Comparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snRNA sequencing
The syncytiotrophoblast (STB) is a multinucleated cell layer that forms the outer surface of human chorionic villi. Its unusual structure, with billions of nuclei in a single cell, makes it difficult to resolve using conventional single-cell methods. To better understand STB differentiation, we perf...
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eLife Sciences Publications Ltd
2025-05-01
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| author | Madeline M Keenen Liheng Yang Huan Liang Veronica J Farmer Rizban E Worota Rohit Singh Amy S Gladfelter Carolyn B Coyne |
| author_facet | Madeline M Keenen Liheng Yang Huan Liang Veronica J Farmer Rizban E Worota Rohit Singh Amy S Gladfelter Carolyn B Coyne |
| author_sort | Madeline M Keenen |
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| description | The syncytiotrophoblast (STB) is a multinucleated cell layer that forms the outer surface of human chorionic villi. Its unusual structure, with billions of nuclei in a single cell, makes it difficult to resolve using conventional single-cell methods. To better understand STB differentiation, we performed single-nucleus and single-cell RNA sequencing on placental tissue and trophoblast organoids (TOs). Single-nucleus RNA-seq was essential for capturing STB populations, revealing three nuclear subtypes: a juvenile subtype co-expressing CTB and STB markers, one enriched in oxygen sensing genes, and another in transport and GTPase signaling. Organoids grown in suspension culture (STBout) showed higher expression of STB markers, hormones, and a greater proportion of the transport-associated nuclear subtype while TOs grown with an inverted polarity (STBin) exhibited a higher proportion of the oxygen sensing nuclear subtype. Gene regulatory analysis identified conserved STB markers, including the chromatin remodeler RYBP. Although RYBP knockout did not impair fusion, it downregulated CSH1 and upregulated oxygen-sensing genes. Comparing STB expression in first trimester, term, and TOs revealed shared features but context-dependent variability. These findings establish TOs as a robust platform to model STB differentiation and nuclear heterogeneity, providing insight into the regulatory networks that shape placental development and function. |
| format | Article |
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| spelling | doaj-art-ed8ba5ff5e0f4eee9c474bdbb5d1f92f2025-08-20T02:30:14ZengeLife Sciences Publications LtdeLife2050-084X2025-05-011310.7554/eLife.101170Comparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snRNA sequencingMadeline M Keenen0https://orcid.org/0000-0002-9585-3705Liheng Yang1https://orcid.org/0000-0001-6842-086XHuan Liang2https://orcid.org/0009-0000-4846-2499Veronica J Farmer3https://orcid.org/0000-0003-3857-5793Rizban E Worota4https://orcid.org/0009-0007-3732-8463Rohit Singh5https://orcid.org/0000-0002-4084-7340Amy S Gladfelter6https://orcid.org/0000-0002-2490-6945Carolyn B Coyne7https://orcid.org/0000-0002-1884-6309Duke University School of Medicine, Department of Cell Biology, Durham, United StatesDuke University School of Medicine, Department of Integrative Immunobiology, Durham, United StatesDuke University School of Medicine, Department of Cell Biology, Durham, United States; Duke University School of Medicine, Department of Biostatistics and Bioinformatics, Durham, United StatesDuke University School of Medicine, Department of Cell Biology, Durham, United StatesDuke University School of Medicine, Department of Integrative Immunobiology, Durham, United StatesDuke University School of Medicine, Department of Cell Biology, Durham, United States; Duke University School of Medicine, Department of Biostatistics and Bioinformatics, Durham, United StatesDuke University School of Medicine, Department of Cell Biology, Durham, United StatesDuke University School of Medicine, Department of Integrative Immunobiology, Durham, United States; Duke Human Vaccine Institute, Durham, United StatesThe syncytiotrophoblast (STB) is a multinucleated cell layer that forms the outer surface of human chorionic villi. Its unusual structure, with billions of nuclei in a single cell, makes it difficult to resolve using conventional single-cell methods. To better understand STB differentiation, we performed single-nucleus and single-cell RNA sequencing on placental tissue and trophoblast organoids (TOs). Single-nucleus RNA-seq was essential for capturing STB populations, revealing three nuclear subtypes: a juvenile subtype co-expressing CTB and STB markers, one enriched in oxygen sensing genes, and another in transport and GTPase signaling. Organoids grown in suspension culture (STBout) showed higher expression of STB markers, hormones, and a greater proportion of the transport-associated nuclear subtype while TOs grown with an inverted polarity (STBin) exhibited a higher proportion of the oxygen sensing nuclear subtype. Gene regulatory analysis identified conserved STB markers, including the chromatin remodeler RYBP. Although RYBP knockout did not impair fusion, it downregulated CSH1 and upregulated oxygen-sensing genes. Comparing STB expression in first trimester, term, and TOs revealed shared features but context-dependent variability. These findings establish TOs as a robust platform to model STB differentiation and nuclear heterogeneity, providing insight into the regulatory networks that shape placental development and function.https://elifesciences.org/articles/101170trophoblastOrganoidsnRNA-Sequencingsyncytiotrophoblast |
| spellingShingle | Madeline M Keenen Liheng Yang Huan Liang Veronica J Farmer Rizban E Worota Rohit Singh Amy S Gladfelter Carolyn B Coyne Comparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snRNA sequencing eLife trophoblast Organoid snRNA-Sequencing syncytiotrophoblast |
| title | Comparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snRNA sequencing |
| title_full | Comparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snRNA sequencing |
| title_fullStr | Comparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snRNA sequencing |
| title_full_unstemmed | Comparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snRNA sequencing |
| title_short | Comparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snRNA sequencing |
| title_sort | comparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snrna sequencing |
| topic | trophoblast Organoid snRNA-Sequencing syncytiotrophoblast |
| url | https://elifesciences.org/articles/101170 |
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