Article
Biotechnology & Applied Microbiology
Peter D. Karp, Peter E. Midford, Ron Caspi, Arkady Khodursky
Summary: The choice of pathway database used in enrichment analyses can have a much stronger effect on the enrichment results than the statistical corrections used in these analyses.
Article
Biochemistry & Molecular Biology
Sofia Tsouka, Mojgan Masoodi
Summary: Pathway analysis is commonly used for functional interpretation of metabolomics data, but lacks standardization and understanding of its impact on functional outcome. In this study, we investigated the consideration of non-human native enzymatic reactions and interconnectivity of pathways in pathway analysis. Exclusion of non-human reactions resulted in loss of information, while considering pathway connectivity provided better emphasis on certain metabolites but occasionally overemphasized central compounds. We proposed a penalization scheme to mitigate the effect of such compounds. We also performed over-representation analysis to compare and assess different methodologies. Our findings raise awareness on the capabilities and shortcomings of current pathway analysis practices in metabolomics.
Article
Biochemical Research Methods
Xiaotao Shen, Chuchu Wang, Michael P. Snyder
Summary: Researchers have developed a tool called massDatabase which allows for the operation of online public databases for biological function mining. The tool is flexible, simple, and powerful, and can be installed on all platforms.
Article
Biochemical Research Methods
Magnus Palmblad, Sebastian Boecker, Sven Degroeve, Oliver Kohlbacher, Lukas Kall, William Stafford Noble, Mathias Wilhelm
Summary: This article discusses the specific guidelines for conducting and reporting machine learning in proteomics and metabolomics, emphasizing the importance of describing molecular structure, function, and physicochemical properties.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Chemistry, Analytical
Bernhard Seidl, Rainer Schuhmacher, Christoph Bueschl
Summary: The use of stable isotopically labeled tracers is an effective method in detecting and tracking metabolites. However, there is currently no software tool available for automatically searching user-defined isotopolog patterns in LC-HRMS data. CPExtract is a versatile software tool that allows high-throughput search for isotopolog patterns in LC-HRMS data.
ANALYTICAL CHEMISTRY
(2022)
Article
Immunology
Adam J. Berlinberg, Emilie H. Regner, Andrew Stahly, Ana Brar, Julie A. Reisz, Mark E. Gerich, Blair P. Fennimore, Frank I. Scott, Alison E. Freeman, Kristine A. Kuhn
Summary: The study identified significant alterations in tryptophan pathway metabolites, including an expansion of indole-3-acetate (IAA) and indole-3-acetaldehyde (I3Ald), in patients with axial spondyloarthritis (SpA) compared to other disease groups and healthy controls, suggesting a possible specificity in the development of axSpA. This indicates that tryptophan metabolism into I3Ald and then IAA may be a mechanism through which the gut microbiome potentially influences the pathophysiology of axSpA.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Clinical Neurology
Zerui You, Chengyu Wang, Xiaofeng Lan, Weicheng Li, Dewei Shang, Fan Zhang, Yanxiang Ye, Haiyan Liu, Yanling Zhou, Yuping Ning
Summary: This study reveals the metabolic differences between patients with treatment-resistant depression (TRD), first-episode drug-naive major depressive disorder (DN-MDD), and healthy controls (HCs), and identifies potential biomarkers. The analysis of metabolic pathways suggests that changes or imbalances in polyamine metabolism and energy metabolism may be primary altered pathways associated with depression.
PROGRESS IN NEURO-PSYCHOPHARMACOLOGY & BIOLOGICAL PSYCHIATRY
(2024)
Article
Biochemistry & Molecular Biology
Yannick Audet-Delage, Michele Rouleau, Lyne Villeneuve, Chantal Guillemette
Summary: Nucleotide sugar-dependent glycosyltransferases (UGTs) play critical roles in cellular metabolism, and this study reveals the impact of UGT expression on cellular metabolism. The expression of UGTs leads to modifications in multiple biochemical pathways, affecting glycolysis, pyrimidine pathways, and precursors of UDP-glucuronic acid metabolism. Furthermore, alternative splicing-derived isoforms of UGTs induce unique metabolic perturbations and extensive connectivity with other metabolic processes.
Article
Biochemical Research Methods
Zhuoru He, Zhongqiu Liu, Lingzhi Gong
Summary: This study revealed the pathogenesis of rheumatoid arthritis through metabolomics, constructed a biomarker panel for accurate prediction, and identified dysregulated metabolic pathways associated with RA.
Article
Agriculture, Multidisciplinary
Joon Hyuk Suh, Robert T. Madden, Jeehye Sung, Alan H. Chambers, Jonathan Crane, Yu Wang
Summary: The study used a metabolomics approach to investigate the biosynthetic mechanisms of key flavor compounds in mango fruits. Correlation analysis revealed the relationships between flavor precursors and compounds. The findings provide insights into the regulation of metabolic flux and the formation of key flavors in mango fruits.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Chemistry, Analytical
Isabel Ten-Domencech, Marta Moreno-Torres, Jose Vicene Castell, Guillermo Quintas, Julia Kuligowski
Summary: Extracting meaningful biological information from metabolomics data is challenging, but the Mantel test can help assess the significance of correlation in metabolic pathway analysis. It allows critical comparisons between different phenotypes, studies, and methods, aiding data interpretation and meta-analysis.
