MicroRNAs: genomics, biogenesis, mechanism, and function

Extracellular Vesicle-Derived miRNAs in Ischemic Stroke: Roles in Neuroprotection, Tissue Regeneration, and Biomarker Potential

Ischemic stroke (IS) is one of the most common causes of death and disability worldwide. Despite its prevalence, knowledge about pathophysiology and diagnostic methods remains limited. Extracellular vesicles (EVs) that are released from cellular membranes constitutively, as well as after activation or damage, may contain various intracellular particles, including microRNAs (miRNAs/miR). miRNAs acting as mRNA transcription regulators are secreted in EVs and may be internalized by other cells. This cellular cross-talk is important for the regeneration of the nervous tissue after ischemic injury. Moreover, miRNAs related to stroke pathophysiology were shown to be differentially expressed after an IS episode. miRNAs associated with various types of stem cell-derived EVs were shown to be involved in post-ischemic neuroprotection and tissue regeneration and may be potential therapeutic agents. Therefore, considering their stability in plasma, they are worth investigating also as potential diagnostic/prognostic biomarkers. The present review summarizes the current knowledge about EV-derived miRNAs in the neuronal injury mechanism and their potential in neuroprotection in IS, and discusses the possibilities of further investigation of their use in preclinical research.

Integrated Analysis of mRNA and miRNA Associated with Reproduction in Female and Male Gonads in Abalone (Haliotis discus hannai)

Reproduction and breeding are crucial to maintaining abalone aquaculture. Understanding the molecular underpinnings of sexual maturation is essential for advancing knowledge in reproductive biology. However, the molecular mechanisms of gonadal development in abalones remain poorly understood, particularly in microRNA (miRNA)-mediated regulation. Thus, this study conducted a comprehensive transcriptomic analysis of abalone Haliotis discus hannai (H. discus hannai) to identify genes and miRNAs associated with ovarian and testicular discovery. This study identified 685 differentially expressed (DE) genes between the H. discus hannai ovary (DD_ovary) and testis (DD_testis) groups, comprising 479 upregulated and 206 downregulated genes in the DD_ovary. Moreover, 137 miRNAs, including 83 novel and 54 known miRNAs, were detected, with 30 upregulated and 27 downregulated in the DD_ovary compared to the DD_testis. Bioinformatics analysis revealed that these miRNAs regulate key processes such as carbohydrate metabolic processes, kinase and hydrolase activity, and starch and sucrose metabolism, all potentially associated with reproductive traits. Further, key mRNA candidates, including Vitelline envelope sperm lysin receptor (Verl) and Testis-specific serine/threonine-protein kinase (Tssk) 1, and miRNAs such as novel_90 and novel_120, were identified as components of a functional miRNA-mRNA network associated with sexual maturity and sex determination. These key genes were verified using qRT-PCR and fluorescence in situ hybridization (FISH). These transcriptomic and miRNA datasets provide valuable resources for understanding abalone reproductive biology and may support molecular breeding strategies.

Circulating MicroRNAs: functional biomarkers for melanoma prognosis and treatment

MicroRNAs (miRNAs) hold significant promise as circulating cancer biomarkers and unlike many other molecular markers, they can provide valuable insights that extend beyond tumour biology. The expression of circulating miRNAs may parallel the cellular composition and dynamic activity within the tumour microenvironment and reveal systemic immune responses. The functional complexity of miRNAs-where a single miRNA can regulate multiple messenger RNAs (mRNAs) to fine tune fundamental processes, and a single mRNA can be targeted by multiple miRNAs-underscores their broad significance and impact. However, this complexity poses significant challenges for translating miRNA research into clinical practice. In melanoma, specific miRNA signatures have shown notable diagnostic, prognostic and predictive value, with lineage-specific and immune-related miRNAs frequently identified as valuable markers. In this review, we explore the role of circulating miRNAs as potential biomarkers in melanoma, and highlight the current status and advances required to translate miRNA research into therapeutic opportunities.

Urinary and Plasma miRNAs in the Early Detection of Acute Kidney Injury and Their Possible Role as Therapeutic Targets

Acute Kidney Injury (AKI) is a severe clinical condition featured by a rapid decrease in kidney function in a short period of time. AKI, which is often secondary to sepsis, ischemia-reperfusion and drug toxicity, is associated to high morbidity and mortality. Moreover, it contributes to the development of chronic kidney disease (CKD), due to maladaptive or incomplete repair mechanisms, resulting in renal fibrosis. Small non-coding RNA has recently emerged as a novel biomarker for the early detection and treatment of AKI. In particular, microRNAs (miRNAs) are non-coding RNA molecules of 21-25 nucleotides regulating the expression of protein-coding genes through sequence-specific recognition. Due to their high stability in biological fluids, such as urine and plasma, they can be reliably analyzed and quantified, and for this reason they can be considered potential diagnostic and therapeutic biomarkers. Specifically, miRNAs have been demonstrated to predict AKI before the increase in creatinine levels, thus improving the management of this syndrome. In this review, we provide a comprehensive overview of the role of urinary and plasma miRNAs in the early detection and treatment of AKI.

MiR-21-5p and miR-223-3p as Treatment Response Biomarkers in Pediatric Eosinophilic Esophagitis

The diagnosis and monitoring of eosinophilic esophagitis (EoE), a common pediatric pathology, typically involves invasive procedures such as an upper endoscopy with biopsies, imposing a significant burden on patients and healthcare systems. We aimed to assess miR-21-5p and miR-223-3p levels in pediatric EoE patients and evaluate their as potential non-invasive biomarkers of disease activity and response to treatments. We enrolled 13 children with EoE and 8 controls. Plasma and esophageal mucosa samples from patients were collected at diagnosis and after 8-10 weeks of therapy and compared with control samples. After microRNA(miRNA) extraction, the levels of miR-21-5p and miR-223-3p and their relevant target genes were analyzed. Bioinformatic analysis was used to identify the predicted target genes and pathways that are potentially relevant for disease pathophysiology. Plasma levels of miR-21-5p and miR-223-3p were significantly higher in EoE patients than in the controls, reflecting their levels in esophageal mucosa. The target genes of these miRNAs are involved in key signaling pathways (MAPK, Ras, and FoxO), relevant for EoE pathophysiology. Among these, STAT3 (Signal Transducer and Activator of Transcription 3) and PTEN (Phosphatase and Tensin Homolog), which are significantly downregulated in patient esophageal mucosa, are implicated in eosinophilic gastroenteropathies and autoimmune diseases. Following therapy (proton pump inhibitors and/or fluticasone propionate), plasma and tissue expression of both miRNAs significantly decreased and were no longer different from the controls. These microRNAs may serve as complementary non-invasive EoE markers and reduce the need for endoscopy/biopsies.

miRNA-based regulation in growth plate cartilage: mechanisms, targets, and therapeutic potential

MicroRNAs (miRNAs) are critical regulators of the skeleton. In the growth plate, these small non-coding RNAs modulate gene networks that drive key stages of chondrogenesis, including proliferation, differentiation, extracellular matrix synthesis and hypertrophy. These processes are orchestrated through the interaction of pivotal pathways including parathyroid hormone-related protein (PTHrP), Indian hedgehog (IHH), and bone morphogenetic protein (BMP) signaling. This review highlights the miRNA-mRNA target networks essential for chondrocyte differentiation. Many miRNAs are differentially expressed in resting, proliferating and hypertrophic cartilage zones. Moreover, differential enrichment of specific miRNAs in matrix vesicles is also observed, providing means for chondrocytes to influence the function and differentiation of their neighbors by via matrix vesicle protein and RNA cargo. Notably, miR-1 and miR-140 emerge as critical modulators of chondrocyte proliferation and hypertrophy by regulating multiple signaling pathways, many of them downstream from their mutual target Hdac4. Demonstration that a human gain-of-function mutation in miR-140 causes skeletal dysplasia underscores the clinical relevance of understanding miRNA-mediated regulation. Further, miRNAs such as miR-26b have emerged as markers for skeletal disorders such as idiopathic short stature, showcasing the translational relevance of miRNAs in skeletal health. This review also highlights some miRNA-based therapeutic strategies, including innovative delivery systems that could target chondrocytes via cartilage affinity peptides, and potential applications related to treatment of physeal bony bridge formation in growing children. By synthesizing current research, this review offers a nuanced understanding of miRNA functions in growth plate biology and their broader implications for skeletal health. It underscores the translational potential of miRNA-based therapies in addressing skeletal disorders and aims to inspire further investigations in this rapidly evolving field.

Circulating miR-20a-5p as a biomarker associated with cabergoline responsiveness in patients with hyperprolactinemia and pituitary adenomas

OBJECTIVE

Dopamine agonist (DA) treatment is effective for hyperprolactinemia and reduces tumor size in patients with prolactinoma; however, prolonged DA administration without prolactinoma causes fibrosis around tumor tissues. Therefore, we aimed to identify circulating microRNAs (miRNAs) as potential biomarkers to predict prolactinoma in patients with hyperprolactinemia and pituitary tumors.

