scholarly journals High throughput microRNAs sequencing profile of serum exosomes in women with and without polycystic ovarian syndrome

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10998
Author(s):  
Feng Zhang ◽  
Su-Ping Li ◽  
Tao Zhang ◽  
Bin Yu ◽  
Juan Zhang ◽  
...  
Keyword(s):  
Sequence Data ◽  
Polycystic Ovary ◽  
Reproductive Age ◽  
Differentially Expressed ◽  
Potential Implication ◽  
Exosomal Mirnas ◽  
Differentially Expressed Mirnas ◽  
Pathway Analyses ◽  
Serum Exosomes

Background Polycystic ovary syndrome (PCOS) is the most common type of endocrine disorder, affecting 5–11% of women of reproductive age worldwide. microRNAs (miRNAs) stably exist in circulating blood encapsulated in extracellular vesicles such as exosomes; therefore, serum miRNAs have the potential to serve as novel PCOS biomarkers. Methods To identify miRNA biomarkers that are associated with PCOS, we performed a comprehensive sequence-based characterization of the PCOS serum miRNA landscape. The serum exosomes were successfully isolated and characterized in a variety of ways. Next, sequence-based analysis was performed on serum exosomes to screen the differentially expressed miRNAs in women with and without PCOS. Results The sequence data revealed that the levels of 54 miRNAs significantly differed between PCOS patients and normal controls. The levels of these miRNAs were detected by RT-qPCR. The results show that hsa-miR-1299, hsa-miR-6818-5p hsa-miR-192-5p, and hsa-miR-145-5p are significantly differentially expressed in PCOS patients serum exosomes and identify these microRNAs as potential biomarkers for PCOS. Furthermore, Gene Ontology (GO) analyses and KEGG pathway analyses of the miRNA targets further allowed to explore the potential implication of the miRNAs in PCOS. Conclusion Our findings suggest that serum exosomal miRNAs serve important roles in PCOS and may be used as novel molecular biomarkers for clinical diagnosis.

scholarly journals Changes of miRNA Expression Profiles from Cervical-Vaginal Fluid-Derived Exosomes in Response to HPV16 Infection

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Ying Wu ◽  
Xinyan Wang ◽  
Li Meng ◽  
Wenqu Li ◽  
Chunyan Li ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Signaling Pathway ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Differentially Expressed ◽  
Vaginal Fluid ◽  
Exosomal Mirnas ◽  
Differentially Expressed Mirnas ◽  
Pathway Analyses ◽  
Hpv16 Infection

As an oncogenic virus, HPV16 can lead to the dysfunction of cervical epithelial cells and contribute to the progression of cervical cancer. Components from the cervical-vaginal fluid (CVF) could be used as the basis for cervical cancer screening. Exosomes are widely present in various body fluids and participate in intercellular communication via its cargos of proteins, mRNAs, and miRNAs. This study was conducted to explore the changes of miRNAs in exosomes isolated form the cervical-vaginal fluid during HPV16 infection and to predict the potential effects of exosomal miRNAs on the development of cervical cancer. CVF was collected from volunteers with or without HPV16 infection. The exosomes in CVF were identified by electron microscopy. Microarray analysis was subjected to find the differentially expressed miRNAs in CVF exosomes. To confirm the results, 16 miRNAs were randomly selected to go through real-time quantitative polymerase chain reaction. In addition, GO and pathway analyses were conducted to reveal potential functions of differentially expressed miRNAs. A total of 2548 conserved miRNAs were identified in the cervical-vaginal fluid-derived exosomes. In response to HPV16 infection, 45 miRNAs are significantly upregulated and 55 miRNAs are significantly downregulated (P<0.05). The GO and KEGG pathway analyses revealed that these differentially expressed miRNAs are tightly associated with cervical cancer tumorigenesis, through interaction with the Notch signaling pathway, TNF signaling pathway, and TGF-β signaling pathway. These results suggest that exosomal miRNAs in CVF are differentially expressed in HPV16 infection patients and HPV16-free volunteers. It provided a novel insight to understand the underlying mechanism of HPV16 infection in regulating cervical cancer progression.

