Identification and characterization of noncoding RNAs-associated competing endogenous RNA networks in major depressive disorder

BACKGROUND Major depressive disorder(MDD)is a common and serious mental illness.Many novel genes in MDD have been characterized by high-throughput methods such as microarrays or sequencing.Recently,noncoding RNAs(ncRNAs)were suggested to be involved in the complicated environmental-genetic regulatory network of MDD occurrence;however,the interplay among RNA species,including protein-coding RNAs and ncRNAs,in MDD remains unclear.AIM To investigate the RNA expression datasets downloaded from a public database and construct a network based on differentially expressed long noncoding RNA(lncRNAs),microRNAs(miRNAs),and mRNAs between MDD and controls.METHODS Gene expression data were searched in NCBI Gene Expression Omnibus using the search term“major depressive disorder.”Six array datasets from humans were related to the search term:GSE19738,GSE32280,GSE38206,GSE52790,GSE76826,and GSE81152.These datasets were processed for initial assessment and subjected to quality control and differential expression analysis.Differentially expressed lncRNAs,miRNAs,and mRNAs were determined,Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed,and protein-protein interaction network was generated.The results were analyzed for their association with MDD.RESULTS After analysis,3 miRNAs,12 lncRNAs,and 33 mRNAs were identified in the competing endogenous RNA network.Two of these miRNAs were earlier shown to be involved in psychiatric disorders,and differentially expressed mRNAs were found to be highly enriched in pathways related to neurogenesis and neuroplasticity as per Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses.The expression of hub gene fatty acid 2-hydroxylase was enriched,and the encoded protein was found to be involved in myelin formation,indicating that neurological development and signal transduction are involved in MDD pathogenesis.CONCLUSION The present study presents candidate nc RNAs involved in the neurogenesis and neuroplasticity pathways related to MDD.

Role of long noncoding RNA-mediated competing endogenous RNA regulatory network in hepatocellular carcinoma

Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) are noncodingRNAs (ncRNAs) that occupy over 90% of the human genome, and their mainfunction is to directly or indirectly regulate messenger RNA (mRNA) expressionand participate in the tumorigenesis and progression of malignances. Inparticular, some lncRNAs can interact with miRNAs as competing endogenousRNAs (ceRNAs) to modulate mRNA expression. Accordingly, these RNAmolecules are interrelated and coordinate to form a dynamic lncRNA-mediatedceRNA regulatory network. Mounting evidence has revealed that lncRNAs thatact as ceRNAs are closely related to tumorigenesis. To date, numerous studieshave established many different regulatory networks in hepatocellular carcinoma(HCC), and perturbations in these ceRNA interactions may result in the initiationand progression of HCC. Herein, we emphasize recent advances concerning thebiological function of lncRNAs as ceRNAs in HCC, with the aim of elucidating themolecular mechanism underlying these HCC-related RNA molecules andproviding novel insights into the diagnosis and treatment of HCC.

Analysis of long noncoding RNA-associated competing endogenous RNA network in glucagon-like peptide-1 receptor agonist-mediated protection inβcells

