miRNA Genes Research Articles

Association of functional variants in miRNA genes with the risk of coronary heart disease

Abstract Background Cardiovascular diseases, especially coronary heart disease (CHD), are currently the leading cause of mortality and morbidity. Environmental and genetic factors contribute to the pathophysiology of CHD. In this study, we investigated the associations of miRNA genes MIR222, MIR423, MIR4274, and MIR3117 with the pathogenesis of CHD. Methods Genetic inheritance models were applied to explore the association between these miRNA genes and CHD. Tetra-Primer Amplification Refractory Mutation System-Polymerase Chain Reaction (T-ARMS-PCR) was used for genotyping, and Sanger sequencing was applied for validation in selected cases. Results The codominant [χ2 = 8.058, 2; P value = 0.0178], and recessive (CC vs GC + GG) [OR = 0.4535 (0.2439–0.8669); P value = 0.0187] models demonstrated a statistically significant association between MIR222 (rs2858060) and CHD. Similarly, the co-dominant [χ2 = 6.105, 2, 2; P value = 0.0472], and additive [OR = 1.494 (1.024–2.211); P value = 0.0428] models revealed a significant association (P value < 0.05) between MIR423 (rs6505162) and CHD. In MIR4242, a novel triplet insertion (CAC) was identified exclusively in CHD samples, predicated to disrupt the stem-loop structure ofmiR-4274. However, MIR3117 showed no association with CHD, as confirmed by Sanger sequencing of 40 samples. Conclusion Our findings suggest that functional variants rs2858060, rs6505162, and a novel triplet insertion (CAC) in MIR222, MIR423, and MIR4274 respectively are strongly associated with CHD. These results underline the potential of miRNA gene variants as genetic biomarkers for CHD susceptibility.

Revealing microRNA regulation in single cells.

MicroRNAs (miRNAs) are key regulators of gene expression and control cellular functions in physiological and pathophysiological states. miRNAs play important roles in disease, stress, and development, and are now being investigated for therapeutic approaches. Alternative processing of miRNAs during biogenesis results in the generation of miRNA isoforms (isomiRs) which further diversify miRNA gene regulation. Single-cell RNA-sequencing (scsRNA-seq) technologies, together with computational strategies, enable exploration of miRNAs, isomiRs, and interacting RNAs at the cellular level. By integration with other miRNA-associated single-cell modalities, miRNA roles can be resolved at different stages of processing and regulation. In this review we discuss (i) single-cell experimental assays that measure miRNA and isomiR abundances, and (ii) computational methods for their analysis to investigate the mechanisms of miRNA biogenesis and post-transcriptional regulation.

Promising Biotechnological Applications of the Artificial Derivatives Designed and Constructed from Plant microRNA Genes

MicroRNAs (miRNAs) are small regulatory RNAs that are expressed in a tissue-specific manner during the development of plants and animals. The genes of miRNAs have been found to produce the following two products: (i) primary transcripts of these genes (pri-miRNA) are processed to give rise to mature miRNA, and (ii) in some cases, the pri-miRNA molecules can be translated to form small peptides, named as miPEPs. Gene silencing by artificial microRNAs (amiRNAs) is one of the potential crucial methods for the regulation of desired genes to improve horticultural plants. Likewise, external application of chemically synthesized miPEPs may help plants to resist biotic/abiotic stresses and grow faster. These potent and reliable derivatives of miRNA genes can be applied for improving useful traits in crop plants. This review summarizes the progress in research on the artificial gene derivatives involved in regulating plant development, virus and pest diseases, and abiotic stress resistance pathways. We also briefly discuss the molecular mechanisms of relevant target genes for future research on breeding in plants. In general, this review may be useful to researchers who are implementing amiRNA and miPEP for accelerating breeding programs and developmental studies in crop plants.

L1CAM+ extracellular vesicles derived from the serum of adolescents with major depressive disorder induce depression-like phenotypes in adolescent mice.

