Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types

Abstract
Data availability
Article and author information
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Abstract

The genesis of broad neuronal classes from multipotential neural progenitor cells has been extensively studied, but less is known about the diversification of a single neuronal class into multiple types. We used single-cell RNA-seq to study how newly-born (postmitotic) mouse retinal ganglion cell (RGC) precursors diversify into ~45 discrete types. Computational analysis provides evidence that RGC transcriptomic type identity is not specified at mitotic exit, but acquired by gradual, asynchronous restriction of postmitotic multipotential precursors. Some types are not identifiable until a week after they are generated. Immature RGCs may be specified to project ipsilaterally or contralaterally to the rest of the brain before their type identity emerges. Optimal transport inference identifies groups of RGC precursors with largely non-overlapping fates, distinguished by selectively expressed transcription factors that could act as fate determinants. Our study provides a framework for investigating the molecular diversification of discrete types within a neuronal class.

Data availability

Sequencing data has been submitted under GSE185671. Reviewer token : evchicgutpqpnoj.Computational scripts are available at : https://github.com/shekharlab/mouseRGCdev

The following data sets were generated

1. Shekhar K
2. Whitney IE
3. Butrus S
4. Peng Y
5. Sanes JR
(2021) Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types
NCBI Gene Expression Omnibus, GSE19373.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185671
1. Shekhar K
(2022) Diversification of multipotential postmitotic mouse retinal ganglion cell precursors into discrete types
GitHub.

https://github.com/shekharlab/mouseRGCdev

The following previously published data sets were used

1. Tran NM
2. Shekhar K et al.
(2019) Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes
GSE137400.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137400

Article and author information

Author details

Karthik Shekhar

Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, United States

For correspondence
kshekhar@berkeley.edu

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-4349-6600
Irene E Whitney

Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States

Competing interests
Irene E Whitney, is affiliated with Honeycomb Biotechnologies. The author has no financial interests to declare..
Salwan Butrus

Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, United States

Competing interests
No competing interests declared.
Yi-Rong Peng

Department of Ophthalmology, University of California, Los Angeles, Los Angeles, United States

Competing interests
No competing interests declared.
Joshua R Sanes

Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States

For correspondence
sanesj@mcb.harvard.edu

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0001-8926-8836

Funding

National Institutes of Health (R37NS029169)

Joshua R Sanes

National Institutes of Health (R01EY022073)

Joshua R Sanes

National Institutes of Health (R00EY028625)

Karthik Shekhar

National Science Foundation (GRP DGE1752814)

Salwan Butrus

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All animal experiments were approved by the Institutional Animal Care and Use Committees (IACUC) at Harvard University. Mice were maintained in pathogen-free facilities under standard housing conditions with continuous access to food and water. Animals used in this study include both males and females. A meta-analysis (not shown) did not show any systematic sex-related effects in either differentially expressed genes or cell-type proportions.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.