Search Results (2,227)

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. Full article

This study describes a novel technique to analyze the extracellular vesicle (EV)-derived microRNA (miRNA) crosstalk between equine chondrocytes and synoviocytes. Donor cells (chondrocytes, n = 8; synoviocytes, n = 9) were labelled with 5-ethynyl uridine (5-EU); EVs were isolated from culture media and incubated with recipient cells (chondrocytes [n = 5] were incubated with synoviocyte-derived EVs, and synoviocytes [n = 4] were incubated with chondrocyte-derived EVs). Total RNA was extracted from recipient cells; the 5-EU-labelled RNA was recovered and sequenced. Differential expression analysis, pathway analysis, and miRNA target prediction were performed. Overall, 198 and 213 miRNAs were identified in recipient synoviocytes and chondrocytes, respectively. The top five most abundant miRNAs were similar for synoviocytes and chondrocytes (eca-miR-21, eca-miR-221, eca-miR-222, eca-miR-100, eca-miR-26a), and appeared to be linked to joint homeostasis. There were nine differentially expressed (p < 0.05) miRNAs (eca-miR-27b, eca-miR-23b, eca-miR-31, eca-miR-191a, eca-miR-199a-5p, eca-miR-143, eca-miR-21, eca-miR-181a, and eca-miR-181b) between chondrocytes and synoviocytes, which appeared to be linked to migration of cells, apoptosis, cell viability of connective tissue cell, and inflammation. In conclusion, the reported technique was effective in recovering and characterizing the EV-derived miRNA crosstalk between equine chondrocytes and synoviocytes and allowed for the identification of EV-communicated miRNA patterns potentially related to cell viability, inflammation, and joint homeostasis. Full article

Adipose tissue metabolism plays a crucial role in sheep meat quality and the optimization of adipose tissue utilization. To reveal the molecular mechanisms of adipose tissue metabolism during growth in naturally grazing sheep, we investigated the mRNA and miRNA profiles in subcutaneous adipose tissue (SAT) from naturally grazing Sunit sheep at 6, 18, and 30 months of age (Mth-6, Mth-18, and Mth-30). We identified 927 differentially expressed (DE) genes and 134 DE miRNAs in the SAT of sheep at different growth stages. Specifically, the expressions of ACACA, FASN, DGAT2, GPAM, SCD, ELOVL6, HSD17B12, TECR, PKM, TKT, PCK1, CD44, and THBS2S genes were significantly upregulated in Mth-18 and Mth-30 compared to that in Mth-6. These genes promoted fatty acid synthesis, triglyceride synthesis, gluconeogenesis, and extracellular matrix–receptor interaction and decreased glycolysis, leading to increased adipocyte proliferation and fat deposition. Notably, our findings suggested that the reduced activity of the AMPK signaling pathway may be regulated by CAMKK2 and PP2A during sheep growth. Furthermore, our results revealed several DE miRNAs, mml-miR-320b, chi-miR-1388-3p, bta-miR-6715, oar-miR-143, and miR-424, that potentially influence fat metabolism. Overall, this study provides a theoretical basis and new insights into the molecular mechanisms of adipose tissue metabolism during growth in naturally grazing sheep. Full article

