Article
Biochemistry & Molecular Biology
Sungtaek Oh, Yura Jang, Chan Hyun Na
Summary: This study used discovery-based approaches and quantitative comparative analyses to identify differential proteins in the cerebrospinal fluid (CSF) of patients with ALS. They found 15 proteins that showed significant differences between ALS and the control group, providing a foundation for biomarker research in ALS.
Article
Cell Biology
Yael Hirschberg, Natalia Valle-Tamayo, Oriol Dols-Icardo, Sebastiaan Engelborghs, Bart Buelens, Roosmarijn E. Vandenbroucke, Yannick Vermeiren, Kurt Boonen, Inge Mertens
Summary: Dementia is a leading cause of death worldwide, and this study focused on analyzing the proteome of cerebrospinal fluid (CSF) and CSF-derived extracellular vesicles (EVs) from patients with Alzheimer's disease, dementia with Lewy bodies, and Parkinson's disease dementia. The analysis identified differentially expressed proteins that can be helpful for differential diagnosis and offer new avenues for research into disease-specific pharmacological therapeutics.
JOURNAL OF EXTRACELLULAR VESICLES
(2023)
Article
Multidisciplinary Sciences
Nathalie Kyalu Ngoie Zola, Clemence Balty, Sebastien Pyr dit Ruys, Axelle A. T. Vanparys, Nicolas D. G. Huyghe, Gaetan Herinckx, Manuel Johanns, Emilien Boyer, Pascal Kienlen-Campard, Mark H. Rider, Didier Vertommen, Bernard J. Hanseeuw
Summary: Tau isoforms in insoluble aggregates differ between tauopathies, but not in soluble brain extracts. This study characterizes the post-translational modifications of aggregated and soluble tau protein in various tauopathies, revealing specific soluble signatures for each tauopathy.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Elodie Lamy, Lea Pilyser, Claire Paquet, Elodie Bouaziz-Amar, Stanislas Grassin-Delyle
Summary: A hydrophilic interaction liquid chromatography - mass spectrometry method was developed for the quantification of acetylcholine and choline in human cerebrospinal fluid, demonstrating high sensitivity and selectivity. The method showed excellent precision and accuracy, making it suitable for the analysis of cholinergic neurotransmission in human pathologies and drug effects study.
Article
Biochemical Research Methods
Shengnan Ji, Xiaomeng Liu, Jing Ha, Lianfeng Ai, Zheng Li
Summary: A sensitive and simple LC-MS/MS method was developed for the determination of orelabrutinib in human plasma and cerebrospinal fluid. The method involved simple protein precipitation, efficient separations, and optimized mass spectrometric conditions to increase selectivity and sensitivity. The method was validated for accuracy, precision, selectivity, linearity, recovery, matrix effect, stability, and limits of quantification. It exhibited a lower limit of quantification of 0.50 ng/mL, with intraday and interday precision RSD both less than 15%, and a recovery rate of 85.7%-92.9%. The method was successfully applied for quantitation in clinical patients treated with orelabrutinib.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Hans-Wolfgang Klafki, Oliver Wirths, Brit Mollenhauer, Thomas Liepold, Petra Rieper, Hermann Esselmann, Jonathan Vogelgsang, Jens Wiltfang, Olaf Jahn
Summary: Neurochemical biomarkers can aid in the diagnosis of Alzheimer's disease, and the A beta-3-40/A beta 1-42 ratio in blood plasma can accurately predict cerebral amyloid-beta pathology. The presence of A beta-3-40 and A beta-3-38 in human cerebrospinal fluid has been confirmed, and the ratio of CSF A beta-3-40/A beta 42 appears to be increased in individuals with amyloid-beta PET-positive results.
JOURNAL OF NEUROCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Sumaiya Nazli, Kip D. Zimmerman, Angelica M. Riojas, Laura A. Cox, Michael Olivier
Summary: The proteomic analysis of plasma has great potential for precision medicine and biomarker identification. However, detecting and quantifying low abundance proteins in plasma is challenging. This study developed a mass spectrometry approach using tandem mass tags (TMT) and a tissue reference sample, which successfully identified and quantified numerous proteins in nonhuman primate plasma samples. The methodology promises to increase the number of putative disease biomarkers by efficiently quantifying plasma proteins released from specific tissues.
