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利用多组学数据集的机器学习在膀胱癌研究中的干预:生物标志物识别的系统评价

Intervention of machine learning in bladder cancer research using multi-omics datasets: systematic review on biomarker identification.

作者信息

Kiruba Blessy, Narayan P S Athul, Raj Badhari, Raj S Rohieth, Mathew Sam George, Lulu Sudhakaran Sajitha, Sundararajan Vino

机构信息

Integrated Multiomics Laboratory, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.

出版信息

Discov Oncol. 2025 Jun 5;16(1):1010. doi: 10.1007/s12672-025-02734-6.


DOI:10.1007/s12672-025-02734-6
PMID:40471489
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12141719/
Abstract

Bladder cancer (BC) is one of the most prevalent types of cancer in developed countries. BC is characterized by its highly heterogeneous and dynamic nature, with significantly higher morbidity and mortality rates in men compared to women. Diagnosing BC requires traditional methods, such as cystoscopy, which can be invasive and costly. Recent research has heavily focused on multi-omics analysis, including genomics, epigenomics, transcriptomics, proteomics, and metabolomics, for biomarker identification. However, challenges such as computational complexity and data integration prevent these methods from achieving robust diagnostic capabilities. Hence, machine learning (ML), with its ability to process high-dimensional data and identify complex patterns, offers a promising patient outcome. By exploiting genomics, epigenomics, transcriptomics, proteomics, and metabolomics data, these models facilitate the discovery of reliable biomarkers, which are critical for early detection, prognosis, and risk stratification of the disease. Integrated models combining computational techniques with large multi-omics datasets have gained significant attention, enabling the identification of significant BC biomarkers that include genes coding for diverse cellular functions, differentially expressed genes, proteins, and metabolites. A substantial amount of multi-omics data collected from clinics and laboratories are utilized to train powerful ML models such as Support Vector Machines (SVM), random forests (RF), decision trees (DT), and gradient boosting methods (e.g., XGBoost) to perform complex tasks, including biomarker discovery, classification of subtypes and feature selection. This comprehensive review highlights the essence of integrated multiomics-ML approaches for the improvement of prognosis and diagnosis of BC.

摘要

膀胱癌(BC)是发达国家中最常见的癌症类型之一。BC的特点是具有高度异质性和动态性,男性的发病率和死亡率明显高于女性。诊断BC需要传统方法,如膀胱镜检查,这种方法可能具有侵入性且成本高昂。最近的研究主要集中在多组学分析,包括基因组学、表观基因组学、转录组学、蛋白质组学和代谢组学,以识别生物标志物。然而,诸如计算复杂性和数据整合等挑战阻碍了这些方法实现强大的诊断能力。因此,机器学习(ML)凭借其处理高维数据和识别复杂模式的能力,为改善患者预后带来了希望。通过利用基因组学、表观基因组学、转录组学、蛋白质组学和代谢组学数据,这些模型有助于发现可靠的生物标志物,这对于疾病的早期检测、预后和风险分层至关重要。将计算技术与大型多组学数据集相结合的综合模型受到了广泛关注,能够识别出重要的BC生物标志物,包括编码多种细胞功能的基因、差异表达基因、蛋白质和代谢物。从临床和实验室收集的大量多组学数据被用于训练强大的ML模型,如支持向量机(SVM)、随机森林(RF)、决策树(DT)和梯度提升方法(如XGBoost),以执行复杂任务,包括生物标志物发现、亚型分类和特征选择。这篇综述重点介绍了整合多组学-ML方法对改善BC预后和诊断的重要性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce71/12141719/0ae6f07f1a04/12672_2025_2734_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce71/12141719/0ae6f07f1a04/12672_2025_2734_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ce71/12141719/0ae6f07f1a04/12672_2025_2734_Fig1_HTML.jpg

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[6]
A Comprehensive Review of Current Approaches in Bladder Cancer Treatment.

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[7]
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[9]
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