Predicting effective microRNA target sites in mammalian mRNAs

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.

Insights into the Regulatory Role of MicroRNAs in Penaeus monodon Under Moderately Low Salinity Stress

MicroRNAs (miRNAs) play crucial roles in regulating various biological processes in crustaceans, including stress responses. Under acute low salinity stress conditions, miRNAs exhibit dynamic expression patterns that significantly influence the physiological and molecular responses of the shrimp. However, research on miRNAs in P. monodon is very limited, and their functions under low salinity stress remain unclear. In this study, by using high-throughput sequencing technology, we identified miRNAs and investigated their regulatory mechanism in P. monodon under low salinity stress. A total of 118 miRNAs were differentially expressed after low salinity exposure. These miRNAs were found to target genes involved in metabolism, pathogen infection, immune response and stress signaling pathways. By modulating the expression of these target genes, miRNAs were able to fine-tune the stress response of P. monodon, thereby enhancing its tolerance to low salinity. This study provides new insights into the regulatory roles of miRNAs in the stress response of aquatic organisms and suggests potential targets for genetic improvement to enhance stress tolerance in P. monodon aquaculture.

Comparative analysis of miRNA-mRNA interaction prediction tools based on experimental head and neck cancer data

BACKGROUND

We evaluated the performance of TargetScan, miRDB, and miRWalk for predicting miRNA-mRNA interactions in HNSCC. Based on clinical tumor and cancer-free tissue data, miRWalk emerged as the most comprehensive tool. Validation using NanoString technology and MiRTarBase confirmed key predictions, highlighting the important roles of the PI3K-Akt and Wnt pathways. This study underscores the importance of integrating bioinformatics and experimental data to better understand HNSCC.

BACKGROUND

■ miRWalk had the highest predicted interactions and validated miRNA networks in HNSCC.

BACKGROUND

■ Around 3.3% of interactions overlapped across tools, emphasizing the need for multitool approaches.

BACKGROUND

■ Dysregulated genes and miRNAs were tied to cancerdriving PI3K-Akt and Wnt pathways.

BACKGROUND

■ The validated approach highlights the importance of integrating computational and molecular data.

OBJECTIVE

Head and neck squamous cell carcinoma (HNSCC) has a poor prognosis largely due to late diagnosis and a lack of reliable biomarkers. MicroRNAs (miRNAs), small non-coding RNAs that regulate gene expression, are promising biomarkers for HNSCC. This study evaluated miRNA-mRNA interactions in HNSCC using conventional computational tools and validated the results using molecular data.

METHODS

We compared three miRNA-mRNA interaction prediction tools, TargetScan, miRDB, and miRWalk, using differentially expressed miRNAs and mRNAs from HNSCC and cancer-free tissues. NanoString nCounter was used to measure miRNA and mRNA expression and the miRTarBase database was used to validate the predicted miRNA-mRNA interactions.

RESULTS

TargetScan and miRWalk provide a comprehensive overview of potential interactions, whereas miRDB provides functional insights. Our results identified 77 and 154 differentially expressed miRNAs and mRNAs in HNSCC, respectively. miRWalk predicted the highest number of miRNA-mRNA interactions, followed by miRDB and TargetScan. Only 3.3% of interactions were common among the tools. The MiRTarBase analysis confirmed a small subset of the predictions. Biological pathway analysis highlighted the dysregulation of PI3K-Akt and Wnt signaling; miRWalk was the best for elucidating how miRNAs modulate target mRNAs in these key pathways during HNSCC progression.

CONCLUSION

miRWalk emerged as the most robust tool for predicting miRNA-mRNA interactions. Our findings highlight the importance of integrating bioinformatics predictions with experimental data to better understand the regulatory networks in HNSCC and identify potential biomarkers for diagnosis and therapy.

Pilot Study on the Profiling and Functional Analysis of mRNA, miRNA, and lncRNA in the Skeletal Muscle of Mongolian Horses, Xilingol Horses, and Grassland-Thoroughbreds

Muscle fibers, as the fundamental units of muscle tissue, play a crucial role in determining skeletal muscle function through their growth, development, and composition. To investigate changes in muscle fiber types and their regulatory mechanisms in Mongolian horses (MG), Xilingol horses (XL), and Grassland-Thoroughbreds (CY), we conducted histological and bioinformatic analyses on the gluteus medius muscle of these three horse breeds. Immunofluorescence analysis revealed that Grassland-Thoroughbreds had the highest proportion of fast-twitch muscle fibers at 78.63%, while Mongolian horses had the lowest proportion at 57.54%. Whole-transcriptome analysis identified 105 differentially expressed genes (DEGs) in the CY vs. MG comparison and 104 DEGs in the CY vs. XL comparison. Time-series expression profiling grouped the DEGs into eight gene sets, with three sets showing significantly up-regulated or down-regulated expression patterns (p < 0.05). Additionally, 280 differentially expressed long non-coding RNAs (DELs) were identified in CY vs. MG, and 213 DELs were identified in CY vs. XL. A total of 32 differentially expressed microRNAs (DEMIRs) were identified in CY vs. MG, while 44 DEMIRs were found in CY vs. XL. Functional enrichment analysis indicated that the DEGs were significantly enriched in essential biological processes, such as actin filament organization, muscle contraction, and protein phosphorylation. KEGG pathway analysis showed their involvement in key signaling pathways, including the mTOR signaling pathway, FoxO signaling pathway, and HIF-1 signaling pathway. Furthermore, functional variation-based analyses revealed associations between non-coding RNAs and mRNAs, with some non-coding RNAs targeting genes potentially related to muscle function regulation. These findings provide valuable insights into the molecular basis for the environmental adaptability, athletic performance, and muscle characteristics in horses, offering new perspectives for the breeding of Grassland-Thoroughbreds.

Evaluation of Thrombomodulin, hsa-miR-18a-5p, and hsa-miR-18b-5p as Potential Prognostic Biomarkers in Uterine Corpus Endometrial Carcinoma

Thrombomodulin (THBD), hsa-miR-18a-5p, and hsa-miR-18b-5p have been frequently mentioned in numerous cancer-related research studies; however, their specific functions in uterine corpus endometrial carcinoma (UCEC) are not well understood. This study aimed to investigate the roles of THBD, hsa-miR-18a-5p, and hsa-miR-18b-5p within a UCEC cohort. We utilized various web-based tools, including GEPIA2, UALCAN, Human Protein Atlas (HPA), TNM Plot, STRING, TargetScan, and ENCORI for our analysis. The expression level of the THBD gene was found to be significantly downregulated (p < 0.05) in UCEC tissue compared to adjacent normal tissue. In contrast, hsa-miR-18a-5p and hsa-miR-18b-5p were both upregulated in UCEC tissue (p < 0.05). Additionally, THBD exhibited a significant hypermethylation level in UCEC tissue (p < 0.05). The elevated expression of hsa-miR-18a-5p was linked to a shorter overall survival (OS) (p = 0.025), while THBD and hsa-miR-18b-5p showed no association with OS (p = 0.87 and p = 0.56, respectively). Notably, THBD expression was significantly negatively correlated with hsa-miR-18a-5p (p = 0.00407), whereas no significant correlation was found between THBD and hsa-miR-18b-5p (p = 0.25). Thus, it can be concluded that increased levels of miR-18a-5p in the UCEC cohort may serve as a negative prognostic marker and a potential therapeutic target. However, further studies are necessary to validate the implications of decreased THBD and increased miR-18b-5p expression levels on the clinical outcomes of these patients.

Computational inference of co-regulatory modules from transcription factors, MicroRNAs, and their targets using CanMod2

Gene regulators such as Transcription Factors (TFs) and microRNAs (miRNAs) regulate genes at the transcriptional and post-transcriptional levels, respectively. There is a complex interplay of regulatory patterns of TFs and miRNAs. Some TFs and miRNAs regulate the activity of their target genes individually, some co-regulate the activity of the same set of genes, some TFs regulate miRNA activity, and some miRNAs regulate TFs. As dysregulation in gene regulation can lead to various diseases like cancer, it is a significant problem to find the interplay among TFs, miRNAs, and their target genes. Here, we propose a computational pipeline, CanMod2, which infers modules of TFs, miRNAs, and their co-regulatory targets that are involved in a common biological process. In this work, we have introduced several algorithmic enhancements to the earlier version of CanMod2. We applied CanMod2 to five cancer types and analyzed the inferred modules extensively. Our results show that the inferred modules were enriched in cancer-related biological processes and pathways. The hub regulators that occur in many modules were among cancer-related genes and miRNAs. The inferred regulator-target interactions were significantly enriched in ground truth interactions. CanMod2 source code and documentation are publicly available at https://github.com/bozdaglab/CanMod2 .

