Preliminary construction of non-coding RNAs and ceRNA regulatory networks mediated by exosomes in porcine follicular fluid.

BACKGROUND: Follicles are fundamental units of the ovary, regulated intricately during development. Exosomes and ovarian granulosa cells (OGCs) play pivotal roles in follicular development, yet the regulatory mechanisms governing exosomes remain elusive. RESULTS: High-throughput sequencing was employed to evaluate the complete transcript expression profiles of six samples (three porcine ovarian granulosa cells-exosome co-culture samples (GCE) and three porcine ovarian granulosa cells (POGCs) samples). Differential expression analysis revealed 924 lncRNAs, 35 circRNAs, 49 miRNAs, and 9823 mRNAs in the GCE group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated enrichment of differentially expressed transcripts in pathways related to cell proliferation and apoptosis. Furthermore, a ceRNA regulatory network comprising 43 lncRNAs, 6 circRNAs, 11 miRNAs, and 126 mRNAs was constructed based on intergene co-expression correlations. Seven miRNAs associated with cell proliferation and apoptosis regulation were identified within this network, encompassing 92 subnet pairs as candidate genes for further exploration of exosome regulatory mechanisms. Additionally, preliminary verification at the cellular level demonstrated that exosomal miR-200b enhances the viability of POGCs. CONCLUSIONS: Transcriptome analysis unveiled a pivotal candidate ceRNA network potentially implicated in exosome-mediated regulation of granulosa cell proliferation and apoptosis, thereby influencing porcine follicular development. These findings offer insights into the molecular mechanisms of follicular fluid exosome regulation, encompassing both coding and non-coding RNA perspectives.

Identification of necroptosis-related genes in ankylosing spondylitis by bioinformatics and experimental validation.

The pathogenesis of ankylosing spondylitis (AS) remains unclear, and while recent studies have implicated necroptosis in various autoimmune diseases, an investigation of its relationship with AS has not been reported. In this study, we utilized the Gene Expression Omnibus database to compare gene expressions between AS patients and healthy controls, identifying 18 differentially expressed necroptosis-related genes (DENRGs), with 8 upregulated and 10 downregulated. Through the application of three machine learning algorithms-least absolute shrinkage and selection operation, support vector machine-recursive feature elimination and random forest-two hub genes, FASLG and TARDBP, were pinpointed. These genes demonstrated high specificity and sensitivity for AS diagnosis, as evidenced by receiver operating characteristic curve analysis. These findings were further supported by external datasets and cellular experiments, which confirmed the downregulation of FASLG and upregulation of TARDBP in AS patients. Immune cell infiltration analysis suggested that CD4+ T cells, CD8+ T cells, NK cells and neutrophils may be associated with the development of AS. Notably, in the group with high FASLG expression, there was a significant infiltration of CD8+ T cells, memory-activated CD4+ T cells and resting NK cells, with relatively less infiltration of memory-resting CD4+ T cells and neutrophils. Conversely, in the group with high TARDBP expression, there was enhanced infiltration of naïve CD4+ T cells and M0 macrophages, with a reduced presence of memory-resting CD4+ T cells. In summary, FASLG and TARDBP may contribute to AS pathogenesis by regulating the immune microenvironment and immune-related signalling pathways. These findings offer new insights into the molecular mechanisms of AS and suggest potential new targets for therapeutic strategies.

Identification of different myofiber types in pigs muscles and construction of regulatory networks.

BACKGROUND: Skeletal muscle is composed of muscle fibers with different physiological characteristics, which plays an important role in regulating skeletal muscle metabolism, movement and body homeostasis. The type of skeletal muscle fiber directly affects meat quality. However, the transcriptome and gene interactions between different types of muscle fibers are not well understood. RESULTS: In this paper, we selected 180-days-old Large White pigs and found that longissimus dorsi (LD) muscle was dominated by fast-fermenting myofibrils and soleus (SOL) muscle was dominated by slow-oxidizing myofibrils by frozen sections and related mRNA and protein assays. Here, we selected LD muscle and SOL muscle for transcriptomic sequencing, and identified 312 differentially expressed mRNA (DEmRs), 30 differentially expressed miRNA (DEmiRs), 183 differentially expressed lncRNA (DElRs), and 3417 differentially expressed circRNA (DEcRs). The ceRNA network included ssc-miR-378, ssc-miR-378b-3p, ssc-miR-24-3p, XR_308817, XR_308823, SMIM8, MAVS and FOS as multiple core nodes that play important roles in muscle development. Moreover, we found that different members of the miR-10 family expressed differently in oxidized and glycolytic muscle fibers, among which miR-10a-5p was highly expressed in glycolytic muscle fibers (LD) and could target MYBPH gene mRNA. Therefore, we speculate that miR-10a-5p may be involved in the transformation of muscle fiber types by targeting the MYHBP gene. In addition, PPI analysis of differentially expressed mRNA genes showed that ACTC1, ACTG2 and ACTN2 gene had the highest node degree, suggesting that this gene may play a key role in the regulatory network of muscle fiber type determination. CONCLUSIONS: We can conclude that these genes play a key role in regulating muscle fiber type transformation. Our study provides transcriptomic profiles and ceRNA interaction networks for different muscle fiber types in pigs, providing reference for the transformation of pig muscle fiber types and the improvement of meat quality.

