Review
Biochemistry & Molecular Biology
Elettra Barberis, Shahzaib Khoso, Antonio Sica, Marco Falasca, Alessandra Gennari, Francesco Dondero, Antreas Afantitis, Marcello Manfredi
Summary: This review discusses the application of recent technological innovations in mass spectrometry to metabolomics analysis, with a focus on the use of artificial intelligence (AI) strategies. The article also explores the challenges and limitations of implementing metabolomics-AI systems, as well as recent tools and studies in disease classification and biomarker identification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Mahbuba Rahman, Herb E. Schellhorn
Summary: Infectious diseases remain a major cause of morbidity and mortality worldwide, and metabolomics has the potential to serve as diagnostic biomarkers and enable personalized treatment. However, achieving personalized medicine requires collaboration across multiple disciplines, including technological development, bioscience, bioinformatics, biostatistics, clinicians, and biotechnology companies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Alessandro Di Minno, Monica Gelzo, Marianna Caterino, Michele Costanzo, Margherita Ruoppolo, Giuseppe Castaldo
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)
Review
Biochemistry & Molecular Biology
Marine P. M. Letertre, Patrick Giraudeau, Pascal de Tullio
Summary: Personalized medicine aims to optimize therapies and patient care based on individual patient characteristics, with clinical metabolomics playing a crucial role in providing relevant information for stratifying patients and improving therapeutic outcomes. However, translating metabolomics from laboratory to clinical practice remains a challenge.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Microbiology
Lightson Ngashangva, Santanu Chattopadhyay
Summary: The gastrointestinal microbiota plays a crucial role in maintaining human health, and dysbiosis is associated with various diseases. Therefore, monitoring the composition and interactions of the gut microbiota is important for health information and disease predisposition. Early detection of pathogens and quantifying beneficial microbial strains is essential in preventing dysbiosis. However, routine monitoring of gut microbiota health is currently limited by conventional methods.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Biochemical Research Methods
Yousef Rasmi, Xiaokang Li, Johra Khan, Tugba Ozer, Jane Ru Choi
Summary: The COVID-19 pandemic poses a serious global health threat and there is an urgent need for rapid and user-friendly diagnostic tools. Point-of-care biosensors, including chip-based and paper-based biosensors, offer a promising solution for remote and resource-limited settings due to their rapid, affordable, and portable nature. The review highlights the importance of early diagnosis of COVID-19 and discusses the advancements in POC biosensors categorized into chip-based, paper-based, and other biosensors, with a focus on detecting key biomarkers. The commercial POC biosensors for COVID-19 are critically evaluated, along with key challenges and future perspectives in developing these emerging technologies.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Fabio Valenti, Italia Falcone, Sara Ungania, Flora Desiderio, Patrizio Giacomini, Chiara Bazzichetto, Fabiana Conciatori, Enzo Gallo, Francesco Cognetti, Gennaro Ciliberto, Aldo Morrone, Antonino Guerrisi
Summary: Treatment and management of metastatic melanoma have evolved significantly in the era of personalized medicine, benefiting from immunotherapy and advancements in multi-omics analyses. While improving clinical management, precision medicine plays a crucial role in guiding treatment decisions for individual patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Chemistry, Multidisciplinary
Celia Fuentes-Chust, Claudio Parolo, Giulio Rosati, Lourdes Rivas, Karla Perez-Toralla, Stephanie Simon, Itziar de Lecuona, Christophe Junot, Jonel Trebicka, Arben Merkoci
Summary: This review article discusses the potential of nanomaterials and nanobiosensing technologies in developing diagnostic devices for the human microbiome, defines the current and future landscape of microbiome-based diagnostics, and addresses the principal ethical, legal, and societal issues related to microbiome research and innovation.
ADVANCED MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Ana Barbosa, Alexander D. Edwards, Nuno M. Reis
Summary: This study conducted a systematic analysis using hundreds of actual microfluidic immunoassay fluoropolymer strips to investigate matrix interference in microflow systems. The experiment revealed that the key factor affecting serum matrix interference is capillary antibody surface coverage. A new approach for eliminating and/or minimizing serum matrix interference was proposed, focusing on antibody surface coverage and sample incubation times.
