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《精心策划的癌细胞图谱》以单细胞分辨率对肿瘤进行了全面表征。

The Curated Cancer Cell Atlas provides a comprehensive characterization of tumors at single-cell resolution.

作者信息

Tyler Michael, Gavish Avishai, Barbolin Chaya, Tschernichovsky Roi, Hoefflin Rouven, Mints Michael, Puram Sidharth V, Tirosh Itay

机构信息

Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.

Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt, Germany.

出版信息

Nat Cancer. 2025 May 8. doi: 10.1038/s43018-025-00957-8.


DOI:10.1038/s43018-025-00957-8
PMID:40341230
Abstract

Recent years have seen a rapid proliferation of single-cell cancer studies, yet most of these studies profiled few tumors, limiting their statistical power. Combining data and results across studies holds great promise but also involves various challenges. We recently began to address these challenges by curating a large collection of cancer single-cell RNA-sequencing datasets, leveraging it for systematic analyses of tumor heterogeneity. Here we greatly extend this repository to 124 datasets for over 40 cancer types, together comprising 2,836 samples, with improved data annotations, visualizations and exploration. Using this vast cohort, we generate an updated map of recurrent expression programs in malignant cells and systematically quantify context-dependent gene expression and cell-cycle patterns across cell types and cancer types. These data, annotations and analysis results are all freely available for exploration and download through the Curated Cancer Cell Atlas, a central community resource that opens new avenues in cancer research.

摘要

近年来,单细胞癌症研究迅速增多,但其中大多数研究仅分析了少数肿瘤,限制了其统计效力。整合不同研究的数据和结果虽前景广阔,但也面临各种挑战。我们最近开始通过整理大量癌症单细胞RNA测序数据集来应对这些挑战,并利用这些数据集对肿瘤异质性进行系统分析。在此,我们将该资源库大幅扩展至涵盖40多种癌症类型的124个数据集,共计2836个样本,并改进了数据注释、可视化和探索功能。利用这个庞大的队列,我们生成了恶性细胞中复发表达程序的更新图谱,并系统地量化了不同细胞类型和癌症类型中依赖于背景的基因表达及细胞周期模式。这些数据、注释和分析结果均可通过“精心策划的癌细胞图谱”免费获取,供探索和下载。该图谱是一个核心社区资源,为癌症研究开辟了新途径。

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本文引用的文献

[1]
snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives.

Commun Biol. 2024-10-16

[2]
A pan-cancer single-cell panorama of human natural killer cells.

Cell. 2023-9-14

[3]
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Nature. 2023-6

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Nat Commun. 2023-5-12

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Annu Rev Biomed Data Sci. 2023-8-10

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Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma.

Nat Genet. 2023-4

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A single-cell atlas of glioblastoma evolution under therapy reveals cell-intrinsic and cell-extrinsic therapeutic targets.

Nat Cancer. 2022-12

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Cancer Res. 2023-2-3

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TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment.

Nucleic Acids Res. 2023-1-6

[10]
Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment.

Nat Genet. 2022-8

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