101
|
Pease NA, Nguyen PHB, Woodworth MA, Ng KKH, Irwin B, Vaughan JC, Kueh HY. Tunable, division-independent control of gene activation timing by a polycomb switch. Cell Rep 2021; 34:108888. [PMID: 33761349 PMCID: PMC8024876 DOI: 10.1016/j.celrep.2021.108888] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/17/2020] [Accepted: 03/01/2021] [Indexed: 01/09/2023] Open
Abstract
During development, progenitors often differentiate many cell generations after receiving signals. These delays must be robust yet tunable for precise population size control. Polycomb repressive mechanisms, involving histone H3 lysine-27 trimethylation (H3K27me3), restrain the expression of lineage-specifying genes in progenitors and may delay their activation and ensuing differentiation. Here, we elucidate an epigenetic switch controlling the T cell commitment gene Bcl11b that holds its locus in a heritable inactive state for multiple cell generations before activation. Integrating experiments and modeling, we identify a mechanism where H3K27me3 levels at Bcl11b, regulated by methyltransferase and demethylase activities, set the time delay at which the locus switches from a compacted, silent state to an extended, active state. This activation delay robustly spans many cell generations, is tunable by chromatin modifiers and transcription factors, and is independent of cell division. With their regulatory flexibility, such timed epigenetic switches may broadly control timing in development.
Collapse
Affiliation(s)
- Nicholas A Pease
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Phuc H B Nguyen
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, USA
| | - Marcus A Woodworth
- Biological Physics, Structure and Design Program, University of Washington, Seattle, WA 98195, USA; Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Kenneth K H Ng
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Blythe Irwin
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
102
|
Mora-Bermúdez F, Taverna E, Huttner WB. From stem and progenitor cells to neurons in the developing neocortex: key differences among hominids. FEBS J 2021; 289:1524-1535. [PMID: 33638923 DOI: 10.1111/febs.15793] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 01/05/2023]
Abstract
Comparing the biology of humans to that of other primates, and notably other hominids, is a useful path to learn more about what makes us human. Some of the most interesting differences among hominids are closely related to brain development and function, for example behaviour and cognition. This makes it particularly interesting to compare the hominid neural cells of the neocortex, a part of the brain that plays central roles in those processes. However, well-preserved tissue from great apes is usually extremely difficult to obtain. A variety of new alternative tools, for example brain organoids, are now beginning to make it possible to search for such differences and analyse their potential biological and biomedical meaning. Here, we present an overview of recent findings from comparisons of the neural stem and progenitor cells (NSPCs) and neurons of hominids. In addition to differences in proliferation and differentiation of NSPCs, and maturation of neurons, we highlight that the regulation of the timing of these processes is emerging as a general foundational difference in the development of the neocortex of hominids.
Collapse
Affiliation(s)
- Felipe Mora-Bermúdez
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Taverna
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| |
Collapse
|
103
|
Bonnefont J, Vanderhaeghen P. Neuronal fate acquisition and specification: time for a change. Curr Opin Neurobiol 2021; 66:195-204. [PMID: 33412482 PMCID: PMC8064025 DOI: 10.1016/j.conb.2020.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
Abstract
During embryonic development, neural stem/progenitor cells generate hundreds of different cell types through the combination of intrinsic and extrinsic cues. Recent data obtained in mouse and human cortical neurogenesis provide novel views about this interplay and how it evolves with time, whether during irreversible cell fate transitions that neural stem cells undergo to become neurons, or through gradual temporal changes of competence that lead to increased neuronal diversity from a common stem cell pool. In each case the temporal changes result from a dynamic balance between intracellular states and extracellular signalling factors. The underlying mechanisms are mostly conserved across species, but some display unique features in human corticogenesis, thereby linking temporal features of neurogenesis and human brain evolution.
Collapse
Affiliation(s)
- Jérôme Bonnefont
- Université Libre de Bruxelles (U.L.B.), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), and ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium; VIB-KULeuven Center for Brain & Disease Research, KULeuven Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium.
| | - Pierre Vanderhaeghen
- Université Libre de Bruxelles (U.L.B.), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), and ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium; VIB-KULeuven Center for Brain & Disease Research, KULeuven Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium.
| |
Collapse
|
104
|
Gong J, Meng T, Yang J, Hu N, Zhao H, Tian T. Three-dimensional in vitro tissue culture models of brain organoids. Exp Neurol 2021; 339:113619. [PMID: 33497645 DOI: 10.1016/j.expneurol.2021.113619] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/03/2021] [Accepted: 01/12/2021] [Indexed: 12/18/2022]
Abstract
Brain organoids are three-dimensional self-assembled structures that are derived from human induced pluripotent stem cells (hiPSCs). They can recapitulate the spatiotemporal organization and function of the brain, presenting a robust system for in vitro modeling of brain development, evolution, and diseases. Significant advances in biomaterials, microscale technologies, gene editing technologies, and stem cell biology have enabled the construction of human specific brain structures in vitro. However, the limitations of long-term culture, necrosis, and hypoxic cores in different culture models obstruct brain organoid growth and survival. The in vitro models should facilitate oxygen and nutrient absorption, which is essential to generate complex organoids and provides a biomimetic microenvironment for modeling human brain organogenesis and human diseases. This review aims to highlight the progress in the culture devices of brain organoids, including dish, bioreactor, and organ-on-a-chip models. With the modulation of bioactive molecules and biomaterials, the generated organoids recapitulate the key features of the human brain in a more reproducible and hyperoxic fashion. Furthermore, an outlook for future preclinical studies and the genetic modifications of brain organoids is presented.
Collapse
Affiliation(s)
- Jing Gong
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Tianyue Meng
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Jun Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Ning Hu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Hezhao Zhao
- Gastrointestinal Cancer Center, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Tian Tian
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China.
| |
Collapse
|
105
|
Adhya D, Chennell G, Crowe JA, Valencia-Alarcón EP, Seyforth J, Hosny NA, Yasvoina MV, Forster R, Baron-Cohen S, Vernon AC, Srivastava DP. Application of Airy beam light sheet microscopy to examine early neurodevelopmental structures in 3D hiPSC-derived human cortical spheroids. Mol Autism 2021; 12:4. [PMID: 33482917 PMCID: PMC7821651 DOI: 10.1186/s13229-021-00413-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 01/08/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The inability to observe relevant biological processes in vivo significantly restricts human neurodevelopmental research. Advances in appropriate in vitro model systems, including patient-specific human brain organoids and human cortical spheroids (hCSs), offer a pragmatic solution to this issue. In particular, hCSs are an accessible method for generating homogenous organoids of dorsal telencephalic fate, which recapitulate key aspects of human corticogenesis, including the formation of neural rosettes-in vitro correlates of the neural tube. These neurogenic niches give rise to neural progenitors that subsequently differentiate into neurons. Studies differentiating induced pluripotent stem cells (hiPSCs) in 2D have linked atypical formation of neural rosettes with neurodevelopmental disorders such as autism spectrum conditions. Thus far, however, conventional methods of tissue preparation in this field limit the ability to image these structures in three-dimensions within intact hCS or other 3D preparations. To overcome this limitation, we have sought to optimise a methodological approach to process hCSs to maximise the utility of a novel Airy-beam light sheet microscope (ALSM) to acquire high resolution volumetric images of internal structures within hCS representative of early developmental time points. RESULTS Conventional approaches to imaging hCS by confocal microscopy were limited in their ability to image effectively into intact spheroids. Conversely, volumetric acquisition by ALSM offered superior imaging through intact, non-clarified, in vitro tissues, in both speed and resolution when compared to conventional confocal imaging systems. Furthermore, optimised immunohistochemistry and optical clearing of hCSs afforded improved imaging at depth. This permitted visualization of the morphology of the inner lumen of neural rosettes. CONCLUSION We present an optimized methodology that takes advantage of an ALSM system that can rapidly image intact 3D brain organoids at high resolution while retaining a large field of view. This imaging modality can be applied to both non-cleared and cleared in vitro human brain spheroids derived from hiPSCs for precise examination of their internal 3D structures. This process represents a rapid, highly efficient method to examine and quantify in 3D the formation of key structures required for the coordination of neurodevelopmental processes in both health and disease states. We posit that this approach would facilitate investigation of human neurodevelopmental processes in vitro.
Collapse
Affiliation(s)
- Dwaipayan Adhya
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - George Chennell
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - James A Crowe
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Eva P Valencia-Alarcón
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - James Seyforth
- M Squared Life Ltd., The Surrey Technology Centre, 40 Occam Road, Guildford, UK
| | - Neveen A Hosny
- M Squared Life Ltd., The Surrey Technology Centre, 40 Occam Road, Guildford, UK
| | - Marina V Yasvoina
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Robert Forster
- M Squared Life Ltd., The Surrey Technology Centre, 40 Occam Road, Guildford, UK
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Anthony C Vernon
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Deepak P Srivastava
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK.
| |
Collapse
|
106
|
Schörnig M, Ju X, Fast L, Ebert S, Weigert A, Kanton S, Schaffer T, Nadif Kasri N, Treutlein B, Peter BM, Hevers W, Taverna E. Comparison of induced neurons reveals slower structural and functional maturation in humans than in apes. eLife 2021; 10:59323. [PMID: 33470930 PMCID: PMC7870144 DOI: 10.7554/elife.59323] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
We generated induced excitatory neurons (iNeurons, iNs) from chimpanzee, bonobo, and human stem cells by expressing the transcription factor neurogenin-2 (NGN2). Single-cell RNA sequencing showed that genes involved in dendrite and synapse development are expressed earlier during iNs maturation in the chimpanzee and bonobo than the human cells. In accordance, during the first 2 weeks of differentiation, chimpanzee and bonobo iNs showed repetitive action potentials and more spontaneous excitatory activity than human iNs, and extended neurites of higher total length. However, the axons of human iNs were slightly longer at 5 weeks of differentiation. The timing of the establishment of neuronal polarity did not differ between the species. Chimpanzee, bonobo, and human neurites eventually reached the same level of structural complexity. Thus, human iNs develop slower than chimpanzee and bonobo iNs, and this difference in timing likely depends on functions downstream of NGN2.
