Immune status assessment based on plasma proteomics with meta graph convolutional networks

BMC Genomics, Год журнала: 2025, Номер 26(1)

Опубликована: Апрель 10, 2025

Plasma proteins, especially immune-related are vital for assessing immune health and predicting disease risks. Despite their significance, the link between these proteins systemic function remains unclear. To bridge this gap, researchers developed ProMetaGCN, a model integrating meta-learning, graph convolutional networks, protein-protein interaction (PPI) data to evaluate status via plasma proteomics. This framework identified 309 factors with associated biological functions pathways. Using six machine learning methods, four algorithms (Random Forest, LightGBM, XGBoost, Lasso) were selected profiling aging analysis, revealing ADAMTS13, GDF15, SERPINF2 as key biomarkers. Validation across two COVID-19 cohorts confirmed model's robustness, showing correlates infection progression recovery. Furthermore, study proposed ImmuneAgeGap, novel metric linking profiles survival rates in non-small-cell lung cancer (NSCLC) patients. These insights advance personalized strategies prevention.

Язык: Английский

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Response Regarding: Using Machine Learning to Predict Weight Gain in Adults: An Observational Analysis from the All of Us Research Program

Journal of Surgical Research, Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

Язык: Английский

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Selective identification of epigenetic regulators at methylated genomic sites by SelectID

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Апрель 18, 2025

DNA methylation is a significant component in proximal chromatin regulation and plays crucial roles regulating gene expression maintaining the repressive state of retrotransposon elements. However, accurate profiling proteomics which simultaneously identifies specific sequences their associated epigenetic modifications remains challenge. Here, we report strategy termed SelectID (selective control at genome targets identified by dCas9), introduces methylated binding domain into dCas9-mediated proximity labeling system to enable situ protein capture repetitive elements with 5-methylcytosine (5mC) modifications. demonstrated as feasible dCas9-TurboID regions, such chromosome 9 satellite. Using SelectID, successfully identify CHD4 potential repressors long interspersed nuclear element-1 (LINE-1) through direct 5' untranslated region (5'UTR) young LINE-1 Overall, our approach has opened up avenues for uncovering regulators regions methylation, will greatly facilitate future studies on regulation.

Язык: Английский

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Dysregulated proteasome activity and steroid hormone biosynthesis are associated with mortality among patients with acute COVID-19

Journal of Translational Medicine, Год журнала: 2024, Номер 22(1)

Опубликована: Июль 4, 2024

Abstract The persistence of coronavirus disease 2019 (COVID-19)-related hospitalization severely threatens medical systems worldwide and has increased the need for reliable detection acute status prediction mortality. We applied a biology approach to discover acute-stage biomarkers that could predict A total 247 plasma samples were collected from 103 COVID-19 (52 surviving patients 51 with mortality), other infectious diseases (IDCs) 41 healthy controls (HCs). Paired obtained survival within 1 day after hospital admission 1–3 days before discharge. There clear differences between controls, as well substantial recovery phases COVID-19. Samples in phase showed suppressed immunity decreased steroid hormone biosynthesis, elevated inflammation proteasome activation. These findings validated by enzyme-linked immunosorbent assays metabolomic analyses larger cohort. Moreover, excessive activity was prominent signature among mortality, indicating it may be key cause poor prognosis. Based on these features, we constructed machine learning panel, including four proteins [C-reactive protein (CRP), subunit alpha type (PSMA)1, PSMA7, beta (PSMB)1)] one metabolite (urocortisone), mortality (area under receiver operating characteristic curve: 0.976) first hospitalization. Our systematic analysis provides novel method early hospitalized patients.

Язык: Английский

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Oral delivery of a chitosan adjuvanted COVID-19 vaccine provides long-lasting and broad-spectrum protection against SARS-CoV-2 variants of concern in golden hamsters

Antiviral Research, Год журнала: 2023, Номер 220, С. 105765 - 105765

Опубликована: Ноя. 28, 2023

Язык: Английский

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SARS-CoV-2 Omicron variant infection affects blood platelets, a comparative analysis with Delta variant

Frontiers in Immunology, Год журнала: 2023, Номер 14

Опубликована: Сен. 27, 2023

In November 2021, the SARS-CoV-2 Omicron variant of concern has emerged and is currently dominating COVID-19 pandemic over world. displays a number mutations, particularly in spike protein, leading to specific characteristics including higher potential for transmission. Although caused significant deaths worldwide, it generally induces less severe clinical signs compared earlier variants. As its impact on blood platelets remains unknown, we investigated platelet behavior patients infected with comparison Delta. Clinical biological (n=9) or Delta (n=11) variants were analyzed. Using complementary methods such as flow cytometry, confocal imaging electron microscopy, examined activation, responsiveness phenotype, presence virus induction selective autophagy. We also explored direct effect proteins from healthy signaling. Severe infection resulted activation partial desensitization, autophagy response. The intraplatelet processing viral cargo was different evidenced by distribution protein-positive structures near plasma membrane colocalization Rab7. Moreover, alone activated signaling pathways phosphorylation AKT, p38MAPK, LIMK SPL76 kinetics. prior variants, leads desensitization previously observed variant. found where autophagy, but mechanisms cargo, part innate response, differs Delta, suggesting that mutations protein modify interactions.

