Small-Molecule Regulators of MicroRNAs in Biomedicine

Drug regulation of microRNA

The scientific review provides the mechanisms of drug regulation of microRNA in the human body. To write the article, information was searched using Scopus, Web of Science, MEDLINE, PubMed, Google Scholar, Embase, Global Health, The Cochrane Library databases. To restore the reduced functional activity of microRNAs, replacement therapy is used, with modified synthetic analogs of endogenous microRNAs, and drugs that enhance the production of the body’s own microRNAs. The authors state that numerous studies have confirmed the effectiveness of miRNA replacement therapy. It is known that there are several groups of drugs among miRNA inhibitors: anti-miRNA oligonucleotides, miRNA traps, miRNA mimics that prevent miRNA binding; peptide nucleic acids, small-molecule inhibitors. The authors suggest that the expression of drug-metabolizing enzymes is controlled by nuclear receptors and transcription factors, epigenetic regulation such as DNA methylation and histone acetylation, and post-translational modification. It is emphasized that ursodeoxycholic acid modulates the expression of some miRNAs. It is known that probiotic bacteria can modulate the expression level of miRNA genes. The use of probiotics is accompanied by a change in the expression of nume­rous genes of the body involved in the regulation of the inflammatory response, allergic reactions, metabolism and other biological processes. Thus, modern science is intensively studying the potential of using drugs that restore miRNA content or inhibit miRNA acti­vity for the therapy of miRNA-dependent conditions. The results of scientific research confirmed the therapeutic effect of ursodeoxycholic acid and probiotic preparations due to the effect on the acti­vity of miRNA generation in hepatobiliary diseases. Therefore, the introduction into clinical practice of drugs than can modulate the content and expression of specific miRNAs will certainly open new perspectives in the treatment of patients with hepatobiliary diseases.

Identification of miRNA-Small Molecule Associations by Continuous Feature Representation Using Auto-Encoders

MicroRNAs (miRNAs) are short non-coding RNAs that play important roles in the body and affect various diseases, including cancers. Controlling miRNAs with small molecules is studied herein to provide new drug repurposing perspectives for miRNA-related diseases. Experimental methods are time- and effort-consuming, so computational techniques have been applied, relying mostly on biological feature similarities and a network-based scheme to infer new miRNA–small molecule associations. Collecting such features is time-consuming and may be impractical. Here we suggest an alternative method of similarity calculation, representing miRNAs and small molecules through continuous feature representation. This representation is learned by the proposed deep learning auto-encoder architecture. Our suggested representation was compared to previous works and achieved comparable results using 5-fold cross validation (92% identified within top 25% predictions), and better predictions for most of the case studies (avg. of 31% vs. 25% identified within the top 25% of predictions). The results proved the effectiveness of our proposed method to replace previous time- and effort-consuming methods.

Ensemble of kernel ridge regression-based small molecule-miRNA association prediction in human disease

MicroRNAs (miRNAs) play crucial roles in human disease and can be targeted by small molecule (SM) drugs according to numerous studies, which shows that identifying SM-miRNA associations in human disease is important for drug development and disease treatment. We proposed the method of Ensemble of Kernel Ridge Regression-based Small Molecule-MiRNA Association prediction (EKRRSMMA) to uncover potential SM-miRNA associations by combing feature dimensionality reduction and ensemble learning. First, we constructed different feature subsets for both SMs and miRNAs. Then, we trained homogeneous base learners based on distinct feature subsets and took the average of scores obtained from these base learners as SM-miRNA association score. In EKRRSMMA, feature dimensionality reduction technology was employed in the process of construction of feature subsets to reduce the influence of noisy data. Besides, the base learner, namely KRR_avg, was the combination of two classifiers constructed under SM space and miRNA space, which could make full use of the information of SM and miRNA. To assess the prediction performance of EKRRSMMA, we conducted Leave-One-Out Cross-Validation (LOOCV), SM-fixed local LOOCV, miRNA-fixed local LOOCV and 5-fold CV based on two datasets. For Dataset 1 (Dataset 2), EKRRSMMA got the Area Under receiver operating characteristic Curves (AUCs) of 0.9793 (0.8871), 0.8071 (0.7705), 0.9732 (0.8586) and 0.9767 ± 0.0014 (0.8560 ± 0.0027). Besides, we conducted four case studies. As a result, 32 (5-Fluorouracil), 19 (17β-Estradiol), 26 (5-Aza-2'-deoxycytidine) and 11 (cyclophosphamide) out of top 50 predicted potentially associated miRNAs were confirmed by database or experimental literature. Above evaluation results demonstrated that EKRRSMMA is reliable for predicting SM-miRNA associations.

