A knowledge base for the discovery of function, diagnostic potential and drug effects on cellular and extracellular miRNAs
- Francesco Russo†1, 4,
- Sebastiano Di Bella†4,
- Vincenzo Bonnici2,
- Alessandro Laganà3,
- Giuseppe Rainaldi1,
- Marco Pellegrini1,
- Alfredo Pulvirenti†4Email author,
- Rosalba Giugno†4Email author and
- Alfredo Ferro4
© Russo et al.; licensee BioMed Central Ltd. 2014
Published: 6 May 2014
MicroRNAs (miRNAs) are small noncoding RNAs that play an important role in the regulation of various biological processes through their interaction with cellular mRNAs. A significant amount of miRNAs has been found in extracellular human body fluids (e.g. plasma and serum) and some circulating miRNAs in the blood have been successfully revealed as biomarkers for diseases including cardiovascular diseases and cancer. Released miRNAs do not necessarily reflect the abundance of miRNAs in the cell of origin. It is claimed that release of miRNAs from cells into blood and ductal fluids is selective and that the selection of released miRNAs may correlate with malignancy. Moreover, miRNAs play a significant role in pharmacogenomics by down-regulating genes that are important for drug function. In particular, the use of drugs should be taken into consideration while analyzing plasma miRNA levels as drug treatment. This may impair their employment as biomarkers.
We enriched our manually curated extracellular/circulating microRNAs database, miRandola, by providing (i) a systematic comparison of expression profiles of cellular and extracellular miRNAs, (ii) a miRNA targets enrichment analysis procedure, (iii) information on drugs and their effect on miRNA expression, obtained by applying a natural language processing algorithm to abstracts obtained from PubMed.
This allows users to improve the knowledge about the function, diagnostic potential, and the drug effects on cellular and circulating miRNAs.
MicroRNAs (miRNAs) are small (~22-nucleotide) non-coding RNA molecules that are single-stranded in their functional form and act as post-transcriptional regulators of gene expression . Their importance was confirmed in several cellular processes like development, proliferation, and apoptosis. Moreover, altered miRNA expression profiles have been linked to a large number of pathological conditions, such as cancer, suggesting that miRNAs are involved in disordered cellular function. miRNA expression profiles have been shown as potential signatures for the classification, diagnosis, and progression of cancer [2, 3]. Recently, a significant amount of miRNAs has been found in extracellular human body fluids [4, 5]. Some circulating miRNAs in the blood have been successfully revealed as biomarkers for several diseases including cardiovascular diseases,  and cancer [4, 7].
miRandola is the first comprehensive database of extracellular circulating miRNAs . The database represents a useful reference tool for anyone investigating the role of extracellular miRNAs as non-invasive biomarkers as well as their physiological function and their involvement in diseases. miRNAs are classified into different categories, based on their main extracellular forms: complexed with Argonaute2 (Ago2) proteins [9, 10], encapsulated within exosomes  or bound to high-density lipoprotein (HDL) . Exosomes are 50-nm to 90-nm vesicles arising from multivesicular bodies and released by exocytosis . They consist of a limiting lipid bilayer, transmembrane proteins and a hydrophilic core containing proteins, mRNAs and miRNAs. Exosomes may horizontally transfer RNAs, including miRNAs that have been shown to be functional after exosome mediated delivery . It has been reported that a significant portion of circulating miRNAs in human plasma and serum is associated with Ago2 [9, 10]. Ago2 is the effector component of the miRNA-induced silencing complex (miRISC) that directly binds miRNAs and mediates messenger RNA repression in cells [14, 15]. The high-density lipoprotein (HDL) is a delivery vehicle for the return of excess cellular cholesterol to the liver for excretion. Recently, it has been reported that HDL transports endogenous miRNAs and delivers them to recipient cells with functional targeting capabilities  providing evidence that HDL-miRNAs could potentially serve as novel diagnostic markers in much the same way exosomal miRNAs have.
This is now emerging as a hot, quickly developing research topic due to the promising role of extracellular miRNAs as non-invasive biomarkers. miRandola constitutes a useful environment for the study of reported circulating miRNAs and may help prioritize their systematic clinical evaluation. Here we present some new tools that we developed and incorporated into miRandola to help the discovery of function, diagnostic potential and drug effects on cellular and extracellular miRNAs in order to facilitate user investigation of circulating miRNAs.
Content and utility
A database for extracellular miRNAs
miRandola is a comprehensive database of extracellular circulating miRNAs. It provides a variety of information including associated diseases, samples, methods used to isolate miRNAs, the description of the experimental protocol and the potential biomarker role.
