Integration of single-cell and spatial transcriptomics by SEU-TCA reveals the spatial origin of early cardiac progenitors

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-06-10 DOI:10.1186/s13059-025-03633-3

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

引用次数: 0

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.

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SEU-TCA对单细胞和空间转录组学的整合揭示了早期心脏祖细胞的空间起源

获取单细胞空间信息仍然是空间转录组学的一个挑战。在这里，我们开发了SEU-TCA，一种利用转移成分分析来提高单细胞空间映射精度的方法。应用于多个单细胞和空间转录组数据集，在空间反褶积和细胞定位方面表现出优越的性能。利用SEU-TCA，我们探索了小鼠原肠胚形成过程中的空间基因表达和调控活性，并鉴定了Irx1调控的前第二心野祖细胞。功能实验显示，Irx1缺失会破坏前第二心野发育并导致室间隔缺损，这凸显了SEU-TCA在推进发育生物学研究方面的潜力。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

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