Article
Biochemical Research Methods
Petra Tomasova, Petra Prochazkova, Radka Roubalova, Jiri Dvorak, Helena Tlaskalova-Hogenova, Martina Cermakova, Helena Pelantova, Blanka Sediva, Marek Vecka, Hana Papezova, Marek Kuzma
Summary: Metabolomic analysis reveals significant metabolic changes in patients with anorexia nervosa, highlighting the severity of system disruption and limited improvement after treatment.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
David J. Degnan, Kelly G. Stratton, Rachel Richardson, Daniel Claborne, Evan A. Martin, Nathan A. Johnson, Damon Leach, Bobbie-Jo M. Webb-Robertson, Lisa M. Bramer
Summary: The pmartR package is designed for QC and analysis of mass spectrometry data, specifically for proteomic, metabolomic, and lipidomic datasets. It has been expanded to include nuclear magnetic resonance metabolomic data and transcriptomic data analysis using DESeq2, edgeR, and limma-voom R packages. The package also offers improved statistics and visualization capabilities, including support for paired data and integration with the trelliscopejs R package.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Agriculture, Dairy & Animal Science
M. Ashokan, Ekta Rana, Kadimetla Sneha, C. Namith, G. S. Naveen Kumar, N. Azharuddin, K. Elango, S. Jeyakumar, K. P. Ramesha
Summary: Advancements in NMR and MS technologies, along with developments in omics sciences, have led to a better understanding of molecular mechanisms and pathways related to the physiological and pathological state of animals. Metabolomics, a post-genomics tool, provides valuable information about an organism's status by analyzing small molecular metabolites within a given time frame. Recently, researchers have focused on metabolomics studies in various fields of livestock management and precision dairying. This review aims to provide insights into the current research and application of metabolomics in different areas of livestock, including nutri-metabolomics, disease diagnosis advancements, reproductive disorders, pharmaco-metabolomics, genomics studies, and dairy production studies.
ANIMAL BIOTECHNOLOGY
(2022)
Review
Chemistry, Analytical
Dongyang Ye, Xiaowei Li, Jianzhong Shen, Xi Xia
Summary: Microbial metabolomics is an important field in systems biology, focusing on the analysis of metabolites in microorganisms. The complexity and diversity of microbial metabolites have hindered its progress, but with the development of new analytical techniques, microbial metabolomics has gained more attention for its ability to elucidate metabolic pathways and microbial-host interactions.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Review
Food Science & Technology
Shubo Li, Yufeng Tian, Pingyingzi Jiang, Ying Lin, Xiaoling Liu, Hongshun Yang
Summary: Metabolomics, as one of the omics fields, has unique advantages in facilitating the understanding of physiological and pathological activities in biology, physiology, pathology, and food science. This review highlights the current applications of metabolomics in food safety, food authenticity and quality, and food traceability, as well as the comprehensive description of combined use of metabolomics with other omics techniques for foodomics. Lastly, the critical discussion on the latest developments, practical challenges and limitations, and requirements related to the application of metabolomics provides new insight into its application in food analysis.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2021)
Review
Food Science & Technology
Tao Zhang, Can Chen, Kaizhou Xie, Jinyu Wang, Zhiming Pan
Summary: Metabolomics has been widely used in meat quality analysis and meat authentication in recent decades, showing promise in providing valuable insights for further research. This review provides a comprehensive overview of the concept, analytical techniques, and analysis workflow of metabolomics in meat science research, while also critically discussing the limitations, challenges, and future trends of its application.
Review
Biochemistry & Molecular Biology
Navneeta Bansal, Manoj Kumar, S. N. Sankhwar, Ashish Gupta
Summary: Prostate cancer presents challenges in early diagnosis and treatment, and there is a need for promising early diagnostic biomarkers. This review summarizes the existing metabolomics biomarkers for prostate cancer and evaluates their potential in clinical diagnosis and monitoring. The study finds that there are significant differences in technical procedures and statistical approaches between laboratories, and further validation is needed.
