301
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Godoy P, Schmidt-Heck W, Hellwig B, Nell P, Feuerborn D, Rahnenführer J, Kattler K, Walter J, Blüthgen N, Hengstler JG. Assessment of stem cell differentiation based on genome-wide expression profiles. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0221. [PMID: 29786556 DOI: 10.1098/rstb.2017.0221] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2018] [Indexed: 12/24/2022] Open
Abstract
In recent years, protocols have been established to differentiate stem and precursor cells into more mature cell types. However, progress in this field has been hampered by difficulties to assess the differentiation status of stem cell-derived cells in an unbiased manner. Here, we present an analysis pipeline based on published data and methods to quantify the degree of differentiation and to identify transcriptional control factors explaining differences from the intended target cells or tissues. The pipeline requires RNA-Seq or gene array data of the stem cell starting population, derived 'mature' cells and primary target cells or tissue. It consists of a principal component analysis to represent global expression changes and to identify possible problems of the dataset that require special attention, such as: batch effects; clustering techniques to identify gene groups with similar features; over-representation analysis to characterize biological motifs and transcriptional control factors of the identified gene clusters; and metagenes as well as gene regulatory networks for quantitative cell-type assessment and identification of influential transcription factors. Possibilities and limitations of the analysis pipeline are illustrated using the example of human embryonic stem cell and human induced pluripotent cells to generate 'hepatocyte-like cells'. The pipeline quantifies the degree of incomplete differentiation as well as remaining stemness and identifies unwanted features, such as colon- and fibroblast-associated gene clusters that are absent in real hepatocytes but typically induced by currently available differentiation protocols. Finally, transcription factors responsible for incomplete and unwanted differentiation are identified. The proposed method is widely applicable and allows an unbiased and quantitative assessment of stem cell-derived cells.This article is part of the theme issue 'Designer human tissue: coming to a lab near you'.
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Affiliation(s)
- Patricio Godoy
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Wolfgang Schmidt-Heck
- Leibniz Institute for Natural Product Research and Infection Biology eV-Hans-Knöll Institute, Jena, Germany
| | - Birte Hellwig
- Department of Statistics, TU Dortmund University, Dortmund, Germany
| | - Patrick Nell
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - David Feuerborn
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | | | - Kathrin Kattler
- Department of Genetics, University of Saarland, Saarbrücken 66123, Germany
| | - Jörn Walter
- Institute of Pathology, Charité Universitätsmedizin, 10117 Berlin, Germany
| | - Nils Blüthgen
- Institute of Pathology, Charité Universitätsmedizin, 10117 Berlin, Germany.,Integrative Research Institute for the Life Sciences, Institute for Theoretical Biology, Humboldt Universität, 10115 Berlin, Germany
| | - Jan G Hengstler
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
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302
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scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets. Proc Natl Acad Sci U S A 2019; 116:9775-9784. [PMID: 31028141 DOI: 10.1073/pnas.1820006116] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Concerted examination of multiple collections of single-cell RNA sequencing (RNA-seq) data promises further biological insights that cannot be uncovered with individual datasets. Here we present scMerge, an algorithm that integrates multiple single-cell RNA-seq datasets using factor analysis of stably expressed genes and pseudoreplicates across datasets. Using a large collection of public datasets, we benchmark scMerge against published methods and demonstrate that it consistently provides improved cell type separation by removing unwanted factors; scMerge can also enhance biological discovery through robust data integration, which we show through the inference of development trajectory in a liver dataset collection.
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303
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Agarwal N, Popovic B, Martucci NJ, Fraunhoffer NA, Soto-Gutierrez A. Biofabrication of Autologous Human Hepatocytes for Transplantation: How Do We Get There? Gene Expr 2019; 19:89-95. [PMID: 30143060 PMCID: PMC6466180 DOI: 10.3727/105221618x15350366478989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Directed differentiation of hepatocytes from induced pluripotent stem cells (iPSCs) holds promise as source material for treating some liver disorders. The unlimited availability of perfectly differentiated iPSC-derived hepatocytes will dramatically facilitate cell therapies. While systems to manufacture large quantities of iPSC-derived cells have been developed, we have been unable to generate and maintain stable and mature adult liver cells ex vivo. This short review highlights important challenges and possible solutions to the current state of hepatocyte biofabrication for cellular therapies to treat liver diseases. Successful cell transplantation will require optimizing the best cell function, overcoming limitations to cell numbers and safety, as well as a number of other challenges. Collaboration among scientists, clinicians, and industry is critical for generating new autologous stem cell-based therapies to treat liver diseases.
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Affiliation(s)
- Nandini Agarwal
- *School of Bioscience and Technology, Vellore Institute of Technology, Vellore, India
- †Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Branimir Popovic
- †Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nicole J. Martucci
- †Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nicolas A. Fraunhoffer
- †Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- ‡Facultad de Ciencias de la Salud, Carrera de Medicina, Universidad Maimónides, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- §Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
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304
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Holloway EM, Capeling MM, Spence JR. Biologically inspired approaches to enhance human organoid complexity. Development 2019; 146:dev166173. [PMID: 30992275 PMCID: PMC6503984 DOI: 10.1242/dev.166173] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Organoids are complex three-dimensional in vitro organ-like model systems. Human organoids, which are derived from human pluripotent stem cells or primary human donor tissue, have been used to address fundamental questions about human development, stem cell biology and organ regeneration. Focus has now shifted towards implementation of organoids for biological discovery and advancing existing systems to more faithfully recapitulate the native organ. This work has highlighted significant unknowns in human biology and has invigorated new exploration into the cellular makeup of human organs during development and in the adult - work that is crucial for providing appropriate benchmarks for organoid systems. In this Review, we discuss efforts to characterize human organ cellular complexity and attempts to make organoid models more realistic through co-culture, transplantation and bioengineering approaches.
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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
| | - Meghan M Capeling
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Jason R Spence
- 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
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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305
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Skinnider MA, Squair JW, Foster LJ. Evaluating measures of association for single-cell transcriptomics. Nat Methods 2019; 16:381-386. [DOI: 10.1038/s41592-019-0372-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/25/2019] [Accepted: 03/05/2019] [Indexed: 12/13/2022]
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306
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Abstract
INTRODUCTION Research has made progress in organ fabrication using an extracellular matrix, cell sheets, or organoids. Human liver tissue has been constructed using a 3-dimensional (3D) bioprinter and showed evidence that an in vitro generated liver bud was reformed in a rodent liver model. This study describes the stages of development of rat fetal organs and liver structure and reviews recent progress in liver organoid transplantation. METHODS The authors developed the procedures for creating a transected plane for use in experimental microsurgery in rats. A liver lobe was fixed vertically with gauze and it was ligated with 6-0 silk suture in the cut line; the parenchyma was cut, and major vessels were ligated to create the transected plane. The ligated tissue was carefully resected. Hemostasis was not required and hepatic components remained on the transected plane. The plane was covered by omentum. RESULTS Using this model, we transplanted fetal liver or a 3D bioprinted liver organoid. This microsurgical method enabled creation of an intact liver parenchyma plane. No bleeding was observed. The transplanted liver components successfully engrafted on the liver. CONCLUSION This method may provide an essential environment for growing liver using portal and arterial blood flow.
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Affiliation(s)
- Eiji Kobayashi
- Department of Organ Fabrication, Keio University School of Medicine 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Shin Enosawa
- Department of Organ Fabrication, Keio University School of Medicine 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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307
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Zhang Y, Liu F. Multidimensional Single-Cell Analyses in Organ Development and Maintenance. Trends Cell Biol 2019; 29:477-486. [PMID: 30928527 DOI: 10.1016/j.tcb.2019.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 02/12/2019] [Accepted: 02/19/2019] [Indexed: 12/15/2022]
Abstract
The revolution of single-cell analysis tools in epigenomics, transcriptomics, lineage tracing, and transcriptome-scale RNA imaging, has boosted our understanding of the underlying molecular mechanisms during organ development and maintenance. Application of these tools enables the multidimensional study of organs, from cell atlas profiling, spatial organization, to cell-cell interaction. Here, we discuss recent progress in employing multidimensional single-cell analyses to address fundamental questions related to the development and maintenance of hematopoietic organs, brain and lung, which will also help provide insights into a better understanding of relevant diseases.
