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1.
Lancet Respir Med ; 9(8): 885-896, 2021 08.
Artículo en Inglés | MEDLINE | ID: mdl-33961805

RESUMEN

BACKGROUND: Infection is a key component of bronchiectasis pathophysiology. Characterisation of the microbiome offers a higher degree of sensitivity and resolution than does traditional culture methods. We aimed to evaluate the role of the microbiome in determining the risk of exacerbation and long-term outcomes, including all-cause mortality, in bronchiectasis. METHODS: We did a prospective observational cohort study of patients with bronchiectasis from eastern Scotland. Patients were enrolled from Sept 11, 2012, to Dec 21, 2015, and followed until Jan 8, 2019, for long-term outcomes. Patients were included if they were aged 18 years or older, and had a high-resolution CT-confirmed diagnosis of bronchiectasis and clinical symptoms consistent with the disease. Sputum samples were obtained when patients were clinically stable. Repeat sputum samples were taken at stable and exacerbation visits during follow-up. The V3-V4 region of the bacterial 16S rRNA gene was sequenced using the Illumina MiSeq platform. The dominant bacterial genus in each sample was assigned on the basis of a previously published method. Microbiome characteristics were analysed for their association with measures of clinical disease severity and long-term outcomes using PERMANOVA, random forest, and survival analyses. FINDINGS: Sequencing data were obtained from the sputum samples of 281 patients with bronchiectasis who were included in the stable baseline cohort. 49 (17%) of 281 patients provided more than one sample when clinically stable and were included in the longitudinal analysis. 64 (23%) patients provided both stable and exacerbation samples. In both stable bronchiectasis and during exacerbations, a sputum microbiome dominated by Proteobacteria and Firmicutes was observed. Individual patients' microbiome profiles were relatively stable over time, during exacerbations and at disease stability. Lower microbiome diversity, measured using the Shannon-Wiener diversity index, was associated with more severe bronchiectasis defined by the bronchiectasis severity index, lower FEV1, and more severe symptoms. Random forest analysis of baseline samples identified Pseudomonas, Enterobacteriaceae, and Stenotrophomonas as being associated with severe bronchiectasis (bronchiectasis severity index ≥9) and greater lung inflammation and Pseudomonas and Enterobacteriaceae with more frequent exacerbations. Patients in whom Pseudomonas was dominant (n=35) were at increased risk of all-cause mortality (hazard ratio 3·12, 95% CI 1·33-7·36; p=0·0091) and had more frequent exacerbations (incident rate ratio 1·69, 95% CI 1·07-2·67; p=0·024) during follow-up compared with patients with other dominant genera (n=246). INTERPRETATION: A reduction in microbiome diversity, particularly one associated with dominance of Pseudomonas, is associated with greater disease severity, higher frequency and severity of exacerbations, and higher risk of mortality. The microbiome might therefore identify subgroups of patients at increased risk of poor outcomes who could benefit from precision treatment strategies. Further research is required to identify the mechanisms of reduced microbiome diversity and to establish whether the microbiome can be therapeutically targeted. FUNDING: British Lung Foundation and European Respiratory Society EMBARC2 consortium.


Asunto(s)
Bronquiectasia/microbiología , Microbiota , Esputo/microbiología , Anciano , Bronquiectasia/mortalidad , Progresión de la Enfermedad , Femenino , Humanos , Estudios Longitudinales , Masculino , Persona de Mediana Edad , Estudios Prospectivos , Calidad de Vida , Pruebas de Función Respiratoria , Índice de Severidad de la Enfermedad
2.
Sci Rep ; 8(1): 6643, 2018 04 27.
Artículo en Inglés | MEDLINE | ID: mdl-29704004

