1
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Ahn S, Jain A, Kasuba KC, Seimiya M, Okamoto R, Treutlein B, Müller DJ. Engineering fibronectin-templated multi-component fibrillar extracellular matrices to modulate tissue-specific cell response. Biomaterials 2024; 308:122560. [PMID: 38603826 DOI: 10.1016/j.biomaterials.2024.122560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/15/2024] [Accepted: 03/30/2024] [Indexed: 04/13/2024]
Abstract
Cells assemble fibronectin, the major extracellular matrix (ECM) protein, into fibrillar matrices, which serve as 3D architectural scaffolds to provide, together with other ECM proteins tissue-specific environments. Although recent approaches enable to bioengineer 3D fibrillar fibronectin matrices in vitro, it remains elusive how fibronectin can be co-assembled with other ECM proteins into complex 3D fibrillar matrices that recapitulate tissue-specific compositions and cellular responses. Here, we introduce the engineering of fibrillar fibronectin-templated 3D matrices that can be complemented with other ECM proteins, including vitronectin, collagen, and laminin to resemble ECM architectures observed in vivo. For the co-assembly of different ECM proteins, we employed their innate fibrillogenic mechanisms including shear forces, pH-dependent electrostatic interactions, or specific binding domains. Through recapitulating various tissue-specific ECM compositions and morphologies, the large scale multi-composite 3D fibrillar ECM matrices can guide fibroblast adhesion, 3D fibroblast tissue formation, or tissue morphogenesis of epithelial cells. In other examples, we customize multi-composite 3D fibrillar matrices to support the growth of signal propagating neuronal networks and of human brain organoids. We envision that these 3D fibrillar ECM matrices can be tailored in scale and composition to modulate tissue-specific responses across various biological length scales and systems, and thus to advance manyfold studies of cell biological systems.
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Affiliation(s)
- Seungkuk Ahn
- Eidgenössische Technische Hochschule (ETH) Zurich, Department of Biosystems Science and Engineering, 4056, Basel, Switzerland.
| | - Akanksha Jain
- Eidgenössische Technische Hochschule (ETH) Zurich, Department of Biosystems Science and Engineering, 4056, Basel, Switzerland
| | - Krishna Chaitanya Kasuba
- Eidgenössische Technische Hochschule (ETH) Zurich, Department of Biosystems Science and Engineering, 4056, Basel, Switzerland
| | - Makiko Seimiya
- Eidgenössische Technische Hochschule (ETH) Zurich, Department of Biosystems Science and Engineering, 4056, Basel, Switzerland
| | - Ryoko Okamoto
- Eidgenössische Technische Hochschule (ETH) Zurich, Department of Biosystems Science and Engineering, 4056, Basel, Switzerland
| | - Barbara Treutlein
- Eidgenössische Technische Hochschule (ETH) Zurich, Department of Biosystems Science and Engineering, 4056, Basel, Switzerland
| | - Daniel J Müller
- Eidgenössische Technische Hochschule (ETH) Zurich, Department of Biosystems Science and Engineering, 4056, Basel, Switzerland.
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2
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Wahle P, Brancati G, Harmel C, He Z, Gut G, Del Castillo JS, Xavier da Silveira Dos Santos A, Yu Q, Noser P, Fleck JS, Gjeta B, Pavlinić D, Picelli S, Hess M, Schmidt GW, Lummen TTA, Hou Y, Galliker P, Goldblum D, Balogh M, Cowan CS, Scholl HPN, Roska B, Renner M, Pelkmans L, Treutlein B, Camp JG. Multimodal spatiotemporal phenotyping of human retinal organoid development. Nat Biotechnol 2023; 41:1765-1775. [PMID: 37156914 PMCID: PMC10713453 DOI: 10.1038/s41587-023-01747-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/13/2023] [Indexed: 05/10/2023]
Abstract
Organoids generated from human pluripotent stem cells provide experimental systems to study development and disease, but quantitative measurements across different spatial scales and molecular modalities are lacking. In this study, we generated multiplexed protein maps over a retinal organoid time course and primary adult human retinal tissue. We developed a toolkit to visualize progenitor and neuron location, the spatial arrangements of extracellular and subcellular components and global patterning in each organoid and primary tissue. In addition, we generated a single-cell transcriptome and chromatin accessibility timecourse dataset and inferred a gene regulatory network underlying organoid development. We integrated genomic data with spatially segmented nuclei into a multimodal atlas to explore organoid patterning and retinal ganglion cell (RGC) spatial neighborhoods, highlighting pathways involved in RGC cell death and showing that mosaic genetic perturbations in retinal organoids provide insight into cell fate regulation.
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Affiliation(s)
- Philipp Wahle
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Giovanna Brancati
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Christoph Harmel
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Gabriele Gut
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Aline Xavier da Silveira Dos Santos
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Pascal Noser
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Bruno Gjeta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Dinko Pavlinić
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Simone Picelli
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Max Hess
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Gregor W Schmidt
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Tom T A Lummen
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Yanyan Hou
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Patricia Galliker
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - David Goldblum
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Marton Balogh
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Cameron S Cowan
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Magdalena Renner
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.
- Department of Ophthalmology, University of Basel, Basel, Switzerland.
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
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3
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Li C, Fleck JS, Martins-Costa C, Burkard TR, Themann J, Stuempflen M, Peer AM, Vertesy Á, Littleboy JB, Esk C, Elling U, Kasprian G, Corsini NS, Treutlein B, Knoblich JA. Author Correction: Single-cell brain organoid screening identifies developmental defects in autism. Nature 2023; 623:E20. [PMID: 37964131 PMCID: PMC10686816 DOI: 10.1038/s41586-023-06836-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Affiliation(s)
- Chong Li
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria.
| | - Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Catarina Martins-Costa
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Jan Themann
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Marlene Stuempflen
- Department of Radiodiagnostics, Medical University of Vienna, Vienna, Austria
| | - Angela Maria Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Ábel Vertesy
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Jamie B Littleboy
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Christopher Esk
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Gregor Kasprian
- Department of Radiodiagnostics, Medical University of Vienna, Vienna, Austria
| | - Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria.
- Department of Neurology, Medical University of Vienna, Vienna, Austria.
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4
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Bressan C, Snapyan M, Snapyan M, Klaus J, di Matteo F, Robertson SP, Treutlein B, Parent M, Cappello S, Saghatelyan A. Metformin rescues migratory deficits of cells derived from patients with periventricular heterotopia. EMBO Mol Med 2023; 15:e16908. [PMID: 37609821 PMCID: PMC10565636 DOI: 10.15252/emmm.202216908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 08/01/2023] [Accepted: 08/10/2023] [Indexed: 08/24/2023] Open
Abstract
Periventricular neuronal heterotopia (PH) is one of the most common forms of cortical malformation in the human cortex. We show that human neuronal progenitor cells (hNPCs) derived from PH patients with a DCHS1 or FAT4 mutation as well as isogenic lines had altered migratory dynamics when grafted in the mouse brain. The affected migration was linked to altered autophagy as observed in vivo with an electron microscopic analysis of grafted hNPCs, a Western blot analysis of cortical organoids, and time-lapse imaging of hNPCs in the presence of bafilomycin A1. We further show that deficits in autophagy resulted in the accumulation of paxillin, a focal adhesion protein involved in cell migration. Strikingly, a single-cell RNA-seq analysis of hNPCs revealed similar expression levels of autophagy-related genes. Bolstering AMPK-dependent autophagy by metformin, an FDA-approved drug, promoted migration of PH patients-derived hNPCs. Our data indicate that transcription-independent homeostatic modifications in autophagy contributed to the defective migratory behavior of hNPCs in vivo and suggest that modulating autophagy in hNPCs might rescue neuronal migration deficits in some forms of PH.
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Affiliation(s)
- Cedric Bressan
- CERVO Brain Research CenterQuebec CityQCCanada
- Université LavalQuebec CityQCCanada
| | - Marta Snapyan
- CERVO Brain Research CenterQuebec CityQCCanada
- Université LavalQuebec CityQCCanada
| | - Marina Snapyan
- CERVO Brain Research CenterQuebec CityQCCanada
- Université LavalQuebec CityQCCanada
- University of OttawaOttawaONCanada
| | | | - Francesco di Matteo
- Max Planck Institute of PsychiatryMunichGermany
- Biomedical Center (BMC)Ludwig Maximilian University of MunichMunichGermany
| | | | - Barbara Treutlein
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Martin Parent
- CERVO Brain Research CenterQuebec CityQCCanada
- Université LavalQuebec CityQCCanada
| | - Silvia Cappello
- Max Planck Institute of PsychiatryMunichGermany
- Biomedical Center (BMC)Ludwig Maximilian University of MunichMunichGermany
| | - Armen Saghatelyan
- CERVO Brain Research CenterQuebec CityQCCanada
- Université LavalQuebec CityQCCanada
- University of OttawaOttawaONCanada
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5
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Li C, Fleck JS, Martins-Costa C, Burkard TR, Themann J, Stuempflen M, Peer AM, Vertesy Á, Littleboy JB, Esk C, Elling U, Kasprian G, Corsini NS, Treutlein B, Knoblich JA. Single-cell brain organoid screening identifies developmental defects in autism. Nature 2023; 621:373-380. [PMID: 37704762 PMCID: PMC10499611 DOI: 10.1038/s41586-023-06473-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/21/2023] [Indexed: 09/15/2023]
Abstract
The development of the human brain involves unique processes (not observed in many other species) that can contribute to neurodevelopmental disorders1-4. Cerebral organoids enable the study of neurodevelopmental disorders in a human context. We have developed the CRISPR-human organoids-single-cell RNA sequencing (CHOOSE) system, which uses verified pairs of guide RNAs, inducible CRISPR-Cas9-based genetic disruption and single-cell transcriptomics for pooled loss-of-function screening in mosaic organoids. Here we show that perturbation of 36 high-risk autism spectrum disorder genes related to transcriptional regulation uncovers their effects on cell fate determination. We find that dorsal intermediate progenitors, ventral progenitors and upper-layer excitatory neurons are among the most vulnerable cell types. We construct a developmental gene regulatory network of cerebral organoids from single-cell transcriptomes and chromatin modalities and identify autism spectrum disorder-associated and perturbation-enriched regulatory modules. Perturbing members of the BRG1/BRM-associated factor (BAF) chromatin remodelling complex leads to enrichment of ventral telencephalon progenitors. Specifically, mutating the BAF subunit ARID1B affects the fate transition of progenitors to oligodendrocyte and interneuron precursor cells, a phenotype that we confirmed in patient-specific induced pluripotent stem cell-derived organoids. Our study paves the way for high-throughput phenotypic characterization of disease susceptibility genes in organoid models with cell state, molecular pathway and gene regulatory network readouts.
