MicroRNAs: genomics, biogenesis, mechanism, and function

Autism spectrum disorder: difficulties in diagnosis and microRNA biomarkers

We performed a PubMed search for microRNAs in autism spectrum disorder that could serve as diagnostic biomarkers in patients and selected 17 articles published from January 2008 to December 2023, of which 4 studies were performed with whole blood, 4 with blood plasma, 5 with blood serum, 1 with serum neural cell adhesion molecule L1-captured extracellular vesicles, 1 with blood cells, and 2 with peripheral blood mononuclear cells. Most of the studies involved children and the study cohorts were largely males. Many of the studies had performed microRNA sequencing or quantitative polymerase chain reaction assays to measure microRNA expression. Only five studies had used real-time polymerase chain reaction assay to validate microRNA expression in autism spectrum disorder subjects compared to controls. The microRNAs that were validated in these studies may be considered as potential candidate biomarkers for autism spectrum disorder and include miR-500a-5p, -197-5p, -424-5p, -664a-3p, -365a-3p, -619-5p, -664a-3p, -3135a, -328-3p, and -500a-5p in blood plasma and miR-151a-3p, -181b-5p, -320a, -328, -433, -489, -572, -663a, -101-3p, -106b-5p, -19b-3p, -195-5p, and -130a-3p in blood serum of children, and miR-15b-5p and -6126 in whole blood of adults. Several important limitations were identified in the studies reviewed, and need to be taken into account in future studies. Further studies are warranted with children and adults having different levels of autism spectrum disorder severity and consideration should be given to using animal models of autism spectrum disorder to investigate the effects of suppressing or overexpressing specific microRNAs as a novel therapy.

CaCO3 nanoparticle-encapsulated CHA circuits for sensitive fluorescence detection of miRNA in living cells

MicroRNAs (miRNAs) serve as important biomarkers for various diseases, including malignant tumors, and have broad applications in diagnosis, treatment, and prognosis. The development of real-time in situ imaging methods for monitoring miRNAs has both scientific and clinical value, and in this regard, catalytic hairpin assemblies (CHAs) can be used as precise and efficient nucleic acid circuits that facilitate hybridization without depleting targets. In this study, we developed a detection system based on CHA circuits encapsulated within CaCO3 nanoparticles, which represents a novel strategy for the detection of human pancreatic cancer. This encapsulation facilitates the pH-sensitive release of DNA probes, thereby ensuring the selective and sensitive detection of cancer-associated miRNAs. Our experimental results confirmed that the fabricated nanoparticles contributed to enhancing the stability and performance of the DNA circuits, thereby enabling precise miRNA detection and effective discrimination between cancerous and non-cancerous cells. Our findings in this study highlight the potential utility of CaCO3 nanoparticle-encapsulated CHA circuits for advancing miRNA-based cancer diagnostics and therapeutics.

Reconfigurable acoustic tweezer for precise tracking and in-situ sensing of trace miRNAs in tumor cells

MicroRNAs (miRNAs) have emerged as critical biomarkers for early cancer diagnosis and monitoring. However, their isolation from clinical samples typically yields only trace amounts, significantly limiting the sensitivity and efficiency of cancer detection. To address this challenge, we present a octangular reconfigurable acoustic tweezer (ORAT) as an integrated platform for precise tumor cell tracking and in-situ detection of trace miRNAs. By simultaneously modulating multidirectional acoustic signals and parameters, the ORAT dynamically reshapes the acoustic field, enabling precise control over manipulation areas, particle spacing, array angles, distribution patterns, and node rotation. This device allows selective particle manipulation across entire regions or specific areas through adaptive adjustments of the microchamber boundary. Notably, the ORAT achieves rapid and accurate localization and labeling of rare tumor cells within a large population of normal cells. Furthermore, it enhances the sensitivity of CRISPR/Cas-based miRNA detection in digital microdroplets by three orders of magnitude, if compared to that of the conventional tube-based method. With its versatile capabilities, the ORAT holds remarkable promise for advancing nucleic acid analysis in a wide range of cancers and related diseases.

Mapping the research landscape of microRNA and stroke: a bibliometric analysis of insights, hotspots, and future directions

MicroRNAs (miRNAs) are critical regulators of stroke pathophysiology, influencing neuroinflammation, neuronal survival, and post-stroke recovery. This study presents a comprehensive bibliometric analysis of 1,988 miRNA-stroke research articles published over the past 42 years, mapping the intellectual landscape, emerging research hotspots, and future directions within the field. Using Python, VOSviewer, and CiteSpace, we identified influential studies, leading authors, collaborative networks, and key thematic clusters that are advancing research. Our analysis highlights several emerging hotspots, including exosomal miRNA biomarkers for stroke diagnosis, miRNA-based therapeutics, and regulatory networks involving circRNAs and lncRNAs, which present promising avenues for precision medicine. Citation burst and timeline analyses highlight the growing focus on miRNA-targeted interventions, epigenetic modifications, and neuroprotective strategies, which are rapidly shaping the evolution of stroke research. Importantly, we emphasize the need for increased research in human-based studies to validate these findings and ensure clinical applicability. This study provides a structured framework to guide future research efforts, promoting international collaboration and bridging the gap between fundamental discoveries and the clinical translation of miRNA-based diagnostics and therapeutics in stroke.

miR-125b-5p regulates FFA-induced hepatic steatosis in L02 cells by targeting estrogen-related receptor alpha

BACKGROUND & AIMS

NAFLD is a global and complex liver disease caused by multiple factors. Intrahepatocellular steatosis is the primary prerequisite for the occurrence and development of NAFLD. It has been shown that miR-125b-5p is highly correlated with NAFLD, and ESRRA is a factor that regulates lipid metabolism. The purpose of our study is to investigate whether miR-125b-5p regulates FFA-induced steatosis in L02 cells by targeting ESRRA.

APPROACHES AND RESULTS

Estrogen-related receptor alpha (ESRRA) was identified as a direct target of miR-125b-5p through database prediction and a dual-luciferase reporter gene assay. L02 cells were induced with free fatty acids (OA:PA, 2:1) at concentrations of 0.3 mM, 0.6 mM, 0.9 mM, 1.2 mM and 1.5 mM for 24 h, 48 h and 72 h, respectively. The degree of hepatocyte steatosis and triglyceride content were separately manifested by oil red O staining and colorimetric method. Cell viability per group was detected by CCK-8 assay. Eventually, 0.9 mM and 24 h were screened out as the optimal concentration and time for establishing the in-vitro model of hepatic steatosis. Followingly, miR-125b-5p and ESRRA were knocked down by transient transfection. We monitored the expressions of lipid metabolism factors SREBP-1c, ACC1 and FAS and determine triglyceride content within the cells per group. The data showed that knockdown of ESRRA led to down-regulation of the expressions of SREBP-1, ACC1, FAS and triglyceride content. Meanwhile, knockdown of ESRRA and miR-125b-5p resulted that the expressions of ESRRA, SREBP-1, ACC1, FAS and triglyceride content rebounded.

CONCLUSIONS

MiR-125b-5p down-regulates the expressions of lipid metabolism-related factors by negatively regulating ESRRA, thereby improving hepatic steatosis.

A portable point-of-care testing platform for rapid and sensitive miRNA-21 detection for heart failure diagnosis

BACKGROUND

MicroRNAs (miRNAs) play a pivotal role in various physiological and pathological processes. In particular, miRNA-21 holds significant potential as a novel biomarker for the diagnosis of heart failure. The development of miRNA detection methods is rapidly advancing, with point-of-care testing (POCT) platforms garnering considerable attention. However, traditional methods are often hampered by their reliance on expensive instruments and complex procedures, limiting clinical applicability. Therefore, there is an urgent need to develop a simple, portable, sensitive, and rapid POCT platform for miRNA-21 detection.

RESULTS

In this work, we proposed a portable POCT platform using a colorimetric biosensor specifically sensitive for miRNA-21. The platform utilized 3,3',5,5'-tetramethylbenzidine as the signaling molecule, and a Linear G-quadruplex loaded with Blocker Nanostructures (LGBN) generated by the RCA reaction as the probe. Furthermore, changes in primary color channels (R/G/B) of TMB for miRNA-21 detection were analyzed via smartphone-based digital image recognition. Under optimal conditions, the platform showed a linear detection range between 0.01 nM and 1 nM, with limits of detection of 8.3 pM (colorimetric methods) and 9.5 pM (digital image colorimetry). Moreover, the colorimetric biosensor exhibited excellent specificity and resistance to interference, successfully detecting miRNA-21 in serum samples from heart failure patients.

SIGNIFICANCE

This detection method has an accuracy consistent with RT-qPCR results, providing a novel and practical approach with POCT for miRNA-21 detection.

Epigenetic alterations and microbiota changes in the saliva of individuals with binge-eating spectrum disorders compared with normal weight healthy controls

AIMS

Binge-eating spectrum disorders, including bulimia nervosa (BN) and binge-eating disorder (BED), have psychological, behavioral, and physical effects, which present significant challenges for accurate diagnosis and treatment. Identifying biomarkers is thus of relevance to improve diagnostic and treatment strategies.

MAIN METHODS

Saliva collected from female individuals with BED (n = 20), BN (n = 17), and normal weight healthy controls (NW-HC) (n = 20) was analyzed to assess salivary microbiome, exosomal miRNA expression, and DNA methylation of dopaminergic system gene components.

