miRNA Expression Research Articles

MicroRNAs in idiopathic childhood nephrotic syndrome.

miRNAs are non-coding RNA that are recognized as biomarkers of kidney disorders. There is limited information on the differential expression of miRNA and their target genes in idiopathic nephrotic syndrome of childhood. We enrolled patients, 2-18years old, with steroid-sensitive nephrotic syndrome, either at onset or during relapse, and steroid-resistant disease, at diagnosis of steroid-resistance. Patients with steroid-sensitive disease were off immunosuppressive medications, while those with steroid-resistance were on therapy with prednisolone at enrollment. Controls were healthy children attending the hospital for vaccinations or for minor non-infectious, non-kidney ailments. Following RNA extraction from whole blood, differential expression of 2549 miRNAs was examined to identify differentially expressed miRNA, defined as those with absolute log2 fold change > 2 and adjusted P < 0.05. Target genes, predicted using miRNet, were compared against the genes for nephrotic syndrome in the NCBI database, and the ontology of selected genes was examined using DAVID. Comparison of miRNA expression in 36 patients and 12 controls led to the identification of 62 and 12 differentially expressed miRNA in patients with steroid-sensitive and steroid-resistant disease, respectively. Of 76 miRNAs that were differentially regulated between the two disease categories, 26 were unique to steroid-sensitive disease and 11 to steroid-resistance. Of 5955 and 2813 genes targeted by the miRNAs specific to steroid-sensitive and steroid-resistant nephrotic syndrome, respectively, 79 were relevant in context of the disease. Steroid-sensitive and steroid-resistant nephrotic syndrome have distinct miRNA expression profiles, which can be examined as biomarkers and in pathogenetic pathways.

MiR-449, identified through antiandrogen exposure, mitigates functional biomarkers associated with ovarian cancer risk

The involvement of the androgen receptor (AR) pathway in developing epithelial ovarian cancer is increasingly acknowledged. However, the specific mechanisms by which anti-androgen agents, such as flutamide, may prevent ovarian cancer and their efficacy remain unknown. This study was initiated by investigating the impact of flutamide on miRNA expression in women at high risk (HR) for ovarian cancer. Ovarian and tubal tissues, free from ovarian, tubal, peritoneal cancers, and serous tubal intraepithelial carcinoma (STIC), were collected from untreated and flutamide-treated HR women as well as low-risk (LR) women controls. We performed miRNA sequencing on these 3 sample cohorts and observed that flutamide normalized miRNA levels in HR tissues, notably upregulating the miR-449 family to levels seen in LR tissues. In subsequent tests in primary ovarian epithelial cells and ovarian cancer cell lines (SKOV3 and Hey), flutamide also increased miR-449a and miR-449b-5p levels. Introducing mimics of these miRNAs reduced the mRNA and protein levels of AR and colony-stimulating factor 1 receptor (CSF1R, also known as c-fms), both of which are known contributors to ovarian cancer progression, with emerging evidence also supporting their roles in ovarian cancer initiation. Ovarian cancer cell migration was inhibited upon introducing miR-449a and miR-449b-5p mimics. Together, our study suggests a novel dual-inhibitory mechanism of flutamide on the AR pathway (AR expression suppression in addition to direct androgen antagonism) and supports its chemopreventive potential in ovarian cancer, especially for HR patients with low miR-449 expression.

Microgravity’s effects on miRNA-mRNA regulatory networks in a mouse model of segmental bone defects

Rehabilitation from musculoskeletal injuries (MSKI) complicate healing dynamics typically by sustained disuse of bone and muscles. Microgravity naturally allows limb disuse and thus an effective model to understand MSKI. The current study examined epigenetic changes in a segmental bone defect (SBD) mouse model in a prolonged unloading condition after spaceflight (FLT). We further connected potential miRNA–mRNA regulatory pathways impacting bone healing. Here, SBD surgery was performed on nine-week-old male mice that were launched into space for approximately 4 weeks. Sham with no surgery and ground controls were included in the study. The midshaft of the ipsilateral femur (with callus on the surgical mice) as well as the ipsilateral quadriceps tissue were used for analysis. Femur and quadriceps had a distinct miRNA profile. There was a stronger surgery effect as observed by miRNA expression when compared to microgravity effects. Leukopoiesis, granulopoiesis, myelopoiesis of leukocytes, differentiation of myeloid leukocytes, and differentiation of progenitor cells were all altered because of surgery in the femur. The biological functions such as apoptosis, necrosis, and activation of cell migration and viability were altered because of surgery in quadriceps. Integrating the transcriptome and microRNA data indicated pronounced changes because of microgravity. According to pathway analysis, microgravity had a greater impact on the quadriceps tissue than the bone tissue in the absence of surgery. The altered biological functions resulting from microgravity were validated by integrating limited proteomics data to miRNA-mRNA. Thus, this study highlights the importance of dynamic interplay of gene-epigene regulations as they appear to be intrinsically interconnected and influence in combination for the biological outcome.

