☆ 4.6 Review

Metabolomics of infectious diseases in the era of personalized medicine

FRONTIERS IN MOLECULAR BIOSCIENCES (2023)

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Review Immunology

Systems-based approaches to study immunometabolism

Vinee Purohit et al.

Summary: Technical advances at the interface of biology and computation, such as single-cell RNA-sequencing (scRNA-seq), have uncovered new levels of complexity in cellular systems. The study of immune cell metabolism has emerged as a new area of investigation using the systems biology approach. However, there are several challenges, including the diversity of immune cell phenotypes, sparse immune cell numbers in vivo, limitations in metabolite identification, dynamic nature of cellular metabolism and metabolic fluxes, tissue specificity, and dependence on the local milieu. This review discusses the systemic nature of immunometabolism, cell- and system-based approaches, mathematical modeling techniques, and applications and challenges in metabolic modeling.

CELLULAR & MOLECULAR IMMUNOLOGY (2022)

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Review Biochemical Research Methods

Metabolomics for personalized medicine: the input of analytical chemistry from biomarker discovery to point-of-care tests

Florence Anne Castelli et al.

Summary: Metabolomics involves detecting, quantifying, and analyzing small molecules in biological samples on a large scale. While it has shown relevance for patient stratification in research projects and clinical studies, challenges related to standardization, metabolite identification, and data processing hinder its implementation in clinical practice, especially in personalized medicine. Streamlining complex molecular signatures and improving interoperability of data are crucial for the future integration of metabolomics into healthcare.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2022)

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Review Biochemistry & Molecular Biology

Challenges in Metabolomics-Based Tests, Biomarkers Revealed by Metabolomic Analysis, and the Promise of the Application of Metabolomics in Precision Medicine

Alessandro Di Minno et al.

Summary: Metabolomics plays a crucial role in characterizing and refining perturbations of biological pathways. Limitations in implementing metabolomics have been addressed, and potential biomarkers have been discovered. Metabolomics is critical for personalized diagnosis and treatment.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

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Editorial Material Genetics & Heredity

Editorial: Metabolomics in Infectious Diseases

Mahbuba Rahman et al.

FRONTIERS IN GENETICS (2022)

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Review Pharmacology & Pharmacy

Overcoming Mycobacterium tuberculosis through small molecule inhibitors to break down cell wall synthesis

Wenbin Kuang et al.

Summary: Mycobacterium tuberculosis (MTB) utilizes various mechanisms to acquire antibiotic resistance and protect itself through biofilm secretion. Developing innovative therapeutic strategies is essential to address the challenges associated with antibiotic resistance and tolerance. This paper discusses the critical roles of potential drug targets in regulating MTB cell wall synthesis and reviews the advanced progress in the development of novel compounds or drug leads for inhibiting cell wall synthesis.

ACTA PHARMACEUTICA SINICA B (2022)

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Review Cell Biology

Quality matters: International standards for biobanking

Georges Dagher

Summary: Human biospecimens are crucial for research in understanding human diseases and developing tailored treatments. Biobanks play a key role in collecting, processing, preserving, storing, and providing access to these resources. The standards outlined here aim to ensure high-quality samples and data for researchers, while maintaining ethical and legal compliance and efficient access procedures.

CELL PROLIFERATION (2022)

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Review Biochemistry & Molecular Biology

Isotope-Assisted Metabolic Flux Analysis: A Powerful Technique to Gain New Insights into the Human Metabolome in Health and Disease

Bilal Moiz et al.

Summary: Cell metabolism represents the coordinated changes in genes, proteins, and metabolites that occur in health and disease; quantifying metabolic fluxes requires sophisticated mathematical and computational analysis of data from isotope labeling experiments; isotope-assisted metabolic flux analysis (iMFA) is a rigorous computational approach for fluxome quantification.

METABOLITES (2022)

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Review Spectroscopy

STRATEGIES AND CHALLENGES IN METHOD DEVELOPMENT AND VALIDATION FOR THE ABSOLUTE QUANTIFICATION OF ENDOGENOUS BIOMARKER METABOLITES USING LIQUID CHROMATOGRAPHY-TANDEM MASS SPECTROMETRY

Mona M. Khamis et al.

Summary: Metabolomics is an important field with challenges in biomarker qualification for clinical applications, due to issues such as inappropriate study designs and insufficient data to support clinical utility. To address these challenges, modifications of existing guidelines and alternative approaches are being developed to facilitate method validation. The main challenges in method development and validation for endogenous metabolites include matrix effects evaluation, alternative analyte-free matrices, and the choice of internal standards.

MASS SPECTROMETRY REVIEWS (2021)

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Review Pharmacology & Pharmacy

Pharmacogenomics of Antiretroviral Drug Metabolism and Transport

Zaikuan J. Yu et al.

Summary: Antiretroviral therapy has greatly reduced morbidity and mortality for HIV patients, and individualized treatment regimens have the potential to further improve long-term management by mitigating treatment failure and drug-induced toxicities. Understanding drug metabolism and genetic influence on these pathways are crucial for personalizing HIV therapy.

ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY, VOL 61, 2021 (2021)

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Review Medicine, General & Internal

Metabolomics: The Stethoscope for the Twenty-First Century

Hutan Ashrafian et al.

Summary: Metabolomics involves the systematic identification and quantification of metabolic products in the human body, offering novel diagnostic biomarkers and personalized treatment response evaluation. Potential applications in clinical practice include disruptive innovations in oncology and metabolic medicine. Challenges to widespread clinical use include data interpretation scalability, sample handling standardization, and e-infrastructure.

MEDICAL PRINCIPLES AND PRACTICE (2021)

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Review Cardiac & Cardiovascular Systems

The evolving landscape of untargeted metabolomics

Alessandro Di Minno et al.

Summary: Untargeted Metabolomics and targeted Metabolomics have made significant progress in the field of life sciences, particularly in the discovery of biomarkers. Expertise in laboratory medicine and bioinformatics helps address challenges and biases in metabolite profiling. Clinical validation and profitability testing are essential steps in identifying potential biomarkers.

NUTRITION METABOLISM AND CARDIOVASCULAR DISEASES (2021)

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Review Immunology

Virus Infections and Host Metabolism-Can We Manage the Interactions?

Deepak Sumbria et al.

Summary: When viruses infect cells, they cause metabolic changes in both the infected and host cells, providing potential targets for therapeutic approaches. The immune system response also involves metabolic changes. The consequences of viral infections may differ in patients with metabolic problems.

FRONTIERS IN IMMUNOLOGY (2021)

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Review Pharmacology & Pharmacy

Metabolomics as a Truly Translational Tool for Precision Medicine

Julian C. Schmidt et al.

Summary: Metabolomics is a versatile omics technology that can be applied to metabolism and toxicity studies in various organisms and biological materials. It provides insights into biological response patterns and supports mechanistic studies, offering a range of resources and tools for analysis and pathway exploration. It is already available as a translational approach to facilitate precision medicine.

INTERNATIONAL JOURNAL OF TOXICOLOGY (2021)

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Review Medicine, Research & Experimental

Translational precision medicine: an industry perspective

Dominik Hartl et al.

Summary: In the era of precision medicine, drug discovery and development are undergoing unprecedented opportunities and challenges. By adopting new technologies and methods, the transition from serendipity-driven to data-driven approach is achieved, promoting the development of modern Translational Precision Medicine methods.

JOURNAL OF TRANSLATIONAL MEDICINE (2021)

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Article Oncology

The current landscape of the FDA approved companion diagnostics

Jan Trost Jorgensen

Summary: Predictive biomarkers play a key role in precision medicine, especially in the development of companion diagnostics for hematological and oncological drugs. The FDA has approved 44 CDx assays by the end of 2020, with diverse analytical platforms requiring rigorous regulatory pathways for approval.

TRANSLATIONAL ONCOLOGY (2021)

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Review Biochemistry & Molecular Biology

Metabolomics: small molecules that matter more

Balasubramanian Chellammal Muthubharathi et al.

Summary: Metabolomics is a high-throughput analytical study that helps understand the status and interactions of a biological system by analyzing small molecule metabolites. Global analysis of metabolome and pathways is needed for therapeutic applications, but understanding the complete network of metabolites in a biological system is challenging.

MOLECULAR OMICS (2021)

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Review Biochemistry & Molecular Biology

Metabolomics in infectious diseases and drug discovery

Vivian Tounta et al.

Summary: Metabolomics is a valuable tool used in conjunction with genomics, transcriptomics, and proteomics to understand host-pathogen interactions at the small-molecule level. Its main applications include prognostic and diagnostic purposes, as well as the discovery of druggable metabolic enzymes and regulators, and elucidation of metabolic mechanisms.

MOLECULAR OMICS (2021)

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Review Pathology

Companion and complementary diagnostics for infectious diseases

Peter J. Dailey et al.

EXPERT REVIEW OF MOLECULAR DIAGNOSTICS (2020)

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Review Biochemistry & Molecular Biology

Current Concepts in Pharmacometabolomics, Biomarker Discovery, and Precision Medicine

Richard D. Beger et al.

METABOLITES (2020)

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Article Biology

Met-Flow, a strategy for single-cell metabolic analysis highlights dynamic changes in immune subpopulations

Patricia J. Ahl et al.

COMMUNICATIONS BIOLOGY (2020)

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Review Biochemical Research Methods

Biobanks for life sciences and personalized medicine: importance of standardization, biosafety, biosecurity, and data management

Heimo Mueller et al.

CURRENT OPINION IN BIOTECHNOLOGY (2020)

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Review Genetics & Heredity

Milestones in Personalized Medicine: From the Ancient Time to Nowadays-the Provocation of COVID-19

Sophie Visvikis-Siest et al.

FRONTIERS IN GENETICS (2020)

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Review Biochemistry & Molecular Biology

Integrative Metabolomics to Identify Molecular Signatures of Responses to Vaccines and Infections

Joann Diray-Arce et al.

METABOLITES (2020)

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Review Microbiology

Factors That Influence the Immune Response to Vaccination

Petra Zimmermann et al.

