Construction of CDKN2A-related competitive endogenous RNA network and identification of GAS5 as a prognostic indicator for hepatocellular carcinoma

BACKGROUND Competitive endogenous RNA(ceRNA)is an innovative way of gene expression modulation,which plays a crucial part in neoplasia.However,the intricacy and behavioral characteristics of the ceRNA network in hepatocellular carcinoma(HCC)remain dismal.AIM To establish a cyclin dependent kinase inhibitor 2A(CDKN2A)-related ceRNA network and recognize potential prognostic indicators for HCC.METHODS The mutation landscape of CDKN2A in HCC was first explored using the cBioPortal database.Differential expression analysis was implemented between CDKN2Ahigh and CDKN2Alow expression HCC samples.The targeted microRNAs were predicted by lncBasev3.0,and the targeted mRNAs were predicted by miRDB,and Targetscan database.The univariate and multivariate analysis were utilized to identify independent prognostic indicators.RESULTS CDKN2A was frequently mutated and deleted in HCC.The single-cell RNA-sequencing analysis revealed that CDKN2A participated in cell cycle pathways.The CDKN2A-related ceRNA network-growth arrest specific 5(GAS5)/miR-25-3p/SRY-box transcription factor 11(SOX11)was successfully established.GAS5 was recognized as an independent prognostic biomarker,whose overexpression was correlated with a poor prognosis in HCC patients.The association between GAS5 expression and methylation,immune infilt-ration was explored.Besides,traditional Chinese medicine effective components targeting GAS5 were obtained.CONCLUSION This CDKN2A-related ceRNA network provides innovative insights into the molecular mechanism of HCC formation and progression.Moreover,GAS5 might be a significant prognostic biomarker and therapeutic target in HCC.

Construction and Analysis of an LncRNA-miRNA-mRNA Network Based on Competitive Endogenous RNA Reveal miRNAs Potentially Involved in In-stent Restenosis after Percutaneous Coronary Intervention

Objective:Percutaneous coronary intervention is one of the most common procedures used for the invasive treatment of patients with coronary heart disease;the incidence of in-stent restenosis(ISR)after percutaneous coronary intervention is 5%to 15%.In this study,a competitive endogenous RNA(ceRNA)network was constructed to investigate potential mechanisms involved in ISR.Methods:The expression data for differentially expressed microRNAs(DEmiRNAs)and messenger RNAs(mRNAs)between patients with and without ISR were obtained using limma package.Long noncoding RNAs(lncRNAs)were predicted based on the DEmiRNAs using the miRDB,miRTarBase,and TargetScan databases.An ISR-specific ceRNA network was subsequently constructed and investigated.To verify the key miRNAs of ceRNA,patients with and without ISR were enrolled from Guangdong Provincial Hospital of Chinese Medicine between January 2017 and December 2018(n=8,respectively);plasma was collected from all enrolled patients.Results:Based on the raw data obtained from the Gene Expression Omnibus database,472 DEmiRNAs and 304 differentilly expressed messenger RNAs between patients with and without ISR were identified.A ceRNA network was constructed by combining 270 IncRNAs,3 miRNAs(miR-125,miR-140,and miR-206),and 4 mRNAs(STRADB,TKT,PCTP,and BTG2).The hub genes of the ceRNA network of ISR included the following:miR-125,miR-206,miR-140,PCDHB9,CASC2,BAK1P1,CSPG4P3Y,CSPG4P4Y,STRCP1,and GRIP2.Verification of miRNAs of ceRNA also showed that the expression of miR-206 was upregulated in patients with ISR vs.those without ISR(P<0.05).In contrast,the expression of miR-140 and miR-125 was downregulated in patients with ISR vs.those without ISR(P<0.05).Conclusions:This study constructed noncoding RNA-related ceRNA networks for ISR.The results indicated that miR-206,miR-125,and miR-140 may be biomarkers of ISR.

