Integrated Bioinformatics Analysis Confirms the Diagnostic Value of Nourin-Dependent miR-137 and miR-106b in Unstable Angina Patients

Abstract

The challenge of rapidly diagnosing myocardial ischemia in unstable angina (UA) patients presenting to the Emergency Department (ED) is due to a lack of sensitive blood biomarkers. This has prompted an investigation into microRNAs (miRNAs) related to cardiac-derived Nourin for potential diagnostic application. The Nourin protein is rapidly expressed in patients with acute coronary syndrome (ACS) (UA and acute myocardial infarction (AMI)). MicroRNAs regulate gene expression through mRNA binding and, thus, may represent potential biomarkers. We initially identified miR-137 and miR-106b and conducted a clinical validation, which demonstrated that they were highly upregulated in ACS patients, but not in healthy subjects and non-ACS controls. Using integrated comprehensive bioinformatics analysis, the present study confirms that the Nourin protein targets miR-137 and miR-106b, which are linked to myocardial ischemia and inflammation associated with ACS. Molecular docking demonstrated robust interactions between the Nourin protein and miR137/hsa-miR-106b, involving hydrogen bonds and hydrophobic interactions, with -10 kcal/mol binding energy. I-TASSER generated Nourin analogs, with the top 10 chosen for structural insights. Antigenic regions and MHCII epitopes within the Nourin SPGADGNGGEAMPGG sequence showed strong binding to HLA-DR/DQ alleles. The Cytoscape network revealed interactions of -miR137/hsa-miR--106b and Phosphatase and tensin homolog (PTEN) in myocardial ischemia. RNA Composer predicted the secondary structure of miR-106b. Schrödinger software identified key Nourin-RNA interactions critical for complex stability. The study identifies miR-137 and miR-106b as potential ACS diagnostic and therapeutic targets. This research underscores the potential of miRNAs targeting Nourin for precision ACS intervention. The analysis leverages RNA Composer, Schrödinger, and I-TASSER tools to explore interactions and structural insights. Robust Nourin-miRNA interactions are established, bolstering the case for miRNA-based interventions in ischemic injury. In conclusion, the study contributes to UA and AMI diagnosis strategies through bioinformatics-guided exploration of Nourin-targeting miRNAs. Supported by comprehensive molecular analysis, the hypoxia-induced miR-137 for cell apoptosis (a marker of cell damage) and the inflammation-induced miR-106b (a marker of inflammation) confirmed their potential clinical use as diagnostic biomarkers. This research reinforces the growing role of miR-137/hsa-miR-106b in the early diagnosis of myocardial ischemia in unstable angina patients.

Keywords: Nourin-dependent miR-137 and miR-106b; integrated bioinformatics analysis; molecular dynamics; myocardial ischemia; unstable angina.

Figure 1

The predicted 3D structure of Nourin protein (a), and the predicted peptide score (b).

Figure 2

The Ell iPro predicted linear epitopes in each protein, MIINHN (a), and GGEA (b).

Figure 3

The NetMHCpan EL 4.1 Prediction method for three proteins, 1 (a), 2 (b), and 3 (c). High score = good binder.

Figure 4

Predicted 3D structure of (a) hsa-miR--106b and (b) hsa-miR-137 using RNA Composer.

Figure 5

Illustrates the interaction network involving PTEN and its targeted miRNAs (miR-137 and miR-106b) that are dependent on the presence of Nourin. (a), miR-137 is shown to regulate the expression of the PTEN gene. Through comprehensive analysis involving sequence complementarity and luciferase reporter assays conducted in both human and mouse model systems, it has been determined that miR-137 binds to the 3’UTR of PTEN mRNA. The exact mechanism of miR-137’s involvement, whether within the nonendonucleolytic or endonucleolytic RISC, or both, remains uncertain (source: https://reactome.org/content/detail/R-HSA-9615570 (accessed on 12 June 2023)). (b), miR-106b is demonstrated to play a role in modulating PTEN gene expression. Specifically, one of the mature products of miR-106b, known as miR-106b-5p, binds to the 3’UTR of PTEN mRNA. This binding event leads to a reduction in both PTEN mRNA and protein levels. This regulatory action is attributed to miR-106b’s participation in the endonucleolytic RISC. Additionally, there is a possibility that miR-106b may contribute to the nonendonucleolytic RISC (source: miR-106b/PTEN network from https://reactome.org/content/detail/R-HSA-8944632 (accessed on 20 June 2023)).

Figure 6

Nourin micro–RNA interaction between (a) miR-106b and (b) miR-137.

Figure 7

Regulation of Hypoxia-Induced Cell Apoptosis by miR-137 and miR-106b. PTEN: Phosphatase and tensin homolog, VEGF: Vascular endothelial growth factor, HIF-α: Hypoxia-inducible factor alpha, and c-Myc (myelocytomatosis viral oncogene homolog).