Integrative analysis of mRNA and microRNA expression of a human alveolar epithelial cell(A549) exposed to water and organic‐soluble extract from particulate matter (PM)2.5

MicroRNA (miRNA) is now attracting attention as a powerful negative regulator of messenger RNA(mRNA) levels, and is implicated in the modulation of important mRNA networks involved in toxicity. In this study, we assessed the effects of particulate matter 2.5 (PM_2.5), one of the most significant air pollutants, on miRNA and target gene expression. We exposed human alveolar epithelial cell (A549) to two types of PM_2.5[water (W‐PM_2.5) and organic (O‐PM_2.5) soluble extracts] and performed miRNA microarray analysis. A total of 37 miRNAs and 62 miRNAs were altered 1.3‐fold in W‐PM_2.5 and O‐PM_2.5, respectively. Integrated analyses of miRNA and mRNA expression profiles identified negative correlations between miRNA and mRNA in both W‐PM_2.5 and O‐PM_2.5 exposure groups. Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses showed that the 35 W‐PM_2.5 target genes are involved in responses to nutrients, positive regulation of biosynthetic processes, positive regulation of nucleobase, nucleoside, and nucleotide, and nucleic acid metabolic processes; while the 69 O‐PM_2.5 target genes are involved in DNA replication, cell cycle processes, the M phase, and the cell cycle check point. We suggest that these target genes may play important roles in PM_2.5‐induced respiratory toxicity by miRNA regulation. These results demonstrate an integrated miRNA‐mRNA approach for identifying molecular events induced by environmental pollutants in an in vitro human model. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 302–310, 2017.     

Differential expression of miRNAs in the visceral adipose tissue of patients with non‐alcoholic fatty liver disease

Aliment Pharmacol Ther 2010; 32: 487–497

Summary

Background Progression of non‐alcoholic fatty liver disease (NAFLD) can be facilitated by soluble molecules secreted by visceral adipose tissue (VAT). MicroRNAs (miRNAs) are likely to regulate some of these molecular pathways involved in pathogenesis of NAFLD. Aim To profile miRNA expression in the visceral adipose tissue of patients with NAFLD. Methods Visceral adipose tissue samples were collected from NAFLD patients and frozen. Patients with biopsy‐proven NAFLD were divided into non‐alcoholic steatohepatitis (NASH) (n = 12) and non‐NASH (n = 12) cohorts controlled for clinical and demographic characteristics. Extracted total RNA was profiled using TaqMan Human MicroRNA arrays. Univariate Mann–Whitney comparisons and multivariate regression analysis were performed to compare miRNA profiles. Results A total of 113 miRNA differentially expressed between NASH patients and non‐NASH patients (P < 0.05). Of these, seven remained significant after multiple test correction (hsa‐miR‐132, hsa‐miR‐150, hsa‐miR‐433, hsa‐miR‐28‐3p, hsa‐miR‐511, hsa‐miR‐517a, hsa‐miR‐671). Predicted target genes for these miRNAs include insulin receptor pathway components (IGF1, IGFR13), cytokines (CCL3, IL6), ghrelin/obestatin gene, and inflammation‐related genes (NFKB1, RELB, FAS). In addition, two miRNA species, hsa‐miR‐197 and hsa‐miR‐99, were significantly associated with pericellular fibrosis in NASH patients (P < 0.05). Levels of IL‐6 in the serum negatively correlated with the expression levels of all seven miRNAs capable of down regulating IL‐6 encoding gene. Conclusions miRNA expression from VAT may contribute to the pathogenesis of NAFLD – a finding which may distinguish relatively simple steatosis from NASH. This could help identify potential targets for pharmacological treatment regimens and candidate biomarkers for NASH.     

