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Article ; Online: Reinforcing the Evidence of Mitochondrial Dysfunction in Long COVID Patients Using a Multiplatform Mass Spectrometry-Based Metabolomics Approach.

Martínez, Sara / Albóniga, Oihane E / López-Huertas, María Rosa / Gradillas, Ana / Barbas, Coral

2024

Abstract: Despite the recent and increasing knowledge surrounding COVID-19 infection, the underlying mechanisms of the persistence of symptoms for a long time after the acute infection are still not completely understood. Here, a multiplatform mass spectrometry- ... ...

Abstract	Despite the recent and increasing knowledge surrounding COVID-19 infection, the underlying mechanisms of the persistence of symptoms for a long time after the acute infection are still not completely understood. Here, a multiplatform mass spectrometry-based approach was used for metabolomic and lipidomic profiling of human plasma samples from Long COVID patients (
Language	English
Publishing date	2024-04-02
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.3c00706
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Article: HPLC-(Q)-TOF-MS-Based Study of Plasma Metabolic Profile Differences Associated with Age in Pediatric Population Using an Animal Model.

Albóniga, Oihane E / González-Mendia, Oskar / Blanco, María E / Alonso, Rosa M

Metabolites

2022 Volume 12, Issue 8

Abstract: A deep knowledge about the biological development of children is essential for appropriate drug administration and dosage in pediatrics. In this sense, the best approximation to study organ maturation is the analysis of tissue samples, but it requires ... ...

Abstract	A deep knowledge about the biological development of children is essential for appropriate drug administration and dosage in pediatrics. In this sense, the best approximation to study organ maturation is the analysis of tissue samples, but it requires invasive methods. For this reason, surrogate matrices should be explored. Among them, plasma emerges as a potential alternative since it represents a snapshot of global organ metabolism. In this work, plasma metabolic profiles from piglets of different ages (newborns, infants, and children) obtained by HPLC-(Q)-TOF-MS at positive and negative ionization modes were studied. Improved clustering within groups was achieved using multiblock principal component analysis compared to classical principal component analysis. Furthermore, the separation observed among groups was better resolved by using partial least squares-discriminant analysis, which was validated by bootstrapping and permutation testing. Thanks to univariate analysis, 13 metabolites in positive and 21 in negative ionization modes were found to be significant to discriminate the three groups of piglets. From these features, an acylcarnitine and eight glycerophospholipids were annotated and identified as metabolites of interest. The findings indicate that there is a relevant change with age in lipid metabolism in which lysophosphatidylcholines and lysophoshatidylethanolamines play an important role.
Language	English
Publishing date	2022-08-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo12080739
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Article: A Novel Approach on the Use of Samples from Faecal Occult Blood Screening Kits for Metabolomics Analysis: Application in Colorectal Cancer Population.

Albóniga, Oihane E / Cubiella, Joaquín / Bujanda, Luis / Blanco, María Encarnación / Lanza, Borja / Alonso, Cristina / Nafría, Beatriz / Falcón-Pérez, Juan Manuel

Metabolites

2023 Volume 13, Issue 3

Abstract: The incidence of colorectal cancer (CRC) is increasing, and currently it is the third most common cancer. Early CRC diagnosis is still difficult and relies on an invasive colonoscopy and tissue biopsy. The globally observed tendency demands non-invasive, ...

Abstract	The incidence of colorectal cancer (CRC) is increasing, and currently it is the third most common cancer. Early CRC diagnosis is still difficult and relies on an invasive colonoscopy and tissue biopsy. The globally observed tendency demands non-invasive, specific, and accurate diagnostic tools for early diagnosis and prognosis. In this work, the main aim was to evaluate for the first time the feasibility of using extracts from the non-invasive sample collection from faecal occult blood (FOB) kits for its use in metabolomics studies taking advantage in this way of the high sensitivity of this technology. Then, a cohort of 131 samples from control individuals (CTL), adenoma (AD) and CRC patients were analysed using a semitargeted approach by ultra-high-performance liquid chromatography-time-of-flight-mass spectrometry (UHPLC-ToF-MS). Multivariate and univariate statistical analysis revealed that cholesteryl esters (ChoE) with polyunsaturated fatty acids (PUFAs) together with FOB were relevant metabolites that could clearly separate CRC patients from AD and CTL individuals, whereas the metabolic profiles of CTL and AD were very similar. These results are in agreement with previous findings and reveal the advantage of using the same FOBT samples for several analyses, which would facilitate sample collection and improve direct connection between FOB measurements and metabolomics analysis. Although the sample size and the number of metabolites should be enhanced to cover a wider range of metabolites, alterations in lipid metabolism clearly point out for future perspectives.
Language	English
Publishing date	2023-02-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo13030321
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Article ; Online: Author Correction: Differential abundance of lipids and metabolites related to SARS-CoV-2 infection and susceptibility.

