Diffuse intimal thickening (DIT) is a pre-clinical stage of atherosclerosis characterized by thickened intima. The molecular basis of its susceptibility to atherogenesis is unknown, and mechanistic investigations cannot be performed in commonly used mouse models, in which DIT does not exist. Vascular smooth muscle cells (SMCs) are the predominant cell type that occupies the intima and media of DIT. The molecular differences between these two layers may reveal the earliest phenotypic changes in SMCs to promote atherosclerosis. We benchmarked the RNA quality of human coronary arteries from autopsies (n = 7) and explanted hearts (n = 7) and performed Visium spatial gene expression on tissue sections with DIT. Although autopsy samples met the RNA quality standard for Visium (DV200 ≥ 30%), only arteries from explanted hearts exhibited reliable sequencing performance. Genes enriched in TGF-β-mediated remodeling of the extracellular matrix were overrepresented in the intima. SMCs enriched in the intima are dedifferentiated, but unlike those in the atherosclerotic lesions, they are not pro-inflammatory. Our findings indicate that autopsy samples are not ideal to distinguish subtle differences among cell phenotypes. SMCs in thickened intima may lead to lipid retention but not necessarily the onset of atherosclerosis.

Although cardiovascular disease is the leading cause of death globally, therapeutic development in this field is slow. Given the high cost of developing new drugs and running clinical trials for cardiovascular disease, repurposing of drugs with approved safety profiles is an attractive strategy for therapeutic development that can significantly reduce the time and cost investment before phase II clinical trials. In the era of “Omics,” various new methods and several large databases have been developed to enable the use of transcriptomics data for drug repurposing. This review summarizes the principles and workflow of signature mapping, which forms the foundation of statistical models used for transcriptome-based drug repurposing. We highlight the features of different analysis pipelines and databases that have been developed for signature mapping. These analysis pipelines prioritize genes that are statistically important, an approach that fundamentally differs from the pharmacological approach of identifying disease-driving and therapeutically targetable pathways. Outcomes of signature mapping pipelines are sensitive to the quality of input data, and results are not always reproducible. Moreover, all widely used RNA-seq databases are derived from cancer research and lack high-quality molecular data for cardiovascular disease. These unmet needs call for interdisciplinary collaboration and large networks of cardiovascular research-oriented biobanks to create the databases needed for transcriptomic-based signature mapping for drug repurposing efforts.

Diffuse intimal thickening (DIT) is a pre-clinical stage of atherosclerosis characterized by thickened intima. The molecular basis of its susceptibility to atherogenesis is unknown, and mechanistic investigations cannot be performed in commonly used mouse models, in which DIT does not exist. Vascular smooth muscle cells (SMCs) are the predominant cell type that occupies the intima and media of DIT. The molecular differences between these two layers may reveal the earliest phenotypic changes in SMCs to promote atherosclerosis. We benchmarked the RNA quality of human coronary arteries from autopsies (n=7) and freshly explanted hearts (n=7) and performed Visium spatial gene expression on tissue sections with DIT. Although autopsy samples met the RNA quality standard for Visium (DV200 ≥ 30%), only arteries from freshly explanted hearts exhibited reliable sequencing performance. Genes enriched in TGF-β-mediated remodeling of the extracellular matrix were overrepresented in the intima. SMCs enriched in the intima are dedifferentiated, but unlike those in the atherosclerotic lesions, they are not proinflammatory. Our findings indicate that autopsy samples are not ideal to distinguish subtle differences among cell phenotypes. SMCs in thickened intima may lead to lipid retention but not necessarily the onset of atherosclerosis.