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吸引子景观分析揭示了结直肠癌发生转变中的一个逆转开关。

Attractor Landscape Analysis Reveals a Reversion Switch in the Transition of Colorectal Tumorigenesis.

作者信息

Shin Dongkwan, Gong Jeong-Ryeol, Jeong Seoyoon D, Cho Youngwon, Kim Hwang-Phill, Kim Tae-You, Cho Kwang-Hyun

机构信息

Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.

Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea.

出版信息

Adv Sci (Weinh). 2025 Feb;12(8):e2412503. doi: 10.1002/advs.202412503. Epub 2025 Jan 22.

DOI:10.1002/advs.202412503
PMID:39840939
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11848608/
Abstract

A cell fate change such as tumorigenesis incurs critical transition. It remains a longstanding challenge whether the underlying mechanism can be unraveled and a molecular switch that can reverse such transition is found. Here a systems framework, REVERT, is presented with which can reconstruct the core molecular regulatory network model and a reversion switch based on single-cell transcriptome data over the transition process is identified. The usefulness of REVERT is demonstrated by applying it to single-cell transcriptome of patient-derived matched organoids of colon cancer and normal colon. REVERT is a generic framework that can be applied to investigate various cell fate transition phenomena.

摘要

诸如肿瘤发生这样的细胞命运改变会引发关键转变。潜在机制能否被揭示以及能否找到可逆转这种转变的分子开关，仍然是一个长期存在的挑战。在此，我们提出了一个系统框架REVERT，它可以重建核心分子调控网络模型，并基于过渡过程中的单细胞转录组数据识别出一个逆转开关。通过将REVERT应用于结肠癌和正常结肠的患者来源匹配类器官的单细胞转录组，证明了其有效性。REVERT是一个通用框架，可用于研究各种细胞命运转变现象。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aab6/11848608/3c972db8c012/ADVS-12-2412503-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aab6/11848608/f9beee098582/ADVS-12-2412503-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aab6/11848608/a8417e3ff5ed/ADVS-12-2412503-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aab6/11848608/59c7d461f0dc/ADVS-12-2412503-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aab6/11848608/94fb68f7aed8/ADVS-12-2412503-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aab6/11848608/3c972db8c012/ADVS-12-2412503-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aab6/11848608/f9beee098582/ADVS-12-2412503-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aab6/11848608/a8417e3ff5ed/ADVS-12-2412503-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aab6/11848608/59c7d461f0dc/ADVS-12-2412503-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aab6/11848608/94fb68f7aed8/ADVS-12-2412503-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/aab6/11848608/3c972db8c012/ADVS-12-2412503-g005.jpg

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Adv Sci (Weinh). 2024 Nov;11(41):e2404854. doi: 10.1002/advs.202404854. Epub 2024 Sep 11.
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Advances in single-cell long-read sequencing technologies.单细胞长读长测序技术的进展
NAR Genom Bioinform. 2024 May 20;6(2):lqae047. doi: 10.1093/nargab/lqae047. eCollection 2024 Jun.
3
Decoding the principle of cell-fate determination for its reverse control.解析细胞命运决定的原理，实现其反向控制。
NPJ Syst Biol Appl. 2024 May 6;10(1):47. doi: 10.1038/s41540-024-00372-2.
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SGAE: single-cell gene association entropy for revealing critical states of cell transitions during embryonic development.SGAE：单细胞基因关联熵，用于揭示胚胎发育过程中细胞转变的关键状态。
Brief Bioinform. 2023 Sep 22;24(6). doi: 10.1093/bib/bbad366.
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Targeting Transcription Factor YY1 for Cancer Treatment: Current Strategies and Future Directions.靶向转录因子YY1用于癌症治疗：当前策略与未来方向
Cancers (Basel). 2023 Jul 5;15(13):3506. doi: 10.3390/cancers15133506.
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High throughput single cell long-read sequencing analyses of same-cell genotypes and phenotypes in human tumors.高通量单细胞长读测序分析人类肿瘤中同一细胞的基因型和表型。
Nat Commun. 2023 Jul 11;14(1):4124. doi: 10.1038/s41467-023-39813-7.
7
Hallmarks of transcriptional intratumour heterogeneity across a thousand tumours.一千个肿瘤中的转录肿瘤内异质性特征。
Nature. 2023 Jun;618(7965):598-606. doi: 10.1038/s41586-023-06130-4. Epub 2023 May 31.
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