scholarly journals MiRNAs expression profiling of rat ovaries displaying PCOS with insulin resistance

2020 ◽  
Vol 302 (5) ◽  
pp. 1205-1213
Author(s):  
Chunren Zhang ◽  
Chuyi Yu ◽  
Zengxian Lin ◽  
Haixia Pan ◽  
Kunyin Li ◽  
...  
Keyword(s):  
Insulin Resistance ◽  
Target Genes ◽  
Kegg Pathway ◽  
Polycystic Ovary ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Real Time Quantitative Pcr ◽  
Qrt Pcr ◽  
Differentially Expressed Mirnas ◽  
Pathway Analyses

Abstract Purpose The present study established microRNA (miRNA) expression profiles for rat ovaries displaying polycystic ovary syndrome (PCOS) with insulin resistance and explored the underlying biological functions of differentially expressed miRNAs. Methods A PCOS with insulin resistance rat model was created by administering letrozole and a high-fat diet. Total RNA was extracted from the ovaries of PCOS with insulin resistance rats and normal rats. Three ovaries from each group were used to identify differentially expressed miRNAs by deep sequencing. A hierarchical clustering heatmap and volcano plot were used to display the pattern of differentially expressed miRNAs. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to explore the potential target genes of the differentially expressed miRNAs and identify their putative biological function. Nine of the differentially expressed miRNAs were selected for validation by Real-time Quantitative PCR (qRT-PCR). Results A total of 58 differentially expressed miRNAs were identified in the rat ovaries exhibiting PCOS with insulin resistance compared with control ovaries, including 23 miRNAs that were upregulated and 35 miRNAs that were downregulated. GO and KEGG pathway analyses revealed that the predicted target genes were related to metabolic processes, cellular processes, and metabolic pathways. Furthermore, qRT-PCR confirmed that miR-3585-5p and miR-30-5p were significantly upregulated and miR-146-5p was downregulated in the ovaries of PCOS with insulin resistance rats compared with the controls. Conclusion These results indicate that differentially expressed miRNAs in rat ovaries may be involved in the pathophysiology of insulin resistance in PCOS. Our study may be beneficial in establishing miRNAs as novel diagnostic and therapeutic biomarkers for insulin resistance in PCOS.

scholarly journals Peripheral Circulating Exosomal miRNAs Potentially Contribute to the Regulation of Molecular Signaling Networks in Aging

2020 ◽  
Vol 21 (6) ◽  
pp. 1908 ◽  
Author(s):  
Hongxia Zhang ◽  
Kunlin Jin
Keyword(s):  
Target Genes ◽  
Differentially Expressed ◽  
Molecular Signaling ◽  
Slow Development ◽  
Exosomal Mirnas ◽  
Pathways Analysis ◽  
Old Rats ◽  
Underlying Mechanisms ◽  
Signaling Components ◽  
Serum Exosomes

People are living longer than ever. Consequently, they have a greater chance for developing a functional impairment or aging-related disease, such as a neurodegenerative disease, later in life. Thus, it is important to identify and understand mechanisms underlying aging as well as the potential for rejuvenation. Therefore, we used next-generation sequencing to identify differentially expressed microRNAs (miRNAs) in serum exosomes isolated from young (three-month-old) and old (22-month-old) rats and then used bioinformatics to explore candidate genes and aging-related pathways. We identified 2844 mRNAs and 68 miRNAs that were differentially expressed with age. TargetScan revealed that 19 of these miRNAs are predicated to target the 766 mRNAs. Pathways analysis revealed signaling components targeted by these miRNAs: mTOR, AMPK, eNOS, IGF, PTEN, p53, integrins, and growth hormone. In addition, the most frequently predicted target genes regulated by these miRNAs were EIF4EBP1, insulin receptor, PDK1, PTEN, paxillin, and IGF-1 receptor. These signaling pathways and target genes may play critical roles in regulating aging and lifespan, thereby validating our analysis. Understanding the causes of aging and the underlying mechanisms may lead to interventions that could reverse certain aging processes and slow development of aging-related diseases.

