Close

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

Julien Delile, Teresa Rayon, Manuela Melchionda, Amelia Edwards, James Briscoe , Andreas Sagner

Posted on: 28 November 2018

Preprint posted on 16 November 2018

Article now published in Development at http://dx.doi.org/10.1242/dev.173807

Using single-cell RNA sequencing 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.

Selected by Reena Lasrado

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

Read preprint (No Ratings Yet)

Author's response

Andreas Sagner shared

Thank you for highlighting our work!

Q1: Would it be also interesting to highlight the crosstalk between the progenitors and the differentiating cells per se?

Yes, absolutely! We believe that our resource may provide a framework to analyse such interactions between progenitors and neurons. Analysing the data, we found multiple known secreted and transmembrane ligands with interesting expression patterns. For example, we found the Wnt ligand Wnt7b to be expressed in late stage progenitors. Previous work in the cortex suggested that Wnt7b controls the timing of gliogenesis by inducing the expression of Notch ligands in neurons, that then signal back to the adjacent neural progenitors to induce gliogenesis (Wang et al., 2016). At the moment it is unclear whether similar principles apply to the spinal cord, however, our resource may provide an entry point for investigating this and similar hypotheses in the future.

Q2: 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?

One of the predictions made by our resource is the existence of a temporal component to the specification of neuronal subtypes in the spinal cord. As you correctly outlined, this temporal component seems to depend on the sequential induction of specific sets of transcription factors that distinguish neurons, independent of their domain of origin, based on their birth date. We agree that a birth-dating analysis, e.g. by EdU incorporation, would be a logical next step towards experimentally validating this hypothesis.

Q3: Is there a pre-requisite of early-born subtypes for the generation of the late-born neuronal subgroups?

We are very keen to investigate the signals and transcriptional networks that promote developmental progression and may change the competency of neural progenitors to give rise to specific neuronal subtypes in the future. At the moment, it is unclear whether developmental progression to a late neural progenitor that can give rise to late-born neuronal subtypes, depends on specific signals from early born neurons or even the presence of neurons at all. Another exciting possibility is that the switch in neuronal subtypes formed from the progenitors depends on the sequential activation of the ‘gliogenic’ gene expression program that is mediated by first Sox9 and later Nfia/Nfib, which are both also markers for late neuronal subtypes. However, to which extent the activation of this transcriptional cascade depends on the presence of neurons is also not known.

Q4: 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?

Differential gene expression tests between the different neuronal domains revealed multiple cell adhesion molecules with domain specific gene expression patterns. Differential cell adhesion has been previously demonstrated to mediate the clustering of motor neurons into specific motor pools in the spinal cord, and thereby provides the basis for the emergence of the topographic map of the spinal cord that underlies the formation of neuronal circuits (Demireva et al., 2011; Price et al., 2002). Furthermore, our analysis revealed the differential expression of Neurexins and Cerebellins in specific classes of inhibitory and excitatory interneurons. As Neurexins and Cerebellins are important for synapse formation, this may suggest the existence of a molecular adhesion code that may mediate the recognition of excitatory and inhibitory synapses by target neurons, and thus contribute to the establishment of neuronal circuitry in the spinal cord.

References

Demireva, E. Y., Shapiro, L. S., Jessell, T. M. and Zampieri, N. (2011). Motor neuron position and topographic order imposed by β- And γ-catenin activities. Cell 147, 641–652.

Price, S. R., De Marco Garcia, N. V., Ranscht, B. and Jessell, T. M. (2002). Regulation of motor neuron pool sorting by differential expression of type II cadherins. Cell 109, 205–216.

Wang, W., Jossin, Y., Chai, G., Lien, W. H., Tissir, F. and Goffinet, A. M. (2016). Feedback regulation of apical progenitor fate by immature neurons through Wnt7-Celsr3-Fzd3 signalling. Nat. Commun. 7, 1–11.

 

Have your say

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Sign up to customise the site to your preferences and to receive alerts

Register here

Also in the developmental biology category:

Cellular signalling protrusions enable dynamic distant contacts in spinal cord neurogenesis

Joshua Hawley, Robert Lea, Veronica Biga, et al.

Selected by 15 November 2024

Ankita Walvekar

Developmental Biology

Actin-based deformations of the nucleus control multiciliated ependymal cell differentiation

Marianne Basso, Alexia Mahuzier, Syed Kaabir Ali, et al.

Selected by 30 October 2024

Ryan Harrison

Developmental Biology

HIF1A contributes to the survival of aneuploid and mosaic pre-implantation embryos

Estefania Sanchez-Vasquez, Marianne E. Bronner, Magdalena Zernicka-Goetz

Selected by 11 October 2024

Anchel De Jaime Soguero

Developmental Biology

Also in the neuroscience category:

Platelet-derived LPA16:0 inhibits adult neurogenesis and stress resilience in anxiety disorder

Thomas Larrieu, Charline Carron, Fabio Grieco, et al.

Selected by 04 December 2024

Harvey Roweth

Neuroscience

Investigating Mechanically Activated Currents from Trigeminal Neurons of Non-Human Primates

Karen A Lindquist, Jennifer Mecklenburg, Anahit H. Hovhannisyan, et al.

