DICER1 dysregulation triggers reprogramming of a specific miRNA subset, promotes mesenchymal cell fates and slows TNBC tumorigenic phenotypes.

Abstract Background T cell activation and polarization drive atherosclerosis. Among the mediators underlying T cell polarization, the epigenetic enzyme EZH2 catalyses the repressive mark H3K27me3. In humans, EZH2 is upregulated in T cells in advanced atherosclerosis, whereas its deficiency in T cells in mice limits plaque formation via an anti-inflammatory response. Emerging evidence indicates that EZH2 can also regulate lncRNAs and miRNAs by depositing H3K27me3 at their loci, repressing transcription. Purpose We hypothesize that EZH2 governs lncRNAs and miRNAs expression in T cells in the context of atherogenesis. Methods CD4+ T cells were isolated from spleens of atherosclerosis-prone T cell-specific Ezh2 (Ezh2cd4)-KO mice and WT littermates. Small RNA-seq (SMARTer® smRNA-Seq) and transcriptomic profiling (Prime-seq) were performed. Differential expression was assessed using edgeR. Selected miRNAs were validated by RT-qPCR. Putative miRNA targets were retrieved from miRTarBase (v. 8) and TargetScan, and gene ontology enrichment was performed using Metascape. Results In CD4+ T cells from Ezh2cd4-KO mice, 41 out of 2,950 mature miRNAs were differentially expressed (log2FC > |0.8|, FDR < 0.05), with 27 upregulated and 14 downregulated. Top upregulated miRNAs included miR-125a-5p, miR-130a-3p, miR-744-5p, miR-181a-5p, miR-181b-5p, miR-374b-5p, miR-99b, miR-3085, and miR-7049-3p. RT-qPCR confirmed that expression of miR-125a-5p, miR-181a-5p, miR-181b-5p, and miR-99b-5p were upregulated in Ezh2-deficient murine CD4+ T cells. GO enrichment analysis of downregulated genes revealed enrichment of IL-4, IL-9, IL-10, and TGF-β pathways, suggesting their relevance in T-cell function and differentiation. In human Jurkat T cells, pharmacological EZH2 inhibition using GSK126 or tazemetostat resulted only in the upregulation of miR-125a-5p and miR-99b-5p, confirming the conservation of the mechanisms in humans. Integration of our Prime-seq transcriptomics and smallRNAseq datasets with human and mouse predicted and experimentally validated targets of miR-125a-5p and miR-99b-5p identified six conserved target genes: STAT1, FAM169B, NDRG3, PSMB9, TRIB1, and RAB3IP. Conclusions Our findings indicate that Ezh2 represses miRNA expression in T cells during atherogenesis, thereby possibly promoting differentiation toward pro-atherogenic subsets while restraining anti-atherogenic transcriptional programs. Further research is needed to elucidate the underlying mechanisms. Ezh2-regulated miRNAs may represent promising targets to direct T cell plasticity to combat atherosclerosis.

Acute myeloid leukemia (AML) is caused by uncontrolled proliferation and impaired differentiation of hematopoietic stem and progenitor cells. Historically, research has emphasized the role of protein-coding genes in the development of AML. However, with the human genome project revealing that 98% of the transcriptome consists of non-protein-coding RNAs, recent studies have explored how the large classes of noncoding RNAs (ncRNAs) contribute to AML. Although there are many types of ncRNAs, much attention has been placed on understanding the function of long ncRNAs (lncRNAs) and small ncRNAs known as microRNAs (miRNAs). lncRNAs are >200 nucleotides, whereas mature miRNAs are typically 18 to 25 nucleotides. lncRNAs are involved in miRNA and protein sequestration and act as transcriptional and translational regulators, whereas miRNAs facilitate mRNA degradation and translational inhibition. In addition to lncRNAs and miRNAs, two additional types of ncRNAs, namely small nucleolar RNAs (snoRNAs) and circular RNAs (circRNAs), have recently garnered attention for their roles in AML. Here, we discuss how these four distinct classes of ncRNAs may aid in disease diagnosis and prognosis as well as the mechanisms by which their dysregulation contributes to AML.

