Target Genes Of miRNAs Research Articles

Association between Yili goose sperm motility and expression profiles of mRNA and miRNA in testis

BackgroundThe study was conducted to find out the candidate microRNA (miRNA) and genes that associated with sperm motility of Yili goose through small RNA sequencing of testicular tissue of Yili goose, and provide a theoretical basis for the study of the regulation mechanism of sperm motility of Yili goose gander.ResultsIn this study, five male geese with high sperm motility and five male geese with low sperm motility were slaughtered to obtain their testis tissues for small RNA sequencing, and biological information methods were used for data analysis. The results showed that a total of 1575 known miRNAs and 68 novel miRNAs were identified in the testis tissue of Yili goose, and 71 differentially expressed miRNAs and 660 differentially expressed genes were screened. GO functional analysis showed that miRNAs target genes were mainly involved in the binding, kinase activity, structural constituent of cytoskeleton and intermediate filament cytoskeleton. KEGG functional analysis showed that miRNAs target genes were significantly enriched in arginine and proline metabolism, glycolysis / gluconeogenesis, fructose and mannose metabolism and beta-Alanine metabolism and other pathways. miRNAs-mRNAs interaction network suggests miR-140/miR-140-3p/miR-140-3p-NKAIN3, let-7d-BTG1 and miR-145-5p/miR -145a-5p-CLEC2E may play an important role in testis development and spermatogenesis.ConclusionsThe results of this study suggest that the sperm motility of Yili goose may be regulated by different miRNAs, and the target genes are significantly enriched in pathways related to sperm metabolism, indicating that miRNAs affect the sperm motility of Yili goose by regulating the metabolic process of sperm and the expression of related genes. This study can provide a reference for revealing the regulation mechanism of Yili goose sperm motility at the molecular level.

Small RNA sequencing of exosomal microRNAs reveals differential expression of microRNAs in preeclampsia.

Preeclampsia (PE) is one of the most common hypertensive disorders of pregnancy. It is a dangerous condition with a high mortality rate in mothers and fetuses and is associated with a lack of early diagnosis and effective treatment. While the etiology of the disease is complex and obscure, it is now clear that the placenta is central to disease progression. Exosomal microRNAs (miRNAs) are possible mediators that regulate placenta-related physiological and pathological processes. Placental mesenchymal stem cells have considerable potential to help us understand the pathogenesis and treatment of pregnancy-related diseases. Here, we investigate the exosomal miRNA profiles of human placenta-derived mesenchymal stem cells between healthy pregnant women and those with PE. We performed small RNA sequencing to obtain miRNA profiles, and conducted enrichment analysis of the miRNA target genes to identify differentially expressed miRNAs associated with PE. Overall, we detected 1795 miRNAs; among them, 206 were differentially expressed in women with PE, including 35 upregulated and 171 downregulated miRNAs, when compared with healthy pregnant women. Moreover, we identified possible functions and pathways associated with PE, including angiogenesis, cell proliferation, migration and invasion, and the coagulation-fibrinolysis balance. Eventually, we proposed hsa-miR-675-5p, hsa-miR-3614-5p, and hsa-miR-615-5p as potential regulators of the pathogenesis of PE, and constructed a miRNA-target gene network. Our study identifies possible candidate biomarkers for the diagnosis of PE, and introduces a new direction for further understanding the pathogenesis of PE.

Integrative bioinformatics analysis of miRNA and mRNA expression profiles identified some potential biomarkers for breast cancer

BackgroundBreast cancer is a common cause of cancer death among women with a complex and heterogeneous picture in histological, molecular and clinical features. The aim of this study was to identify hub gene and their target microRNAs in related pathways for breast cancer.MethodsWe selected screening methods for differentially expressed mRNAs and miRNAs using expression profile data of breast cancer from the cancer genome atlas. Using some databases for annotation, the functional and pathway enrichment for differential expression genes was performed. We selected genes and miRNAs with differential expression pattern. Then we determined target genes for differential expression miRNAs (DEMIs) and intersection between them was selected as differentially expressed miRNA–target genes for breast cancer. In the next step, we constructed miRNA–mRNA regulatory network and protein–protein interaction (PPI) network for more information.ResultsTop 10 DEMIs were identified from miRNA profile. Then, we selected 354 genes as target gene for 10 DEMIs. The miRNA–mRNA and PPI network were constructed, and 10 hub genes and 5 miRNAs identified that some of them are new for breast cancer. Also, miRNA–target genes with differential expressions in this study were all mainly involved in signaling pathways and developmental process.ConclusionThis study identified some candidate biomarkers for breast cancer that they have a potential role in pathways related to breast. These findings can be used for research, early diagnosis and therapeutic goals.

