Endogenous RNA Regulatory Network Research Articles

LncRNA LINC00473 is involved in the progression of invasive pituitary adenoma by upregulating KMT5A via ceRNA-mediated miR-502-3p evasion

Long noncoding RNAs (lncRNAs) and their crosstalks with other RNAs have been revealed to be closely related to tumorigenesis and development, but their role in invasive pituitary adenoma (IPA) remains largely unclear. In our study, LINC00473 was identified as the most upregulated lncRNA in IPA by whole transcriptome RNA sequencing (RNA-Seq). Further, its related signaling pathway LINC00473/miR-502-3p/KMT5A was obtained by constructing a competing endogenous RNA (ceRNA) regulatory network. Their expression in IPA and non-invasive pituitary adenoma (NIPA) tissues was verified by qRT-PCR. Then the effects and mechanisms of LINC00473 and its ceRNA network on the proliferation of pituitary adenoma (PA) cells were confirmed by gene overexpression or silencing techniques combined with CCK-8 assay, EdU staining, flow cytometry assay, and double luciferase reporter gene assay in PA cell lines AtT-20 and GT1-1 in vitro and in a xenograft model in vivo. LINC00473 is overexpressed in IPA and can promote PA cells proliferation. Mechanistically, overexpression of LINC00473 restricts miR-502-3p through the ceRNA mechanism, upregulates KMT5A expression, and promotes the expression of cyclin D1 and CDK2, which is conducive to the cell cycle process, thereby promoting the proliferation of PA cells, involving IPA progression.

Integrated study of circRNA, lncRNA, miRNA, and mRNA networks in mediating the effects of testicular heat exposure.

The World Health Organization has recognized that testicular function is temperature dependent. Testicular heat exposure caused by occupational factors, lifestyle, and clinical diseases can lead to different degrees of reproductive problems. The aim of this study was to reveal the transcriptional regulatory network and its potential crucial roles in mediating the effects of testicular heat exposure. Testicular tissue was collected from a group of mice subjected to scrotal heat exposure as well as a control group. RNA was isolated from both groups and used for high-throughput sequencing. Using differential transcriptome expression analysis, 172 circRNAs, 279 miRNAs, 465 lncRNAs, and 2721 mRNAs were identified as significantly differentially expressed in mouse testicular tissue after heat exposure compared with the control group. Through Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, differentially expressed lncRNAs and mRNAs were found to have potentially important functions in meiotic cell cycle (GO:0051321), cytoplasm (GO:0005737), membrane raft (GO:0045121), MAPK signaling (mmu04010), purine metabolism (mmu00230), and homologous recombination (mmu03440). Some of the most upregulated and downregulated lncRNAs and circRNAs were predicted to be associated with numerous miRNAs and mRNAs through competing endogenous RNA regulatory network analysis, whichwere validated with molecular biology experiments. This research provides high-throughput sequencing data of a testicular heat exposure model and lays the foundation for further study on circRNAs, miRNAs, and lncRNAs that are involved in male reproductive diseases related to elevated testicular temperature.

CeRNA regulatory network of FIH inhibitor as a radioprotector for gastrointestinal toxicity by activating the HIF-1 pathway

Given the relentless renewal ability of intestinal crypt-base stem cells, small intestine in the gastrointestinal (GI) tract is more vulnerable to radiation-induced disruption. Through promoting epithelial integrity and reducing intracellular reactive oxygen species (ROS) levels, hypoxia-inducible factors (HIFs) have been proved to exhibit radioprotective effects in the GI tract. Therefore, enhancing stability or transcriptional activity of HIFs might be a therapeutic strategy for developing radioprotectors. Factor inhibiting HIF (FIH or HIF-1AN) can hamper transcriptional capacity of HIF-1α via interacting with Asn803 in its C-terminal domain. Previously, we discovered promoting HIF-1α transcriptional activity in vitro by FIH inhibitor-N-oxalyl-D-phenylalanine (NOFD) exerts radioprotection on cells. However, the radioprotective effect of FIH inhibitor on the GI tract and its competing endogenous RNA (ceRNA) regulatory network from the FIH/HIF axis has never been addressed. Here we verified radioprotection of NOFD for the GI tract by an animal model and performed whole-transcriptome analysis to fully elucidate the radioprotective mechanism from the FIH/HIF axis against GI syndrome. We identified two novel circular RNAs (circRNAs) (circRNA_2909 and circRNA_0323) and two long non-coding RNAs (lncRNAs) (NONMMUT140549.1 and NONMMUT148249.1) that promote expression of HIF1A and NOS2 in the HIF-1 pathway by sponging microRNAs (miRNAs), especially mmu-miR-92a-1-5p. The de-repression of HIF-1α transcriptional capacity by inhibiting FIH proteomic activity suggests a new therapeutic strategy in alleviating radiation-induced GI syndrome.

