Article
Biochemical Research Methods
Matthias S. Klein
Summary: Data from untargeted metabolomics studies using NMR spectroscopy often have negative values, which hinder data processing and multiomics integration. This study introduces a novel algorithm, ATNV, implemented in the R package mrbin, which successfully identifies relevant metabolites in human urinary NMR spectra.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Michael Altenbuchinger, Henry Berndt, Robin Kosch, Iris Lang, Juergen Doenitz, Peter J. Oefner, Wolfram Gronwald, Helena U. Zacharias
Summary: Untargeted metabolomics is a powerful tool for discovering disease biomarkers and understanding the underlying mechanisms. Nuclear magnetic resonance (NMR) spectroscopy, due to its reproducibility and cost effectiveness, is well-suited for large-scale untargeted metabolomics studies. This study introduces a novel 1D NMR feature extraction procedure called Bucket Fuser (BF), which improves the detection of metabolic biomarkers by dynamically constructing NMR metabolite features. BF outperforms existing methods in extracting metabolite signals and identifying statistically significant features in differential metabolite analyses. The BF algorithm is computationally efficient and can handle small sample sizes.
Article
Biochemical Research Methods
Frans A. A. Mulder, Leonardo Tenori, Cristina Licari, Claudio Luchinat
Summary: NMR is an important technology in metabolomics, but there are practical considerations that need to be addressed, such as the limitations of spin relaxation times, temperature regulation during sample exchanges, and the use of metabolomic fingerprinting techniques. By addressing these issues, NMR metabolomics can become more versatile.
JOURNAL OF MAGNETIC RESONANCE
(2023)
Article
Biochemistry & Molecular Biology
Tianqi Li, Tuulia Tynkkynen, Andrei Ihanus, Siyu Zhao, Ville-Petteri Makinen, Mika Ala-Korpela
Summary: This study systematically compared the effects of seven different normalization schemes in quantitative urinary metabolomics. It found that normalization methods have a significant impact on the associations between intra-urine metabolites, but only minor influences on epidemiological regression analyses with clinical/physiological measures. Multimetabolite normalization schemes showed consistent results with the customary creatinine reference. However, further research is needed for better understanding of intra-urine metabolite associations and nuanced interpretation of epidemiological associations.
Article
Chemistry, Multidisciplinary
Alvaro Mallagaray, Lorena Rudolph, Melissa Lindloge, Jarne Moelbitz, Henrik Thomsen, Franziska Schmelter, Mohamad Ward Alhabash, Mohammed R. Abdullah, Roza Saraei, Marc Ehlers, Tobias Graf, Christian Sina, Astrid Petersmann, Matthias Nauck, Ulrich L. Guenther
Summary: Nuclear Magnetic Resonance (NMR) spectra of human serum and plasma can identify the signals GlycA and GlycB, which come from the acetyl groups of glycoprotein glycans and serve as markers for inflammatory processes. This study provides a detailed assignment of glycoprotein glycan NMR signals in human serum, revealing that GlycA and GlycB signals correspond to specific N-glycans. The concentrations of acute phase glycoproteins, determined conventionally, show a strong correlation with distinctive features in the NMR spectra, enabling the simultaneous quantification of multiple acute phase inflammation proteins.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Greg A. Somerville, Allison A. Parrett, Joseph M. Reed, Stewart G. Gardner, Martha Morton, Robert Powers
Summary: The metabolic adaptation of Staphylococcus aureus in a complex environment is crucial for its antibiotic resistance.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Krzysztof Jan Abram, Douglas McCloskey
Summary: This study assesses the impact of commonly used and newly developed data preprocessing methods on the performance of deep learning in life science data analysis. It provides a set of best practices for researchers to start downstream tasks using deep learning.
