Physiologically relevant miRNAs in mammalian oocytes are rare and highly abundant

miRNAs, ~22nt small RNAs associated with Argonaute (AGO) proteins, are important negative regulators of gene expression in mammalian cells. However, mammalian maternal miRNAs show negligible repressive activity and the miRNA pathway is dispensable for oocytes and maternal‐to‐zygotic transition. The stoichiometric hypothesis proposed that this is caused by dilution of maternal miRNAs during oocyte growth. As the dilution affects miRNAs but not mRNAs, it creates unfavorable miRNA:mRNA stoichiometry for efficient repression of cognate mRNAs. Here, we report that porcine ssc‐miR‐205 and bovine bta‐miR‐10b are exceptional miRNAs, which resist the diluting effect of oocyte growth and can efficiently suppress gene expression. Additional analysis of ssc‐miR‐205 shows that it has higher stability, reduces expression of endogenous targets, and contributes to the porcine oocyte‐to‐embryo transition. Consistent with the stoichiometric hypothesis, our results show that the endogenous miRNA pathway in mammalian oocytes is intact and that maternal miRNAs can efficiently suppress gene expression when a favorable miRNA:mRNA stoichiometry is established.     

Integrated analysis of miRNA and mRNA expression profiles in response to gut microbiota depletion in the abdomens of female Bactrocera dorsalis

Insect gut microbiota has been reported to participate in regulating host multiple biological processes including metabolism and reproduction. However, the corresponding molecular mechanisms remain largely unknown. Recent studies suggest that microRNAs (miRNAs) are involved in complex interactions between the gut microbiota and the host. Here, we used next-generation sequencing technology to characterize miRNA and mRNA expression profiles and construct the miRNA–gene regulatory network in response to gut microbiota depletion in the abdomens of female Bactrocera dorsalis. A total of 3016 differentially expressed genes (DEGs) and 18 differentially expressed miRNAs (DEMs) were identified. Based on the integrated analysis of miRNA and mRNA sequencing data, 229 negatively correlated miRNA–gene pairs were identified from the miRNA–mRNA network. Gene ontology enrichment analysis indicated that DEMs could target several genes involved in the metabolic process, oxidation–reduction process, oogenesis, and insulin signaling pathway. Finally, real-time quantitative polymerase chain reaction further verified the accuracy of RNA sequencing results. In conclusion, our study provides the profiles of miRNA and mRNA expressions under antibiotics treatment and provides an insight into the roles of miRNAs and their target genes in the interaction between the gut microbiota and its host.     

Circulating microRNA profile in humans and mice with congenital GH deficiency

Reduced inflammation, increased insulin sensitivity, and protection against cancer are shared between humans and mice with GH/IGF1 deficiency. Beyond hormone levels, miRNAs are important regulators of metabolic changes associated with healthy aging. We hypothesized that GH deficiency in humans alters the abundance of circulating miRNAs and that a subset of those miRNAs may overlap with those found in GH‐deficient mice. In this study, subjects with untreated congenital isolated GH deficiency (IGHD; n = 23) and control subjects matched by age and sex (n = 23) were recruited and serum was collected for miRNA sequencing. Serum miRNAs from young (6 month) and old (22 month) Ames dwarf (df/df) mice with GH deficiency and their WT littermates (n = 5/age/genotype group) were used for comparison. We observed 14 miRNAs regulated with a genotype by age effect and 19 miRNAs regulated with a genotype effect independent of age in serum of IGHD subjects. These regulated miRNAs are known for targeting pathways associated with longevity such as mTOR, insulin signaling, and FoxO. The aging function was overrepresented in IGHD individuals, mediated by hsa‐miR‐31, hsa‐miR‐146b, hsa‐miR‐30e, hsa‐miR‐100, hsa‐miR‐181b‐2, hsa‐miR‐195, and hsa‐miR‐181b‐1, which target the FoxO and mTOR pathways. Intriguingly, miR‐181b‐5p, miR‐361‐3p, miR‐144‐3p, and miR‐155‐5p were commonly regulated in the serum of humans and GH‐deficient mice. In vitro assays confirmed target genes for the main up‐regulated miRNAs, suggesting miRNAs regulated in IGHD individuals can regulate the expression of age‐related genes. These findings indicate that systemic miRNAs regulated in IGHD individuals target pathways involved in aging in both humans and mice.     