Review
Chemistry, Analytical
Monika Chhillar, Deepak Kukkar, Preeti Kukkar, Ki-Hyun Kim
Summary: Immunoassays have become an important analytical tool for the early-stage diagnosis and treatment monitoring of common diseases like chronic kidney disease (CKD). This review discusses the merits and demerits of various biomarkers for CKD diagnosis and explores different immunoassay types for detecting these biomarkers. It provides valuable insights into the recent advances in nanomaterial-antibody conjugate-based immunoassays for CKD-associated metabolites and biomarkers.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Health Care Sciences & Services
Umile Giuseppe Longo, Arianna Carnevale, Carlo Massaroni, Daniela Lo Presti, Alessandra Berton, Vincenzo Candela, Emiliano Schena, Vincenzo Denaro
Summary: The study proposes a personalized, predictive, participatory, precision, and preventive (P5) medicine model, highlighting the potential for tailoring diagnosis and therapy for patients with RC diseases by defining genetic predispositions and assessing lifestyle and environmental factors.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Health Care Sciences & Services
Samir Rachid Zaim, Colleen Kenost, Hao Helen Zhang, Yves A. Lussier
Summary: This study introduces a novel approach to develop reference standards for evaluating the accuracy of single-subject analyses in transcriptomes, proteomes, and metabolomes. By optimizing thresholding effect-size and expression-level, the study aimed to improve consensus between different analytical methods. Results demonstrated that robust reference standards can reduce bias and increase concordance among analytical methods.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Review
Chemistry, Multidisciplinary
Daria Semeniak, Daniela F. Cruz, Ashutosh Chilkoti, Maiken H. Mikkelsen
Summary: Fluorescence-based biosensors are widely used in life sciences and biomedical applications due to their low detection limits and the ability to measure multiple biomarkers simultaneously. Recent research efforts have focused on implementing these biosensors in the field of point-of-care testing (POCT), which aims to provide rapid and affordable diagnostic testing. However, fluorescence-based assays often yield weak signals at low analyte concentrations, requiring complex and expensive instrumentation to maintain high detection sensitivity. Metal- and metal oxide-based nanostructures offer a solution to this problem by generating high field enhancements near their surfaces, which can improve the performance of fluorophores. This article provides an overview of existing biosensors that employ nanostructures to enhance fluorescence and have the potential for use in POCT.
ADVANCED MATERIALS
(2023)
Article
Clinical Neurology
Eva Ceskova, Petr Silhan
Summary: Personalised medicine aims to provide individualized treatment for each patient, using quantifiable indicators to make decisions. Precision psychiatry is in its early stages, utilizing artificial intelligence and machine learning to gather and analyze sufficient data for diagnosis assessment and treatment planning.
NEUROPSYCHIATRIC DISEASE AND TREATMENT
(2021)
Review
Oncology
Kazuma Kiyotani, Yujiro Toyoshima, Yusuke Nakamura
Summary: The significant advances in cancer genomics have allowed for precision medicine based on genomic and molecular profiling, but clinical application still faces challenges. Cancer immunotherapies, particularly targeting neoantigens derived from somatic mutations, offer potential for precise treatment based on genomic sequencing results.
CANCER BIOLOGY & MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Christian Moguet, Camille Gonzalez, Antoine Sallustrau, Stephanie Gelhaye, Thierry Naas, Stephanie Simon, Herve Volland
Summary: The LFIA-CTX test is a highly efficient, rapid, low-cost lateral flow immunoassay method for detecting expanded-spectrum cephalosporin (ESC) hydrolytic activity. The results demonstrate the high sensitivity and specificity of this method for detecting cefotaxime-hydrolysing beta-lactamase, making it easy to implement in routine microbiology labs.
MICROBIAL BIOTECHNOLOGY
(2022)
Article
Agriculture, Multidisciplinary
Mariangela Tabone, Jose Angel Garcia-Merino, Carlo Bressa, Nuria Elizabeth Rocha Guzman, Karen Herrera Rocha, Emeline Chu Van, Florence A. Castelli, Francois Fenaille, Mar Larrosa
Summary: This study investigated the effects of cocoa intake on gastrointestinal symptoms, gut microbiota, and metabolites in endurance athletes during training. The results showed that cocoa had no significant impact on gastrointestinal symptoms or metabolites, but it did alter the abundance of certain gut bacteria genera.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemical Research Methods
Donatien Lefebvre, Francois Fenaille, Deborah Merda, Kevin Blanco-Valle, Cecile Feraudet-Tarisse, Stephanie Simon, Jacques-Antoine Hennekinne, Yacine Nia, Francois Becher
Summary: This study highlights the importance of improving the sensitivity of top-down mass spectrometry for the identification, differentiation, and absolute quantification of SEA sequence variants. By utilizing immunoaffinity enrichment, a protein internal standard, and optimized acquisition conditions, the top-down method demonstrated efficient identification and precise quantification of SEA variants, as well as providing a supplementary specificity criterion for quantification. The successful evaluation on enterotoxin-producing strains isolated during food poisoning outbreaks showcases the potential of top-down mass spectrometry in complementing traditional methods for toxin analysis.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Medicine, General & Internal
Christian Moguet, Camille Gonzalez, Thierry Naas, Stephanie Simon, Herve Volland
Summary: A multiplex lateral flow immunoassay (LFIA) was developed to detect cefotaxime-hydrolyzing activity and CTX-M enzymes. The LFIA showed high sensitivity and specificity, making it a rapid and accurate method for routine laboratory work.