Article
Immunology
Larissa van der Maas, Maarten Danial, Gideon F. A. Kersten, Bernard Metz, Hugo D. Meiring
Summary: A mass spectrometric method was developed to identify and quantify antigens in DTaP vaccines. The method can be used for both final batch release and in-process control monitoring, potentially reducing the need for animal testing.
Article
Neurosciences
Shaochun Zhu, David Backstrom, Lars Forsgren, Miles Trupp
Summary: The study identified candidate biomarkers and validated related proteins in parkinsonian disorders. Dopamine-drug naive PD patients at first diagnosis exhibit reduced levels of signaling neuropeptides, chaperones, and processing proteases. Subgroup specific candidate biomarkers were identified for different PD subgroups.
JOURNAL OF PARKINSONS DISEASE
(2022)
Review
Biochemistry & Molecular Biology
Besnik Muqaku, Patrick Oeckl
Summary: Mass spectrometry is an important technique for analyzing biomolecules, especially in the field of neurodegenerative diseases where peptidomics analysis of cerebrospinal fluid samples has played a crucial role.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Neurosciences
Nina Rostgaard, Markus Harboe Olsen, Maud Ottenheijm, Lylia Drici, Anja Hviid Simonsen, Peter Plomgaard, Hanne Gredal, Helle Harding Poulsen, Henrik Zetterberg, Kaj Blennow, Steen Gregers Hasselbalch, Nanna MacAulay, Marianne Juhler
Summary: This study aimed to compare the molecular composition of cerebrospinal fluid (CSF) obtained from the ventricular and the lumbar compartments and evaluate the feasibility of using lumbar CSF as a proxy for ventricular CSF. Results showed differences in protein composition and distribution of clinically employed biomarkers between the two compartments. However, for certain proteins and biomarkers, lumbar CSF can be reliably used as a proxy for ventricular CSF if a lumbar/cranial index has been established. It is important to verify the compartmental preference before extrapolating from lumbar CSF to ventricular fluid.
FLUIDS AND BARRIERS OF THE CNS
(2023)
Article
Biochemistry & Molecular Biology
Svitlana Rozanova, Julian Uszkoreit, Karin Schork, Bettina Serschnitzki, Martin Eisenacher, Lars Toenges, Katalin Barkovits-Boeddinghaus, Katrin Marcus
Summary: Proteomic studies using mass spectrometry (MS)-based quantification are important for discovering new biomarkers, but the accuracy of the outcomes can be affected by various analytical conditions. Therefore, it is crucial to assess the quality of the acquired data, including raw data, identification, and quantification levels. This study demonstrates the assessment of four independent datasets from cerebrospinal fluid, highlighting the impact of sample processing-based differences on the quality of quantitative data. Additionally, a free and open source quality control tool called MaCProQC is provided for systematic and rapid data comparison.
Article
Oncology
Jan Remsik, Jessica A. Wilcox, N. Esther Babady, Tracy A. McMillen, Behroze A. Vachha, Neil A. Halpern, Vikram Dhawan, Marc Rosenblum, Christine A. Iacobuzio-Donahue, Edward K. Avila, Bianca Santomasso, Adrienne Boire
Summary: Cancer patients with neurologic sequelae of COVID-19 have meningeal inflammatory cytokines without viral neuroinvasion, mainly driven by type II interferon and correlated with the degree of neurological dysfunction. The neuroinflammatory process persists weeks after recovery from acute respiratory infection, leading to long-term neurocognitive dysfunction. Anti-inflammatory treatments may play a role in managing neurological complications of COVID-19 infection.