BACKGROUND Long noncoding RNAs(lncRNAs)and mRNAs are widely involved in various physiological and pathological processes.The use of glucagon-like peptide-1 receptor agonists(GLP-1RAs)is a novel therapeutic strategy that could promote insulin secretion and decrease the rate ofβ-cell apoptosis in type 2 diabetes mellitus(T2DM)patients.However,the specific lncRNAs and mRNAs and their functions in these processes have not been fully identified and elucidated.AIM To identify the lncRNAs and mRNAs that are involved in the protective effect of GLP-1RA inβcells,and their roles.METHODS Rat gene microarray was used to screen differentially expressed(DE)lncRNAs and mRNAs inβcells treated with geniposide,a GLP-1RA.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses were performed to assess the underlying functions of DE mRNAs.Hub mRNAs were filtered using the STRING database and the Cytoscape plugin,CytoHubba.In order to reveal the regulatory relationship between lncRNAs and hub mRNAs,their co-expression network was constructed based on the Pearson coefficient of DE lncRNAs and mRNAs,and competing endogenous RNA(ceRNA)mechanism was explored through miRanda and TargetScan databases.RESULTS We identified 308 DE lncRNAs and 128 DE mRNAs with a fold change filter of≥1.5 and P value<0.05.GO and KEGG pathway enrichment analyses indicated that the most enriched terms were G-protein coupled receptor signaling pathway,inflammatory response,calcium signaling pathway,positive regulation of cell proliferation,and ERK1 and ERK2 cascade.Pomc,Htr2a,and Agtr1a were screened as hub mRNAs using the STRING database and the Cytoscape plugin,CytoHubba.This result was further verified using SwissTargetPrediction tool.Through the co-expression network and competing endogenous(ceRNA)mechanism,we identified seven lncRNAs(NONRATT027738,NONRATT027888,NONRATT030038,etc.)co-expressed with the three hub mRNAs(Pomc,Htr2a,and Agtr1a)based on the Pearson coefficient of the expression levels.These lncRNAs regulated hub mRNA functions by competing with six miRNAs(rno-miR-5132-3p,rno-miR-344g,rno-miR-3075,etc.)via the ceRNA mechanism.Further analysis indicated that lncRNA NONRATT027738 interacts with all the three hub mRNAs,suggesting that it is at a core position within the ceRNA network.CONCLUSION We have identified key lncRNAs and mRNAs,and highlighted here how they interact through the ceRNA mechanism to mediate the protective effect of GLP-1RA inβcells.

Delineation of a SMARCA4-specific competing endogenous RNA network and its function in hepatocellular carcinoma

BACKGROUND Hepatocellular carcinoma(HCC)is a common malignancy worldwide,and the mortality rate continues to rise each year.SMARCA4 expression has been associated with poor prognosis in various types of cancer;however,the specific mechanism of action of SMARCA4 in HCC needs to be fully elucidated.AIM To explore the specific mechanism of action of SMARCA4 in HCC.METHODS Herein,the expression level of SMARCA4 as well as its association with HCC prognosis were evaluated using transcriptome profiling and clinical data of 18 different types of cancer collected from The Cancer Genome Atlas database.Furthermore,SMARCA4-high and-low groups were identified.Thereafter,gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to identify the function of SMARCA4,followed by construction of a SMARCA4-specific competing endogenous RNA(ceRNA)network using starBase database.The role of SMARCA4 in immunotherapy and its association with immune cells were assessed using correlation analysis.RESULTS It was observed that SMARCA4 was overexpressed and negatively correlated with prognosis in HCC.Further,SMARCA4 expression was positively associated with tumor mutational burden,microsatellite stability,and immunotherapy efficacy.The SNHG3/THUMP3-AS1-miR-139-5p-SMARCA4 ceRNA network was established and could be assumed to serve as a stimulatory mechanism in HCC.CONCLUSION The findings of this study demonstrated that SMARCA4 plays a significant role in progression and immune infiltration in HCC.Moreover,a ceRNA network was detected,which was found to be correlated with poor prognosis in HCC.The findings of this study could contribute towards the identification of predictive markers for immunotherapy and a novel mechanism of action for HCC treatment.

Circular RNA expression and the competitive endogenous RNA network in pathological,age-related macular degeneration events:A cross-platform normalization study

Age-related macular degeneration(AMD)causes irreversible blindness in people aged over 50 worldwide.The dysfunction of the retinal pigment epithelium is the primary cause of atrophic AMD.In the current study,we used the ComBat and Training Distribution Matching method to integrate data obtained from the Gene Expression Omnibus database.We analyzed the integrated sequencing data by the Gene Set Enrichment Analysis.Peroxisome and tumor necrosis factor-α(TNF-α)signaling and nuclear factor kappa B(NF-κB)were among the top 10 pathways,and thus we selected them to construct AMD cell models to identify differentially expressed circular RNAs(circRNAs).We then constructed a competing endogenous RNA network,which is related to differentially expressed circRNAs.This network included seven circRNAs,15 microRNAs,and 82 mRNAs.The Kyoto Encyclopedia of Genes and Genomes analysis of mRNAs in this network showed that the hypoxia-inducible factor-1(HIF-1)signaling pathway was a common downstream event.The results of the current study may provide insights into the pathological processes of atrophic AMD.