scholarly journals Plasma-Derived Exosomal hsa-miR-4488 and hsa-miR-1228-5p: Novel Biomarkers for Dermatomyositis-Associated Interstitial Lung Disease with Anti-Melanoma Differentiation-Associated Protein 5 Antibody-Positive Subset

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Danli Zhong ◽  
Chanyuan Wu ◽  
Dong Xu ◽  
Jingjing Bai ◽  
Qian Wang ◽  
...  
Keyword(s):  
Interstitial Lung Disease ◽  
Lung Disease ◽  
Target Genes ◽  
Homo Sapiens ◽  
Differentially Expressed ◽  
Transmission Electron ◽  
Exosomal Mirnas ◽  
Differentially Expressed Mirnas ◽  
Novel Biomarkers ◽  
And Gender

The present study is aimed at profiling circulating exosome-derived microRNAs (miRNAs/miRs) from patients with dermatomyositis (DM), in particular those complicated with interstitial lung disease (ILD) with anti-melanoma differentiation-associated protein 5 (MDA5) antibody-positive. Fifteen participants were enrolled, including five patients with DM complicated with ILDs prior to treatment with circulating anti-MDA5 antibody-positive status [DM-ILD-MDA5 Ab(+)], five DM patients without ILDs who were negative for 16 detectable myositis-specific antibodies [DM-nonILD-MSA16(-)], and five age- and gender-matched healthy donor controls (HCs). The characteristics of the exosomes extracted by Ribo™ Exosome Isolation Reagent were identified using transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and flow cytometry. Differentially expressed miRNAs, determined by next-generation deep sequencing, were identified through the criteria of ∣ log 2   fold   change ∣ ≥ 1 and P < 0.01 . A total of 38 miRNAs were significantly upregulated in exosomes from patients with DM-ILD-MDA5 Ab(+) compared to those from HC, while 21 miRNAs were significantly downregulated. Compared to exosomes derived from patients with DM-nonILD-MSA16(-), 51 miRNAs were significantly upregulated and 33 miRNAs were significantly downregulated from patients with DM-ILD-MDA5 Ab(+). A total of 73 exosomal miRNAs were significantly differentially expressed between DM-nonILD-MSA16(-) and HC. In particular, two miRNAs, Homo sapiens- (hsa-) miR-4488 and hsa-miR-1228-5p, were common differentially expressed miRNAs among three comparisons. GO and KEGG analyses suggested that several pathways may contribute the pathogenesis of DM-ILD-MDA5 Ab(+) and DM-nonILD-MSA16(-), while PPI network analysis of hsa-miR-4488 and hsa-miR-1228-5p indicated that their predicted target genes, DExD-box helicase 39B and MDM2, may be involved in the mechanisms of DM-ILD-MDA5 Ab(+).

scholarly journals miRNA Profiling Reveals miRNA-130b-3p Mediates DENND1A Variant 2 Expression and Androgen Biosynthesis

Endocrinology ◽  
2019 ◽  
Vol 160 (8) ◽  
pp. 1964-1981 ◽  
Author(s):  
Jan M McAllister ◽  
Angela X Han ◽  
Bhavi P Modi ◽  
Maria E Teves ◽  
Grace R Mavodza ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Polycystic Ovary ◽  
Reproductive Age ◽  
Differentially Expressed ◽  
Theca Cells ◽  
Small Noncoding Rnas ◽  
Network Analyses ◽  
Heritable Disorder ◽  
Transcriptional Regulatory Mechanisms ◽  
Small Rna Deep Sequencing

