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Article ; Online: Investigation of several chromatographic approaches for untargeted profiling of central carbon metabolism

Girel, Sergey / Guillarme, Davy / Fekete, Szabolcs / Rudaz, Serge / González-Ruiz, Víctor

Journal of Chromatography A. 2023 May, v. 1697 p.463994-

2023

Abstract: Monitoring the central carbon metabolism (CCM) network using liquid chromatography/mass spectrometry (LC-MS) analysis is hampered by the diverse chemical nature of its analytes, which are extremely difficult to analyze using single chromatographic ... ...

Abstract	Monitoring the central carbon metabolism (CCM) network using liquid chromatography/mass spectrometry (LC-MS) analysis is hampered by the diverse chemical nature of its analytes, which are extremely difficult to analyze using single chromatographic conditions. Furthermore, CCM-related compounds present non-specific adsorption on metal surfaces, causing detrimental chromatographic effects and sensitivity loss. In this study, polar reversed-phase, mixed-mode (MMC), and zwitterionic hydrophilic interaction chromatography (HILIC) featuring low-adsorption hardware were investigated towards untargeted analysis of biological samples with a focus on energy metabolism-related analytes. Best results were achieved with sulfoalkylbetaine HILIC with different supports, where polymeric option featured the highest coverage and inert hybrid silica facilitated best throughput and kinetic performance at a cost of less selectivity for small carboxylic acids. MMC demonstrated excellent performance for strongly anionic analytes such as multiresidue phosphates. The obtained experimental data also suggested that an additional hydrophilic modulation might be necessary to facilitate better resolution of carboxylic acids in zHILIC mode, as found during the application of the developed method to study the effect of two different mutations on the energy metabolism of S. aureus.
Keywords	adsorption ; carbon metabolism ; chemical species ; energy ; energy metabolism ; hydrophilic interaction chromatography ; hydrophilicity ; mass spectrometry ; polymers ; silica ; zwitterions ; Central carbon metabolism ; Low adsorption column hardware ; Mixed-mode chromatography ; Zwitterionic HILIC ; Untargeted metabolomics
Language	English
Dates of publication	2023-05
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	Pre-press version ; Use and reproduction
ZDB-ID	218139-3
ISSN	0021-9673 ; 0378-4355 ; 0376-737X
ISSN	0021-9673 ; 0378-4355 ; 0376-737X
DOI	10.1016/j.chroma.2023.463994
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Bioactive Nitrosylated and Nitrated

Girel, Sergey / Schütz, Vadim / Bigler, Laurent / Dörmann, Peter / Schulz, Margot

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 15

Abstract: Incubation ... ...

Abstract	Incubation of
MeSH term(s)	Acetamides ; Acetanilides ; Arabidopsis/metabolism ; Glucosides/metabolism ; Nitrates ; Pantoea ; Tandem Mass Spectrometry
Chemical Substances	Acetamides ; Acetanilides ; Glucosides ; Nitrates ; 2-hydroxyacetanilide (4AS8989RNI)
Language	English
Publishing date	2022-07-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27154786
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Article ; Online: Comprehensive plasma steroidomics reveals subtle alterations of systemic steroid profile in patients at different stages of prostate cancer disease.

Girel, Sergey / Markin, Pavel A / Tobolkina, Elena / Boccard, Julien / Moskaleva, Natalia E / Rudaz, Serge / Appolonova, Svetlana A

Scientific reports

2024 Volume 14, Issue 1, Page(s) 1577

Abstract: The steroid submetabolome, or steroidome, is of particular interest in prostate cancer (PCa) as the dependence of PCa growth on androgens is well known and has been routinely exploited in treatment for decades. Nevertheless, the community is still far ... ...

Abstract	The steroid submetabolome, or steroidome, is of particular interest in prostate cancer (PCa) as the dependence of PCa growth on androgens is well known and has been routinely exploited in treatment for decades. Nevertheless, the community is still far from a comprehensive understanding of steroid involvement in PCa both at the tissue and at systemic level. In this study we used liquid chromatography/high resolution mass spectrometry (LC/HRMS) backed by a dynamic retention time database DynaSTI to obtain a readout on circulating steroids in a cohort reflecting a progression of the PCa. Hence, 60 relevant compounds were annotated in the resulting LC/HRMS data, including 22 unknown steroid isomers therein. Principal component analysis revealed only subtle alterations of the systemic steroidome in the study groups. Next, a supervised approach allowed for a differentiation between the healthy state and any of the stages of the disease. Subsequent clustering of steroid metabolites revealed two groups responsible for this outcome: one consisted primarily of the androgens, whereas another contained corticosterone and its metabolites. The androgen data supported the currently established involvement of a hypothalamic-pituitary-gonadal axis in the development of PCa, whereas biological role of corticosterone remained elusive. On top of that, current results suggested a need for improvement in the dynamic range of the analytical methods to better understand the role of low abundant steroids, as the analysis revealed an involvement of estrogen metabolites. In particular, 2-hydroxyestradiol-3-methylether, one of the compounds present in the disease phenotype, was annotated and reported for the first time in men.
MeSH term(s)	Male ; Humans ; Corticosterone ; Steroids/metabolism ; Prostatic Neoplasms/metabolism ; Androgens/metabolism ; Liquid Chromatography-Mass Spectrometry
Chemical Substances	Corticosterone (W980KJ009P) ; Steroids ; Androgens
Language	English
Publishing date	2024-01-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-51859-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Investigation of several chromatographic approaches for untargeted profiling of central carbon metabolism.

