1
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Scatolin GN, Ming H, Wang Y, Iyyappan R, Gutierrez-Castillo E, Zhu L, Sagheer M, Song C, Bondioli K, Jiang Z. Single-cell transcriptional landscapes of bovine peri-implantation development. iScience 2024; 27:109605. [PMID: 38633001 PMCID: PMC11022056 DOI: 10.1016/j.isci.2024.109605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 03/14/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Supporting healthy pregnancy outcomes requires a comprehensive understanding of the molecular and cellular programs of peri-implantation development, when most pregnancy failure occurs. Here, we present single-cell transcriptomes of bovine peri-implantation embryo development at day 12, 14, 16, and 18 post-fertilization. We defined the cellular composition and gene expression of embryonic disc, hypoblast, and trophoblast lineages in bovine peri-implantation embryos, and identified markers and pathway signaling that represent distinct stages of bovine peri-implantation lineages; the expression of selected markers was validated in peri-implantation embryos. Using detailed time-course transcriptomic analyses, we revealed a previously unrecognized primitive trophoblast cell lineage. We also characterized conserved and divergence peri-implantation lineage programs between bovine and other mammalian species. Finally, we established cell-cell communication signaling underlies embryonic and extraembryonic cell interaction to ensure proper early development. These data provide foundational information to discover essential biological signaling underpinning bovine peri-implantation development.
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Affiliation(s)
| | - Hao Ming
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Yinjuan Wang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Rajan Iyyappan
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | | | - Linkai Zhu
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Masroor Sagheer
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Chao Song
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Kenneth Bondioli
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Zongliang Jiang
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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2
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Pope HF, Pilmane M, Junga A, Pētersons A. The Assessment of CDX1, IHH, SHH, GATA4, FOXA2, FOXF1 in Congenital Intra-Abdominal Adhesions. Acta Med Litu 2024; 31:109-121. [PMID: 38978864 PMCID: PMC11227690 DOI: 10.15388/amed.2024.31.1.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/17/2024] [Accepted: 03/25/2024] [Indexed: 07/10/2024] Open
Abstract
Congenital abdominal adhesions are a rare condition that can result in a small bowel obstruction at any age, more frequently in pediatric populations. The cause remains unknown, and the importance of aberrant congenital bands is related to the difficulty of diagnosis, and cases of death with late detection have been documented. This research examines the expression of Caudal Type Homeobox 1 (CDX1), Indian Hedgehog (IHH), Sonic Hedgehog (SHH), GATA Binding Protein 4 (GATA4), Forkhead Box A2 (FOXA2) and Forkhead Box F1 (FOXF1) gene expression in human abdominal congenital adhesion fibroblast and endothelium cells by chromogenic in situ hybridization, with the aim of elucidating their potential association with the etiology of congenital intra-abdominal adhesion band development. The potential genes' signals were examined using a semi-quantitative approach. Significant correlations were observed between the expression of CDX1 (p <.001) and SHH (p=0.032) genes in fibroblasts from congenital intra-abdominal adhesions compared to fibroblasts from control peritoneal tissue. Statistically significant very strong correlations were found between the CDX1 and IHH comparing endothelium and fibroblast cells in congenital abdominal adhesion bands. There was no statistically significant difference found in the distribution of IHH, FOXA2, GATA4, and FOXF1 between the fibroblasts and endothelium of the patients compared to the control group. The presence of notable distinctions and diverse associations suggests the potential involvement of numerous morpho-pathogenetic processes in the development of intraabdominal adhesions.
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Affiliation(s)
| | - Māra Pilmane
- Institute of Anatomy and Anthropology, Riga Stradiņš University, Riga, Latvia
| | - Anna Junga
- Institute of Anatomy and Anthropology, Riga Stradiņš University, Riga, Latvia
| | - Aigars Pētersons
- Children’s Clinical University Hospital, Riga Stradiņš University, Riga, Latvia
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3
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Kearns NA, Lobo M, Genga RMJ, Abramowitz RG, Parsi KM, Min J, Kernfeld EM, Huey JD, Kady J, Hennessy E, Brehm MA, Ziller MJ, Maehr R. Generation and molecular characterization of human pluripotent stem cell-derived pharyngeal foregut endoderm. Dev Cell 2023; 58:1801-1818.e15. [PMID: 37751684 PMCID: PMC10637111 DOI: 10.1016/j.devcel.2023.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 05/15/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023]
Abstract
Approaches to study human pharyngeal foregut endoderm-a developmental intermediate that is linked to various human syndromes involving pharynx development and organogenesis of tissues such as thymus, parathyroid, and thyroid-have been hampered by scarcity of tissue access and cellular models. We present an efficient stepwise differentiation method to generate human pharyngeal foregut endoderm from pluripotent stem cells. We determine dose and temporal requirements of signaling pathway engagement for optimized differentiation and characterize the differentiation products on cellular and integrated molecular level. We present a computational classification tool, "CellMatch," and transcriptomic classification of differentiation products on an integrated mouse scRNA-seq developmental roadmap confirms cellular maturation. Integrated transcriptomic and chromatin analyses infer differentiation stage-specific gene regulatory networks. Our work provides the method and integrated multiomic resource for the investigation of disease-relevant loci and gene regulatory networks and their role in developmental defects affecting the pharyngeal endoderm and its derivatives.
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Affiliation(s)
- Nicola A Kearns
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Macrina Lobo
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ryan M J Genga
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ryan G Abramowitz
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Krishna M Parsi
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jiang Min
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Eric M Kernfeld
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jack D Huey
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jamie Kady
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Erica Hennessy
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael A Brehm
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael J Ziller
- Department of Psychiatry, University of Münster, Münster, Germany
| | - René Maehr
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA; Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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4
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Trinh LT, Osipovich AB, Liu B, Shrestha S, Cartailler JP, Wright CVE, Magnuson MA. Single-Cell RNA Sequencing of Sox17-Expressing Lineages Reveals Distinct Gene Regulatory Networks and Dynamic Developmental Trajectories. Stem Cells 2023; 41:643-657. [PMID: 37085274 PMCID: PMC10465087 DOI: 10.1093/stmcls/sxad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/04/2023] [Indexed: 04/23/2023]
Abstract
During early embryogenesis, the transcription factor SOX17 contributes to hepato-pancreato-biliary system formation and vascular-hematopoietic emergence. To better understand Sox17 function in the developing endoderm and endothelium, we developed a dual-color temporal lineage-tracing strategy in mice combined with single-cell RNA sequencing to analyze 6934 cells from Sox17-expressing lineages at embryonic days 9.0-9.5. Our analyses showed 19 distinct cellular clusters combined from all 3 germ layers. Differential gene expression, trajectory and RNA-velocity analyses of endothelial cells revealed a heterogenous population of uncommitted and specialized endothelial subtypes, including 2 hemogenic populations that arise from different origins. Similarly, analyses of posterior foregut endoderm revealed subsets of hepatic, pancreatic, and biliary progenitors with overlapping developmental potency. Calculated gene-regulatory networks predict gene regulons that are dominated by cell type-specific transcription factors unique to each lineage. Vastly different Sox17 regulons found in endoderm versus endothelial cells support the differential interactions of SOX17 with other regulatory factors thereby enabling lineage-specific regulatory actions.
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Affiliation(s)
- Linh T Trinh
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Anna B Osipovich
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
| | - Bryan Liu
- College of Arts and Sciences, Vanderbilt University, Nashville, TN, USA
| | - Shristi Shrestha
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
| | | | - Christopher V E Wright
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Mark A Magnuson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN, USA
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5
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Scatolin GN, Ming H, Wang Y, Zhu L, Castillo EG, Bondioli K, Jiang Z. Single-cell transcriptional landscapes of bovine peri-implantation development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544813. [PMID: 37398069 PMCID: PMC10312721 DOI: 10.1101/2023.06.13.544813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Supporting healthy pregnancy outcomes requires a comprehensive understanding of the cellular hierarchy and underlying molecular mechanisms during peri-implantation development. Here, we present a single-cell transcriptome-wide view of the bovine peri-implantation embryo development at day 12, 14, 16 and 18, when most of the pregnancy failure occurs in cattle. We defined the development and dynamic progression of cellular composition and gene expression of embryonic disc, hypoblast, and trophoblast lineages during bovine peri-implantation development. Notably, the comprehensive transcriptomic mapping of trophoblast development revealed a previously unrecognized primitive trophoblast cell lineage that is responsible for pregnancy maintenance in bovine prior to the time when binucleate cells emerge. We analyzed novel markers for the cell lineage development during bovine early development. We also identified cell-cell communication signaling underling embryonic and extraembryonic cell interaction to ensure proper early development. Collectively, our work provides foundational information to discover essential biological pathways underpinning bovine peri-implantation development and the molecular causes of the early pregnancy failure during this critical period. Significance Statement Peri-implantation development is essential for successful reproduction in mammalian species, and cattle have a unique process of elongation that proceeds for two weeks prior to implantation and represents a period when many pregnancies fail. Although the bovine embryo elongation has been studied histologically, the essential cellular and molecular factors governing lineage differentiation remain unexplored. This study profiled the transcriptome of single cells in the bovine peri-implantation development throughout day 12, 14, 16, and 18, and identified peri-implantation stage-related features of cell lineages. The candidate regulatory genes, factors, pathways and embryonic and extraembryonic cell interactions were also prioritized to ensure proper embryo elongation in cattle.
