Major regulators of the multi-step metastatic process are potential therapeutic targets for breast cancer management.

Metastasis is a multi-step process that leads to the dissemination of tumor cells to new sites and, consequently, to multi-organ neoplasia. Although most lethal breast cancer cases are related to metastasis occurrence, little is known about the dysregulation of each step, and clinicians still lack reliable therapeutic targets for metastasis impairment. To fill these gaps, we constructed and analyzed gene regulatory networks for each metastasis step (cell adhesion loss, epithelial-to-mesenchymal transition, and angiogenesis). Through topological analysis, we identified E2F1, EGR1, EZH2, JUN, TP63, and miR-200c-3p as general hub-regulators, FLI1 for cell-adhesion loss specifically, and TRIM28, TCF3, and miR-429 for angiogenesis. Applying the FANMOD algorithm, we identified 60 coherent feed-forward loops regulating metastasis-related genes associated with distant metastasis-free survival prediction. miR-139-5p, miR-200c-3p, miR-454-3p, and miR-1301-3p, among others, were the FFL's mediators. The expression of the regulators and mediators was observed to impact overall survival and to go along with metastasis occurrence. Lastly, we selected 12 key regulators and observed that they are potential therapeutic targets for canonical and candidate antineoplastics and immunomodulatory drugs, like trastuzumab, goserelin, and calcitriol. Our results highlight the relevance of miRNAs in mediating feed-forward loops and regulating the expression of metastasis-related genes. Altogether, our results contribute to understanding the multi-step metastasis complexity and identifying novel therapeutic targets and drugs for breast cancer management.

MIR146A and ADIPOQ genetic variants are associated with birth weight in relation to gestational age: a cohort study.

PURPOSE: To evaluate the genetic variants related to polycystic ovary syndrome (PCOS) and its metabolic complications in girls born small for gestational age (SGA). DESIGN: Retrospective birth cohort study. MATERIALS AND METHODS: We evaluated 66 women of reproductive age born at term (37-42 weeks of gestational age) according to the birth weight in relation to gestational age: 26 SGA and 40 AGA (Adequate for gestational age). Anthropometric and biochemical characteristics were measured, as well as the PCOS prevalence. We analyzed 48 single nucleotide polymorphisms (SNPs) previously associated with PCOS and its comorbidities using TaqMan Low-Density Array (TLDA). miRNet and STRING databases were used to predict target and disease networks. RESULTS: Anthropometric and biochemical characteristics did not differ between the SGA and AGA groups, as well as insulin resistance and PCOS prevalence. Two SNPs were not in Hardy-Weinberg equilibrium, the rs2910164 (MIR146A C > G) and rs182052 (ADIPOQ G > A). The rs2910164 minor allele frequency (MAF) was increased in SGA (OR, 2.77; 95%; CI, 1.22-6.29), while the rs182052 was increased AGA (OR, 0.34; 95%; CI, 0.13 - 0.88). The alleles related to reduced miRNA-146a (C) and ADIPOQ (A) activity showed increased frequency in SGA. The mature miR-146a targets 319 genes, been the CXCR4, TMEM167A and IF144L common targets and contributes to PCOS. The ADIPOQ main protein interactions were ERP44, PPARGCIA and CDH13. CONCLUSIONS: The miR-146a (rs2910164) and ADIPOQ (rs182052) allelic variants are related to birth weight in SGA and may predict health-related outcomes, such as PCOS and obesity risk.

Micro-RNAs 518d-3p and 618 Are Upregulated in Individuals With Type 1 Diabetes With Multiple Microvascular Complications.