Identification and characterization of circular RNAs involved in the fertility stability of cotton CMS-D2 restorer line under heat stress.

BACKGROUND: As a vital type of noncoding RNAs, circular RNAs (circRNAs) play important roles in plant growth and development and stress response. However, little is known about the biological roles of circRNAs in regulating the stability of male fertility restoration for cytoplasmic male sterility (CMS) conditioned by Gossypium harknessii cytoplasm (CMS-D2) cotton under high-temperature (HT) stress. RESULTS: In this study, RNA-sequencing and bioinformatics analysis were performed on pollen grains of isonuclear alloplasmic near-isogenic restorer lines NH [N(Rf1rf1)] and SH [S(Rf1rf1)] with obvious differences in fertility stability under HT stress at two environments. A total of 967 circRNAs were identified, with 250 differentially expressed under HT stress. We confirmed the back-splicing sites of eight selected circRNAs using divergent primers and Sanger sequencing. Tissue-specific expression patterns of five differentially expressed circRNAs (DECs) were also verified by RT-PCR and qRT-PCR. Functional enrichment and metabolic pathway analysis revealed that the parental genes of DECs were significantly enriched in fertility-related biological processes such as pollen tube guidance and cell wall organization, as well as the Pentose and glucuronate interconversions, Steroid biosynthesis, and N-Glycan biosynthesis pathways. Moreover, we also constructed a putative circRNA-mediated competing endogenous RNA (ceRNA) network consisting of 21 DECs, eight predicted circRNA-binding miRNAs, and their corresponding 22 mRNA targets, especially the two ceRNA modules circRNA346-miR159a-MYB33 and circRNA484-miR319e-MYB33, which might play important biological roles in regulating pollen fertility stability of cotton CMS-D2 restorer line under HT stress. CONCLUSIONS: Through systematic analysis of the abundance, characteristics and expression patterns of circRNAs, as well as the potential functions of their parent genes, our findings suggested that circRNAs and their mediated ceRNA networks acted vital biological roles in cotton pollen development, and might be also essential regulators for fertility stability of CMS-D2 restorer line under heat stress. This study will open a new door for further unlocking complex regulatory mechanisms underpinning the fertility restoration stability for CMS-D2 in cotton.

Source leaves are regulated by sink strengths through non-coding RNAs and alternative polyadenylation in cucumber (Cucumis sativus L.).

BACKGROUND: The yield of major crops is generally limited by sink capacity and source strength. Cucumber is a typical raffinose family oligosaccharides (RFOs)-transporting crop. Non-coding RNAs and alternative polyadenylation (APA) play important roles in the regulation of growth process in plants. However, their roles on the sink‒source regulation have not been demonstrated in RFOs-translocating species. RESULTS: Here, whole-transcriptome sequencing was applied to compare the leaves of cucumber under different sink strength, that is, no fruit-carrying leaves (NFNLs) and fruit-carrying leaves (FNLs) at 12th node from the bottom. The results show that 1101 differentially expressed (DE) mRNAs, 79 DE long non-coding RNAs (lncRNAs) and 23 DE miRNAs were identified, which were enriched in photosynthesis, energy production and conversion, plant hormone signal transduction, starch and carbohydrate metabolism and protein synthesis pathways. Potential co-expression networks like, DE lncRNAs-DE mRNAs/ DE miRNAs-DE mRNAs, and competing endogenous RNA (ceRNA) regulation models (DE lncRNAs-DE miRNAs-DE mRNAs) associated with sink‒source allocation, were constructed. Furthermore, 37 and 48 DE genes, which enriched in MAPK signaling and plant hormone signal transduction pathway, exist differentially APA, and SPS (CsaV3_2G033300), GBSS1 (CsaV3_5G001560), ERS1 (CsaV3_7G029600), PNO1 (CsaV3_3G003950) and Myb (CsaV3_3G022290) may be regulated by both ncRNAs and APA between FNLs and NFNLs, speculating that ncRNAs and APA are involved in the regulation of gene expression of cucumber sink‒source carbon partitioning. CONCLUSIONS: These results reveal a comprehensive network among mRNAs, ncRNAs, and APA in cucumber sink-source relationships. Our findings also provide valuable information for further research on the molecular mechanism of ncRNA and APA to enhance cucumber yield.