Transcriptomic and bioinformatics analysis of the mechanism by which erythropoietin promotes recovery from traumatic brain injury in mice

Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive days.RNA sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular RNAs.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK pathway.Constructing competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and mRNAs.Because the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was assessed.Ephb6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro poietin.These findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway.

Long noncoding RNA protein-disulfide isomerase-associated 3 regulated high glucose-induced podocyte apoptosis in diabetic nephropathy through targeting miR-139-3p

BACKGROUND Podocyte apoptosis plays a vital role in proteinuria pathogenesis in diabetic nephropathy(DN).The regulatory relationship between long noncoding RNAs(lncRNAs)and podocyte apoptosis has recently become another research hot spot in the DN field.AIM To investigate whether lncRNA protein-disulfide isomerase-associated 3(Pdia3)could regulate podocyte apoptosis through miR-139-3p and revealed the underlying mechanism.METHODS Using normal glucose or high glucose(HG)-cultured podocytes,the cellular functions and exact mechanisms underlying the regulatory effects of lncRNA Pdia3 on podocyte apoptosis and endoplasmic reticulum stress(ERS)were explored.LncRNA Pdia3 and miR-139-3p expression were measured through quantitative real-time polymerase chain reaction.Relative cell viability was detected through the cell counting kit-8 colorimetric assay.The podocyte apoptosis rate in each group was measured through flow cytometry.The interaction between lncRNA Pdia3 and miR-139-3p was examined through the dual luciferase reporter assay.Finally,western blotting was performed to detect the effect of lncRNA Pdia3 on podocyte apoptosis and ERS via miR-139-3p.RESULTS The expression of lncRNA Pdia3 was significantly downregulated in HG-cultured podocytes.Next,lncRNA Pdia3 was involved in HG-induced podocyte apoptosis.Furthermore,the dual luciferase reporter assay confirmed the direct interaction between lncRNA Pdia3 and miR-139-3p.LncRNA Pdia3 overexpression attenuated podocyte apoptosis and ERS through miR-139-3p in HG-cultured podocytes.CONCLUSION Taken together,this study demonstrated that lncRNA Pdia3 overexpression could attenuate HG-induced podocyte apoptosis and ERS by acting as a competing endogenous RNA of miR-139-3p,which might provide a potential therapeutic target for DN.

Comprehensive Analysis of Key mRNAs and lncRNAs in Osteosarcoma Response to Preoperative Chemotherapy with Prognostic Values

Objective:Osteosarcoma is one of the most common types of bone sarcoma with a poor prognosis.However,identifying the predictive factors that contribute to the response to neoadjuvant chemotherapy remains a significant challenge.Methods:A public data series(GSE87437)was downloaded to identify differentially expressed genes(DEGs)and differentially expressed lncRNAs(DElncRNAs)between osteosarcoma patients that do and do not respond to preoperative chemotherapy.Subsequently,functional analysis of the transcriptome expression profile,regulatory networks of DEGs and DElncRNAs,competing endogenous RNAs(ceRNA)and protein-protein interaction networks were performed.Furthermore,the function,pathway,and survival analysis of hub genes was performed and drug and disease relationship prediction of DElncRNA was carried out.Results:A total of 626 DEGs,26 DElncRNAs,and 18 hub genes were identified.However,only one gene and two lncRNAs were found to be suitable as candidate gene and lncRNAs respectively.Conclusion:The DEGs,hub genes,candidate gene,and candidate lncRNAs screened out in this context were considered as potential biomarkers for the response to neoadjuvant chemotherapy of osteosarcoma.