Sequencing and analysis of micro RNAs incamelmilk exosomes.

In order to study the species and functions of micro (mi)RNAs in the exosomes of camel milk, non-coding small (s)RNAs were sequenced and identified by Illumina sequencing technology, and the miRNA fraction was analysed by bioinformatics. After quality control, the average length of sRNA of camel milk exosomes was 18-24 nucleotides. A total of 2,659 miRNAs were identified, including 2,458 known, and 201 new miRNAs. Among the known miRNAs, miR-148a and let-7i had the highest expression levels. The results of gene ontology enrichment analysis indicated that the target genes of camel milk exosome miRNAs were involved in multicellular organismal, catabolic and other biological processes. They play role in the extracellular region, in the cytoskeleton and other cell components, in protein binding, but also have structural molecule activity and other molecular functions. According to the results of the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, the target genes of camel milk exosome miRNAs are involved in Alzheimer's disease, non-alcoholic fatty liver disease, Staphylococcus aureus infection and other pathological pathways. We speculate that the reportedbeneficial effect of camel milk in various pathologic conditions may be closely related to the regulatory function of the exosomal miRNAs exerted on target genes of the diseases.

Identifying Genetic Signatures from Single-Cell RNA Sequencing Data by Matrix Imputation and Reduced Set Gene Clustering

In this current era, the identification of both known and novel cell types, the representation of cells, predicting cell fates, classifying various tumor types, and studying heterogeneity in various cells are the key areas of interest in the analysis of single-cell RNA sequencing (scRNA-seq) data. Due to the nature of the data, cluster identification in single-cell sequencing data with high dimensions presents several difficulties. In this paper, we introduce a new framework that combines various strategies such as imputed matrix, minimum redundancy maximum relevance (MRMR) feature selection, and shrinkage clustering to discover gene signatures from scRNA-seq data. Firstly, we conducted the pre-filtering of the “drop-out” value in the data focusing solely on imputing the identified “drop-out” values. Next, we applied the MRMR feature selection method to the imputed data and obtained the top 100 features based on the MRMR feature selection optimization scores for further downstream analysis. Thereafter, we employed shrinkage clustering on the selected feature matrix to identify the cell clusters using a global optimization approach. Finally, we applied the Limma-Voom R tool employing voom normalization and an empirical Bayes test to detect differentially expressed features with a false discovery rate (FDR) < 0.001. In addition, we performed the KEGG pathway and gene ontology enrichment analysis of the identified biomarkers using David 6.8 software. Furthermore, we conducted miRNA target detection for the top gene markers and performed miRNA target gene interaction network analysis using the Cytoscape online tool. Subsequently, we compared our detected 100 markers with our previously detected top 100 cluster-specified markers ranked by FDR of the latest published article and discovered three common markers; namely, Cyp2b10, Mt1, Alpi, along with 97 novel markers. In addition, the Gene Set Enrichment Analysis (GSEA) of both marker sets also yields similar outcomes. Apart from this, we performed another comparative study with another published method, demonstrating that our model detects more significant markers than that model. To assess the efficiency of our framework, we apply it to another dataset and identify 20 strongly significant up-regulated markers. Additionally, we perform a comparative study of different imputation methods and include an ablation study to prove that every key phase of our framework is essential and strongly recommended. In summary, our proposed integrated framework efficiently discovers differentially expressed stronger gene signatures as well as up-regulated markers in single-cell RNA sequencing data.

Nasopharyngeal carcinoma derived exosomes regulate the proliferation and migration of nasopharyngeal carcinoma cells by mediating the miR-99a-5p BAZ2A axis

ObjectivesNasopharyngeal Carcinoma (NPC) is a common malignant tumor of nasopharyngeal mucosal epithelium in clinical practice. Radiotherapy and chemotherapy are the main treatment methods at present, but the therapeutic effect is still unsatisfactory. Studies have shown that exosomes and microRNAs (miRNAs) play an important role in the development of cancer. Therefore, this study aimed to investigate the effects of NPC derived exosomes on NPC and their molecular mechanisms. MethodsSerum was collected from healthy subjects, Epstein–Barr Virus (EBV) infected patients and NPC patients (n = 9 group) and exosomes were extracted separately. High-throughput sequencing of exosomes was performed to screen differentially expressed miRNAs. The function of the screened miRNA was identified by treating NPC cells with exosomes. The target gene of miRNA was identified using the dual-luciferase assay. Real-Time quantitative Polymerase Chain Reaction (RT-qPCR) was used to determine the levels of miR-99a-5p and Bromodomain Adjacent Tozinc finger domain protein 2A (BAZ2A). Cell Counting Kit-8 assay, flow cytometry, and wound healing assay were utilized to detect cell viability, cell cycle and apoptosis, and migration ability. The protein levels were evaluated by Western blot. ResultsMiR-99a-5p was identified as the most significant differentially expressed miRNA in exosomes (p < 0.05). The proliferation and migration of NPC cells were extremely facilitated by exosomes, accompanied by the suppressed apoptosis, upregulated BAZ2A, Monocyte Chemotactic Protein-1 (MCP1), and Vascular Endothelial Growth Factor A (VEGFA), and downregulation of Interleukin (IL)-1β and Nuclear Transcription Factor-κB (NF-κB) (p < 0.05). BAZ2A was a target gene of miR-99a-5p. Furthermore, the regulatory effect of exosomes on the proliferation, migration, and apoptosis was significantly abolished by overexpression of miR-99a-5p or downregulation of BAZ2A (p < 0.05). ConclusionNPC derived exosomes facilitated the proliferation and migration of NPC through regulating the miR-99a-5p/BAZ2A axis.

Regulation of cashmere fineness traits by noncoding RNA in Jiangnan cashmere goats

BackgroundCashmere has long been used as the raw material for wool textiles. The diameter of the cashmere fibre determines its quality and economic value. However, the regulatory role of noncoding RNAs (ncRNAs) in cashmere fineness remains unclear, especially regarding the interaction between ncRNAs and coding RNAs.ResultsTranscriptome sequencing was used to identify the expression profiles of long noncoding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs) in the skin tissues of Jiangnan cashmere goats with different cashmere fineness levels. Integration analysis of ncRNA and coding RNA was performed in combination with previous research results. The results showed that 16,437 lncRNAs, 2234 circRNAs, and 1322 miRNAs were identified in 8 skin samples of cashmere goats. A total of 403 differentially expressed (DE) lncRNAs, 62 DE circRNAs and 30 DE miRNAs were identified in the skin tissues of the fine groups (Fe) and coarse groups (Ce). We predicted the target gene of DE lncRNA, the target gene of DE miRNA and the host gene of DE circRNA. Based on functional annotation and enrichment analysis of target genes, we found that DE lncRNAs could be involved in regulating the fineness traits of cashmere. The most potential lncRNAs were MSTRG.42054.1, MSTRG.18602.3, and MSTRG.2199.13.ConclusionsThe data from this study enriched the cashmere goat noncoding RNA database and helped to supplement the annotation of the goat genome. The results provided a new direction for the breeding of cashmere characters.

Identification and analysis of differentially expressed microRNAs in endometrium to explore the regulation of sheep fecundity

BackgroundMicroRNAs (miRNAs) play an important regulatory role in mammalian reproduction. Currently, most studies are primarily concentrated on ovarian miRNAs, ignoring the influence of endometrial miRNAs on the fecundity of female sheep. To uncover potential regulators of sheep fecundity, RNA-seq was used to comparatively analyze miRNA expression profiles of endometrium between high prolificacy sheep (HP, litter size = 3) and low prolificacy sheep (LP, litter size = 1) with FecB genotype.ResultsFirstly, genomic features of miRNAs from endometrium were analyzed. Furthermore, 58 differentially expressed (DE) miRNAs were found in the endometrium of Hu sheep with different litter size. A co-expression network of DE miRNAs and target genes has been constructed, and hub genes related litter size are included, such as DE miRNA unconservative_NC_019472.2_1229533 and unconservative_NC_019481.2_1637827 target to estrogen receptor α (ESR1) and unconservative_NC_019481.2_1637827 targets to transcription factor 7 (TCF7). Moreover, functional annotation analysis showed that the target genes (NRCAM and NEGR1) of the DE miRNAs were significantly enriched in cell adhesion molecules (CAMs) signaling pathway, which was related to uterine receptivity.ConclusionTaken together, this study provides a new valuable resource for understanding the molecular mechanisms underlying Hu sheep prolificacy.

Ovarian carcinoma immune-related microRNA affects the heterogeneity of the endocrine microenvironment and anti-tumor immune pattern.

The eighth-leading cause of cancer-related mortality and the seventh-most prevalent malignancy in women globally is ovarian cancer (OV). However, 5-year survival expectancy after conventional treatment is not good. Therefore, there is an urgent need for novel signatures to guide the designation of therapeutic schemes for OV patients. We used univariate Cox analysis to screen hormone secretion regulation axis-related microRNAs (miRNAs), least absolute shrinkage and selection operator analysis to select candidate miRNAs and multivariate Cox analysis to build the risk model. To evaluate possible route and functional differences, enrichment analysis using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed on the differentially expressed genes (DEGs) across various risk groups. We compared Tumor Immune Dysfunction and Exclusion (TIDE) scores across risk categories by analyzing immune cell infiltration, immune checkpoint gene expression, immunological function and TIDE scores. In the end, we determined the half maximal inhibitory concentration (IC50 ) of chemotherapy and targeted medicines for individual patients. Cell assays were determined to test the migration of the miRNA-target genes and western blotting was used to test the correlation of the miRNA-target genes and the pathways. We finally identified hormone secretion regulation axis-related 13 microRNAs to build a risk model. The validation of observed and anticipated values revealed a fair level of agreement. To evaluate the molecular pathways between various groups in accordance with the GO and KEGG analyses, we then discovered 173 DEGs between distinct risk groups. The risk score was shown to be inversely related to the number of immune cells, including myeloid dendritic, granulocytes, M1 and M2 macrophages, B cells, t-lymphocytes, and CD4+ and CD8+ cells, suggesting that immune cells are more frequent in the low-risk group. Immune cell infiltration investigation yielded these results. Finally, we recognized 11 chemotherapeutic drugs and 30 novels targeted drugs on the basis of IC50 between the different risk groups. GJB5 was determined to be the mir-219 target gene and was identified as promoting the cell cycle process. In addition, hormone secretion regulation axis related miRNAs were reported to affects the heterogeneity of endocrine microenvironment and anti-tumor immune pattern. In conclusion, a 13-miRNA prognostic model was constructed to know the immune status, prognosis, immunotherapeutic response and anti-tumor drug sensitivity for OV, which provides theoretical guidance for the effective and individualized treatment of OV patients.

Identification of miRNAs Involved in Intracranial Aneurysm Rupture in Cigarette-Smoking Patients.

Smoking is an independent risk factor for the formation and rupture of intracranial aneurysms (IA). However, the underlying mechanism remains unclear. In this study, we performed miRNA sequencing on plasma from 10 smoking patients with IA, 10 non-smoking patients with IA, and 10 healthy controls. The differentially expressed miRNAs (DE miRNAs) between smoking and non-smoking patients with IA were identified. Functional and pathway enrichment analysis is employed to investigate the potential functions of those DE miRNA target genes. The correlations with the clinical parameters were assessed using receiver operating characteristic curve (ROC) analysis. In total, we identified 428 DE miRNAs. Functional enrichment analysis showed the target genes were significantly enriched in biological aspects related to cell characteristics, such as cell cycle, cell differentiation, and cell migration. Pathway analysis showed DE miRNAs mainly enriched in the PI3K-Akt signaling pathway, Focal adhesion, and JAK-STAT signaling pathway. The expressions of miR-574-5p, miR-151a-3p, and miR-652-3p correlated well with aneurysm parameters. The AUC of miR-574-5p, miR-151a-3p, and miR-652-3p were 97%, 92%, and 99%, respectively. Our study indicated that smoking significantly altered the plasma miRNA profile in patients with IA. The expression of miR-574-5p, miR-151a-3p, and miR-652-3p correlated with aneurysm parameters, which may play a significant role in the formation and rupture of IA.

Characterization of MicroRNAs and Gene Expression in ACC Oxidase RNA Interference-Based Transgenic Bananas.

