STHD：全转录组空间数据中单个点的高清晰度概率细胞分型

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2025-07-18 DOI:10.1186/s13059-025-03608-4

Chuhanwen Sun, Yi Zhang

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引用次数: 0

摘要

空间转录组学技术的最新进展使亚细胞分辨率的转录组基因表达谱成为可能，但高稀疏性和高维度带来了重大的计算挑战。我们提出了高清晰度的全转录组空间转录组中单个点的概率细胞分型的STHD。通过结合计数统计和邻居正则化的机器学习模型，STHD准确预测亚细胞斑点的细胞类型身份，揭示全局组织结构和局部多细胞邻居。我们通过对肿瘤微环境中细胞类型特异性基因表达和免疫相互作用中心的空间分析，以及其在样本、组织和疾病中的普遍性，证明了STHD。

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STHD: probabilistic cell typing of single spots in whole transcriptome spatial data with high definition

Recent advances in spatial transcriptomics technologies have enabled gene expression profiling across the transcriptome in spots with subcellular resolution, but high sparsity and dimensionality present significant computational challenges. We present STHD for probabilistic cell typing of single spots in whole-transcriptome spatial transcriptomics with high definition. With a machine learning model combining count statistics with neighbor regularization, STHD accurately predicts cell type identities of subcellular spots, revealing both global tissue architecture and local multicellular neighborhoods. We demonstrate STHD in spatial analyses of cell type-specific gene expression and immune interaction hubs in tumor microenvironment, and its generalizability across samples, tissues, and diseases.

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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

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.