Identification of Competing Endogenous RNA and Micro-RNA Profiles and Regulatory Networks in 4-Nonylphenol-induced Impairment of Sertoli Cells.

The xenoestrogens nonylphenols (NPs), which are materials used in the plastic polymer industry, are considered endocrine disruptors in a wide range of organisms. Studies have shown that human health problems, such as infertility and reproductive toxicology, are linked with NPs. However, the mechanism by which NPs interfere with male reproduction is not fully elucidated. Here, we found that 4-NP can result in male reproductive impairment and reduce androgen receptor (AR) protein levels in rat sertoli cells in vitro and in vivo. Moreover, we performed RNA sequencing to assess the differential expression of ceRNAs in rat primary sertoli cells treated with 4-NP. Bioinformatics methods, such as Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) database and ceRNA functional network analyses, were used to investigate the sequencing data and gain further understanding of the biological processes. Our analysis revealed a core set of mRNAs (Ar, Atf6 and Cbp), and circRNAs (circ673, circ1377, circ1789, and circPTEN) that were selected and validated by RT-qPCR. In addition, the head-to-tail splicing of circ673, circ1377, circ1789, and circPTEN was identified by Sanger sequencing. These findings provide the first insight into the ceRNA expression profiles of rat sertoli cells and reveal that ceRNAs participate in 4-NP-induced impairment of sertoli cell function, thereby indicating potential therapies for both reproductive toxicology and male infertility.

Signature RNAS and related regulatory roles in type 1 diabetes mellitus based on competing endogenous RNA regulatory network analysis

BackgroundOur study aimed to investigate signature RNAs and their potential roles in type 1 diabetes mellitus (T1DM) using a competing endogenous RNA regulatory network analysis.MethodsExpression profiles of GSE55100, deposited from peripheral blood mononuclear cells of 12 T1DM patients and 10 normal controls, were downloaded from the Gene Expression Omnibus to uncover differentially expressed long non-coding RNAs (lncRNAs), mRNAs, and microRNAs (miRNAs). The ceRNA regulatory network was constructed, then functional and pathway enrichment analysis was conducted. AT1DM-related ceRNA regulatory network was established based on the Human microRNA Disease Database to carry out pathway enrichment analysis. Meanwhile, the T1DM-related pathways were retrieved from the Comparative Toxicogenomics Database (CTD).ResultsIn total, 847 mRNAs, 41 lncRNAs, and 38 miRNAs were significantly differentially expressed. The ceRNA regulatory network consisted of 12 lncRNAs, 10 miRNAs, and 24 mRNAs. Two miRNAs (hsa-miR-181a and hsa-miR-1275) were screened as T1DM-related miRNAs to build the T1DM-related ceRNA regulatory network, in which genes were considerably enriched in seven pathways. Moreover, three overlapping pathways, including the phosphatidylinositol signaling system (involving PIP4K2A, INPP4A, PIP4K2C, and CALM1); dopaminergic synapse (involving CALM1 and PPP2R5C); and the insulin signaling pathway (involving CBLB and CALM1) were revealed by comparing with T1DM-related pathways in the CTD, which involved four lncRNAs (LINC01278, TRG-AS1, MIAT, and GAS5-AS1).ConclusionThe identified signature RNAs may serve as important regulators in the pathogenesis of T1DM.

Identification of crucial noncoding RNAs and mRNAs in hypertrophic scars via RNA sequencing.

