The use of brain organoids to investigate neural development and disease

In the paper

“The production of radial glial cells, intermediate progenitors, and deep- and superficial-layer neurons in an ordered temporal fashion has been reported by studies using all of the protocols currently in use2,3,5,25.”

What the sources say

• Not checked yetcites [2] Lancaster, M. A. et al. Cerebral organoids model human brain development and microcephaly. Nature 501, 373–379 (2013). This was the first paper to introduce a method for generating cerebral organoids. The organoids were used to model microcephaly. source
• Not checked yetcites [3] Kadoshima, T. et al. Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell-derived neocortex. Proc. Natl Acad. Sci. USA 110, 20284–20289 (2013). This study provided a detailed exploration of brain organoid tissue including the temporal and spatial organization of cell type diversity and patterning. source
• Not checked yetcites [5] Qian, X. et al. Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell 165, 1238–1254 (2016). This study used mini bioreactors to produce forebrain organoids with a well-defined OSVZ and demonstrated the presence of oRGs with defined molecular markers. Diverse neuronal cell types expressing molecular markers of all six cortical layers were observed. source
• Not checked yetcites [25] Paşca, A. M. et al. Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture. Nat. Methods 12, 671–678 (2015). source

In the paper

“However, protocols have also been published for the generation of organoids that model the development of other human brain regions, including the hippocampus7, midbrain4,5,8, hypothalamus5, cerebellum5,9, anterior pituitary10 and retina10,11.”

What the sources say

• Not checked yetcites [7] Sakaguchi, H. et al. Generation of functional hippocampal neurons from self-organizing human embryonic stem cell-derived dorsomedial telencephalic tissue. Nat. Commun. 6, 8896 (2015). source
• Not checked yetcites [4] Jo, J. et al. Midbrain-like organoids from human pluripotent stem cells contain functional dopaminergic and neuromelanin-producing neurons. Cell Stem Cell 19, 248–257 (2016). source
• Not checked yetcites [5] Qian, X. et al. Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell 165, 1238–1254 (2016). This study used mini bioreactors to produce forebrain organoids with a well-defined OSVZ and demonstrated the presence of oRGs with defined molecular markers. Diverse neuronal cell types expressing molecular markers of all six cortical layers were observed. source
• Not checked yetcites [8] Monzel, A. S. et al. Derivation of human midbrain-specific organoids from neuroepithelial stem cells. Stem Cell Rep. 8, 1144–1154 (2017). source
• Not checked yetcites [9] Muguruma, K., Nishiyama, A., Kawakami, H., Hashimoto, K. & Sasai, Y. Self-organization of polarized cerebellar tissue in 3D culture of human pluripotent stem cells. Cell Rep. 10, 537–550 (2015). source

In the paper

“Most protocols therefore optimize neural induction by mimicking endogenous patterning through the application of exogenous cues (TABLE 1).”

What the sources say

• Not checked yetcites TABLE 1

In the paper

“Nevertheless, several key features of in vivo brain organogenesis are recapitulated by in vitro organoids, making them attractive models for studies of certain aspects of brain development.”

In the paper

“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.”

What the sources say

• Not checked yetcites [2] Lancaster, M. A. et al. Cerebral organoids model human brain development and microcephaly. Nature 501, 373–379 (2013). This was the first paper to introduce a method for generating cerebral organoids. The organoids were used to model microcephaly. source
• Not checked yetcites [27] Lindborg, B. A. et al. Rapid induction of cerebral organoids from human induced pluripotent stem cells using a chemically defined hydrogel and defined cell culture medium. Stem Cells Transl Med. 5, 970–979 (2016). source
• Not checked yetcites [28] Quadrato, G. et al. Cell diversity and network dynamics in photosensitive human brain organoids. Nature 545, 48–53 (2017). This study analysed gene expression in over 80,000 individual cells and found that organoids can generate a broad diversity of cells that are related to endogenous classes, including cells from the cerebral cortex and the retina. Neuronal activity within organoids was also controlled using light stimulation of photosensitive cells. source
• Not checked yetcites [29] 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). source

In the paper

“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.”

