Discovery of new MicroRNAs and their mRNA targets in patients with acute ischemic stroke

Background: In this study, we applied microarray, bioinformatics, and qRT-PCR techniques to identify miRNAs and their target genes in plasma obtained from acute ischemic stroke patients and matching controls. Methods: Microarray analyses were performed with 24-h acute ischemic stroke vs. healthy individuals and CV-risk factors matched control group plasma samples. Statistical analysis of gene expression was performed using TAC and R, with a focus on robust methods suitable for the small sample size, and miRNA target prediction was conducted using a previously established in-house wizbionet R package. Top non-coding regulators of ischemia (miR-18a-5p, miR-4467, miR-199a-5p and miR-3135b) and their predicted target genes (ANKRD12, HIF1A, GNAI2, GRIN1) were detected via qRT-PCR. Results: 146 upregulated and 258 downregulated differentially expressed RNAs were detected by microarray analysis. Using the multiMiR R package for target prediction, 67 upregulated and 125 downregulated mRNAs were mapped. Functional enrichment analysis revealed that upregulated miRNAs were associated with pathways like BDNF and IL-2 signaling, while downregulated miRNAs were linked to neurodevelopmental and NGF pathways. MiR-18a-5p and miR-199a-5p were significantly elevated in stroke patients at both day 1 and day 7 compared to healthy individuals and CV-matched controls (p < 0.05 for all). miR-4467 was lower at day 1 versus both controls (p < 0.05) but markedly increased by day 7 (p < 0.001), remaining higher than in controls (p < 0.05). miR-3135b showed persistent downregulation at both time points (p < 0.05). ROC analysis confirmed diagnostic value for all miRNAs, with the highest AUC for miR-199a-5p (0.89, 95% CI: 0.81–0.97, p < 0.001), followed by miR-3135b (0.88), miR-4467 (0.80), and miR-18a-5p (0.73; p = 0.002). For potential role in dynamic post-stroke molecular responses perspective, utility, miR-4467 increased significantly during hospitalization (p < 0.001). GNAI2 mRNA was significantly elevated at day 1 versus controls (p < 0.05). ANKRD12 was consistently lower at both day 1 and day 7 compared to controls (p < 0.05). GRIN1 was reduced at admission (p = 0.006) but normalized by day 7 (p > 0.05). ROC analysis showed diagnostic significance for ANKRD12, GNAI2, and GRIN1 (AUC = 0.683, 0.698, 0.693). Conclusion: Our integrated miRNA/mRNA analysis identified distinct molecular signatures in acute ischemic stroke, with 146 upregulated and 258 downregulated RNAs, implicating key neuroinflammatory and neuroprotective pathways, including BDNF, IL-2, and NGF signaling. Among the validated candidates, miR-199a-5p, miR-3135b, miR-4467, and miR-18a-5p demonstrated diagnostic potential, while miR-4467, together with GNAI2 and HIF1A, showed post-stroke dynamic relevance, reflecting early transcriptomic adaptations following ischemic injury. Graphical abstract: [Image: see text] Supplementary information: The online version contains supplementary material available at 10.1186/s12920-025-02302-5.