Month: December 2015

Non-coding RNAs (ncRNAs), for example microRNAs (miRNAs), are frequently dysregulated in cancer and other diseases, and have shown great potential as tissue-based markers for cancer classification and prognostication. ncRNAs are present in membrane-bound vesicles, such as exosomes, in extracellular human body fluids. Circulating miRNAs are also present in human plasma and serum and cofractionate with the Argonaute2 (Ago2) protein and high-density lipoprotein (HDL). Since miRNAs and other ncRNAs circulate in the bloodstream in highly stable forms, they may be used as blood-based biomarkers for cancer and other diseases. A knowledge base of non-invasive biomarkers is a fundamental tool for biomedical research in this field.

In 2012, miRandola was developed as the first database of circulating extracellular miRNAs (Russo et al., 2012). miRandola is a comprehensive, manually curated collection and classification of circulating extracellular miRNAs. We recently updated miRandola with 271 papers, 2695 entries, 673 miRNAs and 12 long non-coding RNAs. The future direction of the database is to be a resource for all potential non-invasive circulating nucleic acid biomarkers.

miRandola_schema

miRandola is the first online resource which gathers all the available data on circulating RNAs into one environment (see Figure). It represents a useful reference tool for anyone investigating the role of extracellular RNAs as biomarkers, as well as their physiological function and their involvement in pathologies.

The database is constantly updated as soon as new data is available, and the online submission system is a crucial feature which helps to ensure that the system is always up-to-date. We are working on a second version of the database to increase the amount of data and to improve usability. miRandola is available online at http://mirandola.iit.cnr.it/.

The exRNA portal at WikiPathways continues to grow. It now includes 46 exRNA-related pathways, including 15 from publications by the Extracellular RNA Communication consortium. We are committed to capturing every published pathway figure from the consortium as a properly modeled pathway at WikiPathways. If your work involves pathways, especially if you are publishing it, then look into contributing to WikiPathways.

The latest pathways to be curated from consortium publications are

  • 1) EV release from cardiac cells and their functional effects (WP3297),
  • 2) the Rac1/Pak1/p38/MMP-2 pathway (WP3303),
  • 3) eIF5A regulation in response to inhibition of the nuclear export system (WP3302), and
  • 4) MFAP5-mediated ovarian cancer cell motility and invasiveness (WP3301).

The goal of the Wikipathways exRNA portal is to build a collection of pathway models for exRNA researchers to use for illustration, data visualization, and analysis. Each pathway is a self-contained data model that connects to identifier and annotation databases. In addition to providing static images for figures and presentations, these pathways can also be used by bioinformatics and network analysis packages such as Cytoscape and PathVisio. Furthermore, as a wiki, anyone can sign up to improve and grow the content. We invite you all to edit, fix, and add to the pathway models in the exRNA portal at WikiPathways.