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Tambalo M, Lodato S. Brain organoids: Human 3D models to investigate neuronal circuits assembly, function and dysfunction. Brain Res 2020; 1746:147028. [PMID: 32717276 DOI: 10.1016/j.brainres.2020.147028] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/12/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
Abstract
The human brain is characterized by an extraordinary complexity of neuronal and nonneuronal cell types, wired together into patterned neuronal circuits, which represent the anatomical substrates for the execution of high-order cognitive functions. Brain circuits' development and function is metabolically supported by an intricate network of selectively permeable blood vessels and finely tuned by short-range interactions with immune factors and immune cells. The coordinated cellular and molecular events governing the assembly of this unique and complex structure are at the core of intense investigation and pose legitimate questions about the best modeling strategies. Unceasing advancements in stem cell technologies coupled with recent demonstration of cell self-assembly capacity have enabled the exponential growth of brain organoid protocols in the past decade. This provides a compelling solution to investigate human brain development, a quest often halted by the inaccessibility of brain tissues and the lack of suitable models. We review the current state-of-the-art on the generation of brain organoids, describing the latest progresses in unguided, guided, and assembloids protocols, as well as organoid-on-a-chip strategies and xenograft approaches. High resolution genome wide sequencing technologies, both at the transcriptional and epigenomic level, enable the molecular comparative analysis of multiple brain organoid protocols, as well as to benchmark them against the human fetal brain. Coupling the molecular profiling with increasingly detailed analyses of the electrophysiological properties of several of these systems now allows a more accurate estimation of the protocol of choice for a given biological question. Thus, we summarize strengths and weaknesses of several brain organoid protocols and further speculate on some potential future endeavors to model human brain development, evolution and neurodevelopmental and neuropsychiatric diseases.
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Affiliation(s)
- M Tambalo
- Humanitas Clinical and Research Center-IRCCS, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - S Lodato
- Humanitas Clinical and Research Center-IRCCS, Via Manzoni 56, 20089 Rozzano, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy.
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Abstract
Segmentation of the vertebrate hindbrain leads to the formation of rhombomeres, each with a distinct anteroposterior identity. Specialised boundary cells form at segment borders that act as a source or regulator of neuronal differentiation. In zebrafish, there is spatial patterning of neurogenesis in which non-neurogenic zones form at boundaries and segment centres, in part mediated by Fgf20 signalling. To further understand the control of neurogenesis, we have carried out single cell RNA sequencing of the zebrafish hindbrain at three different stages of patterning. Analyses of the data reveal known and novel markers of distinct hindbrain segments, of cell types along the dorsoventral axis, and of the transition of progenitors to neuronal differentiation. We find major shifts in the transcriptome of progenitors and of differentiating cells between the different stages analysed. Supervised clustering with markers of boundary cells and segment centres, together with RNA-seq analysis of Fgf-regulated genes, has revealed new candidate regulators of cell differentiation in the hindbrain. These data provide a valuable resource for functional investigations of the patterning of neurogenesis and the transition of progenitors to neuronal differentiation.
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Affiliation(s)
- Monica Tambalo
- Neural Development Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David G Wilkinson
- Neural Development Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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Abstract
Vertebrate ear progenitors are induced by fibroblast growth factor signalling, however the molecular mechanisms leading to the coordinate activation of downstream targets are yet to be discovered. The ear, like other sensory placodes, arises from the pre-placodal region at the border of the neural plate. Using a multiplex NanoString approach, we determined the response of these progenitors to FGF signalling by examining the changes of more than 200 transcripts that define the otic and other placodes, neural crest and neural plate territories. This analysis identifies new direct and indirect FGF targets during otic induction. Investigating changes in histone marks by ChIP-seq reveals that FGF exposure of pre-placodal cells leads to rapid deposition of active chromatin marks H3K27ac near FGF-response genes, while H3K27ac is depleted in the vicinity of non-otic genes. Genomic regions that gain H3K27ac act as cis-regulatory elements controlling otic gene expression in time and space and define a unique transcription factor signature likely to control their activity. Finally, we show that in response to FGF signalling the transcription factor dimer AP1 recruits the histone acetyl transferase p300 to selected otic enhancers. Thus, during ear induction FGF signalling modifies the chromatin landscape to promote enhancer activation and chromatin accessibility.
