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2. Systematic Bioinformatic Analyses of Nutrigenomic Modifications by Polyphenols Associated with Cardiometabolic Health in Humans—Evidence from Targeted Nutrigenomic Studies

Author

Ruskovska, Tatjana, Budić-Leto, Irena, Corral-Jara, Karla Fabiola, Ajdžanović, Vladimir, Arola-Arnal, Anna, Bravo, Francisca Isabel, Deligiannidou, Georgia-Eirini, Havlik, Jaroslav, Janeva, Milkica, Kistanova, Elena, Kontogiorgis, Christos, Krga, Irena, Massaro, Marika, Miler, Marko, Milosevic, Verica, Morand, Christine, Scoditti, Egeria, Suárez, Manuel, Vauzour, David, and Milenkovic, Dragan

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Biotechnology, Complementary and Integrative Health, Nutrition, Clinical Research, Genetics, Aetiology, 2.1 Biological and endogenous factors, Generic health relevance, Cardiovascular, Good Health and Well Being, Adult, Cardiometabolic Risk Factors, Computational Biology, Female, Humans, Male, Metabolic Syndrome, MicroRNAs, Middle Aged, Nutrigenomics, Nutritional Physiological Phenomena, Polyphenols, Protective Agents, RNA, Messenger, Real-Time Polymerase Chain Reaction, Signal Transduction, systematic literature search, nutrigenomics, integrative bioinformatics, polyphenols, cardiometabolic health, human, Food Sciences, Nutrition and Dietetics, Clinical sciences, Nutrition and dietetics, Public health
Abstract

Cardiometabolic disorders are among the leading causes of mortality in the human population. Dietary polyphenols exert beneficial effects on cardiometabolic health in humans. Molecular mechanisms, however, are not completely understood. Aiming to conduct in-depth integrative bioinformatic analyses to elucidate molecular mechanisms underlying the protective effects of polyphenols on cardiometabolic health, we first conducted a systematic literature search to identify human intervention studies with polyphenols that demonstrate improvement of cardiometabolic risk factors in parallel with significant nutrigenomic effects. Applying the predefined inclusion criteria, we identified 58 differentially expressed genes at mRNA level and 5 miRNAs, analyzed in peripheral blood cells with RT-PCR methods. Subsequent integrative bioinformatic analyses demonstrated that polyphenols modulate genes that are mainly involved in the processes such as inflammation, lipid metabolism, and endothelial function. We also identified 37 transcription factors that are involved in the regulation of polyphenol modulated genes, including RELA/NFKB1, STAT1, JUN, or SIRT1. Integrative bioinformatic analysis of mRNA and miRNA-target pathways demonstrated several common enriched pathways that include MAPK signaling pathway, TNF signaling pathway, PI3K-Akt signaling pathway, focal adhesion, or PPAR signaling pathway. These bioinformatic analyses represent a valuable source of information for the identification of molecular mechanisms underlying the beneficial health effects of polyphenols and potential target genes for future nutrigenetic studies.

Published
2021

5. Omics-based analysis of honey bee (Apis mellifera) response to Varroa sp. parasitisation and associated factors reveals changes impairing winter bee generation

Author

Kunc, Martin, Dobeš, Pavel, Ward, Rachel, Lee, Saetbyeol, Čegan, Radim, Dostálková, Silvie, Holušová, Kateřina, Hurychová, Jana, Eliáš, Sara, Pinďáková, Eliška, Čukanová, Eliška, Prodělalová, Jana, Petřivalský, Marek, Danihlík, Jiří, Havlík, Jaroslav, Hobza, Roman, Kavanagh, Kevin, and Hyršl, Pavel

Published
2022
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10. Faecal Bacteriome and Metabolome Profiles Associated with Decreased Mucosal Inflammatory Activity Upon Anti-TNF Therapy in Paediatric Crohn’s Disease