It has been reported that L1 cell adhesion molecule (L1CAM) antibody can capture neuron-derived extracellular vesicles (NDEVs) derived from peripheral blood. This antibody is significantly associated with occurrence of adult psychiatric disorders. However, the role and mechanism of L1CAM+ EVs (L1+ EVs) in adolescent with major depressive disorder (AMDD) is not well understood. This research aimed to explore the function and potential mechanism of L1+ EVs and miRNAs genes in AMDD. L1+ EVs derived from the serum of AMDD and healthy controls (HC) were transplanted into adolescent mice via tail vein. Their effects were explored using behavioral tests, hippocampal Nissl staining, and whole genome mRNA sequencing. MiRNAs expression in L1+ EVs was evaluated by whole-genome sequencing and qRT-PCR. Bioinformatics analysis was employed to explore the possible pathogenic molecular mechanisms of these miRNAs in AMDD. Transplantation of L1+ EVs from AMDD induced depression-like behavior and hippocampal neuronal damage in adolescent mice and aberrant expression of 298 mRNA genes. The molecular signals related to MDD were enriched in the top pathways of the differentially expressed genes. Compared with HC, miR-375-3p and miR-200a-3p were upregulated in L1+ EVs from AMDD, miR-375-3p was also increased in the hippocampus of AMDD serum L1+ EVs-recipient mice. Bioinformatics analysis revealed that miR-375-3p might modulate the network of molecules associated with the MAPK pathway via protein interaction involving hippocampal differential genes Cadm2, Cacna2d1, and Casz1. MiR-375-3p might contribute to L1+ EVs-induced AMDD. L1+ EVs miR-375-3p and miR-200a-3p could potentially serve as potential biomarkers for AMDD.

Exploring the Mechanism of Acupuncture in Improving Ovarian Function in Rats with Poor Ovarian Response Using High-Throughput Sequencing.

This study aimed to investigate the possible mechanism through which acupuncture protects ovaries with Poor Ovarian Response (POR) in rats based on microRNA (miRNA). Thirty-six SPF SD female non-pregnant rats aged 8 weeks were randomly divided into the blank group, model group, and acupuncture group, with 12 rats in each group. According to the group, the rats were given gavage of Tripterygium wilfordii polyglycosides suspension for 14 days to establish the model of POR, and then the rats were treated with acupuncture for 2 weeks, once a day, for 20 minutes. Afterward, their hormone levels were measured, and HE staining was performed on the ovaries after the intervention. Three rats from each group were randomly selected for ovarian tissue miRNA sequencing, and differential miRNAs were subjected to Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway analysis, and Quantitative Polymerase Chain Reaction (QPCR) verification. By using TargetScan to predict the target genes of differential miRNAs, we validated the results with a dual luciferase reporter gene assay. Compared with the blank group, the estrus cycle of the model group was significantly prolonged (P<0.01). Anti-Müllerian Hormone (AMH) (P<0.01) and Estrogen (E2) were significantly decreased (P<0.05). Follicle-Stimulating Hormone (FSH)(P<0.05) and Luteinizing Hormone (LH) increased sharply (P<0.01). Compared with the model group, the estrus cycle was significantly shortened in the acupuncture group (P<0.01). AMH and E2 were markedly raised (P<0.05). FSH (P<0.05) and LH (P<0.01) were significantly declined. miRNA sequencing showed that there were 23 miRNAs significantly different between the model group and the blank group (P<0.05), and 30 miRNAs significantly different between the acupuncture group and the model group (P<0.05). GO demonstrated that the network was mainly involved in cellular components, cells, cellular metabolic processes, binding, and single biological processes; KEGG signaling pathway enrichment showed that it was mainly related to MAPK, adhesion junction, calcium signaling pathways, etc. Q-PCR results showed that after modeling, the expression rose, and after acupuncture, the expression of the following miRNA decreased: miR-154-5p (P<0.01), miR-300-5p (P < 0.05), miR-376c-5p (P<0.05). The dual luciferase reporter assay showed that the relative luciferase activity of the miR-300-5p mimics+MAP3K1-WT group was significantly lower than that of the NC+MAP3K1-WT group (P<0.01). HE results demonstrated that the number of primordial follicles and primary follicles in the model group was significantly lower than that in the blank group (P<0.05). Moreover, the morphology was poorer, and the granulosa cell layer was thinner. Compared with the model group, the number of primary follicles in the acupuncture group increased (P<0.05); the morphology and granulosa cell structure of the ovary were improved to different degrees, and mature follicles could be seen. Acupuncture may improve the ovarian responsiveness of POR rats by regulating miR-154- 5p,miR-300-5p, and miR-376c-5p. Furthermore, miR-300-5p can specifically bind to the 3'-UTR of MAP3K1, and MAP3K1 may be the target of miR-300-5p.

Scenarios for the emergence of new miRNA genes in the plant Arabidopsis halleri.

