Mapping signaling pathways related to chemoresistance in leukemic cells: a computational approach

Author(s)

Renato Milani

• Document type: Doctoral Thesis
• Press: Campinas, SP.
• Institution: Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia
• Defense date: 2014-11-08

Examining board members

Eduardo Galembeck; Claudio Chrysostomo Werneck; Luciana de Campos Leite Medeiros; Willian Fernando Zambuzzi; Jose Mauro Granjeiro

• Advisor: Eduardo Galembeck; Carmen Veríssima Ferreira

Abstract

Chronic myeloid leukemia, characterized by the BCR-ABL fusion gene, still poses challenges to patient treatment. One of them is chemoresistance, a major barrier for successful therapy approaches. Still, the molecular mechanisms responsible for promoting and keeping the multiple drug resistance (MDR) phenotype are largely unknown. The mapping of phosphorylation events in resistant cells may improve disease understanding at the cellular level and suggest new targets for pharmacological intervention. Here we present a comparative analysis of the proteome and phosphoproteome in K562, a chronic myeloid leukemia cell line, and Lucena-1, a K562-derived chemoresistant line. We developed several bioinformatics tools to help analyze the data, such as a phosphoproteomics dataset enrichment tool, titled PhosphoActivity, that is able to retrieve documented sites responsible for the activation or inhibition of the proteins related to each phosphorylated fragment. These tools were employed to sift through 2290 proteins and 4257 phosphorylated peptides corresponding to 2053 phosphoproteins previously identified by mass spectrometry. Combining experimental data with support vector machine-based predictions, we selected 145 proteins and phosphoproteins for validation. The selection includes transcription regulators and structural proteins, such as ?-catenin, HDAC6 and the intermediary filament vimentin. Proteins and phosphoproteins identified and validated through computational and epxerimental methods suggest the involvement of pathways such as cytoskeleton rearrangement, cell lproliferation and carbohydrate metabolism in the chemoresistance of Lucena-1. Furthermore, the identification of LMW-PTP, a protein tyrosine phosphatase, as having a pivotal role in the resistance process in Lucena-1, suggests it as a complex and multifactorial process (AU)

• FAPESP's process: 09/18424-6 - Mapping signaling pathways related to chemoresistance in leukemic cells: a computational approach
• Grantee: Renato Milani
• Support Opportunities: Scholarships in Brazil - Doctorate