Author

Hurych, Jakub, primary, Mascellani Bergo, Anna, additional, Lerchova, Tereza, additional, Hlinakova, Lucie, additional, Kubat, Michal, additional, Malcova, Hana, additional, Cebecauerova, Dita, additional, Schwarz, Jan, additional, Karaskova, Eva, additional, Hecht, Tomas, additional, Vyhnanek, Radim, additional, Toukalkova, Lenka, additional, Dotlacil, Vojtech, additional, Greinerova, Katerina, additional, Cizkova, Anabela, additional, Horvath, Rudolf, additional, Bronsky, Jiri, additional, Havlik, Jaroslav, additional, Hradsky, Ondrej, additional, and Cinek, Ondrej, additional

Published
2023
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13. Faecal Bacteriome and Metabolome Profiles Associated with Decreased Mucosal Inflammatory Activity Upon Anti-TNF Therapy in Paediatric Crohn's Disease.

Author

Hurych, Jakub, Bergo, Anna Mascellani, Lerchova, Tereza, Hlinakova, Lucie, Kubat, Michal, Malcova, Hana, Cebecauerova, Dita, Schwarz, Jan, Karaskova, Eva, Hecht, Tomas, Vyhnanek, Radim, Toukalkova, Lenka, Dotlacil, Vojtech, Greinerova, Katerina, Cizkova, Anabela, Horvath, Rudolf, Bronsky, Jiri, Havlik, Jaroslav, Hradsky, Ondrej, and Cinek, Ondrej

Abstract

Background and Aims Treatment with anti-tumour necrosis factor α antibodies [anti-TNF] changes the dysbiotic faecal bacteriome in Crohn's disease [CD]. However, it is not known whether these changes are due to decreasing mucosal inflammatory activity or whether similar bacteriome reactions might be observed in gut-healthy subjects. Therefore, we explored changes in the faecal bacteriome and metabolome upon anti-TNF administration [and therapeutic response] in children with CD and contrasted those to anti-TNF-treated children with juvenile idiopathic arthritis [JIA]. Methods Faecal samples collected longitudinally before and during anti-TNF therapy were analysed with regard to the bacteriome by massively parallel sequencing of the 16S rDNA [V4 region] and the faecal metabolome by 1H nuclear magnetic resonance imaging. The response to treatment by mucosal healing was assessed by the MINI index at 3 months after the treatment started. We also tested several representative gut bacterial strains for in vitro growth inhibition by infliximab. Results We analysed 530 stool samples from 121 children [CD 54, JIA 18, healthy 49]. Bacterial community composition changed on anti-TNF in CD: three members of the class Clostridia increased on anti-TNF, whereas the class Bacteroidia decreased. Among faecal metabolites, glucose and glycerol increased, whereas isoleucine and uracil decreased. Some of these changes differed by treatment response [mucosal healing] after anti-TNF. No significant changes in the bacteriome or metabolome were noted upon anti-TNF in JIA. Bacterial growth was not affected by infliximab in a disc diffusion test. Conclusions Our findings suggest that gut mucosal healing is responsible for the bacteriome and metabolome changes observed in CD, rather than any general effect of anti-TNF. [ABSTRACT FROM AUTHOR]

Published
2024
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16. Changes in the gut bacteriome upon gluten-free diet intervention do not mediate beta cell preservation

Author

Neuman, Vit, primary, Pruhova, Stepanka, additional, Kulich, Michal, additional, Kolouskova, Stanislava, additional, Vosahlo, Jan, additional, Romanova, Martina, additional, Petruzelkova, Lenka, additional, Havlik, Jaroslav, additional, Mascellani, Anna, additional, Henke, Svatopluk, additional, Sumnik, Zdenek, additional, and Cinek, Ondrej, additional

Published
2022
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17. Antioxidant and Anti-Inflammatory Activity of Five Medicinal Mushrooms of the Genus Pleurotus