MicroRNAs (miRNAs) are central players of the regulation of gene expression in Eukaryotes. The repertoires of miRNA genes vary drastically even among closely related species, indicating that they are evolutionarily labile. However, the processes by which they originate over the course of evolution and the nature of their progenitors across the genome remain poorly understood. Here we analyzed miRNA genes in Arabidopsis halleri, a plant species where we recently documented a large number of species-specific miRNA genes, likely to represent recent events of emergence. Analysis of sequence homology across the genome indicates that a diversity of sources contributes to the emergence of new miRNA genes, including inverted duplications from protein-coding genes, rearrangements of transposable element sequences and duplications of preexisting miRNA genes. Our observations indicate that the origin from protein-coding genes was less common than was previously considered. In contrast, we estimate that almost half of the new miRNA genes likely emerged from transposable elements. Miniature inverted transposable elements (MITE) seem to be particularly important contributors to new miRNA genes, with the Harbinger and Mariner transposable element superfamilies representing disproportionate sources for their emergence. We further analyzed the recent expansion of a miRNA family derived from MuDR elements, and the duplication of miRNA genes formed by two hAT transposons. Overall, our results illustrate the rapid pace at which new regulatory elements can arise from the modification of preexisting sequences in a genome, and highlight the central role of certain categories of transposable elements in this process.

Prenatal maternal stress in rats alters the epigenetic and transcriptomic landscape of the maternal-fetal interface across four generations

Prenatal maternal stress (PNMS) determines lifetime mental and physical health. Here, we show in rats that PNMS has consequences for placental function and fetal brain development across four generations (F0-F3). Using a systems biology approach, comprehensive DNA methylation (DNAm), miRNA, and mRNA profiling revealed a moderate impact of PNMS in the F1 generation, but drastic changes in F2 and F3 generations, suggesting compounding effects of PNMS with each successive generation. Both maternal and placental miRNA gene targets included de novo DNA methyltransferases, indicating robust PNMS-induced disruption in the complex epigenetic regulatory network between miRNAs and DNAm. Transgenerational programming mainly involved genes and biological pathways associated with neurological and psychiatric diseases which were linked to maternal-fetal crosstalk facilitated by the placenta. The highly correlated placenta-brain profiles support the use of placenta as a noninvasive biomarker resource to predict pathological changes in the neonatal brain. The transgenerational persistence of critical DNAm, miRNA and mRNA signatures may explain familial non-genetic disease risks.

An intron-split microRNA mediates cleavage of the mRNA encoded by low phosphate root in Solanaceae

Main conclusionA microRNA with a non-canonical precursor structure harbours an intron in between its miRNA-5p and miRNA-3p relevant for its biogenesis, is conserved across Solanaceae, and targets the mRNA of low phosphate root.Hundreds of miRNAs have been identified in plants and great advances have been accomplished in the understanding of plant miRNA biogenesis, mechanisms and functions. Still, many miRNAs, particularly those with less conventional features, remain to be discovered. Likewise, additional layers of regulation from miRNA generation to action and turnover are still being revealed. The current study describes a microRNA not previously identified given its unusual intron-split stem-loop structure, that has been previously observed only within the monocot-specific miRNA444 family. It shows its conservation across a branch of Solanales including agriculturally relevant Solanaceae family, where its transcripts had already been predicted in several species within sequence databases. The miRNA is absent in Arabidopsis thaliana but present in Solanum lycopersicum, Nicotiana benthamiana, Petunia axillaris, and Ipomoea nil. It proves that at least two different pri-miRNA variants are produced from this miRNA gene, one spliced and the other one retaining the intron. It demonstrates the dual function of its intron in the miRNA biogenesis. On the one hand, its presence in the pri-miRNA positively influences mature miRNA accumulation, but on the other hand, it needs to be removed from the pri-miRNA for efficient mature miRNA production. Finally, it sets low phosphate root as one of its targets, a protein known to be involved in root growth regulation under phosphate starvation in other plant species.

A genome-wide scan of non-coding RNAs and enhancers for refractive error and myopia