Identification and diagnostic potential of hsa_circ_101303 in colorectal cancer: unraveling a regulatory network.

BACKGROUND: The role of novel circular RNAs (circRNAs) in colorectal cancer (CRC) remains to be determined. This study aimed to identify a novel circRNA involved in CRC pathogenesis, assess its diagnostic value, and construct a regulatory network. METHODS: Differential expression analysis was conducted using circRNA datasets to screen for differentially expressed circRNAs. The expression of selected circRNAs was validated in external datasets and clinical samples. Diagnostic value of plasma circRNA levels in CRC was assessed. A competing endogenous RNA (ceRNA) network was constructed for the circRNA using TCGA dataset. RESULTS: Analysis of datasets revealed that hsa_circ_101303 was significantly overexpressed in CRC tissues compared to normal tissues. The upregulation of hsa_circ_101303 in CRC tissues was further confirmed through the GSE138589 dataset and clinical samples. High expression of hsa_circ_101303 was associated with advanced N stage, M stage, and tumor stage in CRC. Plasma levels of hsa_circ_101303 were markedly elevated in CRC patients and exhibited moderate diagnostic ability for CRC (AUC = 0.738). The host gene of hsa_circ_101303 was also found to be related to the TNM stage of CRC. Nine miRNAs were identified as target miRNAs for hsa_circ_101303, and 27 genes were identified as targets of these miRNAs. Subsequently, a ceRNA network for hsa_circ_101303 was constructed to illustrate the interactions between the nine miRNAs and 27 genes. CONCLUSIONS: The study identifies hsa_circ_101303 as a highly expressed circRNA in CRC, which is associated with the progression of the disease. Plasma levels of hsa_circ_101303 show promising diagnostic potential for CRC. The ceRNA network for hsa_circ_101303 provides valuable insights into the regulatory mechanisms underlying CRC.

Systemic whole transcriptome analysis identified underlying molecular characteristics and regulatory networks implicated in the retina following optic nerve injury.

Optic nerve injuries are severely disrupt the structural and functional integrity of the retina, often leading to visual impairment or blindness. Despite the profound impact of these injuries, the molecular mechanisms involved remain poorly understood. In this study, we performed a comprehensive whole-transcriptome analysis of mouse retina samples after optic nerve crush (ONC) to elucidate changes in gene expression and regulatory networks. Transcriptome analysis revealed a variety of molecular alterations, including 256 mRNAs, 530 lncRNAs, and 37 miRNAs, associated with metabolic, inflammatory, signaling, and biosynthetic pathways in the injured retina. The integrated analysis of co-expression and protein-protein interactions identified an active interconnected module comprising 5 co-expressed proteins (Fga, Serpina1a, Hpd, Slc38a4, and Ahsg) associated with the complement and coagulation cascades. Finally, 5 mRNAs (Fga, Serpinala, Hpd, Slc38a4, and Ahsg), 2 miRNAs (miR-671-5p and miR-3057-5p), and 6 lncRNAs (MSTRG. 1830.1, Gm10814, A530013C23Rik, Gm40634, MSTRG.9514.1, A330023F24Rik) were identified by qPCR in the injured retina, and some of them were validated as critical components of a ceRNA network active in 661W and HEK293T cells through dual-luciferase reporter assays. In conclusion, our study provides comprehensive insight into the complex and dynamic biological mechanisms involved in retinal injury responses and highlights promising potential targets to enhance neuroprotection and restore vision.

Transcriptional landscape of intestinal environment in DSS-induced ulcerative colitis mouse model.