Язык: Английский

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Randomised controlled trial reveals no benefit to a 3-month delay in COVID-19 mRNA booster vaccine

Journal of Clinical Investigation, Год журнала: 2024, Номер 134(17)

Опубликована: Июль 11, 2024

BACKGROUNDThere is uncertainty about the timing of booster vaccination against COVID-19 in highly vaccinated populations during present endemic phase COVID-19. Studies focused on primary have previously suggested improved immunity with a longer interval between first and second vaccine doses.METHODSWe conducted randomized, controlled trial (November 2022-August 2023) assigned 52 fully adults to an immediate or 3-month delayed bivalent Spikevax mRNA vaccine. Follow-up visits were completed for 48 participants (n = 24 per arm), collection saliva plasma samples following each visit.RESULTSThe rise neutralizing antibody responses ancestral Omicron strains almost identical arms. Analyses salivary (IgG, IgA), antibody-dependent phagocytic activity, decay kinetics similar 2 Symptomatic asymptomatic SARS-CoV-2 infections occurred 49% (21 49) over median 11.5 months follow-up also arms.CONCLUSIONSOur data suggest that there was no benefit delaying preimmune COVID-19.TRIAL REGISTRATIONAustralian New Zealand Clinical Trials Registry number 12622000411741 (https://anzctr.org.au/Trial/Registration/TrialReview.aspx?ACTRN=12622000411741).FUNDINGNational Health Medical Research Council, Australia (program grant App1149990) Future Fund (App2005544).

Язык: Английский

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Ceramides As Potential New Predictors of the Severity of Acute Coronary Syndrome in Conjunction with SARS-CoV-2 Infection

Acta Naturae, Год журнала: 2024, Номер 16(2), С. 53 - 60

Опубликована: Авг. 21, 2024

Acute coronary events (ACEs) associated with a SARS-CoV-2 infection can significantly differ from classic ACEs. New biomarkers, such as ceramides, may help in the diagnosis and treatment of this disease. This study included 73 ACE patients for whom was verified. Two subgroups were formed: favorable outcome subgroup fatal subgroup. Plasma samples collected all at time admission metabolomic analysis. The analysis metabolites revealed that ceramide levels lower than survivor Therefore, determining ACEs conjunction COVID-19 assess prognosis these manage their risks.

Язык: Английский

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Integrative proteomics and metabolomics study reveal enhanced immune responses by COVID‐19 vaccine booster shot against Omicron SARS‐CoV‐2 infection

Journal of Medical Virology, Год журнала: 2023, Номер 95(11)

Опубликована: Ноя. 1, 2023

Since its outbreak in late 2021, the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely reported to be able evade neutralizing antibodies, becoming more transmissible while causing milder symptoms than previous SARS-CoV-2 strains. Understanding underlying molecular changes infection and corresponding host responses are important control COVID-19 pandemic. In this study, we report an integrative proteomics metabolomics investigation serum samples from 80 patients infected with SARS-CoV-2, as well 160 healthy individuals who had flu-like but were negative for infection. The multiomics results indicated that caused significant proteome metabolome comparing controls without COVID-19. Protein metabolite also pointed liver dysfunctions potential damage other organs by could roughly divided into two subgroups based on their differences. Interestingly, subgroup mostly received full vaccination booster shot fewer coughing symptom, changed sphingomyelin lipid metabolism, stronger immune including higher numbers lymphocytes, monocytes, neutrophils, upregulated proteins related CD4+ T cells, CD8+ effector memory cells (Tem), conventional dendritic revealing beneficial effects against through changes.

Язык: Английский

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COVID-19-Omics Report: From Individual Omics Approaches to Precision Medicine

Reports — Medical Cases Images and Videos, Год журнала: 2023, Номер 6(4), С. 45 - 45

Опубликована: Сен. 22, 2023

During the COVID-19 pandemic, it became apparent that precision medicine relies heavily on biological multi-omics discoveries. High throughput omics technologies, such as host genomics, transcriptomics, proteomics, epigenomics, metabolomics/lipidomics, and microbiomics, have become an integral part of diagnostics. The large number data generated by technologies allows for identification vulnerable demographic populations are susceptible to poor disease outcomes. Additionally, these help pinpoint omics-based biomarkers currently driving advancements in preventive medicine, early diagnosis prognosis, individualized treatments, vaccination. This report summarizes COVID-19-omic studies, highlights results completed ongoing investigations individuals who experienced severe outcomes, examines impact repurposed/novel antiviral drugs, targeted immunotherapeutics, vaccines had individual public health.

Язык: Английский

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