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Marquina M.,Autonomous University of Barcelona | Queralt E.,Cancer Epigenetics and Biology Program PEBC | Casamayor A.,Autonomous University of Barcelona | Arino J.,Autonomous University of Barcelona
International Journal of Biochemistry and Cell Biology | Year: 2012

Ypi1 is an essential regulator of the Saccharomyces cerevisiae Glc7 protein phosphatase. Although lack of Ypi1 results in a dramatic blockage in the G2/M cell cycle transition, with abnormally shaped large buds and short spindles, the molecular bases for this phenotype are still obscure. We report here that depletion of Ypi1 results in stabilization of the Pds1 securin, suggesting the activation of a G2/M checkpoint. Depletion of Ypi1 in cells deleted for MAD1/MAD2 or RAD9 still resulted in G2/M blockage, in spite that these cells lack key components of the spindle assembly and DNA damage checkpoints signaling, respectively. In contrast, deletion of SWE1, which encodes a protein kinase required for the morphogenesis checkpoint signaling, allowed passage through G2/M and recovery of normal cell morphology, although the cells did not proliferate. Depletion of Ypi1 caused stabilization of the Swe1 kinase, persistent phosphorylation of protein kinase Cdc28 at Y19, a landmark for morphogenesis checkpoint activation, and depletion of the Cdc11 septin, which explains the failure to form properly assembled septin rings at the bud necks. Deletion of SWE1 restored normal Cdc11 levels in the absence of Ypi1. These results demonstrate that Ypi1 plays an important role in the morphogenesis checkpoint, possibly by regulating Swe1. © 2012 Elsevier Ltd.

Martinez M.,Research Laboratory | Ichaso N.,Research Laboratory | Setien F.,Cancer Epigenetics and Biology Program PEBC | Durany N.,International University of Catalonia | And 2 more authors.
Lipids in Health and Disease | Year: 2010

Background. Docosahexaenoic acid (DHA, 22:63) is a fundamental component of cell membranes, especially in the brain and retina. In the experimental animal, DHA deficiency leads to suboptimal neurological performance and visual deficiencies. Children with the Zellweger syndrome (ZS) have a profound DHA deficiency and symptoms that can be attributed to their extremely low DHA levels. These children seem to have a metabolic defect in DHA biosynthesis, which has never been totally elucidated. Treatment with DHA ethyl ester greatly improves these patients, but if we could normalize their endogenous DHA production we could get additional benefits. We examined whether DHA biosynthesis by 4-desaturation could be enhanced in the human species by transfecting the enzyme, and if this could normalize the DHA levels in cells from ZS patients. Results. We showed that the 4-desaturase gene (Fad4) from Thraustochytrium sp, which can be expressed by heterologous transfection in other plant and yeast cells, can also be transfected into human lymphocytes, and that it expresses the enzyme (FAD4, 4-desaturase) by producing DHA from direct 4-desaturation of 22:53. We also found that the other substrate for 4-desaturase, 22:46, was parallely desaturated to 22:56. Conclusions. The present "in vitro" study demonstrates that 4-desaturase can be transfected into human cells and synthesize DHA (as well as 22:56, DPA) from 22:53 and 22:46, respectively, by putative 4-desaturation. Even if this pathway may not be the physiological route for DHA biosynthesis "in vivo", the present study opens new perspectives for the treatment of patients within the ZS spectrum. © 2010 Martinez et al; licensee BioMed Central Ltd.

Bonifaci N.,Catalan Institute of Oncology ICO | Colas E.,Autonomous University of Barcelona | Serra-Musach J.,Catalan Institute of Oncology ICO | Serra-Musach J.,Girona Biomedical Research Institute IDIBGI | And 16 more authors.
Carcinogenesis | Year: 2014

