Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord

Summary

Using the 10X platform to perform single-cell transcriptomics on early mouse embryonic stages, the authors recapitulate the development of the neural tube and unravel the molecular mechanisms that underlie spatial and temporal neuronal diversity in the spinal cord.

Background

In the vertebrate neural tube, morphogen gradients induce a transcriptional network that produces distinct progenitor domains, each generating diverse neuronal subtypes. The progressive organization of the domains in the dorso-ventral axis and the formation of the neural circuits are important to coordinate sensory input and motor output. The transcriptionally distinct domains (Briscoe and Small, 2015) harbor distinct neuronal subtypes (Jessell, 2000) in each region. Each transcriptionally distinct domain consists of different subtypes of neurons that function to give a specific physiological output (Hayashi et al., 2018). Although previous studies have characterized gene regulatory networks which define neural tube patterning and neuronal differentiation, they have lacked systematic molecular profiling of the developing neural tube. This can be attributed mainly to the complexity of the tissue, use of population-based techniques and previous focus on late time points.

Key findings

Using the 10X platform for single-cell transcriptomics, the authors recapitulate neural tube development and decipher the growth and progenitor dynamics of the spinal cord. Computational methods used have helped the authors to predict novel gene patterns that support the generation of an expression atlas by focusing on genes related to neurotransmitter biogenesis and release (glutamate decarboxylases and vesicular transporters), cell adhesion molecules (claudins, cerebellins) and transcription factors (Hmx2, Sp9). This study also identifies gene modules that subdivide the major neuronal populations into further groups. Using this technique, the authors show that domain-shared transcriptional programs and sequentially- induced molecular signatures underlie the generation of diverse neuronal subtypes. Finally, by analyzing changes in gene expression the authors reconstruct the transition of a progenitor to a neuron using a pseudo-temporal approach.

Figure S5: Pseudotime analysis reveals gene expression dynamics underlying neurogenesis in several domains. Heatmap showing the 4 gene modules identified as similarly expressed in all dorsal-ventral domains and involved in neurogenesis and progenitor maturation. Among the 114 genes, red gene labels indicate genes excluded from the following analysis because of significant dorsal-ventral bias.

What I like about the work and why is it important

The spinal cord contains many different neuronal subtypes with distinct gene expression patterns that assist to form well defined circuits. Abnormal neural circuit development often translates into prominent neurodevelopmental diseases. Key questions in developmental neuroscience are associated with understanding how these neurons are produced in a precise sequence during embryonic development. This work dissects the properties of neuronal subtypes and reveals novel transcription factors that underlie the genetic program of subgroups. Furthermore, this type of study is essential to unravel the mechanisms fundamental to the function of these diverse neurons.

Future directions and questions for the authors

As the authors have clearly mentioned, this work provides a platform that reveals the molecular diversity at single-cell resolution of the developing spinal cord. This study is a great resource to inform further targeted approaches which promise to enable detailed insight into the development and function of the neural tube.

The authors discuss the results mainly in view of the crosstalk between the morphogen driven gradients and the neural tube progenitors. Would it be also interesting to highlight the crosstalk between the progenitors and the differentiating cells per se? Would the temporal aspect that is revealed in this study suggest a timeline of neuronal subtype generation which would then require birth-dating experiments to support transcriptional data? Is there a pre-requisite of early-born subtypes for the generation of the late-born neuronal subgroups? The crosstalk between cell adhesion molecules and progenitors has not been suggested in this study. Which cellular process in particular would you think it might affect?

References

Briscoe, J. and Small, S. (2015). Morphogen rules: design principles of gradient-mediated embryo patterning. Development 142, 3996–4009.

Jessell, T. M. (2000). Neuronal specification in the spinal cord: inductive signals and transcriptional codes. Nat Rev Genet 1, 20–29.

Hayashi, M., Hinckley, C. A., Driscoll, S. P., Moore, N. J., Levine, A. J., Hilde, K. L., Sharma, K. and Pfaff, S. L. (2018). Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control. Neuron 1–16.

 

 

doi: https://doi.org/10.1242/prelights.5877

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