MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(W1), P. W398 - W406

Published: April 8, 2024

Abstract We introduce MetaboAnalyst version 6.0 as a unified platform for processing, analyzing, and interpreting data from targeted well untargeted metabolomics studies using liquid chromatography - mass spectrometry (LC–MS). The two main objectives in developing are to support tandem MS (MS2) processing annotation, the analysis of exposomics related experiments. Key features include: (i) significantly enhanced Spectra Processing module with MS2 asari algorithm; (ii) Peak Annotation based on comprehensive reference databases fragment-level annotation; (iii) new Statistical Analysis dedicated handling complex study design multiple factors or phenotypic descriptors; (iv) Causal estimating metabolite phenotype causal relations two-sample Mendelian randomization, (v) Dose-Response benchmark dose calculations. In addition, we have also improved MetaboAnalyst's visualization functions, updated its compound database sets, expanded pathway around 130 species. is freely available at https://www.metaboanalyst.ca.

Language: Английский

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Small molecule metabolites: discovery of biomarkers and therapeutic targets

Signal Transduction and Targeted Therapy, Journal Year: 2023, Volume and Issue: 8(1)

Published: March 20, 2023

Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks diseases. Metabolite signatures that have close proximity subject's phenotypic informative dimension, are useful for predicting diagnosis prognosis diseases as well monitoring treatments. The lack early biomarkers could poor serious outcomes. Therefore, noninvasive methods with high specificity selectivity desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool biomarker pathway analysis, revealing possible mechanisms human various deciphering therapeutic potentials. It help identify functional related variation delineate biochemical changes indicators pathological damage prior disease development. Recently, scientists established large number profiles reveal underlying networks target exploration in biomedicine. This review summarized analysis on potential value small-molecule candidate metabolites clinical events, may better diagnosis, prognosis, drug screening treatment. We also discuss challenges need be addressed fuel next wave breakthroughs.

Language: Английский

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Applications of multi‐omics analysis in human diseases

MedComm, Journal Year: 2023, Volume and Issue: 4(4)

Published: July 31, 2023

Multi-omics usually refers to the crossover application of multiple high-throughput screening technologies represented by genomics, transcriptomics, single-cell proteomics and metabolomics, spatial so on, which play a great role in promoting study human diseases. Most current reviews focus on describing development multi-omics technologies, data integration, particular disease; however, few them provide comprehensive systematic introduction multi-omics. This review outlines existing technical categories multi-omics, cautions for experimental design, focuses integrated analysis methods especially approach machine learning deep integration corresponding tools, medical researches (e.g., cancer, neurodegenerative diseases, aging, drug target discovery) as well open-source tools databases, finally, discusses challenges future directions precision medicine. With algorithms, important disease research, also provided detailed introduction. will guidance researchers, who are just entering into research.

Language: Английский

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Comprehensive investigation of pathway enrichment methods for functional interpretation of LC–MS global metabolomics data

Briefings in Bioinformatics, Journal Year: 2022, Volume and Issue: 24(1)

Published: Nov. 15, 2022

Global or untargeted metabolomics is widely used to comprehensively investigate metabolic profiles under various pathophysiological conditions such as inflammations, infections, responses exposures interactions with microbial communities. However, biological interpretation of global data remains a daunting task. Recent years have seen growing applications pathway enrichment analysis based on putative annotations liquid chromatography coupled mass spectrometry (LC-MS) peaks for functional LC-MS-based data. due intricate peak-metabolite and metabolite-pathway relationships, considerable variations are observed among results obtained using different approaches. There an urgent need benchmark these approaches inform the best practices.We conducted study common peak annotation methods in current studies. Representative approaches, including three four methods, were selected benchmarked scenarios. Based results, we provided set recommendations regarding annotation, ranking metrics feature selection. The overall better performance was mummichog approach. We that ~30% rate sufficient achieve high recall (~90% mummichog), semi-annotated improves interpretation. platforms further propose identifiability index indicate possibility being reliably identified. Finally, evaluated all 11 COVID-19 8 inflammatory bowel diseases (IBD) datasets.