Urinary miRNA Expression in Pre-Eclampsia During Early and Mid-Pregnancy

Background: Pre-eclampsia (PE) is a serious condition affecting 2–8% of pregnancies worldwide, leading to high maternal and fetal morbidity and mortality. MicroRNAs (miRNAs), small non-coding RNA molecules, have emerged as potential biomarkers for various pregnancy-related pathologies, including PE. MiRNAs in plasma and serum have been extensively studied, but urinary miRNAs remain underexplored, especially during early pregnancy. This study aimed to investigate the urinary miRNA expression profiles in women with pre-eclampsia during the first and second trimesters. Materials and Methods: A prospective study was conducted using 48 urine samples from 24 pregnant women (n = 12 pre-eclampsia and n = 12 controls). Urine samples were collected in the first (9–13 weeks) and second (22–24 weeks) trimesters. MiRNA isolation, library preparation, and high-throughput sequencing were performed, followed by differential expression and enrichment analyses. Results: In the first trimester, five miRNAs were dysregulated in PE in comparison with the control group (hsa-miR-184, hsa-miR-203a-3p, hsa-miR-205-5p, hsa-miR-223-3p—downregulated; hsa-miR-1-3p—upregulated). In the second trimester, hsa-miR-205-5p and hsa-miR-223-3p were downregulated, and hsa-miR-9-5p, hsa-miR-1-3p, and hsa-miR-206 were upregulated. Conclusions: Our study identified differentially expressed miRNAs in the urine of pre-eclamptic patients during early pregnancy. These findings suggest that specific urinary miRNAs could serve as non-invasive biomarkers for the early detection and risk assessment of pre-eclampsia. The changes in the level of differential expression of miRNAs during gestation highlight their role in the progression of PE. Further research and validation with a larger cohort are needed to explore their clinical potential for improving maternal and fetal outcomes through early intervention.

Integrated miRNA-seq and functional analyses reveal the regulatory role of sha-miR-92a_L + 2R + 4 via targeting vegfaa in rainbow trout (Oncorhynchus mykiss) responding to acute hypoxia and reoxygenation stress

BackgroundHypoxia negatively affects the behavior, growth, reproduction and survival of fish, causing serious economic losses to aquaculture. Rainbow trout (Oncorhynchus mykiss), an important economic fish worldwide, belongs to a hypoxia-sensitive fish species, however, little is known about the regulatory mechanism of microRNAs (miRNAs) under hypoxia stress.ResultsRainbow trout were subjected to hypoxia stress for 3 h (H3h_L), 12 h (H12h_L), 24 h (H24h_L) and 3 h reoxygenation (R3h_L) to systemically evaluate the changes of miRNA expression profiles in liver, and functions of sha-miR-92a_L + 2R + 4 were investigated. We found 17, 144, 57 and 55 differentially expressed (DE) miRNAs in the H3h_L vs. control (N_L), H12h_L vs. N_L, H24h_L vs. N_L and R3h_L vs. N_L comparisons, respectively. Enrichment analysis revealed that the targets of DE miRNAs were significantly enriched in HIF signaling pathway, VEGF signaling pathway, FoxO signaling pathway and glycolysis/gluconeogenesis. Through miRNA-mRNA interaction and weighted gene co-expression network analysis (WGCNA), five key DE miRNAs (sha-miR-92a_L + 2R + 4, ssa-miR-128-3p, ssa-miR-101b-3p_R + 1, ola-miR-199a-5p_R + 2 and tni-miR-199_1ss18CG) were identified, which can target at least two hypoxia-responsive genes, such as vegfaa, ho, glut1a and junb. Functional analysis found that sha-miR-92a_L + 2R + 4 directly regulated vegfaa expression by targeting its 3′-UTR, overexpression of sha-miR-92a_L + 2R + 4 significantly decreased vegfaa expression in rainbow trout liver cells, while opposite results were obtained after transfection of sha-miR-92a_L + 2R + 4 inhibitor. Furthermore, overexpressed sha-miR-92a_L + 2R + 4 promoted rainbow trout liver cell proliferation and inhibited apoptosis.ConclusionThis study deepens our understanding of the crucial roles of miRNAs under hypoxia stress in rainbow trout. These results can contribute to devise strategies for improving rainbow trout survival rate and aquaculture production during hypoxia stress and help speeding up the selective breeding of hypoxia-tolerant rainbow trout.

