Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors
Abstract Obtaining single-cell spatial information remains a challenge in spatial transcriptomics. Here we develop SEU-TCA, a method that leverages transfer component analysis to improve single-cell spatial mapping accuracy. Application to multiple single-cell and spatial transcriptomic datasets sho...
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| Format: | Article |
| Language: | English |
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BMC
2025-06-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-025-03633-3 |
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| author | Jingjing He Yi Yang Rui Jiang Yanying Zheng Xianfa Yang Xu Jiang Xin Xue Zhongzhou Yang Naihe Jing Hailong Cao Zhuojuan Luo Ke Wei Peng Xie Chengqi Lin |
| author_facet | Jingjing He Yi Yang Rui Jiang Yanying Zheng Xianfa Yang Xu Jiang Xin Xue Zhongzhou Yang Naihe Jing Hailong Cao Zhuojuan Luo Ke Wei Peng Xie Chengqi Lin |
| author_sort | Jingjing He |
| collection | DOAJ |
| description | Abstract Obtaining single-cell spatial information remains a challenge in spatial transcriptomics. Here we develop SEU-TCA, a method that leverages transfer component analysis to improve single-cell spatial mapping accuracy. Application to multiple single-cell and spatial transcriptomic datasets shows superior performance in spatial deconvolution and cell mapping. Using SEU-TCA, we explore spatial gene expression and regulon activity during mouse gastrulation and identify anterior second heart field progenitors regulated by Irx1. Functional experiments reveal that Irx1 deletion disrupts anterior second heart field development and causes ventricular septal defects, underscoring SEU-TCA’s potential for advancing developmental biology research. |
| format | Article |
| id | doaj-art-da32964649244a708b515b5d2bf1451f |
| institution | DOAJ |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-da32964649244a708b515b5d2bf1451f2025-08-20T02:39:24ZengBMCGenome Biology1474-760X2025-06-0126113010.1186/s13059-025-03633-3Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitorsJingjing He0Yi Yang1Rui Jiang2Yanying Zheng3Xianfa Yang4Xu Jiang5Xin Xue6Zhongzhou Yang7Naihe Jing8Hailong Cao9Zhuojuan Luo10Ke Wei11Peng Xie12Chengqi Lin13Department of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast UniversityDepartment of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast UniversityInstitute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Shanghai East Hospital, Tongji UniversityDepartment of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast UniversityGuangzhou LaboratoryDepartment of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast UniversityDepartment of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast UniversityState Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Model Animal Research Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Nanjing UniversityGuangzhou LaboratoryDepartment of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast UniversityDepartment of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast UniversityInstitute for Regenerative Medicine, State Key Laboratory of Cardiology and Medical Innovation Center, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Shanghai East Hospital, Tongji UniversityState Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast UniversityDepartment of Cardiac Surgery, Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Zhongda Hospital, Southeast UniversityAbstract Obtaining single-cell spatial information remains a challenge in spatial transcriptomics. Here we develop SEU-TCA, a method that leverages transfer component analysis to improve single-cell spatial mapping accuracy. Application to multiple single-cell and spatial transcriptomic datasets shows superior performance in spatial deconvolution and cell mapping. Using SEU-TCA, we explore spatial gene expression and regulon activity during mouse gastrulation and identify anterior second heart field progenitors regulated by Irx1. Functional experiments reveal that Irx1 deletion disrupts anterior second heart field development and causes ventricular septal defects, underscoring SEU-TCA’s potential for advancing developmental biology research.https://doi.org/10.1186/s13059-025-03633-3Single-cell RNA sequencingSpatial transcriptomicCardiac progenitorsRegulatory factors |
| spellingShingle | Jingjing He Yi Yang Rui Jiang Yanying Zheng Xianfa Yang Xu Jiang Xin Xue Zhongzhou Yang Naihe Jing Hailong Cao Zhuojuan Luo Ke Wei Peng Xie Chengqi Lin Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors Genome Biology Single-cell RNA sequencing Spatial transcriptomic Cardiac progenitors Regulatory factors |
| title | Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors |
| title_full | Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors |
| title_fullStr | Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors |
| title_full_unstemmed | Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors |
| title_short | Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors |
| title_sort | integration of single cell and spatial transcriptomics by seu tca reveals the spatial origin of early cardiac progenitors |
| topic | Single-cell RNA sequencing Spatial transcriptomic Cardiac progenitors Regulatory factors |
| url | https://doi.org/10.1186/s13059-025-03633-3 |
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