Objective: To compare the serum micro-RNAs (miRNAs) profile of individuals with type 1 diabetes without microvascular complications vs. those with multiple severe microvascular complications, in order to identify epigenetically modulated pathways in these two groups of individuals. Research Design and Methods: A total of 10 subjects were selected among individuals followed in the Diabetes Outpatient Clinic and sorted according to the absence or presence of all microvascular complications. Samples from these participants were used for evaluation of serum miRNA expression profile employing a qRT-PCR assay with hydrolysis probes based on the Taqman Low Density Arrays (TLDA) system. The top six most differentially expressed miRNAs between the aforementioned groups were validated by qRT-PCR in additional 47 type 1 diabetes individuals sorted according to the absence or presence of all microvascular complications and matched for age, sex, degree of metabolic control, diabetes duration, and age at diagnosis. Results: Twenty one out of three hundred and seventy seven miRNAs were upregulated in the group of individuals with all microvascular complications vs. the group without complications. The following miRs were validated: 518-3p, 34a-5p, 126-5p, 425-5p, 618, and 139-5p and logistic regression analyses showed that miRNA-518-3p and miRNA-618 were positively associated with multiple microvascular complications after adjustment for age, sex, diabetes duration, HbA1c and use of statin, angiotensin-converting enzyme inhibitors and amlodipine. Conclusions: In this cohort of type 1 diabetes individuals, serum miR-518d-3p and miR-618 were upregulated in those with diabetes kidney disease, diabetes retinopathy, peripheral neuropathy, and cardiovascular autonomic neuropathy in comparison to individuals with no microvascular complications.

Role of miRNAs on the Pathophysiology of Cardiovascular Diseases / Papel dos miRNAs na Fisiopatologia das Doenças Cardiovasculares

Abstract MiRNA (or microRNA) is a subclass of non-coding RNAs that is responsible for post-transcriptional gene regulation. It has approximately 22 nucleotides and regulates gene expression in plants and animals at the post-transcriptional level, by the cleavage of a target mRNA or by suppression of its translation. Although many of the processes and mechanisms have not yet been fully elucidated, there is a strong association between miRNA expression and several diseases. It is known that miRNAs are expressed in the cardiovascular system, but their role in cardiovascular diseases (CVDs) has not been clearly established. In this non-systematic review of the literature, we first present the definition of miRNAs and their action at the cellular level. Afterward, we discuss the role of miRNAs as circulating biomarkers of CVDs, and then their role in cardiac remodeling and atherosclerosis. Despite the complexity and challenges, it is crucial to identify deregulated miRNAs in CVDs, as it allows a better understanding of underlying cellular and molecular mechanisms and helps in the development of more accurate diagnostic and prognostic circulating biomarkers, and new therapeutic strategies for different stages of CVDs.

Resumo O miRNA (ou microRNA) constitui uma subclasse de RNAs não codificantes responsáveis pela regulação gênica pós-transcricional. Ele possui aproximadamente 22 nucleotídeos e regula a expressão gênica em plantas e animais ao nível pós-transcricional, pela clivagem de um mRNA alvo ou da repressão de sua tradução. Embora muitos processos e mecanismos ainda não estejam completamente elucidados, existe uma forte associação entre a expressão de miRNAs e diversas doenças que acometem o organismo. Os miRNAs são expressos no sistema cardiovascular, contudo o seu papel no desenvolvimento das doenças cardiovasculares (DCVs) ainda não está totalmente elucidado. Diante disso, realizou-se uma revisão não sistemática da literatura a fim de se discutir a relação entre os miRNAs e as DCVs. Nesta revisão, primeiramente é discutido o que são os miRNAs e a sua ação a nível celular. Após, é discutido o papel dos miRNAs como biomarcadores circulantes de DCVs e então o seu papel no remodelamento cardíaco e na aterosclerose. Apesar da complexidade e dos desafios, a identificação dos miRNAs desregulados nas DCVs é crucial, uma vez que possibilita uma melhor compressão dos mecanismos celulares e moleculares envolvidos, assim como auxilia o desenvolvimento de marcadores circulantes de diagnóstico e prognóstico mais acurados e de novas estratégias terapêuticas para os diferentes estágios da DCV.

Measuring plasma levels of three microRNAs can improve the accuracy for identification of malignant breast lesions in women with BI-RADS 4 mammography.