Ulcerative colitis (UC) is a chronic inflammatory disease that targets the colon and has seen an increasing prevalence worldwide. In our pursuit of new diagnostic and therapeutic approaches for UC, we undertook a sequencing of colons from UC mouse models. We focused on analyzing their differentially expressed genes (DEGs), enriching pathways, and constructing protein-protein interaction (PPI) and Competing Endogenous RNA (ceRNA) networks. Our analysis highlighted novel DEGs such as Tppp3, Saa3, Cemip, Pappa, and Nr1d1. These DEGs predominantly play roles in pathways like cytokine-mediated signaling, extracellular matrix organization, extracellular structure organization, and external encapsulating structure organization. This suggests that the UC pathogenesis is intricately linked to the interactions between immune and non-immune cells with the extracellular matrix (ECM). To corroborate our findings, we also verified certain DEGs through quantitative real-time PCR. Within the PPI network, nodes like Stat3, Il1b, Mmp3, and Lgals3 emerged as significant and were identified to be involved in the crucial cytokine-mediated signaling pathway, which is central to inflammation. Our ceRNA network analysis further brought to light the role of the Smad7 Long non-coding RNA (lncRNA). Key MicroRNA (miRNAs) in the ceRNA network were pinpointed as mmu-miR-17-5p, mmu-miR-93-5p, mmu-miR-20b-5p, mmu-miR-16-5p, and mmu-miR-106a-5p, while central mRNAs included Egln3, Plagl2, Sema7a, Arrdc3, and Stat3. These insights imply that ceRNA networks are influential in UC progression and could provide further clarity on its pathogenesis. In conclusion, this research deepens our understanding of UC pathogenesis and paves the way for potential new diagnostic and therapeutic methods. Nevertheless, to solidify our findings, additional experiments are essential to confirm the roles and molecular interplay of the identified DEGs in UC.

Integrated analysis and validation of ferroptosis-related genes and immune infiltration in acute myocardial infarction.

BACKGROUND: Acute myocardial infarction (AMI) is indeed a significant cause of mortality and morbidity in individuals with coronary heart disease. Ferroptosis, an iron-dependent cell death, is characterized by the accumulation of intracellular lipid peroxides, which is implicated in cardiomyocyte injury. This study aims to identify biomarkers that are indicative of ferroptosis in the context of AMI, and to examine their potential roles in immune infiltration. METHODS: Firstly, the GSE59867 dataset was used to identify differentially expressed ferroptosis-related genes (DE-FRGs) in AMI. We then performed gene ontology (GO) and functional enrichment analysis on these DE-FRGs. Secondly, we analyzed the GSE76591 dataset and used bioinformatic methods to build ceRNA networks. Thirdly, we identified hub genes in protein-protein interaction (PPI) network. After obtaining the key DE-FRGs through the junction of hub genes with ceRNA and least absolute shrinkage and selection operator (LASSO). ImmucellAI was applied to estimate the immune cell infiltration in each sample and examine the relationship between key DE-FRGs and 24 immunocyte subsets. The diagnostic performance of these genes was further evaluated using the receiver operating characteristic (ROC) curve analysis. Ultimately, we identified an immune-related ceRNA regulatory axis linked to ferroptosis in AMI. RESULTS: Among 56 DE-FRGs identified in AMI, 41 of them were integrated into the construction of competitive endogenous RNA (ceRNA) networks. TLR4 and PIK3CA were identified as key DE-FRGs and PIK3CA was confirmed as a diagnostic biomarker for AMI. Moreover, CD4_native cells, nTreg cells, Th2 cells, Th17 cells, central-memory cells, effector-memory cells, and CD8_T cells had higher infiltrates in AMI samples compared to control samples. In contrast, exhausted cells, iTreg cells, and Tfh cells had lower infiltrates in AMI samples. Spearman analysis confirmed the correlation between 24 immune cells and PIK3CA/TLR4. Ultimately, we constructed an immune-related regulatory axis involving XIST and OIP5-AS1/miR-216a/PIK3CA. CONCLUSION: Our comprehensive analysis has identified PIK3CA as a robust and promising biomarker for this condition. Moreover, we have also identified an immune-related regulatory axis involving XIST and OIP5-AS1/miR-216a/PIK3CA, which may play a key role in regulating ferroptosis during AMI progression.

Core competing endogenous RNA network based on mRNA and non-coding RNA expression profiles in chicken fatty liver.

Fatty liver disease is a common metabolic disease in chickens. This disease can lead to a decrease in egg production and increase the risk of death in chickens. Long non-coding RNAs (lncRNAs) are involved in fatty liver formation by directly targeting genes or regulating gene expression by competitively binding microRNAs. However, a large proportion of competing endogenous RNA (ceRNA) networks in fatty liver diseases are still unclear. The total of 300 Jingxing-Huang chickens were used for fatty liver model construction. Then, differentially expressed (DE) genes (DEGs) identified through whole-transcriptome sequencing from four chickens with fatty liver and four chickens without fatty liver were chosen from the F1 generation. A total of 953 DEGs were identified between the fatty liver group and the control group, including 26 DE micro (mi)RNAs and 56 DE lncRNAs. Differential expression heatmaps and volcano plots were obtained after clustering expression analysis. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that these DEGs were involved in many biological processes and signaling pathways related to fatty acid metabolism and lipid synthesis. Furthermore, cytoscape was used to construct a ceRNA network of the DE miRNAs, DE mRNAs, and DE lncRNAs. Eleven DE lncRNAs, seven DE miRNAs, and 13 DE mRNAs were found to be associated with the pathogenesis of fatty liver disease. An lncRNA-miRNA-mRNA ceRNA network was constructed to elucidate the mechanisms of fatty liver diseases, and the ENSGALT00000079786-miR-140/miR-143/miR-1a/miR-22/miR-375 network was identified. These results provide a valuable resource for further elucidating the posttranscriptional regulatory mechanisms of chicken liver and adipose fat development or deposition.

