4D single-cell spatial transcriptomics reveals dynamic morphogenetic gradients and regenerative domains in planarians.
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| Autori principali: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Natura: | Artículo científico |
| Lingua: | en |
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GigaScience
2026
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| author | Han, Kai Wang, Yuxiaofei Li, Yao Guo, Lidong Chen, Yue Liu, Xiawei Lin, Yaru Huang, Zhi Liu, Qun Guo, Wenjie Zhang, Rui Zhao, Wandong Liang, Langchao Wei, Xiaoyu Zhou, Li Mao, Xuebin Wang, Jiaqi Wu, Weijian Pan, Hongwei Yang, Tao Zhang, He Su, Xiaoshan Liu, Shanshan Zhang, Wenwei Liu, Longqi Christensen, Søren Tvorup Fei, Jifeng Liu, Xin Fan, Guangyi Li, Hanbo Gu, Ying Wang, Jian Yang, Huanming Pei, Gang Xu, Xun Zeng, An Xu, Mengyang |
| author_facet | Han, Kai Wang, Yuxiaofei Li, Yao Guo, Lidong Chen, Yue Liu, Xiawei Lin, Yaru Huang, Zhi Liu, Qun Guo, Wenjie Zhang, Rui Zhao, Wandong Liang, Langchao Wei, Xiaoyu Zhou, Li Mao, Xuebin Wang, Jiaqi Wu, Weijian Pan, Hongwei Yang, Tao Zhang, He Su, Xiaoshan Liu, Shanshan Zhang, Wenwei Liu, Longqi Christensen, Søren Tvorup Fei, Jifeng Liu, Xin Fan, Guangyi Li, Hanbo Gu, Ying Wang, Jian Yang, Huanming Pei, Gang Xu, Xun Zeng, An Xu, Mengyang Han, Kai Wang, Yuxiaofei Li, Yao Guo, Lidong Chen, Yue Liu, Xiawei Lin, Yaru Huang, Zhi Liu, Qun Guo, Wenjie Zhang, Rui Zhao, Wandong Liang, Langchao Wei, Xiaoyu Zhou, Li Mao, Xuebin Wang, Jiaqi Wu, Weijian Pan, Hongwei Yang, Tao Zhang, He Su, Xiaoshan Liu, Shanshan Zhang, Wenwei Liu, Longqi Christensen, Søren Tvorup Fei, Jifeng Liu, Xin Fan, Guangyi Li, Hanbo Gu, Ying Wang, Jian Yang, Huanming Pei, Gang Xu, Xun Zeng, An Xu, Mengyang |
| collection | PubMed - marine biology |
| contents | 4D single-cell spatial transcriptomics reveals dynamic morphogenetic gradients and regenerative domains in planarians. Han, Kai Wang, Yuxiaofei Li, Yao Guo, Lidong Chen, Yue Liu, Xiawei Lin, Yaru Huang, Zhi Liu, Qun Guo, Wenjie Zhang, Rui Zhao, Wandong Liang, Langchao Wei, Xiaoyu Zhou, Li Mao, Xuebin Wang, Jiaqi Wu, Weijian Pan, Hongwei Yang, Tao Zhang, He Su, Xiaoshan Liu, Shanshan Zhang, Wenwei Liu, Longqi Christensen, Søren Tvorup Fei, Jifeng Liu, Xin Fan, Guangyi Li, Hanbo Gu, Ying Wang, Jian Yang, Huanming Pei, Gang Xu, Xun Zeng, An Xu, Mengyang Animals Morphogenesis Planarians Regeneration Single-Cell Gene Expression Analysis Spatial Transcriptomics Transcriptome Understanding how organisms reconstruct complex tissue architectures following injury requires precise mapping of gene expression and cellular responses across space and time. Although planarians serve as a classic model for whole-body regeneration, capturing the continuous spatiotemporal dynamics of positional information and cell fate decisions at the organismal scale remains a significant challenge. Using high-definition spatial transcriptomics, we generated a 4-dimensional atlas encompassing over 3.5 million cells from whole animals across 8 distinct regeneration timepoints. This comprehensive dataset enabled the definition of 36 spatial domains and the tracing of body axis restoration, revealing that positional control genes recover through self-organizing dynamics analogous to an underdamped control system. We identified an injury-induced spatial domain termed the anterior regenerative zone. This unique region is characterized by the convergence of epidermal, muscular, and neural lineages enriched with positional signals. Furthermore, we demonstrated that the transcriptional co-factor Mediator 8 is a critical regulator of this zone. Depletion of Mediator 8 impairs the formation of the anterior regenerative zone, disrupts polarity establishment, and prevents successful blastema formation. Our study provides a holistic molecular and cellular reconstruction of whole-body regeneration, directly linking dynamic gene expression gradients to morphological restoration. The discovery of the Mediator 8-regulated anterior regenerative zone highlights the importance of spatial domains in coordinating tissue repair. The resulting interactive atlas serves as a foundational resource for deciphering the logic of spatiotemporal patterning in regeneration. |