Collapse
Affiliation(s)
- Maria Schörnig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Xiangchun Ju
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Luise Fast
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sebastian Ebert
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anne Weigert
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sabina Kanton
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Theresa Schaffer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nael Nadif Kasri
- Department of Human Genetics and Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Radboudumc, Nijmegen, Netherlands
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Wulf Hevers
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Taverna
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| |
Collapse
|
107
|
Govindan S, Batti L, Osterop SF, Stoppini L, Roux A. Mass Generation, Neuron Labeling, and 3D Imaging of Minibrains. Front Bioeng Biotechnol 2021; 8:582650. [PMID: 33598450 PMCID: PMC7883898 DOI: 10.3389/fbioe.2020.582650] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/23/2020] [Indexed: 01/09/2023] Open
Abstract
Minibrain is a 3D brain in vitro spheroid model, composed of a mixed population of neurons and glial cells, generated from human iPSC derived neural stem cells. Despite the advances in human 3D in vitro models such as aggregates, spheroids and organoids, there is a lack of labeling and imaging methodologies to characterize these models. In this study, we present a step-by-step methodology to generate human minibrain nurseries and novel strategies to subsequently label projection neurons, perform immunohistochemistry and 3D imaging of the minibrains at large multiplexable scales. To visualize projection neurons, we adapt viral transduction and to visualize the organization of cell types we implement immunohistochemistry. To facilitate 3D imaging of minibrains, we present here pipelines and accessories for one step mounting and clearing suitable for confocal microscopy. The pipelines are specifically designed in such a way that the assays can be multiplexed with ease for large-scale screenings using minibrains and other organoid models. Using the pipeline, we present (i) dendrite morphometric properties obtained from 3D neuron morphology reconstructions, (ii) diversity in neuron morphology, and (iii) quantified distribution of progenitors and POU3F2 positive neurons in human minibrains.
Collapse
Affiliation(s)
- Subashika Govindan
- Tissue Engineering Laboratory, Haute école du paysage, d'ingénierie et d'architecture de Genève, Haute école spécialisée de Suisse occidentale (HEPIA HES-SO), University of Applied Sciences and Arts Western Switzerland, Geneva, Switzerland.,ARIMA Lifesciences PVT Ltd., Chennai, India
| | - Laura Batti
- Wyss Center for Bio and Neuroengineering, Geneva, Switzerland
| | | | - Luc Stoppini
- Tissue Engineering Laboratory, Haute école du paysage, d'ingénierie et d'architecture de Genève, Haute école spécialisée de Suisse occidentale (HEPIA HES-SO), University of Applied Sciences and Arts Western Switzerland, Geneva, Switzerland.,Swiss Center for Applied Human Toxicology (SCAHT), Bern, Switzerland
| | - Adrien Roux
- Tissue Engineering Laboratory, Haute école du paysage, d'ingénierie et d'architecture de Genève, Haute école spécialisée de Suisse occidentale (HEPIA HES-SO), University of Applied Sciences and Arts Western Switzerland, Geneva, Switzerland.,Swiss Center for Applied Human Toxicology (SCAHT), Bern, Switzerland
| |
Collapse
|
108
|
Imaizumi K, Okano H. Modeling neurodevelopment in a dish with pluripotent stem cells. Dev Growth Differ 2021; 63:18-25. [PMID: 33141454 PMCID: PMC7984205 DOI: 10.1111/dgd.12699] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 01/29/2023]
Abstract
Pluripotent stem cells (PSCs) can differentiate into all cell types in the body, and their differentiation procedures recapitulate the developmental processes of embryogenesis. Focusing on neurodevelopment, we describe here the application of knowledge gained from embryology to the neural induction of PSCs. Furthermore, PSC-based neural modeling provides novel insights into neurodevelopmental processes. In particular, human PSC cultures are a powerful tool for the study of human-specific neurodevelopmental processes and could even enable the elucidation of the mechanisms of human brain evolution. We also discuss challenges and potential future directions in further improving PSC-based neural modeling.
Collapse
Affiliation(s)
- Kent Imaizumi
- Department of PhysiologyKeio University School of MedicineTokyoJapan
| | - Hideyuki Okano
- Department of PhysiologyKeio University School of MedicineTokyoJapan
| |
Collapse
|
109
|
Zhang XY, Li J, Li CJ, Lin YQ, Huang CH, Zheng X, Song XC, Tu ZC, Li XJ, Yan S. Differential development and electrophysiological activity in cultured cortical neurons from the mouse and cynomolgus monkey. Neural Regen Res 2021; 16:2446-2452. [PMID: 33907033 PMCID: PMC8374592 DOI: 10.4103/1673-5374.313056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In vitro cultures of primary cortical neurons are widely used to investigate neuronal function. However, it has yet to be fully investigated whether there are significant differences in development and function between cultured rodent and primate cortical neurons, and whether these differences influence the utilization of cultured cortical neurons to model pathological conditions. Using in vitro culture techniques combined with immunofluorescence and electrophysiological methods, our study found that the development and maturation of primary cerebral cortical neurons from cynomolgus monkeys were slower than those from mice. We used a microelectrode array technique to compare the electrophysiological differences in cortical neurons, and found that primary cortical neurons from the mouse brain began to show electrical activity earlier than those from the cynomolgus monkey. Although cultured monkey cortical neurons developed slowly in vitro, they exhibited typical pathological features-revealed by immunofluorescent staining-when infected with adeno-associated viral vectors expressing mutant huntingtin (HTT), the Huntington's disease protein. A quantitative analysis of the cultured monkey cortical neurons also confirmed that mutant HTT significantly reduced the length of neurites. Therefore, compared with the primary cortical neurons of mice, cultured monkey cortical neurons have longer developmental and survival times and greater sustained physiological activity, such as electrophysiological activity. Our findings also suggest that primary cynomolgus monkey neurons cultured in vitro can simulate a cell model of human neurodegenerative disease, and may be useful for investigating time-dependent neuronal death as well as treatment via neuronal regeneration. All mouse experiments and protocols were approved by the Animal Care and Use Committee of Jinan University of China (IACUC Approval No. 20200512-04) on May 12, 2020. All monkey experiments were approved by the IACUC protocol (IACUC Approval No. LDACU 20190820-01) on August 23, 2019 for animal management and use.
Collapse
Affiliation(s)
- Xue-Yan Zhang
- Guangdong Key Laboratory of Non-Human Primate Models, Guangdong-Hongkong-Macau Institute of CNS Regeneration; Key Laboratory of CNS Regeneration, Ministry of Education, Jinan University, Guangzhou, Guangdong Province, China
| | - Jun Li
- Guangdong Key Laboratory of Non-Human Primate Models, Guangdong-Hongkong-Macau Institute of CNS Regeneration; Key Laboratory of CNS Regeneration, Ministry of Education, Jinan University, Guangzhou, Guangdong Province, China
| | - Cai-Juan Li
- Guangdong Key Laboratory of Non-Human Primate Models, Guangdong-Hongkong-Macau Institute of CNS Regeneration; Key Laboratory of CNS Regeneration, Ministry of Education, Jinan University, Guangzhou, Guangdong Province, China
| | - Ying-Qi Lin
- Guangdong Key Laboratory of Non-Human Primate Models, Guangdong-Hongkong-Macau Institute of CNS Regeneration; Key Laboratory of CNS Regeneration, Ministry of Education, Jinan University, Guangzhou, Guangdong Province, China
| | - Chun-Hui Huang
- Guangdong Key Laboratory of Non-Human Primate Models, Guangdong-Hongkong-Macau Institute of CNS Regeneration; Key Laboratory of CNS Regeneration, Ministry of Education, Jinan University, Guangzhou, Guangdong Province, China
| | - Xiao Zheng
- Guangdong Key Laboratory of Non-Human Primate Models, Guangdong-Hongkong-Macau Institute of CNS Regeneration; Key Laboratory of CNS Regeneration, Ministry of Education, Jinan University, Guangzhou, Guangdong Province, China
| | - Xi-Chen Song
- Guangdong Key Laboratory of Non-Human Primate Models, Guangdong-Hongkong-Macau Institute of CNS Regeneration; Key Laboratory of CNS Regeneration, Ministry of Education, Jinan University, Guangzhou, Guangdong Province, China
| | - Zhu-Chi Tu
- Guangdong Key Laboratory of Non-Human Primate Models, Guangdong-Hongkong-Macau Institute of CNS Regeneration; Key Laboratory of CNS Regeneration, Ministry of Education, Jinan University, Guangzhou, Guangdong Province, China
| | - Xiao-Jiang Li
- Guangdong Key Laboratory of Non-Human Primate Models, Guangdong-Hongkong-Macau Institute of CNS Regeneration; Key Laboratory of CNS Regeneration, Ministry of Education, Jinan University, Guangzhou, Guangdong Province, China
| | - Sen Yan
- Guangdong Key Laboratory of Non-Human Primate Models, Guangdong-Hongkong-Macau Institute of CNS Regeneration; Key Laboratory of CNS Regeneration, Ministry of Education, Jinan University, Guangzhou, Guangdong Province, China
| |
Collapse
|
110
|
Learning about cell lineage, cellular diversity and evolution of the human brain through stem cell models. Curr Opin Neurobiol 2020; 66:166-177. [PMID: 33246264 DOI: 10.1016/j.conb.2020.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023]
Abstract
Here, we summarize the current knowledge on cell diversity in the cortex and other brain regions from in vivo mouse models and in vitro models based on pluripotent stem cells. We discuss the mechanisms underlying cell proliferation and temporal progression that leads to the sequential generation of neurons dedicated to different layers of the cortex. We highlight models of corticogenesis from stem cells that recapitulate specific transcriptional and connectivity patterns from different cortical areas. We overview state-of-the art of human brain organoids modeling different brain regions, and we discuss insights into human cortical evolution from stem cells. Finally, we interrogate human brain organoid models for their competence to recapitulate the essence of human brain development.
