100 of Salmonella typhimurium. All compounds showed a positive mutagenic response with both TA100 and TA98 in the presence of S-9. A correlation between the electronic character of the bridging group and mutagenic activity for the chrysene derivatives is proposed.

Amount of antibody is critical for immune complex displacement by charge competition from both rabbit glomeruli and anionic beads

The purpose of this study was to determine the feasibility of displacing cationized bovine serum albumin (CBSA) immune complexes from glomeruli by charge competition. An in vitro model identified protamine as an effective agent for displacing 125I-CBSA from anionic beads (dextran sulfate-coated Sepharose 4B). Anti-CBSA serum prevented displacement of 125I-CBSA from anionic beads in a dose-dependent fashion. When 125I-CBSA was injected intravenously into rabbits 98% of 125I-CBSA disappeared from blood within 5 min, at which time CBSA was visualized by immunofluorescence in glomerular capillary walls but not in liver, muscle, skin, spleen or lung. By 24 h 90% of 125I-CBSA had disappeared from glomeruli. In contrast, injection of anti-CBSA antibody caused persistence of 125I-CBSA in kidney (particularly along glomerular capillary walls) for more than 7 days (detected by counting 125I in kidney, by radionuclide imaging and by immunofluorescence). Protamine administration (50 mg intravenously daily for 6 days) caused significant reduction of 125I-CBSA trapped in kidney only if the amount of anti-CBSA injected was small. Protamine did not significantly displace 125I-CBSA from glomeruli if the anti-CBSA dose was larger. Therefore both in vivo and in vitro displacement of 125I-CBSA by protamine depended upon the amount of antibody. We conclude that although charge dependent displacement of immune complexes from glomeruli is probably feasible using protamine this approach would only work in the presence of small amounts of antibody.

Beta-carotene as an inhibitor of benzo(a)pyrene and mitomycin C induced chromosomal breaks in the bone marrow of mice

Female mice of hybrid strain B6C3F1, 8-10 weeks old, were fed on powdered food with or without beta-carotene (100 mg/kg food). After 1 week of these diets, some of each group of mice were injected i.p. with either benzo(a)pyrene (150 mg/kg) in dimethyl sulfoxide, or mitomycin C (1 mg/kg) in distilled water. In the course of separate experiments, bone marrow samples were collected at various intervals after injection for analysis in the in vivo bone marrow micronucleus assay. At the time at which the maximum induction was observed, which coincided between experiments, the frequency of micronuclei induced by benzo(a)pyrene was reduced by 41-61% and that induced by mitomycin C was reduced by 44-71% in the presence of beta-carotene. Beta-carotene is widely distributed in plant material such as carrots and green leafy vegetables and, as such, is a component of the human diet. Our results suggest that beta-carotene provides significant protection against the genotoxicity of benzo(a)pyrene and mitomycin C.

Corn oil and its minor constituents as inhibitors of DMBA-induced chromosomal breaks in vivo

Inhibitory effects of corn oil and its constituents have been studied against 7,12-dimethylbenz[a]anthracene (DMBA)-induced chromosomal breaks in B6C3F1 female mice using the in vivo bone-marrow micronucleus assay. We tested propyl gallate, alpha-tocopherol and beta-sitosterol as constituents of corn oil. In addition, sunflower oil was tested also to check whether corn oil differs from any other vegetable oil. Corn oil, propyl gallate, beta-sitosterol or sunflower oil were injected i.p. to mice for 2 days at 24-h intervals, prior to injecting DMBA i.p. alpha-Tocopherol was mixed in powdered food and the mice were fed on it for 4 days before receiving DMBA. Bone-marrow samples were collected at various 24-h intervals. About 50-70% reduction in number of micronucleated polychromatic erythrocytes (MNPCE)/500 PCEs were observed in all the treatments wherever corn oil was used. Significant inhibitory effects were noted in treatments with alpha-tocopherol and beta-sitosterol. Sunflower oil also showed an inhibitory effect, similar to that with corn oil.

Inhibitory effects of alpha- and beta-naphthoflavones on DMBA-induced anomalies in germ cells assessed by sperm abnormality assay

Frequencies of abnormal sperms in B6C3F1 male mice were analyzed after injection with 7,12-dimethylbenz[a]anthracene (DMBA), alpha-naphthoflavone (alpha-NF or 7,8-benzoflavone), beta-naphthoflavone (beta-NF or 5,6-benzoflavone) and combinations of either alpha-NF and DMBA or beta-NF and DMBA. Either alpha-NF or beta-NF was injected 48 and 24 h before injecting mice twice with DMBA for 2 days at 24-h intervals. Prior injection of mice with alpha-NF and beta-NF was based on the assumption that enhanced activity of monooxygenase enzymes (P-450) in the mouse system so as to modify the metabolism of DMBA towards increased detoxification. Both flavones showed inhibitory effects in the genotoxic action of DMBA to the extent of 83% reduction by alpha-NF and 60% by beta-NF in the number of abnormal sperms as compared with those found in germ cells due to DMBA alone. compared with those found in germ cells due to DMBA alone.

