A ceRNA network of BBOX1-AS1-hsa-miR-125b-5p/hsa-miR-125a-5p-CDKN2A shows prognostic value in cervical cancer

ObjectiveCervical cancer (CC) ranks fourth most diagnosed cancer and cancer mortality in women. Long non-coding RNAs (lncRNAs) take important roles in CC development. This study aimed to identify more and novel competing endogenous RNA (ceRNA) mechanisms of lncRNAs in CC.Materials and methodsThe miRNA expression dataset GSE20592 and lncRNA/mRNA expression dataset GSE63514 were downloaded from Gene Expression Omnibus. The differentially expressed genes (DEGs), differentially expressed lncRNAs (DElncRNAs), and differentially expressed miRNAs (DEmiRNAs) between CC tumor and normal samples were identified with the criteria of adj.P.Value < 0.05 (Benjamini & Hochberg) and |log₂(fold change)|>2. Functional enrichment analysis was performed for DEGs. The interaction pairs among lncRNAs, miRNAs and mRNAs were predicted and the ceRNA network was then constructed. Survival analysis was performed based on the TCGA dataset.ResultsTotally, 42 DEmiRNAs, 25 DElncRNAs, and 518 DEGs were identified in CC tumor samples versus normal tissues. The DEGs were associated with ‘GO:0006260: DNA replication’, ‘GO:0051301: cell division’, and ‘hsa01100:Metabolic pathways’. The ceRNA network consisted of 878 lncRNA-miRNA-mRNA pairs. Of the miRNAs, lncRNAs, and genes with the top 10 interaction degrees in the ceRNA network, the upregulated cyclin dependent kinase inhibitor 2A gene (CDKN2A) was targeted by the downregulated DEmiRNAs including hsa-miR-125b-5p and hsa-miR-125a-5p, which were targeted by the upregulated DElncRNA BBOX1-AS1. The high expression level of CDKN2A contributed to the poor overall survival of patients with CC.ConclusionsThe BBOX1-AS1-hsa-miR-125b-5p/hsa-miR-125a-5p-CDKN2A ceRNA network is of great value in CC development.     

Analysis of key candidate genes and pathways of endometriosis pathophysiology by a genomics-bioinformatics approach

Endometriosis is a common disease in women, but the signaling pathways and driven genes involved remain unclear. This study integrated four datasets to elucidate potential key candidate genes and pathways in endometriosis. Four expression profile datasets including 29 endometriosis lesions and 37 normal tissues were integrated and analyzed. Differentially expressed genes (DEGs) were sorted, and the gene ontology, pathway enrichment, and protein–protein interaction network of candidate genes were then analyzed. A total of 94 shared DEGs were identified from the four datasets. The DEGs were clustered based on functions and signaling pathways through the analysis of significant enrichment. Among the DEG protein-protein interaction network complex, 87 nodes/DEGs were identified. Furthermore, 18 central node genes were identified, and most of the corresponding genes were involved in the angiotensin system, smooth muscle contraction, cell junction organization, and lipoxin pathways. Through integrated bioinformatic analysis, we identified candidate genes and pathways in endometriosis, which could improve our understanding of endometriosis.     

RETRACTED ARTICLE: Investigation of the hub genes and related mechanism in ovarian cancer via bioinformatics analysis

Background

Ovarian cancer is a cancerous growth arising from the ovary.

Objective

This study was aimed to explore the molecular mechanism of the development and progression of the ovarian cancer.

Methods

We first identified the differentially expressed genes (DEGs) between the ovarian cancer samples and the healthy controls by analyzing the GSE14407 affymetrix microarray data, and then the functional enrichments of the DEGs were investigated. Furthermore, we constructed the protein-protein interaction network of the DEGs using the STRING online tools to find the genes which might play important roles in the progression of ovarian cancer. In addition, we performed the enrichment analysis to the PPI network.

Results

Our study screened 659 DEGs, including 77 up- and 582 down-regulated genes. These DEGs were enriched in pathways such as Cell cycle, p53 signaling pathway, Pathways in cancer and Drug metabolism. CCNE1, CCNB2 and CYP3A5 were the significant genes identified from these pathways. Protein-protein interaction (PPI) network was constructed and network Module A was found closely associated with ovarian cancer. Hub nodes such as VEGFA, CALM1, BIRC5 and POLD1 were found in the PPI network. Module A was related to biological processes such as mitotic cell cycle, cell cycle, nuclear division, and pathways namely Cell cycle, Oocyte meiosis and p53 signaling pathway.