Abstract Polycystic ovary syndrome (PCOS) is a common endocrine disorder of reproductive-age women involving overproduction of ovarian androgens and, in some cases, from the adrenal cortex. Family studies have established that PCOS is a complex heritable disorder with genetic and epigenetic components. Several small, noncoding RNAs (miRNAs) have been shown to be differentially expressed in ovarian cells and follicular fluid and in the circulation of women with PCOS. However, there are no reports of global miRNA expression and target gene analyses in ovarian theca cells isolated from normal cycling women and women with PCOS, which are key to the elucidation of the basis for the hyperandrogenemia characteristic of PCOS. With the use of small RNA deep sequencing (miR-seq), we identified 18 differentially expressed miRNAs in PCOS theca cells; of these, miR-130b-3p was predicted to target one of the PCOS genome-wide association study candidates, differentially expressed in neoplastic vs normal cells domain containing 1A (DENND1A). We previously reported that DENND1A variant 2 (DENND1A.V2), a truncated isoform of DENND1A, is upregulated in PCOS theca cells and mediates augmented androgen biosynthesis in PCOS theca cells. The comparison of miR-130b-3p in normal and PCOS theca cells demonstrated decreased miR-130b-3p expression in PCOS theca cells, which was correlated with increased DENND1A.V2, cytochrome P450 17α-hydroxylase (CYP17A1) mRNA and androgen biosynthesis. miR-130b-3p mimic studies established that increased miR130b-3p is correlated with decreased DENND1A.V2 and CYP17A1 expression. Thus, in addition to genetic factors, post-transcriptional regulatory mechanisms via miR-130b-3p underly androgen excess in PCOS. Ingenuity® Pathway Analysis Core Pathway and Network Analyses suggest a network by which miR-130b-3p, DENND1A, the luteinizing hormone/choriogonadotropin receptor, Ras-related protein 5B, and signaling pathways that they potentially target may mediate hyperandrogenism in PCOS.

Identification and characterization of microRNAs in white and black coated yak

2018 ◽  
Author(s):  
Wang-Dui Basang ◽  
Tian-Wu An ◽  
Xiao-Lin Luo ◽  
Yan-Bin Zhu ◽  
Luo-Bu Danjiu Danjiu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Coat Color ◽  
Wnt Signaling Pathway ◽  
Differentially Expressed ◽  
Black And White ◽  
Kegg Pathways ◽  
Differentially Expressed Mirnas ◽  
Paired End Sequencing ◽  
Identification And Characterization

In this study, we used high-throughput technology to provide the first transcriptome dataset for differentially expressed miRNA in mixed pools of dermis tissue from black- and white-coated yak to research the possible molecular mechanisms of yak coat pigmentation. In this study, 92,636,002 and 95,917,842 clear reads were generated through Illumina paired-end sequencing. A total of 78 differentially expressed miRNAs (DEMs) were identified, including 59 upregulated and 19 downregulated miRNAs in the mixed pools of white-coated yak compared with the mixed pools of black-coated yak. In addition, 3634 genes were predicted as putative targets of DEMs. These DEGs related to 59 GO categories and were enriched in 216 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including melanogenesis and the Wnt signaling pathway. The results of the current study indicated that the coat color of the yak involved the transcriptional regulation process of miRNAs. These results provide helpful data to understand the molecular mechanisms of yak coat pigmentation.

scholarly journals Identification and Characterization of miRNAs in Self-Rooted and Grafted Malus Reveals Critical Networks Associated with Flowering

2018 ◽  
Vol 19 (8) ◽  
pp. 2384 ◽  
Author(s):  
Na An ◽  
Sheng Fan ◽  
Yang Yang ◽  
Xilong Chen ◽  
Feng Dong ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Fruit Trees ◽  
Differentially Expressed ◽  
Flowering Genes ◽  
Differentially Expressed Mirnas ◽  
Flowering Rate ◽  
Carbohydrate Contents