Collapse
|
111
|
Lin Y, Yang J, Shen Z, Ma J, Simons BD, Shi SH. Behavior and lineage progression of neural progenitors in the mammalian cortex. Curr Opin Neurobiol 2020; 66:144-157. [PMID: 33227588 DOI: 10.1016/j.conb.2020.10.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 12/17/2022]
Abstract
The cerebral cortex is a central structure in the mammalian brain that enables higher cognitive functions and intellectual skills. It is the hallmark of the mammalian nervous system with enormous complexity, consisting of a large number of neurons and glia that are diverse in morphology, molecular expression, biophysical properties, circuit connectivity and physiological function. Cortical neurons and glia are generated by neural progenitor cells during development. Ensuring the correct cell cycle kinetics, fate behavior and lineage progression of neural progenitor cells is essential to determine the number and types of neurons and glia in the cerebral cortex, which together constitute neural circuits for brain function. In this review, we discuss recent findings on mammalian cortical progenitor cell types and their lineage behaviors in generating neurons and glia, cortical evolution and expansion, and advances in brain organoid technology that allow the modeling of human cortical development under normal and disease conditions.
Collapse
Affiliation(s)
- Yang Lin
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center of Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiajun Yang
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center of Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhongfu Shen
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center of Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jian Ma
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center of Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Benjamin D Simons
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, UK
| | - Song-Hai Shi
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center of Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
112
|
Charvet CJ, Palani A, Kabaria P, Takahashi E. Evolution of Brain Connections: Integrating Diffusion MR Tractography With Gene Expression Highlights Increased Corticocortical Projections in Primates. Cereb Cortex 2020; 29:5150-5165. [PMID: 30927350 DOI: 10.1093/cercor/bhz054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/20/2019] [Indexed: 12/19/2022] Open
Abstract
Diffusion MR tractography permits investigating the 3D structure of cortical pathways as interwoven paths across the entire brain. We use high-resolution scans from diffusion spectrum imaging and high angular resolution diffusion imaging to investigate the evolution of cortical pathways within the euarchontoglire (i.e., primates, rodents) lineage. More specifically, we compare cortical fiber pathways between macaques (Macaca mulatta), marmosets (Callithrix jachus), and rodents (mice, Mus musculus). We integrate these observations with comparative analyses of Neurofilament heavy polypeptide (NEFH) expression across the cortex of mice and primates. We chose these species because their phylogenetic position serves to trace the early evolutionary history of the human brain. Our comparative analysis from diffusion MR tractography, cortical white matter scaling, and NEFH expression demonstrates that the examined primates deviate from mice in possessing increased long-range cross-cortical projections, many of which course across the anterior to posterior axis of the cortex. Our study shows that integrating gene expression data with diffusion MR data is an effective approach in identifying variation in connectivity patterns between species. The expansion of corticocortical pathways and increased anterior to posterior cortical integration can be traced back to an extension of neurogenetic schedules during development in primates.
Collapse
Affiliation(s)
| | - Arthi Palani
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Medical Sciences in the College of Arts and Sciences, Boston University, Boston, MA 02215, USA
| | - Priya Kabaria
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA.,Department of Behavioral Neuroscience, Northeastern University, Boston, MA 02115, USA
| | - Emi Takahashi
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| |
Collapse
|
113
|
Chiaradia I, Lancaster MA. Brain organoids for the study of human neurobiology at the interface of in vitro and in vivo. Nat Neurosci 2020; 23:1496-1508. [PMID: 33139941 DOI: 10.1038/s41593-020-00730-3] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023]
Abstract
Brain development is an extraordinarily complex process achieved through the spatially and temporally regulated release of key patterning factors. In vitro neurodevelopmental models seek to mimic these processes to recapitulate the steps of tissue fate acquisition and morphogenesis. Classic two-dimensional neural cultures present higher homogeneity but lower complexity compared to the brain. Brain organoids instead have more advanced cell composition, maturation and tissue architecture. They can thus be considered at the interface of in vitro and in vivo neurobiology, and further improvements in organoid techniques are continuing to narrow the gap with in vivo brain development. Here we describe these efforts to recapitulate brain development in neural organoids and focus on their applicability for disease modeling, evolutionary studies and neural network research.
Collapse
Affiliation(s)
- Ilaria Chiaradia
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
| |
Collapse
|
114
|
Shi Y, Wu Q, Wang X. Modeling brain development and diseases with human cerebral organoids. Curr Opin Neurobiol 2020; 66:103-115. [PMID: 33130409 DOI: 10.1016/j.conb.2020.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/03/2020] [Accepted: 09/13/2020] [Indexed: 12/12/2022]
Abstract
Understanding the mechanisms that underlie human brain development and neurological and neuropsychiatric disorders is one of the key topics of neurobiology. Because of the poor accessibility of human and non-human primate brain tissues, the current perception and understanding of human brain development have been mainly derived from studies of rodents. However, some human-specific features of neural development cannot be well characterized by these animal models. Thanks to the advances in stem cell technologies, brain organoids are being under rapid development, showing the promising applications in decoding the human brain development and uncovering the pathology of brain diseases. In this review, we mainly summarized the recent advances in the development of brain organoid technology and discussed the limitations, applications and future prospects of this promising field.
Collapse
Affiliation(s)
- Yingchao Shi
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China; IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
| | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Bioland Laboratory (Guangzhou), Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Advanced Innovation Center for Human Brain Protection, Beijing Institute for Brain Disorders, Capital Medical University, Beijing, 100069, China.
| |
Collapse
|
115
|
Lovett ML, Nieland TJ, Dingle YTL, Kaplan DL. Innovations in 3-Dimensional Tissue Models of Human Brain Physiology and Diseases. ADVANCED FUNCTIONAL MATERIALS 2020; 30:1909146. [PMID: 34211358 PMCID: PMC8240470 DOI: 10.1002/adfm.201909146] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Indexed: 05/04/2023]
Abstract
3-dimensional (3D) laboratory tissue cultures have emerged as an alternative to traditional 2-dimensional (2D) culture systems that do not recapitulate native cell behavior. The discrepancy between in vivo and in vitro tissue-cell-molecular responses impedes understanding of human physiology in general and creates roadblocks for the discovery of therapeutic solutions. Two parallel approaches have emerged for the design of 3D culture systems. The first is biomedical engineering methodology, including bioengineered materials, bioprinting, microfluidics and bioreactors, used alone or in combination, to mimic the microenvironments of native tissues. The second approach is organoid technology, in which stem cells are exposed to chemical and/or biological cues to activate differentiation programs that are reminiscent of human (prenatal) development. This review article describes recent technological advances in engineering 3D cultures that more closely resemble the human brain. The contributions of in vitro 3D tissue culture systems to new insights in neurophysiology, neurological diseases and regenerative medicine are highlighted. Perspectives on designing improved tissue models of the human brain are offered, focusing on an integrative approach merging biomedical engineering tools with organoid biology.
Collapse
Affiliation(s)
- Michael L. Lovett
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155
| | - Thomas J.F. Nieland
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155
| | - Yu-Ting L. Dingle
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, 4 Colby Street, Medford, MA 02155
| |
Collapse
|
116
|
Rayon T, Stamataki D, Perez-Carrasco R, Garcia-Perez L, Barrington C, Melchionda M, Exelby K, Lazaro J, Tybulewicz VLJ, Fisher EMC, Briscoe J. Species-specific pace of development is associated with differences in protein stability. Science 2020; 369:eaba7667. [PMID: 32943498 PMCID: PMC7116327 DOI: 10.1126/science.aba7667] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022]
Abstract
Although many molecular mechanisms controlling developmental processes are evolutionarily conserved, the speed at which the embryo develops can vary substantially between species. For example, the same genetic program, comprising sequential changes in transcriptional states, governs the differentiation of motor neurons in mouse and human, but the tempo at which it operates differs between species. Using in vitro directed differentiation of embryonic stem cells to motor neurons, we show that the program runs more than twice as fast in mouse as in human. This is not due to differences in signaling, nor the genomic sequence of genes or their regulatory elements. Instead, there is an approximately two-fold increase in protein stability and cell cycle duration in human cells compared with mouse cells. This can account for the slower pace of human development and suggests that differences in protein turnover play a role in interspecies differences in developmental tempo.
Collapse
Affiliation(s)
- Teresa Rayon
- The Francis Crick Institute, London NW1 1AT, UK.
| | | | - Ruben Perez-Carrasco
- The Francis Crick Institute, London NW1 1AT, UK
- Department of Mathematics, University College London, London WC1E 6BT, UK
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | | | | | | | | | | | - Victor L J Tybulewicz
- The Francis Crick Institute, London NW1 1AT, UK
- Department of Immunology and Inflammation, Imperial College, London W12 0NN, UK
| | - Elizabeth M C Fisher
- UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | | |
Collapse
|
117
|
Lindhout FW, Kooistra R, Portegies S, Herstel LJ, Stucchi R, Snoek BL, Altelaar AFM, MacGillavry HD, Wierenga CJ, Hoogenraad CC. Quantitative mapping of transcriptome and proteome dynamics during polarization of human iPSC-derived neurons. eLife 2020; 9:e58124. [PMID: 32940601 PMCID: PMC7498259 DOI: 10.7554/elife.58124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022] Open
Abstract
The differentiation of neuronal stem cells into polarized neurons is a well-coordinated process which has mostly been studied in classical non-human model systems, but to what extent these findings are recapitulated in human neurons remains unclear. To study neuronal polarization in human neurons, we cultured hiPSC-derived neurons, characterized early developmental stages, measured electrophysiological responses, and systematically profiled transcriptomic and proteomic dynamics during these steps. The neuron transcriptome and proteome shows extensive remodeling, with differential expression profiles of ~1100 transcripts and ~2200 proteins during neuronal differentiation and polarization. We also identified a distinct axon developmental stage marked by the relocation of axon initial segment proteins and increased microtubule remodeling from the distal (stage 3a) to the proximal (stage 3b) axon. This developmental transition coincides with action potential maturation. Our comprehensive characterization and quantitative map of transcriptome and proteome dynamics provides a solid framework for studying polarization in human neurons.