Data is collected from ExoCarta , a database of exosomal proteins, RNA and lipids and PubMed (www.ncbi.nlm.nih.gov/pubmed/). The database is manually curated and constantly updated by the authors and the scientific community who can give its contribution to the project by submitting new data about extracellular miRNAs. The current version of the database contains 119 papers, 2276 entries, 590 unique mature miRNAs and 23 types of samples.
miRNAs are classified into four categories, based on their extracellular form: miRNA-Ago2 (173 entries), miRNA-exosome (856 entries), miRNA-HDL (20 entries) and miRNA-circulating (1227 entries). The latter is used when information about the specific miRNA carrier is not available and constitutes the largest group.
The database is implemented in MySQL running on an Apache server and it is equipped with a PHP web interface. Users may query the database by mature miRNA, miRNA family, sample, diseases, malignant cell lines, and potential biomarker role, to get information about the diseases, processes and functions in which the corresponding miRNAs are involved and the tissues in which they are expressed. Results consist of published data about the searched items and predictions computed by miRo', a web knowledge base which contains miRNA functional annotation inferred through their validated and predicted targets.
A systematic comparison of expression profiles of cellular and extracellular miRNAs
In order to infer the effect of drugs on miRNA expression we downloaded the lists of all miRNAs and drug names from miRBase  and drugbank , respectively. For each miRNA, we queried PubMed through the Entrez utilities  in order to retrieve all the papers whose titles and abstracts contained the name of the miRNA. We selected the abstracts that contained the name of the miRNA and the name of a drug. If such miRNA and drug co-occured in the same sentence, this sentence was stored as support of the relation miRNA-Drug. Sentences were extracted from the text by using the Stanford NLP software [21, 22]. We parsed each sentence in order to find triples containing subject, verb and object, where subject and object were either miRNA or drug names and the verb indicated the effect of the relationship miRNA-Drug. We performed this task by using the software ReVerb [23, 24]. Next, we manually parsed the selected data in order to keep only those relations concerning drugs that are known to up or down regulate a miRNA, together with the related disease and the used experimental platform (microarray, Northern blot, etc.). We enriched our knowledge base by adding supportive information taken from SM2mir , a manually curated databases which maintains experimentally validated effects of small molecules on miRNA expressions (last update refers to June 2012). The final results thus obtained from the above pipeline are presented in the Drug summary and consist of the PubMed ID of the paper, the support sentence and, if specified, the related disease and the experimental techniques.
miRNA targets enrichment analysis
DAVID  is a system for gene functional annotation and enrichment. We now extended miRandola with miRto, a tool which integrates DAVID functional annotation (through the available web service module ) with target prediction (TargetScan www.targetscan.org/vert_61/ and miRanda www.microrna.org/microrna/home.do) and validated targets (miRTarbase mirtarbase.mbc.nctu.edu.tw/) tools.
Drugs can also determine the up-regulation of extracellular miRNAs. For instance, by selecting acetaminophen in miRNAexpress users will see that this drug up-regulates miR-122 and miR-192 in acetaminophen-induced acute liver injury (APAP-ALI) providing the evidence for the potential use of miRNAs as biomarkers of human drug-induced liver injury . One apparent premise to using extracellular miRNAs for disease diagnose is the notion that the abundance of the miRNAs in body fluids reflects their abundance in the malignant cells causing the disease, thus researchers have focused on miRNAs that are abundant in the cells of origin.
Using miRNAexpress users can systematically compare cellular and extracellular expression profiles for a specific disease, and find instead that extracellular miRNAs do not necessarily reflect the abundance of miRNAs in the cell, as demonstrated by recent studies . For instance, by selecting prostate cancer disease (in step 3 of the tool), for both extracellular and cellular miRNAs, users will see that there is no difference in the expression profile patterns for some miRNAs (e.g. let-7c, let-7e and miR-107), while there are some differences for other miRNA signatures (e.g. miR-141 is up-regulated in the plasma of prostate cancer patients , and is down-regulated in prostate cancer cell lines ).
We presented useful tools for further understanding the role of cellular and extracellular miRNAs in the context of their targets, regulation and drug effects on their expressions and annotations. These tools extended the miRandola database, the only online resource collecting information about extracellular miRNAs.