MicroRNA Profiles in Critically Ill Patients.

The use of biomarkers to expedite diagnosis, prognostication, and treatment could significantly improve patient outcomes. The early diagnosis and treatment of critical illnesses can greatly reduce mortality and morbidity. Therefore, there is great interest in the discovery of biomarkers for critical illnesses. Micro-ribonucleic acids (miRNAs) are a highly conserved group of non-coding RNA molecules. They regulate the expression of genes involved in several developmental, physiological, and pathological processes. The characteristics of miRNAs suggest that they could be versatile biomarkers. Assay panels to measure the expression of several miRNAs could facilitate clinical decision-- making for a range of diseases. We have, in this paper, reviewed the current understanding of the role of miRNAs as biomarkers in critically ill patients.

Self-priming dumbbell probe-mediated cascade isothermal amplification for sensitive and label-free MICRORNA detection using fluorescence light-up silver nanocluster

Given the critical significance of microRNAs (miRNAs) in cancer diagnosis and classification (e.g., glioma), there is a need for the advancement of sensitive, specific, quantitative, and cost-effective approach for assessing miRNA expression levels. We present an effective amplification technology for ultrasensitive miRNA analysis by combining a self-priming dumbbell probe-mediated cascade isothermal amplification strategy with fluorescence-enhanced silver nanoclusters (DNA-AgNCs). The approach depends on the disassociation of the stem portion of the dumbbell probe through the binding of target miRNA, followed by self-priming mediated target recycling, DNA polymerase/endonuclease facilitated chain extension, and catalytic hairpin assembly (CHA) to provide an amplified signal. The CHA procedure generates an LP-AgNCs/LP-G duplex, wherein the fluorescence signals of DNA-AgNCs can be significantly amplified when in close proximity to guanine-rich (G-rich) DNA sequences. The proposed label-free assay, characterized by high sensitivity, a wide dynamic range (spanning 6 orders of magnitude), excellent specificity (capable of detecting single-base differences), and simple operation, has been successfully utilized for the detection of miRNA in real samples. This demonstrates its potential as a compelling alternative for miRNA analysis in gene expression profiling and molecular diagnostics, especially for early glioma cancer detection.

LET-7a and LET-7b as Potential Signatures for Glioma Recurrence, Regardless of WHO Tumor Grade.

Micro RNAs (miRs; miRNAs) are small, non-coding RNA segments that influence gene expression. To do this, they bind to corresponding mRNA segments and inhibit the subsequent protein translation. Currently, about 200 transcripts are thought to be regulated by a single miRNA. Dysregulated miRNAs can act as tumor promoters as well as tumor suppressors. The aim of this study was to verify miR-LET-7a and miR-LET-7b as a signature for glioma recurrence detection by analyzing their expression in glioma tissue. Only patients with two or more recurrences of glioma (n=25) were included in the study (tissue samples, n=89). Tissue was obtained during neurosurgical procedures and shock-frozen in liquid nitrogen. The patient cohort (female:male=12:13) had an average age of 35 years when first diagnosed (primary tumor: 13 WHO grade II, 7 WHO grade III and 5 WHO grade IV) and 48 years in the fifth relapse. Quantitative real-time polymerase chain reaction was performed to analyze miRNA expression. miR-151a-3p was used as an internal reference. Expression of miR-LET-7a and miR-LET-7b was significantly lower in the first recurrence than in the primary tumor. The expression of miR-LET-7a and -7b significantly decreased with increasing tumor grade. The strongest down-regulation was found between WHO grade III and IV. In paired samples in which tumor grade did not change between the primary and the first recurrence, the expression of both miRNAs remained significantly lower in the recurrent than in the primary tumor. miR-LET-7a and miR-LET-7b represent a potential signature for glioma recurrence regardless of WHO grade.