Genomic sequence analysis of EGFR regulation by microRNAs in lung cancer

Lung cancer is known as the top cancer killer in most developed countries. Epidermal growth factor receptor (EGFR) is frequently found to be activated by mutation or amplification in lung cancer. MicroRNA (miRNA) is a new class of small molecules that has emerged as important markers of lung cancer development and therapeutic target. There are queries on which miRNAs can regulate EGFR and it is important to predict the candidate miRNAs that target EGFR by bioinformatics and to investigate on the availability of these candidate miRNA regulators in lung cancer. Systematic and rigorous searches for miRNAs targeting EGFR were performed on 10 representative databases. The identified miRNAs that target EGFR were formulated into a conditional regulation matrix and then hierarchical clustering algorithm was applied for the analysis. The systematic search came up with 138 miRNAs that potentially target EGFR. Among them, 11 miRNAs including miR-7 and miR-128b were confirmed by published experimental data or literatures. There were 14 candidate miRNAs predicted by at least 3 prediction pipelines in this study which have never been previously reported to target EGFR. Further studies of these novel identified miRNAs may provide insight on the regulation of EGFR in lung cancer. To the best of our knowledge, this is the first bioinformatic study applying genomic sequence analysis for the prediction of miRNAs that target EGFR in lung cancer. This new strategy that integrates computational and published data approaches provides a fast and effective prediction of miRNAs in specific target genes involved in various diseases.     

mRNAs and miRNAs in whole blood associated with lung hyperplasia,fibrosis, and bronchiolo‐alveolar adenoma and adenocarcinoma after multi‐walled carbon nanotube inhalation exposure in mice

Inhalation exposure to multi‐walled carbon nanotubes (MWCNT) in mice results in inflammation, fibrosis and the promotion of lung adenocarcinoma; however, the molecular basis behind these pathologies is unknown. This study determined global mRNA and miRNA profiles in whole blood from mice exposed by inhalation to MWCNT that correlated with the presence of lung hyperplasia, fibrosis, and bronchiolo‐alveolar adenoma and adenocarcinoma. Six‐week‐old, male, B6C3F1 mice received a single intraperitoneal injection of either the DNA‐damaging agent methylcholanthrene (MCA, 10 µg g^?1 body weight) or vehicle (corn oil). One week after injections, mice were exposed by inhalation to MWCNT (5 mg m^?3, 5 hours per day, 5 days per week) or filtered air (control) for a total of 15 days. At 17 months post‐exposure, mice were euthanized and examined for the development of pathological changes in the lung, and whole blood was collected and analyzed using microarray analysis for global mRNA and miRNA expression. Numerous mRNAs and miRNAs in the blood were significantly up‐ or down‐regulated in animals developing pathological changes in the lung after MCA/corn oil administration followed by MWCNT/air inhalation, including fcrl5 and miR‐122‐5p in the presence of hyperplasia, mthfd2 and miR‐206‐3p in the presence of fibrosis, fam178a and miR‐130a‐3p in the presence of bronchiolo‐alveolar adenoma, and il7r and miR‐210‐3p in the presence of bronchiolo‐alveolar adenocarcinoma, among others. The changes in miRNA and mRNA expression, and their respective regulatory networks, identified in this study may potentially serve as blood biomarkers for MWCNT‐induced lung pathological changes. Copyright © 2015 John Wiley & Sons, Ltd.     

Differential expression of microRNAs and their predicted targets in renal cells exposed to amphotericin B and its complex with copper (II) ions