Collapse
Affiliation(s)
- Feline W Lindhout
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Robbelien Kooistra
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Sybren Portegies
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Lotte J Herstel
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Riccardo Stucchi
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht UniversityUtrechtNetherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
| | - AF Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht UniversityUtrechtNetherlands
| | - Harold D MacGillavry
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Corette J Wierenga
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Casper C Hoogenraad
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
- Department of Neuroscience, Genentech, IncSan FranciscoUnited States
| |
Collapse
|
118
|
|
119
|
Lee H, Nowosiad P, Dutan Polit LM, Price J, Srivastava DP, Thuret S. Apolipoprotein E expression pattern in human induced pluripotent stem cells during in vitro neural induction. F1000Res 2020; 9:353. [PMID: 32685135 PMCID: PMC7355222 DOI: 10.12688/f1000research.23580.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/20/2020] [Indexed: 11/20/2022] Open
Abstract
Apolipoprotein E (APOE) is a multifunctional protein that plays significant roles in important cellular mechanisms in peripheral tissues and is as well expressed in the central nervous system, notably by adult neural stem cells (NSCs) in the hippocampus. Evidence from animal studies suggest that APOE is critical for adult NSC maintenance. However, whether APOE has the potential to play a similar role in human NSCs has not been directly investigated. To address this question, we conducted a focused study characterising APOE gene and protein expression in an in vitro model of neural differentiation utilising human induced pluripotent stem cells. We found that APOE gene expression was dramatically decreased as the cells became more differentiated, indicating that APOE expression levels reflect the degree of cellular differentiation during neural induction. Furthermore, qualitative analysis results of immunocytochemistry showed that intracellular localisation of APOE protein becomes more pronounced as neural differentiation progresses. Taken together, our findings suggest a potential role for APOE in human NSC maintenance and justify further investigations being carried out to understand whether changes in APOE levels can directly impact the neurogenic capacity of human stem cells.
Collapse
Affiliation(s)
- Hyunah Lee
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Paulina Nowosiad
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Lucia M Dutan Polit
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Jack Price
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Deepak P Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Sandrine Thuret
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| |
Collapse
|
120
|
Badai J, Bu Q, Zhang L. Review of Artificial Intelligence Applications and Algorithms for Brain Organoid Research. Interdiscip Sci 2020; 12:383-394. [PMID: 32833194 DOI: 10.1007/s12539-020-00386-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/04/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
The human brain organoid is a miniature three-dimensional tissue culture that can simulate the structure and function of the brain in an in vitro culture environment. Although we consider that human brain organoids could be used to understand brain development and diseases, experimental models of human brain organoids are so highly variable that we apply artificial intelligence (AI) techniques to investigate the development mechanism of the human brain. Therefore, this study briefly reviewed commonly used AI applications for human brain organoid-magnetic resonance imaging, electroencephalography, and gene editing techniques, as well as related AI algorithms. Finally, we discussed the limitations, challenges, and future study direction of AI-based technology for human brain organoids.
Collapse
Affiliation(s)
- Jiayidaer Badai
- College of Computer Science, Sichuan University, Chengdu, 610065, China
| | - Qian Bu
- Department of Food Engineering, College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China
| | - Le Zhang
- College of Computer Science, Sichuan University, Chengdu, 610065, China. .,Medical Big Data Center of Sichuan University, Chengdu, 610065, China. .,PERA Corporation Ltd., Beijing, 100025, China.
| |
Collapse
|
121
|
Studying Human Neurodevelopment and Diseases Using 3D Brain Organoids. J Neurosci 2020; 40:1186-1193. [PMID: 32024767 DOI: 10.1523/jneurosci.0519-19.2019] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/12/2019] [Accepted: 09/16/2019] [Indexed: 02/01/2023] Open
Abstract
In vitro differentiation of pluripotent stem cells provides a systematic platform to study development and disease. Recent advances in brain organoid technology have created new opportunities to investigate the formation and function of the human brain, under physiological and pathological conditions. Brain organoids can be generated to model the cellular and structural development of the human brain, and allow the investigation of the intricate interactions between resident neural and glial cell types. Combined with new advances in gene editing, imaging, and genomic analysis, brain organoid technology can be applied to address questions pertinent to human brain development, disease, and evolution. However, the current iterations of brain organoids also have limitations in faithfully recapitulating the in vivo processes. In this perspective, we evaluate the recent progress in brain organoid technology, and discuss the experimental considerations for its utilization.Dual Perspectives Companion Paper: Integrating CRISPR Engineering and hiPSC-Derived 2D Disease Modeling Systems, by Kristina Rehbach, Michael B. Fernando, and Kristen J. Brennand.
Collapse
|
122
|
Biophysical studies of protein misfolding and aggregation in in vivo models of Alzheimer's and Parkinson's diseases. Q Rev Biophys 2020; 49:e22. [PMID: 32493529 DOI: 10.1017/s0033583520000025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Neurodegenerative disorders, including Alzheimer's (AD) and Parkinson's diseases (PD), are characterised by the formation of aberrant assemblies of misfolded proteins. The discovery of disease-modifying drugs for these disorders is challenging, in part because we still have a limited understanding of their molecular origins. In this review, we discuss how biophysical approaches can help explain the formation of the aberrant conformational states of proteins whose neurotoxic effects underlie these diseases. We discuss in particular models based on the transgenic expression of amyloid-β (Aβ) and tau in AD, and α-synuclein in PD. Because biophysical methods have enabled an accurate quantification and a detailed understanding of the molecular mechanisms underlying protein misfolding and aggregation in vitro, we expect that the further development of these methods to probe directly the corresponding mechanisms in vivo will open effective routes for diagnostic and therapeutic interventions.
Collapse
|
123
|
Prodromidou K, Vlachos IS, Gaitanou M, Kouroupi G, Hatzigeorgiou AG, Matsas R. MicroRNA-934 is a novel primate-specific small non-coding RNA with neurogenic function during early development. eLife 2020; 9:e50561. [PMID: 32459171 PMCID: PMC7295570 DOI: 10.7554/elife.50561] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 05/21/2020] [Indexed: 12/12/2022] Open
Abstract
Integrating differential RNA and miRNA expression during neuronal lineage induction of human embryonic stem cells we identified miR-934, a primate-specific miRNA that displays a stage-specific expression pattern during progenitor expansion and early neuron generation. We demonstrate the biological relevance of this finding by comparison with data from early to mid-gestation human cortical tissue. Further we find that miR-934 directly controls progenitor to neuroblast transition and impacts on neurite growth of newborn neurons. In agreement, miR-934 targets are involved in progenitor proliferation and neuronal differentiation whilst miR-934 inhibition results in profound global transcriptome changes associated with neurogenesis, axonogenesis, neuronal migration and neurotransmission. Interestingly, miR-934 inhibition affects the expression of genes associated with the subplate zone, a transient compartment most prominent in primates that emerges during early corticogenesis. Our data suggest that mir-934 is a novel regulator of early human neurogenesis with potential implications for a species-specific evolutionary role in brain function.
Collapse
Affiliation(s)
- Kanella Prodromidou
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur InstituteAthensGreece
| | - Ioannis S Vlachos
- Department of Pathology, Beth Israel Deaconess Medical CenterBostonUnited States
- DIANA-Lab, Hellenic Pasteur InstituteAthensGreece
- Harvard Medical SchoolBostonUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Maria Gaitanou
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur InstituteAthensGreece
| | - Georgia Kouroupi
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur InstituteAthensGreece
| | | | - Rebecca Matsas
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur InstituteAthensGreece
| |
Collapse
|
124
|
Muchnik SK, Lorente-Galdos B, Santpere G, Sestan N. Modeling the Evolution of Human Brain Development Using Organoids. Cell 2020; 179:1250-1253. [PMID: 31778651 DOI: 10.1016/j.cell.2019.10.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In a recent issue of Nature, Kanton et al. explore human brain evolution and development by profiling the single-cell transcriptomes and epigenomes of cerebral organoids derived from human, chimpanzee, and macaque stem cells. Their results reveal key molecular characteristics that differentiate humans and non-human primates at the earliest stages of brain development.
Collapse
Affiliation(s)
- Sydney Keaton Muchnik
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Belen Lorente-Galdos
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Gabriel Santpere
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA; Neurogenomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
| | - Nenad Sestan
- Departments of Genetics, Psychiatry, and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA.
| |
Collapse
|
125
|
Ou MY, Ju XC, Cai YJ, Sun XY, Wang JF, Fu XQ, Sun Q, Luo ZG. Heterogeneous nuclear ribonucleoprotein A3 controls mitotic progression of neural progenitors via interaction with cohesin. Development 2020; 147:dev185132. [PMID: 32321712 DOI: 10.1242/dev.185132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 04/03/2020] [Indexed: 01/13/2023]
Abstract
Cortex development is controlled by temporal patterning of neural progenitor (NP) competence with sequential generation of deep and superficial layer neurons, but underlying mechanisms remain elusive. Here, we report a role for heterogeneous nuclear ribonucleoprotein A3 (HNRNPA3) in regulating the division of early cortical NPs that mainly give rise to deep-layer neurons via direct neurogenesis. HNRNPA3 is expressed at high levels in NPs of mouse and human cortex at early stages, with a unique peri-chromosome pattern. Intriguingly, downregulation of HNRNPA3 caused chromosome disarrangement, which hindered normal separation of chromosomes during NP division, leading to mitotic delay. Furthermore, HNRNPA3 is associated with the cohesin-core subunit SMC1A and controls its association with chromosomes, implicating a mechanism for the role of HNRNPA3 in regulating chromosome segregation in dividing NPs. Hnrnpa3-deficient mice exhibited reduced cortical thickness, especially of deep layers. Moreover, downregulation of HNRNPA3 in cultured human cerebral organoids led to marked reduction in NPs and deep-layer neurons. Thus, this study has identified a crucial role for HNRNPA3 in NP division and highlighted the relationship between mitosis progression and early neurogenesis.