Selected by 04 December 2024

Vanessa Ehlers

Neuroscience

Circadian modulation of mosquito host-seeking persistence by Pigment-Dispersing Factor impacts daily biting patterns

Linhan Dong, Richard Hormigo, Jord M. Barnett, et al.

Selected by 29 November 2024

Javier Cavieres

Neuroscience

preLists in the developmental biology category:

BSDB/GenSoc Spring Meeting 2024

A list of preprints highlighted at the British Society for Developmental Biology and Genetics Society joint Spring meeting 2024 at Warwick, UK.

 



List by Joyce Yu, Katherine Brown

GfE/ DSDB meeting 2024

This preList highlights the preprints discussed at the 2024 joint German and Dutch developmental biology societies meeting that took place in March 2024 in Osnabrück, Germany.

 



List by Joyce Yu

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

preLights peer support – preprints of interest

This is a preprint repository to organise the preprints and preLights covered through the 'preLights peer support' initiative.

 



List by preLights peer support

The Society for Developmental Biology 82nd Annual Meeting

This preList is made up of the preprints discussed during the Society for Developmental Biology 82nd Annual Meeting that took place in Chicago in July 2023.

 



List by Joyce Yu, Katherine Brown

CSHL 87th Symposium: Stem Cells

Preprints mentioned by speakers at the #CSHLsymp23

 



List by Alex Eve

Journal of Cell Science meeting ‘Imaging Cell Dynamics’

This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.

 



List by Helen Zenner

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

2nd Conference of the Visegrád Group Society for Developmental Biology

Preprints from the 2nd Conference of the Visegrád Group Society for Developmental Biology (2-5 September, 2021, Szeged, Hungary)

 



List by Nándor Lipták

Fibroblasts

The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!

 



List by Osvaldo Contreras

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.

 



List by Alex Eve

EMBL Conference: From functional genomics to systems biology

Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020

 



List by Jesus Victorino

Single Cell Biology 2020

A list of preprints mentioned at the Wellcome Genome Campus Single Cell Biology 2020 meeting.

 



List by Alex Eve

Society for Developmental Biology 79th Annual Meeting

Preprints at SDB 2020

 



List by Irepan Salvador-Martinez, Martin Estermann

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

Planar Cell Polarity – PCP

This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.

 



List by Ana Dorrego-Rivas

Cell Polarity

Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.

 



List by Yamini Ravichandran

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

3D Gastruloids

A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.

 



List by Paul Gerald L. Sanchez and Stefano Vianello

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

EDBC Alicante 2019

Preprints presented at the European Developmental Biology Congress (EDBC) in Alicante, October 23-26 2019.

 



List by Sergio Menchero et al.

EMBL Seeing is Believing – Imaging the Molecular Processes of Life

Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019

 



List by Dey Lab

SDB 78th Annual Meeting 2019

A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.

 



List by Alex Eve

Lung Disease and Regeneration

This preprint list compiles highlights from the field of lung biology.

 



List by Rob Hynds

Young Embryologist Network Conference 2019

Preprints presented at the Young Embryologist Network 2019 conference, 13 May, The Francis Crick Institute, London

 



List by Alex Eve

Pattern formation during development

The aim of this preList is to integrate results about the mechanisms that govern patterning during development, from genes implicated in the processes to theoritical models of pattern formation in nature.

 



List by Alexa Sadier

BSCB/BSDB Annual Meeting 2019

Preprints presented at the BSCB/BSDB Annual Meeting 2019

 



List by Dey Lab

Zebrafish immunology

A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.

 



List by Shikha Nayar

Also in the neuroscience category:

2024 Hypothalamus GRC

This 2024 Hypothalamus GRC (Gordon Research Conference) preList offers an overview of cutting-edge research focused on the hypothalamus, a critical brain region involved in regulating homeostasis, behavior, and neuroendocrine functions. The studies included cover a range of topics, including neural circuits, molecular mechanisms, and the role of the hypothalamus in health and disease. This collection highlights some of the latest advances in understanding hypothalamic function, with potential implications for treating disorders such as obesity, stress, and metabolic diseases.

 



List by Nathalie Krauth

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

CSHL 87th Symposium: Stem Cells

Preprints mentioned by speakers at the #CSHLsymp23

 



List by Alex Eve

Journal of Cell Science meeting ‘Imaging Cell Dynamics’

This preList highlights the preprints discussed at the JCS meeting 'Imaging Cell Dynamics'. The meeting was held from 14 - 17 May 2023 in Lisbon, Portugal and was organised by Erika Holzbaur, Jennifer Lippincott-Schwartz, Rob Parton and Michael Way.

 



List by Helen Zenner

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

SDB 78th Annual Meeting 2019

A curation of the preprints presented at the SDB meeting in Boston, July 26-30 2019. The preList will be updated throughout the duration of the meeting.

 



List by Alex Eve

Autophagy

Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.

 



List by Sandra Malmgren Hill

Young Embryologist Network Conference 2019

Preprints presented at the Young Embryologist Network 2019 conference, 13 May, The Francis Crick Institute, London

 



List by Alex Eve
Close