Epigenetic alternations of microRNAs and DNA methylation contribute to gestational diabetes mellitus

This study aimed to identify epigenetic alternations of microRNAs and DNA methylation for gestational diabetes mellitus (GDM) diagnosis and treatment using in silico approach. Data of mRNA and miRNA expression microarray ({"type":"entrez-geo","attrs":{"text":"GSE103552","term_id":"103552"}}GSE103552 and {"type":"entrez-geo","attrs":{"text":"GSE104297","term_id":"104297"}}GSE104297) and DNA methylation data set ({"type":"entrez-geo","attrs":{"text":"GSE106099","term_id":"106099"}}GSE106099) were obtained from the GEO database. Differentially expressed genes (DEGs), differentially expressed miRNAs (DEMs) and differentially methylated genes (DMGs) were obtained by limma package. Functional and enrichment analyses were performed with the DAVID database. The protein‐protein interaction (PPI) network was constructed by STRING and visualized in Cytoscape. Simultaneously, a connectivity map (CMap) analysis was performed to screen potential therapeutic agents for GDM. In GDM, 184 low miRNA‐targeting up‐regulated genes and 234 high miRNA‐targeting down‐regulated genes as well as 364 hypomethylation–high‐expressed genes and 541 hypermethylation–low‐expressed genes were obtained. They were mainly enriched in terms of axon guidance, purine metabolism, focal adhesion and proteasome, respectively. In addition, 115 genes (67 up‐regulated and 48 down‐regulated) were regulated by both aberrant alternations of miRNAs and DNA methylation. Ten chemicals were identified as putative therapeutic agents for GDM and four hub genes (IGF1R, ATG7, DICER1 and RANBP2) were found in PPI and may be associated with GDM. Overall, this study identified a series of differentially expressed genes that are associated with epigenetic alternations of miRNA and DNA methylation in GDM. Ten chemicals and four hub genes may be further explored as potential drugs and targets for GDM diagnosis and treatment, respectively.     

Identification of lncRNA–miRNA–mRNA regulatory network associated with epithelial ovarian cancer cisplatin-resistant

To construct a long noncoding RNA (lncRNA)–microRNA (miRNA)–messenger RNA (mRNA) regulatory network related to epithelial ovarian cancer (EOC) cisplatin-resistant, differentially expressed genes (DEGs), differentially expressed lncRNAs (DELs), and differentially expressed miRNAs (DEMs) between MDAH and TOV-112D cells lines were identified. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to analyze the biological functions of DEGs. Downstream mRNAs or upstream lncRNAs for miRNAs were analyzed at miRTarBase 7.0 or DIANA-LncBase V2, respectively. A total of 485 significant DEGs, 85 DELs, and 5 DEMs were identified. Protein–protein interaction (PPI) network of DEGs contrains 81 nodes and 141 edges was constructed, and 25 hub genes related to EOC cisplatin-resistant were identified. Subsequently, a lncRNA–miRNA–mRNA regulatory network contains 4 lncRNAs, 4 miRNAs, and 35 mRNAs was established. Taken together, our study provided evidence concerning the alteration genes involved in EOC cisplatin-resistant, which will help to unravel the mechanisms underlying drug resistant.     

Integrative analysis provides multi‐omics evidence for the pathogenesis of placenta percreta