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6
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Smith RJ, Zhang H, Hu SS, Yung T, Francis R, Lee L, Onaitis MW, Dirks PB, Zang C, Kim TH. Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions. Nat Commun 2022; 13:2965. [PMID: 35618699 PMCID: PMC9135761 DOI: 10.1038/s41467-022-30624-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/06/2022] [Indexed: 01/07/2023] Open
Abstract
Development of the gastrointestinal system occurs after gut tube closure, guided by spatial and temporal control of gene expression. However, it remains unclear what forces regulate these spatiotemporal gene expression patterns. Here we perform single-cell chromatin profiling of the primitive gut tube to reveal organ-specific chromatin patterns that reflect the anatomical patterns of distinct organs. We generate a comprehensive map of epigenomic changes throughout gut development, demonstrating that dynamic chromatin accessibility patterns associate with lineage-specific transcription factor binding events to regulate organ-specific gene expression. Additionally, we show that loss of Sox2 and Cdx2, foregut and hindgut lineage-specific transcription factors, respectively, leads to fate shifts in epigenomic patterns, linking transcription factor binding, chromatin accessibility, and lineage fate decisions in gut development. Notably, abnormal expression of Sox2 in the pancreas and intestine impairs lineage fate decisions in both development and adult homeostasis. Together, our findings define the chromatin and transcriptional mechanisms of organ identity and lineage plasticity in development and adult homeostasis. The primitive gut tube gives rise to all major internal organs, while underlying regulatory mechanisms are unclear. Here, the authors analyze its chromatin landscape at the single-cell level and define the epigenetic regulation of lineage fate decisions and plasticity in organ development and homeostasis.
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Affiliation(s)
- Ryan J Smith
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Hongpan Zhang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Shengen Shawn Hu
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Theodora Yung
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Roshane Francis
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Lilian Lee
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Mark W Onaitis
- Division of Cardiovascular and Thoracic Surgery, University of California San Diego Medical Center, San Diego, CA, USA
| | - Peter B Dirks
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA. .,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA. .,Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
| | - Tae-Hee Kim
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.
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7
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Bérenger-Currias NM, Mircea M, Adegeest E, van den Berg PR, Feliksik M, Hochane M, Idema T, Tans SJ, Semrau S. A gastruloid model of the interaction between embryonic and extra-embryonic cell types. J Tissue Eng 2022; 13:20417314221103042. [PMID: 35707767 PMCID: PMC9189523 DOI: 10.1177/20417314221103042] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/10/2022] [Indexed: 12/11/2022] Open
Abstract
Stem-cell derived in vitro systems, such as organoids or embryoids, hold great
potential for modeling in vivo development. Full control over their initial
composition, scalability, and easily measurable dynamics make those systems
useful for studying specific developmental processes in isolation. Here we
report the formation of gastruloids consisting of mouse embryonic stem cells
(mESCs) and extraembryonic endoderm (XEN) cells. These XEN-enhanced gastruloids
(XEGs) exhibit the formation of neural epithelia, which are absent in
gastruloids derived from mESCs only. By single-cell RNA-seq, imaging, and
differentiation experiments, we demonstrate the neural characteristics of the
epithelial tissue. We further show that the mESCs induce the differentiation of
the XEN cells to a visceral endoderm-like state. Finally, we demonstrate that
local inhibition of WNT signaling and production of a basement membrane by the
XEN cells underlie the formation of the neuroepithelial tissue. In summary, we
establish XEGs to explore heterotypic cellular interactions and their
developmental consequences in vitro.
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Affiliation(s)
- Noémie Mlp Bérenger-Currias
- Department of Physics, Leiden University, Leiden, The Netherlands.,Delft University of Technology, Department of Bionanoscience, Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Maria Mircea
- Department of Physics, Leiden University, Leiden, The Netherlands
| | - Esmée Adegeest
- Department of Physics, Leiden University, Leiden, The Netherlands
| | | | - Marleen Feliksik
- Department of Physics, Leiden University, Leiden, The Netherlands
| | - Mazène Hochane
- Department of Physics, Leiden University, Leiden, The Netherlands
| | - Timon Idema
- Delft University of Technology, Department of Bionanoscience, Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Sander J Tans
- Delft University of Technology, Department of Bionanoscience, Kavli Institute of Nanoscience, Delft, The Netherlands.,AMOLF, Amsterdam, The Netherlands
| | - Stefan Semrau
- Department of Physics, Leiden University, Leiden, The Netherlands
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8
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Lotto J, Drissler S, Cullum R, Wei W, Setty M, Bell EM, Boutet SC, Nowotschin S, Kuo YY, Garg V, Pe'er D, Church DM, Hadjantonakis AK, Hoodless PA. Single-Cell Transcriptomics Reveals Early Emergence of Liver Parenchymal and Non-parenchymal Cell Lineages. Cell 2020; 183:702-716.e14. [PMID: 33125890 PMCID: PMC7643810 DOI: 10.1016/j.cell.2020.09.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 07/06/2020] [Accepted: 09/01/2020] [Indexed: 02/08/2023]
Abstract
The cellular complexity and scale of the early liver have constrained analyses examining its emergence during organogenesis. To circumvent these issues, we analyzed 45,334 single-cell transcriptomes from embryonic day (E)7.5, when endoderm progenitors are specified, to E10.5 liver, when liver parenchymal and non-parenchymal cell lineages emerge. Our data detail divergence of vascular and sinusoidal endothelia, including a distinct transcriptional profile for sinusoidal endothelial specification by E8.75. We characterize two distinct mesothelial cell types as well as early hepatic stellate cells and reveal distinct spatiotemporal distributions for these populations. We capture transcriptional profiles for hepatoblast specification and migration, including the emergence of a hepatomesenchymal cell type and evidence for hepatoblast collective cell migration. Further, we identify cell-cell interactions during the organization of the primitive sinusoid. This study provides a comprehensive atlas of liver lineage establishment from the endoderm and mesoderm through to the organization of the primitive sinusoid at single-cell resolution.
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Affiliation(s)
- Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Wei Wei
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Manu Setty
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Erin M Bell
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | | | - Sonja Nowotschin
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ying-Yi Kuo
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dana Pe'er
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, BC V5Z 1L3, Canada; Cell and Developmental Biology Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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9
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Single-cell patterning and axis characterization in the murine and human definitive endoderm. Cell Res 2020; 31:326-344. [PMID: 33106598 DOI: 10.1038/s41422-020-00426-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022] Open
Abstract
Defining the precise regionalization of specified definitive endoderm progenitors is critical for understanding the mechanisms underlying the generation and regeneration of respiratory and digestive organs, yet the patterning of endoderm progenitors remains unresolved, particularly in humans. We performed single-cell RNA sequencing on endoderm cells during the early somitogenesis stages in mice and humans. We developed molecular criteria to define four major endoderm regions (foregut, lip of anterior intestinal portal, midgut, and hindgut) and their developmental pathways. We identified the cell subpopulations in each region and their spatial distributions and characterized key molecular features along the body axes. Dorsal and ventral pancreatic progenitors appear to originate from the midgut population and follow distinct pathways to develop into an identical cell type. Finally, we described the generally conserved endoderm patterning in humans and clear differences in dorsal cell distribution between species. Our study comprehensively defines single-cell endoderm patterning and provides novel insights into the spatiotemporal process that drives establishment of early endoderm domains.
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10
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Chan MM, Smith ZD, Grosswendt S, Kretzmer H, Norman TM, Adamson B, Jost M, Quinn JJ, Yang D, Jones MG, Khodaverdian A, Yosef N, Meissner A, Weissman JS. Molecular recording of mammalian embryogenesis. Nature 2019; 570:77-82. [PMID: 31086336 PMCID: PMC7229772 DOI: 10.1038/s41586-019-1184-5] [Citation(s) in RCA: 206] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 04/10/2019] [Indexed: 01/04/2023]
Abstract
Ontogeny describes the emergence of complex multicellular organisms from single totipotent cells. This field is particularly challenging in mammals, owing to the indeterminate relationship between self-renewal and differentiation, variation in progenitor field sizes, and internal gestation in these animals. Here we present a flexible, high-information, multi-channel molecular recorder with a single-cell readout and apply it as an evolving lineage tracer to assemble mouse cell-fate maps from fertilization through gastrulation. By combining lineage information with single-cell RNA sequencing profiles, we recapitulate canonical developmental relationships between different tissue types and reveal the nearly complete transcriptional convergence of endodermal cells of extra-embryonic and embryonic origins. Finally, we apply our cell-fate maps to estimate the number of embryonic progenitor cells and their degree of asymmetric partitioning during specification. Our approach enables massively parallel, high-resolution recording of lineage and other information in mammalian systems, which will facilitate the construction of a quantitative framework for understanding developmental processes.
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Affiliation(s)
- Michelle M Chan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Zachary D Smith
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Stefanie Grosswendt
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thomas M Norman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Britt Adamson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Molecular Biology, Lewis Sigler Institute, Princeton University, Princeton, NJ, USA
| | - Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey J Quinn
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Dian Yang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew G Jones
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Alex Khodaverdian
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA
| | - Alexander Meissner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA.
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11
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Nowotschin S, Setty M, Kuo YY, Liu V, Garg V, Sharma R, Simon CS, Saiz N, Gardner R, Boutet SC, Church DM, Hoodless PA, Hadjantonakis AK, Pe'er D. The emergent landscape of the mouse gut endoderm at single-cell resolution. Nature 2019; 569:361-367. [PMID: 30959515 PMCID: PMC6724221 DOI: 10.1038/s41586-019-1127-1] [Citation(s) in RCA: 228] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/29/2019] [Indexed: 01/04/2023]
Abstract
Here we delineate the ontogeny of the mammalian endoderm by generating 112,217 single-cell transcriptomes, which represent all endoderm populations within the mouse embryo until midgestation. We use graph-based approaches to model differentiating cells, which provides a spatio-temporal characterization of developmental trajectories and defines the transcriptional architecture that accompanies the emergence of the first (primitive or extra-embryonic) endodermal population and its sister pluripotent (embryonic) epiblast lineage. We uncover a relationship between descendants of these two lineages, in which epiblast cells differentiate into endoderm at two distinct time points-before and during gastrulation. Trajectories of endoderm cells were mapped as they acquired embryonic versus extra-embryonic fates and as they spatially converged within the nascent gut endoderm, which revealed these cells to be globally similar but retain aspects of their lineage history. We observed the regionalized identity of cells along the anterior-posterior axis of the emergent gut tube, which reflects their embryonic or extra-embryonic origin, and the coordinated patterning of these cells into organ-specific territories.