Collapse
Affiliation(s)
- Min-Yi Ou
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang-Chun Ju
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi-Jun Cai
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xin-Yao Sun
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun-Feng Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiu-Qing Fu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qiang Sun
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhen-Ge Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| |
Collapse
|
126
|
Chen A, Guo Z, Fang L, Bian S. Application of Fused Organoid Models to Study Human Brain Development and Neural Disorders. Front Cell Neurosci 2020; 14:133. [PMID: 32670022 PMCID: PMC7326106 DOI: 10.3389/fncel.2020.00133] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Human brain organoids cultured from human pluripotent stem cells provide a promising platform to recapitulate histological features of the human brain and model neural disorders. However, unlike animal models, brain organoids lack a reproducible topographic organization, which limits their application in modeling intricate biology, such as the interaction between different brain regions. To overcome these drawbacks, brain organoids have been pre-patterned into specific brain regions and fused to form an assembloid that represents reproducible models recapitulating more complex biological processes of human brain development and neurological diseases. This approach has been applied to model interneuron migration, neuronal projections, tumor invasion, oligodendrogenesis, forebrain axis establishment, and brain vascularization. In this review article, we will summarize the usage of this technology to understand the fundamental biology underpinning human brain development and disorders.
Collapse
Affiliation(s)
- Augustin Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China.,Molecular Physiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), University of Saarland, Homburg, Germany
| | - Zhenming Guo
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China.,Bio-X Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Lipao Fang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China.,Molecular Physiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), University of Saarland, Homburg, Germany
| | - Shan Bian
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
| |
Collapse
|
127
|
Kanton S, Treutlein B, Camp JG. Single-cell genomic analysis of human cerebral organoids. Methods Cell Biol 2020; 159:229-256. [PMID: 32586444 DOI: 10.1016/bs.mcb.2020.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Investigating early brain development has previously relied on using primary developing brain tissue or two-dimensional cell culture models. Recently, stem cell-derived three-dimensional cell culture systems, collectively called brain organoids, have been developed that can faithfully recapitulate many aspects of early brain development. Together with the ability to reprogram fibroblast or blood cells into induced pluripotent stem cells from humans with neurodevelopmental disorders, this opens new inroads to study patient-specific brain development in a personalized cell culture model. Studying the transcriptomes and regulatory landscape of single cells within brain organoids presents a major advance to understand cell-type specific features and transient states during development, and to link these states to their underlying regulatory logic at high resolution. In this protocol, we describe how to generate single-cell RNA-seq and ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data from the same suspension of organoid cells and focus on reducing batch effects by multiplexing multiple individuals in one experiment. Moreover, we outline basic data processing, analysis, and strategies to correct for batch effects, to account for variability in organoids and for integrating gene expression and open chromatin data.
Collapse
Affiliation(s)
- Sabina Kanton
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Barbara Treutlein
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - J Gray Camp
- Institute of Clinical Ophthalmology (IOB), University of Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland.
| |
Collapse
|
128
|
Lee H, Nowosiad P, Dutan Polit LM, Price J, Srivastava DP, Thuret S. Apolipoprotein E expression pattern in human induced pluripotent stem cells during in vitro neural induction. F1000Res 2020; 9:353. [PMID: 32685135 PMCID: PMC7355222 DOI: 10.12688/f1000research.23580.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/20/2020] [Indexed: 09/23/2023] Open
Abstract
Apolipoprotein E (APOE) is a multifunctional protein that plays significant roles in important cellular mechanisms in peripheral tissues and is as well expressed in the central nervous system, notably by adult neural stem cells (NSCs) in the hippocampus. Evidence from animal studies suggest that APOE is critical for adult NSC maintenance. However, whether APOE has the potential to play a similar role in human NSCs has not been directly investigated. To address this question, we conducted a focused study characterising APOE gene and protein expression in an in vitro model of neural differentiation utilising human induced pluripotent stem cells. We found that APOE gene expression was dramatically decreased as the cells became more differentiated, indicating that APOE expression levels reflect the degree of cellular differentiation during neural induction. Furthermore, qualitative analysis results of immunocytochemistry showed that intracellular localisation of APOE protein becomes more pronounced as neural differentiation progresses. Taken together, our findings suggest a potential role for APOE in human NSC maintenance and justify further investigations being carried out to understand whether changes in APOE levels can directly impact the neurogenic capacity of human stem cells.
Collapse
Affiliation(s)
- Hyunah Lee
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Paulina Nowosiad
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Lucia M. Dutan Polit
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Jack Price
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Deepak P. Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| | - Sandrine Thuret
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, SE5 9NU, UK
| |
Collapse
|
129
|
Grogan KE, Perry GH. Studying human and nonhuman primate evolutionary biology with powerful in vitro and in vivo functional genomics tools. Evol Anthropol 2020; 29:143-158. [PMID: 32142200 PMCID: PMC10574139 DOI: 10.1002/evan.21825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/18/2019] [Accepted: 02/06/2020] [Indexed: 12/19/2022]
Abstract
In recent years, tools for functional genomic studies have become increasingly feasible for use by evolutionary anthropologists. In this review, we provide brief overviews of several exciting in vitro techniques that can be paired with "-omics" approaches (e.g., genomics, epigenomics, transcriptomics, proteomics, and metabolomics) for potentially powerful evolutionary insights. These in vitro techniques include ancestral protein resurrection, cell line experiments using primary, immortalized, and induced pluripotent stem cells, and CRISPR-Cas9 genetic manipulation. We also discuss how several of these methods can be used in vivo, for transgenic organism studies of human and nonhuman primate evolution. Throughout this review, we highlight example studies in which these approaches have already been used to inform our understanding of the evolutionary biology of modern and archaic humans and other primates while simultaneously identifying future opportunities for anthropologists to use this toolkit to help answer additional outstanding questions in evolutionary anthropology.
Collapse
Affiliation(s)
- Kathleen E. Grogan
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
| | - George H. Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
| |
Collapse
|
130
|
Gordon A, Geschwind DH. Human in vitro models for understanding mechanisms of autism spectrum disorder. Mol Autism 2020; 11:26. [PMID: 32299488 PMCID: PMC7164291 DOI: 10.1186/s13229-020-00332-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/01/2020] [Indexed: 02/06/2023] Open
Abstract
Early brain development is a critical epoch for the development of autism spectrum disorder (ASD). In vivo animal models have, until recently, been the principal tool used to study early brain development and the changes occurring in neurodevelopmental disorders such as ASD. In vitro models of brain development represent a significant advance in the field. Here, we review the main methods available to study human brain development in vitro and the applications of these models for studying ASD and other psychiatric disorders. We discuss the main findings from stem cell models to date focusing on cell cycle and proliferation, cell death, cell differentiation and maturation, and neuronal signaling and synaptic stimuli. To be able to generalize the results from these studies, we propose a framework of experimental design and power considerations for using in vitro models to study ASD. These include both technical issues such as reproducibility and power analysis and conceptual issues such as the brain region and cell types being modeled.
Collapse
Affiliation(s)
- Aaron Gordon
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
| |
Collapse
|
131
|
Moriano J, Boeckx C. Modern human changes in regulatory regions implicated in cortical development. BMC Genomics 2020; 21:304. [PMID: 32299352 PMCID: PMC7161147 DOI: 10.1186/s12864-020-6706-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Recent paleogenomic studies have highlighted a very small set of proteins carrying modern human-specific missense changes in comparison to our closest extinct relatives. Despite being frequently alluded to as highly relevant, species-specific differences in regulatory regions remain understudied. Here, we integrate data from paleogenomics, chromatin modification and physical interaction, and single-cell gene expression of neural progenitor cells to identify derived regulatory changes in the modern human lineage in comparison to Neanderthals/Denisovans. We report a set of genes whose enhancers and/or promoters harbor modern human single nucleotide changes and are active at early stages of cortical development. RESULTS We identified 212 genes controlled by regulatory regions harboring modern human changes where Neanderthals/Denisovans carry the ancestral allele. These regulatory regions significantly overlap with putative modern human positively-selected regions and schizophrenia-related genetic loci. Among the 212 genes, we identified a substantial proportion of genes related to transcriptional regulation and, specifically, an enrichment for the SETD1A histone methyltransferase complex, known to regulate WNT signaling for the generation and proliferation of intermediate progenitor cells. CONCLUSIONS This study complements previous research focused on protein-coding changes distinguishing our species from Neanderthals/Denisovans and highlights chromatin regulation as a functional category so far overlooked in modern human evolution studies. We present a set of candidates that will help to illuminate the investigation of modern human-specific ontogenetic trajectories.
Collapse
Affiliation(s)
- Juan Moriano
- Universitat de Barcelona, Gran Via de les Corts Catalanes, Barcelona, Spain.
- Universitat de Barcelona Institute of Complex Systems, Martı́ Franquès, Barcelona, Spain.
| | - Cedric Boeckx
- Universitat de Barcelona, Gran Via de les Corts Catalanes, Barcelona, Spain.
