miRNA Network Research Articles

Side-Directed Release of Differential Extracellular Vesicle-associated microRNA Profiles from Bronchial Epithelial Cells of Healthy and Asthmatic Subjects.

Extracellular vesicles (EVs) are released by virtually all cells and may serve as intercellular communication structures by transmitting molecules such as proteins, lipids, and nucleic acids between cells. MicroRNAs (miRNAs) are an abundant class of vesicular RNA playing a pivotal role in regulating intracellular processes. In this work, we aimed to characterize vesicular miRNA profiles released in a side-directed manner by bronchial epithelial cells from healthy and asthmatic subjects using an air−liquid interface cell culture model. EVs were isolated from a culture medium collected from either the basolateral or apical cell side of the epithelial cell cultures and characterized by nano-flow cytometry (NanoFCM) and bead-based flow cytometry. EV-associated RNA profiles were assessed by small RNA sequencing and subsequent bioinformatic analyses. Furthermore, miRNA-associated functions and targets were predicted and miRNA network analyses were performed. EVs were released at higher numbers to the apical cell side of the epithelial cells and were considerably smaller in the apical compared to the basolateral compartment. EVs from both compartments showed a differential tetraspanins surface marker expression. Furthermore, 236 miRNAs were differentially expressed depending on the EV secretion side, regardless of the disease phenotype. On the apical cell side, 32 miRNAs were significantly altered in asthmatic versus healthy conditions, while on the basolateral cell side, 23 differentially expressed miRNAs could be detected. Downstream KEGG pathway analysis predicted mTOR and MAPK signaling pathways as potential downstream targets of apically secreted miRNAs. In contrast, miRNAs specifically detected at the basolateral side were associated with processes of T and B cell receptor signaling. The study proves a compartmentalized packaging of EVs by bronchial epithelial cells supposedly associated with site-specific functions of cargo miRNAs, which are considerably affected by disease conditions such as asthma.

Significance of chromobox protein (CBX) expression in diffuse LBCL.

Diffuse large B-cell lymphoma (DLBCL) is the main pathological type of non-Hodgkin lymphoma (NHL). Chromobox (CBX) family proteins are classical components of polycomb group (PcG) complexes in many cancer types, resulting in accelerated carcinogenesis. Nevertheless, the prognostic, functional and expression significance of these CBX family members in DLBCL remain unclear and elusive. CBX transcriptional levels were confirmed using Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA) and Cancer Cell Line Encyclopedia (CCLE) databases. The protein levels of CBX family members were analysed using The Human Protein Atlas (HPA) database. Information on the PPI network, functional enrichment, drug sensitivity, prognostic value, miRNA network, protein structure, genetic alteration and immune cell infiltration were generated using the GeneMANIA, Metascape, GSCALite, GEPIA, PDB, cBioPortal, and TIMER databases, and the correlation of these factors with CBX expression levels in DLBCL was assessed. CBX1/2/3/5/6/8 mRNA levels were significantly enhanced in DLBCL tissues compared to corresponding normal tissues. CBX1/3/4/5/8 protein expression levels were obviously increased, whereas CBX7 was obviously decreased. This difference might be attributed to miRNA regulation based on the miRNA network. Overall survival (OS) analysis showed that CBX levels were not correlated with prognosis in DLBCL patients, indicating that CBXs are not good biomarkers for DLBCL patients. Furthermore, functional enrichment analyses indicated that CBXs were closely related to DNA duplex unwinding, covalent chromatin modification, and histone lysine methylation. The levels of CBXs were also significantly associated with diverse immune cell infiltration in DLBCL. This study reveals that dysregulated CBXs are involved in DLBCL development and might represent potential therapeutic targets for DLBCL.

Human Urine-Derived Stem Cells Improve Partial Bladder Outlet Obstruction in Rats: Preliminary Data and microRNA-mRNA Expression Profile

