Transcriptomic atlas of midbrain dopamine neurons uncovers differential vulnerability in a Parkinsonism lesion model

Abstract

Midbrain dopamine (mDA) neurons comprise diverse cells with unique innervation targets and functions. This is illustrated by the selective sensitivity of mDA neurons of the substantia nigra compacta (SNc) in patients with Parkinson’s disease, while those in the ventral tegmental area (VTA) are relatively spared. Here we used single nuclei RNA sequencing (snRNA-seq) of approximately 70,000 mouse midbrain cells to build a high-resolution atlas of mouse mDA neuron diversity at the molecular level. The results showed that differences between mDA neuron groups could best be understood as a continuum without sharp differences between subtypes. Thus, we assigned mDA neurons to several “territories” and “neighborhoods” within a shifting gene expression landscape where boundaries are gradual rather than discrete. Based on the enriched gene expression patterns of these territories and neighborhoods, we were able to localize them in the adult mouse midbrain. Moreover, because the underlying mechanisms for the variable sensitivities of diverse mDA neurons to pathological insults are not well understood, we analyzed surviving neurons after partial 6-hydroxydopamine (6-OHDA) lesions to unravel gene expression patterns that correlate with mDA neuron vulnerability and resilience. Together, this atlas provides a basis for further studies on the neurophysiological role of mDA neurons in health and disease.

Molecular and spatial transcriptomic classification of midbrain dopamine neurons and their alterations in a LRRK2G2019Smodel of Parkinson’s disease

“…The Sox6 family is split into two branches with six subtypes, the Calb1 family is split into two branches with ten subtypes, whereas the Gad2 family can be further split into two subtypes. This scheme represents a more granular taxonomy than previous studies 19 – 21 , 23 , 25 , 38 , 41 , and bears some resemblance to a recent study 86 . Key congruencies between these studies include: 1) parsing midbrain DAergic system into broad groups of subtypes based on expression of Sox6 and Calb1 , and to a lesser extent Gad2 , populations, 2) greater diversity observed in Calb1 + clusters, 3) the identification of some consensus and homogenous subtypes.…”

“…Key discrepancies include the extent to which each cluster further subdivided and the final number and molecular signature of DA subtypes. In the latter study 86 , they refer to levels as territories and neighborhoods. For simplicity of communication, we refer to the lowest level of our dendrogram of molecularly defined DA neuron clusters, as subtypes.…”

“…In addition, Langlieb et al 48 , provide a molecular atlas of the adult mouse brain in which they identified 13 clusters of midbrain DA neurons and located these using Slide-Seq. By contrast, Salmani et al 86 used established markers to locate seven DA neuron territories and 16 neighborhoods. They report a distribution of Gad2 + cells in the midline including CLi, RLi and IF, which bears similarity with our Gad2 family.…”

“…This suggests that our taxonomic scheme is impervious to the context of a mild perturbation such as LRRK2 G2019S , suggesting that our clusters are reflective of cell types, rather than cell states. It is likely, that with more severe perturbations, such as a toxin lesion, more substantial alterations of taxonomic schemes are observed 86 , 92 . However, we expect that for mild insults, day to day behavioral changes, or pharmacological paradigms, our clusters will be resistant to changes, although individual genes may vary.…”