The "dorsal pons", or "dorsal pontine tegmentum" (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in the regulation of many vital functions. Notable among them are the parabrachial nucleus, the Kolliker Fuse, the Barrington nucleus, the locus coeruleus, and the laterodorsal, ventral, and dorsal tegmental nuclei. In this study, we applied single-nucleus RNA-seq (snRNA-seq) to resolve neuronal subtypes based on their unique transcriptional profiles and then used multiplexed error robust fluorescence in situ hybridization (MERFISH) to map them spatially. We sampled ~1 million cells across the dPnTg and defined the spatial distribution of over 120 neuronal subtypes. Our analysis identified an unpredicted high transcriptional diversity in this region and pinpointed many neuronal subtypes9 unique marker genes. We also demonstrated that many neuronal subtypes found in mice were transcriptionally similar to those found in humans, enhancing this study9s translational value. Finally, we developed a freely-accessible, GPU-powered interactive dashboard (http://harvard.heavy.ai:6273/) to provide access to this spatially-resolved transcriptional dataset.

A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution