MicroRNAs profiling in murine models of acute and chronic asthma: a relationship with mRNAs targets

Regulating the Regulators: microRNA and Asthma

One obstacle to developing an effective therapeutic strategy to treat or prevent asthma is that the fundamental causes of asthma are not totally understood. Asthma is thought to be a chronic T_H2 immune-mediated inflammatory disease. Epigenetic changes are recognized to play a role in the initiation and maintenance of a T_H2 response. MicroRNAs (miRNAs) are key epigenetic regulators of gene expression, and their expression is highly regulated, therefore, deregulation of miRNAs may play an important role in the pathogenesis of asthma. Profiling circulating miRNA might provide the highest specificity and sensitivity to diagnose asthma; similarly, correcting potential defects in the miRNA regulation network may lead to new therapeutic modalities to treat this disease.

Decreased miR-192 expression in peripheral blood of asthmatic individuals undergoing an allergen inhalation challenge

Background

MicroRNAs are small non-coding RNAs that regulate gene expression at the post-transcriptional level. While they have been implicated in various diseases, the profile changes in allergen inhalation challenge are not clarified in human. We aimed to evaluate changes in the microRNA profiles in the peripheral blood of asthmatic subjects undergoing allergen inhalation challenge.

Results

Seven mild asthmatic subjects participated in the allergen inhalation challenge. In addition, four healthy control subjects (HCs) were recruited. MicroRNA profiles in peripheral blood samples (pre-challenge and 2 hours post-challenge) were measured by the NanoString nCounter assay to determine changes in miRNA levels as these asthmatic subjects underwent an allergen inhalation challenge. One common miRNA, miR-192, was significantly expressed in both comparisons; HCs vs. pre-challenge and pre- vs. post-challenge, showing that miR-192 was significantly under-expressed in asthmatics compared to HCs and decreased in post-challenge at an FDR of 1%. Cell-specific statistical deconvolution attributed miR-192 expression in whole blood to PBMCs. MiR-192 was technically validated using real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR) showing that the level in asthmatics (pre-challenge) was significantly lower than HCs and that post-challenge was significantly lower than pre-challenge. The normalized relative miR-192 expression quantified using RT-qPCR specific to PBMCs was also validated. Ontology enrichment and canonical pathway analyses for target genes suggested several functions and pathways involved in immune response and cell cycle.

Conclusions

The miRNA profile in peripheral blood was altered after allergen inhalation challenge. Change in miR-192 levels may be implicated in asthma mechanisms. These results suggest that allergen inhalation challenge is a suitable method to characterize peripheral miRNA profiles and potentially elucidate the mechanism of human asthma.

Differential microRNA epression in asthma and the role of miR-1248 in regulation of IL-5

Asthma is a chronic inflammatory disease that can be difficult to manage due to a lack of diagnostic biomarkers and an incomplete understanding of the molecular pathogenesis. MicroRNAs (miRNAs) are small, single-stranded, non-coding RNAs with increasing importance in regulation of immune function and as biomarkers. We profiled miRNAs in the serum of asthmatics and non-asthmatic controls to identify miRNAs that could serve as diagnostic markers and potential regulators of allergic inflammation. Differential expression of miR-1248, miR-26a, Let-7a, and Let-7d were observed in asthmatic patients compared to controls. Predictive algorithm analyses of these miRNAs revealed their specificity for different Th2 cytokines, including IL-5, which has not previously been shown to be post-transcriptionally regulated. Using multiple approaches, we showed that miR-1248 physically interacts with the IL-5 transcript in the 3' untranslated region and serves as a positive regulator to increase IL-5 expression. Collectively, our results demonstrate a previously uncharacterized mode of regulation of IL-5 expression and potential use for miRNAs in the diagnosis and clinical management of asthma.