Partial bladder outlet obstruction (pBOO) often results in bladder tissue inflammation and remodeling. As human urine-derived stem cells (USCs) have demonstrated therapeutic benefits, we used a rat model to investigate the effect of USCs on bladder function and explore the miRNA and gene expression profiles in bladder tissue using RNA sequencing. Eighteen rats were assigned to a sham surgery group, pBOO group, and pBOO+USC group (six biweekly treatments). Routine urodynamic monitoring, analysis of detrusor muscle strips, and pathophysiology assessments were conducted. Finally, altered miRNA and mRNA expression profiles of bladder tissue were examined using RNA sequencing and bioinformatics analysis. After USC treatment, elevated bladder compliance and maximal voiding pressure, declined end filling pressure and voided volume, and improved detrusor muscle contractility and carbachol sensitivity were found. Histology and TUNEL assay revealed reduced collagen deposition and muscle cell apoptosis in bladder tissue. The differential expression of eight miRNAs was reversed by USC treatment. Two large nodes (miR-142 and miR-9a) were identified in the miRNA-gene interaction network in the USC-treated group. The Kyoto Encyclopedia of Genes and Genomes analysis revealed enrichment of multiple significant pathways, including those involved in necroptosis and cytokine-cytokine receptor interactions. This is the first study to demonstrate the protective effect of USCs on bladder function and remodeling in pBOO rats. The miRNA and mRNA expression levels differed in the bladder of pBOO rats with and without USC treatment. Although the mechanism underlying these effects has not been fully elucidated, necroptosis and cytokine-cytokine receptor interaction-related pathways may be involved.Graphical abstract

The Differential Expression of Circular RNAs in Type 2 Diabetes Mellitus and Latent Autoimmune Diabetes in Adults.

Objective: Expression of circular RNAs (circRNAs) in the peripheral blood of individuals with latent autoimmune diabetes in adults (LADA) and type 2 diabetes mellitus (T2DM) were quantified to identify dysregulated circRNAs compared with control individuals. Methods: circRNAs were obtained from the peripheral blood serum of 12 healthy adults and 12 individuals with LADA and 12 type 2 diabetics. The circRNA expression profiles were analyzed by high-throughput RNA sequencing. The most highly dysregulated circular RNAs were validated by quantitative real-time polymerase chain reaction. A circular RNA-microRNA (miRNA) network diagram predicted the interactions of circular RNAs, miRNAs, and coding genes. Results: A total of 2334 differentially expressed circRNAs were detected among the three groups, with 277 circRNAs in the Group DM versus Group NG; 992 circRNAs in the Group LADA versus Group NG and 1065 circRNAs in the Group DM versus Group LADA. Six circRNAs were identified as the most distinctive differentially expressed targets (p < 0.05). The proposed molecular functions of these differentially expressed circRNAS included the tumor necrosis factor signaling pathway, the FoxO signaling pathway, cellular senescence, and long-term potentiation (all false discovery rate p < 0.05) which may contribute to T2DM and LADA. Conclusion: circRNAs are aberrantly expressed in the peripheral blood of patients with T2DM and LADA and may interact with miRNA and circRNA-derived peptides in the development of diabetes. Further investigations may illustrate the partial pathogenesis of diabetes mellitus. Clinical Trial Registration number: ChiCTR1900020644.

Human pancreatic islet miRNA-mRNA networks of altered miRNAs due to glycemic status

SummaryMicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression via mRNA targeting, playing important roles in the pancreatic islets. We aimed to identify molecular pathways and genomic regulatory regions associated with altered miRNA expression due to glycemic status, which could contribute to the development of type 2 diabetes (T2D). To this end, miRNAs were identified by a combination of differential miRNA expression and correlation analysis in human islet samples from donors with normal and elevated blood glucose levels. Analysis and clustering of highly correlated, experimentally validated gene targets of these miRNAs revealed two islet-specific clusters, which were associated with key aspects of islet functions and included a high number of T2D-related genes. Finally, cis-eQTLs and public GWAS data integration uncovered suggestive genomic signals of association with insulin secretion and T2D. The miRNA-driven network-based approach presented in this study contributes to a better understanding of impaired insulin secretion in T2D pathogenesis.

Involvement of CircRNA Expression Profile in Diabetic Retinopathy and Its Potential Diagnostic Value.

