Predicting effective microRNA target sites in mammalian mRNAs

Comprehensive analysis of circRNAs and lncRNAs involvement in the development of skeletal muscle in myostatin-deficient rabbits

Myostatin (MSTN) protein, lncRNAs, and circRNAs regulate skeletal muscle growth and development. This work aims to compare the expression patterns of circRNAs and lncRNAs in the gluteus maximus tissue of wild-type (WT) and MSTN gene knockout (KO) rabbits. Within the gluteus maximus tissue of three WT and four MSTN KO rabbits, we analyzed the expression profiles of circRNAs and lncRNAs. After identifying the differently expressed RNAs, the biological pathways implicated were ascertained by performing enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). We identified differences in the expression of 251 circRNAs (79 upregulated and 172 downregulated), 176 lncRNAs (53 upregulated and 123 downregulated), and 1178 mRNAs (408 upregulated and 770 downregulated) between WT and MSTN KO rabbits. Target genes were significantly enriched in pathways associated with protein synthesis and catabolism, such as oxidative phosphorylation, ubiquitin-mediated proteolysis, the FoxO signaling pathway, and the pentose phosphate pathway, as identified through GO and KEGG enrichment analyses. The constructed network indicates that a class of circRNAs and lncRNAs is engaged in MSTN-mediated regulation of skeletal muscle development. These findings provide valuable insights for innovative therapeutic, diagnostic, and preventive approaches to muscle disorders.

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

BACKGROUND & AIMS

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

APPROACHES AND RESULTS

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

CONCLUSIONS

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

Isoliquiritigenin reduces brain metastasis by circNAV3-ST6GALNAC5-EGFR axis in triple-negative breast cancer

Brain metastasis (BM) is a serious complication of increasing incidence in patients with advanced breast cancer, which is characterized by swift deterioration in quality of life with few efficient therapy strategies. There is an urgent clinical requirement to devise potent therapeutic strategies for the prevention and management of brain metastases. Here, we report isoliquiritigenin (ISL), a key bioactive substance extracted from licorice root, which effectively inhibited triple-negative breast cancer (TNBC) brain metastasis (BM) by downregulation of circNAV3. CircRNAs expression analyses and functional studies, coupled with clinical significance investigations identified circNAV3 as a key molecule promoting TNBC BM. Functionally, circNAV3 could promote proliferation, migration, invasion, angiogenesis and capacity to penetrate the blood-brain barrier of TNBC cells. Mechanistically, circNAV3 could competitively bind with miR-4262, hence intercepting the suppressive effect of miR-4262 on ST6GALNAC5. Subsequently, this interplay enhanced EGFR sialylation and activation, initiating the PI3K/Akt pathway and ultimately fostering the development of TNBC brain metastases. In conclusion, our research establishes that ISL impede the initiation and advancement of TNBC brain metastasis by modulation of circNAV3/miR-4262/ST6GALNAC5/EGFR axis, laying a theoretical groundwork for the therapeutic use of ISL in this scenario.

Brain microRNAs differentially expressed in age-related cerebral pathologies

Multiple brain pathologies accumulate with age, but their underlying biology remains unclear. We investigated the role of microRNAs (miRNAs) in ten age-related cerebral pathologies. Using miRNA sequencing profiles from the dorsolateral prefrontal cortex of 617 brain donors, we identified miRNAs associated with Alzheimer's disease (AD) pathology, Lewy body pathology, arteriolosclerosis, cerebral amyloid angiopathy, and LATE-NC after adjusting for age, sex, and education. After additionally adjusting for co-existing cerebral pathologies, we found miRNAs specifically associated with AD pathology (n = 75), Lewy body pathology (n = 45), arteriolosclerosis (n = 3), cerebral amyloid angiopathy (n = 1), and LATE-NC (n = 4). While some miRNAs were pathology-specific, 14 miRNAs (including those in the miR-132/212 cluster) were associated with both AD pathology and Lewy body pathology, and one (miR-193a-5p) was associated with both AD pathology and cerebral amyloid angiopathy. Gene set enrichment analysis showed that miRNAs associated with arteriolosclerosis target genes involved in glutathione metabolism, synaptic functions, cellular transport, and innate immune response. These findings highlight the role of miRNAs in age-related cerebral pathologies and provide a foundation for future mechanistic studies.

Epigenetic mechanism of iPSC-MSC-EVs in colonic epithelial cell pyroptosis in ulcerative colitis cell models via modulation of ELF3/miR-342-3p/KDM6B axis and histone methylation

Ulcerative colitis (UC) is a chronic inflammatory bowel disease in the colon and rectum. Mesenchymal stem cell-derived extracellular vesicles (MSCs-EVs) have emerged as promising cell-free therapeutics for UC, leveraging their immunomodulatory and tissue-protective properties. However, the specific epigenetic mechanisms by which EVs regulate pyroptosis (an inflammatory cell death pathway) remain poorly understood. This study explores how EVs derived from induced pluripotent stem cell-derived mesenchymal stem cells (iPSC-MSCs) regulate pyroptosis in colonic epithelial cells of UC by targeting the histone-modifying protein KDM6B, aiming to provide new therapeutic insights for UC. iPSCs were differentiated into MSCs, and their EVs were isolated and characterized. EVs were engineered to carry the circular RNA circ-CCND1 and co-cultured with UC model cells induced by DSS. Cell viability, inflammatory cytokine levels, and key molecular markers related to pyroptosis (NLRP3, cleaved Caspase-1, GSDMD-N) were measured. The molecular mechanism was dissected using RNA-protein binding assays and gene expression analysis, focusing on the circ-CCND1/KDM6B/ELF3/miR-342-3p signaling axis. EV treatment reduced pyroptosis in UC model cells, with enhanced efficacy when EVs carried circ-CCND1. Mechanistically, circ-CCND1 in EVs entered cells and bound to KDM6B, inhibiting its activation of the ELF3 gene, leading to increased miR-342-3p, which in turn suppressed KDM6B expression, forming a feedback loop that dampened pyroptosis. In conclusions, iPSC-MSC-derived EVs inhibit inflammatory cell death in colonic epithelial cells by regulating histone modification-related pathways, highlighting their potential as a novel therapeutic strategy for UC.

miRNAs in oral cancer; diagnostic and prognostic roles

Oral cancer (OC) has become increasingly prevalent in recent years, making it one of the most often occurring types of cancer in patients. The clinical identification of OC is usually a time-consuming procedure, and the outlook for individuals with OC is generally unfavorable, as no particular biomarkers have been established to far. The main risk factors linked to OC are high levels of tobacco and alcohol intake, together with a reduced occurrence of viral infections, such as human papillomavirus. Furthermore, there is evidence suggesting that genetic characteristics that can be passed down from parents to offspring play a role in increasing the likelihood of getting ovarian cancer. MicroRNAs (miRNAs) are brief RNA molecules that do not code for proteins and have the ability to either repress or promote the growth of tumors during cancer development. They have been discovered to control multiple signaling pathways within cells, and their abnormal regulation has been demonstrated to be crucial in initiating and furthering the development of cancer. Additionally, they have the ability to either facilitate or impede the entire multi-stage process of cancer metastasis, including epithelial-mesenchymal transition (EMT), migration, and invasion, by selectively targeting essential genes involved in these pathways. Several microRNAs have the ability to regulate gene expression through various ways. In addition, like other types of cancer, OC has shown alterations in the expression of miRNAs, and certain miRNAs may have the ability to be used for diagnosis and treatment. The investigation of these miRNA could perhaps result in advancements in the specified instances of OC.

Micro-RNAs targeting the estrogen receptor alpha involved in endocrine therapy resistance in breast cancer

Endocrine therapy resistance (ETR) in breast cancer (BC) is a multicausal phenomenon with diverse alterations in the tumor cell interactome. Within these alterations, non-coding RNAs (ncRNAs) such as micro-RNAs (miRNAs) modulate the expression of tumor suppressor genes and proto-oncogenes, such as the ESR1 gene encoding estrogen receptor alpha (ERα). This work aims to review the effects of miRNAs targeting ERα mRNA and their mechanisms related to ETR in BC. A thorough review of the literature and an in silico study were carried out to elucidate the involvement of each miRNA, thus contributing to the understanding of ETR in BC.

Serum exosomal hsa-miR-142-5p, hsa-miR-1908-5p, and hsa-miR-450b-5p as candidate biomarkers for recurrent depressive disorder diagnosis and ECT treatment response: A preliminary investigation

PURPOSE

This study investigated the differential expression of serum exosomal miRNAs in female patients with recurrent depressive disorder (RDD) before and after non-convulsive electroconvulsive therapy (ECT), aiming to explore potential diagnostic and therapeutic biomarkers.

METHOD

Serum samples were collected from three groups: healthy female volunteers aged 30-50, female patients with RDD prior to ECT, and female patients post-ECT who had achieved remission. Exosomes were isolated from serum, identified through transmission electron microscopy, nanoparticle tracking analysis, and Western blot analysis of exosomal markers. Total RNA was extracted from exosomes, and miRNA sequencing was conducted to identify differentially expressed miRNAs. Gene target prediction, Gene Ontology, and KEGG pathway enrichment analyses were also performed.

RESULTS

miRNA sequencing revealed significant differences in exosomal miRNA profiles among the three groups. Compared to controls, 69 miRNAs were upregulated and 98 downregulated in the model group, while the recovery group showed 41 upregulated and 51 downregulated miRNAs compared to the model group. Furthermore, the recovery group exhibited 35 upregulated and 59 downregulated miRNAs compared to controls. Analysis identified hsa-miR-142-5p, hsa-miR-1908-5p, and hsa-miR-450b-5p as potential biomarkers for RDD diagnosis and ECT treatment response, with functional roles likely related to inflammation, neurotransmission, and synaptic plasticity.

