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结直肠癌中免疫细胞群体的高清空间转录组分析

High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer.

作者信息

Oliveira Michelli Faria de, Romero Juan Pablo, Chung Meii, Williams Stephen R, Gottscho Andrew D, Gupta Anushka, Pilipauskas Susan E, Mohabbat Seayar, Raman Nandhini, Sukovich David J, Patterson David M, Taylor Sarah E B

机构信息

10x Genomics, Inc, Pleasanton, CA, USA.

出版信息

Nat Genet. 2025 Jun;57(6):1512-1523. doi: 10.1038/s41588-025-02193-3. Epub 2025 Jun 5.


DOI:10.1038/s41588-025-02193-3
PMID:40473992
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12165841/
Abstract

A comprehensive understanding of cellular behavior and response to the tumor microenvironment (TME) in colorectal cancer (CRC) remains elusive. Here, we introduce the high-definition Visium spatial transcriptomic technology (Visium HD) and investigate formalin-fixed paraffin-embedded human CRC samples (n = 5). We demonstrate the high sensitivity, single-cell-scale resolution and spatial accuracy of Visium HD, generating a highly refined whole-transcriptome spatial profile of CRC samples. We identify transcriptomically distinct macrophage subpopulations in different spatial niches with potential pro-tumor and anti-tumor functions via interactions with tumor and T cells. In situ gene expression analysis validates our findings and localizes a clonally expanded T cell population close to macrophages with anti-tumor features. Our study demonstrates the power of high-resolution spatial technologies to understand cellular interactions in the TME and paves the way for larger studies that will unravel mechanisms and biomarkers of CRC biology, improving diagnosis and disease management strategies.

摘要

对结直肠癌(CRC)中细胞行为以及对肿瘤微环境(TME)的反应的全面理解仍然难以捉摸。在此,我们引入了高清Visium空间转录组技术(Visium HD),并对福尔马林固定石蜡包埋的人类CRC样本(n = 5)进行研究。我们展示了Visium HD的高灵敏度、单细胞尺度分辨率和空间准确性,生成了CRC样本高度精细的全转录组空间图谱。通过与肿瘤和T细胞的相互作用,我们在不同空间微环境中鉴定出具有潜在促肿瘤和抗肿瘤功能的转录组学上不同的巨噬细胞亚群。原位基因表达分析验证了我们的发现,并将一个克隆扩增的具有抗肿瘤特征的T细胞群体定位在靠近巨噬细胞的位置。我们的研究展示了高分辨率空间技术在理解TME中细胞相互作用方面的强大作用,并为更大规模的研究铺平了道路,这些研究将揭示CRC生物学的机制和生物标志物,改善诊断和疾病管理策略。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/f868b99832bc/41588_2025_2193_Fig17_ESM.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/f868b99832bc/41588_2025_2193_Fig17_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/20f8e9536103/41588_2025_2193_Fig1_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/92306cf3acd4/41588_2025_2193_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/dba94b35dd66/41588_2025_2193_Fig8_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/596d3ec743df/41588_2025_2193_Fig9_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/2141c8238e2c/41588_2025_2193_Fig10_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/d11986141262/41588_2025_2193_Fig11_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/a16cbe323ab6/41588_2025_2193_Fig12_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/5af2f584c048/41588_2025_2193_Fig13_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/022d4962f2ef/41588_2025_2193_Fig14_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/f63a50d3b978/41588_2025_2193_Fig15_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/ad4a938468b4/41588_2025_2193_Fig16_ESM.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1bfc/12165841/f868b99832bc/41588_2025_2193_Fig17_ESM.jpg

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引用本文的文献

[1]
Integrated multi-omics analysis identifies SELENOP and PKMYT1 as immune-metabolic hub genes in breast cancer.

Biochem Biophys Rep. 2025-8-6

[2]
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本文引用的文献

[1]
Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium dataset.

Genome Biol. 2025-3-28

[2]
FICTURE: scalable segmentation-free analysis of submicron-resolution spatial transcriptomics.

Nat Methods. 2024-10

[3]
LIANA+ provides an all-in-one framework for cell-cell communication inference.

Nat Cell Biol. 2024-9

[4]
Nova-ST: Nano-patterned ultra-dense platform for spatial transcriptomics.

Cell Rep Methods. 2024-8-19

[5]
Open-ST: High-resolution spatial transcriptomics in 3D.

Cell. 2024-7-25

[6]
T-cell infiltration and its regulatory mechanisms in cancers: insights at single-cell resolution.

J Exp Clin Cancer Res. 2024-2-2

[7]
High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis.

Nat Commun. 2023-12-19

[8]
Cellular crosstalk of macrophages and therapeutic implications in non-small cell lung cancer revealed by integrative inference of single-cell transcriptomics.

Front Pharmacol. 2023-11-15

[9]
N-methyladenosine modification of REG1α facilitates colorectal cancer progression via β-catenin/MYC/LDHA axis mediated glycolytic reprogramming.

Cell Death Dis. 2023-8-25

[10]
Single-cell and spatial transcriptome analysis reveals the cellular heterogeneity of liver metastatic colorectal cancer.

Sci Adv. 2023-6-16

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