101
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Zheng Y, Yang X. Application and prospect of single-cell sequencing in cancer metastasis. Future Oncol 2022; 18:2723-2736. [PMID: 35686493 DOI: 10.2217/fon-2022-0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cancer metastasis is a complicated process driven by internal genetic variations and developed through interactions with the external environment. This process usually causes therapeutic resistance and results in a low survival rate. In recent years, single-cell sequencing has become a popular method for revealing the tumor evolutionary genetic lineage, intra-tumoral heterogeneity and tumor microenvironment of the metastasis process. So as to find more therapeutic targets for clinical application, the spatial transcriptomics method has become a new rising field of cancer studies, which promotes the combination between clinical medicine and molecular biology. In future prospects, more accurate and personalized treatment models will come into reality.
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Affiliation(s)
- Yue Zheng
- Department of Biochemistry & Molecular Biology, Basic Medical College, Shanxi Medical University, Taiyuan City, Shanxi Province, 030000, China
| | - Xiaofeng Yang
- Department of Urology, First Hospital of Shanxi Medical University,Taiyuan City, Shanxi Province, 030000, China
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102
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Duan Y, Huang W, Zhan B, Li Y, Xu X, Li K, Li X, Liu X, Ding S, Wang S, Guo J, Wang Y, Gu Q. A Bioink Derived From Human Placenta Supporting Angiogenesis. Biomed Mater 2022; 17. [PMID: 35732166 DOI: 10.1088/1748-605x/ac7b5b] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/22/2022] [Indexed: 11/11/2022]
Abstract
Bioprinting is an emerging approach for constructing sophisticated tissue analogues with detailed architectures such as vascular networks, which requires bioink fulfill the highly printable property and provide a cell-friendly microenvironment mimicking native extracellular matrix (ECM). Here, we developed a human placental ECM-derived bioink (hp-bioink) meeting the requirements of 3D printing for printability and bioactivity. We first decellularized the human placenta, followed by enzymatic digestion, dialysis, lyophilization, and re-solubilization to convert the extracts into hp-bioink. Then, we demonstrated that 3%-5% of hp-bioink can be printed with self-standing and 1%-2% of hp-bioink can be embedded with suspended hydrogels. Moreover, hp-bioink supports HUVEC assembly in vitro and angiogenesis in mice in vivo. Our research enriched the bank of human-derived bioink, and provided a new opportunity to further accelerate bioprinting research and application.
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Affiliation(s)
- Yongchao Duan
- Institute of Zoology Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China, Chaoyang District, Beijing, 100101, CHINA
| | - Wenhui Huang
- Institute of Zoology Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China, Chaoyang District, Beijing, 100101, CHINA
| | - Bo Zhan
- Institute of Zoology Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China, Chaoyang District, Beijing, 100101, CHINA
| | - Yuanyuan Li
- Shanxi Provincial Peoples Hospital, No 29 Shuangtadong Street, Yinze district, Taiyuan, Taiyuan, Shanxi , 030012, CHINA
| | - Xue Xu
- Peking University People's Hospital, 11 Xizhimen South Street, Xicheng District, Beijing, Beijing, 100044, CHINA
| | - Kai Li
- Institute of Zoology Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China, Chaoyang District, Beijing, 100101, CHINA
| | - Xia Li
- Institute of Zoology Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China, Chaoyang District, Beijing, 100101, CHINA
| | - Xin Liu
- Institute of Zoology Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China, Chaoyang District, Beijing, 100101, CHINA
| | - Shenglong Ding
- Beijing Tongren Hospital, 2 Chongwenmennei Dajie Dongcheng District, Beijing, Beijing, 100730, CHINA
| | - Shuo Wang
- Institute of Zoology Chinese Academy of Sciences, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, CHINA
| | - Jia Guo
- Institute of Zoology Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China, Chaoyang District, Beijing, 100101, CHINA
| | - Yukai Wang
- Institute of Zoology Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China, Chaoyang District, Beijing, 100101, CHINA
| | - Qi Gu
- Institute of Zoology Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District District, Beijing, 100101, CHINA
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103
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Cooper F, Tsakiridis A. Towards clinical applications of in vitro-derived axial progenitors. Dev Biol 2022; 489:110-117. [PMID: 35718236 DOI: 10.1016/j.ydbio.2022.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/28/2022] [Accepted: 06/14/2022] [Indexed: 11/19/2022]
Abstract
The production of the tissues that make up the mammalian embryonic trunk takes place in a head-tail direction, via the differentiation of posteriorly-located axial progenitor populations. These include bipotent neuromesodermal progenitors (NMPs), which generate both spinal cord neurectoderm and presomitic mesoderm, the precursor of the musculoskeleton. Over the past few years, a number of studies have described the derivation of NMP-like cells from mouse and human pluripotent stem cells (PSCs). In turn, these have greatly facilitated the establishment of PSC differentiation protocols aiming to give rise efficiently to posterior mesodermal and neural cell types, which have been particularly challenging to produce using previous approaches. Moreover, the advent of 3-dimensional-based culture systems incorporating distinct axial progenitor-derived cell lineages has opened new avenues toward the functional dissection of early patterning events and cell vs non-cell autonomous effects. Here, we provide a brief overview of the applications of these cell types in disease modelling and cell therapy and speculate on their potential uses in the future.
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Affiliation(s)
- Fay Cooper
- Centre for Stem Cell Biology, School of Bioscience, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom; Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Anestis Tsakiridis
- Centre for Stem Cell Biology, School of Bioscience, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom; Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom.
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104
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Signaling oscillations in embryonic development. Curr Top Dev Biol 2022; 149:341-372. [PMID: 35606060 DOI: 10.1016/bs.ctdb.2022.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Tight spatiotemporal control of cellular behavior and cell fate decisions is paramount to the formation of multicellular organisms during embryonic development. Intercellular communication via signaling pathways mediates this control. Interestingly, these signaling pathways are not static, but dynamic and change in activity over time. Signaling oscillations as a specific type of dynamics are found in various signaling pathways and model systems. Functions of oscillations include the regulation of periodic events or the transmission of information by encoding signals in the dynamic properties of a signaling pathway. For instance, signaling oscillations in neural or pancreatic progenitor cells modulate their proliferation and differentiation. Oscillations between neighboring cells can also be synchronized, leading to the emergence of waves traveling through the tissue. Such population-wide signaling oscillations regulate for example the consecutive segmentation of vertebrate embryos, a process called somitogenesis. Here, we outline our current understanding of signaling oscillations in embryonic development, how signaling oscillations are generated, how they are studied and how they contribute to the regulation of embryonic development.
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105
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Kim HJ, Booth G, Saunders L, Srivatsan S, McFaline-Figueroa JL, Trapnell C. Nuclear oligo hashing improves differential analysis of single-cell RNA-seq. Nat Commun 2022; 13:2666. [PMID: 35562344 PMCID: PMC9106741 DOI: 10.1038/s41467-022-30309-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/26/2022] [Indexed: 11/09/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) offers a high-resolution molecular view into complex tissues, but suffers from high levels of technical noise which frustrates efforts to compare the gene expression programs of different cell types. "Spike-in" RNA standards help control for technical variation in scRNA-seq, but using them with recently developed, ultra-scalable scRNA-seq methods based on combinatorial indexing is not feasible. Here, we describe a simple and cost-effective method for normalizing transcript counts and subtracting technical variability that improves differential expression analysis in scRNA-seq. The method affixes a ladder of synthetic single-stranded DNA oligos to each cell that appears in its RNA-seq library. With improved normalization we explore chemical perturbations with broad or highly specific effects on gene regulation, including RNA pol II elongation, histone deacetylation, and activation of the glucocorticoid receptor. Our methods reveal that inhibiting histone deacetylation prevents cells from executing their canonical program of changes following glucocorticoid stimulation.
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Affiliation(s)
- Hyeon-Jin Kim
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Greg Booth
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Lauren Saunders
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA. .,Brotman Baty Institute of Precision Medicine, Seattle, WA, 98195, USA. .,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, 98195, USA.
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106
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Shao Y, Fu J. Engineering multiscale structural orders for high-fidelity embryoids and organoids. Cell Stem Cell 2022; 29:722-743. [PMID: 35523138 PMCID: PMC9097334 DOI: 10.1016/j.stem.2022.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Embryoids and organoids hold great promise for human biology and medicine. Herein, we discuss conceptual and technological frameworks useful for developing high-fidelity embryoids and organoids that display tissue- and organ-level phenotypes and functions, which are critically needed for decoding developmental programs and improving translational applications. Through dissecting the layers of inputs controlling mammalian embryogenesis, we review recent progress in reconstructing multiscale structural orders in embryoids and organoids. Bioengineering tools useful for multiscale, multimodal structural engineering of tissue- and organ-level cellular organization and microenvironment are also discussed to present integrative, bioengineering-directed approaches to achieve next-generation, high-fidelity embryoids and organoids.