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Affiliation(s)
- Chong Li
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria.
| | - Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Catarina Martins-Costa
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Jan Themann
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Marlene Stuempflen
- Department of Radiodiagnostics, Medical University of Vienna, Vienna, Austria
| | - Angela Maria Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Ábel Vertesy
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Jamie B Littleboy
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Christopher Esk
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Gregor Kasprian
- Department of Radiodiagnostics, Medical University of Vienna, Vienna, Austria
| | - Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna, Austria.
- Department of Neurology, Medical University of Vienna, Vienna, Austria.
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6
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Fleck JS, Jansen SMJ, Wollny D, Zenk F, Seimiya M, Jain A, Okamoto R, Santel M, He Z, Camp JG, Treutlein B. Inferring and perturbing cell fate regulomes in human brain organoids. Nature 2023; 621:365-372. [PMID: 36198796 PMCID: PMC10499607 DOI: 10.1038/s41586-022-05279-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 08/25/2022] [Indexed: 02/06/2023]
Abstract
Self-organizing neural organoids grown from pluripotent stem cells1-3 combined with single-cell genomic technologies provide opportunities to examine gene regulatory networks underlying human brain development. Here we acquire single-cell transcriptome and accessible chromatin data over a dense time course in human organoids covering neuroepithelial formation, patterning, brain regionalization and neurogenesis, and identify temporally dynamic and brain-region-specific regulatory regions. We developed Pando-a flexible framework that incorporates multi-omic data and predictions of transcription-factor-binding sites to infer a global gene regulatory network describing organoid development. We use pooled genetic perturbation with single-cell transcriptome readout to assess transcription factor requirement for cell fate and state regulation in organoids. We find that certain factors regulate the abundance of cell fates, whereas other factors affect neuronal cell states after differentiation. We show that the transcription factor GLI3 is required for cortical fate establishment in humans, recapitulating previous research performed in mammalian model systems. We measure transcriptome and chromatin accessibility in normal or GLI3-perturbed cells and identify two distinct GLI3 regulomes that are central to telencephalic fate decisions: one regulating dorsoventral patterning with HES4/5 as direct GLI3 targets, and one controlling ganglionic eminence diversification later in development. Together, we provide a framework for how human model systems and single-cell technologies can be leveraged to reconstruct human developmental biology.
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Affiliation(s)
- Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | | | - Damian Wollny
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fides Zenk
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Makiko Seimiya
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Akanksha Jain
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ryoko Okamoto
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Malgorzata Santel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
- Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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7
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Fleck JS, Camp JG, Treutlein B. What is a cell type? Science 2023; 381:733-734. [PMID: 37590360 DOI: 10.1126/science.adf6162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
A next step for cell atlases should be to chart perturbations in human model systems.
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Affiliation(s)
- Jonas Simon Fleck
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
| | - J Gray Camp
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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8
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Blair JD, Hartman A, Zenk F, Dalgarno C, Treutlein B, Satija R. Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells. bioRxiv 2023:2023.03.27.534442. [PMID: 37034703 PMCID: PMC10081255 DOI: 10.1101/2023.03.27.534442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
Cell signaling plays a critical role in regulating cellular behavior and fate. While multimodal single-cell sequencing technologies are rapidly advancing, scalable and flexible profiling of cell signaling states alongside other molecular modalities remains challenging. Here we present Phospho-seq, an integrated approach that aims to quantify phosphorylated intracellular and intranuclear proteins, and to connect their activity with cis-regulatory elements and transcriptional targets. We utilize a simplified benchtop antibody conjugation method to create large custom antibody panels for simultaneous protein and scATAC-seq profiling on whole cells, and integrate this information with scRNA-seq datasets via bridge integration. We apply our workflow to cell lines, induced pluripotent stem cells, and 3-month-old brain organoids to demonstrate its broad applicability. We demonstrate that Phospho-seq can define cellular states and trajectories, reconstruct gene regulatory relationships, and characterize the causes and consequences of heterogeneous cell signaling in neurodevelopment.
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Affiliation(s)
- John D. Blair
- New York Genome Center, New York, NY
- New York University, Center for Genomics and Systems Biology, New York, NY
| | | | | | | | | | - Rahul Satija
- New York Genome Center, New York, NY
- New York University, Center for Genomics and Systems Biology, New York, NY
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9
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Cahan P, Treutlein B. A conversation with ChatGPT on the role of computational systems biology in stem cell research. Stem Cell Reports 2023; 18:1-2. [PMID: 36630899 PMCID: PMC9860153 DOI: 10.1016/j.stemcr.2022.12.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023] Open
Affiliation(s)
- Patrick Cahan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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10
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Lust K, Maynard A, Gomes T, Fleck JS, Camp JG, Tanaka EM, Treutlein B. Single-cell analyses of axolotl telencephalon organization, neurogenesis, and regeneration. Science 2022; 377:eabp9262. [PMID: 36048956 DOI: 10.1126/science.abp9262] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Salamanders are tetrapod models to study brain organization and regeneration; however, the identity and evolutionary conservation of brain cell types are largely unknown. We delineated the cell populations in the axolotl telencephalon during homeostasis and regeneration using single-cell genomic profiling. We identified glutamatergic neurons with similarities to amniote neurons of hippocampus, dorsal and lateral cortex, and conserved γ-aminobutyric acid-releasing (GABAergic) neuron classes. We inferred transcriptional dynamics and gene regulatory relationships of postembryonic, region-specific neurogenesis and unraveled conserved differentiation signatures. After brain injury, ependymoglia activate an injury-specific state before reestablishing lost neuron populations and axonal connections. Together, our analyses yield insights into the organization, evolution, and regeneration of a tetrapod nervous system.
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Affiliation(s)
- Katharina Lust
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030 Vienna, Austria
| | - Ashley Maynard
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Tomás Gomes
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - J Gray Camp
- Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.,University of Basel, 4001 Basel, Switzerland
| | - Elly M Tanaka
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030 Vienna, Austria
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
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11
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Pașca SP, Arlotta P, Bateup HS, Camp JG, Cappello S, Gage FH, Knoblich JA, Kriegstein AR, Lancaster MA, Ming GL, Muotri AR, Park IH, Reiner O, Song H, Studer L, Temple S, Testa G, Treutlein B, Vaccarino FM. A nomenclature consensus for nervous system organoids and assembloids. Nature 2022; 609:907-910. [PMID: 36171373 PMCID: PMC10571504 DOI: 10.1038/s41586-022-05219-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 07/10/2022] [Indexed: 12/20/2022]
Abstract
Self-organizing three-dimensional cellular models derived from human pluripotent stem cells or primary tissue have great potential to provide insights into how the human nervous system develops, what makes it unique and how disorders of the nervous system arise, progress and could be treated. Here, to facilitate progress and improve communication with the scientific community and the public, we clarify and provide a basic framework for the nomenclature of human multicellular models of nervous system development and disease, including organoids, assembloids and transplants.
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Affiliation(s)
- Sergiu P Pașca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute and Bio-X, Stanford University, Stanford, CA, USA.
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Helen S Bateup
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - J Gray Camp
- Roche Institute for Translational Bioengineering, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Arnold R Kriegstein
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | | | - Guo-Li Ming
- Department of Neuroscience, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alysson R Muotri
- Departments of Pediatrics and Cellular & Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Stem Cell Program, Archealization Center, Center for Academic Research and Training in Anthropogeny, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
| | - Orly Reiner
- Weizmann Institute of Science, Rehovot, Israel
| | - Hongjun Song
- Department of Neuroscience, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | | | - Giuseppe Testa
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Human Technopole, Milan, Italy
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT, USA
- Department of Neuroscience, Yale University, New Haven, CT, USA
- Yale Kavli Institute for Neuroscience, New Haven, CT, USA
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12
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Oskolkov N, Santel M, Parikh HM, Ekström O, Camp GJ, Miyamoto-Mikami E, Ström K, Mir BA, Kryvokhyzha D, Lehtovirta M, Kobayashi H, Kakigi R, Naito H, Eriksson KF, Nystedt B, Fuku N, Treutlein B, Pääbo S, Hansson O. High-throughput muscle fiber typing from RNA sequencing data. Skelet Muscle 2022; 12:16. [PMID: 35780170 PMCID: PMC9250227 DOI: 10.1186/s13395-022-00299-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/07/2022] [Indexed: 11/10/2022] Open
Abstract
Background Skeletal muscle fiber type distribution has implications for human health, muscle function, and performance. This knowledge has been gathered using labor-intensive and costly methodology that limited these studies. Here, we present a method based on muscle tissue RNA sequencing data (totRNAseq) to estimate the distribution of skeletal muscle fiber types from frozen human samples, allowing for a larger number of individuals to be tested. Methods By using single-nuclei RNA sequencing (snRNAseq) data as a reference, cluster expression signatures were produced by averaging gene expression of cluster gene markers and then applying these to totRNAseq data and inferring muscle fiber nuclei type via linear matrix decomposition. This estimate was then compared with fiber type distribution measured by ATPase staining or myosin heavy chain protein isoform distribution of 62 muscle samples in two independent cohorts (n = 39 and 22). Results The correlation between the sequencing-based method and the other two were rATPas = 0.44 [0.13–0.67], [95% CI], and rmyosin = 0.83 [0.61–0.93], with p = 5.70 × 10–3 and 2.00 × 10–6, respectively. The deconvolution inference of fiber type composition was accurate even for very low totRNAseq sequencing depths, i.e., down to an average of ~ 10,000 paired-end reads. Conclusions This new method (https://github.com/OlaHanssonLab/PredictFiberType) consequently allows for measurement of fiber type distribution of a larger number of samples using totRNAseq in a cost and labor-efficient way. It is now feasible to study the association between fiber type distribution and e.g. health outcomes in large well-powered studies. Supplementary Information The online version contains supplementary material available at 10.1186/s13395-022-00299-4.
