Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages

• Published in: Cell stem cell Vol. 20; no. 1; pp. 29 - 40
• Main Authors: Kee, Nigel, Volakakis, Nikolaos, Kirkeby, Agnete, Dahl, Lina, Storvall, Helena, Nolbrant, Sara, Lahti, Laura, Björklund, Åsa K., Gillberg, Linda, Joodmardi, Eliza, Sandberg, Rickard, Parmar, Malin, Perlmann, Thomas
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 05.01.2017
• Subjects: Basic Medicine; Biomarkers - metabolism; Body Patterning - genetics; Cancer and Oncology; Cancer och onkologi; Cell and Molecular Biology; Cell Differentiation - genetics; Cell Lineage - genetics; Cell- och molekylärbiologi; Clinical Medicine; development; dopamine; Dopaminergic Neurons - cytology; Dopaminergic Neurons - metabolism; embryogenesis; Embryonic Stem Cells - cytology; Embryonic Stem Cells - metabolism; Gene Expression Profiling; Gene Regulatory Networks; graph clustering; Humans; hypothalamus; Immunohistochemistry; Klinisk medicin; LIM-Homeodomain Proteins - metabolism; Medical and Health Sciences; Medicin och hälsovetenskap; Medicinska och farmaceutiska grundvetenskaper; neurogenesis; Neurogenesis - genetics; Parkinson's disease; Sequence Analysis, RNA; Signal Transduction - genetics; single cell RNA-seq; Single-Cell Analysis - methods; stem cell; subthalamic nucleus; Subthalamic Nucleus - cytology; Transcription Factors - metabolism; single cell RNA-seq; development; embryogenesis; stem cell; subthalamic nucleus; neurogenesis; dopamine; Parkinson’s disease; hypothalamus; graph clustering
• ISSN: 1934-5909; 1875-9777; 1875-9777
• DOI: 10.1016/j.stem.2016.10.003

Stem cell engineering and grafting of mesencephalic dopamine (mesDA) neurons is a promising strategy for brain repair in Parkinson’s disease (PD). Refinement of differentiation protocols to optimize this approach will require deeper understanding of mesDA neuron development. Here, we studied this process using transcriptome-wide single-cell RNA sequencing of mouse neural progenitors expressing the mesDA neuron determinant Lmx1a. This approach resolved the differentiation of mesDA and neighboring neuronal lineages and revealed a remarkably close relationship between developing mesDA and subthalamic nucleus (STN) neurons, while also highlighting a distinct transcription factor set that can distinguish between them. While previous hESC mesDA differentiation protocols have relied on markers that are shared between the two lineages, we found that application of these highlighted markers can help to refine current stem cell engineering protocols, increasing the proportion of appropriately patterned mesDA progenitors. Our results, therefore, have important implications for cell replacement therapy in PD. [Display omitted] •Single-cell RNA-seq can reconstruct Lmx1a+ neuronal development•The Lmx1a+ population contains distinct mesDA and STN lineages•The STN and mesDA lineages have related, yet distinct, transcription factor profiles•Application of distinct markers can help optimize mesDA differentiation of hESCs Kee et al. use single-cell RNA-seq to reconstruct Lmx1a+ differentiation in silico, revealing an unexpectedly close relationship between mesDA and STN neuronal lineages during differentiation. Application of markers that distinguish the two can help optimize mesDA differentiation of hESCs with a view to improving therapeutic translation.