RESUMEN

Sporulation in Dictyostelium fruiting bodies evolved from amoebozoan encystation with both being induced by cAMP acting on PKA, but with downstream components still being unknown. Using tagged mutagenesis to find missing pathway components, we identified a sporeless mutant defective in a nuclear protein, SpaA. Expression of prespore genes was strongly reduced in spaA- cells, while expression of many spore stage genes was absent. Chromatin immunoprecipitation (ChIP) of a SpaA-YFP gene fusion showed that (pre)spore gene promoters bind directly to SpaA, identifying SpaA as a transcriptional regulator. SpaA dependent spore gene expression required PKA in vivo and was stimulated in vitro by the membrane-permeant PKA agonist 8Br-cAMP. The PKA agonist also promoted SpaA binding to (pre)spore promoters, placing SpaA downstream of PKA. Sequencing of SpaA-YFP ChIPed DNA fragments revealed that SpaA binds at least 117 (pre)spore promoters, including those of other transcription factors that activate some spore genes. These factors are not in turn required for spaA expression, identifying SpaA as the major trancriptional inducer of sporulation.


Asunto(s)
Proteínas Quinasas Dependientes de AMP Cíclico/metabolismo , Dictyostelium/crecimiento & desarrollo , Esporas Protozoarias/crecimiento & desarrollo , Factores de Transcripción/metabolismo , Inmunoprecipitación de Cromatina , Análisis Mutacional de ADN , ADN Protozoario/metabolismo , Dictyostelium/enzimología , Dictyostelium/genética , Dictyostelium/metabolismo , Eliminación de Gen , Perfilación de la Expresión Génica , Regiones Promotoras Genéticas , Unión Proteica , Esporas Protozoarias/enzimología , Esporas Protozoarias/genética , Esporas Protozoarias/metabolismo , Factores de Transcripción/genética
3.
Thorax ; 73(6): 510-518, 2018 06.
Artículo en Inglés | MEDLINE | ID: mdl-29101284

RESUMEN

BACKGROUND: In cystic fibrosis and bronchiectasis, genetic mannose binding lectin (MBL) deficiency is associated with increased exacerbations and earlier mortality; associations in COPD are less clear. Preclinical data suggest MBL interferes with phagocytosis of Haemophilus influenzae, a key COPD pathogen. We investigated whether MBL deficiency impacted on clinical outcomes or microbiota composition in COPD. METHODS: Patients with COPD (n=1796) underwent MBL genotyping; linkage to health records identified exacerbations, lung function decline and mortality. A nested subcohort of 141 patients, followed for up to 6 months, was studied to test if MBL deficiency was associated with altered sputum microbiota, through 16S rRNA PCR and sequencing, or airway inflammation during stable and exacerbated COPD. FINDINGS: Patients with MBL deficiency with COPD were significantly less likely to have severe exacerbations (incidence rate ratio (IRR) 0.66, 95% CI 0.48 to 0.90, p=0.009), or to have moderate or severe exacerbations (IRR 0.77, 95% CI 0.60 to 0.99, p=0.047). MBL deficiency did not affect rate of FEV1 decline or mortality. In the subcohort, patients with MBL deficiency had a more diverse lung microbiota (p=0.008), and were less likely to be colonised with Haemophilus spp. There were lower levels of airway inflammation in patients with MBL deficiency. INTERPRETATION: Patients with MBL deficient genotype with COPD have a lower risk of exacerbations and a more diverse lung microbiota. This is the first study to identify a genetic association with the lung microbiota in COPD.


Asunto(s)
Lectina de Unión a Manosa/deficiencia , Errores Innatos del Metabolismo/genética , Enfermedad Pulmonar Obstructiva Crónica/genética , Enfermedad Pulmonar Obstructiva Crónica/microbiología , Adulto , Anciano , Progresión de la Enfermedad , Femenino , Estudios de Asociación Genética , Genotipo , Humanos , Masculino , Lectina de Unión a Manosa/genética , Microbiota , Persona de Mediana Edad , Reacción en Cadena de la Polimerasa , Polimorfismo de Nucleótido Simple , Enfermedad Pulmonar Obstructiva Crónica/mortalidad , Enfermedad Pulmonar Obstructiva Crónica/fisiopatología , Pruebas de Función Respiratoria , Esputo/microbiología
4.
Phys Chem Chem Phys ; 17(23): 15181-92, 2015 Jun 21.
Artículo en Inglés | MEDLINE | ID: mdl-25990541