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Affiliation(s)
- Sonja Nowotschin
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Manu Setty
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying-Yi Kuo
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vincent Liu
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roshan Sharma
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Claire S Simon
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nestor Saiz
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rui Gardner
- Flow Cytometry Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Dana Pe'er
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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12
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Joseph DB, Chandrashekar AS, Abler LL, Chu LF, Thomson JA, Vezina CM. Epithelial DNA methyltransferase-1 regulates cell survival, growth and maturation in developing prostatic buds. Dev Biol 2019; 447:157-169. [PMID: 30659795 DOI: 10.1016/j.ydbio.2019.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/17/2018] [Accepted: 01/14/2019] [Indexed: 02/07/2023]
Abstract
DNA methyltransferase 1 (DNMT1) is required for embryogenesis but roles in late forming organ systems including the prostate, which emerges from the urethral epithelium, have not been fully examined. We used a targeted genetic approach involving a Shhcre recombinase to demonstrate requirement of epithelial DNA methyltransferase-1 (Dnmt1) in mouse prostate morphogenesis. Dnmt1 mutant urethral cells exhibit DNA hypomethylation, DNA damage, p53 accumulation and undergo cell cycle arrest and apoptosis. Urethral epithelial cells are disorganized in Dnmt1 mutants, leading to impaired prostate growth and maturation and failed glandular development. We evaluated oriented cell division as a mechanism of bud elongation and widening by demonstrating that mitotic spindle axes typically form parallel or perpendicular to prostatic bud elongation axes. We then deployed a ShhcreERT allele to delete Dnmt1 from a subset of urethral epithelial cells, creating mosaic mutants with which to interrogate the requirement for cell division in specific prostatic bud epithelial populations. DNMT1- cell distribution within prostatic buds is not random as would be expected in a process where DNMT1 was not required. Instead, replication competent DNMT1 + cells primarily accumulate in prostatic bud margins and tips while replication impeded DNMT1- cells accumulate in prostatic bud cores. Together, these results highlight the role of DNMT1 in regulating epithelial bud formation by maintaining cell cycle progression and survival of rapidly dividing urethral epithelial cells, which can be extended to the study of other developing epithelial organs. In addition, our results show that prostatic buds consist of two epithelial cell populations with distinct molecular and functional characteristics that could potentially contribute to specialized lineages in the adult prostate.
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Affiliation(s)
- Diya B Joseph
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anoop S Chandrashekar
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lisa L Abler
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Li-Fang Chu
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53707-7365, USA
| | - Chad M Vezina
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA.
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13
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Chal J, Al Tanoury Z, Oginuma M, Moncuquet P, Gobert B, Miyanari A, Tassy O, Guevara G, Hubaud A, Bera A, Sumara O, Garnier JM, Kennedy L, Knockaert M, Gayraud-Morel B, Tajbakhsh S, Pourquié O. Recapitulating early development of mouse musculoskeletal precursors of the paraxial mesoderm in vitro. Development 2018; 145:145/6/dev157339. [DOI: 10.1242/dev.157339] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 02/06/2018] [Indexed: 12/13/2022]
Abstract
ABSTRACT
Body skeletal muscles derive from the paraxial mesoderm, which forms in the posterior region of the embryo. Using microarrays, we characterize novel mouse presomitic mesoderm (PSM) markers and show that, unlike the abrupt transcriptome reorganization of the PSM, neural tube differentiation is accompanied by progressive transcriptome changes. The early paraxial mesoderm differentiation stages can be efficiently recapitulated in vitro using mouse and human pluripotent stem cells. While Wnt activation alone can induce posterior PSM markers, acquisition of a committed PSM fate and efficient differentiation into anterior PSM Pax3+ identity further requires BMP inhibition to prevent progenitors from drifting to a lateral plate mesoderm fate. When transplanted into injured adult muscle, these precursors generated large numbers of immature muscle fibers. Furthermore, exposing these mouse PSM-like cells to a brief FGF inhibition step followed by culture in horse serum-containing medium allows efficient recapitulation of the myogenic program to generate myotubes and associated Pax7+ cells. This protocol results in improved in vitro differentiation and maturation of mouse muscle fibers over serum-free protocols and enables the study of myogenic cell fusion and satellite cell differentiation.
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Affiliation(s)
- Jérome Chal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Ziad Al Tanoury
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Masayuki Oginuma
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Philippe Moncuquet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Bénédicte Gobert
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Anagenesis Biotechnologies, Parc d'innovation, Illkirch Graffenstaden 67400, France
| | - Ayako Miyanari
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Olivier Tassy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Getzabel Guevara
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Alexis Hubaud
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Agata Bera
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Olga Sumara
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Jean-Marie Garnier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Leif Kennedy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
| | - Marie Knockaert
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Barbara Gayraud-Morel
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
- CNRS UMR 3738, Institut Pasteur, Paris 75015, France
| | - Shahragim Tajbakhsh
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris 75015, France
- CNRS UMR 3738, Institut Pasteur, Paris 75015, France
| | - Olivier Pourquié
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), Inserm U964, Université de Strasbourg, Illkirch Graffenstaden 67400, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Boston, MA 02115, USA
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14
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Ibarra-Soria X, Jawaid W, Pijuan-Sala B, Ladopoulos V, Scialdone A, Jörg DJ, Tyser RCV, Calero-Nieto FJ, Mulas C, Nichols J, Vallier L, Srinivas S, Simons BD, Göttgens B, Marioni JC. Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation. Nat Cell Biol 2018; 20:127-134. [PMID: 29311656 PMCID: PMC5787369 DOI: 10.1038/s41556-017-0013-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/21/2017] [Indexed: 02/02/2023]
Abstract
During gastrulation, cell types from all three germ layers are specified and the basic body plan is established 1 . However, molecular analysis of this key developmental stage has been hampered by limited cell numbers and a paucity of markers. Single-cell RNA sequencing circumvents these problems, but has so far been limited to specific organ systems 2 . Here, we report single-cell transcriptomic characterization of >20,000 cells immediately following gastrulation at E8.25 of mouse development. We identify 20 major cell types, which frequently contain substructure, including three distinct signatures in early foregut cells. Pseudo-space ordering of somitic progenitor cells identifies dynamic waves of transcription and candidate regulators, which are validated by molecular characterization of spatially resolved regions of the embryo. Within the endothelial population, cells that transition from haemogenic endothelial to erythro-myeloid progenitors specifically express Alox5 and its co-factor Alox5ap, which control leukotriene production. Functional assays using mouse embryonic stem cells demonstrate that leukotrienes promote haematopoietic progenitor cell generation. Thus, this comprehensive single-cell map can be exploited to reveal previously unrecognized pathways that contribute to tissue development.
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Affiliation(s)
- Ximena Ibarra-Soria
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Wajid Jawaid
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatric Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Blanca Pijuan-Sala
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Vasileios Ladopoulos
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Antonio Scialdone
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
| | - David J Jörg
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Richard C V Tyser
- Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Fernando J Calero-Nieto
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Carla Mulas
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Ludovic Vallier
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Shankar Srinivas
- Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Benjamin D Simons
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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15
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Dey KK, Hsiao CJ, Stephens M. Visualizing the structure of RNA-seq expression data using grade of membership models. PLoS Genet 2017; 13:e1006599. [PMID: 28333934 PMCID: PMC5363805 DOI: 10.1371/journal.pgen.1006599] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 01/24/2017] [Indexed: 02/07/2023] Open
Abstract
Grade of membership models, also known as “admixture models”, “topic models” or “Latent Dirichlet Allocation”, are a generalization of cluster models that allow each sample to have membership in multiple clusters. These models are widely used in population genetics to model admixed individuals who have ancestry from multiple “populations”, and in natural language processing to model documents having words from multiple “topics”. Here we illustrate the potential for these models to cluster samples of RNA-seq gene expression data, measured on either bulk samples or single cells. We also provide methods to help interpret the clusters, by identifying genes that are distinctively expressed in each cluster. By applying these methods to several example RNA-seq applications we demonstrate their utility in identifying and summarizing structure and heterogeneity. Applied to data from the GTEx project on 53 human tissues, the approach highlights similarities among biologically-related tissues and identifies distinctively-expressed genes that recapitulate known biology. Applied to single-cell expression data from mouse preimplantation embryos, the approach highlights both discrete and continuous variation through early embryonic development stages, and highlights genes involved in a variety of relevant processes—from germ cell development, through compaction and morula formation, to the formation of inner cell mass and trophoblast at the blastocyst stage. The methods are implemented in the Bioconductor package CountClust. Gene expression profile of a biological sample (either from single cells or pooled cells) results from a complex interplay of multiple related biological processes. Consequently, for example, distal tissue samples may share a similar gene expression profile through some common underlying biological processes. Our goal here is to illustrate that grade of membership (GoM) models—an approach widely used in population genetics to cluster admixed individuals who have ancestry from multiple populations—provide an attractive approach for clustering biological samples of RNA sequencing data. The GoM model allows each biological sample to have partial memberships in multiple biologically-distinct clusters, in contrast to traditional clustering methods that partition samples into distinct subgroups. We also provide methods for identifying genes that are distinctively expressed in each cluster to help biologically interpret the results. Applied to a dataset of 53 human tissues, the GoM approach highlights similarities among biologically-related tissues and identifies distinctively-expressed genes that recapitulate known biology. Applied to gene expression data of single cells from mouse preimplantation embryos, the approach highlights both discrete and continuous variation through early embryonic development stages, and genes involved in a variety of relevant processes. Our study highlights the potential of GoM models for elucidating biological structure in RNA-seq gene expression data.