Conclusions

It indicated that ovarian cancer was closely associated to the dysregulation of p53 signaling pathway, drug metabolism, tyrosine metabolism and cell cycle. Besides, we also predicted genes such as CCNE1, CCNB2, CYP3A5 and VEGFA might be target genes for diagnosing the ovarian cancer.

     

Comparative transcriptome analysis of embryo invasion in the mink uterus

IntroductionIn mink, as many as 65% of embryos die during gestation. The causes and the mechanisms of embryonic mortality remain unclear. The purpose of our study was to examine global gene expression changes during embryo invasion in mink, and thereby to identify potential signaling pathways involved in implantation failure and early pregnancy loss.MethodsIllumina's next-generation sequencing technology (RNA-Seq) was used to analyze the differentially expressed genes (DEGs) in implantation (IMs) and inter-implantation sites (inter-IMs) of uterine tissue.ResultsWe identified a total of 606 DEGs, including 420 up- and 186 down-regulated genes in IMs compared to inter-IMs. Gene annotation analysis indicated multiple biological pathways to be significantly enriched for DEGs, including immune response, ECM complex, cytokine activity, chemokine activity and protein binding. The KEGG pathway including cytokine-cytokine receptor interaction, Jak-STAT, TNF and the chemokine signaling pathway were the most enriched. A gene network was constructed, and hub nodes such as CSF3, ICAM1, FOS, IL1B, IL8, CD14 and MYC were found through network analysis.DiscussionThis report provides a valuable resource for understanding the mechanisms of embryo implantation in mink.     

Epigenetic analysis of the Notch superfamily in high-grade serous ovarian cancer

ObjectivesGene methylation and other epigenetic modifications of gene regulation have been implicated in the growth of ovarian cancer, but the clinical significance of such modifications in the Notch pathway in high-grade serous ovarian cancer (HGS-OvCa) is not well understood. We used The Cancer Genome Atlas (TCGA) data to study the clinical relevance of epigenetic modifications of Notch superfamily genes.MethodsWe analyzed the interaction of DNA methylation and miRNAs with gene expression data for Notch superfamily members with the Spearman rank correlation test and explored potential relationships with overall survival (OS) with the log-rank test. We downloaded clinical data, level 3 gene expression data, and level 3 DNA methylation data for 480 patients with stage II–IV HGS-OvCa from the TCGA data portal. Patients were randomly divided into training and validation cohorts for survival analyses. In each set, patients were grouped into percentiles according to methylation and microRNA (miRNA) or messenger RNA (mRNA) levels. We used several algorithms to predict miRNA–mRNA interaction.ResultsThere were significant inverse relationships between methylation status and mRNA expression for PPARG, CCND1, and RUNX1. For each of these genes, patients with a lower methylation level and higher expression level had significantly poorer OS than did patients with a higher methylation level and lower expression level. We also found a significant inverse relationship between miRNAs and mRNA expression for CCND1, PPARG, and RUNX1. By further analyzing the effect of miRNAs on gene expression and OS, we found that patients with higher levels of CCND1, PPARG, and RUNX1 expression and lower expression levels of their respective miRNAs (502-5p, 128, and 215/625) had significantly poorer OS.ConclusionsEpigenetic alterations of multiple Notch target genes and pathway interacting genes (PPARG, CCND1, and RUNX1) may relate to activation of this pathway and poor survival of patients with HGS-OvCa.     

Identifying miRNA regulatory mechanisms in preeclampsia by systems biology approaches

Background: Preeclampsia (PE) is the major cause of maternal and fetal morbidity and mortality, affecting 3–8% of all pregnancies around the globe. miRNAs are small, noncoding RNA molecules, which negatively regulate gene expression. Abnormally expressed miRNAs contribute to pregnancy complications such as PE. The aim of our study was to find possible regulatory mechanisms by system biology approaches, which are connected to the pathogenesis of PE. Methods: We integrated publicly available miRNA and gene expression profiles and created a network from the significant miRNA–mRNA pairs with the help of MAGIA and Cytoscape softwares. Two subnetworks were expanded by adding protein–protein interactions. Differentially expressed miRNAs were identified for the evaluation of their regulatory effect. We analyzed the miRNAs and their targets using different bioinformatics tools and through literature research. Results: Altogether, 52,603 miRNA–mRNA interactions were generated by the MAGIA web tool. The top 250 interactions were visualized and pairs with q < 0.0001 were analyzed, which included 85 nodes and 80 edges signalizing the connections between 52 regulated genes and 33 miRNAs. A total of 11 of the regulated genes are PE related and 9 of them were targeted by multiple miRNAs. A total of 8 miRNAs were associated with PE before, and 13 miRNAs regulated more than 1 mRNA. Hsa-mir-210 was the highest degree node in the network and its role in PE is well established. Conclusions: We identified several miRNA–mRNA regulatory mechanisms which may contribute to the pathogenesis of PE. Further investigations are needed to validate these miRNA–mRNA interactions and to enlighten the possibilities of developing potential therapeutic targets.     

