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Ventilator-induced diaphragmatic dysfunction (VIDD) is characterized by diaphragmatic atrophy and contractile failure, leading to prolonged intensive care unit (ICU) stays and increases mortality. While phrenic nerve stimulation (PNS) has demonstrated efficacy in mitigating VIDD by preserving diaphragmatic activity, its underlying molecular mechanisms remain unclear. This study aimed to elucidate the role of competing endogenous RNA (ceRNA) networks in PNS-mediated protection against VIDD through integrated miRNA-Seq and RNA-Seq analyses in a rabbit model. Eleven adult male New Zealand white rabbits were divided into control (n = 4), MV (n = 3) and PNS groups (n = 4). MV and PNS groups underwent 24 h of MV, with intermittent bilateral transvenous PNS applied only to the PNS group. Differentially expressed (DE) analysis of mRNAs, miRNAs and circRNAs across pairwise group comparisons was performed via RNA-seq and miRNA-seq. Functional enrichment analyses (Gene Ontology and Kyoto Encyclopedia of Genes and Genomes) identified key pathways. Potential miRNA targets and interacting circRNAs were computationally predicted. An integrated ceRNA network was constructed using major DE RNAs to identify PNS-associated core regulators. CeRNA network was validated by quantitative real-time polymerase chain reaction (RT-qPCR) and dual-luciferase assays. High-throughput sequencing revealed significant dysregulation of miRNAs, circRNAs and mRNAs in the diaphragm following MV which was partially reversed by PNS. Bioinformatic screening identified a ceRNA network, wherein two key miRNAs emerged: miR-500-3p (targeting RAB37 , an autophagy-related gene) and miR-133b-3p (targeting L-selectin , a cell adhesion molecule regulating immune responses and fibrosis). Both miRNAs were down-regulated after MV and restored by PNS. Computational prediction also identified five circRNAs (circRNA_12437, 24673, 14127, 14942, 12463) as putative sponges for these miRNAs, although this interaction lacks experimental confirmation. Dual-luciferase assays confirmed direct binding of miR-500-3p to RAB37 and miR-133b-3p to L-selectin , functionally linking them to PNS-mediated VIDD protection. Enrichment analyses indicated that DE genes were predominantly enriched in phagosome activity and cell adhesion molecule pathways. Collectively, these findings suggest that PNS preserves diaphragmatic function by modulating ceRNA networks to suppress excessive autophagy and immune cell infiltration. This study identifies the first PNS-responsive ceRNA network in VIDD pathogenesis. Our data highlight the potential critical roles of miR-500-3p- RAB37 and miR-133b-3p- L-selectin axes in regulating autophagy and immune responses. These results provide mechanistic insights and suggest potential therapeutic targets for diaphragm dysfunction.

Gastric cancer (GC), which primarily originates from gastric mucosal epithelium, is driven by factors such as Helicobacter pylori infection, genetic susceptibility and lifestyle. GC poses a serious threat to patient survival and quality of life. Metabolic reprogramming, a hallmark of tumorigenesis and progression, enables cancer cells to continuously adapt their energy metabolism to support proliferation, invasion, metastasis and drug resistance. Circular RNAs (circRNAs) are a class of non-coding RNAs characterized by a covalently closed circular structure, which confers high stability. They are differentially expressed in tumor cells and facilitate tumor proliferation and metastasis through multiple mechanisms such as microRNA sponging, protein binding, short peptide translation and N6-methyladenosine modification. Furthermore, circRNAs contribute to tumor metabolic remodeling, meeting the energy demands of tumor cells by regulating key enzymes and transporters involved in metabolic pathways, thereby modulating the synthesis or degradation of metabolites. The present review summarizes the mechanisms by which circRNAs mediate different metabolic modes during the initiation and progression of GC as well as discusses their potential as biomarkers for GC. By systematically elucidating the intricate interactions between circRNAs and metabolic reprogramming in GC, the present study aims to provide a theoretical foundation for the development of innovative therapeutic strategies against GC.

Type 2 diabetes mellitus (T2DM) is a metabolically heterogeneous disease for which current approaches to early diagnosis and risk stratification remain limited. Circular RNAs (circRNAs) have emerged as promising molecular candidates because of their stability, disease relevance, and regulatory versatility. Circular RNAs (circRNAs) have emerged as a promising class of non-coding RNAs that exhibit unique advantages, such as high stability, disease specificity, and the ability to act as regulators in competing endogenous RNA (ceRNA) networks. This review summarizes the current understanding of circRNAs in T2DM, highlighting their potential as diagnostic biomarkers and their roles in metabolic dysfunction. We explore how circRNAs contribute to key pathogenic processes in T2DM, including insulin resistance, glucose uptake, β-cell survival, inflammation, and vascular dysfunction. Additionally, we discuss the challenges in circRNA research, including technical biases, cohort heterogeneity, and the need for rigorous mechanistic validation. The review concludes by outlining future directions for circRNA-based research, including multicenter prospective studies, single-cell and spatial transcriptomic integration, and the development of circRNA-based companion diagnostics for precision medicine in T2DM.

