Single-cell transcriptomes reveal molecular specializations of neuronal cell types in the developing cerebellum

Abstract

The cerebellum is critical for controlling motor and non-motor functions via cerebellar circuit that is composed of defined cell types, which approximately account for more than half of neurons in mammals. The molecular mechanisms controlling developmental progression and maturation processes of various cerebellar cell types need systematic investigation. Here, we analyzed transcriptome profiles of 21119 single cells of the postnatal mouse cerebellum and identified eight main cell clusters. Functional annotation of differentially expressed genes revealed trajectory hierarchies of granule cells (GCs) at various states and implied roles of mitochondrion and ATPases in the maturation of Purkinje cells (PCs), the sole output cells of the cerebellar cortex. Furthermore, we analyzed gene expression patterns and co-expression networks of 28 ataxia risk genes, and found that most of them are related with biological process of mitochondrion and around half of them are enriched in PCs. Our results also suggested core transcription factors that are correlated with interneuron differentiation and characteristics for the expression of secretory proteins in glia cells, which may participate in neuronal modulation. Thus, this study presents a systematic landscape of cerebellar gene expression in defined cell types and a general gene expression framework for cerebellar development and dysfunction.

Sequencing the landscape of cerebellar gene expression

“…Given by a number of ataxia risk genes (Ashizawa et al, 2018), susceptible cell types in the cerebellum remain unclear. Peng et al (2019) analyzed 28 ataxia risk genes and found that the majority of them were highly expressed in Purkinje cells, in consistent with the current hypothesis that the dysfunction of Purkinje cells is closely related with the occurrence of ataxia. They showed that most significantly enriched genes were related with organizations of organelle and mitochondrial inner membrane and were largely consistent with DEGs of Purkinje cells between P0 and P8, suggesting that mitochondrial function is highly correlated with the development of Purkinje cells and motor behavior disorders.…”

“…This technique is particularly useful to detect the expressions of molecules that determine the fate of diversified cerebellar neurons. By using the droplet-based scRNA-seq (Figure 1), Peng et al (2019) analyzed transcriptome profiles of 21119 single cells of postnatal mouse cerebellum at P0 and P8 ages. For analyzing 58994 unique molecule identifiers (UMIs) and a median of 2615 genes, they used a series of known cerebellar cell lineage markers to annotate each cell cluster, such as granule cell precursor, granule cells, Purkinje cells, astrocytes, interneurons, oligodendrocytes, and endothelial cells.…”

“…Interestingly, the population of mitochondrial transcripts in Purkinje cells was significantly larger than that in other cell types, suggesting that the mitochondria in Purkinje cells may exert essential roles. Peng et al (2019) analyzed temporal mechanisms underlying the development of mouse Purkinje cells. They identified 618 differentially expressed genes (DEGs) by comparing P0 and P8 stages.…”

Dystroglycan Mediates Clustering of Essential GABAergic Components in Cerebellar Purkinje Cells

“…Thus, α-DG joins the list of secreted synaptic organizers that reside in the extracellular matrix and act bidirectionally to coordinate selective interactions between the pre- and post-synaptic compartments ( Johnson-Venkatesh and Umemori, 2010 ; Sassoe-Pognetto and Patrizi, 2017 ; Yuzaki, 2018 ). In the future, it will be important to implement transcriptional and proteomic analyses, such as single-cell RNA sequencing ( Carter et al, 2018 ; Peng et al, 2019 ) and immunoprecipitation of α-DG from murine cerebellum in combination with mass spectrometry to identify new bridge molecules.…”

A transcriptomic atlas of the mouse cerebellum reveals regional specializations and novel cell types

“…Recent advances in single-cell RNA sequencing (scRNAseq) technology [2][3][4] have increased the throughput of profiling to now enable the systematic identification of cell types and states throughout the central nervous system [5][6][7][8] . Several recent studies have harnessed such techniques to examine cell populations in the mouse cerebellum across developmental stages [9][10][11] , but none has yet surveyed cell types in the adult.…”