Caffeic acid as an inhibitor of DMBA-induced chromosomal breakage in mice assessed by bone-marrow micronucleus test

Female mice of hybrid strain B6C3F1, 8-10 weeks old, were fed on powdered food with or without 2% caffeic acid. After one week on these diets, some of each group of mice were injected i.p., with 7,12-dimethyl benz[a]anthracene (25 mg/kg) dissolved in dimethyl disulfoxide. In the course of separate experiments, bone-marrow samples were taken at various intervals after injection for analysis in the micronucleus assay. From each mouse 500 polychromatic erythrocytes were scored to determine the frequency with micronuclei. At the time at which the maximum response was observed, which differed between experiments, the frequency of micronuclei induced by DMBA was reduced by 50% by the presence of caffeic acid. Caffeic acid (3,4-dihydroxy cinnamic acid) is widely distributed in plant materials in both free and combined forms and, as such, is a component of the human diet. Our results suggest that caffeic acid provides significant protection against the genotoxicity of DMBA.

The use of two-dimensional electrophoresis to detect mutations induced in mouse spermatogonia by ethylnitrosourea

Two-dimensional electrophoresis should, in theory, be a suitable method for the measurement of induced mutation rates in the germ cells of mice. Not only can the polypeptide products of a large number of genes be resolved on a single gel but the detection of mutations which lead to proteins with altered electrophoretic properties (but not necessarily altered function) is possible. Our attempts to apply two-dimensional electrophoresis to the detection of mutation in vivo have involved three stages: (i) the rapid production of gels of high resolution and reproducibility; (ii) the identification of eight interstrain protein variants and demonstration of their simple genetic basis; and (iii) a pilot experiment using the powerful germ-cell mutagen ethylnitrosourea. It was found that although interstrain protein variants could be detected and shown to be inherited in a codominant manner, induced variants were rarely detected even on high quality gels. Only 2 variants were detected among 67 offspring of male mice treated with 150 mg/kg ethylnitrosourea. This represented a mutation rate of 0.88 X 10(-4) mutations per locus per gamete.

Inhibitory effect of 7,8-benzoflavone on DMBA- and BaP-induced bone marrow micronuclei in mouse

Frequencies of micronucleated polychromatic erythrocytes (PCE) were analyzed in bone-marrow cells of mice injected with 7,12-dimethylbenz[a]anthracene (DMBA), benzo[a]pyrene (BaP), 7,8-benzoflavone (alpha-naphthoflavone) and the combination of either 7,8-benzoflavone and DMBA or 7,8-benzoflavone and BaP. 7,8-Benzoflavone was injected 48 and 24 h before injecting mice either with DMBA or BaP. Bone-marrow samples were collected at 24, 48, 72 and 96 h. The observed maximum mean number of micronucleated PCE per 500 PCE was 8.6 at 48 h with DMBA and 11.6 at 72 h with BaP. 7,8-Benzoflavone reduced the number of micronucleated PCE in the above treatments with DMBA by 90% and in the case of BaP by 75%. In other words, 7,8-benzoflavone acted as a potent inhibitor in preventing chromosomal breaks caused by DMBA or BaP.

Simultaneous detection of chromosomal aberrations and sister-chromatid exchanges: experience with DNA intercalating agents

Micronuclei that arise from chromosomal fragments can be used as an index of cytogenetic damage in a number of mammalian cell-culture systems. Since sister-chromatid exchanges (SCE) can be scored at the second metaphase after treatment, micronuclei that have arisen from acentric fragments at the first mitosis should be present in the same preparations. When a series of 8 mutagens, most of them intercalating agents, was studied in Chinese hamster ovary (CHO) cells, increased frequencies of micronuclei were detected at all doses which induced increased frequencies of SCE. The time required to score the slides for micronuclei was about one tenth that required for SCE. Since it is clear that aberrations and SCE have different genetic consequences and that they arise by mechanisms that differ at least in part, we find it useful to be able to measure both on the same slides. In this way mutagenic agents such as X-rays and bleomycin that produce few, if any, SCE but much chromosomal breakage would not be missed, nor would any agent that produced SCE without aberrations.