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Affiliation(s)
- Yue Shao
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China; State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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107
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Cermola F, Patriarca EJ, Minchiotti G. Generation of Gastruloids from Epiblast-Like Cells. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2490:197-204. [PMID: 35486247 DOI: 10.1007/978-1-0716-2281-0_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The different states of mouse pluripotency described so far rely on a combination of molecular, phenotypic, and functional analysis. Embryonic Stem cells (ESCs) aggregated in suspension culture are able to form 3D embryo-like structures called gastruloids that mimic features of the gastrulation process. Recent findings indicate that gastruloid formation efficiency decreases as pluripotency progresses from naïve to primed state, and suggest that gastruloids formation may represent a functional assay to discriminate different states of mouse pluripotency.Here we describe a method to generate gastruloids from Epiblast-like cells (EpiLCs), which are transiently induced from ESCs by Activin A and bFGF and represent an intermediate state from naïve ESCs to primed Epiblast Stem cells.
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Affiliation(s)
- Federica Cermola
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, Naples, Italy
| | - Eduardo J Patriarca
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, Naples, Italy
| | - Gabriella Minchiotti
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati Traverso", CNR, Naples, Italy.
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108
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Tension hones body segmentation around the clock. Nature 2022; 605:432-433. [PMID: 35478017 DOI: 10.1038/d41586-022-00840-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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109
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Olmsted ZT, Paluh JL. A Combined Human Gastruloid Model of Cardiogenesis and Neurogenesis. iScience 2022; 25:104486. [PMID: 35721464 PMCID: PMC9198845 DOI: 10.1016/j.isci.2022.104486] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 03/28/2022] [Accepted: 05/20/2022] [Indexed: 11/28/2022] Open
Abstract
Multi-lineage development from gastruloids is enabling unprecedented opportunities to model and study human embryonic processes and is expected to accelerate ex vivo strategies in organ development. Reproducing human cardiogenesis with neurogenesis in a multi-lineage context remains challenging, requiring spatiotemporal input of paracrine and mechanical cues. Here we extend elongating multi-lineage organized (EMLO) gastruloids to include cardiogenesis (EMLOC) and describe interconnected neuro-cardiac lineages in a single gastruloid model. Contractile EMLOCs recapitulate numerous interlinked developmental features including heart tube formation and specialization, cardiomyocyte differentiation and remodeling phases, epicardium, ventricular wall morphogenesis, chamber-like structures and formation of a putative outflow tract. The EMLOC cardiac region, which originates anterior to gut tube primordium, is progressively populated by neurons in a spatial pattern mirroring the known distribution of neurons in the innervated human heart. This human EMLOC model represents a multi-lineage advancement for the study of coincident neurogenesis and cardiogenesis. A trunk-biased microenvironment primed for cardiogenesis Gastruloid-derived spatiotemporal features of cardiogenesis Neurogenesis coupled with neuronal population of cardiac regions Neuro-cardiac multi-lineage, multi-tissue linked developmental model
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Affiliation(s)
- Zachary T. Olmsted
- State University of New York Polytechnic Institute, College of Nanoscale Science and Engineering, Nanobioscience, Nanofab East, 257 Fuller Road, Albany, NY 12203, USA
| | - Janet L. Paluh
- State University of New York Polytechnic Institute, College of Nanoscale Science and Engineering, Nanobioscience, Nanofab East, 257 Fuller Road, Albany, NY 12203, USA
- Corresponding author
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110
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Sanaki-Matsumiya M, Matsuda M, Gritti N, Nakaki F, Sharpe J, Trivedi V, Ebisuya M. Periodic formation of epithelial somites from human pluripotent stem cells. Nat Commun 2022; 13:2325. [PMID: 35484123 PMCID: PMC9050736 DOI: 10.1038/s41467-022-29967-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 04/11/2022] [Indexed: 12/19/2022] Open
Abstract
During embryonic development, epithelial cell blocks called somites are periodically formed according to the segmentation clock, becoming the foundation for the segmental pattern of the vertebral column. The process of somitogenesis has recently been recapitulated with murine and human pluripotent stem cells. However, an in vitro model for human somitogenesis coupled with the segmentation clock and epithelialization is still missing. Here, we report the generation of human somitoids, organoids that periodically form pairs of epithelial somite-like structures. Somitoids display clear oscillations of the segmentation clock that coincide with the segmentation of the presomitic mesoderm. The resulting somites show anterior-posterior and apical-basal polarities. Matrigel is essential for epithelialization but dispensable for the differentiation into somite cells. The size of somites is rather constant, irrespective of the initial cell number. The amount of WNT signaling instructs the proportion of mesodermal lineages in somitoids. Somitoids provide a novel platform to study human somitogenesis. Somitogenesis has been well characterized in model organisms, resulting in detailed description of the somite segmentation clock. Here they generate somitogenic organoids from human pluripotent stem cells that recapitulate somitogenesis, periodic segmentation, and proper polarity.
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Affiliation(s)
| | - Mitsuhiro Matsuda
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
| | - Nicola Gritti
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
| | - Fumio Nakaki
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
| | - James Sharpe
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
| | - Vikas Trivedi
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain.,EMBL Heidelberg, Developmental Biology Unit, Heidelberg, Germany
| | - Miki Ebisuya
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain.
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111
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Gordeeva O, Gordeev A, Erokhov P. Archetypal Architecture Construction, Patterning, and Scaling Invariance in a 3D Embryoid Body Differentiation Model. Front Cell Dev Biol 2022; 10:852071. [PMID: 35573693 PMCID: PMC9091174 DOI: 10.3389/fcell.2022.852071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Self-organized patterning and architecture construction studying is a priority goal for fundamental developmental and stem cell biology. To study the spatiotemporal patterning of pluripotent stem cells of different origins, we developed a three-dimensional embryoid body (EB) differentiation model quantifying volumetric parameters and investigated how the EB architecture formation, patterning, and scaling depend on the proliferation, cavitation, and differentiation dynamics, external environmental factors, and cell numbers. We identified three similar spatiotemporal patterns in the EB architectures, regardless of cell origin, which constitute the EB archetype and mimick the pre-gastrulation embryonic patterns. We found that the EB patterning depends strongly on cellular positional information, culture media factor/morphogen content, and free diffusion from the external environment and between EB cell layers. However, the EB archetype formation is independent of the EB size and initial cell numbers forming EBs; therefore, it is capable of scaling invariance and patterning regulation. Our findings indicate that the underlying principles of reaction-diffusion and positional information concepts can serve as the basis for EB architecture construction, patterning, and scaling. Thus, the 3D EB differentiation model represents a highly reproducible and reliable platform for experimental and theoretical research on developmental and stem cell biology issues.
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Affiliation(s)
- Olga Gordeeva
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Olga Gordeeva,
| | - Andrey Gordeev
- National Institutes of Health’s National Library of Medicine, Bethesda, MD, United States
| | - Pavel Erokhov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
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112
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Rajam SM, Varghese PC, Dutta D. Histone Chaperones as Cardinal Players in Development. Front Cell Dev Biol 2022; 10:767773. [PMID: 35445016 PMCID: PMC9014011 DOI: 10.3389/fcell.2022.767773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/03/2022] [Indexed: 11/25/2022] Open
Abstract
Dynamicity and flexibility of the chromatin landscape are critical for most of the DNA-dependent processes to occur. This higher-order packaging of the eukaryotic genome into the chromatin is mediated by histones and associated non-histone proteins that determine the states of chromatin. Histone chaperones- “the guardian of genome stability and epigenetic information” controls the chromatin accessibility by escorting the nucleosomal and non-nucleosomal histones as well as their variants. This distinct group of molecules is involved in all facets of histone metabolism. The selectivity and specificity of histone chaperones to the histones determine the maintenance of the chromatin in an open or closed state. This review highlights the functional implication of the network of histone chaperones in shaping the chromatin function in the development of an organism. Seminal studies have reported embryonic lethality at different stages of embryogenesis upon perturbation of some of the chaperones, suggesting their essentiality in development. We hereby epitomize facts and functions that emphasize the relevance of histone chaperones in orchestrating different embryonic developmental stages starting from gametogenesis to organogenesis in multicellular organisms.
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Affiliation(s)
- Sruthy Manuraj Rajam
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India.,Manipal Academy of Higher Education, Manipal, India
| | - Pallavi Chinnu Varghese
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India.,Manipal Academy of Higher Education, Manipal, India
| | - Debasree Dutta
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, India
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113
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Jiang S, Feng W, Chang C, Li G. Modeling Human Heart Development and Congenital Defects Using Organoids: How Close Are We? J Cardiovasc Dev Dis 2022; 9:jcdd9050125. [PMID: 35621836 PMCID: PMC9145739 DOI: 10.3390/jcdd9050125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 02/01/2023] Open
Abstract
The emergence of human-induced Pluripotent Stem Cells (hiPSCs) has dramatically improved our understanding of human developmental processes under normal and diseased conditions. The hiPSCs have been differentiated into various tissue-specific cells in vitro, and the advancement in three-dimensional (3D) culture has provided a possibility to generate those cells in an in vivo-like environment. Tissues with 3D structures can be generated using different approaches such as self-assembled organoids and tissue-engineering methods, such as bioprinting. We are interested in studying the self-assembled organoids differentiated from hiPSCs, as they have the potential to recapitulate the in vivo developmental process and be used to model human development and congenital defects. Organoids of tissues such as those of the intestine and brain were developed many years ago, but heart organoids were not reported until recently. In this review, we will compare the heart organoids with the in vivo hearts to understand the anatomical structures we still lack in the organoids. Specifically, we will compare the development of main heart structures, focusing on their marker genes and regulatory signaling pathways.