Bioinformatics and Experimental Insights Into miR‐182, hsa_circ_0070269, and circ‐102,166 as Therapeutic Targets for HCV‐Associated HCC

ABSTRACTAimsHepatocellular carcinoma (HCC) is a type of malignant tumor and the sixth leading cause of death worldwide. It is caused by HBV, HCV infection, and alcohol consumption. MicroRNAs are typically small, non‐coding RNAs that are involved in the regulation of mRNA expression. Recent studies revealed miRNAs' regulatory roles in liver cancer, linked to risk factors like HCV, HBV infection, alcoholism, drug use, and auto‐immune hepatic disorders. Circular RNAs also belong to the class of non‐coding RNAs; they act as ceRNAs to regulate miRNA expression and regulate different oncogenic pathways in HCC progression. This study aimed to check the hsa_circ_0070269, circ‐102,166 (hsa_circ_0004913), and miR‐182 expression in HCV induced HCC patients.MethodsData analysis was used to find out studies related to the role of hsa_circ_0070269, circ‐102,166, and miR‐182 in HCC; miR‐182 targeted genes, their role in different diseases; and miR‐182 interactions with hsa_circ_0070269 and circ‐102,166 in the HCC. It was revealed that the hsa_circ_0070269, circ‐102,166, and miR‐182 correlations in HCV induced HCC have not been explored yet. Therefore, to validate data from literature mining, expression analysis of dysregulated hsa_circ_0070269, circ‐102,166, and miR‐182 was performed in HCV induced HCC patients using RT‐PCR.ResultsIt was found that miR‐182 was significantly upregulated and acts as an oncomiRNA in HCV induced HCC, and hsa_circ_0070269 and circ‐102,166 were downregulated in HCV induced HCC. We have identified that miR‐182 relative expression level was significantly high (p &lt; 0.0029), while has_circ_0070269 (p &lt; 0.002) and circ‐102,166 (p &lt; 0.002) were significantly downregulated in HCV‐HCC patients as compared to expression in healthy individuals.ConclusionOur data revealed that miR‐182 acts as an oncomiRNA in HCC development. Hsa_circ_0070269 and circ‐102,166 are highly expressed in healthy controls compared to HCV induced HCC patients, can sponge miR‐182 expression by acting as tumor suppressors, and can be used as biomarkers and targets for HCC treatment.

Age-Related sncRNAs in Human Hippocampal Tissue Samples: Focusing on Deregulated miRNAs

Small non-coding RNAs (sncRNAs), particularly microRNAs (miRNAs), play an important role in transcriptome regulation by binding to mRNAs and post-transcriptionally inhibiting protein production. This regulation occurs in both physiological and pathological conditions, where the expression of many miRNAs is altered. Previous reports by our group and others have demonstrated that miRNA expression is also altered during aging. However, most studies have analyzed human peripheral blood samples or brain samples from animal models, leaving a gap in knowledge regarding miRNA expression in the human brain. In this work, we analyzed the expression of sncRNAs from coronal sections of human hippocampal samples, a tissue with a high vulnerability to deleterious conditions such as aging. Samples from young (n = 5, 27–49 years old), old (n = 8, 58–88 years old), and centenarian (n = 3, 97, 99, and 100 years old) individuals were included. Our results reveal that sncRNAs, particularly miRNAs, are differentially expressed (DE) in the human hippocampus with aging. Besides, miRNA-mediated regulatory networks revealed significant interactions with mRNAs deregulated in the same hippocampal samples. Surprisingly, 80% of DE mRNA in the centenarian vs. old comparison are regulated by hsa-miR-192-5p and hsa-miR-3135b. Additionally, validated hsa-miR-6826-5p, hsa-let-7b-3p, hsa-miR-7846, and hsa-miR-451a emerged as promising miRNAs that are deregulated with aging and should be further investigated.

Differential analysis of microRNAs in plasma exosomes in patients with cerebral ischemic stroke.