CONCLUSION

Serum exosomal miRNAs, particularly hsa-miR-142-5p, hsa-miR-1908-5p, and hsa-miR-450b-5p, emerged as promising candidates for further investigation as biomarkers for RDD diagnosis and treatment monitoring. Larger, multi-center studies are warranted to validate these findings.

Current updates regarding biogenesis, functions and dysregulation of microRNAs in cancer: Innovative approaches for detection using CRISPR/Cas13‑based platforms (Review)

MicroRNAs (miRNAs) are short non‑coding RNAs, which perform a key role in cellular differentiation and development. Most human diseases, particularly cancer, are linked to miRNA functional dysregulation implicated in the expression of tumor‑suppressive or oncogenic targets. Cancer hallmarks such as continued proliferative signaling, dodging growth suppressors, invasion and metastasis, triggering angiogenesis, and avoiding cell death have all been demonstrated to be affected by dysregulated miRNAs. Thus, for the treatment of different cancer types, the detection and quantification of this type of RNA is significant. The classical and current methods of RNA detection, including northern blotting, reverse transcription‑quantitative PCR, rolling circle amplification and next‑generation sequencing, may be effective but differ in efficiency and accuracy. Furthermore, these approaches are expensive, and require special instrumentation and expertise. Thus, researchers are constantly looking for more innovative approaches for miRNA detection, which can be advantageous in all aspects. In this regard, an RNA manipulation tool known as the CRISPR and CRISPR‑associated sequence 13 (CRISPR/Cas13) system has been found to be more advantageous in miRNA detection. The Cas13‑based miRNA detection approach is cost effective and requires no special instrumentation or expertise. However, more research and validation are required to confirm the growing body of CRISPR/Cas13‑based research that has identified miRNAs as possible cancer biomarkers for diagnosis and prognosis, and as targets for treatment. In the present review, current updates regarding miRNA biogenesis, structural and functional aspects, and miRNA dysregulation during cancer are described. In addition, novel approaches using the CRISPR/Cas13 system as a next‑generation tool for miRNA detection are discussed. Furthermore, challenges and prospects of CRISPR/Cas13‑based miRNA detection approaches are described.

METTL14-mediated m6A methylation of pri-miR-5099 to facilitate cardiomyocyte pyroptosis in myocardial infarction

N6-methyladenosine (m6A) modification is an important mechanism in microRNA processing and maturation. Previous studies show the involvement of pri-miRNA methylation in regulating the occurrence and development of tumor-related diseases. In this study, we investigated the role of its aberrant regulation in cardiac diseases. Myocardial infarction (MI) mouse were established by ligation of the left anterior descending branch of the coronary artery. We showed that the expression of methyltransferase 14 (METTL14) was significantly increased in myocardium of MI mice. We demonstrated that METTL14 methylated the primary transcript miRNA (pri-miR-5099), promoting the recognition by DiGeorge critical region 8 (DGCR8) and the maturation processing of pri-miR-5099. Mature microRNA-5099-3p (miR-5099-3p) inhibited the expression of E74 like ETS transcription factor 1 (ELF1), which transcriptionally regulated pyroptosis factors such as acysteinyl aspartate-specific proteinase 1 (caspase-1) and gasdermin D (GSDMD), ultimately leading to cardiomyocyte pyroptosis. This study reveals that myocardial infarction-induced miR-5099-3p excessive maturation via m6A modification promotes the development and progression of cardiomyocyte pyroptosis.

Sequential macrophage DENV and ZIKV infection shows differential expression of CD86, IFN-β, and regulation of TNF-α and IL-1β depending on DENV serotype

Dengue virus (DENV) is an RNA virus belonging to the Flaviviridae family, comprising four antigenically distinct serotypes. Dengue is the primary arthropod-transmitted virus globally, posing a significant public health challenge, especially in Brazil, where the largest outbreak of Zika virus (ZIKV) was also recorded in 2016. ZIKV shares genomic and structural similarities with DENV, and their co-circulation in Brazil provides evidence of co-infection. The innate immune response against DENV and ZIKV is mediated by pattern recognition receptors that initiate intracellular signaling, leading to antiviral or inflammatory responses. This study aims to better understand the innate immune response to ZIKV in macrophages previously infected with DENV. To achieve this, bone marrow cells from C57BL/6 mice were differentiated into macrophages (BMDMs) and independently infected with each of the four DENV serotypes for 12 h, followed by ZIKV infection for an additional 12 h. Twenty-four hours post-infection, macrophage activation markers CD86 were assessed using flow cytometry and fluorescence microscopy. Pro-inflammatory and antiviral gene expressions were evaluated by qPCR. IFN-β was found to be down-regulated in all analyzed groups. No differences in CD86 expression were observed in ZIKV-infected BMDMs previously infected with DENV, except for serotype 4, which showed an increase in both activation markers. Conversely, TNF-α and IL-1β were down-regulated compared to non-infected or only DENV4-infected cells, correlating with increased cell viability and decreased production of the cytokine TNF-α. Bioinformatic analysis suggested that the expression of both cytokines might be regulated by miRNAs, including miR-181a-5p, which is also up-regulated in the innate immune response. Taken together, the results indicated that co-infection with DENV serotype 4 and ZIKV in mice BMDMs increases the expression of CD86, promoting macrophage activation, but reduces the expression of pro-inflammatory genes TNF-α and IL-1β, indicating enhanced cell viability what can be modulated by miRNAs.

Integrating Bulk RNA and Single-Cell Sequencing Data Unveils Efferocytosis Patterns and ceRNA Network in Ischemic Stroke

Excessive inflammatory response following ischemic stroke (IS) injury is a key factor affecting the functional recovery of patients. The efferocytic clearance of apoptotic cells within ischemic brain tissue is a critical mechanism for mitigating inflammation, presenting a promising avenue for the treatment of ischemic stroke. However, the cellular and molecular mechanisms underlying efferocytosis in the brain after IS and its impact on brain injury and recovery are poorly understood. This study explored the roles of inflammation and efferocytosis in IS with bioinformatics. Three Gene Expression Omnibus Series (GSE) (GSE137482-3 m, GSE137482-18 m, and GSE30655) were obtained from NCBI (National Center for Biotechnology Information) and GEO (Gene Expression Omnibus). Differentially expressed genes (DEGs) were processed for GSEA (Gene Set Enrichment Analysis), GO (Gene Ontology Functional Enrichment Analysis), and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses. Efferocytosis-related genes were identified from the existing literature, following which the relationship between Differentially Expressed Genes (DEGs) and efferocytosis-related genes was examined. The single-cell dataset GSE174574 was employed to investigate the distinct expression profiles of efferocytosis-related genes. The identified hub genes were verified using the dataset of human brain and peripheral blood sample datasets GSE56267 and GSE122709. The dataset GSE215212 was used to predict competing endogenous RNA (ceRNA) network, and GSE231431 was applied to verify the expression of differential miRNAs. At last, the middle cerebral artery (MCAO) model was established to validate the efferocytosis process and the expression of hub genes. DEGs in two datasets were significantly enriched in pathways involved in inflammatory response and immunoregulation. Based on the least absolute shrinkage and selection operator (LASSO) analyses, we identified hub efferocytosis-related genes (Abca1, C1qc, Ptx3, Irf5, and Pros1) and key transcription factors (Stat5). The scRNA-seq analysis showed that these hub genes were mainly expressed in microglia and macrophages which are the main cells with efferocytosis function in the brain. We then identified miR-125b-5p as a therapeutic target of IS based on the ceRNA network. Finally, we validated the phagocytosis and clearance of dead cells by efferocytosis and the expression of hub gene Abca1 in MCAO mice models.

An antisense oligonucleotide-based strategy to ameliorate cognitive dysfunction in the 22q11.2 Deletion Syndrome

Adults and children with the 22q11.2 Deletion Syndrome demonstrate cognitive, social, and emotional impairments and high risk for schizophrenia. Work in mouse model of the 22q11.2 deletion provided compelling evidence for abnormal expression and processing of microRNAs. A major transcriptional effect of the microRNA dysregulation is upregulation of Emc10, a component of the ER membrane complex, which promotes membrane insertion of a subset of polytopic and tail-anchored membrane proteins. We previously uncovered a key contribution of EMC10 in mediating the behavioral phenotypes observed in 22q11.2 deletion mouse models. Here, we show that expression and processing of miRNAs is abnormal and EMC10 expression is elevated in neurons derived from 22q11.2 deletion carriers. Reduction of EMC10 levels restores defects in neurite outgrowth and calcium signaling in patient neurons. Furthermore, antisense oligonucleotide administration and normalization of Emc10 in the adult mouse brain not only alleviates cognitive deficits in social and spatial memory but remarkably sustains these improvements for over 2 months post-injection, indicating its therapeutic potential. Broadly, our study integrates findings from both animal models and human neurons to elucidate the translational potential of modulating EMC10 levels and downstream targets as a specific venue to ameliorate disease progression in 22q11.2 Deletion Syndrome.

Utilizing RNA-seq data in monotone iterative generalized linear model to elevate prior knowledge quality of the circRNA-miRNA-mRNA regulatory axis

BACKGROUND

Current experimental data on RNA interactions remain limited, particularly for non-coding RNAs, many of which have only recently been discovered and operate within complex regulatory networks. Researchers often rely on in-silico interaction detection algorithms, such as TargetScan, which are based on biochemical sequence alignment. However, these algorithms have limited performance. RNA-seq expression data can provide valuable insights into regulatory networks, especially for understudied interactions such as circRNA-miRNA-mRNA. By integrating RNA-seq data with prior interaction networks obtained experimentally or through in-silico predictions, researchers can discover novel interactions, validate existing ones, and improve interaction prediction accuracy.

