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

Andani Eka Putra,

Fenty Anggrainy

и другие.

Heliyon, Год журнала: 2023, Номер 10(1), С. e23579 - e23579

Опубликована: Дек. 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

Язык: Английский

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

и другие.

Frontiers in Molecular Biosciences, Год журнала: 2023, Номер 10

Опубликована: Фев. 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.

Язык: Английский

Процитировано

32
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

и другие.

Journal of Translational Medicine, Год журнала: 2025, Номер 23(1)

Опубликована: Апрель 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

Язык: Английский

Процитировано

2
Comprehensive proteomics and meta-analysis of COVID-19 host response DOI Creative Commons
Haris Babačić, Wanda Christ, J.E. Araújo

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 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.

Язык: Английский

Процитировано

21
Viral PIC-pocketing: RSV sequestration of translational preinitiation complexes into bi-phasic biomolecular condensates DOI Creative Commons
Fatoumatta Jobe, James T. Kelly,

Jennifer Simpson

и другие.

Journal of Virology, Год журнала: 2024, Номер 98(3)

Опубликована: Фев. 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 .

Язык: Английский

Процитировано

7
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

и другие.

Metabolomics, Год журнала: 2023, Номер 19(2)

Опубликована: Янв. 24, 2023

Язык: Английский

Процитировано

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

Csilla Uličná

и другие.

Clinica Chimica Acta, Год журнала: 2024, Номер 562, С. 119881 - 119881

Опубликована: Июль 20, 2024

Язык: Английский

Процитировано

3
SARS-CoV2 variants differentially impact on the plasma metabolome DOI Creative Commons

Tina Kramarić,

Onn Shaun Thein, Dhruv Parekh

и другие.

Metabolomics, Год журнала: 2025, Номер 21(2)

Опубликована: Апрель 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.

Язык: Английский

Процитировано

0
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

и другие.

International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(9), С. 7865 - 7865

Опубликована: Апрель 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.

Язык: Английский

Процитировано

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

и другие.

International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(18), С. 14371 - 14371

Опубликована: Сен. 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.

Язык: Английский

Процитировано

8
Circulating Peptidome Is Strongly Altered in COVID-19 Patients DOI Open Access
Gianluca Baldanzi, Beatrice Purghè, Beatrice Ragnoli

и другие.

International Journal of Environmental Research and Public Health, Год журнала: 2023, Номер 20(2), С. 1564 - 1564

Опубликована: Янв. 14, 2023

Whilst the impact of coronavirus disease 2019 (COVID-19) on host proteome, metabolome, and lipidome has been largely investigated in different bio-fluids, to date, circulating peptidome remains unexplored. Thus, present study aimed apply an untargeted peptidomic approach provide insight into alterations peptides development severity SARS-CoV-2 infection. The from COVID-19 severe mildly symptomatic patients negative controls was characterized using LC-MS/MS analysis for identification quantification purposes. Database search statistical allowed a complete characterization plasma detection most significant modulated that were impacted by Our results highlighted not only peptide abundance inversely correlates with severity, but also involvement biomolecules belonging inflammatory, immune-response, coagulation proteins/processes. Moreover, our data suggested possible changes protein degradation patterns. In research, first time, enabled potentially playing crucial role progression COVID-19.

Язык: Английский

Процитировано

6