Modeling the role of peroxisome proliferator-activated receptor γ and microRNA-146 in mucosal immune responses to Clostridium difficile

Clostridium difficile is an anaerobic bacterium that has re-emerged as a facultative pathogen and can cause nosocomial diarrhea, colitis or even death. Peroxisome proliferator-activated receptor (PPAR) γ has been implicated in the prevention of inflammation in autoimmune and infectious diseases; however, its role in the immunoregulatory mechanisms modulating host responses to C. difficile and its toxins remains largely unknown. To characterize the role of PPARγ in C. difficile-associated disease (CDAD), immunity and gut pathology, we used a mouse model of C. difficile infection in wild-type and T cell-specific PPARγ null mice. The loss of PPARγ in T cells increased disease activity and colonic inflammatory lesions following C. difficile infection. Colonic expression of IL-17 was upregulated and IL-10 downregulated in colons of T cell-specific PPARγ null mice. Also, both the loss of PPARγ in T cells and C. difficile infection favored Th17 responses in spleen and colonic lamina propria of mice with CDAD. MicroRNA (miRNA)-sequencing analysis and RT-PCR validation indicated that miR-146b was significantly overexpressed and nuclear receptor co-activator 4 (NCOA4) suppressed in colons of C. difficile-infected mice. We next developed a computational model that predicts the upregulation of miR-146b, downregulation of the PPARγ co-activator NCOA4, and PPARγ, leading to upregulation of IL-17. Oral treatment of C. difficile-infected mice with the PPARγ agonist pioglitazone ameliorated colitis and suppressed pro-inflammatory gene expression. In conclusion, our data indicates that miRNA-146b and PPARγ activation may be implicated in the regulation of Th17 responses and colitis in C. difficile-infected mice.

Profiling of miRNAs in pediatric asthma: upregulation of miRNA-221 and miRNA-485-3p

The aim of this study was to investigate the expression profiles of microRNAs (miRNAs) in pediatric asthma and to determine candidate miRNAs responsible for the pathogenesis of this disease. Microarrays were used to detect the differences in the miRNA expression levels between asthmatic children and controls. Airway inflammation was evaluated by cell counting and tissue biopsy in an ovalbumin (OVA)-induced murine asthma model. Real-time polymerase chain reaction (PCR) was used to verify the differentially expressed miRNAs. The targets of the identified miRNAs were analyzed by bioinformatic analysis. The sprouty-related protein with an EVH1 domain-2 (Spred-2) protein content was assessed by western blotting. Differences were observed in the expression of miRNAs between the asthmatic children and controls. Upregulation of miRNA-221 and miRNA-485-3p in pediatric asthmatics and murine asthma models were verified by real-time PCR. Spred-2, a predicted target of miRNA-221 and miRNA-485-3p, was downregulated in murine asthma models. Upregulation of miRNA-221 and miRNA-485-3p may regulate the pathogenesis of asthma.

Epigenetics and childhood asthma: current evidence and future research directions

Asthma is the most common chronic disease of childhood, affecting one in eight children in the USA and worldwide. It is a complex disease, influenced by both environmental exposures and genetic factors. Although epigenetic modifications (DNA methylation, histone modification and miRNA) can affect transcriptional activity in multiple genetic pathways relevant for asthma development, very limited work has been carried out so far to examine the role of epigenetic variations on asthma development and management. This review provides a brief overview of epigenetic modifications, summarizes recent findings, and discusses some of the major methodological concerns that are relevant for asthma epigenetics.

MicroRNA profiling in mucosal biopsies of eosinophilic esophagitis patients pre and post treatment with steroids and relationship with mRNA targets

Background

The characterization of miRNAs and their target mRNAs involved in regulation of the immune process is an area of intense research and relatively little is known governing these processes in allergic inflammation. Here we present novel findings defining the miRNA and mRNA transcriptome in eosinophilic esophagitis (EoE), an increasing recognized allergic disorder.

Methods

Esophageal epithelial miRNA and mRNA from five paired biopsies pre- and post-treatment with glucocorticosteroids were profiled using Taqman and Affymetrix arrays. Validation was performed on additional paired biopsies, untreated EoE specimens and normal controls. Differentially regulated miRNAs and mRNAs were generated, within which miRNA-mRNA target pairs with high predicted confidence were identified.