Comprehensive Analysis of the Molecular Mechanism for Gastric Cancer Based on Competitive Endogenous RNA Network

Objective: To explore the regulatory mechanism of competitive endogenous RNAs(ce RNA) in gastric cancer(GC) and to predict the prognosis of GC. Materials and Methods: Expression profiles of long noncoding RNAs(lnc RNAs), micro RNAs(mi RNAs), and m RNAs were obtained from The Cancer Genome Atlas platform. Differentially expressed RNAs(DERNAs) were screened to construct a lnc RNA-mi RNA-m RNA ce RNA network. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed on the ce RNA network-related differentially expressed m RNAs(DEm RNAs). Next, the DERNAs were subjected to Cox regression and survival analyses to identify crucial prognostic factors for patients with GC. Results: We detected 1029 differentially expressed lnc RNAs, 104 differentially expressed mi RNAs, and 1659 DEm RNAs in patients with GC. Next, we performed bioinformatic analysis to construct the lnc RNA-mi RNA-m RNA ce RNA network, which included 10 mi RNAs, 65 lnc RNAs, and 10 m RNAs. Subsequently, Kaplan Meier(K-M) analysis showed that the survival rate of the high-risk group was significantly lower than that of the low-risk group, and the area under the curve value of the receiver operating characteristic curve revealed that the polygenic model had good predictive ability. The results indicated that ADAMTS9-AS1, ATAD2, and CADM2 might be potential therapeutic targets and prognostic biomarkers for GC. Conclusions: Our study has implications for predicting prognosis and monitoring surveillance of GC and provides a new theoretical and experimental basis for the clinical prognosis of GC.

HOXA11-AS aggravates microglia-induced neuroinflammation after traumatic brain injury

Long noncoding RNAs(lnc RNAs)participate in many pathophysiological processes after traumatic brain injury by mediating neuroinflammation and apoptosis.Homeobox A11 antisense RNA(HOXA11-AS)is a member of the lnc RNA family that has been reported to participate in many inflammatory reactions;however,its role in traumatic brain injury remains unclear.In this study,we established rat models of traumatic brain injury using a weight-drop hitting device and injected LV-HOXA11-AS into the right lateral ventricle 2 weeks before modeling.The results revealed that overexpression of HOXA11-AS aggravated neurological deficits in traumatic brain injury rats,increased brain edema and apoptosis,promoted the secretion of proinflammatory factors interleukin-1β,interleukin-6,and tumor necrosis factorα,and promoted the activation of astrocytes and microglia.Microglia were treated with 100 ng/m L lipopolysaccharide for 24 hours to establish in vitro cell models,and then transfected with pc DNA-HOXA11-AS,mi R-124-3 p mimic,or sh-MDK.The results revealed that HOXA11-AS inhibited mi R-124-3 p expression and boosted MDK expression and TLR4-nuclear factor-κB pathway activation.Furthermore,lipopolysaccharide enhanced potent microglia-induced inflammatory responses in astrocytes.Forced overexpression of mi R-124-3 p or downregulating MDK repressed microglial activation and the inflammatory response of astrocytes.However,the mi R-124-3 p-mediated anti-inflammatory effects were reversed by HOXA11-AS.These findings suggest that HOXA11-AS can aggravate neuroinflammation after traumatic brain injury by modulating the mi R-124-3 p-MDK axis.This study was approved by the Animal Protection and Use Committee of Southwest Medical University(approval No.SMU-2019-042)on February 4,2019.