The circ_0002538/miR-138-5p/plasmolipin axis regulates Schwann cell migration and myelination in diabetic peripheral neuropathy

Circular RNAs(circRNAs)play a vital role in diabetic peripheral neuropathy.However,their expression and function in Schwann cells in individuals with diabetic peripheral neuropathy remain poorly understood.Here,we performed protein profiling and circRNA sequencing of sural nerves in patients with diabetic peripheral neuropathy and controls.Protein profiling revealed 265 differentially expressed proteins in the diabetic peripheral neuropathy group.Gene Ontology indicated that differentially expressed proteins were mainly enriched in myelination and mitochondrial oxidative phosphorylation.A real-time polymerase chain reaction assay performed to validate the circRNA sequencing results yielded 11 differentially expressed circRNAs.circ_0002538 was markedly downregulated in patients with diabetic peripheral neuropathy.Further in vitro experiments showed that overexpression of circ_0002538 promoted the migration of Schwann cells by upregulating plasmolipin(PLLP)expression.Moreover,overexpression of circ_0002538 in the sciatic nerve in a streptozotocin-induced mouse model of diabetic peripheral neuropathy alleviated demyelination and improved sciatic nerve function.The results of a mechanistic experiment showed that circ_0002538 promotes PLLP expression by sponging miR-138-5p,while a lack of circ_0002538 led to a PLLP deficiency that further suppressed Schwann cell migration.These findings suggest that the circ_0002538/miR-138-5p/PLLP axis can promote the migration of Schwann cells in diabetic peripheral neuropathy patients,improving myelin sheath structure and nerve function.Thus,this axis is a potential target for therapeutic treatment of diabetic peripheral neuropathy.

Potential targets and mechanisms of photobiomodulation for spinal cord injury

As a classic noninvasive physiotherapy,photobiomodulation,also known as low-level laser therapy,is widely used for the treatment of many diseases and has anti-inflammatory and tissue repair effects.Photobiomodulation has been shown to promote spinal cord injury repair.In our previous study,we found that 810 nm low-level laser therapy reduced the M1 polarization of macrophages and promoted motor function recovery.However,the mechanism underlying this inhibitory effect is not clear.In recent years,transcriptome sequencing analysis has played a critical role in elucidating the progression of diseases.Therefore,in this study,we performed M1 polarization on induced mouse bone marrow macrophages and applied low-level laser therapy.Our sequencing results showed the differential gene expression profile of photobiomodulation regulating macrophage polarization.We analyzed these genes using gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses.Networks of protein-protein interactions and competing RNA endogenous networks were constructed.We found that photobiomodulation inhibited STAT3 expression through increasing the expression of miR-330-5p,and that miR-330-5p binding to STAT3 inhibited STAT3 expression.Inducible nitric oxide synthase showed trends in changes similar to the changes in STAT3 expression.Finally,we treated a mouse model of spinal cord injury using photobiomodulation and confirmed that photobiomodulation reduced inducible nitric oxide synthase and STAT3 expression and promoted motor function recovery in spinal cord injury mice.These findings suggest that STAT3 may be a potential target of photobiomodulation,and the miR-330-5p/STAT3 pathway is a possible mechanism by which photobiomodulation has its biological effects.

CircDOCK7 facilitates the proliferation and adipogenic differentiation of chicken abdominal preadipocytes through the gga‑miR‑301b‑3p/ACSL1 axis