Hypertrophic scarring (HS) is a dermal fibroproliferative disorder characterized by excessive deposition of collagen and other extracellular matrix components. The aim of this study is to explore crucial long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) associated with HS and provide a better understanding of the molecular mechanism of HS. To investigate the lncRNA, circRNA and mRNA expression profiles, we performed RNA sequencing of human HS and normal skin tissues. After the identification of differentially expressed mRNAs (DEmRNAs), lncRNAs (DElncRNAs) and circRNAs (DEcircRNAs), we performed functional enrichment of DEmRNAs. Further on, we constructed DElncRNA/DEcircRNA–DEmRNA coexpression networks and competing endogenous RNA regulatory networks, and performed functional analyses of the DEmRNAs in the constructed networks. In total, 487 DEmRNAs, 92 DElncRNAs and 17 DEcircRNAs were identified. DEmRNAs were significantly enriched in processes such as collagen fibril organization, extracellular matrix–receptor interaction and the phosphatidylinositol 3‐kinase (PI3K)–Akt signaling pathway. In addition, we detected 580 DElncRNA–DEmRNA and 505 DEcircRNA–DEmRNA coexpression pairs. The competing endogenous RNA network contained 18 circRNA–microRNA (miRNA) pairs, 18 lncRNA–miRNA pairs and 409 miRNA–mRNA pairs, including 10 circRNAs, 5 lncRNAs, 15 miRNAs and 160 mRNAs. We concluded that MIR503HG/hsa‐miR‐204‐3p/ACAN, MIR503HG/hsa‐miR‐431‐5p/TNFRSF9, MEG3/hsa‐miR‐6884‐5p/ADAMTS14, AC000035.1‐ADAMTS14 and hsa_circ_0069865‐COMP/ADAM12 interaction pairs may play a central role in HS.

Competitive Endogenous RNAs Participate in Benzene Hematotoxicity by Promoting Ferroptosis

Background: Benzene exposure leads to hematotoxicity, but we still lack sensitive biomarkers for its monitoring and prevention owing to the complex mechanisms. We previously constructed a competitive endogenous RNA(ceRNA) regulatory network (Lnc-TC-miR-142-5p-CUL4B), which may be potential biomarkers for benzene hematotoxicity, and further explored the mechanism of these ceRNAs mediating benzene toxicity. Methods: Peripheral hemogram and ceRNA expression were detected in benzene-exposed workers and controls. Cell viability, ultrastructural changes, lipid ROS and expressions of cell ferroptosis related genes GPX4, SLC7A11 and FTH were examined to detect the occurrence of benzene metabolite 1, 4-benzoquinone (1,4-BQ)-induced ferroptosis. Lentiviral transfected cell models of regulating Lnc-TC, miR-142-5p and CUL4B were constructed to explore their regulatory relationships and roles in 1,4-BQ induced ferroptosis. Results: We confirmed that the expression of ceRNAs Lnc-TC-miR-142-5p-CUL4B were significantly changed and associated with decreased blood cell counts in benzene-exposed workers compared with controls. 1,4-BQ promoted cell ferroptosis characterized by mitochondria damages, increased lipid ROS level, and down-regulation of GPX4, SLC7A11 and FTH. Lnc-TC-miR-142-5p-CUL4B ceRNA network regulated 1,4-BQ-induced cell ferroptosis by targeting GPX4, thus participated in benzene hematotoxicity. Conclusion: The Lnc-TC-miR-142-5p-CUL4B ceRNA network mediated benzene hematotoxicity by promoting ferroptosis, and these ceRNAs may be potential biomarkers for early monitoring and warning of disease. Funding Information: This research was supported by the Beijing Natural Science Foundation Program and Scientific Research Key Program of Beijing Municipal Commission of Education (KZ201810025032), the Support Project of High-level Teachers in Beijing Municipal Universities in the Period of 13th Five-year Plan (CIT&TCD20170323) and National Culture Science Foundation of China (81773397). Declaration of Interests: The authors of this article declare that there are no conflicts of interest. Ethics Approval Statement: The study was approved by Ethics committee of Capital Medical University, each individual signed an informed consent form.

LncRNA-Associated Competitive Endogenous RNA Regulatory Network in an Aβ25-35-Induced AD Mouse Model Treated with Tripterygium Glycoside.