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Affiliation(s)
- Kushal K. Dey
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - Chiaowen Joyce Hsiao
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Matthew Stephens
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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16
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Koshida R, Oishi H, Hamada M, Takei Y, Takahashi S. MafB is required for development of the hindbrain choroid plexus. Biochem Biophys Res Commun 2016; 483:288-293. [PMID: 28025141 DOI: 10.1016/j.bbrc.2016.12.150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
Abstract
The choroid plexus (ChP) is a non-neural epithelial tissue that produces cerebrospinal fluid (CSF). The ChP differentiates from the roof plate, a dorsal midline structure of the neural tube. However, molecular mechanisms underlying ChP development are poorly understood compared to neural development. MafB is a bZip transcription factor that is known to be expressed in the roof plate. Here we investigated the role of MafB in embryonic development of the hindbrain ChP (hChP) using Mafb-deficient mice. Immunohistochemical analyses revealed that MafB is expressed in the roof plate and early hChP epithelial cells but its expression disappears at a later embryonic stage. We also found that the Mafb-deficient hChP exhibits delayed differentiation and results in hypoplasia compared to the wild-type hChP. Furthermore, the Mafb-deficient hChP exhibits increased apoptotic cell death and decreased proliferating cells at E12.5, an early stage of hChP development. Collectively, our findings reveal that MafB play an important role in promoting hChP development during embryogenesis.
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Affiliation(s)
- Ryusuke Koshida
- Department of Anatomy and Neuroscience, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan.
| | - Hisashi Oishi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan
| | - Michito Hamada
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan
| | - Yosuke Takei
- Department of Anatomy and Neuroscience, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan
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17
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Woolnough JL, Atwood BL, Liu Z, Zhao R, Giles KE. The Regulation of rRNA Gene Transcription during Directed Differentiation of Human Embryonic Stem Cells. PLoS One 2016; 11:e0157276. [PMID: 27299313 PMCID: PMC4907514 DOI: 10.1371/journal.pone.0157276] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 05/26/2016] [Indexed: 11/18/2022] Open
Abstract
It has become increasingly clear that proper cellular control of pluripotency and differentiation is related to the regulation of rRNA synthesis. To further our understanding of the role that the regulation of rRNA synthesis has in pluripotency we monitored rRNA synthesis during the directed differentiation of human embryonic stem cells (hESCs). We discovered that the rRNA synthesis rate is reduced ~50% within 6 hours of ACTIVIN A treatment. This precedes reductions in expression of specific stem cell markers and increases in expression of specific germ layer markers. The reduction in rRNA synthesis is concomitant with dissociation of the Pol I transcription factor, UBTF, from the rRNA gene promoter and precedes any increase to heterochromatin throughout the rRNA gene. To directly investigate the role of rRNA synthesis in pluripotency, hESCs were treated with the Pol I inhibitor, CX-5461. The direct reduction of rRNA synthesis by CX-5461 induces the expression of markers for all three germ layers, reduces the expression of pluripotency markers, and is overall similar to the ACTIVIN A induced changes. This work indicates that the dissociation of UBTF from the rRNA gene, and corresponding reduction in transcription, represent early regulatory events during the directed differentiation of pluripotent stem cells.
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Affiliation(s)
- Jessica L Woolnough
- UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Blake L Atwood
- UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Zhong Liu
- UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Rui Zhao
- UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
| | - Keith E Giles
- UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States of America
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18
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Garside VC, Cullum R, Alder O, Lu DY, Vander Werff R, Bilenky M, Zhao Y, Jones SJM, Marra MA, Underhill TM, Hoodless PA. SOX9 modulates the expression of key transcription factors required for heart valve development. Development 2015; 142:4340-50. [PMID: 26525672 DOI: 10.1242/dev.125252] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 10/28/2015] [Indexed: 01/10/2023]
Abstract
Heart valve formation initiates when endothelial cells of the heart transform into mesenchyme and populate the cardiac cushions. The transcription factor SOX9 is highly expressed in the cardiac cushion mesenchyme, and is essential for heart valve development. Loss of Sox9 in mouse cardiac cushion mesenchyme alters cell proliferation, embryonic survival, and valve formation. Despite this important role, little is known about how SOX9 regulates heart valve formation or its transcriptional targets. Therefore, we mapped putative SOX9 binding sites by ChIP-Seq in E12.5 heart valves, a stage at which the valve mesenchyme is actively proliferating and initiating differentiation. Embryonic heart valves have been shown to express a high number of genes that are associated with chondrogenesis, including several extracellular matrix proteins and transcription factors that regulate chondrogenesis. Therefore, we compared regions of putative SOX9 DNA binding between E12.5 heart valves and E12.5 limb buds. We identified context-dependent and context-independent SOX9-interacting regions throughout the genome. Analysis of context-independent SOX9 binding suggests an extensive role for SOX9 across tissues in regulating proliferation-associated genes including key components of the AP-1 complex. Integrative analysis of tissue-specific SOX9-interacting regions and gene expression profiles on Sox9-deficient heart valves demonstrated that SOX9 controls the expression of several transcription factors with previously identified roles in heart valve development, including Twist1, Sox4, Mecom and Pitx2. Together, our data identify SOX9-coordinated transcriptional hierarchies that control cell proliferation and differentiation during valve formation.
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Affiliation(s)
- Victoria C Garside
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada V5Z 1L3 Program in Cell and Developmental Biology, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Olivia Alder
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Daphne Y Lu
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Ryan Vander Werff
- Biomedical Research Centre, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Mikhail Bilenky
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada V5Z 1L3
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada V5Z 1L3 Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6T 1Z4 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada V5A 1S6
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada V5Z 1L3 Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - T Michael Underhill
- Program in Cell and Developmental Biology, University of British Columbia, Vancouver, Canada V6T 1Z4 Biomedical Research Centre, University of British Columbia, Vancouver, Canada V6T 1Z4 Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6T 1Z4
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, Canada V5Z 1L3 Program in Cell and Developmental Biology, University of British Columbia, Vancouver, Canada V6T 1Z4 Department of Medical Genetics, University of British Columbia, Vancouver, Canada V6T 1Z4
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19
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Kulinski TM, Casari MRT, Guenzl PM, Wenzel D, Andergassen D, Hladik A, Datlinger P, Farlik M, Theussl HC, Penninger JM, Knapp S, Bock C, Barlow DP, Hudson QJ. Imprinted expression in cystic embryoid bodies shows an embryonic and not an extra-embryonic pattern. Dev Biol 2015; 402:291-305. [PMID: 25912690 PMCID: PMC4454777 DOI: 10.1016/j.ydbio.2015.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 04/08/2015] [Accepted: 04/16/2015] [Indexed: 12/24/2022]
Abstract
A large subset of mammalian imprinted genes show extra-embryonic lineage (EXEL) specific imprinted expression that is restricted to placental trophectoderm lineages and to visceral yolk sac endoderm (ysE). Isolated ysE provides a homogenous in vivo model of a mid-gestation extra-embryonic tissue to examine the mechanism of EXEL-specific imprinted gene silencing, but an in vitro model of ysE to facilitate more rapid and cost-effective experiments is not available. Reports indicate that ES cells differentiated into cystic embryoid bodies (EBs) contain ysE, so here we investigate if cystic EBs model ysE imprinted expression. The imprinted expression pattern of cystic EBs is shown to resemble fetal liver and not ysE. To investigate the reason for this we characterized the methylome and transcriptome of cystic EBs in comparison to fetal liver and ysE, by whole genome bisulphite sequencing and RNA-seq. Cystic EBs show a fetal liver pattern of global hypermethylation and low expression of repeats, while ysE shows global hypomethylation and high expression of IAPEz retroviral repeats, as reported for placenta. Transcriptome analysis confirmed that cystic EBs are more similar to fetal liver than ysE and express markers of early embryonic endoderm. Genome-wide analysis shows that ysE shares epigenetic and repeat expression features with placenta. Contrary to previous reports, we show that cystic EBs do not contain ysE, but are more similar to the embryonic endoderm of fetal liver. This explains why cystic EBs reproduce the imprinted expression seen in the embryo but not that seen in the ysE.
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Affiliation(s)
- Tomasz M Kulinski
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria.
| | - M Rita T Casari
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria.
| | - Philipp M Guenzl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria.
| | - Daniel Wenzel
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, 1030 Vienna, Austria.
| | - Daniel Andergassen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria.
| | - Anastasiya Hladik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria; Department of Medicine 1, Laboratory of Infection Biology, Medical University of Vienna, 1090 Vienna, Austria.
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria.
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria.
| | - H-Christian Theussl
- IMP/IMBA Transgenic Service, Institute of Molecular Pathology (IMP), Dr. Bohr Gasse 7, 1030 Vienna, Austria.
| | - Josef M Penninger
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, 1030 Vienna, Austria.
| | - Sylvia Knapp
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria; Department of Medicine 1, Laboratory of Infection Biology, Medical University of Vienna, 1090 Vienna, Austria.
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria.
| | - Denise P Barlow
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria.
| | - Quanah J Hudson
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH-BT25.3, 1090 Vienna, Austria.
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20
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Kurek D, Neagu A, Tastemel M, Tüysüz N, Lehmann J, van de Werken HJG, Philipsen S, van der Linden R, Maas A, van IJcken WFJ, Drukker M, Ten Berge D. Endogenous WNT signals mediate BMP-induced and spontaneous differentiation of epiblast stem cells and human embryonic stem cells. Stem Cell Reports 2014; 4:114-128. [PMID: 25544567 PMCID: PMC4297870 DOI: 10.1016/j.stemcr.2014.11.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 11/26/2014] [Accepted: 11/26/2014] [Indexed: 12/22/2022] Open
Abstract
Therapeutic application of human embryonic stem cells (hESCs) requires precise control over their differentiation. However, spontaneous differentiation is prevalent, and growth factors induce multiple cell types; e.g., the mesoderm inducer BMP4 generates both mesoderm and trophoblast. Here we identify endogenous WNT signals as BMP targets that are required and sufficient for mesoderm induction, while trophoblast induction is WNT independent, enabling the exclusive differentiation toward either lineage. Furthermore, endogenous WNT signals induce loss of pluripotency in hESCs and their murine counterparts, epiblast stem cells (EpiSCs). WNT inhibition obviates the need to manually remove differentiated cells to maintain cultures and improves the efficiency of directed differentiation. In EpiSCs, WNT inhibition stabilizes a pregastrula epiblast state with novel characteristics, including the ability to contribute to blastocyst chimeras. Our findings show that endogenous WNT signals function as hidden mediators of growth factor-induced differentiation and play critical roles in the self-renewal of hESCs and EpiSCs. BMP induces WNT-dependent and -independent differentiation pathways in hESCs Modulating WNT and BMP directs differentiation toward mesoderm or trophoblast WNT inhibition returns epiblast stem cells to a chimera-competent pregastrula state WNT inhibition prevents spontaneous differentiation of hESCs and epiblast stem cells
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Affiliation(s)
- Dorota Kurek
- Erasmus MC Stem Cell Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands; Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Alex Neagu
- Erasmus MC Stem Cell Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands; Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Melodi Tastemel
- Erasmus MC Stem Cell Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands; Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Nesrin Tüysüz
- Erasmus MC Stem Cell Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands; Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Johannes Lehmann
- Erasmus MC Stem Cell Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands; Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | | | - Sjaak Philipsen
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Reinier van der Linden
- Erasmus MC Stem Cell Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands; Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Alex Maas
- Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Wilfred F J van IJcken
- Erasmus MC Center for Biomics, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Micha Drukker
- Institute of Stem Cell Research, German Research Center for Environmental Health, Helmholtz Center Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Derk Ten Berge
- Erasmus MC Stem Cell Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands; Department of Cell Biology, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands.