DESIGN

Plasma samples were collected from 3 comparison groups: (1) patients clinically diagnosed with prolactinoma vs nonfunctioning pituitary adenoma (NFPA) based on response to cabergoline treatment, (2) patients with surgically confirmed prolactinoma vs NFPA, and (3) patients before and after cabergoline treatment. Candidate miRNAs from the initial nCounter assay were validated using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) in a larger cohort of 247 patients with hyperprolactinemia and 37 controls.

METHODS

The nCounter assay was used for miRNA expression profiling, and the qRT-PCR validated the candidate miRNAs in the plasma and tumor tissue samples. Total RNA sequencing was conducted on pituitary tumor tissues to identify transcriptomic alterations. Furthermore, candidate miRNA target genes and their biological roles were analyzed using prolactinoma cell lines.

RESULTS

Three miRNA candidates (miR-20a-5p, miR-424-5p, and miR-514a-5p) were selected by analyzing 3 sets of expression comparisons between the 2 groups. Furthermore, the relative miR-20a-5p expression significantly increased in prolactinoma compared with that in normal pituitary glands, NFPA, growth hormone-secreting pituitary adenoma, and adrenocorticotropic hormone-secreting pituitary adenoma. In MMQ and GH4 cells, miR-20a-5p inhibition decreased prolactinoma cell proliferation and prolactin secretion.

CONCLUSIONS

Circulating miR-20a-5p is a potential biomarker for prolactinoma, which could be associated with responsiveness to DAs.

Harnessing the Role of ESR1 in Breast Cancer: Correlation with microRNA, lncRNA, and Methylation

Breast cancer (BC) is a multifactorial condition and it primarily expresses the estrogen receptor α (ERα) that is encoded by the gene estrogen receptor 1 (ESR1), which modulates estrogen signaling. ESR1, by facilitating estrogen overproduction, plays an indispensable role in the progression and survival of the majority of BCs. To obtain molecular insights into these phenomena, we analyzed The Cancer Genome Atlas (TCGA) breast invasive carcinoma (BRCA) RNA-Seq datasets for the expression of ESR1 and its correlation to microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), along with its methylation patterns. Regulation of ESR1 was also assessed with a total of 43 cancerous and non-cancerous breast cell lines. Analyses of both TCGA BRCA and breast cell line RNA-Seq data revealed that specific lncRNAs, i.e., MEG3, BIK, MLL, and FAS are negatively correlated with the ESR1, in which PARP1 demonstrates a positive association. Additionally, both miR-30a and miR-145 showed negative correlations with the ESR1 expression. Of the 54 ESR1 methylation loci analyzed, the majority of them exhibited a negative correlation with the ESR1 expression, highlighting a potentially modifiable regulatory mechanism. These findings underscore the complex regulatory events influencing ESR1 expression and its interaction with diverse signaling pathways, demonstrating novel insights into breast pathogenesis and its potential therapeutics.

Up-regulated microRNAs in blastocoel fluid of human implanted embryos could control circuits of pluripotency and be related to embryo competence

PURPOSE

The paper aims to investigate the biological role of microRNAs secreted by preimplantation embryo into the blastocoel fluid and to detect a distinctive molecular signature for identifying embryos with the highest implantation potential.

METHODS

We carried on a multicenter retrospective study involving five European IVF centers. We collected 112 blastocoel fluid samples from embryos on day 5 post-fertilization, cultured individually, along with data on blastocyst grade and embryo transfer outcomes. Using a custom TLDA Array, we compared the expression levels of 89 miRNAs between 33 fluids from high-quality implanted embryos and 30 fluids from high-quality not-implanted embryos. Expression differences were assessed using SAM and t-test. Additionally, correlation and function enrichment analysis and network construction were conducted to identify the biological roles of deregulated microRNAs.

RESULTS

We identified six up-regulated microRNAs in the blastocoel fluid from implanted embryos, significantly and positively correlated across all samples (r ≥ 0.7; P ≤ 0.05). They could take part in pluripotency circuits, regulating and being regulated by transcription factors associated with stemness, cell growth, and embryo development. The ROC curve analysis confirmed the potential of these miRNAs as implantation classifiers.

CONCLUSION

The six miRNAs up-regulated in blastocoel fluid from implanted embryos may represent a functional molecular signature for evaluating blastocyst quality and identifying the most competent embryos. Their evaluation associated with non-invasive preimplantation genetic testing, integrating epigenetic and genomic analyses, could enhance implantation grade and allow for identification of the euploid embryo not able to implant.

UCL23 hierarchically regulated by WRKY51-miR528 mediates cadmium uptake, tolerance, and accumulation in rice

In humans, cadmium (Cd) toxicity caused by contaminated environments is associated with numerous chronic diseases. Breeding rice with low Cd accumulation is now deemed critical for sustainable agriculture development. Here, we elucidate the crucial functions of UCLACYANIN 23 (UCL23), a small copper protein, in Cd absorption, tolerance, and accumulation through modulation of reactive oxygen signals in rice. Additionally, we demonstrate that WRKY51 binds to promoters of UCL23 and miR528, a post-transcriptional regulator of UCL23, thereby contributing to Cd regulation in a dual-modulatory manner. Furthermore, we show that the natural variation of UCL23 is important for the differential accumulation of Cd in rice grains. Finally, we reveal that Indica rice harboring the major Japonica haplotype of UCL23 significantly reduces Cd uptake in roots and Cd accumulation in grains. Together, our study not only reveals a regulatory cascade in Cd regulation but also provides valuable resources for breeding low-Cd rice cultivars.

Involvement of microRNAs-449/FASN axis in response to trastuzumab therapy in HER2-positive breast cancer

The anti-HER2 monoclonal antibody trastuzumab and new derivative formulations are the standard treatment for HER2-positive breast cancer. However, after 1 to 5 years of treatment, some patients acquire resistance to therapy, leading to relapse. The microRNA-449 family members were downregulated in HER2-positive breast cancer cell lines and low levels were associated with patients' worse prognosis. Moreover, trastuzumab-resistant HER2-positive breast cancer cell lines showed lower microRNAs-449 and higher Fatty Acid Synthase (FASN) expression, compared to sensitive cell lines. The direct regulation of FASN by microRNA-449a and microRNA-449b-5p was demonstrated. Moreover, microRNAs-449 overexpression and FASN inhibition decreased cell proliferation and sensitized cells to trastuzumab treatment by inhibiting the PI3K/AKT signaling pathway. Together, these results suggest the microRNAs-449/FASN axis as a potential therapeutic target in combination with anti-HER2 agents to overcome trastuzumab resistance and to improve treatment response in HER2-positive breast cancer patients.

Comprehensive study of tRNA-derived fragments in plants for biotic stress responses

Plant growth and development are often disrupted by biological stressors as they interfere with the regulatory pathways. Among the key regulators, transfer-RNA-derived fragments (tRFs) have emerged as key players in plant defense mechanisms. While tRF-mediated responses to abiotic stress have been well studied, their role in biotic stress remains less understood, as various stressors may elicit different regulatory systems. In this study, tRF-mediated biotic responses in three species, viz. Arabidopsis thaliana, Oryza sativa, and Solanum lycopersicum are investigated using in-silico approaches. Analysis of predicted tRFs across various biotic stress conditions reveals specific interactions with mRNA targets, microRNAs (miRNAs), and transposable elements (TEs), highlighting their regulatory significance in plant adaptation mechanisms. These findings provide new insights into tRF-mediated stress responses and establish a computational framework for further functional studies. The study's database is publicly available at http://www.nipgr.ac.in/PbtRFdb .

MiR-7a-Klf4 axis as a regulator and therapeutic target of neuroinflammation and ferroptosis in Alzheimer's disease

Neuroinflammation and ferroptosis significantly contribute to neuronal death in Alzheimer's disease (AD) and other neurodegenerative disorders. MicroRNAs (miRNAs) are crucial regulators of these pathological processes. We employed transcriptomic analysis in an APP/PSEN1 Tg AD mouse model to identify dysregulated miRNAs and construct a miRNA-mRNA-pathway network. We discovered increased miR7a expression in the AD brain, targeting Krüppel-like factor 4 (Klf4), a transcriptional factor implicated in Aβ oligomer-induced neuroinflammation and RSL3-induced neuronal ferroptosis. Elevated Klf4 levels in AD mice brains suggest its involvement in AD pathology. The miR-7a mediated silencing of Klf4 alleviates neuroinflammation by modulating NF-κB, iNOS, and NLRP3 pathways, and inhibition of ferroptosis by targeting labile iron levels, GPX4, Nrf2 pathway, and mitochondrial damage. These findings highlight the neuroprotective role of miR-7a and its potential as RNA therapeutic. Pharmacological targeting of the miR-7a-Klf4 axis with blood-brain-barrier (BBB)-permeable compound effectively mitigates neuroinflammation and ferroptosis, suggesting the miR-7a-Klf4 axis as a novel therapeutic target for AD.

