Serum integrative omics reveals predictive signatures for coronary artery disease

Identifying serum biomarkers that accurately reflect the progression of coronary artery disease (CAD) remains a major challenge. Integrative proteomic and metabolomic profiling can provide novel insights into disease pathogenesis and improve clinical prediction. We conducted a four-phase study. In the discovery phase, serum from 40 patients (controls, stable CAD, and acute coronary syndrome (ACS)) was analyzed using data-independent acquisition (DIA) proteomics and liquid chromatography-tandem mass spectrometry (LC-MS)/gas chromatography-mass spectrometry (GC-MS) metabolomics to identify differentially expressed proteins (DEPs) and metabolites. In the verification phase, selected DEPs were validated by parallel reaction monitoring (PRM) in an independent 40-patient cohort. In the derivation phase, six validated proteins were measured by ELISA in 207 angina patients to assess their association with coronary obstruction (≥ 50% stenosis). In the validation phase, a support vector machine (SVM) model incorporating clinical risk factors and these biomarkers was developed in the derivation cohort and tested in an independent 97-patient cohort. Model performance was evaluated using receiver operating characteristic (ROC) curves and decision curve analysis. Coronary obstruction is defined as ≥ 50% luminal diameter stenosis in at least one major coronary artery on angiography. Proteomic analysis identified 97 DEPs, and metabolomic profiling revealed 322 DEMs (including 289 from LC-MS and 33 from GC-MS analyses). Seven proteins showed consistent changes in both DIA and PRM validation. Among these, thrombospondin-1 (TSP-1) was significantly upregulated in stable CAD compared with controls, while serum amyloid A1 (SAA1) was markedly elevated in ACS compared with stable CAD. In an independent angina cohort (n = 207), serum levels of TSP-1 and SAA1 were significantly higher in patients with coronary obstruction. Multivariate logistic regression adjusted for conventional cardiovascular risk factors (including age, sex, homocysteine, and other clinical variables) demonstrated that TSP-1 remained independently associated with coronary artery occlusion (OR = 1.424, 95% CI 1.057-1.918, P = 0.020). A support vector machine (SVM) model incorporating conventional clinical risk factors was constructed, and the addition of TSP-1 and SAA1 significantly improved diagnostic performance for CAD severity (AUC = 0.919 in derivation, 0.992 in validation). In conclusion, our dual-omics approach identified novel biomarkers and pathways in CAD progression. The SVM-based prediction model offers a promising non-invasive tool for early CAD detection, potentially reducing unnecessary invasive procedures.