EXPERT REVIEWS IN MOLECULAR MEDICINE
(2022)
Review
Pharmacology & Pharmacy
Abdul-Hamid Emwas, Kacper Szczepski, Inas Al-Younis, Joanna Izabela Lachowicz, Mariusz Jaremko
Summary: Fluxomics is an innovative research field that measures intracellular flux rates in biological systems, providing insights into molecular interactions and metabolic pathways. It has become increasingly relevant in studying metabolic phenotypes.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Food Science & Technology
Mingchun Wen, Mengting Zhu, Zisheng Han, Chi-Tang Ho, Daniel Granato, Liang Zhang
Summary: This review summarizes the recent advances in tea metabolomics research. By using different analytical tools, the metabolite variation of tea leaves and the changes of chemical composition under different processing technologies were studied. The importance of metabolite identification process was also discussed.
COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY
(2023)
Article
Chemistry, Analytical
Tom van der Laan, Hyung Elfrink, Fatemeh Azadi-Chegeni, Anne-Charlotte Dubbelman, Amy C. Harms, Doris M. Jacobs, Ulrich Braumann, Aldrik H. Velders, John van Duynhoven, Thomas Hankemeier
Summary: In the field of metabolomics, the accurate identification of unknown compounds is crucial. A comprehensive identification workflow including LC-MS and NMR techniques was developed and successfully used to identify five taste-related features in soy sauce. Directed two-dimensional chromatography allowed for tailored fractionation of each feature, leading to the successful identification of proline-based 2,5-diketopiperazines which may contribute to taste through bitter or umami flavors.
ANALYTICA CHIMICA ACTA
(2021)
Review
Chemistry, Analytical
M. Fraga-Corral, M. Carpena, P. Garcia-Oliveira, A. G. Pereira, M. A. Prieto, J. Simal-Gandara
Summary: Metabolomics is a young field of knowledge that seeks to understand metabolites and their mechanisms of action. Various techniques such as NMR, MS, and VS are used to study the metabolome of biological samples. Each technique has its own advantages and limitations, and the choice depends on the research objectives and nature of the samples. Metabolomics has applications in environmental, food, and health sciences, and its growth is supported by advances in analytical techniques and integration with other omics.
CRITICAL REVIEWS IN ANALYTICAL CHEMISTRY
(2022)
Review
Agronomy
Nozomu Sakurai
Summary: Metabolomics plays a central role in crop improvement by monitoring chemical composition changes, clarifying cellular mechanisms, discovering markers and diagnostics, and predicting metabolite-genome relationships. However, a challenge lies in the wide array of instruments used and the ambiguity in metabolite identification and quantification.
Article
Chemistry, Analytical
Joanna Niziol, Krzysztof Ossolinski, Brian P. Tripet, Valerie Copie, Adrian Arendowski, Tomasz Ruman
Summary: Metabolic profiling of urine samples from kidney cancer patients and healthy volunteers using H-1 NMR and LDI MS identified potential urine biomarkers and significantly different mass spectral features, providing a framework for biomarker discovery in kidney cancer.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2021)
Review
Biochemistry & Molecular Biology
Miguel Esperanca-Martins, Iola F. Duarte, Mara Rodrigues, Joaquim Soares do Brito, Dolores Lopez-Presa, Luis Costa, Isabel Fernandes, Sergio Dias
Summary: The prognosis of soft tissue sarcomas (STS) is disappointing due to the lack of individualized treatment strategies and the neglect of specificities and genetic/metabolic differences among sarcoma subtypes. There is a need for more studies to decipher the mechanisms of sarcomagenesis, improve STS diagnosis precision, refine STS classification criteria, and identify prognostic biomarkers. Metabolomics, either as a single-omics approach or as part of a multi-omics strategy, provides valuable insights into the metabolic adaptations that support sarcomagenesis. Further studies employing various data acquisition methods have provided important information for the characterization of the STS metabolome. New methods based on chromatography, mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy, and flow cytometry will offer opportunities to target metabolic pathways therapeutically and monitor the response to such therapies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Federica Murgia, Lorena Lorefice, Antonio Noto, Martina Spada, Jessica Frau, Giuseppe Fenu, Giancarlo Coghe, Antonella Gagliano, Luigi Atzori, Eleonora Cocco
Summary: Current treatment for Multiple Sclerosis (MS) involves multidisciplinary approach and disease-modifying therapies. Metabolomics is used to identify biomarkers/predictors of treatment response. This study evaluated metabolic changes in MS patients starting Fingolimod treatment, finding specific metabolomic features that predict therapeutic response and potential side effects. The results showed that Fingolimod influences aminoacidic and energy metabolisms and reduces oxidative stress and immune system activity, characteristic of MS.
