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Article ; Online: MeRgeION: a Multifunctional R Pipeline for Small Molecule LC-MS/MS Data Processing, Searching, and Organizing.

Liu, Youzhong / Zhang, Yingjie / Vennekens, Tom / Lippens, Jennifer L / Duijsens, Luc / Bui-Thi, Danh / Laukens, Kris / de Vijlder, Thomas

Analytical chemistry

2023 Volume 95, Issue 22, Page(s) 8433–8442

Abstract: ... flexible R-based toolbox to streamline spectral database building, automated structural elucidation, and ... algorithms in the same pipeline. As an open-source R package, meRgeION is ideally suited for building ...

Abstract	Small molecule structure elucidation using tandem mass spectrometry (MS/MS) plays a crucial role in life science, bioanalytical, and pharmaceutical research. There is a pressing need for increased throughput of compound identification and transformation of historical data into information-rich spectral databases. Meanwhile, molecular networking, a recent bioinformatic framework, provides global displays and system-level understanding of complex LC-MS/MS data sets. Herein we present meRgeION, a multifunctional, modular, and flexible R-based toolbox to streamline spectral database building, automated structural elucidation, and molecular networking. The toolbox offers diverse tuning parameters and the possibility to combine various algorithms in the same pipeline. As an open-source R package, meRgeION is ideally suited for building spectral databases and molecular networks from privacy-sensitive and preliminary data. Using meRgeION, we have created an integrated spectral database covering diverse pharmaceutical compounds that was successfully applied to annotate drug-related metabolites from a published nontargeted metabolomics data set as well as reveal the chemical space behind this complex data set through molecular networking. Moreover, the meRgeION-based processing workflow has demonstrated the usefulness of a spectral library search and molecular networking for pharmaceutical forced degradation studies. meRgeION is freely available at: https://github.com/daniellyz/meRgeION2.
MeSH term(s)	Tandem Mass Spectrometry ; Chromatography, Liquid/methods ; Algorithms ; Metabolomics/methods ; Pharmaceutical Preparations ; Software
Chemical Substances	Pharmaceutical Preparations
Language	English
Publishing date	2023-05-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04343
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Article ; Online: MeRgeION: a Multifunctional R Pipeline for Small Molecule LC-MS/MS Data Processing, Searching, and Organizing

Liu, Youzhong / Zhang, Yingjie / Vennekens, Tom / Lippens, Jennifer L. / Duijsens, Luc / Bui-Thi, Danh / Laukens, Kris / de Vijlder, Thomas

Analytical Chemistry. 2023 May 23, v. 95, no. 22 p.8433-8442

2023

Abstract	Small molecule structure elucidation using tandem mass spectrometry (MS/MS) plays a crucial role in life science, bioanalytical, and pharmaceutical research. There is a pressing need for increased throughput of compound identification and transformation of historical data into information-rich spectral databases. Meanwhile, molecular networking, a recent bioinformatic framework, provides global displays and system-level understanding of complex LC-MS/MS data sets. Herein we present meRgeION, a multifunctional, modular, and flexible R-based toolbox to streamline spectral database building, automated structural elucidation, and molecular networking. The toolbox offers diverse tuning parameters and the possibility to combine various algorithms in the same pipeline. As an open-source R package, meRgeION is ideally suited for building spectral databases and molecular networks from privacy-sensitive and preliminary data. Using meRgeION, we have created an integrated spectral database covering diverse pharmaceutical compounds that was successfully applied to annotate drug-related metabolites from a published nontargeted metabolomics data set as well as reveal the chemical space behind this complex data set through molecular networking. Moreover, the meRgeION-based processing workflow has demonstrated the usefulness of a spectral library search and molecular networking for pharmaceutical forced degradation studies. meRgeION is freely available at: https://github.com/daniellyz/meRgeION2.
Keywords	analytical chemistry ; bioinformatics ; data collection ; databases ; metabolites ; metabolomics ; tandem mass spectrometry
Language	English
Dates of publication	2023-0523
Size	p. 8433-8442.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04343
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Article ; Online: Exploring the role of TRPM4 in calcium-dependent triggered activity and cardiac arrhythmias.

