STRIDE: accurately decomposing and integrating spatial transcriptomics using single-cell RNA sequencing.
STRIDE: accurately decomposing and integrating spatial transcriptomics using single-cell RNA sequencing.
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STRIDE：使用单细胞 RNA 测序准确分解和整合空间转录组学
DOI：
10.1093/nar/gkac150
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发表时间：
2022-04-22
影响因子：
14.9
通讯作者：
Wang, Chenfei
中科院分区：
文献类型：
--
作者：
Sun, Dongqing;Liu, Zhaoyang;Li, Taiwen;Wu, Qiu;Wang, Chenfei
空间转录组学的最新进展为理解细胞在空间背景下的异质性提供了前所未有的机会。然而，目前空间技术的局限性阻碍了在单细胞水平上探索细胞的定位和相互作用。在这里，我们提出了通过主题建模的空间转录去卷积(STRIDE)，这是一种通过利用从单细胞转录建模训练的主题轮廓来从空间混合中分解细胞类型的计算方法。与现有方法相比，STRIDE准确地估计了细胞类型比例，并显示出平衡的特异性和敏感性。我们通过将STRIDE应用于不同的空间平台和生物系统来演示STRIDE的有效性。STRIDE去卷积不仅将稀有细胞类型映射到空间位置，而且改进了空间定位基因和结构域的识别。此外，STRIDE发现的主题与细胞类型特定的功能相关，并可进一步用于整合连续的切片和重建组织的三维结构。总而言之，STRIDE是一种用于空间和单细胞转录的集成分析的通用和可扩展的工具，可在https://github.com/wanglabtongji/STRIDE.上公开获得
The recent advances in spatial transcriptomics have brought unprecedented opportunities to understand the cellular heterogeneity in the spatial context. However, the current limitations of spatial technologies hamper the exploration of cellular localizations and interactions at single-cell level. Here, we present spatial transcriptomics deconvolution by topic modeling (STRIDE), a computational method to decompose cell types from spatial mixtures by leveraging topic profiles trained from single-cell transcriptomics. STRIDE accurately estimated the cell-type proportions and showed balanced specificity and sensitivity compared to existing methods. We demonstrate STRIDE’s utility by applying it to different spatial platforms and biological systems. Deconvolution by STRIDE not only mapped rare cell types to spatial locations but also improved the identification of spatial localized genes and domains. Moreover, topics discovered by STRIDE were associated with cell-type-specific functions, and could be further used to integrate successive sections and reconstruct the three-dimensional architecture of tissues. Taken together, STRIDE is a versatile and extensible tool for integrated analysis of spatial and single-cell transcriptomics and is publicly available at https://github.com/wanglabtongji/STRIDE.
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