KEY FINDINGS

Microbial diversity was significantly reduced in BED and BN groups compared to NW-HC. Differential abundance analysis revealed that Bacilli (class-level) were enriched in BN and BED, while Lachnospirales (order-level) were significantly depleted in BN compared to NW-HC. In total, 79 miRNAs were differentially expressed in patients compared with controls. Alteration in four of these miRNAs (let-7b-5p, mir-15b-5p, mir-429, and mir-221-3p) identified via network analysis as potentially relevant to psychiatric disorders, were confirmed to be significantly upregulated in both BED and BN compared with controls. Significant hypomethylation at specific CpG sites of the DAT1 gene was also observed in BED and BN groups relative to controls. Correlation analysis highlighted significant associations between specific microbiota genera, miRNA expression, and DNA methylation of DAT1 in both the BED and BN groups.

SIGNIFICANCE

Our findings provide new evidence on the role of epigenetic modifications linked to alterations in salivary microbial composition and diversity in BED and BN, opening new avenues for future research and therapeutic interventions in eating disorders targeting miRNAs and microbiota.

Peripheral blood miR-16-5p as a potential biomarker for distinguishing unmedicated bipolar disorder type II from major depressive disorder

OBJECTIVE

major depressive disorder (MDD) and bipolar disorder type II (BD-II) are difficult to distinguish clinically due to similar depressive symptoms and unrecognizable hypomania symptoms in the early stages. The study aims to identify these two disorders in the early stages through differential expression of microRNAs.

METHODS

93 subjects including 66 unmedicated patients (33 MDD, 33 BD-II), and 27 healthy controls (HC) were enrolled. At the time of enrollment, all subjects' demographic data, HAMD, HCL-32, and YMRS scales were assessed. 5 ml of peripheral blood for all subjects was collected for microRNA second-generation sequencing. MicroRNA differential expression, target gene GO and KEGG analyses were performed.

RESULTS

No statistical differences in demographic data were found except for age (BD-II < MDD, P = 0.002). In terms of clinical data, there are differences in the course of the disease (BD-II > MDD, P = 0.037) and the HCL-32 (BD-II > MDD, P < 0.01). A variance analysis of microRNA expressions across all three groups identified eight highly expressed differential miRNAs (P < 0.001), Pairwise comparisons revealed that the expression level of miR-16-5p was lower in both MDD group (P < 0.05) and BD-II group (P < 0.001) than in HC group, and it was even lower in BD-II group compared to MDD group (P < 0.01). The area under the curve (AUC) for miR-16-5p in differentiating BD-II from MDD groups was 0.723 (P = 0.003).

CONCLUSIONS

Peripheral blood miR-16-5p may serve as a potential biomarker for distinguishing unmedicated BD-II from MDD patients.

Exponential rolling circle amplification-hybridization chain reaction (EXRCA-HCR) for AgNPs@gel-enhanced fluorescence ultrasensitive detection of miRNA-21

MicroRNA (miRNA) is a common tumor marker, whose abnormal expression is often closely related to the occurrence of various diseases. However, the conventional method for detecting miRNA is qRT-PCR, requiring additional reverse transcription steps, well-trained professionals, and expensive thermal cycling equipment. In this work, we propose a novel isothermal amplification technique (exponential rolling circle amplification-hybridization chain reaction, EXRCA-HCR) for AgNPs@gel-enhanced fluorescence specific and ultrasensitive detection of miRNA-21. This novel technique consists of rolling circle amplification (RCA), exponential isothermal amplification reaction (EXPAR) and hybridization chain reaction (HCR). Combining these three amplification methods, EXRCA-HCR provides a unique cascade amplification strategy, inheriting the advantages of linear amplification and exponential amplification. Under optimal conditions, this novel EXRCA-HCR exhibits a wide fluorescent detection range from 200 fM to 200 nM for miRNA-21, with low detection limit of 21.47 fM. By introducing AgNPs@gel, the fabricated paper-based fluorosensor based on EXRCA-HCR provides a simple and rapid visual detection of miRNA-21. This research puts forward a promising approach for detecting miRNA-21, which can be applied for early diagnosis.

miR‑34a induces apoptosis and pyroptosis in D‑Galactose‑induced aging cochlear hair cells via inhibiting TFAM and promoting mitochondrial dysfunction in vitro and in vivo

Aging of the auditory system causes progressive hearing deficit and affects millions of people; however, the underlying mechanism remains largely unknown. D‑galactose (D‑gal)‑induced aging models were established in vitro using HEI‑OC1 cells and in vivo using C57BL/6 mice to investigate the role of miR‑34a in age‑related hearing loss (ARHL). HEI‑OC1 cells were treated with D‑gal for, while mice received daily intraperitoneal injections of D‑gal for six weeks. Molecular and functional analyses, including reverse transcription‑quantitative PCR, Western blot, flow cytometry, immunofluorescence, and dual‑luciferase reporter assays, were performed to evaluate oxidative stress, mitochondrial dysfunction, apoptosis, and pyroptosis, with miR‑34a inhibitor and DRP1 inhibitor (Mdivi‑1) used to assess their regulatory effects. D‑gal induced hair cell loss by apoptosis and pyroptosis, which was modulated by microRNA (miR)‑34a via mitochondrial dysfunction in vitro and in vivo. Inhibition of mitochondrial transcription factor A (TFAM), which is the target gene of miR‑34a, was involved in the underlying molecular mechanism. miR‑34a mediated apoptosis and pyroptosis in D‑gal‑induced cochlear hair cells via inhibiting TFAM and promoting mitochondrial dysfunction in vitro and in vivo and may serve as a new potential target for future ARHL treatment.

The miR-21-5p/DUSP8/MAPK signaling pathway mediates inflammation and apoptosis in vascular endothelial cells induced by intermittent hypoxia and contributes to the protective effects of N-acetylcysteine

Obstructive sleep apnoea hypopnea syndrome (OSAHS) is a sleep disorder associated with significant cardiovascular complications, characterized by intermittent hypoxia (IH). IH causes endothelial dysfunction, an early event in cardiovascular disease. We investigated the role of dual-specificity phosphatase 8 (DUSP8), a key negative regulator of the mitogen-activated protein kinase (MAPK) signalling pathway, in IH-induced endothelial cell damage, and the therapeutic effects of N-acetylcysteine (NAC) by establishing IH models in human umbilical vein endothelial cells and C57BL/6 mice. DUSP8 and MAPK signalling pathway-related proteins were analysed by western blotting, and DUSP8 mRNA and miR-21-5p expression was assessed by RT-qPCR. Inflammatory cytokines were detected by an enzyme-linked immunosorbent assay, apoptosis-related proteins were analysed by western blotting, and apoptosis was assessed using flow cytometry. IH stimulation induced inflammation and apoptosis in endothelial cells, downregulated DUSP8 expression, and upregulated the phosphorylation of key molecules involved in the MAPK signalling pathway. However, DUSP8 overexpression alleviated IH-induced inflammation and apoptosis in endothelial cells and reduced the phosphorylation of key molecules in the MAPK signalling pathway. Bioinformatic analysis and dual-luciferase reporter assays confirmed that DUSP8 is a direct target of miR-21-5p. DUSP8 overexpression effectively reversed the damage caused by miR-21-5p upregulation under IH conditions. Furthermore, in cell and animal models of IH, NAC demonstrated protective effects against inflammation, apoptosis, and oxidative stress through a mechanism linked to the miR-21-5p/DUSP8/MAPK signalling pathway. Overall, this study elucidated the protective role of DUSP8 against IH-induced endothelial injury and confirmed the potential of NAC as a therapeutic agent for OSAHS-related diseases.

Fate reversal: Exosome-driven macrophage rejuvenation and bacterial-responsive drug release for infection immunotherapy in diabetes

Superficial surgical site infection (SSI) is a significant risk factor for the development of periprosthetic joint infection (PJI), particularly in diabetic patients. A high-glucose microenvironment is observed to compromise phagocytosis by inducing cellular senescence, which leads to impaired antibacterial immune function. Exosomes derived from umbilical cord stem cells (H-Exos) can reverse the immunosuppressive microenvironment by rejuvenating senescent cells, thereby terminating excessive, persistent, and ineffective inflammatory responses. Thus, a novel exosome-based immunotherapeutic antibacterial strategy to reverse fate is proposed. Vancomycin & lysostaphin-loaded exosomes are incorporated in a customizable microneedle patch (ExoV-ExoL@MN) for controlled release, enabling tailored treatments for diverse clinical scenarios. While rejuvenating macrophage senescent phenotype, the antibiotics encapsulated within exosomes can be responsively released by the hemolysin secreted by bacteria, triggering rapid bacterial killing. Post-infection clearance, they induce a shift from M1 to M2 macrophage polarization, thereby enhancing anti-inflammatory and reparative responses. Furthermore, the components can be mixed on demand and at any time, allowing for real-time customization and fabrication directly at the clinic (fabrication@clinic). This strategy reverses the immunosuppressive microenvironment by rejuvenating senescent macrophages and effectively combats bacterial invasion into deep tissues through bacteria-responsive antibiotic release, providing a promising approach for preventing and treating SSI-induced PJI.

Transcriptome analysis and lncRNA expression profile in brain tissues of neonatal hypoxic-ischemic brain damage rat model

BACKGROUND AND OBJECTIVE

Neonatal hypoxic-ischemic encephalopathy (HIE) remains a critical challenge in perinatal medicine. This study aimed to elucidate the transcriptomic landscape, focusing on long non-coding RNAs (lncRNAs) expression patterns in the brain tissues of a neonatal rat model of HIE.