Girel, Sergey / Guillarme, Davy / Fekete, Szabolcs / Rudaz, Serge / González-Ruiz, Víctor

Journal of chromatography. A

2023 Volume 1697, Page(s) 463994

Abstract	Monitoring the central carbon metabolism (CCM) network using liquid chromatography/mass spectrometry (LC-MS) analysis is hampered by the diverse chemical nature of its analytes, which are extremely difficult to analyze using single chromatographic conditions. Furthermore, CCM-related compounds present non-specific adsorption on metal surfaces, causing detrimental chromatographic effects and sensitivity loss. In this study, polar reversed-phase, mixed-mode (MMC), and zwitterionic hydrophilic interaction chromatography (HILIC) featuring low-adsorption hardware were investigated towards untargeted analysis of biological samples with a focus on energy metabolism-related analytes. Best results were achieved with sulfoalkylbetaine HILIC with different supports, where polymeric option featured the highest coverage and inert hybrid silica facilitated best throughput and kinetic performance at a cost of less selectivity for small carboxylic acids. MMC demonstrated excellent performance for strongly anionic analytes such as multiresidue phosphates. The obtained experimental data also suggested that an additional hydrophilic modulation might be necessary to facilitate better resolution of carboxylic acids in zHILIC mode, as found during the application of the developed method to study the effect of two different mutations on the energy metabolism of S. aureus.
MeSH term(s)	Carboxylic Acids ; Chromatography, Liquid/methods ; Hydrophobic and Hydrophilic Interactions ; Mass Spectrometry/methods ; Metabolome ; Organic Chemicals ; Staphylococcus aureus ; Carbon/metabolism
Chemical Substances	Carboxylic Acids ; Organic Chemicals ; Carbon (7440-44-0)
Language	English
Publishing date	2023-04-14
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1171488-8
ISSN	1873-3778 ; 0021-9673
ISSN (online)	1873-3778
ISSN	0021-9673
DOI	10.1016/j.chroma.2023.463994
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Article ; Online: Teg58, a small regulatory RNA, is involved in regulating arginine biosynthesis and biofilm formation in Staphylococcus aureus.

Manna, Adhar C / Leo, Stefano / Girel, Sergey / González-Ruiz, Víctor / Rudaz, Serge / Francois, Patrice / Cheung, Ambrose L

Scientific reports

2022 Volume 12, Issue 1, Page(s) 14963

Abstract: Staphylococcus aureus adapts to different environments by sensing and responding to diverse environmental cues. The responses are coordinately regulated by regulatory proteins, and small regulatory RNAs at the transcriptional and translational levels. ... ...

Abstract	Staphylococcus aureus adapts to different environments by sensing and responding to diverse environmental cues. The responses are coordinately regulated by regulatory proteins, and small regulatory RNAs at the transcriptional and translational levels. Here, we characterized teg58, a SarA repressed sRNA, using ChIP-Seq and RNA-Seq analysis of a sarA mutant. Phenotypic and genetic analyses indicated that inactivation of teg58 led to reduced biofilm formation in a process that is independent of SarA, agr, PIA, and PSMs. RNA-Seq analysis of teg58 mutant revealed up-regulation of arginine biosynthesis genes (i.e., argGH) as well as the ability of the mutant to grow in a chemical defined medium (CDM) lacking L-arginine. Exogenous L-arginine or endogenous induction of argGH led to decreased biofilm formation in parental strains. Further analysis in vitro and in vivo demonstrated that the specific interaction between teg58 and the argGH occurred at the post-transcriptional level to repress arginine synthesis. Biochemical and genetic analyses of various arginine catabolic pathway genes demonstrated that the catabolic pathway did not play a significant role in reduced biofilm formation in the teg58 mutant. Overall, results suggest that teg58 is a regulatory sRNA that plays an important role in modulating arginine biosynthesis and biofilm formation in S. aureus.
MeSH term(s)	Arginine/metabolism ; Bacterial Proteins/metabolism ; Biofilms ; Gene Expression Regulation, Bacterial ; Humans ; RNA, Small Untranslated/genetics ; RNA, Small Untranslated/metabolism ; Staphylococcal Infections/genetics ; Staphylococcus aureus/physiology ; Trans-Activators/metabolism
Chemical Substances	Bacterial Proteins ; RNA, Small Untranslated ; Trans-Activators ; Arginine (94ZLA3W45F)
Language	English
Publishing date	2022-09-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-18815-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Low-polarity untargeted metabolomic profiling as a tool to gain insight into seminal fluid.