CLINICAL MICROBIOLOGY REVIEWS (2019)

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Review Immunology

OMIC Technologies and Vaccine Development: From the Identification of Vulnerable Individuals to the Formulation of Invulnerable Vaccines

Nicola Cotugno et al.

JOURNAL OF IMMUNOLOGY RESEARCH (2019)

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Article Multidisciplinary Sciences

A framework for tracer-based metabolism in mammalian cells by NMR

Raquel Saborano et al.

SCIENTIFIC REPORTS (2019)

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Review Medical Laboratory Technology

Preanalytical Processing and Biobanking Procedures of Biological Samples for Metabolomics Research: A White Paper, Community Perspective (for Precision Medicine and Pharmacometabolomics Task Group-The Metabolomics Society Initiative)

Jennifer A. Kirwan et al.

CLINICAL CHEMISTRY (2018)

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Article Biochemical Research Methods

Metabolomics in the clinic: A review of the shared and unique features of untargeted metabolomics for clinical research and clinical testing

Adam D. Kennedy et al.

JOURNAL OF MASS SPECTROMETRY (2018)

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Editorial Material Pathology

Clinical metabolomics: a pivotal tool for companion diagnostic development and precision medicine

Vladimir Tolstikov et al.

EXPERT REVIEW OF MOLECULAR DIAGNOSTICS (2017)

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Review Immunology

Metabolic Adaptations of Uropathogenic E. coli in the Urinary Tract

Riti Mann et al.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2017)

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Review Medicine, General & Internal

Host-Directed Therapeutic Strategies for Tuberculosis

Afsal Kolloli et al.

FRONTIERS IN MEDICINE (2017)

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Article Microbiology

1H NMR spectroscopy-based metabolomics analysis for the diagnosis of symptomatic E. coli-associated urinary tract infection (UTI)

Milena Lussu et al.

BMC MICROBIOLOGY (2017)

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Review Medicine, Research & Experimental

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Sunil Mathur et al.

BIOMEDICAL REPORTS (2017)

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Article Critical Care Medicine

Plasma metabolomics for the diagnosis and prognosis of H1N1 influenza pneumonia

Mohammad M. Banoei et al.

CRITICAL CARE (2017)

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Review Microbiology

Challenges of metabolomics in human gut microbiota research

Kirill S. Smirnov et al.

INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY (2016)

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Article Chemistry, Medicinal

Metabolomics as a Challenging Approach for Medicinal Chemistry and Personalized Medicine

Michel Frederich et al.

JOURNAL OF MEDICINAL CHEMISTRY (2016)

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Article Multidisciplinary Sciences

Genetic Influences on Metabolite Levels: A Comparison across Metabolomic Platforms

Idil Yet et al.

PLOS ONE (2016)

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Article Microbiology

Metabolic Requirements of Escherichia coli in Intracellular Bacterial Communities during Urinary Tract Infection Pathogenesis

Matt S. Conover et al.

MBIO (2016)

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Editorial Material Medicine, Research & Experimental

Companion diagnostics at the intersection of personalized medicine and healthcare delivery Foreword

Scott A. Waldman et al.

BIOMARKERS IN MEDICINE (2015)

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Review Genetics & Heredity

From big data analysis to personalized medicine for all: challenges and opportunities

Akram Alyass et al.

BMC MEDICAL GENOMICS (2015)

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Review Pharmacology & Pharmacy

Beyond traditional pharmacology: new tools and approaches

E. V. Gurevich et al.

BRITISH JOURNAL OF PHARMACOLOGY (2015)

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Editorial Material Pathology

Companion diagnostics: the key to personalized medicine

Jan Trost Jorgensen

EXPERT REVIEW OF MOLECULAR DIAGNOSTICS (2015)

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Review Gastroenterology & Hepatology

Role of IL28B for chronic hepatitis C treatment toward personalized medicine

Kentaro Matsuura et al.

JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY (2014)

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Review Biochemical Research Methods

Metabolomics plafforms for genome wide association studies-linking the genome to the metabolome

Jerzy Adamski et al.

CURRENT OPINION IN BIOTECHNOLOGY (2013)

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Article Pharmacology & Pharmacy

P4 medicine: how systems medicine will transform the healthcare sector and society

Mauricio Flores et al.

PERSONALIZED MEDICINE (2013)

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Article Endocrinology & Metabolism

Biomarker Discovery and Translation in Metabolomics

G. A. Nagana Gowda et al.

CURRENT METABOLOMICS (2013)

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Review Health Care Sciences & Services

Infectious Disease Management through Point-of-Care Personalized Medicine Molecular Diagnostic Technologies

Luc Bissonnette et al.

JOURNAL OF PERSONALIZED MEDICINE (2012)

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Review Oncology

Biobanking: the foundation of personalized medicine

Robert E. Hewitt

CURRENT OPINION IN ONCOLOGY (2011)

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Review Neurosciences

Metabolomics: Moving to the Clinic

Anders Nordstrom et al.

JOURNAL OF NEUROIMMUNE PHARMACOLOGY (2010)

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Review Pharmacology & Pharmacy

Metabolomics: A global biochemical approach to drug response and disease

Rima Kaddurah-Daouk et al.

ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY (2008)

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