Spatial RNA Sequencing Identifies Robust Markers of Vulnerable and Resistant Human Midbrain Dopamine Neurons and Their Expression in Parkinson’s Disease

• Published in: Frontiers in molecular neuroscience Vol. 14; p. 699562
• Main Authors: Aguila, Julio, Cheng, Shangli, Kee, Nigel, Cao, Ming, Wang, Menghan, Deng, Qiaolin, Hedlund, Eva
• Format: Journal Article
• Language: English
• Published: Lausanne Frontiers Research Foundation 08.07.2021; Frontiers Media S.A
• Subjects: Apoptosis; Cytoskeleton; Dopamine; Ethics; Extracellular matrix; Gene expression; human midbrain dopamine neurons; Human subjects; laser microdissection; Lasers; Mesencephalon; Mitochondria; Movement disorders; Neurodegenerative diseases; Neurons; Neuroscience; Parkinson's disease; RNA sequencing; Sample size; spatial transcriptomics; Stem cells; Substantia nigra; substantia nigra compacta; Transcription; Transcriptomes; ventral tegmental area; Ventral tegmentum
• ISSN: 1662-5099; 1662-5099
• DOI: 10.3389/fnmol.2021.699562

Defining transcriptional profiles of substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) dopamine neurons is critical to understanding their differential vulnerability in Parkinson’s Disease (PD). Here, we determine transcriptomes of human SNc and VTA dopamine neurons using LCM-seq on a large sample cohort. We apply a bootstrapping strategy as sample input to DESeq2 and identify 33 stably differentially expressed genes (DEGs) between these two subpopulations. We also compute a minimal sample size for identification of stable DEGs, which highlights why previous reported profiles from small sample sizes display extensive variability. Network analysis reveal gene interactions unique to each subpopulation and highlight differences in regulation of mitochondrial stability, apoptosis, neuronal survival, cytoskeleton regulation, extracellular matrix modulation as well as synapse integrity, which could explain the relative resilience of VTA dopamine neurons. Analysis of PD tissues showed that while identified stable DEGs can distinguish the subpopulations also in disease, the SNc markers SLIT1 and ATP2A3 were down-regulated and thus appears to be biomarkers of disease. In summary, our study identifies human SNc and VTA marker profiles, which will be instrumental for studies aiming to modulate dopamine neuron resilience and to validate cell identity of stem cell-derived dopamine neurons.