Olesti, Eulalia / Boccard, Julien / Rahban, Rita / Girel, Sergey / Moskaleva, Natalia E / Zufferey, Fanny / Rossier, Michel F / Nef, Serge / Rudaz, Serge / González-Ruiz, Víctor

Metabolomics : Official journal of the Metabolomic Society

2023 Volume 19, Issue 6, Page(s) 53

Abstract: Introduction: A decrease in sperm cell count has been observed along the last several decades, especially in the most developed regions of the world. The use of metabolomics to study the composition of the seminal fluid is a promising approach to gain ... ...

Abstract	Introduction: A decrease in sperm cell count has been observed along the last several decades, especially in the most developed regions of the world. The use of metabolomics to study the composition of the seminal fluid is a promising approach to gain access to the molecular mechanisms underlying this fact. Objectives: In the present work, we aimed at relating metabolomic profiles of young healthy men to their semen quality parameters obtained from conventional microscopic analysis. Methods: An untargeted metabolomics approach focusing on low- to mid-polarity compounds was used to analyze a subset of seminal fluid samples from a cohort of over 2700 young healthy men. Results: Our results show that a broad metabolic profiling comprising several families of compounds (including acyl-carnitines, steroids, and other lipids) can contribute to effectively distinguish samples provided by individuals exhibiting low or high absolute sperm counts. Conclusion: A number of metabolites involved in sexual development and function, signaling, and energy metabolism were highlighted as being distinctive of samples coming from either group, proving untargeted metabolomics as a promising tool to better understand the pathophysiological processes responsible for male fertility impairment.
MeSH term(s)	Humans ; Male ; Semen Analysis ; Semen/metabolism ; Metabolomics/methods ; Spermatozoa/metabolism ; Sperm Count
Language	English
Publishing date	2023-06-05
Publishing country	United States
Document type	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/s11306-023-02020-y
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Article ; Online: Separation and determination of cysteine enantiomers in plasma after derivatization with 4-fluoro-7-nitrobenzofurazan.

Ferré, Sabrina / González-Ruiz, Víctor / Zangari, Joséphine / Girel, Sergey / Martinou, Jean-Claude / Sardella, Roccaldo / Rudaz, Serge

Journal of pharmaceutical and biomedical analysis

2021 Volume 209, Page(s) 114539

Abstract: The importance of D-amino acids in mammals associated with enantio-dependent biological functions has been increasingly highlighted. In addition to naturally occurring, D-amino acid supplementation could have a positive biological impact, including ... ...

Abstract	The importance of D-amino acids in mammals associated with enantio-dependent biological functions has been increasingly highlighted. In addition to naturally occurring, D-amino acid supplementation could have a positive biological impact, including cytoprotective implications. In this context, supplementation with D-cysteine has revealed beneficial effects. Quantification of cysteine enantiomers in rodent plasma has been achieved by using 4-fluoro-7-nitrobenzofurazan derivatization of the target analytes. Cystine, the main form of cysteine in the plasma, was initially reduced to cysteine using DL-dithiothreitol. Baseline enantioseparation was then achieved in less than 3 min using a (R,R)-Whelk-O 1 stationary phase and isocratic elution using CH
MeSH term(s)	Animals ; Chromatography, High Pressure Liquid ; Cysteine ; Mice ; Plasma ; Stereoisomerism
Chemical Substances	Cysteine (K848JZ4886)
Language	English
Publishing date	2021-12-18
Publishing country	England
Document type	Journal Article
ZDB-ID	604917-5
ISSN	1873-264X ; 0731-7085
ISSN (online)	1873-264X
ISSN	0731-7085
DOI	10.1016/j.jpba.2021.114539
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Article ; Online: Anti-microtubule activity of the traditional Chinese medicine herb Northern Ban Lan (Isatis tinctoria) leads to glucobrassicin.

