AI-Driven Proteomics: PUMCH Team Pioneers New Strategy for Precision Diagnosis and Management of Behçet's Disease
CopyFrom: PUMCH UpdateTime: 2025.12.19

Recently, a collaborative team led by Li Yongzhe, Researcher in the Department of Clinical Laboratory, PUMCH; Zheng Wenjie, Chief Physician in the Department of Rheumatology, PUMCH; Liu Yudong, associate researcher at the National Center for Clinical Laboratories; and partners at the National Center for Protein Sciences have successfully applied, for the first time globally, artificial intelligence-driven proteomics to construct a diagnosis and stratification model for Behçet's disease (BD). This breakthrough offers new strategies for early diagnosis and precision treatment of the condition. The findings were published in Advanced Science (IF=14.1), a leading international journal.

Behçet's disease (BD) is a chronic multisystem inflammatory disorder characterized by a heterogeneous spectrum of clinical manifestations. The absence of disease-specific blood biomarkers has long hindered clinical stratification and treatment efficacy assessment.


Figures: AI+proteomics approach for developing BD diagnosis and stratification models

The research team integrated two cutting-edge technologies—data-independent acquisition mass spectrometry (DIA-MS) and customizable antibody microarray analysis—to perform in-depth proteomic profiling of plasma samples from BD patients. With 159 differentially expressed proteins identified in the training cohort, the team trained an XGBoost machine learning model, which was subsequently validated in an independent cohort. The model displayed a favorable performance in BD diagnosis. In the training set, the area under the curve (AUC) of the diagnosis model was 0.984 with an accuracy of 0.935. In the validation set, the AUC was 0.967 with an accuracy of 0.871. The model displayed an equally favorable performance in BD stratification. In the training set, AUCs ranged from 0.897 to 0.986. In the validation set, AUCs ranged from 0.718 to 0.960.


The study identified dozens of proteins with critical roles in BD pathogenesis, including complement component C4B. Protein-protein interaction (PPI) network analysis identified C4B as the hub protein with the highest degree centrality, suggesting a potentially critical role in disease progression. Functional annotation indicated that severity-associated upregulated proteins were primarily involved in protein activation cascades, complement activation, and humoral immune responses. In the study, FXI (coagulation factor XI) emerged as the top-ranked feature in both diagnosis and stratification models, suggesting a potentially important role in the vasculitic mechanisms of BD.

This study demonstrates the power of "AI-driven proteomics" in constructing high-precision diagnosis and stratification models. The findings reveal complex interactive networks among infection, complement activation, coagulation dysfunction, and immune-inflammatory responses in BD pathogenesis—providing a crucial theoretical foundation for developing targeted therapies and personalized intervention strategies. With ongoing multicenter, prospective studies, this model has the potential to translate into a practical clinical tool, facilitating early diagnosis, timely treatment initiation, and comprehensive disease management of BD.

Co-first authors are Cheng Linlin, Resident Physician in the Department of Clinical Laboratory, PUMCH; Li Mansheng, Associate Researcher at the National Center for Protein Sciences. Corresponding authors are Researcher Li Yongzhe, Chief Physician Zheng Wenjie, and Associate Researcher Liu Yudong.


Written by and pictures courtesy of Cheng Linlin
Reviewed by Yang Qiwen
Edited by Dong Jingge
Chief Editor Duan Wenli
Supervised by Wu Peixin