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解析肿瘤进化:一种系统发育学方法。

Resolving tumor evolution: a phylogenetic approach.

作者信息

Li Lin, Xie Wenqin, Zhan Li, Wen Shaodi, Luo Xiao, Xu Shuangbin, Cai Yantong, Tang Wenli, Wang Qianwen, Li Ming, Xie Zijing, Deng Lin, Zhu Hongyuan, Yu Guangchuang

机构信息

Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.

Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital, Nanjing, China.

出版信息

J Natl Cancer Cent. 2024 Mar 21;4(2):97-106. doi: 10.1016/j.jncc.2024.03.001. eCollection 2024 Jun.

DOI:10.1016/j.jncc.2024.03.001
PMID:39282584
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11390690/
Abstract

The evolutionary dynamics of cancer, characterized by its profound heterogeneity, demand sophisticated tools for a holistic understanding. This review delves into tumor phylogenetics, an essential approach bridging evolutionary biology with oncology, offering unparalleled insights into cancer's evolutionary trajectory. We provide an overview of the workflow, encompassing study design, data acquisition, and phylogeny reconstruction. Notably, the integration of diverse data sets emerges as a transformative step, enhancing the depth and breadth of evolutionary insights. With this integrated perspective, tumor phylogenetics stands poised to redefine our understanding of cancer evolution and influence therapeutic strategies.

摘要

癌症的进化动力学具有高度异质性,需要精密工具来进行全面理解。本综述深入探讨肿瘤系统发育学,这是一种将进化生物学与肿瘤学联系起来的重要方法,能为癌症的进化轨迹提供无与伦比的见解。我们概述了工作流程,包括研究设计、数据获取和系统发育重建。值得注意的是,整合不同数据集成为一个变革性步骤,增强了进化见解的深度和广度。从这种综合视角来看,肿瘤系统发育学有望重新定义我们对癌症进化的理解,并影响治疗策略。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7f7/11390690/3b26a6e883f2/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7f7/11390690/b54cb0095edb/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7f7/11390690/e396eda08bc6/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7f7/11390690/3b26a6e883f2/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7f7/11390690/b54cb0095edb/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7f7/11390690/e396eda08bc6/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c7f7/11390690/3b26a6e883f2/gr3.jpg

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Resolving tumor evolution: a phylogenetic approach.解析肿瘤进化:一种系统发育学方法。
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本文引用的文献

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phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things).phytools 2.0:一个更新的用于系统发育比较方法(和其他内容)的 R 生态系统。
PeerJ. 2024 Jan 5;12:e16505. doi: 10.7717/peerj.16505. eCollection 2024.
2
Integrated multi-omics profiling to dissect the spatiotemporal evolution of metastatic hepatocellular carcinoma.整合多组学分析以剖析转移性肝细胞癌的时空演变。
Cancer Cell. 2024 Jan 8;42(1):135-156.e17. doi: 10.1016/j.ccell.2023.11.010. Epub 2023 Dec 14.
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Lineage tracing for multiple lung cancer by spatiotemporal heterogeneity using a multi-omics analysis method integrating genomic, transcriptomic, and immune-related features.
使用整合基因组、转录组和免疫相关特征的多组学分析方法,通过时空异质性对多种肺癌进行谱系追踪。
Front Oncol. 2023 Sep 14;13:1237308. doi: 10.3389/fonc.2023.1237308. eCollection 2023.
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Quantitative estimates of preventable and treatable deaths from 36 cancers worldwide: a population-based study.全球 36 种癌症可预防和可治疗死亡的定量估计:一项基于人群的研究。
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Phylogenetic inference from single-cell RNA-seq data.基于单细胞 RNA-seq 数据的系统发育推断。
Sci Rep. 2023 Aug 8;13(1):12854. doi: 10.1038/s41598-023-39995-6.
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Loss of chromosome Y in primary tumors.原发性肿瘤中Y染色体缺失。
Cell. 2023 Jun 22. doi: 10.1016/j.cell.2023.06.006.
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Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients.肿瘤内空间异质性与肺腺癌患者的生存相关。
Cell Genom. 2022 Aug 10;2(8). doi: 10.1016/j.xgen.2022.100165.
8
Clone Phylogenetics Reveals Metastatic Tumor Migrations, Maps, and Models.克隆系统发育学揭示转移性肿瘤的迁移、图谱和模型。
Cancers (Basel). 2022 Sep 4;14(17):4326. doi: 10.3390/cancers14174326.
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Identification of epithelial and mesenchymal circulating tumor cells in clonal lineage of an aggressive prostate cancer case.在一例侵袭性前列腺癌病例的克隆谱系中鉴定上皮和间充质循环肿瘤细胞。
NPJ Precis Oncol. 2022 Jun 21;6(1):41. doi: 10.1038/s41698-022-00289-1.
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Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution.谱系追踪揭示了肿瘤进化的系统发育动力学、可塑性和途径。
Cell. 2022 May 26;185(11):1905-1923.e25. doi: 10.1016/j.cell.2022.04.015. Epub 2022 May 5.