CoEN: Investigating chromatin landscapes in neurodegenerative disease models

Neurodegenerative diseases (NDs) are highly debilitating conditions that represent a major economic burden for the developed world. While progress has been made in controlling symptoms pharmacologically, virtually no therapeutic options exist for the treatment of these conditions. This is due to the small number of known ND-causing genetic changes and their limited use as therapeutic targets. It is therefore critical to investigate how additional, nongenetic molecular alterations can drive ND initiation and progression. In this respect, alteration of the way the DNA is packed in the nucleus (chromatin) and its consequences on gene expression have been suggested to contribute to ND pathogenesis. However, our understanding of NDassociated chromatin modifications is mostly based on analysis of human post-mortem tissues or on in vitro preclinical models that do not recapitulate the complexity of NDs. The present application aims to provide an in-depth analysis of chromatin changes over the course of ND pathogenesis using faithful in vivo preclinical models and to correlate these changes back to ND hallmark pathological features. Overall, this study will provide key insights into the dynamic nature of ND-associated chromatin alterations and will constitute the basis for further work aimed at identifying new targets for therapeutic intervention.

In line with the aims of this "pathfinder" call, we will investigate the role of chromatin remodelling in neurodegenerative processes and test the hypothesis that development of
pathology in human neurodegenerative diseases is modulated, at least in part, by short- and long-term chromatin responses to specific tissue challenges. In particular, we will investigate restrictive and permissive chromatin changes in animal models that mimic pathologic features of Parkinson's disease, prion disease and tauopathies. Chromatin changes and ensuing transcriptional alterations will be analysed over time prior to, during and after the development of pathology (e.g., protein aggregation and neurodegeneration). Bioinformatic analysis will help identify similarities as well as differences across disease models and elucidate metabolic/toxic pathways involved in cell-specific vulnerability. Our present lack of disease-modifying intervention for human neurodegenerative diseases is due to a limited knowledge of pathogenetic mechanisms. Although chromatin remodelling could be one of these mechanisms, it remains relatively unexplored from the experimental and translational standpoints. This proposed study is designed to provide key insights into the dynamic nature of neurodegenerative diseaseassociated chromatin alterations and will constitute the seed for further work aimed at targeting these epigenetic modifications as a novel therapeutic approach.

This study represents to our knowledge the first in-depth and cross-disease investigation into the chromatin response to pathological processes mimicking human NDs. Data
concerning the dynamic and heterogeneous nature of this response and its implications on transcription will constitute the seed for further funding applications to i) functionally validate genomic changes in preclinical models and in human clinical samples; ii) provide insights into how the chromatin response is initiated and maintained or modified in affected neuronal subpopulations; iii) to explore opportunities for pharmacological targeting of chromatin remodelers in the context of disease onset and/or progression with the ultimate aim to translate our findings into early phase clinical trials. These are among the research opportunities stemming out of the proposed study:

1) Involvement of the PRC2 complex in the response to ND pathological hallmarks. If this study will point at a PRC2 role in the response to ND drivers, we will employ both genetic and pharmacological approaches to modulate PRC2 activity in vivo.

2) Molecular heterogeneity of the chromatin response. We will seek additional funding to perform single-cell transcriptomics on neurons/neuronal nuclei from the above mentioned models. This will provide key insights into the heterogeneity and the plasticity of chromatin response to neurodegenerative processes at single cell resolution between susceptible and resistant neuronal subtypes.

3) Profiling heterogeneity and plasticity of the immune response in ND models. We will investigate chromatin changes in non-neuronal cells and, in particular, immune cells in tissues from the different models utilized in this study using IHC and bulk/single cell genomics on sorted immune cells (trialed during the life of the proposed study).