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探索用于伤口愈合单细胞转录组分析的机器学习策略。

Exploring machine learning strategies for single-cell transcriptomic analysis in wound healing.

作者信息

Cui Jianzhou, Wang Mei, Lin Chenshi, Xu Xu, Zhang Zhenqing

机构信息

Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.

Immunology Program, Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.

出版信息

Burns Trauma. 2025 May 13;13:tkaf032. doi: 10.1093/burnst/tkaf032. eCollection 2025.


DOI:10.1093/burnst/tkaf032
PMID:40718702
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12291542/
Abstract

Wound healing is a highly orchestrated, multiphase process that involves various cell types and molecular pathways. Recent advances in single-cell transcriptomics and machine learning have provided unprecedented insights into the complexity of this process, enabling the identification of novel cellular subpopulations and molecular mechanisms underlying tissue repair. In particular, single-cell RNA sequencing (scRNA-seq) has revealed significant cellular heterogeneity, especially within fibroblast populations, and has provided valuable information on immune cell dynamics during healing. Machine learning algorithms have enhanced data analysis by improving cell clustering, dimensionality reduction, and trajectory inference, leading to a better understanding of wound healing at the single-cell level. This review synthesizes the latest findings on the application of scRNA-seq and machine learning in wound healing research, with a focus on fibroblast diversity, immune responses, and spatial organization of cells. The integration of these technologies has the potential to revolutionize therapeutic strategies for chronic wounds, fibrosis, and tissue regeneration, offering new opportunities for precision medicine. By combining computational approaches with biological insights, this review highlights the transformative impact of scRNA-seq and machine learning on wound healing research.

摘要

伤口愈合是一个高度协调的多阶段过程,涉及多种细胞类型和分子途径。单细胞转录组学和机器学习的最新进展为这一过程的复杂性提供了前所未有的见解,能够识别组织修复背后的新型细胞亚群和分子机制。特别是,单细胞RNA测序(scRNA-seq)揭示了显著的细胞异质性,尤其是在成纤维细胞群体中,并提供了愈合过程中免疫细胞动态的宝贵信息。机器学习算法通过改进细胞聚类、降维和轨迹推断增强了数据分析,从而在单细胞水平上更好地理解伤口愈合。本综述综合了scRNA-seq和机器学习在伤口愈合研究中的最新应用成果,重点关注成纤维细胞多样性、免疫反应和细胞的空间组织。这些技术的整合有可能彻底改变慢性伤口、纤维化和组织再生的治疗策略,为精准医学提供新的机会。通过将计算方法与生物学见解相结合,本综述突出了scRNA-seq和机器学习对伤口愈合研究的变革性影响。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf54/12291542/8b2d6e9713cb/tkaf032f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf54/12291542/097e07bd7fa6/tkaf032f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf54/12291542/7e1f7f3143c7/tkaf032f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf54/12291542/5bb124d0bbf7/tkaf032f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf54/12291542/c1bffbf7ea66/tkaf032f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf54/12291542/8b2d6e9713cb/tkaf032f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf54/12291542/097e07bd7fa6/tkaf032f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf54/12291542/7e1f7f3143c7/tkaf032f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf54/12291542/5bb124d0bbf7/tkaf032f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf54/12291542/c1bffbf7ea66/tkaf032f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cf54/12291542/8b2d6e9713cb/tkaf032f5.jpg

相似文献

[1]
Exploring machine learning strategies for single-cell transcriptomic analysis in wound healing.

Burns Trauma. 2025-5-13

[2]
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[8]
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[10]
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本文引用的文献

[1]
Role of artificial intelligence in revolutionizing drug discovery.

Fundam Res. 2024-5-9

[2]
Single-cell RNA sequencing reveals the impaired epidermal differentiation and pathological microenvironment in diabetic foot ulcer.

Burns Trauma. 2025-3-4

[3]
Demystifying the black box: A survey on explainable artificial intelligence (XAI) in bioinformatics.

Comput Struct Biotechnol J. 2025-1-10

[4]
AI-driven multi-omics integration for multi-scale predictive modeling of genotype-environment-phenotype relationships.

Comput Struct Biotechnol J. 2025-1-2

[5]
Spatiotemporal single-cell roadmap of human skin wound healing.

Cell Stem Cell. 2025-3-6

[6]
Avoiding common machine learning pitfalls.

Patterns (N Y). 2024-8-28

[7]
SELF-Former: multi-scale gene filtration transformer for single-cell spatial reconstruction.

Brief Bioinform. 2024-9-23

[8]
Assessing and mitigating batch effects in large-scale omics studies.

Genome Biol. 2024-10-3

[9]
Deep learning for rapid analysis of cell divisions in vivo during epithelial morphogenesis and repair.

Elife. 2024-9-23

[10]
Joint trajectory inference for single-cell genomics using deep learning with a mixture prior.

Proc Natl Acad Sci U S A. 2024-9-10

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