Article
Biochemistry & Molecular Biology
Lukasz Boguszewicz, Agata Bielen, Mateusz Ciszek, Jacek Wendykier, Krzysztof Szczepanik, Agnieszka Skorupa, Jolanta Mrochem-Kwarciak, Krzysztof Skladowski, Maria Sokol
Summary: This study analyzed the nuclear magnetic resonance (NMR) blood serum metabolic profiles of 106 head and neck squamous cell carcinoma (HNSCC) patients during radio- and concurrent radio-chemotherapy, finding that seven metabolites were significantly altered by radiotherapy. The influence of irradiated volume on metabolic profile was weak, mainly correlating with inflammatory markers, creatinine, lymphocyte count, and branched-chain amino acids.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Obstetrics & Gynecology
Mathilde Bourdon, Pietro Santulli, Fatiha Kateb, Khaled Pocate-Cheriet, Frederic Batteux, Chloe Maignien, Sandrine Chouzenoux, Corinne Bordonne, Louis Marcellin, Gildas Bertho, Charles Chapron
Summary: The study found differences in serum metabolic profiles between patients with adenomyosis and the control group, with specific metabolic profiles observed in different adenomyosis phenotypes. These metabolic changes are associated with processes such as immune activation, cell proliferation, and cell migration.
FERTILITY AND STERILITY
(2021)
Article
Biochemical Research Methods
Alessia Vignoli, Leonardo Tenori, Cristina Morsiani, Paola Turano, Miriam Capri, Claudio Luchinat
Summary: Blood derivatives are commonly used in metabolomic clinical studies due to their low invasiveness and rich biological information. However, the choice of blood collection tubes can affect the metabolic content of plasma and serum. In this study, the metabolomic and lipoprotein profiles of blood samples collected using different tubes were compared. Results showed significant alterations in metabolites and correlations among the three blood matrices. The influence of blood collection tubes on lipoprotein profiles was also observed but to a lesser extent. Overcoming the issue of different collection tubes is crucial for scaling metabolomics and lipoprotein analysis in epidemiological studies. A statistical solution based on regression was proposed to reduce the alterations induced by different collection tubes for both metabolomic and lipoprotein profiles.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Clinical Neurology
Alireza M. Salehi, Ida A. K. Nilsson, Joao Figueirae, Laura M. Thornton, Israa Abdulkarim, Erik Palsson, Cynthia M. Bulik, Mikael Landen
Summary: The study found that lower serum concentrations of methanol in patients with anorexia nervosa and those who have recovered from the disorder may serve as either a trait marker or a scar effect of anorexia nervosa.
EUROPEAN NEUROPSYCHOPHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
R. Conde, R. Laires, L. G. Goncalves, A. Rizvi, C. Barroso, M. Villar, R. Macedo, M. J. Simoes, S. Gaddam, P. Lamosa, L. Puchades-Carrasco, A. Pineda-Lucena, A. B. Patel, S. C. Mande, S. Banerjee, M. Matzapetakis, A. Coelho
Summary: This study utilized Nuclear Magnetic Resonance based metabolomics to discover a signature of biomarkers for tuberculosis diagnosis. Six metabolites associated with TB infection were validated, in line with the recommendations of the World Health Organization.
BIOMEDICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Katarina Simic, Nina Todorovic, Snezana Trifunovic, Zoran Miladinovic, Aleksandra Gavrilovic, Silvana Jovanovic, Natasa Avramovic, Dejan Godevac, Ljubodrag Vujisic, Vele Tesevic, Ljubica Tasic, Boris Mandic
Summary: Schizophrenia is a common mental disorder that significantly impairs patients' functioning and leads to premature death. There are gaps in the understanding and diagnosis of this disease, but personalized and precise approaches are needed for patients through customized medical treatment and reliable monitoring of treatment response. Metabolomic investigations of serum samples of Serbian patients with schizophrenia led to the identification of 26 metabolites/biomarkers for this disorder. These findings provide a good starting point for the establishment of a universal set of biomarkers for schizophrenia, including metabolites that are common among different ethnic and geographic origins.
Article
Biochemistry & Molecular Biology
Melissa Quintero Escobar, Ljubica Tasic, Tassia Brena Barroso Carneiro da Costa, Danijela Stanisic, Silmara Montalvao, Stephany Huber, Joyce Maria Annichino-Bizzacchi
Summary: Deep venous thrombosis (DVT) is closely related to significant morbidity and mortality, and metabolomic analysis may provide valuable insights into detecting, diagnosing, monitoring, and treating the disease. Research has shown important serum differences in glucose, lipids, unsaturated lipids, and glycoprotein A between DVT patients and healthy individuals.
Article
Endocrinology & Metabolism
James Gerard Wolfsberger, Emily C. Hunt, Sai Sumedha Bobba, Sharifa Love-Rutledge, Bernhard Vogler
Summary: This study describes a pre-acquisition method of urine normalization, which adjusts for differences in the hydration state of each organism and results in a narrower concentration range in a targeted analysis.