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114
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Hashmi A, Tlili S, Perrin P, Lowndes M, Peradziryi H, Brickman JM, Martínez Arias A, Lenne PF. Cell-state transitions and collective cell movement generate an endoderm-like region in gastruloids. eLife 2022; 11:59371. [PMID: 35404233 PMCID: PMC9033300 DOI: 10.7554/elife.59371] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 04/08/2022] [Indexed: 12/04/2022] Open
Abstract
Shaping the animal body plan is a complex process that involves the spatial organization and patterning of the different germ layers. Recent advances in live imaging have started to unravel the cellular choreography underlying this process in mammals, however, the sequence of events transforming an unpatterned cell ensemble into structured territories is largely unknown. Here, using gastruloids –3D aggregates of mouse embryonic stem cells- we study the formation of one of the three germ layers, the endoderm. We show that the endoderm is generated from an epiblast-like homogeneous state by a three-step mechanism: (i) a loss of E-cadherin mediated contacts in parts of the aggregate leading to the appearance of islands of E-cadherin expressing cells surrounded by cells devoid of E-cadherin, (ii) a separation of these two populations with islands of E-cadherin expressing cells flowing toward the aggregate tip, and (iii) their differentiation into an endoderm population. During the flow, the islands of E-cadherin expressing cells are surrounded by cells expressing T-Brachyury, reminiscent of the process occurring at the primitive streak. Consistent with recent in vivo observations, the endoderm formation in the gastruloids does not require an epithelial-to-mesenchymal transition, but rather a maintenance of an epithelial state for a subset of cells coupled with fragmentation of E-cadherin contacts in the vicinity, and a sorting process. Our data emphasize the role of signaling and tissue flows in the establishment of the body plan.
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Affiliation(s)
- Ali Hashmi
- IBDM, Aix Marseille University, CNRS, Marseille, France
| | - Sham Tlili
- IBDM, Aix Marseille University, CNRS, Marseille, France
| | - Pierre Perrin
- IBDM, Aix Marseille University, CNRS, Marseille, France
| | - Molly Lowndes
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Hanna Peradziryi
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
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115
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Gao F, Li C, Danopoulos S, Al Alam D, Peinado N, Webster S, Borok Z, Kohbodi GA, Bellusci S, Minoo P. Hedgehog-responsive PDGFRa(+) fibroblasts maintain a unique pool of alveolar epithelial progenitor cells during alveologenesis. Cell Rep 2022; 39:110608. [PMID: 35385750 PMCID: PMC9199394 DOI: 10.1016/j.celrep.2022.110608] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 12/06/2021] [Accepted: 03/11/2022] [Indexed: 01/08/2023] Open
Abstract
The lung alveolus is lined with alveolar type 1 (AT1) and type 2 (AT2) epithelial cells. During alveologenesis, increasing demand associated with expanding alveolar numbers is met by proliferating progenitor AT2s (pAT2). Little information exists regarding the identity of this population and their niche microenvironment. We show that during alveologenesis, Hedgehog-responsive PDGFRa(+) progenitors (also known as SCMFs) are a source of secreted trophic molecules that maintain a unique pAT2 population. SCMFs are in turn maintained by TGFβ signaling. Compound inactivation of Alk5 TβR2 in SCMFs reduced their numbers and depleted the pAT2 pool without impacting differentiation of daughter cells. In lungs of preterm infants who died with bronchopulmonary dysplasia, PDGFRa is reduced and the number of proliferative AT2s is diminished, indicating that an evolutionarily conserved mechanism governs pAT2 behavior during alveologenesis. SCMFs are a transient cell population, active only during alveologenesis, making them a unique stage-specific niche mesodermal cell type in mammalian organs.
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Affiliation(s)
- Feng Gao
- Division of Neonatology, Department of Pediatrics, LAC+USC Medical Center and Childrens Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Changgong Li
- Division of Neonatology, Department of Pediatrics, LAC+USC Medical Center and Childrens Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Soula Danopoulos
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Denise Al Alam
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Neil Peinado
- Division of Neonatology, Department of Pediatrics, LAC+USC Medical Center and Childrens Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Sha Webster
- Division of Neonatology, Department of Pediatrics, LAC+USC Medical Center and Childrens Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Zea Borok
- Hastings Center for Pulmonary Research, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA; Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego School of Medicine, San Diego, CA 92093, USA
| | - GoleNaz Adeli Kohbodi
- Division of Neonatology, Department of Pediatrics, LAC+USC Medical Center and Childrens Hospital Los Angeles, Los Angeles, CA 90033, USA
| | - Saverio Bellusci
- Division of Neonatology, Department of Pediatrics, LAC+USC Medical Center and Childrens Hospital Los Angeles, Los Angeles, CA 90033, USA; Universities of Giessen and Marburg Lung Center (UGMLC), Justus-Liebig-University Giessen, German Center for Lung Research (DZL), 35390 Giessen, Germany
| | - Parviz Minoo
- Division of Neonatology, Department of Pediatrics, LAC+USC Medical Center and Childrens Hospital Los Angeles, Los Angeles, CA 90033, USA; Hastings Center for Pulmonary Research, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA.
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116
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Clinical and translational values of spatial transcriptomics. Signal Transduct Target Ther 2022; 7:111. [PMID: 35365599 PMCID: PMC8972902 DOI: 10.1038/s41392-022-00960-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
The combination of spatial transcriptomics (ST) and single cell RNA sequencing (scRNA-seq) acts as a pivotal component to bridge the pathological phenomes of human tissues with molecular alterations, defining in situ intercellular molecular communications and knowledge on spatiotemporal molecular medicine. The present article overviews the development of ST and aims to evaluate clinical and translational values for understanding molecular pathogenesis and uncovering disease-specific biomarkers. We compare the advantages and disadvantages of sequencing- and imaging-based technologies and highlight opportunities and challenges of ST. We also describe the bioinformatics tools necessary on dissecting spatial patterns of gene expression and cellular interactions and the potential applications of ST in human diseases for clinical practice as one of important issues in clinical and translational medicine, including neurology, embryo development, oncology, and inflammation. Thus, clear clinical objectives, designs, optimizations of sampling procedure and protocol, repeatability of ST, as well as simplifications of analysis and interpretation are the key to translate ST from bench to clinic.
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117
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Gsell S, Merkel M. Phase separation dynamics in deformable droplets. SOFT MATTER 2022; 18:2672-2683. [PMID: 35311835 DOI: 10.1039/d1sm01647d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phase separation can drive spatial organization of multicomponent mixtures. For instance in developing animal embryos, effective phase separation descriptions have been used to account for the spatial organization of different tissue types. Similarly, separation of different tissue types is also observed in stem cell aggregates, where the emergence of a polar organization can mimic early embryonic axis formation. Here, we describe such aggregates as deformable two-phase fluid droplets, which are suspended in a fluid environment (third phase). Using hybrid finite-volume Lattice-Boltzmann simulations, we numerically explore the out-of-equilibrium routes that can lead to the polar equilibrium state of such a droplet. We focus on the interplay between spinodal decomposition and advection with hydrodynamic flows driven by interface tensions, which we characterize by a Peclet number Pe. Consistent with previous work, for large Pe the coarsening process is generally accelerated. However, for intermediate Pe we observe long-lived, strongly elongated droplets, where both phases form an alternating stripe pattern. We show that these "croissant" states are close to mechanical equilibrium and coarsen only slowly through diffusive fluxes in an Ostwald-ripening-like process. Finally, we show that a surface tension asymmetry between both droplet phases leads to transient, rotationally symmetric states whose resolution leads to flows reminiscent of Marangoni flows. Our work highlights the importance of advection for the phase separation process in finite, deformable systems.
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Affiliation(s)
- Simon Gsell
- Aix Marseille Univ, Université de Toulon, CNRS, CPT (UMR 7332), Turing Centre for Living Systems, Marseille, France.
- Aix Marseille Univ, CNRS, IBDM (UMR 7288), Turing Centre for Living Systems, Marseille, France
| | - Matthias Merkel
- Aix Marseille Univ, Université de Toulon, CNRS, CPT (UMR 7332), Turing Centre for Living Systems, Marseille, France.