Refractive error (RE) and myopia are complex polygenic conditions with the majority of genome-wide associated genetic variants in non-exonic regions. Given this, and the onset during childhood, gene-regulation is expected to play an important role in its pathogenesis. This prompted us to explore beyond traditional gene finding approaches. We performed a genetic association study between variants in non-coding RNAs and enhancers, and RE and myopia. We obtained single-nucleotide polymorphisms (SNPs) in microRNA (miRNA) genes, miRNA-binding sites, long non-coding RNAs genes (lncRNAs) and enhancers from publicly available databases: miRNASNPv2, PolymiRTS, VISTA Enhancer Browser, FANTOM5 and lncRNASNP2. We investigated whether SNPs overlapping these elements were associated with RE and myopia leveraged from a large GWAS meta-analysis (N = 160,420). With genetic risk scores (GRSs) per element, we investigated the joint effect of associated variants on RE, axial length (AL)/corneal radius (CR), and AL progression in an independent child cohort, the Generation R Study (N = 3638 children). We constructed a score for biological plausibility per SNP in highly confident miRNA-binding sites and enhancers in chromatin accessible regions. We found that SNPs in two miRNA genes, 14 enhancers and 81 lncRNA genes in chromatin accessible regions and 54 highly confident miRNA-binding sites, were in RE and myopia-associated loci. GRSs from SNPs in enhancers were significantly associated with RE, AL/CR and AL progression. GRSs from lncRNAs were significantly associated with all AL/CR and AL progression. GRSs from miRNAs were not associated with any ocular biometric measurement. GRSs from miRNA-binding sites showed suggestive but inconsistent significance. We prioritized candidate miRNA binding sites and candidate enhancers for future functional validation. Pathways of target and host genes of highly ranked variants included eye development (BMP4, MPPED2), neurogenesis (DDIT4, NTM), extracellular matrix (ANTXR2, BMP3), photoreceptor metabolism (DNAJB12), photoreceptor morphogenesis (CHDR1), neural signaling (VIPR2) and TGF-beta signaling (ANAPC16). This is the first large-scale study of non-coding RNAs and enhancers for RE and myopia. Enhancers and lncRNAs could be of large importance as they are associated with childhood myopia. We provide a confident blueprint for future functional validation by prioritizing candidate miRNA binding sites and candidate enhancers.

Polymorphic Single-Nucleotide Variants in miRNA Genes and the Susceptibility to Colorectal Cancer: Combined Evaluation by Pairwise and Network Meta-Analysis, Thakkinstian's Algorithm and FPRP Criterium.

Considerable epidemiological studies have examined the correlation between polymorphic single-nucleotide variants (SNPs) in miRNA genes and colorectal carcinoma (CRC) risk, yielding inconsistent results. Herein, we sought to systematically investigate the association between miRNA-SNPs and CRC susceptibility by combined evaluation using pairwise and network meta-analysis, the FPRP analysis (false positive report probability), and the Thakkinstian's algorithm. The MEDLINE, EMBASE, WOS, and Cochrane Library databases were searched through May 2024 to find relevant association literatures. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were computed by the pairwise meta-analysis. Network meta-analysis and the Thakkinstian's method were applied for determining the potentially optimal genetic models; additionally, the FPRP was used to identify noteworthy associations. Totally, 39 case-control trials involving 18,028 CRC cases, and 21,816 normal participants were included in the study. Eleven SNPs within nine genes were examined for their predisposition to CRC. miR-27a (rs895819) was found to significantly increase CRC risk among overall population (OR 1.58, 95% CI: 1.32-1.89) and Asians (OR 1.62, 95% CI: 1.31-2.01), with the recessive models identified as the optimal models. Furthermore, miR-196a2 (rs11614913), miR-143/145 (rs41291957), and miR-34b/c (rs4938723) were significantly related to reduced CRC risk among Asian descendants under the optimal dominant (OR 0.75, 95% CI: 0.65-0.86), recessive (OR 0.72, 95% CI: 0.60-0.85), and recessive models (OR 0.69, 95% CI: 0.56-0.85), respectively. The results were also proposed by the network meta-analysis or the Thakkinstian's method and confirmed by the FPRP criterion. The miR-27a (rs895819) is correlated with elevated CRC risk among overall population and Asians, and the recessive model is found to be optimal for predicting CRC risk. Additionally, the miR-196a2 (rs11614913), miR-143/145 (rs41291957), and miR-34b/c (rs4938723), with the dominant, recessive, and recessive models identified as the optimal, might confer protective effects against CRC among Asians.

Role of miRNA regulation in IGFBP-2 overexpression and neuronal ferroptosis: Insights into the Nrf2/SLC7A11/GPX4 pathway in Alzheimer's disease.