Background Abdominal fat deposition depends on both the proliferation of preadipocytes and their maturation into adipocytes,which is a well-orchestrated multistep process involving many regulatory molecules.Circular RNAs(circRNAs)have emergingly been implicated in mammalian adipogenesis.However,circRNA-mediated regulation in chicken adipogenesis remains unclear.Our previous circRNA sequencing data identified a differentially expressed novel circRNA,8:27,886,180|27,889,657,during the adipogenic differentiation of chicken abdominal preadipocytes.This study aimed to investigate the regulatory role of circDOCK7 in the proliferation and adipogenic differentiation of chicken abdominal preadipocytes,and explore its molecular mechanisms of competing endogenous RNA underlying chicken adipogenesis.Results Our results showed that 8:27,886,180|27,889,657 is an exonic circRNA derived from the head-to-tail splicing of exons 19–22 of the dedicator of cytokinesis 7(DOCK7)gene,abbreviated as circDOCK7.CircDOCK7 is mainly distributed in the cytoplasm of chicken abdominal preadipocytes and is stable because of its RNase R resistance and longer half-life.CircDOCK7 is significantly upregulated in the abdominal fat tissues of fat chickens compared to lean chickens,and its expression gradually increases during the proliferation and adipogenic differentiation of chicken abdominal preadipocytes.Functionally,the gain-and loss-of-function experiments showed that circDOCK7 promoted proliferation,G0/G1-to S-phase progression,and glucose uptake capacity of chicken abdominal preadipocytes,in parallel with adipogenic differentiation characterized by remarkably increased intracellular lipid droplet accumulation and triglyceride and acetyl coenzyme A content in differentiated chicken abdominal preadipocytes.Mechanistically,a pull-down assay and a dual-luciferase reporter assay confirmed that circDOCK7 interacted with gga-miR-301b-3p,which was identified as an inhibitor of chicken abdominal adipogenesis.Moreover,the ACSL1 gene was demonstrated to be a direct target of gga-miR-301b-3p.Chicken ACSL1 protein is localized in the endoplasmic reticulum and mitochondria of chicken abdominal preadipocytes and acts as an adipogenesis accelerator.Rescue experiments showed that circDOCK7 could counteract the inhibitory effects of gga-miR-301b-3p on ACSL1 mRNA abundance as well as the proliferation and adipogenic differentiation of chicken abdominal preadipocytes.Conclusions CircDOCK7 serves as a miRNA sponge that directly sequesters gga-miR-301b-3p away from the ACSL1 gene,thus augmenting adipogenesis in chickens.These findings may elucidate a new regulatory mechanism underlying abdominal fat deposition in chickens.

Diagnostic and prognostic value of lnc RNA cancer susceptibility candidate 9 in hepatocellular carcinoma

BACKGROUND Hepatocellular carcinoma(HCC)is a common malignant gastrointestinal tumor.There are currently few clinical diagnostic and prognostic markers for HCC.LncRNA cancer susceptibility candidate 9(CASC9)is a long-chain non-coding RNA discovered in recent years,and previous studies have found that lncRNA CASC9 participates in the occurrence and development of HCC,but its clinical value remains unclear.AIM To determine the expression of lncRNA CASC9 in HCC and its diagnostic and prognostic value.METHODS Data on CASC9 expression in patients with HCC were collected from the Cancer Genome Atlas(TCGA)database to analyze the relationship between CASC9 and patient survival.A total of 80 HCC patients treated in The First Affiliated Hospital of Guangxi Medical University from May 2012 to January 2014 were enrolled in the patient group,and 50 healthy subjects were enrolled in the control group during the same period.CASC9 expression in the two groups was determined using quantitative real-time polymerase chain reaction,and its diagnostic and prognostic value was analyzed based on the CASC9 data and pathological data in these HCC patients.The relationship between CASC9 and patient survival was assessed during the 5-year follow-up period.RESULTS Analysis of data from TCGA database revealed that control samples showed significantly lower CASC9 expression than carcinoma tissue samples(P<0.001);the low CASC9 expression group had a higher survival rate than the high CASC9 expression group(P=0.011),and the patient group showed significantly increased expression of serum CASC9,with the area under the curve(AUC)of 0.933.CASC9 expression was related to tumor size,combined hepatitis,tumor,node,metastasis(TNM)staging,lymph node metastasis,differentiation and alpha fetoprotein,and the high CASC9 expression group showed lower 1-year,3-year and 5-year survival rates than the low CASC9 expression group(all aP<0.05).Multivariate Cox regression analysis revealed that TNM staging,lymph node metastasis,differentiation,alpha fetoprotein and CASC9 were independent factors affecting the prognosis of patients.Stage I+II patients with lymph node metastasis,low differentiation,and alpha fetoprotein>200 ng/mL had a poor 5-year survival rate.CONCLUSION High CASC9 expression is beneficial in the prognosis of HCC patients.CASC9 is expected to be a potential diagnostic and prognostic indicator of HCC.