Background: Circular RNAs (circRNAs), a class of non-coding and undegradable RNAs, play many pathological functions by acting as miRNA sponges, interacting with RNA-binding proteins, and others. The recent literature indicates that circRNAs possess the advanced superiority for the early screening of diabetic retinopathy (DR). Methods: CircRNA sources of peripheral blood mononuclear cells (PBMCs) from healthy controls (n = 4), diabetes mellitus patients (DM) (n = 4), and DR patients (n = 4) were extracted for circular RNA microarray analysis. Enriched biological modules and signaling pathways were analyzed by Gene Ontology Enrichment and Kyoto Encyclopedia of Genes and Genomes analysis, respectively. Real-time quantitative reverse transcription PCR (RT-qPCR) was performed to validate differentiated levels of several circRNAs (fold change ≥2, p < .05) in different groups of healthy control subjects (n = 20), DM patients (n = 60), and DR patients (n = 42). Based on our clinical data from DR, the diagnostic performance of candidate circRNAs was measured by operating characteristic curves (ROCs). Subsequently, their circRNA–miRNA networks were constructed by bioinformatics analysis. Results: Circular RNA microarray analysis was performed, and 2,452 and 289 circRNAs were screened with differential expression in DR patients compared to healthy controls and DM patients, respectively. Enrichment analyses showed that circRNAs in DR patients were enriched in extracellular matrix (ECM)–receptor interaction and focal adhesion pathways. The top 5 differential circRNAs in circRNA microarray analysis were subsequently quantified and verified by RT-qPCR. Consistently, a significant 2.2-fold reduction of hsa_circ_0095008 and 1.7-fold increase in hsa_circ_0001883 were identified in DR patients compared to DM patients. Meanwhile, the area under curves of hsa_circ_0095008 and hsa_circ_0001883 were 0.6710 (95% CI, 0.5646–0.7775) (p = 0.003399) and 0.6071 (95% CI, 0.4953–0.7189) (p = 0.06644), respectively, indicating a good diagnostic value. Conclusion: Our study provided a new sight for the pathological mechanism of DR and revealed the potential value of hsa_circ_0095008 and hsa_circ_0001883 as diagnostic biomarkers for the early diagnosis of DR patients.

Dissecting miRNA-Gene Networks to Map Clinical Utility Roads of Pharmacogenomics-Guided Therapeutic Decisions in Cardiovascular Precision Medicine.

MicroRNAs (miRNAs) create systems networks and gene-expression circuits through molecular signaling and cell interactions that contribute to health imbalance and the emergence of cardiovascular disorders (CVDs). Because the clinical phenotypes of CVD patients present a diversity in their pathophysiology and heterogeneity at the molecular level, it is essential to establish genomic signatures to delineate multifactorial correlations, and to unveil the variability seen in therapeutic intervention outcomes. The clinically validated miRNA biomarkers, along with the relevant SNPs identified, have to be suitably implemented in the clinical setting in order to enhance patient stratification capacity, to contribute to a better understanding of the underlying pathophysiological mechanisms, to guide the selection of innovative therapeutic schemes, and to identify innovative drugs and delivery systems. In this article, the miRNA–gene networks and the genomic signatures resulting from the SNPs will be analyzed as a method of highlighting specific gene-signaling circuits as sources of molecular knowledge which is relevant to CVDs. In concordance with this concept, and as a case study, the design of the clinical trial GESS (NCT03150680) is referenced. The latter is presented in a manner to provide a direction for the improvement of the implementation of pharmacogenomics and precision cardiovascular medicine trials.

Systematic analysis of gene expression alteration of BIRC5/survivn in gastric cancer.

353 Background: BIRC5/survivin gene is a member of the inhibitor of apoptosis (IAP) gene family, which encode negative regulatory proteins that prevent apoptotic cell death. Abnormal BIRC5/survivin expression is associated with carcinogenesis. Methods: We used sequencing data from The Cancer Genome Atlas database，Oncomine database and GTEx database, analyzed BIRC5/survivin expression and gene regulation networks in gastric carcinoma (STAD).Kaplan-Meier plotter database was used to assess the BIRC5/survivin prognostic potential. ULACAN was used to further analyze the relationship between the expression of BIRC5/survivin and the clinical stage of gastric cancer, and the methylation data of the promoter region of BIRC5/survivin. LinkedOmics was used to identify differential gene expression with BIRC5/survivin and to analyze Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. Gene enrichment analysis examined target networks of kinases, miRNAs and transcription factors. We investigated the correlation of BIRC5/survivin expression in gastric cancer with immune infiltration levels from TIMER database and TISID database. Results: We found that BIRC5/survivin is overexpressed in gastric cancer. The patient with high expression of this gene is associated with poor prognosis. The expression of BIRC5/survivin is positive with ERBB2 expression,TMB,MSI,MSH2,MSH6,PMS2.BIRC5/surviving expression is significantly positively correlated to tumor purity and has significant negative correlation with the immune cell infiltration level of B cells,CD8+T cells,CD4+T cells, Macrophage cells, Neutrophil cells and Dendritic cells. BIRC5/survivin expression is significantly positively correlated CD274，LAG3 and PDCD1. Our results show a detailed landscape map of BIRC5/survivin gene mutation in STAD. Our results showed the associations between BIRC5/survivin expression and six immune subtypes: C1 (wound healing); C2 (IFN-gamma dominant);C3 (inflammatory); C4 (lymphocyte depleted); C6 (TGF-b dominant) in STAD. Conclusions: Our results demonstrate that data mining efficiently reveals information about BIRC5/survivin expression and potential regulatory networks in gastric cancer, laying a foundation for further study of the role of BIRC5/survivin in carcinogenesis and tumor immunotherapy.

