肿瘤微环境
转录组
生物
病理
细胞
电池类型
计算生物学
癌症研究
肿瘤细胞
医学
基因
基因表达
遗传学
作者
Zhenzhen Xun,Xinyu Ding,Yao Zhang,Benyan Zhang,Shih‐Wei Lai,Duowu Zou,Junke Zheng,Guo-Qiang Chen,Bing Su,Leng Han,Youqiong Ye
标识
DOI:10.1038/s41467-023-36560-7
摘要
Although advances in spatial transcriptomics (ST) enlarge to unveil spatial landscape of tissues, it remains challenging to delineate pathology-relevant and cellular localizations, and interactions exclusive to a spatial niche (e.g., tumor boundary). Here, we develop Cottrazm, integrating ST with hematoxylin and eosin histological image, and single-cell transcriptomics to delineate the tumor boundary connecting malignant and non-malignant cell spots in tumor tissues, deconvolute cell-type composition at spatial location, and reconstruct cell type-specific gene expression profiles at sub-spot level. We validate the performance of Cottrazm along the malignant-boundary-nonmalignant spatial axis. We identify specific macrophage and fibroblast subtypes localized around tumor boundary that interacted with tumor cells to generate a structural boundary, which limits T cell infiltration and promotes immune exclusion in tumor microenvironment. In this work, Cottrazm provides an integrated tool framework to dissect the tumor spatial microenvironment and facilitates the discovery of functional biological insights, thereby identifying therapeutic targets in oncologic ST datasets.
科研通智能强力驱动
Strongly Powered by AbleSci AI