METHODOLOGY

We employed a modified Rice-Vannucci model to induce HIE in postnatal day 4 (P4) rats. The experimental groups were subjected to either 5 or 7 min of hypoxia (0 % O2, 100 % N2), while control animals were exposed to normoxic conditions.

RESULTS

RNA sequencing revealed a complex transcriptomic landscape in HIE brains, with approximately 80 million differentially expressed lncRNAs compared to controls. ELISA results demonstrated a significant upregulation of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and a concomitant decrease in anti-inflammatory IL-10 levels in brain tissue of HIE rats. qRT-PCR analysis revealed aberrant expression of several miRNAs. Biochemical assays indicated a marked reduction in superoxide dismutase (SOD) activity and an increase in malondialdehyde (MDA) content in HIE brain tissues.

CONCLUSIONS

This study highlights the potential regulatory roles of lncRNAs in HIE brains. The intricate interplay between lncRNAs, miRNAs, and mRNAs and alterations in inflammatory and oxidative stress markers suggests a complex regulatory network governing HIE pathogenesis.

Diabetes and Early Development: Epigenetics, Biological Stress, and Aging

Pregestational diabetes, either type 1 or type 2 diabetes, induces structural birth defects including neural tube defects and congenital heart defects in human fetuses. Rodent models of type 1 and type 2 diabetic embryopathy have been established and faithfully mimic human conditions. Hyperglycemia of maternal diabetes triggers oxidative stress in the developing neuroepithelium and the embryonic heart leading to the activation of proapoptotic kinases and excessive cell death. Oxidative stress also activates the unfolded protein response and endoplasmic reticulum stress. Hyperglycemia alters epigenetic landscapes by suppressing histone deacetylation, perturbing microRNA (miRNA) expression, and increasing DNA methylation. At cellular levels, besides the induction of cell apoptosis, hyperglycemia suppresses cell proliferation and induces premature senescence. Stress signaling elicited by maternal diabetes disrupts cellular organelle homeostasis leading to mitochondrial dysfunction, mitochondrial dynamic alteration, and autophagy impairment. Blocking oxidative stress, kinase activation, and cellular senescence ameliorates diabetic embryopathy. Deleting the mir200c gene or restoring mir322 expression abolishes maternal diabetes hyperglycemia-induced senescence and cellular stress, respectively. Both the autophagy activator trehalose and the senomorphic rapamycin can alleviate diabetic embryopathy. Thus, targeting cellular stress, miRNAs, senescence, or restoring autophagy or mitochondrial fusion is a promising approach to prevent poorly controlled maternal diabetes-induced structural birth defects. In this review, we summarize the causal events in diabetic embryopathy and propose preventions for this pathological condition. · Maternal diabetes induces structural birth defects.. · Kinase signaling and cellular organelle stress are critically involved in neural tube defects.. · Maternal diabetes increases DNA methylation and suppresses developmental gene expression.. · Cellular apoptosis and senescence are induced by maternal diabetes in the neuroepithelium.. · microRNAs disrupt mitochondrial fusion leading to congenital heart diseases in diabetic pregnancy..

Update in the molecular mechanism and biomarkers of diabetic retinopathy

Diabetic retinopathy (DR) is a serious complication of diabetes caused by long-term hyperglycemia that leads to microvascular and neuronal damage in the retina. The molecular mechanisms of DR involve oxidative stress, inflammatory responses, neurodegenerative changes, and vascular dysfunction triggered by hyperglycemia. Oxidative stress activates multiple metabolic pathways, such as the polyol, hexosamine, and protein kinase C (PKC) pathways, resulting in the production of, which in turn promote the formation of advanced glycation end products (AGEs). These pathways exacerbate vascular endothelial damage and the release of inflammatory factors, activating inflammatory signaling pathways such as the NF-κB pathway, leading to retinal cell damage and apoptosis. Additionally, DR involves neurodegenerative changes, including the activation of glial cells, neuronal dysfunction, and cell death. Research on the multiomics molecular markers of DR has revealed complex mechanisms at the genetic, epigenetic, and transcriptional levels. Genome-wide association studies (GWASs) have identified multiple genetic loci associated with DR that are involved in metabolic and inflammatory pathways. Noncoding RNAs, such as miRNAs, circRNAs, and lncRNAs, participate in the development of DR by regulating gene expression. Proteomic, metabolomic and lipidomic analyses have revealed specific proteins, metabolites and lipid changes associated with DR, providing potential biomarkers for the early diagnosis and treatment of this disease. This review provides a comprehensive perspective for understanding the molecular network of DR and facilitates the exploration of innovative therapeutic approaches.

Advances in the study of epithelial mesenchymal transition in cancer progression: Role of miRNAs

Epithelial-mesenchymal transition (EMT) has been extensively studied for its roles in tumor metastasis, the generation and maintenance of cancer stem cells and treatment resistance. Epithelial mesenchymal plasticity allows cells to switch between various states within the epithelial-mesenchymal spectrum, resulting in a mixed epithelial/mesenchymal phenotypic profile. This plasticity underlies the acquisition of multiple malignant features during cancer progression and poses challenges for EMT in tumors. MicroRNAs (miRNAs) in the microenvironment affect numerous signaling processes through diverse mechanisms, influencing physiological activities. This paper reviews recent advances in EMT, the role of different hybrid states in tumor progression, and the important role of miRNAs in EMT. Furthermore, it explores the relationship between miRNA-based EMT therapies and their implications for clinical practice, discussing how ongoing developments may enhance therapeutic outcomes.

miR-4537 curtails ferroptosis by targeting MIOX in renal cell carcinoma

Ferroptosis, an iron-dependent mode of cell death, has gained prominence for its critical role in the advancement of various cancers, notably clear cell renal carcinoma (ccRCC). The intricacies of ferroptosis's involvement in ccRCC, however, remain largely undefined. This study aimed to dissect the contribution of ferroptosis to ccRCC by examining differentially expressed genes (DEGs) identified within the TCGA ccRCC database and ferroptosis driver genes catalogued in the FerrDb database (dedicates to ferroptosis regulators and ferroptosis-disease associations). We employed 786-O and ACHN ccRCC cell lines, alongside HK2 (human kidey-2) cells and HKC (human kidney cells), to confirm the expression of 9 shared genes. Among these, MIOX (myo-inositol oxygenase) emerged as significantly downregulated in ccRCC cells compared to HK2 and HKC cells. Subsequent survival analysis illuminated a positive correlation between MIOX expression and improved patient survival, underscoring its prognostic significance. Further investigations into MIOX regulation identified four miRNAs via TargetScan predictions, with miR-4537 significantly upregulated in ccRCC cell lines. Functional assays involving miR-4537 mimics and inhibitors, combined with ferroptosis inducers and inhibitors, elucidated its impact on ccRCC cell growth and ferroptosis modulation. The results revealed that miR-4537 expression was diminished following ferroptosis induction, and the miR-4537 inhibitor markedly curbing ccRCC cell proliferation by fostering ferroptosis, while the mimic exerted opposite effects. Mechanistically, miR-4537 targets the 3'-UTR of MIOX to manipulate its expression, ultimately inhibiting ferroptosis in ccRCC cells. Our research indicated that miR-4537 restrained ferroptosis by regulating MIOX in ccRCC, offering novel insights into the mechanisms of ferroptosis in cancer biology and highlighting latent therapeutic avenues for cancer treatment through ferroptosis modulation.

MiR-21-5p enhances differentiation and mitigates oleic acid-induced lipid droplet accumulation in C2C12 myoblasts by targeting FBXO11

OBJECTIVE

This study aimed to investigate the role of miRNA 21-5p in regulating the differentiation of C2C12 myoblasts and intramuscular lipid droplets accumulation in myotubes.

METHODS

The role of miR-21-5p in the proliferation and differentiation of myofibroblasts and intracellular lipid accumulation was analyzed using bioinformatics, CCK-8 assay, quantitative real-time polymerase chain reaction, immunoblotting, immunofluorescence staining, and Oil Red O staining.

RESULTS

The analysis of porcine BodyMap transcriptome data revealed differential expression of miRNA 21-5p in skeletal muscle and adipose tissue. Bioinformatics analysis combined with a dual-luciferase reporter assay demonstrated that FBXO11 serves as a direct target of miR-21-5p. Transfection experiments involving a miR-21-5p mimic, miR-21-5p inhibitor, and si-FBXO11 in C2C12 cells showed that overexpression of miR-21-5p or silencing of FBXO11 significantly enhanced the proliferation of C2C12 cells, upregulated myogenesis-related factors, and promoted myotube formation. Furthermore, oleic acid-induced lipid accumulation in myotubes was suppressed, accompanied by reduced expression of adipogenesis-related genes. Conversely, inhibition of miR-21-5p expression produced opposite effects.

CONCLUSION

These findings indicate that miR-21-5p promotes proliferation and differentiation while inhibiting intramyocellular lipid deposition by targeting the 3'-untranslated region of FBXO11 in myogenic cell. The results suggest that miR-21-5p could serve as a potential miRNA biomarker for regulating intramuscular adipogenesis.

