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Understanding how arterial and venous blood vessels differ at the molecular level is essential for advancing vascular biology and developing targeted therapies for cardiovascular disease. In a recent International Journal of Molecular Sciences study, researchers from BioInfoRx and University of North Carolina at Chapel Hill performed a comprehensive bulk RNA-Seq analysis of porcine arterial and venous vascular smooth muscle cells (ApSMCs and VpSMCs) (Lee et al., 2025). 

This study is based on a porcine model because growing evidence indicates that pigs are excellent models for studying human pathophysiology. They are anatomically, physiologically, and genetically much closer to humans than commonly used rodent models, while also sharing similar drug metabolism and pharmacokinetic profiles, although non-human primates are even more similar to humans, ethical and societal concerns limit their use. Recent success in engineered porcine kidney xenotransplantation—where a patient survived for nine months with a pig kidney—further highlights the strong physiological relevance of pigs as a biomedical research model.

This study uncovered hundreds of differentially expressed genes (DEGs) and pathway-level differences that help explain vessel-specific behaviors such as proliferation, migration, inflammation, and calcification. Notably, all genomic analyses and figures in this study were generated using the BxGenomics Bulk RNA-Seq View, developed by researchers in BioInfoRx, highlighting how modern, no-code genomics platforms can transform complex transcriptomic datasets into publication-ready insights.

From Raw RNA-Seq Data to Biological Insight—All in One Platform

Bulk RNA-Seq studies often involve multiple disconnected steps: data preprocessing, differential expression analysis, pathway enrichment, and figure generation—frequently requiring scripting expertise and custom pipelines. In this study, BxGenomics streamlined the entire process. Using the Bulk RNA-Seq View, researchers:

• Identified 466 genes enriched in ApSMCs and 358 genes enriched in VpSMCs (Fig. 1)
• Applied standard statistical cutoffs (≥2-fold change, FDR ≤ 0.05)
• Performed Gene Set Enrichment Analysis (GSEA) and Overrepresentation Analysis (ORA) for pathway enrichment
• Visualized gene expression differences across multiple KEGG pathways between ApSMCs and VpSMCs.

Figure 1. Volcano plot comparing gene expression in ApSMCs and VpSMCs groups without the ApSMC3 outlier.

Clear Visualization of Complex Biology

The Bulk RNA-Seq View enabled intuitive visualization of pathway-level gene expression differences between arterial and venous VSMCs. For example:

• Cell cycle and proliferation pathways clearly showed elevated expression of DNA replication and mitotic genes (e.g., CDK1, CCNB1, SKP2) in venous VSMCs, consistent with their higher proliferative capacity (Fig. 2).
• ECM–receptor interaction and focal adhesion pathways revealed distinct integrin and cytoskeletal gene usage between arterial and venous cells, helping explain differences in migration and mechanical adaptation.
• Inflammatory signaling pathways, including TGF-β, TNF, and Toll-like receptor signaling, highlighted vessel-specific immune responses.
• Wnt signaling and cellular senescence pathways provided mechanistic insight into arterial calcification versus venous remodeling.

By mapping DEGs directly onto curated KEGG pathways, BxGenomics allowed researchers to move beyond gene lists, rapidly interpret biological meaning, and understand key processes in diseases such as PAD, DVT, and AVF failure.

Figure 2. KEGG Pathway of the cell cycle with visualization of gene expression differences between ApSMCs and VpSMCs. Red represents high expression in ApSMCs, while green represents high expression in VpSMCs.

Accelerating Discovery with BxGenomics

This study illustrates an important contribution of BxGenomics to biological research: the ability to go from sequencing data to biologically meaningful insights without coding barriers. The BxGenomics Bulk RNA-Seq View empowers wet-lab scientists, translational researchers, and clinicians to explore gene expression interactively and generate publication-quality figures in minutes. 

References:

Lee, K. A., Li, W., Uriyanghai, U., Wai, C., Su, H., Yang, A., Li, L., Sudarsanam, V. A., Poulton, J. S., Roy-Chaudhury, P., & Xi, G. (2025). Bulk RNA sequencing reveals signature differences in key cell signaling pathways between porcine venous and arterial smooth muscle cells. International Journal of Molecular Sciences, 26(24), 11948. https://doi.org/10.3390/ijms262411948