GRAPHICAL ABSTRACT

The Role of Exosomal miRNAs in Female Infertility: Therapeutic Potential and Mechanisms of Action

Reproductive disorders, including preeclampsia (PE), endometriosis, premature ovarian failure (POF), and polycystic ovary syndrome (PCOS), present substantial challenges to women's reproductive health. Exosomes (EXOs) are cell-derived vesicles containing molecules that influence target cells' gene expression and cellular behavior. Among their cargo, microRNAs (miRNAs)-short, non-coding RNAs typically 19-25 nucleotides in length-play a crucial role in post-transcriptional gene regulation and have been extensively studied for their therapeutic potential. miRNAs are considered therapeutic targets because they regulate key cellular pathways such as proliferation, apoptosis, angiogenesis, and tissue repair. This review examines the role of exosomal miRNAs from sources such as mesenchymal stem cells (MSCs), plasma, and amniotic fluid in female reproductive disorders, including PE, POF, PCOS, and endometriosis. We discuss their biological origins, mechanisms of miRNA sorting and packaging, and their therapeutic applications in modulating disease progression. By categorizing miRNAs according to their beneficial or detrimental effects in specific conditions, we aim to simplify the understanding of their roles in female infertility.

Functional Characterization of miR-216a-5p and miR-125a-5p on Pancreatic Cancer Stem Cells

Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer-related death. Its poor prognosis is closely related to late-stage diagnosis, which results from both nonspecific symptoms and the absence of biomarkers for early diagnosis. MicroRNAs (miRNAs) exert a regulatory role in numerous biological processes and their aberrant expression has been found in a broad spectrum of diseases, including cancer. Cancer stem cells (CSCs) represent a driving force for PDAC initiation, progression, and metastatic spread. Our previous research highlighted the interesting behavior of miR-216a-5p and miR-125a-5p related to PDAC progression and the CSC phenotype. The present study aimed to evaluate the effect of miR-216a-5p and miR-125a-5p on the acquisition or suppression of pancreatic CSC traits. BxPC-3, AsPC-1 cell lines, and their CSC-like models were transfected with miR-216a-5p and miR-125a-5p mimics and inhibitors. Following transfection, we evaluated their impact on the expression of CSC surface markers (CD44/CD24/CxCR4), ALDH1 activity, pluripotency- and EMT-related gene expression, and clonogenic potential. Our results show that miR-216a-5p enhances the expression of CD44/CD24/CxCR4 while negatively affecting the activity of ALDH1 and the expression of EMT genes. MiR-216a-5p positively influenced the clonogenic property. MiR-125a-5p promoted the expression of CD44/CD24/CxCR4 while inhibiting ALDH1 activity. It enhanced the expression of Snail, Oct-4, and Sox-2, while the clonogenic potential appeared to be affected. Comprehensively, our results provide further knowledge on the role of miRNAs in pancreatic CSCs. Moreover, they corroborate our previous findings about miR-216a-5p's potential dual role and miR-125a-5p's promotive function in PDAC.

Role of miRNAs in Bovine Oocyte Maturation and Reproductive Regulation

MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that regulate target gene expression in many eukaryotes. MiRNAs are essential for post-transcriptional regulation, influencing various biological functions, including oocyte growth and maturation, fertilization, early embryo development, and implantation. In recent decades, numerous studies have identified a substantial number of miRNAs associated with mammalian oocyte maturation and early embryo development, utilizing methods such as small RNA sequencing and modulating miRNA expression through overexpression or inhibition. In this review, we introduce the biosynthesis of miRNAs and their regulatory roles in germ cells, summarizing the expression patterns and post-transcriptional regulation of miRNAs during bovine oocyte maturation and early embryo development, as well as their potential application in bovine assisted reproductive technology (ART).

Dipeptidyl peptidase DPF-3 is a gatekeeper of microRNA Argonaute compensation in animals

MicroRNAs (miRNAs) are essential regulators involved in multiple biological processes. To achieve their gene repression function, they are loaded in miRNA-specific Argonautes to form the miRNA-induced silencing complex (miRISC). Mammals and C. elegans possess more than one paralog of miRNA-specific Argonautes, but the dynamic between them remains unclear. Here, we report the conserved dipeptidyl peptidase DPF-3 as an interactor of the miRNA-specific Argonaute ALG-1 in C. elegans. Knockout of dpf-3 increases ALG-2 levels and miRISC formation in alg-1 loss-of-function animals, thereby compensating for ALG-1 loss and rescuing miRNA-related defects observed. DPF-3 can cleave an ALG-2 N-terminal peptide in vitro but does not appear to rely on this catalytic activity to regulate ALG-2 in vivo. This study uncovers the importance of DPF-3 in the miRNA pathway and provides insights into how multiple miRNA Argonautes contribute to achieving proper miRNA-mediated gene regulation in animals.

Spatiotemporal single-cell architecture of gene expression in the Caenorhabditis elegans germ cells

Spermatogenesis is an intricate and tightly controlled process encompassing various layers of gene expression regulation. Despite the advance of our current understanding, the developmental trajectory and regulatory mechanisms dictating spermatogenesis remain elusive. In this study, we have generated single-cell gene expression profiles for Caenorhabditis elegans sperm cells and constructed gene regulatory networks alongside the developmental trajectories of these cells. Our findings indicate that each pre- and post-developmental stage is closely linked by co-expressed genes, while simultaneously being uniquely identified by the combined expression of specific gene families. To illustrate the applicability of this exhaustive gene expression catalog, we used gene regulatory networks to uncover potential transcription factors for (1) the expression of genes in the phosphorylation pathway, identifying NHR-23-to-phosphatase regulation for the meiotic cell division process; and (2) the expression of constituent components of small RNA pathways, identifying ELT-1-to-Argonaute protein regulation for siRNA maintenance and sperm activation. We expect that this sperm cell-specific gene expression directory will prompt investigations into the underlying mechanisms determining anatomy, differentiation, and function across the reproductive system. Finally, our expression data can be explored using the web application CelegansGermAtlas ( https://scgerm-atlas.sjtu.edu.cn/website/#/home ).

Identification and Characterization of Copper-Responsive miRNAs and Their Target Genes in Jerusalem Artichoke

microRNAs (miRNAs) are key regulators of gene expression in plants, significantly contributing to various biological processes and stress responses. While their roles have been extensively studied in Arabidopsis thaliana and other model plants, the response of miRNAs to copper (Cu) stress in Jerusalem artichoke remains unknown. This study addresses this gap by investigating Cu-responsive miRNAs and their regulatory roles in Jerusalem artichoke under Cu stress. Through small RNA library analysis, six miRNA families-miR168, miR394, miR397, miR398, miR408, and miR858-were identified in Cu-stressed and control plants of the Jerusalem artichoke cv. NY1. These miRNAs possess characteristic stem-loop precursor structures and detectable miRNA* sequences, with miR858 having unusually long precursors (1524-6448 nt). This study outlines a framework for miRNA-mediated Cu stress responses in Jerusalem artichoke, highlighting the roles of both well-established Cu-responsive miRNAs (miR397, miR398, and miR408) and other conserved miRNAs (miR168, miR394, and miR858). These miRNAs are suggested to influence Cu stress adaptation by modulating target genes involved in essential metabolic, physiological, and morphological processes, offering new insights into miRNA-mediated stress regulation in plants.

New Insights on the Potential Role of Pyroptosis in Parkinson's Neuropathology and Therapeutic Targeting of NLRP3 Inflammasome with Recent Advances in Nanoparticle-Based miRNA Therapeutics

Parkinson's disease (PD) is a widespread neurodegenerative disorder characterized by the gradual degeneration of dopaminergic neurons in the substantia nigra pars compacta (SNc). This review aims to summarize the recent advancements in the pathophysiological mechanisms of pyroptosis, mediated by NLRP3 inflammasome, in advancing PD and the anti-pyroptotic agents that target NLRP3 inflammatory pathways and miRNA. PD pathophysiology is primarily linked to the aggregation of α-synuclein, the overproduction of reactive oxygen species (ROS), and the development of neuroinflammation due to microglial activation. Prior research indicated that a significant quantity of microglia is activated in both PD patients and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse models, triggering neuroinflammation and resulting in a cascade of cellular death. Microglia possess an inflammatory complex pathway termed the nucleotide-binding oligomerization domain-, leucine-rich repeat, and pyrin domain-containing 3 (NLRP3) inflammasome. Activation of the NLRP-3 inflammasome results in innate cytokines maturation, including IL-18 and IL-1β, which initiates the neuroinflammatory signal and induces a type of inflammatory cell death known as pyroptosis. Upon neuronal damage, intracellular levels of damage-associated molecular patterns (DAMPs), including reactive oxygen species (ROS), would build. DAMPs induce unregulated cell death and subsequent release of oxidative intermediates and pro-inflammatory cytokines, leading to the progression of PD. Thus, targeting of neuroinflammation using antipyroptotic medications can be efficiently achieved by blocking NLRP3 and obstructing IL-1β signaling and release. Furthermore, many research studies showed that miRNAs have been identified as regulators of the NLRP3 inflammasome and Nrf2 signal, which subsequently modulate the NLRP3-Nrf2 axis in PD. Nanotechnology promises potential for the advancement of miRNA-based therapies. Nanoparticles that ensure miRNA stability, traverse the blood-brain barrier (BBB) and distribute miRNA targeting regions needed to be created. In conclusion, targeting the pyroptosis pathway via NLRP3 or miRNA may serve as a prospective therapeutic strategy for PD in the future.