Novel therapeutic target for diabetic kidney disease through downregulation of miRNA-192-5p and miRNA-21-5p by celastrol: implication of autophagy, oxidative stress, and fibrosis

One of the most common microvascular effects of diabetes mellitus (DM) that may result in end-stage renal failure is diabetic kidney disease (DKD). Current treatments carry a substantial residual risk of disease progression regardless of treatment. By modulating various molecular targets, pentacyclic triterpenoid celastrol has been found to possess curative properties in the treatment of diabetes and other inflammatory diseases. Therefore, the present study investigated whether celastrol has anti-inflammatory, antioxidant, and antifibrotic effects as a natural compound against experimental DKD. Streptozotocin (55 mg/kg) was utilized for inducing DKD in a rat model. Antioxidant enzymes and renal function tests were assessed in serum samples. In kidney homogenate, relative miRNA-192-5p and miRNA-21-5p gene expressions were measured. Furthermore, using real-time PCR to evaluate the gene expressions of nucleus erythroid 2-related factor-2 (Nrf-2), matrix metalloproteinase-2 (MMP-2), proapoptotic caspase-3, antiapoptotic Bcl-2, LC-3, and Beclin-1. Moreover, the transforming growth factor β1 (TGF-β1), LC-3, Bcl-2, caspase-3 and NADPH oxidase 4 (NOX4) renal expressions were assessed semi-quantitatively using immunohistochemistry. Seven weeks of celastrol (1.5 mg/kg/day) treatment significantly ameliorated DKD. Celastrol improves kidney functions. Moreover, celastrol treatment demonstrated potent antioxidant effect. The mechanism of apoptosis resulting from the administration of celastrol included the modulation of Bcl-2 and caspase-3 expression in the kidney. Celasterol administration leads to an increase in LC-3 and Beclin-1 renal expression that resulting in autophagy. Celastrol treatment improved renal fibrosis by decreasing TGF-β1 and MMP-2 renal expression. These antifibrotic effects could be due to their ability to inhibit miRNA-192-5p and miRNA-21-5p expression in renal tissues. Celastrol exerts a renoprotective effect by targeting miRNA-21 and miRNA-192, as well as their downstream pathways, such as autophagy, apoptosis, and fibrosis.

The role and research progress of epigenetic modifications in obstructive sleep apnoea-hypopnea syndrome and related complications

Epigenetic modifications are heritable changes in gene expression that do not alter the DNA sequence. Histone modifications, non-coding RNA expression, and DNA methylation are examples of common epigenetic changes. Obstructive sleep apnoea-hypopnea syndrome (OSAHS) is the most common sleep-related breathing disorder, and its incidence is increasing annually, making it a hotspot of clinical research and significantly impacting health and well-being. The main cause of OSAHS is related to complications caused by repeated chronic intermittent hypoxia (CIH). Currently, polysomnography (PSG) and continuous positive airway pressure (CPAP) remain the gold standards for the diagnosis and treatment of OSAHS. However, their limitations-such as time consumption, high cost, and poor patient comfort-contribute to the paradox of high disease prevalence yet low rates of diagnosis and treatment, resulting in a substantial disease burden. In recent years, rapid advances in epigenetics have revealed that biomarkers such as microRNAs (miRNAs), circular RNAs (circRNAs), and other epigenetic modifications hold promise as non-invasive tools for the diagnosis and treatment of OSAHS and its related complications. Although numerous studies have explored epigenetic modifications in other diseases, this study focuses on how epigenetic modifications participate in the process of OSAHS and its related complications, with an aim of elucidating the pathogenesis of OSAHS from an epigenetic perspective and provide new directions for identifying molecular targets for the diagnosis and treatment of OSAHS and related complications.

miR3398-VqMYB15 Regulates the Synthesis of Stilbene in Vitis quinquangularis

Grapevine (Vitis vinifera L.) is an economically important fruit crop grown worldwide. Grapevine is cultivated extensively in China, and certain wild grapes exhibit excellent resistance to pathogens and stress. MicroRNAs (miRNAs) act as key regulators of plant growth, development, and immunity; however, their functions in grape stilbene synthesis are poorly understood. We identified an miRNA (miR3398) that negatively regulates the transcription factor MYB15 and participates in the synthesis of stilbene from Vitis quinquangularis (V. quinquangularis). MiR3398 and VqMYB15 showed completely opposite expression patterns after AlCl3 treatment, and the interaction between miR3398 and VqMYB15 was confirmed using 5'-RACE ligase-mediated rapid amplification of cDNA ends, dual-luciferase reporter gene system, and western blot analysis. VqMYB15 could bind to the VqSTS48 promoter by using yeast one-hybrid and electrophoretic mobility shift assay, and overexpression of VqMYB15 promoted stilbene accumulation in grape leaves. Using an overexpression and silencing system, we found that miR3398 negatively targets VqMYB15 to synthesis of stilbenes. We used Al3+ as an elicitor, indicating that miR3398 plays an important role in the plant immunity of V. quinquangularis. We also found that miR3398 is involved in plant immunity by detecting its promoter activity in grape protoplasts, luciferase imaging, and transgenic Arabidopsis thaliana. More importantly, we found that an ethylene transcription factor, ERF057, can bind to the promoter of miR3398 using Y1H and EMSA assays and inhibit its transcription using DLR, luciferase imaging, and β-glucuronidase transcript assays. Overexpression of VqERF057 reduced miR3398 transcript in V. quinquangularis and transgenic grapevine calli, but increased the stilbene content. These findings contribute to the understanding of the biological functions of miR3398 regulates stilbene synthesis in grapevines and clarify the molecular mechanism underlying the interaction between miR3398 and VqMYB15.

M2 macrophage derived exosomal miR-20a-5p ameliorates trophoblast pyroptosis and placental injuries in obstetric antiphospholipid syndrome via the TXNIP/NLRP3 axis

AIM

Obstetric antiphospholipid syndrome (OAPS) is a pregnancy-related complication characterized by trophoblast pyroptosis and placental injury induced by antiphospholipid antibodies (aPLs). M2-polarized macrophage-derived exosomes (M2-exos) exert anti-inflammatory, immunomodulatory, and growth-promoting effects in various autoimmune diseases and tumors. However, their role in OAPS is not yet clear. Therefore, in this study, we isolated M2-exos from M2 macrophages and investigated their effects on trophoblast proliferation, death, migration, invasion, and pyroptosis following stimulation using aPLs.

MAIN METHODS

First, we established an animal model of OAPS and thereafter treated the OAPS mice with exogenous M2-exos via injection through the tail vein. Then to clarify the roles of miR-20a-5p and thioredoxin-interacting protein (TXNIP) in OAPS, we performed gain- or loss-of-function assays, and used GraphPad Prism software to analyze the collected data with statistical significance set at P < 0.05.

KEY FINDINGS

MicroRNAs (miRNAs) sequencing revealed the enrichment of miR-20a-5p in M2-exos, and these M2-exos significantly alleviated aPLs-induced trophoblast dysfunction. Our results also indicated that M2-exos delivered miR-20a-5p to trophoblast cells directly targeted thioredoxin-interacting protein (TXNIP), and thus suppressed the TXNIP/NLRP3 pathway, reduced pyroptosis and inflammation in trophoblast cells, and improved placental function and fetal development.

SIGNIFICANCE

M2-exos improve pregnancy outcomes in OAPS via the miR-20a-5p/TXNIP/NLRP3 axis, and thus represent as a novel therapeutic approach for aPLs-induced OAPS.

Crosstalk between Hepatic Stellate Cells and Hepatic Macrophages in Metabolic Dysfunction-Associated Steatohepatitis

Metabolic dysfunction-associated steatotic liver disease is the most prevalent liver condition worldwide. Its more severe manifestation, metabolic dysfunction-associated steatohepatitis (MASH), is accompanied by distinctive hepatocellular injury and inflammation with fibrosis. The involvement of chronic inflammation and accompanying immune cell activation in the maturation phases of MASH progression, mediated through hepatic stellate cells (HSCs), plays a central role. This review highlights the detailed molecular and cellular mechanisms of MASH, with special attention to the dynamic dialogue between HSCs and hepatic macrophages. This review will help narrow the existing gaps, with a summary of key roles HSCs and hepatic macrophages play within liver immunity to inflammation, discussing critical intercellular communication pathways as well as proposing new venues for research toward a better understanding of MASH pathobiology, which could pave ways toward breakthroughs in the clinical condition.

miR-23a-mediated TRF2 repression in CD4 T cells from PLWH

CD4 T cells in people living with HIV (PLWH) on antiretroviral therapy (ART) often exhibit an inflammaging phenotype, characterized by persistent inflammation, immune activation, exhaustion, senescence, and apoptosis. We have previously demonstrated that inhibition of telomeric repeat factor 2 (TRF2) protein causes accelerated telomere erosion and premature CD4 T cell aging in PLWH. In this study, we further investigated how TRF2 protein is inhibited in CD4 T cells from PLWH, focusing on the miRNA-mediated mechanism. We found that miR-23a is significantly increased, whereas TRF2 protein is repressed, in CD4 T cells from PLWH compared to healthy subjects (HS). Bioinformatics analysis revealed that the TRF2 3'UTR is a potential target of miR-23a. Co-transfection of miR-23a with a luciferase construct containing TRF2 3'UTR into HEK293T cells revealed that miR-23a suppresses TRF2 protein translation. Notably, T cell receptor (TCR) activation in CD4 T cells from both PLWH and HS increased miR-23a and decreased TRF2 protein expression. Furthermore, increasing miR-23a in CD4 T cells from HS led to a decrease in TRF2 protein level and an increase in cellular apoptosis - a phenotype similar to what we observed in PLWH. Moreover, the knockdown of miR-23a in CD4 T cells from PLWH increased TRF2, but not TRF1, protein levels. These results suggest that miR-23a negatively regulates TRF2 protein expression in CD4 T cells; thus, targeting miR-23a may increase TRF2 protein level, and thereby protect telomere integrity and restore CD4 T cell functions in PLWH.

