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使用可解释人工智能将细胞外囊泡作为代谢功能障碍相关脂肪性肝病分期的生物标志物

Extracellular vesicles as biomarkers for metabolic dysfunction-associated steatotic liver disease staging using explainable artificial intelligence.

作者信息

Trifylli Eleni Myrto, Angelakis Athanasios, Kriebardis Anastasios G, Papadopoulos Nikolaos, Fortis Sotirios P, Pantazatou Vasiliki, Koskinas John, Kranidioti Hariklia, Koustas Evangelos, Sarantis Panagiotis, Manolakopoulos Spilios, Deutsch Melanie

机构信息

Gastrointestinal-Liver Unit, The 2 Department of Internal Medicine, National and Kapodistrian University of Athens, General Hospital of Athens "Hippocratio," Athens 11521, Greece.

Laboratory of Reliability and Quality Control in Laboratory Hematology, Department of Biomedical Sciences, Section of Medical Laboratories, School of Health & Caring Sciences, University of West Attica, Egaleo 12243, Attikí, Greece.

出版信息

World J Gastroenterol. 2025 Jun 14;31(22):106937. doi: 10.3748/wjg.v31.i22.106937.


DOI:10.3748/wjg.v31.i22.106937
PMID:40539197
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12175857/
Abstract

BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a leading cause of chronic liver disease globally. Current diagnostic methods, such as liver biopsies, are invasive and have limitations, highlighting the need for non-invasive alternatives. AIM: To investigate extracellular vesicles (EVs) as potential biomarkers for diagnosing and staging steatosis in patients with MASLD using machine learning (ML) and explainable artificial intelligence (XAI). METHODS: In this single-center observational study, 798 patients with metabolic dysfunction were enrolled. Of these, 194 met the eligibility criteria, and 76 successfully completed all study procedures. Transient elastography was used for steatosis and fibrosis staging, and circulating plasma EV characteristics were analyzed through nanoparticle tracking. Twenty ML models were developed: Six to differentiate non-steatosis (S0) from steatosis (S1-S3); and fourteen to identify severe steatosis (S3). Models utilized EV features (size and concentration), clinical (advanced fibrosis and presence of type 2 diabetes mellitus), and anthropomorphic (sex, age, height, weight, body mass index) data. Their performance was assessed using receiver operating characteristic (ROC)-area under the curve (AUC), specificity, and sensitivity, while correlation and XAI analysis were also conducted. RESULTS: The CatBoost C1a model achieved an ROC-AUC of 0.71/0.86 (train/test) on average across ten random five-fold cross-validations, using EV features alone to distinguish S0 from S1-S3. The CatBoost C2h-21 model achieved an ROC-AUC of 0.81/1.00 (train/test) on average across ten random three-fold cross-validations, using engineered features including EVs, clinical features like diabetes and advanced fibrosis, and anthropomorphic data like body mass index and weight for identifying severe steatosis (S3). Key predictors included EV mean size and concentration. Correlation, XAI, and SHapley Additive exPlanations analysis revealed non-linear feature relationships with steatosis stages. CONCLUSION: The EV-based ML models demonstrated that the mean size and concentration of circulating plasma EVs constituted key predictors for distinguishing the absence of significant steatosis (S0) in patients with metabolic dysfunction, while the combination of EV, clinical, and anthropomorphic features improved the diagnostic accuracy for the identification of severe steatosis. The algorithmic approach using ML and XAI captured non-linear patterns between disease features and provided interpretable MASLD staging insights. However, further large multicenter studies, comparisons, and validation with histopathology and advanced imaging methods are needed.

摘要

背景:代谢功能障碍相关脂肪性肝病(MASLD)是全球慢性肝病的主要病因。目前的诊断方法,如肝活检,具有侵入性且存在局限性,这凸显了对非侵入性替代方法的需求。 目的:利用机器学习(ML)和可解释人工智能(XAI)研究细胞外囊泡(EVs)作为诊断MASLD患者脂肪变性及进行分期的潜在生物标志物。 方法:在这项单中心观察性研究中,纳入了798例代谢功能障碍患者。其中,194例符合纳入标准,76例成功完成了所有研究程序。采用瞬时弹性成像进行脂肪变性和纤维化分期,并通过纳米颗粒跟踪分析循环血浆EV的特征。开发了20个ML模型:6个用于区分非脂肪变性(S0)和脂肪变性(S1 - S3);14个用于识别重度脂肪变性(S3)。模型利用了EV特征(大小和浓度)、临床特征(晚期纤维化和2型糖尿病的存在)以及人体测量学特征(性别、年龄、身高、体重、体重指数)数据。使用受试者操作特征(ROC)曲线下面积(AUC)、特异性和敏感性评估其性能,同时还进行了相关性和XAI分析。 结果:在十次随机五折交叉验证中,仅使用EV特征区分S0和S1 - S3时,CatBoost C1a模型平均ROC - AUC为0.71/0.86(训练/测试)。在十次随机三折交叉验证中,使用包括EVs的工程特征、糖尿病和晚期纤维化等临床特征以及体重指数和体重等人体测量学数据来识别重度脂肪变性(S3)时,CatBoost C2h - 21模型平均ROC - AUC为0.81/1.00(训练/测试)。关键预测因素包括EV平均大小和浓度。相关性、XAI和SHapley加法解释分析揭示了与脂肪变性阶段的非线性特征关系。 结论:基于EV的ML模型表明,循环血浆EV的平均大小和浓度是区分代谢功能障碍患者是否存在显著脂肪变性(S0)的关键预测因素,而EV、临床和人体测量学特征的组合提高了识别重度脂肪变性的诊断准确性。使用ML和XAI的算法方法捕捉了疾病特征之间的非线性模式,并提供了可解释的MASLD分期见解。然而,需要进一步开展大型多中心研究、比较,并与组织病理学和先进成像方法进行验证。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/14db/12175857/3e78efbcfe1f/wjg-31-22-106937-g007.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/14db/12175857/ce4108889f3c/wjg-31-22-106937-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/14db/12175857/3e78efbcfe1f/wjg-31-22-106937-g007.jpg

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本文引用的文献

[1]
Extracellular Vesicles: Advanced Tools for Disease Diagnosis, Monitoring, and Therapies.

Int J Mol Sci. 2024-12-29

[2]
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[3]
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Biogenesis and delivery of extracellular vesicles: harnessing the power of EVs for diagnostics and therapeutics.

Front Mol Biosci. 2024-1-3

[9]
Diagnosis of acute myeloid leukaemia on microarray gene expression data using categorical gradient boosted trees.

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[10]
Digital pathology for nonalcoholic steatohepatitis assessment.

Nat Rev Gastroenterol Hepatol. 2024-1

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