Author

Stastny, Jan, primary, Marsik, Petr, additional, Tauchen, Jan, additional, Bozik, Matej, additional, Mascellani, Anna, additional, Havlik, Jaroslav, additional, Landa, Premysl, additional, Jablonsky, Ivan, additional, Treml, Jakub, additional, Herczogova, Petra, additional, Bleha, Roman, additional, Synytsya, Andriy, additional, and Kloucek, Pavel, additional

Published
2022
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18. Systematic analysis of nutrigenomic effects of polyphenols related to cardiometabolic health in humans – Evidence from untargeted mRNA and miRNA studies

Author

Ruskovska, Tatjana, primary, Budić-Leto, Irena, additional, Corral-Jara, Karla Fabiola, additional, Ajdžanović, Vladimir, additional, Arola-Arnal, Anna, additional, Bravo, Francisca Isabel, additional, Deligiannidou, Georgia-Eirini, additional, Havlik, Jaroslav, additional, Janeva, Milkica, additional, Kistanova, Elena, additional, Kontogiorgis, Christos, additional, Krga, Irena, additional, Massaro, Marika, additional, Miler, Marko, additional, Harnafi, Hicham, additional, Milosevic, Verica, additional, Morand, Christine, additional, Scoditti, Egeria, additional, Suárez, Manuel, additional, Vauzour, David, additional, and Milenkovic, Dragan, additional

Published
2022
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19. Systematic analysis of nutrigenomic effects of polyphenols related to cardiometabolic health in humans – Evidence from untargeted mRNA and miRNA studies

Author

Ruskovska, Tatjana, Ruskovska, Tatjana, Budić-Leto, Irena, Corral-Jara, Karla Fabiola, Ajdžanović, Vladimir, Arola-Arnal, Anna, Bravo, Francisca Isabel, Deligiannidou, Georgia Erini, Havlik, Jaroslav, Janeva, Milkica, Kistanova, Elena, Kontogiorgis, Christos, Krga, Irena, Massaro, Marika, Miler, Marko, Harnafi, Hicham, Milosevic, Verica, Morand, Christine, Scoditti, Egeria, Suárez, Manuel, Vauzour, David, Milenkovic, Dragan, Ruskovska, Tatjana, Ruskovska, Tatjana, Budić-Leto, Irena, Corral-Jara, Karla Fabiola, Ajdžanović, Vladimir, Arola-Arnal, Anna, Bravo, Francisca Isabel, Deligiannidou, Georgia Erini, Havlik, Jaroslav, Janeva, Milkica, Kistanova, Elena, Kontogiorgis, Christos, Krga, Irena, Massaro, Marika, Miler, Marko, Harnafi, Hicham, Milosevic, Verica, Morand, Christine, Scoditti, Egeria, Suárez, Manuel, Vauzour, David, and Milenkovic, Dragan

Abstract

Cardiovascular and metabolic disorders present major causes of mortality in the ageing population. Polyphenols present in human diets possess cardiometabolic protective properties, however their underlying molecular mechanisms in humans are still not well identified. Even though preclinical and in vitro studies advocate that these bioactives can modulate gene expression, most studies were performed using targeted approaches. With the objective to decipher the molecular mechanisms underlying polyphenols cardiometabolic preventive properties in humans, we performed integrative multi-omic bioinformatic analyses of published studies which reported improvements of cardiometabolic risk factors following polyphenol intake, together with genomic analyses performed using untargeted approach. We identified 5 studies within our criteria and nearly 5000 differentially expressed genes, both mRNAs and miRNAs, in peripheral blood cells. Integrative bioinformatic analyses (e.g. pathway and gene network analyses, identification of transcription factors, correlation of gene expression profiles with those associated with diseases and drug intake) revealed that these genes are involved in the processes such as cell adhesion and mobility, immune system, metabolism, or cell signaling. We also identified 27 miRNAs known to regulate processes such as cell cytoskeleton, chemotaxis, cell signaling, or cell metabolism. Gene expression profiles negatively correlated with expression profiles of cardiovascular disease patients, while a positive correlation was observed with gene expression profiles following intake of drugs against cardiometabolic disorders. These analyses further advocate for health protective effects of these bioactives against age-associated diseases. In conclusion, polyphenols can exert multi-genomic modifications in humans and use of untargeted methods coupled with bioinformatic analyses represent the best approach to decipher molecular mechanisms underlying healthy-ageing