Reciprocal regulation between m6 A modifications and non-coding RNAs: emerging roles in cancer therapeutic resistance

In recent years, the interplay between N6-methyladenosine (m6A) modifications and non-coding RNAs (ncRNAs) has emerged as a pivotal research area, owing to their crucial involvement in the pathophysiological mechanisms underlying various diseases. A significant hurdle in cancer therapy is therapeutic resistance, which frequently contributes to adverse patient outcomes. Recent investigations have underscored the vital role that interactions between m6A modifications and ncRNAs play in mediating cancer therapeutic resistance via the MAPK, PI3K/Akt/mTOR, Wnt/β-catenin, HIPPO, and NF-κB pathways. This review elucidates how these interactions drive tumor therapeutic resistance by modulating these pathways. By dissecting the regulatory dynamics between m6A and ncRNAs in the context of cancer therapeutic resistance, this review aims to deepen the understanding of m6A-ncRNA interaction in cancer therapeutic resistance and identify potential therapeutic targets to improve cancer treatment efficacy.

Efficient delivery of small RNAs to podocytes in vitro by direct exosome transfection

BACKGROUND

Podocytes are a crucial component of the glomerular filtration barrier, and changes in their 3D structure contribute to over 80% of chronic kidney disease (CKD) cases. Exosomal small RNAs play a key role in cell-cell communication in CKD and may serve as nanocarriers for delivering small RNAs into podocytes. However, the uptake of exosomal cargo by podocytes remains poorly understood. This study explores the use of isolated exosomes, directly transfected with fluorescently-labeled small RNAs, for tracking and delivering small RNAs to cultured podocytes.

METHODS

Exosomes were isolated from immortalized murine podocytes and transfected with Cy3-labeled siRNA and miRNA controls using the ExoFect siRNA/miRNA Transfection Kit. We characterized the transfected exosomes via transmission electron microscopy (TEM) and Western blot for exosomal markers CD9 and TSG101. Subsequently, we co-cultured these exosomes with podocytes and used confocal laser-scanning microscopy (cLSM), and structured illumination microscopy (SIM) to visualize cargo uptake, confirmed through flow cytometry, imaging flow cytometry and immunofluorescence staining for Rab5, Rab7, and CD9. The isolated exosomes were also transfected with pre-miR-21 and filamin A (FlnA)-siRNAs before being co-cultured with podocytes. We confirmed the efficiency of transfection and knockdown using RT-qPCR, Western blotting, and immunofluorescence staining.

RESULTS

TEM revealed that the exosomes maintained a consistent shape and size of approximately 20 nm posttransfection and exhibited a stable expression of CD9 and TSG101. Flow cytometry and immunofluorescence imaging showed that podocytes take up Cy3-labeled exosomal miRNAs and siRNAs time-dependently, utilizing various mechanisms, including encapsulation within vesicular structures, endocytosis and free distribution within the cells. Transfection of exosomes with FlnA-siRNAs resulted in a significant 2.8-fold reduction of filamin A expression in co-cultured podocytes, while pre-miR-21-transfected exosomes led to a remarkable 338-fold increase in mature miR-21 levels.

CONCLUSIONS

These findings demonstrate that direct exosome transfection with fluorescently-labeled small RNAs is an effective method for tracking exosomal cargo in podocytes. This study is the first to show that directly transfected exosomes can deliver small RNAs to podocytes in vitro, suggesting their potential as RNA carriers for therapeutic strategies in more complex settings.

Emerging roles of non-coding RNA derived from extracellular vesicles in regulating PD-1/PD-L1 pathway: insights into cancer immunotherapy and clinical applications

Numerous studies have demonstrated that extracellular vesicles (EVs) carry a variety of noncoding RNAs (ncRNAs), which can be taken up by neighboring cells or transported to distant sites via bodily fluids, thereby facilitating intercellular communication and regulating multiple cellular functions. Within the tumor microenvironment, EV-ncRNA, on the one hand, regulate the expression of PD-L1, thereby influencing tumor immune evasion, promoting tumor cell proliferation, and enhancing tumor growth, invasion, and metastasis in vivo. On the other hand, these specific EV-ncRNAs can also modulate the functions of immune cells (such as CD8 + T cells, macrophages, and NK cells) through various molecular mechanisms, inducing an immunosuppressive microenvironment and promoting resistance to anti-PD-1 therapy. Therefore, delving into the molecular mechanisms underlying EV-ncRNA regulation of immune checkpoints presents compelling therapeutic prospects for strategies that selectively target EV-ncRNAs. In this review, we elaborate on the cutting-edge research progress related to EV-ncRNAs in the context of cancer and dissect their pivotal roles in the PD-1/PD-L1 immune checkpoint pathway. We also highlight the promising clinical applications of EV-ncRNAs in anti-PD-1/PD-L1 immunotherapy, bridging basic research with practical clinical applications.

Atrial fibrillation is not associated with altered left atrial microRNA expression profile in advanced heart failure patients

BACKGROUND

Atrial fibrillation (AF) is common in patients with chronic heart failure (HF). Nevertheless, some patients with HF remain in sinus rhythm (SR) even with marked left atrial (LA) dilatation and fibrosis. The underlying mechanisms for the differences in atrial arrhythmogenicity are poorly uncovered. Recent findings indicate that distinct microRNAs (miRNA) might induce LA structural and molecular alterations. However, the impact of miRNA dysregulation on AF development in the context of HF has not been studied independently of LA remodeling.

OBJECTIVE

This study aimed to evaluate the differences in LA miRNA expressions in HF patients with AF or SR.

METHODS

LA myocardial samples were obtained from advanced HF patients with AF (n=12; paroxysmal n=4, chronic as persistent/permanent n=8) or SR (n=12) undergoing heart transplantation. The extent of LA interstitial fibrosis was evaluated using picrosirius red-staining. The LA load was estimated by measuring LA mRNA expression of the NPPA gene encoding atrial natriuretic peptide with qRT-PCR and circulating N-terminal proatrial natriuretic peptide (NT-proANP) by ELISA. The LA miRNA screening was performed using the NanoString technology.

RESULTS

LA dilatation, fibrosis, NPPA gene expression, as well as circulating NT-proANP levels were similar between the AF and SR groups, suggesting a comparable extent of atrial remodeling and load among the study groups. The miRNA analysis revealed no differences in atrial miRNA expression between the groups, even after AF subgroup analysis.

CONCLUSION

The LA miRNA expression profile shows no distinction between AF and SR in advanced HF patients with similar levels of pathological atrial remodeling.

A dual-cycle DNA walker sensor for sensitive clinical detection of microRNAs

BACKGROUND

MicroRNAs (miRNAs) play crucial roles in both physiological and pathological processes, and are increasingly recognized as important biomarkers for cancers and other diseases. However, current detection methods for miRNA face challenges, including inadequate sensitivity and the need for temperature-controlled instruments, which hinder their clinical application. It is a pressing need for new strategies suitable for clinical miRNA detection.

RESULTS

We designed a dual-cycle DNA walker sensor (DDWS) by coupling duplex-specific nucleases enzyme-assisted signal amplification (DSNSA) with a DNA walker sensor. In the DSNSA process, the DSN enzyme specifically hydrolyzes DNA in DNA/target miRNA hybrid duplexes to facilitate the target cycling. The DNA walker sensor is activated by the trigger released from the DSNSA process, enabling a DNA walker cycle via the CHA reaction on magnetic microparticles (MMPs). The DDWS exhibited a strong linear relationship over a range of 600 fM to 600 nM and demonstrated excellent specificity for target miRNA. Furthermore, the DDWS was successfully applied to miRNA detection in real samples, including total RNAs extracted in cell samples and clinical papillary thyroid carcinoma (PTC) tissue samples.

SIGNIFICANCE

This DDWS assay holds great potential for evaluating miRNA expression levels across various biological matrices, contributing to the clinical diagnosis and prognosis of cancers.

Emerging Role of Blood-based Biomarkers in Sarcomas

We assess the emerging role of liquid biopsies, particularly circulating tumor DNA (ctDNA), in sarcoma management. Preliminary studies suggest that ctDNA has multiple potential applications including, early detection in patients with cancer predisposition syndromes, diagnosis, prognostication, therapy selection, and monitoring treatment response. Among patients with gastrointestinal stromal tumors, studies have demonstrated the capacity for identification of clinically relevant resistance mutations. In other sarcoma subtypes such as Ewing sarcoma and osteosarcoma, early findings indicate that ctDNA levels might correlate with tumor burden and outcomes, potentially aiding in risk stratification. Clinical utility has not been established for these applications.

Association of MTMR3 rs12537 at miR-181a Binding Site with Ischemic Stroke in Southern Chinese Han Population

Background

Single nucleotide polymorphisms (SNPs) at microRNA (miRNA)--binding sites influence the development of ischemic stroke (IS) by affecting the expression of specific target genes. Myotubularin-related protein 3 (MTMR3), which is involved in autophagy, is directly targeted by miR-181a. This research examined the potential association between the SNP rs12537 in the miRNA-181a binding location within the 3' untranslated region (3'-UTR) of MTMR3 and the incidence and prognosis of IS.

