From Complexity to Clarity: Expanding Metabolome Coverage With Innovative Analytical Strategies

Journal of Separation Science, Journal Year: 2025, Volume and Issue: 48(2)

Published: Feb. 1, 2025

ABSTRACT Metabolomics, a powerful discipline within systems biology, aims at comprehensive profiling of small molecules in biological samples. The challenges sample complexity are addressed through innovative preparation methods, including solid‐phase extraction and microextraction techniques, enhancing the detection quantification low‐abundance metabolites. Advances chromatographic separation, particularly liquid chromatography (LC) gas (GC), coupled with high‐resolution (HR) mass spectrometry (MS), have significantly improved sensitivity, selectivity, throughput metabolomic studies. Cutting‐edge such as ion‐mobility (IM‐MS) tandem MS (MS/MS), further expand capacity for metabolite profiling. These advanced analytical platforms each offer unique advantages metabolomics, continued technological improvements driving deeper insights into metabolic pathways biomarker discovery. By providing detailed overview current trends this review to valuable future metabolomics human health research its translational potential clinical settings. Toward end, also highlights biomedical applications emphasizing role discovery, disease diagnostics, personalized medicine, drug development.

Language: Английский

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Multi-omics approaches for understanding gene-environment interactions in noncommunicable diseases: techniques, translation, and equity issues

Human Genomics, Journal Year: 2025, Volume and Issue: 19(1)

Published: Jan. 31, 2025

Non-communicable diseases (NCDs) such as cardiovascular diseases, chronic respiratory cancers, diabetes, and mental health disorders pose a significant global challenge, accounting for the majority of fatalities disability-adjusted life years worldwide. These arise from complex interactions between genetic, behavioral, environmental factors, necessitating thorough understanding these dynamics to identify effective diagnostic strategies interventions. Although recent advances in multi-omics technologies have greatly enhanced our ability explore interactions, several challenges remain. include inherent complexity heterogeneity multi-omic datasets, limitations analytical approaches, severe underrepresentation non-European genetic ancestries most omics which restricts generalizability findings exacerbates disparities. This scoping review evaluates landscape data related NCDs 2000 2024, focusing on advancements integration, translational applications, equity considerations. We highlight need standardized protocols, harmonized data-sharing policies, advanced approaches artificial intelligence/machine learning integrate study gene-environment interactions. also opportunities translating insights (GxE) research into precision medicine strategies. underscore potential advancing enhancing patient outcomes across diverse underserved populations, emphasizing fairness-centered strategic investments build local capacities underrepresented populations regions.

Language: Английский

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Redefining modern food analysis: Significance of omics analytical techniques integration, chemometrics and bioinformatics

TrAC Trends in Analytical Chemistry, Journal Year: 2024, Volume and Issue: 175, P. 117706 - 117706

Published: April 15, 2024

Language: Английский

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Exploring Molecular Mechanisms and Biomarkers in COPD: An Overview of Current Advancements and Perspectives

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(13), P. 7347 - 7347

Published: July 4, 2024

Chronic obstructive pulmonary disease (COPD) plays a significant role in global morbidity and mortality rates, typified by progressive airflow restriction lingering respiratory symptoms. Recent explorations molecular biology have illuminated the complex mechanisms underpinning COPD pathogenesis, providing critical insights into progression, exacerbations, potential therapeutic interventions. This review delivers thorough examination of latest progress research related to COPD, involving fundamental pathways, biomarkers, targets, cutting-edge technologies. Key areas focus include roles inflammation, oxidative stress, protease-antiprotease imbalances, alongside genetic epigenetic factors contributing susceptibility heterogeneity. Additionally, advancements omics technologies-such as genomics, transcriptomics, proteomics, metabolomics-offer new avenues for comprehensive profiling, aiding discovery novel biomarkers targets. Comprehending foundation carries substantial creation tailored treatment strategies enhancement patient outcomes. By integrating clinical practice, there is promising pathway towards personalized medicine approaches that can improve diagnosis, treatment, overall management ultimately reducing its burden.