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Affiliation(s)
- Yifan Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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308
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Mucenski ML, Mahoney R, Adam M, Potter AS, Potter SS. Single cell RNA-seq study of wild type and Hox9,10,11 mutant developing uterus. Sci Rep 2019; 9:4557. [PMID: 30872674 PMCID: PMC6418183 DOI: 10.1038/s41598-019-40923-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/25/2019] [Indexed: 12/17/2022] Open
Abstract
The uterus is a remarkable organ that must guard against infections while maintaining the ability to support growth of a fetus without rejection. The Hoxa10 and Hoxa11 genes have previously been shown to play essential roles in uterus development and function. In this report we show that the Hoxa9,10,11, Hoxc9,10,11, Hoxd9,10,11 genes play a redundant role in the formation of uterine glands. In addition, we use single cell RNA-seq to create a high resolution gene expression atlas of the developing wild type mouse uterus. Cell types and subtypes are defined, for example dividing endothelial cells into arterial, venous, capillary, and lymphatic, while epithelial cells separate into luminal and glandular subtypes. Further, a surprising heterogeneity of stromal and myocyte cell types are identified. Transcription factor codes and ligand/receptor interactions are characterized. We also used single cell RNA-seq to globally define the altered gene expression patterns in all developing uterus cell types for two Hox mutants, with 8 or 9 mutant Hox genes. The mutants show a striking disruption of Wnt signaling as well as the Cxcl12/Cxcr4 ligand/receptor axis.
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Affiliation(s)
- Michael L Mucenski
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Robert Mahoney
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Andrew S Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
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309
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Yu J, Peng J, Chi H. Systems immunology: Integrating multi-omics data to infer regulatory networks and hidden drivers of immunity. ACTA ACUST UNITED AC 2019; 15:19-29. [PMID: 32789283 DOI: 10.1016/j.coisb.2019.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The immune system is a highly complex and dynamic biological system. It operates through intracellular molecular networks and intercellular (cell-cell) interaction networks. Systems immunology is an emerging discipline that applies systems biology approaches of integrating high-throughput multi-omics measurements with computational network modeling to better understand immunity at various scales. In this review, we summarize key omics technologies and computational approaches used for immunological studies at both population and single-cell levels. We highlight the hidden driver analysis based on data-driven networks and comment on the potential of translating systems immunology discoveries to immunotherapy of cancer and other human diseases.
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Affiliation(s)
- Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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310
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Abstract
Diabetes mellitus is a multifactorial disease affecting increasing numbers of patients worldwide. Progression to insulin-dependent diabetes mellitus is characterized by the loss or dysfunction of pancreatic β-cells, but the pathomechanisms underlying β-cell failure in type 1 diabetes mellitus and type 2 diabetes mellitus are still poorly defined. Regeneration of β-cell mass from residual islet cells or replacement by β-like cells derived from stem cells holds great promise to stop or reverse disease progression. However, the development of new treatment options is hampered by our limited understanding of human pancreas organogenesis due to the restricted access to primary tissues. Therefore, the challenge is to translate results obtained from preclinical model systems to humans, which requires comparative modelling of β-cell biology in health and disease. Here, we discuss diverse modelling systems across different species that provide spatial and temporal resolution of cellular and molecular mechanisms to understand the evolutionary conserved genotype-phenotype relationship and translate them to humans. In addition, we summarize the latest knowledge on organoids, stem cell differentiation platforms, primary micro-islets and pseudo-islets, bioengineering and microfluidic systems for studying human pancreas development and homeostasis ex vivo. These new modelling systems and platforms have opened novel avenues for exploring the developmental trajectory, physiology, biology and pathology of the human pancreas.
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Affiliation(s)
- Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany.
- Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
| | - Anika Böttcher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany.
- Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, Neuherberg, Germany.
- Institute of Stem Cell Research, Helmholtz Zentrum München, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
- Technical University of Munich, Medical Faculty, Munich, Germany.
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311
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LIM homeobox 2 promotes interaction between human iPS-derived hepatic progenitors and iPS-derived hepatic stellate-like cells. Sci Rep 2019; 9:2072. [PMID: 30765795 PMCID: PMC6376133 DOI: 10.1038/s41598-018-37430-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/06/2018] [Indexed: 02/01/2023] Open
Abstract
Human induced pluripotent stem (iPS) cells can differentiate into hepatocyte lineages, although the phenotype of the differentiated cells is immature compared to adult hepatocytes. Improvement of cell-cell interactions between epithelium and mesenchyme is a potential approach to address this phenotype issue. In this study, we developed a model system for improving interactions between human iPS-derived hepatic progenitor cells (iPS-HPCs) and human iPS-derived hepatic stellate cell-like cells (iPS-HSCs). The phenotype of iPS-HSCs, including gene and protein expression profiles and vitamin A storage, resembled that of hepatic stellate cells. Direct co-culture of iPS-HSCs with iPS-HPCs significantly improved hepatocytic maturation in iPS-HPCs, such as their capacity for albumin production. Next, we generated iPS cell lines overexpressing LIM homeobox 2 (LHX2), which suppresses myofibroblastic changes in HSCs in mice. Hepatocytic maturation in iPS-HPCs was significantly increased in direct co-culture with iPS-HSCs overexpressing LHX2, but not in co-culture with a human hepatic stellate cell line (LX-2) overexpressing LHX2. LHX2 regulated the expression of extracellular matrices, such as laminin and collagen, in iPS-HSCs. In conclusion, this study provides an evidence that LHX2 upregulation in iPS-HSCs promotes hepatocytic maturation of iPS-HPCs, and indicates that genetically modified iPS-HSCs will be of value for research into cell-cell interactions.
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312
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Homan KA, Gupta N, Kroll KT, Kolesky DB, Skylar-Scott M, Miyoshi T, Mau D, Valerius MT, Ferrante T, Bonventre JV, Lewis JA, Morizane R. Flow-enhanced vascularization and maturation of kidney organoids in vitro. Nat Methods 2019; 16:255-262. [PMID: 30742039 PMCID: PMC6488032 DOI: 10.1038/s41592-019-0325-y] [Citation(s) in RCA: 497] [Impact Index Per Article: 99.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/21/2018] [Indexed: 01/01/2023]
Abstract
Kidney organoids derived from human pluripotent stem cells have glomerular- and tubular-like compartments that are largely avascular and immature in static culture. Here we report an in vitro method for culturing kidney organoids under flow on millifluidic chips, which expands their endogenous pool of endothelial progenitor cells and generates vascular networks with perfusable lumens surrounded by mural cells. We found that vascularized kidney organoids cultured under flow had more mature podocyte and tubular compartments with enhanced cellular polarity and adult gene expression compared with that in static controls. Glomerular vascular development progressed through intermediate stages akin to those involved in the embryonic mammalian kidney's formation of capillary loops abutting foot processes. The association of vessels with these compartments was reduced after disruption of the endogenous VEGF gradient. The ability to induce substantial vascularization and morphological maturation of kidney organoids in vitro under flow opens new avenues for studies of kidney development, disease, and regeneration.
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Affiliation(s)
- Kimberly A Homan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Navin Gupta
- Renal Division, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Katharina T Kroll
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - David B Kolesky
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Mark Skylar-Scott
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Tomoya Miyoshi
- Renal Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Donald Mau
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - M Todd Valerius
- Renal Division, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Thomas Ferrante
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
| | - Joseph V Bonventre
- Renal Division, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Stem Cell Institute, Cambridge, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jennifer A Lewis
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA.
| | - Ryuji Morizane
- Renal Division, Brigham and Women's Hospital, Boston, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.