Alzheimer's disease (AD) is a common neurodegenerative disease with pathological features including amyloid plaque deposits and neurofibrillary tangles. In this study, the expressions of miRNA, IGFBP-2 and neuronal ferritin were detected by qPCR, Western blot and immunohistochemistry. The regulatory effects of miRNA on IGFBP-2 and neuronal ferritin were further verified by intervention experiments with miRNA mimics and inhibitors. Double luciferase reporter gene assay and RNA immunoprecipitation were used to investigate the interaction between miRNA and target genes. Finally, the effect of miRNA on Nrf2/SLC7A11/GPX4 pathway was evaluated by antioxidant enzyme activity and oxidative stress marker detection. The overexpression of IGFBP-2 was found to be significantly increased with the deposition of neuronal ferritin. Expression levels of specific mirnas were significantly down-regulated in AD models and negatively correlated with IGFBP-2 and neuronal ferritin expression. Intervention experiments with miRNA mimics and inhibitors have confirmed that these mirnas can regulate the expression of IGFBP-2 and neuronal ferritin. Further studies revealed that these mirnas affect antioxidant enzyme activity and oxidative stress levels by targeting key genes in the Nrf2/SLC7A11/GPX4 pathway, thereby regulating the deposition of neuronal ferritin.

Detection and quantification of miRNA 148a expression in infant formulas.

MiRNA 148a, which is associated with various biological processes such as immunity and cell differentiation, is one of the most abundant miRNAs in breast milk. This study aimed to determine the amount of miRNA 148a in different infant formulas, which are used for infants who cannot receive breast milk. The study analyzed 20 formulas, including stage one infant formulas (0-6 months of age), stage two follow-up formulas (6-12 months of age), stage three toddler formulas (above 12 months of age), and premature ones, analyzing miRNA 148a expression and qPCR miRNA gene expression, with significance set at p<0.05. The expression levels of miRNA 148a in different infant formulas were compared, and no statistically significant difference was observed (p>0.05). Also, there was no difference in relative miRNA 148a expression across formulas with and without probiotics (p>0.05). Protein levels in probiotic formulas (0 month-1 year+) were positively correlated with relative miRNA 148a expression (p=0.022). Although miRNA 148a expression has been shown to be present in formulas, it has been revealed that the amount is low compared to breast milk in line with the literature. In this direction, it is important to increase current data on the mechanisms of action of miRNAs in breast milk and the efforts to ensure that infant formulas reach a composition closest to breast milk in line with their biological effects. PRACTICAL APPLICATION: The miRNAs found in exosomal compounds in human breast milk are very diverse in terms of number and health effects, and can control various biological processes in cells, including immunity, cell differentiation, and apoptosis. One of these is miRNA 148a, which is the most abundant in human breast milk. For this reason, in this study, the miRNA 148a content of infant formulas, which are commonly used in healthy babies who cannot receive enough human breast milk (breastfeeding recommended for at least 6 months and up to 2 years) for a valid reason, was analyzed. In conclusion, miRNA expression has been detected in infant formulas, but it has been shown that this expression is at a low level.

MiR- 146b-5p inhibits Candida albicans-induced inflammatory response through targeting HMGB1 in mouse primary peritoneal macrophages.

Candida albicans (C. albicans) is one of the most common pathogens associated with deep fungal infection, which represents a serious threat to human health. Although high mobility group box 1 (HMGB1) plays a key role in C. albicans infection, its mechanism is unclear. We aimed to explore the regulation of small-molecule non-coding RNA (miRNA) for HMGB1 in C. albicans infection. Mouse primary peritoneal macrophages (MPMs) were isolated successfully. The optimum conditions for C. albicans infection were selected by Western blot and ELISA. The miRNA differential expression profiles of C. albicans infection were screened and verified by 6 miRNA gene chips and qRT-PCR. The direct regulation of the target gene HMGB1 by mmu-miR-146b-5p was confirmed through a dual-luciferase assay. The levels of mmu-miR-146b-5p, HMGB1, inflammatory mediators, p-IKK, IKK, p-IκBα, IκBα and NF-κB p65 were tested by qRT-PCR, Western blot, and ELISA. The nuclear and cytoplasm translocation of HMGB1 and NF-κB p65 were detected by Western blot and laser confocal microscopy. After siHMGB1 transfection, the expression levels of HMGB1, inflammatory mediators, p-IKK, IKK, p-IκBα, IκBα and NF-κB p65 were assessed using Western blot, qRT-PCR and ELISA. In our study, MPMs were successfully extracted and infected with C. albicans at optimum conditions of 1.5×107CFU/mL for 36h. Through miRNA gene chips analysis, 40 differential genes were screened. mmu-miR-146b-5p could directly and negatively regulate the expression and translocation of HMGB1, inhibit the expression of inflammatory mediators, and might participate in the NF-κB signaling pathway in a HMGB1-dependent manner under C. albicans infection. mmu-miR-146b-5p may play an anti-inflammatory role in treating C. albicans infection and provide a novel target for it.