Published
2022

30. Molecular Determinants of the Cardiometabolic Improvements of Dietary Flavanols Identified by an Integrative Analysis of Nutrigenomic Data from a Systematic Review of Animal Studies

Author

Monfoulet, Laurent‐Emmanuel, primary, Ruskovska, Tatjana, additional, Ajdžanović, Vladimir, additional, Havlik, Jaroslav, additional, Vauzour, David, additional, Bayram, Banu, additional, Krga, Irena, additional, Corral‐Jara, Karla‐Fabiola, additional, Kistanova, Elena, additional, Abadjieva, Desislava, additional, Massaro, Marika, additional, Scoditti, Egeria, additional, Deligiannidou, Eirini, additional, Kontogiorgis, Christos, additional, Arola‐Arnal, Anna, additional, Schothorst, Evert M., additional, Morand, Christine, additional, and Milenkovic, Dragan, additional

Published
2021
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31. Molecular Determinants of the Cardiometabolic Improvements of Dietary Flavanols Identified by an Integrative Analysis of Nutrigenomic Data from a Systematic Review of Animal Studies

Author

Monfoulet, Laurent-Emmanuel, Monfoulet, Laurent-Emmanuel, Ruskovska, Tatjana, Ajdžanović, Vladimir, Havlik, Jaroslav, Vauzour, David, Bayram, Banu, Krga, Irena, Corral-Jara, Karla-Fabiola, Kistanova, Elena, Abadjieva, Desislava, Massaro, Marika, Scoditti, Egeria, Deligiannidou, Eirini, Kontogiorgis, Christos, Arola-Arnal, Anna, van Schothorst, Evert M., Morand, Christine, Milenković, Dragan, Monfoulet, Laurent-Emmanuel, Monfoulet, Laurent-Emmanuel, Ruskovska, Tatjana, Ajdžanović, Vladimir, Havlik, Jaroslav, Vauzour, David, Bayram, Banu, Krga, Irena, Corral-Jara, Karla-Fabiola, Kistanova, Elena, Abadjieva, Desislava, Massaro, Marika, Scoditti, Egeria, Deligiannidou, Eirini, Kontogiorgis, Christos, Arola-Arnal, Anna, van Schothorst, Evert M., Morand, Christine, and Milenković, Dragan

Abstract

Scope: Flavanols are important polyphenols of the human diet with extensive demonstrations of their beneficial effects on cardiometabolic health. They contribute to preserve health acting on a large range of cellular processes. The underlying mechanisms of action of flavanols are not fully understood but involve a nutrigenomic regulation. Methods and Results: To further capture how the intake of dietary flavanols results in the modulation of gene expression, nutrigenomics data in response to dietary flavanols obtained from animal models of cardiometabolic diseases have been collected and submitted to a bioinformatics analysis. This systematic analysis shows that dietary flavanols modulate a large range of genes mainly involved in endocrine function, fatty acid metabolism, and inflammation. Several regulators of the gene expression have been predicted and include transcription factors, miRNAs and epigenetic factors. Conclusion: This review highlights the complex and multilevel action of dietary flavanols contributing to their strong potential to preserve cardiometabolic health. The identification of the potential molecular mediators and of the flavanol metabolites driving the nutrigenomic response in the target organs is still a pending question which the answer will contribute to optimize the beneficial health effects of dietary bioactives.