MicroRNAs as monitoring markers for right-sided heart failure and congestive hepatopathy

The last decades showed a worrying increase in the evolution of cardiovascular diseases towards different stages of heart failure (HF), as a stigma of the western lifestyle. MicroRNAs (miRNAs), non-coding RNAs, which are approximately 22-nucleotide long, were shown to regulate gene expression at the post-transcriptional level and play a role in the pathogenesis and progression of HF. miRNAs research is of high interest nowadays, as these molecules display mechanisms of action that can influence the course of evolution of common chronic diseases, including HF. The potential of post-transcriptional regulation by miRNAs concerning the diagnosis, management, and therapy for HF represents a new promising approach in the accurate assessment of cardiovascular diseases. This review aims to assess the current knowledge of miRNAs in cardiovascular diseases, especially right-sided heart failure and hepatomegaly. Moreover, attention is focused on their role as potential molecular biomarkers and more promising aspects involving miRNAs as future therapeutic targets in the pathophysiology of HF.

Solubility, thermal and photoluminescence properties of triphenyl imidazole-containing polyimides

In this paper, three kinds of triphenyl imidazole-containing diamines including 2-phenyl-4,5-bis(4-(4-amino-2-trifluoromethylphenoxy)phenyl)imidazole (PBAI), 2-(4-methylphenyl)-4,5-bis(4-(4-amino-2-trifluoromethyl phenoxy)phenyl)imidazole (MPBAI) and 2-(4-trifluoromethylphenyl)-4,5-bis(4-(4-amino-2-trifluoromethylphenoxy)phenyl)imidazole (TFPBAI) were synthesized. Then, a series of polyimide (PI) films were prepared by the solution polymerization of the three diamines and various dianhydrides, such as 4,4′-(hexafluoroisopropylidene)diphthalic anhydride (6FDA), 1,2,4,5-pyromellitic dianhydride (PMDA) and 1,2,3,4-cyclobutanetetracarboxylic dianhydride (CBDA), followed by thermal imidization. The effects of chemical structures on the solubilities and thermal, optical and electrochemical properties of polyimides were explored. All the polyimides exhibited higher glass transition temperatures around 300 °C and excellent solubilities in common polar solvents. The polyimide films derived from CBDA or 6FDA showed better optical properties with light color and transparent characteristics. The fluorescence test showed that the photoluminescence color of CBDA-based polyimide films is in the blue range in the CIE 1931 spectrum, while the polyimide film based on PMDA and 6FDA presented black or weak yellow light. However, all these polyimides in solution exhibited similar blue luminescence. Electrochemical tests indicated that the HOMO and LUMO values of these films were around −6.5 and −3.6 eV, and the energy gap difference was about 3.0 eV. Therefore, the triphenyl imidazole-containing polyimides exhibit comprehensive performance, which will be expected as a new kind of functional material for certain application in the optical and optoelectronics fields.

The triphenyl imidazole-containing polyimide films exhibit excellent solubility and thermal and photoluminescence properties.

Impact of Polypharmacy on Candidate Biomarker miRNomes for the Diagnosis of Fibromyalgia and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: Striking Back on Treatments

Fibromyalgia (FM) and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) are diseases of unknown etiology presenting complex and often overlapping symptomatology. Despite promising advances on the study of miRNomes of these diseases, no validated molecular diagnostic biomarker yet exists. Since FM and ME/CFS patient treatments commonly include polypharmacy, it is of concern that biomarker miRNAs are masked by drug interactions. Aiming at discriminating between drug-effects and true disease-associated differential miRNA expression, we evaluated the potential impact of commonly prescribed drugs on disease miRNomes, as reported by the literature. By using the web search tools SM2miR, Pharmaco-miR, and repoDB, we found a list of commonly prescribed drugs that impact FM and ME/CFS miRNomes and therefore could be interfering in the process of biomarker discovery. On another end, disease-associated miRNomes may incline a patient's response to treatment and toxicity. Here, we explored treatments for diseases in general that could be affected by FM and ME/CFS miRNomes, finding a long list of them, including treatments for lymphoma, a type of cancer affecting ME/CFS patients at a higher rate than healthy population. We conclude that FM and ME/CFS miRNomes could help refine pharmacogenomic/pharmacoepigenomic analysis to elevate future personalized medicine and precision medicine programs in the clinic.

