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Identification of Signaling Pathways and Specifically Mirnas Altered in Familial and Sporadic Forms Of UNIVERSIDAD AUTÓNOMA DE MADRID DEPARTAMENTO DE BIOQUÍMICA Identification of signaling pathways and specifically miRNAs altered in familial and sporadic forms of medullary thyroid tumors Doctoral Thesis Agnieszka Maliszewska Madrid, 2012 BIOCHEMISTRY DEPARTMENT FACULTY OF MEDICINE AUTONOMA UNIVERSITY OF MADRID Identification of signaling pathways and specifically miRNAs altered in familial and sporadic forms of medullary thyroid tumors Agnieszka Maliszewska Thesis co-directors Dr. Mercedes Robledo Batanero Dr. Xavier Matías-Guiu Guia HEREDITARY ENDOCRINE CANCER GROUP HUMAN CANCER GENETICS PROGRAMME SPANISH NATIONAL CANCER RESEARCH CENTRE Dra. Pilar Santisteban, Investigadora del Instituto de Investigaciones Biomédicas Investigaciones Biomédicas Alberto Sols, CSIC-UAM y como la Tutora de la Tesis CERTIFICA: Que Doña Agnieszka Maliszewska, ha realizado la presente Tesis Doctoral titulada “Identification of signaling pathways and specifically miRNAs altered in familial and sporadic forms of medullary thyroid tumors”, en el Centro Nacional de Investigaciones Oncológicas y que en su juicio, reúne plenamente todos los requisitos necesarios para optar al Grado de Doctor, a cuyos efectos será presentado en la Universidad Autónoma de Madrid. Y para que conste se extiende el presente certificado, Madrid, 23 de Julio de 2012 Vo Bo de la Tutora de la Tesis: Dra. Pilar Santisteban This thesis work was carried out at the Spanish National Cancer Research Centre (CNIO) in Madrid from 2008-2012; under the supervision of Dr. Mercedes Robledo-Batanero and Dr. Xavier Matías-Guiu Guia The following fellowships and scientific projects have permitted the realization of this thesis. Fellowship for "la Caixa"/CNIO International PhD Programme in Biomedicine from 2008- 2012 . Grant from the Fundación Mutua Madrileña (project AP2775/2008 to MR) . Grant from the Fondo de Investigaciones Sanitarias (project PI080883 to MR), . The Spanish Ministry of Science and Innovation MICINN (BFU2010-17628 to ME) . Grants 2009SGR794, RD06/0020/1034 and the programa de intensificación de la investigación, Instituto Carlos III. I wish to dedicate my PhD thesis to my parents and my lovely grandmother for their unconditional love and support Acknowledgements I would like to thank all the people thanks to whom I get so far and this PhD thesis was possible to defend and my parents for their unconditional love and support. Table of Contents Table of contents Table of Contents Table of Contents.............................................................................................................................. 19 Abstract ........................................................................................................................................... …35 Resumen ........................................................................................................................................ ….37 Introduction ...................................................................................................................................... 39 1.Thyroid carcinoma ...................................................................................................................... 41 1.1 Multiple Endocrine Neoplasia type 2 (MEN2) syndrome and general background ........... 41 2. RET proto-oncogene .................................................................................................................. 43 2.1 RET structure and protein ................................................................................................... 44 2.2 Activation mechanism of RET ............................................................................................. 44 2.3 Signaling pathways ............................................................................................................. 45 2.3.1 Tyrosine 1062 residue ................................................................................................. 46 2.3.2 Other tyrosine residues ............................................................................................... 47 2.4 Function of RET .................................................................................................................. 48 3. Relation of RET with MEN2 ....................................................................................................... 50 3.1 Germline RET mutations ..................................................................................................... 50 3.2 Somatic RET mutations ...................................................................................................... 53 4. MTC management, detection and targeted therapies .............................................................. 53 4.1 Targeted therapies for MTC ................................................................................................ 54 5. Genomics ................................................................................................................................... 56 5.1 Transcriptomics ................................................................................................................... 56 5.2 microRNAs .......................................................................................................................... 56 Resumen de la introducción…. ......................................................................................................... 61 Objectives ......................................................................................................................................... 69 Objetivos ........................................................................................................................................... 73 Material and methods ...................................................................................................................... 77 1.1 Medullary Thyroid Carcinoma patients ............................................................................... 79 1.2 Frozen MTC tissue samples ................................................................................................ 79 1.3 Formalin fixed embedded (FFPE) samples and tissue microarray (TMA) .......................... 80 1.4 MTC cell line models ........................................................................................................... 80 19 | P a g e Table of contents 2. DNA extraction .......................................................................................................................... 81 2.1 DNA extraction from the peripheral blood ......................................................................... 81 2.2 DNA extraction from the frozen material ........................................................................... 81 2.3 DNA extraction from formalin fixed paraffin embedded (FFPE) material ......................... 82 3. RNA extraction and analysis ...................................................................................................... 83 3.1 RNA extraction from the frozen material ........................................................................... 83 3.2 RNA extraction from formalin fixed paraffin embedded (FFPE) material .......................... 83 3.3 RNA extraction from cell lines ............................................................................................. 84 3.4 Analysis of RNA integrity and quality .................................................................................. 84 4. RET genetic screening ............................................................................................................... 85 5. Gene expression characterization by using microarrays .......................................................... 86 5.1 cDNA synthesis and cRNA labeling ...................................................................................... 87 5.2 Hybridization ....................................................................................................................... 88 5.3 Washing and scanning ........................................................................................................ 88 5.4 Data analysis – extraction, normalization and preprocessing ........................................... 88 6. MicroRNA expression microarrays ........................................................................................... 89 6.1 Labeling and hybridization : miRCURY LNATM microRNA Array ......................................... 89 6.2 Washing and scanning: miRCURY LNATM microRNA Array ................................................. 90 6.3 miRNA normalization and preprocessing ........................................................................... 90 7. Bioinformatic analysis of gene expression and miRNA data .................................................... 91 7.1 Unsupervised clustering ..................................................................................................... 91 7.2 Supervised clustering ......................................................................................................... 91 7.3 Functional profiling and pathways analysis ....................................................................... 92 7.3.1 Gene Ontology analysis .............................................................................................. 92 7.3.2 Gene Set Enrichment Analysis (GSEA) ........................................................................ 92 7.3.3 Ingenuity Pathway Analysis (IPA) 9.0 ........................................................................
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