What the sources say

• Not checked yetcites [28] Quadrato, G. et al. Cell diversity and network dynamics in photosensitive human brain organoids. Nature 545, 48–53 (2017). This study analysed gene expression in over 80,000 individual cells and found that organoids can generate a broad diversity of cells that are related to endogenous classes, including cells from the cerebral cortex and the retina. Neuronal activity within organoids was also controlled using light stimulation of photosensitive cells. source
• Not checked yetcites [29] 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). source

In the paper

“Thus, human brain organoids could produce human-relevant cell types (as had been shown earlier in 2D PSC-derived cell cultures24), spurring an intense interest in organoid technologies as a model system to study human-specific features of brain development.”

What the sources say

• Not checked yetcites [24] Shi, Y., Kirwan, P. & Livesey, F. J. Directed differentiation of human pluripotent stem cells to cerebral cortex neurons and neural networks. Nat. Protoc. 7, 1836–1846 (2012). source

In the paper

“Bioreactors designed to improve oxygen diffusion and nutrient distribution have been used to produce larger and more viable structures that can grow for longer periods2,5 (BOX 1).”

What the sources say

• Not checked yetcites [2] Lancaster, M. A. et al. Cerebral organoids model human brain development and microcephaly. Nature 501, 373–379 (2013). This was the first paper to introduce a method for generating cerebral organoids. The organoids were used to model microcephaly. source
• Not checked yetcites [5] Qian, X. et al. Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell 165, 1238–1254 (2016). This study used mini bioreactors to produce forebrain organoids with a well-defined OSVZ and demonstrated the presence of oRGs with defined molecular markers. Diverse neuronal cell types expressing molecular markers of all six cortical layers were observed. source

In the paper

“It was also demonstrated that cell aggregation was not essential for efficient neural differentiation16, and a number of protocols for generating cortical neurons from monolayer cultures were developed17,18.”

What the sources say

• Not checked yetcites [16] Ying, Q.-L., Stavridis, M., Griffiths, D., Li, M. & Smith, A. Conversion of embryonic stem cells into neuroectodermal precursors in adherent monoculture. Nat. Biotechnol. 21, 183–186 (2003). source

In the paper

“A recent study further demonstrated the production of cortical neuron subtypes expressing markers found in all six cortical layers5 (FIG. 1).”

What the sources say

• Not checked yetcites [5] Qian, X. et al. Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell 165, 1238–1254 (2016). This study used mini bioreactors to produce forebrain organoids with a well-defined OSVZ and demonstrated the presence of oRGs with defined molecular markers. Diverse neuronal cell types expressing molecular markers of all six cortical layers were observed. source

In the paper

“Importantly, these organoids displayed features of human development that are not found in the mouse, such as the presence of outer radial glial cells (oRGs, also known as basal radial glial cells) in a subventricular- like zone22,23 (FIG. 1).”

What the sources say

• Not checked yetcites [22] Fietz, S. A. et al. OSVZ progenitors of human and ferret neocortex are epithelial-like and expand by integrin signaling. Nat. Neurosci. 13, 690–699 (2010). source
• Not checked yetcites [23] Hansen, D. V., Lui, J. H., Parker, P. R. L. & Kriegstein, A. R. Neurogenic radial glia in the outer subventricular zone of human neocortex. Nature 464, 554–561 (2010). source

In the paper

“Apart from growth factor cues, other modulators — such as scaffold support provided by the extracellular matrix — are important features of current protocols2,5,28.”

What the sources say

• Not checked yetcites [2] Lancaster, M. A. et al. Cerebral organoids model human brain development and microcephaly. Nature 501, 373–379 (2013). This was the first paper to introduce a method for generating cerebral organoids. The organoids were used to model microcephaly. source
• Not checked yetcites [5] Qian, X. et al. Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell 165, 1238–1254 (2016). This study used mini bioreactors to produce forebrain organoids with a well-defined OSVZ and demonstrated the presence of oRGs with defined molecular markers. Diverse neuronal cell types expressing molecular markers of all six cortical layers were observed. source
• Not checked yetcites [28] Quadrato, G. et al. Cell diversity and network dynamics in photosensitive human brain organoids. Nature 545, 48–53 (2017). This study analysed gene expression in over 80,000 individual cells and found that organoids can generate a broad diversity of cells that are related to endogenous classes, including cells from the cerebral cortex and the retina. Neuronal activity within organoids was also controlled using light stimulation of photosensitive cells. source

In the paper

“Commonly, neural induction in brain organoids includes inhibition of SMAD signalling to inhibit mesoderm and endoderm formation, followed by the provision of specific morphogens and fate-specifying molecules18.”