Mutant huntingtin induces neuronal apoptosis via derepressing the non-canonical poly(A) polymerase PAPD5

MicroRNAs (miRNAs) are small non-coding RNAs that play crucial roles in post-transcriptional gene regulation. Poly(A) RNA polymerase D5 (PAPD5) catalyzes the addition of adenosine to the 3' end of miRNAs. In this study, we demonstrate that the Yin Yang 1 protein, a transcriptional repressor of PAPD5, is recruited to both RNA foci and protein aggregates, resulting in an upregulation of PAPD5 expression in Huntington's disease (HD). Additionally, we identify a subset of PAPD5-regulated miRNAs with increased adenylation and reduced expression in our disease model. We focus on miR-7-5p and find that its reduction causes the activation of the TAB2-mediated TAK1-MKK4-JNK pro-apoptotic pathway. This pathway is also activated in induced pluripotent stem cell-derived striatal neurons and post-mortem striatal tissues isolated from HD patients. In addition, we discover that a small molecule PAPD5 inhibitor, BCH001, can mitigate cell death and neurodegeneration in our disease models. This study highlights the importance of PAPD5-mediated miRNA dysfunction in HD pathogenesis and suggests a potential therapeutic direction for the disease.

Reconstruction of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveals functional miRNAs and lncRNAs in burns and keloids

BACKGROUNDS

Long non-coding RNAs (lncRNAs) exert their pharmacological functions by serving as sponges for related microRNAs (miRNAs), thereby modulating gene expression. Nevertheless, the regulatory roles of the lncRNA-mediated competing endogenous RNA (ceRNA) mechanism in the interplay between burns and keloids remain largely elusive.

OBJECTIVE

To construct the ceRNA regulatory network of burns, leveraging network pharmacology and bioinformatics analyses.

RESULTS

3576 DELs (Differentially Expressed lncRNAs), 1427 DEMis (Differentially Expressed miRNAs), and 2555 DEMs (Differentially Expressed mRNAs) were identified as differentially expressed genes. A ceRNA network composed of DELs-DEMis-DEMs in burns and keloids was constructed, with a prominent sub-network consisting of 23 DELs, 330 DEMs, and 8 DEMis. Subsequently, the clusterProfiler package in the R programming language was utilized to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The sub-network within the ceRNA network was extracted, in which three lncRNAs, namely lnc-WRB, lnc-SCNN1G, and LINC00271, and three miRNAs, namely hsa-miR-21, hsa-miR-34a, and hsa-miR-155, were identified as key genes.

CONCLUSION

All nodes within the sub-ceRNA network exert either a direct or an indirect influence on the pathological processes of burns and post-burn keloids. The current study successfully constructed the ceRNA network in burns and keloids and provided a potentially novel perspective on the DELs-DEMis-DEMs ceRNA network, contributing to the elucidation of the ceRNA regulatory mechanisms in the pathogenesis of burns and keloids. Nevertheless, systematic and rigorous experimental validations are indispensable to confirm our findings.

microRNA-218-5p coordinates scaling of excitatory and inhibitory synapses during homeostatic synaptic plasticity

Homeostatic synaptic plasticity (HSP) is a neuronal mechanism that allows networks to compensate for prolonged changes in activity by adjusting synaptic strength. This process is crucial for maintaining stable brain function and has been implicated in memory consolidation during sleep. While scaling of both excitatory and inhibitory synapses plays an important role during homeostatic synaptic plasticity, molecules coordinating these processes are unknown. In this study, we investigate the role of miR-218-5p as a regulator of inhibitory and excitatory synapses in the context of picrotoxin (PTX)-induced homeostatic synaptic downscaling (HSD) in rat hippocampal neurons. Using enrichment analysis of microRNA-binding sites in genes changing upon PTX-induced HSD, we bioinformatically predict and experimentally validate increased miR-218-5p activity upon PTX treatment. By electrophysiological recordings and confocal microscopy, we demonstrate that inhibiting miR-218-5p activity exerts a dual effect during HSD: It occludes the downscaling of excitatory synapses and dendritic spines, while at the same time attenuating inhibitory synapse upscaling. Furthermore, we identify the Neuroligin2 interacting molecule Mdga1 as a direct miR-218-5p target which potentially mediates the effect of miR-218-5p on homeostatic upscaling of inhibitory synapses. By performing long-term electroencephalographic recordings, we further reveal that local inhibition of miR-218-5p in the somatosensory cortex reduces local slow-wave activity during non-rapid-eye-movement sleep. In summary, this study uncovers miR-218-5p as a key player in coordinating inhibitory and excitatory synapses during homeostatic plasticity and sleep. Our findings contribute to a deeper understanding of how neural circuits maintain stability in the face of activity-induced perturbations, with implications for pathophysiology.

Telocyte-derived exosomes promote angiogenesis and alleviate acute respiratory distress syndrome via JAK/STAT-miR-221-E2F2 axis

Acute respiratory distress syndrome (ARDS) is characterized by severe respiratory failure and significant inflammation, leading to vascular and epithelial cell damage. The absence of effective pharmacologic treatments underscores the need for novel therapeutic approaches. Telocytes (TCs), a newly identified type of interstitial cells, have shown potential in tissue repair and angiogenesis, particularly through the release of exosomal microRNAs (miRNAs). Exosomes were isolated from LPS (lipopolysaccharide)-stimulated TCs and characterized using western blotting and nanoparticle tracking analysis. The role of exosomal miR-221 in angiogenesis was assessed through tube formation, migration, and proliferation assays in mouse vascular endothelial cells (MVECs). The JAK/STAT pathway's involvement in miR-221 regulation was determined using western blotting and qRT-PCR. A dual-luciferase assay confirmed E2F2 as a direct target of miR-221. ARDS mouse model was established via LPS instillation, and the therapeutic effects of TCs-derived exosomes were evaluated by histopathological scoring, cytokine analysis, and endothelial barrier integrity assays. Our findings demonstrated that exosomes from LPS-stimulated TCs significantly promoted angiogenesis, proliferation, and migration in MVECs. These effects were mediated by miR-221, which downregulated E2F2 expression, an important regulator of endothelial cell functions. The JAK/STAT pathway played a crucial role in miR-221 production, with pathway inhibition reducing miR-221 levels and attenuating its pro-angiogenic effects. In vivo, TCs-derived exosomes reduced lung inflammation and tissue damage in ARDS mice, effects that were reversed by miR-221 inhibition. These results suggested that TCs-derived exosomes promoted angiogenesis and alleviated ARDS through the JAK/STAT-miR-221-E2F2 axis.

MicroRNAs as Endocrine Modulators of Breast Cancer

Breast cancer is an aggressive disease of multiple subtypes with varying phenotypic, hormonal, and clinicopathological features, offering enhanced resistance to conventional therapeutic regimens. There is an unmet need for reliable molecular biomarkers capable of detecting the malignant transformation from the early stages of the disease to enhance diagnosis and treatment outcomes. A subset of small non-coding nucleic acid molecules, micro ribonucleic acids (microRNAs/miRNAs), have emerged as promising biomarkers due to their role in gene regulation and cancer pathogenesis. This review discusses, in detail, the different origins and hormone-like regulatory functionalities of miRNAs localized in tumor tissue and in the circulation, as well as their inherent stability and turnover that determines the utility of miRNAs as biomarkers for disease detection, monitoring, prognosis, and therapeutic targets.

The potential of miR-29 in modulating tumor angiogenesis: a comprehensive review

MicroRNAs (miRNAs) are a class of short non-coding RNAs that play a crucial role in the post-transcriptional regulation of gene expression. They are associated with various biological processes related to tumors. Among the numerous miRNAs, miR-29 has garnered attention for its role in regulating tumor angiogenesis. In numerous human tumors, miR-29 has been demonstrated to negatively correlate with the capacity for angiogenesis and the degree of malignancy, as well as with the expression levels of pro-angiogenic factors such as vascular endothelial growth factor vascular endothelial growth factor (VEGF), platelet-derived growth factor (PDGF), and matrix metalloproteinase (MMP)-2. Multiple studies, utilizing techniques like dual-luciferase reporter assays, have confirmed that miR-29 directly targets the 3'-untranslated region (UTR) of mRNAs for VEGF, PDGF, and MMP-2. Extensive investigations involving tumor cell lines and animal models have shown that the overexpression of miR-29, achieved through miRNA transfection or the introduction of miRNA mimics, effectively inhibits angiogenesis by upregulating these pro-angiogenic factors. Conversely, downregulation of miR-29 using specific inhibitors promotes angiogenesis. While small molecule inhibitors and antibodies targeting VEGF constitute a primary strategy in anti-angiogenesis therapies, miR-29's ability to target multiple pro-angiogenic molecules positions it as a promising candidate for future therapeutic interventions, especially with ongoing advancements in nucleic acid drug design and delivery systems.

