DRB2, DRB3 and DRB5 function in a non-canonical microRNA pathway in Arabidopsis thaliana

DOUBLE-STRANDED RNA BIN DIN G (DRB) proteins have been functionally characterized in viruses, prokaryotes and eukaryotes and are involved in all aspects of RNA biology. Arabidopsis thaliana (Arabidopsis) encodes five closely related DRB proteins, DRB1 to DRB5. DRB1 and DRB4 are required by DICER-LIKE (DCL) proteins DCL1 and DCL4 to accurately and efficiently process structurally distinct double-stranded RNA (dsRNA) precursor substrates in the microRNA (miRNA) and trans-acting small-interfering RNA (tasiRNA) biogenesis pathways respectively. We recently reported that DRB2 is also involved in the biogenesis of specific miRNA subsets. Furthermore, the severity of the developmental phenotype displayed by the drb235 triple mutant plant, compared with those expressed by either drb2, drb3 and drb5 single mutants, or double mutant combinations thereof, indicates that DRB3 and DRB5 function in the same non-canonical miRNA pathway as DRB2. Through the use of our artificial miRNA (amiRNA) plant expression vector, pBlueGreen 2,3 we demonstrate here that unlike DRB2, DRB3 and DRB5 are not involved in the dsRNA processing stages of the miRNA biogenesis pathway, but are required to mediate RNA silencing of target genes of DRB2-associated miRNA s. © 2012 Landes Bioscience.

Study of miRNA polymorphisms and their potential association with breast cancer risk in Australian Caucasian populations

This project established a large and well characterised prospective breast cancer DNA biobank and used this biobank to conduct genetic studies in breast cancer. The thesis presented the results of these high-throughput genotyping studies in two separate Australian Caucasian case-control populations and identified association between three novel genetic variants in microRNA genes and breast cancer risk.

A Ten-microRNA Expression Signature Predicts Survival in Glioblastoma

Glioblastoma (GBM) is the most common and aggressive primary brain tumor with very poor patient median survival. To identify a microRNA (miRNA) expression signature that can predict GBM patient survival, we analyzed the miRNA expression data of GBM patients (n = 222) derived from The Cancer Genome Atlas (TCGA) dataset. We divided the patients randomly into training and testing sets with equal number in each group. We identified 10 significant miRNAs using Cox regression analysis on the training set and formulated a risk score based on the expression signature of these miRNAs that segregated the patients into high and low risk groups with significantly different survival times (hazard ratio HR] = 2.4; 95% CI = 1.4-3.8; p < 0.0001). Of these 10 miRNAs, 7 were found to be risky miRNAs and 3 were found to be protective. This signature was independently validated in the testing set (HR = 1.7; 95% CI = 1.1-2.8; p = 0.002). GBM patients with high risk scores had overall poor survival compared to the patients with low risk scores. Overall survival among the entire patient set was 35.0% at 2 years, 21.5% at 3 years, 18.5% at 4 years and 11.8% at 5 years in the low risk group, versus 11.0%, 5.5%, 0.0 and 0.0% respectively in the high risk group (HR = 2.0; 95% CI = 1.4-2.8; p < 0.0001). Cox multivariate analysis with patient age as a covariate on the entire patient set identified risk score based on the 10 miRNA expression signature to be an independent predictor of patient survival (HR = 1.120; 95% CI = 1.04-1.20; p = 0.003). Thus we have identified a miRNA expression signature that can predict GBM patient survival. These findings may have implications in the understanding of gliomagenesis, development of targeted therapy and selection of high risk cancer patients for adjuvant therapy.

Molecular evolution of a primate-specific microRNA family

Lineage-specific microRNA (miRNA) families may contribute to developmental novelties during evolution. However, little is known about the origin and evolution of new miRNA families. We report evidence of an Alu-mediated rapid expansion of miRNA genes in a

Diversity and evolution of MicroRNA gene clusters

microRNA (miRNA) gene clusters are a group of miRNA genes clustered within a proximal distance on a chromosome. Although a large number of miRNA clusters have been uncovered in animal and plant genomes, the functional consequences of this arrangement are