What the sources say

• Not checked yetcites [18] Chambers, S. M. et al. Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nat. Biotechnol. 27, 275–280 (2009). source

In the paper

“It was later shown that ESCs were able to produce neural precursors in the absence of serum, growth factors, or other inductive signals16, demonstrating the remarkable ability of PSCs to spontaneously acquire neural identity.”

What the sources say

• Not checked yetcites [16] Ying, Q.-L., Stavridis, M., Griffiths, D., Li, M. & Smith, A. Conversion of embryonic stem cells into neuroectodermal precursors in adherent monoculture. Nat. Biotechnol. 21, 183–186 (2003). source

In the paper

“Additionally, it has been shown that when canonical WNT signalling is activated in PSCs during neural differentiation, neural progenitors of a caudal identity are induced in a dose-dependent manner, mimicking in vivo patterning35.”

What the sources say

• Not checked yetcites [35] Kirkeby, A. et al. Generation of regionally specified neural progenitors and functional neurons from human embryonic stem cells under defined conditions. Cell Rep. 1, 703–714 (2012). source

In the paper

“Both of these protocols generated organoids containing a dorsalized neuroepithelium that reproduced certain aspects of cortical development, both structurally and in terms of cell behaviour.”

What the sources say

• Not checked yetcites [2] Lancaster, M. A. et al. Cerebral organoids model human brain development and microcephaly. Nature 501, 373–379 (2013). This was the first paper to introduce a method for generating cerebral organoids. The organoids were used to model microcephaly. source
• Not checked yetcites [3] Kadoshima, T. et al. Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell-derived neocortex. Proc. Natl Acad. Sci. USA 110, 20284–20289 (2013). This study provided a detailed exploration of brain organoid tissue including the temporal and spatial organization of cell type diversity and patterning. source

In the paper

“The results show that the transcriptional profiles of organoids cultured for up to 100 days are similar to those of developing human cortex at post-conceptional weeks 17–24 (REFS 25,29).”

What the sources say

• Not checked yetcites [25] Paşca, A. M. et al. Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture. Nat. Methods 12, 671–678 (2015). source
• Not checked yetcites [29] 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). source

In the paper

“These findings were further supported by another report documenting interneuron migration following fusion of dorsal and ventral brain organoids26, and both studies demonstrated disruption of migration by antagonism of C-X-C chemokine receptor type 4 (CXCR4), which has an important role in interneuron migration6,26.”

What the sources say

• Not checked yetcites [6] Birey, F. et al. Assembly of functionally integrated human forebrain spheroids. Nature 545, 54–59 (2017). This study used pre-patterned pallial and subpallial spheroids to form fused forebrain spheroids, demonstrating interneuron diversity, migration and integration. This organoid model was used to model Timothy syndrome. source
• Not checked yetcites [26] Bagley, J. A., Reumann, D., Bian, S., Lévi-Strauss, J. & Knoblich, J. A. Fused cerebral organoids model interactions between brain regions. Nat. Methods 14, 743–751 (2017). source

In the paper

“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.”

What the sources say

• Not checked yetcites [25] Paşca, A. M. et al. Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture. Nat. Methods 12, 671–678 (2015). source
• Not checked yetcites [28] Quadrato, G. et al. Cell diversity and network dynamics in photosensitive human brain organoids. Nature 545, 48–53 (2017). This study analysed gene expression in over 80,000 individual cells and found that organoids can generate a broad diversity of cells that are related to endogenous classes, including cells from the cerebral cortex and the retina. Neuronal activity within organoids was also controlled using light stimulation of photosensitive cells. source

In the paper

“Brain organoids currently lack some of the cell types present in primary cortex, such as endothelial cells (which have been shown to influence progenitor cell behaviour62,63) and microglia (which also have a role in early stages of cortical development64) (FIG. 2b).”

