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Torres-Ruiz R.,Viral Vector Technical Unit | Rodriguez-Perales S.,Molecular Cytogenetics Group
International Journal of Molecular Sciences

The cancer-modelling field is now experiencing a conversion with the recent emergence of the RNA-programmable CRISPR-Cas9 system, a flexible methodology to produce essentially any desired modification in the genome. Cancer is a multistep process that involves many genetic mutations and other genome rearrangements. Despite their importance, it is difficult to recapitulate the degree of genetic complexity found in patient tumors. The CRISPR-Cas9 system for genome editing has been proven as a robust technology that makes it possible to generate cellular and animal models that recapitulate those cooperative alterations rapidly and at low cost. In this review, we will discuss the innovative applications of the CRISPR-Cas9 system to generate new models, providing a new way to interrogate the development and progression of cancers. © 2015 by the authors; licensee MDPI, Basel, Switzerland. Source

Torres R.,Viral Vector Facility | Garcia A.,Viral Vector Facility | Jimenez M.,Viral Vector Facility | Rodriguez S.,Molecular Cytogenetics Group | Ramirez J.C.,Viral Vector Facility
Gene Therapy

Optimized gene transfer into human cells are still challenging the promise of human stem and induced pluripotent stem cells as resources for disease models, diagnostic screens and personalized cell therapy. These potential applications require precise control of the spatio-temporal action of gene switches and the coordinated regulation of modulators, effectors and differentiation factors during pluripotency, differentiation and homeostasis. Most studies require identical transgene environments for comparable analysis; however, this cannot be achieved by standard methods for transgenesis in human cells because of unintended epigenetic modifications, genetic instability, dose-dependent effects, and disruption or activation of host genes. Although gene targeting can circumvent these problems, human cells have proved difficult to target, and there is therefore a need to develop tools for targeted transgenesis at efficiencies similar to those achieved in mice. We present a simple strategy, KASTRINA 2.0, for reliable transgenesis in human cells, based on targeted recombinase-mediated cassette exchange and the safe episomal status conferred by integrase-deficient lentivirus (IDLV). By driving limited cre recombinase expression, the IDLV yields single site-specific recombination of a selectable donor cassette (TRINA) at the 'safe-harbour' AAVS1 locus previously edited by zinc-finger nuclease to contain an acceptor site (KAS2.0). © 2014 Macmillan Publishers Limited. Source

Sbacchi S.,University of Palermo | Acquadro F.,Molecular Cytogenetics Group | Calo I.,University of Palermo | Cali F.,Associazione Oasi Maria SS. I.R.C.C.S. | Romano V.,University of Palermo
Current Genomics

We have used Gene Ontology (GO) and pathway analyses to uncover the common functions associated to the genes overlapping Copy Number Variants (CNVs) in autistic patients. Our source of data were four published studies [1-4]. We first applied a two-step enrichment strategy for autism-specific genes. We fished out from the four mentioned studies a list of 2928 genes overall overlapping 328 CNVs in patients and we first selected a sub-group of 2044 genes after excluding those ones that are also involved in CNVs reported in the Database of Genomic Variants (enrichment step 1). We then selected from the step 1-enriched list a sub-group of 514 genes each of which was found to be deleted or duplicated in at least two patients (enrichment step 2). The number of statistically significant processes and pathways identified by the Database for Annotation, Visualization and Integrated Discovery and Ingenuity Pathways Analysis softwares with the step 2-enriched list was significantly higher compared to the step 1-enriched list. In addition, statistically significant GO terms, biofunctions and pathways related to nervous system development and function were exclusively identified by the step 2-enriched list of genes. Interestingly, 21 genes were associated to axon growth and pathfinding. The latter genes and other ones associated to nervous system in this study represent a new set of autism candidate genes deserving further investigation. In summary, our results suggest that the autism's "connectivity genes" in some patients affect very early phases of neurodevelopment, i.e., earlier than synaptogenesis. © 2010 Bentham Science Publishers Ltd. Source

Perez C.,University of Navarra | Pascual M.,University of Navarra | Martin-Subero J.I.,University of Barcelona | Bellosillo B.,Hospital Del Mar | And 11 more authors.

Most DNA methylation studies in classic Philadelphia-negative myeloproliferative neoplasms have been performed on a gene-by-gene basis. Therefore, a more comprehensive methylation profiling is needed to study the implications of this epigenetic marker in myeloproliferative neoplasms. Here, we have analyzed 71 chronic (24 polycythemia vera, 23 essential thrombocythemia and 24 primary myelofibrosis) and 13 transformed myeloproliferative neoplasms using genome-wide DNA methylation arrays. The three types of chronic Philadelphia-negative myeloproliferative neoplasms showed a similar aberrant DNA methylation pattern when compared to control samples. Differentially methylated regions were enriched in a gene network centered on the NF-κB pathway, indicating that they may be involved in the pathogenesis of these diseases. In the case of transformed myeloproliferative neoplasms, we detected an increased number of differentially methylated regions with respect to chronic myeloproliferative neoplasms. Interestingly, these genes were enriched in a list of differentially methylated regions in primary acute myeloid leukemia and in a gene network centered around the IFN pathway. Our results suggest that alterations in the DNA methylation landscape play an important role in the pathogenesis and leukemic transformation of myeloproliferative neoplasms. The therapeutic modulation of epigenetically-deregulated pathways may allow us to design targeted therapies for these patients. © 2013 Ferrata Storti Foundation. Source

Balbas-Martinez C.,Epithelial Carcinogenesis Group | Sagrera A.,Epithelial Carcinogenesis Group | Carrillo-De-Santa-Pau E.,Epithelial Carcinogenesis Group | Earl J.,Epithelial Carcinogenesis Group | And 26 more authors.
Nature Genetics

Urothelial bladder cancer (UBC) is heterogeneous at the clinical, pathological and genetic levels. Tumor invasiveness (T) and grade (G) are the main factors associated with outcome and determine patient management. A discovery exome sequencing screen (n = 17), followed by a prevalence screen (n = 60), identified new genes mutated in this tumor coding for proteins involved in chromatin modification (MLL2, ASXL2 and BPTF), cell division (STAG2, SMC1A and SMC1B) and DNA repair (ATM, ERCC2 and FANCA). STAG2, a subunit of cohesin, was significantly and commonly mutated or lost in UBC, mainly in tumors of low stage or grade, and its loss was associated with improved outcome. Loss of expression was often observed in chromosomally stable tumors, and STAG2 knockdown in bladder cancer cells did not increase aneuploidy. STAG2 reintroduction in non-expressing cells led to reduced colony formation. Our findings indicate that STAG2 is a new UBC tumor suppressor acting through mechanisms that are different from its role in preventing aneuploidy. Source

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