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118
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Quan Y, Wang X, Li L. In vitro investigation of mammalian peri-implantation embryogenesis†. Biol Reprod 2022; 107:205-211. [PMID: 35294001 DOI: 10.1093/biolre/ioac055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/14/2022] Open
Abstract
The embryos attach and invade into the uterus and establish the connection with their mother in peri-implantation development. During this period, the pluripotent epiblast cells of embryo undergo symmetry breaking, cell lineage allocation, and morphogenetic remodeling, accompanying with the dramatic changes of transcriptome, epigenome, and signal pathways, to prepare a state for their differentiation and gastrulation. The progresses in mouse genetics and stem cell biology have largely advanced the knowledge of these transformations which are largely hindered by the hard accessibility of natural embryos. To gain insight into mammalian peri-implantation development, great efforts have been made in the field. Recently, the advances in the prolonged in vitro culture of blastocysts, the derivation of multiple pluripotent stem cells, as well as the construction of stem cell-based embryo-like models have opened novel avenues to investigate peri-implantation development in mammals, especially for the humans. Combining with other emerging new technologies, these new models will substantially promote the comprehension of mammalian peri-implantation development, accelerating the progress of reproductive and regenerative medicine.
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Affiliation(s)
- Yujun Quan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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119
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Abstract
Embryonic cells grow in environments that provide a plethora of physical cues, including mechanical forces that shape the development of the entire embryo. Despite their prevalence, the role of these forces in embryonic development and their integration with chemical signals have been mostly neglected, and scrutiny in modern molecular embryology tilted, instead, towards the dissection of molecular pathways involved in cell fate determination and patterning. It is now possible to investigate how mechanical signals induce downstream genetic regulatory networks to regulate key developmental processes in the embryo. Here, we review the insights into mechanical control of early vertebrate development, including the role of forces in tissue patterning and embryonic axis formation. We also highlight recent in vitro approaches using individual embryonic stem cells and self-organizing multicellular models of human embryos, which have been instrumental in expanding our understanding of how mechanics tune cell fate and cellular rearrangements during human embryonic development.
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120
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Needham J, Metzis V. Heads or tails: Making the spinal cord. Dev Biol 2022; 485:80-92. [DOI: 10.1016/j.ydbio.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/15/2021] [Accepted: 03/02/2022] [Indexed: 12/14/2022]
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121
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Qin HC, Luo ZW, Zhu YL. Physical energy-based ultrasound shifts M1 macrophage differentiation towards M2 state. World J Stem Cells 2022; 14:214-218. [PMID: 35432733 PMCID: PMC8963378 DOI: 10.4252/wjsc.v14.i2.214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/12/2021] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Recently, we read with interest the article entitled “Unveiling the Morphogenetic Code: A New Path at the Intersection of Physical Energies and Chemical Signaling”. In this paper, the investigation into the systematic and comprehensive bio-effects of physical energies prompted us to reflect on our research. We believe that ultrasound, which possesses a special physical energy, also has a certain positive regulatory effect on macrophages, and we have already obtained some preliminary research results that support our hypothesis.
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Affiliation(s)
- Hao-Cheng Qin
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zhi-Wen Luo
- Department of Sports Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Yu-Lian Zhu
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
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122
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Barhouse PS, Andrade MJ, Smith Q. Home Away From Home: Bioengineering Advancements to Mimic the Developmental and Adult Stem Cell Niche. FRONTIERS IN CHEMICAL ENGINEERING 2022. [DOI: 10.3389/fceng.2022.832754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The inherent self-organizing capacity of pluripotent and adult stem cell populations has advanced our fundamental understanding of processes that drive human development, homeostasis, regeneration, and disease progression. Translating these principles into in vitro model systems has been achieved with the advent of organoid technology, driving innovation to harness patient-specific, cell-laden regenerative constructs that can be engineered to augment or replace diseased tissue. While developmental organization and regenerative adult stem cell niches are tightly regulated in vivo, in vitro analogs lack defined architecture and presentation of physicochemical cues, leading to the unhindered arrangement of mini-tissues that lack complete physiological mimicry. This review aims to highlight the recent integrative engineering approaches that elicit spatio-temporal control of the extracellular niche to direct the structural and functional maturation of pluripotent and adult stem cell derivatives. While the advances presented here leverage multi-pronged strategies ranging from synthetic biology to microfabrication technologies, the methods converge on recreating the biochemical and biophysical milieu of the native tissue to be modeled or regenerated.
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123
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Essay the (unusual) heuristic value of Hox gene clusters; a matter of time? Dev Biol 2022; 484:75-87. [PMID: 35182536 DOI: 10.1016/j.ydbio.2022.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/22/2022]
Abstract
Ever since their first report in 1984, Antennapedia-type homeobox (Hox) genes have been involved in such a series of interesting observations, in particular due to their conserved clustered organization between vertebrates and arthropods, that one may legitimately wonder about the origin of this heuristic value. In this essay, I first consider different examples where Hox gene clusters have been instrumental in providing conceptual advances, taken from various fields of research and mostly involving vertebrate embryos. These examples touch upon our understanding of genomic evolution, the revisiting of 19th century views on the relationships between development and evolution and the building of a new framework to understand long-range and pleiotropic gene regulation during development. I then discuss whether the high value of the Hox gene family, when considered as an epistemic object, is related to its clustered structure (and the absence thereof in some animal species) and, if so, what is it in such particular genetic oddities that made them so generous in providing the scientific community with interesting information.
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124
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Spatial components of molecular tissue biology. Nat Biotechnol 2022; 40:308-318. [PMID: 35132261 DOI: 10.1038/s41587-021-01182-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 12/03/2021] [Indexed: 02/06/2023]
Abstract
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly evolving, making it possible to comprehensively characterize cells and tissues in health and disease. To maximize the biological insights obtained using these techniques, it is critical to both clearly articulate the key biological questions in spatial analysis of tissues and develop the requisite computational tools to address them. Developers of analytical tools need to decide on the intrinsic molecular features of each cell that need to be considered, and how cell shape and morphological features are incorporated into the analysis. Also, optimal ways to compare different tissue samples at various length scales are still being sought. Grouping these biological problems and related computational algorithms into classes across length scales, thus characterizing common issues that need to be addressed, will facilitate further progress in spatial transcriptomics and proteomics.
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125
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Pourquié O. A brief history of the segmentation clock. Dev Biol 2022; 485:24-36. [DOI: 10.1016/j.ydbio.2022.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022]
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126
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Shaping axial identity during human pluripotent stem cell differentiation to neural crest cells. Biochem Soc Trans 2022; 50:499-511. [PMID: 35015077 PMCID: PMC9022984 DOI: 10.1042/bst20211152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/07/2021] [Accepted: 12/21/2021] [Indexed: 12/18/2022]
Abstract
The neural crest (NC) is a multipotent cell population which can give rise to a vast array of derivatives including neurons and glia of the peripheral nervous system, cartilage, cardiac smooth muscle, melanocytes and sympathoadrenal cells. An attractive strategy to model human NC development and associated birth defects as well as produce clinically relevant cell populations for regenerative medicine applications involves the in vitro generation of NC from human pluripotent stem cells (hPSCs). However, in vivo, the potential of NC cells to generate distinct cell types is determined by their position along the anteroposterior (A–P) axis and, therefore the axial identity of hPSC-derived NC cells is an important aspect to consider. Recent advances in understanding the developmental origins of NC and the signalling pathways involved in its specification have aided the in vitro generation of human NC cells which are representative of various A–P positions. Here, we explore recent advances in methodologies of in vitro NC specification and axis patterning using hPSCs.
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127
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Umemura Y, Koike N, Tsuchiya Y, Watanabe H, Kondoh G, Kageyama R, Yagita K. Circadian key component CLOCK/BMAL1 interferes with segmentation clock in mouse embryonic organoids. Proc Natl Acad Sci U S A 2022; 119:e2114083119. [PMID: 34930826 PMCID: PMC8746294 DOI: 10.1073/pnas.2114083119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2021] [Indexed: 11/18/2022] Open
Abstract
In mammals, circadian clocks are strictly suppressed during early embryonic stages, as well as in pluripotent stem cells, by the lack of CLOCK/BMAL1-mediated circadian feedback loops. During ontogenesis, the innate circadian clocks emerge gradually at a late developmental stage, and with these, the circadian temporal order is invested in each cell level throughout a body. Meanwhile, in the early developmental stage, a segmented body plan is essential for an intact developmental process, and somitogenesis is controlled by another cell-autonomous oscillator, the segmentation clock, in the posterior presomitic mesoderm (PSM). In the present study, focusing upon the interaction between circadian key components and the segmentation clock, we investigated the effect of the CLOCK/BMAL1 on the segmentation clock Hes7 oscillation, revealing that the expression of functional CLOCK/BMAL1 severely interferes with the ultradian rhythm of segmentation clock in induced PSM and gastruloids. RNA sequencing analysis implied that the premature expression of CLOCK/BMAL1 affects the Hes7 transcription and its regulatory pathways. These results suggest that the suppression of CLOCK/BMAL1-mediated transcriptional regulation during the somitogenesis may be inevitable for intact mammalian development.