RESULTS

This paper introduces Pi-GMIFS, an extension of the generalized monotone incremental forward stagewise (GMIFS) regression algorithm that incorporates prior knowledge. The algorithm first estimates prior response values through a prior-only regression, interpolates between these prior values and the original data, and then applies the GMIFS method. Our experimental results on circRNA-miRNA-mRNA regulatory interaction networks demonstrate that Pi-GMIFS consistently enhances precision and recall in RNA interaction prediction by leveraging implicit information from bulk RNA-seq expression data, outperforming the initial prior knowledge.

CONCLUSION

Pi-GMIFS is a robust algorithm for inferring acyclic interaction networks when the variable ordering is known. Its effectiveness was confirmed through extensive experimental validation. We proved that RNA-seq data of a representative size help infer previously unknown interactions available in TarBase v9 and improve the quality of circRNA disease annotation.

Cellular hierarchies of embryonal tumors with multilayered rosettes are shaped by oncogenic microRNAs and receptor-ligand interactions

Embryonal tumor with multilayered rosettes (ETMR) is a pediatric brain tumor with dismal prognosis. Characteristic alterations of the chromosome 19 microRNA cluster (C19MC) are observed in most ETMR; however, the ramifications of C19MC activation and the complex cellular architecture of ETMR remain understudied. Here we analyze 11 ETMR samples from patients using single-cell transcriptomics and multiplexed spatial imaging. We reveal a spatially distinct cellular hierarchy that spans highly proliferative neural stem-like cells and more differentiated neuron-like cells. C19MC is predominantly expressed in stem-like cells and controls a transcriptional network governing stemness and lineage commitment, as resolved by genome-wide analysis of microRNA-mRNA binding. Systematic analysis of receptor-ligand interactions between malignant cell types reveals fibroblast growth factor receptor and Notch signaling as oncogenic pathways that can be successfully targeted in preclinical models and in one patient with ETMR. Our study provides fundamental insights into ETMR pathobiology and a powerful rationale for more effective targeted therapies.

Hsa_circ_0006837 suppresses gastric cancer cell proliferation, migration, and invasion via the modulation of miR-424-5p

BACKGROUND

The mechanism by which circRERE (hsa_circ_0006837) modulates the malignant progression of gastric cancer was investigated to identify a novel biomarker and therapeutic target for this disease.

METHODS

Hsa_circ_0006837 expression in GC tissues and cells was detected by RT-qPCR. Several data analysis methods were used to evaluate the significance of dysregulated hsa_circ_0006837 in GC. The patients were followed up for five years, and survival analysis was conducted using Kaplan-Meier curves. Cox regression was subsequently performed to analyze the risk factors for prognosis. The malignant behaviors of the cells were detected by the CCK-8 and Transwell assays. The relationship between hsa_circ_0006837 and miR-424-5p was assessed by conducting Spearman correlation analysis and verified by dual-luciferase reporter assay.

RESULTS

Hsa_circ_0006837 expression decreased in patients with GC, indicating a poorer patient prognosis. In GC cells, hsa_circ_0006837 overexpression suppressed malignant behaviors. Mechanistically, miR-424-5p was identified as a target of hsa_circ_0006837. The overexpression of miR-424-5p partially counteracted the suppressive effects of upregulated hsa_circ_0006837 on the malignant behaviors of GC cells. FBXO21 was identified as a downstream gene of the hsa_circ_0006837/miR-424-5p axis.

CONCLUSIONS

To summarize, hsa_circ_0006837 is a biomarker for the prognosis of GC. Mechanistically, hsa_circ_0006837 overexpression can modulate the malignant behaviors of GC cells through miR-424-5p.

MicroRNA mechanisms instructing Purkinje cell specification

MicroRNAs (miRNAs) are critical for brain development; however, if, when, and how miRNAs drive neuronal subtype specification remains poorly understood. To address this, we engineered technologies with vastly improved spatiotemporal resolution that allow the dissection of cell-type-specific miRNA-target networks. Fast and reversible miRNA loss of function showed that miRNAs are necessary for Purkinje cell (PC) differentiation, which previously appeared to be miRNA independent, and identified distinct critical miRNA windows for dendritogenesis and climbing fiber synaptogenesis, structural features defining PC identity. Using new mouse models that enable miRNA-target network mapping in rare cell types, we uncovered PC-specific post-transcriptional programs. Manipulation of these programs revealed that the PC-enriched miR-206 and targets Shank3, Prag1, En2, and Vash1, which are uniquely repressed in PCs, are critical regulators of PC-specific dendritogenesis and synaptogenesis, with miR-206 knockdown and target overexpression partially phenocopying miRNA loss of function. Our results suggest that gene expression regulation by miRNAs, beyond transcription, is critical for neuronal subtype specification.

miRNA-200a suppresses GNAI1 and PLCB4 to modulate skin pigmentation in cashmere goats

Coat colour formation in mammals is influenced by melanogenesis and pigmentation processes regulated by miRNAs, including miRNA-200a. Although miRNA-200a is differentially expressed in the skin of cashmere goats with varying coat colours, its regulatory mechanism remains unclear. In this study, miRNA-200a target genes were predicted using miRBase and TargetScan, identifying GNAI1 and PLCB4 as the target genes through GO and KEGG analyses. Dual-luciferase assays using wild-type and mutant plasmids confirmed a direct interaction between miRNA-200a and the 3'UTR regions of these genes. RT-qPCR and Western blot analyses demonstrated that the expression levels of miRNA-200a and its target genes differed significantly between black and white goat skin. In HaCaT cells, transfection with miRNA-200a mimics or inhibitors altered GNAI1 and PLCB4 expression at both mRNA and protein levels. To validate these findings in vivo, subcutaneous injection of antagomiR-200a into BALB/c mice significantly reduced melanin content (P < 0.01) and increased the expression of GNAI1 and PLCB4. These results indicate that miRNA-200a modulates skin pigmentation by suppressing GNAI1 and PLCB4, thereby influencing coat colour in cashmere goats. This study provides a foundational understanding for leveraging genetic regulation to enhance coat colour diversity and develop naturally pigmented breeds.

Single-Cell Transcriptomic Profiling Reveals Regional Differences in the Prefrontal and Entorhinal Cortex of Alzheimer's Disease Brain

Previous studies have largely overlooked cellular differential alterations across differentially affected brain regions in both disease mechanisms and therapeutic development of Alzheimer's disease (AD). This study aimed to compare the differential cellular and transcriptional changes in the prefrontal cortex (PFC) and entorhinal cortex (EC) of AD patients through an integrated single-cell transcriptomic analysis. We integrated three single-cell RNA sequencing (scRNA-seq) datasets comprising PFC and EC samples from AD patients and age-matched healthy controls. A total of 124,658 nuclei and 31 cell clusters were obtained and classified into eight major cell types, with EC exhibiting much more pronounced transcriptional alterations than PFC. Through network analysis, we pinpointed hub regulatory genes that form interconnected networks driving AD pathogenesis, findings validated by RT-qPCR showing more pronounced expression changes in EC versus PFC of AD mice. Moreover, dysregulation of the LINC01099-associated regulatory networks in the PFC and EC, showing correlation with AD progression, may present new therapeutic targets for AD. Together, these results suggest that effective AD biomarkers and therapeutic strategies may require simultaneous, precise targeting of specific cell populations across multiple brain regions.

TarP: A microRNA target gene prediction tool utilizing a polymorphic structured alignment approach

MicroRNAs (miRNAs) represent a vital class of small non-coding RNAs that play key regulatory roles in gene expression. Accurate identification of miRNA-mRNA interactions is essential for understanding their biological functions. However, current computational prediction tools suffer from several limitations, including species-specific biases, suboptimal accuracy, high false discovery rates, and incomplete target gene coverage. To address these challenges, we present TarP, a novel miRNA target prediction algorithm employing a Polymorphic structured alignment (PMS) approach. Our method mimics the natural binding process between miRNAs and their target mRNAs by integrating key biological interaction features. The algorithm utilizes five distinct nucleotide-binding motifs to perform a structured decomposition and alignment of potential mRNA targets. Predictions are then rigorously evaluated through a dual scoring system: a Structure (St) coefficient assessing binding conformation and an Energy (En) coefficient evaluating thermodynamic stability, ensuring high-confidence target selection. Using experimentally validated human miRNA-mRNA interaction datasets, we benchmarked TarP against four widely used prediction tools (miRanda, RNAhybrid, PITA, and TargetScan). Comparative analyses demonstrate that TarP achieves superior performance in both sensitivity and specificity, exhibiting enhanced accuracy in positive target identification and improved discrimination between true and false interactions. The TarP algorithm is freely available at: https://github.com/Whimonk/TarP.