MicroRNAs (miRNAs) have been reported to regulate essential biological processes, and their expression was shown to be affected by pathological processes and drug-induced toxicity. Amphotericin B (AmB) can cause liver and kidney injury, but a recently developed complex of AmB with copper (II) ions (AmB–Cu²⁺) exhibits a lower toxicity to human renal cells while retaining a high antifungal activity. The aim of our study was to assess AmB–Cu²⁺-induced changes in the miRNA profile of renal cells and examine which biological processes are significantly affected by AmB–Cu²⁺. We also aimed to predict whether differentially expressed miRNAs would influence observed changes in the mRNA profile. miRNA and mRNA profiles in normal human renal proximal tubule epithelial cells (RPTEC) treated with AmB–Cu²⁺ or AmB were appointed with the use of microarray technology. For differentially expressed mRNAs, the PANTHER overrepresentation binomial test was performed. miRNA target interactions (MTIs) were predicted using the miRTar tool. The mRNA profile was much more strongly affected than the miRNA profile, in both AmB–Cu²⁺- and AmB-treated cells. AmB–Cu²⁺ influenced both the miRNA and mRNA profiles much more strongly than AmB. The most affected biological processes were intracellular signal transduction (AmB–Cu²⁺) and signal transduction (AmB). Only a few interactions between differentiating miRNAs and mRNAs were found. Changes in the profiles of genes involved in signal transduction and intracellular signal transduction may not result from interactions with differentially expressed miRNAs. Changes in the miRNA profile suggest the possible influence of tested drugs on the regulation of fibrosis via a miRNA-dependent mechanism.     

Microvesicle‐associated microRNA expression is altered upon particulate matter exposure in healthy workers and in A549 cells

Cardiovascular disease risk has been consistently linked with particulate matter (PM) exposure. Cell‐derived microvesicles (MVs) are released into plasma and transfer microRNAs (miRNAs) between tissues. MVs can be produced by the respiratory system in response to proinflammatory triggers, enter the circulatory system and remotely modify gene expression in cardiovascular tissues. However, whether PM affects MV signaling has never been investigated. In this study, we evaluated expression of microRNAs contained within plasma MVs upon PM exposure both in vivo and in vitro. In the in vivo study, we isolated plasma MVs from healthy steel plant workers before and after workplace PM exposure. We measured the expression of 88 MV‐associated miRNAs by real‐time polymerase chain reaction. To assess a possible source of the MV miRNAs identified in vivo, we measured their miRNA expression in PM‐treated A549 pulmonary cell lines in vitro. MiRNA profiling of plasma MVs showed 5.62‐ and 13.95‐fold increased expression of miR‐128 and miR‐302c, respectively, after 3 days of workplace PM exposure (P < 0.001). According to Ingenuity Pathway Analysis, miR‐128 is part of coronary artery disease pathways, and miR‐302c is part of coronary artery disease, cardiac hypertrophy and heart failure pathways. In vitro experiments confirmed a dose‐dependent expression of miR‐128 in MVs released from A549 cells after 6 h of PM treatment (P = 0.030). MiR‐302c was expressed neither from A549 cells nor in reference lung RNA. These results suggest novel PM‐activated molecular mechanisms that may mediate the effects of air pollution and could lead to the identification of new diagnostic and therapeutic interventions. Copyright © 2014 The Authors. Journal of Applied Toxicology Published by John Wiley & Sons Ltd.     

Genomic instability and mouse microRNAs

Tumor progression is the continual selection of variant subpopulations of malignant cells that have acquired increasing levels of genetic instability (Nowell Science 1976, 194, 23–28). This instability is manifested as chromosomal aneuploidy or translocations, viral integration or somatic mutations that typically affect the expression of a gene (oncogene) that is especially damaging to the proper function of a cell. With the recent discovery of non-coding RNAs such as microRNAs (miRNAs), the concept that a target of genetic instability must be a protein-encoding gene is no longer tenable. Over the years, we have conducted several studies comparing the location of miRNA genes to positions of genetic instability, principally retroviral integration sites and chromosomal translocations in the mouse as a means of identifying miRNAs of importance in carcinogenesis. In this current study, we have used the most recent annotation of the mouse miRome (miRBase, release 16.0), and several datasets reporting the sites of integration of different retroviral vectors in a variety of mouse strains and mouse models of cancer, including for the first time a model that shows a propensity to form solid tumors, as a means to further identify or define, candidate oncogenic miRNAs. Several miRNA genes and miRNA gene clusters stand out as interesting new candidate oncogenes due to their close proximity to common retroviral integration sites including miR-29a/b/c and miR106a~363. We also discussed some recently identified miRNAs including miR-1965, miR-1900, miR-1945, miR-1931, miR-1894, and miR-1936 that are close to common retroviral integration sites and are therefore likely to have some role in cell homeostasis.     