The high incidence, disability, mortality, and recurrence rates of cerebral infarction impose a heavy burden on both the Chinese and global populations. It is essential for the early diagnosis, prevention, and protection against brain cell injury. To identify differentially expressed microRNAs (miRNAs) in plasma exosomes of patients with cerebral ischemic stroke, determine relevant biomarkers, and explore their potential signaling pathways. High-throughput sequencing was used to detect the expression of plasma exosomal miRNAs in patients with cerebral ischemic stroke and in a control group. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes enrichment, and target gene network analyses were performed to investigate the target genes and signaling pathways of the differentially expressed miRNAs. The sequencing results identified 95 differentially expressed miRNAs, with 40 upregulated and 55 downregulated miRNAs. Among these, hsa-miR-1303, hsa-miR-125b-1-3p, and hsa-miR-548ab were significantly upregulated in the stroke group and downregulated in the normal control group, whereas hsa-miR-1289 was downregulated in the stroke group and upregulated in the normal group. Gene Ontology, Kyoto Encyclopedia of Genes, and genomes enrichment analyses indicated that the differentially expressed miRNAs and their target genes were mainly concentrated in the PI3K-AKt, mitogen-activated protein kinase, calcium, Ras, Rap1, and cAMP signaling pathways. The expression of plasma exosomal hsa-miR-1303, hsa-miR-125b-1-3p, and hsa-miR-1289 was significantly different in stroke patients than in the control group. These miRNAs may be involved in various signaling pathways related to cerebral infarction, providing a reference for further experimental research.

Deciphering the Interlinked CXCR4-Mediated Feedback Loop Among Signaling Pathways in Diabetic Wound Healing

Abstract: Diabetic chronic wounds and amputations are very serious complications of diabetes mellitus (DM) that result from an integration factor, including oxygen deprivation, elevated reactive oxygen species (ROS), reduced angiogenesis, and microbial invasion. These causative factors lead to tenacious wounds in an inflammatory state, which eventually results in tissue aging and necrosis. Wound healing in DM potentially targets C-X-C chemokine receptor type 4 (CXCR4) regulates several signalling pathways. The CXCR4 signalling pathway integrated with phospholipase C (PLC)/protein kinase-C (PKC) Ca2+ pathways, stromal cell-derived factor-1 (SDF-1), and mitogen- activated protein kinases (MAPKs) pathway for enhancing cell chemotaxis, proliferation, and survival. The dysregulated CXCR4 pathway is connected with poor wound healing in DM patients. Therapeutic strategies targeting CXCR4-based molecules such as UCUF-728, UCUF-965, and AMD3100 have been shown to enhance diabetic wound healing by altering miRNA expression, promoting angiogenesis, and accelerating wound closure. This study indicates that CXCR4 participation in various signalling pathways makes it essential for Understanding the healing of diabetic wounds. Using specific compounds to target CXCR4 offers a potentially effective treatment strategy to improve wound healing in diabetes. Our understanding of CXCR4 signalling and its regulation processes will enable us to develop more potent wound care solutions for diabetic chronic wounds. This report concludes that CXCR4's potential therapeutic targeting shows improvements in diabetic wound repair. This review will demonstrate that CXCR4 plays a major role in wound healing through its various signalling pathways. Targeting CXCR4 with certain agonist molecules shows a therapeutic approach to potentially increasing wound healing in diabetes. By enhancing our understanding of the CXCR4 signalling mechanism in future studies, we can develop more potential treatments for chronic diabetic wounds.

Blood-based microRNAs as the potential biomarkers for Alzheimer's disease: evidence from a systematic review.

Alzheimer's disease (AD) is a neurodegenerative disorder that progresses over time and is identified by the development of neurofibrillary tangles and amyloid deposits in the brain. Mounting evidence has revealed that microRNAs (miRNAs) are significantly involved in AD progression, and may be used as promising biomarkers for diagnosis and prognosis. Nevertheless, the existing body of data regarding dysregulated circulating miRNAs in AD and their therapeutic applications are characterized by a lack of consistency. A comprehensive search was performed across various databases (PubMed, EMBASE, Web of Science, Scopus, Google Scholar, Cochrane, and ProQuest), starting from its inception and ending in January 2023. The criteria for inclusion consisted of original research studies written in English, which utilized Real-Time PCR to analyze miRNA expression in the blood, serum, or plasma of AD patients and healthy controls. The extracted data included the miRNA(s) investigated, dysregulation status, study type, human sample(s), and major findings. The search produced 608 records, which after careful examination, resulted in 48 suitable articles for data extraction. The research revealed a wide range of sample types used, with whole blood (39.59%) and serum (27.09%, including serum-exosome at 4.17%) emerging as the most prominent. The compiled dataset featured 4001 AD patients and 3886 healthy controls, revealing intricate regulatory patterns among 83 up-regulated (35.78%), 66 down-regulated (28.44%), and 83 not significantly altered (35.78%) miRNAs. Our results demonstrated that specific circulating miRNAs are consistently dysregulated in AD and could serve as non-intrusive biomarkers for the identification, prognosis, and prediction of cognitive decline. Further large-scale prospective studies are required to validate their clinical applications.