Repression of AGO1 by AGO2 via let-7 microRNAs facilitates embryonic stem cell differentiation

Argonaute (AGO) proteins are critical regulators of gene expression. Of the four AGOs in mammals, AGO1 and AGO2 are expressed in mouse embryonic stem cells (mESCs). These two proteins have opposing functions in controlling mESCs' fate decisions between pluripotency and differentiation. AGO2 promotes differentiation predominantly via the let-7 microRNAs, whereas AGO1 maintains pluripotency via modulating protein folding independent of small RNAs. These recent findings raise the question of whether and how these two AGOs are mutually regulated in mESCs. Here, using loss-of-function and gain-of-function approaches, we show that AGO2 represses the expression of AGO1 mRNA via a conserved let-7-microRNA-binding site in its 3' UTR. Mutating this binding site at the endogenous locus abolishes the AGO2-mediated repression of AGO1 mRNA and compromises the exit pluripotency of mESCs. These results indicate that the posttranscriptional regulation of AGO1 by AGO2 and let-7 microRNAs is important for stem cell differentiation, but also reveal a regulatory mechanism between the two AGO paralogs with opposing functions in controlling stem cell fate decisions.

Arg-Gly-Asp engineered mesenchymal stem cells as targeted nanotherapeutics against kidney fibrosis by modulating m6A

Background The recent surge in research on extracellular vesicles has generated considerable interest in their clinical applications. Extracellular vesicles derived from mesenchymal stem cells (MSC-EV) have emerged as a promising cell-free therapy for chronic kidney disease (CKD), offering an alternative to traditional Mesenchymal stem/stromal cells (MSCs) in extracellular vesicle-based nanotherapeutics. However, challenges such as in vivo off-target effects and limited bioavailability have impeded the wider adoption of MSC-EV in clinical settings. Methods Arginyl-glycyl-aspartic acid peptide-modified MSC-EV (RGD-MSC-EV) were developed using a donor cell-assisted membrane modification strategy. The targeting capability and therapeutic efficacy of RGD-MSC-EV were thoroughly evaluated both in vitro and in vivo. Additionally, the mechanisms of RNA N6-methyladenosine (m6A) methylation-mediated angiogenesis were extensively investigated to elucidate how RGD-MSC-EV mitigates renal fibrosis. Results RGD-MSC-EV demonstrated exceptional targeted delivery efficiency, exhibiting optimal biodistribution and retention within the target tissue. This breakthrough positions them as significantly enhanced anti-fibrotic therapeutics. Notably, RGD-MSC-EV sustains the viability of renal peritubular capillary (PTCs) endothelial cells by transporting microRNA-126-5p (miR-126-5p) and modulating alkB homolog 5 (ALKBH5)-mediated m6A modification of SIRT1(Sirtuin 1), a crucial regulator in angiogenesis. By revitalizing endothelial cells and promoting microcirculation, this approach restored oxygen metabolism homeostasis, ultimately delaying fibrogenesis associated with CKD. Conclusions RGD-MSC-EV offers a feasible and effective strategy to alleviate renal interstitial fibrosis by restoring m6A and mitigating the loss of renal PTCs. STATEMENT OF SIGNIFICANCE: Chronic kidney disease (CKD) often leads to renal fibrosis, which worsens disease progression. This study introduces a novel strategy using engineered extracellular vesicles (EVs) derived from mesenchymal stem cells (MSC-EV). By modifying these EVs with RGD peptides, we significantly enhance their targeting ability to hypoxic kidney tissues. The research reveals how these EVs deliver microRNA (miR-126-5p) to restore key molecular mechanisms, stabilizing SIRT1 expression through m6A RNA modifications. This approach promotes blood vessel health and delays fibrosis. Compared to current treatments, RGD-MSC-EV offers a safe, effective, and cell-free therapeutic alternative. These findings advance the understanding of EV-based therapies and their clinical potential, bridging basic research and real-world CKD treatment applications.

CiR-EIS alleviates metabolic dysfunction-associated steatohepatitis by modulating macrophage polarization involving the miR-548m/IGF1 axis

BACKGROUND & AIMS

Metabolic dysfunction-associated steatohepatitis (MASH) is a significant public health concern, with macrophage phenotypes implicated in its progression. Although extensive inflammation-suppressing circular RNA (ciR-EIS, formerly named as hsa_circ_0008882) has been implicated in inflammation regulation, its role in macrophage polarization within the context of MASH remains unexplored. This study aimed to clarify the effect of ciR-EIS on macrophage polarization in MASH.

METHODS

Immunofluorescence-fluorescence in situ hybridization was used to evaluate the localization of ciR-EIS in human liver sections. THP-1-derived macrophages (TDMs) were utilized to study ciR-EIS functions in vitro. Flow cytometry and RT-qPCR were employed to evaluate macrophage polarization after transfection. Bodipy assay was used to measure lipid buildup in HepG2 cells. Immunohistochemistry was used to confirm liver insulin-like growth factor 1 (IGF1) expression. Retrospective clinical records were analyzed to examine the association between cir-EIS, IGF1, and MASH.

RESULTS

CiR-EIS was downregulated in patients with MASH and colocalized with the macrophage marker CD68. CiR-EIS and mitochondrially encoded NADH dehydrogenase 5 (MT-ND5) were downregulated in M1 macrophages and upregulated in M2 macrophages. TDM-derived supernatants overexpressed ciR-EIS, significantly reducing HepG2 lipid deposition and inhibiting LX2 proliferation. Overexpression of ciR-EIS in TDMs significantly inhibited M1 macrophage markers CD86, interleukin-1 beta, and tumor necrosis factor-alpha while enhancing M2 macrophage markers CD163 and CD206. CiR-EIS regulated macrophage polarization in a manner involving the miR-548m/IGF1 axis. Serum IGF1 levels were positively correlated with ciR-EIS, and both of them were notably reduced in patients with MASH and inversely correlated with APRI and FIB-4 scores.

CONCLUSIONS

CiR-EIS regulates macrophage polarization in a manner involving the miR-548/IGF1 axis, thereby reducing hepatocyte lipid accumulation and stellate cell proliferation in MASH. It demonstrates potential as a diagnostic marker and therapeutic target for MASH.

Identification of dysregulated competitive endogenous RNA network driven by copy number variation in colon adenocarcinoma

Competitive endogenous RNA (ceRNA) network modulation plays a crucial role in pathogenesis of colon adenocarcinoma (COAD). This study analyzed The Cancer Genome Atlas(TCGA) data to identify 151 copy number variation (CNV)-driven lncRNAs in COAD, constructing a ceRNA network (6 lncRNAs-14 miRNAs-68 mRNAs). Functional enrichment revealed their roles in muscle system processes , blood vessel development and extracellular matrix organization. Survival analysis linked LINC00941 amplification to poor prognosis. Two CNV-driven lncRNA-targeting drugs were identified, offering insights into COAD mechanisms and potential biomarkers.

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

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

Integrating gonadal RNA-seq and small RNA-seq to analyze mRNA and miRNA changes in medaka sex differentiation

MicroRNAs are important post-transcriptional regulators, yet the molecular crosstalk between miRNAs and their target genes during sex differentiation remains poorly understood. Medaka (Oryzias latipes), the first fish in which the sex determination gene was identified, serves as an ideal model for studying this process. Here, we generated gonadal RNA-seq and small RNA-seq data from XYDMY- females, wild-type females and males to explore this crosstalk. A total of twenty-seven RNA-seq datasets, comprising 188 Gb of raw reads, and twenty-seven small RNA-seq datasets, totaling 18 Gb of raw reads, were collected, covering 10, 30 and 120 days. After optimizing the mapping and normalizing, we conducted transcriptional and post-transcriptional dynamic analyses of differentially expressed genes and miRNAs between WT females and males, as well as between WT females and XYDMY- females. Additionally, we integrated the RNA-seq and small RNA-seq data to construct comprehensive interaction networks and performed a detailed analysis of the temporal dynamics in gene and miRNA expression. These resources offer valuable insights into the transcriptional regulation of gonadal differentiation and development in vertebrates.

Transcriptome analysis reveals PTBP1 as a key regulator of circRNA biogenesis

BACKGROUND

Circular RNAs (circRNAs) are a class of non-coding RNAs generated through back splicing. High expression of circRNAs is often associated with numerous abnormal cellular biological processes. However, the regulatory factors of circRNAs are not fully understood.

RESULTS

In this study, we identified PTBP1 as a crucial regulator of circRNA biogenesis through a comprehensive analysis of the whole transcriptome profiles across 10 diverse cell lines. Knockdown of PTBP1 led to a significant decrease in circRNA expression, concomitant with a distinct reduction in cell proliferation. To investigate the regulatory mechanism of PTBP1 on circRNA biogenesis, we constructed a minigene reporter based on SPPL3 gene. The results showed that PTBP1 can bind to the flanking introns of circSPPL3, and the mutation of PTBP1 motif impedes the back splicing of circSPPL3. Subsequently, to demonstrate that this observation is not an exception, the comprehensive regulatory effects of PTBP1 on circRNAs were confirmed by miniGFP, reflecting the necessity of the binding site in the flanking introns. Analysis of data from clinical samples showed that both PTBP1 and circRNAs exhibited substantial upregulation in acute myeloid leukemia, further demonstrating a potential role for PTBP1 in promoting circRNA biogenesis under in vivo conditions. Competitive endogenous RNA (ceRNA) network revealed that PTBP1-associated circRNAs participated in biological processes associated with cell proliferation.

CONCLUSIONS

In summary, our study is the first to identify the regulatory effect of PTBP1 on circRNA biogenesis and indicates a possible link between PTBP1 and circRNA expression in leukemia.