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313
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Affiliation(s)
- Mo Li
- From the King Abdullah University of Science and Technology, Thuwal, Saudi Arabia (M.L.); and the Salk Institute for Biological Studies, La Jolla, CA (J.C.I.B.)
| | - Juan C Izpisua Belmonte
- From the King Abdullah University of Science and Technology, Thuwal, Saudi Arabia (M.L.); and the Salk Institute for Biological Studies, La Jolla, CA (J.C.I.B.)
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314
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Wang F, Li G, Wu Z, Fan Z, Yang M, Wu T, Wang J, Zhang C, Wang S. Tracking diphyodont development in miniature pigs in vitro and in vivo. Biol Open 2019; 8:bio.037036. [PMID: 30683673 PMCID: PMC6398454 DOI: 10.1242/bio.037036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abnormalities of tooth number in humans, such as agenesis and supernumerary tooth formation, are closely related to diphyodont development. There is an increasing demand to understand the molecular and cellular mechanisms behind diphyodont development through the use of large animal models, since they are the most similar to the mechanism of human tooth development. However, attempting to study diphyodont development in large animals remains challenging due to large tooth size, prolonged growth stage and embryo manipulation. Here, we characterized the expression of possible genes for diphyodont development and odontogenesis of an organoid bud from single cells of tooth germs in vitro using Wzhishan pig strain (WZSP). Following this, we used a method of ectopic transplantation of tooth germs at cap stage to dynamically track diphyodont development of tooth germs in mouse subrenal capsules to overcome the restrictions in pig embryos. The results showed that pig tooth germ at cap stage could restore diphyodont development and maintain efficient long-term survival and growth in mouse subrenal capsules, which is suitable for future manipulation of large mammalian tooth development. Our pilot study provided an alternative for studying diphyodont development in large mammals, which will further promote the use of pig as a diphyodont model similar to humans for craniofacial development study. Summary: Little is known about diphyodont development in large animals. Our pilot trial characterized this gene expression and developed an alternative method to track diphyodont development in pigs.
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Affiliation(s)
- Fu Wang
- Molecular Laboratory for Gene Therapy & Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing 100050, China.,Department of Basic Oral Sciences, School of Stomatology, Dalian Medical University, Dalian 116044, China
| | - Guoqing Li
- Molecular Laboratory for Gene Therapy & Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing 100050, China
| | - Zhifang Wu
- Molecular Laboratory for Gene Therapy & Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing 100050, China
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing 100050, China
| | - Min Yang
- Department of Basic Oral Sciences, School of Stomatology, Dalian Medical University, Dalian 116044, China
| | - Tingting Wu
- Molecular Laboratory for Gene Therapy & Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing 100050, China
| | - Jinsong Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Chunmei Zhang
- Molecular Laboratory for Gene Therapy & Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing 100050, China
| | - Songlin Wang
- Molecular Laboratory for Gene Therapy & Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing 100050, China .,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
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315
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Jang S, Collin de l'Hortet A, Soto-Gutierrez A. Induced Pluripotent Stem Cell-Derived Endothelial Cells: Overview, Current Advances, Applications, and Future Directions. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:502-512. [PMID: 30653953 DOI: 10.1016/j.ajpath.2018.12.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 11/12/2018] [Accepted: 12/05/2018] [Indexed: 12/13/2022]
Abstract
Endothelial cells are prevalent in our bodies and serve multiple functions. By lining the vasculature, they provide a barrier to tissues and facilitate the transport of molecules and cells. They also maintain hemostasis and modulate blood flow by reacting to chemokines and releasing signal molecules. Thus, endothelial dysfunction leads to a wide variety of diseases, including atherosclerosis and coronary artery disease. In today's era of stem cell research, induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) have emerged for research and engineering purposes. They are not only tools for studying disease states but are also a crucial part of efforts to engineer vessel and organ grafts. As the techniques in cell culture, microfluidics, and personalized medicine concomitantly improve, the potential for iPSC-ECs is enormous. We review functions of endothelium in our bodies, the development and uses of iPSC-ECs, and the possible avenues to explore in the future.
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Affiliation(s)
- Sae Jang
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota.
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316
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Hu Q, Greene CS. Parameter tuning is a key part of dimensionality reduction via deep variational autoencoders for single cell RNA transcriptomics. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2019. [PMID: 30963075 DOI: 10.1101/385534] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful tool to profile the transcriptomes of a large number of individual cells at a high resolution. These data usually contain measurements of gene expression for many genes in thousands or tens of thousands of cells, though some datasets now reach the million-cell mark. Projecting high-dimensional scRNA-seq data into a low dimensional space aids downstream analysis and data visualization. Many recent preprints accomplish this using variational autoencoders (VAE), generative models that learn underlying structure of data by compress it into a constrained, low dimensional space. The low dimensional spaces generated by VAEs have revealed complex patterns and novel biological signals from large-scale gene expression data and drug response predictions. Here, we evaluate a simple VAE approach for gene expression data, Tybalt, by training and measuring its performance on sets of simulated scRNA-seq data. We find a number of counter-intuitive performance features: i.e., deeper neural networks can struggle when datasets contain more observations under some parameter configurations. We show that these methods are highly sensitive to parameter tuning: when tuned, the performance of the Tybalt model, which was not optimized for scRNA-seq data, outperforms other popular dimension reduction approaches - PCA, ZIFA, UMAP and t-SNE. On the other hand, without tuning performance can also be remarkably poor on the same data. Our results should discourage authors and reviewers from relying on self-reported performance comparisons to evaluate the relative value of contributions in this area at this time. Instead, we recommend that attempts to compare or benchmark autoencoder methods for scRNA-seq data be performed by disinterested third parties or by methods developers only on unseen benchmark data that are provided to all participants simultaneously because the potential for performance differences due to unequal parameter tuning is so high.
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Affiliation(s)
- Qiwen Hu
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA,
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA,
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317
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Giladi A, Amit I. Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries. Cell 2018; 172:14-21. [PMID: 29328909 DOI: 10.1016/j.cell.2017.11.011] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/01/2017] [Accepted: 11/06/2017] [Indexed: 02/08/2023]
Abstract
The immunology field has invested great efforts and ingenuity to characterize the various immune cell types and elucidate their functions. However, accumulating evidence indicates that current technologies and classification schemes are limited in their ability to account for the functional heterogeneity of immune processes. Single-cell genomics hold the potential to revolutionize the way we characterize complex immune cell assemblies and study their spatial organization, dynamics, clonal distribution, pathways, function, and crosstalks. In this Perspective, we consider recent and forthcoming technological and analytical advances in single-cell genomics and the potential impact of those advances on the future of immunology research and immunotherapy.
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Affiliation(s)
- Amir Giladi
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | - Ido Amit
- Department of Immunology, Weizmann Institute, Rehovot 76100, Israel.
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318
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Abstract
The essential liver exocrine and endocrine functions require a precise spatial arrangement of the hepatic lobule consisting of the central vein, portal vein, hepatic artery, intrahepatic bile duct system, and hepatocyte zonation. This allows blood to be carried through the liver parenchyma sampled by all hepatocytes and bile produced by the hepatocytes to be carried out of the liver through the intrahepatic bile duct system composed of cholangiocytes. The molecular orchestration of multiple signaling pathways and epigenetic factors is required to set up lineage restriction of the bipotential hepatoblast progenitor into the hepatocyte and cholangiocyte cell lineages, and to further refine cell fate heterogeneity within each cell lineage reflected in the functional heterogeneity of hepatocytes and cholangiocytes. In addition to the complex molecular regulation, there is a complicated morphogenetic choreography observed in building the refined hepatic epithelial architecture. Given the multifaceted molecular and cellular regulation, it is not surprising that impairment of any of these processes can result in acute and chronic hepatobiliary diseases. To enlighten the development of potential molecular and cellular targets for therapeutic options, an understanding of how the intricate hepatic molecular and cellular interactions are regulated is imperative. Here, we review the signaling pathways and epigenetic factors regulating hepatic cell lineages, fates, and epithelial architecture.