Exploring the Role of microRNAs as Blood Biomarkers in Alzheimer's Disease and Frontotemporal Dementia

Alzheimer's disease (AD) and frontotemporal dementia (FTD) are the most common forms of dementia globally. AD is characterized by the accumulation of amyloid-β (Aβ) plaques and hyperphosphorylated tau in the brain, leading to progressive memory loss and cognitive decline, significantly impairing daily life. In contrast, FTD is marked by selective degeneration of the frontal and/or temporal lobes, typically resulting in profound changes in personality and social behavior, speech disorders, and psychiatric symptoms. Numerous studies have found microRNAs (miRNAs)-small, non-coding RNA molecules that regulate gene expression post-transcriptionally-to be dysregulated in AD and FTD. As a result, miRNAs have emerged as promising novel biomarkers for these diseases. This review examines the current understanding of miRNAs in AD and FTD, emphasizing their potential as accessible, noninvasive biomarkers for diagnosing these prevalent neurodegenerative disorders.

Characterization of the global bovine microRNAome of peripheral blood mononuclear cells isolated from Mycobacterium bovis exposed cattle

Accurate diagnostics are urgently needed for bovine TB - an economically devastating disease posing a re-emerging threat to veterinary and public health worldwide. MicroRNAs, post-transcriptional gene regulators involved in a range of biological processes and immunological pathways, have emerged as promising diagnostic biomarkers for numerous diseases. In human TB, microRNAs have been widely studied, but not much is currently known about their role in bovine TB. This study aimed to investigate the diagnostic potential of microRNAs in bTB through comprehensive analysis of their expression profiles in disparate states of M. bovis exposure. We used RNA-sequencing to characterize the global microRNAome of peripheral blood mononuclear cells from cattle that were either unvaccinated, BCG-vaccinated, unprotected or protected. A total of 468 microRNAs were detected across all samples, none of which were uniquely expressed in any group. Significant differential expression was observed for bta-miR-6122-3p, bta-miR-3533 and bta-miR29b in various comparisons. Subsequent target analysis of bta-miR-29b, a candidate biomarker in human tuberculosis, revealed that several genes (ACVR2A, PIK3R1, TBX21, TGFBR1 and TGFBR2) involved in a number of relevant T-cell and immune signaling pathways, were amongst the predicted targets. Overall, this study provides evidence that microRNAs could be promising novel biomarkers for bovine TB diagnostics.

MiRNA Omics Reveal the Mechanisms of the Dual Effects of Selenium Supplementation on the Development of the Silkworm (Bombyx mori)

This study explores the dual effects of selenium (Se) supplementation on silkworm development by analyzing miRNA expression profiles of fat bodies in silkworms under different Se concentrations (50 µM and 200 µM). Compared to the control, 84 miRNAs displayed different expression levels in the F_50 µM group, with 72 miRNAs up-regulated and 12 down-regulated; 152 miRNAs were differentially expressed in the F_200 µM group, with 124 up-regulated and 28 down-regulated. In the F_50 µM group, the target genes of differentially expressed miRNAs were mainly enriched in Toll and Imd signaling pathways, oxidative phosphorylation, and ribosome biogenesis in eukaryotes; however, mainly oxidative phosphorylation, ribosome biogenesis in eukaryotes, and the spliceosome were enriched in the F_200 µM group. Based on the results of the protein-protein interaction network and miRNA-target network, bmo-miR-2a-1-5p and bmo-miR-317-3p_L-2R+2 were screened as key miRNAs in the F_50 µM group and the F_200 µM group, respectively. The bmo-miR-2a-1-5p mainly targeted 10014128 (DREDD), 100862750 (ATF2), and 101744000 (Tak1) genes, which were enriched in Toll and Imd signaling pathways. The bmo-miR-317-3p_L-2R+2 primarily regulated 101738508 (SF3b) and 101746688 (Prp19) genes, which were in the spliceosome pathway. Thus, our results demonstrated that Se supplementation improved the silkworm development via bmo-miR-2a-1-5p miRNA regulation of the Toll and Imd signaling pathways and inhibited it via bmo-miR-317-3p_L-2R+2 miRNA targeting the spliceosome pathway. Our data revealed that 50 µM Se supplementation could improve silkworm productivity; meanwhile, a 200 µM Se treatment displayed toxic effects, leading to impaired development.

Identification of a circRNA-miRNA-mRNA interactome associated with Parkinson's disease progression

BackgroundCircular RNAs (circRNAs) constitute a distinctive subclass of RNAs that are known for their regulatory roles in fundamental cellular processes. Due to their increased stability and ubiquitous expression, circular RNAs have been widely studied as potential molecular targets in various diseases, including neurodegenerative diseases. While several studies have found differentially expressed circRNAs associated with Parkinson's disease (PD), none has looked specifically into PD progression.ObjectiveTo elucidate the role of circRNAs in the progression of PD by identifying dysregulated circRNAs associated with PD progression and to pinpoint potential downstream miRNAs and associated differentially expressed gene targets.MethodsIn this study, we have utilized large-scale, longitudinal, and deep RNA-seq data from two independent cohorts, namely the Parkinson's Progression Marker Initiative (PPMI) and the Parkinson's Disease Biomarker Program (PDBP), to characterize circRNA expression in patients of early PD stage.ResultsWe identified six circRNAs significantly differentially expressed in whole blood samples obtained from PD patients over time. Additionally, we were able to map a competing endogenous RNA (ceRNA) network with potential downstream miRNA-mRNA targets and, with the help of co-expression analysis, to identify genes associated with PD progression. Our findings provide compelling evidence for a dysregulated circRNA interactome as an indicator of PD progression, with changes in the expression of these circRNAs and downstream gene targets being significantly associated with changes in UPDRS III scores in PD patients.ConclusionsOur results strongly indicate the association of circular RNAs with PD progression and emphasize its significance as a critical molecular marker.

Bone-Induced HER2 Promotes Secondary Metastasis in HR+/HER2- Breast Cancer

SIGNIFICANCE

Given the urgent need for alternative strategies to block metastasis progression, we demonstrate that blocking HER2-mediated secondary metastasis improves clinical outcome and establish HER2 as a biomarker for bone metastasis in patients with initial HR+/HER2- breast cancer, which represents ∼70% of all cases.

Exosome-like vesicles encapsulated with specific microRNAs accelerate burn wound healing and ameliorate scarring

Burn injuries are prevalent, yet effective treatments remain elusive. Exosomes derived from mesenchymal stem cells (MSC-Ex) possess remarkable pro-regenerative properties for wound healing. Despite their potential, the challenge of mass production limits their clinical application. To address this, preparing exosome-like vesicles has become an international trend. In this study, 28 key microRNAs (miRNAs) with significant pro-proliferation, anti-inflammation, and anti-fibrosis functions were screened from MSC-Ex. These miRNAs were encapsulated into liposomes and then hybridized with extracellular vesicles derived from watermelon to create synthetic exosome-like vesicles. The fabricated vesicles exhibited similar particle size and zeta potential to MSC-Ex, demonstrating high serum stability and effectively resisting the degradation of miRNA by RNase. They were efficiently internalized by cells and enabled a high rate of lysosomal escape for miRNAs post cellular uptake, thereby effectively exerting their pro-proliferative, anti-inflammatory, and anti-fibrotic functions. Further experiments demonstrated that these vesicles efficiently accelerated burn wound healing and reduced scarring, with effects comparable to those of natural MSC-Ex. Based on these findings, the exosome-like vesicles fabricated in this study present a promising alternative to MSC-Ex in burn wound treatment.

Profiling the regulatory landscape of sialylation through miRNA targeting of CMP- sialic acid synthetase

Cell surface sialic acid is an important glycan modification that contributes to both normal and pathological physiology. The enzyme cytidine monophosphate N-acetylneuraminic acid synthetase (CMAS) biosynthesizes the activated sugar donor cytidine monophosphate (CMP) sialic acid, which is required for all sialylation. CMAS levels impact sialylation with corresponding biological effects. The mechanisms that regulate CMAS are relatively uncharacterized. Herein, we use a high throughput genetically encoded fluorescence assay (miRFluR) to comprehensively profile the posttranscriptional regulation of CMAS by miRNA. These small non-coding RNAs have been found to impact glycosylation. Mapping the interactions of the human miRNAome with the 3'-untranslated region of CMAS, we identified miRNA whose impact on CMAS expression was either downregulatory or upregulatory. This follows previous work from our laboratory and others showing that miRNA regulation is bidirectional. Validation of the high-throughput results confirmed our findings. We also identified the direct binding sites for two upregulatory and two downregulatory miRNAs. Functional enrichment analysis for miRNAs upregulating CMAS revealed associations with pancreatic cancer, where sialic acid metabolism and the α-2,6-sialyltransferase ST6GAL1 have been found to be important. We found that miRNA associated with the enriched signature enhanced pancreatic cell-surface α-2,6-sialylation via CMAS expression in the absence of effects on ST6GAL1. We also find overlap between the miRNA regulation of CMAS and that of previously analyzed sialyltransferases. Overall, our work points to the importance of miRNA in regulating sialylation levels in disease and add further evidence to the bidirectional nature of miRNA regulation.

