A wide variety of human diseases, including Alzheimer’s, Parkinson’s, Huntington’s, and diabetes type II, are associated with the deposition of insoluble protein aggregates composed of amyloid fibrils. The conversion of monomeric protein into amyloid fibrils has been studied extensively in test tube reactions, but how protein aggregation takes place in living cells and organisms remains poorly understood. Notably, cells and organisms have evolved intricate networks for protein quality control, such as molecular chaperones that aid correct protein folding, and degradation machineries that eliminate aberrant protein species. Furthermore, amyloid formation is likely affected by the presence of other cellular components including membranes.

In our lab, we use the roundworm Caenorhabditis elegans as a model organism to study disease-related protein aggregation in vivoC. elegans is relatively short-lived and optically transparent, allowing us to track the aggregation of fluorescently labelled proteins across its lifespan. Using a combination of different microscopy techniques, genetics, biochemistry, structural biology, and mathematical modelling, we aim to obtain a molecular and quantitative understanding of protein aggregation and its relation to ageing and disease.

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In vivo protein aggregation kinetics

Amyloid formation has been studied extensively in test tube reactions, and using kinetic assays combined with mathematical modelling it is possible to decipher the microscopic reaction steps and the associated rates. This knowledge is very important e.g. to develop therapeutics that prevent certain reaction steps, in particular those that lead to the generation of toxic protein species. In living organisms, the steps that lead to amyloid deposition remain largely elusive, and the process had not yet been examined in a quantitative manner. In this project, we are using C. elegans expressing expanded polyglutamine (polyQ), which is associated with Huntington’s disease, as a model system to quantitatively examine the kinetics of amyloid formation in vivo. The use of this simple animal model allowed us to identify a mechanism of stochastic nucleation in each cell, followed by rapid aggregate growth (see recent preprint and figure below). Based on this model we are continuing to investigate the interplay with cellular components, the difference between different tissues and cell types, as well as the role of ageing as a main risk factor for protein aggregation.

Schematic mechanism of polyQ aggregation in C. elegans muscle cells.
Stars represent nucleation events and spheres (growing) protein aggregates.

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Protein aggregation and cellular membranes

A number of disease-associated proteins that form amyloids have been found to interact with cellular membranes, such as IAPP in diabetes type II, amyloid-β in Alzheimer’s disease and α-synuclein in Parkinson’s disease. We aim to investigate the mechanisms by which these proteins aggregate in vivo in the presence of native biological membranes, and how these processes can be modulated by small molecules.

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In situ structural biology

The molecular structures of amyloid fibrils and intermediate aggregate species are typically studied in isolation, in the absence of the native biological environment. In order to understand how amyloid-like aggregates arise and cause cellular toxicity, we aim to establish methods to elucidate protein aggregation pathways and the structural features of aggregate species at molecular resolution in a biological context.