Cell diversity and network dynamics in photosensitive human brain organoids
Open accessAbstract
In vitro models of the developing brain such as three-dimensional brain organoids offer an unprecedented opportunity to study aspects of human brain development and disease. However, the cells generated within organoids and the extent to which they recapitulate the regional complexity, cellular diversity and circuit functionality of the brain remain undefined. Here we analyse gene expression in over 80,000 individual cells isolated from 31 human brain organoids. We find that organoids can generate a broad diversity of cells, which are related to endogenous classes, including cells from the cerebral cortex and the retina. Organoids could be developed over extended periods (more than 9 months), allowing for the establishment of relatively mature features, including the formation of dendritic spines and spontaneously active neuronal networks. Finally, neuronal activity within organoids could be controlled using light stimulation of photosensitive cells, which may offer a way to probe the functionality of human neuronal circuits using physiological sensory stimuli.
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hiPSC-derived astrocytes can be generated with a fast protocol in 2D layers or integrated in 3D systems such as spheroids and organoids.
“hiPSC-derived astrocytes, which can be generated with a fast protocol in 2D layers104 or integrated in 3D systems such as spheroids and organoids105–108”
From Reactive astrocyte nomenclature, definitions, and future directions (2021) · cites this paper as [107]
Protocols using medium free of neural induction signalling molecules promote generation of diverse brain regions and cell populations.
“Some protocols build on the principles of spontaneous neural induction by using medium that is free of neural induction signalling molecules2,27. This promotes the generation of diverse brain regions and cell populations2,28,29.”
From The use of brain organoids to investigate neural development and disease (2017) · cites this paper as [28]
Scaffold support provided by the extracellular matrix is an important feature of current protocols.
“Apart from growth factor cues, other modulators — such as scaffold support provided by the extracellular matrix — are important features of current protocols2,5,28.”
From The use of brain organoids to investigate neural development and disease (2017) · cites this paper as [28]
Such regional diversity leads to relatively variable outcomes and differentiation of some cells into non-ectodermal cell types.
“Although such regional diversity is appealing, it also leads to a relatively variable outcome and the differentiation of some cells into non-ectodermal cell types28,29.”
From The use of brain organoids to investigate neural development and disease (2017) · cites this paper as [28]
Organoids derived from the same cell line under the same conditions can often produce tissues with different regional identities and spatial and cellular heterogeneity.
“One important issue is that organoids derived from the same cell line under the same conditions can often produce tissues with different regional identities and spatial and cellular heterogeneity28,29.”
From The use of brain organoids to investigate neural development and disease (2017) · cites this paper as [28]
Single-cell mRNA sequencing of 80,000 cells from 31 brain organoids after 3 and 6 months identified 10 distinct populations in 6-month-old organoids.
“A recent paper used droplet-based single-cell mRNA sequencing to analyse gene expression in 80,000 cells from 31 brain organoids after 3 and 6 months in vitro28. Using principal component analysis, 10 distinct populations of cells (clusters) were identified in 6-month old organoids.”
From The use of brain organoids to investigate neural development and disease (2017) · cites this paper as [28]
6-month-old organoids presented greater diversity of cell types than 3-month-old organoids, as well as enrichment of genes associated with neuronal and glial maturation.
“As one might expect, 6-month-old organoids presented a greater diversity of cell types than 3-month-old organoids, as well as enrichment of genes associated with neuronal and glial maturation.”
From The use of brain organoids to investigate neural development and disease (2017) · cites this paper as [28]
Photosensitive cells in retinal-like regions of brain organoids can respond to light.
“Recently, it was demonstrated that photosensitive cells in retinal-like regions of brain organoids can respond to light28.”
From The use of brain organoids to investigate neural development and disease (2017) · cites this paper as [28]
Some cell types were only produced by a subset of organoids, and organoids grown in the same bioreactor tended to be similar, suggesting that batch effects and local microenvironments are important in patterning.
“Also, the authors observed that some cell types were only produced by a subset of organoids and that organoids grown in the same bioreactor tended to be similar in terms of their ability to make cells of each cluster, suggesting that batch effects and local microenvironments are important in patterning and possibly that organoids secrete signalling factors that influence sister organoids.”
From The use of brain organoids to investigate neural development and disease (2017) · cites this paper as [28]
Electrophysiological studies demonstrated functional synapses in several brain organoid models.
“In addition to these findings, electrophysiological studies have demonstrated functional synapses in several brain organoid models25,28, and electron microscopy has confirmed the presence of structurally defined synaptic junctions28.”
From The use of brain organoids to investigate neural development and disease (2017) · cites this paper as [28]
Long-term organoid culture can improve the correlation between molecular signatures of organoid and endogenous cells.
“Several reports suggest that long-term organoid culture can improve the correlation between the molecular signatures of organoid and endogenous cells28,52.”
From The use of brain organoids to investigate neural development and disease (2017) · cites this paper as [28]
A large number of cells were assigned to a mesodermal lineage, emphasizing variability inherent in the protocol.
“For example, a large number of cells were assigned to a mesodermal lineage, emphasizing the variability inherent in the protocol.”
From The use of brain organoids to investigate neural development and disease (2017) · cites this paper as [28]
Initial reports identified striking parallels among organoid development, human primary tissue and in vivo organogenesis.
“These initial reports identified striking parallels among organoid development, human primary tissue and in vivo organogenesis”
From The organoid cell atlas (2021) · cites this paper as [10]
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- Authors
- Quadrato, G., Nguyen, T., Macosko, E. Z., Sherwood, J. L., Min Yang, S., Berger, D. R., Maria, N., Scholvin, J., Goldman, M., Kinney, J. P., Boyden, E. S., Lichtman, J. W., Williams, Z. M., McCarroll, S. A., & Arlotta, P.
- Affiliations
- Broad Institute (US)
- Harvard University (US)
- Leaflabs (United States) (US)
- McGovern Institute for Brain Research (US)
- Corresponding author
- Quadrato, Giorgia
- Arlotta, Paola
- ORCID
- Venue
- Nature
- Published
- 2017-04-26
- Volume
- 545
- Issue
- 7652
- Pages
- 48-53
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5659341
- OpenAlex
- W2609844460
- Cited by
- 1,321
- References
- 45
- Citations by year
- 2026: 118 · 2025: 131 · 2024: 167 · 2023: 131 · 2022: 162 · 2021: 168 · 2020: 178 · 2019: 137 · 2018: 91 · 2017: 35 · 2013: 1
- FWCI
- 51.12
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- Funders
- National Institute of Mental Health (P50MH094271)
- National Institute of Neurological Disorders and Stroke (DP1NS087724, R01NS073124)
- Topics
- Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- human brain organoids, cellular diversity, neuronal network dynamics, spontaneous neuronal activity, photostimulation, dendritic spines, cortical development, retinal development, single-cell gene expression, pluripotent stem cell differentiation, interneuron migration, synaptogenesis
- MeSH terms
- Brain, Cell Line, Cell Separation, Cerebral Cortex, Dendrites, Humans, Light, Nerve Net, Neural Pathways, Organ Specificity, Organoids, Retina, Time Factors, Sequence Analysis, RNA, Photoreceptor Cells, Vertebrate, Gene Expression Profiling, Pluripotent Stem Cells, Neurogenesis, Single-Cell Analysis, Transcriptome, In Vitro Techniques
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