Expression Profile and Potential Functions of Circulating Long Noncoding RNAs in Acute Ischemic Stroke in the Southern Chinese Han Population

Unveiling the role of HIST2H2AC in stroke through single-cell and transcriptome analysis

Stroke is a leading cause of death and disability, and genetic risk factors play a significant role in its development. Unfortunately, effective therapies for stroke are currently limited. Early detection and diagnosis are critical for improving outcomes and developing new treatment strategies. In this study, we aimed to identify potential biomarkers and effective prevention and treatment strategies for stroke by conducting transcriptome and single-cell analyses. Our analysis included screening for biomarkers, functional enrichment analysis, immune infiltration, cell-cell communication, and single-cell metabolism. Through differential expression analysis, enrichment analysis, and protein-protein interaction (PPI) network construction, we identified HIST2H2AC as a potential biomarker for stroke. Our study also highlighted the diagnostic role of HIST2H2AC in stroke, its relationship with immune cells in the stroke environment, and our improved understanding of metabolic pathways after stroke. Overall, our research provided important insights into the pathogenesis of stroke, including potential biomarkers and treatment strategies that can be explored further to improve outcomes for stroke patients.

Identification of significant m6A regulators and immune microenvironment characterization in ischemic stroke

The role of m6A modification in the regulation of the immune microenvironment (IME) of ischemic stroke (IS) is barely known. Thus, we aim to investigate the impact of m6A modification on the IME of IS and its diagnostic value in IS. We comprehensively assessed the m6A modification patterns, the relationship between these modification patterns and the characteristics of the IME. The m6A modification patterns of individual IS sample were quantified by m6Ascore. The performance of m6A phenotype-related genes as potential biomarkers was evaluated by the area under the receiver operating characteristic curve. Experimental validation was also performed by qRT-PCR. Six dysregulated m6A regulators were identified and a classification model consisting of four key m6A regulators (METLL3, RBMX, RBM15B, YTDHF3) could distinguish IS and healthy control samples well. METTL3 and YTHDF3 are closely related to circulating neutrophil abundance. Two distinct m6A modification patterns were determined which differed in immunocyte abundance. We also identified six m6A phenotype-related genes (APOBEC3A, PTMA, FCGR3A, LOC440926, LOC649946, and FTH1L11), and further explored their biological function. Among them, APOBEC3A, FCGR3A, and FTH1L11 were positively associated with neutrophil abundance. APOBEC3A and FCGR3A were stable diagnostic m6A-associated genes in both the discovery and validation cohorts. This study reveals that m6A modification plays a non-negligible role in the formation of a diversified and complex IME in IS. The m6A phenotype-related genes could be diagnostic biomarkers of IS.

In Silico Insights into Micro-Mechanism Understanding of Extracts of Taxus Chinensis Fruits Against Alzheimer's Disease

BACKGROUND

The taxus chinensis fruit (TCF) shows promises in treatment of aging-related diseases such as Alzheimer's disease (AD). However, its related constituents and targets against AD have not been deciphered.

OBJECTIVE

This study was to uncover constituents and targets of TCF extracts against AD.

METHODS

An integrated approach including ultrasound extractions and constituent identification of TCF by UPLC-QE-MS/MS, target identification of constituents and AD by R data-mining from Pubchem, Drugbank and GEO databases, network construction, molecular docking and the ROC curve analysis was carried out.

RESULTS

We identified 250 compounds in TCF extracts, and obtained 3,231 known constituent targets and 5,326 differential expression genes of AD, and 988 intersection genes. Through the network construction and KEGG pathway analysis, 19 chemicals, 31 targets, and 11 biological pathways were obtained as core compounds, targets and pathways of TCF extracts against AD. Among these constituents, luteolin, oleic acid, gallic acid, baicalein, naringenin, lovastatin and rutin had obvious anti-AD effect. Molecular docking results further confirmed above results. The ROC AUC values of about 87% of these core targets of TCF extracts was greater than 0.5 in the two GEO chips of AD, especially 10 targets with ROC AUC values greater than 0.7, such as BCL2, CASP7, NFKBIA, HMOX1, CDK2, LDLR, RELA, and CCL2, which mainly referred to neuron apoptosis, response to oxidative stress and inflammation, fibroblast proliferation, etc.Conclusions:The TCF extracts have diverse active compounds that can act on the diagnostic genes of AD, which deserve further in-depth study.

