ATACing pain – exploring the gene regulatory network of the mouse dorsal root ganglia for analgesic strategies in chronic pain

• Applicant: Dr. Doris Krauter
• Subject Area: Experimental Models for the Understanding of Nervous System Diseases ; Experimental and Theoretical Network Neuroscience ; Molecular Biology and Physiology of Neurons and Glial Cells
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 544943340

Pain is a result of the activation of molecularly unique sensory cell types that form assemblies of different neuronal and glial cells, located in the dorsal root ganglion (DRG). Under normal circumstances, pain is beneficial as a protective mechanism. However, under pathological conditions, painful stimuli cause stronger pain, and even non-painful stimuli can cause unpleasantness. To understand mechanisms of chronic pain we need to identify the causative molecular perturbations in the pain causing cell types. In this proposal, I will employ multiomics sequencing on the single cell level in the mouse DRG, namely single cell RNA sequencing to determine molecularly defined sensory cell types combined with single cell ATAC sequencing to identify open chromatin regions, which allows to identify enhancer gene regulatory networks in the respective sensory cell types. I will compare the gene expression and chromatin topology in the naïve mouse to chronic pain mouse models to find enhancer elements responsible for chronic pain. I aim at utilizing the discovered cell-type and disease specific DNA regulatory elements to silence the activity in the pain causing cell types in vivo. Therefore, I will designing pain specific enhancer constructs which will be delivered to the mouse sensory cell types in vivo using adeno-associated viruses and lipid nanoparticles. The constructs will drive the expression of a optogenetic tool fused to a flourescent protein to allow validation of the delivery using immunohistochemical methods and functional silencing of the neurons by light stimulation and sensory behavior analysis in the mice. This application is timely, since technologies for identifying accessible chromatin in single cells, deep learning methods to design optimal cell type-specific enhancers and lipid nanoparticle technologies are just emerging, opening for discoveries previously unreachable. I anticipate that deep insights into the cellular and molecular basis of chronic pain will be enabling for highly needed new therapeutic options to treat pain.

• DFG Programme: WBP Fellowship
• International Connection: Sweden
• Host: Professor Dr. Patrik Ernfors