Article
Chemistry, Analytical
Tamas Gyongyosi, Istvan Timari, Davy Sinnaeve, Burkhard Luy, Katalin E. Kover
Summary: The article introduces the important step of resonance assignment in nuclear magnetic resonance analysis, as well as a new method combining HSQC and COSY experiments for faster structure elucidation.
ANALYTICAL CHEMISTRY
(2021)
Article
Plant Sciences
Mohammad Reza Atighi, Bruno Verstraeten, Tim De Meyer, Tina Kyndt
Summary: Epigenetic processes, particularly histone modifications, play a crucial role in plant-nematode interactions, with a specific focus on H3K9 targeting plant defence-related genes.
MOLECULAR PLANT PATHOLOGY
(2021)
Article
Oncology
Rianne J. Hendriks, Marloes M. G. van der Leest, Bas Israel, Gerjon Hannink, Anglita YantiSetiasti, Erik B. Cornel, Christina A. Hulsbergen-van de Kaa, O. Sjoerd Klaver, J. P. Michiel Sedelaar, Wim Van Criekinge, Hans de Jong, Peter F. A. Mulders, E. David Crawford, Jeroen Veltman, Jack A. Schalken, Jelle O. Barentsz, Inge M. van Oort
Summary: This study evaluated the SelectMDx test as a tool to detect high-grade prostate cancer in biopsy-naive men, showing that it can avoid unnecessary biopsies in 38% of cases and minimize detection of low-grade PCa. The combination strategy with mpMRI showed the highest net benefit in clinical utility.
PROSTATE CANCER AND PROSTATIC DISEASES
(2021)
Article
Chemistry, Multidisciplinary
Bruno Linclau, Zhong Wang, Benjamin Jeffries, Jerome Graton, Rodrigo J. Carbajo, Davy Sinnaeve, Jean-Yves Le Questel, James S. Scott, Elisabetta Chiarparin
Summary: Efficient drug discovery relies on optimizing bioactivity and compound properties such as lipophilicity, guided by efficiency metrics; the use of conformer-specific lipophilicities is a less explored strategy; optimizing lipophilicity values for different conformers can create a novel avenue in drug discovery.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biotechnology & Applied Microbiology
Lea Girard, Niels Geudens, Brent Pauwels, Monica Hofte, Jose C. Martins, Rene De Mot
Summary: Pseudomonas lipopeptides are secondary metabolites with diverse ecological functions and biotechnological applications, and a reliable transporter gene-guided approach allows for the detection and classification of lipopeptide producers among Pseudomonas strains, providing a valuable tool for strain prioritization.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Aniko Meijer, Tim De Meyer, Klaas Vandepoele, Tina Kyndt
Summary: By investigating the expression of sRNAs in different stages of rice development, this study identified many potential regulators of rice yield and quality, highlighting their importance in optimizing rice production.
Article
Oncology
Maartje Massen, Kim Lommen, Kim A. D. Wouters, Johan Vandersmissen, Wim van Criekinge, James G. Herman, Veerle Melotte, Leo J. Schouten, Manon van Engeland, Kim M. Smits
Summary: DNA methylation biomarkers for cancer have great potential for early detection and treatment response, but their clinical implementation is limited. This study evaluated technical pitfalls in the development of DNA methylation biomarkers for colorectal cancer, including variation in assay location and design quality.
CLINICAL EPIGENETICS
(2022)
Review
Chemistry, Multidisciplinary
Isabelle Landrieu, Elian Dupre, Davy Sinnaeve, Lea El Hajjar, Caroline Smet-Nocca
Summary: Protein aggregation into amyloid fibrils is associated with human disorders and the mechanisms and co-factors involved in amyloid formation are still poorly understood. The role of amyloid fibrils in neurodegenerative diseases remains to be elucidated and finding drugs or therapies targeting amyloid formation is challenging. Chemical biology tools and protein engineering methods provide new insights into amyloid formation.
