Publications (18)81.64 Total impact
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Article: Position-dependent expression of GADD45α in rat brain tumours
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ABSTRACT: Although the complex and multifactorial process of tumour growth has been extensively studied for decades, our understanding of the fundamental relationship between tumour growth dynamics and genetic expression profile remains incomplete. Recent studies of tumour dynamics indicate that gene expression in solid tumours would depend on the distance from the centre of the tumour. Since tumour proliferative activity is mainly localised to its external zone, and taking into account that generation and expansion of genetic mutations depend on the number of cell divisions, important differences in gene expression between central and peripheral sections of the same tumour are to be expected. Here, we have studied variations in the genetic expression profile between peripheral and internal samples of the same brain tumour. We have carried out microarray analysis of mRNA expression, and found a differential profile of genetic expression between the two cell subsets. In particular, one major nuclear protein that regulates cell responses to DNA-damaging and stress signals, GADD45α, was expressed at much lower levels in the peripheral zone, as compared to tumour core samples. These differences in GADD45α mRNA transcription levels have been confirmed by quantitative analysis via real time PCR, and protein levels of GADD45α also exhibit the same pattern of differential expression. Our findings suggest that GADD45α might play a major role in the regulation of brain tumour invasive potential.Medical Oncology 04/2012; 24(4):436-444. · 2.14 Impact Factor -
Article: Early peroxisome proliferator-activated receptor gamma regulated genes involved in expansion of pancreatic beta cell mass.
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ABSTRACT: The progression towards type 2 diabetes depends on the allostatic response of pancreatic beta cells to synthesise and secrete enough insulin to compensate for insulin resistance. The endocrine pancreas is a plastic tissue able to expand or regress in response to the requirements imposed by physiological and pathophysiological states associated to insulin resistance such as pregnancy, obesity or ageing, but the mechanisms mediating beta cell mass expansion in these scenarios are not well defined. We have recently shown that ob/ob mice with genetic ablation of PPARγ2, a mouse model known as the POKO mouse failed to expand its beta cell mass. This phenotype contrasted with the appropriate expansion of the beta cell mass observed in their obese littermate ob/ob mice. Thus, comparison of these models islets particularly at early ages could provide some new insights on early PPARγ dependent transcriptional responses involved in the process of beta cell mass expansion Here we have investigated PPARγ dependent transcriptional responses occurring during the early stages of beta cell adaptation to insulin resistance in wild type, ob/ob, PPARγ2 KO and POKO mice. We have identified genes known to regulate both the rate of proliferation and the survival signals of beta cells. Moreover we have also identified new pathways induced in ob/ob islets that remained unchanged in POKO islets, suggesting an important role for PPARγ in maintenance/activation of mechanisms essential for the continued function of the beta cell. Our data suggest that the expansion of beta cell mass observed in ob/ob islets is associated with the activation of an immune response that fails to occur in POKO islets. We have also indentified other PPARγ dependent differentially regulated pathways including cholesterol biosynthesis, apoptosis through TGF-β signaling and decreased oxidative phosphorylation.BMC Medical Genomics 12/2011; 4:86. · 3.69 Impact Factor -
Article: Progress and challenges in developing a molecular diagnostic test for neurofibromatosis type 1.
Expert Review of Molecular Diagnostics 09/2011; 11(7):671-3. · 4.86 Impact Factor -
Article: Characterization of host genetic expression patterns in HIV-infected individuals with divergent disease progression.
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ABSTRACT: The course of HIV-1 infection shows a variety of clinical phenotypes with an important involvement of host factors. We compare host gene expression patterns in CD3+ T cells from two of these phenotypes: long-term non-progressor patients (LTNP) and matched control patients with standard HIV disease progression. Array analysis revealed over-expression of 322 genes in progressors and 136 in LTNP. Up-regulated genes in progressors were mainly implicated in the regulation of DNA replication, cell cycle and DNA damage stimulus and mostly localized into cellular organelles. In contrast, most up-regulated genes in LTNP were located at the plasmatic membrane and involved in cytokine-cytokine receptor interaction, negative control of apoptosis or regulation of actin cytoskeleton. Regarding gene interactions, a higher number of viral genes interacting with cellular factors were seen in progressors. Our study offers new comparative insights related to disease status and can distinguish differentiated patterns of gene expression among clinical phenotypes.Virology 03/2011; 411(1):103-12. · 3.35 Impact Factor -
Article: Formin1 mediates the induction of dendritogenesis and synaptogenesis by neurogenin3 in mouse hippocampal neurons.