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Affiliation(s)
- Yasuhiro Umemura
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Nobuya Koike
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Yoshiki Tsuchiya
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Hitomi Watanabe
- Laboratory of Integrative Biological Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Gen Kondoh
- Laboratory of Integrative Biological Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Ryoichiro Kageyama
- Laboratory of Growth Regulation System, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan;
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128
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Bérenger-Currias NM, Mircea M, Adegeest E, van den Berg PR, Feliksik M, Hochane M, Idema T, Tans SJ, Semrau S. A gastruloid model of the interaction between embryonic and extra-embryonic cell types. J Tissue Eng 2022; 13:20417314221103042. [PMID: 35707767 PMCID: PMC9189523 DOI: 10.1177/20417314221103042] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/10/2022] [Indexed: 12/11/2022] Open
Abstract
Stem-cell derived in vitro systems, such as organoids or embryoids, hold great
potential for modeling in vivo development. Full control over their initial
composition, scalability, and easily measurable dynamics make those systems
useful for studying specific developmental processes in isolation. Here we
report the formation of gastruloids consisting of mouse embryonic stem cells
(mESCs) and extraembryonic endoderm (XEN) cells. These XEN-enhanced gastruloids
(XEGs) exhibit the formation of neural epithelia, which are absent in
gastruloids derived from mESCs only. By single-cell RNA-seq, imaging, and
differentiation experiments, we demonstrate the neural characteristics of the
epithelial tissue. We further show that the mESCs induce the differentiation of
the XEN cells to a visceral endoderm-like state. Finally, we demonstrate that
local inhibition of WNT signaling and production of a basement membrane by the
XEN cells underlie the formation of the neuroepithelial tissue. In summary, we
establish XEGs to explore heterotypic cellular interactions and their
developmental consequences in vitro.
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Affiliation(s)
- Noémie Mlp Bérenger-Currias
- Department of Physics, Leiden University, Leiden, The Netherlands.,Delft University of Technology, Department of Bionanoscience, Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Maria Mircea
- Department of Physics, Leiden University, Leiden, The Netherlands
| | - Esmée Adegeest
- Department of Physics, Leiden University, Leiden, The Netherlands
| | | | - Marleen Feliksik
- Department of Physics, Leiden University, Leiden, The Netherlands
| | - Mazène Hochane
- Department of Physics, Leiden University, Leiden, The Netherlands
| | - Timon Idema
- Delft University of Technology, Department of Bionanoscience, Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Sander J Tans
- Delft University of Technology, Department of Bionanoscience, Kavli Institute of Nanoscience, Delft, The Netherlands.,AMOLF, Amsterdam, The Netherlands
| | - Stefan Semrau
- Department of Physics, Leiden University, Leiden, The Netherlands
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129
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Lohoff T, Ghazanfar S, Missarova A, Koulena N, Pierson N, Griffiths JA, Bardot ES, Eng CHL, Tyser RCV, Argelaguet R, Guibentif C, Srinivas S, Briscoe J, Simons BD, Hadjantonakis AK, Göttgens B, Reik W, Nichols J, Cai L, Marioni JC. Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. Nat Biotechnol 2022; 40:74-85. [PMID: 34489600 PMCID: PMC8763645 DOI: 10.1038/s41587-021-01006-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023]
Abstract
Molecular profiling of single cells has advanced our knowledge of the molecular basis of development. However, current approaches mostly rely on dissociating cells from tissues, thereby losing the crucial spatial context of regulatory processes. Here, we apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes in tissue sections of mouse embryos at the 8-12 somite stage. By integrating spatial context and multiplexed transcriptional measurements with two single-cell transcriptome atlases, we characterize cell types across the embryo and demonstrate that spatially resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain-hindbrain boundary (MHB) and the developing gut tube. We uncover axes of cell differentiation that are not apparent from single-cell RNA-sequencing (scRNA-seq) data, such as early dorsal-ventral separation of esophageal and tracheal progenitor populations in the gut tube. Our method provides an approach for studying cell fate decisions in complex tissues and development.
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Affiliation(s)
- T Lohoff
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - S Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - A Missarova
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - N Koulena
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - N Pierson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - J A Griffiths
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Genomics Plc, Cambridge, UK
| | - E S Bardot
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - C-H L Eng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - R C V Tyser
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - R Argelaguet
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - C Guibentif
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Sahlgrenska Center for Cancer Research, Department of Microbiology and Immunology, University of Gothenburg, Gothenburg, Sweden
| | - S Srinivas
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - J Briscoe
- The Francis Crick Institute, London, UK
| | - B D Simons
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- The Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - A-K Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - B Göttgens
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - W Reik
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Epigenetics Programme, Babraham Institute, Cambridge, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
| | - J Nichols
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - L Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - J C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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130
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Filimonow K, de la Fuente R. Specification and role of extraembryonic endoderm lineages in the periimplantation mouse embryo. Theriogenology 2021; 180:189-206. [PMID: 34998083 DOI: 10.1016/j.theriogenology.2021.12.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022]
Abstract
During mammalian embryo development, the correct formation of the first extraembryonic endoderm lineages is fundamental for successful development. In the periimplantation blastocyst, the primitive endoderm (PrE) is formed, which gives rise to the parietal endoderm (PE) and visceral endoderm (VE) during further developmental stages. These PrE-derived lineages show significant differences in both their formation and roles. Whereas differentiation of the PE as a migratory lineage has been suggested to represent the first epithelial-to-mesenchymal transition (EMT) in development, organisation of the epithelial VE is of utmost importance for the correct axis definition and patterning of the embryo. Despite sharing a common origin, the striking differences between the VE and PE are indicative of their distinct roles in early development. However, there is a significant disparity in the current knowledge of each lineage, which reflects the need for a deeper understanding of their respective specification processes. In this review, we will discuss the origin and maturation of the PrE, PE, and VE during the periimplantation period using the mouse model as an example. Additionally, we consider the latest findings regarding the role of the PrE-derived lineages and early embryo morphogenesis, as obtained from the most recent in vitro models.
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Affiliation(s)
- Katarzyna Filimonow
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Jastrzębiec, Poland.
| | - Roberto de la Fuente
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Jastrzębiec, Poland.
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131
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Isakova A, Neff N, Quake SR. Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states. Proc Natl Acad Sci U S A 2021; 118:e2113568118. [PMID: 34911763 PMCID: PMC8713755 DOI: 10.1073/pnas.2113568118] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2021] [Indexed: 12/22/2022] Open
Abstract
The ability to interrogate total RNA content of single cells would enable better mapping of the transcriptional logic behind emerging cell types and states. However, current single-cell RNA-sequencing (RNA-seq) methods are unable to simultaneously monitor all forms of RNA transcripts at the single-cell level, and thus deliver only a partial snapshot of the cellular RNAome. Here we describe Smart-seq-total, a method capable of assaying a broad spectrum of coding and noncoding RNA from a single cell. Smart-seq-total does not require splitting the RNA content of a cell and allows the incorporation of unique molecular identifiers into short and long RNA molecules for absolute quantification. It outperforms current poly(A)-independent total RNA-seq protocols by capturing transcripts of a broad size range, thus enabling simultaneous analysis of protein-coding, long-noncoding, microRNA, and other noncoding RNA transcripts from single cells. We used Smart-seq-total to analyze the total RNAome of human primary fibroblasts, HEK293T, and MCF7 cells, as well as that of induced murine embryonic stem cells differentiated into embryoid bodies. By analyzing the coexpression patterns of both noncoding RNA and mRNA from the same cell, we were able to discover new roles of noncoding RNA throughout essential processes, such as cell cycle and lineage commitment during embryonic development. Moreover, we show that independent classes of short-noncoding RNA can be used to determine cell-type identity.
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Affiliation(s)
- Alina Isakova
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA 94305;
- Chan Zuckerberg Biohub, San Francisco, CA 94158
- Department of Applied Physics, Stanford University, Stanford, CA 94305
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132
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133
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Veenvliet JV, Lenne PF, Turner DA, Nachman I, Trivedi V. Sculpting with stem cells: how models of embryo development take shape. Development 2021; 148:dev192914. [PMID: 34908102 PMCID: PMC8722391 DOI: 10.1242/dev.192914] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During embryogenesis, organisms acquire their shape given boundary conditions that impose geometrical, mechanical and biochemical constraints. A detailed integrative understanding how these morphogenetic information modules pattern and shape the mammalian embryo is still lacking, mostly owing to the inaccessibility of the embryo in vivo for direct observation and manipulation. These impediments are circumvented by the developmental engineering of embryo-like structures (stembryos) from pluripotent stem cells that are easy to access, track, manipulate and scale. Here, we explain how unlocking distinct levels of embryo-like architecture through controlled modulations of the cellular environment enables the identification of minimal sets of mechanical and biochemical inputs necessary to pattern and shape the mammalian embryo. We detail how this can be complemented with precise measurements and manipulations of tissue biochemistry, mechanics and geometry across spatial and temporal scales to provide insights into the mechanochemical feedback loops governing embryo morphogenesis. Finally, we discuss how, even in the absence of active manipulations, stembryos display intrinsic phenotypic variability that can be leveraged to define the constraints that ensure reproducible morphogenesis in vivo.
