Abstract:
Neurodegenerative diseases such as Alzheimer’s Disease remain a leading socio-economic challenge and have been intensely studied on the genetic level, demonstrating a significant contribution of the immune system to disease pathogenesis. However, how environmental factors influence pathology remains to be fully understood. As microglia are the main resident immune cell population in the brain, they have been studied intensely regarding their contribution to neurological and neurodegenerative diseases. In the last years, several transcriptomic studies independently identified different microglia subpopulations with a variety of functions in health and disease. However, despite many genetic studies, it is still not clear how microglia influence disease pathology, how they change during healthy aging and which regulatory factors drive the development of a specific microglia activation state. Therefore, the first study presented here used scRNA-Seq and scATAC-Seq to characterize microglia of wildtype and APP-transgenic mice of different ages. Single-cell transcriptomic and open-chromatin profiling revealed that microglia are a heterogenous cell population showing differences in number, gene expression and chromatin accessibility, not only with progressive β-amyloid deposition in the brain, but also during healthy aging. Furthermore, we describe for the first time an age-related decline of one homeostatic microglia population and a simultaneous increase of an aging-associated subpopulation, that develops and persists independent of Aβ pathology. Multimodal analysis of the microglia subpopulations identified several disease-relevant transcription factors, such as Arnt and Hif1α, and their candidate target genes. Finally, this study shows that Hif1α regulates a subset of genes that define the so-called disease-associated microglia (DAM) phenotype, and microglial knockout of Hif1α induced a shift in microglia subpopulations, reducing neuroinflammation and increasing plaque-compaction, which, in turn, limits neuritic damage.
The onset and progression of neurodegenerative diseases can be influenced by peripheral inflammatory insults such as certain diseases (e.g. diabetes, arthritis) or infections. As it has recently been shown in our lab that microglia can develop long-lasting immune memory effects in response to peripheral inflammatory insults, the second part of my PhD project was aimed at analyzing the molecular mechanisms of how peripheral inflammatory insults cause microglial immune memory. To this end, wildtype mice were stimulated with a set of pro- and anti-inflammatory cytokines or exposed to live bacterial infections and multiplex cytokine profiles were generated. In addition, a method was established that will allow us to profile fixed nuclei from mouse as well as post-mortem human tissue. In a proof of principle experiment, we could show that analyzing chromatin accessibility and gene expression in the same single-nucleus circumvents the issue of data sparsity and allows co-embedding of both datasets. This multi-omic analysis enables the identification of cell type-specific epigenetic and transcriptomic dysregulation in this and future studies.