ANALYTICA CHIMICA ACTA
(2021)
Article
Plant Sciences
Hui Li, Shangling Han, Yiqiong Huo, Guifang Ma, Zhaoxia Sun, Hongying Li, Siyu Hou, Yuanhuai Han
Summary: This study identified and analyzed genes related to carotenoid metabolism in foxtail millet, revealing their correlation with carotenoid content and constructing a gene coexpression network. The findings provide insights into the regulatory network of carotenoid metabolism in foxtail millet, laying the foundation for genetic modification to enhance carotenoid content in the future.
Article
Biochemistry & Molecular Biology
Yajun Huang, Xuzhi Wan, Zexu Zhao, Hanqi Liu, Yuxi Wen, Weihao Wu, Xiaodong Ge, Chao Zhao
Summary: Paramylon produced by Euglena gracilis has antioxidant, antitumor, and hypolipidaemic functions. Glucose, as a carbon source, regulates the metabolism of E. gracilis, resulting in the differential expression of metabolites and the regulation of carbon and nitrogen balance through the GABA shunt. This study provides new insights into E. gracilis metabolism during paramylon synthesis.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Endocrinology & Metabolism
Yingxin Zheng, Yuemeng Zhu, Ting Zhuge, Bin Li, Chao Gu
Summary: Estrogen therapy is commonly used as a supplementary treatment for female infertility patients post-hysteroscopy, with protective functions that enhance endometrial regeneration and menstruation, inhibit recurrent adhesions, and improve conception rates. The pre-surgery endometrial protective function of estrogen administration remains controversial, but recent research suggests that estrogen can promote cell proliferation in endometrial tissues.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Agricultural Engineering
Manish Paul, Niteesh Kumar Pandey, Ayan Banerjee, Gireesh Kumar Shroti, Preeti Tomer, Rajesh Kumar Gazara, Hrudayanath Thatoi, Thallada Bhaskar, Saugata Hazra, Debashish Ghosh
Summary: This review focuses on the research progress of lignin-degrading microorganisms and enzymes associated with ligninolytic activity, which play a crucial role in the breakdown of lignocellulosic biomass. Analyzing multi-omics data highlights the potential value of fungal-produced enzymes in lignocellulosic material degradation, giving them an advantage in their ecological niches.
BIORESOURCE TECHNOLOGY
(2023)
Article
Chemistry, Analytical
Goncalo Graca, Yuheng Cai, Chung-Ho E. Lau, Panagiotis A. Vorkas, Matthew R. Lewis, Elizabeth J. Want, David Herrington, Timothy M. D. Ebbels
Summary: This paper proposes a novel approach for automated annotation of isotopologues, adducts, and in-source fragments from untargeted metabolomics and lipidomics LC-MS datasets. The method combines correlation-based parent-fragment linking with molecular fragment matching. The workflow demonstrates high precision and recall values and outperforms current state-of-the-art software for AIF data annotation.
ANALYTICAL CHEMISTRY
(2022)
Article
Nutrition & Dietetics
Queenie Chan, Gina M. Wren, Chung-Ho E. Lau, Timothy M. D. Ebbels, Rachel Gibson, Ruey Leng Loo, Ghadeer S. Aljuraiban, Joram M. Posma, Alan R. Dyer, Lyn M. Steffen, Beatriz L. Rodriguez, Lawrence J. Appel, Martha L. Daviglus, Paul Elliott, Jeremiah Stamler, Elaine Holmes, Linda Van Horn
Summary: Adherence to the DASH diet is associated with lower blood pressure and increased potassium intake. The DASH diet recommends consuming more fruits, vegetables, and potassium-rich foods to replace sodium-rich processed foods and influence blood pressure through metabolic pathways.
AMERICAN JOURNAL OF CLINICAL NUTRITION
(2022)
Article
Chemistry, Analytical
Rui Climaco Pinto, Ibrahim Karaman, Matthew R. Lewis, Jenny Hallqvist, Manuja Kaluarachchi, Goncalo Graca, Elena Chekmeneva, Brenan Durainayagam, Mohsen Ghanbari, M. Arfan Ikram, Henrik Zetterberg, Julian Griffin, Paul Elliott, Ioanna Tzoulaki, Abbas Dehghan, David Herrington, Timothy Ebbels
Summary: This article introduces a method to find feature correspondence between two similar LC-MS metabolomics experiments or batches using only the features' retention time, mass-to-charge ratio, and feature intensity. The effectiveness of the method is demonstrated through experiments on real and synthetic datasets.
