Identification of Heterogeneous Prognostic Subtypes in Primary Membranous Nephropathy Based on Unsupervised Machine Learning

 

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Identification of Heterogeneous Prognostic Subtypes in Primary Membranous Nephropathy Based on Unsupervised Machine Learning

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Yuzhu
Xu
Yuzhu Xu xuyzh8@mail2.sysu.edu.cn The First Affiliated Hospital of Sun Yat-Sen University Department of Nephrology GuangDong China *
Shuqin Liu liushq58@mail2.sysu.edu.cn The First Affiliated Hospital of Sun Yat-Sen University Department of Nephrology GuangDong China -
Dingding Wang wangdd29@mail2.sysu.edu.cn The First Affiliated Hospital of Sun Yat-Sen University Department of Nephrology GuangDong China -
Yiqin Wang wangyq99@mail2.sysu.edu.cn The First Affiliated Hospital of Sun Yat-Sen University Department of Nephrology GuangDong China -
Xiaohui Lu luxh33@mail2.sysu.edu.cn The First Affiliated Hospital of Sun Yat-Sen University Department of Nephrology GuangDong China -
Dan Wang wangd256@mail.sysu.edu.cn The First Affiliated Hospital of Sun Yat-Sen University Department of Nephrology GuangDong China -
Naya Huang huangny5@mail.sysu.edu.cn The First Affiliated Hospital of Sun Yat-Sen University Department of Nephrology GuangDong China -
Qiong Wen wenqiong@mail.sysu.edu.cn The First Affiliated Hospital of Sun Yat-Sen University Department of Nephrology GuangDong China -
Qian Zhou zhouq49@mail.sysu.edu.cn The First Affiliated Hospital of Sun Yat-Sen University Clinical Trials Unit GuangDong China -
Jinjin Fan fanjinj@mail.sysu.edu.cn The First Affiliated Hospital of Sun Yat-Sen University Department of Nephrology GuangDong China -
Xin Wang wangxin8@mail.sysu.edu.cn The First Affiliated Hospital of Sun Yat-Sen University Department of Nephrology GuangDong China -
Wei Chen chenwei99@mail.sysu.edu.cn The First Affiliated Hospital of Sun Yat-Sen University Department of Nephrology GuangDong China -
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Primary membranous nephropathy (PMN) is the leading cause of adult nephrotic syndrome. Current risk stratification relies on six-month changes in proteinuria, estimated glomerular filtration rate (eGFR), and anti-phospholipase A2 receptor (PLA2R) antibody levels, lacks accurate baseline prognostic tools. We aimed to develop an early and precise subtyping system to identify heterogeneous PMN subgroups using machine learning.

We enrolled 1,109 biopsy-proven PMN adults from Southern China (2010-2022), with a follow-up of at least two years. The primary endpoint was end-stage renal disease (ESRD) or ≥50% eGFR decline. The secondary endpoint was all-cause mortality. Unsupervised hierarchical clustering (Ward’s method), principal component analysis, and decision tree modeling were employed to integrate key baseline features for subtype identification and validation.

Three distinct subtypes were identified: Cluster 1a (low-risk) had the mildest disease, frequent conservative treatment (41·3%), and the best prognosis(only 11.0% experienced primary endpoint, while 54.9% showed eGFR decline <20%). Cluster 2 (high-risk) featured oldest age, highest comorbidities, most severe pathology, most intensive immunosuppression (72·3%), and poorest prognosis (69.2%experienced primary endpoint, HR=3·538, 95%CI:1·803–6·943 vs. Cluster 1a). Cluster 1b (moderate-risk) showed nephrotic proteinuria, hyperlipidemia, intermediate clinicopathological severity, and poorer prognosis than Cluster 1a (HR=1·532, 95%CI:1·036–2·265). The new classification achieved 0·821 accuracy for the primary endpoint, outperforming conventional methods. A decision tree model incorporating eGFR, mean blood pressure (MBP), urine β2-microglobulin (β2M), glomerulosclerosis percentage, total protein (TP), fibrinogen (Fbg), and segmental glomerulosclerosis percentage achieved effective risk stratification, with Area Under the Curve (AUC) of 0·882 (training) and 0·856 (validation).

The three novel phenotypes identified by machine learning-based clustering demonstrated superior predictive performance compared to conventional methods. This approach enables accurate identification of heterogeneous PMN patients, thereby optimizing clinical decision-making and prognostic assessment.


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