大脑表达 miRNA 在大脑进化中的作用及其遗传机制初步研究

人类区别于其它动物的最本质特征是其拥有其他动物所无法比拟的大脑容量及高 级的认知能力。即使与其近亲－非人灵长类相比，人也拥有比非人灵长类大好几倍的脑 容量和更为发达的认知能力。现在一般认为，人类大脑的形成是适应性选择(达尔文正 选择)的结果。但是到目前为止，对人类起源过程中大脑容量增大及认知能力提高的遗 传学机制却知之甚少。以前的研究表明，几个与大脑发育相关的蛋白质编码基因在人类 起源中受到了正向选择。同时，也有证据表明人类大脑的进化也可能是基因表达调控变 化的结果。因此寻找人与非人灵长类大脑表达基因的调控差异或许能够进一步为人与非 人灵长类为何有如此巨大的差异提供分子生物学水平上的解释。 MicroRNA(miRNA)是一类在转录后水平调控基因表达的不编码蛋白质的小 RNA(长度20－24个碱基)。通过调控靶基因的表达，miRNA参与了众多的生理过程。而 很多大脑表达的miRNA的表达量在大脑发育过程中呈显著的变化，这表明miRNA参与 了大脑的发育调控。由此可知，miRNA对其靶基因调控效率的改变很可能引起大脑发育 调控的改变。 本文通过寻找大脑表达的保守microRNA 及对其靶基因的预测，同时用比较基因组 学的方法发现：有很多microRNA 的靶基因3’UTR 的靶位点中存在人类特异突变位点。 我们推测这些人类特异突变位点可能改变microRNA 对其靶基因的表达调控效应，而调 控效应的改变可能在进化过程中对认知能力的提高发挥重要作用。利用体外报告基因系 统，我们发现有几个预测的靶基因是对应miRNA 的真实靶基因。其中，miR-127 的靶 基因（SEMA3F）3’UTR 的靶位点中所含的一个人类特有的突变增强了miR-127 对 SEMA3F 的调控效率。将该位点突变回复为黑猩猩的位点使得miR-127 对SEMA3F 的 调控效率降低到黑猩猩的水平。这表明miR-127 对SEMA3F 的调控效率的改变确实是 由该人类特异突变位点引起的。我们提供了人类特异突变位点能够引起miR-127 对SEMA3F 的调控效率的改变的体外证据，但是体内的调控模式是否如此尚需进一步的工 作。 总之，本文通过体外试验表明，miRNA靶基因3’UTR的序列变异具有功能效应，它 有可能是人类中枢神经系统在起源和演化中发挥关键作用的重要遗传机制之一。

MicroRNA发现的研究现状及重离子辐照相关应用前景

MicroRNA(miRNA)是一类大小为19—24个核苷酸的非编码RNA,它们通过与靶基因的信使RNA(mRNA)结合在转录后水平调节靶基因的表达,因而在广泛的生物学过程中发挥重要作用。首先从miRNA的获得和鉴定两方面对目前miRNA发现工作进行了概括,然后分析和总结了近年来人源miRNA发现工作的现状,最后提出有关新miRNA发现工作的新想法。

MicroRNA 203 Expression in Keratinocytes Is Dependent on Regulation of p53 Levels by E6.

A screen of microRNA (miRNA) expression following differentiation in human foreskin keratinocytes (HFKs) identified changes in several miRNAs, including miRNA 203 (miR-203), which has previously been shown to play an important role in epithelial cell biology by regulating p63 levels. We investigated how expression of human papillomavirus type 16 (HPV16) oncoproteins E6 and E7 affected miR-203 expression during proliferation and differentiation of HFKs. We demonstrated that miR-203 expression is reduced in HFKs where p53 function is compromised, either by the viral oncoprotein E6 or by knockout of p53 using short hairpin RNAs (p53i). We show that the induction of miR-203 observed during calcium-induced differentiation of HFKs is significantly reduced in HFKs expressing E6 and in p53i HFKs. Induction of miR-203 in response to DNA damage is also reduced in the absence of p53. We report that proliferation of HFKs is dependent on the level of miR-203 expression and that overexpression of miR-203 can reduce overproliferation in E6/E7-expressing and p53i HFKs. In summary, these results indicate that expression of miR-203 is dependent on p53, which may explain how expression of HPV16 E6 can disrupt the balance between proliferation and differentiation, as well as the response to DNA damage, in keratinocytes.