The complex post-transcriptional regulation of genes coding for methionine adenosyl transferase: New insights for liver cancer

Methionine adenosyltransferases (MATs) catalyze the synthesis of S-adenosylmethionine (SAM), the universal methyl donor involved in methylation reactions, redox balance, and polyamine synthesis. In mammals, three MAT genes, MAT1A, MAT2A, and MAT2B, exhibit tissue-specific expression, with MAT1A predominating in healthy liver and MAT2A/MAT2B upregulated during liver injury and malignancy. A shift from MAT1A to MAT2A/MAT2B expression is a hallmark of hepatocellular carcinoma (HCC), contributing to decreased SAM levels and promoting tumorigenesis. Recent findings highlight the pivotal role of post-transcriptional regulation in controlling MAT gene expression. N6-methyladenosine (m6A) modification, the most prevalent internal mRNA modification, plays a dynamic role in determining the fate of MAT2A mRNA. m6A marks regulate MAT2A mRNA splicing and stability in response to stress and metabolic changes. Additionally, RNA-binding proteins (RBPs) such as ELAVL1 and hnRNPD bind to MAT mRNAs, modulating their stability and translation. Dysregulation of these RBPs in liver disease alters MAT expression profiles. Non-coding RNAs, including microRNAs such as miR-29, miR-21, and miR-485, and long non-coding RNAs such as LINC00662 and SNGH6, modulate MAT expression post-transcriptionally by targeting MAT transcripts directly or influencing RNA-binding proteins (RBPs) and m6A writers/readers. Together, these mechanisms form a complex and intricate post-transcriptional regulatory network that governs MAT activity in physiological and pathological states. This review examines emerging insights into MAT post-transcriptional regulation, focusing on its implications for liver cancer, and opens new avenues for developing therapies that target these regulatory mechanisms.

Differences in microRNA within plasma extracellular vesicles at various time points during early pregnancy in sheep revealed by high-throughput sequencing data

Exosome microRNAs are vital for gene transcription and expression, influencing target genes. They may play direct and indirect roles in pregnancy across animal models and humans. The objective of this research was to comprehensively explore the expression profiles of plasma exosomal miRNAs during the early pregnancy stage in sheep. This study specifically delved into the differences in the expression of plasma exosomal miRNAs between Chinese Merino and Suffolk sheep. The primary focus was on clearly elucidating the changes in plasma exosomal miRNAs, pinpointing potential biomarkers that might exert an impact on early pregnancy, and thoroughly exploring their biological functions as well as the possible underlying molecular mechanisms. Chinese Merino and Suffolk sheep were divided into two groups of 20 for artificial insemination. Blood samples were collected at various pregnancy stages (day 0, day 14, and day 30), Ultrasound diagnosis was carried out five weeks following artificial insemination. Three pregnant sheep from each group were selected for isolating extracellular vesicle-derived miRNAs from plasma. High-throughput sequencing identified differentially expressed miRNAs, and their target genes were analyzed using bioinformatics methods. In plasma exosomal samples derived from all sheep of both breeds at various time points during the early pregnancy stage, a cumulative total of 80 known miRNAs and 182 novel miRNAs were successfully identified. Compared to day 0 gestation controls, both sheep breeds showed differential expression of six known miRNAs: four were up- regulated and two down- regulated. Pathway analysis linked these miRNAs to biological processes such as ECM receptor interactions, growth hormone synthesis, carbohydrate digestion, adrenergic signaling in cardiomyocytes, and MAPK signaling regulation. Notably, Oar-mir-27a differed between the two groups at various time points. In summary, this research meticulously carried out a profiling analysis of the expression of plasma exosomal miRNAs in Chinese Merino and Suffolk sheep. Through this analysis, several exosomal miRNAs were identified, which display distinct abundance levels during the early pregnancy period. These findings strongly imply that these miRNAs have the potential to serve as biomarkers for precisely assessing the reproductive status of sheep.

Renal ischemia alters the mRNA and miRNA profile of vasculature-related genes in scattered tubular-like cells from female pigs

Scattered tubular-like cells (STCs) are renal tubular cells that survive episodes of renal injury and acquire progenitor-like characteristics to repair other damaged kidney cells. STCs release proangiogenic factors in culture and induce microvascular proliferation in injured murine kidneys in vivo. Renovascular disease (RVD) compromises the reparative capacity of STCs, but the underlying mechanisms remain unknown. We hypothesized that RVD alters the expression of vasculature-related genes in swine STCs and impair their vasculoprotective properties. CD24+/CD133+ STCs were harvested from female pig kidneys after 10 wk of RVD or sham (n = 6 each), and the mRNA profiles of vasculature-related genes were analyzed using mRNA and microRNA seq (n = 3/group). STC expression of candidate differentially expressed (DE) genes and their capacity to induce human umbilical endothelial cells (HUVECs) to form tube-like networks were subsequently assessed in vitro before and after micro-RNA (miRNA) modulation (n = 6 each). mRNA-seq identified 67 upregulated and 42 downregulated vasculature-related genes in RVD-STCs. Four miRNAs were upregulated and 12 downregulated in RVD-STCs and found to target 31.3% to 40.5% of DE vasculature-related genes. Modulation in vitro of representative miRNAs decreased RVD-STC expression of anti-angiogenic and increased expression of proangiogenic target genes, respectively. Furthermore, this restored the ability of STCs to induce HUVEC tube formation on Matrigel that was impaired in RVD. Chronic renal ischemia alters the expression of vasculature-related genes in swine STCs, likely through posttranscriptional mechanisms, impairing their proangiogenic activity. These observations may contribute to develop novel approaches to preserve the reparative capacity of STCs in individuals with RVD.NEW & NOTEWORTHY The intrinsic reparative capacity of the adult mammalian kidney is restricted to the ability of scattered tubular-like cells (STCs) to repair damaged kidney cells. Our study provides evidence that chronic renal ischemia alters the mRNA/miRNA profile of angiogenic/vascular development genes of swine STCs, limiting their potential to repair injured tubular cells. Our observations may assist in developing new therapies to improve renal repair in individuals with chronic renal ischemia.

Circulating miRNAs involved in the immune response of the European seabass (Dicentrarchus labrax)

Understanding the immune response in fish through transcriptomic and microRNA (miRNA) profiling may unlock critical insights into disease resistance mechanisms. The objective of the present study was to examine the immune modulation of the European seabass (Dicentrarchus labrax) following bacterial infection and vaccination. Therefore, sequencing of circulating miRNA isolated from blood serum and 3'UTR transcriptome sequencing of head kidney was conducted. In the infected fish 19 miRNAs were found to be differentially expressed. This included two novel miRNAs exhibiting high levels in the infected fish. Regarding circulating miRNAs following vaccination, three specific miRNAs have been identified that demonstrated a substantial increase in expression. Two of them, miR-216b and miR-30a-5p, have been documented to possess the capacity to delay the progression of viral infections. 3'UTR sequencing analysis of the infected fish revealed no significant enrichment of down-regulated transcripts. However, there was a significant enrichment of up-regulated transcripts related to ribosome biogenesis and protein processing. In vaccinated fish up-regulated transcripts did not demonstrate substantial enrichment. Down-regulated genes on the other hand were involved in cytoskeleton organization and apoptosis, indicating that cellular disruption might be a potential hindrance to effective immunity. Overall, these results provide first insights into the progression and regulation of host immune responses to pathogen infection and vaccination. Moreover, the detection of in total 13 differential expressed circulating miRNAs, including regulators of critical innate immunity-related genes such as Toll-like receptor 18, suggests a potential for circulating miRNAs to play a significant role in the post-transcriptional control of fish immune defenses.

c-Myc knockdown restores tamoxifen sensitivity in triple-negative breast cancer by reactivating the expression of ERα: the central role of miR-152 and miR-148a

BACKGROUND

Poor prognosis of triple-negative breast cancer (TNBC) is owing to its intrinsic heterogeneity and lack of targeted therapies. Emerging evidence has characterized that targeting c-Myc might be a promising way to treat TNBC.

METHODS

c-Myc knocked down TNBC cells were generated and the tamoxifen sensitivity was determined. Methylation-specific PCR analysis was used to detect the methylation status of ERα promoter, and c-Myc-mediated miRNA transcription was examined using chromatin immunoprecipitation and dual-luciferase reporter assays. The in vivo tamoxifen sensitivity was determined by mouse xenograft model.

RESULTS

c-Myc knockdown in TNBC cells leads to the reactivation of ERα and consequent acquisition its sensitivity to tamoxifen. c-Myc depletion decreased the methylation in the promoter of ERα and DNMT1 was identified as the main executor. c-Myc knockdown-induced tamoxifen sensitivity was reversed by DNMT1 overexpression. The expression of miR-152-3p and miR-148a-3p was largely induced in c-Myc knockdown TNBC cells, and both miR-152-3p and miR-148a-3p could target DNMT1 to regulate its expression. c-Myc binds to the promoter regions of miR-152-3p and miR-148a-3p to exert transcriptional suppression. By suppressing miR-152-3p or miR-148a-3p expression using inhibitors, enhanced sensitivity to tamoxifen induced by c-Myc knockdown was partially reversed. In vivo xenograft tumor model demonstrated that c-Myc knockdown mildly inhibits the growth of tumor, and a dramatic decline was observed when administrated with tamoxifen combined with c-Myc knockdown.

CONCLUSION

Our study first illustrated that c-Myc knockdown in TNBC cells reactivate ERα expression in a miR-152/miR-148a-DNMT1-dependent manner, and brought new sights into treating TNBC using hormonal therapies.