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ABSTRACT: Neurogenin3, a proneural transcription factor controlled by Notch receptor, has been recently shown to regulate dendritogenesis and synaptogenesis in mouse hippocampal neurons. However, little is known about the molecular mechanisms involved in these actions of Ngn3. We have used a microarray analysis to identify Ngn3 regulated genes related with cytoskeleton dynamics. One of such genes is Fmn1, whose protein, Formin1, is associated with actin and microtubule cytoskeleton. Overexpression of the Fmn1 isoform-Ib in cultured mouse hippocampal neurons induced an increase in the number of primary dendrites and in the number of glutamatergic synaptic inputs at 4 days in vitro. The same changes were provoked by overexpression of Ngn3. In addition downregulation of Fmn1 by the use of Fmn1-siRNAs impaired such morphological and synaptic changes induced by Ngn3 overexpression in neurons. These results reveal a previously unknown involvement of Formin1 in dendritogenesis and synaptogenesis and indicate that this protein is a key component of the Ngn3 signaling pathway that controls neuronal differentiation.PLoS ONE 01/2011; 6(7):e21825. · 4.09 Impact Factor -
Article: Automatic genomics: a user-friendly program for the automatic designing and plate loading of medium-throughput qPCR experiments.
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ABSTRACT: Quantitative PCR (qPCR) remains the method of choice for gene and microRNA (miRNA) expression studies. Many laboratories wish to automate some or all of the steps of medium-throughput qPCR experiments through the use of various types of liquid handling robots. However, it is not uncommon to find cases in which scripts provided by the robot supplier are too rigid for user-specific applications, do not include all the desired options, or are too complicated to be modified by a nonprofessional programmer. Here, we present Automatic Genomics, a program that allows users with a limited programming background to automate medium-throughput qPCR experiments by using commercially available liquid-handling robots. The user is able to optimize the plate design in terms of number of genes, number of samples, and controls.BioTechniques 01/2011; 50(1):46-50. · 2.67 Impact Factor -
Article: Cux1 and Cux2 regulate dendritic branching, spine morphology, and synapses of the upper layer neurons of the cortex.
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ABSTRACT: Dendrite branching and spine formation determines the function of morphologically distinct and specialized neuronal subclasses. However, little is known about the programs instructing specific branching patterns in vertebrate neurons and whether such programs influence dendritic spines and synapses. Using knockout and knockdown studies combined with morphological, molecular, and electrophysiological analysis, we show that the homeobox Cux1 and Cux2 are intrinsic and complementary regulators of dendrite branching, spine development, and synapse formation in layer II-III neurons of the cerebral cortex. Cux genes control the number and maturation of dendritic spines partly through direct regulation of the expression of Xlr3b and Xlr4b, chromatin remodeling genes previously implicated in cognitive defects. Accordingly, abnormal dendrites and synapses in Cux2(-/-) mice correlate with reduced synaptic function and defects in working memory. These demonstrate critical roles of Cux in dendritogenesis and highlight subclass-specific mechanisms of synapse regulation that contribute to the establishment of cognitive circuits.Neuron 05/2010; 66(4):523-35. · 14.74 Impact Factor -
Article: Large-scale gene expression in bone marrow mesenchymal stem cells: a putative role for COL10A1 in osteoarthritis.
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ABSTRACT: To elucidate disease-specific molecular changes occurring in osteoarthritis (OA) by analysing the differential gene expression profiles of bone marrow mesenchymal stem cells (BM-MSCs) from patients with OA compared with those without OA. Expression profiles of BM-MSCs from eight paired patients with OA and patients with hip fracture without signs of OA were compared by DNA microarray expression analysis and significant differences were evaluated by computational Gene Set Enrichment Analysis. To validate the involvement of COL10A1 as part of the most downregulated gene set in OA, three tagging single nucleotide polymorphisms were genotyped in 191 patients with OA and 283 controls. COL10A1 expression was also assessed by quantitative RT-PCR in additional subjects. Expression levels in 9% (1967) of the overall transcripts were significantly different (p<0.05) between MSCs from patients with OA and controls (532 genes reached twofold differences: 240 were upregulated and 292 were downregulated). Cell development and differentiation were the functional categories accounting for most genes with altered expression. Interestingly, several genes related to the Wnt/-catenin pathway and collagen genes were downregulated in MSCs from patients with OA. The collagen gene set was clearly downregulated in OA. Furthermore, the expression of COL10A1 was significantly reduced in patients with OA. A genetic association between the COL10A1 rs11965969 polymorphism and OA was also found. COL10A1 downregulation seems to have a role in the establishment of a defective and/or unstable subchondral cartilage matrix in OA disease. It is proposed that OA may be linked to the intrinsic defective regenerative potential of BM-MSCs resulting from its reduced expression of fate commitment-related genes.Annals of the rheumatic diseases 05/2010; 69(10):1880-5. · 8.11 Impact Factor -
Article: Processing of Agilent microRNA array data.
