HAL Id: hal-01607393
https://hal.archives-ouvertes.fr/hal-01607393
Submitted on 2 Jun 2020
HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-entific research documents, whether they are pub-lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.
L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
Copyright
A systems biology network analysis of nutri(epi)genomic changes in endothelial cells exposed to epicatechin
metabolites
Dragan Milenkovic, Wim Vanden Berghe, Christine Morand, Sylvain Claude, Annette van de Sandt, Simone Gorressen, Laurent-Emmanuel Monfoulet,
Dominique Bayle, Céline Boby, Chandra Chirumamilla, et al.
To cite this version:
Dragan Milenkovic, Wim Vanden Berghe, Christine Morand, Sylvain Claude, Annette van de Sandt, et al.. A systems biology network analysis of nutri(epi)genomic changes in endothelial cells exposed to epicatechin metabolites. 2. COST POSITIVe Scientific Workshop on “ Omics breakthroughs in the Health effects of plant food bioactives, Sep 2017, Thessalonique, Greece. Scientific Reports, 8 (1), 2017, 2nd COST POSITIVe Scientific Workshop on “ Omics breakthroughs in the Health effects of plant food bioactives. �10.1038/s41598-018-33959-x�. �hal-01607393�
A systems biology network analysis of nutri(epi)genomic changes in endothelial cells
exposed to epicatechin metabolites
D. Milenkovic
a,, W. Vanden Berghe
c,d, C. Morand
a, S. Claude
a, A. van de Sandt
e, S. Gorressen
e, L-E. Monfoulet
a, D. Bayle
a, C. Boby
f, C. S. Chirumamilla
c, K. Declerck
c, K.
Szarc vel Szic
c, M. Lahtela-Kakkonen
g, C.Gerhauser
h, M. W. Merx
d♯, Malte Kelm
ca INRA, UMR 1019, UNH, CRNH Auvergne, F-63000 Clermont-Ferrand ; Clermont Université, Université d'Auvergne, Unité de Nutrition Humaine, BP 10448, F-63000 Clermont-Ferrand, France; c PPES, Department of Biomedical
Sciences, University of Antwerp (UA), Wilrijk, Belgium; d L-GEST, Department of Biochemistry and Microbiology, UGent, Ghent, Belgium; e Department of Medicine, Division of Cardiology, Pneumology and Angiology, University
Hospital Düsseldorf, Germany; f INRA, UMR1213 Herbivores, Plate-Forme d'Exploration du Métabolisme, Saint-Genès-Champanelle, France. g School of Pharmacy, University of Eastern Finland, Kuopio, Finland; h Division of
Epigenomics and Cancer Risk Factors, DKFZ, Heidelberg, Germany
Flavan-3-ols represent a major group of flavonoids found in the Western diet and are found in most foods and are particularly abundant in cocoa, green tea, red wine and various fruits. Epidemiologcal, clinical and pre-clinical studies have shown convincing evidences of their cardiovascular protective properties. However their mechanism of action remains unknown as most sutides have been performed in non-physiolgoically relevant conditions and not taking into account the metabolism of these compounds.
In this study, our systems biology based integration of transcriptomic, microRNomic and epigenomic data of inflammed HUVEC cells exposed to a mixture of plasma metabolites
of epicatechin revealed common pathway associated with reduced endothelial cell adhesion and transmigration functions. Biological proof of predicted impact of epicatechin
metabolites on endothelial cell adhesion and transmigration was obtained using cell in-vitro assays performed in the same experimental conditions as those used for nutrigenomic
analyses. In accordance with our hypothesis, we showed that the pre-incubation of endothelial cells with epicatechin metabolites did not only result only in the reduction of
monocyte adhesion, but also in that of endothelial permeability as shown by a decrease in monocyte transendothelial migration. Taken together, results from our study provide
convincing evidence pointing that epicatechin metabolites trigger complex nutri(epi)genomic changes that modulate endothelial cell adhesion function and permeability.