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21
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Hou J, Wei W, Saund RS, Xiang P, Cunningham TJ, Yi Y, Alder O, Lu DYD, Savory JGA, Krentz NAJ, Montpetit R, Cullum R, Hofs N, Lohnes D, Humphries RK, Yamanaka Y, Duester G, Saijoh Y, Hoodless PA. A regulatory network controls nephrocan expression and midgut patterning. Development 2014; 141:3772-81. [PMID: 25209250 DOI: 10.1242/dev.108274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Although many regulatory networks involved in defining definitive endoderm have been identified, the mechanisms through which these networks interact to pattern the endoderm are less well understood. To explore the mechanisms involved in midgut patterning, we dissected the transcriptional regulatory elements of nephrocan (Nepn), the earliest known midgut specific gene in mice. We observed that Nepn expression is dramatically reduced in Sox17(-/-) and Raldh2(-/-) embryos compared with wild-type embryos. We further show that Nepn is directly regulated by Sox17 and the retinoic acid (RA) receptor via two enhancer elements located upstream of the gene. Moreover, Nepn expression is modulated by Activin signaling, with high levels inhibiting and low levels enhancing RA-dependent expression. In Foxh1(-/-) embryos in which Nodal signaling is reduced, the Nepn expression domain is expanded into the anterior gut region, confirming that Nodal signaling can modulate its expression in vivo. Together, Sox17 is required for Nepn expression in the definitive endoderm, while RA signaling restricts expression to the midgut region. A balance of Nodal/Activin signaling regulates the anterior boundary of the midgut expression domain.
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Affiliation(s)
- Juan Hou
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Wei Wei
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Ranajeet S Saund
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Ping Xiang
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Thomas J Cunningham
- Development, Aging and Regeneration Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Yuyin Yi
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada Cell and Developmental Biology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Olivia Alder
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Daphne Y D Lu
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Joanne G A Savory
- Cellular and Molecular Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Nicole A J Krentz
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Rachel Montpetit
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Nicole Hofs
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - David Lohnes
- Cellular and Molecular Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - R Keith Humphries
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada Experimental Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Yojiro Yamanaka
- Goodman Cancer Research Centre, Department of Human Genetics, McGill University, Montreal, Quebec H2W 1S6, Canada
| | - Gregg Duester
- Development, Aging and Regeneration Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Yukio Saijoh
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada Cell and Developmental Biology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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22
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Rodríguez-Seguel E, Mah N, Naumann H, Pongrac IM, Cerdá-Esteban N, Fontaine JF, Wang Y, Chen W, Andrade-Navarro MA, Spagnoli FM. Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence. Genes Dev 2013; 27:1932-46. [PMID: 24013505 PMCID: PMC3778245 DOI: 10.1101/gad.220244.113] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A key question in stem cell biology is how distinct cell types arise from common multipotent progenitor cells. It is unknown how liver and pancreas cells diverge from a common endoderm progenitor population and adopt specific fates. Using RNA-seq, Spagnoli and colleagues define the gene expression programs of liver and pancreas progenitors and identify the noncanonical Wnt pathway as a potential developmental regulator of this fate decision. Furthermore, this study provides a framework for lineage-reprogramming strategies to convert adult hepatic cells into pancreatic cells. Understanding how distinct cell types arise from multipotent progenitor cells is a major quest in stem cell biology. The liver and pancreas share many aspects of their early development and possibly originate from a common progenitor. However, how liver and pancreas cells diverge from a common endoderm progenitor population and adopt specific fates remains elusive. Using RNA sequencing (RNA-seq), we defined the molecular identity of liver and pancreas progenitors that were isolated from the mouse embryo at two time points, spanning the period when the lineage decision is made. The integration of temporal and spatial gene expression profiles unveiled mutually exclusive signaling signatures in hepatic and pancreatic progenitors. Importantly, we identified the noncanonical Wnt pathway as a potential developmental regulator of this fate decision and capable of inducing the pancreas program in endoderm and liver cells. Our study offers an unprecedented view of gene expression programs in liver and pancreas progenitors and forms the basis for formulating lineage-reprogramming strategies to convert adult hepatic cells into pancreatic cells.
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23
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Wei W, Hou J, Alder O, Ye X, Lee S, Cullum R, Chu A, Zhao Y, Warner SM, Knight DA, Yang D, Jones SJM, Marra MA, Hoodless PA. Genome-wide microRNA and messenger RNA profiling in rodent liver development implicates mir302b and mir20a in repressing transforming growth factor-beta signaling. Hepatology 2013; 57:2491-501. [PMID: 23315977 DOI: 10.1002/hep.26252] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 12/19/2012] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are recently discovered small RNA molecules that regulate developmental processes, such as proliferation, differentiation, and apoptosis; however, the identity of miRNAs and their functions during liver development are largely unknown. Here we investigated the miRNA and gene expression profiles for embryonic day (E)8.5 endoderm, E14.5 Dlk1(+) liver cells (hepatoblasts), and adult liver by employing Illumina sequencing. We found that miRNAs were abundantly expressed at all three stages. Using K-means clustering analysis, 13 miRNA clusters with distinct temporal expression patterns were identified. mir302b, an endoderm-enriched miRNA, was identified as an miRNA whose predicted targets are expressed highly in E14.5 hepatoblasts but low in the endoderm. We validated the expression of mir302b in the endoderm by whole-mount in situ hybridization. Interestingly, mir20a, the most highly expressed miRNA in the endoderm library, was also predicted to regulate some of the same targets as mir302b. We found that through targeting Tgfbr2, mir302b and mir20a are able to regulate transforming growth factor beta (TGFβ) signal transduction. Moreover, mir302b can repress liver markers in an embryonic stem cell differentiation model. Collectively, we uncovered dynamic patterns of individual miRNAs during liver development, as well as miRNA networks that could be essential for the specification and differentiation of liver progenitors. (HEPATOLOGY 2013).
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Affiliation(s)
- Wei Wei
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, B.C., Canada
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24
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Chuykin I, Schulz H, Guan K, Bader M. Activation of the PTHRP/adenylate cyclase pathway promotes differentiation of rat XEN cells into parietal endoderm, whereas Wnt/β-catenin signaling promotes differentiation into visceral endoderm. J Cell Sci 2012; 126:128-38. [PMID: 23038778 DOI: 10.1242/jcs.110239] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
During early mammalian development, primitive endoderm (PrE) is specified and segregated away from the pluripotent epiblast. At a later developmental stage, PrE forms motile parietal endoderm (PE) lying proximal to the trophectoderm, and visceral endoderm (VE) that contacts the developing epiblast and extraembryonic ectoderm. Mouse extraembryonic endoderm (XEN) cells were isolated and became widely used to study signals governing lineage specification. Rat XEN cell lines have also been derived, but were distinguished from mouse by expression of SSEA1 and Oct4. We showed here that rat XEN cells grown in the presence of a GSK3 inhibitor or overexpressing β-catenin exhibited enhanced formation of cell contacts and decreased motility. Rat XEN cells treated with BMP4 revealed similar morphological changes. Furthermore, we observed that rat XEN cells cultured with GSK3 inhibitor formed adhesion and tight junctions, and acquired bottom-top polarity, indicating the formation of VE cells. In contrast, forskolin, an activator of the cAMP pathway, induced the disruption of cell contacts in rat XEN cells. Treatment with forskolin induced PE formation and epithelial-mesenchymal transition (EMT) in rat XEN cells. Using microarray and real-time PCR assays, we found that VE versus PE formation of rat XEN cells was correlated with change in expression levels of VE or PE marker genes. Similar to forskolin, EMT was prompted upon treatment of rat XEN cells with recombinant parathyroid hormone related peptide (PTHRP), an activator of the cAMP pathway in vivo. Taken together, our data suggest that rat XEN cells are PrE-like cells. The activation of Wnt or BMP4 pathways in rat XEN cells leads to the acquisition of VE characteristics, whereas the activation of the PTHRP/cAMP pathway leads to EMT and the formation of PE.
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Affiliation(s)
- Ilya Chuykin
- Max-Delbrück Center for Molecular Medicine 13125, Berlin, Robert-Rossle Strasse 10, Germany.