BackgroundTripterygium glycoside (TG) has been suggested to have protective effects on the diseases of the central nervous system including Alzheimer’s disease (AD). The mechanisms involving lncRNA-associated competing endogenous RNAs (ceRNAs) were shown to play important roles in the development of AD. However, the ceRNA mechanism of TG in treating AD is still unknown. Thus, we aimed to explore the ceRNA mechanism in the treatment of AD with TG.MethodsA total of 32 C57BL/6J mice were administered 3 µL of Aβ25-35 (dual side, 1 mg/mL) by a single stereotactic injection in the brain to conduct AD mouse model. AD mouse models were randomly selected and divided into the AD+normal saline (NS) group (n=16) and the AD+TG group (n=16). The expression data of lncRNAs, mRNAs, and miRNAs in the hippocampus of mice from AD+NS group (n=3) and the AD+TG group (n=3) were obtained by microarray analysis. The MuTaME method was used to predict the ceRNA regulatory network. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using the DAVID database. A protein–protein interaction (PPI) network was constructed by using STRING software.ResultsTG can significantly improve spatial memory and inhibit the production of p-tau in an Aβ25-35-induced AD mouse model. A total of 661 differentially expressed lncRNAs, 503 mRNAs, and 13 miRNAs were identified. A ceRNA network involving the top 200 mRNA-miRNA-lncRNA pairs with 16 lncRNAs, 11 miRNAs, and 52 mRNAs was visualized. And a PPI network complex filtered 26 gene nodes in DEGs was predicted.ConclusionWe have identified 503 DEGs, 661 DElncRNAs, and 13 DEmiRNAs during treatment with TG in Aβ25-35-induced AD mouse model. A ceRNA network based on the DElncRNAs, DEmRNAs, and DEmiRNAs was conducted, which provided new insight into the lncRNA-mediated ceRNA regulatory mechanisms underlying the effects of TG in the treatment of AD.

Expression profiles and potential functions of long noncoding RNAs and mRNAs in autoimmune pulmonary alveolar proteinosis patients.

Autoimmune pulmonary alveolar proteinosis (APAP) is a rare lung disease that may be associated with surfactant overaccumulation. To assess the function of long noncoding RNAs (lncRNAs) in APAP, we performed microarray analyses to identify differentially expressed (DE) lncRNAs and mRNAs between peripheral blood samples from five APAP patients and five healthy volunteers. In total, 12459 DE lncRNAs and 9331 DE mRNAs were identified in APAP patient samples. A qRT-PCR validation of 20 DE lncRNAs and 20 mRNAs indicated that 12 DE lncRNAs may be involved in the pathogenesis of APAP. Coding and noncoding co-expression (CNC) and competing endogenous RNA (ceRNA) regulatory networks were constructed with these 12 DE lncRNAs. Gene Ontology analysis of the downregulated mRNAs and the CNC network revealed that “ubiquitin-like protein transferase activity” was suppressed in APAP patient samples. Kyoto Encyclopedia of Genes and Genomes analysis demonstrated that the “MAPK signaling pathway” was enriched in the ceRNA network. Gene Ontology analysis also indicated that mRNAs involved in many transmembrane ion transport processes were upregulated in APAP patients. The DE lncRNAs and mRNAs discovered in this study have elucidated the pathogenesis of APAP, and the CNC and ceRNA networks have provided novel insights for future functional research.

Identification of circRNA-miRNA-mRNA Regulatory Network in Bladder Cancer by Integrated Analysis

Introduction: Bladder cancer (BC) is a common malignant tumor in the urinary system with high mortality and recurrence rates. This study sought to identify crucial circular RNAs (circRNAs) associated with BC. Methods: The mRNA, miRNA, and circRNA expression profiles of BC were downloaded from GEO database. The differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), and circRNAs (DEcircRNAs) were identified using bioinformatics method. Combining circRNA-miRNA pairs with miRNA-mRNA pairs, the competing endogenous RNA (ceRNA; DEcircRNA-DEmi­RNA-DEmRNA) regulatory network was constructed. Functional annotation of host gene of DEcircRNAs and DEmRNAs in ceRNA regulatory network were performed. qRT-PCR validation was performed. Results: A total of 4,003 DEmRNAs, 25 DEmiRNAs, and 119 DEcircRNAs were obtained. The ceRNA network contained 18 circRNA-miRNA pairs and 699 mi­RNA-mRNA pairs, including 17 circRNAs, 4 miRNAs, and 624 mRNAs. Functional annotation of DEmRNAs in ceRNA regulatory network revealed that these DEmRNAs were significantly enriched in glycerolipid metabolism, p53 signaling pathway, and oocyte meiosis. Except for hsa_circ_0028173, expression of the others in the qRT-PCR results was consistent with that in our integrated analysis, generally. Conclusion: We speculate that hsa_circ_0008035/hsa-miR-107/MSRB3 and hsa_circ_0028173/hsa-miR-338-3p/TPX2/GATA3 interaction pairs may play a vital role in BC.

Integrated Analysis of ceRNA Regulatory Network Associated With Tumor Stage in Cervical Cancer.