Published
2021

32. Systematic Bioinformatic Analyses of Nutrigenomic Modifications by Polyphenols Associated with Cardiometabolic Health in Humans-Evidence from Targeted Nutrigenomic Studies

Author

Universitat Rovira i Virgili, Ruskovska, Tatjana; Budic-Leto, Irena; Corral-Jara, Karla Fabiola; Ajdzanovic, Vladimir; Arola-Arnal, Anna; Bravo, Francisca Isabel; Deligiannidou, Georgia-Eirini; Havlik, Jaroslav; Janeva, Milkica; Kistanova, Elena; Kontogiorgis, Christos; Krga, Irena; Massaro, Marika; Miler, Marko; Milosevic, Verica; Morand, Christine; Scoditti, Egeria; Suarez, Manuel; Vauzour, David; Milenkovic, Dragan, Universitat Rovira i Virgili, and Ruskovska, Tatjana; Budic-Leto, Irena; Corral-Jara, Karla Fabiola; Ajdzanovic, Vladimir; Arola-Arnal, Anna; Bravo, Francisca Isabel; Deligiannidou, Georgia-Eirini; Havlik, Jaroslav; Janeva, Milkica; Kistanova, Elena; Kontogiorgis, Christos; Krga, Irena; Massaro, Marika; Miler, Marko; Milosevic, Verica; Morand, Christine; Scoditti, Egeria; Suarez, Manuel; Vauzour, David; Milenkovic, Dragan

Abstract

Cardiometabolic disorders are among the leading causes of mortality in the human population. Dietary polyphenols exert beneficial effects on cardiometabolic health in humans. Molecular mechanisms, however, are not completely understood. Aiming to conduct in-depth integrative bioinformatic analyses to elucidate molecular mechanisms underlying the protective effects of polyphenols on cardiometabolic health, we first conducted a systematic literature search to identify human intervention studies with polyphenols that demonstrate improvement of cardiometabolic risk factors in parallel with significant nutrigenomic effects. Applying the predefined inclusion criteria, we identified 58 differentially expressed genes at mRNA level and 5 miRNAs, analyzed in peripheral blood cells with RT-PCR methods. Subsequent integrative bioinformatic analyses demonstrated that polyphenols modulate genes that are mainly involved in the processes such as inflammation, lipid metabolism, and endothelial function. We also identified 37 transcription factors that are involved in the regulation of polyphenol modulated genes, including RELA/NFKB1, STAT1, JUN, or SIRT1. Integrative bioinformatic analysis of mRNA and miRNA-target pathways demonstrated several common enriched pathways that include MAPK signaling pathway, TNF signaling pathway, PI3K-Akt signaling pathway, focal adhesion, or PPAR signaling pathway. These bioinformatic analyses represent a valuable source of information for the identification of molecular mechanisms underlying the beneficial health effects of polyphenols and potential target genes for future nutrigenetic studies.

Published
2021

40. Effect of Selected Stilbenoids on Human Fecal Microbiota

Author

Jaimes, Jose, primary, Jarosova, Veronika, additional, Vesely, Ondrej, additional, Mekadim, Chahrazed, additional, Mrazek, Jakub, additional, Marsik, Petr, additional, Killer, Jiri, additional, Smejkal, Karel, additional, Kloucek, Pavel, additional, and Havlik, Jaroslav, additional

Published
2019
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42. Screening of medicinal plants traditionally used in Peruvian Amazon for in vitro antioxidant and anticancer potential

Author

Tauchen, Jan, primary, Huml, Lukas, additional, Bortl, Ludvik, additional, Doskocil, Ivo, additional, Jarosova, Veronika, additional, Marsik, Petr, additional, Frankova, Adela, additional, Clavo Peralta, Zoyla Mirella, additional, Chuspe Zans, Maria-Elena, additional, Havlik, Jaroslav, additional, Lapcik, Oldrich, additional, and Kokoska, Ladislav, additional