CircHECTD1 up-regulates mucin 1 expression to accelerate hepatocellular carcinoma development by targeting microRNA-485-5p via a competing endogenous RNA mechanism

Background::Non-coding RNAs have attracted considerable attention for their vital role in cancer.The purpose of this study was to determine the effects of non-coding RNAs on hepatocellular carcinoma(HCC)and reveal their regulatory mechanism in the pathophysiological process.Methods::We measured the expression of mucin 1(MUC1)and miR-485-5p in tissues from 15 HCC patients and in liver cancer cell lines by quantitative real-time polymerase chain reaction and Western blot,screened for aberrantly expressed microRNAs(miRNAs)by miRNA microarrays.Bioinformatics tools were used to find the miRNA and circular RNA that regulated MUC1,which were validated by RNA immunoprecipitation assay and luciferase reporter assay.Cell counting kit-8,Transwell assays,and flow cytometry were used to conduct functional experiments.Proteins were examined by western blot and immunohistochemical staining assays.Significant differences between groups were estimated using the one-way analysis of variance.A P<0.05 was considered statistically significant.Results::MUC1 was overexpressed in HCC tissues compared with that in paratumor tissues(normal vs.tumor,1.007±0.215 vs.75.213±18.403,t=18.401,P<0.001)while miR-485-5p was down-regulated(normal vs.tumor,4.894±0.684 vs.1.586±0.398,t=16.191,P<0.001).Inhibition of miR-485-5p promoted cell proliferation(73.33%±5.13%vs.41.33%±3.51%,t=8.913,P<0.001),migration(102±8 cells vs.46±8 cells,t=8.681,P<0.001),invasion(59±7 cells vs.28±2 cells,t=8.034,P<0.01),and suppressed apoptosis(22.64%±6.97%vs.36.33%±3.96%,t=2.958,P<0.05)of HepG2 cells with which MUC1 is knocked down.Mechanically,miR-485-5p binds to MUC1,while circHECTD1 binds to miR-485-5p,resulting in the indirect up-regulation of the MUC1 level.Conclusions::Our findings reveal that circHECTD1 facilitates HCC progression by sponging miR-485-5p to up-regulate MUC1.

Comprehensive circRNA-microRNA-mRNA network analysis revealed the novel regulatory mechanism of Trichosporon asahii infection

Background:Invasive Trichosporon asahii(T.asahii)infection frequently occurs with a high mortality in immunodeficient hosts,but the pathogenesis of T.asahii infection remains elusive.Circular RNAs(circRNAs)are a type of endogenous noncoding RNA that participate in various disease processes.However,the mechanism of circRNAs in T.asahii infection remains completely unknown.Methods:RNA sequencing(RNA-seq)was performed to analyze the expression profiles of circRNAs,microRNAs(miRNAs),and mRNAs in THP-1 cells infected with T.asahii or uninfected samples.Some of the RNA-seq results were verified by RT-qPCR.Gene Ontology(GO)enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analyses were used to analyze the differentially expressed mRNAs.A circRNA-miRNA-mRNA network was constructed and verified by dual-luciferase reporter assay and overexpression experiments.Results:A total of 46 circRNAs,412 mRNAs and 47 miRNAs were differentially expressed at 12 h after T.asahii infection.GO and KEGG analyses showed that the differentially expressed mRNAs were primarily linked to the leukocyte migration involved in the inflammatory response,the Toll-like receptor signaling pathway,and the TNF signaling pathway.A competing endogenous RNA(ceRNA)network was constructed with 5 differentially expressed circRNAs,5 differentially expressed miRNAs and 42 differentially expressed mRNAs.Among them,hsa_circ_0065336 was found to indirectly regulate PTPN11 expression by sponging miR-505-3p.Conclusions:These data revealed a comprehensive circRNA-associated ceRNA network during T.asahii infection,thus providing new insights into the pathogenesis of the T.asahii-host interactions.