ANALYTICAL CHEMISTRY
(2022)
Article
Immunology
Stanley Kimbung Mbandi, Hannah Painter, Adam Penn-Nicholson, Asma Toefy, Mzwandile Erasmus, Willem A. Hanekom, Thomas J. Scriba, Rachel P. J. Lai, Suzaan Marais, Helen A. Fletcher, Graeme Meintjes, Robert J. Wilkinson, Mark F. Cotton, Savita Pahwa, Mark J. Cameron, Elisa Nemes
Summary: Immune reconstitution inflammatory syndrome (IRIS) is a complication of antiretroviral therapy (ART) in patients with advanced HIV, but its pathogenesis is uncertain. This study found that immune-based blood transcriptomic signatures (RISK6 and Sweeney3) have the potential to predict and diagnose IRIS in HIV+ children and adults.
EUROPEAN JOURNAL OF IMMUNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Adam Amara, Clement Frainay, Fabien Jourdan, Thomas Naake, Steffen Neumann, Elva Maria Novoa-del-Toro, Reza M. Salek, Liesa Salzer, Sarah Scharfenberg, Michael Witting
Summary: Both targeted and untargeted mass spectrometry-based metabolomics approaches can be used to understand metabolic processes through network analysis. Network-based methods can provide insights into metabolism by connecting metabolites based on various relationships. These methods can address the challenges in metabolite identification and interpretation in untargeted metabolomics data analysis.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Oncology
Johnny R. Ostman, Rui C. Pinto, Timothy M. D. Ebbels, Elin Thysell, Goran Hallmans, Ali A. Moazzami
Summary: Prostate cancer is the most common cancer form in males in many European and American countries, but its etiology is still unclear. This study used untargeted metabolomics to analyze plasma samples from 752 PCa case-control pairs and identified new metabolites associated with PCa risk. The associations between different metabolites and risk varied depending on disease aggressiveness and baseline age.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Editorial Material
Engineering, Environmental
Cecilia Wieder, Jacob G. Bundy, Clement Frainay, Nathalie Poupin, Pablo Rodriguez-Mier, Florence Vinson, Juliette Cooke, Rachel P. J. Lai, Fabien Jourdan, Timothy M. D. Ebbels
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Biochemical Research Methods
Cecilia Wieder, Rachel P. J. Lai, Timothy M. D. Ebbels
Summary: This study evaluates the applicability of single sample pathway analysis methods in metabolomics, demonstrating the potential of ssPA methods through benchmarking with semi-synthetic metabolomics data and a case study on inflammatory bowel disease. Clustering/dimensionality reduction-based methods provide higher precision at moderate-to-high effect sizes, offering a deeper level of interpretation that conventional methods cannot provide.
BMC BIOINFORMATICS
(2022)
Review
Biochemistry & Molecular Biology
Timothy M. D. Ebbels, Justin J. J. van der Hooft, Haley Chatelaine, Corey Broeckling, Nicola Zamboni, Soha Hassoun, Ewy A. Mathe
Summary: The computational metabolomics field brings together experts from various disciplines to maximize the impact of metabolomics research. Advances in technology have generated complex datasets that require processing, annotation, modeling, and interpretation. Techniques for visualization, integration, and interpretation of metabolomics data have evolved alongside the development of databases and knowledge resources. This review highlights recent advances and discusses opportunities and innovations in response to challenges in the field.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2023)
Article
Nutrition & Dietetics
Alexis C. Wood, Goncalo Graca, Meghana Gadgil, Mackenzie K. Senn, Matthew A. Allison, Ioanna Tzoulaki, Philip Greenland, Timothy Ebbels, Paul Elliott, Mark O. Goodarzi, Russell Tracy, Jerome I. Rotter, David Herrington
Summary: This study investigated the relationship between red meat intake and inflammation. The results showed no significant association between processed or unprocessed red meat and markers of inflammation. However, unprocessed red meat intake was inversely associated with the plasma metabolite glutamine, which was also inversely associated with C-reactive protein levels.
AMERICAN JOURNAL OF CLINICAL NUTRITION
(2023)
Article
Nutrition & Dietetics
Alexis C. Wood, Mark O. Goodarzi, Mackenzie K. Senn, Meghana D. Gadgil, Goncalo Graca, Matthew A. Allison, Ioanna Tzoulaki, Michael Y. Mi, Philip Greenland, Timothy Ebbels, Paul Elliott, Russell P. Tracy, David M. Herrington, Jerome I. Rotter
Summary: Avocado intake is associated with metabolomic biomarkers related to glycemia. These biomarkers are strongly associated with lower fasting glucose, lower fasting insulin, and lower incidence of type 2 diabetes. However, the association between avocado intake and fasting insulin is attenuated when controlling for body mass index.
JOURNAL OF NUTRITION
(2023)
Review
Endocrinology & Metabolism
Michael T. Judge, Timothy M. D. Ebbels
Summary: This review aims to broaden the application of automated annotation tools by discussing the key ideas of spectral matching and describing a set of terms for classifying this information, thus advancing standards for communicating annotation confidence. Additionally, it hopes to facilitate collaboration between chemical data scientists, software developers, and the NMR metabolomics community for long-term software solutions.