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Affiliation(s)
- Nikolay Oskolkov
- Department of Clinical Sciences, Lund University, Malmö, Sweden.,Department of Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Lund University, Lund, Sweden
| | - Malgorzata Santel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hemang M Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Gainesville, USA
| | - Ola Ekström
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Gray J Camp
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Eri Miyamoto-Mikami
- Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
| | - Kristoffer Ström
- Department of Clinical Sciences, Lund University, Malmö, Sweden.,Swedish Winter Sports Research Centre, Mid Sweden University, Östersund, Sweden
| | - Bilal Ahmad Mir
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | | | - Mikko Lehtovirta
- Department of Clinical Sciences, Lund University, Malmö, Sweden.,Institute for Molecular Medicine Finland (FIMM), Helsinki University, Helsinki, Finland
| | | | - Ryo Kakigi
- Faculty of Management & Information Science, Josai International University, Chiba, Japan
| | - Hisashi Naito
- Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
| | | | - Björn Nystedt
- Department of Cell and Molecular Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Noriyuki Fuku
- Graduate School of Health and Sports Science, Juntendo University, Chiba, Japan
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Okinawa Institute of Science and Technology, Onna-son, Japan
| | - Ola Hansson
- Department of Clinical Sciences, Lund University, Malmö, Sweden. .,Institute for Molecular Medicine Finland (FIMM), Helsinki University, Helsinki, Finland.
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13
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Krumm J, Sekine K, Samaras P, Brazovskaja A, Breunig M, Yasui R, Kleger A, Taniguchi H, Wilhelm M, Treutlein B, Camp JG, Kuster B. High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development. Cell Rep 2022; 38:110604. [PMID: 35354033 DOI: 10.1016/j.celrep.2022.110604] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/29/2021] [Accepted: 03/09/2022] [Indexed: 11/29/2022] Open
Abstract
Primary human hepatocytes are widely used to evaluate liver toxicity of drugs, but they are scarce and demanding to culture. Stem cell-derived hepatocytes are increasingly discussed as alternatives. To obtain a better appreciation of the molecular processes during the differentiation of induced pluripotent stem cells into hepatocytes, we employ a quantitative proteomic approach to follow the expression of 9,000 proteins, 12,000 phosphorylation sites, and 800 acetylation sites over time. The analysis reveals stage-specific markers, a major molecular switch between hepatic endoderm versus immature hepatocyte-like cells impacting, e.g., metabolism, the cell cycle, kinase activity, and the expression of drug transporters. Comparing the proteomes of two- (2D) and three-dimensional (3D)-derived hepatocytes with fetal and adult liver indicates a fetal-like status of the in vitro models and lower expression of important ADME/Tox proteins. The collective data enable constructing a molecular roadmap of hepatocyte development that serves as a valuable resource for future research.
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Affiliation(s)
- Johannes Krumm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Keisuke Sekine
- Laboratory of Cancer Cell Systems, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-004, Japan
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany
| | - Agnieska Brazovskaja
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Markus Breunig
- Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany
| | - Ryota Yasui
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-004, Japan
| | - Alexander Kleger
- Department of Internal Medicine I, Ulm University Hospital, 89081 Ulm, Germany
| | - Hideki Taniguchi
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-004, Japan; Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; Computational Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, 4056 Basel, Switzerland
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, 85354 Freising, Germany; Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, 85354 Freising, Germany.
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14
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Gerber T, Loureiro C, Schramma N, Chen S, Jain A, Weber A, Weigert A, Santel M, Alim K, Treutlein B, Camp JG. Spatial transcriptomic and single-nucleus analysis reveals heterogeneity in a gigantic single-celled syncytium. eLife 2022; 11:69745. [PMID: 35195068 PMCID: PMC8865844 DOI: 10.7554/elife.69745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 02/07/2022] [Indexed: 11/25/2022] Open
Abstract
In multicellular organisms, the specification, coordination, and compartmentalization of cell types enable the formation of complex body plans. However, some eukaryotic protists such as slime molds generate diverse and complex structures while remaining in a multinucleate syncytial state. It is unknown if different regions of these giant syncytial cells have distinct transcriptional responses to environmental encounters and if nuclei within the cell diversify into heterogeneous states. Here, we performed spatial transcriptome analysis of the slime mold Physarum polycephalum in the plasmodium state under different environmental conditions and used single-nucleus RNA-sequencing to dissect gene expression heterogeneity among nuclei. Our data identifies transcriptome regionality in the organism that associates with proliferation, syncytial substructures, and localized environmental conditions. Further, we find that nuclei are heterogenous in their transcriptional profile and may process local signals within the plasmodium to coordinate cell growth, metabolism, and reproduction. To understand how nuclei variation within the syncytium compares to heterogeneity in single-nucleus cells, we analyzed states in single Physarum amoebal cells. We observed amoebal cell states at different stages of mitosis and meiosis, and identified cytokinetic features that are specific to nuclei divisions within the syncytium. Notably, we do not find evidence for predefined transcriptomic states in the amoebae that are observed in the syncytium. Our data shows that a single-celled slime mold can control its gene expression in a region-specific manner while lacking cellular compartmentalization and suggests that nuclei are mobile processors facilitating local specialized functions. More broadly, slime molds offer the extraordinary opportunity to explore how organisms can evolve regulatory mechanisms to divide labor, specialize, balance competition with cooperation, and perform other foundational principles that govern the logic of life.
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Affiliation(s)
- Tobias Gerber
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cristina Loureiro
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Nico Schramma
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Siyu Chen
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany.,Physics Department, Technical University of Munich, München, Germany
| | - Akanksha Jain
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Anne Weber
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Anne Weigert
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Malgorzata Santel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Karen Alim
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany.,Physics Department, Technical University of Munich, München, Germany
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - J Gray Camp
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland.,University of Basel, Basel, Switzerland
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15
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Kyrousi C, O’Neill AC, Brazovskaja A, He Z, Kielkowski P, Coquand L, Di Giaimo R, D’ Andrea P, Belka A, Forero Echeverry A, Mei D, Lenge M, Cruceanu C, Buchsbaum IY, Khattak S, Fabien G, Binder E, Elmslie F, Guerrini R, Baffet AD, Sieber SA, Treutlein B, Robertson SP, Cappello S. Extracellular LGALS3BP regulates neural progenitor position and relates to human cortical complexity. Nat Commun 2021; 12:6298. [PMID: 34728600 PMCID: PMC8564519 DOI: 10.1038/s41467-021-26447-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 09/26/2021] [Indexed: 12/15/2022] Open
Abstract
Basal progenitors (BPs), including intermediate progenitors and basal radial glia, are generated from apical radial glia and are enriched in gyrencephalic species like humans, contributing to neuronal expansion. Shortly after generation, BPs delaminate towards the subventricular zone, where they further proliferate before differentiation. Gene expression alterations involved in BP delamination and function in humans are poorly understood. Here, we study the role of LGALS3BP, so far known as a cancer biomarker, which is a secreted protein enriched in human neural progenitors (NPCs). We show that individuals with LGALS3BP de novo variants exhibit altered local gyrification, sulcal depth, surface area and thickness in their cortex. Additionally, using cerebral organoids, human fetal tissues and mice, we show that LGALS3BP regulates the position of NPCs. Single-cell RNA-sequencing and proteomics reveal that LGALS3BP-mediated mechanisms involve the extracellular matrix in NPCs' anchoring and migration within the human brain. We propose that its temporal expression influences NPCs' delamination, corticogenesis and gyrification extrinsically.