Article
Chemistry, Analytical
Fanny Noirmain, Julie Dano, Nathalie Hue, Jesus M. Gonzalez-Jartin, Luis M. Botana, Denis Servent, Stephanie Simon, Romulo Araoz
Summary: This study presents a lateral flow test for the detection of cyclic imine toxins in shellfish. The test strips utilize lipoprotein vesicles immobilized in the test line, the high affinity of neurotoxins for their receptor targets, and high porosity glass fiber filter membranes as support. A novel GF/C glass fiber membrane stationary phase is used, and the mechanism of immobilization of electrocyte membrane vesicles in the membrane is investigated. The developed NeuroTorp is a portable and low-cost device for rapid detection of cyclic imine toxins in shellfish.
ANALYTICA CHIMICA ACTA
(2022)
Article
Oncology
Bryann Pardieu, Justine Pasanisi, Frank Ling, Reinaldo Dal Bello, Justine Penneroux, Angela Su, Romane Joudinaud, Laureen Chat, Hsin Chieh Wu, Matthieu Duchmann, Gaetano Sodaro, Clementine Chauvel, Florence A. Castelli, Loic Vasseur, Kim Pacchiardi, Yannis Belloucif, Marie-Charlotte Laiguillon, Eshwar Meduri, Camille Vaganay, Gabriela Alexe, Jeannig Berrou, Chaima Benaksas, Antoine Forget, Thorsten Braun, Claude Gardin, Emmanuel Raffoux, Emmanuelle Clappier, Lionel Ades, Hugues de The, Francois Fenaille, Brian J. Huntly, Kimberly Stegmaier, Herve Dombret, Nina Fenouille, Camille Lobry, Alexandre Puissant, Raphael Itzykson
Summary: By analyzing multiple AML datasets, we identified SLC7A11 as a potential gene that is essential for AML cell survival. Inhibition of SLC7A11 using genetic and chemical methods reduced the viability and clonogenic capacity of AML cell lines. Sulfasalazine, a drug with xCT inhibitory activity, showed anti-leukemic effects against primary AML samples in vitro. Inhibition of xCT affected multiple metabolic pathways, leading to depletion of glutathione pools and oxidative stress-induced cell death in leukemic cells.
Article
Biochemistry & Molecular Biology
Nihel Bekhti, Florence Castelli, Alain Paris, Blanche Guillon, Christophe Junot, Clemence Moiron, Francois Fenaille, Karine Adel-Patient
Summary: This study aimed to provide a comprehensive view of the metabolic composition of meconium by collecting 33 samples from 11 healthy newborns and analyzing its evolution during the first 3 days of life. A total of 229 metabolites from diverse origins and chemical classes were successfully identified. Statistical analysis revealed that sugars, amino acids, and some bacteria-derived metabolites were among the most impacted compounds during the first 3 days after birth.
Article
Biochemistry & Molecular Biology
Imene Bousahba, Jeremie David, Florence Castelli, Celine Chollet, Sadia Ouzia, Francois Fenaille, Didier Remond, Nathalie Poupin, Sergio Polakof
Summary: Obesity is a major contributor to the development of type 2 diabetes. This study aims to identify early phenotypes that precede T2D in diet-induced obese minipigs. Through analysis of various parameters, four distinct phenotypes were differentiated, and specific metabolomic signatures were identified in insulin resistant and progressively obese minipigs, potentially serving as biomarkers for early progression to T2D.
JOURNAL OF PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Baptiste Duceau, Michael Blatzer, Jean Bardon, Thibault Chaze, Quentin Giai Gianetto, Florence Castelli, Francois Fenaille, Lucie Duarte, Thomas Lescot, Christophe Tresallet, Bruno Riou, Mariette Matondo, Olivier Langeron, Pierre Rocheteau, Fabrice Chretien, Adrien Bougle
Summary: This study investigated the skeletal muscle of patients with septic shock using an integrative multi-omics approach and found that changes in mitochondrial pathways, metabolic reprogramming, and depletion of antioxidant capacities may be important factors in the distinctive signature of septic shock in skeletal muscle.