| format | Artículo científico |
| id | pubmed_42172041 |
| institution | PubMed |
| language | en |
| publishDate | 2026 |
| publisher | GigaScience |
| record_format | pubmed |
| spellingShingle | 4D single-cell spatial transcriptomics reveals dynamic morphogenetic gradients and regenerative domains in planarians. Han, Kai Wang, Yuxiaofei Li, Yao Guo, Lidong Chen, Yue Liu, Xiawei Lin, Yaru Huang, Zhi Liu, Qun Guo, Wenjie Zhang, Rui Zhao, Wandong Liang, Langchao Wei, Xiaoyu Zhou, Li Mao, Xuebin Wang, Jiaqi Wu, Weijian Pan, Hongwei Yang, Tao Zhang, He Su, Xiaoshan Liu, Shanshan Zhang, Wenwei Liu, Longqi Christensen, Søren Tvorup Fei, Jifeng Liu, Xin Fan, Guangyi Li, Hanbo Gu, Ying Wang, Jian Yang, Huanming Pei, Gang Xu, Xun Zeng, An Xu, Mengyang Animals Morphogenesis Planarians Regeneration Single-Cell Gene Expression Analysis Spatial Transcriptomics Transcriptome 4D single-cell spatial transcriptomics reveals dynamic morphogenetic gradients and regenerative domains in planarians. Han, Kai Wang, Yuxiaofei Li, Yao Guo, Lidong Chen, Yue Liu, Xiawei Lin, Yaru Huang, Zhi Liu, Qun Guo, Wenjie Zhang, Rui Zhao, Wandong Liang, Langchao Wei, Xiaoyu Zhou, Li Mao, Xuebin Wang, Jiaqi Wu, Weijian Pan, Hongwei Yang, Tao Zhang, He Su, Xiaoshan Liu, Shanshan Zhang, Wenwei Liu, Longqi Christensen, Søren Tvorup Fei, Jifeng Liu, Xin Fan, Guangyi Li, Hanbo Gu, Ying Wang, Jian Yang, Huanming Pei, Gang Xu, Xun Zeng, An Xu, Mengyang Animals Morphogenesis Planarians Regeneration Single-Cell Gene Expression Analysis Spatial Transcriptomics Transcriptome Understanding how organisms reconstruct complex tissue architectures following injury requires precise mapping of gene expression and cellular responses across space and time. Although planarians serve as a classic model for whole-body regeneration, capturing the continuous spatiotemporal dynamics of positional information and cell fate decisions at the organismal scale remains a significant challenge. Using high-definition spatial transcriptomics, we generated a 4-dimensional atlas encompassing over 3.5 million cells from whole animals across 8 distinct regeneration timepoints. This comprehensive dataset enabled the definition of 36 spatial domains and the tracing of body axis restoration, revealing that positional control genes recover through self-organizing dynamics analogous to an underdamped control system. We identified an injury-induced spatial domain termed the anterior regenerative zone. This unique region is characterized by the convergence of epidermal, muscular, and neural lineages enriched with positional signals. Furthermore, we demonstrated that the transcriptional co-factor Mediator 8 is a critical regulator of this zone. Depletion of Mediator 8 impairs the formation of the anterior regenerative zone, disrupts polarity establishment, and prevents successful blastema formation. Our study provides a holistic molecular and cellular reconstruction of whole-body regeneration, directly linking dynamic gene expression gradients to morphological restoration. The discovery of the Mediator 8-regulated anterior regenerative zone highlights the importance of spatial domains in coordinating tissue repair. The resulting interactive atlas serves as a foundational resource for deciphering the logic of spatiotemporal patterning in regeneration. |
| title | 4D single-cell spatial transcriptomics reveals dynamic morphogenetic gradients and regenerative domains in planarians. |
| topic | Animals Morphogenesis Planarians Regeneration Single-Cell Gene Expression Analysis Spatial Transcriptomics Transcriptome |
| url | https://pubmed.ncbi.nlm.nih.gov/42172041/ |