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Affiliation(s)
- Christina Kyrousi
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.5216.00000 0001 2155 0800Present Address: First Department of Psychiatry, Medical School, National and Kapodistrian University of Athens, Greece and University Mental Health, Neurosciences and Precision Medicine Research Institute “Costas Stefanis”, Athens, Greece
| | - Adam C. O’Neill
- grid.29980.3a0000 0004 1936 7830Department of Women’s and Children’s Health, University of Otago, 9054 Dunedin, New Zealand
| | - Agnieska Brazovskaja
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Zhisong He
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany ,grid.5801.c0000 0001 2156 2780ETH Zurich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - Pavel Kielkowski
- grid.6936.a0000000123222966Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany ,grid.5252.00000 0004 1936 973XPresent Address: Department Chemie Ludwig-Maximilians-Universität München Butenandtstr. 5-13, 81377 München, Germany
| | - Laure Coquand
- grid.4444.00000 0001 2112 9282Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d’Ulm, F-75005 Paris, France
| | - Rossella Di Giaimo
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Pierpaolo D’ Andrea
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Alexander Belka
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | | | - Davide Mei
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Matteo Lenge
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Cristiana Cruceanu
- grid.419548.50000 0000 9497 5095Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Isabel Y. Buchsbaum
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany ,grid.5252.00000 0004 1936 973XGraduate School of Systemic Neurosciences, Ludwig-Maximilians-University, 82152 Munich Planegg, Germany
| | - Shahryar Khattak
- grid.4488.00000 0001 2111 7257DFG-Research Center and Cluster of Excellence for Regenerative Therapies (CRTD), School of Medicine, Technical University Dresden, 01307 Dresden, Germany ,grid.4912.e0000 0004 0488 7120Present Address: Royal College of Surgeons Ireland (RCSI) in Bahrain, Adliya, Kingdom of Bahrain
| | - Guimiot Fabien
- grid.50550.350000 0001 2175 4109Unité de Foetopathologie, Assistance Publique-Hôpitaux de Paris, CHU Robert Debré, F-75019 Paris, France
| | - Elisabeth Binder
- grid.419548.50000 0000 9497 5095Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Frances Elmslie
- grid.4464.20000 0001 2161 2573South West Thames Regional Genetics Service, St George’s, University of London, London, SW17 0RE UK
| | - Renzo Guerrini
- grid.413181.e0000 0004 1757 8562Neuroscience Department, Children’s Hospital A. Meyer-University of Florence, 50139 Florence, Italy
| | - Alexandre D. Baffet
- grid.4444.00000 0001 2112 9282Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d’Ulm, F-75005 Paris, France
| | - Stephan A. Sieber
- grid.6936.a0000000123222966Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany
| | - Barbara Treutlein
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany ,grid.5801.c0000 0001 2156 2780ETH Zurich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - Stephen P. Robertson
- grid.29980.3a0000 0004 1936 7830Department of Women’s and Children’s Health, University of Otago, 9054 Dunedin, New Zealand
| | - Silvia Cappello
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, 80804 Munich, Germany
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16
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Born G, Nikolova M, Scherberich A, Treutlein B, García-García A, Martin I. Engineering of fully humanized and vascularized 3D bone marrow niches sustaining undifferentiated human cord blood hematopoietic stem and progenitor cells. J Tissue Eng 2021; 12:20417314211044855. [PMID: 34616539 PMCID: PMC8488506 DOI: 10.1177/20417314211044855] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/21/2021] [Indexed: 01/01/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are frequently located around the bone marrow (BM) vasculature. These so-called perivascular niches regulate HSC function both in health and disease, but they have been poorly studied in humans due to the scarcity of models integrating complete human vascular structures. Herein, we propose the stromal vascular fraction (SVF) derived from human adipose tissue as a cell source to vascularize 3D osteoblastic BM niches engineered in perfusion bioreactors. We show that SVF cells form self-assembled capillary structures, composed by endothelial and perivascular cells, that add to the osteogenic matrix secreted by BM mesenchymal stromal cells in these engineered niches. In comparison to avascular osteoblastic niches, vascularized BM niches better maintain immunophenotypically-defined cord blood (CB) HSCs without affecting cell proliferation. In contrast, HSPCs cultured in vascularized BM niches showed increased CFU-granulocyte-erythrocyte-monocyte-megakaryocyte (CFU-GEMM) numbers. The vascularization also contributed to better preserve osteogenic gene expression in the niche, demonstrating that niche vascularization has an influence on both hematopoietic and stromal compartments. In summary, we have engineered a fully humanized and vascularized 3D BM tissue to model native human endosteal perivascular niches and revealed functional implications of this vascularization in sustaining undifferentiated CB HSPCs. This system provides a unique modular platform to explore hemato-vascular interactions in human healthy/pathological hematopoiesis.
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Affiliation(s)
- Gordian Born
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.,Department of Biomedical Engineering, University of Basel, Allschwill, Switzerland
| | - Marina Nikolova
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Arnaud Scherberich
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.,Department of Biomedical Engineering, University of Basel, Allschwill, Switzerland
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Andrés García-García
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Ivan Martin
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.,Department of Biomedical Engineering, University of Basel, Allschwill, Switzerland
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17
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Lin HC, He Z, Ebert S, Schörnig M, Santel M, Nikolova MT, Weigert A, Hevers W, Kasri NN, Taverna E, Camp JG, Treutlein B. NGN2 induces diverse neuron types from human pluripotency. Stem Cell Reports 2021; 16:2118-2127. [PMID: 34358451 PMCID: PMC8452516 DOI: 10.1016/j.stemcr.2021.07.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/22/2023] Open
Abstract
Human neurons engineered from induced pluripotent stem cells (iPSCs) through neurogenin 2 (NGN2) overexpression are widely used to study neuronal differentiation mechanisms and to model neurological diseases. However, the differentiation paths and heterogeneity of emerged neurons have not been fully explored. Here, we used single-cell transcriptomics to dissect the cell states that emerge during NGN2 overexpression across a time course from pluripotency to neuron functional maturation. We find a substantial molecular heterogeneity in the neuron types generated, with at least two populations that express genes associated with neurons of the peripheral nervous system. Neuron heterogeneity is observed across multiple iPSC clones and lines from different individuals. We find that neuron fate acquisition is sensitive to NGN2 expression level and the duration of NGN2-forced expression. Our data reveal that NGN2 dosage can regulate neuron fate acquisition, and that NGN2-iN heterogeneity can confound results that are sensitive to neuron type. NGN2-iNs are molecularly heterogeneous NGN2-iNs subtypes have signatures of central and peripheral nervous system Neural fate acquisition is sensitive to the level and duration of NGN2 expression
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Affiliation(s)
- Hsiu-Chuan Lin
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Sebastian Ebert
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Maria Schörnig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Malgorzata Santel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Marina T Nikolova
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Anne Weigert
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Wulf Hevers
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nael Nadif Kasri
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboudumc, Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboudumc, Nijmegen, the Netherlands
| | - Elena Taverna
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Human Technopole, Milan, Italy
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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18
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Yu Q, Kilik U, Holloway EM, Tsai YH, Harmel C, Wu A, Wu JH, Czerwinski M, Childs CJ, He Z, Capeling MM, Huang S, Glass IA, Higgins PDR, Treutlein B, Spence JR, Camp JG. Charting human development using a multi-endodermal organ atlas and organoid models. Cell 2021; 184:3281-3298.e22. [PMID: 34019796 PMCID: PMC8208823 DOI: 10.1016/j.cell.2021.04.028] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/11/2021] [Accepted: 04/16/2021] [Indexed: 12/11/2022]
Abstract
Organs are composed of diverse cell types that traverse transient states during organogenesis. To interrogate this diversity during human development, we generate a single-cell transcriptome atlas from multiple developing endodermal organs of the respiratory and gastrointestinal tract. We illuminate cell states, transcription factors, and organ-specific epithelial stem cell and mesenchyme interactions across lineages. We implement the atlas as a high-dimensional search space to benchmark human pluripotent stem cell (hPSC)-derived intestinal organoids (HIOs) under multiple culture conditions. We show that HIOs recapitulate reference cell states and use HIOs to reconstruct the molecular dynamics of intestinal epithelium and mesenchyme emergence. We show that the mesenchyme-derived niche cue NRG1 enhances intestinal stem cell maturation in vitro and that the homeobox transcription factor CDX2 is required for regionalization of intestinal epithelium and mesenchyme in humans. This work combines cell atlases and organoid technologies to understand how human organ development is orchestrated.
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Affiliation(s)
- Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Umut Kilik
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Christoph Harmel
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael Czerwinski
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Charlie J Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Sha Huang
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ian A Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Peter D R Higgins
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland.
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19
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Fleck JS, Sanchís-Calleja F, He Z, Santel M, Boyle MJ, Camp JG, Treutlein B. Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases. Cell Stem Cell 2021; 28:1177-1180. [PMID: 34087154 DOI: 10.1016/j.stem.2021.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Holloway EM, Czerwinski M, Tsai YH, Wu JH, Wu A, Childs CJ, Walton KD, Sweet CW, Yu Q, Glass I, Treutlein B, Camp JG, Spence JR. Mapping Development of the Human Intestinal Niche at Single-Cell Resolution. Cell Stem Cell 2021; 28:568-580.e4. [PMID: 33278341 PMCID: PMC7935765 DOI: 10.1016/j.stem.2020.11.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 08/27/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022]
Abstract
The human intestinal stem cell niche supports self-renewal and epithelial function, but little is known about its development. We used single-cell mRNA sequencing with in situ validation approaches to interrogate human intestinal development from 7-21 weeks post conception, assigning molecular identities and spatial locations to cells and factors that comprise the niche. Smooth muscle cells of the muscularis mucosa, in close proximity to proliferative crypts, are a source of WNT and RSPONDIN ligands, whereas EGF is expressed far from crypts in the villus epithelium. Instead, an PDGFRAHI/F3HI/DLL1HI mesenchymal population lines the crypt-villus axis and is the source of the epidermal growth factor (EGF) family member NEUREGULIN1 (NRG1). In developing intestine enteroid cultures, NRG1, but not EGF, permitted increased cellular diversity via differentiation of secretory lineages. This work highlights the complexities of intestinal EGF/ERBB signaling and delineates key niche cells and signals of the developing intestine.
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Affiliation(s)
- Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael Czerwinski
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joshua H Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Charlie J Childs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Katherine D Walton
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Caden W Sweet
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
| | - Ian Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA.