CLHGNNMDA: Hypergraph Neural Network Model Enhanced by Contrastive Learning for miRNA-Disease Association Prediction.

Numerous biological experiments have demonstrated that microRNA (miRNA) is involved in gene regulation within cells, and mutations and abnormal expression of miRNA can cause a myriad of intricate diseases. Forecasting the association between miRNA and diseases can enhance disease prevention and treatment and accelerate drug research, which holds considerable importance for the development of clinical medicine and drug research. This investigation introduces a contrastive learning-augmented hypergraph neural network model, termed CLHGNNMDA, aimed at predicting associations between miRNAs and diseases. Initially, CLHGNNMDA constructs multiple hypergraphs by leveraging diverse similarity metrics related to miRNAs and diseases. Subsequently, hypergraph convolution is applied to each hypergraph to extract feature representations for nodes and hyperedges. Following this, autoencoders are employed to reconstruct information regarding the feature representations of nodes and hyperedges and to integrate various features of miRNAs and diseases extracted from each hypergraph. Finally, a joint contrastive loss function is utilized to refine the model and optimize its parameters. The CLHGNNMDA framework employs multi-hypergraph contrastive learning for the construction of a contrastive loss function. This approach takes into account inter-view interactions and upholds the principle of consistency, thereby augmenting the model's representational efficacy. The results obtained from fivefold cross-validation substantiate that the CLHGNNMDA algorithm achieves a mean area under the receiver operating characteristic curve of 0.9635 and a mean area under the precision-recall curve of 0.9656. These metrics are notably superior to those attained by contemporary state-of-the-art methodologies.

The Role of microRNA Expression and DNA Methylation in HPV-Related Cervical Cancer: A Systematic Review

Human papillomavirus (HPV) infection is a major etiologic factor in cervical cancer, a major cause of cancer-related morbidity and mortality among women worldwide. The role of microRNA (miRNA) dysregulation in cervical carcinogenesis is still largely unknown, but epigenetic changes, including DNA methylation and miRNA regulation, are crucial factors. The integration of HPV DNA into the host genome can lead to alterations in DNA methylation patterns and miRNA expression, contributing to the progression from normal epithelium to cervical intraepithelial neoplasia and, ultimately, to cervical cancer. This review aimed to examine the relationship between epigenetic changes in the development and progression of HPV associated with cervical cancer. A systematic literature search was conducted in major databases using predefined inclusion and exclusion criteria. Studies that investigated the expression, function, and clinical significance of miRNAs, DNA methylation, and the expression of oncoproteins in HPV-related cervical cancer were included. Data extraction, quality assessment, and synthesis were performed to provide a comprehensive overview of the current state of knowledge. We provide an overview of the studies investigating miRNA expression in relation to cervical cancer progression, highlighting their common outcomes and their weaknesses/strengths. To achieve this, we systematically searched the Pubmed database for all articles published between January 2018 and December 2023. Our systematic review revealed a substantial body of evidence supporting the pivotal role of miRNA dysregulation in the pathogenesis of HPV-related cervical cancer and related oncoproteins. From the 28 studies retrieved, miR-124, FAM194/miR-124-2, and DNA methylation are the most frequently down- or up-regulated in CC progression. Notably, FAM194/miR-124-2 and DNA methylation emerged as a promising molecular marker for distinguishing between cases requiring immediate surgical intervention and those amenable to a more conservative wait-and-see approach. This systematic review underscores the critical involvement of microRNA in the context of HPV-related cervical cancer and sheds light on the potential clinical utility of FAM194/miR-124-2 and DNA methylation as a discriminatory tool for guiding treatment decisions. The identification of patients who may benefit from early surgical intervention versus those suitable for observation has important implications for personalized and targeted management strategies in the era of precision medicine.