Comprehensive Genomic Analysis Reveals Novel Transposable Element-Derived MicroRNA Regulating Caste Differentiation in Honeybees

The honeybee (Apis mellifera) is a highly social insect whose caste differentiation is regulated by epigenetic mechanisms, representing a classic example of phenotypic plasticity in social insects. Although the importance of transposable elements (TEs) in epigenetic research is well recognized, their specific role in honeybee caste differentiation has not been fully explored. This study reveals a novel regulatory mechanism where the microRNA (miRNA) ame-mir-3721-3p, derived from ApME (Apis miniature inverted-repeat TEs), suppresses DNA methyltransferase gene DNMT3, promoting queen-like development in honeybee larvae. Genome-wide analysis identified 43 ApME elements in Apis, with ApMETm15 being particularly abundant and species-specific. These elements gave rise to 6 miRNAs, including ame-mir-3721-3p which showed notable regulatory potential. Target gene prediction and luciferase reporter assays confirmed that ame-mir-3721-3p binds to and suppresses DNMT3 expression. Spatiotemporal expression analysis indicated that ame-mir-3721-3p is significantly upregulated during the critical L3 larval stage, exhibiting a similar expression pattern to DNMT3. Larval feeding experiments with agomir demonstrated that ame-mir-3721-3p suppresses DNMT3 expression and significantly impacts the expression of genes related to the juvenile hormone and ecdysone pathways. Further physiological evidence showed that when larvae were treated with agomir-3721 during the critical caste differentiation window (L3-L4 stage), the emerging adult bees exhibited increased body size, doubled ovarian area, and significantly higher frequency of ovary development, with significant upregulation of ovarian-specific marker genes. These findings provide direct evidence for ame-mir-3721-3p's role in promoting queen-like developmental trajectories during caste differentiation, uncovering a new regulatory pathway in honeybee development and offering insights into epigenetic mechanisms in social insects.

Genome-wide profiling and functional characterization of circular RNAs in neural development and injury: insights from a rat model research

Circular RNAs (circRNAs) have re-emerged as promising gene regulators in various physiological and pathological conditions. However, the expression patterns of circRNAs in the developing spinal cord of mammals and the comprehensive distribution of circRNAs across different tissues remain poorly understood. In this study, rats were used as the model organism. We conducted a comprehensive analysis of 15 RNA-Seq datasets comprising 217 rat samples and developed a web-based resource, CiRNat, to facilitate access to these data. We identified 15,251 credible circRNAs and validated them through experimental approaches. Notably, we observed two significant time points for circRNA increase during spinal cord development, approximately at embryonic day 14 (E14d) and postnatal week 4 (P4w). Analysis of circRNA expression in various rat tissues revealed higher expression levels in central nervous system tissues compared to peripheral nervous system tissues and other tissues. Furthermore, some highly abundant circRNAs exhibited tissue- and species-specific expression patterns and differed from their cognate linear RNAs, such as those derived from Gigyf2. Integrating polysome profiling and bioinformatic predictions suggested potential functions of certain circRNAs as miRNA sponges and translational templates. Collectively, this study provides the first comprehensive landscape of circRNAs in the developing spinal cord, offering an important resource and new insights for future exploration of functional circRNAs in central nervous system development and related diseases.

MicroRNA-130b Suppresses Malignant Behaviours and Inhibits the Activation of the PI3K/Akt Signaling Pathway by Targeting MET in Pancreatic Cancer

There has been interested in the microRNAs' roles in pancreatic cancer (PC) cell biology, particularly in regulating pathways related to tumorigenesis. The study aimed to explore the hub miRNAs in PC and underlying mechanisms by bioinformatics and fundamental experiments. RNA datasets collected from the Gene Expression Omnibus were analysed to find out differentially expressed RNAs (DERNAs). The miRNA-mRNA and protein-protein interaction (PPI) networks were built. The clinicopathological features and expressions of hub miRNAs and hub mRNAs were explored. Dual-luciferase reporter gene assay was performed to assess the interaction between microRNA and target gene. RT-qPCR and western blot were employed to explore RNA expression. The roles of RNA were detected by CCK-8 test, wound healing, transwell, and flow cytometry experiment. We verified 40 DEmiRNAs and 1613 DEmRNAs, then detected a total of 69 final functional mRNAs (FmRNAs) and 23 DEmiRNAs. In the miRNA-mRNA networks, microRNA-130b (miR-130b) was the hub RNA with highest degrees. Clinical analysis revealed that miR-130b was considerably lower expressed in cancerous tissues than in healthy ones, and patients with higher-expressed miR-130b had a better prognosis. Mechanically, miR-130b directly targeted MET in PC cells. Cell functional experiments verified that miR-130b suppressed cell proliferation, migration, promoted apoptosis, and inhibited the PI3K/Akt pathway by targeting MET in PC cells. Our findings illustrated the specific molecular mechanism of miR-130b regulating PC progress. The miR-130b/MET axis may be an alternative target in the therapeutic intervention of PC and provide an opportunity to deepen our understanding of the pathogenesis of PC.

Pseudogene Lamr1-ps1 Aggravates Early Spatial Learning Memory Deficits in Alzheimer's Disease Model Mice

Alzheimer's disease (AD), a neurodegenerative disorder with complex etiologies, manifests through a cascade of pathological changes before clinical symptoms become apparent. Among these early changes, alterations in the expression of non-coding RNAs (ncRNAs) have emerged as pivotal events. In this study, we focused on the aberrant expression of ncRNAs and revealed that Lamr1-ps1, a pseudogene of the laminin receptor, significantly exacerbates early spatial learning and memory deficits in APP/PS1 mice. Through a combination of bioinformatics prediction and experimental validation, we identified the miR-29c/Bace1 pathway as a potential regulatory mechanism by which Lamr1-ps1 influences AD pathology. Importantly, augmenting the miR-29c-3p levels in mice ameliorated memory deficits, underscoring the therapeutic potential of targeting miR-29c-3p in early AD intervention. This study not only provides new insights into the role of pseudogenes in AD but also consolidates a foundational basis for considering miR-29c as a viable therapeutic target, offering a novel avenue for AD research and treatment strategies.

Environmentally induced variation in sperm sRNAs is linked to gene expression and transposable elements in zebrafish offspring

Environmental factors affect not only paternal condition but may translate into the following generations where sperm-mediated small RNAs (sRNAs) can contribute to the transmission of paternal effects. sRNAs play a key role in the male germ line in genome maintenance and repair, and particularly in response to environmental stress and the resulting increase in transposable element (TE) activity. Here, we investigated how the social environment (high competition, low competition) of male zebrafish Danio rerio affects sRNAs in sperm and how these are linked to gene expression and TE activity in their offspring. In a first experiment, we collected sperm samples after exposing males to each social environment for 2 weeks to test for differentially expressed sperm micro- (miRNA) and piwi-interacting RNAs (piRNA). In a separate experiment, we performed in vitro fertilisations after one 2-week period using a split-clutch design to control for maternal effects and collected embryos at 24 h to test for differentially expressed genes and TEs. We developed new computational prediction tools to link sperm sRNAs with differentially expressed TEs and genes in the embryos. Our results support the idea that the molecular stress response in the male germ line has significant down-stream effects on the molecular pathways, and we provide a direct link between sRNAs, TEs and gene expression.

Mechanisms of apoptosis-related non-coding RNAs in ovarian cancer: a narrative review

Ovarian cancer remains a major challenge in oncology due to its complex biology and late-stage diagnosis. Recent advances in molecular biology have highlighted the crucial role of non-coding RNAs (ncRNAs) in regulating apoptosis and cancer progression. NcRNAs, including microRNAs, long non-coding RNAs, and circular RNAs, have emerged as significant players in the molecular networks governing ovarian cancer. Despite these insights, the precise mechanisms by which ncRNAs influence ovarian cancer pathology are not fully understood. This complexity, combined with the heterogeneity of the disease and the development of treatment resistance, poses substantial obstacles to effective therapeutic development. Additionally, the lack of reliable early detection methods further complicates treatment strategies. This manuscript reviews the current state of research on ncRNAs in ovarian cancer, discusses the challenges in translating these findings into clinical applications, and outlines potential future directions. Emphasis is placed on the need for integrated approaches to unravel the intricate roles of ncRNAs, improve early detection, and develop personalized treatment strategies to address the diverse and evolving nature of ovarian cancer. While these findings provide valuable insights, it is crucial to recognize that many results are based on preclinical studies and require further validation to establish their clinical applicability.

Mitochondrial calcium uniporter as biomarker and therapeutic target for breast cancer: Prognostication, immune microenvironment, epigenetic regulation and precision medicine

INTRODUCTION

Mitochondrial calcium uniporter (MCU) is a central subunit of MCU complex that regulate the levels of calcium ions within mitochondria. A comprehensive understanding the implications of MCU in clinical prognostication, biological understandings and therapeutic opportunity of breast cancer (BC) is yet to be determined.

OBJECTIVES

This study aims to investigate the role of MCU in predictive performance, tumor progression, epigenetic regulation, shaping of tumor immune microenvironment, and pharmacogenetics and the development of anti-tumor therapy for BC.

