Molecular architecture of the developing mouse brain.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
08 2021
08 2021
Historique:
received:
01
07
2020
accepted:
28
06
2021
pubmed:
30
7
2021
medline:
21
8
2021
entrez:
29
7
2021
Statut:
ppublish
Résumé
The mammalian brain develops through a complex interplay of spatial cues generated by diffusible morphogens, cell-cell interactions and intrinsic genetic programs that result in probably more than a thousand distinct cell types. A complete understanding of this process requires a systematic characterization of cell states over the entire spatiotemporal range of brain development. The ability of single-cell RNA sequencing and spatial transcriptomics to reveal the molecular heterogeneity of complex tissues has therefore been particularly powerful in the nervous system. Previous studies have explored development in specific brain regions
Identifiants
pubmed: 34321664
doi: 10.1038/s41586-021-03775-x
pii: 10.1038/s41586-021-03775-x
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
92-96Informations de copyright
© 2021. The Author(s), under exclusive licence to Springer Nature Limited.
Références
Camp, J. G. et al. Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proc. Natl Acad. Sci. USA 112, 15672–15677 (2015).
doi: 10.1073/pnas.1520760112
Pollen, A. A. et al. Molecular identity of human outer radial glia during cortical development. Cell 163, 55–67 (2015).
doi: 10.1016/j.cell.2015.09.004
Nowakowski, T. J. et al. Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex. Science 358, 1318–1323 (2017).
doi: 10.1126/science.aap8809
Zhong, S. et al. A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. Nature 555, 524–528 (2018).
doi: 10.1038/nature25980
Telley, L. et al. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science 364, eaav2522 (2019).
doi: 10.1126/science.aav2522
La Manno, G. et al. Molecular diversity of midbrain development in mouse, human, and stem cells. Cell 167, 566–580.e19 (2016).
doi: 10.1016/j.cell.2016.09.027
Carter, R. A. et al. A single-cell transcriptional atlas of the developing murine cerebellum. Curr. Biol. 28, 2910–2920.e2 (2018).
doi: 10.1016/j.cub.2018.07.062
Zeisel, A. et al. Molecular architecture of the mouse nervous system. Cell 174, 999–1014.e22 (2018).
doi: 10.1016/j.cell.2018.06.021
Rosenberg, A. B. et al. Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding. Science 360, 176–182 (2018).
doi: 10.1126/science.aam8999
Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019).
doi: 10.1038/s41586-019-0969-x
Siegenthaler, J. A. & Pleasure, S. J. in Patterning and Cell Type Specification in the Developing CNS and PNS (eds. Rubenstein, J. L. R. & Rakic, P.) 835–849 (Elsevier, 2013).
Niwa, H., Miyazaki, J. & Smith, A. G. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat. Genet. 24, 372–376 (2000).
doi: 10.1038/74199
Burtscher, I. & Lickert, H. Foxa2 regulates polarity and epithelialization in the endoderm germ layer of the mouse embryo. Development 136, 1029–1038 (2009).
doi: 10.1242/dev.028415
Li, L. et al. Location of transient ectodermal progenitor potential in mouse development. Development 140, 4533–4543 (2013).
doi: 10.1242/dev.092866
Zhang, X. et al. Pax6 is a human neuroectoderm cell fate determinant. Cell Stem Cell 7, 90–100 (2010).
doi: 10.1016/j.stem.2010.04.017
Hatakeyama, J. et al. Hes genes regulate size, shape and histogenesis of the nervous system by control of the timing of neural stem cell differentiation. Development 131, 5539–5550 (2004).
doi: 10.1242/dev.01436
Pijuan-Sala, B. et al. A single-cell molecular map of mouse gastrulation and early organogenesis. Nature 566, 490–495 (2019).
doi: 10.1038/s41586-019-0933-9
Tamai, H. et al. Pax6 transcription factor is required for the interkinetic nuclear movement of neuroepithelial cells. Genes Cells 12, 983–996 (2007).
doi: 10.1111/j.1365-2443.2007.01113.x
Alves dos Santos, M. T. M. & Smidt, M. P. En1 and Wnt signaling in midbrain dopaminergic neuronal development. Neural Dev. 6, 23 (2011).
doi: 10.1186/1749-8104-6-23
Schwarz, M. et al. Pax2/5 and Pax6 subdivide the early neural tube into three domains. Mech. Dev. 82, 29–39 (1999).
doi: 10.1016/S0925-4773(99)00005-2
Sato, S. et al. Regulation of Six1 expression by evolutionarily conserved enhancers in tetrapods. Dev. Biol. 368, 95–108 (2012).
doi: 10.1016/j.ydbio.2012.05.023
Dasgupta, K. & Jeong, J. Developmental biology of the meninges. Genesis 57, e23288 (2019).
doi: 10.1002/dvg.23288
DeSisto, J. et al. Single-cell transcriptomic analyses of the developing meninges reveal meningeal fibroblast diversity and function. Dev. Cell 54, 43–59.e4 (2020).
doi: 10.1016/j.devcel.2020.06.009
Hammond, T. R. et al. Single-cell RNA sequencing of microglia throughout the mouse lifespan and in the injured brain reveals complex cell-state changes. Immunity 50, 253–271.e6 (2019).
doi: 10.1016/j.immuni.2018.11.004
Lein, E. S. et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature 445, 168–176 (2007).
doi: 10.1038/nature05453
Murdoch, J. N., Eddleston, J., Leblond-Bourget, N., Stanier, P. & Copp, A. J. Sequence and expression analysis of Nhlh1: a basic helix-loop-helix gene implicated in neurogenesis. Dev. Genet. 24, 165–177 (1999).
doi: 10.1002/(SICI)1520-6408(1999)24:1/2<165::AID-DVG15>3.0.CO;2-V
Gyllborg, D. et al. Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue. Nucleic Acids Res. 48, e112 (2020).
doi: 10.1093/nar/gkaa792
Biancalani, T. et al. Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with Tangram. Preprint at https://doi.org/10.1101/2020.08.29.272831 (2020).
Kinameri, E. et al. Prdm proto-oncogene transcription factor family expression and interaction with the Notch-Hes pathway in mouse neurogenesis. PLoS ONE 3, e3859 (2008).
doi: 10.1371/journal.pone.0003859
Sakamoto, T. & Ishibashi, T. Hyalocytes: essential cells of the vitreous cavity in vitreoretinal pathophysiology? Retina 31, 222–228 (2011).
doi: 10.1097/IAE.0b013e3181facfa9
La Manno, G. et al. RNA velocity of single cells. Nature 560, 494–498 (2018).
doi: 10.1038/s41586-018-0414-6
Gyllborg, D. & Nilsson, M. HybISS: hybridization-based in situ sequencing. protocols.io., https://doi.org/10.17504/protocols.io.xy4fpyw (2020).
doi: 10.17504/protocols.io.xy4fpyw
Gopalan, P., Hofman, J. M. & Blei, D. M. Scalable recommendation with Poisson factorization. Preprint at https://arxiv.org/abs/1311.1704 (2013).
Kobak, D. & Berens, P. The art of using t-SNE for single-cell transcriptomics. Nat. Commun. 10, 5416 (2019).
doi: 10.1038/s41467-019-13056-x
Chalfoun, J. et al. MIST: accurate and scalable microscopy image stitching tool with stage modeling and error minimization. Sci. Rep. 7, 4988 (2017).
doi: 10.1038/s41598-017-04567-y