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21
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Schörnig M, Ju X, Fast L, Ebert S, Weigert A, Kanton S, Schaffer T, Nadif Kasri N, Treutlein B, Peter BM, Hevers W, Taverna E. Comparison of induced neurons reveals slower structural and functional maturation in humans than in apes. eLife 2021; 10:59323. [PMID: 33470930 PMCID: PMC7870144 DOI: 10.7554/elife.59323] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
We generated induced excitatory neurons (iNeurons, iNs) from chimpanzee, bonobo, and human stem cells by expressing the transcription factor neurogenin-2 (NGN2). Single-cell RNA sequencing showed that genes involved in dendrite and synapse development are expressed earlier during iNs maturation in the chimpanzee and bonobo than the human cells. In accordance, during the first 2 weeks of differentiation, chimpanzee and bonobo iNs showed repetitive action potentials and more spontaneous excitatory activity than human iNs, and extended neurites of higher total length. However, the axons of human iNs were slightly longer at 5 weeks of differentiation. The timing of the establishment of neuronal polarity did not differ between the species. Chimpanzee, bonobo, and human neurites eventually reached the same level of structural complexity. Thus, human iNs develop slower than chimpanzee and bonobo iNs, and this difference in timing likely depends on functions downstream of NGN2.
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Affiliation(s)
- Maria Schörnig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Xiangchun Ju
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Luise Fast
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sebastian Ebert
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anne Weigert
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sabina Kanton
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Theresa Schaffer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nael Nadif Kasri
- Department of Human Genetics and Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Radboudumc, Nijmegen, Netherlands
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Wulf Hevers
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Taverna
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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22
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Affiliation(s)
- Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland.
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23
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Miller AJ, Yu Q, Czerwinski M, Tsai YH, Conway RF, Wu A, Holloway EM, Walker T, Glass IA, Treutlein B, Camp JG, Spence JR. In Vitro and In Vivo Development of the Human Airway at Single-Cell Resolution. Dev Cell 2020; 54:818. [PMID: 32991836 PMCID: PMC7540720 DOI: 10.1016/j.devcel.2020.09.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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24
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He Z, Brazovskaja A, Ebert S, Camp JG, Treutlein B. CSS: cluster similarity spectrum integration of single-cell genomics data. Genome Biol 2020; 21:224. [PMID: 32867824 PMCID: PMC7460789 DOI: 10.1186/s13059-020-02147-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/17/2020] [Indexed: 01/24/2023] Open
Abstract
It is a major challenge to integrate single-cell sequencing data across experiments, conditions, batches, time points, and other technical considerations. New computational methods are required that can integrate samples while simultaneously preserving biological information. Here, we propose an unsupervised reference-free data representation, cluster similarity spectrum (CSS), where each cell is represented by its similarities to clusters independently identified across samples. We show that CSS can be used to assess cellular heterogeneity and enable reconstruction of differentiation trajectories from cerebral organoid and other single-cell transcriptomic data, and to integrate data across experimental conditions and human individuals.
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Affiliation(s)
- Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | | | - Sebastian Ebert
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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25
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Dannemann M, He Z, Heide C, Vernot B, Sidow L, Kanton S, Weigert A, Treutlein B, Pääbo S, Kelso J, Camp JG. Human Stem Cell Resources Are an Inroad to Neandertal DNA Functions. Stem Cell Reports 2020; 15:214-225. [PMID: 32559457 PMCID: PMC7363959 DOI: 10.1016/j.stemcr.2020.05.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 02/07/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) from diverse humans offer the potential to study human functional variation in controlled culture environments. A portion of this variation originates from an ancient admixture between modern humans and Neandertals, which introduced alleles that left a phenotypic legacy on individual humans today. Here, we show that a large iPSC repository harbors extensive Neandertal DNA, including alleles that contribute to human phenotypes and diseases, encode hundreds of amino acid changes, and alter gene expression in specific tissues. We provide a database of the inferred introgressed Neandertal alleles for each individual iPSC line, together with the annotation of the predicted functional variants. We also show that transcriptomic data from organoids generated from iPSCs can be used to track Neandertal-derived RNA over developmental processes. Human iPSC resources provide an opportunity to experimentally explore Neandertal DNA function and its contribution to present-day phenotypes, and potentially study Neandertal traits.
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Affiliation(s)
- Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Christian Heide
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Leila Sidow
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sabina Kanton
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anne Weigert
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - J Gray Camp
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland.
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26
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Khrameeva E, Kurochkin I, Han D, Guijarro P, Kanton S, Santel M, Qian Z, Rong S, Mazin P, Sabirov M, Bulat M, Efimova O, Tkachev A, Guo S, Sherwood CC, Camp JG, Pääbo S, Treutlein B, Khaitovich P. Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains. Genome Res 2020; 30:776-789. [PMID: 32424074 PMCID: PMC7263190 DOI: 10.1101/gr.256958.119] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/30/2020] [Indexed: 12/14/2022]
Abstract
Identification of gene expression traits unique to the human brain sheds light on the molecular mechanisms underlying human evolution. Here, we searched for uniquely human gene expression traits by analyzing 422 brain samples from humans, chimpanzees, bonobos, and macaques representing 33 anatomical regions, as well as 88,047 cell nuclei composing three of these regions. Among 33 regions, cerebral cortex areas, hypothalamus, and cerebellar gray and white matter evolved rapidly in humans. At the cellular level, astrocytes and oligodendrocyte progenitors displayed more differences in the human evolutionary lineage than the neurons. Comparison of the bulk tissue and single-nuclei sequencing revealed that conventional RNA sequencing did not detect up to two-thirds of cell-type-specific evolutionary differences.
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Affiliation(s)
| | - Ilia Kurochkin
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia
| | - Dingding Han
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Patricia Guijarro
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China
| | - Sabina Kanton
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Malgorzata Santel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Zhengzong Qian
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China
| | - Shen Rong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China
| | - Pavel Mazin
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
| | - Marat Sabirov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Matvei Bulat
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia
| | - Olga Efimova
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia
| | - Anna Tkachev
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.,Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
| | - Song Guo
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China
| | - Chet C Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology, Basel, 4057, Switzerland
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology in Zurich, Basel, 4058, Switzerland
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China.,Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
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27
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Abstract
Investigating early brain development has previously relied on using primary developing brain tissue or two-dimensional cell culture models. Recently, stem cell-derived three-dimensional cell culture systems, collectively called brain organoids, have been developed that can faithfully recapitulate many aspects of early brain development. Together with the ability to reprogram fibroblast or blood cells into induced pluripotent stem cells from humans with neurodevelopmental disorders, this opens new inroads to study patient-specific brain development in a personalized cell culture model. Studying the transcriptomes and regulatory landscape of single cells within brain organoids presents a major advance to understand cell-type specific features and transient states during development, and to link these states to their underlying regulatory logic at high resolution. In this protocol, we describe how to generate single-cell RNA-seq and ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data from the same suspension of organoid cells and focus on reducing batch effects by multiplexing multiple individuals in one experiment. Moreover, we outline basic data processing, analysis, and strategies to correct for batch effects, to account for variability in organoids and for integrating gene expression and open chromatin data.
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Affiliation(s)
- Sabina Kanton
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Barbara Treutlein
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - J Gray Camp
- Institute of Clinical Ophthalmology (IOB), University of Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland.
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28
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Miller AJ, Yu Q, Czerwinski M, Tsai YH, Conway RF, Wu A, Holloway EM, Walker T, Glass IA, Treutlein B, Camp JG, Spence JR. In Vitro and In Vivo Development of the Human Airway at Single-Cell Resolution. Dev Cell 2020; 53:117-128.e6. [PMID: 32109386 PMCID: PMC7396815 DOI: 10.1016/j.devcel.2020.01.033] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/09/2019] [Accepted: 01/28/2020] [Indexed: 12/13/2022]
Abstract
Bud tip progenitor cells give rise to all murine lung epithelial lineages and have been described in the developing human lung; however, the mechanisms controlling human bud tip differentiation into specific lineages are unclear. Here, we used homogeneous human bud tip organoid cultures and identified SMAD signaling as a key regulator of the bud tip-to-airway transition. SMAD induction led to the differentiation of airway-like organoids possessing functional basal cells capable of clonal expansion and multilineage differentiation. To benchmark in vitro-derived organoids, we developed a single-cell mRNA sequencing atlas of the human lung from 11.5 to 21 weeks of development, which revealed high degrees of similarity between the in vitro-derived and in vivo airway. Together, this work sheds light on human airway differentiation in vitro and provides a single-cell atlas of the developing human lung.
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Affiliation(s)
- Alyssa J Miller
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; University of Basel, Basel, Switzerland; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael Czerwinski
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Renee F Conway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Emily M Holloway
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Taylor Walker
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ian A Glass
- Department of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; University of Basel, Basel, Switzerland; Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Jason R Spence
- Program in Cell and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA.
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29
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Abstract
The cumulative activity of all of the body's cells, with their myriad interactions, life histories, and environmental experiences, gives rise to a condition that is distinctly human and specific to each individual. It is an enduring goal to catalog our human cell types, to understand how they develop, how they vary between individuals, and how they fail in disease. Single-cell genomics has revolutionized this endeavor because sequencing-based methods provide a means to quantitatively annotate cell states on the basis of high-information content and high-throughput measurements. Together with advances in stem cell biology and gene editing, we are in the midst of a fascinating journey to understand the cellular phenotypes that compose human bodies and how the human genome is used to build and maintain each cell. Here, we will review recent advances into how single-cell genomics is being used to develop personalized phenotyping strategies that cross subcellular, cellular, and tissue scales to link our genome to our cumulative cellular phenotypes.
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Affiliation(s)
- J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Randall Platt
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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30
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Parra RG, Papadopoulos N, Ahumada-Arranz L, Kholtei JE, Mottelson N, Horokhovsky Y, Treutlein B, Soeding J. Reconstructing complex lineage trees from scRNA-seq data using MERLoT. Nucleic Acids Res 2019; 47:8961-8974. [PMID: 31428793 PMCID: PMC6755101 DOI: 10.1093/nar/gkz706] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 07/22/2019] [Accepted: 08/01/2019] [Indexed: 11/20/2022] Open
Abstract
Advances in single-cell transcriptomics techniques are revolutionizing studies of cellular differentiation and heterogeneity. It has become possible to track the trajectory of thousands of genes across the cellular lineage trees that represent the temporal emergence of cell types during dynamic processes. However, reconstruction of cellular lineage trees with more than a few cell fates has proved challenging. We present MERLoT (https://github.com/soedinglab/merlot), a flexible and user-friendly tool to reconstruct complex lineage trees from single-cell transcriptomics data. It can impute temporal gene expression profiles along the reconstructed tree. We show MERLoT’s capabilities on various real cases and hundreds of simulated datasets.