LncRNA SNHG14 is beneficial to oxygen glucose deprivation/reoxygenation-induced neuro-2a cell injury via mir-98-5p sequestration-caused BCL2L13 upregulation

BACKGROUND

The deregulation of long non-coding RNA (lncRNA) is associated with diverse human disorders, including cerebral ischemia/reperfusion injury (CI/RI). LncRNA SNHG14 was reported to function in CI/RI. Whereas, molecular mechanisms regulated by SNHG14 are not fully unveiled.

METHODS

Mice subjected to middle cerebral artery occlusion/reperfusion (MCAO/R) were used as CI/RI animal models. Neuro-2a (N2A) cells subjected to oxygen glucose deprivation/reoxygenation (OGD/R) were used as CI/RI cell models. The expression of SNHG14, miR-98-5p and BCL2 like 13 (BCL2L13) was examined using quantitative real-time PCR (qPCR) or western blot. Apoptosis was monitored by flow cytometry assay. Apoptosis-related markers and endoplasmic reticulum (ER) stress-related markers were quantified by western blot. Inflammatory factors and oxidative stress were detected using matched commercial kits. The predicted relationship between miR-98-5p and SNHG14 or BCL2L13 was validated by dual-luciferase reporter assay, RIP assay and pull-down assay.

RESULTS

The high expression of SNHG14 was monitored in MCAO/R-treated mice and OGD/R-treated N2A cells. OGD/R-induced N2A cell apoptosis, ER stress, inflammation and oxidative stress were attenuated by SNHG14 knockdown. SNHG14 targeted miR-98-5p to positively regulate BCL2L13 expression. Inhibition of miR-98-5p recovered cell apoptosis, ER stress, inflammation and oxidative stress that were repressed by SNHG14 knockdown. Overexpression of BCL2L13 enhanced cell apoptosis, ER stress, inflammation and oxidative stress that were repressed by miR-98-5p enrichment.

CONCLUSIONS

SNHG14 knockdown alleviated OGD/induced N2A cell apoptosis, ER stress, inflammation and oxidative stress by depleting BCL2L13 via increasing miR-98-5p.

Long noncoding RNAs regulated spermatogenesis in varicocele-induced spermatogenic dysfunction

Objectives

To evaluate the expression, potential functions and mechanisms of long noncoding RNAs (lncRNAs) in the pathogenesis of varicocele (VC)‐induced spermatogenic dysfunction.

Materials and Methods

We established a rat model with left experimental VC and divided rats into the sham group, the VC group, and the surgical treatment group (each group, n = 10). Haematoxylin and eosin (HE) staining and sperm quality were analysed to evaluate spermatogenesis function. LncRNA expression profiles were analysed using lncRNA‐Seq (each group n = 3) and validated using quantitative real‐time polymerase chain reaction (each group n = 10). Correlation analysis and gene target miRNA prediction were used to construct competing endogenous RNA network. The regulated signalling pathway and spermatogenic dysfunction of differentially expressed lncRNAs (DE lncRNAs) were validated by Western blot.

Results

HE detection and sperm quality analysis showed that VC could induce spermatogenic dysfunction. Eight lncRNAs were upregulated and three lncRNAs were downregulated in the VC group compared with the sham group and surgical treatment group. The lncRNA of NONRATG002949.2, NONRATG001060.2, NONRATG013271.2, NONRATG022879.2, NONRATG023424.2, NONRATG005667.2 and NONRATG010686.2 were significantly negatively related to sperm quality, while NONRATG027523.1, NONRATG017183.2 and NONRATG023747.2 were positively related to sperm quality. The lncRNAs promote spermatogenic cell apoptosis and inhibit spermatogonia and spermatocyte proliferation and meiotic spermatocytes by regulating the PI3K–Akt signalling pathway.

Conclusion

DE lncRNAs may be potential biomarkers for predicting the risk of spermatogenic dysfunction in VC and the effect of surgical repair. These DE lncRNAs promote spermatogenic dysfunction by regulating the PI3K–Akt signalling pathway.