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ABSTRACT: The Agilent microRNA microarray platform interrogates each microRNA with several copies of distinct oligonucleotide probes and integrates the results into a total gene signal (TGS), using a proprietary algorithm that makes use of the background subtracted signal. The TGS can be normalized between arrays, and the Agilent recommendation is either not to normalize or to normalize to the 75th percentile signal intensity. The robust multiarray average algorithm (RMA) is an alternative method, originally developed to obtain a summary measure of mRNA Affymetrix gene expression arrays by using a linear model that takes into account the probe affinity effect. The RMA method has been shown to improve the accuracy and precision of expression measurements relative to other competing methods. There is also evidence that it might be preferable to use non-corrected signals for the processing of microRNA data, rather than background-corrected signals. In this study we assess the use of the RMA method to obtain a summarized microRNA signal for the Agilent arrays. We have adapted the RMA method to obtain a processed signal for the Agilent arrays and have compared the RMA summarized signal to the TGS generated with the image analysis software provided by the vendor. We also compared the use of the RMA algorithm with uncorrected and background-corrected signals, and compared quantile normalization with the normalization method recommended by the vendor. The pre-processing methods were compared in terms of their ability to reduce the variability (increase precision) of the signals between biological replicates. Application of the RMA method to non-background corrected signals produced more precise signals than either the RMA-background-corrected signal or the quantile-normalized Agilent TGS. The Agilent TGS normalized to the 75% percentile showed more variation than the other measures. Used without background correction, a summarized signal that takes into account the probe effect might provide a more precise estimate of microRNA expression. The variability of quantile normalization was lower compared with the normalization method recommended by the vendor.BMC Research Notes 01/2010; 3:18. -
Article: Estradiol activates beta-catenin dependent transcription in neurons.
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ABSTRACT: Estradiol may fulfill a plethora of functions in neurons, in which much of its activity is associated with its capacity to directly bind and dimerize estrogen receptors. This hormone-protein complex can either bind directly to estrogen response elements (ERE's) in gene promoters, or it may act as a cofactor at non-ERE sites interacting with other DNA-binding elements such as AP-1 or c-Jun. Many of the neuroprotective effects described for estrogen have been associated with this mode of action. However, recent evidence suggests that in addition to these "genomic effects", estrogen may also act as a more general "trophic factor" triggering cytoplasmic signals and extending the potential activity of this hormone. We demonstrated that estrogen receptor alpha associates with beta-catenin and glycogen synthase kinase 3 in the brain and in neurons, which has since been confirmed by others. Here, we show that the action of estradiol activates beta-catenin transcription in neuroblastoma cells and in primary cortical neurons. This activation is time and concentration-dependent, and it may be abolished by the estrogen receptor antagonist ICI 182780. The transcriptional activation of beta-catenin is dependent on lymphoid enhancer binding factor-1 (LEF-1) and a truncated-mutant of LEF-1 almost completely blocks estradiol TCF-mediated transcription. Transcription of a TCF-reporter in a transgenic mouse model is enhanced by estradiol in a similar fashion to that produced by Wnt3a. In addition, activation of a luciferase reporter driven by the engrailed promoter with three LEF-1 repeats was mediated by estradiol. We established a cell line that constitutively expresses a dominant-negative LEF-1 and it was used in a gene expression microarray analysis. In this way, genes that respond to estradiol or Wnt3a, sensitive to LEF-1, could be identified and validated. Together, these data demonstrate the existence of a new signaling pathway controlled by estradiol in neurons. This pathway shares some elements of the insulin-like growth factor-1/Insulin and Wnt signaling pathways, however, our data strongly suggest that it is different from that of both these ligands. These findings may reveal a set of new physiological roles for estrogens, at least in the Central Nervous System (CNS).PLoS ONE 02/2009; 4(4):e5153. · 4.09 Impact Factor -
Article: Modifications in host cell structure and functions mediated by Tat intracellular expression are greatly dependent on the second exon
Retrovirology. 01/2009; -
Article: Transcriptional expression of cis-acting and trans-acting splicing mutations cause autosomal dominant retinitis pigmentosa.