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Affiliation(s)
- Stacey S Huppert
- Division of Gastroenterology, Hepatology & Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.
| | - Makiko Iwafuchi-Doi
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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319
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Xu H, Jiao Y, Qin S, Zhao W, Chu Q, Wu K. Organoid technology in disease modelling, drug development, personalized treatment and regeneration medicine. Exp Hematol Oncol 2018; 7:30. [PMID: 30534474 PMCID: PMC6282260 DOI: 10.1186/s40164-018-0122-9] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 11/29/2018] [Indexed: 12/13/2022] Open
Abstract
Organoid technology bridges the gap between conventional two-dimensional cell line culture and in vivo models. The near-physiological technology can virtually recapitulates organ development and human diseases, such as infectious diseases, genetic abnormality and even cancers. In addition, organoids can more accurately predict drug responses, and serve as an excellent platform for drug development, including efficacy evaluation, toxicity testing and pharmacokinetics analysis. Furthermore, organoids can also be exploited to explore the possible optimized treatment strategies for each individual patient. Besides, organoid technology is a promising strategy for regeneration medicine and transplantation use, which can overcome the deficiency in the supply of healthy donor tissues and inherent immunological rejection through establishing isogenic organoids from minuscule amounts of patient biopsies. Collectively, organoids hold enormous potential for clinical applications and bring basic research closer to clinical practice. In this review, we described common organoid lines, summarized the potential clinical applications, and outlined the current limitations.
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Affiliation(s)
- Hanxiao Xu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030 China
| | - Ying Jiao
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030 China
| | - Shuang Qin
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030 China
| | - Weiheng Zhao
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030 China
| | - Qian Chu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030 China
| | - Kongming Wu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030 China
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320
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Bioengineering the innate vasculature of complex organs: what have we learned so far. Curr Opin Organ Transplant 2018; 23:657-663. [DOI: 10.1097/mot.0000000000000577] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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321
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Aranda-Anzaldo A, Dent MA. Landscaping the epigenetic landscape of cancer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 140:155-174. [DOI: 10.1016/j.pbiomolbio.2018.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/16/2018] [Accepted: 06/07/2018] [Indexed: 02/07/2023]
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322
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McCracken IR, Taylor RS, Henderson NC, Sluimer JC, Baker AH. Unravelling atherosclerotic heterogeneity by single cell RNA sequencing. Curr Opin Lipidol 2018; 29:488-489. [PMID: 30379738 DOI: 10.1097/mol.0000000000000559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
| | - Richard S Taylor
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Neil C Henderson
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Judith C Sluimer
- Centre for Cardiovascular Science
- Department of Pathology, CARIM School for Cardiovascular Diseases, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Andrew H Baker
- Centre for Cardiovascular Science
- Department of Pathology, CARIM School for Cardiovascular Diseases, Maastricht University Medical Center, Maastricht, The Netherlands
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323
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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: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [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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324
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Cohen M, Giladi A, Gorki AD, Solodkin DG, Zada M, Hladik A, Miklosi A, Salame TM, Halpern KB, David E, Itzkovitz S, Harkany T, Knapp S, Amit I. Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting. Cell 2018; 175:1031-1044.e18. [DOI: 10.1016/j.cell.2018.09.009] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 07/16/2018] [Accepted: 09/07/2018] [Indexed: 12/20/2022]
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325
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Vento-Tormo R, Efremova M, Botting RA, Turco MY, Vento-Tormo M, Meyer KB, Park JE, Stephenson E, Polański K, Goncalves A, Gardner L, Holmqvist S, Henriksson J, Zou A, Sharkey AM, Millar B, Innes B, Wood L, Wilbrey-Clark A, Payne RP, Ivarsson MA, Lisgo S, Filby A, Rowitch DH, Bulmer JN, Wright GJ, Stubbington MJT, Haniffa M, Moffett A, Teichmann SA. Single-cell reconstruction of the early maternal-fetal interface in humans. Nature 2018; 563:347-353. [PMID: 30429548 PMCID: PMC7612850 DOI: 10.1038/s41586-018-0698-6] [Citation(s) in RCA: 1257] [Impact Index Per Article: 209.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 10/15/2018] [Indexed: 11/08/2022]
Abstract
During early human pregnancy the uterine mucosa transforms into the decidua, into which the fetal placenta implants and where placental trophoblast cells intermingle and communicate with maternal cells. Trophoblast-decidual interactions underlie common diseases of pregnancy, including pre-eclampsia and stillbirth. Here we profile the transcriptomes of about 70,000 single cells from first-trimester placentas with matched maternal blood and decidual cells. The cellular composition of human decidua reveals subsets of perivascular and stromal cells that are located in distinct decidual layers. There are three major subsets of decidual natural killer cells that have distinctive immunomodulatory and chemokine profiles. We develop a repository of ligand-receptor complexes and a statistical tool to predict the cell-type specificity of cell-cell communication via these molecular interactions. Our data identify many regulatory interactions that prevent harmful innate or adaptive immune responses in this environment. Our single-cell atlas of the maternal-fetal interface reveals the cellular organization of the decidua and placenta, and the interactions that are critical for placentation and reproductive success.
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Affiliation(s)
- Roser Vento-Tormo
- Wellcome Sanger Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | | | - Rachel A Botting
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Margherita Y Turco
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | | | | | | | - Emily Stephenson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | - Angela Goncalves
- Wellcome Sanger Institute, Cambridge, UK
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lucy Gardner
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Staffan Holmqvist
- Department of Paediatrics, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Angela Zou
- Wellcome Sanger Institute, Cambridge, UK
| | - Andrew M Sharkey
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ben Millar
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Barbara Innes
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Wood
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Rebecca P Payne
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | - Steve Lisgo
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Filby
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - David H Rowitch
- Department of Paediatrics, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Judith N Bulmer
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Muzlifah Haniffa
- Wellcome Sanger Institute, Cambridge, UK.
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Ashley Moffett
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK.
- Theory of Condensed Matter Group, The Cavendish Laboratory, University of Cambridge, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
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326
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Grandy R, Tomaz RA, Vallier L. Modeling Disease with Human Inducible Pluripotent Stem Cells. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2018; 14:449-468. [PMID: 30355153 DOI: 10.1146/annurev-pathol-020117-043634] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding the physiopathology of disease remains an essential step in developing novel therapeutics. Although animal models have certainly contributed to advancing this enterprise, their limitation in modeling all the aspects of complex human disorders is one of the major challenges faced by the biomedical research field. Human induced pluripotent stem cells (hiPSCs) derived from patients represent a great opportunity to overcome this deficiency because these cells cover the genetic diversity needed to fully model human diseases. Here, we provide an overview of the history of hiPSC technology and discuss common challenges and approaches that we and others have faced when using hiPSCs to model disease. Our emphasis is on liver disease, and consequently, we review the progress made using this technology to produce functional liver cells in vitro and how these systems are being used to recapitulate a diversity of developmental, metabolic, genetic, and infectious liver disorders.