Methods

An improved multitemperature ligase detection reaction assay was used to perform genotyping analysis in two independent case-control datasets consisting of 1128 subjects with IS and 1140 healthy controls with matched ages.

Results

The distribution frequencies of the T allele (p = 5.2×10-4) of SNP rs12537 in MTMR3 were elevated significantly in IS patients as compared to healthy controls. Further categorization based on IS subtypes revealed that individuals carrying the variation T allele were linked with a higher risk of suffering large-artery (p = 1.2×10-3) and small-artery (p = 7.0×10-4) atherosclerotic stroke subtypes. The T allele of rs12537 was shown to be linked to both moderate and severe stroke (NIHSS ≥ 6) (p = 0.011), as well as a poor short-term outcome (p = 0.016) of IS. A significant correlation was also found between the rs12537 T allele mutation and a decrease in MTMR3 (p = 0.019), as well as an elevated miR-181a (p = 0.021) and LC3B (p = 0.026) in individuals with IS.

Conclusion

This study identified a novel role for the rs12537 variant in influencing IS susceptibility and prognosis, potentially by modulating MTMR3 expression and leading to increased autophagy.

MiR-133a-5p Facilitates Cuproptosis in Hepatocellular Carcinoma Through Targeting of ATP7B

Purpose

We explored the effects of miR-133a-5p and ATP7B on cuproptosis in hepatocellular carcinoma.

Methods

Initially, we assessed the impact of miR-133a-5p on hepatocellular carcinoma (HCC) using CCK-8 assays, cell scratch assays, and flow cytometry. Subsequently, we utilized elesclomol in combination with copper ions to induce cuproptosis in the HCC cell lines PLC/PRF/5 and Huh-7. We evaluated the influence of miR-133a-5p on cuproptosis using CCK-8 assays, cell scratch assays, flow cytometry, and Western blotting. To elucidate the underlying mechanisms, we employed bioinformatics to identify potential downstream target genes of miR-133a-5p and conducted dual-luciferase reporter assays to confirm the binding sites. Finally, we validated the regulatory effect of miR-133a-5p on ATP7B by modulating miR-133a-5p expression through cell transfection experiments.

Results

The results from the CCK-8 assay, cell scratch assay, and flow cytometry demonstrated that miR-133a-5p significantly inhibits the proliferation and migration of HCC cells while promoting their apoptosis. Furthermore, Elesclomol in combination with copper ions induces cuproptosis in HCC cells. Compared to the cuproptosis observed in HCC as a control, miR-133a-5p further suppresses the proliferation and migration of HCC cells, enhances their death, and increases the expression of cuproptosis-related proteins more prominently. Bioinformatics analysis suggested that ATP7B might be a downstream target gene of miR-133a-5p. This was confirmed by dual luciferase assays, which identified a binding site between miR-133a-5p and ATP7B. Additionally, the expression levels of ATP7B were found to decrease or increase in response to the regulation by miR-133a-5p.

Conclusion

MiR-133a-5p facilitates cuproptosis in hepatocellular carcinoma through targeting of ATP7B.

CoupleMDA: Metapath-Induced Structural-Semantic Coupling Network for miRNA-Disease Association Prediction

The prediction of microRNA-disease associations (MDAs) is crucial for understanding disease mechanisms and biomarker discovery. While graph neural networks have emerged as promising tools for MDA prediction, existing methods face critical limitations: (1) data leakage caused by improper use of Gaussian interaction profile (GIP) kernel similarity during feature construction, (2) self-validation loops in calculating miRNA functional similarity using known MDA data, and (3) information bottlenecks in conventional graph neural network (GNN) architectures that flatten heterogeneous relationships and employ over-simplified decoders. To address these challenges, we propose CoupleMDA, a metapath-guided heterogeneous graph learning framework coupling structural and semantic features. The model constructs a biological heterogeneous network using independent data sources to eliminate feature-target space coupling. Our framework implements a two-stage encoding strategy: (1) relational graph convolutional networks (RGCN) for pre-encoding and (2) metapath-guided semantic aggregation for secondary encoding. During decoding, common metapaths between node pairs structurally guide feature pooling, mitigating information bottlenecks. The comprehensive evaluation shows that CoupleMDA achieves a 2-5% performance improvement over the current state-of-the-art baseline methods in the heterogeneous graph link prediction task. Ablation studies confirm the necessity of each proposed component, while case analyses reveal the framework's capability to recover cancer-related miRNA-disease associations through biologically interpretable metapaths.

Epigenetic Modifications in Sensorineural Hearing Loss: Protective Mechanisms and Therapeutic Potential

Hearing loss, which currently affects more than 430 million individuals globally and is projected to exceed 700 million by 2050, predominantly manifests as sensorineural hearing loss (SNHL), for which existing technologies such as hearing aids and cochlear implants fail to restore natural auditory function. Research focusing on protecting inner ear hair cells (HCs) from harmful factors through the regulation of epigenetic modifications has gained significant attention in otology for its role in regulating gene expression without altering the DNA sequence, suggesting potential strategies for preventing and treating SNHL. By synthesizing relevant studies on the inner ear, this review summarizes the emerging roles of histone modifications, DNA methylation, and noncoding RNAs in HC damage, with a focus on their therapeutic potential through epigenetic modulation. Moreover, this review examines the therapeutic potential of epigenetic regulation for the prevention and treatment of SNHL, emphasizing the application of small-molecule epigenetic compounds and their efficacy in modulating gene expression to preserve and restore auditory function.

miRNA-1229-5p promotes migration and invasion and suppresses apoptosis of endometrial cells via the STMN1/p38 MAPK axis in endometriosis

BACKGROUND

Emerging evidence suggests that aberrantly expressed microRNAs (miRNAs) participate in endometriosis pathogenesis. miR-1229-5p participates in the pathogenesis of several disease, but its precise role and mechanism in endometriosis is unclear.

METHODS

Endometrial tissues were obtained from patients with endometriosis and healthy controls. RT-qPCR and western blotting were employed to detect the expression levels of genes and proteins, respectively. Transcriptome sequencing and luciferase reporter assay were utilized to identify the target of miR-1229-5p. CCK-8, transwell assay, wound healing assay and flow cytometry assay were performed to evaluate the functional roles of miR-1229-5p. Finally, the clinical significance of miR-1229-5p was furtherly analyzed.

RESULTS

MiR-1229-5p was upregulated in ectopic endometrium of ovarian endometriosis patients (n = 60) compared to normal endometria of controls (n = 40), and its expression also served as an indicator for endometriosis severity. STMN1 was identified as the target of miR-1229-5p by luciferase experiments, and its expression was significantly downregulated in ectopic endometrium. Functionally, miR-1229-5p overexpression promoted migration, invasion, and inhibited apoptosis of ESCs and Ishikawa cells. Meanwhile, upregulation of miR-1229-5p also facilitated the protein expression of Bcl-2, MMP2, MMP9, N-cadherin, and ZEB1, and repressed the protein levels of Bax and E-cadherin. Whereas downregulation of miR-1229-5p exerted opposite effects. Importantly, STMN1 overexpression could partially reverse the effects of miR-1229-5p upregulation. Mechanistically, miR-1229-5p activates the p38 mitogen-activated protein kinase (p38 MAPK) signaling via targeting STMN1.

CONCLUSION

The newly identified miR-1229-5p-STMN1-p38 MAPK axis illustrates the molecular mechanism of endometriosis progression and offers a potential therapeutic target for treating endometriosis.

Machine learning approaches for predicting the small molecule-miRNA associations: a comprehensive review

MicroRNAs (miRNAs) are evolutionarily conserved small regulatory elements that are ubiquitous in cells and are found to be abnormally expressed during the onset and progression of several human diseases. miRNAs are increasingly recognized as potential diagnostic and therapeutic targets that could be inhibited by small molecules (SMs). The knowledge of SM-miRNA associations (SMAs) is sparse, mainly because of the dynamic and less predictable 3D structures of miRNAs that restrict the high-throughput screening of SMs. Toward augmenting the costly and laborious experiments determining the SM-miRNA interactions, machine learning (ML) has emerged as a cost-effective and efficient platform. In this article, various aspects associated with the ML-guided predictions of SMAs are thoroughly reviewed. Firstly, a detailed account of the SMA data resources useful for algorithms training is provided, followed by an elaboration of various feature extraction methods and similarity measures utilized on SMs and miRNAs. Subsequent to a summary of the ML algorithms basics and a brief description of the performance measures, an exhaustive census of all the 32 ML-based SMA prediction methods developed so far is outlined. Distinctive features of these methods have been described by classifying them into six broad categories, namely, classical ML, deep learning, matrix factorization, network propagation, graph learning, and ensemble learning methods. Trend analyses are performed to investigate the patterns in ML algorithms usage and performance achievement in SMA prediction. Outlining key principles behind the up-to-date methodologies and comparing their accomplishments, this review offers valuable insights into critical areas for future research in ML-based SMA prediction.

Integrating exosome wide associations study and Mendelian randomization identified causal miRNAs for type 2 diabetes mellitus and its complications

BACKGROUND

Type 2 diabetes mellitus (T2DM) and its complications, including diabetic lower extremity arterial disease (DLEAD) and diabetic foot (DF), impose significant health burdens worldwide. However, the differential expression of microRNAs (miRNAs) between T2DM and its complications and its causal effects remain poorly understood.

