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  1. Article ; Online: Cross-Validation of Metabolic Phenotypes in SARS-CoV-2 Infected Subpopulations Using Targeted Liquid Chromatography-Mass Spectrometry (LC-MS).

    Whiley, Luke / Lawler, Nathan G / Zeng, Annie Xu / Lee, Alex / Chin, Sung-Tong / Bizkarguenaga, Maider / Bruzzone, Chiara / Embade, Nieves / Wist, Julien / Holmes, Elaine / Millet, Oscar / Nicholson, Jeremy K / Gray, Nicola

    Journal of proteome research

    2024  Volume 23, Issue 4, Page(s) 1313–1327

    Abstract: To ensure biological validity in metabolic phenotyping, findings must be replicated in independent sample sets. Targeted workflows have long been heralded as ideal platforms for such validation due to their robust quantitative capability. We evaluated ... ...

    Abstract To ensure biological validity in metabolic phenotyping, findings must be replicated in independent sample sets. Targeted workflows have long been heralded as ideal platforms for such validation due to their robust quantitative capability. We evaluated the capability of liquid chromatography-mass spectrometry (LC-MS) assays targeting organic acids and bile acids to validate metabolic phenotypes of SARS-CoV-2 infection. Two independent sample sets were collected: (1) Australia: plasma, SARS-CoV-2 positive (
    MeSH term(s) Humans ; SARS-CoV-2 ; Liquid Chromatography-Mass Spectrometry ; Chromatography, Liquid/methods ; COVID-19 ; Tandem Mass Spectrometry/methods ; Phenotype ; Bile Acids and Salts
    Chemical Substances Bile Acids and Salts
    Language English
    Publishing date 2024-03-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.3c00797
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  2. Article ; Online: Zona Pellucida sperm-binding protein 3 receptor distribution during Gopc

    Bizkarguenaga, Maider / Gomez-Santos, Laura / Madrid, Juan Francisco / Sáez, Francisco José / Alonso, Edurne

    Microscopy research and technique

    2021  Volume 85, Issue 4, Page(s) 1454–1464

    Abstract: Globozoospermia is a type of teratozoospermia characterized by round morphology of the sperm head. ... ...

    Abstract Globozoospermia is a type of teratozoospermia characterized by round morphology of the sperm head. Gopc
    MeSH term(s) Acrosome/metabolism ; Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Golgi Matrix Proteins/metabolism ; Male ; Mice ; Receptors, Cell Surface/metabolism ; Seminal Plasma Proteins ; Spermatids ; Spermatogenesis ; Spermatozoa/physiology ; Zona Pellucida
    Chemical Substances Adaptor Proteins, Signal Transducing ; Golgi Matrix Proteins ; Gopc protein, mouse ; Receptors, Cell Surface ; Seminal Plasma Proteins ; sp56 protein, mouse ; spermadhesin
    Language English
    Publishing date 2021-12-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1099714-3
    ISSN 1097-0029 ; 1059-910X
    ISSN (online) 1097-0029
    ISSN 1059-910X
    DOI 10.1002/jemt.24009
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  3. Article ; Online: Characterization of preovulatory follicular fluid secretome and its effects on equine oocytes during in vitro maturation.

    Luis-Calero, Marcos / Marinaro, Federica / Fernández-Hernández, Pablo / Ortiz-Rodríguez, José M / G Casado, Javier / Pericuesta, Eva / Gutiérrez-Adán, Alfonso / González, Esperanza / Azkargorta, Mikel / Conde, Ricardo / Bizkarguenaga, Maider / Embade, Nieves / Elortza, Félix / Falcón-Pérez, Juan M / Millet, Óscar / González-Fernández, Lauro / Macías-García, Beatriz

    Research in veterinary science

    2024  Volume 171, Page(s) 105222

    Abstract: In vitro maturation (IVM) of oocytes is clinically used in horses to produce blastocysts but current conditions used for horses are suboptimal. We analyzed the composition of equine preovulatory follicular fluid (FF) secretome and tested its effects on ... ...

