Dmitry Ter-Ovanesyan

Highly efficient Cas9-mediated transcriptional programming

The RNA-guided nuclease Cas9 can be reengineered as a programmable transcription factor. However, modest levels of gene activation have limited potential applications. We describe an improved transcriptional regulator obtained through the rational design of a tripartite activator, VP64-p65-Rta (VPR), fused to nuclease-null Cas9. We demonstrate its utility in activating endogenous coding and noncoding genes, targeting several genes simultaneously and stimulating neuronal differentiation of human induced pluripotent stem cells (iPSCs).

ISEV position paper: extracellular vesicle RNA analysis and bioinformatics

Extracellular vesicles (EVs) are the collective term for the various vesicles that are released by cells into the extracellular space. Such vesicles include exosomes and microvesicles, which vary by their size and/or protein and genetic cargo. With the discovery that EVs contain genetic material in the form of RNA (evRNA) has come the increased interest in these vesicles for their potential use as sources of disease biomarkers and potential therapeutic agents. Rapid developments in the availability of deep sequencing technologies have enabled the study of EV-related RNA in detail. In October 2012, the International Society for Extracellular Vesicles (ISEV) held a workshop on “evRNA analysis and bioinformatics.” Here, we report the conclusions of one of the roundtable discussions where we discussed evRNA analysis technologies and provide some guidelines to researchers in the field to consider when performing such analysis.

High‐Throughput Multiplex Sequencing of miRNA

Next-generation sequencing offers many advantages over other methods of microRNA (miRNA) expression profiling, such as sample throughput and the capability to discover novel miRNAs. As the sequencing depth of current sequencing platforms exceeds what is necessary to quantify miRNAs, multiplexing several samples in one sequencing run offers a significant cost advantage. Although previous studies have achieved this goal by adding bar codes to miRNA libraries at the ligation step, this was recently shown to introduce significant bias into the miRNA expression data. This bias can be avoided, however, by bar coding the miRNA libraries at the PCR step instead. Here, we describe a user-friendly PCR bar-coding method of preparing multiplexed microRNA libraries for Illumina-based sequencing. The method also prevents the production of adapter dimers and can be completed in one day.

Extracellular Vesicle Isolation and Analysis by Western Blotting

Extracellular vesicles (EVs) are released by mammalian cells and are thought to be important mediators of intercellular communication. There are many methods for isolating EVs from cell culture media, but the most popular methods involve purification based on ultracentrifugation . Here, we provide a detailed protocol for isolating EVs by differential ultracentrifugation and analyzing EV proteins (such as the tetraspanins CD9 , CD63 and CD81 ) by western blotting.

UK–Russia Researcher Links Workshop: extracellular vesicles – mechanisms of biogenesis and roles in disease pathogenesis, M.V. Lomonosov Moscow State University, Moscow, Russia, 1–5 March 2015

The UK–Russia extracellular vesicles (EVs) workshop was held at the Medical Center of the M.V. Lomonosov Moscow State University, Moscow, Russia, with 56 attendees from UK and Russian universities and research institutes. The program consisted of 6 research sessions and was focused on studies of EVs isolated from in vitro model systems or biological fluids, including blood and urine. The multidisciplinary program included presentations on mechanisms of EV biogenesis, the role of EVs in disease pathogenesis, the diagnostic value of EVs, including their quantitation and cargo load, as well as the clinical use of EVs in regenerative medicine. Methodological challenges imposed by the nanoscale size of EVs as well as targeted delivery approaches for therapeutics were considered in a separate session on technologies. The main aim of the workshop was to overview challenges confronting EV researchers and to facilitate knowledge exchange between researchers with different backgrounds and skills. Given the lack of definitive EV nomenclature, specific terms (exosomes or microvesicles) were only applied in the meeting report to studies that carried out full EV characterization, including differential ultracentrifugation isolation approaches, comprehensive protein marker characterization, and single vesicle analysis (electron microscopy and nanoparticle analysis), to ascertain EV size and morphology following the International Society for Extracellular Vesicles standardization recommendations (1,2). In studies where characterization was not conclusive, the term EV is used.

Imaging of Isolated Extracellular Vesicles Using Fluorescence Microscopy

High-resolution fluorescence microscopy approaches enable the study of single objects or biological complexes. Single object studies have the general advantage of uncovering heterogeneity that may be hidden during the ensemble averaging which is common in any bulk conventional biochemical analysis. The implementation of single object analysis in the study of extracellular vesicles (EVs) may therefore be used to characterize specific properties of vesicle subsets which would be otherwise undetectable. We present a protocol for staining isolated EVs with a fluorescent lipid dye and attaching them onto a glass slide in preparation for imaging with total internal reflection fluorescence microscopy (TIRF-M) or other high-resolution microscopy techniques.