Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development

Katarína Tiklová,Thomas Perlmann,Fredrik Holmström,Linda Gillberg,Laura Lahti,Sara Nolbrant,Nikolaos Volakakis,Malin Parmar,Mats Nilsson,Markus M Hilscher,Chika Yokota,Alessandro Fiorenzano,Eliza Joodmardi,Åsa K Björklund,Thomas Hauling

doi:10.1038/s41467-019-08453-1

Abstract

Midbrain dopamine (mDA) neurons constitute a heterogenous group of cells that have been intensely studied, not least because their degeneration causes major symptoms in Parkinson’s disease. Understanding the diversity of mDA neurons – previously well characterized anatomically – requires a systematic molecular classification at the genome-wide gene expression level. Here, we use single cell RNA sequencing of isolated mouse neurons expressing the transcription factor Pitx3, a marker for mDA neurons. Analyses include cells isolated during development up until adulthood and the results are validated by histological characterization of newly identified markers. This identifies seven neuron subgroups divided in two major branches of developing Pitx3-expressing neurons. Five of them express dopaminergic markers, while two express glutamatergic and GABAergic markers, respectively. Analysis also indicate evolutionary conservation of diversity in humans. This comprehensive molecular characterization will provide a valuable resource for elucidating mDA neuron subgroup development and function in the mammalian brain.

Highlights

Midbrain dopamine neurons constitute a heterogenous group of cells that have been intensely studied, not least because their degeneration causes major symptoms in Parkinson’s disease
Results scRNAseq establishes a trajectory for Midbrain dopamine (mDA) neuron maturation
Consistent with previous studies[10,11], immunohistochemistry using antibodies against GFP and TH showed that GFP was expressed in virtually all TH-positive mDA neurons throughout the adult mouse ventral midbrain region (Fig. 1a)

Summary

Introduction

Midbrain dopamine (mDA) neurons constitute a heterogenous group of cells that have been intensely studied, not least because their degeneration causes major symptoms in Parkinson’s disease. The full extent of mDA neuron diversity remains to be elucidated, and functional properties of distinct mDA neuron subgroups are far from being understood It still remains unknown when and how this diversity is generated during development, and it is so far not possible to control this subtype diversity during stem cell differentiation. A scRNAseq study of developing and adult mouse ventral midbrain cells, including mDA neurons, analyzed genomewide gene expression in individual cells[7]. Both studies sampled a relatively low number of differentiated mDA neurons and in the qPCR study only 96 genes were analyzed

Methods

Results

Conclusion