A Network Analysis Approach to Detect and Differentiate Usher Syndrome Types Using miRNA Expression Profiles: A Pilot Study

Background: Usher syndrome (USH) is a rare genetic disorder that affects both hearing and vision. It presents in three clinical types—USH1, USH2, and USH3—with varying onset, severity, and disease progression. Existing diagnostics primarily rely on genetic profiling to identify variants in USH genes; however, accurate detection before symptom onset remains a challenge. MicroRNAs (miRNAs), which regulate gene expression, have been identified as potential biomarkers for disease. The aim of this study is to develop a data-driven system for the identification of USH using miRNA expression profiles. Methods: We collected microarray miRNA-expression data from 17 samples, representing four patient-derived USH cell lines and a non-USH control. Supervised feature selection was utilized to identify key miRNAs that differentiate USH cell lines from the non-USH control. Subsequently, a network model was constructed by measuring pairwise correlations based on these identified features. Results: The proposed system effectively distinguished between control and USH samples, demonstrating high accuracy. Additionally, the model could differentiate between the three USH types, reflecting its potential and sensitivity beyond the primary identification of affected subjects. Conclusions: This approach can be used to detect USH and differentiate between USH subtypes, suggesting its potential as a future base model for the identification of Usher syndrome.

Interleukin-33 mediated regulation of microRNAs in human cord blood-derived mast cells: Implications for infection, immunity, and inflammation.

Mast cell (MCs) activation is the driving force of immune responses in several inflammatory diseases, including asthma and allergies. MCs are immune cells found throughout the body and are equipped with numerous surface receptors that allow them to respond to external signals from parasites and bacteria as well as to intrinsic signals such as cytokines. Upon activation, MCs release various mediators and proteases that contribute to inflammation. This study aimed to identify microRNAs (miRNAs) that regulate MC response to interleukin-33 and their target genes using a model of human cord blood-derived mast cells (hCBMCs). hCBMCs were induced with 10 and 20 ng of recombinant human interleukin-33 (rhIL-33) for 6 and 24 h, respectively. Total RNA was extracted from these cells and miRNA profiling was performed using high-throughput microarrays. Differential expression of miRNAs and target analysis were performed using Transcriptome Analysis Console and Ingenuity Pathway Analysis. The most significant miRNAs in each condition were miR-6836-5p (fold change = 1.76, p = 3E-03), miR-6883-5p (fold change = -2.13, p = 7E-05), miR-1229-5p (fold change = 2.46, p = 8E-04), and miR-3613-5p (fold change = 66.7, p = 1E-06). Target analysis revealed that these miRNAs regulate mast cell responsiveness and degranulation by modulating the expression of surface receptors, adaptors, and signaling molecules in response to rhIL-33 stimulation. This study is the first miRNA profiling and target analysis of hCBMCs that will further enhance our understanding of the role of miRNAs in the immune response in a timely manner and their relevance for the development of a new therapeutic target for inflammatory disorders.

The dual actions of miRNA16a in restricting Bovine Coronavirus replication through downregulation of Furin and enhancing the host immune response.

The roles of host cell miRNAs have not been well studied in the context of BCoV replication and immune regulation. This study aimed to identify miRNA candidates that regulate essential host genes involved in BCoV replication, tissue tropism, and immune regulation. To achieve these goals, we used two isolates of BCoV (enteric and respiratory) to infect bovine endothelial cells (BECs) and Madine Darby Bovine Kidney (MDBK) cells. We determined the miRNA expression profiles of these cells after BCoV infection. The expression of miRNA16a is differentially altered during BCoV infection. Our data show that miRNA16a is a significantly downregulated miRNA in both in vitro and ex vivo models. We confirmed the miRNA16aexpression profile by qRT-PCR. Overexpression of pre-miRNA16ain the BEC and the MDBK cell lines markedly inhibited BCoV infection, as determined by the viral genome copy numbers measured by qRT‒PCR, viral protein expression (S and N) measured by Western blot, and virus infectivity using a plaque assay. Our bioinformatic prediction showed that Furin is a potential target of miRNA16a. We compared the Furin protein expression level in pre-miRNA16a-transfected/BCoV-infected cells to that in pre-miRNA-scrambled-transfected cells. Our qRT-PCR and Western blot data revealed marked inhibition of Furin expression at the mRNA and protein levels, respectively. BCoV-S protein expression was markedly inhibited at both the mRNA and protein levels. To further confirm the impact of the downregulation of the Furin enzyme on the replication of BCoV, we transfected cells with specific Furin-siRNAs parallel to the scrambled siRNA. Marked inhibition of BCoV replication was observed in the Furin-siRNA-treated group. To further validate Furin as a novel target for miRNA16a, we cloned the 3'UTR of bovine Furin carrying the seed region of miRNA16a in the dual luciferase vector. Our data showed that luciferase activity in pre-miRNA16a-transfected cells decreased by more than 50% compared to cells transfected with the construct carrying the mutated Furin seed region. Our data confirmed that miRNA16ainhibits BCoV replication by targeting the host cell line Furin and the BCoV-S glycoprotein. It also enhances the host immune response, which contributes to the inhibition of viral replication. This is the first study to confirm that Furin is a valid target of miRNA16a. Our findings highlight the clinical applications of host miRNA16a as a potential miRNA-based vaccine/antiviral therapy.

