title: Investigating miRNA-mRNA regulatory networks using crosslinking immunoprecipitation methods for biomarker and target discovery in cancer.
abstract: MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level. Recently, different experimental approaches, such as RNA Sequencing, crosslinking immunoprecipitation (CLIP) methods and its variations, together with computational approaches have been developed to elucidate the miRNA-mRNA targetome. Areas covered: This report focuses on comparing the different experimental and computational approaches, describing their advantages and disadvantages and providing several examples of preclinical (in vitro and in vivo) and clinical studies that have identified miRNA target genes in various tumour types, including breast, ovary, colorectal and pancreas. Expert commentary: The combination of CLIP methods with bioinformatic analyses is essential to better predict miRNA-mRNA interactions and associate their specific pathways within the extensive regulatory network. Nevertheless, further studies are needed to overcome the difficulties these methods have, in order to find a gold standard method that identifies, without any bias, the regulatory association between miRNAs and their target mRNAs.
authors: a Division of Cancer, Dept. of Surgery & Cancer, Imperial Centre for Translational and Experimental Medicine (ICTEM) , Imperial College , London , UK.
authors: Mireia
authors: M
authors: Mato Prado
authors: a Division of Cancer, Dept. of Surgery & Cancer, Imperial Centre for Translational and Experimental Medicine (ICTEM) , Imperial College , London , UK.|b HPB Surgical Unit, Dept. of Surgery & Cancer , Imperial College , London , UK.
authors: Adam E
authors: AE
authors: Frampton
authors: c Dept. of Medical Oncology , VU University Medical Center , Amsterdam , The Netherlands.|d Cancer Pharmacology Lab, AIRC Start-Up Unit , University of Pisa , Pisa , Italy.|e CNR-Nano , Institute of Nanoscience and Nanotechnology , Pisa , Italy.
authors: Elisa
authors: E
authors: Giovannetti
authors: a Division of Cancer, Dept. of Surgery & Cancer, Imperial Centre for Translational and Experimental Medicine (ICTEM) , Imperial College , London , UK.
authors: Justin
authors: J
authors: Stebbing
authors: a Division of Cancer, Dept. of Surgery & Cancer, Imperial Centre for Translational and Experimental Medicine (ICTEM) , Imperial College , London , UK.
authors: Leandro
authors: L
authors: Castellano
authors: a Division of Cancer, Dept. of Surgery & Cancer, Imperial Centre for Translational and Experimental Medicine (ICTEM) , Imperial College , London , UK.
authors: Jonathan
authors: J
authors: Krell
mesh_terms: D000818:Animals; D014408:Biomarkers, Tumor; D019295:Computational Biology / Q000379:methods; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics*; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D014408:Biomarkers, Tumor; D035683:MicroRNAs; D012333:RNA, Messenger
keywords: CLASH; PAR-CLIP; RNA sequencing; biomarker; cancer; microRNA; pancreatic Cancer; targetome; therapy