LncRNA AC136007.2 alleviates cerebral ischemic-reperfusion injury by suppressing autophagy

Differential expression and diagnostic significance of the long noncoding RNA (lncRNA) AC136007.2 has been reported in patients with acute ischemic stroke (AIS). However, its role on disease progression and outcome remains unclear. Here, we employed an oxygen-glucose deprivation/reperfusion (OGD/R) model in neuronal SH-SY5Y cells and performed middle cerebral artery occlusion (MCAO) surgery in rats to investigate the function of AC136007.2 in ischemia-reperfusion (I/R) injury. AC136007.2 expression was determined by RT-qPCR and cell viability was examined using CCK-8, Edu, LDH, and apoptosis assays. Pro-inflammatory cytokine expression was assessed using ELISA. OGD/R downregulated AC136007.2 expression in SH-SY5Y cells, decreased viability by inducing apoptosis, and stimulated secretion of TNF-α, IL-6, and IL-1β. In turn, lentivirus-mediated AC136007.2 overexpression significantly reversed these phenomena. LC3 immunofluorescence and western blotting analyses of LC3-I/II and Beclin-1 expression and AMPK/mTOR phosphorylation status showed that AC136007.2 suppressed autophagy in SH-SY5Y cells via inactivation of AMPK/mTOR signaling. Notably, incubation with the AMPK activator AICAR abolished the pro-survival effect of AC136007.2 upon OGD/R treatment. Importantly, intraventricular injection of AC136007.2 significantly reduced cerebral infarction and brain edema in MCAO rats, as shown by TTC staining and water content measurements. We conclude that AC136007.2 alleviates cerebral I/R injury by suppressing AMPK/mTOR-dependent autophagy.

Construction of lncRNA-Mediated ceRNA Network for Investigating Immune Pathogenesis of Ischemic Stroke

Ischemic stroke (IS) is a common and serious neurological disease. Extensive evidence indicates that activation of the immune system contributes significantly to the development of IS pathology. In recent years, some long non-coding RNAs (lncRNAs), acting as competing endogenous RNAs (ceRNAs), have been reported to affect IS process, especially the immunological response after stroke. However, the roles of lncRNA-mediated ceRNAs in immune pathogenesis of IS are not systemically investigated. In the present study, we generated a global immune-related ceRNA network containing immune-related genes (IRGs), miRNAs, and lncRNAs based on experimentally verified interactions. Further, we excavated an IS immune-related ceRNA (ISIRC) network through mapping significantly differentially expressed IRGs, miRNAs, and lncRNAs of patients with IS into the global network. We analyzed the topological properties of the two networks, respectively, and found that lncRNA NEAT1 and lncRNA KCNQ1OT1 played core roles in aforementioned two immune-related networks. Moreover, the results of functional enrichment analyses revealed that lncRNAs in the ISIRC network were mainly involved in several immune-related biological processes and pathways. Finally, we identified 17 lncRNAs which were highly related to the immune mechanism of IS through performing random walk with restart for the ISIRC network. Importantly, it has been confirmed that NEAT1, KCNQ1OT1, GAS5, and RMRP could regulate immuno-inflammatory response after stroke, such as production of inflammatory factors and activation of the immune cells. Our results suggested that lncRNAs exerted an important role in the immune pathogenesis of IS and provided a new strategy to do research on IS.

Identification of key genes in lung adenocarcinoma based on a competing endogenous RNA network

Lung adenocarcinoma (LUAD) is the most commonly diagnosed type of lung cancer and exhibits a high morbidity. The present study aimed to investigate the long non-coding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) mechanisms in LUAD. The receptor activity modifying protein 2-antisense RNA 1 (RAMP2-AS1) was identified using GSE113852 and GSE130779 datasets downloaded from the Gene Expression Omnibus database, and the downregulation of RAMP2-AS1 was the most significant in LUAD. In addition, microRNA (miR)-296-5p was identified to bind to RAMP2-AS1 via bioinformatics analysis. Subsequently, CD44, cyclin D3 (CCND3), neurocalcin δ (NCALD), microtubule actin crosslinking factor 1 (MACF1) and potassium channel tetramerization domain containing 15 were obtained by intersecting the predicted target genes of miR-296-5p and 368 differentially expressed mRNAs in LUAD. According to the Gene Expression Profiling Interactive Analysis and UALCAN databases, these five mRNAs were downregulated in LUAD, and their expression levels were positively correlated with those of RAMP2-AS1. CD44, CCND3, NCALD and MACF1 were selected as key mRNAs in LUAD based on prognostic analyses. Furthermore, functional enrichment analyses were performed and an interaction network was constructed to reveal the functions of the RAMP2-AS1-associated ceRNA in LUAD. The results indicated that the functions were mainly enriched in generic transcription pathways, cyclin D-associated events in G₁ and epithelial stromal transformation. Reverse transcription-quantitative PCR assays revealed that RAMP2-AS1, CD44, CCND3, NCALD and MACF1 expression was lower in tumor tissues than in normal tissues, while miR-296-5p expression was higher in tumor tissues compared with in normal tissues. The association between RAMP2-AS1 and MACF1 was further confirmed using in vitro experiments. Overall, the present results indicated that RAMP2-AS1, miR-296-5p, CD44, CCND3, NCALD and MACF1 may be involved in LUAD progression and may therefore serve as potential biomarkers and provide a theoretical basis for the study of the pathogenesis of LUAD.

