miRNome landscape analysis reveals a 30 miRNA core in retinoblastoma.

BACKGROUND: miRNAs exert their effect through a negative regulatory mechanism silencing expression upon hybridizing to their target mRNA, and have a prominent position in the control of many cellular processes including carcinogenesis. Previous miRNA studies on retinoblastoma (Rb) have been limited to specific miRNAs reported in other tumors or to medium density arrays. Here we report expression analysis of the whole miRNome on 12 retinoblastoma tumor samples using a high throughput microarray platform including 2578 mature miRNAs. METHODS: Twelve retinoblastoma tumor samples were analyzed using an Affymetrix platform including 2578 mature miRNAs. We applied RMA analysis to normalize raw data, obtained categorical data from detection call values, and also used signal intensity derived expression data. We used Diana-Tools-microT-CDS to find miRNA targets and ChromDraw to map miRNAs in chromosomes. RESULTS: We discovered a core-cluster of 30 miRNAs that were highly expressed in all the cases and a cluster of 993 miRNAs that were uniformly absent in all cases. Another 1022 miRNA were variably present in the samples reflecting heterogeneity between tumors. We explored mRNA targets, pathways and biological processes affected by some of these miRNAs. We propose that the core-cluster of 30 miRs represent miRNA machinery common to all Rb, and affecting most pathways considered hallmarks of cancer. In this core, we identified miR-3613 as a potential and critical down regulatory hub, because it is highly expressed in all the samples and its potential mRNA targets include at least 36 tumor suppressor genes, including RB1. In the variably expressed miRNA, 36 were differentially expressed between males and females. Some of the potential pathways targeted by these 36 miRNAs were associated with hormonal production. CONCLUSION: These findings indicate that Rb tumor samples share a common miRNA expression profile regardless of tumor heterogeneity, and shed light on potential novel therapeutic targets such as mir-3613 This is the first work to delineate the miRNA landscape in retinoblastoma tumor samples using an unbiased approach.

Circulating miRNome detection analysis reveals 537 miRNAS in plasma, 625 in extracellular vesicles and a discriminant plasma signature of 19 miRNAs in children with retinoblastoma from which 14 are also detected in corresponding primary tumors.

miRNAs regulate post-transcriptional gene expression in metazoans, and thus are involved in many fundamental cellular biological processes. Extracellular miRNAs are also found in most human biofluids including plasma. These circulating miRNAs constitute a long distance inter cellular communication system and are potentially useful biomarkers. High throughput technologies like microarrays are able to scan a complete miRNome providing useful detection scores that are underexplored. We proposed to answer how many and which miRNAs are detectable in plasma or extracellular vesicles as these questions have not yet been answered. We set out to address this knowledge gap by analyzing the mirRNome in plasma and corresponding extracellular vesicles (EVs) from 12 children affected by retinoblastoma (Rb) a childhood intraocular malignant tumor, as well as from 12 healthy similarly aged controls. We calculated an average of 537 detectable miRNAs in plasma and 625 in EVs. The most miRNA enriched compartment were EVs from Rb cases with an average of 656 detectable elements. Using hierarchical clustering with the detection scores, we generated broad detection mirnome maps and identified a plasma signature of 19 miRNAs present in all Rb cases that is able to discriminate cases from controls. An additional 9 miRNAs were detected in all the samples; within this group, miRNA-5787 and miRNA-6732-5p were highly abundant and displayed very low variance across all the samples, suggesting both are good candidates to serve as plasma references or normalizers. Further exploration considering participant's sex, allowed discovering 5 miRNAs which corresponded only to females and 4 miRNAs corresponding only to males. Target and pathway analysis of these miRNAs revealed hormonal function including estrogen, thyroid signaling pathways and testosterone biosynthesis. This approach allows a comprehensive unbiased survey of a circulating miRNome landscape, creating the possibility to define normality in mirnomic profiles, and to locate where in these miRNome profiles promising and potentially useful circulating miRNA signatures can be found.

Aislamiento y caracterización celular de exosomas de plasma para su uso como biomarcadores de diagnóstico / Isolation and cellular characterization of exosomes from plasma for their use as diagnostic biomarkers / Purificação e caracterização celular de exossomos para seu uso como biomarcadores de diagnóstico

Los exosomas son vesículas membranosas extracelulares esenciales en la comunicación intercelular a larga distancia, viajan en los fluidos corporales y entregan mensajes moleculares dirigidos a la mayoría de las células de todo el organismo. La liberación de mensajes vía exosomas ocurre en forma de ADN, ARN o proteínas; dicha liberación se ha asociado a diferentes condiciones fisiológicas normales y patológicas, como el cáncer. Por lo anterior, el aislamiento eficiente y caracterización celular de exosomas de plasma es clave para su uso como biomarcadores no invasivos de diversas enfermedades. En el presente estudio se purificaron exosomas a partir de muestras clínicas de plasmas de pacientes previamente diagnosticados con retinoblastoma y de individuos sanos como control. Los exosomas recuperados fueron caracterizados a nivel celular por microscopia electrónica de transmisión empleando una técnica de criogenia. Para demostrar la correcta purificación de exosomas se confirmó la presencia de las proteínas transmembranales CD63 y CD81 mediante immunoblot. Adicionalmente de los exosomas purificados, se identificaron ARNs pequeños no codificantes llamados microARNs. En general, se describe la purificación y caracterización celular de exosomas obtenidos de plasma humano para su potencial uso como biomarcadores.

Exosomes are small extracellular vesicles essential in intercellular communication; they act as vehicles of broad scope. They are travelling in body fluids and delivering molecular messages to cells in the organism. Messages released by exosomes like DNA, RNA and proteins are associated with different pathological conditions including cancer. Therefore, the efficient isolation and cellular characterization of exosomes from plasma is essential to use them as biomarkers in many diseases. Here, exosomes were purified from patients diagnosed with pediatric cancer and healthy individuals as control. The exosomes recovered were characterized using cryogenic transmission electron microscopy. Moreover, the presence of CD63 and CD81 transmembrane proteins was confirmed using Western blot. Besides, miRNAs presence was identified from exosomes. This work describes a complete technique to isolate and characterize exosomes from human plasma, recognizing their potential as biomarkers.

Os exossomos são vesículas membranosas extracelulares essenciais na comunicação intercelular de longa distância; eles viajam em fluidos corporais e entregam mensagens moleculares dirigidas à maioria das células de todo o organismo. A liberação de mensagens através dos exossomos ocorre em forma de DNA, RNA ou proteínas; essa liberação foi associada a diferentes condições fisiológicas normais e patológicas, tais como o câncer. Por tudo isso, o eficiente isolamento e caracterização celular de exossomos de plasma é chave para sua utilização como biomarcadores não invasivos de várias doenças. No presente estudo, exossomos foram purificados a partir de amostras clínicas de plasmas de pacientes que tinham sido diagnosticados previamente com retinoblastoma e de indivíduos saudáveis como controle. Os exossomos recuperados foram caracterizados a nível celular por microscopia eletrônica de transmissão usando uma técnica de criogenia. Para demonstrar a correta purificação dos exossomos, foi confirmada a presença de proteínas transmembranares CD63 e CD81 usando inmunoblot. Além dos exossomos purificados foram identificados ARNs não codificantes pequenos chamados microARNs. Em geral os métodos de purificação e caracterização celular de exossomos obtidos de plasma humano são descritos por seu potencial utilização como biomarcadores.