Results

Compared to the post-glucocorticoid treated esophageal mucosa, of all the 377 miRNA sequences examined, 32 miRNAs were significantly upregulated and four downregulated in the pre-treated biopsies. MiR-214 was the most upregulated (150 fold) and miR-146b-5b, 146a, 145, 142-3p and 21 were upregulated by at least 10 fold. Out of 12 miRNAs chosen for validation by qRT-PCR, five (miR-214, 146b-5p, 146a, 142-3p and 21) were confirmed and 11 shared the same trend. When the expression of the 12 miRNAs in the EoE mucosa was compared to unrelated normal mucosa, six (miR-214, 146b-5p, 146a, 21, 203, and 489) showed similar significant changes as in the paired samples and 10 of them shared the same trend. In the same five pairs of samples used to profile miRNA, 311 mRNAs were down-regulated and 35 were up-regulated in pre-treated EoE mucosa. Among them, 164 mRNAs were identified as potential targets of differentially regulated miRNAs. Further analysis revealed that immune-related genes, targeted and non-targeted by miRNAs, were among the most important genes involved in the pathogenesis of EoE.

Conclusions

Our findings add to the accumulating body of data defining a regulatory role for miRNA in immune and allergic processes.

The role and regulation of microRNAs in asthma

PURPOSE OF REVIEW

Asthma is a common chronic inflammatory airway disorder that is characterized by variable and recurring airflow obstruction, chronic airway inflammation and bronchial hyper-responsiveness. The etiopathogenesis of asthma remains a complex issue. The intricacy in developing a more effective therapeutic strategy may be due to a large diversity in causative agents and a lack of understanding of the precise molecular mechanism involved in asthma. However, recent identification of microRNAs (miRs) has enhanced technological abilities to understand the disease process.

RECENT FINDINGS

miRs regulate gene expression by controlling the translation of a specific type of messenger RNA. miRs have been recently identified as key regulatory RNAs with immense significance in numerous biological processes including asthma. miRs have been implicated to have a fundamental role in acute and chronic asthma and in airway remodeling by the regulation of multiple signal transduction pathways that are involved in the pathogenesis of asthma. It is possible that miRs may bring a fundamental change to our understanding of the pathophysiology of asthma. This may then lead to the development of novel efficacious therapeutic strategies in asthma.

SUMMARY

In this review, we highlight the current understanding of the role and regulation of miRs in asthma.

Therapeutic modulation of miRNA for the treatment of proinflammatory lung diseases

miRNAs are short, nonprotein coding RNAs that regulate target gene expression principally by causing translational repression and/or mRNA degradation. miRNAs are involved in most mammalian biological processes and have pivotal roles in controlling the expression of factors involved in basal and stimulus-induced signaling pathways. Considering their central role in the regulation of gene expression, miRNAs represent therapeutic drug targets. Here we describe how miRNAs are involved in the regulation of aspects of innate immunity and inflammation, what happens when this goes awry, such as in the chronic inflammatory lung diseases cystic fibrosis and asthma, and discuss the current state-of-the-art miRNA-targeted therapeutics.

Antagonism of mmu-mir-106a attenuates asthma features in allergic murine model

MicroRNAs (miRs) regulate immunological pathways in health and disease, and a number of miRs have been shown to be altered in mouse models of asthma. The secretion of interleukin-10 (IL-10), an anti-inflammatory cytokine, has been shown to be defective in many inflammatory diseases including asthma. We recently demonstrated that miR-106a inhibits IL-10 in a post-transcriptional manner. In this study, we investigated the effect of inhibition of mmu-miR106a in asthmatic condition to find its possible role as a therapeutic target. Our in vitro experiments with mouse macrophage, RAW264.7, revealed that mmu-miR-106a potentially decreased IL-10 along with increase in proinflammatory cytokine. Furthermore, administration of mmu-miR-106a to naive mice reduced IL-10 levels in lungs in a dose-dependent manner without altering lung histology. Most interestingly, knockdown of mmu-miR-106a in an established allergic airway inflammation has significantly alleviated most of the features of asthma such as airway hyperresponsiveness, airway inflammation, increased Th2 response, goblet cell metaplasia, and subepithelial fibrosis along with increase in IL-10 levels in lung. This represents the first in vivo proof of a miRNA-mediated regulation of IL-10 with a potential to reverse an established asthmatic condition.