BmADARa-mediated RNA editing regulates silk gland development and silk protein expression via miR-3315 targeting BmSuc1 in Bombyx mori.

The majority of pri-miRNAs acquire a 5' cap and 3' poly(A) tail. Mature miRNAs recruit deadenylases that shorten poly(Α) tails triggering target mRNA degradation. Poly(A)-specific ribonuclease (PARN) is a deadenylase that also mediates late steps of noncoding RNA maturation. Herein, we show that PARN affects the expression of a subset of miRNAs in NCI-H520 cells of lung cancer origin, including miR-29a and miR-1207, which are also predicted to target PARN mRNA. PARN associates with pri-miR-29a and pri-miR-1207 regulating their poly(A) lengths. Conversely, miR-29a-3p and miR-1207-5p bind the 3' UTR of PARN mRNA and regulate its expression. Cleavage and polyadenylation specificity factor 6 (CPSF6) recruits PARN to pri-miRNAs and together they affect primary and mature miR-29a-3p levels. Modulation of PARN, miR-29a-3p, or miR-1207-5p expression affects cell migration. We present a model to describe the dynamic relation between PARN and miR-29a and discuss its biological significance.

Initially thought to localize at the cytosol and nucleus only, emerging evidence indicates that miRNAs also localize within mitochondria where they could regulate diverse pathological and physiological processes. Therefore, the aim of the current study was to profile the population of miRNAs in isolated mitochondria and whole-tissue from human skeletal muscle at rest and in response to acute endurance exercise. Twelve healthy males (age 26 ± 4 years, mean ± SD) cycled for 60 min at 70% VO2peak and muscle biopsies were collected at rest, immediately after and 3 h after exercise. The mitochondria were isolated by immunoprecipitation, enzymatically purified, then the resident RNA was sequenced to assess the mitochondrial transcriptome. Small RNA sequencing revealed that mitochondria isolated from male skeletal muscle tissue contain a distinct population of miRNAs. Of the approximately 127 mature miRNAs detected in skeletal muscle mitochondria at each time point, the canonical muscle-specific miRs (myo-miRs) miR-1, miR-133 and miR-206 families constituted on average 45% of total mitochondria miRNA reads. However, none of these canonical myo-miRs were differentially expressed in mitochondria following endurance exercise. One miRNA, hsa-miR-146b-5p, was differentially expressed 3 h after exercise when compared to pre-exercise in both mitochondria (log2 fold-change = 5.4, p = 0.003, FDR = 0.82) and whole muscle tissue (log2 fold-change = 2.3, p < 0.0001, FDR = 0.060) but not when adjusted for multiple testing. Future research is now required to investigate miRNA-mRNA interactions in the mitochondria of skeletal muscle tissue.

Small RNA pathways play key roles in the regulation of gene expression in the germ line and in somatic cells. The germ line in Caenorhabditis elegans has multiple classes of small RNAs that can interact with its 19 Argonaute family proteins, including microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs) and endogenous small interfering RNAs (endo-siRNAs). The pathway for miRNA biogenesis and activity requires stepwise processing before the mature miRNA is bound to an Argonaute protein and can function in a miRNA induced silencing complex (miRISC). To understand whether the small RNA pathway responsible for producing miRNAs is required for optimal male fertility and fecundity, we analyzed male fertility, sperm production, and gonad morphology in mutants with reduced Microprocessor activity and miRNA-associated Argonaute activity. Optimal male fertility requires the Microprocessor genes, drsh-1 and pash-1, as well as multiple miRNA-associated Argonaute genes. Although mutant male sperm display normal in vitro sperm activation, multiple mutants displayed defects in the ability to generate cross progeny upon successful mating. Together, our results support a role for small RNA pathway genes in germline or somatic cells to promote optimal male fertility and fecundity.

