The exploration of glucocorticoid pathway based on disease severity in COVID-19 patients DOI Creative Commons
Gestina Aliska,

Andani Eka Putra,

Fenty Anggrainy

et al.

Heliyon, Journal Year: 2023, Volume and Issue: 10(1), P. e23579 - e23579

Published: Dec. 10, 2023

Systemic inflammation is a hallmark of Coronavirus Disease 2019 (COVID-19) and the key to pathophysiology its severe cases with host cytokine involvement. Glucocorticoids can moderate this inflammatory effect due receptor binding (NRC31-the gene encoded), influencing expression effector genes pro-inflammatory cytokines. Another important pathway in processes immune responses nuclear factor-κB (NF-κB) signaling (NFKBIA-the encoded). We aimed explore glucocorticoid mild COVID-19. performed cross-sectional, observational study on COVID-19 cases, assessing RNA white blood cells. The Illumina® platform was used for sequencing, FASTQ data were quality-checked Multiqc. raw analyzed using CLC Genomics Workbench®. Our included 23 patients 21 an average age 49.9 ± 18.2 years old. NR3C1 NFKBIA expressions did not show significantly significant difference between groups (log2 fold change 0.5, p = 0.1; 0.82, 0.09). However, TSC22D3, DUSP-1, JAK-1 MAPK-1 higher 1.3, < 0.001; 2.6, 0.9, 1.48, p-value<0.001; respectively). Furthermore, TNF, IL-1β, IL-6 lower 4.05, 3.33, 6.86, In conclusion, our results showed that although NRC31 statistically groups, TSC22D3 cases. These highlight importance genes, specifically combatting systemic inflammation. recent findings have potential lead identification novel pharmacological targets could prove be vital fight against diseases associated

Language: Английский

Algorithms and tools for data-driven omics integration to achieve multilayer biological insights: a narrative review DOI Creative Commons
Aurelia Morabito, Giulia De Simone, Roberta Pastorelli

et al.

Journal of Translational Medicine, Journal Year: 2025, Volume and Issue: 23(1)

Published: April 10, 2025

Systems biology is a holistic approach to biological sciences that combines experimental and computational strategies, aimed at integrating information from different scales of processes unravel pathophysiological mechanisms behaviours. In this scenario, high-throughput technologies have been playing major role in providing huge amounts omics data, whose integration would offer unprecedented possibilities gaining insights on diseases identifying potential biomarkers. the present review, we focus strategies applied literature integrate genomics, transcriptomics, proteomics, metabolomics year range 2018-2024. Integration approaches were divided into three main categories: statistical-based approaches, multivariate methods, machine learning/artificial intelligence techniques. Among them, statistical (mainly based correlation) ones with slightly higher prevalence, followed by learning Integrating multiple layers has shown great uncovering molecular mechanisms, putative biomarkers, aid classification, most time resulting better performances when compared single analyses. However, significant challenges remain. The nature platforms introduces issues such as variable data quality, missing values, collinearity, dimensionality. These further increase combining datasets, complexity heterogeneity integration. We report found cope these challenges, but some open still remain should be addressed disclose full

Language: Английский

Citations

2
Metabolomics as a powerful tool for diagnostic, pronostic and drug intervention analysis in COVID-19 DOI Creative Commons
Chiara Bruzzone, Ricardo Conde, Nieves Embade

et al.

Frontiers in Molecular Biosciences, Journal Year: 2023, Volume and Issue: 10

Published: Feb. 15, 2023

COVID-19 currently represents one of the major health challenges worldwide. Albeit its infectious character, with onset affectation mainly at respiratory track, it is clear that pathophysiology has a systemic ultimately affecting many organs. This feature enables possibility investigating SARS-CoV-2 infection using multi-omic techniques, including metabolomic studies by chromatography coupled to mass spectrometry or nuclear magnetic resonance (NMR) spectroscopy. Here we review extensive literature on metabolomics in COVID-19, unraveled aspects disease including: characteristic metabotipic signature associated discrimination patients according severity, effect drugs and vaccination treatments characterization natural history metabolic evolution disease, from full recovery long-term long sequelae COVID.