METHODS

The downloaded TCGA datasets were used to identify predictive ability of MCU expressions via supervised learning principle. Functional enrichment, mutation landscape, immunological profile, drug sensitivity were examined using bioinformatics analysis and confirmed by experiments exploiting human specimens, in vitro and in vivo models.

RESULTS

MCU copy numbers increase with MCU gene expression. MCU expression, but not MCU genetic alterations, had a positive correlation with known BC prognostic markers. Higher MCU levels in BC showed modest efficacy in predicting overall survival. In addition, high MCU expression was associated with known BC prognostic markers and with malignancy. In BC tumor and sgRNA-treated cell lines, enrichment pathways identified the involvement of cell cycle and immunity. miR-29a was recognized as a negative epigenetic regulator of MCU. High MCU levels were associated with increased mutation levels in oncogene TP53 and tumor suppression gene CDH1, as well as with an immunosuppressive microenvironment. Sigle-cell sequencing indicated that MCU mostly mapped on to tumor cell and CD8 T-cells. Inter-databases verification further confirmed the aforementioned observation. miR-29a-mediated knockdown of MCU resulted in tumor suppression and mitochondrial dysfunction, as well as diminished metastasis. Furthermore, MCU present pharmacogenetic significance in cellular docetaxel sensitivity and in prediction of patients' response to chemotherapeutic regimen.

CONCLUSION

MCU shows significant implication in prognosis, outcome prediction, microenvironmental shaping and precision medicine for BC. miR-29a-mediated MCU inhibition exerts therapeutic effect in tumor growth and metastasis.

A Gallbladder-Specific Hydrophobic Bile Acid-FXR-MUC1 Signaling Axis Mediates Cholesterol Gallstone Formation

Differences in the distribution of hydrophilic and hydrophobic bile acids (BA) are observed in mouse models of non-alcoholic fatty liver disease (NAFLD) induced by a high-fat-cholesterol "Western-style" diet (WD), and cholesterol gallstone disease (CGD) induced by a lithogenic diet. Despite sharing common pathological processes, these models exhibit distinct characteristics in their BA pools. The study investigates the impact of hydrophobic BA (HphoBA) and hydrophilic BA (HphilBA) on CGD development using cytochrome-P450-2c70 knockout (C70-KO) mice (miceC70-KO), genetically modified to resemble humans with a hydrophobic BA pool. All miceC70-KO fed the WD develop CGD, resembling human cholelithiasis patients, while WD-fed wild-type (WT) mice (miceWT) show cholesterol-saturated bile but rarely form gallstones. Compared to miceWT, WD-fed miceC70-KO display caveolae microdomain redistribution in the gallbladder mediated by the HphoBA, FXR, and miR30c/e axis, which enhances the Sp1 transcriptional activity of mucin-1 (MUC1) genes through nuclear translocation of protein kinase Cζ (PKCζ). These changes contribute to increased production of pronucleating agents (MUC1 and MUC5ac) and accelerate crystallization of gallbladder cholesterol. The data also suggest that WD-fed miceC70-KO appropriately model human CGD since lithogenic diet-fed miceWT have a larger BA pool that masks the negative effects of gallbladder FXR on CGD development.

HGF/c-Met Promotes Breast Cancer Tamoxifen Resistance Through the EZH2/HOTAIR-miR-141/200a Feedback Signaling Pathway

Tamoxifen is one of the most frequently used endocrine medications for the treatment of estrogen receptor-positive (ER + ) breast cancer (BC). Unfortunately, tamoxifen resistance (TR) brings more challenges to the clinical treatment, and the mechanisms of TR have not yet been fully clarified. HGF/c-Met is closely associated with cancer metastasis, but whether it is involved in TR remains unclear. In our study, we found that the activation of HGF/c-Met was crucial for TR maintenance. Synergistic interaction with HOTAIR and EZH2 accelerated HGF expression by repressing miR-141/200a. Additionally, HGF/c-Met activated NF-κB, forming a positive feedback loop of EZH2/HOTAIR-miR-141/200a-HGF/c-Met-NF-κB. Our findings indicated that HGF/c-Met functioned as an important biomarker for TR, and HGF/c-Met inhibition provided a novel approach to TR treatment.

In vivo AGO-APP identifies a module of microRNAs cooperatively preserving neural progenitors

MicroRNAs are essential regulators of gene expression. Their function is particularly important during neurogenesis, when the production of large numbers of neurons from a limited number of neural stem cells depends on the precise control of determination, proliferation and differentiation. However, microRNAs can target many mRNAs and vice-versa, raising the question of how specificity is achieved to elicit a precise regulatory response. Here we introduce in vivo AGO-APP, a novel approach to purify Argonaute-bound, and therefore active microRNAs from specific cell types. Using AGO-APP in the larval Drosophila central nervous system, we identify a module of microRNAs predicted to redundantly target all iconic genes known to control the transition from neuroblasts to neurons. While microRNA overexpression generally validated predictions, knockdown of individual microRNAs did not induce detectable phenotypes. In contrast, neuroblasts were induced to differentiate precociously when several microRNAs were knocked down simultaneously. Our data supports the concept that at physiological expression levels, the cooperative action of miRNAs allows efficient targeting of entire gene networks.

miR-708-5p is elevated in bipolar patients and can induce mood disorder-associated behavior in mice

Mood disorders (MDs) are caused by an interplay of genetic and environmental (GxE) risk factors. However, molecular pathways engaged by GxE risk factors are poorly understood. Using small-RNA sequencing in peripheral blood mononuclear cells (PBMCs), we show that the bipolar disorder (BD)-associated microRNA miR-708-5p is upregulated in healthy human subjects with a high genetic or environmental predisposition for MDs. miR-708-5p is further upregulated in the hippocampus of rats which underwent juvenile social isolation, a model of early life stress. Hippocampal overexpression of miR-708-5p in adult male mice is sufficient to elicit MD-associated behavioral endophenotypes. We further show that miR-708-5p directly targets Neuronatin (Nnat), an endoplasmic reticulum protein. Restoring Nnat expression in the hippocampus of miR-708-5p-overexpressing mice rescues miR-708-5p-dependent behavioral phenotypes. Finally, miR-708-5p is upregulated in PBMCs from patients diagnosed with MD. Peripheral miR-708-5p expression allows to differentiate male BD patients from patients suffering from major depressive disorder (MDD). In summary, we describe a potential functional role for the miR-708-5p/Nnat pathway in MD etiology and identify miR-708-5p as a potential biomarker for the differential diagnosis of MDs.

Analysis of genetic polymorphism and expression of SOX2 in oral leukoplakia: a case-control study

PURPOSE

To investigate the association of SOX2 polymorphisms with oral leukoplakia with dysplasia (OLD) and compare it with the immunohistochemical expression of SOX-2.

METHODS

The samples comprised 64 patients with oral leukoplakia and 20 with normal oral mucosa who were subjected to SOX2 polymorphism rs77677339 genotyping by real-time polymerase chain reaction and immunohistochemistry for SOX-2 (basal epithelium expression, suprabasal and total; nuclear area and intensity). Statistical tests included the Chi-square and Fisher's exact tests.

RESULTS

No significant difference was observed in genotype distribution between the OLD and control groups. The GG genotype (96.9%) was observed in the OLD group and 100% in the control group. The GA genotype was not observed in the control group. Statistical comparisons between the immunohistochemistry and genetic results were not statistically significant. No association was identified between rs77677339 and immunohistochemistry in OLD; however, the presence of allele A in heterozygotes with OLD suggests that this allele may serve as a risk marker.

CONCLUSION

The variant rs77677339 is localized in a region that contains different micro-RNA-binding sites, which can lead to changes in gene expression, contributing to OLD development through unclear molecular mechanisms. This study presents the preliminary results for this single nucleotide polymorphism in the literature.

An integrated multi-omics biomarker approach using molecular profiling and microRNAs for evaluation of pancreatic cyst fluid

BACKGROUND

Classification and risk stratification of pancreatic cysts are challenging because of limited radiographic and cytomorphologic features. Although molecular profiling has emerged as an ancillary test for pancreatic cyst fluid (PCF), additional high-sensitivity and -specificity biomarkers are still needed for improved classification.

METHODS

In this study, PCF from 93 patients, including intraductal papillary mucinous neoplasms (n = 65), mucinous cystic neoplasms (n = 9), serous cystadenomas (n = 9), pancreatic cyst not otherwise specified (n = 8), and pseudocysts (n = 2), were evaluated for biomarkers. Molecular profiling by next-generation sequencing was performed, and a subset of the cases (n = 32) were interrogated with 2083 microRNAs (miRNAs) to evaluate their use for pancreatic cyst risk stratification.