RESUMEN

We study surface functionalisation by uracil and 2-thiouracil, and immobilisation of several DNA moieties on functionalised gold surfaces. The combination of X-ray photoelectron and near-edge X-ray absorption spectroscopy allowed us to obtain a complete understanding of complex interfacial processes, starting from adsorption of biomolecules onto the metallic surface and progressing towards a specific surface functionality for interactions with other biologically related adsorbates. Au(110) surfaces were functionalised by deposition of uracil and 2-thiouracil molecules under vacuum conditions, and then tested for their selectivity by immobilisation of different DNA moieties deposited from aqueous solutions. We observed that adenine, adenosine, and RNA polymer (polyadenylic acid) from saturated solutions were immobilized successfully on the 2-thiouracil, but those from dilute (1%) solutions were not. However, cytosine failed to adsorb even from saturated solution. The chemical states of the biologically related adsorbates were investigated and the geometrical orientation of uracil and 2-thiouracil on the Au(110) surface was determined using both spectroscopic techniques.


Asunto(s)
Oro/química , Tiouracilo/química , Uracilo/química , Adsorción , Ácidos Nucleicos Inmovilizados/química , Propiedades de Superficie , Termodinámica , Espectroscopía de Absorción de Rayos X
5.
PLoS One ; 8(6): e67306, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-23825651

RESUMEN

Fixed, paraffin-embedded (FPE) tissues are a potentially rich resource for studying the role of NOTCH1 in cancer and other pathologies, but tests that reliably detect activated NOTCH1 (NICD1) in FPE samples have been lacking. Here, we bridge this gap by developing an immunohistochemical (IHC) stain that detects a neoepitope created by the proteolytic cleavage event that activates NOTCH1. Following validation using xenografted cancers and normal tissues with known patterns of NOTCH1 activation, we applied this test to tumors linked to dysregulated Notch signaling by mutational studies. As expected, frequent NICD1 staining was observed in T lymphoblastic leukemia/lymphoma, a tumor in which activating NOTCH1 mutations are common. However, when IHC was used to gauge NOTCH1 activation in other human cancers, several unexpected findings emerged. Among B cell tumors, NICD1 staining was much more frequent in chronic lymphocytic leukemia than would be predicted based on the frequency of NOTCH1 mutations, while mantle cell lymphoma and diffuse large B cell lymphoma showed no evidence of NOTCH1 activation. NICD1 was also detected in 38% of peripheral T cell lymphomas. Of interest, NICD1 staining in chronic lymphocytic leukemia cells and in angioimmunoblastic lymphoma was consistently more pronounced in lymph nodes than in surrounding soft tissues, implicating factors in the nodal microenvironment in NOTCH1 activation in these diseases. Among carcinomas, diffuse strong NICD1 staining was observed in 3.8% of cases of triple negative breast cancer (3 of 78 tumors), but was absent from 151 non-small cell lung carcinomas and 147 ovarian carcinomas. Frequent staining of normal endothelium was also observed; in line with this observation, strong NICD1 staining was also seen in 77% of angiosarcomas. These findings complement insights from genomic sequencing studies and suggest that IHC staining is a valuable experimental tool that may be useful in selection of patients for clinical trials.