Identification of a novel mitovirus in Colocasia esculenta through high‑throughput sequencing and in-silico miRNA prediction for sequence-specific gene silencing.

ABSTRACT Strand separation of the RNA duplex is vital for miRNA maturation, enabling the guide strand to form miRISC. The erythroid miRNA miR-486-5p requires AGO2-mediated catalytic cleavage of its passenger strand, miR-486-3p, but the regulatory factors remain unclear. We identify CSDE1 as a cofactor that facilitates AGO2-dependent removal of the passenger strand and the maturation of miR-486-5p. Loss of CSDE1 increases miR-486-3p levels in leukaemia cells, decreases cleavage efficiency in vitro, and derepresses miR-486-5p targets. Reintroducing the full-length CSDE1 restores AGO2-dependent duplex cleavage in vitro, a function that depends on its N-terminal cold-shock domain (CSD1) for interaction with AGO2. Overall, these findings indicate that CSDE1 contributes to AGO2-mediated miR-486 strand separation, with implications for target gene silencing in leukaemia.

Pluripotent stem cell (PSC) differentiation is orchestrated by intricate autocrine and paracrine signaling networks. Among these, exosomes, key components of the cellular secretome, are implicated as crucial mediators of intercellular communication via delivery of bioactive molecules, including microRNAs (miRNAs). This study investigated the role of exosomal miRNAs in stem cell differentiation using Dgcr8-deficient mouse embryonic stem cells (mESCs), which are incapable of producing mature miRNAs. Although the differentiation capacity was markedly impaired in these cells, partial restoration was observed following treatment with exosomes derived from differentiating wild-type mESCs. Exosomal miRNA uptake was confirmed, and gene ontology analysis revealed significant enrichment of pathways associated with cell fate determination, morphogenesis, and apoptosis regulation. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that exosomal miRNAs modulated multiple osteoinductive signaling cascades, notably the MAPK and TGF-β pathways, in Dgcr8-deficient cells. Apoptotic markers were also downregulated, suggesting a protective effect conferred by the exosomal cargo. Collectively, our results suggest that exosome-mediated delivery of miRNAs may represent a fundamental mechanism by which pluripotent stem cells coordinate stress responses and differentiation trajectories, providing novel insights into the regulation of embryogenesis.

MicroRNAs (miRNAs) are ~ 22-nucleotide-long noncoding RNAs that regulate gene expression at the post-transcriptional level through mRNA cleavage or translational repression. To date, approximately 2,700 mature human miRNAs have been identified, although biological functions have been assigned to fewer than 600. Among these, miR-155 has emerged as a regulatory miRNA with important roles in metabolism, immune homeostasis, and disease pathogenesis. Dysregulated miR-155 expression has been implicated in metabolic disorders, including diabetes and preeclampsia, as well as autoimmune diseases such as rheumatoid arthritis, multiple sclerosis, and systemic lupus erythematosus. Mechanistic and preclinical evidence indicates that aberrant miRNA-155 expression contributes to tumorigenesis by modulating tumor suppressor genes in hematologic malignancies and solid tumors. This review summarizes the current updates on the physiological and pathological roles of miRNA-155.

Plant subspecies that have colonized distinct natural habitats must evolve different phenotypic and physiological features to ensure survival. However, the underlying molecular mechanisms remain poorly understood. In this study, we selected seven Arabidopsis accessions and six rice varieties with significantly different natural habitat parameters to investigate the molecular mechanisms behind the differential expression and activity of microRNAs (miRNAs) at the subspecies level. Compared to Col-0, 24–35 differentially expressed miRNA precursors and 36–110 differentially expressed mature miRNAs were identified in the other six Arabidopsis accessions. Compared to Nipponbare, 19–40 differentially expressed precursors and 8–101 mature miRNAs were identified in the other five rice varieties. The expression patterns of the precursors correlate well with those of the mature miRNAs. Both m6A modification and single nucleotide polymorphisms (SNPs) associated with miRNA genes were closely linked to precursor transcription and miRNA maturation. Degradome sequencing data analysis revealed that the high miRNA level likely caused intense target cleavages in a specific subspecies. In some cases, the affinity of miRNA—target interactions was significantly influenced by SNPs. Notably, many target genes were functionally involved in organ development, reproduction or stress responses. The data presented here provide molecular hints into the different developmental processes and environmental responses among plant subspecies with distinct natural habitats.