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Affiliation(s)
- Monica Tambalo
- Centre for Craniofacial and Regenerative Biology, Faculty of Dental, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Maryam Anwar
- Centre for Craniofacial and Regenerative Biology, Faculty of Dental, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Mohi Ahmed
- Centre for Craniofacial and Regenerative Biology, Faculty of Dental, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Andrea Streit
- Centre for Craniofacial and Regenerative Biology, Faculty of Dental, Oral and Craniofacial Sciences, King's College London, London, SE1 9RT, UK.
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Fassier C, Fréal A, Gasmi L, Delphin C, Ten Martin D, De Gois S, Tambalo M, Bosc C, Mailly P, Revenu C, Peris L, Bolte S, Schneider-Maunoury S, Houart C, Nothias F, Larcher JC, Andrieux A, Hazan J. Motor axon navigation relies on Fidgetin-like 1-driven microtubule plus end dynamics. J Cell Biol 2018. [PMID: 29535193 PMCID: PMC5940295 DOI: 10.1083/jcb.201604108] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Fassier et al. identify Fidgetin-like 1 (Fignl1) as a key growth cone (GC)-enriched microtubule (MT)-associated protein in motor circuit wiring. They show that Fignl1 modulates motor GC morphology and steering behavior by down-regulating EB binding at MT plus ends and promoting MT depolymerization beneath the cell cortex. During neural circuit assembly, extrinsic signals are integrated into changes in growth cone (GC) cytoskeleton underlying axon guidance decisions. Microtubules (MTs) were shown to play an instructive role in GC steering. However, the numerous actors required for MT remodeling during axon navigation and their precise mode of action are far from being deciphered. Using loss- and gain-of-function analyses during zebrafish development, we identify in this study the meiotic clade adenosine triphosphatase Fidgetin-like 1 (Fignl1) as a key GC-enriched MT-interacting protein in motor circuit wiring and larval locomotion. We show that Fignl1 controls GC morphology and behavior at intermediate targets by regulating MT plus end dynamics and growth directionality. We further reveal that alternative translation of Fignl1 transcript is a sophisticated mechanism modulating MT dynamics: a full-length isoform regulates MT plus end–tracking protein binding at plus ends, whereas shorter isoforms promote their depolymerization beneath the cell cortex. Our study thus pinpoints Fignl1 as a multifaceted key player in MT remodeling underlying motor circuit connectivity.
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Affiliation(s)
- Coralie Fassier
- Sorbonne Universités, Université Pierre et Marie Curie-Université Paris 6, Institut de Biologie Paris-Seine, Unité de Neuroscience Paris Seine, Centre National de la Recherche Scientifique UMR 8246, Institut National de la Santé et de la Recherche Médicale U1130, Paris, France
| | - Amélie Fréal
- Sorbonne Universités, Université Pierre et Marie Curie-Université Paris 6, Institut de Biologie Paris-Seine, Unité de Neuroscience Paris Seine, Centre National de la Recherche Scientifique UMR 8246, Institut National de la Santé et de la Recherche Médicale U1130, Paris, France
| | - Laïla Gasmi
- Sorbonne Universités, Université Pierre et Marie Curie-Université Paris 6, Institut de Biologie Paris-Seine, Unité de Neuroscience Paris Seine, Centre National de la Recherche Scientifique UMR 8246, Institut National de la Santé et de la Recherche Médicale U1130, Paris, France
| | - Christian Delphin
- Institut National de la Santé et de la Recherche Médicale U1216, Université Grenoble Alpes, Grenoble Institut Neurosciences, Grenoble, France
| | - Daniel Ten Martin
- Sorbonne Universités, Université Pierre et Marie Curie-Université Paris 6, Institut de Biologie Paris-Seine, Unité de Neuroscience Paris Seine, Centre National de la Recherche Scientifique UMR 8246, Institut National de la Santé et de la Recherche Médicale U1130, Paris, France
| | - Stéphanie De Gois