Availability and requirements
miRandola is available at http://atlas.dmi.unict.it/mirandola/
Francesco Russo has been supported by a fellowship sponsored by Progetto Istituto Toscano Tumori Grant 2012 Prot.A00GRT. The present work is partially supported by the Flagship project InterOmics(PB.P05), funded by the Italian MIUR and CNR organizations, and by the joint IIT-IFC Lab for Integrative System Medicine (LISM). We wish to thank Dr. Dario Veneziano for his precious support in the preparation of the final version of the article.
This article is published as part of a supplement. The publication costs for this article were funded by PROGETTO BANDIERA INTEROMICS "Sviluppo di una piattaforma integrata per l'applicazione delle scienze "omiche" alla definizione dei biomarcatori e profili diagnostici, predittivi e teranostici" CUP B91J12000270001.
This article has been published as part of BMC Genomics Volume 15 Supplement 5, 2014: Italian Society of Bioinformatics (BITS): Annual Meeting 2013: Genomics. The full contents of the supplement are available online at http://www.biomedcentral.com/bmcgenomics/supplements/15/S3
- Bartel D: MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell. 2004, 116: 281-297.View ArticlePubMedGoogle Scholar
- Cortez M, Bueso-Ramos C, Ferdin J, Lopez-Berestein G, Sood A, Calin G: MicroRNAs in body fluids n the mix of hormones and biomarkers. Nat Rev Clin Oncol. 2011, 8: 467-477.PubMed CentralView ArticlePubMedGoogle Scholar
- Kunej T, Godnic I, Ferdin J, Horvat S, Dovc P, Calin G: Epigenetic regulation of microRNAs in cancer: an integrated review of literature. Mutat Res. 2011, 717: 77-84.View ArticlePubMedGoogle Scholar
- Mitchell P, Parkin R, Kroh E, Fritz B, Wyman S, Pogosova-Agadjanyan E, Peterson A, Noteboom J, O'Briant K, Allen A, Lin D, Urban N, Drescher C, Knudsen B, Stirewalt D, Gentleman R, Vessella R, Nelson P, Martin D, Tewari M: Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA. 2008, 105: 10513-10518.PubMed CentralView ArticlePubMedGoogle Scholar
- Hanke M, Hoefig K, Merz H, Feller A, Kausch I, Jocham D, Warnecke J, Sczakiel G: A robust methodology to study urine microRNA as tumor marker: microRNA-126 and microRNA-182 are related to urinary bladder cancer. Urol Oncol. 2009, 28 (6): 655-661.View ArticlePubMedGoogle Scholar
- Gupta S, Bang C, Thum T: Circulating microRNAs as biomarkers and potential paracrine mediators of cardiovascular disease. Circ Cardiovasc Genet. 2010, 3: 655-661.View ArticleGoogle Scholar
- Tomimaru Y, Eguchi H, Nagano H, Wada H, Kobayashi S, Marubashi S, Tanemura M, Tomokuni A, Take-masa I, Umeshita K, Kanto T, Doki Y, Mori M: Circulating microRNA-21 as a novel biomarker for hepatocellular carcinoma. J Hepatol. 2012, 56: 167-175.View ArticlePubMedGoogle Scholar
- Russo F, Di Bella S, Nigita G, Macca V, Lagana A, Giugno R, Pulvirenti A, Ferro A: miRandola: extracellular circulating microRNAs database. PLoS One. 2012, 7 (10): e47786-PubMed CentralView ArticlePubMedGoogle Scholar
- Turchinovich A, Weiz L, Langheinz A, Burwinkel B: Characterization of extracellular circulating mi-croRNA. Nucleic Acids Res. 2011, 39 (16): 7223-7233.PubMed CentralView ArticlePubMedGoogle Scholar
- Arroyo J, Chevillet J, Kroh E, Ruf I, Pritchard C, Gibson D, Mitchell P, Bennett C, Pogosova-Agadjanyan E, Stirewalt D, Tait J, M T: Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci USA. 2011, 108 (12): 5003-5008.PubMed CentralView ArticlePubMedGoogle Scholar
- Valadi H, Ekstrom K, Bossios A, Sjostrand M, Lee J, Lotvall J: Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol. 2007, 9 (6): 654-659.View ArticlePubMedGoogle Scholar
- Vickers K, Palmisano B, Shoucri B, Shamburek R, Remaley A: MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins. Nat Cell Biol. 2011, 13 (4): 423-433.PubMed CentralView ArticlePubMedGoogle Scholar
- Fevrier B, Raposo G: Exosomes: Endosomal-derived vesicles shipping extracellular messages. Curr Opin Cell Biol. 2004, 16 (4): 415-421.View ArticlePubMedGoogle Scholar