MicroRNAs in the Diagnosis of Digestive Diseases: A Comprehensive Review

MicroRNAs (miRNAs) have emerged as crucial regulators in digestive pathologies, including inflammatory bowel disease (miR-31, miR-155, and miR-21), colorectal cancer (miR-21, miR-598, and miR-494), and non-alcoholic fatty liver disease (miR-21, miR-192, and miR-122). Their capacity to modulate gene expression at the post-transcriptional level makes them highly promising candidates for biomarkers and therapeutic interventions. However, despite considerable progress, their clinical application remains challenging. Research has shown that miRNA expression is highly dynamic, varying across patients, disease stages, and different intestinal regions. Their dual function as both oncogenes and tumor suppressors further complicates their therapeutic use, as targeting miRNAs may yield unpredictable effects. Additionally, while miRNA-based therapies hold great potential, significant hurdles persist, including off-target effects, immune activation, and inefficiencies in delivery methods. The intricate interplay between miRNAs and gut microbiota adds another layer of complexity, influencing disease mechanisms and treatment responses. This review examined the role of miRNAs in digestive pathologies, emphasizing their diagnostic and therapeutic potential. While they offer new avenues for disease management, unresolved challenges underscore the need for further research to refine their clinical application.

Circulating microRNAs as Potential Biomarkers of Overweight and Obesity in Adults: A Narrative Review

In an obesogenic environment, such as the one we have been experiencing in recent decades, epigenetics provides answers to the relationship between hereditary and environmentally acquired patterns that have significantly contributed to the global rise in obesity prevalence. MicroRNA (miRNA) constitutes a diminutive non-coding small RNA molecule, 20 to 24 nucleotides in length, that functions as a regulator of gene regulation at the post-translational level. Circulating miRNAs (c-miRNAs) have been detected in multiple body fluids, including blood, plasma, serum, saliva, milk from breastfeeding mothers, and urine. These molecules hold significant therapeutic value and serve as extracellular biomarkers in metabolic diseases. They aid in the diagnosis and tracking of therapy responses, as well as dietary and physical habit modifications. Researchers have studied c-miRNAs as potential biomarkers for diagnosing and characterizing systemic diseases in people of all ages and backgrounds since then. These conditions encompass dyslipidemia, type 2 diabetes mellitus (T2DM), cardiovascular risk, metabolic syndrome, cardiovascular diseases, and obesity. This review therefore analyzes the usefulness of c-miRNAs as therapeutic markers over the past decades. It also provides an update on c-miRNAs associated with general obesity and overweight, as well as with the most prevalent pathologies in the adult population. It also examines the effect of different nutritional approaches and physical activity regarding the activity of miRNAs in circulation in adults with overweight or general obesity. All of this is done with the aim of evaluating their potential use as biomarkers in various research contexts related to overweight and obesity in adults.

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 (miRNA) expression across the mouse lifespan (7 time points) and two aging interventions composed of 1009 samples. MiRNAs are promising therapeutic targets, as they silence genes by complementary base-pair binding of messenger RNAs and are known to mediate aging speed. We first established sex- and brain-region-specific miRNA expression patterns in young adult samples. Then we focused on sex-dependent and independent brain-region-specific miRNA expression changes during aging. The corpus callosum in males and the choroid plexus in females exhibited strong sex-specific age-related signatures. In this work, we identified three sex-independent brain aging miRNAs (miR-146a-5p, miR-155-5p and miR-5100). We showed for miR-155-5p that these expression changes are driven by aging microglia. MiR-155-5p targets mTOR signaling pathway components and other cellular communication pathways and is hence a promising therapeutic target.

Epigenetic Regulation of Chromatin Functions by MicroRNAs and Long Noncoding RNAs and Implications in Human Diseases

The bulk of RNA produced from the genome of complex organisms consists of a very large number of transcripts lacking protein translational potential and collectively known as noncoding RNAs (ncRNAs). Initially thought to be mere products of spurious transcriptional noise, ncRNAs are now universally recognized as pivotal players in cell regulatory networks across a broad spectrum of biological processes. Owing to their critical regulatory roles, ncRNA dysfunction is closely associated with the etiopathogenesis of various human malignancies, including cancer. As such, ncRNAs represent valuable diagnostic biomarkers as well as potential targets for innovative therapeutic intervention. In this review, we focus on microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), the two most extensively studied classes in the field of ncRNA biology. After outlining key concepts of miRNA and lncRNA biogenesis pathways, we examine their multiple roles in mediating epigenetic regulation of gene expression and chromatin organization. Finally, by providing numerous examples of specific miRNAs and lncRNAs, we discuss how dysregulation of these mechanisms contributes to the onset and/or progression of various human diseases.

Redox-stimulated catalytic DNA circuit for high-fidelity imaging of microRNA and in situ interpretation of the relevant regulatory pathway

Biomolecules play essential roles in regulating the orderly progression of biochemical reaction networks. DNA-based biocircuits supplement an attractive and ideal approach for the visual imaging of endogenous biomolecules, yet their sensing performance is commonly encumbered by the undesired signal leakage. To solve this issue, here we proposed a glutathione (GSH)-activated DNA circuit for achieving the spatio-selective microRNA imaging through the successive response of a GSH-specific activation procedure and a non-enzymatic catalytic signal amplification procedure. In this design, by incorporating a disulfide bond into the pre-sealed nucleic acid probe, the uncontrolled circuitry leakage could be effectively ameliorated. In target cancer cells with high-abundant GSH and miR-21, endogenous GSH recognized and cleaved the pre-installed disulfide bond within DNA probes, thereby restoring the activity of circuitry components. The miR-21 then catalyzed the specific operation of circuitry for generating an amplified readout signal. We demonstrate that this system not only enables the effective discriminations of various cell types, but also contributes to the exploration of the correlationship between GSH and miR-21. This on-site activated DNA circuit can be extended to the robust analysis and exploration of different biomolecular interactions, offering a reliable reference for the in-depth understanding of biochemical interaction networks.

Perspectives of exosomal ncRNAs in the treatment of bone metabolic diseases: Focusing on osteoporosis, osteoarthritis, and rheumatoid arthritis

Bone metabolic disorders, constituting a group of prevalent and grave conditions, currently have a scarcity of therapeutic alternatives. Over the recent past, exosomes have been at the forefront of research interest, owing to their nanoparticulate nature and potential for therapeutic intervention. ncRNAs are a class of heterogeneous transcripts that they lack protein-encoding capacity, yet they can modulate the expression of other genes through multiple mechanisms. Mounting evidence underscores the intricate role of exosomes as ncRNAs couriers implicated in the pathogenesis of bone metabolic disorders. In this review, we endeavor to elucidate recent insights into the roles of three ncRNAs - miRNAs, lncRNAs, and circRNAs - in bone metabolic ailments such as osteoporosis, osteoarthritis, and rheumatoid arthritis. Additionally, we examine the viability of exosomal ncRNAs as innovative, cell-free modalities in the diagnosis and therapeutic management of bone metabolic disorders. We aim to uncover the critical function of exosomal ncRNAs within the context of bone metabolic diseases.

Biomarkers of endometriosis

Endometriosis represents a diverse disease characterized by three distinct phenotypes: superficial peritoneal lesions, ovarian endometriomas, and deep infiltrating endometriosis. The most widely accepted pathophysiological hypothesis for endometriosis is rooted in retrograde menstruation, a phenomenon observed in most patients. Endometriosis is closely linked to infertility, but having endometriosis does not necessarily imply infertility. The disease can impact fertility through various mechanisms affecting the pelvic cavity, ovaries, and the uterus itself. MicroRNAs (miRNAs) indeed represent a fascinating and essential component of the regulatory machinery within cells. Discovered in the early 1990s, miRNAs have since been identified as critical players in gene expression control. Unfortunately, ovarian endometrioma is a common gynecologic disorder for which specific serum markers are currently lacking. Some have examined urocortin for its ability to differentiate endometriomas from other benign ovarian cysts. Another potential marker, Cancer Antigen 125 (CA-125) is a well-established indicator for epithelial cell ovarian cancer and its levels can be elevated in conditions such as endometriosis. CA-125 is derived from coelomic epithelia, including the endometrium, fallopian tube, ovary, and peritoneum. In this review we examine the pathophysiologic basis for endometriosis and highlight potential markers to more fully characterize the underlying biochemical processes linked to this multifaceted disease state.