Background and Objectives: Laryngeal cancer poses a significant clinical challenge, with late-stage diagnosis contributing to high morbidity and mortality. Circulating microRNAs (miRNAs) represent promising, minimally invasive biomarkers for earlier detection and improved therapeutic monitoring. This pilot study focused exclusively on miRNAs found to be upregulated in laryngeal carcinoma patients, aiming to elucidate their diagnostic and prognostic relevance. Methods: A total of 50 participants meeting standardized inclusion criteria were recruited from the ENT Clinic in Timișoara. Of these, 30 patients provided paired blood samples before and after treatment (surgical or non-surgical). Samples were pooled into three preoperative groups (P1, P2, P3) and three corresponding postoperative groups (C1, C2, C3). miRNAs were extracted from plasma and exosomes, and relative expression was measured by qPCR (Qiagen platform). Statistical analyses included Mann–Whitney U tests, receiver operating characteristic (ROC) curves, and logistic regression. Results: Seven miRNAs consistently exhibited significant upregulation preoperatively. Notably, hsa-miR-424-5p displayed a mean fold change of 4.59 (p = 0.0091) relative to postoperative samples, while hsa-miR-186-5p increased by 2.19-fold (p = 0.0030). hsa-miR-15b-5p also showed a substantial preoperative upregulation of 1.77-fold (p = 0.0057). In ROC analyses, hsa-miR-424-5p yielded an area under the curve (AUC) of 0.82 (95% CI 0.70–0.94), with 78% sensitivity and 80% specificity in distinguishing preoperative from postoperative status. Logistic regression indicated that elevated levels of hsa-miR-424-5p (OR = 1.56, 95% CI 1.10–2.20) and hsa-miR-186-5p (OR = 1.32, 95% CI 1.02–1.68) significantly predicted the preoperative disease state. Conclusions: These data underscore the potential of upregulated circulating miRNAs to serve as biomarkers for active laryngeal cancer and to monitor treatment response. Although preliminary, the findings encourage further research with larger cohorts and additional endpoints. With thorough validation, upregulated miRNAs could be integrated into clinical workflows, enhancing diagnostic precision, risk stratification, and postoperative surveillance in laryngeal cancer. Full article

Understanding the resistance mechanisms of plants against pests contributes to the sustainable deployment of plant resistance in Integrated Pest Management (IPM) programmes. The Mi-1 gene in tomato is the only one described with the capacity to provide resistance to different types of harmful organisms such as plant parasitic nematodes and pest insects, including the whitefly Bemisia tabaci MED (Mediterranean species). In this work, gene expression in the interaction of B. tabaci with susceptible tomato plants lacking the Mi-1 gene (cv. Moneymaker, compatible interaction), and with resistant plants carrying the Mi-1 gene (cv. Motelle, incompatible interaction) was studied using the oligonucleotide microarray technique. Both interactions were studied 2 and 12 days post infestation (dpi) of plants with adult insects. At 2 dpi, 159 overexpressed and 189 repressed transcripts were detected in the incompatible interaction, while these figures were 32 and 47 in the compatible one. Transcriptional reprogramming was more intense at 12 dpi but, as at 2 dpi, the number of transcripts overexpressed and repressed was higher in the incompatible (595 and 437, respectively) than in the compatible (71 and 52, respectively) interaction. According to the Mapman classification, these transcripts corresponded mainly to genes in the protein and RNA categories, some of which are involved in the defence response (signalling, respiratory burst, regulation of transcription, PRs, HSPs, cell wall or hormone signalling). These results provide a wealth of information about possible genes related to the resistance provided by the Mi-1 gene to B. tabaci, and whose role deserves further investigation. Full article

Background: Atopic dermatitis (AD), allergic rhinitis (AR), and chronic rhinosinusitis with nasal polyps (CRSwNP) represent interconnected conditions within the spectrum of type 2 inflammatory diseases. While these conditions share common genetic and epigenetic pathways, the precise molecular mechanisms remain underexplored. Methods: This review integrates the latest insights on the genetic and epigenetic factors linking AD, AR, and CRSwNP, focusing on genome-wide association studies, DNA methylation patterns, histone modifications, and microRNA regulation. Results: In all three conditions, epigenetic modifications, including DNA methylation (Me) and histone acetylation (Ac) and methylation, regulate inflammatory and barrier-related genes, influencing disease severity. Notably, miRNAs such as miR-146a and miR-155 play pivotal roles in modulating inflammation across all three diseases, while disease-specific miRNAs contribute to airway remodeling (miR-125b and miR-21 in AR and CRSwNP). Emerging evidence underscores the role of microbiome-driven inflammasome activation and matrix metalloproteinases (MMP-2, MMP-9, and MMP-12) in perpetuating chronic inflammation and remodeling. Conclusions: The interplay between genetic predispositions, epigenetic modifications, and exposomal factors underscores the systemic nature of type 2 inflammation. A deeper understanding of these interconnected mechanisms could lead to transformative, personalized diagnostic and therapeutic advancements. Full article