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Affiliation(s)
- Rodrigo Grandy
- Wellcome and MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom; .,Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
| | - Rute A Tomaz
- Wellcome and MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom; .,Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
| | - Ludovic Vallier
- Wellcome and MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom; .,Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
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327
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Dynamic intercellular transport modulates the spatial patterning of differentiation during early neural commitment. Nat Commun 2018; 9:4111. [PMID: 30291250 PMCID: PMC6173785 DOI: 10.1038/s41467-018-06693-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 09/17/2018] [Indexed: 01/01/2023] Open
Abstract
The initiation of heterogeneity within a population of phenotypically identical progenitors is a critical event for the onset of morphogenesis and differentiation patterning. Gap junction communication within multicellular systems produces complex networks of intercellular connectivity that result in heterogeneous distributions of intracellular signaling molecules. In this study, we investigate emergent systems-level behavior of the intercellular network within embryonic stem cell (ESC) populations and corresponding spatial organization during early neural differentiation. An agent-based model incorporates experimentally-determined parameters to yield complex transport networks for delivery of pro-differentiation cues between neighboring cells, reproducing the morphogenic trajectories during retinoic acid-accelerated mouse ESC differentiation. Furthermore, the model correctly predicts the delayed differentiation and preserved spatial features of the morphogenic trajectory that occurs in response to intercellular perturbation. These findings suggest an integral role of gap junction communication in the temporal coordination of emergent patterning during early differentiation and neural commitment of pluripotent stem cells.
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328
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Wang D, Gu J. VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder. GENOMICS, PROTEOMICS & BIOINFORMATICS 2018; 16:320-331. [PMID: 30576740 PMCID: PMC6364131 DOI: 10.1016/j.gpb.2018.08.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/09/2018] [Accepted: 08/08/2018] [Indexed: 02/08/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful technique to analyze the transcriptomic heterogeneities at the single cell level. It is an important step for studying cell sub-populations and lineages, with an effective low-dimensional representation and visualization of the original scRNA-Seq data. At the single cell level, the transcriptional fluctuations are much larger than the average of a cell population, and the low amount of RNA transcripts will increase the rate of technical dropout events. Therefore, scRNA-seq data are much noisier than traditional bulk RNA-seq data. In this study, we proposed the deep variational autoencoder for scRNA-seq data (VASC), a deep multi-layer generative model, for the unsupervised dimension reduction and visualization of scRNA-seq data. VASC can explicitly model the dropout events and find the nonlinear hierarchical feature representations of the original data. Tested on over 20 datasets, VASC shows superior performances in most cases and exhibits broader dataset compatibility compared to four state-of-the-art dimension reduction and visualization methods. In addition, VASC provides better representations for very rare cell populations in the 2D visualization. As a case study, VASC successfully re-establishes the cell dynamics in pre-implantation embryos and identifies several candidate marker genes associated with early embryo development. Moreover, VASC also performs well on a 10× Genomics dataset with more cells and higher dropout rate.
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Affiliation(s)
- Dongfang Wang
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division & Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Jin Gu
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division & Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China.
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329
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330
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Lukassen S, Bosch E, Ekici AB, Winterpacht A. Single-cell RNA sequencing of adult mouse testes. Sci Data 2018; 5:180192. [PMID: 30204153 PMCID: PMC6132189 DOI: 10.1038/sdata.2018.192] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/20/2018] [Indexed: 11/30/2022] Open
Abstract
Spermatogenesis is an efficient and complex system of continuous cell differentiation. Previous studies investigating the transcriptomes of different cell populations in the testis relied either on sorting cells, cell depletion, or juvenile animals where not all stages of spermatogenesis have been completed. We present single-cell RNA sequencing (scRNA-Seq) data of 2,500 cells from the testes of two 8-week-old C57Bl/6J mice. Our dataset includes all spermatogenic stages from preleptotene to condensing spermatids as well as individual spermatogonia, Sertoli and Leydig cells. The data capture the full continuity of the meiotic and postmeiotic stages of spermatogenesis, and is thus ideally suited for marker discovery, network inference and similar analyses for which temporal ordering of differentiation processes can be exploited. Furthermore, it can serve as a reference for future studies involving single-cell RNA-Seq in mice where spermatogenesis is perturbed.
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Affiliation(s)
- Soeren Lukassen
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Elisabeth Bosch
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
| | - Andreas Winterpacht
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Schwabachanlage 10, 91054 Erlangen, Germany
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331
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Matsuzaki T, Matsumoto S, Kasai T, Yoshizawa E, Okamoto S, Yoshikawa HY, Taniguchi H, Takebe T. Defining Lineage-Specific Membrane Fluidity Signatures that Regulate Adhesion Kinetics. Stem Cell Reports 2018; 11:852-860. [PMID: 30197117 PMCID: PMC6178887 DOI: 10.1016/j.stemcr.2018.08.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/10/2018] [Accepted: 08/11/2018] [Indexed: 12/13/2022] Open
Abstract
Cellular membrane fluidity is a critical modulator of cell adhesion and migration, prompting us to define the systematic landscape of lineage-specific cellular fluidity throughout differentiation. Here, we have unveiled membrane fluidity landscapes in various lineages ranging from human pluripotency to differentiated progeny: (1) membrane rigidification precedes the exit from pluripotency, (2) membrane composition modulates activin signaling transmission, and (3) signatures are relatively germ layer specific presumably due to unique lipid compositions. By modulating variable lineage-specific fluidity, we developed a label-free “adhesion sorting (AdSort)” method with simple cultural manipulation, effectively eliminating pluripotent stem cells and purifying target population as a result of the over 1,150 of screened conditions combining compounds and matrices. These results underscore the important role of tunable membrane fluidity in influencing stem cell maintenance and differentiation that can be translated into lineage-specific cell purification strategy. Membrane rigidification precedes the exit from pluripotency Germ layer-specific membrane fluidity signature exists Identification of polyphenols as a membrane fluidity modulator Fluidity-based adhesion sorting purify differentiated progeny from pluripotency
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Affiliation(s)
- Takahisa Matsuzaki
- Institute of Research, Tokyo Medical and Dental University (TMDU), 15-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan
| | - Shinya Matsumoto
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan
| | - Toshiharu Kasai
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan
| | - Emi Yoshizawa
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan
| | - Satoshi Okamoto
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan
| | - Hiroshi Y Yoshikawa
- Department of Chemistry, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Hideki Taniguchi
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan; Advanced Medical Research Center, Yokohama City University, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan
| | - Takanori Takebe
- Institute of Research, Tokyo Medical and Dental University (TMDU), 15-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Kanazawa-ku 3-9, Yokohama, Kanagawa 236-0004, Japan; Advanced Medical Research Center, Yokohama City University, 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.
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332
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Miranda CC, Fernandes TG, Pinto SN, Prieto M, Diogo MM, Cabral JM. A scale out approach towards neural induction of human induced pluripotent stem cells for neurodevelopmental toxicity studies. Toxicol Lett 2018; 294:51-60. [DOI: 10.1016/j.toxlet.2018.05.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/28/2018] [Accepted: 05/04/2018] [Indexed: 12/30/2022]
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333
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Tam PKH, Yiu RS, Lendahl U, Andersson ER. Cholangiopathies - Towards a molecular understanding. EBioMedicine 2018; 35:381-393. [PMID: 30236451 PMCID: PMC6161480 DOI: 10.1016/j.ebiom.2018.08.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/06/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
Liver diseases constitute an important medical problem, and a number of these diseases, termed cholangiopathies, affect the biliary system of the liver. In this review, we describe the current understanding of the causes of cholangiopathies, which can be genetic, viral or environmental, and the few treatment options that are currently available beyond liver transplantation. We then discuss recent rapid progress in a number of areas relevant for decoding the disease mechanisms for cholangiopathies. This includes novel data from analysis of transgenic mouse models and organoid systems, and we outline how this information can be used for disease modeling and potential development of novel therapy concepts. We also describe recent advances in genomic and transcriptomic analyses and the importance of such studies for improving diagnosis and determining whether certain cholangiopathies should be viewed as distinct or overlapping disease entities.