Neuropeptide Ecdysis-Triggering Hormone and Its Receptor Mediate the Fecundity Improvement of 'Candidatus Liberibacter Asiaticus'-Infected Diaphorina citri Females and CLas Proliferation

The severe Asiatic form of huanglongbing (HLB), caused by "Candidatus Liberibacter asiaticus" (CLas), threatens global citrus production via the citrus psyllid, Diaphorina citri. Culturing challenges of CLas necessitate reducing D. citri populations for disease management. CLas boosts the fecundity of CLas-positive (CLas+) D. citri and fosters its own proliferation by modulating the insect host's juvenile hormone (JH), but the intricate endocrine regulatory mechanisms remain elusive. Here, it is reported that the D. citri ecdysis-triggering hormone (DcETH) and its receptor DcETHR play pivotal roles in the reciprocal benefits between CLas and D. citri within the ovaries, influencing energy metabolism and reproductive development in host insects; miR-210, negatively regulates DcETHR expression, contributing to this symbiotic interaction. CLas infection reduces 20-hydroxyecdysone (20E) levels and stimulates DcETH release, elevating JH production via DcETHR, enhancing fecundity and CLas proliferation. Furthermore, circulating JH levels suppress 20E production in CLas+ ovaries. Collectively, the orchestrated functional interplay involving 20E, ETH, and JH increases energy metabolism and promotes the fecundity of CLas+ D. citri and CLas proliferation. These insights not only broaden the knowledge of how plant pathogens manipulate the reproductive behavior of insect hosts but also offer novel targets and strategies for combatting HLB and D. citri.

Epigenetic regulation of HOXA3 and its impact on oral squamous cell carcinoma progression

OBJECTIVE

The role of homeobox A3 (HOXA3) in cancer progression is gaining prominence, however, to date, no studies have investigated its regulatory function in oral cancer. In this study, we explored the role of HOXA3 through epigenetic mechanisms.

METHODS

Clinical samples were collected from 25 potentially malignant oral lesions and 50 oral squamous cell carcinoma (OSCC) patients, categorized into low-stage and high-stage tumors. The promoter activity of HOXA3 was determined through cloning and luciferase assays. CpG methylation patterns across the gene were identified using methyl-capture sequencing. Gene expression was analyzed using RT‒qPCR. The Survminer R package was used to assess the clinical significance of 3' UTR methylation associated with overall survival. RNA‒RNA interactions were analyzed using RNAInter and TargetScan v8.0.

RESULTS

HOXA3 expression was upregulated in dysplasia and downregulated in advanced cancer stages, showing an inverse correlation with promoter methylation, suggesting epigenetic regulation by DNA methylation. Hypermethylation of the 3' UTR was associated with poor overall survival in advanced stages. Long noncoding RNAs and microRNAs may post-transcriptionally modulate HOXA3 in oral carcinogenesis.

CONCLUSION

CpG-specific hypermethylation in the 3' UTR may serve as a potential biomarker in OSCC.

Relationships between liver and rumen fluke infections, milk somatic cells and polymorphisms in the Toll-like receptor 5 gene and vitamin D metabolism-related genes in Holstein dairy cows

This study investigated polymorphisms in the genes CYP3A4, CYP2R1, and TLR5, and their associations with liver fluke (Fasciola hepatica) and rumen fluke (Calicophoron / Paramphistomum spp.) infections as well as with milk somatic cell count (SCC) as an indicator for mastitis in Holstein Friesian dairy cows. DNA sequencing of the genes' exons, 5'-, 3'-untranslated regions (UTR), introns, and flanking regions of 24 cows revealed 442 variants (388 SNPs and 54 InDels) including 116 previously unknown variants. We detected three novel non-synonymous variants leading to the derived amino acid exchanges, i.e. CYP3A4 p.Gly197Ser, CYP3A4 p.Ile388Val, and CYP2R1 p.Val11Ala. The newly identified SNP 25:36589922 T > C (ss11846100002) is positioned in the splice site of CYP3A4, but showed no impact on the binding score of the splice enzymes. The CYP2R1 and TLR5 genes presented 11 SNPs in the 5'- and 3'-UTR, partly influencing transcription factor binding or microRNA target sites. Associations between polymorphisms and constructed haplotypes with infection traits were analysed via (generalized) linear mixed models including further potential confounders. In total, 109 variants in CYP3A4, 37 variants in CYP2R1, and 18 variants in TLR5 were significantly associated with F. hepatica and rumen fluke infections, and with SCC. The CYP2R1 and TLR5 variants were mostly linked to SCC, indicating the genes' roles in immune responses to bacterial infections. Haplotype analysis revealed significant associations between specific CYP3A4 haplotypes and F. hepatica worm count and faecal egg counts. This study revealed significant insights into gene polymorphisms related to vitamin D metabolism and immune response, which seem to play a role in helminth and udder infections.

Mechanism of KMT2D-mediated epigenetic modification in IL-1β-induced nucleus pulposus cell degeneration

BACKGROUND

Intervertebral disc (IVD) degeneration (IVDD) is characterized by structural destruction accompanied by accelerated signs of aging. This study aimed to investigate the mechanism of lysine methyltransferase 2D (KMT2D) in the proliferation, apoptosis, and inflammation of nucleus pulposus cells (NPCs) in IVDD.

METHODS

Mouse-derived NPCs were cultured and induced with interleukin-1 beta (IL-1β) to establish cell models. KMT2D expression was detected by western blot and reverse transcription-quantitative polymerase chain reaction (RT-qPCR). KMT2D expression was interfered with, and the contents of IL-18, IL-6, and tumor necrosis factor (TNF) were detected by enzyme-linked immunosorbent assay. Cell proliferation, apoptosis, and the expression of miR-133a-5p and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (PFKFB2) were measured. The enrichment of KMT2D and Histone 3 Lysine 4 monomethylation/dimethylation (H3K4me1/2) on the miR-133a-5p promoter was analyzed by chromatin immunoprecipitation and qPCR. The binding of miR-133a-5p and PFKFB2 was analyzed by a dual-luciferase assay.

RESULTS

IL-1β treatment promoted KMT2D expression in NPCs. KMT2D knockdown reduced inflammation and apoptosis and promoted the proliferation of IL-1β-induced NPCs. Mechanistically, KMT2D upregulated miR-133a-5p expression by increasing the level of H3K4me2 at the miR-133a-5p promoter, thereby promoting the binding between miR-133a-5p and PFKFB2 and downregulating the transcription of PFKFB2. miR-133a-5p overexpression or PFKFB2 knockdown alleviated the protective effect of KMT2D knockdown on IL-1β-induced NPCs.

CONCLUSION

KMT2D promoted miR-133a-5p expression through H3K4me2 methylation, thereby promoting the binding of miR-133a-5p to PFKFB2, reducing the mRNA level of PFKFB2, promoting inflammation and apoptosis of IL-1β-induced NPCs, and inhibiting NPC proliferation.

Identification of potential crucial genes and mechanisms associated with metabolically unhealthy obesity based on the gene expression profile

Background

Obesity is an epidemic and systemic metabolic disease that seriously endangers human health. This study aimed to understand the transcriptomic characteristics of the blood of metabolically unhealthy obesity (MUO) and provide insight into the target genes of differently expressed microRNAs in the occurrence and development of MUO.

Methods

The GSE146869, GSE145412, GSE23561, and GSE169290 datasets were analyzed to understand the transcriptome characteristics of the blood of MUO and provide insights into the target genes of differently expressed microRNAs (DEMs) in MUO. Functional and pathway enrichment analyses and gene interaction network analyses were performed to profile the function of differentially expressed genes (DEGs). In addition, miRNet 2.0, TransmiR v2.0, RNA22, TargetScan 7.2, miRDB, and miRWalk databases were used to predict the target genes of effective microRNAs.

Results

A total of 189 co-DEGs were identified in at least two datasets. The 156 co-upregulated genes were enriched into 29 biological process (BP) terms and 12 KEGG pathways. Among the 29 BP terms, the immune- and metabolism-related BP terms were enriched. The 33 co-downregulated genes were enriched into two BP terms, including apoptotic process and regulation of the apoptotic process, with no KEGG pathway. The hub genes EGF, STAT3, IL1B, PF4, SELP, and ITGA2B in the gene interaction network might play important roles in abnormal BP in MUO. Among the 19 DEMs identified in the blood of the MUO group by the GSE169290 dataset, 18 microRNAs targeted 85 genes as risk factors in MUO.

Conclusion

A network consisting of 18 microRNAs and 85 target genes might serve as a risk factor for metabolically unhealthy obesity.

Serum miR-26a level is decreased in cataract patients with glaucoma and related to visual quality

CLINICAL RELEVANCE

microRNAs have been found to be involved in the progression of a variety of ocular diseases.

BACKGROUND

Cataract and glaucoma often coexist, and combined surgery is a common treatment. The aim of this study is to analyse the correlation between miR-26a and visual quality in cataract patients with glaucoma.

METHODS

Seventy patients with cataract and glaucoma and 70 healthy volunteers were enrolled and received phacoemulsification and trabeculectomy. The patients were divided into low and high miR-26a expression groups according to miR-26a mean expression. The objective scattering index, strehl ratio, and modulated transfer function cut-off were analysed by optical quality analysis system II. The changes of miR-26a, objective scattering index, strehl ratio, modulated transfer function cut-off, and the correlation between the indicators were analysed. The downstream genes of miR-26a were analysed by Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes functional enrichment.

RESULTS

There were significant differences between patients and controls in lipid biomarker levels and visual indicators. miR-26a was decreased in the patient group. Strehl ratio and modulated transfer function cut-off in the miR-26a low-expression group were lower than in high-expression group, while mean defect of the visual field and objective scattering index were higher than in high-expression group. The miR-26a expression was negatively correlated with the severity of disease and objective scattering index, and positively correlated with strehl ratio and modulated transfer function cut-off. After surgery, miR-26a, strehl ratio, and modulated transfer function cut-off were increased, and objective scattering index was decreased. The downstream genes of miR-26a were related to several biological processes and signalling pathways.