Article
Multidisciplinary Sciences
Wade Self, Khader Awwad, John Paul Savaryn, Michael Schulz
Summary: We developed a method to quantify extracellular tau protein concentrations in human cerebrospinal fluid (CSF) without the need for antibody-based enrichment strategies. Our study demonstrated that the method can be used for quasi quantitative measurement of tau surrogate peptides in Alzheimer's Disease CSF. We also provided evidence that CSF total Tau measures by LC-MS are feasible even in the presence of monoclonal therapeutic antibodies in human CSF. Overall, our Tau LC-MS/MS method serves as a translational bioanalytical tool for assessing target engagement and pharmacodynamics in anti-tau antibody drug development.
Article
Biochemistry & Molecular Biology
Hilal A. Rather, Shalini Mishra, Yixin Su, Ashish Kumar, Sangeeta Singh, Biswapriya B. Misra, Jingyun Lee, Cristina M. Furdui, Lindsey R. Hamilton, Robert W. Gould, Susan H. Nader, Michael A. Nader, Gagan Deep
Summary: This study investigates the effects of prenatal cocaine use on postnatal development and long-term neurobiological outcomes. The researchers found that extracellular vesicles (EVs) could potentially serve as biomarkers to assess the adverse effects due to prenatal cocaine exposure.
Article
Biochemistry & Molecular Biology
Umberto De Marchi, Antonio Nunez Galindo, Jonathan Thevenet, Aurelie Hermant, Flavien Bermont, Steve Lassueur, Jaime Santo Domingo, Martin Kussmann, Loic Dayon, Andreas Wiederkehr
Article
Cell Biology
Jaime Santo-Domingo, Antonio Nunez Galindo, Ornella Cominetti, Umberto De Marchi, Pedro Cutillas, Loic Dayon, Andreas Wiederkehr
CELL COMMUNICATION AND SIGNALING
(2019)
Article
Biochemical Research Methods
Loic Dayon, Ornella Cominetti, Jerome Wojcik, Antonio Nunez Galindo, Aikaterini Oikonomidi, Hugues Henry, Eugenia Migliavacca, Martin Kussmann, Gene L. Bowman, Julius Popp
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Biochemical Research Methods
Roland Bruderer, Jan Muntel, Sebastian Muller, Oliver M. Bernhard, Tejas Gandhi, Ornella Cominetti, Charlotte Macron, Jerome Carayol, Oliver Rinner, Arne Astrup, Wim H. M. Saris, Jorg Hager, Armand Valsesia, Loic Dayon, Lukas Reiter
MOLECULAR & CELLULAR PROTEOMICS
(2019)
Review
Biochemistry & Molecular Biology
Jaime Santo-Domingo, Loiec Dayon, Andreas Wiederkehr
JOURNAL OF MOLECULAR BIOLOGY
(2020)
Review
Biochemical Research Methods
Loic Dayon, Michael Affolter
EXPERT REVIEW OF PROTEOMICS
(2020)
Article
Endocrinology & Metabolism
Isabelle Chareyron, Stefan Christen, Sofia Moco, Armand Valsesia, Steve Lassueur, Loic Dayon, Claes B. Wollheim, Jaime Santo Domingo, Andreas Wiederkehr
Article
Biochemical Research Methods
Loic Dayon, Charlotte Macron, Sabine Lahrichi, Antonio Nunez Galindo, Michael Affolter
Summary: A highly automated proteomic workflow for human milk sample analysis was developed, utilizing liquid chromatography mass spectrometry. Different workflows were evaluated and optimized, with the aim of allowing analysis of large sample cohorts in clinical research. This efficient workflow provides a new approach to studying the proteome of human milk.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Cell Biology
Miriam Valera-Alberni, Magali Joffraud, Joan Miro-Blanch, Jordi Capellades, Alexandra Junza, Loic Dayon, Antonio Nunez Galindo, Jose L. Sanchez-Garcia, Armand Valsesia, Angelique Cercillieux, Flavia Soellner, Andreas G. Ladurner, Oscar Yanes, Carles Canto
Summary: This study demonstrates the regulation of mitochondrial dynamics through the phosphorylation of Drp1 at the S579 and S600 sites, and its impact on mitochondrial remodeling, metabolic function, and glucose tolerance. The findings suggest an interplay between the phosphorylation sites of Drp1, which can modulate lipid oxidation, respiratory capacity, and thermogenic response. The results provide evidence for the potential use of Drp1 phosphorylation modulation in the treatment and prevention of metabolic diseases.