RESULTS
1) Circulating flavanol metabolites modulate expression of genes in endothelial cells 2) Flavanol metabolites modulate phosphorylation of cell signaling proteins and p65
The aims of this study were to provide molecular biological
evidence of the vasculo-protective effect of epicatechin, by
evaluating its effect on the interactions between circulating
immune cells and vascular endothelium which constitute
initial steps of atherosclerosis development, and to decipher
the underlying mechanisms of action using systems biology
approach.
Epicatechin metabolites attenuate TNFα-induced phosphorylation of p38 and Akt kinase signaling in endothelial cells associated with reduced phosphorylation of the NF-κB subunit p65 by favorable binding properties to the ATP binding cavity of the p38-MAPK protein.
3) Flavanol metabolites modulate expression of miRNA and DNA methylation profile
Epicatechin metabolite responsive miRNAs contributes in fine-tuning transcriptional regulation of cell adhesion and
transendothelial migration pathways and module DNA
methylation of genes regulating cell adhesion, migration or cytoskeleton organization.
INTRODUCTION
STUDY DESIGN
CONCLUSION
Adherent junctionS Focal adhesionChemokine pathway VEGF pathway Tight junction
MAPK pathway
Leukocyte extravation
Leukocyte transendothelial migration
Cytoskeleton remodeling
Gene expression analysis using microarrays showed that mixtures of flavanol metabolites modulate the expression of genes involved in the regulation of cell-cell adhesion, cytoskeleton organization or focal adhesion, suggesting of lower monocyte to endothelial cell adhesion and transmigration.
In-silico docking of (-)-epicatechin-4’-sulfate to P38-MAPK hsa-let-7a hsa-let-7f hsa-miR-10a hsa-miR-10b hsa-miR-1246 hsa-miR-1290 hsa-miR-130b hsa-miR-134 hsa-miR-139-5p hsa-miR-146a hsa-miR-148a hsa-miR-155 hsa-miR-181a* hsa-miR-195 hsa-miR-199a-3p hsa-miR-199a-5p hsa-miR-214 hsa-miR-221* hsa-miR-224 hsa-miR-29b-1* hsa-miR-30a* hsa-miR-30c hsa-miR-30e* hsa-miR-320a hsa-miR-320c hsa-miR-320d hsa-miR-361-5p hsa-miR-365 hsa-miR-369-5p hsa-miR-455-3p hsa-miR-543 hsa-miR-574-5p hsa-miR-575 hsa-miR-584 hsa-miR-638 hsa-miR-769-5p hsa-miR-98 MIX + TNFα / +TNFα + TNFα / -TNFα
miRNA expression profile
1549 972
Hyper-methylated
Hypo-methylated
Changes in DNA methylation
4) Integrative analyses of nutri(epi)genomic data
5) Impact of flavanol on monocyte adhesion and transendothelial migration
Mixture of epicatechin metabolites significantly reduced the adhesion of monocytes to a TNFα-activated endothelial cell monolayer (-32%) and their transendothelial migration (27%).
ATP binding cavity THP1 t = 23h THP1/HUVEC co-incubation Signaling pathway analysis Western-blotting Protein extraction Nutrigenomics transcriptomics RNA extraction miRNA expression transcriptomics miRNA extraction HUVECs
(Human Umbilical Vein Endothelial Cells)
Monocytes
Exposure of HUVECs to flavanol metabolite mix at
1microM: - 4’Methyl Epicatechin - 4’Methyl Epicatechin 7 Glucuronide - Epicatechin-4’-Sulfate t = 0 t = 3h Induction of inflammatory stress t = 18h t = 22h +TNFα (0.1ng/ml) Epigenetics global methylation genomic DNA Fixation and labelling Monocytes adhesion to endothelial cells Counting of attached monocytes Transwell assay Monocytes transendothelial migration In-silico