Plasma microRNA profiles distinguish lethal injury in acetaminophen toxicity: A research study

AIM: To investigate plasma microRNA (miRNA) profiles indicative of hepatotoxicity in the setting of lethal acetaminophen (APAP) toxicity in mice.

METHODS: Using plasma from APAP poisoned mice, either lethally (500 mg/kg) or sublethally (150 mg/kg) dosed, we screened commercially available murine microRNA libraries (SABiosciences, Qiagen Sciences, MD) to evaluate for unique miRNA profiles between these two dosing parameters.

RESULTS: We distinguished numerous, unique plasma miRNAs both up- and downregulated in lethally compared to sublethally dosed mice. Of note, many of the greatest up- and downregulated miRNAs, namely 574-5p, 466g, 466f-3p, 375, 29c, and 148a, have been shown to be associated with asthma in prior studies. Interestingly, a relationship between APAP and asthma has been previously well described in the literature, with an as yet unknown mechanism of pathology. There was a statistically significant increase in alanine aminotransferase levels in the lethal compared to sublethal APAP dosing groups at the 12 h time point (P < 0.001). There was 90% mortality in the lethally compared to sublethally dosed mice at the 48 h time point (P = 0.011).

CONCLUSION: We identified unique plasma miRNAs both up- and downregulated in APAP poisoning which are correlated to asthma development.

MicroRNA-181a, -146a and -146b in spleen CD4+ T lymphocytes play proinflammatory roles in a murine model of asthma

CD4+ T lymphocytes can be primarily polarized to differentiate into Th2 cells, and are heavily involved in the Th2 inflammation of asthma. Little is known about the correlation between microRNAs and Th2 inflammation in asthma, therefore we explore the roles of five microRNAs (microRNA-181a, -155, -150, -146a and -146b) in Th2 inflammation of asthma by tracking their expression levels in splenic CD4+ T lymphocytes under different conditions. Using quantitative real-time polymerase chain reaction (qPCR), the dynamic changes of these microRNAs in murine models of acute asthma (i.e. the OVA group) were analyzed, in comparison to a control group. The effects of dexamethasone on the miRNA expression levels were also investigated. The results showed that the expression levels of microRNA-181a, -150, -146a and -146b were higher in the OVA group compared to the control group in the beginning of the disease, and after 5days dropped to control group levels because there was no new airway challenge. Moreover, the miRNA-146a expression was down-regulated by treatment with dexamethasone. MicroRNA-181a had a positive linear correlation with the numbers of inflammatory cells (i.e. the numbers of total cells or of the eosinophils in the BALF) by Spearman correlation analysis, so did miRNA-146a and miRNA-146b. These observations suggest that microRNA-181a, -146a and -146b are proinflammatory factors in asthma, and that down-regulation of miRNA-146a may partially account for the anti-inflammatory effect of dexamethasone.

Identification of an interleukin 13-induced epigenetic signature in allergic airway inflammation

Epigenetic changes have been implicated in the pathogenesis of asthma. We sought to determine if IL13, a key cytokine in airway inflammation and remodeling, induced epigenetic DNA methylation and miRNAs expression changes in the airways in conjunction with its transcriptional gene regulation. Inducible expression of an IL13 transgene in the airways resulted in significant changes in DNA methylation in 177 genes, most of which were associated with the IL13 transcriptional signature in the airways. A large number of genes whose expression was induced by IL13 were found to have decreased methylation, including those involved in tissue remodeling (Olr1), leukocyte influx (Cxcl3, Cxcl5, CSFr2b), and the Th2 response (C3ar1, Chi3l4). Reciprocally, some genes whose expression was suppressed were found to have increased methylation (e.g. Itga8). In addition, miRNAs were identified with targets for lung development and Wnt signaling, amongst others. These results indicate that IL13 confers an epigenetic methylation and miRNA signature that accompanies its transcriptional program in the airways, which may play a critical role in airway inflammation and remodeling.