Banana (Musa acuminata, AAA group) is a typically respiratory climacteric fruit. Previously, genes encoding ACC oxidase, one of the key enzymes in ethylene biosynthesis, Mh-ACO1 and Mh-ACO2 in bananas were silenced individually using RNAi interference technology, and fruit ripening of transgenic bananas was postponed. Here, the differential expression of miRNAs and their targeted mRNAs were analyzed in the transcriptomes of fruits at the third ripening stage, peel color more green than yellow, from the untransformed and RNAi transgenic bananas. Five significantly differentially expressed miRNAs (mac-miR169a, mac-miR319c-3p, mac-miR171a, mac-miR156e-5p, and mac-miR164a-5p) were identified. The predicted miRNA target genes were mainly enriched in six KEGG pathways, including 'sulfur relay system', 'protein digestion and absorption', 'histidine metabolism', 'pathogenic E. coli infection', 'sulfur metabolism', and 'starch and sucrose metabolism'. After ethylene treatment, the expression of ACC oxidase silencing-associated miRNAs was down-regulated, and that of their target genes was up-regulated along with fruit ripening. The evolutionary clustering relationships of miRNA precursors among 12 gene families related to fruit ripening were analyzed. The corresponding expression patterns of mature bodies were mainly concentrated in flowers, fruits, and leaves. Our results indicated that ethylene biosynthesis is associated with miRNAs regulating the expression of sulfur metabolism-related genes in bananas.

Interleukin-17A stimulation induces alterations in Microglial microRNA expression profiles.

Increased maternal interleukin (IL)-17A and activated microglia are pivotal factors contributing to the pathological phenotypes of maternal immune activation (MIA), developing neurodevelopmental disorders in offspring. This study aimed to determine whether IL-17A affects the microglial microRNA (miRNA) profiles. The miRNA expression profiles of primary cultured microglia stimulated with recombinant IL-17A were examined comprehensively using miRNA sequencing and validated through qRT-PCR. The expressions of miRNAs target genes identified using bioinformatics, were investigated in microglia transfected with mimic miRNA. The target gene's expression was also examined in the fetal brains of the MIA mouse model induced by maternal lipopolysaccharide (LPS) administration. Primary cultured microglia expressed the IL-17A receptor and increased proinflammatory cytokines and nitric oxide synthase 2 upon treatment with IL-17A. Among the three miRNAs with |log2FC | >1, only mmu-miR-206-3p expression was significantly up-regulated by IL-17A. Transfection with the mmu-miR-206-3p mimic resulted in a significant decrease in the expression of Hdac4 and Igf1, target genes of mmu-miR-206-3p. Hdac4 expression also significantly decreased in the LPS-induced MIA model. IL-17A affected microglial miRNA profiles with upregulated mmu-miR-206-3p. These findings suggest that targeting the IL-17A/mmu-miR-206-3p pathway may be a new strategy for predicting MIA-related neurodevelopmental deficits and providing preventive interventions. Despite the growing evidence of interleukin (IL)-17A and microglia in the pathology of maternal immune activation (MIA), the downstream of IL-17A in microglia is not fully known. IL-17A altered microRNA profiles and upregulated the mmu-miR-206-3p expression in microglia. The mmu-miR-206-3p reduced autism spectrum disorder (ASD) related gene expressions, Hdac4 and Igf1. The Hdac4 expression was also reduced in the brain of MIA offspring. The hsa-miR-206 sequence is consistent with that of mmu-miR-206-3p. This study may provide clues to pathological mechanisms leading to predictions and interventions for ASD children born to mothers with IL-17A-related disorders.

Interaction between Rumen Epithelial miRNAs-Microbiota-Metabolites in Response to Cold-Season Nutritional Stress in Tibetan Sheep.

Tibetan sheep are already well adapted to cold season nutrient stress on the Tibetan Plateau. Rumen, an important nutrient for metabolism and as an absorption organ in ruminants, plays a vital role in the cold stress adaptations of Tibetan sheep. Ruminal microbiota also plays an indispensable role in rumen function. In this study, combined multiomics data were utilized to comprehensively analyze the interaction mechanism between rumen epithelial miRNAs and microbiota and their metabolites in Tibetan sheep under nutrient stress in the cold season. A total of 949 miRNAs were identified in the rumen epithelium of both cold and warm seasons. A total of 62 differentially expressed (DE) miRNAs were screened using FC > 1.5 and p value < 0.01, and a total of 20,206 targeted genes were predicted by DE miRNAs. KEGG enrichment analysis revealed that DE miRNA-targeted genes were mainly enriched in axon guidance(ko04360), tight junction(ko04530), inflammatory mediator regulation of TRP channels(ko04750) and metabolism-related pathways. Correlation analysis revealed that rumen microbiota, rumen VFAs and DE miRNAs were all correlated. Further study revealed that the targeted genes of cold and warm season rumen epithelial DE miRNAs were coenriched with differential metabolites of microbiota in glycerophospholipid metabolism (ko00564), apoptosis (ko04210), inflammatory mediator regulation of TRP channels (ko04750), small cell lung cancer (ko05222), and choline metabolism in cancer (ko05231) pathways. There are several interactions between Tibetan sheep rumen epithelial miRNAs, rumen microbiota, and microbial metabolites, mainly through maintaining rumen epithelial barrier function and host homeostasis of choline and cholesterol, improving host immunity, and promoting energy metabolism pathways, thus enabling Tibetan sheep to effectively respond to cold season nutrient stress. The results also suggest that rumen microbiota have coevolved with their hosts to improve the adaptive capacity of Tibetan sheep to cold season nutrient stress, providing a new perspective for the study of cold season nutritional stress adaptation in Tibetan sheep.