Pironet, Andy / Vandewiele, Frone / Vennekens, Rudi

The Journal of physiology

2023 Volume 602, Issue 8, Page(s) 1605–1621

Abstract: Cardiac arrhythmias pose a major threat to a patient's health, yet prove to be often difficult to predict, prevent and treat. A key mechanism in the occurrence of arrhythmias is disturbed ... ...

Abstract	Cardiac arrhythmias pose a major threat to a patient's health, yet prove to be often difficult to predict, prevent and treat. A key mechanism in the occurrence of arrhythmias is disturbed Ca
MeSH term(s)	Humans ; Mice ; Animals ; Calcium/metabolism ; Arrhythmias, Cardiac/genetics ; Myocytes, Cardiac/metabolism ; Calcium, Dietary ; TRPM Cation Channels/genetics
Chemical Substances	Calcium (SY7Q814VUP) ; Calcium, Dietary ; TRPM Cation Channels ; TRPM4 protein, human ; TRPM4 protein, mouse
Language	English
Publishing date	2023-05-14
Publishing country	England
Document type	Journal Article
ZDB-ID	3115-x
ISSN	1469-7793 ; 0022-3751
ISSN (online)	1469-7793
ISSN	0022-3751
DOI	10.1113/JP283831
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Article ; Online: Putting the pressure on endocytosis in the kidney.

Van Giel, Dorien / Vennekens, Rudi

Cell calcium

2020 Volume 94, Page(s) 102338

Abstract: In Science Signaling, Gualdani and colleagues provide evidence that the ion channel TRPV4 functions as a mechanosensor in the renal proximal tubules and show that TRPV4 activity modulates protein reabsorption. ...

Abstract	In Science Signaling, Gualdani and colleagues provide evidence that the ion channel TRPV4 functions as a mechanosensor in the renal proximal tubules and show that TRPV4 activity modulates protein reabsorption.
MeSH term(s)	Albumins ; Endocytosis ; Kidney Tubules, Proximal ; TRPV Cation Channels
Chemical Substances	Albumins ; TRPV Cation Channels
Language	English
Publishing date	2020-12-26
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	757687-0
ISSN	1532-1991 ; 0143-4160
ISSN (online)	1532-1991
ISSN	0143-4160
DOI	10.1016/j.ceca.2020.102338
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Article ; Online: A TRiP to heart failure.

Vennekens, Rudi

Cardiovascular research

2013 Volume 99, Issue 4, Page(s) 590–591

MeSH term(s)	Animals ; Calcium Channels/physiology ; Cardiomyopathy, Dilated/etiology ; Humans ; Sarcolemma/metabolism ; TRPV Cation Channels/physiology
Chemical Substances	Calcium Channels ; TRPV Cation Channels ; TRPV2 protein, human ; Trpv2 protein, mouse
Language	English
Publishing date	2013-09-01
Publishing country	England
Document type	Comment ; Editorial ; Research Support, Non-U.S. Gov't
ZDB-ID	80340-6
ISSN	1755-3245 ; 0008-6363
ISSN (online)	1755-3245
ISSN	0008-6363
DOI	10.1093/cvr/cvt186
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Article ; Online: Continuous glucose monitoring during pregnancy in healthy mice.

Wuyts, Caroline / Simoens, Caroline / Pinto, Silvia / Philippaert, Koenraad / Vennekens, Rudi

Scientific reports

2021 Volume 11, Issue 1, Page(s) 4450

Abstract: During pregnancy, metabolic adaptations occur to maintain the balance between maternal and foetal growth, including increased insulin secretion and decreased insulin sensitivity. When the body fails to adjust, gestational diabetes mellitus develops. To ... ...

