Background:
While several interventions can effectively lower lipid levels in people at risk for atherosclerotic cardiovascular disease (ASCVD), cardiovascular event (CVE) risks remain, suggesting an unmet medical need to identify factors contributing to CVE risk. Monocytes and macrophages play central roles in atherosclerosis, but previous work has yet to provide a detailed view of macrophage populations involved in increased ASCVD risk.
Methods:
A novel macrophage foaming analytics tool, AtheroSpectrum, was developed using two quantitative indices depicting lipid metabolism and the inflammatory status of macrophages. Next, a machine-learning algorithm was developed to analyze gene expression patterns in the peripheral monocyte transcriptome of Multi-Ethnic Study of Atherosclerosis participants (MESA-set1, n=911). A list of 30 genes was generated and integrated with traditional risk factors to create an ASCVD risk prediction model (CR-30), which was subsequently validated in the remaining MESA-set2 (n=228); performance of CR-30 was also tested in two independent human atherosclerotic tissue transcriptome datasets (GTEx and GSE43292).
Results:
Using single-cell transcriptomic profiles (GSE97310, GSE116240, GSE97941, FR-FCM-Z23S), AtheroSpectrum detected two distinct programs in plaque macrophages: homeostatic-foaming and inflammatory pathogenic-foaming, the latter was positively associated with severity of atherosclerosis in multiple studies. A pool of 2209 pathogenic foaming genes was extracted and screened to select a subset of 30 genes correlated with CVE in MESA-set1. A CVD risk score model (CR-30) was then developed by incorporating this gene-set with traditional variables sensitive to CVE in MESA-set1 after cross-validation generalizability analysis. The performance of CR-30 was then tested in MESA-set2 (p=2.60×10
−4
, AUC=0.742), and two independent datasets (GTEx, p=7.32×10
−17
, AUC=0.664; GSE43292, p=7.04×10
−2
, AUC=0.633). Model sensitivity tests confirmed the contribution of the 30-gene panel to the prediction model (likelihood ratio test, df=31, p=0.03).
Conclusions:
Our novel computational program (AtheroSpectrum) identified a specific gene expression profile associated with inflammatory macrophage foam cells. A subset of 30 genes expressed in circulating monocytes jointly contributed to prediction of symptomatic atherosclerotic vascular disease. Incorporating a pathogenic foaming gene-set with known risk factors can significantly strengthen the power to predict ASCVD risk. Our programs may facilitate both mechanistic investigations and development of therapeutic and prognostic strategies for ASCVD risk.