A hallmark of Parkinson’s Disease (PD) is the degeneration of dopamine (DA) releasing neurons in a midbrain structure of the basal ganglia called the substantia nigra pars compacta (SNpc). Yet, some DA neurons survive in the SNpc even at advanced stages of PD. This suggests some neurons are more vulnerable than others in the progression of the disease.

Knowing specifically which DA neurons die in PD could help scientists identify the mechanisms leading to their loss, define accurate disease models and help develop precise therapies that target, renew, or replace the specific DA neurons lost in PD.

In a study published in Nature Neuroscience (“Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s disease”), scientists have developed and implemented a new method to enrich DA neurons from patients with PD and matched controls and profile their gene expression.

“It was known that cells in this area of the brain die, and that they make dopamine, but the exact subset that are vulnerable had not been identified definitively before,” said Evan Macosko, PhD, a professor at the Broad Institute of Harvard and MIT, and the senior author of the study. “By knowing the gene expression of these cells, we have a ‘recipe book’ for making them in a dish. Cell replacement therapies can therefore be informed by these data.”

Using a transcriptomic profiling protocol called Slide-Seq, invented in Macosko’s lab and published in an earlier study, the investigators sampled 387,483 nuclei, including 22,048 DA neuron profiles to identify ten distinct populations of DA neurons and spatially localized each within the SNpc.

“Our study used cutting-edge single cell and Slide-seq spatial transcriptomics technology to identify a very specific subtype of cell most vulnerable to death in Parkinson’s disease,” said Macosko.

Comparing profiling data from PD patients and controls, the researchers identified a single population of DA neurons that expresses the gene AGTR1 and is restricted to the front (ventral tier) of the SNpc, which was selectively lost in PD. This population of DA neurons showed upregulation of targets of the transcription factors TP53 and NR2F2, suggesting molecular processes associated with their selective degeneration.

“We identified pathways that are activated in the vulnerable cells of Parkinson’s patients, including P53, which is known to promote cell death. The identification of these pathway activations in the actual cells of Parkinson’s patients nominates these as good therapeutic targets,” said Macosko.

Additionally, in contrast to studies on late-onset Alzheimer’s disease that indicate microglia and other immune cells are involved in the pathogenesis of the disease, the current study indicates that the genetic risks of DA neuron degeneration in PD are intrinsic to the vulnerable cells.

“We discovered that these vulnerable cells express the genes most at risk in PD (by genomewide association studies). This suggests that human genetic risk within the vulnerable cells influences their survival. In Alzheimer’s disease, this is not the case,” said Macosko.

To arrive at this conclusion, the scientists examined the enrichment of common genetic risk factors of sporadic PD within the markers of the ten populations of DA neurons in the SNpc identified in this study. They found that the same population of vulnerable DA neurons also had the highest expression of genes that confer risk for developing PD, providing a potential explanation for their vulnerability and highlighting the importance of cell-intrinsic processes in their degeneration.

In their next experiments, Macosko and his team intend to conduct single-cell analyses on other vulnerable brain regions in larger populations. Macosko said, “We expect this will teach us a lot about the mechanisms of Parkinson’s disease.”