Midbrain dopamine neurons of the substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) are important for motor, cognitive and limbic functions through substantial projections to forebrain structures. Dysfunction of the midbrain dopamine system is associated with several disorders, including Parkinson´s disease (PD) and substance use disorder. PD is characterized by the loss of dopaminergic neurons leading to severe motor dysfunction and by the brain distribution of aggregated α-Synuclein protein. Mutations in the α-Synuclein gene (SNCA) have been associated with PD.

The overall aim of this thesis was to increase the understanding of anatomical and histological features of dopamine neurons by identifying and characterizing gene expression differences between dopamine neurons, primarily those located within VTA but also the SNc. This knowledge should help towards increased understanding of the roles exerted by different dopamine neurons in behavior during healthy conditions and in disease. For this purpose, unbiased microarray analysis was first performed to identify genes that are differentially expressed in the VTA and SNc. Identified genes, e.g. Trpv1, NeuroD6, Calbindin and Grp, were analyzed on mRNA level primarily in mouse brain sections to determine their distribution patterns. Several were found to localize only in restricted neurons within the VTA, thus defining subpopulations of dopamine neurons in the mouse VTA. Further analysis revealed several interesting findings. For example, in clinical samples of PD biopsies, most dopamine neurons were degenerated, but those remaining were positive for Grp. VTA dopamine neurons positive for NeuroD6 or Calbindin2 were investigated using optogenetics. Activation of the NeuroD6-neurons, but not Calbindin2-neurons, was unexpectedly revealed as sufficient to drive place preference. To address the integrity of midbrain dopamine neurons in mouse models of PD, fluorescent in situ hybridization analyses was performed in two transgenic mouse lines expressing the human SNCA gene and in one dopamine degeneration lesion model, the 6-OHDA method. Despite near-ubiquitous presence of SNCA mRNA, all markers for midbrain dopamine cells remained intact in both transgenic models. Dopamine neurons thus showed an unanticipated robustness towards α-Synuclein pathology not described before. In contrast, most dopamine neurons were lost in the lesion model.

In summary, by identifying and characterizing dopamine neurons using established and new markers, histological analyses revealed the presence of distinct gene expression patterns within the VTA that allowed anatomical and functional assessments of discrete subpopulations of midbrain neurons. The thesis contributes new knowledge of the midbrain dopamine system.