Title: Genome-wide expression approaches applied to biomedical research: long-term adaptation of Burkholderia cenocepacia to cystic fibrosis patients’ airways and extended ex-vivo cultivation of human mesenchymal stem cells
Abstract: Omics approaches allow a global understanding of biological systems, opening new avenues in biomedical research. In this field, during this thesis, two research projects were performed using genome-wide expression approaches. The first project was focused on the exploitation of a quantitative proteomic analysis based on 2-Dimensional Difference Gel Electrophoresis (2-D DIGE) (Madeira et al., 2011) and a transcriptomic analysis (Mira et al., 2011), based on DNA microarrays, to get insights into the adaptive molecular strategies employed by the opportunistic pathogenBurkholderia cenocepacia, during long-term colonization of a cystic fibrosis (CF) patients’ lungs. The proteome and transcriptome of two B. cenocepacia clonal variants selected among 11 sequential isolates retrieved from the same CF patient (Coutinho et al., 2011a), chronically infected for 3.5 years, were compared (Madeira et al., 2011; Miraet al., 2011; Coutinho et al., 2011a; Coutinho et al., 2011b). Results suggest a genetic adaptation to antimicrobial therapy and to other stressing conditions to which bacteria are exposed over time in the CF lungs, promoting successful colonization and long-term survival. In the second project developed, a quantitative proteomics approach based on 2-Dimensional Gel Electrophoresis (2-DE) has proven useful to unveil the molecular mechanisms underlying cellular senescence of human bone marrow mesenchymal stem cells, during extended ex-vivo cultivation, paving the way to set up a proteome profiling strategy for quality control in order to assure safe and clinically effective expansion of these cells for therapeutical use (Madeira et al., 2012).
Acknowledgments: This study was financially supported by FEDER and “Fundação para a Ciência e a Tecnologia” (contracts PTDC/SAU-MII/69591/2006, ERA-PTG/SAU/0001/2008, in the context of the EraNet Pathogenomics ADHRES Signature Project, PTDC/EQU-EQU/114231/2009 (PEst-OE/EQB/LA0023/2011 research lines: Systems and Synthetic Biology and Stem Cell Engineering and Regenerative Medicine), and PhD grant SFRH/BD/37012/2007). The microarray analysis was sponsored by Cystic Fibrosis Foundation Therapeutics Inc. (CFFT) under the scope of theBurkholderia Array project (BA-009-A). This research was also performed under the COST Action BM1003 “Microbial cell surface determinants of virulence as targets for new therapeutics in Cystic Fibrosis”.
Madeira A, Santos PM, Coutinho CP, Pinto-de-Oliveira A, Sá-Correia I. (2011), Quantitative proteomics (2-D DIGE) reveals molecular strategies employed byBurkholderia cenocepacia to adapt to the airways of cystic fibrosis patients under antimicrobial therapy”, Proteomics. 11:1313-1328.
Mira NP, Madeira A, Moreira AS, Coutinho CP, Sá-Correia I. (2011), Genomic expression analysis reveals strategies of Burkholderia cenocepacia to adapt to the airways of cystic fibrosis patients and antimicrobial therapy. PLoS One. 6:e28831.
Coutinho CP, de Carvalho CCCR, Madeira A, Pinto-de-Oliveira A, Sá-Correia I. (2011a), Burkholderia cenocepacia phenotypic clonal variation during a 3.5-year colonization in the lungs of a cystic fibrosis patient. Infect. Immun. 79:2950-60.
Coutinho CP, dos Santos SC, Madeira A, Mira NP, Moreira AS, Sá-Correia I. (2011b), Long-term colonization of the cystic fibrosis lung by Burkholderia cepaciacomplex bacteria: epidemiology, clonal variation and genome-wide expression alterations”. Front. Cell. Infect. Microbiol. 1. Article 12.
Madeira A, da Silva CL, dos Santos F, Camafeita E, Cabral JMS, Sá-Correia I. (2012), Human Mesenchymal Stem Cell Expression Program upon Extended Ex-VivoCultivation, as Revealed by 2-DE-Based Quantitative Proteomics. PLoS One. 7:e43523.
PhD Degree: Biotechnology; Year of conlusion: 2012
Institution: Instituto Superior Técnico, Universidade Técnica de Lisboa
Supervision: Isabel Sá-Correia and Joaquim Sampaio Cabral