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Affiliation(s)
- R Gonzalo Parra
- Quantitative and Computational Biology Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany.,Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Nikolaos Papadopoulos
- Quantitative and Computational Biology Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Laura Ahumada-Arranz
- Quantitative and Computational Biology Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Jakob El Kholtei
- Quantitative and Computational Biology Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Noah Mottelson
- Quantitative and Computational Biology Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Yehor Horokhovsky
- Quantitative and Computational Biology Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
| | - Barbara Treutlein
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.,Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Johannes Soeding
- Quantitative and Computational Biology Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany
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31
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Kanton S, Boyle MJ, He Z, Santel M, Weigert A, Sanchís-Calleja F, Guijarro P, Sidow L, Fleck JS, Han D, Qian Z, Heide M, Huttner WB, Khaitovich P, Pääbo S, Treutlein B, Camp JG. Organoid single-cell genomic atlas uncovers human-specific features of brain development. Nature 2019; 574:418-422. [DOI: 10.1038/s41586-019-1654-9] [Citation(s) in RCA: 312] [Impact Index Per Article: 62.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 09/06/2019] [Indexed: 12/22/2022]
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32
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Affiliation(s)
- Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Barbara Treutlein
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
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33
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Koh W, Wu A, Penland L, Treutlein B, Neff NF, Mantalas GL, Blumenfeld YJ, El-Sayed YY, Stevenson DK, Shaw GM, Quake SR. Single Cell Transcriptomes Derived from Human Cervical and Uterine Tissue during Pregnancy. ACTA ACUST UNITED AC 2019; 3:e1800336. [PMID: 32648692 DOI: 10.1002/adbi.201800336] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/16/2019] [Indexed: 12/20/2022]
Abstract
This work presents the workflow for generating single cell transcriptomes derived from primary human uterine and cervical tissue obtained during planned cesarean hysterectomies. In total, a catalogue of 310 single cell transcriptomes are obtained, cell types present in these biopsies are inferred, and specific genes defining each of the cellular types present in the tissue are identified. Further validation of the inferred cell identity is also demonstrated via meta-analysis of independent repositories in literature generated by bulk sequenced data of fluorescence-activated cell sorting sorted cells.
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Affiliation(s)
- Winston Koh
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.,Molecular Engineering Lab, Agency of Science, Technology & Research, 61 Biopolis Drive, #03-13 Proteos, Singapore, 138673, Singapore
| | - Angela Wu
- Division of Life Science and Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China
| | - Lolita Penland
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Barbara Treutlein
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Norma F Neff
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Gary L Mantalas
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Yair J Blumenfeld
- Division of Maternal-Fetal Medicine and Obstetrics, Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yasser Y El-Sayed
- Division of Maternal-Fetal Medicine and Obstetrics, Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - David K Stevenson
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Gary M Shaw
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
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34
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Treutlein B, Camp JG. Evaluation of Wu et al.: Strengthening Single-Cell Bioinformatic Comparisons for Improving Organoid Differentiation. Cell Stem Cell 2019; 24:343-344. [PMID: 30849359 DOI: 10.1016/j.stem.2019.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
An example of the peer review process, for "Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics" (Wu et al., 2018), is presented herein.
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Affiliation(s)
- Barbara Treutlein
- ETH Zürich, Department of Biosystems Science and Engineering, Basel, Switzerland.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.
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35
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Brazovskaja A, Treutlein B, Camp JG. High-throughput single-cell transcriptomics on organoids. Curr Opin Biotechnol 2018; 55:167-171. [PMID: 30504008 DOI: 10.1016/j.copbio.2018.11.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/07/2018] [Indexed: 01/08/2023]
Abstract
Three-dimensional (3D) tissues grown in culture from human stem cells offer the incredible opportunity to analyze and manipulate human development, and to generate patient-specific models of disease. Methods to sequence DNA and RNA in single cells are being used to analyze these so-called 'organoid' systems in high-resolution. Single-cell transcriptomics has been used to quantitate the similarity of organoid cells to primary tissue counterparts in the brain, intestine, liver, and kidney, as well as identify cell-specific responses to environmental variables and disease conditions. The merging of these two technologies, single-cell genomics and organoids, will have profound impact on personalized medicine in the near future.
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Affiliation(s)
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Technical University Munich, 80333 Munich, Germany.
| | - J Gray Camp
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
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36
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Gerber T, Murawala P, Knapp D, Masselink W, Schuez M, Hermann S, Gac-Santel M, Nowoshilow S, Kageyama J, Khattak S, Currie JD, Camp JG, Tanaka EM, Treutlein B. Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration. Science 2018; 362:eaaq0681. [PMID: 30262634 PMCID: PMC6669047 DOI: 10.1126/science.aaq0681] [Citation(s) in RCA: 204] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 09/05/2018] [Indexed: 12/29/2022]
Abstract
Amputation of the axolotl forelimb results in the formation of a blastema, a transient tissue where progenitor cells accumulate prior to limb regeneration. However, the molecular understanding of blastema formation had previously been hampered by the inability to identify and isolate blastema precursor cells in the adult tissue. We have used a combination of Cre-loxP reporter lineage tracking and single-cell messenger RNA sequencing (scRNA-seq) to molecularly track mature connective tissue (CT) cell heterogeneity and its transition to a limb blastema state. We have uncovered a multiphasic molecular program where CT cell types found in the uninjured adult limb revert to a relatively homogenous progenitor state that recapitulates an embryonic limb bud-like phenotype including multipotency within the CT lineage. Together, our data illuminate molecular and cellular reprogramming during complex organ regeneration in a vertebrate.
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Affiliation(s)
- Tobias Gerber
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Prayag Murawala
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
- Deutsche Forschungsgemeinschaft (DFG) Center for Regenerative Therapies (CRTD), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Dunja Knapp
- Deutsche Forschungsgemeinschaft (DFG) Center for Regenerative Therapies (CRTD), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Wouter Masselink
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Maritta Schuez
- Deutsche Forschungsgemeinschaft (DFG) Center for Regenerative Therapies (CRTD), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Sarah Hermann
- Deutsche Forschungsgemeinschaft (DFG) Center for Regenerative Therapies (CRTD), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Malgorzata Gac-Santel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Sergej Nowoshilow
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
- Deutsche Forschungsgemeinschaft (DFG) Center for Regenerative Therapies (CRTD), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Jorge Kageyama
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Shahryar Khattak
- Deutsche Forschungsgemeinschaft (DFG) Center for Regenerative Therapies (CRTD), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Joshua D Currie
- Deutsche Forschungsgemeinschaft (DFG) Center for Regenerative Therapies (CRTD), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - J Gray Camp
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
- Deutsche Forschungsgemeinschaft (DFG) Center for Regenerative Therapies (CRTD), Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Barbara Treutlein
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, 108 Pfotenhauerstraße, 01307 Dresden, Germany
- Department of Biosciences, Technical University Munich, 85354 Freising, Germany
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37
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Vaid S, Camp JG, Hersemann L, Eugster Oegema C, Heninger AK, Winkler S, Brandl H, Sarov M, Treutlein B, Huttner WB, Namba T. A novel population of Hopx-dependent basal radial glial cells in the developing mouse neocortex. Development 2018; 145:dev.169276. [PMID: 30266827 DOI: 10.1242/dev.169276] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/18/2018] [Indexed: 01/10/2023]
Abstract
A specific subpopulation of neural progenitor cells, the basal radial glial cells (bRGCs) of the outer subventricular zone (OSVZ), are thought to have a key role in the evolutionary expansion of the mammalian neocortex. In the developing lissencephalic mouse neocortex, bRGCs exist at low abundance and show significant molecular differences from bRGCs in developing gyrencephalic species. Here, we demonstrate that the developing mouse medial neocortex (medNcx), in contrast to the canonically studied lateral neocortex (latNcx), exhibits an OSVZ and an abundance of bRGCs similar to that in developing gyrencephalic neocortex. Unlike bRGCs in developing mouse latNcx, the bRGCs in medNcx exhibit human bRGC-like gene expression, including expression of Hopx, a human bRGC marker. Disruption of Hopx expression in mouse embryonic medNcx and forced Hopx expression in mouse embryonic latNcx demonstrate that Hopx is required and sufficient, respectively, for bRGC abundance as found in the developing gyrencephalic neocortex. Taken together, our data identify a novel bRGC subpopulation in developing mouse medNcx that is highly related to bRGCs of developing gyrencephalic neocortex.
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Affiliation(s)
- Samir Vaid
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, D-01307 Dresden, Germany
| | - J Gray Camp
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Lena Hersemann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, D-01307 Dresden, Germany
| | - Christina Eugster Oegema
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, D-01307 Dresden, Germany
| | - Anne-Kristin Heninger
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, D-01307 Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, D-01307 Dresden, Germany
| | - Holger Brandl
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, D-01307 Dresden, Germany
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, D-01307 Dresden, Germany
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, D-01307 Dresden, Germany
| | - Takashi Namba
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, D-01307 Dresden, Germany
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38
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Camp JG, Wollny D, Treutlein B. Single-cell genomics to guide human stem cell and tissue engineering. Nat Methods 2018; 15:661-667. [PMID: 30171231 DOI: 10.1038/s41592-018-0113-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/02/2018] [Indexed: 12/15/2022]
Abstract
To understand human development and disease, as well as to regenerate damaged tissues, scientists are working to engineer certain cell types in vitro and to create 3D microenvironments in which cells behave physiologically. Single-cell genomics (SCG) technologies are being applied to primary human organs and to engineered cells and tissues to generate atlases of cell diversity in these systems at unparalleled resolution. Moving beyond atlases, SCG methods are powerful tools for gaining insight into the engineering and disease process. Here we discuss how scientists can use single-cell sequencing to optimize human cell and tissue engineering by measuring precision, detecting inefficiencies, and assessing accuracy. We also provide a perspective on how emerging SCG methods can be used to reverse-engineer human cells and tissues and unravel disease mechanisms.