Identification of key immune-related genes and potential therapeutic targets in immune checkpoint inhibitor-associated myocarditis.

BACKGROUND: Immune checkpoint inhibitors (ICIs) are widely used in cancer treatment; however, the emergence of ICI-associated myocarditis (ICI-MC) presents a severe and potentially fatal complication with poorly understood pathophysiological mechanisms. This study aimed to identify crucial immune-related genes in ICI-MC and uncover potential therapeutic targets using bioinformatics. METHODS: Using the GSE180045 dataset, which includes three groups-Group A: ICI patients without immune adverse events, Group B: ICI patients with non-myocarditis immune adverse events, and Group C: ICI patients with myocarditis-we analyzed differentially expressed genes (DEGs) between ICI-MC samples (Group C) and non-myocarditis controls (Groups A and B). These DEGs were then cross-referenced with 1796 immune-related genes from the immPort database to identify immune-related DEGs. We conducted functional enrichment analyses (Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, gene set enrichment analysis), constructed a protein-protein interaction network, and identified hub genes. Validation using the GSE4172 dataset led to the identification of optimal feature genes from the overlap between hub genes and DEGs. Predictions of target MicroRNAs (miRNAs) were made, and a competing endogenous RNA (ceRNA) network was constructed. Target drugs for hub genes were predicted using the Connectivity Map database. RESULTS: We identified 58 DEGs between ICI-MC and controls, which led to the identification of 32 immune-related DEGs after intersection with 1796 immune-related genes. Functional analyses revealed enrichment in cell lysis, CD8+ T-cell receptor, natural killer cell-mediated cytotoxicity, and RAGE signaling. Notably upregulated hub genes included IL7R, PRF1, GNLY, CD3G, NKG7, GZMH, GZMB, KLRB1, KLRK1, and CD247. In the validation dataset, 407 DEGs were uncovered, resulting in the identification of 3 optimal feature genes (KLRB1, NKG7, GZMH). The predicted target miRNAs, lincRNAs, and circRNAs constituted a comprehensive ceRNA network. Among the top 10 drugs with elevated connectivity scores was acetohydroxamic acid, indicating a need for caution in ICI treatment. CONCLUSION: KG7, GZMH, and KLRB1 were identified as pivotal immune-related genes in ICI-MC. Biological enrichments included pathways involved in cell lysis, the CD8+ T-cell receptor pathway, natural killer cell-mediated cytotoxicity, RAGE signaling, and proinflammatory responses. The ceRNA network illuminated the role of critical molecules and underscored the importance of avoiding drugs such as acetohydroxamic acid in ICI treatment. Key message What is already known on this topic  Myocarditis is recognized as a serious ICI-associated toxicity, seemingly infrequent yet often fulminant and lethal. The underlying mechanisms of ICI-associated myocarditis remain not fully understood. Although the significance of T cells and cytotoxic T lymphocyte-associated protein 4 (CTLA-4) is evident, the inciting antigens, the reasons for their recognition, and the mechanisms causing cardiac cell injury are not well characterized. An improved understanding of ICI-associated myocarditis will provide insights into the equilibrium between the immune and cardiovascular systems. What this study adds  Our study further validates the significance of T cells and CTLA-4 in ICI-associated myocarditis. More importantly, we identified three genes-NKG7, GZMH, and KLRB1-essential for the development of ICI-MC and proposed ceRNA networks involving these three key genes. How this study might affect research, practice or policy  The newly discovered key genes and their intricate molecular interactions offer a comprehensive perspective on the mechanisms underlying ICI-MC. Furthermore, our findings advise caution regarding the use of drugs like acetohydroxamic acid during ICI treatment. As our understanding of these regulatory networks deepens, our study provides valuable insights that could inform future therapeutic strategies for ICI-MC.

MiR-485-3p/MiR-543/MiR-337-3p is Required for the Oncogenic Potential of the Hsa_circ_0007385-MEMO1 Axis in Colorectal Cancer.