ObjectiveTo analyze the abnormally expressed genes involved in cervical cancer occurrence and development.Materials and MethodsIntegrated bioinformatics methods were used to analyze differentially expressed (DE) RNAs, including mRNAs, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs), in stage I, II, III, and IV cervical cancer patients from the TCGA database to fully reveal the dynamic changes caused by cervical cancer.ResultsFirst, DE RNAs in cervical cancer tissues from stage I, II, III, and IV patients and normal cervical tissues were identified and divided into different profiles. Several DE RNA profiles were down-regulated or up-regulated in stage I, III, and IV patients. GO and KEGG analysis of DE mRNA profile 1, 2, 4, 5, 6 and 22 which were significantly down-regulated or up-regulated showed that DE mRNAs are involved in cell division, DNA replication, cell adhesion, the positive and negative regulation of RNA polymerase ll promoter transcription. Besides, DE RNA profiles with significant differences in patient stages were analyzed to perform a competing endogenous RNA (ceRNA) regulatory network of lncRNA, miRNA, and mRNA. The protein-protein interaction (PPI) network of DE mRNAs in the ceRNA regulatory network was also constructed. The network had nine central genes (up-regulated genes: CDKN2A, GSK3B, BIRC5, CYCS, MAD2L1; down-regulated genes: PTEN, FOXO3, CCND2, TGFBR2). Survival analysis found that 5 lncRNAs, 9 mRNAs, and 4 miRNAs can be used as prognostic indicators of cervical cancer. Finally, combined with cluster analysis results, we further screened 2 DE RNAs (AMZ2P1 and HDAC5) using clinical samples, suggesting that AMZ2P1, and HDAC5 may act as diagnostic biomarkers for the development of cervical cancer.ConclusionThis research provides new effective targets and reliable biological markers for the diagnosis and prognosis of cervical cancer.

Differential mRNA expression profile and competitive endogenous RNA regulatory network in osteoarthritis

Differential mRNA expression profile and competitive endogenous RNA regulatory network in osteoarthritis

Bioinformatics identification of the candidate microRNAs and construction of a competing endogenous RNA regulatory network in lacrimal gland adenoid cystic carcinoma high-grade transformation.

Adenoid cystic carcinoma of the lacrimal gland (LACC) is a major orbital malignancy. The recurrence rate and mortality rate are higher in LACC high-grade transformation (LACC-HGT) compared with in LACC. The present study aimed to identify the candidate microRNAs (miRNAs/miRs) and construct a competing endogenous RNA (ceRNA) regulatory network for LACC-HGT. A miRNA microarray on paraffin-embedded tissues was performed to identify the differentially expressed miRNAs (DEMs) of LACC-HGT. The overlap with the salivary adenoid cystic carcinoma miRNA/RNA sequencing dataset in the Gene Expression Omnibus was used to identify candidate miRNAs. In order to construct a ceRNA regulatory network of LACC-HGT, a microarray of mRNA and circRNA in primary cell lines was performed. The circRNAs and genes with high expression in LACC-HGT were predicted as targeting miRNAs, and the circRNA-miRNA-mRNA regulatory network was constructed. miR-140-3p was identified as part of the ceRNA network and as a candidate miRNA, therefore this was further analyzed using reverse transcription-quantitative (RT-q)PCR. Overall, the Agilent Human microarray analysis identified a total of 16 DEMs from the LACC-HGT paraffin-embedded tissues. A total of 653 DECs and 9,566 DEGs of LACC-HGT primary cell lines were screened via the microarray of mRNA and circRNA. The ceRNA regulatory network was constructed using the cross-binding of circRNA-miRNA, miRNA-mRNA and the downregulated miRNAs in LACC-HGT to clearly demonstrate the circRNA-miRNA-mRNA interaction relationship. RT-qPCR results confirmed that miR-140-3p was downregulated in LACC-HGT tissues and primary cell lines compared with LACC. Target genes CD200 and parathyroid hormone-related protein were significantly upregulated in LACC-HGT primary cell lines. miR-140-3p and its target genes may play an important role in LACC-HGT pathogenesis. In conclusion, the current bioinformatics study constructed a ceRNA network based on a microarray, which may help identify novel miRNA therapeutic targets for LACC-HGT.