Dozens of common genetic variants associated with cancer risk have been identified through genome-wide association studies (GWASs). However, these variants only explain a modest fraction of the heritability of disease. The missing heritability has been attributed to several factors, among them the existence of genetic interactions (G × G). Systematic screens for G × G in model organisms have revealed their fundamental influence in complex phenotypes. In this scenario, G × G overlap significantly with other types of gene and/or protein relationships. Here, by integrating predicted G × G from GWAS data and complex- and context-defined gene coexpression profiles, we provide evidence for G × G associated with cancer risk. G × G predicted from a breast cancer GWAS dataset identified significant overlaps [relative enrichments (REs) of 8-36%, empirical P values < 0.05 to 10-4] with complex (non-linear) gene coexpression in breast tumors. The use of gene or protein data not specific for breast cancer did not reveal overlaps. According to the predicted G × G, experimental assays demonstrated functional interplay between lipoma-preferred partner and transforming growth factor-β signaling in the MCF10A non-tumorigenic mammary epithelial cell model. Next, integration of pancreatic tumor gene expression profiles with pancreatic cancer G × G predicted from a GWAS corroborated the observations made for breast cancer risk (REs of 25-59%). The method presented here can potentially support the identification of genetic interactions associated with cancer risk, providing novel mechanistic hypotheses for carcinogenesis. © The Author 2013. Published by Oxford University Press. All rights reserved.

Moran S.,Cancer Epigenetics and Biology Program PEBC | Arribas C.,Cancer Epigenetics and Biology Program PEBC | Esteller M.,Cancer Epigenetics and Biology Program PEBC | Esteller M.,University of Barcelona | Esteller M.,Catalan Institution for Research and Advanced Studies
Epigenomics | Year: 2016

Aim: DNA methylation is the best known epigenetic mark. Cancer and other pathologies show an altered DNA methylome. However, delivering complete DNA methylation maps is compromised by the price and labor-intensive interpretation of single nucleotide methods. Material & methods: Following the success of the HumanMethylation450 BeadChip (Infinium) methylation microarray (450K), we report the technical and biological validation of the newly developed MethylationEPIC BeadChip (Infinium) microarray that covers over 850,000 CpG methylation sites (850K). The 850K microarray contains >90% of the 450K sites, but adds 333,265 CpGs located in enhancer regions identified by the ENCODE and FANTOM5 projects. Results & conclusion: The 850K array demonstrates high reproducibility at the 450K CpG sites, is consistent among technical replicates, is reliable in the matched study of fresh frozen versus formalin-fixed paraffin-embeded samples and is also useful for 5-hydroxymethylcytosine. These results highlight the value of the MethylationEPIC BeadChip as a useful tool for the analysis of the DNA methylation profile of the human genome. © 2015 Future Medicine Ltd.

Sandoval J.,Cancer Epigenetics and Biology Program PEBC | Heyn H.A.,Cancer Epigenetics and Biology Program PEBC | Moran S.,Cancer Epigenetics and Biology Program PEBC | Serra-Musach J.,Catalan Institute of Nanoscience and Nanotechnology | And 5 more authors.
Epigenetics | Year: 2011

DNA methylation is the most studied epigenetic mark and CpG methylation is central to many biological processes and human diseases. Since cancer has highlighted the contribution to disease of aberrant DNA methylation patterns, such as the presence of promoter CpG island hypermethylation-associated silencing of tumor suppressor genes and global DNA hypomethylation defects, their importance will surely become apparent in other pathologies. However, advances in obtaining comprehensive DNA methylomes are hampered by the high cost and time-consuming aspects of the single nucleotide methods currently available for whole genome DNA methylation analyses. Following the success of the standard CpG methylation microarrays for 1,505 CpG sites and 27,000 CpG sites, we have validated in vivo the newly developed 450,000 (450K) cytosine microarray (Illumina). The 450K microarray includes CpG and CNG sites, CpG islands/shores/shelves/open sea, non-coding RNA (microRNAs and long non-coding RNAs) and sites surrounding the transcription start sites (-200 bp to -1,500 bp, 5'-UTRs and exons 1) for coding genes, but also for the corresponding gene bodies and 3'-UTRs, in addition to intergenic regions derived from GWAS studies. Herein, we demonstrate that the 450K DNA methylation array can consistently and significantly detect CpG methylation changes in the HCT-116 colorectalcancer cell line in comparison with normal colon mucosa or HCT-116 cells with defective DNA methyltransferases (DKO). The provided validation highlights the potential use of the 450K DNA methylation microarray as a useful tool for ongoing and newly designed epigenome projects. © 2011 Landes Bioscience.

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