Novel strategy for hair regeneration: Exosomes and collagenous sequences of human a1(XVII) chain enhance hair follicle stem cell activity by regulating the hsa-novel-238a-CASP9 axis

The regenerative capacity of hair follicles is fundamentally influenced by the intricate interactions between hair follicle stem cells (HFSCs) and their microenvironment. Our study presents a novel strategy for hair regeneration, highlighting the synergistic relationship between dermal papilla cell-derived exosomes (DPC-Exos) and collagenous sequences of Human a1(XVII) Chain (CS-COL17A1) in modulating HFSC activity via the hsa-novel-238a-CASP9 axis. We characterized DPC-Exos using nanoparticle tracking analysis and transmission electron microscopy and confirmed, their purity with the exosomal markers CD81, CD63, and CD9.A dose-dependent CCK-8 assay showed that both DPC-Exos and CS-COL17A1 significantly improved HFSC viability. Scratch and Transwell assays showed improved HFSC migration after treatment. MiRNA sequencing revealed a significant upregulation of hsa-novel-238a in HFSCs after treatment with DPC-Exos and CS-COL17A1, suggesting its involvement in the regulation of HFSCs activity. A dual-luciferase assay confirmed that hsa-novel-238a directly targets the CASP9 gene, elucidating the underlying molecular mechanisms. The combined application of DPC-Exos and CS-COL17A1 significantly improved HFSC migration and proliferation (p < 0.01), highlighting the importance of the hsa-novel-238a-CASP9 axis. This research provides insights into the regulatory network of exosomes and CS-COL17A1, paving the way for innovative therapeutic approaches to treat hair loss and enhance hair follicle regeneration through modulation of the hsa-novel-238a-CASP9 axis.

Molecular mechanisms of miR-192 in cancer: a biomarker and therapeutic target

Cancer remains a major global health challenge due to its rising prevalence and high mortality rates. The field of microRNAs (miRNAs) has made significant progress in the understanding of tumorigenesis and has broadened our knowledge of their targeting, especially in cancer therapy. miRNAs, a class of small non-coding RNAs, participate in post-transcriptional gene regulation by translational inhibition or mRNA degradation. Among these, microRNA-192 (miR-192) is located on human chromosome 11q13.1, and is highly correlated with the occurrence and development of various human cancers. Dysregulation of miR-192 has been extensively studied in various pathological processes, including tumorigenesis, making it a valuable biomarker for cancer diagnosis and prognosis. The functional role of miR-192 varies across cancer types, acting as either a tumor suppressor or as an oncogene through the modulation of multiple gene expressions and downstream signaling pathways. However, the roles of miR-192 in cancer appear inconsistent across types, with current research often focused on specific genes or pathways, limiting insight into its broader impact on cellular signaling networks. Therefore, this review aims to provide a comprehensive overview of miR-192 research. The paper reviews differences in miR-192 expression in cancer and systematically summarizes the role of miR-192 in cancers. The review further explores the complex roles of miR-192 in various pathological processes, emphasizing its regulatory pathways, interaction networks, and association with tumor progression. This review also illustrates the clinical application of miR-192 as a diagnostic and prognostic biomarker for non-invasive cancer detection, as it is consistently present in both serum and exosomes. A comprehensive summary and analysis of the relationship between miR-192 and various cancers may provide valuable insights, potentially guiding novel approaches in clinical diagnosis, therapeutic strategies, and foundational cancer research.

Nanotechnology-leveraged CRISPR/Cas systems: icebreaking in trace cancer-related nucleic acids biosensing

As promising noninvasive biomarkers, nucleic acids provide great potential to innovate cancer early detection methods and promote subsequent diagnosis to improve the survival rates of patient. Accurate, straightforward and sensitive detection of such nucleic acid-based cancer biomarkers in complex biological samples holds significant clinical importance. However, the low abundance creates huge challenges for their routine detection. As the next-generation diagnostic tool, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas) with their high programmability, sensitivity, fidelity, single-base resolution, and precise nucleic acid positioning capabilities are extremely attractive for trace nucleic acid-based cancer biomarkers (NABCBs), permitting rapid, ultra-sensitive and specific detection. More importantly, by combing with nanotechnology, it can solve the long-lasting problems of poor sensitivity, accuracy and simplicity, as well as to achieve integrated miniaturization and portable point-of-care testing (POCT) detection. However, existing literature lacks specific emphasis on this topic. Thus, we intend to propose a timely one for the readers. This review will bridge this gap by providing insights for CRISPR/Cas-based nano-biosensing development and highlighting the current state-of-art, challenges, and prospects. We expect that it can provide better understanding and valuable insights for trace NABCBs detection, thereby facilitating advancements in early cancer screening/detection/diagnostics and win practical applications in the foreseeable future.

Insect metamorphosis and chitin metabolism under miRNA regulation: a review with current advances

Insect metamorphosis is a complex developmental process regulated by microRNAs (miRNAs) and hormonal signaling pathways. Key genes driving insect ontogenic changes are precisely modulated by miRNAs, which interact with 20-hydroxyecdysone (20E) and juvenile hormone (JH) to coordinate developmental transitions. Over the past decade, significant progress has been made in understanding miRNA biogenesis, their regulatory roles in gene expression, and their involvement in critical biological processes, including metamorphosis and chitin metabolism. miRNAs are now recognized as essential regulators of chitin metabolism and hormonal signaling, ensuring precise control of insect development. Disrupting the expression of participating genes in hormone signaling pathways through miRNAs leads to aberrant metamorphosis and consequent lethal outcomes, highlighting their potential as targets for pest control. This review summarizes current advances in miRNA-mediated regulation of insect metamorphosis and chitin metabolism, with a focus on their interactions with 20E and JH signaling pathways. By integrating recent findings, we provide insights into the molecular mechanisms underlying miRNA function in developmental transitions and their potential applications in insect pest management strategies. © 2025 Society of Chemical Industry.

Unlocking the Potential of MicroRNA Expression: Biomarkers for Platelet Reactivity and Coronary Artery Disease

Coronary artery disease (CAD) is a leading cause of morbidity and mortality worldwide, with platelet reactivity playing a central role in its pathogenesis. Recent research has identified microRNAs (miRNAs; miRs) as potential biomarkers for CAD, due to their ability to regulate platelet function and reactivity. This review focuses on four key miRNAs-miR-223, miR-126, miR-21, and miR-150-known to influence platelet reactivity and their implications in CAD. miR-223, which is highly expressed in platelets, has shown associations with CAD and myocardial infarction, while miR-126 has been linked to thrombus formation and vascular health. Additionally, miR-21 and miR-150 have also emerged as important players, with roles in platelet reactivity and cardiovascular outcomes. However, despite their potential, the use of miRNAs as clinical biomarkers faces several challenges, including variability in reported results across studies. These inconsistencies often arise from differences in sample material, preanalytical conditions, and normalization strategies. Furthermore, the influence of antiplatelet therapy on miRNA expression adds another layer of complexity, making it difficult to determine whether observed changes in miRNA levels are due to disease states or therapeutic interventions. This review therefore highlights the need for standardization in miRNA research to enhance the reliability of findings. By addressing these methodological challenges, miRNAs could become powerful tools in personalized medicine, aiding in the development of tailored therapeutic strategies for CAD patients and ultimately improving clinical outcomes.

Differential miRNA expression and regulatory mechanisms in pigmentation and fiber development of white and brown cotton (Gossypium hirsutum)

Cotton (Gossypium hirsutum) is a major global natural fiber crop used in the textile industry. Although white colored cotton remains the most popular form of cultivated cotton, colored varieties could replace chemically dyed fibers and provide more environmental friendly alternatives. In order to investigate the role of miRNAs in fiber color, we selected white and brown cotton varieties for comparative investigations. Through small RNA sequencing, a number of known miRNA families were discovered (74 in white cotton and 61 in brown cotton, with 44 shared) in which 11 miRNA families were significantly elevated in brown cotton variety. Functional enrichment and network analysis of target genes of these miRNAs revealed their regulatory role in secondary metabolite biosynthesis pathway, particularly the flavonoids pathway, which are known to be associated with fiber coloration. Pigmentation and developmental-related miRNA members such as miR396e-5p, miR167l, and miR1446 were also significantly enriched. Real-time PCR results suggest the regulatory role of miRNAs in these two cotton varieties. Furthermore, 30 and 25 novel miRNAs were also identified in white and brown cotton, respectively. Our findings also show miRNAs associated with fiber coloration and development through the intricate networks of miRNA and targets. Understanding these systems may provide novel insights on improving the fiber color and quality.

Methods for Extracellular Vesicle Isolation: Relevance for Encapsulated miRNAs in Disease Diagnosis and Treatment

Extracellular vesicles (EVs) are nanovesicles that facilitate intercellular communication by carrying essential biomolecules under physiological and pathological conditions including microRNAs (miRNAs). They are found in various body fluids, such as blood, urine, and saliva, and their levels fluctuate with disease progression, making them valuable diagnostic tools. However, isolating EVs is challenging due to their small size and biological complexity. Here, we summarize the principles behind the most common EV isolation methods including ultracentrifugation, precipitation, immunoaffinity, sorting, ultrafiltration, size exclusion chromatography, and microfluidics while highlighting protocol strengths and weaknesses. We also review the main strategies to identify and quantify circulating miRNAs with a particular focus on EV-encapsulated miRNAs. Since these miRNAs hold special clinical interest derived from their superior stability and therapeutic potential, the information provided here should provide valuable guidance for future research initiatives in the promising field of disease diagnostic and treatment based on EV-encapsulated miRNAs.