Pernicious placenta previa with placenta percreta (PP) is a catastrophic condition during pregnancy. However, the underlying pathogenesis remains unclear. In the present study, the placental tissues of normal cases and PP tissues of pernicious placenta previa cases were collected to determine the expression profile of protein‐coding genes, miRNAs, and lncRNAs through sequencing. Weighted gene co‐expression network analysis (WGCNA), accompanied by miRNA target prediction and correlation analysis, were employed to select potential hub protein‐coding genes and lncRNAs. The expression levels of selected protein‐coding genes, Wnt5A and MAPK13, were determined by quantitative PCR and immunohistochemical staining, and lncRNA PTCHD1‐AS and PAPPA‐AS1 expression levels were determined by quantitative PCR and fluorescence in situ hybridization. The results indicated that 790 protein‐coding genes, 382 miRNAs, and 541 lncRNAs were dysregulated in PP tissues, compared with normal tissues. WGCNA identified coding genes in the module (ME) black and ME turquoise modules that may be involved in the pathogenesis of PP. The selected potential hub protein‐coding genes, Wnt5A and MAPK13, were down‐regulated in PP tissues, and their expression levels were positively correlated with the expression levels of PTCHD1‐AS and PAPPA‐AS1. Further analysis demonstrated that PTCHD1‐AS and PAPPA‐AS1 regulated Wnt5A and MAPK13 expression by interacting with specific miRNAs. Collectively, our results provided multi‐omics data to better understand the pathogenesis of PP and help identify predictive biomarkers and therapeutic targets for PP.     

Declined miR‐181a‐5p expression is associated with impaired natural killer cell development and function with aging

MicroRNAs (miRNAs) regulate gene expression and thereby influence cell development and function. Numerous studies have shown the significant roles of miRNAs in regulating immune cells including natural killer (NK) cells. However, little is known about the role of miRNAs in NK cells with aging. We previously demonstrated that the aged C57BL/6 mice have significantly decreased proportion of mature (CD27⁻CD11b⁺) NK cells compared with young mice, indicating impaired maturation of NK cells with aging. Here, we performed deep sequencing of CD27⁺ NK cells from young and aged mice. Profiling of the miRNome (global miRNA expression levels) revealed that 49 miRNAs displayed a twofold or greater difference in expression between young and aged NK cells. Among these, 30 miRNAs were upregulated and 19 miRNAs were downregulated in the aged NK cells. We found that the expression level of miR‐l8la‐5p was increased with the maturation of NK cells, and significantly decreased in NK cells from the aged mice. Knockdown of miR‐181a‐5p inhibited NK cell development in vitro and in vivo. Furthermore, miR‐181a‐5p is highly conserved in mice and human. MiR‐181a‐5p promoted the production of IFN‐γ and cytotoxicity in stimulated NK cells from both mice and human. Importantly, miR‐181a‐5p level markedly decreased in NK cells from PBMC of elderly people. Thus, our results demonstrated that the miRNAs profiles in NK cells change with aging, the decreased level of miR‐181a‐5p contributes to the defective NK cell development and function with aging. This opens new strategies to preserve or restore NK cell function in the elderly.     

Joint efficacy of the three biomarkers SNCA,GYPB and HBG1 for atrial fibrillation and stroke: Analysis via the support vector machine neural network

Atrial fibrillation (AF) is the most common type of persistent arrhythmia. Although its incidence has been increasing, the pathogenesis of AF in stroke remains unclear. In this study, a total of 30 participants were recruited, including 10 controls, 10 patients with AF and 10 patients with AF and stroke (AF + STROKE). Differentially expressed genes (DEGs) were identified, and functional annotation of DEGs, comparative toxicogenomic database analysis associated with cardiovascular diseases, and predictions of miRNAs of hub genes were performed. Using RT‐qPCR, biological process and support vector machine neural networks, numerous DEGs were found to be related to AF. HBG1, SNCA and GYPB were found to be upregulated in the AF group. Higher expression of hub genes in AF and AF + STROKE groups was detected via RT‐PCR. Upon training the biological process neural network of SNCA and GYPB for HBG1, only small differences were detected. Based on the support vector machine, the predicted value of SNCA and GYPB for HBG1 was 0.9893. Expression of the hub genes of HBG1, SNCA and GYPB might therefore be significantly correlated to AF. These genes are involved in the incidence of AF complicated by stroke, and may serve as targets for early diagnosis and treatment.     

