Integrative Bioinformatics and Exploratory Experimental Validation of Expression Changes in miR-214-3p, miR-1b, miR-133b-3p, and Directionally Concordant mRNAs in a Rat Model of Acute Myocardial Infarction
- 1Department of Biophysics, Faculty of Medicine, Trakya University, 22030 Edirne, Türkiye; (B.E.Y.); (M.Y.)
- 2Department of Biostatistics, Faculty of Medicine, Trakya University, 22030 Edirne, Türkiye
Abstract
Background and Objectives: Acute myocardial infarction (AMI) induces inflammatory, cell-death, and fibrotic responses. MicroRNAs modulate these processes by regulating specific mRNA targets, but the contribution of individual miRNA–mRNA axes remains incompletely defined. Materials and Methods: Transcriptomic datasets GSE35088 (mRNA) and GSE95855 (miRNA) were analyzed to identify differentially expressed mRNAs and miRNAs. Pooled predicted targets of upregulated miRNAs were intersected with upregulated mRNAs, and those of downregulated miRNAs with downregulated mRNAs, to prioritize directionally concordant candidate sets. The canonical inverse-direction intersections were computed for comparison. An isoproterenol-induced model of myocardial injury in male Wistar rats, with injury verified by creatine kinase-MB and troponin-I, was used for exploratory RT-qPCR. Results: The analysis yielded 143 differentially expressed mRNAs and 35 miRNAs. The same-direction intersection prioritized Fbn1, Col3a1, Hamp, and Cyp2e1, grouped by direction with the most strongly changed miRNAs: upregulated miR-214-3p and downregulated miR-1b and miR-133b-3p. Among these molecules, only Fbn1 has predicted interactions with these miRNAs in the multiMiR output, with miR-214-3p in the same direction and miR-133b-3p in the inverse direction. The canonical intersection identified 28 upregulated mRNAs as predicted targets of downregulated miRNAs, twelve of which, including Col3a1, are targets of the miR-29 family. RT-qPCR showed directionally concordant, statistically supported changes for miR-214-3p, miR-1b, miR-133b-3p, Col3a1, and Cyp2e1, reported as fold changes with 95% confidence intervals. Hamp and Fbn1 were not statistically supported, with intervals wide enough to include decreases as well as several-fold increases. Conclusions: The candidate sets reflect directional concordance, not demonstrated miRNA–target regulation. The upregulated set (miR-214-3p, Col3a1) and the downregulated set (miR-1b, miR-133b-3p, Cyp2e1) comprise molecules previously implicated in fibrotic and oxidative remodeling, while the canonical analysis nominates the miR-29 family for future testing. These molecules warrant evaluation in circulating samples and larger cohorts.
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BibTeX
@article{yamasan2026integrative,
title = {{Integrative Bioinformatics and Exploratory Experimental Validation of Expression Changes in miR-214-3p, miR-1b, miR-133b-3p, and Directionally Concordant mRNAs in a Rat Model of Acute Myocardial Infarction}},
author = {Bilge Eren Yamasan and Mustafa Yıldız and Selçuk Korkmaz},
journal = {Medicina (Kaunas, Lithuania)},
year = {2026},
month = sep,
doi = {10.3390/medicina62101860},
url = {https://europepmc.org/article/PMC/PMC13706966},
note = {CC BY},
}
RIS
TY - JOUR
TI - Integrative Bioinformatics and Exploratory Experimental Validation of Expression Changes in miR-214-3p, miR-1b, miR-133b-3p, and Directionally Concordant mRNAs in a Rat Model of Acute Myocardial Infarction
AU - Bilge Eren Yamasan
AU - Mustafa Yıldız
AU - Selçuk Korkmaz
PY - 2026
DA - 2026/09/01
JO - Medicina (Kaunas, Lithuania)
DO - 10.3390/medicina62101860
UR - https://europepmc.org/article/PMC/PMC13706966
AB - Background and Objectives: Acute myocardial infarction (AMI) induces inflammatory, cell-death, and fibrotic responses. MicroRNAs modulate these processes by regulating specific mRNA targets, but the contribution of individual miRNA–mRNA axes remains incompletely defined. Materials and Methods: Transcriptomic datasets GSE35088 (mRNA) and GSE95855 (miRNA) were analyzed to identify differentially expressed mRNAs and miRNAs. Pooled predicted targets of upregulated miRNAs were intersected with upregulated mRNAs, and those of downregulated miRNAs with downregulated mRNAs, to prioritize directionally concordant candidate sets. The canonical inverse-direction intersections were computed for comparison. An isoproterenol-induced model of myocardial injury in male Wistar rats, with injury verified by creatine kinase-MB and troponin-I, was used for exploratory RT-qPCR. Results: The analysis yielded 143 differentially expressed mRNAs and 35 miRNAs. The same-direction intersection prioritized Fbn1, Col3a1, Hamp, and Cyp2e1, grouped by direction with the most strongly changed miRNAs: upregulated miR-214-3p and downregulated miR-1b and miR-133b-3p. Among these molecules, only Fbn1 has predicted interactions with these miRNAs in the multiMiR output, with miR-214-3p in the same direction and miR-133b-3p in the inverse direction. The canonical intersection identified 28 upregulated mRNAs as predicted targets of downregulated miRNAs, twelve of which, including Col3a1, are targets of the miR-29 family. RT-qPCR showed directionally concordant, statistically supported changes for miR-214-3p, miR-1b, miR-133b-3p, Col3a1, and Cyp2e1, reported as fold changes with 95% confidence intervals. Hamp and Fbn1 were not statistically supported, with intervals wide enough to include decreases as well as several-fold increases. Conclusions: The candidate sets reflect directional concordance, not demonstrated miRNA–target regulation. The upregulated set (miR-214-3p, Col3a1) and the downregulated set (miR-1b, miR-133b-3p, Cyp2e1) comprise molecules previously implicated in fibrotic and oxidative remodeling, while the canonical analysis nominates the miR-29 family for future testing. These molecules warrant evaluation in circulating samples and larger cohorts.
SN - 1010-660X
SN - 1648-9144
ER -