玉麦microRNAs类活性物质的筛选及功能分析

目的 鉴定玉麦中可吸收入血的microRNAs(miRNAs)类活性物质,并分析其靶基因功能。方法 采用二代高通量测序法,以正常小鼠血浆miRNAs为空白对照,测定喂食玉麦匀浆液小鼠血浆中miRNAs的总量,并与玉麦miRNAs比对,鉴定吸收入体内的玉麦miRNAs。采用TargetScan与MiRanda软件,预测玉麦miRNAs可能作用于人类mRNA靶基因,并通过Gene Ontology(GO)与Kyoto Encyclopedia of Genes and Genomes(KEGG)分析靶基因的相关功能和信号途径。结果 共鉴定出12个可吸收入体内的玉麦miRNAs。GO与KEGG分析显示这些miRNAs可能调控的靶基因及其参与的生物学功能包括胰岛素信号通路、癌症通路、MAPK通路等相关信号通路,其中miR4995、miR156a、miR396e为玉麦可能的主要核酸活性物质。结论 miRNAs可能为玉麦中的一种新的活性物质。     

Absence of mature microRNAs inactivates the response of gene expression to carcinogenesis induced by N‐ethyl‐N‐nitrosourea in mouse liver

This study aims to evaluate the role of microRNAs (miRNAs) in chemical tumorigenesis by evaluating genomic gene expression in miRNA knockout mice. Previous studies showed that mice without mature miRNAs due to hepatocyte‐specific Dicer1 knockout (KO) had a much higher liver tumor incidence than wild‐type mice. In this study, Dicer1 KO or the wild‐type mice were treated intraperitoneally with genotoxic carcinogen N‐ethyl‐N‐nitrosourea (ENU) at a single dose (150 mg kg^–1 that resulted in liver tumorigenesis) or the vehicle at 3 weeks of age. The animals were killed 2 weeks after treatment and the liver samples were collected for the gene expression study. Principal components analysis and hierarchical cluster analysis showed that gene expression was globally altered by the Dicer1 KO and ENU exposure. There were 5621, 3286 and 2565 differentially expressed genes for Dicer1 disruption, ENU treatment in wild‐type mice and ENU treatment in Dicer1 KO mice, respectively. Functional analysis of the differentially expressed genes suggests that the Dicer1 KO mouse liver lost their capability to suppress the carcinogenesis induced by ENU exposure in genomic level. In addition, the miRNA‐mediated BRCA1 and P53 signaling pathways were identified as the main pathways responsible for the tumorigenesis. We conclude that the mouse livers in the absence of mature miRNAs could not appropriately respond to carcinogenic insults from ENU treatment, indicating that miRNAs play a critical role in chemical carcinogenesis. Copyright © 2014 John Wiley & Sons, Ltd.     