    Abstract In vitro maturation (IVM) of oocytes is clinically used in horses to produce blastocysts but current conditions used for horses are suboptimal. We analyzed the composition of equine preovulatory follicular fluid (FF) secretome and tested its effects on meiotic competence and gene expression in oocytes subjected to IVM. Preovulatory FF was obtained, concentrated using ultrafiltration with cut-off of 10 kDa, and stored at -80 °C. The metabolic and proteomic composition was analyzed, and its ultrastructural composition was assessed by cryo-transmission microscopy. Oocytes obtained post-mortem or by ovum pick up (OPU) were subjected to IVM in the absence (control) or presence of 20 or 40 μg/ml (S20 or S40) of secretome. Oocytes were then analyzed for chromatin configuration or snap frozen for gene expression analysis. Proteomic analysis detected 255 proteins in the Equus caballus database, mostly related to the complement cascade and cholesterol metabolism. Metabolomic analysis yielded 14 metabolites and cryo-transmission electron microscopy analysis revealed the presence of extracellular vesicles (EVs). No significant differences were detected in maturation rates among treatments. However, the expression of GDF9 and BMP15 significantly increased in OPU-derived oocytes compared to post-mortem oocytes (fold increase ± SEM: 9.4 ± 0.1 vs. 1 ± 0.5 for BMP15 and 9.9 ± 0.3 vs. 1 ± 0.5 for GDF9, respectively; p < 0.05). Secretome addition increased the expression of TNFAIP6 in S40 regardless of the oocyte source. Further research is necessary to fully understand whether secretome addition influences the developmental competence of equine oocytes.
    MeSH term(s) Female ; Horses ; Animals ; Follicular Fluid/chemistry ; Follicular Fluid/metabolism ; Proteomics ; Secretome ; Meiosis ; Oocytes/metabolism ; In Vitro Oocyte Maturation Techniques/veterinary
    Language English
    Publishing date 2024-03-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 840961-4
    ISSN 1532-2661 ; 0034-5288
    ISSN (online) 1532-2661
    ISSN 0034-5288
    DOI 10.1016/j.rvsc.2024.105222
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  4. Article: Metabolic Features of Increased Gut Permeability, Inflammation, and Altered Energy Metabolism Distinguish Agricultural Workers at Risk for Mesoamerican Nephropathy.

    Raines, Nathan H / Leone, Dominick A / O'Callaghan-Gordo, Cristina / Ramirez-Rubio, Oriana / Amador, Juan José / Lopez Pilarte, Damaris / Delgado, Iris S / Leibler, Jessica H / Embade, Nieves / Gil-Redondo, Rubén / Bruzzone, Chiara / Bizkarguenaga, Maider / Scammell, Madeleine K / Parikh, Samir M / Millet, Oscar / Brooks, Daniel R / Friedman, David J

    Metabolites

    2023  Volume 13, Issue 3

    Abstract: Mesoamerican nephropathy (MeN) is a form of chronic kidney disease found predominantly in young men in Mesoamerica. Strenuous agricultural labor is a consistent risk factor for MeN, but the pathophysiologic mechanism leading to disease is poorly ... ...

    Abstract Mesoamerican nephropathy (MeN) is a form of chronic kidney disease found predominantly in young men in Mesoamerica. Strenuous agricultural labor is a consistent risk factor for MeN, but the pathophysiologic mechanism leading to disease is poorly understood. We compared the urine metabolome among men in Nicaragua engaged in sugarcane harvest and seed cutting (
    Language English
    Publishing date 2023-02-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662251-8
    ISSN 2218-1989
    ISSN 2218-1989
    DOI 10.3390/metabo13030325
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  5. Article: Prospective Metabolomic Studies in Precision Medicine: The AKRIBEA Project.

    Bizkarguenaga, Maider / Gil-Redondo, Rubén / Bruzzone, Chiara / Bernardo-Seisdedos, Ganeko / Laín, Ana / González-Valle, Beatriz / Embade, Nieves / Mato, José M / Millet, Oscar

    Handbook of experimental pharmacology

    2022  Volume 277, Page(s) 275–297

    Abstract: For a long time, conventional medicine has analysed biomolecules to diagnose diseases. Yet, this approach has proven valid only for a limited number of metabolites and often through a bijective relationship with the disease (i.e. glucose relationship ... ...

