Dissecting cellular heterogeneity dynamics 

Cell fate commitment is the key process for understanding how a multicellular organism’s genotype gives rise to phenotypic traits including disease development and progression. To understand the role of epigenetically-induced cell heterogeneity and its importance for development and pathogenesis, we analyse population dynamics of hematopoietic stem and human breast cancer cells at single cell resolution. We quantify cellular heterogeneity dynamics by combining flux cytometry, microarray, single cell qPCR and RNAseq approaches including our Drop-Seq tool with microscopy and bioinformatics analyses. The resulting multi-scale data enables to get a comprehensive picture of cell fate dynamics and is integrated into a developmental modelling framework. The methods developed to characterise critical transition of cell states in this project are also applied to changes of mitochondrial dynamics.

Brain energy metabolism in neurodegeneration

Brain energy metabolism is based on the fine-tuned interplay of glycolysis and mitochondrial activity, as the energy providing pathways, and intercellular energy transfer. It represents a promising unifying perspective for neurodegenerative diseases because mitochondrial dysfunction, as a common hallmark, interrelates several known pathological processes including dopamine synthesis, oxidative stress and proteostasis. To account for the complex interplay of different cell types in brain energy metabolism, we combine high-resolution imaging and mechanistic spatial modelling of intra- and intercellular energy homeostasis. In collaboration with Mark Ellisman at the National Center of Microscopy and Imaging Research (NCMIR) at La Jolla, we use super-resolution 3D electron microscopy (EM) to image astrocytic morphologies and mitochondria to develop spatiotemporal in silico models of intracellular energy metabolism that allow us to investigate the dynamic consequences of potentially disease related morphological and molecular impairments. This project receives funding by the FNR.

Mitochondrial dynamics

Mitochondrial dysfunction plays an important role in the aetiology of neurodegeneration. To elucidate the underlying mechanisms, we study mitochondrial dynamics at different levels. First, we analyse the crosstalk between Ca2+ signalling and mitochondrial activity by live cell fluorescent imaging and dynamic modelling, and show how the coupling can increase robustness of energy homeostasis within cells. Second, we use PD-related iPS cell lines and pharmacological perturbations together with multiscale modelling to study mitochondrial transport and its impact on mitochondrial turnover. This fission- and fusion based processes ultimately determine the energy profiles along neurites and their functionality. Finally, we develop a microscopic in silico model of mitochondria to investigate how mitochondrial morphology is affecting energy production. This project is partially funded by the FNR.

Identifying genetic interactions

Phenotypic variations, including those that underlie health and disease in humans, result from multiple genetic variations and environmental factors and combinations thereof. Detecting these potentially non-additive genetic interactions is key to understand complex diseases like PD and other neurodegenerative diseases. In collaboration with the Galas and Dudley groups at the Pacific North West Research Center in Seattle, USA, we are developing information theory-based methods to detect pairwise effects of genetic markers on phenotypic traits that have negligible effect when considered alone. Accuracy and computational efficiency of our recent interaction distance approach is validated in large datasets of yeast, mouse and synthetic human data. The method will help to study genetic interactions in patient cohorts and can even be used to optimize the composition of case and control groups depending on expected allele frequencies.

The role of intercellular interaction in neurodegeneration

Besides neurons, glial cells like microglia and astrocytes play a critical role in the pathogenesis of neurodegenerative diseases. For example, a subfraction of microglia seem to lose their protective functions and become harmful to the brain. These subgroups of microglia engage maladaptive inflammatory or phagocytic responses that promote neuroinflammation and neuronal cell death and may contribute to the progression of Alzheimer’s disease (AD). To characterise this intercellular phenomenon, we image post mortem human brain samples from AD subjects and controls, and develop an unbiased automatic image analysis pipeline that extracts a wide range of cellular features from individual cells including standard morphological characteristics to more innovative graph-based features accounting different patterns of arborisation and complexity. Comparing brain tissues from patients and controls for different brain regions, we identify alterations of the potentially harmful microglia, characterise their key phenotypic features and impact on the disease. Additionally, this methodology provides new tools for the understanding of microglia, and its involvement in neurodegenerative processes and other brain alterations.