Autophagy regulation at the level of the acetylproteome – Acetauto

We use a series of approaches from cell and molecular biology, as well as systems biology methods (protein mass spectrometry, metabolomics, medium and high-throughput screenings).

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We hope to obtain insights into the therapeutic modulation of autophagy with important implications for metabolism and aging.

We have published multiple high-profile papers including in Science, Molecular Cell, Oncogen, Journal of Biological Chemistry, Cell Research, Cell Cycle, Autophagy Nature Reviews Drug Discover, Nature Reviews Cancer Research, Science Signaling.

The current state of the art suggest that autophagy is essential for the adaptation of stress, that deregulated autophagy is involved in multiple human diseases, and that the healthspan and lifespan of multiple model organisms including mice and primates correlates with their autophagic potential. The post-translational modification of multiple cellular proteins by acetylation or deacetylation rivals with the importance of (de)phosphorylation reactions. Multiple acetyl transferases and deacetylases connect signaling and metabolism at multiple levels.

In this fundamental research project, we aim at responding at the following important questions:

• Which pharmacological or genetic modulators of protein (de)acetylases are the most potent inhibitors and inducers of autophagy? And do they elicit the canonical or non-canonical autophagic pathway?

• Which are the functional links between the acetylproteome and autophagy? Which are the elements in the cytoplasmic and nuclear acetylproteomes that are decisive for autophagy regulation?

• What is the precise role of acetyl CoA in the regulation of autophagy? Does acetyl CoA play a major role in the control of autophagy by caloric restriction/starvation? And can this knowledge taken advantage of to manipulate autophagy?

• How is autophagy regulated by acyl CoA binding protein (ACBP)? Is this regulatory function relevant to mammalian physiology? And how do intracellular regulation of autophagy (by acyl CoA, acetyl CoA etc.) and its putative paracrine regulation (by acyl CoA binding protein) crosstalk?

Our project can be subdivided into five major tasks.

The first task deals with the coordination of the project.

The second task will consist in the quantitative comparison of autophagy stimulation by pharmacological agents and siRNAs that inhibit or activate (histone) deacetylases and acetylases in different mammalian cell lines, insisting on epistatic analyses. Moreover, we will systematically test different modulators of histone (de)acetylases for their capacity to induce classical (Beclin 1-dependent) and non-canonical (Beclin 1-independent) autophagy.

The third task involves the exploration of functional links between the acetylproteome and autophagy. For this, we will determine alterations in the acetylproteome induced by starvation and rapamycin. These results will be confronted with our databases of (de)acetylations stimulated by spermidine or resveratrol. We will chose selected proteins and subject them to direct manipulations (siRNA-mediated knockdown or cDNA-enforced overexpression) or mutations (to create acetylation-mimetic or acetylation-refractary sites) for the modulation of autophagy.

The fourth task concerns the role of the acetyl CoA in autophagic regulation. We will determine the impact of genetic or biochemical manipulations that increase or reduce acetyl CoA concentrations or affect the metabolism of acetyl CoA or more generally of acyl CoA. Epistatic analyses involving acetyl CoA-targeted experimental interventions with known inducers of autophagy will be performed to understand the importance of acetyl CoA in autophagic control.

The fifth task deals with the regulation of autophagy by extracellular acyl CoA binding protein (ACBP). We will determine whether and to which extent the release of ACBP is determined by autophagy. We will determine to which extent intracellular acetyl CoA (and more generally acyl CoA) and intracellular/extracellular ACBP crosstalk in autophagy regulation. Finally, we will assess the impact of exogenous ACBP or its neutralization in several model systems of autophagy induction, in vitro and in vivo.

We surmise that responding to these questions will provide insights into the regulation of autophagy and facilitate the development of novel genetic, pharmacological and nutritional interventions aiming at an optimal induction for autophagy for therapeutic purposes.