What the sources say

• Not checked yetcites [62] Javaherian, A. & Kriegstein, A. A stem cell niche for intermediate progenitor cells of the embryonic cortex. Cereb. Cortex 19, i70–i77 (2009). source
• Not checked yetcites [63] Stubbs, D. et al. Neurovascular congruence during cerebral cortical development. Cereb. Cortex 19, i32–i41 (2009). source
• Not checked yetcites [64] Cunningham, C. L., Martínez- Cerdeño, V. & Noctor, S. C. Microglia regulate the number of neural precursor cells in the developing cerebral cortex. J. Neurosci. 33, 4216–4233 (2013). source

In the paper

“A recent study characterized cerebral organoids by demonstrating the presence of both distinct cerebral brain regions and forebrain organizing centres56.”

What the sources say

• Not checked yetcites [56] Renner, M. et al. Self-organized developmental patterning and differentiation in cerebral organoids. EMBO J. 36, 1316–1329 (2017). source

In the paper

“For example, the fusion of human cortical spheroids and human subpallial spheroids was used to model the migration of interneurons from the subpallium to the cortex6.”

What the sources say

• Not checked yetcites [6] Birey, F. et al. Assembly of functionally integrated human forebrain spheroids. Nature 545, 54–59 (2017). This study used pre-patterned pallial and subpallial spheroids to form fused forebrain spheroids, demonstrating interneuron diversity, migration and integration. This organoid model was used to model Timothy syndrome. source

In the paper

“The organoid-derived interneurons migrated in a manner similar to that of their in vivo counterparts.”

What the sources say

• Not checked yetcites [6] Birey, F. et al. Assembly of functionally integrated human forebrain spheroids. Nature 545, 54–59 (2017). This study used pre-patterned pallial and subpallial spheroids to form fused forebrain spheroids, demonstrating interneuron diversity, migration and integration. This organoid model was used to model Timothy syndrome. source

In the paper

“Most protocols show transcriptional correlation with only early to mid-gestational stages of brain development5,25,29.”

What the sources say

• Not checked yetcites [5] Qian, X. et al. Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell 165, 1238–1254 (2016). This study used mini bioreactors to produce forebrain organoids with a well-defined OSVZ and demonstrated the presence of oRGs with defined molecular markers. Diverse neuronal cell types expressing molecular markers of all six cortical layers were observed. source
• Not checked yetcites [25] Paşca, A. M. et al. Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture. Nat. Methods 12, 671–678 (2015). source
• Not checked yetcites [29] 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). source

In the paper

“Time-lapse confocal microscopy of organoid cells displaying the characteristic mitotic behaviour of oRGs provided further evidence of their identity49,50, and single-cell transcriptome sequencing has been used to confirm the presence of cells with oRG gene expression signatures50.”

What the sources say

• Not checked yetcites [49] Ostrem, B., Di Lullo, E. & Kriegstein, A. oRGs and mitotic somal translocation - a role in development and disease. Curr. Opin. Neurobiol. 42, 61–67 (2017). source
• Not checked yetcites [50] Bershteyn, M. et al. Human iPSC-derived cerebral organoids model cellular features of lissencephaly and reveal prolonged mitosis of outer radial glia. Cell Stem Cell 20, 435–449.e4 (2017). This study used brain organoids to model lissencephaly. The authors identified a mitotic defect in oRGs and used single-cell RNA sequencing to identify cells presenting an oRG transcriptional signature in human brain organoids. source

In the paper

“Although the presence of a cortical-hem-like region had been noted in an earlier report3, the organoid tissue examined in the later study also expressed signalling molecules, including WNT2B and BMP6.”