Screening of Biomarkers for Hypertension Susceptibility in Pregnancy

Objective:To study the differential lncRNA/mRNA expression profiles of placental tissues in patients with gestational hypertension,analyze their possible mechanisms of action,and explore their target genes and small molecule drug-related lncRNAs.Methods:Three patients with gestational hypertension who were treated in our hospital from May 2018 to May 2019 were selected as the research subjects and three healthy pregnant women who underwent a prenatal examination in the same hospital were selected as the control group.The placental tissues were taken from the patients.RNA-sequencing was performed to construct lncRNA/mRNA differential expression profiles;screening differentially expressed lncRNAs were used to predict target genes,and GO and KEGG enrichment analysis predicted the biological functions of target genes and the enriched signal pathways,respectively.Protein-protein interaction network,lncRNA-miRNAmRNA network,and differentially expressed genesmall molecule drug association networks were constructed.Results:RNA-seq analysis revealed 19 differentially expressed lncRNA(4 up-regulated;15 down-regulated)(P<0.05).Moreover,423 differentially expressed genes(DEGs)(84 up-regulated;339 downregulated)(P<0.05).GO and KEGG enrichment analysis found that gestational hypertension is mainly related to endothelial cell damage,inflammatory response,abnormal immune regulation,and abnormal trophoblast invasion.The PPI network and lncRNA-miRNA-mRNA network were constructed.Differentially expressed gene-drug small molecule prediction results found 19 pairs of differentially gene-small drug relationship pairs,mainly including antibody,inhibitor et al.Conclusion:Differently expressed lncRNAs in the placenta of patients with gestational hypertension can participate in the regulation of multiple biological functional levelrelated signal pathways through targeted regulation of their target genes,and play an important role in the occurrence and development of gestational hypertension.The predicted small molecule drug can be used as a reference for clinical treatment.

LncRNA-m18as1 competitively binds with miR-18a-5p to regulate follicle-stimulating hormone secretion through the Smad2/3 pathway in rat primary pituitary cells

Long noncoding RNAs(lncRNAs)are expressed in different species and different tissues,and perform different functions,but little is known about their involvement in the synthesis or secretion of follicle-stimulating hormone(FSH).In general,we have revealed lnc RNA-micro RNA(mi RNA)-messenger RNA(m RNA)interactions that may play important roles in rat primary pituitary cells.In this study,a new lncRNA was identified for the first time.First,we analyzed the gene expression of lncRNA-m18as1 in different tissues and different stages by reverse transcription-quantitative polymerase chain reaction(RT-qPCR)and observed the localization of lncRNA-m18as1 with fluorescence in situ hybridization,which indicated that this lncRNA was distributed mainly in the cytoplasm.Next,we used RT-qPCR and enzyme-linked immunosorbent assay(ELISA)to analyze the regulation of FSH synthesis and secretion after overexpression or knockdown of lncRNA-m18as1 and found that lncRNA-m18as1 was positively correlated with FSH synthesis and secretion.In addition,mothers against decapentaplegic homolog 2(Smad2)was highly expressed in our sequencing results.We also screened miR-18a-5p from our sequencing results as a miRNA that may bind to lncRNA-m18as1 and Smad2.We used RNA immunoprecipitation-qPCR(RIP-qPCR)and/or dual luciferase assays to confirm that lncRNA-m18as1 interacted with miR-18a-5p and miR-18a-5p interacted with Smad2.Fluorescence in situ hybridization(FISH)showed that lncRNA-m18as1 and miR-18a-5p were localized mainly in the cytoplasm.Finally,we determined the relationship among lncRNA-m18as1,miR-18a-5p,and the Smad2/3 pathway.Overall,we found that lncRNA-m18as1 acts as a molecular sponge of miR-18a-5p to regulate the synthesis and secretion of FSH through the Smad2/3 pathway.

The role of long noncoding RNAs in cancer metastasis

Signaling pathways are tightly controlled systems that regulate the appropriate timing of gene expression required for the differentiation of cells down a particular lineage essential for proper tissue development.Proliferation,apoptosis and metabolic pathways are just a few examples of the signaling pathways that require fine-tuning,so as to control the proper development of a particular tissue type or organ system.An estimated 70%of the genome is actively transcribed,only 2%of which codes for known protein-coding genes.Long noncoding RNAs(lncRNAs)in particular,are a large and diverse class of RNAs>200 nucleotides in length,and not translated into protein.lncRNAs are essential transcriptional and post-transcriptional regulators that control the expression of genes in a spatial,temporal,and cell context-dependent manner.The aberrant expression of lncRNAs is therefore linked with a number of chronic diseases including cardiac dysfunction,diabetes,and cancer.In this review,we highlight the specific role lncRNAs have in promoting the metastatic cascade across a number of epithelial cancer models.