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ABSTRACT: Two types of mutations may lead to deficient pre-mRNA splicing: cis-acting mutations that inactivate a constitutive or alternative splice site within the pre-mRNA, and trans-acting mutations that affect the function of a basal factor of the splicing machinery. Autosomal dominant retinitis pigmentosa (adRP) is caused by mutations in at least 12 genes, with mutations in rhodopsin being the most prevalent. Two cis-acting mutations, g.3811A>G and g.5167G>T at the splice site in the rhodopsin gene (RHO; GenBank U49742.1) are linked to adRP in a Spanish population; while a cis-acting mutation, g.4335G>T, has been linked to recessive RP (arRP). Transcriptional expression analysis showed that the cis-acting splicing mutations linked to adRP promoted alternative splice sites, while the arRP linked mutation results in exclusion of exon 4. Trans-acting splicing mutations associated with adRP have also been found, and mutations in the pre-mRNA splicing factors PRPF3, PRPF8, PRPF31, and RP9 are associated with adRP in several populations. This report describes a new mutation in PRPF3 in a Spanish adRP family. We also investigated the transcriptional patterns in Epstein-Barr virus (EBV)-transformed lymphoblastoid cells from patients carrying a mutation in PRPF8. Despite the role of PRPF8 in the minor U12 splicing processes, microarray analysis revealed that mutations in PRPF8 not only did not result in significant differences in splicing efficiency of rhodopsin, but no apparent changes in expression of U12-type intron genes and splicing processes was observed. Microarray analysis revealed a panel of differentially expressed genes mapped to the RP loci, and future work will determine their role in RP.Human Mutation 07/2008; 29(6):869-78. · 5.69 Impact Factor -
Article: Codelink: an R package for analysis of GE healthcare gene expression bioarrays.
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ABSTRACT: MOTIVATION: Microarray-based expression profiles have become a standard methodology in any high-throughput analysis. Several commercial platforms are available, each with its strengths and weaknesses. The R platform for statistical analysis and graphics is a powerful environment for the analysis of microarray data, because it has many integrated statistical methods available as well as the specialized microarray analysis project Bioconductor. Many packages have been added in the last few years increasing the range of possible analysis. Here, we report the availability of a package for reading and analyzing data from GE Healthcare Gene Expression Bioarrays within the R environment. AVAILABILITY: The software is implemented in the R language, is open source and available for download free of charge through the Bioconductor (http://www.bioconductor.org) project.Bioinformatics 06/2007; 23(9):1168-9. · 5.47 Impact Factor -
Article: Position-dependent expression of GADD45alpha in rat brain tumours.
[show abstract] [hide abstract]
ABSTRACT: Although the complex and multifactorial process of tumour growth has been extensively studied for decades, our understanding of the fundamental relationship between tumour growth dynamics and genetic expression profile remains incomplete. Recent studies of tumour dynamics indicate that gene expression in solid tumours would depend on the distance from the centre of the tumour. Since tumour proliferative activity is mainly localised to its external zone, and taking into account that generation and expansion of genetic mutations depend on the number of cell divisions, important differences in gene expression between central and peripheral sections of the same tumour are to be expected. Here, we have studied variations in the genetic expression profile between peripheral and internal samples of the same brain tumour. We have carried out microarray analysis of mRNA expression, and found a differential profile of genetic expression between the two cell subsets. In particular, one major nuclear protein that regulates cell responses to DNA-damaging and stress signals, GADD45alpha, was expressed at much lower levels in the peripheral zone, as compared to tumour core samples. These differences in GADD45alpha mRNA transcription levels have been confirmed by quantitative analysis via real time PCR, and protein levels of GADD45alpha also exhibit the same pattern of differential expression. Our findings suggest that GADD45alpha might play a major role in the regulation of brain tumour invasive potential.Medical Oncology 02/2007; 24(4):436-44. · 2.14 Impact Factor -
Article: The molecular signature of mantle cell lymphoma reveals multiple signals favoring cell survival.
