A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo
Directed differentiation of pluripotent stem cells provides an accessible system to model development. However, the distinct cell types that emerge, their dynamics, and their relationship to progenitors in the early embryo has been difficult to decipher because of the cellular heterogeneity inherent...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2018-08-01
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| Series: | Stem Cell Research |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1873506118301909 |
| _version_ | 1818500899620782080 |
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| author | Abby Spangler Emily Y. Su April M. Craft Patrick Cahan |
| author_facet | Abby Spangler Emily Y. Su April M. Craft Patrick Cahan |
| author_sort | Abby Spangler |
| collection | DOAJ |
| description | Directed differentiation of pluripotent stem cells provides an accessible system to model development. However, the distinct cell types that emerge, their dynamics, and their relationship to progenitors in the early embryo has been difficult to decipher because of the cellular heterogeneity inherent to differentiation. Here, we used a combination of bulk RNA-Seq, single cell RNA-Seq, and bioinformatics analyses to dissect the cell types that emerge during directed differentiation of mouse embryonic stem cells as embryoid bodies and we compared them to spatially and temporally resolved transcriptional profiles of early embryos. Our single cell analyses of the day 4 embryoid bodies revealed three populations which had retained related yet distinct pluripotent signatures that resemble the pre- or post-implantation epiblast, one population of presumptive neuroectoderm, one population of mesendoderm, and four populations of neural progenitors. By day 6, the neural progenitors predominated the embryoid bodies, but both a small population of pluripotent-like cells and an anterior mesoderm-like Brachyury-expressing population were present. By comparing the day 4 and day 6 populations, we identified candidate differentiation paths, transcription factors, and signaling pathways that mark the in vitro correlate of the transition from the mid-to-late primitive streak stage. Keywords: Directed differentiation, Embryoid body, Mesendoderm, Single cell rna-seq, Noggin, Transcriptional profiling, Neuroectoderm |
| first_indexed | 2024-12-10T20:48:54Z |
| format | Article |
| id | doaj.art-1c935b8feb4347cea3da80a898e29e7a |
| institution | Directory Open Access Journal |
| issn | 1873-5061 |
| language | English |
| last_indexed | 2024-12-10T20:48:54Z |
| publishDate | 2018-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Stem Cell Research |
| spelling | doaj.art-1c935b8feb4347cea3da80a898e29e7a2022-12-22T01:34:10ZengElsevierStem Cell Research1873-50612018-08-0131201215A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryoAbby Spangler0Emily Y. Su1April M. Craft2Patrick Cahan3Department of Biomedical Engineering, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USADepartment of Biomedical Engineering, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USADepartment of Orthopaedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USADepartment of Biomedical Engineering, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Corresponding author.Directed differentiation of pluripotent stem cells provides an accessible system to model development. However, the distinct cell types that emerge, their dynamics, and their relationship to progenitors in the early embryo has been difficult to decipher because of the cellular heterogeneity inherent to differentiation. Here, we used a combination of bulk RNA-Seq, single cell RNA-Seq, and bioinformatics analyses to dissect the cell types that emerge during directed differentiation of mouse embryonic stem cells as embryoid bodies and we compared them to spatially and temporally resolved transcriptional profiles of early embryos. Our single cell analyses of the day 4 embryoid bodies revealed three populations which had retained related yet distinct pluripotent signatures that resemble the pre- or post-implantation epiblast, one population of presumptive neuroectoderm, one population of mesendoderm, and four populations of neural progenitors. By day 6, the neural progenitors predominated the embryoid bodies, but both a small population of pluripotent-like cells and an anterior mesoderm-like Brachyury-expressing population were present. By comparing the day 4 and day 6 populations, we identified candidate differentiation paths, transcription factors, and signaling pathways that mark the in vitro correlate of the transition from the mid-to-late primitive streak stage. Keywords: Directed differentiation, Embryoid body, Mesendoderm, Single cell rna-seq, Noggin, Transcriptional profiling, Neuroectodermhttp://www.sciencedirect.com/science/article/pii/S1873506118301909 |
| spellingShingle | Abby Spangler Emily Y. Su April M. Craft Patrick Cahan A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo Stem Cell Research |
| title | A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo |
| title_full | A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo |
| title_fullStr | A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo |
| title_full_unstemmed | A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo |
| title_short | A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo |
| title_sort | single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo |
| url | http://www.sciencedirect.com/science/article/pii/S1873506118301909 |
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