Abstract	During pregnancy, metabolic adaptations occur to maintain the balance between maternal and foetal growth, including increased insulin secretion and decreased insulin sensitivity. When the body fails to adjust, gestational diabetes mellitus develops. To gain insight in the pregnancy-induced adaptations, we applied continuous glucose monitoring via telemetric transmitters. We show that continuous glucose monitoring in conscious, non-stressed, freely moving mice throughout the full pregnancy is feasible, accurate and safe. We show that healthy mice during a full pregnancy develop adaptations in glucose homeostasis reminiscent of those in pregnant women. Furthermore, continuous glucose monitoring allows the complete analysis of all aspects of glucose excursions associated with spontaneous feeding episodes, and the thorough analysis of glycaemic variability. In conclusion, continuous glucose monitoring allows a detailed description of the glycaemic status during pregnancy, which will help to unravel specific mechanisms for gestational diabetes mellitus.
MeSH term(s)	Animals ; Blood Glucose/metabolism ; Blood Glucose Self-Monitoring/methods ; Diabetes, Gestational/blood ; Diabetes, Gestational/metabolism ; Female ; Insulin/metabolism ; Insulin Resistance/physiology ; Mice ; Mice, Inbred C57BL ; Pregnancy ; Pregnancy Outcome ; Pregnancy in Diabetics/blood ; Pregnancy in Diabetics/metabolism
Chemical Substances	Blood Glucose ; Insulin
Language	English
Publishing date	2021-02-24
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/s41598-021-83901-x
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Article ; Online: The emerging role of the apelinergic system in kidney physiology and disease.

Janssens, Peter / Decuypere, Jean-Paul / Bammens, Bert / Llorens-Cortes, Catherine / Vennekens, Rudi / Mekahli, Djalila

Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association

2022 Volume 37, Issue 12, Page(s) 2314–2326

Abstract: The apelinergic system (AS) is a novel pleiotropic system with an essential role in renal and cardiovascular physiology and disease, including water homeostasis and blood pressure regulation. It consists of two highly conserved peptide ligands, apelin ... ...

Abstract	The apelinergic system (AS) is a novel pleiotropic system with an essential role in renal and cardiovascular physiology and disease, including water homeostasis and blood pressure regulation. It consists of two highly conserved peptide ligands, apelin and apela, and a G-protein-coupled apelin receptor. The two ligands have many isoforms and a short half-life and exert both similar and divergent effects. Vasopressin, apelin and their receptors colocalize in hypothalamic regions essential for body fluid homeostasis and interact at the central and renal levels to regulate water homeostasis and diuresis in inverse directions. In addition, the AS and renin-angiotensin system interact both systemically and in the kidney, with implications for the cardiovascular system. A role for the AS in diverse pathological states, including disorders of sodium and water balance, hypertension, heart failure, pre-eclampsia, acute kidney injury, sepsis and diabetic nephropathy, has recently been reported. Furthermore, several metabolically stable apelin analogues have been developed, with potential applications in diverse diseases. We review here what is currently known about the physiological functions of the AS, focusing on renal, cardiovascular and metabolic homeostasis, and the role of the AS in associated diseases. We also describe several hurdles and research opportunities worthy of the attention of the nephrology community.
MeSH term(s)	Humans ; Apelin/metabolism ; Intercellular Signaling Peptides and Proteins/metabolism ; Kidney/metabolism ; Ligands ; Receptors, G-Protein-Coupled/metabolism ; Water/metabolism ; Kidney Diseases
Chemical Substances	Apelin ; Intercellular Signaling Peptides and Proteins ; Ligands ; Receptors, G-Protein-Coupled ; Water (059QF0KO0R)
Language	English
Publishing date	2022-11-10
Publishing country	England
Document type	Review ; Journal Article
ZDB-ID	90594-x
ISSN	1460-2385 ; 0931-0509
ISSN (online)	1460-2385
ISSN	0931-0509
DOI	10.1093/ndt/gfab070
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Article ; Online: Is autosomal dominant polycystic kidney disease an early sweet disease?

Dachy, Angélique / Decuypere, Jean-Paul / Vennekens, Rudi / Jouret, François / Mekahli, Djalila

Pediatric nephrology (Berlin, Germany)

2022 Volume 37, Issue 9, Page(s) 1945–1955

Abstract: The clinical course of autosomal dominant polycystic kidney disease (ADPKD) starts in childhood. Evidence of the beneficial impact of early nephron-protective strategies and lifestyle modifications on ADPKD prognosis is accumulating. Recent studies have ... ...