RESULTS

As independent PCF biomarkers in 32 cases with histologic diagnoses, three miRNAs performed significantly better than mutant KRAS, mutant GNAS, carcinoembryonic antigen (CEA), and serum carbohydrate antigen 19-9 (CA19-9) in discriminating high-risk from low-risk cysts. The three elevated miRNAs in combination with mutant KRAS, mutant GNAS, and serum CA19-9 displayed similar diagnostic performance (miR-4461: area under the curve [AUC], 0.950; 95% confidence interval [CI], 0.800-1; miR-6723-5p: AUC, 0.958; 95% CI, 0.850-1; miR-6755-3p: AUC, 0.942; 95% CI, 0.816-1) in discriminating high-risk from low-risk cysts, when compared to mutant KRAS, mutant GNAS, CEA, and serum CA19-9 (AUC, 0.950; 95% CI, 0.825-1). In the absence of CA19-9, the three-marker panel of KRAS, GNAS, and miRNAs showed marginally improved performance compared with KRAS, GNAS, and CEA, which highlights the potential utility of miRNAs as biomarkers in PCF analysis.

CONCLUSIONS

These findings demonstrate that a multiomics biomarker approach with elevated PCF miRNAs with mutant KRAS, mutant GNAS, and serum CA19-9 may help in better detecting high-risk cysts for early clinical intervention.

EasyCircR: Detection and reconstruction of circular RNAs post-transcriptional regulatory interaction networks

Circular RNAs (circRNAs) are regulatory RNAs that play a crucial role in various biological activities and have been identified as potential biomarkers for neurological disorders and cancer. CircRNAs have emerged as significant regulators of gene expression through different mechanisms, including regulation of transcription and splicing, modulation of translation, and post-translational modifications. Additionally, some circRNAs operate as microRNA (miRNA) sponges in the cytoplasm, boosting post-transcriptional expression of target genes by inhibiting miRNA activity. Although existing pipelines can reconstruct circRNAs, identify miRNAs sponged by them, retrieve cascade-regulated mRNAs, and represent the regulatory interactions as complex circRNA-miRNA-mRNA networks, none of the state-of-the-art approaches can discriminate the biological level at which the mRNAs involved in the interactions are regulated, avoiding considering potential target mRNAs not regulated at the post-transcriptional level. EasyCircR is a novel R package that combines circRNA detection and reconstruction with post-transcriptional gene expression analysis (exon-intron split analysis) and miRNA response element prediction. The package enables estimation and visualization of circRNA-miRNA-mRNA interactions through an intuitive Shiny application, leveraging the post-transcriptional regulatory nature of circRNA-miRNA relationship and excluding unrealistic regulatory interactions at the biological level. EasyCircR source code, Docker container and user guide are available at: https://github.com/InfOmics/EasyCircR.

The impact of extracellular glucose concentrations on antioxidant capacity, viability, and microRNA expression in TM4 Sertoli cells

This study investigates the impact of extracellular glucose concentrations on antioxidant capacity, viability, and microRNA (miR) expression in TM4 Sertoli cell lines. TM4 cells were cultured in high-glucose (115 µm) and low-glucose (<505 µm) conditions to simulate hyperglycemia and glucose starvation, respectively. The study measured total antioxidant capacity (TAC), malondialdehyde (MDA), total oxidant status (TOS), glutathione (GSH), glutathione disulfide (GSSG), NADP/NADPH, glutathione peroxidase (GPX), and glutathione reductase (GR) levels. MiR-17, miR-34, miR-106a, and miR-200a expression levels were assessed. Cell viability and apoptosis were evaluated using MTT assay and acridine-orange staining. Results indicated that high glucose reduced miR-17 expression while low glucose increased it. Both glucose conditions elevated miR-34, miR-106a, and miR-200a expressions. TAC levels decreased, while TOS and MDA levels increased significantly under both conditions. High glucose had no significant effect on GPX and GR levels, whereas low glucose decreased them. Both conditions led to reduced GSH levels, increased GSSG levels, and altered NADP/NADPH ratio. Increased apoptosis and decreased cell viability were observed under both glucose conditions. These findings suggest that extracellular glucose levels significantly dysregulate miRNA expression, antioxidant capacities, and redox buffer systems in TM4 cells. High glucose conditions suppress miR-17 expression, increase miR-34 and miR-106a levels, and induce reductive buffer imbalance. Conversely, low glucose conditions trigger compensatory mechanisms via increased miR-17 expression to enhance antioxidant status while reducing GPX and GR levels. These results provide insights into the molecular responses of Sertoli cells under varying glucose environments, highlighting potential therapeutic pathways for conditions like diabetes and metabolic dysfunctions.

Circulating MicroRNAs: functional biomarkers for melanoma prognosis and treatment

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

Loss of tricellular tight junction tricellulin leads to hyposalivation in Sjögren's syndrome

Tricellulin, a key tricellular tight junction (TJ) protein, is essential for maintaining the barrier integrity of acinar epithelia against macromolecular passage in salivary glands. This study aims to explore the role and regulatory mechanism of tricellulin in the development of salivary gland hypofunction in Sjögren's syndrome (SS). Employing a multifaceted approach involving patient biopsies, non-obese diabetic (NOD) mice as a SS model, salivary gland acinar cell-specific tricellulin conditional knockout (TricCKO) mice, and IFN-γ-stimulated salivary gland epithelial cells, we investigated the role of tricellulin in SS-related hyposalivation. Our data revealed diminished levels of tricellulin in salivary glands of SS patients. Similarly, NOD mice displayed a reduction in tricellulin expression from the onset of the disease, concomitant with hyposecretion and an increase in salivary albumin content. Consistent with these findings, TricCKO mice exhibited both hyposecretion and leakage of macromolecular tracers when compared to control animals. Mechanistically, the JAK/STAT1/miR-145 axis was identified as mediating the IFN-γ-induced downregulation of tricellulin. Treatment with AT1001, a TJ sealer, ameliorated epithelial barrier dysfunction, restored tricellulin expression, and consequently alleviated hyposalivation in NOD mice. Importantly, treatment with miR-145 antagomir to specifically recover the expression of tricellulin in NOD mice significantly alleviated hyposalivation and macromolecular leakage. Collectively, we identified that tricellulin deficiency in salivary glands contributed to hyposalivation in SS. Our findings highlight tricellulin as a potential therapeutic target for hyposecretion, particularly in the context of reinforcing epithelial barrier function through preventing leakage of macromolecules in salivary glands.

The Identification of Novel Therapeutic Biomarkers in Rheumatoid Arthritis: A Combined Bioinformatics and Integrated Multi-Omics Approach

Rheumatoid arthritis (RA) is a multifaceted autoimmune disease that is marked by a complex molecular profile influenced by an array of factors, including genetic, epigenetic, and environmental elements. Despite significant advancements in research, the precise etiology of RA remains elusive, presenting challenges in developing innovative therapeutic markers. This study takes an integrated multi-omics approach to uncover novel therapeutic markers for RA. By analyzing both transcriptomics and epigenomics datasets, we identified common gene candidates that span these two omics levels in patients diagnosed with RA. Remarkably, we discovered eighteen multi-evidence genes (MEGs) that are prevalent across transcriptomics and epigenomics, twelve of which have not been previously linked directly to RA. The bioinformatics analyses of the twelve novel MEGs revealed they are part of tightly interconnected protein-protein interaction networks directly related to RA-associated KEGG pathways and gene ontology terms. Furthermore, these novel MEGs exhibited direct interactions with miRNAs linked to RA, underscoring their critical role in the disease's pathogenicity. Overall, this comprehensive bioinformatics approach opens avenues for identifying new candidate markers for RA, empowering researchers to validate these markers efficiently through experimental studies. By advancing our understanding of RA, we can pave the way for more effective therapies and improved patient outcomes.

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

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

miR-1297 is frequently downmodulated in flat epithelial atypia of the breast and promotes mammary neoplastic transformation via EphrinA2 regulation

Breast cancer ranks as the most prevalent form of cancer globally. Currently, advanced screening methods have significantly improved early detection rates. These achievements have led to more non-invasive cancer diagnoses and underscored the clinical relevance of precursor lesions like flat epithelial atypia (FEA), a histological condition characterized by mild atypical changes in the normal epithelium lining the mammary ducts. Despite the increasing detection of FEA in mammary biopsy, our understanding of the biological behavior of this entity remains limited and, as a consequence, the clinical management of patients is still being debated. Evidence from the literature indicates that dysregulation of microRNAs contributes to all stages of breast cancer progression, potentially serving as valuable markers of disease evolution. In this study, through a comparison of the microRNA profiles of normal mammary epithelium, FEA, and non-invasive breast cancer in three cohorts of patients, we identified downregulation of miR-1297 as a common feature in both FEA and non-invasive breast cancer compared to the normal counterpart. Mechanistically, overexpression of miR-1297 inhibits the growth of breast cancer cells by targeting the oncogenic receptor tyrosine kinase EphrinA2. In contrast, downregulation of miR-1297 increases proliferation and alters the morphology of normal mammary epithelial cells in a three-dimensional context. These findings pinpoint the downregulation of miR-1297 as an early event in mammary transformation and suggest its potential role as a driver of progression in FEA, harboring the capacity to evolve into malignancy.