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Affiliation(s)
- Paul K H Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, and Dr. Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, and The University of Hong Kong, Hong Kong.
| | - Rachel S Yiu
- Department of Surgery, Li Ka Shing Faculty of Medicine, and Dr. Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, and The University of Hong Kong, Hong Kong
| | - Urban Lendahl
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Emma R Andersson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
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334
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Packer J, Trapnell C. Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation. Trends Genet 2018; 34:653-665. [PMID: 30007833 PMCID: PMC6097890 DOI: 10.1016/j.tig.2018.06.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/05/2018] [Accepted: 06/07/2018] [Indexed: 12/12/2022]
Abstract
Cells in a multicellular organism fulfill specific functions by enacting cell-type-specific programs of gene regulation. Single-cell RNA sequencing technologies have provided a transformative view of cell-type-specific gene expression, the output of cell-type-specific gene regulatory programs. This review discusses new single-cell genomic technologies that complement single-cell RNA sequencing by providing additional readouts of cellular state beyond the transcriptome. We highlight regression models as a simple yet powerful approach to relate gene expression to other aspects of cellular state, and in doing so, gain insights into the biochemical mechanisms that are necessary to produce a given gene expression output.
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Affiliation(s)
- Jonathan Packer
- Department of Genome Sciences, Room S333, Foege Building, Box 355065, Seattle, WA 98105, USA
| | - Cole Trapnell
- Department of Genome Sciences, Room S333, Foege Building, Box 355065, Seattle, WA 98105, USA.
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335
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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] [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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336
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Rashidi H, Luu NT, Alwahsh SM, Ginai M, Alhaque S, Dong H, Tomaz RA, Vernay B, Vigneswara V, Hallett JM, Chandrashekran A, Dhawan A, Vallier L, Bradley M, Callanan A, Forbes SJ, Newsome PN, Hay DC. 3D human liver tissue from pluripotent stem cells displays stable phenotype in vitro and supports compromised liver function in vivo. Arch Toxicol 2018; 92:3117-3129. [PMID: 30155720 PMCID: PMC6132688 DOI: 10.1007/s00204-018-2280-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 07/31/2018] [Indexed: 12/15/2022]
Abstract
Liver disease is an escalating global health issue. While liver transplantation is an effective mode of therapy, patient mortality has increased due to the shortage of donor organs. Developing renewable sources of human liver tissue is therefore attractive. Pluripotent stem cell-derived liver tissue represents a potential alternative to cadaver derived hepatocytes and whole organ transplant. At present, two-dimensional differentiation procedures deliver tissue lacking certain functions and long-term stability. Efforts to overcome these limiting factors have led to the building of three-dimensional (3D) cellular aggregates. Although enabling for the field, their widespread application is limited due to their reliance on variable biological components. Our studies focused on the development of 3D liver tissue under defined conditions. In vitro generated 3D tissues exhibited stable phenotype for over 1 year in culture, providing an attractive resource for long-term in vitro studies. Moreover, 3D derived tissue provided critical liver support in two animal models, including immunocompetent recipients. Therefore, we believe that our study provides stable human tissue to better model liver biology 'in the dish', and in the future may permit the support of compromised liver function in humans.
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Affiliation(s)
- Hassan Rashidi
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Nguyet-Thin Luu
- Centre for Liver Research, Institute of Immunology and Immunotherapy and National Institute for Health Research Biomedical Research Centre at University Hospitals Birmingham NHS Foundation Trust and the University of Birmingham, Birmingham, UK
| | - Salamah M Alwahsh
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Maaria Ginai
- Institute of Bioengineering, The University of Edinburgh, King's Buildings, Edinburgh, EH9 3DW, UK
| | - Sharmin Alhaque
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Hua Dong
- School of Chemistry, University of Edinburgh, Kings Buildings, EH9 3FJ, Edinburgh, UK
| | - Rute A Tomaz
- Anne McLaren Laboratory, Wellcome Trust-MRC Stem Cell Institute, University of Cambridge, Cambridge, CB2 0SZ, UK
| | - Bertrand Vernay
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Vasanthy Vigneswara
- Centre for Liver Research, Institute of Immunology and Immunotherapy and National Institute for Health Research Biomedical Research Centre at University Hospitals Birmingham NHS Foundation Trust and the University of Birmingham, Birmingham, UK
| | - John M Hallett
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Anil Chandrashekran
- Child Health Clinical Academic Group, MRC Centre for Transplantation, King's College London, London, UK
| | - Anil Dhawan
- Child Health Clinical Academic Group, MRC Centre for Transplantation, King's College London, London, UK
| | - Ludovic Vallier
- Anne McLaren Laboratory, Wellcome Trust-MRC Stem Cell Institute, University of Cambridge, Cambridge, CB2 0SZ, UK
| | - Mark Bradley
- School of Chemistry, University of Edinburgh, Kings Buildings, EH9 3FJ, Edinburgh, UK
| | - Anthony Callanan
- Institute of Bioengineering, The University of Edinburgh, King's Buildings, Edinburgh, EH9 3DW, UK
| | - Stuart J Forbes
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Philip N Newsome
- Centre for Liver Research, Institute of Immunology and Immunotherapy and National Institute for Health Research Biomedical Research Centre at University Hospitals Birmingham NHS Foundation Trust and the University of Birmingham, Birmingham, UK.,Liver Unit, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - David C Hay
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK.
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337
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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] [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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338
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Mertz DR, Ahmed T, Takayama S. Engineering cell heterogeneity into organs-on-a-chip. LAB ON A CHIP 2018; 18:2378-2395. [PMID: 30040104 PMCID: PMC6081245 DOI: 10.1039/c8lc00413g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Organ-on-a-chip development is an application that will benefit from advances in cell heterogeneity characterization because these culture models are intended to mimic in vivo microenvironments, which are complex and dynamic. Due in no small part to advances in microfluidic single cell analysis methods, cell-to-cell variability is an increasingly understood feature of physiological tissues, with cell types from as common as 1 out of every 2 cells to as rare as 1 out of every 100 000 cells having important roles in the biochemical and biological makeup of tissues and organs. Variability between neighboring cells can be transient or maintained, and ordered or stochastic. This review covers three areas of well-studied cell heterogeneity that are informative for organ-on-a-chip development efforts: tumors, the lung, and the intestine. Then we look at how recent single cell analysis strategies have enabled better understanding of heterogeneity within in vitro and in vivo tissues. Finally, we provide a few work-arounds for adapting current on-chip culture methods to better mimic physiological cell heterogeneity including accounting for crucial rare cell types and events.
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Affiliation(s)
- David R Mertz
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech College of Engineering and Emory School of Medicine, USA.
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339
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O'Donoghue SI, Baldi BF, Clark SJ, Darling AE, Hogan JM, Kaur S, Maier-Hein L, McCarthy DJ, Moore WJ, Stenau E, Swedlow JR, Vuong J, Procter JB. Visualization of Biomedical Data. Annu Rev Biomed Data Sci 2018. [DOI: 10.1146/annurev-biodatasci-080917-013424] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The rapid increase in volume and complexity of biomedical data requires changes in research, communication, and clinical practices. This includes learning how to effectively integrate automated analysis with high–data density visualizations that clearly express complex phenomena. In this review, we summarize key principles and resources from data visualization research that help address this difficult challenge. We then survey how visualization is being used in a selection of emerging biomedical research areas, including three-dimensional genomics, single-cell RNA sequencing (RNA-seq), the protein structure universe, phosphoproteomics, augmented reality–assisted surgery, and metagenomics. While specific research areas need highly tailored visualizations, there are common challenges that can be addressed with general methods and strategies. Also common, however, are poor visualization practices. We outline ongoing initiatives aimed at improving visualization practices in biomedical research via better tools, peer-to-peer learning, and interdisciplinary collaboration with computer scientists, science communicators, and graphic designers. These changes are revolutionizing how we see and think about our data.