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Affiliation(s)
- Jesse V. Veenvliet
- Stembryogenesis Lab, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany
| | - Pierre-François Lenne
- Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, 13288, Marseille, France
| | - David A. Turner
- Institute of Life Course and Medical Sciences, William Henry Duncan Building, University of Liverpool, Liverpool, L7 8TX, UK
| | - Iftach Nachman
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Vikas Trivedi
- European Molecular Biology Laboratories (EMBL), Barcelona, 08003, Spain
- EMBL Heidelberg, Developmental Biology Unit, 69117, Heidelberg, Germany
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134
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Abstract
Primordial germ cells (PGCs) form early in embryo development and are crucial precursors to functioning gamete cells. Considerable research has focussed on identifying the transcriptional characteristics and signalling pathway requirements that confer PGC specification and development, enabling the derivation of PGC-like cells (PGCLCs) in vitro using specific signalling cocktails. However, full maturation to germ cells still relies on co-culture with supporting cell types, implicating an additional requirement for cellular- and tissue-level regulation. Here, we discuss the experimental evidence that highlights the nature of intercellular interactions between PGCs and neighbouring cell populations during mouse PGC development. We posit that the role that tissue interactions play on PGCs is not limited solely to signalling-based induction but extends to coordination of development by robust regulation of the proportions and position of the cells and tissues within the embryo, which is crucial for functional germ cell maturation. Such tissue co-development provides a dynamic, contextual niche for PGC development. We argue that there is evidence for a clear role for inter-tissue dependence of mouse PGCs, with potential implications for generating mammalian PGCLCs in vitro.
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Affiliation(s)
- Christopher B Cooke
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.,Abcam Plc, Discovery Drive, Cambridge Biomedical Campus, Cambridge, CB2 0AX, UK.,The Francis Crick Institute, 1 Midland Road, Somers Town, London, NW1 1AT, UK
| | - Naomi Moris
- The Francis Crick Institute, 1 Midland Road, Somers Town, London, NW1 1AT, UK
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135
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Loh CH, van Genesen S, Perino M, Bark MR, Veenstra GJC. Loss of PRC2 subunits primes lineage choice during exit of pluripotency. Nat Commun 2021; 12:6985. [PMID: 34848733 PMCID: PMC8632979 DOI: 10.1038/s41467-021-27314-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 11/09/2021] [Indexed: 12/11/2022] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) is crucial for the coordinated expression of genes during early embryonic development, catalyzing histone H3 lysine 27 trimethylation. Two distinct PRC2 complexes, PRC2.1 and PRC2.2, contain respectively MTF2 and JARID2 in embryonic stem cells (ESCs). In this study, we explored their roles in lineage specification and commitment, using single-cell transcriptomics and mouse embryoid bodies derived from Mtf2 and Jarid2 null ESCs. We observe that the loss of Mtf2 results in enhanced and faster differentiation towards cell fates from all germ layers, while the Jarid2 null cells are predominantly directed towards early differentiating precursors, with reduced efficiency towards mesendodermal lineages. These effects are caused by derepression of developmental regulators that are poised for activation in pluripotent cells and gain H3K4me3 at their promoters in the absence of PRC2 repression. Upon lineage commitment, the differentiation trajectories are relatively similar to those of wild-type cells. Together, our results uncover a major role for MTF2-containing PRC2.1 in balancing poised lineage-specific gene activation, whereas the contribution of JARID2-containing PRC2 is more selective in nature compared to MTF2. These data explain how PRC2 imposes thresholds for lineage choice during the exit of pluripotency.
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Affiliation(s)
- Chet H. Loh
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Siebe van Genesen
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Matteo Perino
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands ,grid.4709.a0000 0004 0495 846XPresent Address: Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Magnus R. Bark
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Gert Jan C. Veenstra
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
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136
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Weijts B, Yvernogeau L, Robin C. Recent Advances in Developmental Hematopoiesis: Diving Deeper With New Technologies. Front Immunol 2021; 12:790379. [PMID: 34899758 PMCID: PMC8652083 DOI: 10.3389/fimmu.2021.790379] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
The journey of a hematopoietic stem cell (HSC) involves the passage through successive anatomical sites where HSCs are in direct contact with their surrounding microenvironment, also known as niche. These spatial and temporal cellular interactions throughout development are required for the acquisition of stem cell properties, and for maintaining the HSC pool through balancing self-renewal, quiescence and lineage commitment. Understanding the context and consequences of these interactions will be imperative for our understanding of HSC biology and will lead to the improvement of in vitro production of HSCs for clinical purposes. The aorta-gonad-mesonephros (AGM) region is in this light of particular interest since this is the cradle of HSC emergence during the embryonic development of all vertebrate species. In this review, we will focus on the developmental origin of HSCs and will discuss the novel technological approaches and recent progress made to identify the cellular composition of the HSC supportive niche and the underlying molecular events occurring in the AGM region.
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Affiliation(s)
- Bart Weijts
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) & University Medical Center Utrecht, Utrecht, Netherlands
| | - Laurent Yvernogeau
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) & University Medical Center Utrecht, Utrecht, Netherlands
| | - Catherine Robin
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) & University Medical Center Utrecht, Utrecht, Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands
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137
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Chen Y, Shao Y. Stem Cell-Based Embryo Models: En Route to a Programmable Future. J Mol Biol 2021; 434:167353. [PMID: 34774563 DOI: 10.1016/j.jmb.2021.167353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/04/2021] [Accepted: 11/04/2021] [Indexed: 01/10/2023]
Abstract
Early-stage human embryogenesis, such as implantation, gastrulation, and neurulation, are critical for successful pregnancy. For decades, our knowledge about these stages has been limited by the inaccessibility to such embryo specimens in vivo and the difficulty in rebuilding them in vitro. Although human embryos could be cultured in vitro beyond implantation, it remains challenging for the cultured embryos to recapitulate the continuous, coordinated morphogenesis and cytodifferentiation as seen in vivo. Stem cell-based embryo models, mainly derived from human pluripotent stem cells, are organized structures mimicking essential developmental processes in the early-stage human embryos. Despite their invaluable potentials, most embryo models are based on the self-organization of human pluripotent stem cells, which are limited in controllability, reproducibility, and developmental fidelity. Recently, the integration of bioengineered tools and stem cell biology has fueled a technological transformation towards programmable, highly complex, high-fidelity stem cell-based embryo models. Given its scientific and clinical significance, we present an overview of recent paradigm-shifting advances as well as historical perspectives regarding the past, present, and future of synthetic human embryology. Following the developmental roadmap of human embryogenesis, we critically review existing stem cell-based models for implantation, gastrulation, and neurulation, respectively. We highlight the limitations encountered by autonomous self-organization strategy and discuss the concept and application of guided cell organization as a game-changer for innovating next-generation embryo models. Future endeavors in synthetic human embryology should rationally leverage both the self-organizing power and programmable microenvironmental guidance to secure faithful reconstructions of the hierarchical orders of human embryogenesis in vitro.
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Affiliation(s)
- Yunping Chen
- Institute of Biomechanics and Medical Engineering, Applied Mechanics Laboratory, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
| | - Yue Shao
- Institute of Biomechanics and Medical Engineering, Applied Mechanics Laboratory, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China.
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138
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Mayeur H, Lanoizelet M, Quillien A, Menuet A, Michel L, Martin KJ, Dejean S, Blader P, Mazan S, Lagadec R. When Bigger Is Better: 3D RNA Profiling of the Developing Head in the Catshark Scyliorhinus canicula. Front Cell Dev Biol 2021; 9:744982. [PMID: 34746140 PMCID: PMC8569936 DOI: 10.3389/fcell.2021.744982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
We report the adaptation of RNA tomography, a technique allowing spatially resolved, genome-wide expression profiling, to a species occupying a key phylogenetic position in gnathostomes, the catshark Scyliorhinus canicula. We focused analysis on head explants at an embryonic stage, shortly following neural tube closure and of interest for a number of developmental processes, including early brain patterning, placode specification or the establishment of epithalamic asymmetry. As described in the zebrafish, we have sequenced RNAs extracted from serial sections along transverse, horizontal and sagittal planes, mapped the data onto a gene reference taking advantage of the high continuity genome recently released in the catshark, and projected read counts onto a digital model of the head obtained by confocal microscopy. This results in the generation of a genome-wide 3D atlas, containing expression data for most protein-coding genes in a digital model of the embryonic head. The digital profiles obtained for candidate forebrain regional markers along antero-posterior, dorso-ventral and left-right axes reproduce those obtained by in situ hybridization (ISH), with expected relative organizations. We also use spatial autocorrelation and correlation as measures to analyze these data and show that they provide adequate statistical tools to extract novel expression information from the model. These data and tools allow exhaustive searches of genes exhibiting any predefined expression characteristic, such a restriction to a territory of interest, thus providing a reference for comparative analyses across gnathostomes. This methodology appears best suited to species endowed with large embryo or organ sizes and opens novel perspectives to a wide range of evo-devo model organisms, traditionally counter-selected on size criterion.