METHODS

We conducted an exosome-wide association study (EWAS) comparing miRNA profiles between T2DM and its complications, including DLEAD and DF, without healthy controls. The significant miRNAs identified between DM and its complications were further validated by integrating cis-miRNA expression quantitative trait loci (cis-miR-eQTLs) and genome-wide association study (GWAS) summary data of T2DM and peripheral arterial disease (PAD) through two-sample Mendelian randomization (MR) analysis.

RESULTS

We identified several differential expressions of miRNAs between T2DM, DLEAD, and DF, such as hsa-miR-409-3p between T2DM and DLEAD, hsa-miR-543 between T2DM and DF and hsa-miR-206 between DLEAD and DF. The two sample MR analysis revealed potential causal relationships between dysregulated miRNAs and T2DM and its complications, such as hsa-miR-30b-3p and hsa-miR-30b-5p showed causal associations with T2DM and PAD respectively.

CONCLUSIONS

Our study elucidates the miRNA signatures associated with T2DM and its complications. These findings provide insights into the pathogenesis of T2DM and its complications and suggest potential therapeutic targets for intervention.

Suppressing proteasome activity enhances sensitivity to actinomycin D in diffuse anaplastic Wilms tumor

Wilms tumor is the most common pediatric kidney cancer, and diffuse anaplastic Wilms tumor is the most chemoresistant subtype. Here, we explore how Wilms tumor cells evade the chemotherapy actinomycin D, which inhibits ribosomal RNA biogenesis. Using ribosome profiling, protein arrays, and a genome-wide knockout screen, we describe how actinomycin D disrupts protein homeostasis and blocks cell-cycle progression. When ribosomal capacity is limited by actinomycin D treatment, anaplastic Wilms tumor cells preferentially translate proteasome components. Next, we find that the proteasome inhibitor bortezomib sensitizes cells to actinomycin D treatment in vitro and prolongs survival in xenograft models. Lastly, increased levels of proteasome components are associated with anaplastic histology and worse prognosis in Wilms tumor patients. In sum, maintaining protein homeostasis is critical for Wilms tumor proliferation, and it can be therapeutically disrupted by blocking protein synthesis or turnover.

Optimizing siRNA Therapeutics Targeting HIF-1α: Computational Design, Screening, and Molecular Dynamics Simulation Studies

Hypoxia-inducible factor-1 alpha (HIF-1α) is an important transcription factor regulating glycolysis, angiogenesis, metastasis, and erythropoiesis under hypoxic conditions in solid tumors. Small interfering RNAs (siRNAs) have emerged as a promising therapeutic approach for solid tumors by selectively silencing target genes. This study explored siRNA-mediated degradation of HIF-1α by specifically targeting HIF-1α mRNA. We retrieved the HIF-1α gene sequence from the database and used various computational tools like siDirect and OligoWalk to get potential 19-21nts long siRNAs. Furthermore, these siRNAs were screened using parameters like sequence specificity, BLASTn, secondary structure formation, GC content, binding affinity between siRNA and mRNA, and thermodynamic properties. The potential siRNAs were further evaluated through molecular docking studies for interaction with the human Argonaute-2 protein (hAgo2), followed by molecular dynamics simulation studies. Post-MD studies revealed S4 (5'UAUAUGGUGAUGAUGUGGC3') as the most potential siRNA candidate against HIF-1α, based on root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and H-bond analysis. Molecular mechanics Poisson-Boltzmann surface area (MMPBSA) analysis was also performed to further validate the selected siRNA candidates, which further affirmed S4 (5'UAUAUGGUGAUGAUGUGGC3') as a potential candidate against HIF-1α.

Histomorphological variations in progressive multifocal leukoencephalopathy correlated with JCV replication in brain lesions: insights from 91 patients

Progressive multifocal leukoencephalopathy (PML) is a demyelinating disease caused by JC polyomavirus (JCV). The histopathology of PML is morphologically diverse and characterized by the classical triad of demyelination, enlarged oligodendroglial nuclei, and bizarre astrocytes. Pathological diagnostic criteria for PML require both the classical triad and viral detection in brain tissue. However, the frequency of this triad in surgical pathology specimens and its correlation with disease progression and viral loads remain unclear. In this study, 117 brain tissues from 91 pathologically confirmed PML patients were investigated. PML histopathology was found to be spatially and temporally pleomorphic, and not all brain tissues exhibited the complete classical triad. The sensitivity of quantitative PCR for detecting JCV in brain tissues was 100%, whereas that of immunohistochemistry (IHC) was 83.5-87.8%. Viral loads in biopsy samples were significantly higher than those in autopsy samples and decreased over time after disease onset. To systematically characterize PML lesions from the outer border to the demyelinated center, we developed a histological classification based on the classical triad and macrophage infiltration. This classification correlated with viral loads, with subtypes characterized by abundant enlarged oligodendroglial nuclei at the demyelination border exhibiting the highest levels of JCV DNA. Pathological variability was influenced by spatial and temporal factors rather than by underlying diseases, although PML associated with acquired immunodeficiency syndrome exhibited more severe demyelination. In conclusion, histomorphological variability in PML reflects viral replication activity, emphasizing the importance of comprehensive pathological evaluation. Combining histomorphology, tissue-based PCR for viral DNA detection, and IHC for viral antigens is crucial for assessing disease progression. Early brain biopsy from the demyelination border offers the best opportunity for a definitive diagnosis of PML and may guide therapy targeting active lesions.

Fungus-targeted nanomicelles enable microRNA delivery for suppression of virulence in Aspergillus fumigatus as a novel antifungal approach

Aspergillus fumigatus, which causes aspergillosis, has developed resistance to azole antifungal agents in recent years. As only three main classes of antifungal drugs are available, the development of novel therapeutic strategies is crucial. We aimed to control the expression of virulence factors by introducing microRNAs (miRNAs) into fungi as an innovative therapeutic approach. To test our hypothesis, we selected miRNA mimics targeting alb1, which is involved in the synthesis of 1,8-dihydroxynaphthalene (DHN)-melanin, a virulence factor of A. fumigatus, and transfected them into the protoplast of the fungus, resulting in a two-fold reduction in alb1 expression. Next, we created a 3×HA-tagged Alb1 protein (Alb1-HAp)-expressing strain and confirmed the regulation of translation using western blotting with an anti-HA antibody. The protein amount of Alb1-HAp was reduced by one-third after the introduction of the miRNA. Moreover, the reduction in melanin after miRNA transfection promoted the killing of fungus by hydrogen peroxide-induced oxidative stress and sensitised the fungus to neutrophil attack. Additionally, by loading miRNAs into a fungus-targeted delivery system, we demonstrated the potential of transferring miRNAs into intact fungal cells in vitro. These results indicate the potential of miRNAs to regulate target virulence factors in fungi, leading to the development of novel therapies.

The crosstalk between glutathione metabolism and non-coding RNAs in cancer progression and treatment resistance

Excessive reactive oxygen species (ROS) are closely associated with the initiation and progression of cancers. As the most abundant intracellular antioxidant, glutathione (GSH) plays a critical role in regulating cellular ROS levels, modulating physiological processes, and is intricately linked to tumor progression and drug resistance. However, the underlying mechanisms remain not fully elucidated. Non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), are key regulators of GSH levels. Different ncRNAs modulate various pathways involved in GSH metabolism, and these regulatory targets have the potential to serve as therapeutic targets for enhancing cancer treatment. In this review, we summarize the functions of GSH metabolism and highlight the significance of ncRNA-mediated regulation of GSH in cancer progression, drug resistance, and clinical applications.

A spatio-temporal brain miRNA expression atlas identifies sex-independent age-related microglial driven miR-155-5p increase

An in-depth understanding of the molecular processes composing aging is crucial to develop therapeutic approaches that decrease aging as a key risk factor for cognitive decline. Herein, we present a spatio-temporal brain atlas (15 different regions) of microRNA expression across the mouse lifespan (7 time points) and two aging interventions. MicroRNAs are promising therapeutic targets, as they silence genes by complementary base-pair binding of messenger RNAs and mediate aging speed. We first established sex- and brain-region-specific microRNA expression patterns in young adult samples. Then we focused on sex-dependent and independent brain-region-specific microRNA expression changes during aging. We identified three sex-independent brain aging microRNAs (miR-146a-5p, miR-155-5p, and miR-5100). For miR-155-5p, we showed that these expression changes are driven by aging microglia and target mTOR signaling pathway components and other cellular communication pathways. In this work, we identify strong sex-brain-region-specific aging microRNAs and microglial miR-155-5p as a promising therapeutic target.

Scenarios for the emergence of new microRNA genes in the plant Arabidopsis halleri

MicroRNAs (miRNAs) are central players in the regulation of gene expression in eukaryotes. The repertoires of miRNA genes vary drastically even among closely related species, indicating that they are evolutionarily labile. However, the processes by which they originate over the course of evolution and the nature of their progenitors across the genome remain poorly understood. Here, we analyzed miRNA genes in Arabidopsis halleri, a plant species where we recently documented a large number of species-specific miRNA genes, likely to represent recent events of emergence. Analysis of sequence homology across the genome indicates that a diversity of sources contributes to the emergence of new miRNA genes, including inverted duplications from protein-coding genes, rearrangements of transposable element (TE) sequences, and duplications of preexisting miRNA genes. Our observations indicate that the origin from protein-coding genes was less common than was previously considered. In contrast, we estimate that almost half of the new miRNA genes likely emerged from TEs. Miniature inverted-repeat TEs (MITEs) seem to be particularly important contributors to new miRNA genes, with the Harbinger and Mariner TE superfamilies representing disproportionate sources for their emergence. We further analyzed the recent expansion of a miRNA family derived from MuDR elements and the duplication of miRNA genes formed by two hAT transposons. Overall, our results illustrate the rapid pace at which new regulatory elements can arise from the modification of preexisting sequences in a genome and highlight the central role of certain categories of TEs in this process.