Grafting can improve the agricultural traits of crop plants, especially fruit trees. However, the regulatory networks and differentially expressed microRNAs (miRNAs) related to grafting in apple remain unclear. Herein, we conducted high-throughput sequencing and identified differentially expressed miRNAs among self-rooted Fuji, self-rooted M9, and grafted Fuji/M9. We analyzed the flowering rate, leaf morphology, and nutrient and carbohydrate contents in the three materials. The flowering rate, element and carbohydrate contents, and expression levels of flowering genes were higher in Fuji/M9 than in Fuji. We detected 206 known miRNAs and 976 novel miRNAs in the three materials, and identified those that were up- or downregulated in response to grafting. miR156 was most abundant in Fuji, followed by Fuji/M9, and then self-rooted M9, while miR172 was most abundant in M9, followed by Fuji/M9, and then Fuji. These expression patterns suggest that that these miRNAs were related to grafting. A Gene Ontology (GO) analysis showed that the differentially expressed miRNAs controlled genes involved in various biological processes, including cellular biosynthesis and metabolism. The expression of differentially expressed miRNAs and flowering-related genes was verified by qRT-PCR. Altogether, this comprehensive analysis of miRNAs related to grafting provides valuable information for breeding and grafting of apple and other fruit trees.

Identification and characterization of differentially expressed miRNAs between bamboo shoot and rhizome shoot

2016 ◽  
Vol 59 (4) ◽  
pp. 322-335 ◽  
Author(s):  
Qun-Ying Jin ◽  
Hua-Zheng Peng ◽  
Er-Pei Lin ◽  
Nan Li ◽  
Dan-Ni Huang ◽  
...  
Keyword(s):  
Differentially Expressed ◽  
Bamboo Shoot ◽  
Differentially Expressed Mirnas ◽  
Identification And Characterization

scholarly journals Identification and characterization of differentially expressed miRNAs in HepG2 cells under normoxic and hypoxic conditions

RSC Advances ◽  
2019 ◽  
Vol 9 (29) ◽  
pp. 16884-16891 ◽  
Author(s):  
Fanzhi Kong ◽  
Wei Ran ◽  
Ning Jiang ◽  
Shize Li ◽  
Dongjie Zhang ◽  
...  
Keyword(s):  
Hepg2 Cells ◽  
Transcriptional Regulators ◽  
Differentially Expressed ◽  
Hypoxic Conditions ◽  
Differentially Expressed Mirnas ◽  
Identification And Characterization

MicroRNAs (miRNAs) are important post-transcriptional regulators involved in hypoxia conditions; however, their roles in HepG2 cells remain poorly understood.

scholarly journals Pancreatic Acinar Cells Employ miRNAs as Mediators of Intercellular Communication to Participate in the Regulation of Pancreatitis-Associated Macrophage Activation

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Yong Zhao ◽  
Hao Wang ◽  
Ming Lu ◽  
Xin Qiao ◽  
Bei Sun ◽  
...  
Keyword(s):  
Macrophage Activation ◽  
Target Genes ◽  
Culture Media ◽  
Mapk Pathway ◽  
Acinar Cells ◽  
Differentially Expressed ◽  
Pancreatic Acinar Cells ◽  
Supernatant Fraction ◽  
Exosomal Mirnas ◽  
Differentially Expressed Mirnas

Macrophage activation plays an important role in the inflammatory response in acute pancreatitis. In the present study, the activation of AR42J pancreatic acinar cells was induced by taurolithocholate treatment. The results showed that the culture medium from the activated AR42J cells significantly enhanced NFκB activation in the macrophages compared to that without taurolithocholate treatment. Additionally, the precipitates obtained from ultracentrifugation of the culture media that were rich in exosomes were markedly more potent in activating macrophages compared with the supernatant fraction lacking exosomes. The results indicated that the mediators carried by the exosomes played important roles in macrophage activation. Exosomal miRNAs were extracted and examined using microarrays. A total of 115 differentially expressed miRNAs were identified, and 30 showed upregulated expression, while 85 displayed downregulated expression. Target genes of the differentially expressed miRNAs were predicted using TargetScan, MiRanda, and PicTar software programs. The putative target genes were subjected to KEGG functional analysis. The functions of the target genes were primarily enriched in MAPK pathways. Specifically, the target genes regulated macrophage activation through the TRAF6-TAB2-TAK1-NIK/IKK-NFκB pathway. As the mediators of signal transduction, miRNAs and their predicted target mRNAs regulate every step in the MAPK pathway.

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