SCIENTIFIC REPORTS
(2022)
Article
Nanoscience & Nanotechnology
Lei Zhao, Giulio Rosati, Andrew Piper, Cecilia de Carvalho Castro e Silva, Liming Hu, Qiuyue Yang, Flavio Della Pelle, Ruslan R. Alvarez-Diduk, Arben Merkoci
Summary: Graphene-based materials have unique properties that make them suitable for electro-chemical biosensing. However, the production of graphene electrodes on a large scale remains challenging. This study presents a simple and fast method for fabricating reduced graphene oxide electrodes using direct writing and stamp-transferring techniques. The biosensors developed using these electrodes demonstrated excellent sensitivity and detection limits for Escherichia coli, making them suitable for real-world applications.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Gastroenterology & Hepatology
Emmanuel Weiss, Carlos de la Pena-Ramirez, Ferran Aguilar, Juan-Jose Lozano, Cristina Sanchez-Garrido, Patricia Sierra, Pedro Izquierdo-Bueno Martin, Juan Manuel Diaz, Francois Fenaille, Florence A. Castelli, Thierry Gustot, Wim Laleman, Agustin Albillos, Carlo Alessandria, Marco Domenicali, Paolo Caraceni, Salvatore Piano, Faouzi Saliba, Stefan Zeuzem, Alexander L. Gerbes, Julia A. Wendon, Christian Jansen, Wenyi Gu, Maria Papp, Raj Mookerjee, Carmine Gabriele Gambino, Cesar Jimenez, Ilaria Giovo, Giacomo Zaccherini, Manuela Merli, Antonella Putignano, Frank Erhard Uschner, Thomas Berg, Tony Bruns, Christian Trautwein, Alexander Zipprich, Rafael Banares, Jose Presa, Joan Genesca, Victor Vargas, Javier Fernandez, Mauro Bernardi, Paolo Angeli, Rajiv Jalan, Joan Claria, Christophe Junot, Richard Moreau, Jonel Trebicka, Vicente Arroyo
Summary: This study aimed to identify metabolites associated with short-term death in patients with acutely decompensated cirrhosis and design metabolomic prognostic models. Three prognostic metabolites strongly associated with death were selected and two models were built, which were found to be more accurate in predicting death within 7, 14, and 28 days compared to traditional scoring systems.
Article
Immunology
Karine Adel-Patient, Florence Campeotto, Marta Grauso, Blanche Guillon, Marco Moroldo, Eric Venot, Celine Dietrich, Francois Machavoine, Florence A. A. Castelli, Francois Fenaille, Thierry Jo Molina, Patrick Barbet, Christophe Delacourt, Maria Leite-de-Moraes, Guillaume Lezmi
Summary: This study provides a detailed description of local immunological and molecular components of EoE in children and identifies potential circulating EoE biomarkers. The results indicate that EoE is associated with dysregulation of both innate and adaptive immunity, as well as altered pathways related to epithelial cells and barrier functions. Combining metabolomics and cytokines data may offer a set of potential plasma biomarkers for EoE diagnosis.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jessica Michieletto, Aurelie Delvaux, Emeline Chu-Van, Christophe Junot, Francois Fenaille, Florence A. A. Castelli
Summary: The goal of this study was to develop a reliable and accurate untargeted metabolomics workflow to gain a deeper understanding of the metabolism of dendritic cells upon exposure to an infectious agent. The study found that dendritic cells undergo significant metabolic alterations upon infection, specifically in nucleotides, nucleotide sugars, polyamines, the TCA cycle, and the arginine pathway.
Article
Chemistry, Multidisciplinary
Yang Qiuyue, Emily P. Nguyen, David Panacek, Veronika Sedajova, Vitezslav Hruby, Giulio Rosati, de Carvalho Castro Silva Cecilia, Aristides Bakandritsos, Michal Otyepka, Arben Merkoci
Summary: Heavy metal pollutants are highly toxic and pose great concern in environmental monitoring. Electrochemical detection, hindered by mutual interferences of heavy metal ions, is a main technique with limited sensitivity to Cd2+ ions. This study introduces a metal-free and sustainable nanomaterial, cysteamine covalently functionalized graphene (GSH), which significantly enhances the sensitivity of screen-printed carbon electrode (SPCE) to Cd2+ ions while maintaining sensitivity to other heavy metals. The enhancement is attributed to the grafted thiols on the GSH sheets with strong affinity to Cd2+ ions, based on Pearson's principle. The GSH-modified SPCE also exhibits high reusability and outperforms existing SPCEs modified by non-covalently functionalized graphene derivatives. The GSH-SPCE is successfully validated in tap water.