Asunto(s)
Receptor Notch1/metabolismo , Animales , Línea Celular Tumoral , Xenoinjertos , Humanos , Inmunohistoquímica , Ratones , Mutación , Receptor Notch1/genética
6.
Neuropharmacology ; 63(4): 750-60, 2012 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-22683514

RESUMEN

In utero exposure of rodents to valproic acid (VPA), a histone deacetylase (HDAC) inhibitor, has been proposed to induce an adult phenotype with behavioural characteristics reminiscent of those observed in autism spectrum disorder (ASD). We have evaluated the face validity of this model in terms of social cognition deficits which are a major core symptom of ASD. We employed the social approach avoidance paradigm as a measure of social reciprocity, detection of biological motion that is crucial to social interactions, and spatial learning as an indicator of dorsal stream processing of social cognition and found each parameter to be significantly impaired in Wistar rats with prior in utero exposure to VPA. We found no significant change in the expression of neural cell adhesion molecule polysialylation state (NCAM PSA), a measure of construct validity, but a complete inability to increase its glycosylation state which is necessary to mount the neuroplastic response associated with effective spatial learning. Finally, in all cases, we found chronic HDAC inhibition, with either pan-specific or HDAC1-3 isoform-specific inhibitors, to significantly ameliorate deficits in both social cognition and its associated neuroplastic response. We conclude that in utero exposure to VPA provides a robust animal model for the social cognitive deficits of ASD and a potential screen for the development of novel therapeutics for this condition.


Asunto(s)
Trastornos Generalizados del Desarrollo Infantil/tratamiento farmacológico , Trastornos del Conocimiento/prevención & control , Modelos Animales de Enfermedad , Histona Desacetilasa 1/antagonistas & inhibidores , Inhibidores de Histona Desacetilasas/uso terapéutico , Molécula L1 de Adhesión de Célula Nerviosa/metabolismo , Plasticidad Neuronal/efectos de los fármacos , Ácidos Siálicos/metabolismo , Animales , Conducta Animal/efectos de los fármacos , Niño , Trastornos Generalizados del Desarrollo Infantil/metabolismo , Trastornos Generalizados del Desarrollo Infantil/patología , Trastornos Generalizados del Desarrollo Infantil/fisiopatología , Trastornos del Conocimiento/etiología , Giro Dentado/efectos de los fármacos , Giro Dentado/metabolismo , Giro Dentado/patología , Femenino , Histona Desacetilasa 1/metabolismo , Inhibidores de Histona Desacetilasas/toxicidad , Humanos , Masculino , Terapia Molecular Dirigida , Proteínas del Tejido Nervioso/metabolismo , Neuronas/efectos de los fármacos , Neuronas/enzimología , Neuronas/metabolismo , Neuronas/patología , Embarazo , Efectos Tardíos de la Exposición Prenatal , Ratas , Ratas Wistar , Conducta Social
7.
Histopathology ; 60(5): 838-42, 2012 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-22296244

RESUMEN

AIMS: Ovarian gynandroblastomas are rare tumours that, by definition, comprise a combination of components resembling both female, typically granulosa cell tumour (GCT), and male, typically Sertoli or Sertoli/Leydig cell tumour (ST/SLT), sex cord/stromal differentiation. The histogenesis of these tumours is unknown and, in view of the very strong association between the C134W (402 C>G) FOXL2 mutation and adult-type GCT, we analysed a series of gynandroblastomas for this mutation. METHODS AND RESULTS: Both components of each lesion were isolated by laser capture microdissection and the C134W (402 C>G) FOXL2 mutation was analysed by polymerase chain reaction sequencing. No mutation was identified in either the GCT or ST/SLT component of six cases, three of which contained adult-type GCT. CONCLUSIONS: This suggests that, despite their similar morphological appearances, the GCT-like component of gynandroblastoma has a different molecular basis from conventional adult-type GCT. This finding underscores a more general principle that morphological similarity does not necessarily indicate molecular identity.


