Circulando MicroRNA Quantificação Usando DNA de ligação Dye Química e Gota Digital PCR
Summary
A sensitive and accurate method for cell-free microRNAs quantification using a dye-based chemistry and droplet digital PCR technology is described.
Abstract
Circulating (da isentos de células) microARNs (miARNs) são libertados a partir de células para a corrente sanguínea. A quantidade de microARNs específicos na circulação tem sido associada a um estado de doença e tem o potencial de ser utilizado como biomarcador da doença. Um método sensível e preciso para a circulação de microARN quantificação usando uma química à base de corantes e gota a tecnologia de PCR digital foi desenvolvido recentemente. Especificamente, utilizando Locked Nucleic Acid (LNA) à base de iniciadores específicos de miARN com um corante de ligação a ADN fluorescente verde num sistema de PCR compatível gota digital, é possível obter a quantificação absoluta de miARNs específicos. Aqui, nós descrevemos como realizar esta técnica para avaliar a quantidade de miARN em fluidos biológicos, tais como plasma e soro, é viável e eficaz.
Introduction
MicroRNAs (miRNAs) are released into blood circulation by potentially all the cells of the organism, as a consequence of active release or necrotic and apoptotic processes. Cell-free miRNAs have been detected in the bloodstream either as free stable molecules or linked to lipoproteins or enveloped inside exosomes and microvesicles 1-3. They are believed to function as cell-to-cell communicators 4, and their amount changes in the presence of cancer, cardiac disorders or autoimmune diseases 5-7. Their accurate and reproducible quantification is the basis for their evaluation as disease biomarkers. However, for several reasons already described elsewhere 8,9, miRNA quantification in serum or plasma, as well as other body fluids, could be very challenging 10,11. We recently developed a method for the absolute quantification of circulating miRNAs, based on miRNA-specific LNA primers and DNA-binding dye droplet digital PCR (ddPCR) technology 12. This methodology has been applied to the validation of miRNA breast cancer biomarkers 13,14.
After the partitioning of each reverse-transcribed miRNA molecule inside a nanoliter-sized droplet, it is possible to count the copy number of each miRNA in each sample, basically counting the number of green, and therefore positive, fluorescent droplets. As soon as a PCR reaction occurs, a positive count is achieved, without the need to establish a standard curve or taking PCR efficiency into account in target amount calculation, as it happens with quantitative RT-PCR (RT-qPCR). In addition, ddPCR proved to be more sensitive and accurate than RT-qPCR in circulating miRNA quantification 15. In this article we present the detailed protocol of this methodology, discussing the most relevant steps andspecifically considering serum and plasma clinical samples.
Protocol
Representative Results
Discussion
miARNs circulantes estão presentes no sangue em concentrações extremamente baixas e a quantidade de ARN que pode ser extraída a partir de amostras de plasma e soro é baixa. Por esta razão, eles são difíceis de quantificar com outras técnicas tais como a sequenciação de ARN e micro-arranjo. Além disso, há uma falta generalizada de acordo com a normalização de dados e a presença de miARNs endógenos de "referência" no sangue. Neste contexto, uma tecnologia de PCR sensíveis, como digitais gota, …
Divulgations
The authors have nothing to disclose.
Acknowledgements
Apoiado pelo financiamento da Associação Italiana de Investigação do Cancro (AIRC) para MF (MFAG 11676) e MN (Oncologia Clínica Programa Especial Molecular -. 5 por mille n 9980, 2010/15) e do Ministério Italiano da Instrução, da Universidade e FIRB Research 2011 para MN (Project RBAPIIBYNP).
Materials
| miRNeasy Mini Kit | Qiagen | 217004 | Columns for total RNA, including miRNA, extraction from serum/plasma |
| 100 nmole RNA oligo Cel-miR-39-3p | Integrated DNA Technologies | Custom | Sequence: UCACCGGGUGUAAAUCAGCUUG |
| Universal cDNA synthesis kit II, 8-64 rxns | Exiqon | 203301 | Kit for microRNA reverse transcription |
| MicroRNA LNA PCR primer set | Exiqon | 204000-206xxx and 2100000-21xxxxx | Primers for miRNA amplification inside droplets |
| QX200 droplet generator | BioRad | 186-4002 | Instrument used for droplet reading |
| QX200 droplet reader | BioRad | 186-4003 | Instrument used for droplet generation |
| QuantaSoft software | BioRad | 186-3007 | Software for data collection and analysis |
| PX1 PCR plate sealer | BioRad | 181-4000 | Plate sealer |
| DG8 droplet generator cartridges and gaskets | BioRad | 186-4008 | Cartridges used to mix sample and oil to generate droplets |
| QX200 ddPCR EvaGreen supermix | BioRad | 186-4033/36 | PCR supermix |
| QX200 droplet generator oil for EvaGreen dye | BioRad | 186-4005 | Oil for droplet generation |
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