Extracellular viral microRNAs as biomarkers of virus infection in human cells

Nucleic acid amplification tests (NAATs) have enabled fast and sensitive detection of virus infections but are unable to discriminate between live and dead/inert viral fragments or between latent and reactivated virus infections. Here, we show that extracellular viral microRNAs (viral exmiRs) are cell-free candidate biomarkers of live, latent, and reactivated virus infections, achieving fast (under 1 day) and sensitive (30 attomolar [aM]) detection by quantitative real-time reverse transcription PCR (real-time RT-qPCR). We report that spent-media-derived Epstein-Barr virus (EBV) miR-BART10-3p and herpes simplex virus 1 (HSV-1) miR-H5 are biomarkers of live EBV-2 and HSV-1 infection of T cell cultures, respectively. We identified extracellular human herpesvirus 6 (HHV-6) miR-Ro6-4 as a biomarker of endogenous latent HHV-6 in healthy human donor T cell cultures and identified human cytomegalovirus (HCMV) miR-US5-2-5p and miR-US22-5p as plasma biomarkers of endogenous latent HCMV infection. Viral exmiR profiling of spent media from EBV- and HHV-8-reactivated B cell models revealed specific signatures of elevated EBV miR-BHRF1-2-3p and HHV-8 miR-K12-10a-3p, miR-K12-10b, and miR-K12-12-3p, respectively, during virus reactivation. Our study thus suggests the utility of viral exmiR biomarkers in enabling NAAT-based detection of live, endogenous latent, and reactivated virus infections of cells.

New Insight Into the Neuroimmune Interplay In Pseudomonas aeruginosa Keratitis

Purpose

The miR-183/96/182 cluster (miR-183C) is required for normal functions of sensory neurons (SN) and various immune cells, including myeloid cells (MC). This research aims to reveal the roles of miR-183C of SN in the interplay of corneal sensory nerves (CSN) and MC during Pseudomonas aeruginosa (PA) keratitis.

Methods

Double-tracing mice with SN-specific (SNS) conditional knockout of miR-183C (CKO) and age- and sex-matched wild type (WT) controls were used. Their CSN are labeled with Red Fluorescent Protein (RFP); MC with Enhanced Green (EG)FP. The left corneas were scarified and infected with ATCC19660 PA. Corneal flatmounts were prepared at 3, 6, and 12 hours post-infection (hpi) and 1, 3, and 5 days (d)pi for confocal microscopy. Myeloperoxidase (MPO) assay and plate count were performed at 1 dpi.

Results

In WT mice, CSN began to degenerate as early as 3 hpi, starting from the fine terminal CSN in the epithelial/subepithelial layers, most prominently in the central region. By 1 dpi, CSN in the epithelium/subepithelial layer were nearly completely destroyed, while stromal nerves persisted. From 3 dpi, CSN were obliterated in both layers. In CKO vs WT mice, CNS followed a slightly slower pace of degeneration. CSN density was decreased at 3 and 6 hpi. However, at 3 dpi, residual large-diameter stromal CSN were better preserved.MC were decreased in the central cornea at 3 and 6 hpi, but increased in the periphery. Both changes were more prominent in CKO vs WT mice. At 12 hpi, densely packed MC formed a ring-shaped band circling a "dark" zone nearly devoid of MC, colocalizing with CSN most degenerated zone in the central cornea. In CKO vs WT, the ring center was larger with fewer MC. At 1 dpi, the entire cornea was filled with MC; however, MC density was lower in CKO mice. An MPO assay showed decreased neutrophils in PA-infected cornea of CKO mice. This led to a decreased severity of PA keratitis at 3 dpi.

Conclusions

This double-tracing model reveals the interplay between CSN and MC during PA keratitis with greater clarity, providing new insights into PA keratitis. CSN-imposed modulation on innate immunity is most impressive within 24 hours after infection. Functionally, the miR-183C in CSN modulates CSN density and the dynamics of MC fluxes- a neuroimmune interaction in display.

Circ_0090100 induces AHNAK expression to inhibit trophoblast cell proliferation and invasion and accelerate cell apoptosis by segregating miR-139-5p in preeclampsia

The etiology of preeclampsia (PE) is complex and is known to involve the expression of circular RNAs (circRNAs). Among these, the function of circ_0090100 in PE is yet to be fully understood. This study was conducted to examine the expression profile of circ_0090100 in placental tissues from PE patients and to assess its influence on trophoblast cell functions. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure the RNA expression levels of circ_0090100, microRNA-139-5p (miR-139-5p), and AHNAK nucleoprotein (AHNAK). Cell viability, proliferation, apoptosis, and invasion were assessed using the CCK-8 assay, EdU incorporation, flow cytometry, and transwell migration assays, respectively. Western blot analysis was performed to detect the protein expression of N-cadherin, Vimentin, and AHNAK. Dualluciferase reporter assay and RNA immunoprecipitation (RIP) assay were conducted to elucidate the relationships between circ_0090100, miR-139-5p, and AHNAK. We found that the expression of circ_0090100 and AHNAK was upregulated, while miR-139-5p. expression was downregulated in PE placental tissues compared to controls. Transfection of a plasmid overexpressing circ_0090100 into JEG-3 and HTR-8/SVneo trophoblast cell lines resulted in reduced cell proliferation and invasion, but increased apoptosis. Mechanistically, circ_0090100 functioned as a miR-139-5p sponge, and miR-139-5p targeted AHNAK. Furthermore, upregulating miR-139-5p reversed the effects of circ_0090100 in JEG-3 and HTR-8/SVneo cells. AHNAK was found to be involved in the regulation of miR-139-5p effects on trophoblast cells. Additionally, circ_0090100 induced the production of AHNAK through miR-139-5p. Therefore, circ_0090100 activated AHNAK to suppress trophoblast cell proliferation and invasion, and promote cell apoptosis, via miR-139-5p.

A Multi-Input Neural Network Model for Accurate MicroRNA Target Site Detection

(1) Background: MicroRNAs are non-coding RNA sequences that regulate cellular functions by targeting messenger RNAs and inhibiting protein synthesis. Identifying their target sites is vital to understanding their roles. However, it is challenging due to the high cost and time demands of experimental methods and the high false-positive rates of computational approaches. (2) Methods: We introduce a Multi-Input Neural Network (MINN) algorithm that integrates diverse biologically relevant features, including the microRNA duplex structure, substructures, minimum free energy, and base-pairing probabilities. For each feature derived from a microRNA target-site duplex, we create a corresponding image. These images are processed in parallel by the MINN algorithm, allowing it to learn a comprehensive and precise representation of the underlying biological mechanisms. (3) Results: Our method, on an experimentally validated test set, detects target sites with an AUPRC of 0.9373, Precision of 0.8725, and Recall of 0.8703 and outperforms several commonly used computational methods of microRNA target-site predictions. (4) Conclusions: Incorporating diverse biologically explainable features, such as duplex structure, substructures, their MFEs, and binding probabilities, enables our model to perform well on experimentally validated test data. These features, rather than nucleotide sequences, enhance our model to generalize beyond specific sequence contexts and perform well on sequentially distant samples.

Expression Analysis of Circulating miR-21, miR-34a and miR-122 and Redox Status Markers in Metabolic Dysfunction-Associated Steatotic Liver Disease Patients with and Without Type 2 Diabetes

Metabolic dysfunction-associated steatotic liver disease (MASLD), a hepatic form of metabolic syndrome, often co-occurs with type 2 diabetes (T2D) and now affects approximately 30% of the global population. MASLD encompasses conditions from simple steatosis to metabolic dysfunction-associated steatohepatitis, with oxidative stress (OS) driving progression through inflammation. This study analyzes the expression levels of circulating miRNAs and redox status markers in MASLD patients with and without T2D, exploring their potential as disease biomarkers. The expressions of miR-21, miR-34a, and miR-122 were analyzed in the platelet-poor plasma of 147 participants, divided into three groups: MASLD + T2D (48), MASLD (50), and a control group (49). Total oxidant status (TOS), total antioxidant status (TAS), ischemia-modified albumin (IMA), and superoxide anion radical (O2•-) were measured in serum and plasma. Logistic regression showed that miR-21, miR-34a, TOS, TAS, O2•-, and IMA were positive predictors of MASLD, while miR-21 and TAS were negative predictors of T2D in MASLD. Although miR-122 did not show a significant association with either condition, in combination with miR-34a and other markers such as lipid status and liver enzymes, a new significant predictor of MASLD was identified. Circulating miRNAs in combination with redox status markers, lipid status and liver enzymes show potential as MASLD biomarkers.

The relationship of miR-155 host gene polymorphism in the susceptibility of cancer: a systematic review and meta-analysis

Background

miR-155 is overexpressed in many cancers, highlighting its potential as a biomarker for cancer diagnosis, treatment, and therapeutic evaluation. miR-155 is processed from the miR-155 host gene (MIR155HG). Genetic variations in MIR155HG may influence cancer susceptibility, but existing evidence is inconclusive. This study aimed to evaluate the association of MIR155HG polymorphisms with cancer risk.