    Abstract For a long time, conventional medicine has analysed biomolecules to diagnose diseases. Yet, this approach has proven valid only for a limited number of metabolites and often through a bijective relationship with the disease (i.e. glucose relationship with diabetes), ultimately offering incomplete diagnostic value. Nowadays, precision medicine emerges as an option to improve the prevention and/or treatment of numerous pathologies, focusing on the molecular mechanisms, acting in a patient-specific dimension, and leveraging multiple contributing factors such as genetic, environmental, or lifestyle. Metabolomics grasps the required subcellular complexity while being sensitive to all these factors, which results in a most suitable technique for precision medicine. The aim of this chapter is to describe how NMR-based metabolomics can be integrated in the design of a precision medicine strategy, using the Precision Medicine Initiative of the Basque Country (the AKRIBEA project) as a case study. To that end, we will illustrate the procedures to be followed when conducting an NMR-based metabolomics study with a large cohort of individuals, emphasizing the critical points. The chapter will conclude with the discussion of some relevant biomedical applications.
    MeSH term(s) Humans ; Precision Medicine ; Prospective Studies ; Metabolomics/methods ; Diabetes Mellitus/metabolism ; Biomarkers
    Chemical Substances Biomarkers
    Language English
    Publishing date 2022-10-18
    Publishing country Germany
    Document type Journal Article
    ISSN 0171-2004
    ISSN 0171-2004
    DOI 10.1007/164_2022_610
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  6. Article: Diagnostic Potential of the Plasma Lipidome in Infectious Disease: Application to Acute SARS-CoV-2 Infection.

    Gray, Nicola / Lawler, Nathan G / Zeng, Annie Xu / Ryan, Monique / Bong, Sze How / Boughton, Berin A / Bizkarguenaga, Maider / Bruzzone, Chiara / Embade, Nieves / Wist, Julien / Holmes, Elaine / Millet, Oscar / Nicholson, Jeremy K / Whiley, Luke

    Metabolites

    2021  Volume 11, Issue 7

    Abstract: Improved methods are required for investigating the systemic metabolic effects of SARS-CoV-2 infection and patient stratification for precision treatment. We aimed to develop an effective method using lipid profiles for discriminating between SARS-CoV-2 ... ...

    Abstract Improved methods are required for investigating the systemic metabolic effects of SARS-CoV-2 infection and patient stratification for precision treatment. We aimed to develop an effective method using lipid profiles for discriminating between SARS-CoV-2 infection, healthy controls, and non-SARS-CoV-2 respiratory infections. Targeted liquid chromatography-mass spectrometry lipid profiling was performed on discovery (20 SARS-CoV-2-positive; 37 healthy controls; 22 COVID-19 symptoms but SARS-CoV-2negative) and validation (312 SARS-CoV-2-positive; 100 healthy controls) cohorts. Orthogonal projection to latent structure-discriminant analysis (OPLS-DA) and Kruskal-Wallis tests were applied to establish discriminant lipids, significance, and effect size, followed by logistic regression to evaluate classification performance. OPLS-DA reported separation of SARS-CoV-2 infection from healthy controls in the discovery cohort, with an area under the curve (AUC) of 1.000. A refined panel of discriminant features consisted of six lipids from different subclasses (PE, PC, LPC, HCER, CER, and DCER). Logistic regression in the discovery cohort returned a training ROC AUC of 1.000 (sensitivity = 1.000, specificity = 1.000) and a test ROC AUC of 1.000. The validation cohort produced a training ROC AUC of 0.977 (sensitivity = 0.855, specificity = 0.948) and a test ROC AUC of 0.978 (sensitivity = 0.948, specificity = 0.922). The lipid panel was also able to differentiate SARS-CoV-2-positive individuals from SARS-CoV-2-negative individuals with COVID-19-like symptoms (specificity = 0.818). Lipid profiling and multivariate modelling revealed a signature offering mechanistic insights into SARS-CoV-2, with strong predictive power, and the potential to facilitate effective diagnosis and clinical management.
    Language English
    Publishing date 2021-07-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662251-8
    ISSN 2218-1989
    ISSN 2218-1989
    DOI 10.3390/metabo11070467
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  7. Article ; Online: Integrative Modeling of Plasma Metabolic and Lipoprotein Biomarkers of SARS-CoV-2 Infection in Spanish and Australian COVID-19 Patient Cohorts.