Bioinformatics analysis of drug-resistant ceRNA in epithelial ovarian cancer

Objective: To explore the possible biological function of long-chain non-coding RNA (lncRNA) on epithelial ovarian cancer (EOC) drug resistance and the value of new diagnostic markers through bioinformatics analysis, clinical testing and verification methods. Methods: (1) Mining the lncRNA related to EOC and constructing the competing endogenous RNA (ceRNA) regulatory network: comprehensively apply text mining, data prediction and network construction and other bioinformatics methods to establish a potential ceRNA regulatory network related to EOC drug resistance, namely lncRNA-microRNA (miRNA)-mRNA regulatory network. (2) Clinical verification: a total of 95 cancer tissue specimens were collected from EOC patients who underwent cytoreductive surgery at the Affiliated Tumor Hospital of Guangxi Medical University from June 2008 to October 2016, of which 54 were platinum-resistant patients (resistance group), 41 platinum-based drug-sensitive patients (sensitive group). Real-time fluorescent quantitative PCR was used to detect the expression of lncRNA in EOC tissues of the two groups, the effect of lncRNA expression on the prognosis of EOC patients, and the diagnostic efficacy of lncRNA expression on resistance to EOC were also analyzed. Results: (1) Text mining preliminarily screened out 25 differentially expressed lncRNA related to the occurrence and development of EOC, and further subcellular localization analysis found that 8 lncRNA exist in the cytoplasm. Through further data mining, collinear literature analysis and construction of ceRNA, the regulatory network predicts that the two lncRNA molecules, GAS5 and HOTAIR, could serve as key ceRNA molecules. (2) Through real-time fluoressent quantitative PCR verification, it was found that both GAS5 and HOTAIR were highly expressed in drug-resistant EOC tissues, which affects the progression-free survival (PFS) and overall survival (OS) time of patients with drug-resistant EOC independent risk factors (P<0.05). The receiver operating characteristic (ROC) area under the curve (AUC) of GAS5 alone was 0.678, the AUC of HOTAIR alone was 0.863, and the AUC of GAS5 combined with HOTAIR was 0.871, and there were statistically significant differences (all P<0.05). Conclusions: The high expression of GAS5 and HOTAIR is closely related to the drug resistance of EOC, which could be used as a potential predictor of response to chemotherapy. At the same time, the combined detection of GAS5 and HOTAIR has a certain diagnostic efficiency for patients with platinum-resistant EOC. This method of using the ceRNA regulatory network to predict key molecules will provide new ideas for the diagnosis and treatment of EOC.

Genome-wide landscape of mRNAs, microRNAs, lncRNAs, and circRNAs in hemorrhagic shock-induced ALI/ARDS in rats.

Hemorrhagic shock (HS) can develop into multiple organ dysfunction syndrome, among which acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) usually lead to poor outcomes. The underlying molecular mechanisms of HS-induced ALI/ARDS remain unclear. This study sought to investigate gene expression profiles and predict competing endogenous RNA (ceRNA) regulatory networks in an HS-induced ALI/ARDS preclinical model. Sprague Dawley rats were subjected to a fixed volume of hemorrhage (HS, 40% estimated total blood volume) or not (sham) randomly. After 8 hours of observation, left lung tissue was harvested to evaluate lung injury. Right lung was collected for RNA sequencing. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed and the long noncoding RNA (lncRNA)/circular RNA (circRNA)-microRNA (miRNA)-messenger RNA (mRNA) linkages were predicted using the ceRNA theory. Quantitative real-time polymerase chain reaction was used to validate the RNA sequencing findings. Hemorrhagic shock lungs showed noticeable ALI/ARDS features, and 437 mRNAs, 31 miRNAs, 734 lncRNAs, and 29 circRNAs were differentially expressed. In Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, the differentially expressed transcripts were enriched in the following terms: the metabolic pathways, signal transduction pathways, necroptosis, DNA damage recognition and repair, inflammatory cell migration and chemotaxis, the NOD-like receptor signaling pathway, the Janus kinase/signal transducer and activator of transcription signaling pathway, the mitogen-activated protein kinase signaling pathway, the phosphatidylinositol-3-kinase/protein kinase B signaling pathway, and so on. Also, this study identified lncRNA-miRNA-mRNA linkages with 12 lncRNAs, 5 miRNAs, 15 mRNAs, and circRNA-miRNA-mRNA linkages with 10 circRNAs, 16 miRNAs, 39 mRNAs. These networks might play important regulatory roles. This is the first high-throughput analysis of gene expression profiles in HS-induced ALI/ARDS. It shows that metabolism, cell signaling, DNA damage and repair, and necroptosis-related RNAs altered, and inflammatory response-associated RNAs and pathways have pivotal roles in HS-induced ALI/ARDS progression. It also prompts some important RNAs and regulatory networks for future research. Basic science article.