Background: Preeclampsia (PE) is a critical complication of pregnancy that affects 3% to 5% of all pregnancies and has been linked to aberrant placentation, causing severe maternal and fetal illness and death. Objectives: This systematic review aims to elucidate the association of in-utero endocrine-disrupting chemical (EDC) exposure and microRNAs and their imprinted genes from prenatal and maternal circulation of PE patients. Methods: Databases such as PubMed, PubMed Central, ScienceDirect, the Comparative Toxicogenomics Database (CTD), ProQuest, EBSCOhost, and Google Scholar were utilized to search for articles that investigate the relationships between selected EDCs and epigenetic events such as DNA methylation and microRNAs that are associated with PE. Results: A total of 29 studies were included in the database search. Altered expression of microRNAs (miR-15a-5p, miR-142-3p, and miR-185) in the placenta of PE patients was positively associated with the urinary concentration of phthalates and phenols in the development of the disease in the first trimester. EDCs such as phenols, phthalates, perfluoroalkyl substances (PFOAs), polybrominated diphenyl ethers (PBDEs), and organochlorine phosphates (OCPs) have been reported to be associated with hypertensive disorders in pregnancy. miRNA-31, miRNA-144, miRNA-145, miRNA-210, placental specific clusters (C14MC, and C19MC) may be used as possible targets for PE because of their potential roles in the onset and progression of PE. Conclusions: Prenatal EDC exposure, including exposure to BPA, showed association with signaling pathways including estrogen, sFlt-1/PlGF, ErbB, MAPK/ERK, and cholesterol mechanisms with placental hemodynamics. Even low EDC exposures leave altered epigenetic marks throughout gestation, which might cause PE complications. Full article

Background: Lung adenocarcinoma (LUAD) is a common histopathological variant of non-small cell lung cancer. Individuals with type 2 diabetes (T2DM) face an elevated risk of developing LUAD. We examined the common genomic characteristics between LUAD and T2DM through bioinformatics analysis. Methods: We acquired the GSE40791, GSE25724, GSE10072, and GSE71416 datasets. Differentially expressed genes (DEGs) were identified through R software, particularly its version 4.1.3 and analyzed via gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Subsequently, we analyzed the relationship between immune cell infiltration and DEGs. we constructed a protein–protein interaction network using STRING and visualized it with Cytoscape. Moreover, gene modules were identified utilizing the MCODE plugin, and hub genes were selected through the CytoHubba plugin. Additionally, we evaluated the predictive significance of hub genes using receiver operating characteristic curves and identified the final central hub genes. Finally, we forecasted the regulatory networks of miRNA and transcription factors for the central hub genes. Results: A total of 748 DEGs were identified. Analysis of immune infiltration showed a notable accumulation of effector-memory CD8 T cells, T follicular helper cells, type 1 T helper cells, activated B cells, natural killer cells, macrophages, and neutrophils in both LUAD and T2DM. Moreover, these DEGs were predominantly enriched in immune-related pathways, including the positive regulation of I-κB kinase/NF-κB signaling, positive regulation of immunoglobulin production, cellular response to interleukin-7, and cellular response to interleukin-4. The TGF-β signaling pathway was significantly important among them. Additionally, seven hub genes were identified, including ATR, RFC4, MCM2, NUP155, NUP107, NUP85, and NUP37. Among them, ATR, RFC4, and MCM2 were identified as pivotal hub genes. Additionally, hsa-mir147a, hsa-mir16-5p, and hsa-mir-1-3p were associated with LUAD and T2DM. SP1 (specific protein 1) and KDM5A (lysine-specific demethylase 5A) regulated MCM2, ATR, and RFC4. Conclusions: Our study elucidates the common mechanisms of immune response, TGF-β signaling pathway, and natural killer cells in LUAD and T2DM, and identifies ATR, RFC4, and MCM2 as key potential biomarkers and therapeutic targets for the comorbidity of these two conditions. Full article

