Spatial transcriptomics and in silico random pooling identify novel markers of vulnerable and resistant midbrain dopamine neurons

SUMMARY Defining transcriptional profiles of substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) dopamine neurons is critical to understand their differential vulnerability in Parkinson’s disease. However, reported transcriptional profiles for these neuron populations rely on studies in rodents and display extensive variability across small sample sizes. Here, we use laser capture microdissection coupled with RNA sequencing to analyze single isolated SNc and VTA dopamine neurons in a large human cohort. By applying a unique iterative random pooling algorithm, with high utility to resolve differences across any two populations, we reveal 33 dopamine population-specific markers We also define the minimal cohort size required to identify these stably differentially expressed genes, explaining inconsistent results from previous studies. Finally, we identify human transcripts, including ZCCHC12 , CDH13 and SERPINE2 , that faithfully classify SNc or VTA dopamine neurons also in the mouse. The novel markers identified will be vital for future studies aiming to validate the identity of stem cell-derived dopamine neurons or to induce dopamine neuron resilience.