Material/Methods

A systematic literature search identified 15 case-control studies on three single nucleotide polymorphisms (SNPs): rs767649 (T > A), rs928883 (G > A), and rs1893650 (T > C). Meta-analysis was performed using RevMan 5.4, with odds ratios (ORs) and 95% confidence intervals (CIs) as effect measures.

Results

No significant association was observed for rs767649 and rs928883 in overall cancer analysis. However, subgroup analysis revealed rs767649 increased susceptibility to respiratory, digestive, and reproductive cancers, while reducing cancer risk after excluding reproductive cancers. rs928883 showed a protective effect for digestive cancers. rs1893650 was not significantly associated with cancer risk.

Conclusion

MIR155HG polymorphisms influence susceptibility to specific cancer subtypes, particularly respiratory and digestive cancers. These findings underscore the importance of genetic and environmental factors in cancer risk and warrant further investigation.

DeepHeteroCDA: circRNA-drug sensitivity associations prediction via multi-scale heterogeneous network and graph attention mechanism

Drug sensitivity is essential for identifying effective treatments. Meanwhile, circular RNA (circRNA) has potential in disease research and therapy. Uncovering the associations between circRNAs and cellular drug sensitivity is crucial for understanding drug response and resistance mechanisms. In this study, we proposed DeepHeteroCDA, a novel circRNA-drug sensitivity association prediction method based on multi-scale heterogeneous network and graph attention mechanism. We first constructed a heterogeneous graph based on drug-drug similarity, circRNA-circRNA similarity, and known circRNA-drug sensitivity associations. Then, we embedded the 2D structure of drugs into the circRNA-drug sensitivity heterogeneous graph and use graph convolutional networks (GCN) to extract fine-grained embeddings of drug. Finally, by simultaneously updating graph attention network for processing heterogeneous networks and GCN for processing drug structures, we constructed a multi-scale heterogeneous network and use a fully connected layer to predict the circRNA-drug sensitivity associations. Extensive experimental results highlight the superior of DeepHeteroCDA. The visualization experiment shows that DeepHeteroCDA can effectively extract the association information. The case studies demonstrated the effectiveness of our model in identifying potential circRNA-drug sensitivity associations. The source code and dataset are available at https://github.com/Hhhzj-7/DeepHeteroCDA.

Optimizing sample size for supervised machine learning with bulk transcriptomic sequencing: a learning curve approach

Accurate sample classification using transcriptomics data is crucial for advancing personalized medicine. Achieving this goal necessitates determining a suitable sample size that ensures adequate classification accuracy without undue resource allocation. Current sample size calculation methods rely on assumptions and algorithms that may not align with supervised machine learning techniques for sample classification. Addressing this critical methodological gap, we present a novel computational approach that establishes the accuracy-versus-sample size relationship by employing a data augmentation strategy followed by fitting a learning curve. We comprehensively evaluated its performance for microRNA and RNA sequencing data, considering diverse data characteristics and algorithm configurations, based on a spectrum of evaluation metrics. To foster accessibility and reproducibility, the Python and R code for implementing our approach is available on GitHub. Its deployment will significantly facilitate the adoption of machine learning in transcriptomics studies and accelerate their translation into clinically useful classifiers for personalized treatment.

Research and progress of microRNA-136 in metastatic tumors

Background

MiR-136 is abnormally expressed in many types of metastatic tumors and is closely associated with tumor cell proliferation, apoptosis, invasion, and metastasis, indicating its important role in tumor development and progression. This review summarizes current knowledge regarding miR-136's molecular mechanisms, functional roles, and impact on chemotherapy in different human cancers.

Methods

A literature search was conducted in PubMed and Web of Science using "miR-136" and "metastatic tumors" as English keywords, and in CNKI and Wanfang databases using the same terms in Chinese. Studies related to miR-136 research in metastatic tumors and high-quality evidence from similar studies were included. Meta-analyses, dissertations, conference papers, low-quality articles, unavailable full-text articles, and republished articles were excluded.

Results

This review synthesizes the current understanding of miR-136's role in various cancers, including osteosarcoma, gastric cancer, gallbladder cancer, esophageal cancer, prostate cancer, colorectal cancer, breast cancer, glioma, and thyroid cancer. miR-136 acts as a tumor suppressor by targeting various genes, including MTDH, PTEN, MAP2K4, MUC1, LRH-1, MIEN1, RASAL2, CYR61, and KLF7. It influences multiple signaling pathways, including the ERK/mitogen-activated protein kinase, Wnt/β-catenin, Ha-Ras, PI3K/Akt, Aurora-A kinase, nuclear factor-κB, and JNK pathways. Furthermore, miR-136 is involved in chemoresistance by modulating ROCK1, PPP2R2A, and the miR-136-Notch3 signaling axis.

Conclusions

MiR-136 demonstrates promising potential as a novel biomarker and therapeutic target in various human cancers. Further research is needed to fully elucidate its complex roles in cancer development, progression, and drug resistance, particularly regarding its potential in immunotherapy.

MicroRNAs in HIV infection: dual regulators of viral replication and host immunity

MicroRNAs (miRNAs) are small non-coding RNAs that play a crucial role in regulating gene expression by binding to target messenger RNAs (mRNAs), leading to their degradation or translational repression. Over the past few years, significant progress has been made in understanding the role of miRNAs in various biological processes, including viral infections such as human immunodeficiency virus (HIV). HIV infection is characterized by a complex interaction between the virus and the host's immune system, where miRNAs have emerged as key regulators. MiRNAs influence HIV infection by modulating both viral replication and the host immune response. Researchers have identified several host miRNAs that suppress or enhance HIV replication by targeting viral genes or host factors essential for the virus life cycle. Conversely, HIV has evolved mechanisms to manipulate the host's miRNA machinery to its advantage. The virus can downregulate or upregulate specific host miRNAs to create a more favorable environment for replication and persistence. Moreover, HIV infection can alter the expression profiles of various miRNAs in infected cells, which can contribute to immune dysregulation and disease progression. Dysregulation of miRNAs is associated with HIV-associated complications, such as neurocognitive disorders and cardiovascular diseases. Understanding the specific roles of miRNAs in HIV pathogenesis could lead to the development of novel therapeutic strategies, such as miRNA-based therapies, to control HIV infection and its associated comorbidities. Understanding the role of miRNAs in HIV infection reveals their significant influence on the complex interactions between the virus and the host, impacting the course of infection and disease progression. Also, continued research in miRNA-mediated mechanisms in HIV holds the potential for uncovering new insights into viral pathogenesis and developing innovative therapeutic approaches.

MicroRNA profiling in umbilical cord plasma: links to maternal metabolism and neonatal metabolic and inflammatory traits

MicroRNAs (miRNAs) are regulators of mRNA translation and play crucial roles in various physiological and pathological processes. In this study, we profiled miRNAs in umbilical cord plasma (UCP) to explore the association of neonatal circulating miRNAs with maternal metabolic parameters and neonatal anthropometric, metabolic and inflammatory characteristics in healthy pregnancies. Data and UCP samples were collected from 16 pregnancies, equally divided between normal-weight and overweight mothers and between male and female newborns. Using next-generation sequencing, we identified and quantified miRNAs in UCP, alongside the analysis of metabolic and inflammatory parameters. Our results revealed that the majority of UCP miRNAs are sensitive to maternal and neonatal characteristics, particularly maternal body mass index, gestational weight gain, placental weight, UCP leptin, UCP C-reactive protein and UCP insulin levels. Notably, we identified a strong association between the placenta-derived chromosome 19 microRNA cluster (C19MC) and placental weight, gestational weight gain, UCP insulin and neonatal weight. Likewise, the pregnancy-specific chromosome 14 microRNA cluster (C14MC) was associated with maternal body mass index and UCP leptin. Our study highlights the sensitivity of UCP miRNAs to maternal metabolic conditions, demonstrates their association with neonatal metabolic and inflammatory traits, and underscores the potential role of circulating cord blood miRNAs in fetal metabolism and development. KEY POINTS: MicroRNAs (miRNAs) are regulatory RNA molecules that modulate protein expression. They are present in all body fluids and umbilical cord plasma and are affected by metabolic changes. Pregnancy is a state of metabolic change in the mother, and maternal metabolism affects fetal development. We found that the composition of umbilical cord blood miRNAs is associated with maternal and neonatal metabolism. Pregnancy-specific groups of miRNAs showed particular patterns, with miRNAs encoded by a region of chromosome 14 associated with maternal body mass index and with miRNAs encoded by a specific region of chromosome 19 associated with umbilical cord plasma insulin. MicroRNAs represent a separate dimension through which maternal metabolism can influence fetal development.

Serum mature microRNA panel: A novel approach for primary prostate cancer diagnosis

BACKGROUND

Prostate cancer (PC) is the second most common malignant tumor in males and a leading cause of cancer-related morbidity and mortality among men. Early detection is essential for improving outcomes. Although prostate-specific antigen (PSA) is widely used for PC screening, it suffers from high false positive and false negative rates. Our study aimed to identify a panel of serum mature microRNAs (miRNAs) for PC diagnosis.

