Elucidating the Molecular Mechanism of Ischemic Stroke Using Integrated Analysis of miRNA, mRNA, and lncRNA Expression Profiles

Combined Analysis of Human and Experimental Rat Samples Identified Biomarkers for Ischemic Stroke

The genetic transcription profile and underlying molecular mechanisms of ischemic stroke (IS) remain elusive. To address this issue, four mRNA and one miRNA expression profile of rats with middle cerebral artery occlusion (MCAO) were acquired from the Gene Expression Omnibus (GEO) database. A total of 780 differentially expressed genes (DEGs) and 56 miRNAs (DEMs) were screened. Gene set and functional enrichment analysis revealed that a substantial number of immune-inflammation-related pathways were abnormally activated in IS. Through weighted gene co-expression network analysis, the turquoise module was identified as meaningful. By taking the intersection of the turquoise module genes, DEM-target genes, and all DEGs, 354 genes were subsequently obtained as key IS-related genes. Among them, six characteristic genes were identified using the least absolute shrinkage and selection operator. After validation with three external datasets, transforming growth factor beta 1 (Tgfb1) was selected as the hub gene. This finding was further confirmed by gene expression pattern analysis in both the MCAO model rats and clinical IS patients. Moreover, the expression of the hub genes exhibited a negative correlation with the modified Rankin scale score (P < 0.05). Collectively, these results expand our knowledge of the genetic profile and molecular mechanisms involved in IS and suggest that the Tgfb1 gene is a potential biomarker of this disease.

AP003352.1/miR-141-3p axis enhances the proliferation of osteosarcoma by LPAR3

Osteosarcoma (OS) is a highly malignant tumor with a poor prognosis and a growing incidence. LncRNAs and microRNAs control the occurrence and development process of osteosarcoma through ceRNA patterns. The LPAR3 gene is important in cancer cell proliferation, apoptosis and disease development. However, the regulatory mechanism of the ceRNA network through which LPAR3 participates in osteosarcoma has not been clarified. Herein, our study demonstrated that the AP003352.1/miR-141-3p axis drives LPAR3 expression to induce the malignant progression of osteosarcoma. First, the expression of LPAR3 is regulated by the changes in AP003352.1 and miR-141-3p. Similar to the ceRNA of miR-141-3p, AP003352.1 regulates the expression of LPAR3 through this mechanism. In addition, the regulation of AP003352.1 in malignant osteosarcoma progression depends to a certain degree on miR-141-3p. Importantly, the AP003352.1/miR-141-3p/LPAR3 axis can better serve as a multi-gene diagnostic marker for osteosarcoma. In conclusion, our research reveals a new ceRNA regulatory network, which provides a novel potential target for the diagnosis and treatment of osteosarcoma.

Competing endogenous RNA network analysis of the molecular mechanisms of ischemic stroke

BACKGROUND

Ischemic stroke (IS) is a serious neurological disease that largely results in long-term disability and death. Extensive evidence has indicated that the activation of inflammation and ferroptosis significantly contribute to the development of IS pathology. However, the underlying molecular mechanism remains unclear. In this study, we aimed to identify potential biomarkers associated with IS through the construction of a competing endogenous RNA (ceRNA) network and to investigate the possible inflammatory and ferroptosis-related molecular mechanisms.

RESULTS

We identified 178 differentially expressed target messenger RNAs (DETmRNAs) associated with IS. As revealed through enrichment analysis, the DEmRNAs were mainly enriched in the inflammatory signaling pathways and also related to ferroptosis mechanism. The CIBERSORT algorithm showed immune infiltration landscapes in which the naïve B cells, naïve T cells, and monocytes had statistically different numbers in the cerebral infarction group compared with the control group. A ceRNA network was constructed in this study involving 44 long non-coding RNAs (lncRNAs), 15 microRNAs (miRNAs), and 160 messenger RNAs (mRNAs). We used the receiver operating characteristic (ROC) analysis to identify three miRNAs (miR-103a-3p, miR-140-3p, and miR-17-5p), one mRNA (TLR4), and one lncRNA (NEAT1) as the potential key biomarkers of the ceRNA network. The key mRNA and lncRNA were shown to be highly related to the ferroptosis mechanism of IS. The expression of these key biomarkers was also further validated by a method of quantitative real-time polymerase chain reaction in SH-SY5Y cells, and the validated results were consistent with the findings predicted by bioinformatics.

CONCLUSION

Our results suggest that the ceRNA network may exert an important role in the inflammatory and ferroptosis molecular mechanisms of IS, providing new insight into therapeutic IS targets.

lncRNA SND1-IT1 delivered via intracerebral hemorrhage-derived exosomes affect the growth of human microglia by regulating the miR-124-3p/MTF1 axis

In this study, we investigated the effects of long noncoding RNA (lncRNA) SND1-IT1 on human microglia (HMC3 cells) delivered by intracerebral hemorrhage (ICH)-derived exosomes (ICH-exos) as well as a competitive endogenous RNA (ceRNA) network. Exosomes obtained from ICH plasma were characterized by nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), and western blot. RNA sequencing was performed to study the lncRNA transcriptome from ICH-exos and the healthy control-derived exosomes (HC-exos) and differentially expressed lncRNAs (DE-lncRNAs) were identified. HMC3 cells were treated with ICH-exos or transfected with pcDNA3.1-SND1-IT1, and then cell viability and apoptosis were measured. The ceRNA network (lncRNA SND1-IT1/miR-124-3p/messenger RNA MTF1) was chosen for further investigation. NTA, TEM, and western blot showed that exosomes were successfully separated and could be absorbed by HMC3 cells. The expression of lncRNA SND1-IT1 in ICH-exos was significantly higher than that of HC-exos (p < 0.05). In addition, lncRNA SND1-IT1 overexpression and ICH-exos significantly inhibited cell viability and enhanced apoptosis. A total of 162 DE-lncRNAs were identified by sequencing, and a ceRNA network was constructed. The dual-luciferase reporter gene indicated that lncRNA SND1-IT1, miR-124-3p, and MTF1 interacted with each other. Cell experiments showed that lncRNA SND1-IT1 affected the growth of HMC3 cells through miR-124-3p/MTF1. In conclusion, ICH-exos delivered lncRNA SND1-IT1 to HMC3 cells, and exosomal lncRNA SND1-IT1 can regulate cell viability and apoptosis to influence HMC3 cell growth via the SND1-IT1/miR-124-3p/MTF1 axis.