基于miRNA-mRNA调控关系对与Cox回归模型的宫颈鳞状细胞癌预后生物标志物综合分析

目的：探究微小RNA（miRNA）-信使RNA（mRNA）关系对在宫颈鳞状细胞癌（CESC）中的表达,分析其预测CESC预后的意义。方法：利用癌症和肿瘤基因图谱（TCGA）数据库筛选CESC和正常宫颈组织中miRNA和mRNA的差异表达谱,利用miRTarBase、TargetScan和miRDB数据库验证miRNA与靶向mRNA的相互作用关系,并通过Cytoscape软件可视化,采用Kaplan-Meier生存分析确定CESC的预后标志物,构建与CESC预后相关的miRNA-mRNA调控网络,并对筛选出的mRNA进行基因本体功能（GO）富集分析和京都基因与基因组百科全书（KEGG）通路富集分析。结果：通过比较CESC组织与正常宫颈组织,共检测到4个miRNA可纳入预后风险评分模型,生存分析筛选出9个与CESC预后相关的差异表达mRNA,最终得到与CESC预后紧密相关的4个miRNA-mRNA调控关系对,hsa-miR-505-5p的靶向mRNA为染色质结构域蛋白8（CBX8）,hsa-miR-142-3p分别靶向Ⅰ型血小板结合蛋白基序的解聚蛋白样金属蛋白酶3（ADAMTS3）、蛋白酪氨酸磷酸酶受体B（PTPRB）和SEC23同源物A（SEC23A）。生物学功能和通路分析显示,差异表达的mRNA主要在生物学过程和磷脂酰肌醇3激酶-蛋白激酶B（PI3K-Akt）、人乳头瘤病毒（HPV）感染的通路中显著富集。结论：miRNA-mRNA关系对与CESC预后相关,可作为今后CESC发病机制研究的新角度以及监测预后的有效指标。     

褪黑素抑制氧化应激和铁死亡缓解妊娠糖尿病大鼠病理损伤

目的:探讨褪黑素对妊娠糖尿病(GDM)大鼠的治疗作用及可能作用机制。方法:将24只雌性大鼠分成4组正常妊娠组、GDM模型组、低剂量褪黑素5mg/(kg·d)治疗组及高剂量褪黑素10mg/(kg·d)治疗组,每组6只。不同剂量褪黑素治疗14天后,检测大鼠胰腺组织形态病理变化及细胞凋亡水平,检测血清生化指标、细胞氧化应激指标及铁含量。检测胰腺组织中褪黑素受体基因及铁死亡通路相关基因的mRNA和蛋白表达水平。结果:褪黑素治疗明显减轻了大鼠胰腺组织病理损伤和细胞凋亡水平,降低了血清中葡萄糖、糖化血红蛋白及胰岛素水平,显著升高了胰腺组织中CAT、GSH-PX、SOD等抗氧化酶活性及抗氧化剂GSH水平,降低了H2O2、MDA及铁含量。褪黑素治疗显著增加了大鼠胰腺中褪黑素受体基因MTNR1B表达,同时调控铁死亡通路相关基因表达,包括增加GPX4及FTH1基因表达水平,降低ACSL4基因表达水平。结论:褪黑素可能通过褪黑素受体介导,抑制组织氧化还原水平失衡,降低组织细胞凋亡和铁死亡,进而缓解GDM所致的病理损伤。     

The expression of the miRNA-200 family in endometrial endometrioid carcinoma

Objective.

Recent reports suggest that targeting the unique miRNAs highly expressed in several cancers may be a promising approach in the development of new cancer therapeutic tools. The purpose of this study was to evaluate the roles of miRNAs as therapeutic targets in human endometrial endometrioid carcinomas (EECs).

Methods.

We evaluated the differential expressions of miRNAs in EECs and normal endometrial tissues using microarrays and cluster analysis. After validation of differentially expressed miRNAs in another set of EECs and normal endometrial tissues, we performed the in vitro experiment using endometrial cancer cells with anti-miRNA (anti-miR) to evaluate the roles of miRNAs that are highly expressed in EECs for cell proliferation and chemosensitivity.

Results.