Albóniga, Oihane E / Moreno, Elena / Martínez-Sanz, Javier / Vizcarra, Pilar / Ron, Raquel / Díaz-Álvarez, Jorge / Rosas Cancio-Suarez, Marta / Sánchez-Conde, Matilde / Galán, Juan Carlos / Angulo, Santiago / Moreno, Santiago / Barbas, Coral / Serrano-Villar, Sergio

Scientific reports

2023 Volume 13, Issue 1, Page(s) 22513

Language	English
Publishing date	2023-12-18
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-47669-6
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Article: Metabolic Snapshot of Plasma Samples Reveals New Pathways Implicated in SARS-CoV-2 Pathogenesis

Albóniga, Oihane E. / Jiménez, Daniel / Sánchez-Conde, Matilde / Vizcarra, Pilar / Ron, Raquel / Herrera, Sabina / Martínez-Sanz, Javier / Moreno, Elena / Moreno, Santiago / Barbas, Coral / Serrano-Villar, Sergio

Journal of proteome research. 2022 Feb. 08, v. 21, no. 3

2022

Abstract: Despite the scientific and human efforts to understand COVID-19, there are questions still unanswered. Variations in the metabolic reaction to SARS-CoV-2 infection could explain the striking differences in the susceptibility to infection and the risk of ... ...

Abstract	Despite the scientific and human efforts to understand COVID-19, there are questions still unanswered. Variations in the metabolic reaction to SARS-CoV-2 infection could explain the striking differences in the susceptibility to infection and the risk of severe disease. Here, we used untargeted metabolomics to examine novel metabolic pathways related to SARS-CoV-2 susceptibility and COVID-19 clinical severity using capillary electrophoresis coupled to a time-of-flight mass spectrometer (CE-TOF-MS) in plasma samples. We included 27 patients with confirmed COVID-19 and 29 healthcare workers heavily exposed to SARS-CoV-2 but with low susceptibility to infection (“nonsusceptible”). We found a total of 42 metabolites of SARS-CoV-2 susceptibility or COVID-19 clinical severity. We report the discovery of new plasma biomarkers for COVID-19 that provide mechanistic explanations for the clinical consequences of SARS-CoV-2, including mitochondrial and liver dysfunction as a consequence of hypoxemia (citrulline, citric acid, and 3-aminoisobutyric acid (BAIBA)), energy production and amino acid catabolism (phenylalanine and histidine), and endothelial dysfunction and thrombosis (citrulline, asymmetric dimethylarginine (ADMA), and 2-aminobutyric acid (2-AB)), and we found interconnections between these pathways. In summary, in this first report several metabolic pathways implicated in SARS-CoV-2 susceptibility and COVID-19 clinical progression were found by CE-MS based metabolomics that could be developed as biomarkers of COVID-19.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; amino acid metabolism ; biomarkers ; capillary electrophoresis ; citric acid ; citrulline ; disease severity ; energy ; health services ; histidine ; humans ; hypoxia ; liver ; metabolites ; metabolomics ; mitochondria ; pathogenesis ; phenylalanine ; proteome ; research ; risk ; spectrometers ; thrombosis
Language	English
Dates of publication	2022-0208
Size	p. 623-634.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00786
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Comparison of liver and plasma metabolic profiles in piglets of different ages as animal models for paediatric population.

Albóniga, Oihane E / González, Oskar / Alonso, Rosa M / Xu, Yun / Goodacre, Royston

The Analyst

2020 Volume 145, Issue 21, Page(s) 6859–6867

Abstract: Liver plays an important role in drug metabolism, so studying the grade of maturation of this organ would help to develop more appropriate dosing regimens for paediatric populations. Nevertheless, considering the invasive nature of liver analyses there ... ...