Language: Английский

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Gut bacterial metabolism contributes to host global purine homeostasis

Cell Host & Microbe, Journal Year: 2023, Volume and Issue: 31(6), P. 1038 - 1053.e10

Published: June 1, 2023

The microbes and microbial pathways that influence host inflammatory disease progression remain largely undefined. Here, we show variation in atherosclerosis burden is partially driven by gut microbiota associated with circulating levels of uric acid (UA) mice humans. We identify bacterial taxa spanning multiple phyla, including Bacillota, Fusobacteriota, Pseudomonadota, use purines, UA as carbon energy sources anaerobically. a gene cluster encodes key steps anaerobic purine degradation widely distributed among gut-dwelling bacteria. Furthermore, colonization gnotobiotic purine-degrading bacteria modulates other purines the systemically. Thus, are important drivers global homeostasis serum levels, catabolism may represent mechanism which health.

Language: Английский

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Web-based multi-omics integration using the Analyst software suite

Nature Protocols, Journal Year: 2024, Volume and Issue: 19(5), P. 1467 - 1497

Published: Feb. 14, 2024

Language: Английский

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Determining a multimodal aging clock in a cohort of Chinese women

Med, Journal Year: 2023, Volume and Issue: 4(11), P. 825 - 848.e13

Published: July 28, 2023

Language: Английский

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Investigation of nephrotoxicity on mice exposed to polystyrene nanoplastics and the potential amelioration effects of DHA-enriched phosphatidylserine

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 892, P. 164808 - 164808

Published: June 10, 2023

Language: Английский

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Cardiometabolic characteristics of people with metabolically healthy and unhealthy obesity

Cell Metabolism, Journal Year: 2024, Volume and Issue: 36(4), P. 745 - 761.e5

Published: April 1, 2024

There is considerable heterogeneity in the cardiometabolic abnormalities associated with obesity. We evaluated multi-organ system metabolic function 20 adults metabolically healthy obesity (MHO; normal fasting glucose and triglycerides, oral tolerance, intrahepatic triglyceride content, whole-body insulin sensitivity), unhealthy (MUO; prediabetes, hepatic steatosis, resistance), 15 who were lean. Compared MUO, people MHO had (1) altered skeletal muscle biology (decreased ceramide content increased expression of genes involved BCAA catabolism mitochondrial structure/function); (2) adipose tissue inflammation extracellular matrix remodeling lipogenesis); (3) lower 24-h plasma glucose, insulin, non-esterified fatty acids, triglycerides; (4) higher adiponectin PAI-1 concentrations; (5) decreased oxidative stress. These findings provide a framework potential mechanisms responsible for This study was registered at ClinicalTrials.gov (NCT02706262).

Language: Английский

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Infant microbes and metabolites point to childhood neurodevelopmental disorders

Cell, Journal Year: 2024, Volume and Issue: 187(8), P. 1853 - 1873.e15

Published: April 1, 2024

This study has followed a birth cohort for over 20 years to find factors associated with neurodevelopmental disorder (ND) diagnosis. Detailed, early-life longitudinal questionnaires captured infection and antibiotic events, stress, prenatal factors, family history, more. Biomarkers including cord serum metabolome lipidome, human leukocyte antigen (HLA) genotype, infant microbiota, stool were assessed. Among the 16,440 Swedish children across time, 1,197 developed an ND. Significant associations emerged future ND diagnosis in general specific subtypes, spanning intellectual disability, speech disorder, attention-deficit/hyperactivity autism. investigation revealed microbiome connections as well early emerging mood gastrointestinal problems. The findings suggest links immunodysregulation metabolism, compounded by infection, antibiotics. convergence of biomarkers risk this prospective, on large-scale population establishes foundation prediction intervention neurodevelopment.

Language: Английский

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