title: Ablation of Dicer leads to widespread perturbation of signaling pathways.
abstract: Dicer is an essential ribonuclease involved in the biogenesis of miRNAs. Previous studies have reported downregulation of Dicer in multiple cancers including hepatocellular carcinoma. To identify signaling pathways that are altered upon Dicer depletion, we carried out quantitative phosphotyrosine profiling of liver tissue from Dicer knockout mice. We employed antibody-based enrichment of phosphotyrosine containing peptides coupled with SILAC spike-in approach for quantitation. High resolution mass spectrometry-based analysis identified 349 phosphotyrosine peptides corresponding to 306 unique phosphosites of which 75 were hyperphosphorylated and 78 were hypophosphorylated. Several receptor tyrosine kinases including MET, PDGF receptor alpha, Insulin-like growth factor 1 and Insulin receptor as well as non-receptor tyrosine kinases such as Src family kinases were found to be hyperphosphorylated upon depletion of Dicer. In addition, signaling molecules such as IRS-2 and STAT3 were hyperphosphorylated. Activation of these signaling pathways has been implicated previously in various types of cancers. Interestingly, we observed hypophosphorylation of molecules including focal adhesion kinase and paxillin. Our study profiles the perturbed signaling pathways in response to dysregulated miRNAs resulting from depletion of Dicer. Our findings warrant further studies to investigate oncogenic effects of downregulation of Dicer in cancers.
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Manipal University, Madhav Nagar, Manipal 576104, India.
authors.forename: Nandini A
authors.initials: NA
authors.lastname: Sahasrabuddhe
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
authors.forename: Tai-Chung
authors.initials: TC
authors.lastname: Huang
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore 560066, India.
authors.forename: Praveen
authors.initials: P
authors.lastname: Kumar
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
authors.forename: Bidyut
authors.initials: B
authors.lastname: Ghosh
authors.affiliation: McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Leach
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Manipal University, Madhav Nagar, Manipal 576104, India; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
authors.forename: Raghothama
authors.initials: R
authors.lastname: Chaerkady
authors.affiliation: Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address: pandey@jhmi.edu.
authors.forename: Akhilesh
authors.initials: A
authors.lastname: Pandey
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002460:Cell Line; D053487:DEAD-box RNA Helicases / Q000235:genetics* / Q000378:metabolism; D051379:Mice; D018345:Mice, Knockout; D008969:Molecular Sequence Data; D010748:Phosphopeptides / Q000032:analysis / Q000378:metabolism; D019000:Phosphotyrosine / Q000032:analysis / Q000378:metabolism*; D060066:Protein Interaction Maps; D020794:Receptor Protein-Tyrosine Kinases / Q000378:metabolism; D043244:Ribonuclease III / Q000235:genetics* / Q000378:metabolism; D015398:Signal Transduction
chemical_list: D010748:Phosphopeptides; D019000:Phosphotyrosine; D020794:Receptor Protein-Tyrosine Kinases; C509781:Dicer1 protein, mouse; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases
keywords: Dicer; Pathways; Phosphotyrosine; Receptor tyrosine kinase; SILAC