Expression profile and bioinformatics analysis of circular RNAs in acute ischemic stroke in a South Chinese Han population

Recent studies have found that circular RNAs (circRNAs) play crucial roles not only in the normal growth and the development of different tissues and organs but also in the pathogenesis and progression of various disorders. However, the expression patterns and the function of circRNAs in acute ischemic stroke (AIS) in the South Chinese Han population are unclear. In the present study, RNA sequencing (RNA-seq) data was generated from 3 AIS patients and 3 healthy controls. The circRNAs were detected and identified by CIRI2 and Find_circ software. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analyses were used to detect the expression of circRNAs. Meanwhile, the potential diagnostic value of the selected circRNAs for AIS was assessed by generating receiver operating characteristic (ROC) curve with area under curve (AUC). The bioinformatic analysis of the host genes of differentially expressed (DE) circRNAs was performed by gene ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, KOBAS for pathway analysis and regulatory network analysis. miRNA-circRNA and miRNA-mRNA interactions were predicted by using TargetScan, miRanda and starBase. CircRNA-miRNA-mRNA interaction networks were created with Cytoscape. Our result showed that there were 2270 DE circRNAs between AIS patients and healthy controls. Among them, 659 were found upregulated and 1611 were downregulated. Bioinformatic analysis showed that the DE circRNAs were related to the following biological processes: endocytosis, energy metabolism, apoptosis, FoxO signaling pathway, platelet activation, neurotrophin signaling pathway and VEGF signaling pathway, which may be associated with the pathological of AIS. Three randomly selected circRNAs were successfully validated by qRT-PCR. The results show that hsa_circ_0005548 was significantly upregulated, while hsa_circ_0000607 and hsa_circ_0002465 were significantly downregulated in AIS. Furthermore, the AUC values for hsa_circ_005548, hsa_circ_0000607 and hsa_circ_0002465 were 0.51, 0.75 and 0.69, respectively, suggesting that hsa_circ_0000607 and hsa_circ_0002465 could be potential biomarkers for AIS. In addition, Bcl2 was predicted to be a direct target of miR-337-3p, and hsa_circRNA_0000607 was predicted to act as a sponge for miR-337-3p. Thus, hsa_circ_0000607 may be involved in AIS by regulating the miR-337-3p/Bcl2 axis. Collectively, our findings indicate that numerous dysregulated circRNAs may play pivotal functional roles in AIS and hsa_circ_0000607 may play a crucial role in the pathogenesis and progression of AIS by regulating the miR-337-3p/Bcl2 axis.

LncRNA SNHG5: A new budding star in human cancers

Long non-coding RNA (LncRNA) belongs to non-coding RNAs longer than 200 nucleic acids. More and more studies have revealed that lncRNA can participate in the occurrence and pathophysiology of diseases, especially in cancers. Although research on lncRNAs has doubled year by year, little is known about the specific regulatory mechanisms of lncRNAs in diseases. The main purpose of this review is to explore the molecular mechanism and clinical significance of SNHG5 in cancers. We systematically search Pubmed to obtain relevant literature on SNHG5. In this review, the functional role, molecular mechanism, and clinical significance of SNHG5 in human cancers are described in detail. Small nucleolar RNA host gene 5 (SNHG5) has been shown to be involved in the development and tumorigenesis of a variety of cancers (colorectal, bladder, gastric, endometrial, acute lymphocytic leukemia, osteosarcoma, etc.). Its disorder is closely related to metastasis, pathological staging, and prognosis. LncRNA SNHG5 might be a potential and novel diagnostic marker for cancer patients, a target for molecular targeted therapy, and a prognostic diagnostic marker.