Small Extracellular Vesicle-Associated MiRNAs in Polarized Retinal Pigmented Epithelium.

Oxidative stress in the retinal pigmented epithelium (RPE) has been implicated in age-related macular degeneration by impacting endocytic trafficking, including the formation, content, and secretion of extracellular vesicles (EVs). Using our model of polarized primary porcine RPE (pRPE) cells under chronic subtoxic oxidative stress, we tested the hypothesis that RPE miRNAs packaged into EVs are secreted in a polarized manner and contribute to maintaining RPE homeostasis. Small EVs (sEVs) enriched for exosomes were isolated from apical and basal conditioned media from pRPE cells grown for up to four weeks with or without low concentrations of hydrogen peroxide using two sEV isolation methods, leading to eight experimental groups. The sEV miRNA expression was profiled using miRNA-Seq with Illumina MiSeq, followed by quality control and bioinformatics analysis for differential expression using the R computing environment. Expression of selected miRNAs were validated using qRT-PCR. We identified miRNA content differences carried by sEVs isolated using two ultracentrifugation-based methods. Regardless of the sEV isolation method, miR-182 and miR-183 were enriched in the cargo of apically secreted sEVs, and miR-122 in the cargo of basally secreted sEVs from RPE cells during normal homeostatic conditions. After oxidative stress, miR-183 levels were significantly decreased in the cargo of apically released sEVs from stressed RPE cells. We curated RPE sEV miRNA datasets based on cell polarity and oxidative stress. Unbiased miRNA analysis identified differences based on polarity, stress, and sEV isolation methods. These findings suggest that miRNAs in sEVs may contribute to RPE homeostasis and function in a polarized manner.

Pralatrexate represses the resistance of HCC cells to molecular targeted agents via the miRNA-34a/Notch pathway

Metabolism-related pathways are important targets for intervention in the treatment of hepatocellular carcinoma (HCC), but few studies have reported on the combination of inhibitors of folate metabolism-related enzymes and molecularly targeted drugs for HCC. The results of the present work are the first to reveal the effects of an inhibitor of dihydrofolate reductase (DHFR), pralatrexate, on the sensitivity of HCC cells to molecularly targeted agents examined using multiple assays. In HCC cells, knockdown of DHFR or treatment with pralatrexate enhanced the sensitivity of HCC cells to molecularly targeted agents, such as sorafenib, regorafenib, lenvatinib, cabozantinib, or anlotinib. Mechanically, pralatrexate decreased the methylation rates of miRNA-34a’s promoter region to enhance the expression of miRNA-34a. Treatment with pralatrexate inhibited the expression of Notch and its downstream factors by enhancing the expression of miRNA-34a in HCC cells. In clinical specimens, the expression of miRNA-34a was negatively correlated with DHFR expression, while DHFR expression was positively correlated with the Notch intracellular domain (NICD) and downstream factors of the Notch pathway. The expression of miRNA-34a was negatively correlated with DHFR expression, while the methylation rates of miRNA-34a’s promoter were positively related to DHFR. The effect of pralatrexate on the metabolic profile of HCC cells is very different from that of small molecule inhibitors related to glycolipid metabolism. Therefore, pralatrexate upregulates the sensitivity of HCC cells to molecularly targeted drugs. These results expand our understanding of folate metabolism and HCC and can help provide more options for HCC treatment.