Asunto(s)
Factores de Transcripción Forkhead/genética , Tumor de Células de la Granulosa/genética , Neoplasias Ováricas/genética , Mutación Puntual , Adolescente , Adulto , Anciano , Análisis Mutacional de ADN , Femenino , Fibroma/genética , Fibroma/patología , Proteína Forkhead Box L2 , Estudios de Asociación Genética , Genotipo , Tumor de Células de la Granulosa/patología , Humanos , Captura por Microdisección con Láser , Persona de Mediana Edad , Neoplasias Ováricas/patología , Adulto Joven
8.
Cancer Res ; 70(6): 2264-73, 2010 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-20215513

RESUMEN

Selumetinib (AZD6244, ARRY-142886) is a selective, non-ATP-competitive inhibitor of mitogen-activated protein/extracellular signal-regulated kinase kinase (MEK)-1/2. The range of antitumor activity seen preclinically and in patients highlights the importance of identifying determinants of response to this drug. In large tumor cell panels of diverse lineage, we show that MEK inhibitor response does not have an absolute correlation with mutational or phospho-protein markers of BRAF/MEK, RAS, or phosphoinositide 3-kinase (PI3K) activity. We aimed to enhance predictivity by measuring pathway output through coregulated gene networks displaying differential mRNA expression exclusive to resistant cell subsets and correlated to mutational or dynamic pathway activity. We discovered an 18-gene signature enabling measurement of MEK functional output independent of tumor genotype. Where the MEK pathway is activated but the cells remain resistant to selumetinib, we identified a 13-gene signature that implicates the existence of compensatory signaling from RAS effectors other than PI3K. The ability of these signatures to stratify samples according to functional activation of MEK and/or selumetinib sensitivity was shown in multiple independent melanoma, colon, breast, and lung tumor cell lines and in xenograft models. Furthermore, we were able to measure these signatures in fixed archival melanoma tumor samples using a single RT-qPCR-based test and found intergene correlations and associations with genetic markers of pathway activity to be preserved. These signatures offer useful tools for the study of MEK biology and clinical application of MEK inhibitors, and the novel approaches taken may benefit other targeted therapies.


Asunto(s)
Bencimidazoles/farmacología , Quinasas Quinasa Quinasa PAM/metabolismo , Sistema de Señalización de MAP Quinasas/efectos de los fármacos , Neoplasias/tratamiento farmacológico , Neoplasias/enzimología , Línea Celular Tumoral , Perfilación de la Expresión Génica , Humanos , Quinasas Quinasa Quinasa PAM/antagonistas & inhibidores , Sistema de Señalización de MAP Quinasas/fisiología , Neoplasias/genética , Fosfohidrolasa PTEN/biosíntesis , Fosfohidrolasa PTEN/genética , Fosfatidilinositol 3-Quinasas/biosíntesis , Fosfatidilinositol 3-Quinasas/genética , Proteínas Proto-Oncogénicas B-raf/biosíntesis , Proteínas Proto-Oncogénicas B-raf/genética , Proteínas Proto-Oncogénicas c-akt/biosíntesis , Proteínas Proto-Oncogénicas c-akt/genética , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa
9.
FEBS Lett ; 583(15): 2493-9, 2009 Aug 06.
Artículo en Inglés | MEDLINE | ID: mdl-19596328

RESUMEN

The most debilitating feature of cystic fibrosis (CF) disease is uncontrolled inflammation of respiratory epithelium. The relationship between the commonest mutated form of CFTR (F508del or DeltaF508) and inflammation has not yet been elucidated. Here, we present a new paradigm suggesting that CFTR can interact with intra-epithelial IgG, establishing a direct link between normal CFTR and the immune system. Further, our data show that the amino-acid sequence local to F508 can bind IgG with high affinity, dependent on F508, such that loss of F508 abolishes this link both in vitro and in the intact cell.