Massively parallel reporter assays identify functional enhancer variants at QT interval GWAS loci

Genome-wide association studies (GWAS) have identified >30 loci with multiple common noncoding variants explaining interindividual electrocardiographic QT interval (QTi) variation. Of the many types of noncoding functional elements, here we sought to identify transcriptional enhancers with sequence variation and their cognate transcription factors (TFs) that alter the expression of proximal cardiac genes to affect QTi variation. We used massively parallel reporter assays (MPRA) in mouse cardiomyocyte HL-1 cells to screen for functional enhancer variants among 1,018 QTi-associated GWAS variants that overlap candidate cardiac enhancers across 31 loci. We identified 445 GWAS variant-containing enhancers of which 79 showed significant allelic difference in enhancer activity across 21 GWAS loci, with multiple enhancer variants per locus. Of these, we predicted differential binding by cardiac TFs, including AP-1, ATF-1, GATA2, MEF2, NKX2.5, SRF and TBX5 which are known to play key roles in development and homeostasis, at 49 enhancer variants. Finally, we used expression quantitative trait locus mapping and predicted promoter-enhancer contacts to identify 14 candidate target genes through analyses of 36 enhancer variants at 16 loci. This study provides strong evidence for 14 cardiac genes, 10 of them novel, impacting on QTi variation, beyond explaining observed genetic associations.

Manuscript title: unravelling the neuroprotective role of miR-27a-3p in the MAPK pathway in Parkinson's disease

Parkinson's disease (PD) is a multifaceted neurodegenerative disorder characterized by dopaminergic neuron loss and the presence of Lewy bodies. Beyond its hallmark motor symptoms, PD involves significant neuroinflammation and immune dysfunction, driven by dysregulated signalling pathways such as the Mitogen-Activated Protein Kinase (MAPK) pathway. This study investigates the therapeutic potential of hsa-miR-27a-3p in modulating these pathways, with a focus on its interaction with MKK7, a key MAPK component. Bioinformatics and experimental analyses, using miRNA-mRNA interactions and construct a protein-protein interaction (PPI) network, confirm that hsa-miR-27a-3p directly binds to the 3' untranslated region (3'UTR) of MKK7, reducing its expression. Overexpression of hsa-miR-27a-3p improves cell viability, mitigates morphological changes, and reduces neurotoxicity in SH-SY5Y (human neuroblastoma cell line for experimental validation) cells exposed to MPP +, a PD neurotoxin. The study further demonstrates that hsa-miR-27a-3p modulates apoptotic pathways by increasing anti-apoptotic BCL2 while downregulating pro-apoptotic BAX and P53, as assessed through Western blot analysis of protein expression in SH-SY5Y cells transfected with miR-27a-3p mimic or negative control, followed by quantification of protein levels. Additionally, hsa-miR-27a-3p suppresses neuroinflammatory responses by significantly reducing TNF-α and IL1β levels. Western blot analysis reveals that hsa-miR-27a-3p inhibits phosphorylation of MKK7 and other MAPK pathway components, such as JNK and p38, highlighting its role in attenuating neuroinflammation and oxidative stress. These findings establish a negative correlation between hsa-miR-27a-3p expression and key neurodegenerative processes, suggesting its potential as a therapeutic target. This study provides comprehensive insights into the neuroprotective mechanisms of hsa-miR-27a-3p, paving the way for innovative interventions in PD management.

Evaluation of Lipid-Based Transfection in Primary Monocytes Within an Ex Vivo Whole-Blood Model

Transfection is a fundamental method in biomedical research to study intracellular molecular mechanisms by manipulating target protein expression. Various methods have been developed to deliver nucleic acids into the cells of interest in vitro, with chemical transfection by cationic lipids being the most widely used for RNA interference (RNAi). However, translating these in vitro results into in vivo remains a significant challenge. In this study, we established an ex vivo transfection model using cationic lipids in human whole blood. Three different lipid-based reagents were evaluated regarding toxicity, transfection efficiency, and immunogenicity across leukocyte populations using spectral flow cytometry. CD14+ monocytes were identified as the primary population to be transfected by cationic lipids in whole blood. To assess immunogenicity, the monocyte-specific activation markers CD80 and human leukocyte antigen DR isotype (HLA-DR) were analyzed upon transfection. Our results demonstrated that Lipofectamine RNAiMAX outperforms the other two reagents, showing low toxicity and high transfection efficiency in combination with a minimal potential for monocyte activation. Functional knockdown experiments using siRNA targeting CIITA and the microRNA mir-3972 targeting HLA-DRA showed dose-dependent suppression in HLA-DR expression. This study provides the framework for preliminary testing of RNAi in a physiologically relevant ex vivo model, enabling assessment of key endpoints such as toxicity, transfection efficiency, and immune activation potential of gene delivery systems.

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

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

Bioinformatics analysis and experimental validation of C6orf120 as a potential prognostic marker and therapeutic target for liver hepatocellular carcinoma

The C6orf120 gene is a novel gene whose function has not been fully defined. Previous studies have associated it with various liver pathologies, but its specific role in hepatocellular carcinoma (LIHC) remains unclear. This study aimed to investigate the diagnostic and prognostic value of C6orf120 in LIHC, as well as its potential biological functions. In this preliminary research, we utilized data from various databases and bioinformatics tools, including TCGA, GEO, TIMER2, HPA, GEPIA, Linkeomics, Metascape, CIBERSORT, TargetScan, DIANA-microT, RNAinter, and ENCORI, to analyze the expression patterns and mechanisms of C6orf120 in LIHC. Our bioinformatics analysis revealed that C6orf120 is upregulated in LIHC and may serve as a diagnostic and prognostic biomarker. The aberrant expression of C6orf120 in LIHC was further supported by clinical samples and cell lines. In vitro experiments demonstrated that the knockdown of C6orf120 in HepG2 cells significantly reduced migration capacity without affecting proliferation. Additionally, the downregulation of C6orf120 in LIHC cells appeared to inhibit endothelial cell migration and angiogenesis, which are critical in tumorigenesis and development. In conclusion, our findings suggest that C6orf120 could serve as a novel diagnostic and prognostic biomarker for LIHC and is expected to be a prognostic marker and a potential therapeutic target in the clinical management of LIHC.

Functional validation to explore the protective role of miR-223 in Staphylococcus aureus-induced bovine mastitis

BACKGROUND

Mastitis caused by Staphylococcus aureus (S. aureus) is one of the most intractable problems for the dairy industry, causing significantly reduced milk yields and early slaughter of cows worldwide. MicroRNAs (miRNAs) can post-transcriptionally regulate gene expression and studies in recent years have shown the importance of miRNA-associated gene regulation in S. aureus-induced mastitis.

RESULTS

In this study, to investigate the role of miR-223 in mastitis, we performed experiments to overexpress and suppress miR-223 in an immortalized bovine mammary epithelial cell line (MAC-T) infected with S. aureus. Overexpression of miR-223 in MAC-T cells repressed cell apoptosis and necrosis induced by S. aureus infection, whereas suppression of miR-223 had the opposite effect. Transcriptome expression profiling with weighted gene co-expression network analysis (WGCNA) and gene set variation analysis (GSVA) showed that miR-223 affects apoptosis and inflammation-related pathways. Furthermore, differentially expressed (DE) genes were evaluated, and genes exhibiting contrasting expression trends in the miR-223 overexpressed and suppressed groups were assessed as potential target genes of miR-223. Potential target genes, including CDC25B, PTPRF, DCTN1, and DPP9, were observed to be associated with apoptosis and necroptosis. Finally, through integrative analysis of genome-wide association study (GWAS) data and the animal quantitative trait loci (QTL) database, we determined that target genes of miR-223 were significantly enriched in single-nucleotide polymorphisms (SNP) and QTLs related to somatic cell count (SCC) and mastitis.

CONCLUSION

In summary, miR-223 has an inhibitory effect on S. aureus-induced cell apoptosis and necrosis by regulating PTPRF, DCTN1, and DPP9. These genes were significantly enriched in QTL regions associated with bovine mastitis resistance, underscoring their relevance in genetic regulation of disease resilience. Our findings provide critical genetic markers for enhancing mastitis resistance, particularly S. aureus-induced mastitis, through selective breeding. This work offers valuable insights for developing cattle with improved resistance to mastitis via targeted genetic selection.

Effects of Clinical Covariates on Serum miRNA Expression among Women without Ovarian Cancer

BACKGROUND

Serum miRNAs are potential biomarkers for ovarian cancer; however, many factors may influence miRNA expression. To understand potential confounders in miRNA analysis, we examined how sociodemographic factors and comorbidities, including known ovarian cancer risk factors, influence serum miRNA levels in women without ovarian cancer.