Language: Английский

Citations

32
Comprehensive proteomics and meta-analysis of COVID-19 host response DOI Creative Commons
Haris Babačić, Wanda Christ, J.E. Araújo

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Sept. 22, 2023

Abstract COVID-19 is characterised by systemic immunological perturbations in the human body, which can lead to multi-organ damage. Many of these processes are considered be mediated blood. Therefore, better understand host response SARS-CoV-2 infection, we performed systematic analyses circulating, soluble proteins blood through global proteomics mass-spectrometry (MS) proteomics. Here, show that a large part proteome altered COVID-19, among them elevated levels interferon-induced and proteasomal proteins. Some have alternating cells after infection vitro different organs patients deregulated blood, suggesting shared infection-related changes.The availability public proteomic resources on alterations leaves uncertainty about change given protein during COVID-19. Hence, review meta-analysis MS studies proteomes, including up 1706 individuals (1039 patients), provide concluding estimates for alteration 1517 Finally, based developed CoViMAPP, an open-access resource effect sizes diagnostic potential publicly available research, clinical, academic community.

Language: Английский

Citations

20
Viral PIC-pocketing: RSV sequestration of translational preinitiation complexes into bi-phasic biomolecular condensates DOI Creative Commons
Fatoumatta Jobe, James T. Kelly,

Jennifer Simpson

et al.

Journal of Virology, Journal Year: 2024, Volume and Issue: 98(3)

Published: Feb. 29, 2024

ABSTRACT Orthopneumoviruses characteristically form membrane-less cytoplasmic inclusion bodies (IBs) wherein RNA replication and transcription occur. Here, we report a strategy whereby the orthopneumoviruses sequester various components of translational pre i nitiation complex machinery into viral to facilitate translation their own mRNAs— PIC -pocketing. Electron microscopy respiratory syncytial virus (RSV)-infected cells revealed bi-phasic organization IBs, specifically, spherical “droplets” nested within larger inclusion. Using correlative light electron microscopy, combined with fluorescence in situ hybridization, showed that observed morphology represents functional compartmentalization body these domains are synonymous previously reported body-associated granules (IBAGs). Detailed analysis demonstrated IBAGs concentrate nascent mRNA, M2-1 protein as well eukaryotic initiation factors (eIF), eIF4F eIF3, 40S complexes involved initiation. Interestingly, although ribopuromycylation-based imaging indicates majority mRNA occurs cytoplasm, there was some evidence for intra-IBAG translation, consistent likely presence ribosomes subset imaged by microscopy. Mass spectrometry sub-cellular fractions from RSV-infected identified significant modification cellular machinery; however, interestingly, ribopuromycylation assays no changes global levels translation. The mechanistic basis this pathway subsequently determined involve interacting eIF4G, its transport between cytoplasm separate phases body. In summary, our data show organelles function spatially regulate early steps highly selective biomolecular condensate. IMPORTANCE Respiratory viruses (RSVs) cows humans cause morbidity mortality respective populations. These replicate infected compartmentalizing cell’s distinct microdomains called (IBs). paper, IBs further compartmentalized smaller structures have significantly different density, Within intra-IB structures, ribosomal active findings highlight RSV may additionally compartmentalize favor cell. contribute understanding how hijack cell genomes provide new targets antiviral therapeutics vivo .

Language: Английский

Citations

7
SARS-CoV2 variants differentially impact on the plasma metabolome DOI Creative Commons

Tina Kramarić,

Onn Shaun Thein, Dhruv Parekh

et al.

Metabolomics, Journal Year: 2025, Volume and Issue: 21(2)

Published: April 5, 2025

Abstract Introduction Infection with severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) leads to COVID19 disease and caused a worldwide pandemic in 2019. Since the first wave of infections, there has been significant antigenic shifts, leading emergence new variants. Today, infections have shifted away from severe, fatal infection seen Objective This study aimed assess how plasma metabolomes patients varied different strains could reflect severity. Methods Patients not requiring intensive care were recruited between January 2021 May 2022 Queen Elizabeth Hospital Birmingham; 33 alpha, 13 delta 14 omicron These compared 26 age matched contemporaneously controls. Plasma samples extracted into chloroform/methanol/water (1:2.5/1 v/v) assessed by flow injection electrospray mass spectrometry (FIE-MS) using an Exactive Orbitrap spectrometer. Derived data R based MetaboAnalyst platform. Results clearly Metabolite variation be related SARS-CoV2 Variant showed levels some phospholipids, ganglioside GD1a dihydroxyvitamin D3 derivative. Correlations indicated negative correlations selected phospholipids C-reactive protein, creatinine, neutrophil D-dimer. Conclusion The show changes, particularly which severity variant infection.

Language: Английский

Citations

0
A metabolic readout of the urine metabolome of COVID-19 patients DOI Open Access
Frutos C. Marhuenda‐Egea, Jennifer Narro-Serrano,

M. J. Shalabi-Benavent

et al.

Metabolomics, Journal Year: 2023, Volume and Issue: 19(2)

Published: Jan. 24, 2023

Language: Английский

Citations

9
Blood proteomics in COVID-19 infection: An update DOI
Michal Alexovič, Tetiana Bondarchuk,

Csilla Uličná

et al.