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25
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Wang P, McKnight KD, Wong DJ, Rodriguez RT, Sugiyama T, Gu X, Ghodasara A, Qu K, Chang HY, Kim SK. A molecular signature for purified definitive endoderm guides differentiation and isolation of endoderm from mouse and human embryonic stem cells. Stem Cells Dev 2012; 21:2273-87. [PMID: 22236333 DOI: 10.1089/scd.2011.0416] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Embryonic definitive endoderm (DE) generates the epithelial compartment of vital organs such as liver, pancreas, and intestine. However, purification of DE in mammals has not been achieved, limiting the molecular "definition" of endoderm, and hindering our understanding of DE development and attempts to produce endoderm from sources such as embryonic stem (ES) cells. Here, we describe purification of mouse DE using fluorescence-activated cell sorting (FACS) and mice harboring a transgene encoding enhanced green fluorescent protein (eGFP) inserted into the Sox17 locus, which is expressed in the embryonic endoderm. Comparison of patterns of signaling pathway activation in native mouse DE and endoderm-like cells generated from ES cells produced novel culture modifications that generated Sox17-eGFP⁺ progeny whose gene expression resembled DE more closely than achieved with standard methods. These studies also produced new FACS methods for purifying DE from nontransgenic mice and mouse ES cell cultures. Parallel studies of a new human SOX17-eGFP ES cell line allowed analysis of endoderm differentiation in vitro, leading to culture modifications that enhanced expression of an endoderm-like signature. This work should accelerate our understanding of mechanisms regulating DE development in mice and humans, and guide further use of ES cells for tissue replacement.
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Affiliation(s)
- Pei Wang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, Califorina, USA
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26
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Artus J, Douvaras P, Piliszek A, Isern J, Baron MH, Hadjantonakis AK. BMP4 signaling directs primitive endoderm-derived XEN cells to an extraembryonic visceral endoderm identity. Dev Biol 2011; 361:245-62. [PMID: 22051107 DOI: 10.1016/j.ydbio.2011.10.015] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 09/19/2011] [Accepted: 10/08/2011] [Indexed: 12/20/2022]
Abstract
The visceral endoderm (VE) is an epithelial tissue in the early postimplantation mouse embryo that encapsulates the pluripotent epiblast distally and the extraembryonic ectoderm proximally. In addition to facilitating nutrient exchange before the establishment of a circulation, the VE is critical for patterning the epiblast. Since VE is derived from the primitive endoderm (PrE) of the blastocyst, and PrE-derived eXtraembryonic ENdoderm (XEN) cells can be propagated in vitro, XEN cells should provide an important tool for identifying factors that direct VE differentiation. In this study, we demonstrated that BMP4 signaling induces the formation of a polarized epithelium in XEN cells. This morphological transition was reversible, and was associated with the acquisition of a molecular signature comparable to extraembryonic (ex) VE. Resembling exVE which will form the endoderm of the visceral yolk sac, BMP4-treated XEN cells regulated hematopoiesis by stimulating the expansion of primitive erythroid progenitors. We also observed that LIF exerted an antagonistic effect on BMP4-induced XEN cell differentiation, thereby impacting the extrinsic conditions used for the isolation and maintenance of XEN cells in an undifferentiated state. Taken together, our data suggest that XEN cells can be differentiated towards an exVE identity upon BMP4 stimulation and therefore represent a valuable tool for investigating PrE lineage differentiation.
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Affiliation(s)
- Jérôme Artus
- Developmental Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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27
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Loebel DAF, Studdert JB, Power M, Radziewic T, Jones V, Coultas L, Jackson Y, Rao RS, Steiner K, Fossat N, Robb L, Tam PPL. Rhou maintains the epithelial architecture and facilitates differentiation of the foregut endoderm. Development 2011; 138:4511-22. [PMID: 21903671 DOI: 10.1242/dev.063867] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Rhou encodes a Cdc42-related atypical Rho GTPase that influences actin organization in cultured cells. In mouse embryos at early-somite to early-organogenesis stages, Rhou is expressed in the columnar endoderm epithelium lining the lateral and ventral wall of the anterior intestinal portal. During foregut development, Rhou is downregulated in regions where the epithelium acquires a multilayered morphology heralding the budding of organ primordia. In embryos generated from Rhou knockdown embryonic stem (ES) cells, the embryonic foregut displays an abnormally flattened shape. The epithelial architecture of the endoderm is disrupted, the cells are depleted of microvilli and the phalloidin-stained F-actin content of their sub-apical cortical domain is reduced. Rhou-deficient cells in ES cell-derived embryos and embryoid bodies are less efficient in endoderm differentiation. Impaired endoderm differentiation of Rhou-deficient ES cells is accompanied by reduced expression of c-Jun/AP-1 target genes, consistent with a role for Rhou in regulating JNK activity. Downregulation of Rhou in individual endoderm cells results in a reduced ability of these cells to occupy the apical territory of the epithelium. Our findings highlight epithelial morphogenesis as a required intermediate step in the differentiation of endoderm progenitors. In vivo, Rhou activity maintains the epithelial architecture of the endoderm progenitors, and its downregulation accompanies the transition of the columnar epithelium in the embryonic foregut to a multilayered cell sheet during organ formation.
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Affiliation(s)
- David A F Loebel
- Embryology Unit, Children's Medical Research Institute, Westmead, NSW 2145, Australia
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28
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Wang P, Rodriguez RT, Wang J, Ghodasara A, Kim SK. Targeting SOX17 in human embryonic stem cells creates unique strategies for isolating and analyzing developing endoderm. Cell Stem Cell 2011; 8:335-46. [PMID: 21362573 PMCID: PMC3063711 DOI: 10.1016/j.stem.2011.01.017] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 11/18/2010] [Accepted: 01/27/2011] [Indexed: 11/18/2022]
Abstract
Human embryonic stem cells (hESCs) can provide insights into development of inaccessible human tissues such as embryonic endoderm. Progress in this area has been hindered by a lack of methods for isolating endodermal cells and tracing fates of their differentiated progeny. By using homologous recombination in human ESCs, we inserted an enhanced green fluorescent protein (eGFP) transgene into the SOX17 locus, a postulated marker of human endoderm. FACS purification and gene expression profiling confirmed that SOX17(+)-hESC progeny expressed endodermal markers and unveiled specific cell surface protein combinations that permitted FACS-based isolation of primitive gut tube endodermal cells produced from unmodified human ESCs and from induced pluripotent stem cells (iPSC). Differentiating SOX17(+) endodermal cells expressed markers of liver, pancreas, and intestinal epithelium in vitro and gave rise to endodermal progeny in vivo. Thus, prospective isolation, lineage tracing, and developmental studies of SOX17(+) hESC progeny have revealed fundamental aspects of human endodermal biology.
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Affiliation(s)
- Pei Wang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Ryan T. Rodriguez
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Jing Wang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Amar Ghodasara
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
| | - Seung K. Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA
- Howard Hughes Medical Institute
- Department of Medicine (Oncology Division), Stanford University School of Medicine, Stanford, CA
- Corresponding author Howard Hughes Medical Institute Department of Developmental Biology B300 Beckman Center 279 Campus Drive, Stanford CA, 94305-5329 T: 650-723-6230 F: 650-725-7739
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29
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Smad1 signaling restricts hematopoietic potential after promoting hemangioblast commitment. Blood 2011; 117:6489-97. [PMID: 21515822 DOI: 10.1182/blood-2010-10-312389] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bone morphogenetic protein (BMP) signaling regulates embryonic hematopoiesis via receptor-mediated activation of downstream SMAD proteins, including SMAD1. In previous work, we showed that Smad1 expression is sufficient to enhance commitment of mesoderm to hemangioblast fate. We also found indirect evidence to support a subsequent repressive function for Smad1 in hematopoiesis. To test this hypothesis directly, we developed a novel system allowing temporal control of Smad1 levels by conditional knockdown in embryonic stem cell derivatives. Depletion of Smad1 in embryoid body cultures before hemangioblast commitment limits hematopoietic potential because of a block in mesoderm development. Conversely, when Smad1 is depleted in FlK1(+) mesoderm, at a stage after hemangioblast commitment, the pool of hematopoietic progenitors is expanded. This involves enhanced expression levels for genes specific to hematopoiesis, including Gata1, Runx1 and Eklf, rather than factors required for earlier specification of the hemangioblast. The phenotype correlates with increased nuclear SMAD2 activity, indicating molecular cross-regulation between the BMP and TGF-β signaling pathways. Consistent with this mechanism, hematopoiesis was enhanced when Smad2 was directly expressed during this same developmental window. Therefore, this study reveals a temporally defined function for Smad1 in restricting the expansion of early hematopoietic progenitors.
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Lionetti V, Bianchi G, Recchia FA, Ventura C. Control of autocrine and paracrine myocardial signals: an emerging therapeutic strategy in heart failure. Heart Fail Rev 2011; 15:531-42. [PMID: 20364318 DOI: 10.1007/s10741-010-9165-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A growing body of evidence supports the hypothesis that autocrine and paracrine mechanisms, mediated by factors released by the resident cardiac cells, could play an essential role in the reparative process of the failing heart. Such signals may influence the function of cardiac stem cells via several mechanisms, among which the most extensively studied are cardiomyocyte survival and angiogenesis. Moreover, besides promoting cytoprotection and angiogenesis, paracrine factors released by resident cardiac cells may alter cardiac metabolism and extracellular matrix turnover, resulting in more favorable post-injury remodeling. It is reasonable to believe that critical intracellular signals are activated and modulated in a temporal and spatial manner exerting different effects, overall depending on the microenvironment changes present in the failing myocardium. The recent demonstration that chemically, mechanically or genetically activated cardiac cells may release peptides to protect tissue against ischemic injury provides a potential route to achieve the delivery of specific proteins produced by these cells for innovative pharmacological regenerative therapy of the heart. It is important to keep in mind that therapies currently used to treat heart failure (HF) and leading to improvement of cardiac function fail to induce tissue repair/regeneration. As a matter of facts, if specific autocrine/paracrine cell-derived factors that improve cardiac function will be identified, pharmacological-based therapy might be more easily translated into clinical benefits than cell-based therapy. This review will focus on the recent development of potential pharmacologic targets to promote and drive at molecular level the cardiac repair/regeneration in HF.
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Affiliation(s)
- Vincenzo Lionetti
- Sector of Medicine, Scuola Superiore Sant'Anna, Via G. Moruzzi, 1, 56124, Pisa, Italy.