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Affiliation(s)
- Hélène Mayeur
- CNRS, Sorbonne Université, UMR 7232-Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls sur Mer, France
| | - Maxence Lanoizelet
- CNRS, Sorbonne Université, UMR 7232-Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls sur Mer, France
| | - Aurélie Quillien
- Molecular, Cellular and Developmental Biology (MCD UMR 5077), Centre de Biologie Intégrative (CBI, FR 3743), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Arnaud Menuet
- UMR 7355, Experimental and Molecular Immunology and Neurogenetics, CNRS and University of Orléans, Orléans, France
| | - Léo Michel
- CNRS, Sorbonne Université, UMR 7232-Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls sur Mer, France
| | - Kyle John Martin
- United Kingdom Research and Innovation, Biotechnology and Biological Sciences Research Council, Swindon, United Kingdom
| | - Sébastien Dejean
- Institut de Mathématiques de Toulouse, Université de Toulouse, CNRS, UPS, UMR 5219, Toulouse, France
| | - Patrick Blader
- Molecular, Cellular and Developmental Biology (MCD UMR 5077), Centre de Biologie Intégrative (CBI, FR 3743), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sylvie Mazan
- CNRS, Sorbonne Université, UMR 7232-Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls sur Mer, France
| | - Ronan Lagadec
- CNRS, Sorbonne Université, UMR 7232-Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, Banyuls sur Mer, France
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139
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Weldon SA, Münsterberg AE. Somite development and regionalisation of the vertebral axial skeleton. Semin Cell Dev Biol 2021; 127:10-16. [PMID: 34690064 DOI: 10.1016/j.semcdb.2021.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/27/2021] [Accepted: 10/06/2021] [Indexed: 11/25/2022]
Abstract
A critical stage in the development of all vertebrate embryos is the generation of the body plan and its subsequent patterning and regionalisation along the main anterior-posterior axis. This includes the formation of the vertebral axial skeleton. Its organisation begins during early embryonic development with the periodic formation of paired blocks of mesoderm tissue called somites. Here, we review axial patterning of somites, with a focus on studies using amniote model systems - avian and mouse. We summarise the molecular and cellular mechanisms that generate paraxial mesoderm and review how the different anatomical regions of the vertebral column acquire their specific identity and thus shape the body plan. We also discuss the generation of organoids and embryo-like structures from embryonic stem cells, which provide insights regarding axis formation and promise to be useful for disease modelling.
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Affiliation(s)
- Shannon A Weldon
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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140
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Indana D, Agarwal P, Bhutani N, Chaudhuri O. Viscoelasticity and Adhesion Signaling in Biomaterials Control Human Pluripotent Stem Cell Morphogenesis in 3D Culture. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2101966. [PMID: 34499389 DOI: 10.1002/adma.202101966] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/27/2021] [Indexed: 06/13/2023]
Abstract
Organoids are lumen-containing multicellular structures that recapitulate key features of the organs, and are increasingly used in models of disease, drug testing, and regenerative medicine. Recent work has used 3D culture models to form organoids from human induced pluripotent stem cells (hiPSCs) in reconstituted basement membrane (rBM) matrices. However, rBM matrices offer little control over the microenvironment. More generally, the role of matrix viscoelasticity in directing lumen formation remains unknown. Here, viscoelastic alginate hydrogels with independently tunable stress relaxation (viscoelasticity), stiffness, and arginine-glycine-aspartate (RGD) ligand density are used to study hiPSC morphogenesis in 3D culture. A phase diagram that shows how these properties control hiPSC morphogenesis is reported. Higher RGD density and fast stress relaxation promote hiPSC viability, proliferation, apicobasal polarization, and lumen formation, while slow stress relaxation at low RGD densities triggers hiPSC apoptosis. Notably, hiPSCs maintain pluripotency in alginate hydrogels for much longer times than is reported in rBM matrices. Lumen formation is regulated by actomyosin contractility and is accompanied by translocation of Yes-associated protein (YAP) from the nucleus to the cytoplasm. The results reveal matrix viscoelasticity as a potent factor regulating stem cell morphogenesis and provide new insights into how engineered biomaterials may be leveraged to build organoids.
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Affiliation(s)
- Dhiraj Indana
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Pranay Agarwal
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nidhi Bhutani
- Department of Orthopaedic Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ovijit Chaudhuri
- Department of Mechanical Engineering, Stanford University, Stanford, CA, 94305, USA
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141
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Diaz-Cuadros M, Pourquié O, El-Sherif E. Patterning with clocks and genetic cascades: Segmentation and regionalization of vertebrate versus insect body plans. PLoS Genet 2021; 17:e1009812. [PMID: 34648490 PMCID: PMC8516289 DOI: 10.1371/journal.pgen.1009812] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Oscillatory and sequential processes have been implicated in the spatial patterning of many embryonic tissues. For example, molecular clocks delimit segmental boundaries in vertebrates and insects and mediate lateral root formation in plants, whereas sequential gene activities are involved in the specification of regional identities of insect neuroblasts, vertebrate neural tube, vertebrate limb, and insect and vertebrate body axes. These processes take place in various tissues and organisms, and, hence, raise the question of what common themes and strategies they share. In this article, we review 2 processes that rely on the spatial regulation of periodic and sequential gene activities: segmentation and regionalization of the anterior-posterior (AP) axis of animal body plans. We study these processes in species that belong to 2 different phyla: vertebrates and insects. By contrasting 2 different processes (segmentation and regionalization) in species that belong to 2 distantly related phyla (arthropods and vertebrates), we elucidate the deep logic of patterning by oscillatory and sequential gene activities. Furthermore, in some of these organisms (e.g., the fruit fly Drosophila), a mode of AP patterning has evolved that seems not to overtly rely on oscillations or sequential gene activities, providing an opportunity to study the evolution of pattern formation mechanisms.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ezzat El-Sherif
- Division of Developmental Biology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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142
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Mechanics of neural tube morphogenesis. Semin Cell Dev Biol 2021; 130:56-69. [PMID: 34561169 DOI: 10.1016/j.semcdb.2021.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 01/07/2023]
Abstract
The neural tube is an important model system of morphogenesis representing the developmental module of out-of-plane epithelial deformation. As the embryonic precursor of the central nervous system, the neural tube also holds keys to many defects and diseases. Recent advances begin to reveal how genetic, cellular and environmental mechanisms work in concert to ensure correct neural tube shape. A physical model is emerging where these factors converge at the regulation of the mechanical forces and properties within and around the tissue that drive tube formation towards completion. Here we review the dynamics and mechanics of neural tube morphogenesis and discuss the underlying cellular behaviours from the viewpoint of tissue mechanics. We will also highlight some of the conceptual and technical next steps.
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143
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Sozen B, Jorgensen V, Weatherbee BAT, Chen S, Zhu M, Zernicka-Goetz M. Reconstructing aspects of human embryogenesis with pluripotent stem cells. Nat Commun 2021; 12:5550. [PMID: 34548496 PMCID: PMC8455697 DOI: 10.1038/s41467-021-25853-4] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/24/2021] [Indexed: 02/01/2023] Open
Abstract
Understanding human development is of fundamental biological and clinical importance. Despite its significance, mechanisms behind human embryogenesis remain largely unknown. Here, we attempt to model human early embryo development with expanded pluripotent stem cells (EPSCs) in 3-dimensions. We define a protocol that allows us to generate self-organizing cystic structures from human EPSCs that display some hallmarks of human early embryogenesis. These structures mimic polarization and cavitation characteristic of pre-implantation development leading to blastocyst morphology formation and the transition to post-implantation-like organization upon extended culture. Single-cell RNA sequencing of these structures reveals subsets of cells bearing some resemblance to epiblast, hypoblast and trophectoderm lineages. Nevertheless, significant divergences from natural blastocysts persist in some key markers, and signalling pathways point towards ways in which morphology and transcriptional-level cell identities may diverge in stem cell models of the embryo. Thus, this stem cell platform provides insights into the design of stem cell models of embryogenesis.
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Affiliation(s)
- Berna Sozen
- Plasticity and Self-Organization Group, Division of Biology and Biological Engineering, Caltech, Pasadena, CA, 91125, USA
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, 06520, USA
| | - Victoria Jorgensen
- Plasticity and Self-Organization Group, Division of Biology and Biological Engineering, Caltech, Pasadena, CA, 91125, USA
| | - Bailey A T Weatherbee
- Mammalian Development and Stem Cell Group, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Sisi Chen
- Plasticity and Self-Organization Group, Division of Biology and Biological Engineering, Caltech, Pasadena, CA, 91125, USA
| | - Meng Zhu
- Mammalian Development and Stem Cell Group, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
- Blavatnik Institute, Harvard Medical School, Department of Genetics, Boston, MA, 02115, USA
| | - Magdalena Zernicka-Goetz
- Plasticity and Self-Organization Group, Division of Biology and Biological Engineering, Caltech, Pasadena, CA, 91125, USA.