What the sources say

• Not checked yetcites [56] Renner, M. et al. Self-organized developmental patterning and differentiation in cerebral organoids. EMBO J. 36, 1316–1329 (2017). source

In the paper

“Immunohistochemical analyses revealed that several organoids contained a cell population that resembled the cortical hem, an important signalling centre implicated in forebrain patterning57,58.”

What the sources say

• Not checked yetcites [56] Renner, M. et al. Self-organized developmental patterning and differentiation in cerebral organoids. EMBO J. 36, 1316–1329 (2017). source

In the paper

“Interestingly, the transcriptomic profiles of organoid-derived neurons show greater neuronal maturation than those of 2D monolayer-derived neurons25.”

What the sources say

• Not checked yetcites [25] Paşca, A. M. et al. Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture. Nat. Methods 12, 671–678 (2015). source

In the paper

“Another important aspect of human development that has been reported in brain organoids is the generation of an outer subventricular zone (OSVZ) containing an abundant population of oRG progenitor cells.”

What the sources say

• Not checked yetcites [5] Qian, X. et al. Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell 165, 1238–1254 (2016). This study used mini bioreactors to produce forebrain organoids with a well-defined OSVZ and demonstrated the presence of oRGs with defined molecular markers. Diverse neuronal cell types expressing molecular markers of all six cortical layers were observed. source

In the paper

“These manipulations are easily applied to organoid systems51,66, fuelling a burgeoning interest in the application of this technology to understand the pathophysiology of a wide range of adult and developmental human brain diseases.”

What the sources say

• Not checked yetcites [51] Li, Y. et al. Induction of expansion and folding in human cerebral organoids. Cell Stem Cell 20, 385–396 (2017). source
• Not checked yetcites [66] Sun, Y. & Ding, Q. Genome engineering of stem cell organoids for disease modeling. Protein Cell 8, 315–327 (2017). source

In the paper

“Several reports suggest that long-term organoid culture can improve the correlation between the molecular signatures of organoid and endogenous cells28,52.”

What the sources say

• Not checked yetcites [28] Quadrato, G. et al. Cell diversity and network dynamics in photosensitive human brain organoids. Nature 545, 48–53 (2017). This study analysed gene expression in over 80,000 individual cells and found that organoids can generate a broad diversity of cells that are related to endogenous classes, including cells from the cerebral cortex and the retina. Neuronal activity within organoids was also controlled using light stimulation of photosensitive cells. source
• Not checked yetcites [52] Luo, C. et al. Cerebral organoids recapitulate epigenomic signatures of the human fetal brain. Cell Rep. 17, 3369–3384 (2016). source

In the paper

“A recent report described expansion and surface folding of cerebral organoids following phosphatase and tensin homologue (PTEN) deletion and enhancement of the phosphoinositide 3-kinase (PI3K)–AKT growth signalling pathway51, suggesting that increased neural progenitor proliferation may be a major contributing factor to expansion and gyrification of the human brain.”

What the sources say

• Not checked yetcites [51] Li, Y. et al. Induction of expansion and folding in human cerebral organoids. Cell Stem Cell 20, 385–396 (2017). source

In the paper

“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.”

What the sources say

• Not checked yetcites [28] Quadrato, G. et al. Cell diversity and network dynamics in photosensitive human brain organoids. Nature 545, 48–53 (2017). This study analysed gene expression in over 80,000 individual cells and found that organoids can generate a broad diversity of cells that are related to endogenous classes, including cells from the cerebral cortex and the retina. Neuronal activity within organoids was also controlled using light stimulation of photosensitive cells. source

In the paper

“Recently, it was demonstrated that photosensitive cells in retinal-like regions of brain organoids can respond to light28.”

What the sources say

• Not checked yetcites [28] Quadrato, G. et al. Cell diversity and network dynamics in photosensitive human brain organoids. Nature 545, 48–53 (2017). This study analysed gene expression in over 80,000 individual cells and found that organoids can generate a broad diversity of cells that are related to endogenous classes, including cells from the cerebral cortex and the retina. Neuronal activity within organoids was also controlled using light stimulation of photosensitive cells. source

In the paper

“A degree of neuronal functional maturation was reported in dorsal telencephalon organoids that were allowed to develop for up to 180 days in vitro25.”