Circular RNAs (circRNAs) play regulatory roles in the biological processes of multiple tumors, colorectal cancer (CRC) included. Our previous study probed the impact of circ_0007385 on CRC cell malignant behaviors, while the underlying mechanism remains obscure. In this work, the potential mechanism of hsa_circ_0007385 in CRC was probed. Functional experiments were implemented for probing the function of hsa_circ_0007385 in CRC. Further analysis revealed the relation between hsa_circ_0007385 and miRNAs. A xenograft mouse model was implemented for probing the influence of hsa_circ_0007385 on CRC growth and metastasis in vivo. Hsa_circ_0007385 was up-regulated in CRC. Hsa_circ_0007385 positively regulated its host gene mediator of cell motility 1 (MEMO1). Hsa_circ_0007385 silencing inhibited CRC progression. Hsa_circ_0007385 and MEMO1 bond to miR-485-3p/miR-543/miR-337-3p, and these three miRNAs were lowly expressed in CRC, and negatively modulated by hsa_circ_0007385. Hsa_circ_0007385 functioned as an oncogene in CRC in a miR-485-3p/miR-543/miR-337-3p- or MEMO1-dependent manner. Hsa_circ_0007385 promoted CRC progression via modulating miR-485-3p/miR-543/miR-337-3p/MEMO1 axis. Thus, circ-MEMO1 might be a promising therapeutic target for CRC.

Integration Analysis of miRNA Circulating Expression Following Cerebellar Transcranial Direct Current Stimulation in Patients with Ischemic Stroke.

The aim of this study was to explore the molecular mechanisms underlying cerebellar transcranial direct current stimulation (ctDCS) as a rehabilitation intervention for patients with ischemic stroke, focusing on the role of microRNAs (miRNAs). Whole-transcriptome sequencing was employed to obtain circulating expression profiles of miRNAs, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and mRNAs in patients with ischemic stroke before and after 3-week ctDCS. miRanda software was used to predict the target genes of miRNAs, while Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to identify biological functions and signaling pathways. Subsequently, competing endogenous RNA (ceRNA) regulatory networks comprising circRNA-miRNA-mRNA and lncRNA-miRNA-mRNA interactions were constructed. Key miRNAs in blood samples were validated through quantitative RT-PCR. In total, 43 miRNAs, 807 lncRNAs, 1,111 circRNAs, and 201 mRNAs were differentially expressed after ctDCS compared with before ctDCS. Bioinformatics analyses revealed significant enrichment of target genes regulated by differentially expressed miRNAs across multiple biological pathways. CeRNA regulatory networks implied that several miRNAs were closely related to the ctDCS. Among them, hsa-miR-181a-5p, hsa-miR-224-5p, and hsa-miR-340-3p showed significantly downregulated expression levels as confirmed by qRT-PCR. This study conducted the first-ever assessment of miRNA expression patterns in patients with ischemic stroke undergoing ctDCS. The findings revealed that ctDCS induces alterations in miRNA levels, suggesting their potential utility as therapeutic markers.

lncRNA TTTY14 participates in the progression of repeated implantation failure by regulating the miR-6088/SEMA5A axis.

PURPOSE: To identify potential biomarkers and the molecular mechanisms associated with repeated implantation failure (RIF), three microarray datasets, GSE71331 (lncRNA + mRNA), GSE111974 (lncRNA + mRNA), and GSE71332 (miRNA), were retrieved from the Gene Expression Omnibus (GEO) database. METHODS: The differentially expressed mRNAs (DEMs), lncRNAs (DElncRNAs), and miRNAs (DEmiRNAs) between normal control samples (C group) and RIF samples (RIF group) were identified, and then a module partition analysis was performed based on weighted correlation network analysis (WGCNA). Following enrichment analysis of the genes, the lncRNA-miRNA-mRNA interactions (ceRNA) were examined. The mRNAs in the ceRNA network were evaluated using the GSE58144 dataset. Finally, the key RNAs were verified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). RESULTS: Fifty-three DEmiRNAs, 327 DEMs, and 13 DElncRNAs were identified between the C and RIF groups. According to WGCNA, the magenta module was positively correlated with RIF disease status. The lncRNA-mRNA interaction analysis based on genes in the magenta module revealed the intersecting lncRNAs, including peptidylprolyl isomerase E-like pseudogene (PPIEL) and the testis-specific transcript, y-Linked 14 (TTTY14); these lncRNAs are mainly involved in functions, such as plasma membrane organization. The ceRNA network analysis revealed several interactions, such as TTTY14-miR-6088-semaphorin 5 A (SEMA5A). Finally, SEMA5A and the zinc finger protein 555 (ZNF555) were identified to be significantly upregulated in the RIF group compared with those in the C group in the GSE58144 dataset. The RT-qPCR results aligned with the above results. CONCLUSIONS: Overall, TTTY14, ZNF555, SEMA5A, PPIEL, and miR-6088 could serve as novel biomarkers of RIF.