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Affiliation(s)
- J Gray Camp
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Damian Wollny
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. .,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany. .,Department of Biosciences, Technical University Munich, Freising, Germany.
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39
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Ayabe H, Anada T, Kamoya T, Sato T, Kimura M, Yoshizawa E, Kikuchi S, Ueno Y, Sekine K, Camp JG, Treutlein B, Ferguson A, Suzuki O, Takebe T, Taniguchi H. Optimal Hypoxia Regulates Human iPSC-Derived Liver Bud Differentiation through Intercellular TGFB Signaling. Stem Cell Reports 2018; 11:306-316. [PMID: 30033085 PMCID: PMC6092760 DOI: 10.1016/j.stemcr.2018.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 12/22/2022] Open
Abstract
Timely controlled oxygen (O2) delivery is crucial for the developing liver. However, the influence of O2 on intercellular communication during hepatogenesis is unclear. Using a human induced pluripotent stem cell-derived liver bud (hiPSC-LB) model, we found hypoxia induced with an O2-permeable plate promoted hepatic differentiation accompanied by TGFB1 and TGFB3 suppression. Conversely, extensive hypoxia generated with an O2-non-permeable plate elevated TGFBs and cholangiocyte marker expression. Single-cell RNA sequencing revealed that TGFB1 and TGFB3 are primarily expressed in the human liver mesenchyme and endothelium similar to in the hiPSC-LBs. Stromal cell-specific RNA interferences indicated the importance of TGFB signaling for hepatocytic differentiation in hiPSC-LB. Consistently, during mouse liver development, the Hif1a-mediated developmental hypoxic response is positively correlated with TGFB1 expression. These data provide insights into the mechanism that hypoxia-stimulated signals in mesenchyme and endothelium, likely through TGFB1, promote hepatoblast differentiation prior to fetal circulation establishment.
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Affiliation(s)
- Hiroaki Ayabe
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan
| | - Takahisa Anada
- Division of Craniofacial Function Engineering, Tohoku University Graduate School of Dentistry, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Takuo Kamoya
- Division of Craniofacial Function Engineering, Tohoku University Graduate School of Dentistry, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Tomoya Sato
- Division of Craniofacial Function Engineering, Tohoku University Graduate School of Dentistry, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Masaki Kimura
- Division of Gastroenterology, Hepatology & Nutrition, Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | - Emi Yoshizawa
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan
| | - Shunyuu Kikuchi
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan
| | - Yasuharu Ueno
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan
| | - Keisuke Sekine
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan
| | - J Gray Camp
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Autumn Ferguson
- Division of Gastroenterology, Hepatology & Nutrition, Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
| | - Osamu Suzuki
- Division of Craniofacial Function Engineering, Tohoku University Graduate School of Dentistry, 4-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Takanori Takebe
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan; Division of Gastroenterology, Hepatology & Nutrition, Developmental Biology, Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA; Institute of Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.
| | - Hideki Taniguchi
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan.
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40
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Kageyama J, Wollny D, Treutlein B, Camp JG. ShinyCortex: Exploring Single-Cell Transcriptome Data From the Developing Human Cortex. Front Neurosci 2018; 12:315. [PMID: 29867326 PMCID: PMC5962798 DOI: 10.3389/fnins.2018.00315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 04/24/2018] [Indexed: 11/22/2022] Open
Abstract
Single-cell mRNA sequencing (scRNA-seq) is a powerful method to identify and classify cell types and reconstruct differentiation trajectories within complex tissues, such as the developing human cortex. scRNA-seq data also enables the discovery of cell type-specific marker genes and genes that regulate developmental transitions. Here we provide a brief overview of how scRNA-seq has been shaping the study of human cortex development, and present ShinyCortex, a resource that brings together data from recent scRNA-seq studies of the developing cortex for further analysis. ShinyCortex is based in R and displays recently published scRNA-seq data from the human and mouse cortex in a comprehensible, dynamic and accessible way, suitable for data exploration by biologists.
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Affiliation(s)
- Jorge Kageyama
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Damian Wollny
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Barbara Treutlein
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Department of Biosciences, Technical University Munich, Munich, Germany
| | - J Gray Camp
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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41
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Gerber T, Willscher E, Loeffler-Wirth H, Hopp L, Schadendorf D, Schartl M, Anderegg U, Camp G, Treutlein B, Binder H, Kunz M. Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq. Oncotarget 2018; 8:846-862. [PMID: 27903987 PMCID: PMC5352202 DOI: 10.18632/oncotarget.13666] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/12/2016] [Indexed: 01/21/2023] Open
Abstract
Recent technological advances in single-cell genomics make it possible to analyze cellular heterogeneity of tumor samples. Here, we applied single-cell RNA-seq to measure the transcriptomes of 307 single cells cultured from three biopsies of three different patients with a BRAF/NRAS wild type, BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant melanoma metastasis, respectively. Analysis based on self-organizing maps identified sub-populations defined by multiple gene expression modules involved in proliferation, oxidative phosphorylation, pigmentation and cellular stroma. Gene expression modules had prognostic relevance when compared with gene expression data from published melanoma samples and patient survival data. We surveyed kinome expression patterns across sub-populations of the BRAF/NRAS wild type sample and found that CDK4 and CDK2 were consistently highly expressed in the majority of cells, suggesting that these kinases might be involved in melanoma progression. Treatment of cells with the CDK4 inhibitor palbociclib restricted cell proliferation to a similar, and in some cases greater, extent than MAPK inhibitors. Finally, we identified a low abundant sub-population in this sample that highly expressed a module containing ABC transporter ABCB5, surface markers CD271 and CD133, and multiple aldehyde dehydrogenases (ALDHs). Patient-derived cultures of the BRAF mutant/NRAS wild type and BRAF wild type/NRAS mutant metastases showed more homogeneous single-cell gene expression patterns with gene expression modules for proliferation and ABC transporters. Taken together, our results describe an intertumor and intratumor heterogeneity in melanoma short-term cultures which might be relevant for patient survival, and suggest promising targets for new treatment approaches in melanoma therapy.
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Affiliation(s)
- Tobias Gerber
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology Leipzig, 04103 Leipzig, Germany
| | - Edith Willscher
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Henry Loeffler-Wirth
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Lydia Hopp
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Dirk Schadendorf
- Department of Dermatology, Venereology and Allergology, University Hospital Essen, 45147 Essen, Germany
| | - Manfred Schartl
- Department of Physiological Chemistry, University of Würzburg, Biozentrum, Am Hubland, 97074 Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, 97080 Würzburg, Germany.,Institute for Advanced Study, 3572 Texas A&M University, College Station, Texas 77843-3572, USA
| | - Ulf Anderegg
- Department of Dermatology, Venereology and Allergology, University of Leipzig, 04103 Leipzig, Germany
| | - Gray Camp
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology Leipzig, 04103 Leipzig, Germany
| | - Barbara Treutlein
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology Leipzig, 04103 Leipzig, Germany
| | - Hans Binder
- Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Manfred Kunz
- Department of Dermatology, Venereology and Allergology, University of Leipzig, 04103 Leipzig, Germany
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Abstract
Innovative methods designed to recapitulate human organogenesis from pluripotent stem cells provide a means to explore human developmental biology. New technologies to sequence and analyze single-cell transcriptomes can deconstruct these 'organoids' into constituent parts, and reconstruct lineage trajectories during cell differentiation. In this Spotlight article we summarize the different approaches to performing single-cell transcriptomics on organoids, and discuss the opportunities and challenges of applying these techniques to generate organ-level, mechanistic models of human development and disease. Together, these technologies will move past characterization to the prediction of human developmental and disease-related phenomena.
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Affiliation(s)
- J Gray Camp
- Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Barbara Treutlein
- Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany .,Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Technical University Munich, Department of Biosciences, 85354 Freising, Germany
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43
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Affiliation(s)
- J Gray Camp
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Barbara Treutlein
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany, and at the Technical University Munich, Germany
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44
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Camp JG, Sekine K, Gerber T, Loeffler-Wirth H, Binder H, Gac M, Kanton S, Kageyama J, Damm G, Seehofer D, Belicova L, Bickle M, Barsacchi R, Okuda R, Yoshizawa E, Kimura M, Ayabe H, Taniguchi H, Takebe T, Treutlein B. Multilineage communication regulates human liver bud development from pluripotency. Nature 2017; 546:533-538. [PMID: 28614297 DOI: 10.1038/nature22796] [Citation(s) in RCA: 346] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 04/27/2017] [Indexed: 12/11/2022]
Abstract
Conventional two-dimensional differentiation from pluripotency fails to recapitulate cell interactions occurring during organogenesis. Three-dimensional organoids generate complex organ-like tissues; however, it is unclear how heterotypic interactions affect lineage identity. Here we use single-cell RNA sequencing to reconstruct hepatocyte-like lineage progression from pluripotency in two-dimensional culture. We then derive three-dimensional liver bud organoids by reconstituting hepatic, stromal, and endothelial interactions, and deconstruct heterogeneity during liver bud development. We find that liver bud hepatoblasts diverge from the two-dimensional lineage, and express epithelial migration signatures characteristic of organ budding. We benchmark three-dimensional liver buds against fetal and adult human liver single-cell RNA sequencing data, and find a striking correspondence between the three-dimensional liver bud and fetal liver cells. We use a receptor-ligand pairing analysis and a high-throughput inhibitor assay to interrogate signalling in liver buds, and show that vascular endothelial growth factor (VEGF) crosstalk potentiates endothelial network formation and hepatoblast differentiation. Our molecular dissection reveals interlineage communication regulating organoid development, and illuminates previously inaccessible aspects of human liver development.