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Kobayashi NR, Hawes SM, Crook JM, Pébay A. G-protein coupled receptors in stem cell self-renewal and differentiation. Stem Cell Rev Rep 2010; 6:351-66. [PMID: 20625855 DOI: 10.1007/s12015-010-9167-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Stem cells have great potential for understanding early development, treating human disease, tissue trauma and early phase drug discovery. The factors that control the regulation of stem cell survival, proliferation, migration and differentiation are still emerging. Some evidence now exists demonstrating the potent effects of various G-protein coupled receptor (GPCR) ligands on the biology of stem cells. This review aims to give an overview of the current knowledge of the regulation of embryonic and somatic stem cell maintenance and differentiation by GPCR ligands.
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Elimination of tumorigenic stem cells from differentiated progeny and selection of definitive endoderm reveals a Pdx1+ foregut endoderm stem cell lineage. Stem Cell Res 2010; 6:143-57. [PMID: 21130058 DOI: 10.1016/j.scr.2010.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 09/21/2010] [Accepted: 10/23/2010] [Indexed: 01/23/2023] Open
Abstract
Embryonic stem cell (ESC) derivatives offer promise for generating clinically useful tissues for transplantation, yet the specter of producing tumors in patients remains a significant concern. We have developed a simple method that eliminates the tumorigenic potential from differentiated ESC cultures of murine and human origin while purifying lineage-restricted, definitive endoderm-committed cells. A three-stage scheme utilizing magnetic bead sorting and specific antibodies to remove undifferentiated ESCs and extraembryonic endoderm cells, followed by positive selection of definitive endoderm cells on the basis of epithelial cell adhesion molecule (EpCAM) expression, was used to isolate a population of EpCAM(+)SSEA1(-)SSEA3(-) cells. Sorted cells do not form teratomas after transplantation into immunodeficient mice, but display gene and protein expression profiles indicative of definitive endoderm cells. Sorted cells could be subsequently expanded in vitro and further differentiated to express key pancreas specification proteins. In vivo transplantation of sorted cells resulted in small, benign tissues that uniformly express PDX1. These studies describe a straightforward method without genetic manipulation that eliminates the risk of teratoma formation from ESC differentiated derivatives. Significantly, enriched populations isolated by this method appear to be lineage-restricted definitive endoderm cells with limited proliferation capacity.
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Trowe MO, Shah S, Petry M, Airik R, Schuster-Gossler K, Kist R, Kispert A. Loss of Sox9 in the periotic mesenchyme affects mesenchymal expansion and differentiation, and epithelial morphogenesis during cochlea development in the mouse. Dev Biol 2010; 342:51-62. [DOI: 10.1016/j.ydbio.2010.03.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 02/24/2010] [Accepted: 03/16/2010] [Indexed: 10/19/2022]
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Hassan AS, Hou J, Wei W, Hoodless PA. Expression of two novel transcripts in the mouse definitive endoderm. Gene Expr Patterns 2010; 10:127-34. [PMID: 20153842 DOI: 10.1016/j.gep.2010.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 02/03/2010] [Accepted: 02/05/2010] [Indexed: 12/19/2022]
Abstract
Here we describe the expression of two novel transcripts, Ende (AK014119) and Npe (AK084355), during early mouse embryogenesis. Ende mRNA was first detected at embryonic day (E) 7.0 in a small population of epiblast cells in the distal half of the embryo. At E7.5, Ende was expressed by newly formed definitive endoderm cells in the proximal half of the embryo, and was not expressed in extra-embryonic endoderm. This expression pattern then changed to the ventral aspect of the developing foregut pocket and the entire hindgut pocket at E8.0-8.5, before becoming restricted to the foregut overlying the heart and the posterior-most hindgut. By E9.25 Ende expression was also observed in the posterior half of the ventral neural tube. Thus, Ende was expressed dynamically and in specific populations of the definitive endoderm from E7.0 to E8.5. We found Npe expression to be restricted to the node/posterior notochord region at the distal tip of the embryo between E7.0 and E8.0. By E9.5, Npe expression was observed in the posterior-most population of dorsal hindgut cells and notochord cells. Given their expression in mouse definitive endoderm populations, Ende and Npe will be valuable tools to study formation and development of this tissue.
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Affiliation(s)
- Ali S Hassan
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
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McKnight KD, Hou J, Hoodless PA. Foxh1 and Foxa2 are not required for formation of the midgut and hindgut definitive endoderm. Dev Biol 2010; 337:471-81. [DOI: 10.1016/j.ydbio.2009.10.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 10/29/2009] [Accepted: 10/29/2009] [Indexed: 11/16/2022]
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Tremblay KD. Formation of the murine endoderm: lessons from the mouse, frog, fish, and chick. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2010; 96:1-34. [PMID: 21075338 DOI: 10.1016/b978-0-12-381280-3.00001-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The mammalian definitive endoderm arises as a simple epithelial sheet. This sheet of cells will eventually produce the innermost tube that comprises the entire digestive tract from the esophagus to the colon as well as the epithelial component of the digestive and respiratory organs including the thymus, thyroid, lung, liver, gallbladder, and pancreas. Thus a wide array of tissue types are derived from the early endodermal sheet, and understanding the morphological and molecular mechanisms used to produce this tissue is integral to understanding the development of all these organs. The goal of this chapter is to summarize what is known about the morphological and molecular mechanisms used to produce this embryonic germ layer. Although this chapter mainly focuses on the mechanisms used to generate the murine endoderm, supportive or suggestive data from other species, including chick, frog (Xenopus laevis), and the Zebrafish (Danio rerio) are also examined.
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Affiliation(s)
- Kimberly D Tremblay
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
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37
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Gadue P, Gouon-Evans V, Cheng X, Wandzioch E, Zaret KS, Grompe M, Streeter PR, Keller GM. Generation of monoclonal antibodies specific for cell surface molecules expressed on early mouse endoderm. Stem Cells 2009; 27:2103-13. [PMID: 19522011 DOI: 10.1002/stem.147] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The development of functional cell populations such as hepatocytes and pancreatic beta cells from embryonic stem cell (ESC) is dependent on the efficient induction of definitive endoderm early in the differentiation process. To monitor definitive endoderm formation in mouse ESC differentiation cultures in a quantitative fashion, we generated a reporter cell line that expresses human CD25 from the Foxa3 locus and human CD4 from the Foxa2 locus. Induction of these reporter ESCs with high concentrations of activin A led to the development of a CD25-Foxa3+CD4-Foxa2+ population within 4-5 days of culture. Isolation and characterization of this population showed that it consists predominantly of definitive endoderm that is able to undergo hepatic specification under the appropriate conditions. To develop reagents that can be used for studies on endoderm development from unmanipulated ESCs, from induced pluripotent stem cells, and from the mouse embryo, we generated monoclonal antibodies against the CD25-Foxa3+CD4-Foxa2+ population. With this approach, we identified two antibodies that react specifically with endoderm from ESC cultures and from the early embryo. The specificity of these antibodies enables one to quantitatively monitor endoderm development in ESC differentiation cultures, to study endoderm formation in the embryo, and to isolate pure populations of culture- or embryo-derived endodermal cells.
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Affiliation(s)
- Paul Gadue
- Department of Pathology, Center for Cellular and Molecular Therapeutics; Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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Roszell B, Mondrinos MJ, Seaton A, Simons DM, Koutzaki SH, Fong GH, Lelkes PI, Finck CM. Efficient derivation of alveolar type II cells from embryonic stem cells for in vivo application. Tissue Eng Part A 2009; 15:3351-65. [PMID: 19388834 PMCID: PMC2811058 DOI: 10.1089/ten.tea.2008.0664] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 04/23/2009] [Indexed: 11/12/2022] Open
Abstract
In the present study, mouse embryonic stem cells (ESCs) were differentiated into alveolar epithelial type II (AEII) cells for endotracheal injection. These enriched lung-like populations expressed lung epithelial markers SP-A, SP-B, SP-C, and CC10. First we show that rapid differentiation of ESCs requires a dissociated seeding method instead of an embryoid body culture method. We then investigated a two-step differentiation of ESCs into definitive endoderm by activin or A549-conditioned medium as a precursor to lung epithelial cells. When conditioned medium from A549 cells was used to derive endoderm, yield was increased above that of activin alone. Further studies showed that Wnt3a may be one of the secreted factors produced by A549 cells and promotes definitive endoderm differentiation, in part, through suppression of primitive endoderm. Activin and Wnt3a together at appropriate doses with dissociated cell seeding promoted greater endoderm yield than activin alone. Next, fibroblast growth factor 2 was shown to induce a dose-dependent expression of SPC, and these cells contained lamellar bodies characteristic of mature AEII cells from ESC-derived endoderm. Finally, ES-derived lung cells were endotracheally injected into preterm mice with evidence of AEII distribution within the lung parenchyma. This study concludes that a recapitulation of development may enhance derivation of an enriched population of lung-like cells for use in cell-based therapy.