Article
Immunology
Kathryn C. Fitzgerald, Christopher A. Mecoli, Morgan Douglas, Samantha Harris, Berna Aravidis, Jemima Albayda, Elias S. Sotirchos, Ahmet Hoke, Ana-Maria Orbai, Michelle Petri, Lisa Christopher-Stine, Alan N. Baer, Julie J. Paik, Brittany L. Adler, Eleni Tiniakou, Homa Timlin, Pavan Bhargava, Scott D. Newsome, Arun Venkatesan, Vinay Chaudhry, Thomas E. Lloyd, Carlos A. Pardo, Barney J. Stern, Mark Lazarev, Brindusa Truta, Shiv Saidha, Edward S. Chen, Michelle Sharp, Nisha Gilotra, Edward K. Kasper, Allan C. Gelber, Clifton O. Bingham, Ami A. Shah, Ellen M. Mowry
Summary: The study shows that glucocorticoid exposure may increase the risk of COVID-19 in people with autoimmune or inflammatory conditions. Those with pandemic-related reduced income may be more vulnerable to disruptions in healthcare services.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Medicine, General & Internal
Sachin P. Gadani, Maria Reyes-Mantilla, Larissa Jank, Samantha Harris, Morgan Douglas, Matthew D. Smith, Peter A. Calabresi, Ellen M. Mowry, Kathryn C. Fitzgerald, Pavan Bhargava
Summary: This study found robust T cell responses in individuals with multiple sclerosis on anti-CD20 therapies despite a reduced humoral response to SARS-CoV-2 vaccination. Follow-up studies are needed to determine if this translates to protection against COVID-19 infection.
Letter
Clinical Neurology
Pavan Bhargava, Norman Haughey, Peter A. Calabresi
MULTIPLE SCLEROSIS JOURNAL
(2022)
Review
Clinical Neurology
Pavan Bhargava, Hans Peter Hartung, Peter A. Calabresi
Summary: This article reviews the role of B cells in mediating cortical demyelination and neuronal damage in multiple sclerosis. The authors summarize the evidence linking B cells to cortical injury, potential mechanisms by which B cells may mediate oligodendrocyte and neuronal death, and treatment strategies that could be used to target pathogenic B cells.
Article
Clinical Neurology
Dimitrios C. Ladakis, Pamela J. Yao, Michael Vreones, Joseph Blommer, Grigorios Kalaitzidis, Elias S. Sotirchos, Kathryn C. Fitzgerald, Shiv Saidha, Peter A. Calabresi, Dimitrios Kapogiannis, Pavan Bhargava
Summary: This study aimed to evaluate the relationship between levels of mitochondrial complex IV and V activity and brain and retinal atrophy in multiple sclerosis (MS). The results showed that higher mitochondrial complex IV activity and lower mitochondrial complex V activity levels were significantly associated with faster whole-brain volume atrophy. The findings suggest that mitochondrial measures in circulating extracellular vesicles could serve as potential biomarkers of disease progression in MS.
MULTIPLE SCLEROSIS JOURNAL
(2022)
Article
Clinical Neurology
Yaewon Kim, Alison W. Rebman, Tory P. Johnson, Hong Wang, Ting Yang, Carlo Colantuoni, Pavan Bhargava, Michael Levy, Peter A. Calabresi, John N. Aucott, Mark J. Soloski, Erika Darrah
Summary: This study investigates the expression of PAD2 gene in the human CNS and the presence of anti-PAD2 antibodies in patients with various neurologic diseases. The results show that anti-PAD2 antibodies are associated with less severe symptoms in subsets of patients with multiple sclerosis (MS) and post-treatment Lyme disease (PTLD).
FRONTIERS IN NEUROLOGY
(2022)
Article
Medicine, General & Internal
Kathryn C. Fitzgerald, Pavan Bhargava, Matthew D. Smith, Diane Vizthum, Bobbie Henry-Barron, Michael D. Kornberg, Sandra D. Cassard, Dimitrios Kapogiannis, Patrick Sullivan, David J. Baer, Peter A. Calabresi, Ellen M. Mowry
Summary: In people with multiple sclerosis, an intermittent calorie restriction diet is associated with reduction in memory T cell subsets and changes in certain lipid markers.
