Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis
Abstract Background Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this process at single-cell resolution remain elusive. Results We perform singl...
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| Format: | Article |
| Language: | English |
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BMC
2018-03-01
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| Series: | Genome Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s13059-018-1416-2 |
| _version_ | 1811314596657496064 |
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| author | Ji Dong Yuqiong Hu Xiaoying Fan Xinglong Wu Yunuo Mao Boqiang Hu Hongshan Guo Lu Wen Fuchou Tang |
| author_facet | Ji Dong Yuqiong Hu Xiaoying Fan Xinglong Wu Yunuo Mao Boqiang Hu Hongshan Guo Lu Wen Fuchou Tang |
| author_sort | Ji Dong |
| collection | DOAJ |
| description | Abstract Background Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this process at single-cell resolution remain elusive. Results We perform single-cell RNA sequencing analysis of 1916 individual cells from eight organs and tissues of E9.5 to E11.5 mouse embryos, namely, the forebrain, hindbrain, skin, heart, somite, lung, liver, and intestine. Based on the regulatory activities rather than the expression patterns, all cells analyzed can be well classified into four major groups with epithelial, mesodermal, hematopoietic, and neuronal identities. For different organs within the same group, the similarities and differences of their features and developmental paths are revealed and reconstructed. Conclusions We identify mutual interactions between epithelial and mesenchymal cells and detect epithelial cells with prevalent mesenchymal features during organogenesis, which are similar to the features of intermediate epithelial/mesenchymal cells during tumorigenesis. The comprehensive transcriptome at single-cell resolution profiled in our study paves the way for future mechanistic studies of the gene-regulatory networks governing mammalian organogenesis. |
| first_indexed | 2024-04-13T11:15:20Z |
| format | Article |
| id | doaj.art-4873e4f6e23742199190757e746726f9 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-04-13T11:15:20Z |
| publishDate | 2018-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-4873e4f6e23742199190757e746726f92022-12-22T02:48:59ZengBMCGenome Biology1474-760X2018-03-0119112010.1186/s13059-018-1416-2Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesisJi Dong0Yuqiong Hu1Xiaoying Fan2Xinglong Wu3Yunuo Mao4Boqiang Hu5Hongshan Guo6Lu Wen7Fuchou Tang8Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking UniversityBeijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking UniversityBeijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking UniversityBeijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking UniversityBeijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking UniversityBeijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking UniversityBeijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking UniversityBeijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking UniversityBeijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking UniversityAbstract Background Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this process at single-cell resolution remain elusive. Results We perform single-cell RNA sequencing analysis of 1916 individual cells from eight organs and tissues of E9.5 to E11.5 mouse embryos, namely, the forebrain, hindbrain, skin, heart, somite, lung, liver, and intestine. Based on the regulatory activities rather than the expression patterns, all cells analyzed can be well classified into four major groups with epithelial, mesodermal, hematopoietic, and neuronal identities. For different organs within the same group, the similarities and differences of their features and developmental paths are revealed and reconstructed. Conclusions We identify mutual interactions between epithelial and mesenchymal cells and detect epithelial cells with prevalent mesenchymal features during organogenesis, which are similar to the features of intermediate epithelial/mesenchymal cells during tumorigenesis. The comprehensive transcriptome at single-cell resolution profiled in our study paves the way for future mechanistic studies of the gene-regulatory networks governing mammalian organogenesis.http://link.springer.com/article/10.1186/s13059-018-1416-2Single-cell RNA-seqOrganogenesisInteractions between mesenchyme and epitheliumEpithelial/mesenchymal hybrid state |
| spellingShingle | Ji Dong Yuqiong Hu Xiaoying Fan Xinglong Wu Yunuo Mao Boqiang Hu Hongshan Guo Lu Wen Fuchou Tang Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis Genome Biology Single-cell RNA-seq Organogenesis Interactions between mesenchyme and epithelium Epithelial/mesenchymal hybrid state |
| title | Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis |
| title_full | Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis |
| title_fullStr | Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis |
| title_full_unstemmed | Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis |
| title_short | Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis |
| title_sort | single cell rna seq analysis unveils a prevalent epithelial mesenchymal hybrid state during mouse organogenesis |
| topic | Single-cell RNA-seq Organogenesis Interactions between mesenchyme and epithelium Epithelial/mesenchymal hybrid state |
| url | http://link.springer.com/article/10.1186/s13059-018-1416-2 |
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