Polystyrene Nanoparticles-coated Astragalus Polysaccharides Affects the Development of Prostate Cancer by Regulating Glycolysis of DAP12/SYK Axis Through miR-370

Background This study aims to explore the use of polystyrene nanoparticles as a carrier to encapsulate astragalus polysaccharides and regulate the glycolytic pathway of the DNAX-activating protein of 12 kDa/spleen tyrosine kinase (DAP12/SYK) axis through miR-370, thereby affecting the development mechanism of prostate cancer. Materials and Methods Polystyrene nanoparticles coated with astragalus polysaccharide nanoparticles (APS/PDA NPs) were prepared, and PC-3 cell experiments were used for culture and further detection of miRNA and other genes, detection of glycolysis-related proteins and genes, and observation of the biology of PC-3 cells behavioral changes, exploring the mechanism of action of APS/PDA NPs. Results We successfully prepared composite materials of APS/PDA NPs, and found that APS/PDA NPs could inhibit glycolysis and induce apoptosis in PC-3 cells. Further experiments showed that APS/PDA NPs could increase miR-370 expression, inhibit glycolysis, and induce apoptosis. APS/PDA NPs play a strong role in inhibiting the DAP12/SYK axis, inhibiting glycolysis, and causing apoptosis. Combined with biological information and multiple experiments, it was confirmed that miR-370 targeted DAP12, and the inhibition of PCa progression by APS/PDA NPs was achieved through targeting miR-370 and negatively regulating the DAP12/SYK axis. Conclusion As a drug carrier, polystyrene nanoparticles can effectively deliver astragalus polysaccharides to prostate cancer cells, thereby increasing the local concentration of drugs and enhancing the therapeutic effect. More encouragingly, this drug carrier not only performed well in inhibiting glycolysis but also significantly upregulated the level of miR-370, which further inhibits the expression of DAP12, providing a new therapeutic idea for inhibiting the development of prostate cancer.

Whole-Transcriptome Analysis Reveals the Regulatory Network of Immune Response in Dapulian Pig.

There is a consensus that indigenous pigs in China are more resistant than modern commercial pigs in terms of disease resistance. Generally, the immune response is an important part of anti-disease capability; however, the related mechanism in pigs is largely puzzling. Here, the public transcriptome data of peripheral blood mononuclear cells (PBMCs) from Dapulian (Chinese local breed) and Landrace (Commercial breed) pigs after stimulation with polyinosinic-polycytidylic acid (poly I:C, a conventional reagent used for simulation of the viral infection) were reanalyzed, and the immune response mechanism in different pig breeds was investigated from a transcriptomic perspective. Of note, through comparative analyses of Dapulian and Landrace pigs, the candidate genes involved in swine broad-spectrum resistance were identified, such as TIMD4, RNF128 and VCAM1. In addition, after differential gene expression, target gene identification and functional enrichment analyses, a potential regulatory network of miRNA genes associated with immune response was obtained in Dapulian pigs, including five miRNAs and 12 genes (such as ssc-miR-181a, ssc-miR-486, IL1R1 and NFKB2). This work provides new insights into the immune response regulation of antiviral responses in indigenous and modern commercial pigs.

MiRNA Expression: I/R Cardiomyocyte and Sevoflurane.

The effects of anesthetic drugs on myocardial cells have been a subject of research for the last 50 years. The clinical benefits of halogenated agents, particularly sevoflurane, have been demonstrated in cardiac surgery patients. These benefits are due to the action of different enzymes and a variety of molecular pathways mediated by the action of small noncoding RNAs (sRNA) such as microRNAs (miRNAs). However, the modulation potential induced by anesthetic drugs on the miRNA expression and their cardioprotective effects is unknown. To analyze the variation in the expression of a panel of miRNAs induced by halogenated agents to identify their cardioprotective effects. Variations in the expression of specific miRNAs induce the potential cardioprotective effects of halogenated agents. An ischemia/reperfusion (I/R) in vitro model of primary human cardiac myocytes (HCMs) was performed. Four study groups were performed: control group (standard culture conditions), I/R group (without hypnotic drugs exposition), I/R-propofol group (I/R-P), and I/R-sevoflurane group (I/R-S). The secretion of p53 and Akt1 cytokines was quantified in the different cell study groups using an Enzyme-Linked ImmunoSorbent Assay, and the differentially expressed miRNAs were identified carrying out a complete genomic sequencing using the Next Generation Sequencing (NGS). HCMs subjected to the I/R procedure and exposed to sevoflurane showed lower secretion levels of p53 factor and higher levels of Akt-1 cytokine compared to HCMs exposed to propofol (p53: I/R-S: 10.43 ± 0.91 ng/mL; I/R-P: 137.92 ± 7.53 ng/mL; p > 0.05); (Akt1: I/R-S: 0.62 ± 0.12 ng/mL; I/R-P: 0.23 ± 0.05 ng/mL; p > 0.05). The miRNA gene expression analysis (NGS) showed significantly increased expression of the hsa-miR-140-5p and hsa-miR-455-5p, both miRNAs associated with cardiac function; the hsa-miR-98-5p and hsa-miR-193a-5p, both related to apoptosis inhibition; and the hsa-let-7d-5p associated with myocardial protection. This increase was observed in the HCMs group exposed to sevoflurane in comparison to the propofol group. Sevoflurane-induced miRNAs overexpression confers cardioprotection through various mechanisms at the DNA level and the different signaling pathways levels, such as Akt/ERK.