METHODS

Data from 1,576 women from the Mass General Brigham Biobank collected between 2012 and 2019, excluding subjects previously or subsequently diagnosed with ovarian cancer, were examined. Using a focused panel of 179 miRNA probes optimized for serum profiling, miRNA expression was measured by flow cytometry using the Abcam FirePlex assay and correlated with subjects' electronic medical records.

RESULTS

The study population broadly reflected the New England population. The median age of subjects was 49 years, 34% were current or prior smokers, 33% were obese (body mass index > 30 kg/m2), 49% were postmenopausal, and 11% had undergone prior bilateral oophorectomy. Significant differences in miRNA expression were observed among ovarian risk factors such as age, obesity, menopause, BRCA1 or BRCA2 germline mutations, or existence of breast cancer in family history. Additionally, miRNA expression was significantly altered by prior bilateral oophorectomy, hypertension, and hypercholesterolemia. Other variables, such as smoking; parity; age at menarche; hormonal replacement therapy; oral contraception; breast, endometrial, or colon cancer; and diabetes, were not associated with significant changes in the panel when corrected for multiple testing.

CONCLUSIONS

Serum miRNA expression patterns are significantly affected by patient demographics, exposure history, and medical comorbidities.

IMPACT

Understanding confounders in serum miRNA expression is important for refining clinical assays for cancer screening.

DNA methylation dynamics in the small intestine of egg-selected laying hens along egg production stages

Decades of artificial selection have markedly enhanced egg production efficiency, yet the epigenetic underpinnings, notably DNA methylation dynamics in the gut, remain largely unexplored. Here, we investigate how breeds and developmental stages influence DNA methylation profiles in laying hens, and their potential relationship to laying performance and gut health. We compared two highly selected laying hen strains, Lohmann Brown-Classic (LB) and Lohmann Selected Leghorn-Classic (LSL), which exhibited similar egg production but divergent physiological, metabolic, and immunological characteristics. Our sampling encompassed key developmental stages: the pullet stage (10 and 16 wk old), peak production (24 and 30 wk old), and later stage (60 wk old) (n = 99; 10 per group), allowing us to elucidate the temporal dynamics of epigenetic regulation. Our findings highlight a crucial window of epigenetic modulation during the prelaying period, characterized by stage-specific methylation alterations and the involvement of predicted transcription factor motifs within methylated regions. This observation was consistent with the expression patterns of DNA methyltransferases (DNMTs), including DNMT1, DNMT3A, and DNMT3B. In addition, a higher methylation level was observed in specific loci or regions in the LSL compared with the LB strain. Notably, we uncover strain-specific differences in methylation levels, particularly pronounced in genomic regions associated with intestinal integrity, inflammation, and energy homeostasis. Our research contributes to the multidisciplinary framework of epigenetics and egg-laying performance, offering valuable implications for poultry production and welfare.NEW & NOTEWORTHY Our study reveals key methylation changes in the jejunum mucosa of laying hens across developmental stages and between strains, with implications for gut health, immune function, and egg production. These findings highlight a crucial role of epigenetic regulation in optimizing performance.

Integrated transcriptomic and regulatory RNA profiling reflects complex pathophysiology and uncovers a conserved gene signature in end stage heart failure

Background

Heart failure (HF) is a complex syndrome. Despite availability of multiple treatment options, the mortality remains high and the quality of life poor. Better understanding of the underlying pathophysiological processes can lead to development of novel therapies. Multiple comparative transcriptomics studies, which revealed gene level changes in the key pathophysiological pathways in failing hearts, point towards heterogeneity from interplay of disease stage, etiologies and ethnicity. Transcriptomic characterization of HF in patients from different ethnicities can potentially help in understanding the heterogeneity imparted by various factors and the core elements in heart failure.

Methods & results

An integrated analysis of bulk transcriptome and microRNA sequencing from the cardiac tissues of 30 South Asian (SA) patients having HF with reduced ejection fraction (HFrEF) and 19 control subjects was conducted. Plasma miRNAs from a subset of HFrEF and control patients were also sequenced to understand their biomarker potential. The altered transcriptome from the myocardium of SA HFrEF patients reflected cardiac muscle contraction, cellular energetics, altered immune signaling and extracellular matrix remodelling as predominant pathophysiological mechanisms. The SA HFrEF patients also showed dysregulation of multiple microRNAs in cardiac tissue like miR-216, miR-217, miR-184 and miR-9983. Many of these miRNAs, such as miR184 and few others, showed altered levels in both the plasma and cardiac tissue of HFrEF patients suggesting their biomarker potential. The diversity in the HFrEF transcriptomes from published studies led us to examine the core HF genes in our cohort. A gene signature generated using machine learning (ML) from the top dysregulated genes in SA HFrEF cohort stratified HF from controls in other cohorts. The sensitivity of the HF gene signature was further improved when union of two cohorts was used as a training set. Our ML analyses developed a core HF gene signature consisting of 21 genes that can stratify HF patients from controls with 98 % sensitivity in all the tested cohorts.

Conclusions

This study reveals molecular changes underlying the pathophysiology as reflected by coding and regulatory non-coding components of transcriptome from South Asian patients and uncovers a conserved gene signature for HF.

A novel frameshift TBX4 variant in a family with ischio-coxo-podo-patellar syndrome and variable severity

BACKGROUND

Congenital anomalies of the knee are a spectrum of rare disorders with wide clinical and genetic variability, which are mainly due to the complex processes underlying knee development. Despite progresses in understanding pathomechanisms and associated genes, many patients remain undiagnosed.

OBJECTIVE

To uncover the genetic bases of a congenital patellar dislocation affecting multiple family members with variable severity.

METHODS

We performed ES in the proband and his father, both showing bilateral patellar dislocation, his sister with a milder similar condition, and his unaffected mother. Sanger sequencing was then performed in the proband's brother and paternal aunt, both affected as well.

RESULTS

ES and Sanger sequencing identified the presence of the novel heterozygous frameshift mutation c.735delT in the TBX4 gene in all affected family members. TBX4 is associated with autosomal dominant ischio-coxo-podo-patellar syndrome with/without pulmonary arterial hypertension (ICPPS, #147891), reaching a diagnosis in the family. Intrafamilial clinical heterogeneity suggests that other factors might be involved, such as additional variants in TBX4 or in other modifier genes. Interestingly, we identified three additional variants in the TBX4 gene in the proband only, whose phenotype is more severe. Despite being classified as benign, one of these variants is predicted to disrupt a splicing protein binding site, and may therefore affect TBX4 alternative splicing, accounting for the more severe phenotype of the proband.

CONCLUSION

We expand and further delineate the genotypic and phenotypic spectrum of ICPPS. Further studies are necessary to shed light on the potential effect of this variant and on the variable phenotypic expressivity of TBX4-related phenotypes.

Regulation of KIF23 by miR-107 controls replicative tumor cell fitness in mouse and human hepatocellular carcinoma

BACKGROUND & AIMS

In hepatocellular carcinoma (HCC), successful translation of experimental targets identified in mouse models to human patients has proven challenging. In this study, we used a comprehensive transcriptomic approach in mice to identify novel potential targets for therapeutic intervention in humans.

METHODS

We analyzed combined genome-wide miRNA and mRNA expression data in three pathogenically distinct mouse models of liver cancer. Effects of target genes on hepatoma cell fitness were evaluated by proliferation, survival and motility assays. TCGA and GEO databases, in combination with tissue microarrays, were used to validate the mouse targets and their impact on human HCC prognosis. Finally, the functional effects of the identified targets on tumorigenesis and tumor therapy were tested in hydrodynamic tail vein injection-based preclinical HCC models in vivo.

RESULTS

The expression of miR-107 was found to be significantly reduced in mouse models of liver tumors of various etiologies and in cohorts of humans with HCC. Overexpression of miR-107 or inhibition of its novel target kinesin family member 23 (Kif23) significantly reduced proliferation by interfering with cytokinesis, thereby controlling survival and motility of mouse and human hepatoma cells. In humans, KIF23 expression was found to be a prognostic marker in liver cancer, with high expression associated with poor prognosis. Hydrodynamic tail vein injection of vectors carrying either pre-miR-107 or anti-Kif23 shRNA inhibited the development of highly aggressive c-Myc-NRAS-induced liver cancers in mice.

CONCLUSIONS

Disruption of the miR-107/Kif23 axis inhibited hepatoma cell proliferation in vitro and prevented oncogene-induced liver cancer development in vivo, offering a novel potential avenue for the treatment of HCC in humans.

IMPACT AND IMPLICATIONS

Our study revealed the central role of the miR-107/KIF23 axis in controlling tumor cell fitness and hepatocellular carcinoma progression. The results demonstrate that the overexpression of miR-107 or silencing of its target, KIF23, markedly suppresses the proliferation, survival, and motility of human and mouse hepatoma cells. In this work, we demonstrate that the disruption of miR-107/Kif23 signaling effectively protects mice from an aggressive form of oncogene-induced liver cancer in vivo, implying that targeting miR-107/KIF23 might be a novel therapeutic approach for hepatocellular carcinoma in humans.