A BI-RADS category of 4 from a mammogram indicates suspicious breast lesions, which require core biopsies for diagnosis and have an approximately one third chance of being malignant. Human plasma contains many circulating microRNAs, and variations in their circulating levels have been associated with pathologies, including cancer. Here, we present a novel methodology to identify malignant breast lesions in women with BI-RADS 4 mammography. First, we used the miRNome array and qRT-PCR to define circulating microRNAs that were differentially represented in blood samples from women with breast tumor (BI-RADS 5 or 6) in comparison to controls (BI-RADS 1 or 2). Next, we used qRT-PCR to quantify the level of this circulating microRNAs in patients with mammograms presenting with BI-RADS category 4. Finally, we developed a machine learning method (Artificial Neural Network - ANN) that receives circulating microRNA levels and automatically classifies BI-RADS 4 breast lesions as malignant or benign. We identified a minimum set of three circulating miRNAs (miR-15a, miR-101 and miR-144) with altered levels in patients with breast cancer. These three miRNAs were quantified in plasma from 60 patients presenting biopsy-proven BI-RADS 4 lesions. Finally, we constructed a very efficient ANN that could correctly classify BI-RADS 4 lesions as malignant or benign with approximately 92.5% accuracy, 95% specificity and 88% sensibility. We believe that our strategy of using circulating microRNA and a machine learning method to classify BI-RADS 4 breast lesions is a non-invasive, non-stressful and valuable complementary approach to core biopsy in women with BI-RADS 4 lesions.

Uso de micro RNA en el manejo de la insuficiencia cardiaca / Use of microRNAs in heart failure management

Resumen: La insuficiencia cardiaca (IC) es una enfermedad de alto impacto que afecta en gran medida a todas las poblaciones humanas, por lo que se ha hecho necesario el desarrollo de nuevas estrategias y métodos para manejarla. Entre estas encontramos a los microRNA, pequeños RNA no codificantes que regulan la expresión genética y que aparecen como una importante opción en el diagnóstico, pronóstico y tratamiento de esta patología. Resultados de múltiples investigaciones han establecido miRNA específicos como notorios biomarcadores de la IC, puesto que estos pueden ser aislados en fluidos corporales como la sangre y la cuantificación de sus niveles se puede correlacionar con la presencia, estado o características específicas de la enfermedad. Desde el punto de la terapéutica, por su importante rol en el control de la expresión génica y la homeostasis celular, se ha explorado su uso en la prevención o tratamiento de las características patológicas de la IC. Por ello, en esta revisión se busca mostrar la importancia de la investigación biomédica en el uso de miRNA como método para el manejo de la IC, mostrando la afectación de enfermedad en el mundo, aspectos importantes sobre la biología de los miRNA, así como avances en su uso como biomarcadores y dianas terapéuticas.

Abstract: Heart failure (HF) is a high impact disease that affects all human populations, demanding the development of new strategies and methods to manage this pathology. That's why microRNAs, small noncoding RNAs that regulate gene expression, appear as an important option in the diagnosis, prognosis and treatment of this disease. MiRNAs seems to have a future on HF handling, because can be isolated from body fluids such as blood, and changes in its levels can be associated with the presence, stage and specific disease features, which makes them an interesting option as biomarkers. Also, due to the important role of these molecules on regulation of gene expression and cell homeostasis, it has been explored its potential use as a therapeutic method to prevent or treat HF. That is why this review seeks to show the importance of biomedical research involving the use of miRNAs as a method to approach the HF, showing the impact of disease in the world, aspects of miRNAs biology, and their use as biomarkers and as important therapeutic targets.

[Use of microRNAs in heart failure management]. / Uso de micro RNA en el manejo de la insuficiencia cardiaca.

Heart failure (HF) is a high impact disease that affects all human populations, demanding the development of new strategies and methods to manage this pathology. That's why microRNAs, small noncoding RNAs that regulate gene expression, appear as an important option in the diagnosis, prognosis and treatment of this disease. MiRNAs seems to have a future on HF handling, because can be isolated from body fluids such as blood, and changes in its levels can be associated with the presence, stage and specific disease features, which makes them an interesting option as biomarkers. Also, due to the important role of these molecules on regulation of gene expression and cell homeostasis, it has been explored its potential use as a therapeutic method to prevent or treat HF. That is why this review seeks to show the importance of biomedical research involving the use of miRNAs as a method to approach the HF, showing the impact of disease in the world, aspects of miRNAs biology, and their use as biomarkers and as important therapeutic targets.

