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metsDB:一个关于癌症转移在整体、单细胞和空间水平的知识库。

metsDB: a knowledgebase of cancer metastasis at bulk, single-cell and spatial levels.

作者信息

Wu Sijia, Zhang Jiajin, Wang Yanfei, Qin Xinyu, Zhang Zhaocan, Lu Zhennan, Kim Pora, Zhou Xiaobo, Huang Liyu

机构信息

School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, PR China.

School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

出版信息

Nucleic Acids Res. 2025 Jan 6;53(D1):D1427-D1434. doi: 10.1093/nar/gkae916.

DOI:10.1093/nar/gkae916
PMID:39436035
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11701579/
Abstract

Cancer metastasis, the process by which tumour cells migrate and colonize distant organs from a primary site, is responsible for the majority of cancer-related deaths. Understanding the cellular and molecular mechanisms underlying this complex process is essential for developing effective metastasis prevention and therapy strategies. To this end, we systematically analysed 1786 bulk tissue samples from 13 cancer types, 988 463 single cells from 17 cancer types, and 40 252 spots from 45 spatial slides across 10 cancer types. The results of these analyses are compiled in the metsDB database, accessible at https://relab.xidian.edu.cn/metsDB/. This database provides insights into alterations in cell constitutions, cell relationships, biological pathways, molecular biomarkers, and drug responses during cancer metastasis at bulk, single-cell, and spatial levels. Users can perform cell or gene searches to obtain multi-view and multi-scale metastasis-related data. This comprehensive resource is invaluable for understanding the metastasis process and for designing molecular therapies.

摘要

癌症转移是肿瘤细胞从原发部位迁移并定植到远处器官的过程,它导致了大多数与癌症相关的死亡。了解这一复杂过程背后的细胞和分子机制对于制定有效的转移预防和治疗策略至关重要。为此,我们系统分析了来自13种癌症类型的1786份大块组织样本、来自17种癌症类型的988463个单细胞以及来自10种癌症类型的45张空间玻片上的40252个斑点。这些分析结果汇总在metsDB数据库中,可通过https://relab.xidian.edu.cn/metsDB/访问。该数据库提供了在大块、单细胞和空间水平上癌症转移过程中细胞组成、细胞关系、生物途径、分子生物标志物和药物反应变化的见解。用户可以进行细胞或基因搜索,以获取多视角和多尺度的转移相关数据。这一综合资源对于理解转移过程和设计分子疗法具有重要价值。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6872/11701579/1866e092f044/gkae916fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6872/11701579/021af255a17b/gkae916figgra1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6872/11701579/edb485a457fa/gkae916fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6872/11701579/1866e092f044/gkae916fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6872/11701579/021af255a17b/gkae916figgra1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6872/11701579/edb485a457fa/gkae916fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6872/11701579/1866e092f044/gkae916fig2.jpg

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本文引用的文献

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The estrogen signaling pathway reprograms prostate cancer cell metabolism and supports proliferation and disease progression.雌激素信号通路重编程前列腺癌细胞代谢,支持增殖和疾病进展。
J Clin Invest. 2024 Apr 16;134(11):e170809. doi: 10.1172/JCI170809.
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Distinct fibroblast subpopulations associated with bone, brain or intrapulmonary metastasis in advanced non-small-cell lung cancer.晚期非小细胞肺癌中与骨、脑或肺内转移相关的不同成纤维细胞亚群。
Clin Transl Med. 2024 Mar;14(3):e1605. doi: 10.1002/ctm2.1605.
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BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis.
班克斯统一了细胞分型和组织领域分割,以实现可扩展的空间组学数据分析。
Nat Genet. 2024 Mar;56(3):431-441. doi: 10.1038/s41588-024-01664-3. Epub 2024 Feb 27.
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Multi-omic profiling of clear cell renal cell carcinoma identifies metabolic reprogramming associated with disease progression.对透明细胞肾细胞癌进行多组学分析,确定与疾病进展相关的代谢重编程。
Nat Genet. 2024 Mar;56(3):442-457. doi: 10.1038/s41588-024-01662-5. Epub 2024 Feb 15.
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Gastric cancer with enhanced myogenesis is associated with less cell proliferation, enriched epithelial-to-mesenchymal transition and angiogenesis, and poor clinical outcomes.具有增强肌生成的胃癌与较少的细胞增殖、丰富的上皮-间质转化和血管生成以及不良临床结果相关。
Am J Cancer Res. 2024 Jan 15;14(1):355-367. doi: 10.62347/NCIM3072. eCollection 2024.
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Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions.Niche-DE:空间转录组学数据中的生态位差异基因表达分析确定了依赖于上下文的细胞-细胞相互作用。
Genome Biol. 2024 Jan 12;25(1):14. doi: 10.1186/s13059-023-03159-6.
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It's all about the base: stromal cells are central orchestrators of metastasis.一切都与基质细胞有关:基质细胞是转移的核心协调者。
Trends Cancer. 2024 Mar;10(3):208-229. doi: 10.1016/j.trecan.2023.11.004. Epub 2023 Dec 9.
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Robust mapping of spatiotemporal trajectories and cell-cell interactions in healthy and diseased tissues.健康和患病组织中时空轨迹和细胞-细胞相互作用的稳健映射。
Nat Commun. 2023 Nov 25;14(1):7739. doi: 10.1038/s41467-023-43120-6.
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Cancer Discov. 2023 Dec 12;13(12):2610-2631. doi: 10.1158/2159-8290.CD-23-0299.
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Cancer-associated fibroblast classification in single-cell and spatial proteomics data.单细胞和空间蛋白质组学数据中的癌症相关成纤维细胞分类。
Nat Commun. 2023 Jul 18;14(1):4294. doi: 10.1038/s41467-023-39762-1.