- Universitat de Barcelona Institute of Complex Systems, Martı́ Franquès, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies, Passeig Lluı́s Companys, Barcelona, Spain.
| |
Collapse
|
132
|
Modeling of early neural development in vitro by direct neurosphere formation culture of chimpanzee induced pluripotent stem cells. Stem Cell Res 2020; 44:101749. [DOI: 10.1016/j.scr.2020.101749] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/17/2020] [Accepted: 02/21/2020] [Indexed: 02/07/2023] Open
|
133
|
Jasinska AJ. Resources for functional genomic studies of health and development in nonhuman primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171 Suppl 70:174-194. [PMID: 32221967 DOI: 10.1002/ajpa.24051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/22/2020] [Accepted: 02/26/2020] [Indexed: 01/01/2023]
Abstract
Primates display a wide range of phenotypic variation underlaid by complex genetically regulated mechanisms. The links among DNA sequence, gene function, and phenotype have been of interest from an evolutionary perspective, to understand functional genome evolution and its phenotypic consequences, and from a biomedical perspective to understand the shared and human-specific roots of health and disease. Progress in methods for characterizing genetic, transcriptomic, and DNA methylation (DNAm) variation is driving the rapid development of extensive omics resources, which are now increasingly available from humans as well as a growing number of nonhuman primates (NHPs). The fast growth of large-scale genomic data is driving the emergence of integrated tools and databases, thus facilitating studies of gene functionality across primates. This review describes NHP genomic resources that can aid in exploration of how genes shape primate phenotypes. It focuses on the gene expression trajectories across development in different tissues, the identification of functional genetic variation (including variants deleterious for protein function and regulatory variants modulating gene expression), and DNAm profiles as an emerging tool to understand the process of aging. These resources enable comparative functional genomics approaches to identify species-specific and primate-shared gene functionalities associated with health and development.
Collapse
Affiliation(s)
- Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, California, USA.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Eye on Primates, Los Angeles, California, USA
| |
Collapse
|
134
|
Mostajo-Radji MA, Schmitz MT, Montoya ST, Pollen AA. Reverse engineering human brain evolution using organoid models. Brain Res 2020; 1729:146582. [PMID: 31809699 PMCID: PMC7058376 DOI: 10.1016/j.brainres.2019.146582] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 02/06/2023]
Abstract
Primate brains vary dramatically in size and organization, but the genetic and developmental basis for these differences has been difficult to study due to lack of experimental models. Pluripotent stem cells and brain organoids provide a potential opportunity for comparative and functional studies of evolutionary differences, particularly during the early stages of neurogenesis. However, many challenges remain, including isolating stem cell lines from additional great ape individuals and species to capture the breadth of ape genetic diversity, improving the reproducibility of organoid models to study evolved differences in cell composition and combining multiple brain regions to capture connectivity relationships. Here, we describe strategies for identifying evolved developmental differences between humans and non-human primates and for isolating the underlying cellular and genetic mechanisms using comparative analyses, chimeric organoid culture, and genome engineering. In particular, we focus on how organoid models could ultimately be applied beyond studies of progenitor cell evolution to decode the origin of recent changes in cellular organization, connectivity patterns, myelination, synaptic development, and physiology that have been implicated in human cognition.
Collapse
Affiliation(s)
- Mohammed A Mostajo-Radji
- Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew T Schmitz
- Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA
| | - Sebastian Torres Montoya
- Health Co-creation Laboratory, Medellin General Hospital, Medellin, Antioquia, Colombia; Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alex A Pollen
- Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
135
|
Seranova E, Palhegyi AM, Verma S, Dimova S, Lasry R, Naama M, Sun C, Barrett T, Rosenstock TR, Kumar D, Cohen MA, Buganim Y, Sarkar S. Human Induced Pluripotent Stem Cell Models of Neurodegenerative Disorders for Studying the Biomedical Implications of Autophagy. J Mol Biol 2020; 432:2754-2798. [PMID: 32044344 DOI: 10.1016/j.jmb.2020.01.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/12/2022]
Abstract
Autophagy is an intracellular degradation process that is essential for cellular survival, tissue homeostasis, and human health. The housekeeping functions of autophagy in mediating the clearance of aggregation-prone proteins and damaged organelles are vital for post-mitotic neurons. Improper functioning of this process contributes to the pathology of myriad human diseases, including neurodegeneration. Impairment in autophagy has been reported in several neurodegenerative diseases where pharmacological induction of autophagy has therapeutic benefits in cellular and transgenic animal models. However, emerging studies suggest that the efficacy of autophagy inducers, as well as the nature of the autophagy defects, may be context-dependent, and therefore, studies in disease-relevant experimental systems may provide more insights for clinical translation to patients. With the advancements in human stem cell technology, it is now possible to establish disease-affected cellular platforms from patients for investigating disease mechanisms and identifying candidate drugs in the appropriate cell types, such as neurons that are otherwise not accessible. Towards this, patient-derived human induced pluripotent stem cells (hiPSCs) have demonstrated considerable promise in constituting a platform for effective disease modeling and drug discovery. Multiple studies have utilized hiPSC models of neurodegenerative diseases to study autophagy and evaluate the therapeutic efficacy of autophagy inducers in neuronal cells. This review provides an overview of the regulation of autophagy, generation of hiPSCs via cellular reprogramming, and neuronal differentiation. It outlines the findings in various neurodegenerative disorders where autophagy has been studied using hiPSC models.
Collapse
Affiliation(s)
- Elena Seranova
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Adina Maria Palhegyi
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Surbhi Verma
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom; Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Simona Dimova
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Rachel Lasry
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, 91120, Israel
| | - Moriyah Naama
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, 91120, Israel
| | - Congxin Sun
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Timothy Barrett
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Tatiana Rosado Rosenstock
- Department of Physiological Science, Santa Casa de São Paulo School of Medical Sciences, São Paulo, SP, 01221-020, Brazil
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Malkiel A Cohen
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem, 91120, Israel
| | - Sovan Sarkar
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom.
| |
Collapse
|
136
|
Prodromidou K, Matsas R. Species-Specific miRNAs in Human Brain Development and Disease. Front Cell Neurosci 2019; 13:559. [PMID: 31920559 PMCID: PMC6930153 DOI: 10.3389/fncel.2019.00559] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/04/2019] [Indexed: 12/20/2022] Open
Abstract
Identification of the unique features of human brain development and function can be critical towards the elucidation of intricate processes such as higher cognitive functions and human-specific pathologies like neuropsychiatric and behavioral disorders. The developing primate and human central nervous system (CNS) are distinguished by expanded progenitor zones and a protracted time course of neurogenesis, leading to the expansion in brain size, prominent gyral anatomy, distinctive synaptic properties, and complex neural circuits. Comparative genomic studies have revealed that adaptations of brain capacities may be partly explained by human-specific genetic changes that impact the function of proteins associated with neocortical expansion, synaptic function, and language development. However, the formation of complex gene networks may be most relevant for brain evolution. Indeed, recent studies identified distinct human-specific gene expression patterns across developmental time occurring in brain regions linked to cognition. Interestingly, such modules show species-specific divergence and are enriched in genes associated with neuronal development and synapse formation whilst also being implicated in neuropsychiatric diseases. microRNAs represent a powerful component of gene-regulatory networks by promoting spatiotemporal post-transcriptional control of gene expression in the human and primate brain. It has also been suggested that the divergence in miRNA expression plays an important role in shaping gene expression divergence among species. Primate-specific and human-specific miRNAs are principally involved in progenitor proliferation and neurogenic processes but also associate with human cognition, and neurological disorders. Human embryonic or induced pluripotent stem cells and brain organoids, permitting experimental access to neural cells and differentiation stages that are otherwise difficult or impossible to reach in humans, are an essential means for studying species-specific brain miRNAs. Single-cell sequencing approaches can further decode refined miRNA-mRNA interactions during developmental transitions. Elucidating species-specific miRNA regulation will shed new light into the mechanisms that control spatiotemporal events during human brain development and disease, an important step towards fostering novel, holistic and effective therapeutic approaches for neural disorders. In this review, we discuss species-specific regulation of miRNA function, its contribution to the evolving features of the human brain and in neurological disease, with respect also to future therapeutic approaches.
Collapse
Affiliation(s)
- Kanella Prodromidou
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | - Rebecca Matsas
- Laboratory of Cellular and Molecular Neurobiology-Stem Cells, Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| |
Collapse
|
137
|
Fischer J, Heide M, Huttner WB. Genetic Modification of Brain Organoids. Front Cell Neurosci 2019; 13:558. [PMID: 31920558 PMCID: PMC6928125 DOI: 10.3389/fncel.2019.00558] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/04/2019] [Indexed: 12/12/2022] Open
Abstract
Brain organoids have become increasingly used systems allowing 3D-modeling of human brain development, evolution, and disease. To be able to make full use of these modeling systems, researchers have developed a growing toolkit of genetic modification techniques. These techniques can be applied to mature brain organoids or to the preceding embryoid bodies (EBs) and founding cells. This review will describe techniques used for transient and stable genetic modification of brain organoids and discuss their current use and respective advantages and disadvantages. Transient approaches include adeno-associated virus (AAV) and electroporation-based techniques, whereas stable genetic modification approaches make use of lentivirus (including viral stamping), transposon and CRISPR/Cas9 systems. Finally, an outlook as to likely future developments and applications regarding genetic modifications of brain organoids will be presented.
Collapse
Affiliation(s)
- Jan Fischer
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Heide
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| |
Collapse
|
138
|
Barry C, Schmitz MT, Argus C, Bolin JM, Probasco MD, Leng N, Duffin BM, Steill J, Swanson S, McIntosh BE, Stewart R, Kendziorski C, Thomson JA, Bacher R. Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics. PLoS Comput Biol 2019; 15:e1007543. [PMID: 31815944 PMCID: PMC6922475 DOI: 10.1371/journal.pcbi.1007543] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 12/19/2019] [Accepted: 11/12/2019] [Indexed: 12/22/2022] Open
Abstract
Pluripotent stem cells retain the developmental timing of their species of origin in vitro, an observation that suggests the existence of a cell-intrinsic developmental clock, yet the nature and machinery of the clock remain a mystery. We hypothesize that one possible component may lie in species-specific differences in the kinetics of transcriptional responses to differentiation signals. Using a liquid-handling robot, mouse and human pluripotent stem cells were exposed to identical neural differentiation conditions and sampled for RNA-sequencing at high frequency, every 4 or 10 minutes, for the first 10 hours of differentiation to test for differences in transcriptomic response rates. The majority of initial transcriptional responses occurred within a rapid window in the first minutes of differentiation for both human and mouse stem cells. Despite similarly early onsets of gene expression changes, we observed shortened and condensed gene expression patterns in mouse pluripotent stem cells compared to protracted trends in human pluripotent stem cells. Moreover, the speed at which individual genes were upregulated, as measured by the slopes of gene expression changes over time, was significantly faster in mouse compared to human cells. These results suggest that downstream transcriptomic response kinetics to signaling cues are faster in mouse versus human cells, and may offer a partial account for the vast differences in developmental rates across species.