Identification of an 11-lncRNA signature with high performance for predicting the prognosis of hepatocellular carcinoma using bioinformatics analysis.

Hepatocellular carcinoma (HCC) is a common primary liver cancer with a high incidence and mortality. This study was conducted to identify a long non-coding RNA (lncRNA) signature that may serve as a predictor for HCC prognosis.RNA-seq data were extracted from The Cancer Genome Atlas database. Differentially expressed genes, lncRNAs, and miRNAs were identified in HCC (n = 374) and control samples (n = 50) and used to screen prognosis-associated lncRNA signatures. The association of the lncRNA signature with HCC prognosis was analyzed and a competitive endogenous RNA regulatory network involving the lncRNA signature was constructed.A total of 199 mRNAs, 1092 lncRNAs, and 251 miRNAs were differentially expressed between HCC and control samples. Among these lncRNAs, 11 prognosis-associated lncRNAs were used to construct a lncRNA signature. Cox regression analysis showed that patients with higher risk scores of the lncRNA signature were at risk of poor prognosis. Four lncRNAs (including LINC01517, DDX11-AS1, LINC01136, and RP11-20J15.2) and 7 miRNAs (including miR-195, miR-199b, miR-326, miR-424, and let-7c) in the ceRNA network interacted with the upregulated gene E2F2, which was associated with the overall prognosis of patients with HCC.The 11-lncRNA signature might be useful for predicting the prognosis of patients with HCC.

Construction of a novel ceRNA network and identification of lncRNA ADAMTS9-AS2 and PVT1 as hub regulators of miRNA and coding gene expression in gastric cancer.

BackgroundStudies on the interactions of single long non-coding RNA, microRNA, and mRNA have many limitations; therefore, it is necessary to study the complex regulatory network of gastric cancer (GC) pathogenesis systematically.MethodsIn this study, gene and miRNA expression data for GC were downloaded from The Cancer Genome Atlas and used for transcriptome profiling, differential gene analysis, and construction of an lncRNA-miRNA-mRNA regulatory network in conjunction with an online database to identify the key genes and subnetworks in GC pathogenesis. Real-time quantitative polymerase chain reaction was used to detect the expression of hub lncRNAs in 54 paired GC and matched normal mucosal tissues.ResultsWe constructed an lncRNA-miRNA-mRNA competitive endogenous RNA regulatory network containing 1,626 network nodes and 2,704 interactions. LncRNA ADAMTS9-AS2 and PVT1 were identified as key node genes in this competitive endogenous RNA network. Quantitative reverse transcription-polymerase chain reaction revealed ADAMTS9-AS2 downregulation and PVT1 upregulation in 54 pairs of GC and normal tissues adjacent to the cancer tissues.ConclusionsThis study systematically analysed the lncRNA-miRNA-mRNA regulatory network in GC and identified ADAMTS9-AS2 and PVT1 as key regulatory genes in this network, providing new understanding of GC pathogenesis and insights for its early diagnosis and treatment.

Exploring the Effect of Differentially Expressed Long Non-coding RNAs Driven by Copy Number Variation on Competing Endogenous RNA Network by Mining Lung Adenocarcinoma Data.

Lung cancer is the first cause of cancer death, and gene copy number variation (CNV) is a vital cause of lung cancer progression. Prognosis prediction of patients followed by medication guidance by detecting CNV of lung cancer is emerging as a promising precise treatment in the future. In this paper, the differences in CNV and gene expression between cancer tissue and normal tissue of lung adenocarcinoma (LUAD) from The Cancer Genome Atlas Lung Adenocarcinoma data set were firstly analyzed, and greater differences were observed. Furthermore, CNV-driven differentially expressed long non-coding RNAs (lncRNAs) were screened out, and then, a competing endogenous RNA (ceRNA) regulatory network related to the gene CNV was established, which involved 9 lncRNAs, seven microRNAs, and 178 downstream messenger RNAs (mRNAs). Pathway enrichment analyses sequentially performed revealed that the downstream mRNAs were mainly enriched in biological pathways related to cell division, DNA repair, and so on, indicating that these mRNAs mainly affected the replication and growth of tumor cells. Besides, the relationship between lncRNAs and drug effects was explored based on previous studies, and it was found that LINC00511 and LINC00942 in the CNV-associated ceRNA network could be used to determine tumor response to drug treatment. As examined, the drugs affected by these two lncRNAs mainly targeted metabolism, target of rapamycin signaling pathway, phosphatidylinositol-3-kinase signaling pathway, epidermal growth factor receptor signaling pathway, and cell cycle. In summary, the present research was devoted to analyzing CNV, lncRNA, mRNA, and microRNA of lung cancer, and nine lncRNAs that could affect the CNV-associated ceRNA network we constructed were identified, two of which are promising in determining tumor response to drug treatment.