Background/Objectives: TDP-43 mutation-driven Amyotrophic Lateral Sclerosis (ALS) motor neuron disease is one of the most prominent forms (approximately 97%) in cases of sporadic ALS. Dysfunctional autophagy and lysosomal function are the prime mechanisms behind ALS. Mitoxantrone (Mito), a synthetic doxorubicin analog, is an inhibitor of DNA and RNA synthesis/repair via intercalating with nitrogenous bases and inhibiting topoisomerase II. The therapeutic potential of miRNAs associated with disease conditions has also been reported. This study explores the therapeutic potential of Mito along with miRNAs against mutated TDP-43 protein-induced proteinopathy in human-induced pluripotent stem cell (hiPSC)-derived human neural progenitor cells (hNPCs). Methods: HiPSCs mutated for TDP-43 were differentiated into hNPCs and used to explore the therapeutic potential of Mito at a concentration of 1 μM for 24 h (the identified non-cytotoxic dose). The therapeutic effects of Mito on miRNA expression and various cellular parameters such as mitochondrial dynamics, autophagy, and stress granules were assessed using the high-throughput Open Array technique, immunocytochemistry, flow cytometry, immunoblotting, and mitochondrial bioenergetic assay. Results: Mutated TDP-43 protein accumulation causes stress granule formation (G3BP1), mitochondrial bioenergetic dysfunction, SOD1 accumulation, hyperactivated autophagy, and ER stress in hNPCs. The mutated hNPCs also show dysregulation in six miRNAs (miR-543, miR-34a, miR-200c, miR-22, miR-29b, and miR-29c) in mutated hNPCs. A significant restoration of TDP-43 mutation-induced alterations could be witnessed upon the exposure of mutated hNPCs to Mito. Conclusions: Our study indicates that miR-543, miR-29b, miR-22, miR-200c, and miR-34a have antisense therapeutic potential alone and in combination with Mitoxantrone. Full article

Extracellular vesicles (EVs) are emerging as crucial biomarkers in molecular diagnostics, providing early detection of disease progression. Although ultracentrifugation remains the gold standard for vesicle isolation from biofluids, it has limitations in scalability and accessibility. This study presents lyophilization as an innovative method for preserving EVs and isolating microRNAs from saliva, utilizing its proven ability to maintain biological activity and prevent unwanted chemical reactions. We assessed five different sample preparation protocols combined with a dual-purification strategy. Structural and molecular integrity analyses revealed that lyophilized samples retained essential EV characteristics, including CD63/CD9 membrane localization. QELS analysis and electron microscopy confirmed distinct vesicle populations in both ultracentrifuged (30–50 nm and 320–360 nm) and lyophilized samples (50–70 nm and 360–380 nm). Importantly, lyophilized samples exhibited higher total RNA concentrations (p < 0.0001) while preserving key microRNA signatures (miR-16, miR-21, miR-33a, and miR-146b) with high fidelity. The efficacy of lyophilization is linked to its ability to systematically reduce solvent content through sublimation while maintaining vesicle integrity and molecular cargo. This method offers a practical, scalable alternative for EV isolation with significant implications for biomarker-based diagnostics. Full article