Prediction of Potential Small Molecule-Associated MicroRNAs Using Graphlet Interaction

MicroRNAs (miRNAs) have been proved to be targeted by the small molecules recently, which made using small molecules to target miRNAs become a possible therapy for human diseases. Therefore, it is very meaningful to investigate the relationships between small molecules and miRNAs, which is still yet in the newly-developing stage. In this paper, we presented a prediction model of Graphlet Interaction based inference for Small Molecule-MiRNA Association prediction (GISMMA) by combining small molecule similarity network, miRNA similarity network and known small molecule-miRNA association network. This model described the complex relationship between two small molecules or between two miRNAs using graphlet interaction which consists of 28 isomers. The association score between a small molecule and a miRNA was calculated based on counting the numbers of graphlet interaction throughout the small molecule similarity network and the miRNA similarity network, respectively. Global and two types of local leave-one-out cross validation (LOOCV) as well as five-fold cross validation were implemented in two datasets to evaluate GISMMA. For Dataset 1, the AUCs are 0.9291 for global LOOCV, 0.9505, and 0.7702 for two local LOOCVs, 0.9263 ± 0.0026 for five-fold cross validation; for Dataset 2, the AUCs are 0.8203, 0.8640, 0.6591, and 0.8554 ± 0.0063, in turn. In case study for small molecules, 5-Fluorouracil, 17β-Estradiol and 5-Aza-2'-deoxycytidine, the numbers of top 50 miRNAs predicted by GISMMA and validated to be related to these three small molecules by experimental literatures are in turn 30, 29, and 25. Based on the results from cross validations and case studies, it is easy to realize the excellent performance of GISMMA.

Small Molecule Inhibition of MicroRNA miR-21 Rescues Chemosensitivity of Renal-Cell Carcinoma to Topotecan

Chemical probes of microRNA (miRNA) function are potential tools for understanding miRNA biology that also provide new approaches for discovering therapeutics for miRNA-associated diseases. MicroRNA-21 (miR-21) is an oncogenic miRNA that is overexpressed in most cancers and has been strongly associated with driving chemoresistance in cancers such as renal cell carcinoma (RCC). Using a cell-based luciferase reporter assay to screen small molecules, we identified a novel inhibitor of miR-21 function. Following structure-activity relationship studies, an optimized lead compound demonstrated cytotoxicity in several cancer cell lines. In a chemoresistant-RCC cell line, inhibition of miR-21 via small molecule treatment rescued the expression of tumor-suppressor proteins and sensitized cells to topotecan-induced apoptosis. This resulted in a >10-fold improvement in topotecan activity in cell viability and clonogenic assays. Overall, this work reports a novel small molecule inhibitor for perturbing miR-21 function and demonstrates an approach to enhancing the potency of chemotherapeutics specifically for cancers derived from oncomir addiction.

Overexpression of miR‑21 promotes neural stem cell proliferation and neural differentiation via the Wnt/β‑catenin signaling pathway in vitro

The primary aim of the present study was to examine the effects of microRNA‑21 (miR‑21) on the proliferation and differentiation of rat primary neural stem cells (NSCs) in vitro. miR‑21 was overexpressed in NSCs by transfection with a miR‑21 mimic. The effects of miR‑21 overexpression on NSC proliferation were revealed by Cell Counting kit 8 and 5‑ethynyl‑2'‑deoxyuridine incorporation assay, and miR‑21 overexpression was revealed to increase NSC proliferation. miR‑21 overexpression was confirmed using reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR). mRNA and protein expression levels of key molecules (β‑catenin, cyclin D1, p21 and miR‑21) in the Wnt/β‑catenin signaling pathway were studied by RT‑qPCR and western blot analysis. RT‑qPCR and western blot analyses revealed that miR‑21 overexpression increased β‑catenin and cyclin D1 expression, and decreased p21 expression. These results suggested that miR‑21‑induced increase in proliferation was mediated by activation of the Wnt/β‑catenin signaling pathway, since overexpression of miR‑21 increased β‑catenin and cyclin D1 expression and reduced p21 expression. Furthermore, inhibition of the Wnt/β‑catenin pathway with FH535 attenuated the influence of miR‑21 overexpression on NSC proliferation, indicating that the factors activated by miR‑21 overexpression were inhibited by FH535 treatment. Furthermore, overexpression of miR‑21 enhanced the differentiation of NSCs into neurons and inhibited their differentiation into astrocytes. The present study indicated that in primary rat NSCs, overexpression of miR‑21 may promote proliferation and differentiation into neurons via the Wnt/β‑catenin signaling pathway in vitro.