Comprehensive analysis of lncRNA-miRNA-mRNA ceRNA network and key genes in granulosa cells of patients with biochemical primary ovarian insufficiency.

Primary ovarian insufficiency (POI) is a common condition leading to the pathological decline of ovarian function in women of reproductive age, resulting in amenorrhea, hypogonadism, and infertility. Biochemical premature ovarian insufficiency (bPOI) is an intermediate stage in the pathogenesis of POI in which the fertility of patients has been reduced. Previous studies suggest that granulosa cells (GCs) play an essential role in the pathogenesis of POI, but their pathogenetic mechanisms remain unclear. To further explore the potential pathophysiological mechanisms of GCs in POI, we constructed a molecular long non-coding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA) network using GC expression data collected from biochemical premature ovarian failure (bPOI) patients in the GEO database. We discovered that the GCs of bPOI patients had differential expression of 131 mRNAs, 191 lncRNAs, and 28 miRNAs. By systematic network analysis, we identified six key genes, including SRSF1, PDIA5, NEURL1B, UNK, CELF2, and CFL2, and five hub miRNAs, namely hsa-miR-27a-3p, hsa-miR-24-3p, hsa-miR-22-3p, hsa-miR-129-5p, and hsa-miR-17-5p, and the results suggest that the expression of these key genes may be regulated by two hub miRNAs, hsa-miR-27a-3p and hsa-miR-17-5p. Additionally, a POI model in vitro was created to confirm the expression of a few important genes. In this study, we discovered a unique lncRNA-miRNA-mRNA network based on the ceRNA mechanism in bPOI for the first time, and we screened important associated molecules, providing a partial theoretical foundation to better understand the pathogenesis of POI.

A transcriptomics-based investigation of the mechanism of pulmonary fibrosis induced by nickel oxide nanoparticles.

Nickel oxide nanoparticles (NiONPs) are an emerging nanomaterial, which poses a huge threat to the health of workplace population. Nanoparticles induce pulmonary fibrosis, and its mechanisms are associated with noncoding RNAs (ncRNAs). However, ncRNAs and competing endogenous RNA (ceRNA) networks which involved in NiONP-induced pulmonary fibrosis are still unclear. This study aimed to identify ncRNA-related ceRNA networks and investigate the role of the Wnt/ß-catenin pathway in pulmonary fibrosis. Male Wistar rats were intratracheally instilled with 0.015, 0.06, and 0.24 mg/kg NiONPs twice a week for 9 weeks. First, we found there were 93 circularRNAs (circRNAs), 74 microRNAs (miRNAs), 124 long non-coding RNAs (lncRNAs), and 1675 messenger RNAs (mRNAs) differentially expressed through microarray analysis. Second, we constructed ceRNA networks among lncRNAs/circRNAs, miRNAs and mRNAs and identified two ceRNA networks (lncMelttl16/miR-382-5p/Hsd17b7 and circIqch/miR-181d-5p/Stat1) after real time-quantitative polymerase chain reaction (RT-qPCR) validation. Furthermore, based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, ncRNAs were found to be involved in biological processes and signaling pathways related to pulmonary fibrosis. KEGG analysis showed that NiONPs activated the Wnt/ß-catenin pathway in rats. In vitro, HFL1 cells were treated with 0, 50, 100, and 200 µg/mL NiONPs for 24 h. We found that NiONPs induced collagen deposition and Wnt/ß-catenin pathway activation. Moreover, a blockade of Wnt/ß-catenin pathway alleviated NiONP-induced collagen deposition. In conclusion, these observations suggested that ncRNAs were crucial in pulmonary fibrosis development and that the Wnt/ß-catenin pathway mediated the deposition of collagen.

Integrative analysis of circRNA networks in postoperative cognitive dysfunction.

OBJECTIVE: In the quest to decipher the molecular intricacies of Postoperative Cognitive Dysfunction (POCD), this study focused on circular RNA (circRNA) and their regulatory networks. MATERIALS AND METHODS: Analyzing the Gene Expression Omnibus Series (GSE) 147277 dataset, we pinpointed 10 differentially expressed circRNAs linked to POCD. RESULTS: The ensuing competing endogenous RNA (ceRNA) network, featuring pivotal players like Homo sapiens(hsa)_circ_0003424 and hsa-miR-193b-5p, provided a comprehensive understanding of the molecular players at play in POCD. CONCLUSION: Additionally, the Protein-Protein Interaction (PPI) network spotlighted 10 core Hub genes, including phosphatase and tensin homolog (PTEN) and signal transducer and activator of transcription 3(STAT3), shedding light on potential therapeutic targets.