A data-driven biocomputing pipeline with meta-analysis on high throughput transcriptomics to identify genome-wide miRNA markers associated with type 2 diabetes

BackgroundMicroRNAs (miRNAs) are sought-after biomarkers of complex, polygenic diseases such as type 2 diabetes (T2D). Data-driven biocomputing provides robust and novel avenues for synthesizing evidence from individual miRNA seq studies. ObjectiveTo identify miRNA markers associated with T2D, via a data-driven, biocomputing approach on high throughput transcriptomics. Materials and methodsThe pipeline consisted of five sequential steps using miRNA seq data retrieved from the National Center for Biotechnology Information Gene Expression Omnibus platform: systematic review; identification of differentially expressed miRNAs (DE-miRNAs); meta-analysis of DE-miRNAs; network analysis; and downstream analyses. Three normalization algorithms (trimmed mean of M-values; upper quartile; relative log expression) and two meta-analytic algorithms (robust rank aggregation; Fisher's method of p-value combining) were integrated into the pipeline. Network analysis was conducted on miRNet 2.0 while enrichment and over-representation analyses were conducted on miEAA 2.0. ResultsA total of 1256 DE-miRNAs (821 downregulated; 435 upregulated) were identified from 5 eligible miRNA seq datasets (3 circulatory; 1 adipose; 1 pancreatic). The meta-signature comprised 9 miRNAs (hsa-miR-15b-5p; hsa-miR-33b-5p; hsa-miR-106b-3p; hsa-miR-106b-5p; hsa-miR-146a-5p; hsa-miR-483-5p; hsa-miR-539-3p; hsa-miR-1260a; hsa-miR-4454), identified via the two meta-analysis approaches. Two hub nodes (hsa-miR-106b-5p; hsa-miR-15b-5p) with above-average degree and betweenness centralities in the miRNA-gene interactions network were identified. Downstream analyses revealed 5 highly conserved- (hsa-miR-33b-5p; hsa-miR-15b-5p; hsa-miR-106b-3p; hsa-miR-106b-5p; hsa-miR-146a-5p) and 7 highly confident- (hsa-miR-33b-5p; hsa-miR-15b-5p; hsa-miR-106b-3p; hsa-miR-106b-5p; hsa-miR-146a-5p; hsa-miR-483-5p; hsa-miR-539-3p) miRNAs. A total of 288 miRNA-disease associations were identified, in which 3 miRNAs (hsa-miR-15b-5p; hsa-miR-106b-3p; hsa-miR-146a-5p) were highly enriched. ConclusionsA meta-signature of DE-miRNAs associated with T2D was discovered via in-silico analyses and its pathobiological relevance was validated against corroboratory evidence from contemporary studies and downstream analyses. The miRNA meta-signature could be useful for guiding future studies on T2D. There may also be avenues for using the pipeline more broadly for evidence synthesis on other conditions using high throughput transcriptomics.

Screening for Regulatory Network of miRNA-Inflammation, Oxidative Stress and Prognosis-Related mRNA in Acute Myocardial Infarction: An in silico and Validation Study.

BackgroundAcute myocardial infarction (AMI), which commonly leads to heart failure, is among the leading causes of mortality worldwide. The aim of this study was to find potential regulatory network for miRNA-inflammation, oxidative stress and prognosis-related mRNA to uncover molecular mechanisms of AMI.MethodsThe expression profiles of miRNA and mRNA in the blood samples from AMI patients were downloaded from the Gene Expression Omnibus (GEO) dataset for differential expression analysis. Weighted gene co-expression network analysis (WGCNA) was used to further identify important mRNAs. The negatively regulatory network construction of miRNA–inflammation, oxidative stress and prognosis-related mRNAs was performed, followed by protein–protein interaction (PPI) and functional analysis of mRNAs.ResultsA total of three pairs of negatively regulatory network of miRNA–inflammation and prognosis-related mRNAs (hsa-miR-636/hsa-miR-491-3p/hsa-miR-188-5p/hsa-miR-188-3p-AQP9, hsa-miR-518a-3p-C5AR1 and hsa-miR-509-3-5p/hsa-miR-127-5p-PLAUR), two pairs of negatively regulatory network of miRNA–oxidative stress and prognosis-related mRNAs (hsa-miR-604-TLR4 and hsa-miR-139-5p-CXCL1) and three pairs of negatively regulatory network of miRNA-inflammation, oxidative stress and prognosis-related mRNA (hsa-miR-634/hsa-miR-591-TLR2, hsa-miR-938-NFKBIA and hsa-miR-520h/hsa-miR-450b-3p-ADM) were identified. In the KEGG analysis, some signaling pathways were identified, such as complement and coagulation cascades, pathogenic Escherichia coli infection, chemokine signaling pathway and cytokine–cytokine receptor interaction and Toll-like receptor signaling pathway.ConclusionIdentified negatively regulatory network of miRNA-inflammation/oxidative stress and prognosis-related mRNA may be involved in the process of AMI. Those inflammation/oxidative stress and prognosis-related mRNAs may be diagnostic and prognostic biomarkers for AMI.

