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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 27 more authors.
Nature Genetics | Year: 2013

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.


Rio-Machin A.,Molecular Cytogenetics Group | Ferreira B.I.,Molecular Cytogenetics Group | Henry T.,Mayo Medical School | Gomez-Lopez G.,Bioinformatics Unit | And 8 more authors.
Leukemia | Year: 2013

Currently, multiple myeloma (MM) patients are broadly grouped into a non-hyperdiploid (nh-MM) group, highly enriched for IgH translocations, or into a hyperdiploid (h-MM) group, which is typically characterized by trisomies of some odd-numbered chromosomes. We compared the micro RNA (miRNA) expression profiles of these two groups and we identified 16 miRNAs that were downregulated in the h-MM group, relative to the nh-MM group. We found that target genes of the most differentially expressed miRNAs are directly involved in the pathogenesis of MM; specifically, the inhibition of hsa-miR-425, hsa-miR-152 and hsa-miR-24, which are all downregulated in h-MM, leads to the overexpression of CCND1, TACC3, MAFB, FGFR3 and MYC, which are the also the oncogenes upregulated by the most frequent IgH chromosomal translocations occurring in nh-MM. Importantly, we showed that the downregulation of these specific miRNAs and the upregulation of their targets also occur simultaneously in primary cases of h-MM. These data provide further evidence on the unifying role of cyclin D pathways deregulation as the key mechanism involved in the development of both groups of MM. Finally, they establish the importance of miRNA deregulation in the context of MM, thereby opening up the potential for future therapeutic approaches based on this molecular mechanism. © 2013 Macmillan Publishers Limited All rights reserved.


Martin M.C.,Molecular Cytogenetics Group | Cigudosa J.C.,Molecular Cytogenetics Group | Rodriguez-Perales S.,Molecular Cytogenetics Group
Nature Communications | Year: 2014

Cancer-related human chromosomal translocations are generated through the illegitimate joining of two non-homologous chromosomes affected by double-strand breaks (DSB). Effective methodologies to reproduce precise reciprocal tumour-associated chromosomal translocations are required to gain insight into the initiation of leukaemia and sarcomas. Here we present a strategy for generating cancer-related human chromosomal translocations in vitro based on the ability of the RNA-guided CRISPR-Cas9 system to induce DSBs at defined positions. Using this approach we generate human cell lines and primary cells bearing chromosomal translocations resembling those described in acute myeloid leukaemia and Ewing's sarcoma at high frequencies. FISH and molecular analysis at the mRNA and protein levels of the fusion genes involved in these engineered cells reveal the reliability and accuracy of the CRISPR-Cas9 approach, providing a powerful tool for cancer studies. © 2014 Macmillan Publishers Limited. All rights reserved.


Menezes J.,Molecular Cytogenetics Group | Acquadro F.,Molecular Cytogenetics Group | Wiseman M.,NIMGenetics | Gomez-Lopez G.,Bioinformatic Unit | And 15 more authors.
Leukemia | Year: 2014

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a very rare disease that currently lacks genomic and genetic biomarkers to assist in its clinical management. We performed whole-exome sequencing (WES) of three BPDCN cases. Based on these data, we designed a resequencing approach to identify mutations in 38 selected genes in 25 BPDCN samples. WES revealed 37-99 deleterious gene mutations per exome with no common affected genes between patients, but with clear overlap in terms of molecular and disease pathways (hematological and dermatological disease). We identified for the first time deleterious mutations in IKZF3, HOXB9, UBE2G2 and ZEB2 in human leukemia. Target sequencing identified 29 recurring genes, ranging in prevalence from 36% for previously known genes, such as TET2, to 12-16% for newly identified genes, such as IKZF3 or ZEB2. Half of the tumors had mutations affecting either the DNA methylation or chromatin remodeling pathways. The clinical analysis revealed that patients with mutations in DNA methylation pathway had a significantly reduced overall survival (P=0.047). We provide the first mutational profiling of BPDCN. The data support the current WHO classification of the disease as a myeloid disorder and provide a biological rationale for the incorporation of epigenetic therapies for its treatment. © 2014 Macmillan Publishers Limited.


Maiques-Diaz A.,Molecular Cytogenetics Group | Chou F.S.,Cincinnati Childrens Hospital Medical Center | Wunderlich M.,Cincinnati Childrens Hospital Medical Center | Gomez-Lopez G.,Bioinformatics Unit | And 7 more authors.
Leukemia | Year: 2012

The AML1-ETO fusion protein, which is present in 10-15% of cases of acute myeloid leukemia, is known to repress myeloid differentiation genes through DNA binding and recruitment of chromatin-modifying proteins and transcription factors in target genes. ChIP-chip analysis of human hematopoietic stem/progenitor cells transduced with the AML1-ETO fusion gene enabled us to identify 1168 AML1-ETO target genes, 103 of which were co-occupied by histone deacetylase 1 (HDAC1) and had lost the hyperacetylation mark at histone H4, and 264 showed a K9 trimethylation at histone H3. Enrichment of genes involved in hematopoietic differentiation and in specific signaling pathways was observed in the presence of these epigenetic modifications associated with an inactive chromatin status. Furthermore, AML1-ETO target genes had a significant correlation between the chromatin marks studied and transcriptional silencing. Interestingly, AML1 binding sites were absent on a large number of selected AML1-ETO promoters and an Sp1 binding site was found in over 50% of them. Reversible silencing induced by the fusion protein in the presence of AML1 and/or Sp1 transcription factor binding site was confirmed. Therefore, this study provides a global analysis of AML1-ETO functional chromatin modifications and identifies the important role of Sp1 in the DNA binding pattern of AML1-ETO, suggesting a role for Sp1-targeted therapy in this leukemia subtype. © 2012 Macmillan Publishers Limited.


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 | Year: 2014

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.


Torres-Ruiz R.,Viral Vector Technical Unit | Rodriguez-Perales S.,Molecular Cytogenetics Group
International Journal of Molecular Sciences | Year: 2015

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.


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.
Haematologica | Year: 2013

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.


Menezes J.,Molecular Cytogenetics Group | Cigudosa J.C.,Molecular Cytogenetics Group
OncoTargets and Therapy | Year: 2015

Chronic neutrophilic leukemia (CNL) is a rare myeloproliferative neoplasm (MPN) that includes only 150 patients described to date meeting the latest World Health Organization (WHO) criteria and the recently reported CSF3R mutations. The diagnosis is based on morphological criteria of granulocytic cells and the exclusion of genetic drivers that are known to occur in others MPNs, such as BCR-ABL1, PDGFRA/B, or FGFR1 rearrangements. However, this scenario changed with the identification of oncogenic mutations in the CSF3R gene in approximately 83% of WHO-defined and no monoclonal gammopathy-associated CNL patients. CSF3R T618I is a highly specific molecular marker for CNL that is sensitive to inhibition in vitro and in vivo by currently approved protein kinase inhibitors. In addition to CSF3R mutations, other genetic alterations have been found, notably mutations in SETBP1, which may be used as prognostic markers to guide therapeutic decisions. These findings will help to understand the pathogenesis of CNL and greatly impact the clinical management of this disease. In this review, we discuss the new genetic alterations recently found in CNL and the clinical perspectives in its diagnosis and treatment. Fortunately, since the diagnosis of CNL is not based on exclusion anymore, the molecular characterization of the CSF3R gene must be included in the WHO criteria for CNL diagnosis. © 2015, Menezes and Cigudosa.


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 | Year: 2010

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.

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