    Masuda, Reika / Lodge, Samantha / Nitschke, Philipp / Spraul, Manfred / Schaefer, Hartmut / Bong, Sze-How / Kimhofer, Torben / Hall, Drew / Loo, Ruey Leng / Bizkarguenaga, Maider / Bruzzone, Chiara / Gil-Redondo, Rubén / Embade, Nieves / Mato, José M / Holmes, Elaine / Wist, Julien / Millet, Oscar / Nicholson, Jeremy K

    Journal of proteome research

    2021  Volume 20, Issue 8, Page(s) 4139–4152

    Abstract: Quantitative plasma lipoprotein and metabolite profiles were measured on an autonomous community of the Basque Country (Spain) cohort consisting of hospitalized COVID-19 patients ( ...

    Abstract Quantitative plasma lipoprotein and metabolite profiles were measured on an autonomous community of the Basque Country (Spain) cohort consisting of hospitalized COVID-19 patients (
    MeSH term(s) Australia ; Biomarkers ; COVID-19 ; Humans ; Lipoproteins ; SARS-CoV-2
    Chemical Substances Biomarkers ; Lipoproteins
    Language English
    Publishing date 2021-07-12
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.1c00458
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  8. Article ; Online: Abnormal concentration of porphyrins in serum from COVID-19 patients.

    San Juan, Itxaso / Bruzzone, Chiara / Bizkarguenaga, Maider / Bernardo-Seisdedos, Ganeko / Laín, Ana / Gil-Redondo, Rubén / Diercks, Tammo / Gil-Martínez, Jon / Urquiza, Pedro / Arana, Eunate / Seco, Marisa / García de Vicuña, Aitor / Embade, Nieves / Mato, José M / Millet, Oscar

    British journal of haematology

    2020  Volume 190, Issue 5, Page(s) e265–e267

    MeSH term(s) Aged ; Aged, 80 and over ; Betacoronavirus/metabolism ; COVID-19 ; Coronavirus Infections/blood ; Female ; Heme/metabolism ; Humans ; Male ; Middle Aged ; Pandemics ; Pneumonia, Viral/blood ; Porphyrins/blood ; SARS-CoV-2
    Chemical Substances Porphyrins ; Heme (42VZT0U6YR)
    Keywords covid19
    Language English
    Publishing date 2020-08-29
    Publishing country England
    Document type Letter ; Research Support, Non-U.S. Gov't
    ZDB-ID 80077-6
    ISSN 1365-2141 ; 0007-1048
    ISSN (online) 1365-2141
    ISSN 0007-1048
    DOI 10.1111/bjh.17060
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  9. Article ; Online: Uneven metabolic and lipidomic profiles in recovered COVID-19 patients as investigated by plasma NMR metabolomics.

    Bizkarguenaga, Maider / Bruzzone, Chiara / Gil-Redondo, Rubén / SanJuan, Itxaso / Martin-Ruiz, Itziar / Barriales, Diego / Palacios, Ainhoa / Pasco, Samuel T / González-Valle, Beatriz / Laín, Ana / Herrera, Lara / Azkarate, Aida / Vesga, Miguel Angel / Eguizabal, Cristina / Anguita, Juan / Embade, Nieves / Mato, José M / Millet, Oscar

    NMR in biomedicine

    2021  Volume 35, Issue 2, Page(s) e4637

    Abstract: COVID-19 is a systemic infectious disease that may affect many organs, accompanied by a measurable metabolic dysregulation. The disease is also associated with significant mortality, particularly among the elderly, patients with comorbidities, and solid ... ...