Abstract TMP111: The Detrimental Effects Of Post-stroke Social Isolation On Microglial Activation Is Mediated By MicroRNAs

Introduction: Social Isolation (SI) is a risk factor for a wide array of psychological disorders. SI significantly enhances the incidence of developing neurological diseases, including stroke within the elderly population. Recent studies have shown microRNA (miRNA) signatures in the brain and the circulation are altered in social defeat models and under stressful environmental conditions. Although SI has shown to influence post-stroke recovery, potential targetable interventions to mitigate these inflammatory events are limited. Hypothesis: Post-stroke SI influences temporally distinct miRNA networks in the brain that regulate acute microglial activation and contribute to chronic depressive phenotypes. Methods: Aged (18-20 month) C57BL/6 male mice were subjected to 60-minute middle cerebral artery occlusion (MCAO) followed by reperfusion. Mice were randomly assigned to either continued pair housing (PH), or SI three days after a 60-minute MCAO. Mice were euthanized at post-stroke SI Day 1, 4, and 27 and ipsilateral hemispheres were collected for miRNA sequencing and downstream analysis. Behavioral tests and brain cell analysis using flow cytometry were performed using independent experimental cohorts. Results: The top 10 differentially expressed miRNAs were identified in SI vs. PH mice across three time points (FC ≥ 1.5, FDR adjusted P &lt;0.05, n=4/group). Interactional network analysis revealed miR-466i-3p, miR-10a-5p, and miR-10b-5p as pivotal nodes that regulated the expression of the largest subset of genes involved in microglial-specific immune activation and chronic depression after stroke at SI D4 and D27, respectively. Flow cytometry analysis showed that microglia are significantly activated at post-stroke SI Day 4, as assessed by the downregulation of microglia-specific homeostatic protein purinergic receptor P2RY12 ( P &lt;0.05, n=7-8/group) and interestingly, chronic SI induced depressive-like behaviors in aged stroke mice; consistent with our miRNA-based pathway analysis. Conclusion: This is the first comprehensive miRNA expression profiling study using NGS technique in aging, stroke, and SI. Our data revealed that SI-specific miRNAs are involved in microglial activation and chronic depression in aged mice.

Deregulatory miRNA-BDNF Network Inferred from Dynamic Expression Changes in Schizophrenia.

(1) Background: Brain-derived neurotrophic factor (BDNF) is one of the promising risk genes for schizophrenia (SZ), a disease with prominent dysregulation of miRNA networks. Here, we present a study of miRNA-BDNF co-expression changes in peripheral blood of SZ patients. (2) Methods: The expression levels of the BDNF mRNA and three validated binding miRNAs—miR-124-3p, miR-132-3p, and miR-206—were quantified in the blood of 48 healthy controls and 32 SZ patients before and after 12 weeks of treatment. The co-expression patterns were evaluated in the three groups. (3) Results: The expression levels of BDNF were significantly downregulated in SZ patients compared to the controls. After the treatment, the expression levels of BDNF were upregulated, while the expression levels of the three miRNAs were downregulated. Co-expression analyses showed positive correlations of this network in the SZ patients, while weak negative correlations were observed in the healthy controls. After the 12-week treatment, the overall correlation between BDNF and the three miRNAs reached the levels comparable to the healthy controls. (4) Conclusions: Our findings suggest the involvement of the miRNA-BDNF network in the onset and treatment of SZ.