Small nucleolar RNA host gene 3 functions as a novel biomarker in liver cancer and other tumour progression

Cancer has become the most life-threatening disease in the world.Mutations in and aberrant expression of genes encoding proteins and mutations in noncoding RNAs,especially long noncoding RNAs(lncRNAs),have significant effects in human cancers.LncRNAs have no protein-coding ability but function extensively in numerous physiological and pathological processes.Small nucleolar RNA host gene 3(SNHG3)is a novel lncRNA and has been reported to be differentially expressed in various tumors,such as liver cancer,gastric cancer,and glioma.However,the interaction mechanisms for the regulation between SNHG3 and tumor progression are poorly understood.In this review,we summarize the results of SNHG3 studies in humans,animal models,and cells to underline the expression and role of SNHG3 in cancer.SNHG3 expression is upregulated in most tumors and is detrimental to patient prognosis.SNHG3 expression in lung adenocarcinoma remains controversial.Concurrently,SNHG3 affects oncogenes and tumor suppressor genes through various mechanisms,including competing endogenous RNA effects.A deeper understanding of the contribution of SNHG3 in clinical applications and tumor development may provide a new target for cancer diagnosis and treatment.

A quantitative understanding of microRNA- mediated competing endogenous RNA regulation

MicroRNA （miRNA） plays key roles in post-transcriptional regulations. Recently, a competing endogenous RNA （ceRNA） hypothesis has been proposed that miRNA targets could communicate and regulate each other through titrating shared miRNAs, which provides a new layer of gene regulation. Though a number of ceRNAs playing biological functions have been identified, the ceRNA hypothesis remains controversial. Recent experimental and theoretical studies argued that the modulation of a single RNA species could hardly change the expression level of competing miRNA targets through ceRNA effect under normal physiological conditions. Here, we reviewed a common framework to model miRNA regulations, and summarized the current theoretical and experimental studies for quantitative understanding ceRNA effect. By revisiting a coarse-grained ceRNA model, we proposed that network topology could significantly influence the competing effect and ceRNA regulation at protein level could be much stronger than that at RNA level. We also provided a conditional independent binding equation to describe miRNA relative repression on different target, which could be applied to quantify siRNA off-target effect.

Multivariate competing endogenous RNA network characterization for cancer microRNA biomarker discovery:a novel bioinformatics model with application to prostate cancer metastasis

Background:MicroRNAs(miRNAs)are post-transcriptional regulators with potential as biomarkers for cancer management.Datadriven competing endogenous RNA(ceRNA)network modeling is an effective way to decipher the complex interplay between miRNAs and spongers.However,there are currently no general rules for ceRNA network-based biomarker prioritization.Methods and results:In this study,a novel bioinformatics model was developed by integrating gene expression with multivariate miRNA-target data for ceRNA network-based biomarker discovery.Compared with traditional methods,the structural vulnerability in the human long non-coding RNA(lncRNA)–miRNA–messenger RNAs(mRNA)network was comprehensively analyzed,and the single-line regulatory or competing mode among miRNAs,lncRNAs,and mRNAs was characterized and quantified as statistical evidence for miRNA biomarker identification.The application of this model to prostate cancer(PCa)metastasis identified a total of 12 miRNAs as putative biomarkers from the metastatic PCa-specific lncRNA–miRNA–mRNA network and nine of them have been previously reported as biomarkers for PCa metastasis.The receiver operating characteristic curve and cell line qRT-PCR experiments demonstrated the power of miR-26b-5p,miR-130a-3p,and miR-363-3p as novel candidates for predicting PCa metastasis.Moreover,PCa-associated pathways such as prostate cancer signaling,ERK/MAPK signaling,and TGF-βsignaling were significantly enriched by targets of identified miRNAs,indicating the underlying mechanisms of miRNAs in PCa carcinogenesis.Conclusions:A novel ceRNA-based bioinformatics model was proposed and applied to screen candidate miRNA biomarkers for PCa metastasis.Functional validations using human samples and clinical data will be performed for future translational studies on the identified miRNAs.