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Affiliation(s)
- Blair Roszell
- School of Biomedical Engineering, Sciences, and Health Systems, Drexel University, Philadelphia, Pennsylvania
- University of Connecticut Health Center, Farmington, Connecticut
| | - Mark J. Mondrinos
- School of Biomedical Engineering, Sciences, and Health Systems, Drexel University, Philadelphia, Pennsylvania
| | - Ariel Seaton
- University of Connecticut Health Center, Farmington, Connecticut
| | - Donald M. Simons
- School of Biomedical Engineering, Sciences, and Health Systems, Drexel University, Philadelphia, Pennsylvania
| | - Sirma H. Koutzaki
- School of Biomedical Engineering, Sciences, and Health Systems, Drexel University, Philadelphia, Pennsylvania
| | - Guo-Hua Fong
- University of Connecticut Health Center, Farmington, Connecticut
| | - Peter I. Lelkes
- School of Biomedical Engineering, Sciences, and Health Systems, Drexel University, Philadelphia, Pennsylvania
| | - Christine M. Finck
- University of Connecticut Health Center, Farmington, Connecticut
- Connecticut Children's Medical Center, Hartford, Connecticut
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Holtzinger A, Rosenfeld GE, Evans T. Gata4 directs development of cardiac-inducing endoderm from ES cells. Dev Biol 2009; 337:63-73. [PMID: 19850025 DOI: 10.1016/j.ydbio.2009.10.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 10/05/2009] [Accepted: 10/06/2009] [Indexed: 01/06/2023]
Abstract
The transcription factor Gata4 is essential for normal heart morphogenesis and regulates the survival, growth, and proliferation of cardiomyocytes. We tested if Gata4 can specify cardiomyocyte fate from an uncommitted stem or progenitor cell population, by developing a system for conditional expression of Gata4 in embryonic stem cells. We find that in embryoid body cultures containing even a low ratio of these cells, expression of Gata4 is sufficient to enhance significantly the generation of cardiomyocytes, via a non-cell-autonomous mechanism. The Gata4-expressing cells do not generate cardiac or other mesoderm derivatives. Rather, Gata4 expression directs the development of two types of Sox17+ endoderm. This includes an epCam+Dpp4+ subtype of visceral endoderm. In addition, Gata4 generates similar amounts of epCam+Dpp4- definitive endoderm enriched for Cxcr4, FoxA2, FoxA3, Dlx5 and other characteristic transcripts. Both types of endoderm express cardiac-inducing factors, including WNT antagonists Dkk1 and Sfrp5, although the visceral endoderm subtype has much higher cardiac-inducing activity correlating with relatively enhanced levels of transcripts encoding BMPs. The Gata4-expressing cells eventually express differentiation markers showing commitment to liver development, even under conditions that normally support mesoderm development. The results suggest that Gata4 is capable of specifying endoderm fates that facilitate, with temporal and spatial specificity, the generation of cardiomyocyte progenitors from associated mesoderm.
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Affiliation(s)
- Audrey Holtzinger
- Department of Surgery, Weill Cornell Medical School, New York, NY 10021, USA
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Burtscher I, Lickert H. Foxa2 regulates polarity and epithelialization in the endoderm germ layer of the mouse embryo. Development 2009; 136:1029-38. [PMID: 19234065 DOI: 10.1242/dev.028415] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the mouse, one of the earliest events in the determination of cell fate is the segregation of cells into germ layers during gastrulation; however, the cellular and molecular details are not well defined due to intrauterine development. We were able to visualize a clear sequence of events occurring in the process of germ-layer formation, using immunohistochemistry and time-lapse confocal imaging. The T-box transcription factor brachyury (T) and the Forkhead transcription factor Foxa2 specify mesoderm and endoderm in the posterior epiblast. Fate-specified epiblast cells lose their polarity and undergo epithelial-mesenchymal transition to invade into the primitive streak region, where these cell populations quickly separate and differentiate into morphologically and molecularly distinct Foxa2-positive endoderm and T-positive mesoderm populations. The endoderm cells flatten and acquire apical-basal polarity during intercalation into the outside epithelium in order to establish proper intracellular junctions with pre-existing cells. By contrast, the mesodermal cells become spherical during migration and acquire a mesenchymal fate. Interestingly, axial mesodermal cells are descended from Foxa2-positive epiblast cells that upregulate T protein in the anterior primitive streak region. These cells, as well as Foxa2-positive endoderm cells, are highly polarized and epithelialized, suggesting that Foxa2 promotes an epithelial fate and suppresses a mesenchymal fate. This observation is supported by the fact that Foxa2 mutant endodermal cells fail to maintain polarity and do not establish proper cellular junctions, and are thus unable to functionally integrate into the endoderm epithelium. We propose that Foxa2 regulates a molecular program that induces an epithelial cellular phenotype.
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Affiliation(s)
- Ingo Burtscher
- Helmholtz Zentrum München, Institute of Stem Cell Research, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
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Hansson M, Olesen DR, Peterslund JML, Engberg N, Kahn M, Winzi M, Klein T, Maddox-Hyttel P, Serup P. A late requirement for Wnt and FGF signaling during activin-induced formation of foregut endoderm from mouse embryonic stem cells. Dev Biol 2009; 330:286-304. [PMID: 19358838 DOI: 10.1016/j.ydbio.2009.03.026] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 03/18/2009] [Accepted: 03/30/2009] [Indexed: 02/07/2023]
Abstract
Here we examine how BMP, Wnt, and FGF signaling modulate activin-induced mesendodermal differentiation of mouse ES cells grown under defined conditions in adherent monoculture. We monitor ES cells containing reporter genes for markers of primitive streak (PS) and its progeny and extend previous findings on the ability of increasing concentrations of activin to progressively induce more ES cell progeny to anterior PS and endodermal fates. We find that the number of Sox17- and Gsc-expressing cells increases with increasing activin concentration while the highest number of T-expressing cells is found at the lowest activin concentration. The expression of Gsc and other anterior markers induced by activin is prevented by treatment with BMP4, which induces T expression and subsequent mesodermal development. We show that canonical Wnt signaling is required only during late stages of activin-induced development of Sox17-expressing endodermal cells. Furthermore, Dkk1 treatment is less effective in reducing development of Sox17(+) endodermal cells in adherent culture than in aggregate culture and appears to inhibit nodal-mediated induction of Sox17(+) cells more effectively than activin-mediated induction. Notably, activin induction of Gsc-GFP(+) cells appears refractory to inhibition of canonical Wnt signaling but shows a dependence on early as well as late FGF signaling. Additionally, we find a late dependence on FGF signaling during induction of Sox17(+) cells by activin while BMP4-induced T expression requires FGF signaling in adherent but not aggregate culture. Lastly, we demonstrate that activin-induced definitive endoderm derived from mouse ES cells can incorporate into the developing foregut endoderm in vivo and adopt a mostly anterior foregut character after further culture in vitro.
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Affiliation(s)
- Mattias Hansson
- Department of Developmental Biology, Hagedorn Research Institute, Niels Steensens Vej 6, DK-2820 Gentofte, Denmark
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Matukumalli LK, Schroeder SG. Sequence Based Gene Expression Analysis. Bioinformatics 2009. [DOI: 10.1007/978-0-387-92738-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Tamplin OJ, Kinzel D, Cox BJ, Bell CE, Rossant J, Lickert H. Microarray analysis of Foxa2 mutant mouse embryos reveals novel gene expression and inductive roles for the gastrula organizer and its derivatives. BMC Genomics 2008; 9:511. [PMID: 18973680 PMCID: PMC2605479 DOI: 10.1186/1471-2164-9-511] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 10/30/2008] [Indexed: 01/05/2023] Open
Abstract
Background The Spemann/Mangold organizer is a transient tissue critical for patterning the gastrula stage vertebrate embryo and formation of the three germ layers. Despite its important role during development, there are still relatively few genes with specific expression in the organizer and its derivatives. Foxa2 is a forkhead transcription factor that is absolutely required for formation of the mammalian equivalent of the organizer, the node, the axial mesoderm and the definitive endoderm (DE). However, the targets of Foxa2 during embryogenesis, and the molecular impact of organizer loss on the gastrula embryo, have not been well defined. Results To identify genes specific to the Spemann/Mangold organizer, we performed a microarray-based screen that compared wild-type and Foxa2 mutant embryos at late gastrulation stage (E7.5). We could detect genes that were consistently down-regulated in replicate pools of mutant embryos versus wild-type, and these included a number of known node and DE markers. We selected 314 genes without previously published data at E7.5 and screened for expression by whole mount in situ hybridization. We identified 10 novel expression patterns in the node and 5 in the definitive endoderm. We also found significant reduction of markers expressed in secondary tissues that require interaction with the organizer and its derivatives, such as cardiac mesoderm, vasculature, primitive streak, and anterior neuroectoderm. Conclusion The genes identified in this screen represent novel Spemann/Mangold organizer genes as well as potential Foxa2 targets. Further investigation will be needed to define these genes as novel developmental regulatory factors involved in organizer formation and function. We have placed these genes in a Foxa2-dependent genetic regulatory network and we hypothesize how Foxa2 may regulate a molecular program of Spemann/Mangold organizer development. We have also shown how early loss of the organizer and its inductive properties in an otherwise normal embryo, impacts on the molecular profile of surrounding tissues.
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Affiliation(s)
- Owen J Tamplin
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, M5G 1X8, Canada.
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Abstract
Coordinated regulation of genetic activity underpins formation of the body plan and morphogenesis of embryonic structures. In this issue of Developmental Cell, Mitiku and Baker describe a chronological series of transcriptomes of postimplantation mouse embryos at gastrulation and early organogenesis, providing a valuable resource for studying the dynamics of both genome-wide and gene-specific transcriptional activities that accompany mouse embryogenesis.
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Affiliation(s)
- Nicolas Fossat
- Embryology Unit, Children's Medical Research Institute, University of Sydney, Locked Bag 23, Wentworthville NSW 2145, Australia
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McKnight KD, Hou J, Hoodless PA. Dynamic expression of thyrotropin-releasing hormone in the mouse definitive endoderm. Dev Dyn 2008; 236:2909-17. [PMID: 17849455 DOI: 10.1002/dvdy.21313] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thyrotropin-releasing hormone (TRH) is a well-characterized regulator of the hypothalamic-pituitary-thyroid endocrine axis. Here, we describe the expression of Trh during early embryonic development in the mouse. We find Trh to be highly expressed during postimplantation stages in the mouse embryo, with expression first observed in the epiblast at embryonic day (E) 6.5. During gastrulation, Trh is expressed in the newly formed definitive endoderm cells, and at embryonic day (E) 7.75, marks the entire definitive endoderm. Subsequently, Trh mRNA levels rapidly decrease such that, by E9.0, expression in the definitive endoderm is no longer detected, after which neural expression predominates. Thus, Trh is expressed dynamically and specifically in the developing mouse definitive endoderm from E7.0 to E8.5. Trh is unique among definitive endoderm markers as it transiently marks the entire definitive endoderm population and is not expressed in the extraembryonic endoderm. Trh will be a valuable tool to study definitive endoderm formation in the mouse embryo.
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Affiliation(s)
- Kristen D McKnight
- Genetics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
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