Identification of candidate targets and mechanisms involved in miRNA regulation in multiple myeloma

BackgroundMultiple myeloma (MM) is a complex disease affected by many factors. The recognition of miRNA networks is helpful for specific detection and personalised treatment.MethodsmRNA expression profiles were obtained from GSE39754 and GSE87830, and differentially expressed mRNAs (DEmRs) between MM and controls were identified. The intersection of the two sets of DEmRs in GSE39754 and GSE87830 was identified as common mRNAs, and enrichment analysis was subsequently performed. Moreover, we analysed differentially expressed miRNAs (DEmiRs) between MM and controls in GSE87830. A regulatory network of target mRNAs related to the overall survival of MM patients was then constructed.ResultsIn this study, a total of 356 common mRNAs were identified that were significantly enriched in neutrophil-mediated immunity, Th17 cell differentiation and PI3K-Akt signalling pathways. Moreover, we identified 103 DEmiRs and predicted 91 differentially expressed mRNAs as target mRNAs. Cox regression analysis was used to screen 14 target mRNAs that significantly affected the survival of MM patients. In the constructed integrated regulatory network, HIF1A and THBS1 were found to participate in Th17 cell differentiation and PI3K-Akt signalling pathways.ConclusionThese findings improve the understanding of the regulatory mechanisms of MM. Genes that are part of integrated regulatory networks may represent candidate targets for MM treatment.

Constructing mRNA, miRNA, circRNA and lncRNA regulatory network by Analysis of microarray data in breast cancer

BackgroundLuminal tumors are the utmost frequent subtype of breast cancer (BC). Despite luminal BC has relatively good prognosis, in a subset of patients, disease relapse occurs to endocrine therapy; hence, there is a critical need to identify new strategies to promote the early detection and more effective therapies. Noncoding RNAs including microRNAs, long noncoding RNAs, and circular RNAs can interact with and modulate each other via diverse molecular mechanisms and make a complicated regulatory network. ncRNAs participate in diverse biological processes and disorders such as breast tumors. Therefore, understanding their regulatory mechanisms allow to develop new field of research and therapeutic options for BC patients. MethodsIn this study, BC-specific RNA expression profiles including mRNAs, miRNAs, lncRNAs, and circRNAs were retrieved from Gene Expression Omnibus microarray datasets, and differentially expressed (DE) items were obtained. Disease ontology, functional and pathway enrichment analyses were executed. The protein-protein interaction network was constructed, and hub mRNAs were extracted. The prognostic value of hub mRNAs in patients of BC was performed. Subsequently, a ceRNA network was established. ResultsIn total, 691 DE genes, 122 DE lncRNAs, 60 DE miRNAs, and 38 DE circRNAs in breast tumor samples were compared with normal samples. Subsequently, 12 hub-genes including FOXO3, RHOA, EZH2, KIT, HSP90B1, NCOA3, RAC1, IGF1, CAV1, CXCR4, CCNB1, and ITGB1 were screened from the network. Kaplan-Meier Plotter results revealed that FOXO3 and RHOA were a suitable prognostic marker for patients with breast cancer. Finally, we determined possible ncRNAs (circ0007535, circ0002727, circ0005240, circ0014130, circ0044927, circ0007001, circ0089153, NORAD, MALAT1, TUG1, ZFAS1, OPI5-AS1, miR183, miR182, miR101, miR200c, miR200b, miR149, miR342, and miR1207) which could crosstalk with each other to regulate FOXO3 and RHOA through different regulatory patterns. ConclusionThese data might improve our perception of the breast tumorigenesis and could develop new field of research and therapeutic options for BC patients.

Bioinformatic-based Identification of Genes Associated with Aortic Valve Stenosis.

Aortic valve stenosis (AS) disease is the most common valvular disease in developed countries. The pathology of AS is complex, and its main processes include calcification of the valve stroma and involve genetic factors, lipoprotein deposition and oxidation, chronic inflammation, osteogenic transition of cardiac valve interstitial cells, and active valve calcification. The aim of this study was to identify potential genes associated with AS. Three original gene expression profiles (GSE153555, GSE12644, and GSE51472) were downloaded from the Gene Expression Omnibus (GEO) database and analyzed by GEO2R tool or 'limma' in R to identify differentially expressed genes (DEGs). Functional enrichment was analyzed using the ClusterProfiler package in R Bioconductor. STRING was utilized for the Protein-Protein Interaction (PPI) Network construct, and tissue-specific gene expression were identified using BioGPS database. The hub genes were screened out using the Cytoscape software. Related miRNAs were predicted in Targetscan, miWalk, miRDB, Hoctar, and TarBase. A total of 58 upregulated genes and 20 downregulated genes were screened out, which were mostly enriched in matrix remodeling and the immune system process. A module was thus clustered into by PPI network analysis, which mainly involved in Fc gamma R-mediated phagocytosis, Osteoclast differentiation. Ten genes (IBSP, NCAM1, MMP9, FCGR3B, COL4A3, FCGR1A, THY1, RUNX2, ITGA4, and COL10A1) with the highest degree scores were subsequently identified as the hub genes for AS by applying the CytoHubba plugin. And hsa-miR-1276 was finally identified as potential miRNA and miRNA-gene regulatory network was constructed using NetworkAnalyst. Our analysis suggested that IBSP, NCAM1, MMP9, FCGR3B, COL4A3, FCGR1A, THY1, RUNX2, ITGA4, and COL10A1 might be hub genes associated with AS, and hsa-miR-1276 was potential miRNA. This result could provide novel insight into pathology and therapy of AS in the future.