The widespread use of food additives, such as butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), and tert-butylhydroquinone (TBHQ), has raised concerns about their potential toxicity, especially their hepatotoxicity, nephrotoxicity, and neurotoxicity. This study explores the targets and mechanisms of food additive-induced toxicity using network toxicology. Toxicity predictions of BHA, BHT, and TBHQ were performed using the ProTox-3.0, ADMETlab 3.0, and Xundrug databases, and potential targets were identified using the SwissTargetPrediction, Batman-TCM, SuperPred, and SEA databases. These were integrated with GeneCards—The Human Gene Database (GeneCards) and the Online Mendelian Inheritance in Man (OMIM) database to extract toxicity-related targets for subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Core-acting genes were further screened through protein–protein interactions (PPIs), and molecular docking was performed to verify the binding free energy between BHA, BHT, and TBHQ and their core targets. Additionally, the mRNA-miRNA-lnRNA interaction regulatory networks of the core targets and potential carcinogenic mechanisms were analyzed. The targets of BHA, BHT, and TBHQ were as follows: ACE, HIF1A, NR1H4, NFKB1, TNF, IL6, IFNG, IL1B, and ESR1 for hepatotoxicity; APP, NFKB1, ACE, FOS, IL10, IL1B, IL6, TNF, and ALB for nephrotoxicity; and GRIN2B, IL1B, and TNF for neurotoxicity. These interactions primarily involved pathways such as interleukin-17 (IL-17) and Janus kinase-signal transducer and activator of transcription (JAK-STAT), as well as various pathways related to non-alcoholic fatty liver disease (NAFLD). This study highlights the potential toxicity of BHA, BHT, and TBHQ to the liver, kidneys, and nerves, providing insights for better safety evaluations. Full article

Pancreatic (PC), colorectal (CRC), hepatocellular (HCC), and gallbladder (GC) cancers together account for nearly 20% of all cancer cases. However, specific biomarkers and therapeutic targets for these cancers are lacking. Diagnosing these cancers early and providing timely, appropriate treatment to improve patient outcomes is crucial. In this context, previous studies, including ours, have highlighted the potential of non-coding RNAs, particularly long non-coding RNAs (lncRNAs), in diagnosing and prognosis of various cancers. This review focuses on the mechanistic role of the recently identified lncRNA LINC00261 in PC, CRC, HCC, and GC. Our comprehensive literature analysis revealed that LINC00261 functions as a tumor suppressor, and its reduced expression is associated with larger tumor size, advanced tumor-node-metastasis (TNM) stages, lymphatic metastasis, and poorer overall survival rates. Additionally, we discovered that LINC00261 acts as a molecular sponge for miRNAs, such as miR-550a-3p, miR-23a-3p, miR-148a, miR-324-3p, and miR-105-5p, regulating critical cancer-related signaling pathways, including PI3K/Akt/mTOR, Protein kinase B, and Mammalian target of rapamycin (mTOR). Further bioinformatic analysis revealed that LINC00261 regulates key cellular processes, such as protein-DNA complex formation, ribonuclease complex activity, histone deacetylase complexes, and nuclear matrix interactions. Overall, we believe that LINC00261 holds significant promise as a future biomarker and, when combined with existing treatment strategies, may enhance cancer patient care and survival. Full article

(1) Background: Glioblastoma (GBM) is one of the most aggressive brain tumors with a poor prognosis. Therefore, new insights into GBM diagnosis and treatment are required. In addition to differentially expressed mRNAs, miRNAs may have the potential to be applied as diagnostic biomarkers. (2) Methods: In this study, profiling of human miRNAs in combination with mRNAs was performed on total RNA isolated from tissue samples of five control and five GBM patients, using a high-throughput RNA sequencing (RNA-Seq) approach. (3) Results: A total of 35 miRNAs and 365 mRNAs were upregulated, while 82 miRNAs and 1225 mRNAs showed significant downregulation between tissue samples of GBM patients compared to the control samples using the iDEP tool to analyze RNA-Seq data. To validate our results, the expression of five miRNAs (hsa-miR-196a-5p, hsa-miR-21-3p, hsa-miR-10b-3p, hsa-miR-383-5p, and hsa-miR-490-3p) and fourteen mRNAs (E2F2, HOXD13, VEGFA, CDC45, AURKB, HOXC10, MYBL2, FABP6, PRLHR, NEUROD6, CBLN1, HRH3, HCN1, and RELN) was determined by RT-qPCR assay. The miRNet tool was used to build miRNA–target interaction. Furthermore, a protein–protein interaction (PPI) network was created from the miRNA targets by applying the NetworkAnalyst 3.0 tool. Based on the PPI network, a functional enrichment analysis of the target proteins was also carried out. (4) Conclusions: We identified an miRNA panel and several deregulated mRNAs that could play an important role in tumor development and distinguish GBM patients from healthy controls with high sensitivity and specificity using total RNA isolated from tissue samples. Full article