CHANGES IN microRNA (miR) PROFILE AND EFFECTS OF miR-320 IN INSULIN-RESISTANT 3T3-L1 ADIPOCYTES

• 1 MicroRNAs (miRNAs) play essential roles in many biological processes. It is known that aberrant miRNA expression contributes to some pathological conditions. However, it is not known whether miRNAs play any role in the development of insulin resistance in adipocytes, a key pathophysiological link between obesity and diabetes.
• 2 To investigate the function of miRNAs in the development of insulin resistance, using miRNA microarray analysis we compared miRNA expression profiles between normal insulin‐sensitive 3T3‐L1 adipocytes and 3T3‐L1 adipocytes rendered insulin resistant following treatment with high glucose (25 mmol/L) and high insulin (1 µmol/L). Furthermore, adipocytes were transfected with specific antisense oligonucleotides against miRNA‐320 (anti‐miR‐320 oligo) and the effects on the development of insulin resistance were evaluated.
• 3 We identified 50 upregulated and 29 downregulated miRNAs in insulin‐resistant (IR) adipocytes, including a 50‐fold increase in miRNA‐320 (miR‐320) expression. Using bioinformatic techniques, the p85 subunit of phosphatidylinositol 3‐kinase (PI3‐K) was found to be a potential target of miR‐320. In experiments with anti‐miR‐320 oligo, insulin sensitivity was increased in IR adipocytes, as evidenced by increases in p85 expression, phosphorylation of Akt and the protein expression of the glucose transporter GLUT‐4, as well as insulin‐stimulated glucose uptake. These beneficial effects of anti‐miR‐320 oligo were observed only in IR adipocytes and not in normal adipocytes.
• 4 In conclusion, the miRNA profile changes in IR adipocytes compared with normal 3T3‐L1 adipocytes. Anti‐miR‐320 oligo was found to regulate insulin resistance in adipocytes by improving insulin–PI3‐K signalling pathways. The findings provide information regarding a potentially new therapeutic strategy to control insulin resistance.

     

MicroRNA changes associated with atypical CYP1A1 inducer BMS-764459

The corticotrophin releasing factor (CRF) receptor I antagonist, BMS-764459 (evaluated as a potential treatment of affective disorders), was orally dosed to female Sprague-Dawley rats once daily for 2 weeks (vehicle control or 175 mg/kg/day). To investigate the mechanism of BMS-764459-related liver weight increases, total liver RNA was isolated and evaluated for mRNA gene expression by microarray analysis (assessing the expression of approximately 24,000 genes) from snap-frozen tissue. Subsequently, mRNA and miRNA (microRNA) were also analyzed 5 years later from FFPE (Formalin Fixed Paraffin Embedded) samples via RT-PCR (about 800 miRNA evaluated). Genomic analyses showed that BMS-764459 induces AhR target genes with additional inductions of CYP2B, CYP3A, and Abcc3 consistent with the gene expression pattern of atypical CYP1A1 inducers. Analysis of miRNA expression identified a number of significantly affected miRNAs. To further evaluate their role in atypical CYP1A1 induction, an in silico evaluation of differentially expressed miRNA was performed and their putative mRNA 3′-UTR (untranslated region) binding sequences were evaluated. MiR-680 and miR-29a were identified as potential regulators and biomarkers of atypical CYP1A1 induction by regulating Abcc3, CYP3A and CYP2B as well as a number of AhR targeted genes.     

The changes of miRNA expression in rat hippocampus following chronic lead exposure

miRNAs have been found to contribute to normal brain functions, nervous system diseases, as well as neurotoxicities induced by external agents. However, whether they are involved in lead-induced neurotoxicities is still not clear. To identify that, a lead-induced chronic neurotoxicity model of rats was built. Both miRNA microarray analysis and qRT-PCR were performed to determine the change of miRNA expression in hippocampus. Then 3 bioinformatics databases were used to analyze the relative target genes of these miRNA, which were further confirmed by qRT-PCR and Western blot. In the present study, lead exposure resulted in the changed expression of 7 miRNAs: miR-204, miR-211, miR-448, miR-449a, miR-34b, and miR-34c were greatly up-regulated while miR-494 was greatly down-regulated. Bioinformatics analysis results showed that the target genes of 6 up-regulated miRNAs were related to neural injury and neurodegeration, axon and synapse function, neural development and regeneration. Correspondingly, the expression levels of mature mRNAs and proteins of three target genes (Bcl-2, Itpr1, and Map2k1) were greatly repressed, verifying the results of bioinformatics analysis. Taken together, our results showed that the expression of several miRNAs reported to be associated with neurophysiological pathways and neurodegenerative diseases changed in rat hippocampus following chronic lead exposure. These miRNAs may play important roles in lead-induced neurotoxicity.