MiRNA and lncRNA Expression Networks Modulate Cell Cycle and DNA Repair Inhibition in Senescent Prostate Cells

Cellular senescence is a state of permanent growth arrest that arises once cells reach the limit of their proliferative capacity. It creates an inflammatory microenvironment favouring the initiation and progression of various age-related diseases, including prostate cancer. Non-coding RNAs (ncRNAs) have emerged as important regulators of cellular gene expression. Nonetheless, very little is known about the interplay of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) and how deregulation of ncRNA networks promotes cellular senescence. To investigate this, human prostate epithelial cells were cultured through different passages until senescent, and their RNA was extracted and sequenced using RNA sequencing (RNAseq) and microRNA sequencing (miRNA-seq) miRNAseq. Differential expression (DE) gene analysis was performed to compare senescent and proliferating cells with Limma, miRNA-target interactions with multiMiR, lncRNA-target interactions using TCGA data and network evaluation with miRmapper. We found that miR-335-3p, miR-543 and the lncRNAs H19 and SMIM10L2A all play central roles in the regulation of cell cycle and DNA repair processes. Expression of most genes belonging to these pathways were down-regulated by senescence. Using the concept of network centrality, we determined the top 10 miRNAs and lncRNAs, with miR-335-3p and H19 identified as the biggest hubs for miRNAs and lncRNA respectively. These ncRNAs regulate key genes belonging to pathways involved in cell senescence and prostate cancer demonstrating their central role in these processes and opening the possibility for their use as biomarkers or therapeutic targets to mitigate against prostate ageing and carcinogenesis.

Transplantation of umbilical cord-derived mesenchymal stem cells promotes the recovery of thin endometrium in rats

The endometrium plays a critical role in embryo implantation and pregnancy, and a thin uterus is recognized as a key factor in embryo implantation failure. Umbilical cord mesenchymal stem cells (UC-MSCs) have attracted interest for the repair of intrauterine adhesions. The current study investigated the repair of thin endometrium in rats using the UC-MSCs and the mechanisms involved. Rats were injected with 95% ethanol to establish a model of thin endometrium. The rats were randomly divided into normal, sham, model, and UC-MSCs groups. Endometrial morphological alterations were observed by hematoxylin–eosin staining and Masson staining, and functional restoration was assessed by testing embryo implantation. The interaction between UC-MSCs and rat endometrial stromal cells (ESCs) was evaluated using a transwell 3D model and immunocytochemistry. Microarray mRNA and miRNA platforms were used for miRNA-mRNA expression profiling. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses were performed to identify the biological processes, molecular functions, cellular components, and pathways of endometrial injury and UC-MSCs transplantation repair and real-time quantitative reverse transcription PCR (qRT-PCR) was performed to further identify the expression changes of key molecules in the pathways. Endometrium thickness, number of glands, and the embryo implantation numbers were improved, and the degree of fibrosis was significantly alleviated by UC-MSCs treatment in the rat model of thin endometrium. In vitro cell experiments showed that UC-MSCs migrated to injured ESCs and enhanced their proliferation. miRNA microarray chip results showed that expression of 45 miRNAs was downregulated in the injured endometrium and upregulated after UC-MSCs transplantation. Likewise, expression of 39 miRNAs was upregulated in the injured endometrium and downregulated after UC-MSCs transplantation. The miRNA-mRNA interactions showed the changes in the miRNA and mRNA network during the processes of endometrial injury and repair. GO and KEGG analyses showed that the process of endometrial injury was mainly attributed to the decomposition of the extracellular matrix (ECM), protein degradation and absorption, and accompanying inflammation. The process of UC-MSCs transplantation and repair were accompanied by the reconstruction of the ECM, regulation of chemokines and inflammation, and cell proliferation and apoptosis. The key molecules involved in ECM-receptor interaction pathways were further verified by qRT-PCR. Itga1 and Thbs expression decreased in the model group and increased by UC-MSCs transplantation, while Laminin and Collagen expression increased in both the model group and MSCs group, with greater expression observed in the latter. This study showed that UC-MSCs transplantation could promote recovery of thin endometrial morphology and function. Furthermore, it revealed the expression changes of miRNA and mRNA after endometrial injury and UC-MSCs transplantation repair processed, and signaling pathways that may be involved in endometrial injury and repair.