Article
Biology
Etienne Dubois, Antonio Nunez Galindo, Loic Dayon, Ornella Cominetti
Summary: Large-scale proteomic studies often deal with unwanted variability caused by multiple centers and analytical batches. Normalization of protein data is performed to remove such variability. However, there is a lack of comparative studies on normalization methods specifically for mass spectrometry-based proteomic data. In this study, different normalization methods were evaluated using a large MS-based proteomic dataset from an overweight and obese population. Results showed that quantile sample normalization, RUV, mean, and median centering performed well compared to other methods.
Review
Biochemical Research Methods
Loic Dayon, Ornella Cominetti, Michael Affolter
Summary: Biological fluids, such as blood and cerebrospinal fluid, are important samples for diagnostic testing and monitoring. Proteomic technologies have been used to identify protein biomarkers in these fluids, but with limited success. Recent advancements in technology and methodologies have allowed for better analysis of human biological fluids, and this review focuses on recent highlights in the field of proteomics using mass spectrometry. Despite being overshadowed by genomics, proteomic tools and methodologies have matured and are now better suited for discovering innovative and robust biofluid biomarkers.
EXPERT REVIEW OF PROTEOMICS
(2022)
Article
Biochemical Research Methods
Ornella Cominetti, Antonio Nunez Galindo, John Corthesy, Jerome Carayol, Natacha Germain, Bogdan Galusca, Bruno Estour, Joerg Hager, Nele Gheldof, Loic Dayon
Summary: This study compared the plasma proteome composition changes in constitutionally thin (CT) individuals and normal-weight individuals after overfeeding. The results showed that CT individuals had specific differences in their plasma proteome compared to normal-weight individuals at baseline, and these differences became more significant during and after overfeeding. CT individuals showed enhanced resilience and more rapid adaptation to changes. The study also identified specific proteins that were differentially regulated during overeating in CT individuals. These findings suggest that the resistance to weight gain in CT individuals is primarily biological.
PROTEOMICS CLINICAL APPLICATIONS
(2022)
Article
Chemistry, Analytical
Anton N. Kozhinov, Alex Johnson, Konstantin O. Nagornov, Michael Stadlmeier, Warham Lance Martin, Loic Dayon, John Corthesy, Martin Wuhr, Yury O. Tsybin
Summary: In multiplexed quantitative proteomics based on tandem mass spectrometry (MS2), complement reporter ion approaches (TMTc and TMTproC) have been developed to solve the ratio-compression problem of conventional MS2-level approaches. However, current mass resolution and scan speeds of OrbitrapTM instruments limit the quantification of complement reporter ions to a limited number of channels. This study demonstrates the feasibility of resolving 6.32 mDa-spaced complement reporter ions using a FusionTM LumosTM Orbitrap instrument with extended acquisition modes, and achieving shotgun proteomics-compatible scan rates through a super-resolution mass spectrometry approach using the least-squares fitting (LSF) method.
ANALYTICAL CHEMISTRY
(2023)
Article
Cell Biology
Jaime Santo-Domingo, Steve Lassueur, Antonio Nunez Galindo, Pilar Alvarez-Illera, Silvia Romero-Sanz, Elena Caldero-Escudero, Sergio de la Fuente, Loic Dayon, Andreas Wiederkehr
Summary: Glucose sensing in pancreatic D-cells relies on mitochondrial signals and oxidative phosphorylation to promote insulin secretion. SLC25A46, an outer mitochondrial membrane protein, was identified as a downstream effector of glucose-dependent signal transduction. It plays a role in mitochondrial dynamics and protects mitochondria from apoptosis under nutrient stress in INS-E cells.
JOURNAL OF CELL SCIENCE
(2023)
Article
Multidisciplinary Sciences
Charlotte Macron, Regis Lavigne, Antonio Nunez Galindo, Michael Affolter, Charles Pineau, Loic Dayon