Comparing RNA extraction methods to face the variations in RNA quality using two human biological matrices

BACKGROUND

Nucleic acids, RNA among them, are widely used in biomedicine and Biotechnology. Because of their susceptibility to degradation by RNases, the handling and extraction process of RNA from cells and tissues require specialized personnel and standardized methods to guarantee high purity and integrity. Due to the diversity of techniques found in the market, a comparative study between different RNA extraction methods is useful to facilitate the best choice for the researcher or in research service platforms such as biobanks to see the traceability of the samples.

METHODS AND RESULTS

In this study, we have compared seven different RNA extraction methods: manual (TRIzol™), semiautomated (QIAGEN™, Bio-Rad, Monarch®, and Canvax™), and fully automated (QIAcube™ and Maxwell®) processes, from two biological matrices: human Jurkat T cells and peripheral blood mononuclear cells (PBMC). Results showed marked differences in the RNA quality and functionality according to the method employed for RNA extraction and the matrix used.

DISCUSSION

QIAcube™ and semi-automated extraction methods were perceived as the best options because of their lower variability, good functionality, and lower cost (P < 0.001). These data contribute to facilitating researchers or research service platforms (Biobanks) in decision-making practices and emphasize the relevance of the selection of the RNA extraction method in each experimental procedure or traceability study to guarantee both quality standards and its reproducibility.

Measurement of yield and quality of DNA in human buffy coat is extraction method dependent

During the last few years, an important element in the improvement of the molecular biology techniques has been the necessity for availability of high quality and functionality DNA. Several DNA extraction procedures with different results in both performance and quality, have been proposed. In this study our objective was to determine the most reliable extraction method that balances DNA quantity, and to assess the sample quantification of the fluorometric DNA quantification methods. For this, blood extracted by venopunction from 20 healthy volunteers was used to obtain DNA from buffy coat, and 4 commercial DNA extraction kits were assessed as well as two fluorometric DNA quantification methods with protocols of different complexity. Results suggest that manual methods achieve higher quality and larger yields of DNA. DNA purity obtained with the 4 extraction kits evaluated through the 260/280 and 260/230 ratio showed that the Qiacube kit fulfilled the criteria established in this work, followed very close by the Flexigene kit. On the other hand, the fluorometric DNA methods used in the samples quantification showed a higher variability when using QuantiFlour method, obtaining better results probably due to the simplicity of this protocol.

Quality assessment on the long-term cryopreservation and nucleic acids extraction processes implemented in the andalusian public biobank

Human samples are commonly collected and long-term stored in biobanks for current and future analyses. Even though techniques for freezing human blood are well established, the storage time can compromise the cell viability as well as the yield and quality of nucleic acids (RNA and DNA) extracted from them. In this study, a protocol to obtain peripheral blood mononuclear cells (PBMCs) from 70 subjects, which were stored at - 196 °C from EDTA tubes for a long-term, was assessed. In parallel; a protocol to obtain DNA from the same subjects, which were stored at - 80 °C from citrate tubes, was also studied. Samples stored from 2008 to 2012 were studied and the results obtained showed that there were no statistically significant differences in the RNA or DNA extracted in terms of purity, integrity and functionality The freezing protocol used by the Málaga Biobank shows that viable PBMCs and DNA could be kept for a period of, at least, 10 years, with a high quality and performance. Furthermore, RNA extracted from these PBMCs presents also a good quality and performance. Therefore, the samples frozen according to the conditions of the protocols assessed in this study could be optimal for biomedical research.

Neutralizing antibodies against IFN beta in patients with multiple sclerosis: a comparative study of two cytopathic effect tests (CPE) for their detection

Neutralizing antibodies (NABs) against IFN beta should be measured in specialized laboratories, using a test of inhibition of the cytopathic effect (bioassay or CPE test), based on the capacity of IFNss to block the infection of live monolayer-cultured cells by a virus, depending on the presence or absence of NABs. The European Federation of Neurological Societies (EFNS) considers this assay to be the gold standard. However, the various different ways to perform this assay complicate comparison of the results between laboratories. The World Health Organization (WHO) has published several recommendations to perform this assay using the A549 cell line and the murine encephalomyocarditis virus (EMCV). In order to validate the results previously obtained in our laboratory with HEP2/VSV, we undertook a comparative analysis of the two bioassays, HEP2/VSV and A549/EMCV, to assess whether the use of different cell lines and viruses influences sensitivity. We also calibrated the A549/EMCV assay with a reference IFNss. Our results confirm that the bioassay with HEP2/VSV is as sensitive as the assay with A549/EMCV and that a significant association and correlation exist in the results between both assays. Thus, past results with HEP2/VSV in our laboratory could be comparable with those obtained with A549/EMCV in both our laboratory and others.