Identification of a PLCE1‑regulated competing endogenous RNA regulatory network for esophageal squamous cell carcinoma.

Phospholipase C epsilon 1 (PLCE1) and the competing endogenous RNA (ceRNA) network are crucial for tumorigenesis and the progression of esophageal squamous cell carcinoma (ESCC). However, whether PLCE1 can regulate the ceRNA network in ESCC has not been clarified. In the present study, we aimed to identify the PLCE1-regulated ceRNA network and further elucidate the regulatory mechanisms by which ESCC is promoted. Microarray analysis was used to identify differentially expressed lncRNAs (DELs) and differentially expressed genes (DEGs) from three pairs of samples of PLCE-silenced Eca109 and control Eca109 cells. Next, the ceRNA regulatory network was established and visualized in Cytoscape, and functional enrichment analysis was performed to analyze DEGs from ceRNAs. Protein-protein interaction (PPI) networks among the DEGs were established by the STRING database to screen hub genes. Kaplan-Meier survival analysis was used to validate hub genes. Finally, PLCE1-related hub gene/lncRNA/miRNA axes were also constructed based on the ceRNA network. A total of 105 DELs and 346 DEGs were found to be dysregulated in the microarray data (|log2FC| >1.5, adjusted P<0.05). We constructed a PLCE1-regulated ceRNA network that incorporated 12 lncRNAs, 43 miRNAs, and 169 mRNAs. Functional enrichment analysis indicated that the DEGs might be associated with ESCC onset and development. A PPI network was established, and 9 hub genes [WD and tetratricopeptide repeats 1 (WDTC1), heat shock protein family A (Hsp70) member 5 (HSPA5), N-ethylmaleimide sensitive factor, vesicle fusing ATPase (NSF), fibroblast growth factor 2 (FGF2), cyclin dependent kinase inhibitor 1A (CDKN1A or P21), bone morphogenetic protein 2 (BMP2), complement C3 (C3), GM2 ganglioside activator (GM2A) and discs large MAGUK scaffold protein 4 (DLG4)] were determined from the network. Kaplan-Meier survival analysis validated four hub genes (BMP2, CDKN1A, GM2A, and DLG4) that were treated as prognostic factors. Ultimately, hub gene/lncRNA/miRNA subnetworks were obtained based on the 4 hub genes, 13 DEmiRNAs, and 10 DELs. In conclusion, the PLCE1-regulated ceRNA contributes to the onset and progression of ESCC and the underlying molecular mechanisms may provide insights into personalized prognosis and new therapies for ESCC patients.

Identification of microRNA hsa-miR-30c-5p as an inhibitory factor in the progression of hepatocellular carcinoma and investigation of its regulatory network via comprehensive analysis

ABSTRACT Hepatocellular carcinoma (HCC) is a primary liver cancer with high morbidity and mortality. An increasing number of abnormal gene expressions were identified to be associated with the progression of HCC. Previous studies showed that the hsa-miR-30 c-5p (miR-30 c), one of the miR-30 family members, might play a role in suppressing tumor progression in a variety of tumors. The present study aims to examine miR-30 c effects in the development of HCC. The role of miR-30 c in HCC was comprehensively investigated by using bioinformatics and experiments in vitro. The multiple databases were combined to predict and screen the target genes and upstream lncRNAs of miR-30 c, and then constructed a competitive endogenous RNA (ceRNA) regulatory network with miR-30 c as the central miRNA. The miR-30 c-related ceRNA regulatory network was also initially validated in vitro. The results showed that miR-30 c over-expression could inhibit proliferation, migration, invasion, induce apoptosis, and increase G0/G1 phase ratio of HCC cells. Three miR-30 c upstream lncRNAs and 12 miR-30 c target genes were expressed in HCC cells with increased expression and poor prognosis, and a miR-30 C-related ceRNA regulatory network was constructed. This study verified miR-30 c as an inhibitory factor in the progression of HCC and performed analyses on the miR-30 c regulatory network, which might provide potential target information for HCC prognoses and therapies. However, further experiments in vivo and studies including clinical trials will be conducted to validate our results.