CeRNA Network and Functional Enrichment Analysis of Preeclampsia by Weighted Gene Coexpression Network Analysis.

Background Preeclampsia (PE) is a multisystemic syndrome which has short- and long-term risk to mothers and children and has pluralistic etiology. Objective This study is aimed at constructing a competitive endogenous RNA (ceRNA) network for pathways most related to PE using a data mining strategy based on weighted gene coexpression network analysis (WGCNA). Methods We focused on pathways involving hypoxia, angiogenesis, and epithelial mesenchymal transition according to the gene set variation analysis (GSVA) scores. The gene sets of these three pathways were enriched by gene set enrichment analysis (GSEA). WGCNA was used to study the underlying molecular mechanisms of the three pathways in the pathogenesis of PE by analyzing the relationship among pathways and genes. The soft threshold power (β) and topological overlap matrix allowed us to obtain 15 modules, among which the red module was chosen for the downstream analysis. We chose 10 hub genes that satisfied ∣log2Fold Change | >2 and had a higher degree of connectivity within the module. These candidate genes were subsequently confirmed to have higher gene significance and module membership in the red module. Coexpression networks were established for the hub genes to unfold the connection between the genes in the red module and PE. Finally, ceRNA networks were constructed to further clarify the underlying molecular mechanism involved in the occurrence of PE. 56 circRNAs, 17 lncRNAs, and 20 miRNAs participated in the regulation of the hub genes. Coagulation factor II thrombin receptor (F2R) and lumican (LUM) were considered the most relevant genes, and ceRNA networks of them were constructed. Conclusion The microarray data mining process based on bioinformatics methods constructed lncRNA and miRNA networks for ten hub genes that were closely related to PE and focused on ceRNAs of F2R and LUM finally. The results of our study may provide insight into the mechanisms underlying PE occurrence.

MicroRNA global profiling in cystic fibrosis cell lines reveals dysregulated pathways related with inflammation, cancer, growth, glucose and lipid metabolism, and fertility: an exploratory study.

Background and aim:Cystic fibrosis (CF), is due to CF transmembrane conductance regulator (CFTR) loss of function, and is associated with comorbidities. The increasing longevity of CF patients has been associated with increased cancer risk besides the other known comorbidities. The significant heterogeneity among patients, suggests potential epigenetic regulation. Little attention has been given to how CFTR influences microRNA (miRNA) expression and how this may impact on biological processes and pathways.Methods:We assessed the changes in miRNAs and subsequently identified the affected molecular pathways using CFBE41o-, and IB3 human immortalized cell lines since they reflect the most common genetic mutations in CF patients, and 16HBE14o- cells were used as controls.Results:In the CF cell lines, 41 miRNAs showed significant changes (FC (log2) ≥ +2 or FC (log2) ≤ -2 and p-value≤0.05). Gene target analysis evidenced 511 validated miRNA target genes. Gene Ontology analysis evidenced cancer, inflammation, body growth, glucose, and lipid metabolism as the biological processes most impacted by these miRNAs. Protein-protein interaction and pathway analysis highlighted 50 significantly enriched pathways among which RAS, TGF beta, JAK/STAT and insulin signaling.Conclusions:CFTR loss of function is associated with changes in the miRNA network, which regulates genes involved in the major comorbidities that affect CF patients suggesting that further research is warranted. (www.actabiomedica.it)

Assays for the Spectrum of Circulating Tumor Cells.

Cancer cells sharing stem cell properties are called "cancer stem cells" (CSCs). CSCs have distinct metabolic properties, are intrinsically drug resistant evading chemotherapies, are regulated by miRNA networks and participate in tumor relapse and metastases. During metastatic dissemination, circulating tumor cells (CTCs) invade distant organs and settle in supportive niches. In this process, the stem cell-like properties within CTCs contribute to CTC survival and eventually seed the growth of a secondary tumor. We herein describe methodologies for the analysis of CTCs as they reside in distinct functional pools with distinct characteristics.