Abstract	The clinical course of autosomal dominant polycystic kidney disease (ADPKD) starts in childhood. Evidence of the beneficial impact of early nephron-protective strategies and lifestyle modifications on ADPKD prognosis is accumulating. Recent studies have described the association of overweight and obesity with rapid disease progression in adults with ADPKD. Moreover, defective glucose metabolism and metabolic reprogramming have been reported in distinct ADPKD models highlighting these pathways as potential therapeutic targets in ADPKD. Several "metabolic" approaches are currently under evaluation in adults, including ketogenic diet, food restriction, and metformin therapy. No data are available on the impact of these approaches in childhood thus far. Yet, according to World Health Organization (WHO), we are currently facing a childhood obesity crisis with an increased prevalence of overweight/obesity in the pediatric population associated with a cardio-metabolic risk profile. The present review summarizes the knowledge about the role of glucose metabolism in the pathophysiology of ADPKD and underscores the possible harm of overweight and obesity in ADPKD especially in terms of long-term cardiovascular outcomes and renal prognosis.
MeSH term(s)	Adult ; Child ; Disease Progression ; Glucose/therapeutic use ; Humans ; Kidney ; Overweight/complications ; Pediatric Obesity/complications ; Polycystic Kidney, Autosomal Dominant/drug therapy ; Polycystic Kidney, Autosomal Dominant/therapy
Chemical Substances	Glucose (IY9XDZ35W2)
Language	English
Publishing date	2022-01-05
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	631932-4
ISSN	1432-198X ; 0931-041X
ISSN (online)	1432-198X
ISSN	0931-041X
DOI	10.1007/s00467-021-05406-z
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Article ; Online: Correction to: Is autosomal dominant polycystic kidney disease an early sweet disease?

Dachy, Angélique / Decuypere, Jean-Paul / Vennekens, Rudi / Jouret, François / Mekahli, Djalila

Pediatric nephrology (Berlin, Germany)

2022 Volume 37, Issue 9, Page(s) 2223–2224

Language	English
Publishing date	2022-06-21
Publishing country	Germany
Document type	Published Erratum
ZDB-ID	631932-4
ISSN	1432-198X ; 0931-041X
ISSN (online)	1432-198X
ISSN	0931-041X
DOI	10.1007/s00467-022-05624-z
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Article ; Online: Emerging concepts for the role of TRP channels in the cardiovascular system.

Vennekens, Rudi

The Journal of physiology

2010 Volume 589, Issue Pt 7, Page(s) 1527–1534

Abstract: The transient receptor potential (TRP) family of ion channels is a large family of cation selective ion channels, which are expressed and functional in a variety of tissues. In this review we focus on the most recent results detailing the role of TRP ... ...

Abstract	The transient receptor potential (TRP) family of ion channels is a large family of cation selective ion channels, which are expressed and functional in a variety of tissues. In this review we focus on the most recent results detailing the role of TRP channels in the cardiovascular system. The presented results underscore the role of TRP channels in cardiomyocytes, smooth cells and endothelium, and in disease states such as hypertension, cardiac conduction block and cardiac hypertrophy.
MeSH term(s)	Animals ; Blood Pressure/physiology ; Cardiomegaly/etiology ; Cardiomegaly/physiopathology ; Cardiovascular Physiological Phenomena ; Endothelium, Vascular/physiology ; Humans ; Models, Cardiovascular ; Muscle, Smooth, Vascular/physiology ; Myocardium/metabolism ; Transient Receptor Potential Channels/physiology
Chemical Substances	Transient Receptor Potential Channels
Language	English
Publishing date	2010-12-20
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	3115-x
ISSN	1469-7793 ; 0022-3751
ISSN (online)	1469-7793
ISSN	0022-3751
DOI	10.1113/jphysiol.2010.202077
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