Guan, Pingyin / Zhou, Jianning / Girel, Sergey / Zhu, Xin / Schwab, Marian / Zhang, Kunxi / Wang-Müller, Qiyan / Bigler, Laurent / Nick, Peter

Journal of integrative plant biology

2021 Volume 63, Issue 12, Page(s) 2058–2074

Abstract: Traditional Chinese medicine (TCM) belongs to the most elaborate and extensive systems of plant-based healing. The herb Northern Ban Lan (Isatis tinctoria) is famous for its antiviral and anti-inflammatory activity. Although numerous components isolated ... ...

Abstract	Traditional Chinese medicine (TCM) belongs to the most elaborate and extensive systems of plant-based healing. The herb Northern Ban Lan (Isatis tinctoria) is famous for its antiviral and anti-inflammatory activity. Although numerous components isolated from I. tinctoria have been characterized so far, their modes of action have remained unclear. Here, we show that extracts from I. tinctoria exert anti-microtubular activity. Using time-lapse microscopy in living tobacco BY-2 (Nicotiana tabacum L. cv Bright Yellow 2) cells expressing green fluorescent protein-tubulin, we use activity-guided fractionation to screen out the biologically active compounds of I. tinctoria. Among 54 fractions obtained from either leaves or roots of I. tinctoria by methanol (MeOH/H
MeSH term(s)	Glucosinolates ; HeLa Cells ; Humans ; Indoles ; Isatis/chemistry ; Medicine, Chinese Traditional ; Microtubules
Chemical Substances	Glucosinolates ; Indoles ; glucobrassicin (EA6EH0IU89)
Language	English
Publishing date	2021-11-10
Publishing country	China (Republic : 1949- )
Document type	Journal Article
ZDB-ID	2130095-1
ISSN	1744-7909 ; 1672-9072
ISSN (online)	1744-7909
ISSN	1672-9072
DOI	10.1111/jipb.13177
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Article: Anti‐microtubule activity of the traditional Chinese medicine herb Northern Ban Lan (Isatis tinctoria) leads to glucobrassicin

Guan, Pingyin / Zhou, Jianning / Girel, Sergey / Zhu, Xin / Schwab, Marian / Zhang, Kunxi / Wang‐Müller, Qiyan / Bigler, Laurent / Nick, Peter

Journal of integrative plant biology. 2021 Dec., v. 63, no. 12

2021

Abstract: Traditional Chinese medicine (TCM) belongs to the most elaborate and extensive systems of plant‐based healing. The herb Northern Ban Lan (Isatis tinctoria) is famous for its antiviral and anti‐inflammatory activity. Although numerous components isolated ... ...

Abstract	Traditional Chinese medicine (TCM) belongs to the most elaborate and extensive systems of plant‐based healing. The herb Northern Ban Lan (Isatis tinctoria) is famous for its antiviral and anti‐inflammatory activity. Although numerous components isolated from I. tinctoria have been characterized so far, their modes of action have remained unclear. Here, we show that extracts from I. tinctoria exert anti‐microtubular activity. Using time‐lapse microscopy in living tobacco BY‐2 (Nicotiana tabacum L. cv Bright Yellow 2) cells expressing green fluorescent protein‐tubulin, we use activity‐guided fractionation to screen out the biologically active compounds of I. tinctoria. Among 54 fractions obtained from either leaves or roots of I. tinctoria by methanol (MeOH/H₂O 8:2), or ethyl acetate extraction, one specific methanolic root fraction was selected, because it efficiently and rapidly eliminated microtubules. By combination of further purification with ultra‐high‐performance liquid chromatography and high‐resolution tandem mass spectrometry most of the bioactivity could be assigned to the glucosinolate compound glucobrassicin. Glucobrassicin can also affect microtubules and induce apoptosis in HeLa cells. In the light of these findings, the antiviral activity of Northern Ban Lan is discussed in the context of microtubules being hijacked by many viral pathogens for cell‐to‐cell spread.
Keywords	Isatis tinctoria ; Nicotiana tabacum ; Oriental traditional medicine ; anti-inflammatory activity ; antiviral properties ; apoptosis ; ethyl acetate ; fluorescence ; fractionation ; glucobrassicin ; medicinal plants ; methanol ; microscopy ; microtubules ; tandem mass spectrometry ; tobacco ; ultra-performance liquid chromatography
Language	English
Dates of publication	2021-12
Size	p. 2058-2074.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2130095-1
ISSN	1744-7909 ; 1672-9072
ISSN (online)	1744-7909
ISSN	1672-9072
DOI	10.1111/jipb.13177
Database	NAL-Catalogue (AGRICOLA)

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