- Sorbonne Universités, Université Pierre et Marie Curie-Université Paris 6, Institut de Biologie Paris-Seine, Unité de Neuroscience Paris Seine, Centre National de la Recherche Scientifique UMR 8246, Institut National de la Santé et de la Recherche Médicale U1130, Paris, France
| | - Monica Tambalo
- Sorbonne Universités, Université Pierre et Marie Curie-Université Paris 6, Institut de Biologie Paris-Seine, Unité de Neuroscience Paris Seine, Centre National de la Recherche Scientifique UMR 8246, Institut National de la Santé et de la Recherche Médicale U1130, Paris, France
| | - Christophe Bosc
- Institut National de la Santé et de la Recherche Médicale U1216, Université Grenoble Alpes, Grenoble Institut Neurosciences, Grenoble, France
| | - Philippe Mailly
- Centre for Interdisciplinary Research in Biology, Collège de France, Paris, France
| | - Céline Revenu
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France
| | - Leticia Peris
- Institut National de la Santé et de la Recherche Médicale U1216, Université Grenoble Alpes, Grenoble Institut Neurosciences, Grenoble, France
| | - Susanne Bolte
- Sorbonne Universités, Université Pierre et Marie Curie-Université Paris 6, Institut de Biologie Paris-Seine, Centre National de la Recherche Scientifique FR3631, Paris, France
| | - Sylvie Schneider-Maunoury
- Sorbonne Universités, Université Pierre et Marie Curie-Université Paris 6, Institut de Biologie Paris-Seine, Biologie du Développement, Centre National de la Recherche Scientifique UMR7622, Paris, France
| | - Corinne Houart
- Medical Research Council Centre for Developmental Neurobiology, King's College London, Guy's Hospital Campus, London, England, UK
| | - Fatiha Nothias
- Sorbonne Universités, Université Pierre et Marie Curie-Université Paris 6, Institut de Biologie Paris-Seine, Unité de Neuroscience Paris Seine, Centre National de la Recherche Scientifique UMR 8246, Institut National de la Santé et de la Recherche Médicale U1130, Paris, France
| | - Jean-Christophe Larcher
- Sorbonne Universités, Université Pierre et Marie Curie-Université Paris 6, Institut de Biologie Paris-Seine, Biologie du Développement, Centre National de la Recherche Scientifique UMR7622, Paris, France
| | - Annie Andrieux
- Institut National de la Santé et de la Recherche Médicale U1216, Université Grenoble Alpes, Grenoble Institut Neurosciences, Grenoble, France
| | - Jamilé Hazan
- Sorbonne Universités, Université Pierre et Marie Curie-Université Paris 6, Institut de Biologie Paris-Seine, Unité de Neuroscience Paris Seine, Centre National de la Recherche Scientifique UMR 8246, Institut National de la Santé et de la Recherche Médicale U1130, Paris, France
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Hintze M, Prajapati RS, Tambalo M, Christophorou NAD, Anwar M, Grocott T, Streit A. Cell interactions, signals and transcriptional hierarchy governing placode progenitor induction. Development 2017; 144:2810-2823. [PMID: 28684624 PMCID: PMC5560042 DOI: 10.1242/dev.147942] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/21/2017] [Indexed: 12/18/2022]
Abstract
In vertebrates, cranial placodes contribute to all sense organs and sensory ganglia and arise from a common pool of Six1/Eya2+ progenitors. Here we dissect the events that specify ectodermal cells as placode progenitors using newly identified genes upstream of the Six/Eya complex. We show in chick that two different tissues, namely the lateral head mesoderm and the prechordal mesendoderm, gradually induce placode progenitors: cells pass through successive transcriptional states, each identified by distinct factors and controlled by different signals. Both tissues initiate a common transcriptional state but over time impart regional character, with the acquisition of anterior identity dependent on Shh signalling. Using a network inference approach we predict the regulatory relationships among newly identified transcription factors and verify predicted links in knockdown experiments. Based on this analysis we propose a new model for placode progenitor induction, in which the initial induction of a generic transcriptional state precedes regional divergence.