Within the context of global warming, understanding the molecular mechanisms behind physiological plasticity and local adaptation is essential for insect populations. This study performed an integrated miRNA and mRNA analysis on Aquatica leii larvae exposed to temperatures of 20 °C, 24 °C, 28 °C, and 32 °C. Under varying thermal conditions, 1983 genes exhibited differential expression (i.e., DEGs). These genes showed significant enrichment in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to carbohydrate metabolism, glycan biosynthesis and metabolism. Notably, we detected that the “neuroactive ligand–receptor interaction” signaling pathway, which is involved in environmental information processing, was significantly upregulated in the 28 °C and 32 °C treatment groups. This indicates that starting at 28 °C, A. leii needs to maintain normal cellular physiological functions by regulating ligand–receptor binding and signal transduction. Furthermore, 220 differentially expressed miRNAs (DEMs) were detected under the different temperature treatment conditions. An interaction network was constructed between key DEMs and DEGs, revealing 12 significant DEM-DEG regulatory pairs in A. leii under different temperature treatments. We found three miRNA-mRNA candidate modules that could be involved in A. leii’s response to high temperature, including ggo-miR-1260b and ptr-miR-1260b/RN001_010114, CM069438.1_43851/RN001_014852, and CM069438.1_43851/RN001_014877. Our data provide deeper insights into the molecular responses of A. leii to the high temperature at the miRNA and mRNA levels. Full article

The identification of molecular markers for fertility is critical for the sustainability of livestock production. We profiled small non-coding RNAs (sncRNAs) in sperm from rams with high fertility (HF) and low fertility (LF) phenotypes to uncover their roles in ram sperm fertility. Rams were categorized into high-fertility (HF, n = 31; 94.5 ± 2.8%) and low-fertility (LF, n = 25; 83.1 ± 5.73%) phenotypes based on pregnancy rates (average 89.4 ± 7.2%). From these, sperm samples of HF (n = 4; pregnancy rate 99.2 ± 1.6%) and LF (n = 4; pregnancy rate 73.6 ± 4.4%) rams underwent sncRNA sequencing. Small RNA sequencing produced 14,962,876 reads in LF rams and 17,401,094 reads in HF rams, showing distinct sncRNA biotypes, including miRNAs, tRNAs, snoRNAs, snRNAs, and rRNAs. Among these, miRNAs comprised 7.12% of reads in LF rams and 3.78% in HF rams, while rRNAs and repeats formed significant proportions in both groups. A total of 1673 known and 627 novel miRNAs were identified, with 227 differentially expressed miRNAs between the HF and LF groups. We showed that key miRNAs, such as oar-miR-200b and oar-miR-370-3p, were upregulated in HF sperm, while downregulated miRNAs in LF, such as oar-miR-26b and oar-let-7d, were associated with impaired sperm function and DNA fragmentation. A functional enrichment analysis of miRNA target genes highlighted pathways related to ribonucleoprotein complex biogenesis, RNA processing, and gene expression regulation. These findings establish the critical role of sperm sncRNAs as regulators of fertility and potential biomarkers in breeding soundness tests for the precision farming of livestock for global food security. Full article