What the sources say

• Not checked yetcites [25] Paşca, A. M. et al. Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture. Nat. Methods 12, 671–678 (2015). source

In the paper

“It was only after the molecular identity of oRGs was established48 that an OSVZ-like zone containing oRGs could be reliably identified based on marker expression5 (FIG. 1).”

What the sources say

• Not checked yetcites [48] Pollen, A. A. et al. Molecular identity of human outer radial glia during cortical development. Cell 163, 55–67 (2015). source
• Not checked yetcites [5] Qian, X. et al. Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell 165, 1238–1254 (2016). This study used mini bioreactors to produce forebrain organoids with a well-defined OSVZ and demonstrated the presence of oRGs with defined molecular markers. Diverse neuronal cell types expressing molecular markers of all six cortical layers were observed. source

In the paper

“For brain-like organoids derived using current protocols, the resemblance is limited, which is not surprising given the complexity of the human brain.”

In the paper

“Correctly mimicking morphogen signalling in in vitro cultures is difficult due to the complex interplay of regional and temporal expression in vivo.”

In the paper

“Thus, pre-patterned organoids can fuse and form functional interconnections.”

In the paper

“Given the resemblance of organoid models to early stages of cortical neurogenesis, they may be best suited for modelling developmental disorders that manifest at embryonic or fetal stages.”

In the paper

“The oRG population is largely missing in mouse brain development47, and human cellular models therefore provide a unique opportunity to study this cell population.”

In the paper

“The oRG population is largely missing in mouse brain development47, and human cellular models therefore provide a unique opportunity to study this cell population.”

What the sources say

• Not checked yetcites [47] Wang, X., Tsai, J.-W., LaMonica, B. & Kriegstein, A. R. A new subtype of progenitor cell in the mouse embryonic neocortex. Nat. Neurosci. 14, 555–561 (2011). source

In the paper

“Human brain organoids are therefore potentially useful for modelling human-specific traits, such as the cell types and structural features of the human brain, or the effects of disease-causing mutations that are difficult to model in the mouse.”

In the paper

“The advantages of in vitro models of human brain disease are numerous. They hold promise for the study of at least some features of disease in a 3D multicellular environment.”

In the paper

“An overriding issue regarding brain organoids as a model of development is their relative immaturity.”

In the paper

“Organoid models are also amenable to studies that require live, functioning tissue, such as the analysis of electrophysiological features or dynamic cell behaviours.”

In the paper

“In some instances, brain organoids have recapitulated disease phenotypes observed in mouse models, validating both models50.”

What the sources say

• Not checked yetcites [50] Bershteyn, M. et al. Human iPSC-derived cerebral organoids model cellular features of lissencephaly and reveal prolonged mitosis of outer radial glia. Cell Stem Cell 20, 435–449.e4 (2017). This study used brain organoids to model lissencephaly. The authors identified a mitotic defect in oRGs and used single-cell RNA sequencing to identify cells presenting an oRG transcriptional signature in human brain organoids. source

In the paper

“The possibilities of disease modelling have expanded with the evolution of genome editing tools65, which allow for the introduction of precise, targeted mutations or targeted gene repair.”

What the sources say

• Not checked yetcites [65] Hockemeyer, D. & Jaenisch, R. Induced pluripotent stem cells meet genome editing. Cell Stem Cell 18, 573–586 (2016). source

In the paper

“A recent report described expansion and surface folding of cerebral organoids following phosphatase and tensin homologue (PTEN) deletion and enhancement of the phosphoinositide 3-kinase (PI3K)–AKT growth signalling pathway51, suggesting that increased neural progenitor proliferation may be a major contributing factor to expansion and gyrification of the human brain.”

In the paper

“The ‘extrinsic’ organoid model whereby patterning is influenced by externally added molecules rather than relying on intrinsic self-organization shows promise with regard to better reproducibility5,6,25.”