Published
2018
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43. Reply to the Letter to the Editor by Paul O. Sheridan, Sylvia H. Duncan, Alan W. Walker, Karen P. Scott, Petra Louis and Harry J. Flint, referring to our paper 'Reclassification of Eubacterium rectale (Prévot et al. 1967) in a new genus Agathobacter gen. nov., as Agathobacter rectalis comb. nov., within the family Lachnospiraceae, and description of Agathobacter ruminis sp. nov., from the rumen', Int J Syst Evol Microbiol, DOI 10.1099/ijsem.0.000788

Author

Rosero, Jaime A., Killer, Jiri, Sechovcova, Hana, Mrazek, Jakub, Oldřich Benada, Fliegerova, Katerina, Havlik, Jaroslav, and Kopecny, Jan

Subjects
General Medicine, Microbiology, Ecology, Evolution, Behavior and Systematics
Published
2016

45. In vitro antistaphylococcal effects of Embelia schimperi extracts and their component embelin with oxacillin and tetracyclin

Author

Rondevaldova, Johana, Leuner, Olga, Teka, Alemtshay, Lulekal, Ermias, Havlik, Jaroslav, Van Damme, Patrick, and Kokoska, Ladislav

Abstract

Bacterial infections are in less-developed countries traditionally treated by remedies prepared from medicinal plants. Embelia schimperi (Vatke) is a plant used as a taenicide or disinfectant in Ethiopia, very often taken mixed with another plant species. In the present study, we examined two extracts prepared from seeds and twigs with leaves of E. schimperi and its main present secondary metabolite embelin for their antibacterial combinatory effect with oxacillin and tetracycline against sensitive and resistant Staphylococcus aureus strains. Minimum inhibitory concentrations were determined through the broth microdilution method, whereas the combinatory effect was evaluated through fractional inhibitory concentration sum (ΣFIC) indices. Results show many positive interactions and synergy occurring in embelin and oxacillin combinations against 4 out of 9 strains (ΣFIC 0.203–0.477) and for embelin and tetracycline combination against 3 out of 9 strains (ΣFIC 0.400–0.496). Moreover, the resistance to oxacillin has been overcome in 2 strains and to tetracycline in 3 strains. According to our knowledge, this is the first study showing antimicrobial combinatory effect of E. schimperi as well as of embelin. These findings can be used for the further research targeted on the development of new antistaphylococcal agents.

Published
2015

46. Screening of medicinal plants traditionally used in Peruvian Amazon for in vitro antioxidant and anticancer potential.

Author

Tauchen, Jan, Huml, Lukas, Bortl, Ludvik, Doskocil, Ivo, Jarosova, Veronika, Marsik, Petr, Frankova, Adela, Clavo Peralta, Zoyla Mirella, Chuspe Zans, Maria-Elena, Havlik, Jaroslav, Lapcik, Oldrich, and Kokoska, Ladislav

Subjects
MEDICINAL plants, ANALYTICAL chemistry, PHENOLS, OXIDATIVE stress, ANTIOXIDANTS
Abstract

Plants mentioned in this study have numerous records in traditional Peruvian medicine being used in treatment of cancer and other diseases likely to be associated with oxidative stress. Amongst the eight plant species tested, only Dysphania ambrosioides exhibited combinatory antioxidant and anti-proliferative effect on a broad spectrum of cancer cells (DPPH and ORAC values = 80.6 and 687.3 μg TE/mg extract, respectively; IC50 against Caco-2, HT-29 and Hep-G2 = 129.2, 69.9 and 130.6, respectively). Alkaloids and phenolic compounds might significantly contribute to anticancer/antioxidant activity of this plant. The results justify the traditional medicinal use of this plant. Our findings further suggest that D. ambrosioides might serve as a prospective material for further development of novel plant-based antioxidant and/or anti-proliferative agents. Detailed analysis of chemical composition together with toxicology assessments and in vivo antioxidant/anti-proliferative activity of this plant should be carried out in order to verify its potential practical use. [ABSTRACT FROM AUTHOR]

Published
2019
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