Effects of exercise on microRNA expression in young males peripheral blood mononuclear cells

MicroRNAs are increasingly seen as targets of drug discovery because they influence gene function acting both to silence and subtly modulate protein translation. Little is known about effects of dynamic physiological states on microRNA regulation in humans. We hypothesized that microRNA expression in peripheral blood mononuclear cells (PBMCs) would be affected by brief exercise. Twelve young men performed brief bouts of heavy exercise. PBMC microRNA was analyzed before and immediately after exercise using the Agilent Human microRNA V2 Microarray. Exercise altered expression level of 34 microRNAs (FDR < 0.05). Many of them play roles in inflammatory processes (e.g., miR-125b[↓], down-regulated by proinflammatory factor LPS; and miR-132[↑], 125b[↓] and let-7e[↓] involved inTLR4 signaling). Using previous exercise data in PBMCs, we linked the microRNA changes to specific gene pathways. This analysis identified 12 pathways including the TGF-β and MAPK signaling. We also compared exercise-associated microRNA changes in PBMCs with the exercise-associated microRNAs previously identified in neutrophils. Nine microRNAs were affected in both PBMCs and neutrophils, but only six changed in the same direction. A commonly occurring physiologic perturbation, brief heavy exercise, changes microRNA profiles in PBMCs, many of which are related to inflammatory processes. The pattern of change suggests that exercise differentially influences microRNAs in leukocyte subtypes.

MicroRNA Regulation of Smooth Muscle Phenotype

Advances in studies of microRNA (miRNA) expression and function in smooth muscles illustrate important effects of small noncoding RNAs on cell proliferation, hypertrophy and differentiation. An emerging theme in miRNA research in a variety of cell types including smooth muscles is that miRNAs regulate protein expression networks to fine tune phenotype. Some widely expressed miRNAs have been described in smooth muscles that regulate important processes in many cell types, such as miR-21 control of proliferation and cell survival. Other miRNAs that are prominent regulators of smooth muscle-restricted gene expression also have targets that control pluripotent cell differentiation. The miR-143~145 cluster which targets myocardin and Kruppel-like factor 4 (KLF4) is arguably the best-described miRNA family in smooth muscles with profound effects on gene expression networks that promote serum response factor (SRF)-dependent contractile and cytoskeletal protein expression and the mature contractile phenotype. Kruppel-family members KLF4 and KLF5 have multiple effects on cell differentiation and are targets for multiple miRNAs in smooth muscles (miR-145, miR-146a, miR-25). The feedback and feedforward loops being defined appear to contribute significantly to vascular and airway remodeling in cardiovascular and respiratory diseases. RNA interference approaches applied to animal models of vascular and respiratory diseases prove that miRNAs and RNA-induced silencing are valid targets for novel anti-remodeling therapies that alter pathological smooth muscle hyperplasia and hypertrophy.

Treatment of allergic asthma: modulation of Th2 cells and their responses

Atopic asthma is a chronic inflammatory pulmonary disease characterised by recurrent episodes of wheezy, laboured breathing with an underlying Th2 cell-mediated inflammatory response in the airways. It is currently treated and, more or less, controlled depending on severity, with bronchodilators e.g. long-acting beta agonists and long-acting muscarinic antagonists or anti-inflammatory drugs such as corticosteroids (inhaled or oral), leukotriene modifiers, theophyline and anti-IgE therapy. Unfortunately, none of these treatments are curative and some asthmatic patients do not respond to intense anti-inflammatory therapies. Additionally, the use of long-term oral steroids has many undesired side effects. For this reason, novel and more effective drugs are needed. In this review, we focus on the CD4+ Th2 cells and their products as targets for the development of new drugs to add to the current armamentarium as adjuncts or as potential stand-alone treatments for allergic asthma. We argue that in early disease, the reduction or elimination of allergen-specific Th2 cells will reduce the consequences of repeated allergic inflammatory responses such as lung remodelling without causing generalised immunosuppression.