Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

Ishaan Gupta; Paul G Collier; Bettina Haase; Ahmed Mahfouz; Anoushka Joglekar; Taylor Floyd; Frank Koopmans; Ben Barres; August B Smit; Steven A Sloan; Wenjie Luo; Olivier Fedrigo; M Elizabeth Ross; Hagen U Tilgner

doi:10.1038/nbt.4259

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

Nature Biotechnology ◽

10.1038/nbt.4259 ◽

2018 ◽

Vol 36 (12) ◽

pp. 1197-1202 ◽

Cited By ~ 76

Author(s):

Ishaan Gupta ◽

Paul G Collier ◽

Bettina Haase ◽

Ahmed Mahfouz ◽

Anoushka Joglekar ◽

...

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Cerebellar Cells

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Single-cell spatial transcriptomic analysis reveals common and divergent features of developing postnatal granule cerebellar cells and medulloblastoma

BMC Biology ◽

10.1186/s12915-021-01071-8 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Wenqin Luo ◽

Guan Ning Lin ◽

Weichen Song ◽

Yu Zhang ◽

Huadong Lai ◽

...

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Granule Cells ◽

Cerebellar Granule Cells ◽

Granule Neurons ◽

Cerebellar Granule ◽

Granule Neuron ◽

Proliferation And Differentiation ◽

Single Cell Rna Sequencing ◽

Cerebellar Cells

Abstract Background Cerebellar neurogenesis involves the generation of large numbers of cerebellar granule neurons (GNs) throughout development of the cerebellum, a process that involves tight regulation of proliferation and differentiation of granule neuron progenitors (GNPs). A number of transcriptional regulators, including Math1, and the signaling molecules Wnt and Shh have been shown to have important roles in GNP proliferation and differentiation, and deregulation of granule cell development has been reported to be associated with the pathogenesis of medulloblastoma. While the progenitor/differentiation states of cerebellar granule cells have been broadly investigated, a more detailed association between developmental differentiation programs and spatial gene expression patterns, and how these lead to differential generation of distinct types of medulloblastoma remains poorly understood. Here, we provide a comparative single-cell spatial transcriptomics analysis to better understand the similarities and differences between developing granule and medulloblastoma cells. Results To acquire an enhanced understanding of the precise cellular states of developing cerebellar granule cells, we performed single-cell RNA sequencing of 24,919 murine cerebellar cells from granule neuron-specific reporter mice (Math1-GFP; Dcx-DsRed mice). Our single-cell analysis revealed that there are four major states of developing cerebellar granule cells, including two subsets of granule progenitors and two subsets of differentiating/differentiated granule neurons. Further spatial transcriptomics technology enabled visualization of their spatial locations in cerebellum. In addition, we performed single-cell RNA sequencing of 18,372 cells from Patched+/− mutant mice and found that the transformed granule cells in medulloblastoma closely resembled developing granule neurons of varying differentiation states. However, transformed granule neuron progenitors in medulloblastoma exhibit noticeably less tendency to differentiate compared with cells in normal development. Conclusion In sum, our study revealed the cellular and spatial organization of the detailed states of cerebellar granule cells and provided direct evidence for the similarities and discrepancies between normal cerebellar development and tumorigenesis.

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