Targeting microRNA methylation: Innovative approaches to diagnosing and treating hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) stands as the most prevalent form of primary liver cancer and is frequently linked to underlying chronic liver conditions such as hepatitis B, hepatitis C, and cirrhosis. Despite the progress achieved in the field of oncology, HCC remains a significant clinical challenge, primarily due to its typically late-stage diagnosis and the complex and multifaceted nature of its tumor biology. These factors contribute to the limited effectiveness of current treatment modalities and result in poor patient prognosis. Emerging research has underscored the vital role of microRNAs (miRNAs)-small, non-coding RNA molecules that play a pivotal part in the post-transcriptional regulation of gene expression. These miRNAs are integral to a wide array of cellular functions, including proliferation, apoptosis, and differentiation, and their dysregulation is closely associated with the pathogenesis of various cancers, notably HCC. A major focus in recent studies has been on the epigenetic regulation of miRNAs through methylation, a key mechanism that modulates gene expression. This process, involving the addition of methyl groups to CpG islands in the promoter regions of miRNA genes, can result in either gene silencing or activation, influencing the expression of oncogenes and tumor suppressor genes. Such alterations have profound implications for tumor growth, metastasis, and resistance to treatment. Evidence suggests that aberrant miRNA methylation can serve as a powerful biomarker for early detection and prognosis in HCC and may present novel opportunities for therapeutic intervention. This review aims to provide a comprehensive overview of the current landscape of miRNA methylation in HCC, elucidating its significance in the molecular mechanisms of liver cancer and examining its potential for clinical application. By exploring the diagnostic and therapeutic potential of miRNA methylation, we seek to highlight its value in enhancing personalized treatment strategies and improving patient outcomes.

Postmortem analyses of myocardial microRNA expression in sepsis

BackgroundSepsis can lead to myocardial depression, playing a significant role in sepsis pathophysiology, clinical care, and outcome. To gain more insight into the pathophysiology of the myocardial response in sepsis, we investigated the expression of microRNA in myocardial autopsy specimens in critically ill deceased with sepsis and non-septic controls.Materials and methodsIn this retrospective observational study, we obtained myocardial tissue samples collected during autopsy from adult patients deceased with sepsis (n = 15) for routine histological examination. We obtained control myocardial tissue specimens (n = 15) from medicolegal autopsies of cadavers whose cause of death was injury or who were found dead at home and the cause of death was coronary artery disease with sudden cardiac arrest. RNA was isolated from formalin-fixed paraffin- embedded (FFPE) cardiac samples using the RecoverAll Total Nucleic Acid Isolation Kit for FFPE (Invitrogen). Differentially expressed miRNAs were identified using edgeR v3.32. MicroRNA was considered up- or down-regulated if the false discovery rate was < 0.05 and logarithmic fold change (log2FC) ≥ 1 for up-regulated or log2FC ≤ -1 for down-regulated miRNAs. The mean difference and 95% confidence interval (CI) were calculated for normalized read counts. Predicted miRNA targets were retrieved using Ingenuity Pathway Analysis (IPA) software, and pathway enrichment and classification were performed using PantherDB. For miRNA – mRNA interaction analysis, differentially expressed genes were analyzed by 3`mRNA sequencing.ResultsDifferential expression analysis identified a total of 32 miRNAs in the myocardial specimens. Eight miRNAs had a significant change in the mean difference based on the 95% CI, with the largest increase in mean counts in septic samples with hsa-miR-12136 and the highest fold change with hsa-miR-146b-5p. The threshold for down-regulated miRNAs in sepsis compared to controls was obtained with hsa-miR-144-5p and hsa-miR-451a, with the latter having the largest decrease in mean counts and fold decrease. The miRNA – mRNA interaction analysis identified eight miRNAs with target genes also differentially expressed in septic hearts. The highest number of potential targets were identified for hsa-miR-363-3p.ConclusionsSeveral regulatory miRNAs were up-or down-regulated in the myocardial tissue of patients deceased with sepsis compared to non-septic subjects. The predicted target genes of miRNAs and miRNA-mRNA interaction analysis are associated with biological functions related to cardiovascular functions, cell viability, cell adhesion, and regulation of inflammatory and immune response.