Serum Extracellular Vesicle-Derived hsa-miR-2277-3p and hsa-miR-6813-3p Are Potential Biomarkers for Major Depression: A Preliminary Study.

The aim of the present study was to examine the association between miRNA levels in extracellular vesicles (EVs) from serum and the severity of Major Depression (MD). Patient sera from 16 MD cases were collected at our university hospital. The miRNAs contained in EVs were extracted using a nanofiltration method, and their expression levels were analyzed using miRNA microarrays. Intergroup comparisons were performed to validate the diagnostic performance of miRNAs in EVs. Furthermore, candidate miRNAs in EVs were added to neural progenitor cells, astrocytes, and microglial cells in vitro, and the predicted target genes of the candidate miRNAs were extracted. The predicted target genes underwent enrichment analysis. The expression levels of hsa-miR-6813-3p and hsa-miR-2277-3p were significantly downregulated with increasing depression severity of MD. The pathway enrichment analysis suggests that hsa-miR-6813-3p may be involved in glucocorticoid receptor and gamma-aminobutyric acid receptor signaling. Additionally, hsa-miR-2277-3p was found to be involved in the dopaminergic neural pathway. The analysis of serum miRNAs in EVs suggests that hsa-miR-6813-3p and hsa-miR-2277-3p could serve as novel biomarkers for MD, reflecting its severity. Moreover, these miRNAs in EVs could help understand MD pathophysiology.

Identification and verification of a prognostic signature based on a miRNA-mRNA interaction pattern in colon adenocarcinoma.

The expression characteristics of non-coding RNA (ncRNA) in colon adenocarcinoma (COAD) are involved in regulating various biological processes. To achieve these functions, ncRNA and a member of the Argonaute protein family form an RNA-induced silencing complex (RISC). The RISC is directed by ncRNA, especially microRNA (miRNA), to bind the target complementary mRNAs and regulate their expression by interfering with mRNA cleavage, degradation, or translation. However, how to identify potential miRNA biomarkers and therapeutic targets remains unclear. Here, we performed differential gene screening based on The Cancer Genome Atlas dataset and annotated meaningful differential genes to enrich related biological processes and regulatory cancer pathways. According to the overlap between the screened differential mRNAs and differential miRNAs, a prognosis model based on a least absolute shrinkage and selection operator-based Cox proportional hazards regression analysis can be established to obtain better prognosis characteristics. To further explore the therapeutic potential of miRNA as a target of mRNA intervention, we conducted an immunohistochemical analysis and evaluated the expression level in the tissue microarray of 100 colorectal cancer patients. The results demonstrated that the expression level of POU4F1, DNASE1L2, and WDR72 in the signature was significantly upregulated in COAD and correlated with poor prognosis. Establishing a prognostic signature based on miRNA target genes will help elucidate the molecular pathogenesis of COAD and provide novel potential targets for RNA therapy.

Plasma-Derived Small Extracellular Vesicles From VKH Patients Suppress T Cell Proliferation Via MicroRNA-410-3p Modulation of CXCL5 Axis.