A miRNA microarray showed that the miR-200 family, including hsa-miR-141, hsa-miR-200a, hsa-miR-200b, hsa-miR-200c, and hsa-miR-429, was up-regulated in EECs as compared with that in normal endometrial tissues. When we treated endometrial cancer cells with specific anti-miRs, including anti-miR-141, -200a, -200b, -200c, or -429, we found that anti-miR-200a, -200b, -200c, and -429 significantly inhibited the growth of HEC-1A cells and anti-miR-141, -200c, and -429 significantly inhibited the growth of Ishikawa cells. Moreover, transfection with anti-miR-429 enhanced the cytotoxic effect of cisplatin in HEC-1A cells.

Conclusions.

These results indicate that the miR-200 family is highly expressed in EECs compared with that of normal endometrial tissues and could play an important role in cancer growth. Specifically, anti-miR-429 could enhance the cytotoxic activity with cisplatin in EECs. Therefore, the miR-200 family may offer new candidate targets to be exploited in therapeutic strategies for patients with these carcinomas.     

Serum microRNAs in clear cell carcinoma of the ovary

ObjectiveTo identify candidate microRNAs (miRNAs) in the serum of patients with clear cell carcinomas in monitoring disease progression.Materials and methodsThe sera of patients with diagnosed ovarian clear cell carcinoma were collected from 2009 to 2012. Real-time quantitative polymerase chain reaction (PCR) analysis for 270 miRNAs was performed. To offset the potential extraction bias, an equal amount of Caenorhabditis elegans cel-miR-238 was added to each serum specimen before miRNA isolation. miRNA expression was analyzed using the ΔCt method, with cel-miR-238 as controls.ResultsTwenty-one patients with clear cell carcinoma were included. In the discovery phase on four pairs of pre- and postoperative sera, 18 differentially expressed miRNAs were selected from 270 miRNAs. In the validation phase on an independent set of 11 pairs of pre- and postoperative sera, 4 miRNAs (hsa-miR-130a, hsa-miR-138, hsa-miR-187, and hsa-miR-202) were confirmed to be higher in the preoperative sera. In the application phase, hsa-miR-130a remained consistent with the different time points in seven of the 10 patients during clinical follow-up periods. More importantly, in three patients, hsa-miR-130a levels were elevated in early disease recurrences before CA125 was found to be elevated.ConclusionHsa-miR-130a may be a useful serum biomarker for detecting recurrence of ovarian clear cell cancer, and warrants further studies.     

LPS-TLR4-NF-κB通路在妊娠期糖尿病、正常孕妇及育龄妇女外周血单核细胞中的表达

目的:研究外周血单核细胞LPS-TLR4-NF-κB通路在妊娠期糖尿病(GDM)、正常孕妇及育龄妇女外周血单核细胞的表达,探讨GDM的发病机制。方法:选取GDM孕妇、正常孕妇以及育龄妇女各20例,抽取外周静脉血5ml,分离单核细胞,用内毒素(LPS)刺激培养,RT-PCR法检测TLR4及NF-κB mRNA的表达,ELISA法检测培养液中IL-1、IL-10、TNF-α水平。结果:3组妇女TLR4、NF-κB mRNA表达的差异有统计学意义(P=0.000)。GDM组及正常孕妇组TLR4与NF-κB mRNA表达水平有良好的相关性(rGDM=0.768,r正常孕妇=0.833)。育龄妇女组TLR4与NF-κB mRNA的表达水平相关性稍差(r育龄妇女=0.719)。3组培养液中IL-1、IL-10、TNF-α水平的差异有统计学意义。结论:GDM孕妇体内TLR4、NF-κB mRNA的大量表达,提示可能LPS-TLR4-NF-κB通路介导了炎症因子释放,参与了GDM的发病。     

Bioinformatics analysis of gene expression profiles in B cells of postmenopausal osteoporosis patients

Objective

The aim of this study was to gain a better understanding of the molecular mechanisms and identify more critical genes associated with the pathogenesis of postmenopausal osteoporosis (PMOP).

MiRNAs与妊娠期糖尿病发病机制的研究进展

妊娠期糖尿病(gestational diabetes mellitus,GDM)是常见的妊娠期合并症之一,并且会对孕妇以及子代造成严重后果甚至有长远影响。随着生活方式的改变,GDM在我国发病率呈逐年升高趋势。微小RNA(microRNAs,miRNAs)是一类长度为19~24个核苷酸的单链小分子非编码RNA,以特异性结合方式抑制靶基因的转录或翻译来调控细胞的发育、分化与增殖、早期胚胎发育、脂肪代谢、神经细胞功能分化及自身免疫调节等生物过程。目前,GDM的发病机制还未完全阐明。近年来,miRNAs在GDM发病机制中的作用备受关注,主要通过胰岛素抵抗、胰岛素分泌异常和脂肪因子等方面参与GDM的发生。