SUMOylation of SND1 drives mature miRNA degradation and tumor progression.

Angiosarcoma (AS) is a rare and aggressive tumor arising within the endothelium, characterized by a high metastatic rate and poor prognosis. Our prior work established that endothelial loss of Dicer1, a key enzyme in microRNA (miRNA) processing, drives AS formation in mice, indicating a tumor suppressive role for miRNAs in tumorigenesis. Here, we corroborated this hypothesis by generating a novel conditional knockout model targeting Dgcr8, a core component of the microprocessor complex required for pri-miRNA processing. Conditional deletion of Dgcr8 phenocopies Dicer1 loss, resulting in spontaneous AS formation and global loss of mature miRNAs. We further demonstrate that treatment with enoxacin (ENX), a repurposed antibiotic known to enhance miRNA processing, reduces viability, migration, and clonogenicity of AS cells. ENX increases the abundance of tumor-suppressive miRNAs and downregulates oncogenic pathways, including pathways related to cell cycle progression, angiogenesis, and cell migration. These results establish the essential role of miRNA biogenesis in suppressing AS and reveal a pharmacologically targetable vulnerability via ENX-mediated enhancement of miRNA expression in tumors.

A growing number of mutations are being identified in the noncoding genome, including microRNA (miRNA) genes; however, little is known about the consequences of these mutations and how harmful they are to the functioning of miRNA genes. To evaluate the effects of miRNA gene mutations, we took advantage of a large collection of somatic mutations identified in miRNA genes in >10,000 The Cancer Genome Atlas cancer samples and compared them with the corresponding miRNA sequencing data. Using different analytical approaches and rigorous statistical criteria, we revealed that a substantial fraction of mutations is deleterious for the proper functioning of miRNA genes affecting the level of mature miRNAs, isomiR profiles (precision of DROSHA/DICER1 cleavage), and/or 5p/3p miRNA strand balance. We also showed that most mutations, especially those identified as deleterious, destabilize the structure of miRNA precursors. The analysis showed that many miRNA gene mutations can damage miRNA genes and, if located in disease-related miRNA genes, may be pathogenic variants.

Gestational diabetes mellitus (GDM) develops silently during early pregnancy, yet its earliest circulating molecular signatures remain poorly defined. In this exploratory biomarker study, we characterized first-trimester circulating microRNA (miRNAs) associated with later GDM using a pool-based small RNA sequencing approach. Using a systematic and unbiased sequencing strategy with locus-level miRNA resolution, we profiled the first-trimester plasma miRNome and prioritized a set of 18 mature miRNAs from among 255 detected species. Set-level functional enrichment analyses based on curated and predicted miRNA-target interactions derived primarily from cellular and tissue-based studies showed annotation-based convergence on pathways related to Ca2+ homeostasis, glucagon-insulin regulatory circuits, and PI3K-AKT signaling. Network analysis indicated coordinated associations among these miRNAs and shared target pathways involved in insulin secretion and insulin sensitivity. Key contributors-including miR-29a-3p, miR-29c-3p, miR-146a-5p, let-7a-5p, and miR-182-5p-were linked, through in silico target annotation, to central metabolic regulators such as PTEN, PIK3R1, AKT1, AKT2, and components of Ca2+ signaling (ATP2A2, CALM1/3, ITPR1, RYR2). These circulating miRNAs should be interpreted primarily as biomarkers reflecting coordinated metabolic states rather than as direct causal mediators. Most identified miRNAs have not been previously reported in the context of first-trimester GDM, supporting the exploratory and hypothesis-generating nature of this circulating miRNA signature in early gestational metabolic research.