What the sources say

• Not checked yetcites [5] Qian, X. et al. Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell 165, 1238–1254 (2016). This study used mini bioreactors to produce forebrain organoids with a well-defined OSVZ and demonstrated the presence of oRGs with defined molecular markers. Diverse neuronal cell types expressing molecular markers of all six cortical layers were observed. source
• Not checked yetcites [6] Birey, F. et al. Assembly of functionally integrated human forebrain spheroids. Nature 545, 54–59 (2017). This study used pre-patterned pallial and subpallial spheroids to form fused forebrain spheroids, demonstrating interneuron diversity, migration and integration. This organoid model was used to model Timothy syndrome. source
• Not checked yetcites [25] Paşca, A. M. et al. Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture. Nat. Methods 12, 671–678 (2015). source

In the paper

“In particular, the use of patient-derived iPSCs provides a unique opportunity to model complex polygenic disorders, including those with unidentified risk loci.”

In the paper

“They hold the promise of better relevance for understanding human brain development and disease than current rodent models.”

In the paper

“Several drugs that have shown promising results in Alzheimer mouse models have failed to prevent cognitive decline in late-phase clinical trials87–89.”

What the sources say

• Not checked yetcites [87] Salloway, S. et al. Two phase 3 trials of bapineuzumab in mild-to-moderate Alzheimer's disease. N. Engl. J. Med. 370, 322–333 (2014). source
• Not checked yetcites [88] Doody, R. S. et al. A phase 3 trial of semagacestat for treatment of Alzheimer's disease. N. Engl. J. Med. 369, 341–350 (2013). source
• Not checked yetcites [89] Doody, R. S. et al. Phase 3 trials of solanezumab for mild-to-moderate Alzheimer's disease. N. Engl. J. Med. 370, 311–321 (2014). source

In the paper

“iPSCs derived from individuals with MDS were used to generate cerebral organoids that exhibited several developmental phenotypes reported in lissencephaly mouse models, including dysregulation of the neuroepithelial stem cell mitotic spindle and neuronal migration defects50.”

What the sources say

• Not checked yetcites [50] Bershteyn, M. et al. Human iPSC-derived cerebral organoids model cellular features of lissencephaly and reveal prolonged mitosis of outer radial glia. Cell Stem Cell 20, 435–449.e4 (2017). This study used brain organoids to model lissencephaly. The authors identified a mitotic defect in oRGs and used single-cell RNA sequencing to identify cells presenting an oRG transcriptional signature in human brain organoids. source

In the paper

“The use of primary tissue also highlighted the vulnerability of microglia to ZIKV infection72.”

What the sources say

• Not checked yetcites [72] Retallack, H. et al. Zika virus cell tropism in the developing human brain and inhibition by azithromycin. Proc. Natl Acad. Sci. USA 113, 14408–14413 (2016). source

In the paper

“the 3D-differentiated neuronal cells expressing FAD mutations exhibited aggregates of phosphorylated tau as well as filamentous tau.”

What the sources say

• Not checked yetcites [85] Choi, S. H. et al. A three-dimensional human neural cell culture model of Alzheimer's disease. Nature 515, 274–278 (2014). source

In the paper

“one study revealed that familial AD (FAD) mutations in β-amyloid precursor protein and presenilin 1 induced robust extracellular deposition of amyloid-β in a human neural stem-cell-derived 3D culture system85.”

What the sources say

• Not checked yetcites [85] Choi, S. H. et al. A three-dimensional human neural cell culture model of Alzheimer's disease. Nature 515, 274–278 (2014). source

In the paper

“the capacity of organoids to differentiate, self-organize, and form distinct, complex, biologically relevant structures makes them ideal in vitro models of development, disease pathogenesis, and platforms for drug screening.”

In the paper

“Such studies offer hope that brain organoids might act as a drug discovery platform for neurodegenerative disease.”

In the paper

“A study using 2D iPSC-derived neural progenitor cells68 and two later studies69,70 that used both 2D neural precursor cells (NPCs) and brain organoids demonstrated this association.”

