Systems biology based characterization of medicinal effects of phytochemicals

Epidemiological, clinical and animal studies support a beneficial role of mangiferin, epicatechin and withaferin A in the prevention or treatment of  metabolic & cardiovascular diseases, cancers and neuronal disorders. By integrating epigenomic, transcriptomic, microRNomic, (chemo)proteomic approaches we want to identify key signalling pathways and molecular targets of phytochemicals involved in chemoprevention, cardioprotection or hormone therapy sensitisation in various disease models.

Investigation of epigenomic plasticity of metastatic and non-metastatic breast cancer cells exposed to withaferin A (Dehousse grant)

Withaferin A isolated from withania somnifera exerts anti-inflammatory, pro-apoptotic, anti-metastastatic and anti-angiogenic effects in various tumor models in vitro/in vivo.

  • In this project, we evaluate the role of DNA methylation and chromatin enzyme (writer/eraser/reader) changes in anti-cancer properties of withaferin A in metastatic and non-metastatic breast cancer cells. We apply Illumina 450K CpG array, Sequenome Epityper and CpG pyrosequencing for quantitative DNA methylation profiling and Illumina bead array for transcriptomic profiling.

Further reading:

  • Hyperactivated NF-{kappa}B and AP-1 transcription factors promote highly accessible chromatin and constitutive transcription across the interleukin-6 gene promoter in metastatic breast cancer cells. Ndlovu N, Van Lint C, Van Wesemael K, Callebert P, Chalbos D, Haegeman G, Vanden Berghe W. Mol Cell Biol. 2009 Oct;29(20):5488-504.
  • Epigenetic impact of dietary polyphenols in cancer chemoprevention: lifelong remodeling of our epigenomes. Vanden Berghe W. Pharmacol Res. 2012 Jun;65(6):565-76. doi: 10.1016/j.phrs.2012.03.007


Circumventing the Biological Obstacles of Anti-Inflammatory Glucocorticoid Therapy (SBO/IWT)

Glucocorticoids (GCs) have been successful steroid therapeutics for the treatment of acute and chronic inflammatory conditions and leukemic cancers. Nevertheless, there are important clinical drawbacks with respect to occurrence of steroid resistance and side effects. The overall objective of this project is to identify key pathways and molecular targets related to GC therapy resistance, or develop new compounds with improved therapeutic profile (less side effects)

  • We investigate the role of microRNAs and DNA methylation in modulation of GC effects in glucocorticoid resistant and sensitive multiple myeloma cell types
  • We perform compound screenings with epigenetic modulator compounds to identify suppressors and enhancers of GR function

Further reading:

  • How glucocorticoid receptors modulate the activity of other transcription factors: A scope beyond tethering.Ratman D, Vanden Berghe W, Dejager L, Libert C, Tavernier J, Beck IM, De Bosscher K. Mol Cell Endocrinol. 2012


Characterisation of the role of jumonji histone demethylases in cancer therapy responses by hypoxia mimetic compounds (BOF/NOI)

Therapy resistant tumors with a bad prognosis typically demonstrate a strong inflammatory gene expression profile and severe hypoxic and hypoglycemic growth conditions.

  • We will study the effect of hypoxia sensitive chromatin enzymes in cancer therapy response in neuroblastoma and leukemia to Withaferin A and hypoxia mimetic compounds (DFO). Chromatin studies involve histone modification specific assays and DNA (hydroxyl)methylation


Molecular characterization and valorization of Cuban natural products, in particular Vimang® and its naturally glucoxylsanthone mangiferin, for therapeutic applications against cancer and inflammation (VLIR).

To reduce the cancer mortality in Cuba, the development of novel cost-effective cancer therapies based on phytomedicinal products from indigenous natural sources, is one of the priorities of the Cuban Ministry of Health.  Previous collaborative studies have already identified pure mangiferin as a major bioactive compound in Mangifera indica L. extract (Vimang), with potent anti-cancer properties in vitro/in vivo.

  • In this project, we will investigate the role chemosensitising and/or anti-angiogenic effects of mangiferin in combination treatment with classic chemotherapeutic drugs (cisplatin, doxorubicin, paclitaxel) in breast, colon or brain cancer cell types in vitro or xenografts in vivo.

Further reading:

  • Gallic acid indanone and mangiferin xanthone are strong determinants of immunosuppressive anti-tumour effects of Mangifera indica L. bark in MDA-MB231 breast cancer cells. García-Rivera D, Delgado R, Bougarne N, Haegeman G, Vanden Berghe W. Cancer Lett. 2011 Jun 1;305(1):21-31.


Integrative bioinformatics analysis of combined epigenome (methylome), transcriptome, miRNome and proteome data (BOF/NOI).

Rapid evolution in analytical technologies including next generation sequencing and mass spectrometry recently boosted the systematic analysis of molecular layers such as the transcriptome, epigenome and proteome. In this doctoral project, novel bioinformatic methodologies will be developed and studied which enable the integrative analysis of these three different quantitative omics data types .