Vascular calcification in atherosclerosis: potential roles of macrophages and non-coding micro-RNAs / Calcificación vascular en aterosclerosis: posibles funciones de macrófagos y micro-ARNs no codificantes

Coronary heart disease, a leading cause of death in western societies, is caused by the presence of atherosclerotic plaques in the coronary arteries. Calcification is a frequent complication of atherosclerotic plaques, and often a contributing factor to their instability and rupture. Endothelial cells, smooth muscle cells and plaque macrophages, all contribute to the calcification process, which is reminiscent of that underlying bone formation. In particular, the role of macrophages in calcification has long been recognized, but whether or not distinct macrophage subsets ­v.g., M1 or inflammatory, and M2 or antinflammatory have specific functions in osteogenic signaling within the context of plaque calcification remains poorly understood. Over the past few years, accumulated evidence has revealed novel roles of non-coding micro-RNAs (miRs) in atherorelevant functions of macrophages and in mechanisms linked to macrophage divergence into different subtypes. In this article we discuss some salient findings on potential roles of miRs in vascular calcification, with focus on those miRs that have also been associated to macrophage differentiation, and speculate on their potential relation to M1 and M2 macrophages in the context of calcification of atherosclerotic plaques. (AU)

La enfermedad cardíaca coronaria, principal causa de muerte en occidente, es causada por la presencia de placas ateroscleróticas en las arterias coronarias. La presencia de depósitos de calcificación es una complicación frecuente de la placa, y puede contribuir a la inestabilidad y ruptura de la misma. El proceso de calcificación de la placa es similar al que ocurre en hueso, y contribuyen al mismo, mecanismos dependientes de células endoteliales, células musculares lisas y macrófagos, células que están presentes en todas las etapas de desarrollo de la placa aterosclerótica. El rol de los macrófagos en la calcificación de la placa se conoce desde hace tiempo, pero la contribución de los distintos tipos de macrófagos ­por ejemplo, M1 o tipo inflamatorio, y M2 o tipo antiinflamatorio a mecanismos de señalización osteogénica en dicho contexto aún no se conoce. Recientemente varios trabajos experimentales han revelado la existencia de nuevos roles de micro-ARNs no codificantes (miRs) en varias funciones de los macrófagos que son de relevancia en el proceso aterogénico, como así también en mecanismos relacionados a la diferenciación de macrófagos en subtipos específicos. En este artículo discutimos algunos de los hallazgos más importantes sobre posibles nuevos roles de miRs en calcificación vascular, poniendo énfasis en aquellos miRs que han sido también asociados a la diferenciación de macrófagos, y especulamos acerca de su posible relación con macrófagos M1 y M2 en el contexto de la calcificación de la placa aterosclerótica. (AU)

Identificação de RNAs longos não-codificadores de proteínas regulados por micro-RNAs / Identification of long non-protein coding RNAs regulated by micro-RNAs

