@article {405,
	title = {Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape.},
	journal = {Cancer Res},
	volume = {78},
	year = {2018},
	month = {2018 Nov 01},
	pages = {6059-6072},
	abstract = {<p>Metabolic reprogramming plays an important role in cancer development and progression and is a well-established hallmark of cancer. Despite its inherent complexity, cellular metabolism can be decomposed into functional modules that represent fundamental metabolic processes. Here, we performed a pan-cancer study involving 9,428 samples from 25 cancer types to reveal metabolic modules whose individual or coordinated activity predict cancer type and outcome, in turn highlighting novel therapeutic opportunities. Integration of gene expression levels into metabolic modules suggests that the activity of specific modules differs between cancers and the corresponding tissues of origin. Some modules may cooperate, as indicated by the positive correlation of their activity across a range of tumors. The activity of many metabolic modules was significantly associated with prognosis at a stronger magnitude than any of their constituent genes. Thus, modules may be classified as tumor suppressors and oncomodules according to their potential impact on cancer progression. Using this modeling framework, we also propose novel potential therapeutic targets that constitute alternative ways of treating cancer by inhibiting their reprogrammed metabolism. Collectively, this study provides an extensive resource of predicted cancer metabolic profiles and dependencies. Combining gene expression with metabolic modules identifies molecular mechanisms of cancer undetected on an individual gene level and allows discovery of new potential therapeutic targets. .</p>},
	keywords = {Cell Line, Tumor, Cluster Analysis, Disease Progression, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Gene Regulatory Networks, Humans, Kaplan-Meier Estimate, Metabolome, mutation, Neoplasms, Oncogenes, Phenotype, Prognosis, RNA, Small Interfering, Sequence Analysis, RNA, Transcriptome, Treatment Outcome},
	issn = {1538-7445},
	doi = {10.1158/0008-5472.CAN-17-2705},
	author = {Cubuk, Cankut and Hidalgo, Marta R and Amadoz, Alicia and Pujana, Miguel A and Mateo, Francesca and Herranz, Carmen and Carbonell-Caballero, Jos{\'e} and Dopazo, Joaquin}
}
@article {521,
	title = {The protease MT1-MMP drives a combinatorial proteolytic program in activated endothelial cells.},
	journal = {FASEB J},
	volume = {26},
	year = {2012},
	month = {2012 Nov},
	pages = {4481-94},
	abstract = {<p>The mechanism by which proteolytic events translate into biological responses is not well understood. To explore the link of pericellular proteolysis to events relevant to capillary sprouting within the inflammatory context, we aimed at the identification of the collection of substrates of the protease MT1-MMP in endothelial tip cells induced by inflammatory stimuli. We applied quantitative proteomics to endothelial cells (ECs) derived from wild-type and MT1-MMP-null mice to identify the substrate repertoire of this protease in TNF-α-activated ECs. Bioinformatics analysis revealed a combinatorial MT1-MMP proteolytic program, in which combined rather than single substrate processing would determine biological decisions by activated ECs, including chemotaxis, cell motility and adhesion, and vasculature development. MT1-MMP-deficient ECs inefficiently processed several of these substrates (TSP1, CYR61, NID1, and SEM3C), validating the model. This novel concept of MT1-MMP-driven combinatorial proteolysis in angiogenesis might be extendable to proteolytic actions in other cellular contexts.</p>},
	keywords = {Animals, Blotting, Western, Combinatorial Chemistry Techniques, Computational Biology, Endothelial Cells, Gene Expression Regulation, Enzymologic, Inflammation, Matrix Metalloproteinase 14, Mice, Protein Array Analysis, Reverse Transcriptase Polymerase Chain Reaction, RNA Interference, RNA, Small Interfering, Transcriptome, Tumor Necrosis Factor-alpha},
	issn = {1530-6860},
	doi = {10.1096/fj.12-205906},
	author = {Koziol, Agnieszka and Gonzalo, Pilar and Mota, Alba and Poll{\'a}n, Angela and Lorenzo, Cristina and Colom{\'e}, Nuria and Montaner, David and Dopazo, Joaquin and Arribas, Joaqu{\'\i}n and Canals, Francesc and Arroyo, Alicia G}
}