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Affiliation(s)
- Mark Hintze
- Department of Craniofacial Development & Stem Cell Biology, King's College London, Dental Institute, London SE1 9RT, UK
| | - Ravindra Singh Prajapati
- Department of Craniofacial Development & Stem Cell Biology, King's College London, Dental Institute, London SE1 9RT, UK
| | - Monica Tambalo
- Department of Craniofacial Development & Stem Cell Biology, King's College London, Dental Institute, London SE1 9RT, UK
| | - Nicolas A D Christophorou
- Department of Craniofacial Development & Stem Cell Biology, King's College London, Dental Institute, London SE1 9RT, UK
| | - Maryam Anwar
- Department of Craniofacial Development & Stem Cell Biology, King's College London, Dental Institute, London SE1 9RT, UK
| | - Timothy Grocott
- Department of Craniofacial Development & Stem Cell Biology, King's College London, Dental Institute, London SE1 9RT, UK
| | - Andrea Streit
- Department of Craniofacial Development & Stem Cell Biology, King's College London, Dental Institute, London SE1 9RT, UK
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Chen J, Tambalo M, Barembaum M, Ranganathan R, Simões-Costa M, Bronner ME, Streit A. A systems-level approach reveals new gene regulatory modules in the developing ear. Development 2017; 144:1531-1543. [PMID: 28264836 PMCID: PMC5399671 DOI: 10.1242/dev.148494] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/24/2017] [Indexed: 01/23/2023]
Abstract
The inner ear is a complex vertebrate sense organ, yet it arises from a simple epithelium, the otic placode. Specification towards otic fate requires diverse signals and transcriptional inputs that act sequentially and/or in parallel. Using the chick embryo, we uncover novel genes in the gene regulatory network underlying otic commitment and reveal dynamic changes in gene expression. Functional analysis of selected transcription factors reveals the genetic hierarchy underlying the transition from progenitor to committed precursor, integrating known and novel molecular players. Our results not only characterize the otic transcriptome in unprecedented detail, but also identify new gene interactions responsible for inner ear development and for the segregation of the otic lineage from epibranchial progenitors. By recapitulating the embryonic programme, the genes and genetic sub-circuits discovered here might be useful for reprogramming naïve cells towards otic identity to restore hearing loss. Summary: Transcriptome analysis and knock down of select transcription factors reveals a genetic hierarchy as cells become committed to inner ear fate.
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Affiliation(s)
- Jingchen Chen
- Department of Craniofacial Development and Stem Cell Biology, King's College London, London SE1 9RT, UK
| | - Monica Tambalo
- Department of Craniofacial Development and Stem Cell Biology, King's College London, London SE1 9RT, UK
| | - Meyer Barembaum
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ramya Ranganathan
- Department of Craniofacial Development and Stem Cell Biology, King's College London, London SE1 9RT, UK
| | - Marcos Simões-Costa
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrea Streit
- Department of Craniofacial Development and Stem Cell Biology, King's College London, London SE1 9RT, UK
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Lleras-Forero L, Tambalo M, Christophorou N, Chambers D, Houart C, Streit A. Neuropeptides: developmental signals in placode progenitor formation. Dev Cell 2013; 26:195-203. [PMID: 23906067 PMCID: PMC3748341 DOI: 10.1016/j.devcel.2013.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 02/20/2013] [Accepted: 07/02/2013] [Indexed: 02/02/2023]
Abstract
Few families of signaling factors have been implicated in the control of development. Here, we identify the neuropeptides nociceptin and somatostatin, a neurotransmitter and neuroendocrine hormone, as a class of developmental signals in both chick and zebrafish. We show that signals from the anterior mesendoderm are required for the formation of anterior placode progenitors, with one of the signals being somatostatin. Somatostatin controls ectodermal expression of nociceptin, and both peptides regulate Pax6 in lens and olfactory progenitors. Consequently, loss of somatostatin and nociceptin signaling leads to severe reduction of lens formation. Our findings not only uncover these neuropeptides as developmental signals but also identify a long-sought-after mechanism that initiates Pax6 in placode progenitors and may explain the ancient evolutionary origin of neuropeptides, predating a complex nervous system.
