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TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development
Early embryonic development is a dynamic process that relies on proper cell-cell communication to form a correctly patterned embryo. Early embryo development-related ligand-receptor pairs (eLRs) have been shown to guide cell fate decisions and morphogenesis. However, the scope of eLRs and their infl...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10475079/ https://www.ncbi.nlm.nih.gov/pubmed/37660148 http://dx.doi.org/10.1038/s42003-023-05283-2 |
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author | Wang, Longteng Zheng, Yang Sun, Yu Mao, Shulin Li, Hao Bo, Xiaochen Li, Cheng Chen, Hebing |
author_facet | Wang, Longteng Zheng, Yang Sun, Yu Mao, Shulin Li, Hao Bo, Xiaochen Li, Cheng Chen, Hebing |
author_sort | Wang, Longteng |
collection | PubMed |
description | Early embryonic development is a dynamic process that relies on proper cell-cell communication to form a correctly patterned embryo. Early embryo development-related ligand-receptor pairs (eLRs) have been shown to guide cell fate decisions and morphogenesis. However, the scope of eLRs and their influence on early embryo development remain elusive. Here, we developed a computational framework named TimeTalk from integrated public time-course mouse scRNA-seq datasets to decipher the secret of eLRs. Extensive validations and analyses were performed to ensure the involvement of identified eLRs in early embryo development. Process analysis identified that eLRs could be divided into six temporal windows corresponding to sequential events in the early embryo development process. With the interpolation strategy, TimeTalk is powerful in revealing paracrine settings and studying cell-cell communication during early embryo development. Furthermore, by using TimeTalk in the blastocyst and blastoid models, we found that the blastoid models share the core communication pathways with the epiblast and primitive endoderm lineages in the blastocysts. This result suggests that TimeTalk has transferability to other bio-dynamic processes. We also curated eLRs recognized by TimeTalk, which may provide valuable clues for understanding early embryo development and relevant disorders. |
format | Online Article Text |
id | pubmed-10475079 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-104750792023-09-04 TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development Wang, Longteng Zheng, Yang Sun, Yu Mao, Shulin Li, Hao Bo, Xiaochen Li, Cheng Chen, Hebing Commun Biol Article Early embryonic development is a dynamic process that relies on proper cell-cell communication to form a correctly patterned embryo. Early embryo development-related ligand-receptor pairs (eLRs) have been shown to guide cell fate decisions and morphogenesis. However, the scope of eLRs and their influence on early embryo development remain elusive. Here, we developed a computational framework named TimeTalk from integrated public time-course mouse scRNA-seq datasets to decipher the secret of eLRs. Extensive validations and analyses were performed to ensure the involvement of identified eLRs in early embryo development. Process analysis identified that eLRs could be divided into six temporal windows corresponding to sequential events in the early embryo development process. With the interpolation strategy, TimeTalk is powerful in revealing paracrine settings and studying cell-cell communication during early embryo development. Furthermore, by using TimeTalk in the blastocyst and blastoid models, we found that the blastoid models share the core communication pathways with the epiblast and primitive endoderm lineages in the blastocysts. This result suggests that TimeTalk has transferability to other bio-dynamic processes. We also curated eLRs recognized by TimeTalk, which may provide valuable clues for understanding early embryo development and relevant disorders. Nature Publishing Group UK 2023-09-02 /pmc/articles/PMC10475079/ /pubmed/37660148 http://dx.doi.org/10.1038/s42003-023-05283-2 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Wang, Longteng Zheng, Yang Sun, Yu Mao, Shulin Li, Hao Bo, Xiaochen Li, Cheng Chen, Hebing TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development |
title | TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development |
title_full | TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development |
title_fullStr | TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development |
title_full_unstemmed | TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development |
title_short | TimeTalk uses single-cell RNA-seq datasets to decipher cell-cell communication during early embryo development |
title_sort | timetalk uses single-cell rna-seq datasets to decipher cell-cell communication during early embryo development |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10475079/ https://www.ncbi.nlm.nih.gov/pubmed/37660148 http://dx.doi.org/10.1038/s42003-023-05283-2 |
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