Long noncoding RNA LINC01124 activates hepatocellular carcinoma cell proliferation, migration, and invasion by absorbing microRNA-1247-5p and overexpressing FOXO3

Long intergenic non-protein coding RNA 1124(LINC01124)has been identified as an important regulator of non-small-cell lung cancer.However,the expression and detailed role of LINC01124 in hepatocellular carcinoma(HCC)remain unestablished to date.Therefore,this study aimed to elucidate the role of LINC01124 in the aggressiveness of HCC cells and identify the underlying regulatory mechanism.Quantitative reverse transcriptase-polymerase chain reaction was performed to measure the expression of LINC01124 in HCC.Cell Counting Kit-8 assay,Transwell cell migration and invasion assays,and a xenograft tumor model were used to investigate the function of LINC01124 in HCC cells,and bioinformatics analysis,RNA immunoprecipitation,luciferase reporter assay,and rescue experiments were used to elucidate the underlying mechanisms.Herein,LINC01124 overexpression was confirmed in HCC tissues as well as cell lines.Further,the downregulation of LINC01124 decreased HCC cell proliferation,migration,and invasion in vitro,whereas the upregulation of LINC01124 triggered the opposite results.Additionally,LINC01124 ablation impaired tumor growth in vivo.Mechanistic analyses revealed that LINC01124 functions as a competing endogenous RNA to sponge microRNA-1247-5p(miR-1247-5p)in HCC cells.Moreover,forkhead box O3(FOXO3)was identified as a direct target of miR-1247-5p.FOXO3 was positively regulated by LINC01124 in HCC cells through the sequestration of miR-1247-5p.Finally,rescue assays revealed that the inhibition of miR-1247-5p or overexpression of FOXO3 reversed the effects of LINC01124 silencing on the HCC cell malignant phenotype.In summary,LINC01124 plays a tumor-promoting role in HCC by regulating the miR-1247-5p-FOXO3 axis.The LINC01124-miR-1247-5p-FOXO3 pathway may provide a foundation for the identification of alternative therapies for HCC.

Current and future perspectives on the regulation and functions of miR-545 in cancer development

Micro ribonucleic acids(miRNAs)are a highly conserved class of single-stranded non-coding RNAs.Within the miR-545/374a cluster,miR-545 resides in the intron of the long non-coding RNA(lncRNA)FTX on Xq13.2.The precursor form,pre-miR-545,is cleaved to generate two mature miRNAs,miR-545-3p and miR-545-5p.Remarkably,these two miRNAs exhibit distinct aberrant expression patterns in different cancers;however,their expression in colorectal cancer remains controversial.Notably,miR-545-3p is affected by 15 circular RNAs(circRNAs)and 10 long non-coding RNAs(lncRNAs),and it targets 27 protein-coding genes(PCGs)that participate in the regulation of four signaling pathways.In contrast,miR-545-5p is regulated by one circRNA and five lncRNAs,it targets six PCGs and contributes to the regulation of one signaling pathway.Both miR-545-3p and miR-545-5p affect crucial cellular behaviors,including cell cycle,proliferation,apoptosis,epithelial-mesenchymal transition,invasion,and migration.Although low miR-545-3p expression is associated with poor prognosis in three cancer types,studies on miR-545-5p are yet to be reported.miR-545-3p operates within a diverse range of regulatory networks,thereby augmenting the efficacy of cancer chemotherapy,radiotherapy,and immunotherapy.Conversely,miR-545-5p enhances immunotherapy efficacy by inhibiting T-cell immunoglobulin and mucin-domain containing-3(TIM-3)expression.In summary,miR-545 holds immense potential as a cancer biomarker and therapeutic target.The aberrant expression and regulatory mechanisms of miR-545 in cancer warrant further investigation.

Circular RNAs:typical biomarkers for bone-related diseases

Bone is a connective tissue that has important functions in the human body.Cells and the extracellular matrix(ECM)are key components of bone and are closely related to bone-related diseases.However,the outcomes of conventional treatments for bone-related diseases are not promising,and hence it is necessary to elucidate the exact regulatory mechanisms of bone-related diseases and identify novel biomarkers for diagnosis and therapy.Circular RNAs(circRNAs)are single-stranded RNAs that form closed circular structures without a 5’cap or 3’tail and polycyclic adenylate tails.Due to their high stability,circRNAs have the potential to be typical biomarkers.Accumulating evidence suggests that circRNAs are involved in bone-related diseases,including osteoarthritis,osteoporosis,osteosarcoma,multiple myeloma,intervertebral disc degeneration,and rheumatoid arthritis.Herein,we summarize the recent research progress on the characteristics and functions of circRNAs,and highlight the regulatory mechanism of circRNAs in bone-related diseases.