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在空间背景下对单细胞进行高分辨率映射。

High-resolution mapping of single cells in spatial context.

作者信息

Ke Jincan, Xu Jian, Liu Jia, Yang Yumeng, Guo Chenkai, Xie Bingbing, Cui Guizhong, Peng Guangdun, Suo Shengbao

机构信息

Center for Cell Lineage Technology and Engineering, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.

University of Chinese Academy of Sciences, Beijing, China.

出版信息

Nat Commun. 2025 Jul 15;16(1):6533. doi: 10.1038/s41467-025-61667-4.


DOI:10.1038/s41467-025-61667-4
PMID:40664667
Abstract

Spatially resolved transcriptomic technologies have emerged as pivotal tools for elucidating molecular regulation and cellular interplay within the intricate tissue microenvironment, but hampered by insufficient gene recovery or challenges in achieving intact single-cell resolution. Here, we develop Cellular Mapping of Attributes with Position (CMAP), a method that efficiently maps large-scale individual cells to their precise spatial locations by integrating single-cell and spatial data through a divide--and--conquer strategy. Analysis of both simulated and real datasets shows that CMAP performs effectively and is adaptable across diverse data types and sequencing platforms. Particularly, CMAP handles scenarios well where discrepancies exist between single-cell and spatial transcriptomics data. Our findings underscore CMAP's capacity to endow single-cells with exact spatial coordinates, facilitating the dissection of nuanced spatial-organ-specific endothelial cell heterogeneity, as well as the intricate cancer immune microenvironments that elude conventional single-cell or spatial data analysis.

摘要

空间分辨转录组技术已成为阐明复杂组织微环境中分子调控和细胞相互作用的关键工具,但受到基因回收率不足或难以实现完整单细胞分辨率的挑战的阻碍。在这里,我们开发了位置属性细胞图谱(CMAP),这是一种通过分治策略整合单细胞和空间数据,将大规模单个细胞高效映射到其精确空间位置的方法。对模拟数据集和真实数据集的分析表明,CMAP 有效地发挥作用,并且适用于各种数据类型和测序平台。特别是,CMAP 能很好地处理单细胞和空间转录组学数据之间存在差异的情况。我们的研究结果强调了 CMAP 赋予单个细胞精确空间坐标的能力,有助于剖析细微的空间器官特异性内皮细胞异质性,以及传统单细胞或空间数据分析难以处理的复杂癌症免疫微环境。

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High-resolution mapping of single cells in spatial context.

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[2]
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[10]
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本文引用的文献

[1]
CellChat for systematic analysis of cell-cell communication from single-cell transcriptomics.

Nat Protoc. 2025-1

[2]
SPADE: spatial deconvolution for domain specific cell-type estimation.

Commun Biol. 2024-4-17

[3]
An immune cell map of human lung adenocarcinoma development reveals an anti-tumoral role of the Tfh-dependent tertiary lymphoid structure.

Cell Rep Med. 2024-3-19

[4]
Molecular and Spatial Signatures of Mouse Embryonic Endothelial Cells at Single-Cell Resolution.

Circ Res. 2024-3

[5]
High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis.

Nat Commun. 2023-12-19

[6]
Molecularly defined and spatially resolved cell atlas of the whole mouse brain.

Nature. 2023-12

[7]
Spatial transcriptomics deconvolution at single-cell resolution using Redeconve.

Nat Commun. 2023-12-1

[8]
Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation.

Nat Commun. 2023-9-14

[9]
SONAR enables cell type deconvolution with spatially weighted Poisson-Gamma model for spatial transcriptomics.

Nat Commun. 2023-8-7

[10]
Three-dimensional molecular architecture of mouse organogenesis.

Nat Commun. 2023-7-31

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