Circulating exosomes regulate immune responses and induce immune tolerance in immune-mediated diseases. This study aimed to investigate the role of circulating small extracellular vesicles (sEVs) derived from patients with Vogt-Koyanagi-Harada (VKH) syndrome, in T-cell responses. The sEVs were isolated from the plasma of healthy controls, patients with VKH, and other uveitis patients. The effects of autologous and allogeneic sEVs on the proliferation of circulating CD4+ T cells were evaluated. Microarray analysis of sEVs was performed to determine their differential miRNA expression profiles. The target genes of the candidate miRNA were predicted and verified. The role of both the candidate miRNA and target genes in T-cell proliferation was tested. Plasma-derived sEVs from patients with VKH inhibited the proliferation of autologous CD4+ T cells. Among all the miRNAs that might be associated with inflammatory activity, we found that miR-410-3p had the largest number of T-cell proliferation target genes. MiR-410-3p mimics inhibited the proliferation of Jurkat cells and CD4+ T cells. C-X-C motif chemokine ligand 5 (CXCL5) was confirmed to be a potential target gene of miR-410-3p, and siRNA-mediated CXCL5 knockdown inhibited cell proliferation. Circulating sEVs exert an inhibitory effect on autologous CD4+ T cells mediated by miR-410-3p by targeting CXCL5, supporting the possibility of using autogenic sEVs to inhibit ocular inflammation.

Evaluation of the Relationship between Aromatase/Sirtuin1 Interaction and miRNA Expression in Human Neuroblastoma Cells.

Changes in activation/inhibition of Sirtuin-1 (SIRT1) and aromatase play an important role in a plethora of diseases. MicroRNAs (miRNAs) modulate multiple molecular pathways and affect a substantial number of physiological and pathological processes. The aim of this study was to investigate any possible interaction between aromatase and SIRT1 in SH-SY5Y cells and to see how there is a connection between this interaction and miRNA expression, if there is an interaction. In this study, cells were incubated in serum-deprived media for 6, 12, and 24 h. Aromatase and SIRT1 expressions were evaluated by Western blot. The IC50 concentration of SIRT1 activator (SRT1720), SIRT1 inhibitor (EX527), and aromatase inhibitors (letrozole and fadrozole) was determined by the XTT method. Then, CYP19A1 and SIRT1 levels were evaluated in the presence of SIRT1 siRNA or IC50 values for each activator/inhibitor. Finally, CYP19A1, SIRT1 expression and miRNA target gene were assessed with bioinformatic approaches. Aromatase and SIRT1 protein levels were significantly elevated in the cells incubated at 24 h in serum-deprived media (p ≤ 0.05). SIRT1 also positively regulated CYP19A1 in SH-SY5Y cells in media with/without FBS. Serum deprivation depending on time course caused changes in the oxidant/ antioxidant system. While oxidative stress index tended to decrease in the absence of FBS at 24 h compared to the control, it showed a significant decrease at 48 h in a serum-deprived manner (p ≤ 0.001). As a result of bioinformatics analysis, we determined 3 miRNAs that could potentially regulate SIRT1 and CYP19A1. hsa-miR-27a-3p and hsa-miR-181a-5p correlated in terms of their expressions at 24 h compared to 12 h, and there was a significant decrease in the expression of these miRNAs. On the contrary, the expression of hsa-miR-30c-5p significantly increased at 24 h compared to 12 h. Considering the results, a direct link between aromatase and SIRT1 was observed in human neuroblastoma cells. The identification of key miRNAs, hsa-miR-27a-3p, hsa-miR-30c-5p, and hsa-miR-181a-5p targeting both aromatase and SIRT1, provides an approach with novel insights on neurology-associated diseases.

Gold nanoparticles attenuate the interferon-γ induced SOCS1 expression and activation of NF-κB p65/50 activity via modulation of microRNA-155-5p in triple-negative breast cancer cells.