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Affiliation(s)
- J Gray Camp
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Keisuke Sekine
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Tobias Gerber
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics, Leipzig University, 16 Härtelstrasse, Leipzig 04107, Germany
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, Leipzig University, 16 Härtelstrasse, Leipzig 04107, Germany
| | - Malgorzata Gac
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Sabina Kanton
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Jorge Kageyama
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Georg Damm
- Department of Hepatobiliary and Transplantation Surgery, University Hospital of Leipzig, Liebigstrasse 20, Leipzig 04103, Germany.,Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, 55 Philipp-Rosenthal-Strasse, Leipzig 04103, Germany
| | - Daniel Seehofer
- Department of Hepatobiliary and Transplantation Surgery, University Hospital of Leipzig, Liebigstrasse 20, Leipzig 04103, Germany.,Saxonian Incubator for Clinical Translation (SIKT), University of Leipzig, 55 Philipp-Rosenthal-Strasse, Leipzig 04103, Germany
| | - Lenka Belicova
- Max Planck Institute of Molecular Cell Biology and Genetics, 108 Pfotenhauerstrasse, Dresden 01307, Germany
| | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, 108 Pfotenhauerstrasse, Dresden 01307, Germany
| | - Rico Barsacchi
- Max Planck Institute of Molecular Cell Biology and Genetics, 108 Pfotenhauerstrasse, Dresden 01307, Germany
| | - Ryo Okuda
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Emi Yoshizawa
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Masaki Kimura
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Hiroaki Ayabe
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Hideki Taniguchi
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Takanori Takebe
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan.,Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, Ohio 45229-3039, USA
| | - Barbara Treutlein
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, 108 Pfotenhauerstrasse, Dresden 01307, Germany
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45
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Sundaramoorthy R, Hughes AL, Singh V, Wiechens N, Ryan DP, El-Mkami H, Petoukhov M, Svergun DI, Treutlein B, Quack S, Fischer M, Michaelis J, Böttcher B, Norman DG, Owen-Hughes T. Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes. eLife 2017; 6. [PMID: 28332978 PMCID: PMC5391205 DOI: 10.7554/elife.22510] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/15/2017] [Indexed: 12/11/2022] Open
Abstract
The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state. DOI:http://dx.doi.org/10.7554/eLife.22510.001
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Affiliation(s)
| | - Amanda L Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Vijender Singh
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Nicola Wiechens
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Daniel P Ryan
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Hassane El-Mkami
- School of Physics and Astronomy, University of St Andrews, St Andrews, United Kingdom
| | - Maxim Petoukhov
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
| | - Dmitri I Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
| | - Barbara Treutlein
- Institute for Biophysics, Faculty of Natural Sciences, Ulm University, Ulm, Germany
| | - Salina Quack
- Institute for Biophysics, Faculty of Natural Sciences, Ulm University, Ulm, Germany
| | - Monika Fischer
- Institute for Biophysics, Faculty of Natural Sciences, Ulm University, Ulm, Germany
| | - Jens Michaelis
- Institute for Biophysics, Faculty of Natural Sciences, Ulm University, Ulm, Germany
| | - Bettina Böttcher
- Lehrstuhl für Biochemie, Rudolf-Virchow Zentrum, Universitat Würzburg, Würzburg, Germany
| | - David G Norman
- Nucleic Acids Structure Research Group, University of Dundee, Dundee, United Kingdom
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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46
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Mora-Bermúdez F, Badsha F, Kanton S, Camp JG, Vernot B, Köhler K, Voigt B, Okita K, Maricic T, He Z, Lachmann R, Pääbo S, Treutlein B, Huttner WB. Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development. eLife 2016; 5:e18683. [PMID: 27669147 PMCID: PMC5110243 DOI: 10.7554/elife.18683] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/22/2016] [Indexed: 12/25/2022] Open
Abstract
Human neocortex expansion likely contributed to the remarkable cognitive abilities of humans. This expansion is thought to primarily reflect differences in proliferation versus differentiation of neural progenitors during cortical development. Here, we have searched for such differences by analysing cerebral organoids from human and chimpanzees using immunohistofluorescence, live imaging, and single-cell transcriptomics. We find that the cytoarchitecture, cell type composition, and neurogenic gene expression programs of humans and chimpanzees are remarkably similar. Notably, however, live imaging of apical progenitor mitosis uncovered a lengthening of prometaphase-metaphase in humans compared to chimpanzees that is specific to proliferating progenitors and not observed in non-neural cells. Consistent with this, the small set of genes more highly expressed in human apical progenitors points to increased proliferative capacity, and the proportion of neurogenic basal progenitors is lower in humans. These subtle differences in cortical progenitors between humans and chimpanzees may have consequences for human neocortex evolution.
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Affiliation(s)
| | - Farhath Badsha
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sabina Kanton
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - J Gray Camp
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kathrin Köhler
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birger Voigt
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keisuke Okita
- Department of Reprogramming Science, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Tomislav Maricic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Zhisong He
- CAS-MPG Partner Institute for Computational Biology, Shanghai, China
| | - Robert Lachmann
- Universitätsklinikum Carl Gustav Carus, Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Technische Universität Dresden, Dresden, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Barbara Treutlein
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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47
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Gokce O, Stanley GM, Treutlein B, Neff NF, Camp JG, Malenka RC, Rothwell PE, Fuccillo MV, Südhof TC, Quake SR. Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq. Cell Rep 2016; 16:1126-1137. [PMID: 27425622 DOI: 10.1016/j.celrep.2016.06.059] [Citation(s) in RCA: 259] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 05/13/2016] [Accepted: 06/11/2016] [Indexed: 11/28/2022] Open
Abstract
The striatum contributes to many cognitive processes and disorders, but its cell types are incompletely characterized. We show that microfluidic and FACS-based single-cell RNA sequencing of mouse striatum provides a well-resolved classification of striatal cell type diversity. Transcriptome analysis revealed ten differentiated, distinct cell types, including neurons, astrocytes, oligodendrocytes, ependymal, immune, and vascular cells, and enabled the discovery of numerous marker genes. Furthermore, we identified two discrete subtypes of medium spiny neurons (MSNs) that have specific markers and that overexpress genes linked to cognitive disorders and addiction. We also describe continuous cellular identities, which increase heterogeneity within discrete cell types. Finally, we identified cell type-specific transcription and splicing factors that shape cellular identities by regulating splicing and expression patterns. Our findings suggest that functional diversity within a complex tissue arises from a small number of discrete cell types, which can exist in a continuous spectrum of functional states.
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Affiliation(s)
- Ozgun Gokce
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität LMU, 81377 Munich, Germany
| | - Geoffrey M Stanley
- Biophysics Program, Stanford University, Stanford, CA 94305, USA; Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Barbara Treutlein
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA; Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Norma F Neff
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - J Gray Camp
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Robert C Malenka
- Nancy Pritzker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Patrick E Rothwell
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Nancy Pritzker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Marc V Fuccillo
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Nancy Pritzker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Stephen R Quake
- Departments of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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48
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Affiliation(s)
- Jens Michaelis
- Biophysics
Institute, Faculty of Natural Sciences, Ulm University, Albert-Einstein-Allee
11, 89081 Ulm, Germany
- Center
for Integrated Protein Science Munich (CIPSM), Department
of Chemistry and Biochemistry, Munich University, Butenandtstrasse 5-13, 81377 München, Germany
| | - Barbara Treutlein
- Department
of Bioengineering, Stanford University, James H. Clark Center, E-300, 318
Campus Drive, Stanford, California 94305-5432, United States
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49
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Treutlein B, Muschielok A, Andrecka J, Jawhari A, Buchen C, Kostrewa D, Hög F, Cramer P, Michaelis J. Dynamic architecture of a minimal RNA polymerase II open promoter complex. Mol Cell 2012; 46:136-46. [PMID: 22424775 DOI: 10.1016/j.molcel.2012.02.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 11/04/2011] [Accepted: 02/10/2012] [Indexed: 01/22/2023]
Abstract
The open promoter complex (OC) is a central intermediate during transcription initiation that contains a DNA bubble. Here, we employ single-molecule Förster resonance energy transfer experiments and Nano-Positioning System analysis to determine the three-dimensional architecture of a minimal OC consisting of promoter DNA, including a TATA box and an 11-nucleotide mismatched region around the transcription start site, TATA box-binding protein (TBP), RNA polymerase (Pol) II, and general transcription factor (TF)IIB and TFIIF. In this minimal OC, TATA-DNA and TBP reside above the Pol II cleft between clamp and protrusion domains. Downstream DNA is dynamically loaded into and unloaded from the Pol II cleft at a timescale of seconds. The TFIIB core domain is displaced from the Pol II wall, where it is located in the closed promoter complex. These results reveal large overall structural changes during the initiation-elongation transition, which are apparently accommodated by the intrinsic flexibility of TFIIB.
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Affiliation(s)
- Barbara Treutlein
- Department of Chemistry and Center for Integrated Protein Science München, Ludwig-Maximilians-Universität München, Butenandtstr.11, 81377 Munich, Germany
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50
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Treutlein B, Muschielok A, Andrecka J, Jawhari A, Buchen C, Kostrewa D, Hög F, Cramer P, Michaelis J. Dynamic Architecture of the RNA Polymerase II Open Promoter Complex. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.1574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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