Introduction Non-coding RNAs (ncRNAs) such as for example microRNAs (miRNAs) are frequently dysregulated in cancer 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 cofractionate with the Argonaute2 (Ago2) protein and the High-density lipoprotein (HDL). Since miRNAs and the other ncRNAs circulate in the bloodstream in a highly stable, extracellular 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. Material and method Data is manually collected from ExoCarta, a database of exosomal proteins, RNA and lipids and PubMed. Articles containing information on circulating miRNAs are collected by querying PubMed database using the keywords “microRNA”, “miRNA”, “extracellular” and “circulating”. Data is then manually extracted from the retrieved papers. General information about the miRNAs is obtained from miRBase. The aim of miRandola is to collect data concerning the miRNAs contained not only in exosomes but in all kind of circulating miRNAs functionally enriched with information such as their family, diseases, processes, functions, associated tissues, and their potential roles as biomarkers. Result and discussion Here, we present an updated version of the miRandola database, a comprehensive manually curated collection and classification of extracellular circulating miRNAs. miRandola contains 2366 entries, with 599 unique mature miRNAs and 23 types of samples, extracted from 139 papers. miRNAs are classified into four categories, based on their extracellular form: miRNA-Ago2 (173 entries), miRNA-exosome (862 entries), miRNA-HDL (20 entries) and miRNA-circulating (1311 entries). Moreover, the database contains several tools, allowing users to infer the potential biological functions of circulating miRNAs, their connections with phenotypes and the drug effects on cellular and extracellular miRNAs. Conclusion miRandola is the first online resource which gathers all the available data on circulating miRNAs in a unique environment. It represents a usufeul reference tool for anyone investigating the role of extracellular miRNAs as biomarkers as well as their physiological function and their involvement in pathologies. miRandola is constantly updated by the staff as soon as new data is available and the online submission system is a crucial feature which helps ensuring that the system is always up-to-date. The future direction of the database is to be a resource for all the potential non-invasive biomarkers such as lncRNAs, cell-free DNA and circulating tumor cells (CTCs). miRandola is available online at: http://atlas.dmi.unict.it/mirandola/
miRandola database: the future of non-invasive diagnosis through circulating miRNA biomarkers
GIUGNO, ROSALBA;
2015-01-01
Abstract
Introduction Non-coding RNAs (ncRNAs) such as for example microRNAs (miRNAs) are frequently dysregulated in cancer 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 cofractionate with the Argonaute2 (Ago2) protein and the High-density lipoprotein (HDL). Since miRNAs and the other ncRNAs circulate in the bloodstream in a highly stable, extracellular 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. Material and method Data is manually collected from ExoCarta, a database of exosomal proteins, RNA and lipids and PubMed. Articles containing information on circulating miRNAs are collected by querying PubMed database using the keywords “microRNA”, “miRNA”, “extracellular” and “circulating”. Data is then manually extracted from the retrieved papers. General information about the miRNAs is obtained from miRBase. The aim of miRandola is to collect data concerning the miRNAs contained not only in exosomes but in all kind of circulating miRNAs functionally enriched with information such as their family, diseases, processes, functions, associated tissues, and their potential roles as biomarkers. Result and discussion Here, we present an updated version of the miRandola database, a comprehensive manually curated collection and classification of extracellular circulating miRNAs. miRandola contains 2366 entries, with 599 unique mature miRNAs and 23 types of samples, extracted from 139 papers. miRNAs are classified into four categories, based on their extracellular form: miRNA-Ago2 (173 entries), miRNA-exosome (862 entries), miRNA-HDL (20 entries) and miRNA-circulating (1311 entries). Moreover, the database contains several tools, allowing users to infer the potential biological functions of circulating miRNAs, their connections with phenotypes and the drug effects on cellular and extracellular miRNAs. Conclusion miRandola is the first online resource which gathers all the available data on circulating miRNAs in a unique environment. It represents a usufeul reference tool for anyone investigating the role of extracellular miRNAs as biomarkers as well as their physiological function and their involvement in pathologies. miRandola is constantly updated by the staff as soon as new data is available and the online submission system is a crucial feature which helps ensuring that the system is always up-to-date. The future direction of the database is to be a resource for all the potential non-invasive biomarkers such as lncRNAs, cell-free DNA and circulating tumor cells (CTCs). miRandola is available online at: http://atlas.dmi.unict.it/mirandola/
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