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.

Extracellular vesicles (EVs) are small capsular bodies released by cells, mediating responses in intercellular communication. The role of EVs in Aβ pathology spreading in the Alzheimer’s disease (AD) brain has been evidenced, although whether this occurs due to the co-transportation of Aβ peptides or contribution of other factors, such as EV-associated transcripts, remains uncertain. In vitro studies of miRNA cargo in neuron-derived extracellular vesicles (NDEVs) show that Aβ hyperexpression alters the transcriptomic profile; however, it is not clear to what extent this causes changes at the organ level. By utilizing datasets from published studies, we generated competing endogenous RNA (ceRNA) networks for miRNAs co-expressed in NDEVs and the brain in different stages of pathology, using both an APP overexpressing neuronal model (in vitro) and brain cortices from 6- and 9-month-old APP/PSEN1 mice (in vivo). Networks integrating information from mRNAs, lncRNAs, and circRNAs showed two candidate lncRNAs (Kcnq1ot1 and Gm42969) and a circRNA (Pum1), while enrichment analyses detected that NDEVs miRNAs signal to other CNS cells and that this signal can be disrupted by Aβ pathology, contributing to the loss of long-term potentiation seen in early AD.

YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), an m6A reader, has a role in the development and progression of breast cancer as well as the immunological microenvironment. The networks of competing endogenous RNA in cancer have received much attention in research. In tumor gene therapy, the regulatory networks of m6A and competing endogenous RNA are increasingly emerging as a new route. We evaluated the relationship between the YTHDF1 expression, overall survival, and clinicopathology of breast cancer using TCGA, PrognoScan, and other datasets. We used Western blot to demonstrate that YTHDF1 is substantially expressed in breast cancer tissues. Furthermore, we explored YTHDF1′s functions in the tumor mutational burden, microsatellite instability, and tumor microenvironment. Our findings indicate that YTHDF1 is a critical component of the m6A regulatory proteins in breast cancer and may have a particular function in the immunological microenvironment. Crucially, we investigated the relationship between YTHDF1 and the associated competitive endogenous RNA regulatory networks, innovatively creating three such networks (Dehydrogenase/Reductase 4-Antisense RNA 1-miR-378g-YTHDF1, HLA Complex Group 9-miR-378g-YTHDF1, Taurine Up-regulated 1-miR-378g-YTHDF1). Furthermore, we showed that miR-378g could inhibit the expression of YTHDF1, and that miR-378g/YTHDF1 could impact MDA-MB-231 proliferation. We speculate that YTHDF1 may serve as a biomarker for poor prognosis and differential diagnosis, impact the growth of breast cancer cells via the ceRNA network axis, and be a target for immunotherapy against breast cancer.

Background Inflammatory cytokines such as Interleukin 1β(IL1β), IL6,Tumor Necrosis Factor-α (TNF-α) can inhibit osteoblast differentiation and induce osteoblast apoptosis. PANoptosis, a newly identified type of programmed cell death (PCD), may be influenced by long noncoding RNA (lncRNAs) which play important roles in regulating inflammation. However, the potential role of lncRNAs in inflammation and PANoptosis during osteogenic differentiation remains unclear. This study aimed to investigate the regulatory functions of lncRNAs in inflammation and apoptosis during osteogenic differentiation. Methods and results High-throughput sequencing was used to identify differentially expressed genes involved in osteoblast differentiation under inflammatory conditions. Two lncRNAs associated with inflammation and PANoptosis during osteogenic differentiation were identified from sequencing data and Gene Expression Omnibus (GEO) databases. Their functionalities were analyzed using diverse bioinformatics methodologies, resulting in the construction of the lncRNA-miRNA-mRNA network. Among these, lncRNA (MIR17HG) showed a high correlation with PANoptosis. Bibliometric methods were employed to collect literature data on PANoptosis, and its components were inferred. PCR and Western Blotting experiments confirmed that lncRNA MIR17HG is related to PANoptosis in osteoblasts during inflammation. Conclusions Our data suggest that TNF-α-induced inhibition of osteogenic differentiation and PANoptosis in MC3T3-E1 osteoblasts is associated with MIR17HG. These findings highlight the critical role of MIR17HG in the interplay between inflammation, PANoptosis, and osteogenic differentiation, suggesting potential therapeutic targets for conditions involving impaired bone formation and inflammatory responses.