Estudos recentes têm revelado que a maior parte dos transcritos gerados em células humanas é composta por RNAs não-codificadores de proteínas (ncRNAs). Uma parte desses ncRNAs compreende a classe de RNAs curtos, que possuem menos que 200 nucleotídeos. Os micro-RNAs (miRNAs) fazem parte dessa classe e têm sido alvo de grande interesse, pois são preditos como possíveis reguladores de mais de 60% dos RNAs mensageiros (mRNAs) humanos. Outra classe dos ncRNAs é composta por ncRNAs longos (lncRNAs, com mais de 200 nucleotídeos), que são transcritos a partir de regiões intergênicas e intrônicas do genoma humano e possuem várias funções, muitas delas relacionadas ao controle da expressão de mRNAs. Recentemente, os lncRNAs têm sido caracterizados quanto à sua estrutura e função. No entanto, muito pouco se sabe sobre os mecanismos pelos quais os lncRNAs são regulados. Este trabalho teve como objetivo avaliar se lncRNAs são regulados por miRNAs em células humanas. Para tanto, identificamos lncRNAs ligados ao complexo de silenciamento induzido por RNA (RISC) em células da linhagem HeLa, utilizando um método aqui desenvolvido de geração de bibliotecas de cDNA direcionadas para sequenciamento em larga escala na plataforma 454/Roche. Em paralelo, sequenciamos os miRNAs ligados ao RISC nestas mesmas células. Os resultados obtidos mostram que centenas de lncRNAs de diversas classes se ligam ao RISC em células HeLa, juntamente com milhares de mRNAs e várias centenas de miRNAs. Entre os miRNAs, encontramos 37 que são preditos como alvejando os lncRNAs detectados. Estes miRNAs constituem possíveis reguladores dos lncRNAs e, portanto, nosso trabalho estabelece um mapa experimental de interações diretas entre lncRNAs e miRNAs. Dentre os lncRNAs identificados ligados ao RISC neste trabalho, destaca-se o TUG1, lincRNA sabidamente envolvido na regulação de genes relacionados à apoptose e ao ciclo celular. Mostramos por ensaio de super-expressão de miRNAs e qPCR que TUG1 é regulado pelo miRNA-148b, um dos miRNAs por nós detectados que possui um sítio alvo altamente conservado em mamíferos localizado na extremidade 3' de TUG1. Em conjunto, este trabalho contribui para o entendimento da regulação dos níveis de expressão de lncRNAs em células humanas e abre perspectivas para a modulação de miRNAs como estratégia de regulação dos níveis e das funções de lncRNAs

Recent studies have revealed that the largest fraction of the transcripts generated in human cells is composed of non-protein coding RNAs (ncRNAs). A portion of these RNAs encompasses the class of short RNAs, which are less than 200 nucleotides in length. Micro-RNAs (miRNAs) are part of this class and are of great interest, as they are predicted to target over 60% of the human messenger RNAs (mRNAs). Another class of ncRNAs is composed of long ncRNAs (lncRNAs, longer than 200 nucleotides), which are transcribed from intergenic and intronic regions of the human genome and have several functions, many of them related to the control of the mRNA expression. Recently, the structure and function of lncRNAs have been characterized. However, little is known about the mechanisms involved in lncRNA regulation. This work aimed to evaluate whether lncRNAs are regulated by miRNAs in human cells. For this purpose, we identified lncRNAs bound to the RNA-induced silencing complex (RISC) in HeLa cells using a method developed here for the generation of strand-specific cDNA libraries for large scale RNA-sequencing in the 454/Roche plataform. In parallel, we sequenced the miRNAs bound to RISC in these cells. Our results show that hundreds of lncRNAs from diverse classes are bound to RISC in HeLa cells, along with thousands of mRNAs and several hundred miRNAs. Among the miRNAs we identified 37 that are predicted to target the detected lncRNAs. These miRNAs are possible regulators of the lncRNAs, and therefore our work establishes an experimental map of direct interactions between lncRNAs and miRNAs. The lncRNA TUG1, a lincRNA involved in the regulation of genes related to apoptosis and cell cycle, was identified among the lncRNAs bound to RISC. We showed by miRNA over-expression and qPCR that TUG-1 is regulated by the miRNA-148b, which is one of the miRNAs detected in our sequencings and has a binding site highly conserved in mammals located at the TUG1 3` end. Taken together, our results contribute to the understanding of the regulation of the lncRNA expression levels in human cells and open perspectives for the modulation of miRNAs as a strategy to regulate the levels and functions of lncRNAs

Análise de expressão de micro RNA em carcinoma urotelial de bexiga / Analysis of micro RNA expression in bladder urothelial carcinoma