- Song J, Liu J, Tolia N, Schneiderman J, Smith S, Martienssen R, Hannon G, Joshua-Tor L: The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat Struct Biol. 2003, 10 (12): 1026-1032.View ArticlePubMedGoogle Scholar
- Ma J, Ye K, Patel D: Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature. 2004, 429: 318-322.View ArticlePubMedGoogle Scholar
- Mathivanan S, Fahner C, Reid G, Simpson R: ExoCarta 2012: database of exosomal proteins, RNA and lipids. Nucleic Acids Res. 2012, 429: D1241-D1244.View ArticleGoogle Scholar
- Ruepp A, Kowarsch A, Schmidl D, Buggenthin F, Brauner B, Dunger I, Fobo G, Frishman G, Montrone C, Theis F: PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol. 2010, 11: R6-PubMed CentralView ArticlePubMedGoogle Scholar
- Griffiths-Jones S, Grocock R, Van Dongen S, Bateman A, Enright A: miRBase: microRNA sequences, targets and gene nomenclature. Nucleic acids research. 2006, 34 (suppl 1): D140-D144.PubMed CentralView ArticlePubMedGoogle Scholar
- Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, et al: DrugBank 3.0: a comprehensive resource for omics research on drugs. Nucleic acids research. 2011, 39 (suppl 1): D1035-D1041.PubMed CentralView ArticlePubMedGoogle Scholar
- Sayers E, Wheeler D: Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils). NCBI Short Courses. 2004Google Scholar
- Stanford N: Stanford NLP (Natural Language Processing). [http://www-nlp.stanford.edu/]
- Baldridge J: The opennlp project. 2005Google Scholar
- Sharma A, Swaminathan R, Yang H: A verb-centric approach for relationship extraction in biomedical text. Semantic Computing (ICSC), 2010 IEEE Fourth International Conference on, IEEE. 2010, 377-385.View ArticleGoogle Scholar
- Fader A, Soderland S, Etzioni O: Identifying relations for open information extraction. Proceedings of the Conference on Empirical Methods in Natural Language Processing, Association for Computational Linguistics. 2011, 1535-1545.Google Scholar
- Liu X, Wang S, Meng F, Wang J, Zhang Y, Dai E, Yu X, Li X, Jiang W: SM2miR: a database of the experimentally validated small molecules effects on microRNA expression. Bioinformatics. 2013, 29 (3): 409-411.View ArticlePubMedGoogle Scholar
- Huang D, Sherman B, Lempicki R: Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc. 2009, 4: 44-57.View ArticleGoogle Scholar
- Jiao X, Sherman B, Huang da W, Stephens R, Baseler M, Lane H, Lempicki R: DAVID-WS: a stateful web service to facilitate gene/protein list analysis. Bioinformatics. 2012, 28 (13): 1805-1806.PubMed CentralView ArticlePubMedGoogle Scholar
- Hosack D, Dennis GJ, Sherman B, Lane H, Lempicki R: Identifying biological themes within lists of genes with EASE. Genome Biol. 2003, 4 (10): R70-PubMed CentralView ArticlePubMedGoogle Scholar
- de Boer H, van Solingen C, Prins J, Duijs J, MV H, Rabelink T, van Zonneveld A: Aspirin treatment hampers the use of plasma microRNA-126 as a biomarker for the progression of vascular disease. Eur Heart J. 2013Google Scholar
- Starkey Lewis P, Dear J, Platt V, Simpson K, Craig D, Antoine D, French N, Dhaun N, Webb D, Costello E, Neoptolemos J, Moggs J, Goldring C, Park B: Circulating microRNAs as potential markers of human drug-induced liver injury. Hepatology. 2011, 54 (5): 1767-1776.View ArticlePubMedGoogle Scholar
- Pigati L, Yaddanapudi S, Iyengar R, Kim D, Hearn S, Danforth D, Hastings M, Duelli D: Selective release of microRNA species from normal and malignant mammary epithelial cells. PLoS One. 2012, 5 (10): e13515-View ArticleGoogle Scholar
- Bryant R, Pawlowski T, Catto J, Marsden G, Vessella R, Rhees B, Kuslich C, Visakorpi T, Hamdy F: Changes in circulating microRNA levels associated with prostate cancer. Br J Cancer. 2012, 106 (4): 768-774.PubMed CentralView ArticlePubMedGoogle Scholar
- Porkka K, Pfeiffer M, Waltering K, Vessella R, Tammela T, Visakorpi T: MicroRNA expression profiling in prostate cancer. Cancer Res. 2007, 67 (13): 6130-6135.View ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.