Triple-negative breast cancer (TNBC) is a very aggressive form of cancer that grows and spreads very fast and generally relapses. Therapeutic options of TNBC are limited and still need to be explored completely. Gold nanoparticles conjugated with citrate (citrate-AuNPs) are reported to have anticancer potential; however, their role in regulating microRNAs (miRNAs) in TNBC has never been investigated. This study investigated the potential of citrate-AuNPs against tumorigenic inflammation via modulation of miRNAs in TNBC cells. Gold nanoparticles were chemically synthesized using the trisodium-citrate method and were characterized by UV-Vis spectrophotometry and dynamic light scattering studies. Targetscan bioinformatics was used to analyze miRNA target genes. Levels of miRNA and mRNA were quantified using TaqMan assays. The pairing of miRNA in 3'untranslated region (3'UTR) of mRNA was validated by luciferase reporter clone, containing the entire 3'UTR of mRNA, and findings were further re-validated via transfection with miRNA inhibitors. Newly synthesized citrate-AuNPs were highly stable, with a mean size was 28.3 nm. The data determined that hsa-miR155-5p is a direct regulator of SOCS1 (suppressor-of-cytokine-signaling) expression and citrate-AuNPs inhibits SOCS1 mRNA/protein expression via modulating hsa-miR155-5p expression. Transfection of TNBC MDA-MB-231 cells with anti-miR155-5p markedly increased SOCS1 expression (p<0.001), while citrate-AuNPs treatment significantly inhibited anti-miR155-5p transfection-induced SOCS1 expression (p<0.05). These findings were validated by IFN-γ-stimulated MDA-MB-231 cells. Moreover, the data also determined that citrate-AuNPs also inhibit IFN-γ-induced NF-κB p65/p50 activation in MDA-MB-231 cells transfected with anti-hsa-miR155-5p. Newly generated citrate-AuNPs were stable and non-toxic to TNBC cells. Citrate-AuNPs inhibit IFN-γ-induced SOCS1 mRNA/protein expression and deactivate NF-κB p65/50 activity via negative regulation of hsa-miR155-5p. These novel pharmacological actions of citrate-AuNPs on IFN-γ-stimulated TNBC cells provide insights that AuNPs inhibit IFN-γ induced inflammation in TNBC cells by modulating the expression of microRNAs.

Characteristics of mesenchymal stem cells and their exosomes derived from giant panda (Ailuropoda melanoleuca) endometrium.

Conservation of genetic resources is an important way to protect endangered species. At present, mesenchymal stem cells (MSCs) have been isolated from the bone marrow and umbilical cords of giant pandas. However, the types and quantities of preserved cell resources were rare and limited, and none of MSCs was derived from female reproductive organs. Here, we first isolated MSCs from the endometrium of giant panda. These cells showed fibroblast morphology and expressed Sox2, Klf4, Thy1, CD73, CD105, CD44, CD49f, and CD105. Endometrium mesenchymal stem cells (eMSCs) of giant panda could induce differentiation into three germ layers in vitro. RNA-seq analysis showed that 833 genes were upregulated and 716 genes were downregulated in eMSCs compared with skin fibroblast cells. The results of GO and the KEGG analysis of differentially expressed genes (DEGs) were mainly focused on transporter activity, signal transducer activity, pathways regulating pluripotency of stem cells, MAPK signaling pathway, and PI3K-Akt signaling pathway. The genes PLCG2, FRK, JAK3, LYN, PIK3CB, JAK2, CBLB, and MET were identified as hub genes by PPI network analysis. In addition, the exosomes of eMSCs were also isolated and identified. The average diameter of exosomes was 74.26 ± 13.75 nm and highly expressed TSG101 and CD9 but did not express CALNEXIN. A total of 277 miRNAs were detected in the exosomes; the highest expression of miRNA was the has-miR-21-5p. A total of 14461 target genes of the whole miRNAs were predicted and proceeded with functional analysis. In conclusion, we successfully isolated and characterized the giant panda eMSCs and their exosomes, and analyzed their functions through bioinformatics techniques. It not only enriched the conservation types of giant panda cell resources and promoted the protection of genetic diversity, but also laid a foundation for the application of eMSCs and exosomes in the disease treatment of giant pandas.

Small RNA-Seq to Unveil the miRNA Expression Patterns and Identify the Target Genes in Panax ginseng.

Panax ginseng, renowned for its medicinal properties, relies on adventitious roots and hairy roots as crucial sources for the production of ginsenosides. Despite the widespread utilization of ginseng, investigations into its miRNAs have remained scarce. To address this gap, two samples of ginseng adventitious roots and ginseng hairy roots were collected, and subsequent construction and sequencing of small RNA libraries of ginseng adventitious roots and hairy roots were performed using the Illumina HiSeq X Ten platform. The analysis of the sequencing data unveiled total miRNAs 2432. The miR166 and miR396 were the most highly expressed miRNA families in ginseng. The miRNA expression analysis results were used to validate the qRT-PCR. Target genes of miRNA were predicted and GO function annotation and KEGG pathway analysis were performed on target genes. It was found that miRNAs are mainly involved in synthetic pathways and biological processes in plants, which include metabolic and bioregulatory processes. The plant miRNAs enriched KEGG pathways are associated with some metabolism, especially amino acid metabolism and carbohydrate metabolism. These results provide valuable insights miRNAs and their roles in metabolic processes in ginseng.