Clinica Chimica Acta, Journal Year: 2024, Volume and Issue: 562, P. 119881 - 119881

Published: July 20, 2024

Language: Английский

Citations

3
A Systematic Review of the Role of Purinergic Signalling Pathway in the Treatment of COVID-19 DOI Open Access
Vitoria Guero Korb, Iago Carvalho Schultz, Liziane Raquel Beckenkamp

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(9), P. 7865 - 7865

Published: April 26, 2023

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome 2 (SARS-CoV-2), has become a global health concern. Three years since its origin, despite the approval of vaccines and specific treatments against this new coronavirus, there are still high rates infection, hospitalization, mortality in some countries. COVID-19 is characterised inflammatory state coagulation disturbances that may be linked to purinergic signalling molecules such as adenosine triphosphate (ATP), diphosphate (ADP), (ADO), receptors (P1 P2). These nucleotides/nucleosides play important roles cellular processes, immunomodulation, blood clot formation, vasodilation, which affected during SARS-CoV-2 infection. Therefore, drugs targeting pathway, currently used for other pathologies, being evaluated preclinical clinical trials COVID-19. In review, we focus on potential these control release, degradation, reuptake extracellular nucleotides nucleosides treat Drugs P1 could have therapeutic efficacy due their capacity modulate cytokine storm immune response. Those acting P2X7, NLRP3 inflammasome activation, also valuable candidates they can reduce release pro-inflammatory cytokines. However, according available data, most promising medications treatment those platelets behaviour factors, mainly through P2Y12 receptor.

Language: Английский

Citations

8
Meta-Analysis of COVID-19 Metabolomics Identifies Variations in Robustness of Biomarkers DOI Open Access
Anthony Onoja, Johanna von Gerichten, Holly-May Lewis

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(18), P. 14371 - 14371

Published: Sept. 21, 2023

The global COVID-19 pandemic resulted in widespread harms but also rapid advances vaccine development, diagnostic testing, and treatment. As the disease moves to endemic status, need identify characteristic biomarkers of for diagnostics or therapeutics has lessened, lessons can still be learned inform biomarker research dealing with future pathogens. In this work, we test five sets research-derived against an independent targeted quantitative Liquid Chromatography–Mass Spectrometry metabolomics dataset evaluate how robustly these proposed panels would distinguish between COVID-19-positive negative patients a hospital setting. We further crowdsourced panel comprising most commonly mentioned literature 2020 2023. best-performing dataset—measured by F1 score (0.76) AUROC (0.77)—included nine biomarkers: lactic acid, glutamate, aspartate, phenylalanine, β-alanine, ornithine, arachidonic choline, hypoxanthine. Panels fewer metabolites performed less well, showing weaker statistical significance cohort than originally reported their respective discovery studies. Whilst studies reviewed here were small may subject confounders, it is desirable that resilient across cohorts if they are find use clinic, highlighting importance assessing robustness reproducibility analyses populations.

Language: Английский

Citations

7
Persisting Gastrointestinal Symptoms in Children with SARS-CoV-2: Temporal Evolution over 18 Months and Possible Role of Lactoferrin DOI Creative Commons
Francesco Mariani,

Saveena Rainaldi,

Giulia Dall’Ara

et al.

Children, Journal Year: 2024, Volume and Issue: 11(1), P. 105 - 105

Published: Jan. 15, 2024

Background and aim: Persisting gastrointestinal symptoms are reported to be relatively common in children with long COVID; however, their detailed characterization long-term outcomes have not yet been described. Methods: We performed a retrospective study aiming investigate the temporal evolution of SARS-CoV-2, from acute infection 18-months follow-up. To further possible therapeutic strategies, we evaluated role lactoferrin improving these children, compared those treated. Results: A total 1224 patients (47.7% females) were included. Of participants, 246 (19.8%) vaccinated 143 (11.5%) presented comorbidities. 175 (14.1%) during infection, 54 (4.4%) at three months, 23 (1.9%) six 6 (3.3%) twelve 2 (2.3%) eighteen months At follow-up, who treated 3 oral had less persisting did receive lactoferrin, although this difference was statistically significant (three (25%) group vs. fourteen (33.3%) treated, p = 0.73), probably due low number GI symptoms. Conclusions: SARS-CoV-2 non-negligible proportion for up 12–18 after infection. In addition, found trend even if nonsignificant toward faster improvement COVID lactoferrin. Despite limitations relating present study’s design, given burden COVID, our findings provide basis perform prospective, placebo-controlled study.

Language: Английский

Citations

2