MicroRNA-130b regulates the tumour suppressor RUNX3 in gastric cancer

Aim: Accumulating evidence indicates that RUNX3 is an important tumour suppressor that is inactivated in many cancer types. This study aimed to assess the role of microRNA (miRNA) in the regulation of RUNX3.

MicroRNA-155 Promotes Resolution of Hypoxia-Inducible Factor 1{alpha} Activity

The hypoxia-inducible factor (HIF) is a key regulator of the transcriptional response to hypoxia. While the mechanism underpinning HIF activation is well understood, little is known about its resolution. Both the protein and the mRNA levels of HIF-1a (but not HIF-2a) were decreased in intestinal epithelial cells exposed to prolonged hypoxia. Coincident with this, microRNA (miRNA) array analysis revealed multiple hypoxia-inducible miRNAs. Among these was miRNA-155 (miR-155), which is predicted to target HIF-1a mRNA. We confirmed the hypoxic upregulation of miR-155 in cultured cells and intestinal tissue from mice exposed to hypoxia. Furthermore, a role for HIF-1a in the induction of miR-155 in hypoxia was suggested by the identification of hypoxia response elements in the miR-155 promoter and confirmed experimentally. Application of miR-155 decreased the HIF-1a mRNA, protein, and transcriptional activity in hypoxia, and neutralization of endogenous miR-155 reversed the resolution of HIF-1a stabilization and activity. Based on these data and a mathematical model of HIF-1a suppression by miR-155, we propose that miR-155 induction contributes to an isoform-specific negative-feedback loop for the resolution of HIF-1a activity in cells exposed to prolonged hypoxia, leading to oscillatory behavior of HIF-1a-dependent transcription.

Enoxacin inhibits growth of prostate cancer cells and effectively restores microRNA processing

Prostate cancer (PCa) is one of the most incident malignancies worldwide. Although efficient therapy is available for early-stage PCa, treatment of advanced disease is mainly ineffective and remains a clinical challenge. microRNA (miRNA) dysregulation is associated with PCa development and progression. In fact, several studies have reported a widespread downregulation of miRNAs in PCa, which highlights the importance of studying compounds capable of restoring the global miRNA expression. The main aim of this study was to define the usefulness of enoxacin as an anti-tumoral agent in PCa, due to its ability to induce miRNA biogenesis in a TRBP-mediated manner. Using a panel of five PCa cell lines, we observed that all of them were wild type for the TARBP2 gene and expressed TRBP protein. Furthermore, primary prostate carcinomas displayed normal levels of TRBP protein. Remarkably, enoxacin was able to decrease cell viability, induce apoptosis, cause cell cycle arrest, and inhibit the invasiveness of cell lines. Enoxacin was also effective in restoring the global expression of miRNAs. This study is the first to show that PCa cells are highly responsive to the anti-tumoral effects of enoxacin. Therefore, enoxacin constitutes a promising therapeutic agent for PCa.

microRNA evaluation of unknown primary lesions in the head and neck

Unknown primary malignancy in the head and neck is not an infrequent diagnosis for patients with metastatic cervical lymph nodes. Although linked with a relatively good prognosis following radiation treatment, widespread radiation is coupled with significant morbidity. Altered microRNA (miRNA) expression has been associated with both cancer progression and metastasis. We sought to determine whether miRNA expression analysis could be used as a diagnostic tool to discover the primary site of malignancy, within the head and neck. We used quantitative real-time PCR to identify miRNA expression profiles of squamous cell carcinoma of the tonsil, base of tongue and post-nasal space, as well as their corresponding metastatic lymph nodes, from 6 patients. Our results revealed that each cancer maintained its expression profile between the primary site and the nodal metastasis (r = 0.82, p < 0.0001). In addition, each anatomical sub-site maintained a distinct miRNA profile between individual patients (r = 0.79, p < 0.0001). Finally, between sub-sites, the miRNA profiles were distinct (p < 0.0001). As proof of principle, our study provides an indication that miRNA expression analysis may be useful to compare the primary lesion and local metastatic disease. This may be clinically relevant to predict the primary site of origin of metastatic disease, when the primary site remains obscure.