CONCLUSION

In cataract patients with glaucoma, miR-26a expression was lower than matched controls and increased following combined cataract removal and trabeculectomy.

LncRNA RMG controls liquid-liquid phase separation of MEIS2 to regulate myogenesis

Long non-coding RNAs (lncRNAs) regulate liquid-liquid phase separation (LLPS), driving the formation of biomolecular condensates essential for cellular function. However, this regulatory mechanism is yet to be reported in skeletal muscles. In this study, we comprehensively analyzed lncRNAs in skeletal muscle across multiple pig breeds, developmental stages, and tissues. Our analysis identified over 10,000 novel lncRNAs. We found that the lnc-regulator of muscle growth (lnc-RMG) regulates myogenesis by modulating the LLPS of Meis homeobox 2 (MEIS2). Lnc-RMG was specifically expressed in the skeletal muscle, with significantly higher expression in the fetal stage than in the embryonic stage. Notably, lnc-RMG was highly conserved between pigs and humans and exhibits similar biological functions in myogenesis. Furthermore, lnc-RMG knockdown promoted skeletal muscle regeneration. Mechanistically, lnc-RMG produces mature microRNA (miR)-133a-3p, which targets and inhibits MEIS2 expression, thereby inhibiting MEIS2 LLPS. This inhibition promoted the transcription of transforming growth factor-β receptor II (TGFβR2), ultimately regulating myogenesis. Overall, our findings revealed a novel lnc-RMG/miR-133a-3p/MEIS2/TGFβR2 axis that regulated myogenesis through LLPS and provided new insights into the molecular mechanisms that drive muscle development and regeneration. These findings highlight potential therapeutic targets for muscle-related diseases and novel strategies for livestock improvement.

MicroRNA-29c-3p and -126a Contribute to the Decreased Angiogenic Potential of Aging Endothelial Progenitor Cells

EPCs play important roles in the maintenance of vascular repair and health. Aging is associated with both reduced numbers and functional impairment of EPCs, leading to diminished angiogenic capacity, impaired cardiac repair, and increased risk for cardiovascular disease (CVD). The molecular mechanisms that govern EPC function in cardiovascular health are not fully understood, but there is increasing evidence that microRNAs (miRNAs) play key roles in modulating EPC functionality, endothelial homeostasis, and vascular repair. We aimed to determine how aging alters endothelial progenitor (EPC) health and functionality by altering key miRNA-mRNA pathways. To identify key miRNA-mRNA pathways contributing to diminished EPC functionality associated with aging, microRNA and mRNA profiling were conducted in EPCs from young and aged C57BL/6 mice. We identified a complex aging-associated regulatory network involving two miRNAs-miR-29c-3p and -126a-that acted in tandem to impair vascular endothelial growth factor signaling through targeting Klf2 and Spred1, respectively. The modulation of components of the miR-29c-3p-Klf2-miR-126a-Spred-1-Vegf signaling pathway altered EPC self-renewal capacity, vascular tube formation, and migration in vitro, as well as cardiac repair in vivo. The miR-29c-3p-Klf2-miR-126a-Spred1-Vegf signaling axis plays a critical role in regulating the aging-associated deficits in EPC-mediated vascular repair and CVD risk.

High expression of miR-7974 predicts poor prognosis and is associated with autophagy in estrogen receptor-positive breast cancer

Estrogen receptor-positive (ER+) breast cancers (BC) cause death despite well-established treatments. MicroRNAs (miRNAs) have potential as biomarkers specific to cancer subtypes and tissues, therefore miRNA-based biomarkers could help improve patient survival. In this study, we investigated a relatively unknown miRNA, miR-7974. We utilized small RNA data from 204 breast tissue samples to study miR-7974 association with clinicopathological features and outcomes for BC patients. Additionally, in vitro and in ovo methods were used to identify miR-7974 role at molecular and cellular level in MCF-7 cells. Findings were validated using MDA-MB-453 cells. MiR-7974 was upregulated in many clinicopathological features of BC (P<0.05). Furthermore, the highest expression of miR-7974 was associated with poor relapse-free survival in ER+ BC patients [hazard ratio (HR)=8.70; 95% confidence interval (CI)=3.28-23.06; P=1.37x10-05] and poor BC-specific survival in patients receiving only surgical treatment (HR=8.36; 95% CI=1.01-69.06; P=0.049). Our studies revealed that miR-7974 targets autophagy gene, MAP1LC3B, identified as direct miR-7974 target (P<0.05) in MCF-7 cells. In vitro analyses indicated overexpressing miR-7974 had anti-proliferative effect in MCF7 and MDA-MB-453 cells. Overall, our results demonstrate potential prognostic role of miR-7974 in ER+ BC.

A multi-omic approach implicates novel protein dysregulation in post-traumatic stress disorder

BACKGROUND

Post-traumatic stress disorder (PTSD) is a common and disabling psychiatric disorder. PTSD involves multiple brain regions and is often comorbid with other psychiatric disorders, such as major depressive disorder (MDD). Recent genome-wide association studies (GWASs) have identified many PTSD risk loci and transcriptomics studies of postmortem brain have found differentially expressed genes associated with PTSD cases. In this study, we integrated genome-wide measures across modalities to identify convergent molecular effects in the PTSD brain.

METHODS

We performed tandem mass spectrometry (MS/MS) on a large cohort of donors (N = 66) in two prefrontal cortical areas, dorsolateral prefrontal cortex (DLPFC), and subgenual prefrontal cortex (sgPFC). We also coupled the proteomics data with transcriptomics and microRNA (miRNA) profiling from RNA-seq and small-RNA sequencing, respectively for the same cohort. Additionally, we utilized published GWAS results of multiple psychiatric disorders for integrative analysis.

RESULTS

We found differentially expressed proteins and co-expression protein modules disrupted by PTSD. Integrative analysis with transcriptomics and miRNA data from the same cohort pointed to hsa-mir-589 as a regulatory miRNA responsible for dysregulation of neuronal protein networks for PTSD, including the gamma-aminobutyric acid (GABA) vesicular transporter, SLC32A1. In addition, we identified significant enrichment of risk genes for other psychiatric disorders, such as autism spectrum disorder (ASD) and major depressive disorder (MDD) within PTSD protein co-expression modules, suggesting shared molecular pathology.

CONCLUSIONS

We integrated genome-wide measures of mRNA and miRNA expression and proteomics profiling from PTSD, MDD, and control (CON) brains to identify convergent and divergent molecular processes across genomic modalities. We substantially expand the number of differentially expressed genes and proteins in PTSD and identify downregulation of GABAergic processes in the PTSD proteome. This provides a novel framework for future studies integrating proteomic profiling with transcriptomics and non-coding RNAs in the human brain studies.

miRNA-29 regulates epidermal and mesenchymal functions in skin repair

MicroRNAs (miRNAs) control organogenesis in mammals by inhibiting translation of mRNA. Skin is an excellent model to study the role of miRNAs in epidermis and the mesenchyme. Previous research demonstrated miRNA-29 family functions in skin; however, the mRNA targets and the downstream mechanisms of miRNA-29-mediated regulation are missing. We used the miRNA crosslinking and immunoprecipitation method to find direct targets of miRNA-29 in keratinocytes and fibroblasts from human skin. miRNA-29 inhibition using modified antisense oligonucleotides in 2D and 3D cultures of keratinocytes and fibroblasts enhanced cell-to-matrix adhesion through autocrine and paracrine mechanisms of miRNA-29-dependent tissue growth. We reveal a full transcriptome of human keratinocytes with enhanced adhesion to the matrix, which supports regeneration of the epidermis and is regulated by miRNA-29. Impact statement The functions of small, therapeutically targetable microRNA molecules identified in our study can provide a new approach to improve wound healing by restoring and enhancing the inner molecular mechanisms of a cell and its surrounding matrix. We also provide a plethora of new mRNA targets for follow-up studies of cell adhesion and extracellular matrix formation in humans.

QKI-induced circ_0001766 inhibits colorectal cancer progression and rapamycin resistance by miR-1203/PPP1R3C/mTOR/Myc axis

Colorectal cancer (CRC) is the third most common cancer and remains a significant challenge due to high rates of drug resistance and limited therapeutic options. Circular RNAs (circRNAs) are increasingly recognized for their roles in CRC initiation, progression, and drug resistance. However, no circRNA-based therapies have yet entered clinical development, underscoring the need for comprehensive detection and mechanistic studies of circRNAs in CRC. Here, we identified and characterized a circular RNA, circ_0001766 (hsa_circ_0001766), through microarray analysis of CRC tissues. Our results showed that circ_0001766 is downregulated in CRC tissues and closely associated with patient survival and metastasis. Functional experiments demonstrated that circ_0001766 inhibits CRC cell proliferation, migration and invasion both in-vitro and in-vivo. Mechanistically, hypoxia downregulates Quaking (QKI), an RNA-binding protein essential for the biogenesis of circ_0001766 by binding to introns 1 and 3 of PDIA4 pre-mRNA. Reduced QKI expression under hypoxic conditions leads to decreased circ_0001766 levels in CRC. Circ_0001766 acts as a competitive endogenous RNA, sponging miR-1203 to prevent the degradation of PPP1R3C mRNA. Loss of circ_0001766 results in decreased PPP1R3C expression, leading to the activation of mTOR signaling and increased phosphorylation of Myc, which promotes CRC progression and rapamycin resistance. Our study reveals that overexpression of circ_0001766 or PPP1R3C in CRC cells inhibits the mTOR and Myc pathway, thereby resensitizing cells to rapamycin. The combination of circ_0001766 or PPP1R3C with rapamycin markedly inhibits CRC cell proliferation and induces apoptosis by reducing rapamycin-induced Myc phosphorylation. In summary, our study elucidates a critical circ_0001766/miR-1203/PPP1R3C axis that modulates CRC progression and rapamycin resistance. Our findings highlight circ_0001766 as a promising therapeutic target in CRC, providing a new avenue for enhancing the efficacy of existing treatments and overcoming drug resistance.