Language: Английский

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Emerging trends and hot topics in the application of multi-omics in drug discovery: A bibliometric and visualized study

Current Pharmaceutical Analysis, Journal Year: 2024, Volume and Issue: 21(1), P. 20 - 32

Published: Dec. 1, 2024

Language: Английский

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Mass Spectrometry Advancements and Applications for Biomarker Discovery, Diagnostic Innovations, and Personalized Medicine

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(18), P. 9880 - 9880

Published: Sept. 12, 2024

Mass spectrometry (MS) has revolutionized clinical chemistry, offering unparalleled capabilities for biomolecule analysis. This review explores the growing significance of mass (MS), particularly when coupled with liquid chromatography (LC), in identifying disease biomarkers and quantifying biomolecules diagnostic prognostic purposes. The unique advantages MS accurately diverse molecules have positioned it as a cornerstone personalized-medicine advancement. MS-based technologies transformed precision medicine, enabling comprehensive understanding mechanisms patient-specific treatment responses. LC-MS shown exceptional utility analyzing complex biological matrices, while high-resolution expanded analytical capabilities, allowing detection low-abundance elucidation pathways. integration other techniques, such ion mobility spectrometry, opened new avenues biomarker discovery validation. As we progress toward will be crucial addressing challenges individualized patient care, driving innovations diagnosis, prognosis, strategies.

Language: Английский

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Proteomic Profiling Towards a Better Understanding of Genetic Based Muscular Diseases: The Current Picture and a Look to the Future

Biomolecules, Journal Year: 2025, Volume and Issue: 15(1), P. 130 - 130

Published: Jan. 15, 2025

Proteomics accelerates diagnosis and research of muscular diseases by enabling the robust analysis proteins relevant for manifestation neuromuscular in following aspects: (i) evaluation effect genetic variants on corresponding protein, (ii) prediction underlying defect based proteomic signature muscle biopsies, (iii) pathophysiologies different entities diseases, key definition new intervention concepts, (iv) patient stratification according to biochemical fingerprints as well (v) monitoring success therapeutic interventions. This review presents—also through exemplary case studies—the various advantages mass proteomics investigation discusses technical limitations, provides an outlook possible future application concepts. Hence, is excellent large-scale analytical tool diagnostic workup (hereditary) warrants systematic profiling pathophysiological processes. The steady development may allow overcome existing limitations including a quenched dynamic range quantification protein isoforms. Future directions include targeted settings using not only biopsies but also liquid address need minimally invasive procedures.

Language: Английский

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PROTRIDER: Protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 5, 2025

Structured abstract Motivation Detection of gene regulatory aberrations enhances our ability to interpret the impact inherited and acquired genetic variation for rare disease diagnostics tumor characterization. While numerous methods calling RNA expression outliers from RNA-sequencing data have been proposed, establishment protein mass spectrometry is lacking. Results Here we propose assess various modeling approaches call across three datasets oncology. We use as independent evidence enrichment outlier calls in matched RNA-seq samples variants likely disrupting expression. show that controlling hidden confounders technical covariates largely beneficial can be achieved using conditional autoencoders. Moreover, find differences between experimental fitted log-transformed intensities by such models exhibit heavy tails are poorly captured with Gaussian distribution report stronger statistical calibration when instead Student’s t-distribution. Our resulting method, PROTRIDER, outperformed baseline based on raw log-intensities Z-scores or differential analysis limma. The application PROTRIDER reveals significant enrichments AlphaMissense pathogenic outliers. Overall, provides a method confidently identify aberrantly expressed proteins applicable cancer proteomics. Availability Implementation freely available at github.com/gagneurlab/PROTRIDER . Contact Julien Gagneur: gagneur in.tum.de

Language: Английский

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Shaping the future of oral cancer diagnosis: advances in salivary proteomics

Expert Review of Proteomics, Journal Year: 2024, Volume and Issue: 21(4), P. 149 - 168

Published: April 2, 2024

Introduction Saliva has gained increasing attention in the quest for disease biomarkers. Because it is a biological fluid that can be collected an easy, painless, and safe way, been increasingly studied identification of oral cancer This particularly important because often diagnosed at late stages with poor prognosis.

Language: Английский

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Circulating Proteins as Diagnostic Markers in Gastric Cancer

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(23), P. 16931 - 16931

Published: Nov. 29, 2023

Gastric cancer (GC) is a highly malignant disease affecting humans worldwide and has poor prognosis. Most GC cases are detected at advanced stages due to the lacking early detectable symptoms. Therefore, there great interest in improving diagnosis by implementing targeted prevention strategies. Markers necessary for detection guide clinicians best personalized treatment. The current semi-invasive endoscopic methods detect invasive, costly, time-consuming. Recent advances proteomics technologies have enabled screening of many samples novel biomarkers disease-related signature signaling networks. These include circulating proteins from different fluids (e.g., plasma, serum, urine, saliva) extracellular vesicles. We review relevant published studies on protein detail their application as potential diagnosis. Identifying sensitive specific diagnostic markers may improve patient survival rates contribute advancing precision/personalized medicine.

Language: Английский

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