Sarcoma histiocítico: análise molecular pela técnica de hibridação genômica comparativa, microRNA e imunoistoquímica

Pós-graduação em Patologia - FMB

Swimming Training in Rats Increases Cardiac MicroRNA-126 Expression and Angiogenesis

DA SILVA, N. D. JR, T. FERNANDES, U. P. R. SOCI, A. W. A. MONTEIRO, M. I. PHILLIPS, and E. M. DE OLIVEIRA. Swimming Training in Rats Increases Cardiac MicroRNA-126 Expression and Angiogenesis. Med. Sci. Sports Exerc., Vol. 44, No. 8, pp. 1453-1462, 2012. Purpose: MicroRNA (miRNA)-126 is angiogenic and has two validated targets: Sprouty-related protein 1 (Spred-1) and phosphoinositol-3 kinase regulatory subunit 2 (PI3KR2), negative regulators of angiogenesis by VEGF pathway inhibition. We investigated the role of swimming training on cardiac miRNA-126 expression related to angiogenesis. Methods: Female Wistar rats were assigned to three groups: sedentary (S), training 1 (T1, moderate volume), and training 2 (T2, high volume). T1 consisted of 60 min.d(-1) of swimming, five times per week for 10 wk with 5% body overload. T2 consisted of the same protocol of T1 until the eighth week; in the ninth week, rats trained for two times a day, and in the 10th week, rats trained for three times a day. MiRNA and PI3KR2 gene expression analysis was performed by real-time polymerase chain reaction in heart muscle. We assessed markers of training, the cardiac capillary-fiber ratio, cardiac protein expression of VEGF, Spred-1, Raf-1/ERK 1/2, and PI3K/Akt/eNOS. Results: The cardiac capillary-fiber ratio increased in T1 (58%) and T2 (101%) compared with S. VEGF protein expression was increased 42% in T1 and 108% in T2. Cardiac miRNA-126 expression increased 26% (T1) and 42% (T2) compared with S, correlated with angiogenesis. The miRNA-126 target Spred-1 protein level decreased 41% (T1) and 39% (T2), which consequently favored an increase in angiogenic signaling pathway Raf-1/ERK 1/2. On the other hand, the gene expression of PI3KR2, the other miRNA-126 target, was reduced 39% (T1) and 78% (T2), and there was an increase in protein expression of components of the PI3K/Akt/eNOS signaling pathway in the trained groups. Conclusions: This study showed that aerobic training promotes an increase in the expression of miRNA-126 and that this may be related to exercise-induced cardiac angiogenesis, by indirect regulation of the VEGF pathway and direct regulation of its targets that converged in an increase in angiogenic pathways, such as MAPK and PI3K/Akt/eNOS.

Studio dei profili di espressione dei microRNA nell'epatocarcinoma umano

Il carcinoma epatocellulare (HCC) è il più frequente tumore maligno del fegato e rappresenta il sesto tipo di tumore più comune nel mondo. Spesso i pazienti con HCC vengono diagnosticati a stadi piuttosto avanzati, quando le uniche opzioni terapeutiche in grado di migliorarne la sopravvivenza sono la chemoembolizzazione dell'arteria epatica ed il trattamento con l'inibitore multi-cinasico, Sorafenib. In questo contesto, la scoperta del ruolo centrale dei microRNA (miRNA) nella tumorigenesi umana risulta di fondamentale importanza per lo sviluppo di nuovi marcatori diagnostici e bersagli terapeutici. I microRNA (miRNA) sono delle piccole molecole di RNA non codificante, della lunghezza di 19-22 nucleotidi, filogeneticamente molto conservati, ed esercitano un ruolo cruciale nella regolazione di importanti processi fisiologici, quali sviluppo, proliferazione, differenziamento, apoptosi e risposta a numerosi segnali extracellulari e di stress. I miRNA sono inoltre responsabile della fine regolazione dell'espressione di centinaia di geni bersaglio attraverso il blocco della traduzione o la degradazione dell'mRNA target. Studi di profiling hanno evidenziato l'espressione aberrante di specifici miRNA in numerosi tipi di tumore umano. Lo scopo del presente lavoro è stato quello di individuare un pannello di miRNA deregolati nell'epatocarcinoma umano e di caratterizzare il ruolo biologico di tre miRNA deregolati nell'HCC, al fine di individuare alcuni dei meccanismi molecolari alla base della trasformazione maligna miRNA-associata. La nostra ricerca è stata inoltre focalizzata nell'individuazione di nuovi bersagli e strumenti terapeutici, quali i microRNA, per il trattamento combinato di HCC in stadio intermedio-avanzato.