- Mammalian Development and Stem Cell Group, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK.
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144
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Steventon B, Busby L, Arias AM. Establishment of the vertebrate body plan: Rethinking gastrulation through stem cell models of early embryogenesis. Dev Cell 2021; 56:2405-2418. [PMID: 34520764 DOI: 10.1016/j.devcel.2021.08.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/20/2021] [Accepted: 08/14/2021] [Indexed: 12/28/2022]
Abstract
A striking property of vertebrate embryos is the emergence of a conserved body plan across a wide range of organisms through the process of gastrulation. As the body plan unfolds, gene regulatory networks (GRNs) and multicellular interactions (cell regulatory networks, CRNs) combine to generate a conserved set of morphogenetic events that lead to the phylotypic stage. Interrogation of these multilevel interactions requires manipulation of the mechanical environment, which is difficult in vivo. We review recent studies of stem cell models of early embryogenesis from different species showing that, independent of species origin, cells in culture form similar structures. The main difference between embryos and in vitro models is the boundary conditions of the multicellular ensembles. We discuss these observations and suggest that the mechanical and geometric boundary conditions of different embryos before gastrulation hide a morphogenetic ground state that is revealed in the stem-cell-based models of embryo development.
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Affiliation(s)
| | - Lara Busby
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Alfonso Martinez Arias
- Systems Bioengineering, DCEXS, Universidad Pompeu Fabra, Doctor Aiguader, 88 ICREA, Pag Lluis Companys 23, Barcelona, Spain.
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145
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146
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Anlas K, Trivedi V. Studying evolution of the primary body axis in vivo and in vitro. eLife 2021; 10:e69066. [PMID: 34463611 PMCID: PMC8456739 DOI: 10.7554/elife.69066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023] Open
Abstract
The metazoan body plan is established during early embryogenesis via collective cell rearrangements and evolutionarily conserved gene networks, as part of a process commonly referred to as gastrulation. While substantial progress has been achieved in terms of characterizing the embryonic development of several model organisms, underlying principles of many early patterning processes nevertheless remain enigmatic. Despite the diversity of (pre-)gastrulating embryo and adult body shapes across the animal kingdom, the body axes, which are arguably the most fundamental features, generally remain identical between phyla. Recently there has been a renewed appreciation of ex vivo and in vitro embryo-like systems to model early embryonic patterning events. Here, we briefly review key examples and propose that similarities in morphogenesis and associated gene expression dynamics may reveal an evolutionarily conserved developmental mode as well as provide further insights into the role of external or extraembryonic cues in shaping the early embryo. In summary, we argue that embryo-like systems can be employed to inform previously uncharted aspects of animal body plan evolution as well as associated patterning rules.
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Affiliation(s)
| | - Vikas Trivedi
- EMBL BarcelonaBarcelonaSpain
- EMBL Heidelberg, Developmental BiologyHeidelbergGermany
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147
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Girgin MU, Broguiere N, Hoehnel S, Brandenberg N, Mercier B, Arias AM, Lutolf MP. Bioengineered embryoids mimic post-implantation development in vitro. Nat Commun 2021; 12:5140. [PMID: 34446708 PMCID: PMC8390504 DOI: 10.1038/s41467-021-25237-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
The difficulty of studying post-implantation development in mammals has sparked a flurry of activity to develop in vitro models, termed embryoids, based on self-organizing pluripotent stem cells. Previous approaches to derive embryoids either lack the physiological morphology and signaling interactions, or are unconducive to model post-gastrulation development. Here, we report a bioengineering-inspired approach aimed at addressing this gap. We employ a high-throughput cell aggregation approach to simultaneously coax mouse embryonic stem cells into hundreds of uniform epiblast-like aggregates in a solid matrix-free manner. When co-cultured with mouse trophoblast stem cell aggregates, the resulting hybrid structures initiate gastrulation-like events and undergo axial morphogenesis to yield structures, termed EpiTS embryoids, with a pronounced anterior development, including brain-like regions. We identify the presence of an epithelium in EPI aggregates as the major determinant for the axial morphogenesis and anterior development seen in EpiTS embryoids. Our results demonstrate the potential of EpiTS embryoids to study peri-gastrulation development in vitro.
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Affiliation(s)
- Mehmet U Girgin
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Nicolas Broguiere
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sylke Hoehnel
- SUN bioscience, EPFL Innovation Park, Lausanne, Switzerland
| | | | - Bastien Mercier
- Faculty of Medicine and Pharmacy, University of Grenoble Alpes, Grenoble, France
| | | | - Matthias P Lutolf
- Laboratory of Stem Cell Bioengineering, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Roche Institute for Translational Bioengineering (ITB), Pharma Research and Early Development (pRED), Roche Innovation Center Basel, Basel, Switzerland.
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148
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Zhai J, Xiao Z, Wang Y, Wang H. Human embryonic development: from peri-implantation to gastrulation. Trends Cell Biol 2021; 32:18-29. [PMID: 34417090 DOI: 10.1016/j.tcb.2021.07.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/25/2021] [Accepted: 07/26/2021] [Indexed: 01/12/2023]
Abstract
The basic body plan of the mammalian embryo is established through gastrulation, a pivotal early postimplantation event during which the three major germ layers (endoderm, ectoderm, and mesoderm) are specified with cellular and spatial diversity. Despite its basic and clinical importance, human embryo development from peri-implantation to gastrulation remains shrouded in mystery. Recent advances in the elongated in vitro culture of rodent and non-primate embryos and the construction of embryo-like structures have helped to improve understanding of the mechanisms of human early embryonic development. Here, we review the recent advances and possible future directions in the development of in vitro models to better understand human embryogenesis from peri-implantation to gastrulation.
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Affiliation(s)
- Jinglei Zhai
- The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, P. R. China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, P. R. China
| | - Zhenyu Xiao
- The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, P. R. China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, P. R. China
| | - Yiming Wang
- The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hongmei Wang
- The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, P. R. China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China.
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149
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Rao A, Barkley D, França GS, Yanai I. Exploring tissue architecture using spatial transcriptomics. Nature 2021; 596:211-220. [PMID: 34381231 PMCID: PMC8475179 DOI: 10.1038/s41586-021-03634-9] [Citation(s) in RCA: 499] [Impact Index Per Article: 166.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/11/2021] [Indexed: 02/08/2023]
Abstract
Deciphering the principles and mechanisms by which gene activity orchestrates complex cellular arrangements in multicellular organisms has far-reaching implications for research in the life sciences. Recent technological advances in next-generation sequencing- and imaging-based approaches have established the power of spatial transcriptomics to measure expression levels of all or most genes systematically throughout tissue space, and have been adopted to generate biological insights in neuroscience, development and plant biology as well as to investigate a range of disease contexts, including cancer. Similar to datasets made possible by genomic sequencing and population health surveys, the large-scale atlases generated by this technology lend themselves to exploratory data analysis for hypothesis generation. Here we review spatial transcriptomic technologies and describe the repertoire of operations available for paths of analysis of the resulting data. Spatial transcriptomics can also be deployed for hypothesis testing using experimental designs that compare time points or conditions-including genetic or environmental perturbations. Finally, spatial transcriptomic data are naturally amenable to integration with other data modalities, providing an expandable framework for insight into tissue organization.
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Affiliation(s)
- Anjali Rao
- Institute for Computational Medicine, NYU Langone Health, New York, NY, USA
| | - Dalia Barkley
- Institute for Computational Medicine, NYU Langone Health, New York, NY, USA
| | - Gustavo S França
- Institute for Computational Medicine, NYU Langone Health, New York, NY, USA
| | - Itai Yanai
- Institute for Computational Medicine, NYU Langone Health, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
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150
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van den Brink SC, van Oudenaarden A. 3D gastruloids: a novel frontier in stem cell-based in vitro modeling of mammalian gastrulation. Trends Cell Biol 2021; 31:747-759. [PMID: 34304959 DOI: 10.1016/j.tcb.2021.06.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022]
Abstract
3D gastruloids, aggregates of embryonic stem cells that recapitulate key aspects of gastrula-stage embryos, have emerged as a powerful tool to study the early stages of mammalian post-implantation development in vitro. Owing to their tractable nature and the relative ease by which they can be generated in large numbers, 3D gastruloids provide an unparalleled opportunity to study normal and pathological embryogenesis from a bottom-up perspective and in a high-throughput manner. Here, we review how gastruloid models can be exploited to deepen our understanding of mammalian development. In addition, we discuss current limitations, potential clinical applications, and ethical implications of this emerging model system.
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Affiliation(s)
- Susanne C van den Brink
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Alexander van Oudenaarden
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, The Netherlands
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