METHODS

We conducted a PubMed search to identify candidate mature miRNAs associated with PC. We then used quantitative reverse transcription-polymerase chain reaction (RT-qPCR) to assess the expression profiles of these mature miRNAs in serum samples from 112 PC patients and 112 healthy controls (HCs). We selected mature miRNAs with favorable diagnostic potential by analyzing receiver operating characteristic (ROC) curves and calculating the area under the curve (AUC). Subsequently, we developed a highly diagnostically efficient panel of three mature miRNAs using stepwise logistic regression based on their expression levels.

RESULTS

We identified three mature miRNAs (hsa-miR-143-5p, hsa-miR-23b-3p, and hsa-miR-148b-3p) with significant diagnostic value, constructing a panel with an AUC of 0.891, sensitivity of 84.15%, and specificity of 80.49%. Bioinformatics analysis also revealed LDB3 and RBMS3 as potential therapeutic targets for PC.

CONCLUSIONS

Our study introduces a novel diagnostic approach by identifying a panel of three mature miRNAs (hsa-miR-143-5p, hsa-miR-23b-3p, and hsa-miR-148b-3p) as novel and non-intrusive biomarkers for PC.

miR-874-3p Alleviates Macrophage-Mediated Inflammatory Injury in Intracerebral Hemorrhage by Targeting HIPK2

Macrophages mediate secondary inflammatory injury after intracerebral hemorrhage (ICH). This study aimed to investigate the role and molecular mechanisms of miR-874-3p in macrophage polarization. A mice model of ICH was constructed by autologous blood injection. Macrophages were treated with erythrocyte lysates to construct an ICH cell model. Real-time quantitative reverse transcription PCR (RT-qPCR) was used to detect miR-874-3p levels. Enzyme-Linked Immunosorbent Assay (ELISA) was used to detect macrophage polarization markers. Brain tissue water content and neurological deficit scores were used to assess the degree of inflammatory injury in ICH mice. RNA immunoprecipitation (RIP) and Dual-luciferase reporter (DLR) assays were used to analyze the targeting relationship between miR-874-3p and target mRNA. miR-874-3p levels were decreased in ICH mice and erythrocyte lysates-treated macrophages. miR-874-3p mimic alleviated inflammatory injury, decreased the levels of M1 macrophage markers, and increased the levels of M2 macrophage markers, suggesting that miR-874-3p is involved in ICH by regulating macrophage polarization. HIPK2 is the target mRNA of miR-874-3p and has the opposite expression pattern of miR-874-3p. Overexpression of HIPK2 attenuates the effect of elevated miR-874-3p levels on macrophage polarization and inflammatory brain injury in ICH mice. miR-874-3p regulates macrophage polarization in ICH by targeting HIPK2. Therefore, the miR-874-3p/HIPK2 axis may be a promising target for ICH treatment.

A review of RNA nanoparticles for drug/gene/protein delivery in advanced therapies: Current state and future prospects

Nanotechnology involves the utilization of materials with exceptional properties at the nanoscale. Over the past few years, nanotechnologies have demonstrated significant potential in improving human health, particularly in medical treatments. The self-assembly characteristic of RNA is a highly effective method for designing and constructing nanostructures using a combination of biological, chemical, and physical techniques from different fields. There is great potential for the application of RNA nanotechnology in therapeutics. This review explores various nano-based drug delivery systems and their unique features through the impressive progress of the RNA field and their significant therapeutic promises due to their unique performance in the COVID-19 pandemic. However, a significant hurdle in fully harnessing the power of RNA drugs lies in effectively delivering RNA to precise organs and tissues, a critical factor for achieving therapeutic effectiveness, minimizing side effects, and optimizing treatment outcomes. There have been many efforts to pursue targeting, but the clinical translation of RNA drugs has been hindered by the lack of clear guidelines and shared understanding. A comprehensive understanding of various principles is essential to develop vaccines using nucleic acids and nanomedicine successfully. These include mechanisms of immune responses, functions of nucleic acids, nanotechnology, and vaccinations. Regarding this matter, the aim of this review is to revisit the fundamental principles of the immune system's function, vaccination, nanotechnology, and drug delivery in relation to the creation and manufacturing of vaccines utilizing nanotechnology and nucleic acids. RNA drugs have demonstrated significant potential in treating a wide range of diseases in both clinical and preclinical research. One of the reasons is their capacity to regulate gene expression and manage protein production efficiently. Different methods, like modifying chemicals, connecting ligands, and utilizing nanotechnology, have been essential in enabling the effective use of RNA-based treatments in medical environments. The article reviews stimuli-responsive nanotechnologies for RNA delivery and their potential in RNA medicines. It emphasizes the notable benefits of these technologies in improving the effectiveness of RNA and targeting specific cells and organs. This review offers a comprehensive analysis of different RNA drugs and how they work to produce therapeutic benefits. Recent progress in using RNA-based drugs, especially mRNA treatments, has shown that targeted delivery methods work well in medical treatments.

Serotonergic-dependent effects of exercise and elevated stress hormone on small non-coding RNA transcriptomics and proteomics in a mouse model of affective disorders

Environmental changes may alter gene expression in depression and anxiety disorders through epigenetic regulation, including via small non-coding RNAs (sncRNAs) and their major subclass, microRNAs (miRNAs). However, underlying mechanisms mediating miRNA regulation in response to changing environmental stimuli are unclear. Using the serotonin transporter (5-HTT) knockout (KO) mouse model of depression/anxiety, this study aimed to compare the effects of voluntary exercise (EX) versus chronic treatment with the stress hormone corticosterone (CT), on hippocampal miRNA transcriptome and proteome in five comparison groups: WT-SH vs. KO-SH; WT-SH vs. WT-EX; KO-SH vs. KO-EX; WT-SH vs. WT-CT; KO-SH vs. KO-CT. We hypothesized that treatment with stress hormone will result in miRNA and proteomics changes observed in genetic model of depression, while exercise will have beneficial effects similar to antidepressant treatment. Using high-throughput sequencing of miRNAs and mass spectrometry (MS)-based approaches for protein expression, we revealed 337 differentially expressed (DE) miRNAs and 67 proteins in 5-HTT KO mice compared to wild-type (WT) control mice in standard-housing conditions. After exercise, there were 200 DE miRNAs and 3 DE proteins in WT mice, and 20 DE miRNAs and 95 DE proteins in 5-HTT KO mice, while corticosterone treatment led to 168 DE miRNAs and 1 DE protein in WT, and 21 DE miRNAs and 21 DE proteins in 5-HTT KO mice. Serotonergic dysfunction (due to the 5-HTT KO gene mutation) induced altered expression of miRNAs and proteins involved in regulation of neurodevelopment, neurogenesis and neuroinflammatory responses. Treatment with the stress hormone corticosterone in WT mice activated pathways which were also found altered in 5-HTT KO mice, while exercise caused antidepressant-like effects. These findings suggest that functional 5-HTT might be required for the beneficial effects of exercise on miRNA expression. Our study is the first to explore how gene-environment interactions affect miRNA/proteomic composition in a mouse model of depression/anxiety, and extends our understanding of gene-environmental interactions underlying these affective disorders.

gma-miR828a Negatively Regulates Resistance to Tea Leaf Spot Caused by Lasiodiplodia theobromae Through Targeting the CsMYB28-CsRPP13 Module

Leaf spot caused by the fungus Lasiodiplodia theobromae severely affects the quality and production of tea (Camellia sinensis) in plantations across southwestern China. Currently, no effective control measures are available, and the damage to tea leaves is also exacerbated by a lack of understanding regarding the epidemiology of the disease. Previous studies have suggested that gma-miR828a is differentially expressed during L. theobromae infection and may target and cleave the mRNA of CsMYB28. In this study, we characterised CsMYB28 as encoding a transcription factor (TF) that localises to the nucleus, cell membrane, and cytoplasm. This gene was found to be differentially and spatiotemporally expressed in leaf tissues following L. theobromae infection of leaves of the tea plant. Altered CsMYB28 expression, achieved by transient overexpression or stable genetic transformation of Nicotiana benthamiana, or transient silencing using antisense oligonucleotides (AsODN) in the tea plant, indicated that CsMYB28 contributes to resistance against L. theobromae. Using DNA affinity purification sequencing, yeast one-hybrid, and dual-luciferase assays, we also identified that CsMYB28 bound to the AATTAATT motif of CsRPP13, thereby activating the expression of CsRPP13. Additionally, degradome sequencing, β-glucuronidase (GUS) assays, and RNA ligase-mediated rapid amplification of cDNA ends revealed that miR828a cleaved CsMYB28 mRNA, negatively regulating its expression. The results from transient overexpression and stable transformation studies, combined with AsODN-mediated silencing in the tea plant, suggested that miR828a plays a negative regulatory role in modulating the response of the tea plant to L. theobromae infection. This study demonstrates that the miR828a-CsMYB28-CsRPP13 mediates the response of the tea plant to L. theobromae infection.