Linking RNA dynamics to heart disease: the lncRNA/miRNA/mRNA axis in myocardial ischemia-reperfusion injury

CoupleMDA: Metapath-Induced Structural-Semantic Coupling Network for miRNA-Disease Association Prediction

The prediction of microRNA-disease associations (MDAs) is crucial for understanding disease mechanisms and biomarker discovery. While graph neural networks have emerged as promising tools for MDA prediction, existing methods face critical limitations: (1) data leakage caused by improper use of Gaussian interaction profile (GIP) kernel similarity during feature construction, (2) self-validation loops in calculating miRNA functional similarity using known MDA data, and (3) information bottlenecks in conventional graph neural network (GNN) architectures that flatten heterogeneous relationships and employ over-simplified decoders. To address these challenges, we propose CoupleMDA, a metapath-guided heterogeneous graph learning framework coupling structural and semantic features. The model constructs a biological heterogeneous network using independent data sources to eliminate feature-target space coupling. Our framework implements a two-stage encoding strategy: (1) relational graph convolutional networks (RGCN) for pre-encoding and (2) metapath-guided semantic aggregation for secondary encoding. During decoding, common metapaths between node pairs structurally guide feature pooling, mitigating information bottlenecks. The comprehensive evaluation shows that CoupleMDA achieves a 2-5% performance improvement over the current state-of-the-art baseline methods in the heterogeneous graph link prediction task. Ablation studies confirm the necessity of each proposed component, while case analyses reveal the framework's capability to recover cancer-related miRNA-disease associations through biologically interpretable metapaths.

miRNA-148a-3p targets to regulate the lipid metabolism gene SOCS3 to reduce myocardial ischemia/reperfusion injury

BACKGROUND

Acute myocardial infarction (AMI) is a major cause of death in cardiovascular patients. SOCS3's protective role in cardiac I/R-I is being explored, and miRNAs, particularly miRNA-148a-3p, are suspected to target SOCS3. To elucidate the role of miRNA-148a-3p targeting lipid metabolism gene SOCS3 in cardiac ischemia-reperfusion injury (I/R-I) in rats.

METHODS

Derived mRNA expression data GSE59867 from GEO, identified 558 lipid metabolism genes from KEGG and GSEA, and screened for differentially expressed genes in acute myocardial infarction (AMI). Predicted miRNA-148a-3p targeting SOCS3 using TargetScanHuman, validated binding via luciferase assay and 3'UTR mutation. Established a rat I/R-I model to assess miRNA-148a-3p and SOCS3 expression, and investigated SOCS3 regulation by miRNA-148a-3p overexpression. Analyzed expression of NF-κB p65, IL-1β, and TNF-α-related proteins, and evaluated cardiac hemodynamics post-SOCS3 regulation by miRNA-148a-3p.

RESULTS

In GSE59867, TSPO, SOCS3, LRP1, PLB1, CYP1B1, PPARG, ACSL1, and CYP27A1 were identified as differentially expressed lipid metabolism genes in AMI. The results of immune infiltration showed a close relationship between the differential lipid metabolism genes and the infiltration of immune cells such as macrophages and monocytes. The random forest algorithm identified SOCS3 as the key gene. The luciferase reporter gene demonstrated the participation of miRNA-148a-3p in the regulation of SOCS3 by binding to its 3'UTR. In vivo experiments revealed low expression of miRNA-148a-3p in myocardial I/R, while SOCS3 was highly expressed. Elevated miRNA-148a-3p expression led to a decrease in SOCS3, NF-κB p65, IL-1β, and TNF-α levels during cardiac I/R-I. Overexpression of miRNA-148a-3p enhanced the cardiac performance in rats experiencing cardiac I/R-I.

CONCLUSIONS

Overexpression of miRNA-148a-3p regulates NF-κB signaling pathway by targeting lipid metabolism gene SOCS3, reduces inflammatory response, and then reduces cardiac I/R-I in rats.

Molecular insights into regulatory RNAs in the cellular machinery

It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.

Non-coding RNAs modulate pyroptosis in myocardial ischemia-reperfusion injury: A comprehensive review

Reperfusion therapy is the most effective treatment for acute myocardial infarction. However, reperfusion itself can also cause cardiomyocytes damage. Pyroptosis has been shown to be an important mode of myocardial cell death during ischemia-reperfusion. Non-coding RNAs (ncRNAs) play critical roles in regulating pyroptosis. The regulation of pyroptosis by microRNAs, long ncRNAs, and circular RNAs may represent a new mechanism of myocardial ischemia-reperfusion injury. This review summarizes the currently known regulatory roles of ncRNAs in myocardial ischemia-reperfusion injury and interactions between ncRNAs. Potential therapeutic strategies using ncRNA modulation are also discussed.

Mechanisms by which silencing long-stranded noncoding RNA KCNQ1OT1 alleviates myocardial ischemia/reperfusion injury (MI/RI)-induced cardiac injury via miR-377-3p/HMOX1

BACKGROUND

The key complication of myocardial infarction therapy is myocardial ischemia/reperfusion injury (MI/RI), and there is no effective treatment. The present study elucidates the mechanism of action of lncRNA KCNQ1OT1 in alleviating MI/RI and provides new perspectives and therapeutic targets for cardiac injury-related diseases.

METHODS

An ischemia/reperfusion (I/R) injury model of human adult cardiac myocytes (HACMs) was constructed, and the expression of KCNQ1OT1 and miR-377-3p was determined by RT‒qPCR. The levels of related proteins were detected by western blot analysis. Cell proliferation was detected by a CCK-8 assay, and cell apoptosis and ROS content were determined by flow cytometry. SOD and MDA expression as well as Fe2+ changes were detected by related analysis kits. The target binding relationships between lncRNA KCNQ1OT1 and miR-377-3p as well as between miR-377-3p and heme oxygenase 1 (HMOX1) were verified by a dual-luciferase reporter gene assay.

RESULTS

Myocardial ischemia‒reperfusion caused oxidative stress in HACMs, resulting in elevated ROS levels, increased Fe2+ levels, decreased cell viability, and increased LDH release (a marker of myocardial injury), and apoptosis. KCNQ1OT1 and HMOX1 were upregulated in I/R-induced myocardial injury, but the level of miR-377-3p was decreased. A dual-luciferase reporter gene assay indicated that lncRNA KCNQ1OT1 targets miR-377-3p and that miR-377-3p targets HMOX1. Inhibition of HMOX1 alleviated miR-377-3p downregulation-induced myocardial injury. Furthermore, lncRNA KCNQ1OT1 promoted the level of HMOX1 by binding to miR-377-3p and aggravated myocardial injury.

CONCLUSION

LncRNA KCNQ1OT1 aggravates ischemia‒reperfusion-induced cardiac injury via miR-377-3P/HMOX1.