    Abstract COVID-19 is a systemic infectious disease that may affect many organs, accompanied by a measurable metabolic dysregulation. The disease is also associated with significant mortality, particularly among the elderly, patients with comorbidities, and solid organ transplant recipients. Yet, the largest segment of the patient population is asymptomatic, and most other patients develop mild to moderate symptoms after SARS-CoV-2 infection. Here, we have used NMR metabolomics to characterize plasma samples from a cohort of the abovementioned group of COVID-19 patients (n = 69), between 3 and 10 months after diagnosis, and compared them with a set of reference samples from individuals never infected by the virus (n = 71). Our results indicate that half of the patient population show abnormal metabolism including porphyrin levels and altered lipoprotein profiles six months after the infection, while the other half show little molecular record of the disease. Remarkably, most of these patients are asymptomatic or mild COVID-19 patients, and we hypothesize that this is due to a metabolic reflection of the immune response stress.
    MeSH term(s) COVID-19/immunology ; COVID-19/metabolism ; Cholesterol, HDL/blood ; Cholesterol, LDL/blood ; Humans ; Lipidomics ; Magnetic Resonance Spectroscopy/methods ; Metabolomics ; SARS-CoV-2
    Chemical Substances Cholesterol, HDL ; Cholesterol, LDL
    Language English
    Publishing date 2021-10-27
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1000976-0
    ISSN 1099-1492 ; 0952-3480
    ISSN (online) 1099-1492
    ISSN 0952-3480
    DOI 10.1002/nbm.4637
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  10. Article ; Online: Metabolic Landscape of the Mouse Liver by Quantitative

    Bernardo-Seisdedos, Ganeko / Bilbao, Jon / Fernández-Ramos, David / Lopitz-Otsoa, Fernando / Gutierrez de Juan, Virginia / Bizkarguenaga, Maider / Mateos, Borja / Fondevila, Marcos F / Abril-Fornaguera, Jordi / Diercks, Tammo / Lu, Shelly C / Nogueiras, Rubén / Mato, José M / Millet, Oscar

    Hepatology (Baltimore, Md.)

    2021  Volume 74, Issue 1, Page(s) 148–163

    Abstract: Background and aims: The liver plays a central role in all metabolic processes in the body. However, precise characterization of liver metabolism is often obscured by its inherent complexity. Phosphorylated metabolites occupy a prominent position in all ...

    Abstract Background and aims: The liver plays a central role in all metabolic processes in the body. However, precise characterization of liver metabolism is often obscured by its inherent complexity. Phosphorylated metabolites occupy a prominent position in all anabolic and catabolic pathways. Here, we develop a
    Approach and results: We applied this technique to define the metabolic landscape in livers from a mouse model of the rare disease disorder congenital erythropoietic porphyria (CEP) as well as two well-known murine models of nonalcoholic steatohepatitis: one genetic, methionine adenosyltransferase 1A knockout mice, and the other dietary, mice fed a high-fat choline-deficient diet. We report alterations in the concentrations of phosphorylated metabolites that are readouts of the balance between glycolysis, gluconeogenesis, the pentose phosphate pathway, the tricarboxylic acid cycle, and oxidative phosphorylation and of phospholipid metabolism and apoptosis. Moreover, these changes correlate with the main histological features: steatosis, apoptosis, iron deposits, and fibrosis. Strikingly, treatment with the repurposed drug ciclopirox improves the phosphoromic profile of CEP mice, an effect that was mirrored by the normalization of liver histology.
    Conclusions: In conclusion, these findings indicate that NMR-based phosphoromics may be used to unravel metabolic phenotypes of liver injury and to identify the mechanism of drug action.
    MeSH term(s) Animals ; Disease Models, Animal ; Feasibility Studies ; Female ; Humans ; Hydrophobic and Hydrophilic Interactions ; Liver/drug effects ; Liver/metabolism ; Liver/pathology ; Magnetic Resonance Spectroscopy ; Male ; Metabolome/drug effects ; Metabolome/physiology ; Metabolomics/methods ; Mice ; Mice, Transgenic ; Models, Animal ; Non-alcoholic Fatty Liver Disease/drug therapy ; Non-alcoholic Fatty Liver Disease/pathology ; Phosphorus ; Phosphorylation/drug effects
    Chemical Substances Phosphorus (27YLU75U4W)
    Language English
    Publishing date 2021-06-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 604603-4
    ISSN 1527-3350 ; 0270-9139
    ISSN (online) 1527-3350
    ISSN 0270-9139
    DOI 10.1002/hep.31676
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