Numerous studies have demonstrated the involvement of messenger RNAs (mRNAs) and non-coding RNAs, including long non-coding RNAs (lncRNA), circular RNAs (circRNAs) and microRNA (miRNAs), in gouty arthritis onset; however, the regulatory mechanism has not yet been elucidated. Here, we applied whole-transcriptome sequencing to identify the differentially expressed circRNAs, lncRNAs, miRNAs and mRNAs between the gout patients and normal people, and constructed co-regulated networks of circRNAs and lncRNAs according to the competitive endogenous RNA (ceRNA) theory for gouty arthritis onset to improve our understanding of the pathogenesis of this disease. The most significant finding of this study is the co-regulated ceRNA network of circRNAs and lncRNAs in gouty arthritis. The circRNA novel_circ_0030384 and the lncRNAs AAMP, TRIM16, PKN1, XLOC_184579 and XLOC_189826 were upstream genes in the co-regulated network. These upstream genes upregulated miR550a-5p and miR550a-3-5p, which downregulated PSME1 and FERMT3 expression. These mRNAs participated in proteasome dynamics, antigen processing and presentation, and platelet activation, which are associated with inflammation in gouty arthritis. In addition, the circRNA and lncRNAs upregulated miR550a-5p, which downregulated GRK2 and OS9 expression. Also, it proved that the down-regulated of PSME1, FERMT3, GRK2 and OS9 can aggravate gouty arthritis in vitro. In summary, these genes mediate inflammation in gouty arthritis through chemokine signaling to regulate neutrophil function.

The present study aimed to identify differentially expressed circRNAs in hypertrophic cardiac tissues and explored the potential regulatory role and mechanism of one differentially expressed circRNA in myocardial hypertrophy. RNA sequencing was used to identify differentially expressed circRNAs in hypertrophic and control cardiac tissues. CircRNA expression levels were verified by reverse transcription-quantitative PCR. Isoproterenol (ISO) was used to induce hypertrophy of AC16 cells. The extent of cell hypertrophy was indicated by the cell size, protein/DNA ratio and levels of B-type natriuretic peptide (BNP) and β-myosin heavy chain (β-MHC). The interactions between hsa_circ_0072107 and miR-516b-5p, as well as between miR-516b-5p and zinc ring finger protein 36 (ZFP36), were confirmed through dual luciferase assays, biotinylated probe pull-down and anti-AGO2 RNA immunoprecipitation assays. hsa_circ_0072107 was one of the most upregulated circRNAs in hypertrophic cardiac tissues. hsa_circ_0072107 overexpression and ISO treatment increased cell size, elevated the protein/DNA ratio and increased the levels of BNP and β-MHC in AC16 cells, indicating that hsa_circ_0072107 aggravates AC16 hypertrophy. These changes induced by ISO treatment could be blocked by the knockdown of hsa_circ_0072107. The dual-luciferase activity assay indicated that miR-516b-5p can bind to hsa_circ_0072107. miR-516b-5p binding site mutation blocked the effect of hsa_circ_0072107. ZFP36 is a target gene of miR-516b-5p, which suppresses AC16 hypertrophy. hsa_circ_0072107 overexpression alleviated the effect of miR-516b-5p overexpression on cell hypertrophy and ZFP36 expression. hsa_circ_0072107 is up-regulated in hypertrophic cardiac tissues and potentially promotes AC16 hypertrophy and may play its role by acting as a competitive endogenous RNA of miR-516b-5p. Thus, hsa_circ_0072107 may be a novel target for the treatment of myocardial hypertrophy.

Ulcerative colitis (UC) is a common chronic disease associated with inflammation and oxidative stress. This study aimed to construct a long noncoding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA) network based on bioinformatics analysis and to explore oxidative stress-related genes underlying the pathogenesis of UC. The GSE75214, GSE48959, and GSE114603 datasets were downloaded from the Gene Expression Omnibus database. Following differentially expressed (DE) analysis, the regulatory relationships among these DERNAs were identified through miRDB, miRTarBase, and TargetScan; then, the lncRNA-miRNA-mRNA network was established. The Molecular Signatures Database (MSigDB) was used to search oxidative stress-related genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for functional annotation and enrichment analyses. Based on the drug gene interaction database DGIdb, drugs that interact with oxidative stress-associated genes were explored. A dextran sulfate sodium (DSS)-induced UC mouse model was used for experimental validation. A total of 30 DE-lncRNAs, 3 DE-miRNAs, and 19 DE-mRNAs were used to construct a lncRNA-miRNA-mRNA network. By comparing these 19 DE-mRNAs with oxidative stress-related genes in MSigDB, three oxidative stress-related genes ( , and ) were found in the 19 DEM sets, which were all negatively associated with miR-194. GO and KEGG analyses showed that , and were associated with immune inflammation and steroid hormone synthesis. In animal experiments, the results showed that dexamethasone, a well-known glucocorticoid drug, could significantly decrease the expression of , and as well as improve UC histology, restore antioxidant activities, inhibit inflammation, and decrease myeloperoxidase activity. was identified as a representative gene associated with glucocorticoid therapy resistance and thus may be a new therapeutic target for the treatment of UC in the clinic.