Value of Bioinformatics Models for Predicting Translational Control of Angiogenesis

• Published in: Circulation research Vol. 136; no. 10; pp. 1147 - 1165
• Main Authors: Shaposhnikov, Michal, Thakar, Juilee, Berk, Bradford C.
• Format: Journal Article
• Language: English
• Published: Hagerstown, MD Lippincott Williams & Wilkins 09.05.2025
• Subjects: Angiogenesis; Animals; Computational Biology - methods; Humans; Neovascularization, Pathologic - genetics; Neovascularization, Physiologic - genetics; Protein Biosynthesis; computational biology; protein biosynthesis; machine learning; angiogenesis
• ISSN: 0009-7330; 1524-4571; 1524-4571
• DOI: 10.1161/CIRCRESAHA.125.325438

Angiogenesis, the formation of new blood vessels, is a fundamental biological process with implications for both physiological functions and pathological conditions. While the transcriptional regulation of angiogenesis, mediated by factors such as HIF-1α (hypoxia-inducible factor 1-alpha) and VEGF (vascular endothelial growth factor), is well-characterized, the translational regulation of this process remains underexplored. Bioinformatics has emerged as an indispensable tool for advancing our understanding of translational regulation, offering predictive models that leverage large data sets to guide research and optimize experimental approaches. However, a significant gap persists between bioinformatics experts and other researchers, limiting the accessibility and utility of these tools in the broader scientific community. To address this divide, user-friendly bioinformatics platforms are being developed to democratize access to predictive analytics and empower researchers across disciplines. Translational control, compared with transcriptional control, offers a more energy-efficient mechanism that facilitates rapid cellular responses to environmental changes. Furthermore, transcriptional regulators themselves are often subject to translational control, emphasizing the interconnected nature of these regulatory layers. Investigating translational regulation requires advanced, accessible bioinformatics tools to analyze RNA structures, interacting micro-RNAs, long noncoding RNAs, and RBPs (RNA-binding proteins). Predictive platforms such as RNA structure, human internal ribosome entry site Atlas, and RBPSuite enable the study of RNA motifs and RNA-protein interactions, shedding light on these critical regulatory mechanisms. This review highlights the transformative role of bioinformatics using widely accessible user-friendly tools with a Web-browser interface to elucidate translational regulation in angiogenesis. The bioinformatics tools discussed extend beyond angiogenesis, with applications in diverse fields, including clinical care. By integrating predictive models and experimental insights, researchers can streamline hypothesis generation, reduce experimental costs, and find novel translational regulators. By bridging the bioinformatics knowledge gap, this review aims to empower researchers worldwide to adopt bioinformatics tools in their work, fostering innovation and accelerating scientific discovery.