ABSTRACTMicroRNAs (miRNAs) are pivotal post‑transcriptional regulators whose single‑cell behavior has remained largely inaccessible due to technical barriers in single‐cell small‑RNA profiling. We present SiCmiR, a two‑layer neural network that predicts miRNA expression profiles from only 977 LINCS L1000 landmark genes, thereby reducing sensitivity to dropout in single‐cell RNA‐seq (scRNA‐seq) data. Proof‑of‑concept analyses illustrate how SiCmiR can uncover candidate hub‑miRNAs in bulk‐seq cell lines and hepatocellular carcinoma, scRNA‐seq pancreatic ductal carcinoma, and ACTH‑secreting pituitary adenoma and extracellular vesicle (EV)‑mediated crosstalk in glioblastoma. Trained on 6,462 TCGA paired miRNA–mRNA samples, SiCmiR attains state‑of‑the‑art accuracy on cancers and generalizes to unseen cancer types and drug perturbations. We next construct SiCmiR‑Atlas, containing 362 public datasets, 9.36 million cells, and 726 cell types, which is the first dedicated database of single‑cell mature miRNA expression, providing interactive visualization, biomarker identification, and cell‑type‑resolved miRNA–target networks. SiCmiR transforms bulk‑derived statistical power into a single‑cell view of miRNA biology and provides a community resource for biomarker discovery. SiCmiR Atlas is available at https://awi.cuhk.edu.cn/∼SiCmiR/.

Hepatocellular carcinoma (HCC) poses significant clinical challenges, including high recurrence, mortality, and drug resistance, underscoring the urgent needs for novel targeted therapies. Lin28B, an RNA-binding protein frequently overexpressed in HCC, promotes tumor progression by enhancing oncogenic signaling pathways and inhibiting the maturation of tumor-suppressive let-7 family miRNAs. However, due to the lack of conventional small-molecule binding pockets, Lin28B has long been considered an undruggable target. In this study, a series of pre-let-7-PROTACs were constructed by conjugating pre-let-7 family miRNAs and E3 ligase ligands. Most pre-let-7-PROTACs achieved efficient and specific degradation of Lin28B and restored endogenous mature let-7 expression, thereby suppressing HCC cell proliferation and migration, promoting apoptosis, and enhancing chemosensitivity. In a Huh-7 xenograft tumor model, pre-let-7-PROTACs exhibited significant synergistic antitumor effects when combined with sorafenib (SFB). This study confirmed that pre-let-7-PROTACs reduce tumor stemness by degrading Lin28B, offering a promising therapeutic approach for HCC.

HASTY-dependent miRNA cell-to-cell movement is required for systemic pathogen resistance in Arabidopsis.

While METTL1 is a well-established m7G writer protein, its protein–protein interaction network remains largely unexplored. To map the METTL1 interactome in HEK293T cells, we employed APEX2-mediated proximity labeling coupled with LC-MS/MS analysis. This approach allowed for the identification of 60 and 18 unique proteins significantly enriched in the METTL1 proximity proteome compared to enhanced green fluorescent protein (EGFP) and nuclear localization signal (NLS) controls, respectively. Among these proteins, we found exportin-5 (XPO5), a nuclear export factor critical for pre-miRNA transport. We validated the METTL1–XPO5 interaction by co-immunoprecipitation and western blot analysis. Strikingly, genetic ablation of METTL1 caused XPO5 to redistribute to the cytosol, which in turn accelerated pre-miRNA export and enhanced miRNA maturation. This function of METTL1 was independent of its canonical m7G methyltransferase activity. Mechanistically, we found that METTL1 facilitates ERK-mediated phosphorylation of XPO5, thereby promoting its nuclear retention. Accordingly, constitutive activation of ERK was sufficient to restore nuclear XPO5 localization in METTL1-deficient cells. In summary, our study uncovers a non-canonical role for METTL1 in regulating the subcellular distribution of XPO5 and pre-miRNA export, revealing a novel mechanism of miRNA maturation that extends METTL1’s function beyond m7G methylation.