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Affiliation(s)
- Seán I. O'Donoghue
- Data61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Eveleigh NSW 2015, Australia
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW), Kensington NSW 2033, Australia
| | - Benedetta Frida Baldi
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
| | - Susan J. Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney NSW 2010, Australia
| | - Aaron E. Darling
- The ithree Institute, University of Technology Sydney, Ultimo NSW 2007, Australia
| | - James M. Hogan
- School of Electrical Engineering and Computer Science, Queensland University of Technology, Brisbane QLD, 4000, Australia
| | - Sandeep Kaur
- School of Computer Science and Engineering, University of New South Wales (UNSW), Kensington NSW 2033, Australia
| | - Lena Maier-Hein
- Division of Computer Assisted Medical Interventions (CAMI), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Davis J. McCarthy
- European Bioinformatics Institute (EBI), European Molecular Biology Laboratory (EMBL), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
- St. Vincent's Institute of Medical Research, Fitzroy VIC 3065, Australia
| | - William J. Moore
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Esther Stenau
- Division of Computer Assisted Medical Interventions (CAMI), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jason R. Swedlow
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Jenny Vuong
- Data61, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Eveleigh NSW 2015, Australia
| | - James B. Procter
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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340
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Massive and Reproducible Production of Liver Buds Entirely from Human Pluripotent Stem Cells. Cell Rep 2018; 21:2661-2670. [PMID: 29212014 DOI: 10.1016/j.celrep.2017.11.005] [Citation(s) in RCA: 243] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 09/01/2017] [Accepted: 10/31/2017] [Indexed: 12/13/2022] Open
Abstract
Organoid technology provides a revolutionary paradigm toward therapy but has yet to be applied in humans, mainly because of reproducibility and scalability challenges. Here, we overcome these limitations by evolving a scalable organ bud production platform entirely from human induced pluripotent stem cells (iPSC). By conducting massive "reverse" screen experiments, we identified three progenitor populations that can effectively generate liver buds in a highly reproducible manner: hepatic endoderm, endothelium, and septum mesenchyme. Furthermore, we achieved human scalability by developing an omni-well-array culture platform for mass producing homogeneous and miniaturized liver buds on a clinically relevant large scale (>108). Vascularized and functional liver tissues generated entirely from iPSCs significantly improved subsequent hepatic functionalization potentiated by stage-matched developmental progenitor interactions, enabling functional rescue against acute liver failure via transplantation. Overall, our study provides a stringent manufacturing platform for multicellular organoid supply, thus facilitating clinical and pharmaceutical applications especially for the treatment of liver diseases through multi-industrial collaborations.
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341
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Hopp L, Loeffler-Wirth H, Nersisyan L, Arakelyan A, Binder H. Footprints of Sepsis Framed Within Community Acquired Pneumonia in the Blood Transcriptome. Front Immunol 2018; 9:1620. [PMID: 30065722 PMCID: PMC6056630 DOI: 10.3389/fimmu.2018.01620] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/29/2018] [Indexed: 12/14/2022] Open
Abstract
We analyzed the blood transcriptome of sepsis framed within community-acquired pneumonia (CAP) and characterized its molecular and cellular heterogeneity in terms of functional modules of co-regulated genes with impact for the underlying pathophysiological mechanisms. Our results showed that CAP severity is associated with immune suppression owing to T-cell exhaustion and HLA and chemokine receptor deactivation, endotoxin tolerance, macrophage polarization, and metabolic conversion from oxidative phosphorylation to glycolysis. We also found footprints of host's response to viruses and bacteria, altered levels of mRNA from erythrocytes and platelets indicating coagulopathy that parallel severity of sepsis and survival. Finally, our data demonstrated chromatin re-modeling associated with extensive transcriptional deregulation of chromatin modifying enzymes, which suggests the extensive changes of DNA methylation with potential impact for marker selection and functional characterization. Based on the molecular footprints identified, we propose a novel stratification of CAP cases into six groups differing in the transcriptomic scores of CAP severity, interferon response, and erythrocyte mRNA expression with impact for prognosis. Our analysis increases the resolution of transcriptomic footprints of CAP and reveals opportunities for selecting sets of transcriptomic markers with impact for translation of omics research in terms of patient stratification schemes and sets of signature genes.
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Affiliation(s)
- Lydia Hopp
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Henry Loeffler-Wirth
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
| | - Lilit Nersisyan
- Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Arsen Arakelyan
- Group of Bioinformatics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Hans Binder
- Interdisciplinary Centre for Bioinformatics, Universität Leipzig, Leipzig, Germany
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342
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RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomas. Oncogene 2018; 37:6136-6151. [PMID: 29995873 DOI: 10.1038/s41388-018-0385-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 12/13/2022]
Abstract
Recent studies revealed trajectories of mutational events in early melanomagenesis, but the accompanying changes in gene expression are far less understood. Therefore, we performed a comprehensive RNA-seq analysis of laser-microdissected melanocytic nevi (n = 23) and primary melanoma samples (n = 57) and characterized the molecular mechanisms of early melanoma development. Using self-organizing maps, unsupervised clustering, and analysis of pseudotime (PT) dynamics to identify evolutionary trajectories, we describe here two transcriptomic types of melanocytic nevi (N1 and N2) and primary melanomas (M1 and M2). N1/M1 lesions are characterized by pigmentation-type and MITF gene signatures, and a high prevalence of NRAS mutations in M1 melanomas. N2/M2 lesions are characterized by inflammatory-type and AXL gene signatures with an equal distribution of wild-type and mutated BRAF and low prevalence of NRAS mutations in M2 melanomas. Interestingly, N1 nevi and M1 melanomas and N2 nevi and M2 melanomas, respectively, cluster together, but there is no clustering in a stage-dependent manner. Transcriptional signatures of M1 melanomas harbor signatures of BRAF/MEK inhibitor resistance and M2 melanomas harbor signatures of anti-PD-1 antibody treatment resistance. Pseudotime dynamics of nevus and melanoma samples are suggestive for a switch-like immune-escape mechanism in melanoma development with downregulation of immune genes paralleled by an increasing expression of a cell cycle signature in late-stage melanomas. Taken together, the transcriptome analysis identifies gene signatures and mechanisms underlying development of melanoma in early and late stages with relevance for diagnostics and therapy.
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343
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Han S, Tan C, Ding J, Wang J, Ma'ayan A, Gouon-Evans V. Endothelial cells instruct liver specification of embryonic stem cell-derived endoderm through endothelial VEGFR2 signaling and endoderm epigenetic modifications. Stem Cell Res 2018; 30:163-170. [PMID: 29936335 DOI: 10.1016/j.scr.2018.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/05/2018] [Accepted: 06/07/2018] [Indexed: 12/19/2022] Open
Abstract
Liver organogenesis requires complex cell-cell interactions between hepatic endoderm cells and adjacent cell niches. Endothelial cells are key players for endoderm hepatic fate decision. We previously demonstrated that the endothelial cell niche promotes hepatic specification of mouse embryonic stem cell(ESC)-derived endoderm through dual repression of Wnt and Notch pathways in endoderm cells. In the present study, we dissected further the mechanisms by which endothelial cells trigger endoderm hepatic specification. Using our previously established in vitro mouse ESC system mimicking the early hepatic specification process, endoderm cells were purified and co-cultured with endothelial cells to induce hepatic specification. The comparison of transcriptome profiles between hepatic endoderm cells isolated from co-cultures and endoderm cells cultured alone revealed that VEGF signaling instructs hepatic specification of endoderm cells through endothelial VEGFR2 activation. Additionally, epigenetic mark inhibition assays upon co-cultures uncovered that histone acetylation and DNA methylation promote hepatic specification while histone methylation inhibits it. This study provides an efficient 2D platform modelling the endothelial cell niche crosstalk with endoderm, and reveals mechanisms by which endothelial cells promote hepatic specification of mouse ESC-derived endoderm cells through endothelial VEGFR2 activation and endoderm epigenetic modifications.
