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FWGDekker Report Summary

Project ID: 309782
Funded under: FP7-IDEAS-ERC
Country: Netherlands

Final Report Summary - FWGDEKKER (Novel tools to read and write the epigenetic code in inflammation)

Protein lysine acetylations play a key regulatory role in signal transduction pathways that are involved in inflammatory responses. Lysine acetylations of histones play a role in the epigenetic regulation of gene transcription. In addition, they play a role in the regulation of the activity and localization of transcription factors such as the nuclear factor kB subunit p65. Acetylations of both the histones and the transcription factor p65 are regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). We aim to develop novel small molecule inhibitors of these enzymes in combination with studies on the selectivity profile of these inhibitors for their cellular substrates in the context of inflammation.

We developed a novel method to study protein lysine acylations using metabolic labelling of lysine acetylation sites using alkene labelled carboxylates. The oxidative Heck reaction has been established as a novel bioorthogonal reaction for labelling of protein bound alkenes that reflect the level of protein lysine acylation.

A model for airway inflammation has been established in which we investigated changes in pro- and anti-inflammatory gene transcription upon LPS/INFg stimulation in relevant cell cultures. The effects in cell cultures are connected to effects in ex vivo lung tissue slices and an in vivo model for airway inflammation in mice. In the in vivo study in mice we found clear anti-inflammatory effects upon treatment with an HDAC inhibitors via inhalation in the airways. Importantly, we found that IL-10 upregulation by HDAC inhibition is consistently observed in all the model systems. In the cultured cells we identified that increased NF-kB transcriptional activity, increased p65 K310 acetylation and increased p65 binding to the IL-10 promotor provide a mechanistic explanation for the observed anti-inflammatory effects.

In parallel, we are developing novel HAT and HDAC inhibitors. Towards this aim we resolved the enzyme kinetic mechanism of the HAT KAT8 and we identified the first inhibitors for this enzyme using a fragment-based screening. We demonstrated that enzyme kinetic analysis is key to a reliable description of the binding of small molecule inhibitors to the HATs as bi-substrate enzymes.

These results provide the basis to develop novel HDAC inhibitors with improved selectivity among the HDAC isoenzymes 1, 2 and 3. Our most recent findings indicate that HDAC1 isoenzyme selective inhibitors have a superior anti-inflammatory profile in cell based studies.

Ultimately, this combined development of novel detection methods and small molecule inhibitors will enable a personalized approach in which patients are treated based on the detection of specific lysine acetylations as biomarkers that guide the selection of specific therapeutics.

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