Highlight talk – Theme: Proteins
Abstract
Colorectal cancer (CRC) transcriptional subtypes have been recently identified by gene expression profiling. Here we describe an analytical pipeline, microRNA master regulator analysis (MMRA), developed to search for microRNAs potentially driving CRC subtypes. Starting from a microRNA–mRNA tumour expression data set, MMRA identifies candidate regulator microRNAs by assessing their subtype-specific expression, target enrichment in subtype mRNA signatures and network analysis-based contribution to subtype gene expression. When applied to a CRC data set of 450 samples, assigned to subtypes by 3 different transcriptional classifiers, MMRA identifies 24 candidate microRNAs, in most cases downregulated in the stem/serrated/mesenchymal (SSM) poor prognosis subtype. Functional validation in CRC cell lines confirms downregulation of the SSM subtype by miR-194, miR-200b, miR-203 and miR-429, which share target genes and pathways mediating this effect. These results show that, by combining statistical tests, target prediction and network analysis, MMRA effectively identifies microRNAs functionally associated to cancer subtypes.
Authors
Laura Cantini, Institut Curie, France
Claudio Isella, Department of Oncology, Universita degli Studi di Torino and Candiolo Cancer Institute, FPO IRCCS, Italy
Consalvo Petti, Candiolo Cancer Institute, FPO IRCCS, Italy
Gabriele Picco, Department of Oncology, Universita degli Studi di Torino and Candiolo Cancer Institute, FPO IRCCS, Italy
Simone Chiola, Department of Oncology, Universita degli Studi di Torino and Candiolo Cancer Institute, FPO IRCCS, Italy
Elisa Ficarra, Department of Control and Computer Engineering, Politecnico di Torino, Italy
Michele Caselle, Department of Physics and INFN, Universita` degli Studi di Torino, Italy
Enzo Medico, Department of Oncology, Universita` degli Studi di Torino and Candiolo Cancer Institute, FPO IRCCS, Italy