Article
Clinical Neurology
Dimitrios C. C. Ladakis, Pavan Bhargava
Summary: It has been found that the composition of gut microbiome is disturbed in patients with multiple sclerosis (MS), and its interaction with the immune system and brain may contribute to the development of the disease. The effects of the gut microbiota on MS may be mediated by direct interactions between bacteria and immune cells or through interactions of products of bacterial metabolism with immune and CNS cells. This review article summarizes the differences in gut microbiome composition between people with MS and controls, and examines the potential role of bacterial metabolites in the pathogenesis of MS, as well as approaches to modify the composition of gut microbiota in order to alleviate gut dysbiosis and impact the course of MS.
Article
Nutrition & Dietetics
Dohyup Kim, Emily E. Witt, Simone Schubert, Elias Sotirchos, Pavan Bhargava, Ellen M. Mowry, Karen Sachs, Biter Bilen, Lawrence Steinman, Avni Awani, Zihuai He, Peter A. Calabresi, Keith Van Haren
Summary: The gene expression profile of vitamin D in the immune system may vary by cell type. Future clinical studies should consider techniques that allow for cell-type resolution.
Article
Clinical Neurology
Akash Virupakshaiah, Dimitrios C. Ladakis, Bardia Nourbakhsh, Pavan Bhargava, Sonam Dilwali, Vinicius Schoeps, Kamil Borkowski, John W. Newman, Emmanuelle Waubant
Summary: This study found that altered serum lipid metabolites are associated with the risk of relapse and disability in children with multiple sclerosis (MS). Acylcarnitines and poly-unsaturated fatty acids were associated with higher relapse rates and disability, while phosphatidylethanolamines, plasmalogens, and primary bile acid metabolites were associated with lower relapse rates and lower disability. Examining lipid metabolism may provide a deeper understanding of pediatric MS.
MULTIPLE SCLEROSIS JOURNAL
(2023)
Article
Clinical Neurology
Dimitrios C. Ladakis, Maria Reyes-Mantilla, Sachin P. Gadani, Jackson W. Mace, Susana C. Dominguez-Penuela, Mayaa J. Appiah, Matthew D. Smith, Pavan Bhargava, Robert J. Fox, Shiv Saidha, Peter A. Calabresi
Summary: This study found that serum MIF levels were associated with brain atrophy in male PPMS patients, but not in SPMS patients. Ibudilast did not affect MIF levels.
MULTIPLE SCLEROSIS JOURNAL
(2023)
Article
Clinical Neurology
Dimitrios C. Ladakis, Jennifer Gould, Jenny M. Khazen, Julia M. Lefelar, Scott Tarpey, Charles J. Bies, Rebecca Salky, Kathryn C. Fitzgerald, Pavan Bhargava, Bardia Nourbakhsh, Elias S. Sotirchos
Summary: Unlike multiple sclerosis and neuromyelitis optica, the burden of fatigue in myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD) is unclear. This study compared fatigue levels between people with MOGAD and household controls (HC) and found that people with MOGAD reported more severe fatigue. Among MOGAD participants, higher age, history of bilateral optic neuritis, and current use of acute treatment were associated with higher fatigue severity.
MULTIPLE SCLEROSIS JOURNAL-EXPERIMENTAL TRANSLATIONAL AND CLINICAL
(2022)
Meeting Abstract
Clinical Neurology
Dimitrios C. Ladakis, Pamela J. Yao, Michael Vreones, Joseph Blommer, Grigorios Kalaitzidis, Elias S. Sotirchos, Kathryn C. Fitzgerald, Shiv Saidha, Peter A. Calabresi, Dimitrios Kapogiannis, Pavan Bhargava
ANNALS OF NEUROLOGY
(2022)
Meeting Abstract
Clinical Neurology
Emily M. Schorr, Alexander J. Gill, Matthew D. Smith, Alyssandra Valenzuela, Rachel Thero, Anna L. Duval, Ryan C. Winger, Jasmin Graziano, Christopher Harp, Alexandria Lewis, Hannah-Noelle Lord, Catherine Siu, Yasmin Resto, Annaelle Deslauriers, Pavan Bhargava, Shiv Saidha, Elias Sotirchos, Ellen M. Mowry, Peter A. Calabresi, Kathryn C. Fitzgerald
ANNALS OF NEUROLOGY
(2022)
Letter
Rheumatology
Pavan Bhargava
LANCET RHEUMATOLOGY
(2022)