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Affiliation(s)
- Songyan Han
- Department of Cell, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christopher Tan
- Department of Pharmacological Science, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Junjun Ding
- Department of Cell, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacological Science, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Valerie Gouon-Evans
- Department of Cell, Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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344
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Towards Multi-Organoid Systems for Drug Screening Applications. Bioengineering (Basel) 2018; 5:bioengineering5030049. [PMID: 29933623 PMCID: PMC6163436 DOI: 10.3390/bioengineering5030049] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/15/2018] [Accepted: 06/19/2018] [Indexed: 12/13/2022] Open
Abstract
A low percentage of novel drug candidates succeed and reach the end of the drug discovery pipeline, mainly due to poor initial screening and assessment of the effects of the drug and its metabolites over various tissues in the human body. For that, emerging technologies involving the production of organoids from human pluripotent stem cells (hPSCs) and the use of organ-on-a-chip devices are showing great promise for developing a more reliable, rapid and cost-effective drug discovery process when compared with the current use of animal models. In particular, the possibility of virtually obtaining any type of cell within the human body, in combination with the ability to create patient-specific tissues using human induced pluripotent stem cells (hiPSCs), broadens the horizons in the fields of drug discovery and personalized medicine. In this review, we address the current progress and challenges related to the process of obtaining organoids from different cell lineages emerging from hPSCs, as well as how to create devices that will allow a precise examination of the in vitro effects generated by potential drugs in different organ systems.
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345
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Porrello ER, Kirkeby A. A symphony of stem cells in Vienna - looking to the future. Development 2018; 145:145/11/dev163501. [PMID: 29884655 DOI: 10.1242/dev.163501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The inaugural 'Symposium for the Next Generation of Stem Cell Research' (SY-Stem) was held on February 22-24 at the Vienna BioCenter in Austria. The meeting focused on having young researchers as speakers, and the program was of an impressively high quality. Here, we summarise key findings from this meeting, which brought together emerging leaders to discuss various topics, including pluripotency, organoids, endogenous regeneration, transcriptional regulation, clinical applications and emerging technologies.
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Affiliation(s)
- Enzo R Porrello
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria 3052, Australia .,Department of Physiology, School of Biomedical Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Agnete Kirkeby
- Human Neural Development, Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200 Copenhagen, Denmark .,Wallenberg Neuroscience Center, Department Experimental Medical Science, Lund University, 22184 Lund, Sweden
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346
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Kernfeld EM, Genga RMJ, Neherin K, Magaletta ME, Xu P, Maehr R. A Single-Cell Transcriptomic Atlas of Thymus Organogenesis Resolves Cell Types and Developmental Maturation. Immunity 2018; 48:1258-1270.e6. [PMID: 29884461 DOI: 10.1016/j.immuni.2018.04.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/18/2018] [Accepted: 04/13/2018] [Indexed: 12/22/2022]
Abstract
Thymus development is critical to the adaptive immune system, yet a comprehensive transcriptional framework capturing thymus organogenesis at single-cell resolution is still needed. We applied single-cell RNA sequencing (RNA-seq) to capture 8 days of thymus development, perturbations of T cell receptor rearrangement, and in vitro organ cultures, producing profiles of 24,279 cells. We resolved transcriptional heterogeneity of developing lymphocytes, and genetic perturbation confirmed T cell identity of conventional and non-conventional lymphocytes. We characterized maturation dynamics of thymic epithelial cells in vivo, classified cell maturation state in a thymic organ culture, and revealed the intrinsic capacity of thymic epithelium to preserve transcriptional regularity despite exposure to exogenous retinoic acid. Finally, by integrating the cell atlas with human genome-wide association study (GWAS) data and autoimmune-disease-related genes, we implicated embryonic thymus-resident cells as possible participants in autoimmune disease etiologies. This resource provides a single-cell transcriptional framework for biological discovery and molecular analysis of thymus organogenesis.
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Affiliation(s)
- Eric M Kernfeld
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ryan M J Genga
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kashfia Neherin
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Margaret E Magaletta
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ping Xu
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - René Maehr
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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347
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Hickey RD, Naugler WE. Ectopic expansion of engineered human liver tissue seeds using mature cell populations. Hepatology 2018; 67:2465-2467. [PMID: 29222915 DOI: 10.1002/hep.29718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/04/2017] [Accepted: 12/04/2017] [Indexed: 12/07/2022]
Affiliation(s)
- Raymond D Hickey
- Department of Surgery, Department of Molecular Medicine, Mayo Clinic, Rochester, MN
| | - Willscott E Naugler
- Department of Medicine, Division of Gastroenterology and Hepatology, Oregon Health & Science Center, Portland, OR; Oregon Stem Cell Center, Oregon Health & Science Center, Portland, OR
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348
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Baker K. Organoids Provide an Important Window on Inflammation in Cancer. Cancers (Basel) 2018; 10:E151. [PMID: 29883385 PMCID: PMC5977124 DOI: 10.3390/cancers10050151] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/17/2018] [Accepted: 05/17/2018] [Indexed: 02/08/2023] Open
Abstract
Inflammation is a primary driver of cancer initiation and progression. However, the complex and dynamic nature of an inflammatory response make this a very difficult process to study. Organoids are a new model system where complex multicellular structures of primary cells can be grown in a 3D matrix to recapitulate the biology of the parent tissue. This experimental model offers several distinct advantages over alternatives including the ability to be genetically engineered, implanted in vivo and reliably derived from a wide variety of normal and cancerous tissue from patients. Furthermore, long-term organoid cultures reproduce many features of their source tissue, including genetic and epigenetic alterations and drug sensitivity. Perhaps most significantly, cancer organoids can be cocultured in a variety of different systems with a patients’ own immune cells, uniquely permitting the study of autologous cancer-immune cell interactions. Experiments with such systems promise to shed light on the mechanisms governing inflammation-associated cancer while also providing prognostic information on an individual patient’s responsiveness to immunotherapeutic anti-cancer drugs. Thanks to their ability to capture important features of the complex relationship between a cancer and its microenvironment, organoids are poised to become an essential tool for unraveling the mechanisms by which inflammation promotes cancer.
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Affiliation(s)
- Kristi Baker
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada.
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349
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Takahashi Y, Takebe T, Taniguchi H. Methods for Generating Vascularized Islet‐Like Organoids Via Self‐Condensation. ACTA ACUST UNITED AC 2018; 45:e49. [DOI: 10.1002/cpsc.49] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yoshinobu Takahashi
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine Yokohama Kanagawa Japan
| | - Takanori Takebe
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine Yokohama Kanagawa Japan
- Advanced Medical Research Center, Yokohama City University Yokohama Kanagawa Japan
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati Cincinnati Ohio
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center Cincinnati Ohio
- Institute of Research, Tokyo Medical and Dental University, Bunkyo‐ku Tokyo Japan
| | - Hideki Taniguchi
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine Yokohama Kanagawa Japan
- Advanced Medical Research Center, Yokohama City University Yokohama Kanagawa Japan
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350
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Characterization of germ cell differentiation in the male mouse through single-cell RNA sequencing. Sci Rep 2018; 8:6521. [PMID: 29695820 PMCID: PMC5916943 DOI: 10.1038/s41598-018-24725-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/04/2018] [Indexed: 11/21/2022] Open
Abstract
Spermatogenesis in the mouse has been extensively studied for decades. Previous methods, such as histological staining or bulk transcriptome analysis, either lacked resolution at the single-cell level or were focused on a very narrowly defined set of factors. Here, we present the first comprehensive, unbiased single-cell transcriptomic view of mouse spermatogenesis. Our single-cell RNA-seq (scRNA-seq) data on over 2,500 cells from the mouse testis improves upon stage marker detection and validation, capturing the continuity of differentiation rather than artificially chosen stages. scRNA-seq also enables the analysis of rare cell populations masked in bulk sequencing data and reveals new insights into the regulation of sex chromosomes during spermatogenesis. Our data provide the basis for further studies in the field, for the first time providing a high-resolution reference of transcriptional processes during mouse spermatogenesis.
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