Identification of Key Genes and Drug Recommendations in Diffuse Large B-Cell Lymphoma Based on Analysis of Glutathione-Related Genes

Background: Various malignancies can be efficiently combated by focusing on glutathione. It is unclear how glutathione-related genes link to diffuse large B-cell lymphoma (DLBCL). Methods: Clinical information was gathered from DLBCL patients, and differences in glutathione-related differentially expressed genes (DEGs) between DLBCL and healthy groups were found. Enrichment analysis was run on the DEGs associated with glutathione. We discovered hub genes in glutathione, confirmed hub genes’ capacity for diagnosis and function prediction, and estimated drug sensitivity. Immune microenvironmental variations between healthy and DLBCL people were assessed, and hub genes for transcription factor (TF) targeting and miRNAs were found. Results: The glutathione-related DEGs were linked to biological processes such as response to oxidative stress and response to xenobiotic stimulus, according to enrichment analysis. Out of DEGs associated with glutathione, six hub genes were chosen. In the DLBCL population, there was a notable upregulation of the six hub genes. All the genes’ AUC values in the diagnostic ability category were more than 0.7, showing strong hub gene diagnostic capacity. The DLBCL population had a high level of T-cell infiltration, according to immune infiltration analysis techniques. Similar activities, such as the cell cycle G2/M phase transition and the negative control of organelle formation, are demonstrated by gene function prediction for hub. According to drug sensitivity prediction, there was a favorable link between KPNA2 with pracinostat, BRCA1 with B-7100, and LEE-011. The gene KPNA2 was shown to be concurrently targeted by many miRNAs and TFs, according to the miRNA-gene-TF interaction network. Conclusion: The relationship between DLBCL and glutathione-related genes was uncovered by our research, and six glutathione genes were linked to DLBCL. These genes might be used as diagnostic biomarkers or targets for treatment for DLBCL patients.

Differential expression profile of miRNAs in maternal amniotic fluid exosomes in fetuses with isolated ventriculomegaly

To investigate the role of miRNAs in maternal amniotic fluid exosomes in development of isolated ventriculomegaly (VM) in fetuses. Amniotic fluid samples were collected from 9 cases of moderate isolated VM and 8 normal control cases to extract exosomal miRNA, and miRNA sequencing technique was used to identify differentially expressed miRNAs between the two groups. Three miRNAs with significant differential expression between the two groups, whose high expression was associated with VM, were selected for verification with RT-qPCR. Dual luciferase reporter assays were used to verify the regulatory effect of miR-122-5p on its predicted target genes AKT3 and CCDC88C. Gene ontology (GO) and KEGG pathway analyses were performed to explore the possible roles of the top 40 significant differential miRNAs in the pathophysiology of VM. We identified a total of 272 differentially expressed miRNAs in VM cases, including 43 up-regulated and 229 down-regulated miRNAs. The target genes of these differential miRNAs were associated with DNA and transcription factor binding, transmembrane transporter and nucleic acid binding transcription factor activity, and cell developmental process. These miRNAs were mostly enriched in the MAPK, cGMP-PKG and Wnt signaling pathways. Verification with RT-qPCR showed that miR-122-5p expression level was significantly lower in VM group than in the control group (P < 0.05), which was consistent with miRNA sequencing results; let-7b-5p expression level was significantly lower in VM group, which was contrary to miRNA sequencing result. Dual luciferase reporter assays showed that miR-122-5p was not capable of regulating AKT3 or CCDC88C expressions. The highly abundant differentially expressed miRNAs in maternal amniotic fluid exosomes play important roles in the occurrence of fetal VM possibly by regulating the MAPK, PI3K-Akt, Wnt and cGMP-PKG signaling pathways.