Mapping effective microRNA pairing beyond the seed using abasic modifications

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression by base-pairing to complementary sites in messenger RNAs (mRNAs). The primary element for site recognition is the seed region (nucleotides 2-8 in the miRNA), but for a minority of sites pairing outside the seed increases efficiency, with the supplementary region (nucleotides 13-16) typically having the greatest impact. However, the structural determinants of effective pairing outside the seed are not fully understood. Here, we use abasic modified nucleotides to disrupt pairing to residues 13 and 14 of miR-34a and measure the effect of this modification compared to wild-type miR-34a on the cellular transcriptome and proteome using RNA-seq and mass spectrometry. We find that a subset of sites with predicted supplementary pairing are affected by miRNA transfection, with up to two-fold decreases in site repression at the mRNA level. We show that miR-34a 3'-pairing is sensitive to GU wobble pairs in a position-specific manner and favors bulges in the miRNA over the target. These results were validated with luciferase reporter assays. Overall, this study demonstrates a novel methodological approach for elucidating the role of specific miRNA residues in target site selection, advancing our understanding of miRNA-mediated gene regulation.

Genome wide analysis of allele-specific circular RNAs in mammals and their role in cell proliferation

Circular RNAs (circRNAs) are a large class of widely expressed RNAs with covalently closed continuous structures. However, it is currently unknown if circRNAs shows allele-specific expression, as are the consequences of genetic variation on their circularization efficiency and subsequent biological function. Here, we propose a novel pipeline, ASE-circRNA, to accurately quantify both circRNA and their related linear RNA for each allele, and then assess the allele-specificity of the expression of a circular RNA. We identified and analyzed allele-specific circRNAs from human tissue, as well as brains from reciprocal crosses between pairs of highly divergent strains of both mice and pigs by next generation sequencing. Droplet digital PCR (ddPCR) was used to confirm the circularization efficiency measured by next generation sequencing. We found that variation in intron sequences affect the circularization efficiency of circRNAs. Furthermore, we demonstrate that a circRNA, circHK1, regulates the expression of POLR2A to influence the rate of cell proliferation. Our study provides new insight into the molecular mechanisms impacted by variation in genome sequence in the origin of human disease and phenotype.

Identification of Key Genes Related to Intramuscular Fat Content of Psoas Major Muscle in Saba Pigs by Integrating Bioinformatics and Machine Learning Based on Transcriptome Data

The psoas major muscle (PMM) is a piece of pork with good tenderness and high value. Intramuscular fat (IMF) content, serving as a pivotal indicator of pork quality, varies greatly among pigs within the same breed. However, there is a paucity of studies focusing on investigating the molecular mechanism of PMM IMF deposition in the same pig breed. The present study aimed to identify the potential genes related to the IMF content of PMM in low- and high-IMF Saba pigs based on transcriptome data analysis. The data used in this study were the RNA sequences of PMM from 12 Saba pigs (PRJNA1223630, from our laboratory) and gene expression profiles (GSE207279) acquired from the NCBI Sequence Read Archive database and the GEO database, respectively, together with data on the fatty acid and amino acid composition of the 12 Saba pigs' PMM. It was found that the high-IMF pigs exhibited significantly elevated levels of saturated fatty acids and (mono)unsaturated fatty acids, especially C14:0, C16:0, C20:0, C16:1, C18:1n9c, and C20:2, compared with those in the low-IMF pigs (p < 0.05 or p < 0.01). A total of 370 differentially expressed genes (DEGs) (221 up- and 149 down-regulated) were identified based on PRJNA1223630. Then, 20 hub genes were identified through protein-protein interaction (PPI) network analysis. Four potential fat-deposition-related genes (DGAT2, PCK1, MELK, and FASN) were further screened via the intersection of the candidate genes identified by the Least Absolute Shrinkage and Selection Operator (LASSO) algorithm and the top five genes ranked by the Random Forest (RF) method based on the 20 hub genes and were validated in the test gene set (GSE207279). The constructed mRNA (gene)-miRNA-lncRNA network, involving miRNAs (miR-103a-3p, miR-107, and miR-485-5p), lncRNAs (XIST, NEAT1, and KCNQ1OT1), and FASN, might be crucial for IMF deposition in pigs. These findings might delineate valuable regulatory molecular mechanisms coordinating IMF deposition and could serve as a beneficial foundation for the genetic improvement of pork quality.

miR-143-3p Promotes TSCM Differentiation and Inhibits Progressive T Cell Differentiation via Inhibiting ABL2 and PAG1

BACKGROUND

Adoptive cell therapy (ACT), including CAR-T and TCR-T therapies, shows promise for cancer treatment, depending on infused T cell expansion, persistence and activity. We previously characterized four T-cell subsets (TN, TSCM, TCM and TEM) and their miRNA profiles.

OBJECTIVES

This study investigates miR-143-3p's role in T cell differentiation.

METHODS

Using qPCR, we analyzed miR-143-3p expression. Target genes were validated by dual-luciferase assays. Functional assays assessed differentiation markers, proliferation, apoptosis and cytokine secretion.

RESULTS

miR-143-3p was upregulated in early-differentiated TSCM but downregulated during progression. We confirmed ABL2 and PAG1 as direct targets suppressed by miR-143-3p. Overexpression increased early markers (LEF1, CCR7 and CD62L) while decreasing late markers (EOMES, KLRG1 and CD45RO). It also enhanced proliferation, reduced apoptosis and suppressed cytokine secretion.

CONCLUSIONS

miR-143-3p promotes TSCM differentiation and inhibits progressive differentiation by targeting ABL2/PAG1, suggesting new ACT optimization strategies.

Reprogramming liver metastasis-associated macrophages toward an anti-tumoral phenotype through enforced miR-342 expression

Upon metastatic seeding in the liver, liver macrophages, including Kupffer cells, acquire a transcriptional profile typical of tumor-associated macrophages (TAMs), which support tumor progression. MicroRNAs (miRNAs) fine-tune TAM pro-tumoral functions, making their modulation a promising strategy for macrophage reprogramming into an anti-tumoral phenotype. Here, we analyze the transcriptomic profiles of liver and splenic macrophages, identifying miR-342-3p as a key regulator of liver macrophage function. miR-342-3p is highly active in healthy liver macrophages but significantly downregulated in colorectal cancer liver metastases (CRLMs). Lentiviral vector-engineered liver macrophages enforcing miR-342-3p expression acquire a pro-inflammatory phenotype and reduce CRLM growth. We identify Slc7a11, a cysteine-glutamate antiporter linked to pro-tumoral activity, as a direct miR-342-3p target, which may be at least partially responsible for TAM phenotypic reprogramming. Our findings highlight the potential of in vivo miRNA modulation as a therapeutic strategy for TAM reprogramming, offering an approach to enhance cancer immunotherapy.

Exploration potential sepsis-ferroptosis mechanisms through the use of CETSA technology and network pharmacology

As an important self-protection response mechanism of the body, inflammation can not only remove the necrotic or even malignant cells in the body, but also take a series of targeted measures to eliminate the pathogen of foreign invasion and block the foreign substances that may affect the life and health of the body. Flavonoids have known anti-inflammatory, anti-oxidation, anti-cancer and other effects, including glycyrrhizin molecules is one of the representatives. Licochalcone D has known anti-inflammatory and antioxidant properties and is effective in the treatment of a variety of inflammatory diseases. However, the underlying mechanism for the treatment of sepsis remains unclear. In this study, the therapeutic potential of Licochalcone D for sepsis was studied by analyzing network pharmacology and molecular dynamics simulation methods. Sepsis-related genes were collected from the database to construct PPI network maps and drug-targeting network profiles. The potential mechanism of Licochalcone D in sepsis was predicted by gene ontology, KEGG and molecular dynamics simulation. Sixty drug-disease genes were subsequently validated. Go analysis showed that monomeric small molecule Licochalcone D could regulate the process of intracellular enzyme system. The KEGG pathway analysis showed that the signal pathway of the main effect was related to the calcium pathway. The results of intersections with iron death-related target genes showed that ALOX5, ALOX15B and other nine targets all had the effect of possibly improving sepsis, while GSE 54,514, GSE 95,233 and GSE 69,528 were used to analyze the survival rate and ROC curve. Five genes were screened, including ALOX5, ALOX15B, NFE2L2 and NR4A1, HIF1A. The results of molecular docking showed that ALOX5 and Licochalcone D had strong binding activity. Finally, the results of molecular dynamics simulation showed that there was good binding power between drug and target. In the present study, we utilized molecular dynamics simulation techniques to assess the binding affinity between the small-molecule ligand and the protein receptor. The simulation outcomes demonstrate that the binding interface between the ligand and receptor remains stable, with a calculated binding free energy (ΔG) of -32.47 kJ/mol. This signifies a high-affinity interaction between the ligand and receptor, suggesting the long-term stability of the small molecule under physiological conditions. These findings provide critical insights for drug development efforts. This study elucidates the therapeutic potential of Licochalcone D, a traditional Chinese medicine monomer, in improving sepsis through the regulation of ferroptosis, thereby providing a new direction and option for subsequent clinical drug development in the treatment of sepsis.