Introdução: O câncer de bexiga é a segunda neoplasia maligna mais frequente do trato urinário, com 386.000 casos estimados e 150.000 mortes para 2011 no mundo. Noventa e cinco por cento são carcinomas uroteliais (CUB) papilíferos não músculo-invasivos de baixo grau, que apresentam altas taxas de recidiva, mas raramente progridem. Tumores invasivos de alto grau representam 10-20% dos diagnósticos, são altamente agressivos levando à mortalidade elevada. O conhecimento das vias moleculares envolvidas na carcinogênese dessa neoplasia é importante para a identificação de novos marcadores para diagnóstico, acompanhamento, prognóstico e desenvolvimento de novas terapias alvo. Micro RNA (miRNA) são pequenas sequências não codificantes de RNA que regulam a expressão dos genes inibindo a tradução da proteína ou promovendo a degradação do RNA mensageiro, estando atualmente envolvidos em vários processos celulares fisiológicos e patológicos, incluindo o câncer. Objetivos: Caracterizar o perfil de expressão de miRNA no CUB, relacionando-o com os parâmetros prognósticos clássicos para a doença: grau histológico e estadiamento. Além disso, relacionar esse padrão de comportamento dos miRNA com a recidiva tumoral e sobrevida câncer-específica em pacientes tratados cirurgicamente para CUB. Material e Métodos: Catorze miRNA (miR-100, miR-10a, miR-21, miR-205, miR-let7c, miR- 125b, miR-143, miR-145, miR-221, miR-223, miR-15a, miR-16-1, miR-199a e miR- 452) foram isolados de espécimes cirúrgicos de 60 pacientes divididos em 2 grupos: 30 pacientes com CUB não invasivo (pTa) de baixo grau submetidos à RTU de bexiga, 30 com CUB invasivo (pT2-3) de alto grau submetidos à cistectomia radical. O grupo controle é representado por cinco pacientes portadores de bexiga normal sem CUB que realizaram tratamento cirúrgico aberto para tratamento da hiperplasia prostática benigna (HPB). O processamento dos miRNA envolveu três fases: (1) extração do miRNA com kit específico, (2) geração do DNA...

Introduction: Bladder cancer (BC) is the second most common malignancy of the urinary tract, with 386,000 cases estimated and 150,000 deaths in 2011. Urothelial carcinomas (UC) represent 95% of BC cases, and knowledge of the molecular pathways associated with BC carcinogenesis is crucial to identify new diagnostic and prognostic biomarkers, and development of new target molecular therapies. MicroRNAs (miRNAs) are short non-coding RNA molecules that play important roles in the regulation of gene expression by acting directly on mRNAs, leading to either mRNA degradation or inhibition of translation, involved in many physiological and pathological processes, including cancer. Objectives: To characterize miRNAs expression profiles in UC, associating with classic prognostic factors: grade and stage. Moreover, correlate miRNA expression with tumor recurrence and survival. Material and Methods: Fourteen miRNAs (miR-100, miR-10a, miR-21, miR-205, miR-let7c, miR-125b, miR-143, miR-145, miR-221, miR-223, miR-15a, miR-16-1, miR- 199a e miR-452) were isolated from surgical specimens from 60 patients classified in two groups: 30 patients with low-grade non-invasive pTa UC that underwent TURB, 30 with high-grade invasive pT2/pT3 UC underwent radical cystectomy. The control group consists in five normal bladder tissue taken from patients that underwent retropubic prostatectomy to treat benign prostatic hyperplasia (BPH). miRNA processing involved three phases: (1) miRNA extraction by specific kits, (2) cDNA generation (3) miRNA amplification through qRT-PCR. Expression profiles were obtained by relative quantification determined by 2-ct method. Endogenous control were RNU-43 and RNU-48. Statistic tests were used to study the prognostic variables and Kaplan-Meyer curves were constructed to analyze disease-free (DFS) and disease-specific (DSS) survivals. Results: All miRNAs were underexpressed in both groups, except miR-10a in pTa and miR-100, 21 and 205 in pT2/pT3 tumors...