FRONTIERS IN CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Laurentijn Tilleman, Kaat Rubben, Wim Van Criekinge, Dieter Deforce, Filip Van Nieuwerburgh
Summary: This study tested the effectiveness of Targeted Locus Amplification (TLA) combined with Illumina or Nanopore sequencing in accurate genotyping and phasing of pharmacogenes. The results showed limited nucleotide mapping on target and incomplete coverage of genes with both sequencing methods. However, the optimized primer pair for the CYP2D6 gene in the Nanopore dataset resulted in correct haplotypes, indicating the potential reliability of this method with patient-specific primer design and optimization.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Catherine Cesa-Luna, Niels Geudens, Lea Girard, Vic De Roo, Hassan R. Maklad, Jose C. Martins, Monica Hofte, Rene De Mot
Summary: By mining the genomes of Pseudomonas species, we have mapped the global Pseudomonas lipopeptidome and found its impressive diversity to be linked to taxonomy of the producers. The synthesis of lipopeptides is facilitated by nonribosomal peptide synthetases (NRPSs), which assemble siderophores and lipopeptides. Our analysis also revealed that lipopeptide production is confined to the Pseudomonas fluorescens lineage and shows a correlation between NRPS and taxonomic affiliation.
Article
Chemistry, Multidisciplinary
Kevin Van Holsbeeck, Baptiste Fischer, Simon Gonzalez, Charlene Gadais, Wim Versees, Jose C. Martins, Charlotte Martin, Alexandre Wohlkoenig, Jan Steyaert, Steven Ballet
Summary: RAS proteins play a crucial role in regulating intracellular signaling networks and mutations that stabilize their active state are associated with cancer development. The study investigated the potential of developing peptide mimetics to modulate RAS signaling by mimicking the complementarity-determining region 3 (CDR3) of the regulatory guanine nucleotide exchange factor (GEF) son of sevenless 1 (SOS1). Through optimization and conformational rigidification, CDR3 mimetics with half of the maximal activation potential of Nanobody14 (Nb14) were obtained, demonstrating the feasibility of modulating protein-protein interactions through structural mimicry of a paratope.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Alessia Lasorsa, Krishnendu Bera, Idir Malki, Elian Dupre, Francois-Xavier Cantrelle, Hamida Merzougui, Davy Sinnaeve, Xavier Hanoulle, Jozef Hritz, Isabelle Landrieu
Summary: Phosphorylation of Tau protein is associated with Alzheimer's disease progression, and the interaction between Tau and BIN1 is modulated by phosphorylation. Nuclear magnetic resonance spectroscopy studies show that phosphorylation affects the local structure and dynamics of Tau peptide, which in turn affects the binding with BIN1.
Article
Biochemistry & Molecular Biology
Carlos A. Elena-Real, Amin Sagar, Annika Urbanek, Matija Popovic, Anna Morato, Alejandro Estana, Aurelie Fournet, Christine Doucet, Xamuel L. Lund, Zhen-Dan Shi, Luca Costa, Aurelien Thureau, Frederic Allemand, Rolf E. Swenson, Pierre-Emmanuel Milhiet, Ramon Crehuet, Alessandro Barducci, Juan Cortes, Davy Sinnaeve, Nathalie Sibille, Pau Bernado
Summary: Huntington's disease is caused by an expansion of CAG repeats in the HTT gene, resulting in an extended polyglutamine tract in huntingtin. Through site-specific isotopic labeling and NMR investigations, researchers have found that the polyglutamine tract adopts long alpha-helical conformations and that alpha-helical stability is more important than the number of glutamines in defining aggregation kinetics and fibril structure. These findings provide insights into the pathogenicity of the expanded huntingtin exon 1 and contribute to a better understanding of polyglutamine-related diseases.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Organic
Gabija Poskaite, David E. Wheatley, Neil Wells, Bruno Linclau, Davy Sinnaeve
Summary: Due to the complexity of the NMR spectra of reducing sugars caused by tautomeric equilibria, it is challenging to determine the coupling constant that is necessary for the analysis and assignment of substituents. This study demonstrates that 1D FESTA technique can be used to obtain individual spectra of both pyranoside and furanoside forms of reducing fluorosugars, providing a more complete characterization compared to the standard sel-TOCSY method. The power of FESTA is illustrated by the first full NMR characterization of several fluorosugars, including the important fluorosugar 2-deoxy-2-fluoroglucose.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Spectroscopy
Davy Sinnaeve
Summary: Selective 2D J-resolved spectroscopy has been improved and expanded upon over the years to observe a wider spectral bandwidth, achieve high-resolution full absorption mode line shapes, suppress couplings to nonselected spins, and avoid spectral overlap.