[Pathogenesis of psoriasis]

Psoriasis is an inflammatory T cell-mediated autoimmune disease of skin and joints that affects 2-4 % of the adult population and 0.1-1 % of children. Genetic susceptibility, environmental triggering factors, and innate immune processes initiate psoriasis pathogenesis that results in an adaptive autoreactive response. The T cell response is orchestrated by CD 8(+) T cells in the epidermis and by CD 4(+) T cells in the dermis that predominantly produce interleukin-17 (IL‑17). Research of the past 15 years unraveled cellular and molecular mechanisms as well as cytokines like TNF-α or IL‑23 that contribute to psoriatic inflammation. This knowledge has been translated into clinical practice and a number of antipsoriatic small molecules and immunobiologics are now available. Here, we discuss the current principles of psoriasis pathogenesis in the context of modern therapies.

Circulating MicroRNAs as Potential Molecular Biomarkers in Pathophysiological Evolution of Pregnancy

MicroRNAs represent nonprotein coding small RNA molecules that are very stable to degradation and responsible for gene silencing in most eukaryotic cells. Increased evidence has been accumulating over the years about their potential value as biomarkers for several diseases. MicroRNAs were predicted to be involved in nearly all biological processes from development to oncogenesis. In this review, we address the importance of circulating microRNAs in different conditions associated with pregnancy starting with the implantation period to preeclampsia and we shortly describe the correlation between placental circulating miRNAs and pregnancy status. We also discuss the importance of microRNAs in recurrent abortion and ectopic pregnancy.

Let-7a suppresses glioma cell proliferation and invasion through TGF-β/Smad3 signaling pathway by targeting HMGA2

It has been shown that let-7a was associated with the tumorigenesis of glioma. Our study was designed to infer how let-7a targets high-mobility AT-hook 2 (HMGA2) and suppresses glioma cell proliferation, invasion, and migration. Glioma tissues from 60 glioma patients and 10 normal brain tissues were collected in this study. Real-time quantitative reverse transcription-PCR (qRT-PCR) and in situ hybridization were used to detect the expression levels of let-7a in tissues and cells. The HMGA2 and the proteins related to transforming growth factor-beta (TGF-β)/Smad3 signaling pathway were measured by immunohistochemistry and western blot. Glioma U87 cells were transfected with either let-7a mimics, HMGA2 small interfering RNA (siRNA), let-7a mimics + HMGA2, HMGA2, or scramble. A cell counting kit-8 (CCK-8) assay was used to detect and compare the difference among various transfection groups. Glioma tumor xenograft models on mice were built to evaluate the effects of let-7a and HMGA2 siRNA on glioma tumors in vivo. The expression level of let-7a significantly downregulated in glioma tissues, while the HMGA2 positive expression rate notably increased compared with those in normal brain tissues (all P < 0.05). Moreover, the expression levels of let-7a and HMGA2 were correlated with glioma grades (all P < 0.05). The proliferation of U87 cells transfected with let-7a mimics or HMGA2 siRNA was significantly inhibited in comparison to the blank control group and the apoptosis rates of U87 cells transfected with let-7a mimics or HMGA2 siRNA were significantly higher than those in the blank control group (all P < 0.05). Let-7a or HMGA2 siRNA could remarkably attenuate the invasion and migration ability of glioma cells (all P < 0.05). Apart from that, over-expressed exogenous HMGA2 could reverse the inhibition of glioma cell metastasis and proliferation induced by let-7a. As suggested by immunohistochemistry and western blot, the expression levels of TGF-β1 and p-Smad3 significantly decreased compared with the blank or scramble group (all P < 0.05). Thus, let-7a and HMGA2 siRNA could effectively suppress the growth of tumors in glioma xenograft models. Let-7a may suppress the proliferation and invasion of glioma cells through mediating TGF-β/Smad3 signaling pathway by targeting HMGA2.