  • To get a comprehensive systems biological view of cellular networks targeted by a potent anti-cancer compound Withaferin A, isolated from Withania somnifera, we will integrate information obtained from transcriptomic experiments (Illumina Array), epigenomic methylation profiling (MBD2seq, Illumina CpG array), microRNA profiling (miRNomics) and chemoproteomic (SILAC/iTrAQ) assays


Targeted delivery of dietary flavanols for optimal cardiovascular cell function (FP7 Flaviola).

Effects on cardiovascular health Flavanols are a group of compounds found in cocoa beans, tea leaves and red wine grapes. There is a growing body of evidence suggesting that a diet rich in flavanols can have a positive impact on cardiovascular health. FLAVIOLA is a pan-European research project addressing how the body absorbs and metabolises flavanols, what impact they have on cardiovascular function and the best diet to benefit from flavanol-containing foods.

  • We investigate DNA methylation changes (Illumina 450K CpG array, CpG pyrosequencing and Sequenom epityper assays) in human vascular cell types (HUVEC) exposed to cocoa metabolites and in blood samples from cocoa flavanol diet intervention studies
  • We investigate actions of flavanols on expression of epigenetic writer/eraser/reader enzymes in human vascular cells
  • We investigate changes in DNA methylation and expression of epigenetic writer/eraser/reader enzymes in monocytes isolated from WT and APOE mouse in early or late stage of atherosclerosis

Further reading:

  • Dietary curcumin inhibits atherosclerosis by affecting the expression of genes involved in leukocyte adhesion and transendothelial migration. Coban D, Milenkovic D, Chanet A, Khallou-Laschet J, Sabbe L, Palagani A, Vanden Berghe W, Mazur A, Morand C. Mol Nutr Food Res. 2012 Aug;56(8):1270-81.
  • Nature or nurture: Let food be your epigenetic medicine in chronic inflammatory disorders. Szarc Vel Szic K, Ndlovu MN, Haegeman G, Vanden Berghe W. Biochem Pharmacol. 2010
  • Natural Products from Mediterranean Diet: From Anti-Inflammatory Agents to Dietary Epigenetic Modulators. Kontogiorgis, C.A.; Bompou, E.M.; Ntella, M.; Vanden Berghe, W. Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry 9: 101-124 (2010).


Hormones and neuroplasticity: image guided discoveries of molecular mechanisms in neuroplasticity (PLASTOSCINE/IUAP).

In this project we want to tackle the question of how brain plasticity is regulated at the molecular level in two songbird models with different song learning and neuroplasticity characteristics, with the help of recently developed tools in brain imaging and epigenetics.

  • In this project, we want to investigate how hormones and environment (light) induced effects contribute to brain plasticity at least in part through epigenetic programming via changes in DNA methylation or histone modifications (acetylation, methylation).
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Quantitative proteomic characterization of cellular targets of withaferin A involved in cancer therapy chemosensitisation in B-cell chronic leukemia cells (FWO).

In the current project we combine medicinal chemistry and affinity tag based proteomics for investigation of cellular targets involved in cancer therapy chemosensitisation. It can be expected that antitumor compounds such as Withaferin A have a wide array of intracellular actions that allows these compounds to attack the tumor from several different molecular fronts. Moreover, it can be expected that some of these pathways act in a synergistic way thereby increasing the potency of the antitumor agent. At the same time however, such a diversity of actions may also explain the nearly unavoidable existence of side-effects when these compounds are administered systemically.

The identification of the intracellular pathways, induced or inhibited by Withaferin A, is therefore of paramount importance to develop agents that influence only part of the Withaferine A spectrum of pathways, yet remain equally potent in their antitumor capacity.

Hence, in order to unravel the many molecular pathways, influenced by Withaferin A, a global, proteomics approach is desired. However as an intracellular proteome can be looked at in several ways like protein expression, posttranslational modifications and protein-protein interactions, different proteomics strategies were set out:

  • Use SILAC to study differential protein expression in Withaferin treated vs. non-treated cells
  • Use biotinylated Withaferin A to determine Withaferin binding partners
  • Use HeLa cells, stabile expressing His-tagged SUMO to determine changing SUMO modifications after Withaferin treatment.

Further reading:

  • Molecular insight in the multifunctional activities of Withaferin A.Vanden Berghe W, Sabbe L, Kaileh M,  Haegeman G, Heyninck K. Biochem Pharmacol. 2012 Nov 15;84(10):1282-91.
  • Withaferin a strongly elicits IkappaB kinase beta hyperphosphorylation concomitant with potent inhibition of its kinase activity.Kaileh M, Vanden Berghe W, Heyerick A, Horion J, Piette J, Libert C, De Keukeleire D, Essawi T, Haegeman G.J Biol Chem. 2007 Feb 16;282(7):4253-64.