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ABSTRACT: Mantle cell lymphoma (MCL) is a prototypical neoplastic disease in which a common cytogenetic alteration, t11;14, leading to cyclin D1 overexpression, is associated with other changes that need to be considered in an explanation of the clinical, morphological, and molecular variability of this disease. Using a cDNA microarray (Oncochip-CNIO) containing clones for 6386 cancer-related genes, we have analyzed the expression profiles of a series of 38 cases. After normalization with the expression profiling of sorted mantle zone lymphocytes, we have related the findings to conventional clinical and molecular variables, including immunoglobulin variable heavy chain somatic mutation, blastoid cytology, increased proliferation, and long-term survival. MCL signature (446 genes) includes genes involved in apoptosis, cell cycle, signal transduction, and cell structure. Especially striking was the presence of multiple concurrent alterations in the tumor necrosis factor and nuclear factor kappaB pathway, and the overexpression of IL10R and SPARC genes. We also identified a molecular signature for the presence of immunoglobulin variable heavy chain somatic mutation, which includes a number of genes potentially relevant in cancer (CDC14A, ras, and others). Signatures for proliferation and blastoid cytology were also found. An integrated analysis of these data yields a gene-expression based survival predictor (26 genes grouped into two clusters), which distinguishes half of the patients with a survival probability of 52% at 5 years. The predictive model has been confirmed by cross-validation. In conclusion, MCL seems to combine a disease-specific signature and different sets of genes of which the expression is associated with key clinical, molecular, and immunophenotypical events.Cancer Research 01/2004; 63(23):8226-32. · 7.86 Impact Factor -
Article: Growth and molecular profile of lung cancer cells expressing ectopic LKB1: down-regulation of the phosphatidylinositol 3'-phosphate kinase/PTEN pathway.
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ABSTRACT: Germ-line mutations in LKB1 gene cause the Peutz-Jeghers syndrome (PJS), a genetic disease with increased risk of malignancies. Recently, LKB1-inactivating mutations have been identified in one-third of sporadic lung adenocarcinomas, indicating that LKB1 gene inactivation is critical in tumors other than those of the PJS syndrome. However, the in vivo substrates of LKB1 and its role in cancer development have not been completely elucidated. Here we show that overexpression of wild-type LKB1 protein in A549 lung adenocarcinomas cells leads to cell-growth suppression. To examine changes in gene expression profiles subsequent to exogenous wild-type LKB1 in A549 cells, we used cDNA microarrays. We detected deregulation of 100 genes involved in cell proliferation, apoptosis, and cell adhesion. Strikingly, modification of the expression of well-known p53-responsive genes such as GADD45, TOP2A, and p21 suggests that growth suppression in A549 cells overexpressing LKB1 may be mediated by p53. In addition, PTEN up-regulation indicates that LKB1 could be involved in the PTEN/phosphatidylinositol-3'-kinase(PI3K)/AKT molecular pathway. Thus, our results give some insights into the understanding of how LKB1 inactivation contributes to lung carcinogenesis.Cancer Research 04/2003; 63(6):1382-8. · 7.86 Impact Factor -
Article: Identification of genes involved in resistance to interferon-alpha in cutaneous T-cell lymphoma.
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ABSTRACT: Interferon-alpha therapy has been shown to be active in the treatment of mycosis fungoides although the individual response to this therapy is unpredictable and dependent on essentially unknown factors. In an effort to better understand the molecular mechanisms of interferon-alpha resistance we have developed an interferon-alpha resistant variant from a sensitive cutaneous T-cell lymphoma cell line. We have performed expression analysis to detect genes differentially expressed between both variants using a cDNA microarray including 6386 cancer-implicated genes. The experiments showed that resistance to interferon-alpha is consistently associated with changes in the expression of a set of 39 genes, involved in signal transduction, apoptosis, transcription regulation, and cell growth. Additional studies performed confirm that STAT1 and STAT3 expression and interferon-alpha induction and activation are not altered between both variants. The gene MAL, highly overexpressed by resistant cells, was also found to be expressed by tumoral cells in a series of cutaneous T-cell lymphoma patients treated with interferon-alpha and/or photochemotherapy. MAL expression was associated with longer time to complete remission. Time-course experiments of the sensitive and resistant cells showed a differential expression of a subset of genes involved in interferon-response (1 to 4 hours), cell growth and apoptosis (24 to 48 hours.), and signal transduction.American Journal Of Pathology 12/2002; 161(5):1825-37. · 4.89 Impact Factor -
Article: Modifications in host cell structure and functions mediated by Tat intracellular expression are greatly dependent on the second exon
Top co-authors
Top Journals
- Cancer Research (2)
- Medical Oncology (2)
- PLoS ONE (2)
- American Journal Of Pathology (1)
- Virology (1)
Institutions
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2012
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Cardiovascular Research Center
Barcelona, Catalonia, Spain
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2011
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Spanish National Centre for Cardiovascular Research
Madrid, Madrid, Spain
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2007
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Institute for Biomedical Research “Alberto Sols“
Madrid, Madrid, Spain
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