A systematic review of the research progress of non-coding RNA in neuroinflammation and immune regulation in cerebral infarction/ischemia-reperfusion injury

Cerebral infarction/ischemia-reperfusion injury is currently the disease with the highest mortality and disability rate of cardiovascular disease. Current studies have shown that nerve cells die of ischemia several hours after ischemic stroke, which activates the innate immune response in the brain, promotes the production of neurotoxic substances such as inflammatory cytokines, chemokines, reactive oxygen species and − nitrogen oxide, and mediates the destruction of blood-brain barrier and the occurrence of a series of inflammatory cascade reactions. Meanwhile, the expression of adhesion molecules in cerebral vascular endothelial cells increased, and immune inflammatory cells such as polymorphonuclear neutrophils, lymphocytes and mononuclear macrophages passed through vascular endothelial cells and entered the brain tissue. These cells recognize antigens exposed by the central nervous system in the brain, activate adaptive immune responses, and further mediate secondary neuronal damage, aggravating neurological deficits. In order to reduce the above-mentioned damage, the body induces peripheral immunosuppressive responses through negative feedback, which increases the incidence of post-stroke infection. This process is accompanied by changes in the immune status of the ischemic brain tissue in local and systemic systems. A growing number of studies implicate noncoding RNAs (ncRNAs) as novel epigenetic regulatory elements in the dysfunction of various cell subsets in the neurovascular unit after cerebral infarction/ischemia-reperfusion injury. In particular, recent studies have revealed advances in ncRNA biology that greatly expand the understanding of epigenetic regulation of immune responses and inflammation after cerebral infarction/ischemia-reperfusion injury. Identification of aberrant expression patterns and associated biological effects of ncRNAs in patients revealed their potential as novel biomarkers and therapeutic targets for cerebral infarction/ischemia-reperfusion injury. Therefore, this review systematically presents recent studies on the involvement of ncRNAs in cerebral infarction/ischemia-reperfusion injury and neuroimmune inflammatory cascades, and elucidates the functions and mechanisms of cerebral infarction/ischemia-reperfusion-related ncRNAs, providing new opportunities for the discovery of disease biomarkers and targeted therapy. Furthermore, this review introduces clustered regularly interspaced short palindromic repeats (CRISPR)-Display as a possible transformative tool for studying lncRNAs. In the future, ncRNA is expected to be used as a target for diagnosing cerebral infarction/ischemia-reperfusion injury, judging its prognosis and treatment, thereby significantly improving the prognosis of patients.

Integrated Analysis of Competitive Endogenous RNA Networks in Acute Ischemic Stroke

Background: Acute ischemic stroke (AIS) is a severe neurological disease with complex pathophysiology, resulting in the disability and death. The goal of this study is to explore the underlying molecular mechanisms of AIS and search for new potential biomarkers and therapeutic targets.

Methods: Integrative analysis of mRNA and miRNA profiles downloaded from Gene Expression Omnibus (GEO) was performed. We explored differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMirs) after AIS. Target mRNAs of DEMirs and target miRNAs of DEGs were predicted with target prediction tools, and the intersections between DEGs and target genes were determined. Subsequently, Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses, Gene set enrichment analysis (GSEA), Gene set variation analysis (GSVA), competitive endogenous RNA (ceRNA) (lncRNA-miRNA-mRNA) network, protein–protein interaction (PPI) network, and gene transcription factors (TFs) network analyses were performed to identify hub genes and associated pathways. Furthermore, we obtained AIS samples with evaluation of immune cell infiltration and used CIBERSORT to determine the relationship between the expression of hub genes and infiltrating immune cells. Finally, we used the Genomics of Drug Sensitivity in Cancer (GDSC) database to predict the effect of the identified targets on drug sensitivity.

Result: We identified 293 DEGs and 26 DEMirs associated with AIS. DEGs were found to be mainly enriched in inflammation and immune-related signaling pathways through enrichment analysis. The ceRNA network included nine lncRNAs, 13 miRNAs, and 21 mRNAs. We used the criterion AUC >0.8, to screen a 3-gene signature (FBL, RPS3, and RPS15) and the aberrantly expressed miRNAs (hsa-miR-125a-5p, hsa-miR-125b-5p, hsa-miR-148b-3p, and hsa-miR-143-3p) in AIS, which were verified by a method of quantitative PCR (qPCR) in HT22 cells. T cells CD8, B cells naïve, and activated NK cells had statistical increased in number compared with the acute cerebral infarction group. By predicting the IC50 of the patient to the drug, AZD0530, Z.LLNle.CHO and NSC-87877 with significant differences between the groups were screened out. AIS demonstrated heterogeneity in immune infiltrates that correlated with the occurrence and development of diseases.

Conclusion: These findings may contribute to a better understanding of the molecular mechanisms of AIS and provide the basis for the development of novel treatment targets in AIS.