Collapse
Affiliation(s)
- Christopher Barry
- Morgridge Institute for Research, Madison, WI, United States of America
| | | | - Cara Argus
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Jennifer M. Bolin
- Morgridge Institute for Research, Madison, WI, United States of America
| | | | - Ning Leng
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Bret M. Duffin
- Morgridge Institute for Research, Madison, WI, United States of America
| | - John Steill
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Scott Swanson
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Brian E. McIntosh
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI, United States of America
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States of America
| | - James A. Thomson
- Morgridge Institute for Research, Madison, WI, United States of America
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, United States of America
| | - Rhonda Bacher
- Department of Biostatistics, University of Florida, Gainesville, FL, United States of America
| |
Collapse
|
139
|
Wei Y, de Lange SC, Scholtens LH, Watanabe K, Ardesch DJ, Jansen PR, Savage JE, Li L, Preuss TM, Rilling JK, Posthuma D, van den Heuvel MP. Genetic mapping and evolutionary analysis of human-expanded cognitive networks. Nat Commun 2019; 10:4839. [PMID: 31649260 PMCID: PMC6813316 DOI: 10.1038/s41467-019-12764-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/24/2019] [Indexed: 01/04/2023] Open
Abstract
Cognitive brain networks such as the default-mode network (DMN), frontoparietal network, and salience network, are key functional networks of the human brain. Here we show that the rapid evolutionary cortical expansion of cognitive networks in the human brain, and most pronounced the DMN, runs parallel with high expression of human-accelerated genes (HAR genes). Using comparative transcriptomics analysis, we present that HAR genes are differentially more expressed in higher-order cognitive networks in humans compared to chimpanzees and macaques and that genes with high expression in the DMN are involved in synapse and dendrite formation. Moreover, HAR and DMN genes show significant associations with individual variations in DMN functional activity, intelligence, sociability, and mental conditions such as schizophrenia and autism. Our results suggest that the expansion of higher-order functional networks subserving increasing cognitive properties has been an important locus of genetic changes in recent human brain evolution.
Collapse
Affiliation(s)
- Yongbin Wei
- Connectome Lab, Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Siemon C de Lange
- Connectome Lab, Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Lianne H Scholtens
- Connectome Lab, Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Dirk Jan Ardesch
- Connectome Lab, Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Philip R Jansen
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Jeanne E Savage
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Longchuan Li
- Marcus Autism Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Todd M Preuss
- Division of Neuropharmacology and Neurologic Diseases, Emory University, Atlanta, GA, 30322, USA
- Center for Translational Social Neuroscience, Emory University, Atlanta, GA, 30322, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30322, USA
| | - James K Rilling
- Center for Translational Social Neuroscience, Emory University, Atlanta, GA, 30322, USA
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, 30322, USA
- Department of Anthropology, Emory University, Atlanta, GA, 30322, USA
- Center for Behavioral Neuroscience, Emory University, Atlanta, GA, 30322, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, 30322, USA
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
- Department of Clinical Genetics, Amsterdam Neuroscience, Amsterdam UMC, 1081 HV, Amsterdam, The Netherlands
| | - Martijn P van den Heuvel
- Connectome Lab, Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands.
- Department of Clinical Genetics, Amsterdam Neuroscience, Amsterdam UMC, 1081 HV, Amsterdam, The Netherlands.
| |
Collapse
|
140
|
Kanton S, Boyle MJ, He Z, Santel M, Weigert A, Sanchís-Calleja F, Guijarro P, Sidow L, Fleck JS, Han D, Qian Z, Heide M, Huttner WB, Khaitovich P, Pääbo S, Treutlein B, Camp JG. Organoid single-cell genomic atlas uncovers human-specific features of brain development. Nature 2019; 574:418-422. [DOI: 10.1038/s41586-019-1654-9] [Citation(s) in RCA: 312] [Impact Index Per Article: 62.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 09/06/2019] [Indexed: 12/22/2022]
|
141
|
Single-cell multimodal transcriptomics to study neuronal diversity in human stem cell-derived brain tissue and organoid models. J Neurosci Methods 2019; 325:108350. [DOI: 10.1016/j.jneumeth.2019.108350] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/24/2019] [Accepted: 07/05/2019] [Indexed: 12/16/2022]
|
142
|
Pinson A, Namba T, Huttner WB. Malformations of Human Neocortex in Development - Their Progenitor Cell Basis and Experimental Model Systems. Front Cell Neurosci 2019; 13:305. [PMID: 31338027 PMCID: PMC6629864 DOI: 10.3389/fncel.2019.00305] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 06/24/2019] [Indexed: 12/31/2022] Open
Abstract
Malformations of the human neocortex in development constitute a heterogeneous group of complex disorders, resulting in pathologies such as intellectual disability and abnormal neurological/psychiatric conditions such as epilepsy or autism. Advances in genomic sequencing and genetic techniques have allowed major breakthroughs in the field, revealing the molecular basis of several of these malformations. Here, we focus on those malformations of the human neocortex, notably microcephaly, and macrocephaly, where an underlying basis has been established at the level of the neural stem/progenitor cells (NPCs) from which neurons are directly or indirectly derived. Particular emphasis is placed on NPC cell biology and NPC markers. A second focus of this review is on experimental model systems used to dissect the underlying mechanisms of malformations of the human neocortex in development at the cellular and molecular level. The most commonly used model system have been genetically modified mice. However, although basic features of neocortical development are conserved across the various mammalian species, some important differences between mouse and human exist. These pertain to the abundance of specific NPC types and/or their proliferative capacity, as exemplified in the case of basal radial glia. These differences limit the ability of mouse models to fully recapitulate the phenotypes of malformations of the human neocortex. For this reason, additional experimental model systems, notably the ferret, non-human primates and cerebral organoids, have recently emerged as alternatives and shown to be of increasing relevance. It is therefore important to consider the benefits and limitations of each of these model systems for studying malformations of the human neocortex in development.
Collapse
Affiliation(s)
| | - Takashi Namba
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Wieland B. Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| |
Collapse
|
143
|
Yang SC, Liu JJ, Wang CK, Lin YT, Tsai SY, Chen WJ, Huang WK, Tu PWA, Lin YC, Chang CF, Cheng CL, Lin H, Lai CY, Lin CY, Lee YH, Chiu YC, Hsu CC, Hsu SC, Hsiao M, Schuyler SC, Lu FL, Lu J. Down-regulation of ATF1 leads to early neuroectoderm differentiation of human embryonic stem cells by increasing the expression level of SOX2. FASEB J 2019; 33:10577-10592. [PMID: 31242772 DOI: 10.1096/fj.201800220rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We reveal by high-throughput screening that activating transcription factor 1 (ATF1) is a novel pluripotent regulator in human embryonic stem cells (hESCs). The knockdown of ATF1 expression significantly up-regulated neuroectoderm (NE) genes but not mesoderm, endoderm, and trophectoderm genes. Of note, down-regulation or knockout of ATF1 with short hairpin RNA (shRNA), small interfering RNA (siRNA), or clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) was sufficient to up-regulate sex-determining region Y-box (SOX)2 and paired box 6 (PAX6) expression under the undifferentiated or differentiated conditions, whereas overexpression of ATF1 suppressed NE differentiation. Endogenous ATF1 was spontaneously down-regulated after d 1-3 of neural induction. By double-knockdown experiments, up-regulation of SOX2 was critical for the increase of PAX6 and SOX1 expression in shRNA targeting Atf1 hESCs. Using the luciferase reporter assay, we identified ATF1 as a negative transcriptional regulator of Sox2 gene expression. A novel function of ATF1 was discovered, and these findings contribute to a broader understanding of the very first steps in regulating NE differentiation in hESCs.-Yang, S.-C., Liu, J.-J., Wang, C.-K., Lin, Y.-T., Tsai, S.-Y., Chen, W.-J., Huang, W.-K., Tu, P.-W. A., Lin, Y.-C., Chang, C.-F., Cheng, C.-L., Lin, H., Lai, C.-Y., Lin, C.-Y., Lee, Y.-H., Chiu, Y.-C., Hsu, C.-C., Hsu, S.-C., Hsiao, M., Schuyler, S. C., Lu, F. L., Lu, J. Down-regulation of ATF1 leads to early neuroectoderm differentiation of human embryonic stem cells by increasing the expression level of SOX2.
Collapse
Affiliation(s)
- Shang-Chih Yang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Jan-Jan Liu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Kai Wang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Tsen Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Su-Yi Tsai
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Wei-Ju Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Wei-Kai Huang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Po-Wen A Tu
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Chen Lin
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | | | - Chih-Lun Cheng
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsuan Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chien-Ying Lai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chun-Yu Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Hsuan Lee
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yen-Chun Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Shu-Ching Hsu
- National Institute of Infectious Diseases and Vaccinology, Zhunan, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Scott C Schuyler
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City, Taiwan.,Division of Head and Neck Surgery, Department of Otolaryngology, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Frank Leigh Lu
- Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jean Lu
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan.,RNAi Core, National Core Facility, Academia Sinica, Taipei, Taiwan.,Department of Life Science, Tzu Chi University, Hualien, Taiwan.,Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
| |
Collapse
|
144
|
Suzuki IK. Molecular drivers of human cerebral cortical evolution. Neurosci Res 2019; 151:1-14. [PMID: 31175883 DOI: 10.1016/j.neures.2019.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/30/2019] [Accepted: 05/31/2019] [Indexed: 01/10/2023]
Abstract
One of the most important questions in human evolutionary biology is how our ancestor has acquired an expanded volume of the cerebral cortex, which may have significantly impacted on improving our cognitive abilities. Recent comparative approaches have identified developmental features unique to the human or hominid cerebral cortex, not shared with other animals including conventional experimental models. In addition, genomic, transcriptomic, and epigenomic signatures associated with human- or hominid-specific processes of the cortical development are becoming identified by virtue of technical progress in the deep nucleotide sequencing. This review discusses ontogenic and phylogenetic processes of the human cerebral cortex, followed by the introduction of recent comprehensive approaches identifying molecular mechanisms potentially driving the evolutionary changes in the cortical development.