Abstract	Liver plays an important role in drug metabolism, so studying the grade of maturation of this organ would help to develop more appropriate dosing regimens for paediatric populations. Nevertheless, considering the invasive nature of liver analyses there are obvious ethical boundaries, particularly in babies and children. In this work, we investigated the suitability of blood plasma as an alternative matrix to evaluate the biological age of liver. With this aim, we studied the correlation of plasma and liver metabolomic profiles obtained by HPLC-TOF-MS for piglets of different ages (newborns, neonates and infants). By means of Pearson correlation analysis we observed that 360 and 1784 pairs of metabolite features were significantly correlated in positive and negative ionization mode, respectively. Procrustes analysis was applied in order to assess the similarity of the clustering resulting from the data obtained from the two matrices and the two ionisation modes. The Procrustes distances were low for both ESI+ (0.3753) and ESI- (0.3673) and, hence, liver and plasma are expected to provide similar discriminatory information. Furthermore, we found that Multiblock Principal Component Analysis (MB-PCA) readily allowed us to combine the data obtained from both matrices and to better understand the clustering according to the three study groups. Considering all these results, we suggest that plasma can provide valuable insight into the maturation grade of liver in order to provide accurate dosing in paediatric population.
MeSH term(s)	Animals ; Child ; Humans ; Infant ; Infant, Newborn ; Liver ; Metabolome ; Models, Animal ; Pharmaceutical Preparations ; Plasma ; Spectrometry, Mass, Electrospray Ionization ; Swine
Chemical Substances	Pharmaceutical Preparations
Language	English
Publishing date	2020-08-28
Publishing country	England
Document type	Journal Article
ZDB-ID	210747-8
ISSN	1364-5528 ; 0003-2654
ISSN (online)	1364-5528
ISSN	0003-2654
DOI	10.1039/d0an00254b
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Article ; Online: Optimization of XCMS parameters for LC-MS metabolomics: an assessment of automated versus manual tuning and its effect on the final results.

Albóniga, Oihane E / González, Oskar / Alonso, Rosa M / Xu, Yun / Goodacre, Royston

Metabolomics : Official journal of the Metabolomic Society

2020 Volume 16, Issue 1, Page(s) 14

Abstract: Introduction: Several software packages containing diverse algorithms are available for processing Liquid Chromatography-Mass Spectrometry (LC-MS) chromatographic data and within these deconvolution packages different parameters settings can lead to ... ...

Abstract	Introduction: Several software packages containing diverse algorithms are available for processing Liquid Chromatography-Mass Spectrometry (LC-MS) chromatographic data and within these deconvolution packages different parameters settings can lead to different outcomes. XCMS is the most widely used peak picking and deconvolution software for metabolomics, but the parameter selection can be hard for inexpert users. To solve this issue, the automatic optimization tools such as Isotopologue Parameters Optimization (IPO) can be extremely helpful. Objectives: To evaluate the suitability of IPO as a tool for XCMS parameters optimization and compare the results with those manually obtained by an exhaustive examination of the LC-MS characteristics and performance. Methods: Raw HPLC-TOF-MS data from two types of biological samples (liver and plasma) analysed in both positive and negative electrospray ionization modes from three groups of piglets were processed with XCMS using parameters optimized following two different approaches: IPO and Manual. The outcomes were compared to determine the advantages and disadvantages of using each method. Results: IPO processing produced the higher number of repeatable (%RSD < 20) and significant features for all data sets and allowed the different piglet groups to be distinguished. Nevertheless, on multivariate level, similar clustering results were obtained by Principal Component Analysis (PCA) when applied to IPO and manual matrices. Conclusion: IPO is a useful optimization tool that helps in choosing the appropriate parameters. It works well on data with a good LC-MS performance but the lack of such adequate data can result in unrealistic parameter settings, which might require further investigation and manual tuning. On the contrary, manual selection criteria requires deeper knowledge on LC-MS, programming language and XCMS parameter interpretation, but allows a better fine-tuning of the parameters, and thus more robust deconvolution.
MeSH term(s)	Animals ; Automation/methods ; Automation/standards ; Calibration ; Chromatography, Liquid/methods ; Chromatography, Liquid/standards ; Mass Spectrometry/methods ; Mass Spectrometry/standards ; Metabolomics/methods ; Metabolomics/standards ; Software ; Swine
Language	English
Publishing date	2020-01-10
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2250617-2
ISSN	1573-3890 ; 1573-3882
ISSN (online)	1573-3890
ISSN	1573-3882
DOI	10.1007/s11306-020-1636-9
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Article ; Online: Differential abundance of lipids and metabolites related to SARS-CoV-2 infection and susceptibility.

Scientific reports

2023 Volume 13, Issue 1, Page(s) 15124

Abstract: The mechanisms driving SARS-CoV-2 susceptibility remain poorly understood, especially the factors determining why unvaccinated individuals remain uninfected despite high-risk exposures. To understand lipid and metabolite profiles related with COVID-19 ... ...

Abstract	The mechanisms driving SARS-CoV-2 susceptibility remain poorly understood, especially the factors determining why unvaccinated individuals remain uninfected despite high-risk exposures. To understand lipid and metabolite profiles related with COVID-19 susceptibility and disease progression. We collected samples from an exceptional group of unvaccinated healthcare workers heavily exposed to SARS-CoV-2 but not infected ('non-susceptible') and subjects who became infected during the follow-up ('susceptible'), including non-hospitalized and hospitalized patients with different disease severity providing samples at early disease stages. Then, we analyzed their plasma metabolomic profiles using mass spectrometry coupled with liquid and gas chromatography. We show specific lipids profiles and metabolites that could explain SARS-CoV-2 susceptibility and COVID-19 severity. More importantly, non-susceptible individuals show a unique lipidomic pattern characterized by the upregulation of most lipids, especially ceramides and sphingomyelin, which could be interpreted as markers of low susceptibility to SARS-CoV-2 infection. This study strengthens the findings of other researchers about the importance of studying lipid profiles as relevant markers of SARS-CoV-2 pathogenesis.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Gas Chromatography-Mass Spectrometry ; Ceramides ; Disease Progression
Chemical Substances	Ceramides
Language	English
Publishing date	2023-09-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-40999-5
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Article: A Comprehensive Metabolomics Analysis of Fecal Samples from Advanced Adenoma and Colorectal Cancer Patients.

