List of communications


Targeted proteomic approaches to study the molecular signature of glioma stem cells.

González-Tejedo C, Functional Proteomics Group, Centro Nacional de Biotecnología-CSIC, Madrid, Spain;
Rodriguez-Fanjul V, Nanomedicine laboratory, IMDEA Nanociencia, Madrid, Spain;
Carrión-Navarro J, Instituto de Medicina Molecular Aplicada (IMMA), Hospital de Madrid Foundation, Madrid, Spain;
Tabas-Madrid D, Functional Bioinformatics Group, Centro Nacional de Biotecnología-CSIC, Madrid, Spain;
Kennedy J, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
Yan P, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
Zhao L, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
Whiteaker JR, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
Paulovich AG, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
Ayuso-Sacido A, Instituto de Medicina Molecular Aplicada (IMMA), Hospital de Madrid Foundation, Madrid, Spain;
Gharbi SI, Functional Proteomics Group, Centro Nacional de Biotecnología-CSIC, Madrid, Spain;
Albar JP, Functional Proteomics Group, Centro Nacional de Biotecnología-CSIC, Madrid, Spain;


High lethality of Glioblastoma multiforme (GBM) is explained by the progression of the disease due to the existence of glioma stem cells (GSCs), which are resistant to current treatments. According to genome-wide expression analyses, GSCs can be classified in 2 subtypes: proneural and mesenchymal. However, GSCs are still poorly characterized. Since proteins are the final performers of biological functions, it would be crucial to study the GSC proteome to identify potential novel biomarkers as well as new therapeutic targets.

Mass spectrometry, in combination with RNA-seq data, enables highly specific identification of proteins and their variants. Therefore, to gain further insight into the molecular biology of GSCs, we applied a deep proteogenomic analysis of a panel of GSC lines isolated from different GBM patients, including proneural and mesenchymal cell lines.

We first performed shotgun proteomic studies of several GSCs and searched this proteomic data against customized protein sequence databases generated using RNA-seq to identify novel splice variants and single-nucleotide polymorphisms. Next, we compared one of these GSCs with a non-stem GBM cell line by quantitative MS using iTRAQ labeling to find proteins potentially involved in GSC resistance and determine specific markers of stemness. Functional pathway analysis of differentially regulated proteins revealed that DNA repair mechanisms, cell adhesion and metabolism were mostly affected.

To validate these preliminary results, we applied a targeted proteomics approach in a panel of GSCs subtypes. We performed Multiple Reaction Monitoring (MRM) to absolutely quantify a panel of stem markers and proteins involved in the DNA repair mechanisms. With this emerging technology, we are able to distinguish GSCs subclasses according to the expression levels of stem markers like nestin or SOX2. We also identified putative biomarkers differentially expressed in our panel of stem cell lines like the DNA repair protein PARP1, whose inhibition has been associated to an increase in drug sensitivity.

We show that targeted proteomics is a powerful tool to quantify proteins involved in pathways related to GBM progression and drug resistence. This will help to better classify patients according to the proteomic profile of their GSCs and select the most adequate treatment.

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