Collapse
Affiliation(s)
- Ikuo K Suzuki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan; VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KULeuven, 3000 Leuven, Belgium; Université Libre de Bruxelles (U.L.B.), Institut de Recherches en Biologie Humaine et Moléculaire (IRIBHM), ULB Neuroscience Institute (UNI), 1070 Brussels, Belgium.
| |
Collapse
|
145
|
Abstract
Human brain organoids, generated from pluripotent stem cells, have emerged as a promising technique for modeling early stages of human neurodevelopment in controlled laboratory conditions. Although the applications for disease modeling in a dish have become routine, the use of these brain organoids as evolutionary tools is only now getting momentum. Here, we will review the current state of the art on the use of brain organoids from different species and the molecular and cellular insights generated from these studies. Besides, we will discuss how this model might be beneficial for human health and the limitations and future perspectives of this technology.
Collapse
Affiliation(s)
- Alysson R. Muotri
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, School of Medicine, La Jolla, CA, USA
- Department of Cellular & Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA
- UCSD Stem Cell Programme, University of California San Diego, School of Medicine, La Jolla, CA, USA
- Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, CA, USA
- Kavli Institute for Brain and Mind, University of California San Diego, School of Medicine, La Jolla, CA, USA
| |
Collapse
|
146
|
Kyrousi C, Cappello S. Using brain organoids to study human neurodevelopment, evolution and disease. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2019; 9:e347. [PMID: 31071759 DOI: 10.1002/wdev.347] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/18/2019] [Accepted: 04/07/2019] [Indexed: 01/12/2023]
Abstract
The brain is one of the most complex organs, responsible for the advanced intellectual and cognitive ability of humans. Although primates are to some extent capable of performing cognitive tasks, their abilities are less evolved. One of the reasons for this is the vast differences in the brain of humans compared to other mammals, in terms of shape, size and complexity. Such differences make the study of human brain development fascinating. Interestingly, the cerebral cortex is by far the most complex brain region resulting from its selective evolution within mammals over millions of years. Unraveling the molecular and cellular mechanisms regulating brain development, as well as the evolutionary differences seen across species and the need to understand human brain disorders, are some of the reasons why scientists are interested in improving their current knowledge on human corticogenesis. Toward this end, several animal models including primates have been used, however, these models are limited in their extent to recapitulate human-specific features. Recent technological achievements in the field of stem cell research, which have enabled the generation of human models of corticogenesis, called brain or cerebral organoids, are of great importance. This review focuses on the main cellular and molecular features of human corticogenesis and the use of brain organoids to study it. We will discuss the key differences between cortical development in human and nonhuman mammals, the technological applications of brain organoids and the different aspects of cortical development in normal and pathological conditions, which can be modeled using brain organoids. This article is categorized under: Comparative Development and Evolution > Regulation of Organ Diversity Nervous System Development > Vertebrates: General Principles.
Collapse
Affiliation(s)
- Christina Kyrousi
- Department of Developmental Neurobiology, Max Planck Institute of Psychiatry, Munich, Germany
| | - Silvia Cappello
- Department of Developmental Neurobiology, Max Planck Institute of Psychiatry, Munich, Germany
| |
Collapse
|
147
|
Abstract
Brain organoids are self-assembled three-dimensional aggregates generated from pluripotent stem cells with cell types and cytoarchitectures that resemble the embryonic human brain. As such, they have emerged as novel model systems that can be used to investigate human brain development and disorders. Although brain organoids mimic many key features of early human brain development at molecular, cellular, structural and functional levels, some aspects of brain development, such as the formation of distinct cortical neuronal layers, gyrification, and the establishment of complex neuronal circuitry, are not fully recapitulated. Here, we summarize recent advances in the development of brain organoid methodologies and discuss their applications in disease modeling. In addition, we compare current organoid systems to the embryonic human brain, highlighting features that currently can and cannot be recapitulated, and discuss perspectives for advancing current brain organoid technologies to expand their applications.
Collapse
Affiliation(s)
- Xuyu Qian
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Biomedical Engineering Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
148
|
Multifunctionalized hydrogels foster hNSC maturation in 3D cultures and neural regeneration in spinal cord injuries. Proc Natl Acad Sci U S A 2019; 116:7483-7492. [PMID: 30923117 PMCID: PMC6462084 DOI: 10.1073/pnas.1818392116] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cells reside in 3D microenvironments in living tissues; consequently, 3D cultures gained great interest because they better mimic the natural conditions of cells. Self-assembling peptides (SAPs) are synthetic bioabsorbable biomaterials that can provide customized 3D microenvironments regulating cell functionalities and tissue repair. Here we introduce a SAP-hydrogel designed to support human neural stem cell (hNSC) differentiation in 3D serum-free conditions, generating mature and active human neurons in vitro. We also demonstrate its functional neurorigenerative potential in rat spinal cord injuries, peaking when seeded with hNSCs progeny predifferentiated in vitro for 6 weeks. Despite these promising results, this approach should be confirmed in the future with medium-size animal models and with additional and refined behavioral tests before entering a clinical trial. Three-dimensional cell cultures are leading the way to the fabrication of tissue-like constructs useful to developmental biology and pharmaceutical screenings. However, their reproducibility and translational potential have been limited by biomaterial and culture media compositions, as well as cellular sources. We developed a construct comprising synthetic multifunctionalized hydrogels, serum-free media, and densely seeded good manufacturing practice protocol-grade human neural stem cells (hNSC). We tracked hNSC proliferation, differentiation, and maturation into GABAergic, glutamatergic, and cholinergic neurons, showing entangled electrically active neural networks. The neuroregenerative potential of the “engineered tissue” was assessed in spinal cord injuries, where hNSC-derived progenitors and predifferentiated hNSC progeny, embedded in multifunctionalized hydrogels, were implanted. All implants decreased astrogliosis and lowered the immune response, but scaffolds with predifferentiated hNSCs showed higher percentages of neuronal markers, better hNSC engraftment, and improved behavioral recovery. Our hNSC-construct enables the formation of 3D functional neuronal networks in vitro, allowing novel strategies for hNSC therapies in vivo.
Collapse
|
149
|
Varrault A, Journot L, Bouschet T. Cerebral Cortex Generated from Pluripotent Stem Cells to Model Corticogenesis and Rebuild Cortical Circuits: In Vitro Veritas? Stem Cells Dev 2019; 28:361-369. [PMID: 30661489 DOI: 10.1089/scd.2018.0233] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Organoids and cells generated in vitro from pluripotent stem cells (PSCs) are considered to be robust models of development and a conceivable source of transplants for putative cell therapy. However, a fundamental question about organoids and cells generated from PSCs is as follows: do they faithfully reproduce the in vivo tissue they are supposed to mimic and replace? This question is particularly relevant to complex tissues such as the cerebral cortex. In this review, we have tackled this issue by comparing cerebral cortices generated in vitro from PSCs to the in vivo cortex, with a particular focus on their respective cellular composition, molecular and epigenetic signatures, and brain connectivity. In short, in vitro cortex generated from PSCs reproduces most of the cardinal features of the in vivo cortex, including temporal corticogenesis and connectivity when PSC-derived cortical cells are grafted in recipient mouse cortex. However, compared to in vivo cortex, in vitro cortex lacks microglia and blood vessels and is less mature. Recent experiments show that the brain of the transplanted host provides these missing cell types together with an environment that promotes the synaptic maturation of the cortical transplant. Taken together, these data suggest that corticogenesis is largely intrinsic and well recapitulated in vitro, while the full maturation of cortical cells requires additional environmental clues. Finally, we propose some lines of work to improve corticogenesis from PSCs as a tool to model corticogenesis and rebuild cortical circuits.
Collapse
Affiliation(s)
- Annie Varrault
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Laurent Journot
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Université de Montpellier, Montpellier, France
| |
Collapse
|
150
|
Field AR, Jacobs FMJ, Fiddes IT, Phillips APR, Reyes-Ortiz AM, LaMontagne E, Whitehead L, Meng V, Rosenkrantz JL, Olsen M, Hauessler M, Katzman S, Salama SR, Haussler D. Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes. Stem Cell Reports 2019; 12:245-257. [PMID: 30639214 PMCID: PMC6372947 DOI: 10.1016/j.stemcr.2018.12.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 01/30/2023] Open
Abstract
The cerebral cortex has expanded in size and complexity in primates, yet the molecular innovations that enabled primate-specific brain attributes remain obscure. We generated cerebral cortex organoids from human, chimpanzee, orangutan, and rhesus pluripotent stem cells and sequenced their transcriptomes at weekly time points for comparative analysis. We used transcript structure and expression conservation to discover gene regulatory long non-coding RNAs (lncRNAs). Of 2,975 human, multi-exonic lncRNAs, 2,472 were structurally conserved in at least one other species and 920 were conserved in all. Three hundred eighty-six human lncRNAs were transiently expressed (TrEx) and many were also TrEx in great apes (46%) and rhesus (31%). Many TrEx lncRNAs are expressed in specific cell types by single-cell RNA sequencing. Four TrEx lncRNAs selected based on cell-type specificity, gene structure, and expression pattern conservation were ectopically expressed in HEK293 cells by CRISPRa. All induced trans gene expression changes were consistent with neural gene regulatory activity.
Collapse
Affiliation(s)
- Andrew R Field
- Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Frank M J Jacobs
- Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ian T Fiddes
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alex P R Phillips
- Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrea M Reyes-Ortiz
- Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Erin LaMontagne
- Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Lila Whitehead
- Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Vincent Meng
- Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jimi L Rosenkrantz
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mari Olsen
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Max Hauessler
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Sol Katzman
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Sofie R Salama
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| |
Collapse
|