Multi‐omics of the expression and clinical outcomes of TMPRSS2 in human various cancers: A potential therapeutic target for COVID‐19

Growing evidence has shown that Transmembrane Serine Protease 2 (TMPRSS2) not only contributes to the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection, but is also closely associated with the incidence and progression of tumours. However, the correlation of coronavirus disease (COVID‐19) and cancers, and the prognostic value and molecular function of TMPRSS2 in various cancers have not been fully understood. In this study, the expression, genetic variations, correlated genes, immune infiltration and prognostic value of TMPRSS2 were analysed in many cancers using different bioinformatics platforms. The observed findings revealed that the expression of TMPRSS2 was considerably decreased in many tumour tissues. In the prognostic analysis, the expression of TMPRSS2 was considerably linked with the clinical consequences of the brain, blood, colorectal, breast, ovarian, lung and soft tissue cancer. In protein network analysis, we determined 27 proteins as protein partners of TMPRSS2, which can regulate the progression and prognosis of cancer mediated by TMPRSS2. Besides, a high level of TMPRSS2 was linked with immune cell infiltration in various cancers. Furthermore, according to the pathway analysis of differently expressed genes (DEGs) with TMPRSS2 in lung, breast, ovarian and colorectal cancer, 160 DEGs genes were found and were significantly enriched in respiratory system infection and tumour progression pathways. In conclusion, the findings of this study demonstrate that TMPRSS2 may be an effective biomarker and therapeutic target in various cancers in humans, and may also provide new directions for specific tumour patients to prevent SARS‐CoV‐2 infection during the COVID‐19 outbreak.     

Population dynamics of the glacial relict amphipods in a subarctic lake: role of density‐dependent and density‐independent factors

Relative role of intrinsic density‐dependent factors (such as inter‐ and intraspecific competition, predation) and extrinsic density‐independent factors (environmental changes) in population dynamics is a key issue in ecology. Density‐dependent mechanisms are considered as important drivers of population dynamics in many vertebrate and insect species; however, their influence on the population dynamics of freshwater invertebrates is not clearly understood. In this study, I examined interannual variations in the abundance of the glacial relict amphipod Monoporeia affinis in a small subarctic lake based on long‐term (2002–2019) monitoring data. The results suggest that the population dynamics of amphipods in the lake is influenced by the combined effects of both intrinsic and extrinsic factors. The reproductive success of amphipod cohorts was inversely related to its initial abundance, indicating it is influenced by density‐dependent factors. M. affinis recruitment was negatively correlated with population density and near‐bottom temperature but positively correlated with food availability, which is defined as the concentration of chlorophyll a. Multiple regression with chlorophyll, temperature, and abundance of parent cohort as independent factors explained about 80% of the variation in the reproductive success of amphipods. The negative correlation between amphipod recruitment and water temperature indicates that the current climate conditions adversely affect the populations of glacial relict amphipods even in cold‐water lakes of the subarctic zone. Results of this study can be useful in environmental assessments to separate population oscillations connected with density‐dependent mechanisms from human‐mediated changes.     

miRTar Hunter: A prediction system for identifying human microRNA target sites

MicroRNAs (miRNAs) are important regulators of gene expression and play crucial roles in many biological processes including apoptosis, differentiation, development, and tumorigenesis. Recent estimates suggest that more than 50% of human protein coding genes may be regulated by miRNAs and that each miRNA may bind to 300–400 target genes. Approximately 1,000 human miRNAs have been identified so far with each having up to hundreds of unique target mRNAs. However, the targets for a majority of these miRNAs have not been identified due to the lack of large-scale experimental detection techniques. Experimental detection of miRNA target sites is a costly and time-consuming process, even though identification of miRNA targets is critical to unraveling their functions in various biological processes. To identify miRNA targets, we developed miRTar Hunter, a novel computational approach for predicting target sites regardless of the presence or absence of a seed match or evolutionary sequence conservation. Our approach is based on a dynamic programming algorithm that incorporates more sequence-specific features and reflects the properties of various types of target sites that determine diverse aspects of complementarities between miRNAs and their targets. We evaluated the performance of our algorithm on 532 known human miRNA:target pairs and 59 experimentally-verified negative miRNA:target pairs, and also compared our method with three popular programs for 481 miRNA:target pairs. miRTar Hunter outperformed three popular existing algorithms in terms of recall and precision, indicating that our unique scheme to quantify the determinants of complementary sites is effective at detecting miRNA targets. miRTar Hunter is now available at http://203.230.194.162/~kbkim.