What the sources say

• Not checked yetcites [68] Tang, H. et al. Zika virus infects human cortical neural progenitors and attenuates their growth. Cell Stem Cell 18, 587–590 (2016). source
• Not checked yetcites [69] Garcez, P. P. et al. Zika virus impairs growth in human neurospheres and brain organoids. Science 352, 816–818 (2016). source
• Not checked yetcites [70] Cugola, F. R. et al. The Brazilian Zika virus strain causes birth defects in experimental models. Nature 534, 267–271 (2016). This report used a brain organoid model to demonstrate that ZIKV infection results in a reduction of proliferative zones and in disrupted cortical layers. source

In the paper

“The diverse cell types that can be represented in an organoid can be an advantage for modelling complex cellular interactions, but future studies must validate the extent and reproducibility of composition differences.”

In the paper

“These findings were supported by another group using brain organoids derived from multiple patients with FAD: again, AD-like pathologies such as amyloid aggregation, hyperphosphorylated tau protein, and endosome abnormalities were seen86.”

What the sources say

• Not checked yetcites [86] Raja, W. K. et al. Self-organizing 3D human neural tissue derived from induced pluripotent stem cells recapitulate alzheimer's disease phenotypes. PLoS ONE 11, e0161969 (2016). This report used Alzheimer disease (AD) patient-derived iPSCs to recapitulate AD-like pathologies such as age-dependent amyloid aggregation, hyperphosphorylated tau protein, and endosome abnormalities in organoids and showed that treatment of patient-derived organoids with β-and γ-secretase inhibitors significantly reduces amyloid and tau pathology. source

In the paper

“another reported reductions in progenitor cell and neuron numbers due to apoptosis70”

What the sources say

• Not checked yetcites [70] Cugola, F. R. et al. The Brazilian Zika virus strain causes birth defects in experimental models. Nature 534, 267–271 (2016). This report used a brain organoid model to demonstrate that ZIKV infection results in a reduction of proliferative zones and in disrupted cortical layers. source

In the paper

“Studies have suggested that brain organoids may be relevant models, even for late-onset diseases such as Alzheimer disease (AD).”

In the paper

“This revealed a cell-autonomous migration defect in Timothy syndrome-derived interneurons.”

What the sources say

• Not checked yetcites [6] Birey, F. et al. Assembly of functionally integrated human forebrain spheroids. Nature 545, 54–59 (2017). This study used pre-patterned pallial and subpallial spheroids to form fused forebrain spheroids, demonstrating interneuron diversity, migration and integration. This organoid model was used to model Timothy syndrome. source

In the paper

“The use of brain organoids helped to demonstrate a causal relationship between ZIKV infection and the selective targeting and destruction of neural progenitor cells.”

In the paper

“These findings are important because this phenotype has not been reported in mouse models with FAD mutations.”

In the paper

“One study showed that brain organoids exposed to ZIKV undergo a growth reduction69”

What the sources say

• Not checked yetcites [69] Garcez, P. P. et al. Zika virus impairs growth in human neurospheres and brain organoids. Science 352, 816–818 (2016). source

In the paper

“this demonstrates how organoid modelling can be used to identify molecular and cellular alterations that may underlie neuropsychiatric disorders.”

In the paper

“However, the organoids used to investigate ZIKV infection do not precisely reflect human brain tissue architecture and cell type composition (see above).”

In the paper

“These neuronal networks can take years to mature in the human brain and rely on subcortical influences, calling into question the ability of organoid models to accurately reflect these complex interrelated features of brain development.”

In the paper

“a study using human iPSC-derived NPCs or early-stage cerebral organoids demonstrated that genetic ablation of AXL did not affect ZIKV entry or ZIKV-mediated cell death74.”

What the sources say

• Not checked yetcites [74] Wells, M. F. et al. Genetic ablation of AXL does not protect human neural progenitor cells and cerebral organoids from zika virus infection. Cell Stem Cell 19, 703–708 (2016). source

In the paper

“Consequently, the interpretation of cell type infectivity and its significance in human disease may be biased.”

In the paper

“Although gyrification is not yet well recapitulated in human brain organoids, they may contain the relevant cell types or developmental programmes necessary to investigate these diseases.”

In the paper

“As noted above, this cell type is usually missing from organoid models, which may be significant when considering viral entry mechanisms.”