Circular RNAs in glioma progression: Fundamental mechanisms and therapeutic potential: A review

Gliomas are the most common primary malignant brain tumors, characterized by aggressive invasion, limited therapeutic options, and poor prognosis. Despite advances in surgery, radiotherapy, and chemotherapy, the median survival of glioma patients remains disappointingly low. Therefore, identifying glioma-associated therapeutic targets and biomarkers is of significant clinical importance. Circular RNAs (circRNAs) are a class of naturally occurring long non-coding RNAs (lncRNAs), notable for their stability and evolutionary conservation. Increasing evidence indicates that circRNA expression is dysregulated in gliomas compared to adjacent non-tumor tissues and contributes to the regulation of glioma-related biological processes. Furthermore, numerous circRNAs function as oncogenes or tumor suppressors, mediating glioma initiation, progression, and resistance to temozolomide (TMZ). Mechanistically, circRNAs regulate glioma biology through diverse pathways, including acting as miRNA sponges, binding RNA-binding proteins (RBPs), modulating transcription, and even encoding functional peptides. These features highlight the potential of circRNAs as diagnostic and prognostic biomarkers, as well as therapeutic targets for glioma. This review summarizes the dysregulation and functions of circRNAs in glioma and explores key mechanisms through which they mediate tumor progression, including DNA damage repair, programmed cell death (PCD), angiogenesis, and metabolic reprogramming. Our aim is to provide a comprehensive perspective on the multifaceted roles of circRNAs in glioma and to highlight their potential for translational application in targeted therapy.

The potential role of miR-450a-1-3p in chromium-associated heart rate variability reduction

Chromium (Cr) exposure has been reported to be associated with heart rate variability (HRV) decline, whereas the underlying mechanism remains unknown. In present study, a cross-sectional study was conducted in Chinese urban adults to explore the potential role of microRNAs (miRNAs) in the relationship between urinary chromium and HRV decline. In the discovery stage, 20 Cr-related miRNAs were screened out by high-throughput sequencing. Both generalized linear model and differential expression analysis were conducted and miR-450a-1-3p was chosen for further analyses. Then, the quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to measure the concentration of plasma miR-450a-1-3p and generalized linear model was used to estimate the association between urinary chromium, plasma miR-450a-1-3p and HRV indices and further to explore the potential role of miR-450a-1-3p in chromium-induced HRV reduction. Precisely, a positive association of chromium exposure with plasma miR-450a-1-3p was observed and HRV indices were negatively related to urinary chromium or plasma miR-450a-1-3p concentrations elevating (all P < 0.05). Furthermore, plasma miR-450a-1-3p significantly mediated and affected the relationship between chromium exposure and HRV reduction. Finally, we used KEGG analysis to study the potential pathway of miR-450a-1-3p and inferred the arrhythmogenic right ventricular cardiomyopathy and calcium signaling pathway were involved in the chromium-induced HRV reduction.

Exploring the potential of Gonolobus condurango as a histone deacetylase inhibitor in triple-negative breast cancer cell lines: in vitro study

BACKGROUND

Triple-negative breast cancer (TNBC) is a subtype associated with poor prognosis, low survival rates, and high expression of histone deacetylases (HDAC). Treatment with HDAC inhibitors (HDACi) induces the acetylation of histones and thereby the expression of tumor suppressive miRNAs that regulate proliferation, apoptosis, migration, and differentiation. Gonolobus condurango (GC) has been reported to exhibit HDAC inhibitory effects, and this study aims to investigate whether GC acts as a HDACi in TNBC cell lines.

METHODS

Expression and acetylation analyses were performed on the TNBC cell lines HCC38, HCC1395, and HCC1937. Cells were treated with HDAC inhibitors Trichostatin A (TSA), suberoylanilide hydroxamic acid (SAHA), or Romidepsin as well as with GC Urtincture and different dilutions of GC. Tumor-relevant functional effects were analyzed using WST-1-based proliferation and Caspase-3/7 based apoptosis assays. Induction of expression of tumor-suppressive miRNAs hsa-miRNA-192-5p (miR-192) and hsa-miR-194-2 (miR-194) was analyzed by qRT-PCR.

RESULTS

Meta-analyses of gene expression showed a significant reduction in HDAC1 and HDAC2 expression in triple-negative breast cancer samples. The TNBC cell lines (HCC38, HCC1395, and HCC1937) used for in vitro assays also exhibited reduced expression of HDAC1, HDAC2, HDAC3, and HDAC4 and low acetylation levels. Treatment with the HDAC inhibitors TSA, SAHA, or Romidepsin induced acetylation, while GC did not. TSA and GC Urtincture induced apoptosis in HCC38, whereas GC dilutions had no effect. Treatment with TSA forced the expression of tumor suppressive miRNAs miR-192 and miR-194, but neither GC Urtincture nor any GC dilution induced the expression of these miRNAs.

CONCLUSION

Several classes of HDAC inhibitors have been shown to be potent and specific anticancer agents. In this study, Gonolobus condurango showed no HDAC inhibitory effect in the TNBC cell lines. Identifying new HDAC inhibitors is important, but they must be well characterized before being used as therapeutic agents in humans.

DNA logic nanomachine for the accurate identification of multiple microRNAs in tumor cells

The use of dynamic DNA logic circuits for disease diagnosis at the molecular level plays a considerable role in biomedical fields. Nevertheless, how to create programmable nanomachines based on molecular logical gates to accurately identify multiple biomarkers from tumor cells remains a pivotal challenge. Herein, we developed a DNA-based nanomachine for analyzing and imaging multiple microRNAs (miRNAs) in cancerous cells with a logical AND operation. The triangular prism design of DNA nanomachine improved its performance in living cell research with high stability and served as a modularized framework for toehold-mediated strand displacement reactions and catalytic hairpin assembly circuits. The results suggested that the nanomachine could efficiently enter cells with great biocompatibility and rapidly recognize the correct biomolecules with high sensitivity. The well-designed DNA-logic gate nanomachine enabled accurate diagnosis on multiple miRNA patterns in different cell lines and differentiation of aberrant expression in target cells, which provided a novel possibility for intelligent disease diagnosis using smart nanomachines at the molecular level.

Plant microRNAs enter the scene of calcium signaling

Recent studies have identified the miRNA391/1432/4376 superfamily (miR391S) in seed plants, which targets the 5' untranslated region (UTR) of mRNAs encoding autoinhibited Ca2+-ATPases (ACAs), a key component of calcium signaling. This superfamily includes miR391 in the Brassicaceae, miR4376 in the Solanaceae, and miR1432 in the Poaceae, all of which share a highly conserved 10-nucleotide (nt) core in their mature miRNA sequences. Notably, miR1432 in the Poaceae targets both ACA and mRNAs encoding calmodulin-like proteins, which are putative Ca2+ sensors. In this opinion article we highlight evidence revealing this miRNA superfamily's ancient origin, regulatory conservation, and sequence diversification linked to functional innovation. Consistent with the central role of calcium signaling, recent studies on Arabidopsis thaliana and rice suggest the broad implications of the ACA-targeting miRNAs in plant development, immunity, and abiotic stress responses.

Evaluation of circulating microRNAs in plasma from horses with non-strangulating intestinal infarction and idiopathic peritonitis

Non-strangulating intestinal infarctions (NSII) associated with Strongylus vulgaris infection and idiopathic peritonitis (IP) share similar clinical presentation but require different treatment approaches. Horses with NSII need surgical intervention, while idiopathic peritonitis cases can be successfully treated with antimicrobials. A correct diagnosis is thus crucial, but because the two diseases overlap in clinicopathological features, differentiation is difficult in clinical practice. MicroRNAs (miRNAs) are non-coding RNAs that exhibit measurable changes in abundance in tissues and circulation during disease. This study aimed to explore differences in plasma miRNA abundance between patients with NSII and IP. Plasma samples were collected from 43 horses, consisting of 21 with NSII and 22 with IP. A subset (n = 12) was submitted for deep small RNA sequencing to identify miRNAs differing between the groups. Next, a panel of nine miRNAs (two were potential normalizers) were selected for evaluation and confirmation by reverse transcription quantitative real-time PCR (RT-qPCR). Small RNA sequencing detected 628 miRNAs in the blood samples, but no miRNAs were differentially abundant between the disease groups. This finding was confirmed by qPCR. In agreement with previous studies, the top abundant miRNAs in both groups included Eca-Mir-122-5p and Eca-Mir-486-5p, as well as Eca-Mir-223-3p, which has previously been associated with inflammation. Target prediction for the most abundant miRNAs additionally predicted targets in inflammatory pathways. Evaluation of clinicopathological parameters revealed differences between the groups in two measures (white blood cell count and blood neutrophil count), which aligns with findings from previous studies. The results demonstrate that NSII and IP elicit similar miRNA profiles in plasma and are characterized by systemic inflammation.