Telleria, Oiana / Alboniga, Oihane E / Clos-Garcia, Marc / Nafría-Jimenez, Beatriz / Cubiella, Joaquin / Bujanda, Luis / Falcón-Pérez, Juan Manuel

Metabolites

2022 Volume 12, Issue 6

Abstract: ... accurate predicted model consisting of the combination of hemoglobin (Hgb) and bilirubin E,E, lactosyl-N ...

Abstract	Accurate diagnosis of colorectal cancer (CRC) still relies on invasive colonoscopy. Noninvasive methods are less sensitive in detecting the disease, particularly in the early stage. In the current work, a metabolomics analysis of fecal samples was carried out by ultra-high-performance liquid chromatography-tandem mass spectroscopy (UPLC-MS/MS). A total of 1380 metabolites were analyzed in a cohort of 120 fecal samples from patients with normal colonoscopy, advanced adenoma (AA) and CRC. Multivariate analysis revealed that metabolic profiles of CRC and AA patients were similar and could be clearly separated from control individuals. Among the 25 significant metabolites, sphingomyelins (SM), lactosylceramides (LacCer), secondary bile acids, polypeptides, formiminoglutamate, heme and cytidine-containing pyrimidines were found to be dysregulated in CRC patients. Supervised random forest (RF) and logistic regression algorithms were employed to build a CRC accurate predicted model consisting of the combination of hemoglobin (Hgb) and bilirubin E,E, lactosyl-N-palmitoyl-sphingosine, glycocholenate sulfate and STLVT with an accuracy, sensitivity and specificity of 91.67% (95% Confidence Interval (CI) 0.7753-0.9825), 0.7 and 1, respectively.
Language	English
Publishing date	2022-06-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662251-8
ISSN	2218-1989
ISSN	2218-1989
DOI	10.3390/metabo12060550
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Article ; Online: Metabolic Snapshot of Plasma Samples Reveals New Pathways Implicated in SARS-CoV-2 Pathogenesis.

Albóniga, Oihane E / Jiménez, Daniel / Sánchez-Conde, Matilde / Vizcarra, Pilar / Ron, Raquel / Herrera, Sabina / Martínez-Sanz, Javier / Moreno, Elena / Moreno, Santiago / Barbas, Coral / Serrano-Villar, Sergio

Journal of proteome research

2022 Volume 21, Issue 3, Page(s) 623–634

Abstract	Despite the scientific and human efforts to understand COVID-19, there are questions still unanswered. Variations in the metabolic reaction to SARS-CoV-2 infection could explain the striking differences in the susceptibility to infection and the risk of severe disease. Here, we used untargeted metabolomics to examine novel metabolic pathways related to SARS-CoV-2 susceptibility and COVID-19 clinical severity using capillary electrophoresis coupled to a time-of-flight mass spectrometer (CE-TOF-MS) in plasma samples. We included 27 patients with confirmed COVID-19 and 29 healthcare workers heavily exposed to SARS-CoV-2 but with low susceptibility to infection ("nonsusceptible"). We found a total of 42 metabolites of SARS-CoV-2 susceptibility or COVID-19 clinical severity. We report the discovery of new plasma biomarkers for COVID-19 that provide mechanistic explanations for the clinical consequences of SARS-CoV-2, including mitochondrial and liver dysfunction as a consequence of hypoxemia (citrulline, citric acid, and 3-aminoisobutyric acid (BAIBA)), energy production and amino acid catabolism (phenylalanine and histidine), and endothelial dysfunction and thrombosis (citrulline, asymmetric dimethylarginine (ADMA), and 2-aminobutyric acid (2-AB)), and we found interconnections between these pathways. In summary, in this first report several metabolic pathways implicated in SARS-CoV-2 susceptibility and COVID-19 clinical progression were found by CE-MS based metabolomics that could be developed as biomarkers of COVID-19.
MeSH term(s)	Biomarkers ; COVID-19 ; Humans ; Metabolome ; Metabolomics/methods ; SARS-CoV-2
Chemical Substances	Biomarkers
Language	English
Publishing date	2022-02-08
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.1c00786
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