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Affiliation(s)
- Laura Lleras-Forero
- Department of Craniofacial Development and Stem Cell Biology, King’s College London, Guy’s Tower Wing, Floor 27, London SE1 9RT, UK
| | - Monica Tambalo
- Department of Craniofacial Development and Stem Cell Biology, King’s College London, Guy’s Tower Wing, Floor 27, London SE1 9RT, UK
| | - Nicolas Christophorou
- Department of Craniofacial Development and Stem Cell Biology, King’s College London, Guy’s Tower Wing, Floor 27, London SE1 9RT, UK
| | - David Chambers
- MRC Centre for Developmental Neurobiology, King’s College London, New Hunts House, London SE1 1UL, UK
| | - Corinne Houart
- MRC Centre for Developmental Neurobiology, King’s College London, New Hunts House, London SE1 1UL, UK
| | - Andrea Streit
- Department of Craniofacial Development and Stem Cell Biology, King’s College London, Guy’s Tower Wing, Floor 27, London SE1 9RT, UK
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Streit A, Tambalo M, Chen J, Grocott T, Anwar M, Sosinsky A, Stern CD. Experimental approaches for gene regulatory network construction: the chick as a model system. Genesis 2012; 51:296-310. [PMID: 23174848 DOI: 10.1002/dvg.22359] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/09/2012] [Accepted: 11/11/2012] [Indexed: 01/23/2023]
Abstract
Setting up the body plan during embryonic development requires the coordinated action of many signals and transcriptional regulators in a precise temporal sequence and spatial pattern. The last decades have seen an explosion of information describing the molecular control of many developmental processes. The next challenge is to integrate this information into logic "wiring diagrams" that visualize gene actions and outputs, have predictive power and point to key control nodes. Here, we provide an experimental workflow on how to construct gene regulatory networks using the chick as model system.
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Affiliation(s)
- Andrea Streit
- Department of Craniofacial Development and Stem Cell Biology, King's College London, London, United Kingdom.
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Grocott T, Tambalo M, Streit A. The peripheral sensory nervous system in the vertebrate head: a gene regulatory perspective. Dev Biol 2012; 370:3-23. [PMID: 22790010 DOI: 10.1016/j.ydbio.2012.06.028] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 06/28/2012] [Accepted: 06/29/2012] [Indexed: 02/06/2023]
Abstract
In the vertebrate head, crucial parts of the sense organs and sensory ganglia develop from special regions, the cranial placodes. Despite their cellular and functional diversity, they arise from a common field of multipotent progenitors and acquire distinct identity later under the influence of local signalling. Here we present the gene regulatory network that summarises our current understanding of how sensory cells are specified, how they become different from other ectodermal derivatives and how they begin to diversify to generate placodes with different identities. This analysis reveals how sequential activation of sets of transcription factors subdivides the ectoderm over time into smaller domains of progenitors for the central nervous system, neural crest, epidermis and sensory placodes. Within this hierarchy the timing of signalling and developmental history of each cell population is of critical importance to determine the ultimate outcome. A reoccurring theme is that local signals set up broad gene expression domains, which are further refined by mutual repression between different transcription factors. The Six and Eya network lies at the heart of sensory progenitor specification. In a positive feedback loop these factors perpetuate their own expression thus stabilising pre-placodal fate, while simultaneously repressing neural and neural crest specific factors. Downstream of the Six and Eya cassette, Pax genes in combination with other factors begin to impart regional identity to placode progenitors. While our review highlights the wealth of information available, it also points to the lack information on the cis-regulatory mechanisms that control placode specification and of how the repeated use of signalling input is integrated.
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Affiliation(s)
- Timothy Grocott
- Department of Craniofacial Development and Stem Cell Biology, King's College London, Guy's Tower Wing, Floor 27, London SE1 9RT, UK
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