A prognostic four-gene signature and a therapeutic strategy for hepatocellular carcinoma: Construction and analysis of a circRNA-mediated competing endogenous RNA network.

BACKGROUND: Hepatocellular carcinoma (HCC) has a poor long-term prognosis. The competition of circular RNAs (circRNAs) with endogenous RNA is a novel tool for predicting HCC prognosis. Based on the alterations of circRNA regulatory networks, the analysis of gene modules related to HCC is feasible. METHODS: Multiple expression datasets and RNA element targeting prediction tools were used to construct a circRNA-microRNA-mRNA network in HCC. Gene function, pathway, and protein interaction analyses were performed for the differentially expressed genes (DEGs) in this regulatory network. In the protein-protein interaction network, hub genes were identified and subjected to regression analysis, producing an optimized four-gene signature for prognostic risk stratification in HCC patients. Anti-HCC drugs were excavated by assessing the DEGs between the low- and high-risk groups. A circRNA-microRNA-hub gene subnetwork was constructed, in which three hallmark genes, KIF4A, CCNA2, and PBK, were subjected to functional enrichment analysis. RESULTS: A four-gene signature (KIF4A, CCNA2, PBK, and ZWINT) that effectively estimated the overall survival and aided in prognostic risk assessment in the The Cancer Genome Atlas (TCGA) cohort and International Cancer Genome Consortium (ICGC) cohort was developed. CDK inhibitors, PI3K inhibitors, HDAC inhibitors, and EGFR inhibitors were predicted as four potential mechanisms of drug action (MOA) in high-risk HCC patients. Subsequent analysis has revealed that PBK, CCNA2, and KIF4A play a crucial role in regulating the tumor microenvironment by promoting immune cell invasion, regulating microsatellite instability (MSI), and exerting an impact on HCC progression. CONCLUSIONS: The present study highlights the role of the circRNA-related regulatory network, identifies a four-gene prognostic signature and biomarkers, and further identifies novel therapy for HCC.

Duodenal-Jejunal bypass improves metabolism and re-models extra cellular matrix through modulating ceRNA network.

BACKGROUND: Bariatric surgery (BS) is an effective approach in treating obesity and ameliorating T2DM with obesity. Our previous studies demonstrated that duodenal-jejunal bypass (DJB) altered long non-coding RNAs (lncRNAs) in the gastrointestinal system, which is associated with modulation of lipid metabolism, and glycemic control through entero-pancreatic axis and gut-brain axis. The adipose non-coding RNA expression profile and the underlying competing endogenous RNA (ceRNA) regulatory network pattern post DJB needs further research and investigation. RESULTS: In this study, we compared the lncRNAs, circular RNAs (circRNAs) and messenger RNAs (mRNAs) expression in adipose tissues between the sham group and the DJB group. 2219 differentially expressed mRNAs (DEmRNAs), 722 differential expression of lncRNAs (DElncRNAs) and 425 differential expression of circRNAs (DEcircRNAs) were identified. GO terms and KEGG pathways analysis of the DEmRNAs implied that the dysregulated adipose mRNAs were associated with lipid, amino acid metabolism, insulin resistance, and extra cellular matrix (ECM)-related pathways. Moreover, via analyzing ceRNA regulatory networks of DElncRNAs and DEcircRNAs, 31 hub DE mRNAs, especially Mpp7, 9330159F19Rik, Trhde. Trdn, Sorbs2, were found on these pathways. CONCLUSIONS: The role of DJB in adipose tends to remodel ECM and improve the energy metabolism through the ceRNA regulatory network.

Nucleus pulposus related lncRNA and mRNA expression profiles in intervertebral disc degeneration.

In the present study, we aimed to have a comprehensive understanding of nucleus pulposus related long noncoding RNA (lncRNA) and mRNA expression profiles in intervertebral disc degeneration (IDD). In total, 2418 mRNAs and 528 lncRNAs were found to be differentially expressed in the IDD group compared with the Control group. Combining microarray datasets and sequencing data, 5 overlapping DEMs and 7 overlapping DELs were identified. NF-κB signaling pathway, PI3K-Akt signaling pathway and Wnt/ß-catenin signaling pathway were strongly linked with enriched GO terms and KEGG pathways. The ceRNA network suggested that lnc-TMEM44-AS1-hsa-miR-206-HDAC4 may be one crucial axis in IDD. PPI network analysis was constructed with 309 nodes and 129 edges. And the highest connectivity degrees were ALB, APOB and CCL2. This study suggested that specific lncRNAs and ceRNA axes may be crucial in the development of IDD. It provides a new perspective for delaying IDD process and enhancing intervertebral disc repair.