Asunto(s)
Regulador de Conductancia de Transmembrana de Fibrosis Quística/metabolismo , Células Epiteliales/inmunología , Células Epiteliales/fisiología , Inmunoglobulina G/metabolismo , Mutación , Secuencia de Aminoácidos , Animales , Fibrosis Quística/inmunología , Fibrosis Quística/patología , Regulador de Conductancia de Transmembrana de Fibrosis Quística/genética , Células Epiteliales/citología , Humanos , Ratones , Ratones Transgénicos , Datos de Secuencia Molecular , Péptidos/genética , Péptidos/metabolismo , Fenilalanina/metabolismo , Poxviridae/genética , Poxviridae/metabolismo , Mucosa Respiratoria/citología , Mucosa Respiratoria/inmunología , Mucosa Respiratoria/patología , Alineación de Secuencia , Ovinos
10.
Clin Transl Sci ; 2(3): 183-92, 2009 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-20443891

RESUMEN

Potential biomarkers were identified for in vitro sensitivity to the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor gefitinib in head and neck cancer. Gefitinib sensitivity was determined in cell lines, followed by transcript profiling coupled with a novel pathway analysis approach. Eleven cell lines were highly sensitive to gefitinib (inhibitor concentration required to give 50% growth inhibition [GI(50)] < 1 microM), three had intermediate sensitivity (GI(50) 1-7 microM), and six were resistant (GI(50) > 7 microM); an exploratory principal component analysis revealed a separation between the genomic profiles of sensitive and resistant cell lines. Subsequently, a hypothesis-driven analysis of Affymetrix data (Affymetrix, Inc., Santa Clara, CA, USA) revealed higher mRNA levels for E-cadherin (CDH1); transforming growth factor, alpha (TGF-alpha); amphiregulin (AREG); FLJ22662; EGFR; p21-activated kinase 6 (PAK6); glutathione S-transferase Pi (GSTP1); and ATP-binding cassette, subfamily C, member 5 (ABCC5) in sensitive versus resistant cell lines. A hypothesis-free analysis identified 46 gene transcripts that were strongly differentiated, seven of which had a known association with EGFR and head and neck cancer (human EGF receptor 3 [HER3], TGF-alpha, CDH1, EGFR, keratin 16 [KRT16], fibroblast growth factor 2 [FGF2], and cortactin [CTTN]). Polymerase chain reaction (PCR) and enzyme-linked immunoabsorbant assay analysis confirmed Affymetrix data, and EGFR gene mutation, amplification, and genomic gain correlated strongly with gefitinib sensitivity. We identified biomarkers that predict for in vitro responsiveness to gefitinib, seven of which have known association with EGFR and head and neck cancer. These in vitro predictive biomarkers may have potential utility in the clinic and warrant further investigation.


Asunto(s)
Antineoplásicos/farmacología , Biomarcadores de Tumor/análisis , Resistencia a Antineoplásicos/efectos de los fármacos , Neoplasias de Cabeza y Cuello/genética , Quinazolinas/farmacología , Antineoplásicos/uso terapéutico , Biomarcadores de Tumor/genética , Línea Celular Tumoral , Análisis Mutacional de ADN , Resistencia a Antineoplásicos/genética , Ensayos de Selección de Medicamentos Antitumorales , Ensayo de Inmunoadsorción Enzimática , Gefitinib , Dosificación de Gen/genética , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Genoma Humano/genética , Humanos , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Quinazolinas/uso terapéutico , ARN Mensajero/genética , ARN Mensajero/metabolismo
11.
BMC Cancer ; 8: 281, 2008 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-18828900

RESUMEN

INTRODUCTION: A functional polymorphism within MDM2, SNP309 T>G, has been linked to early onset cancer. This study examined clinical associations of breast cancer with SNP309 in a Scottish Caucasian population and investigated additional MDM2 intron 1 polymorphisms. METHODS: Intron 1 of MDM2 was PCR amplified and directly sequenced from 299 breast cancer patients and 275 cancer free controls and compared with clinical and pathological parameters. RESULTS: SNP309 was observed, for the control and breast cancer cohorts respectively, at frequencies of: T/T = 44.7% and 39.5%; G/T = 42.2% and 47.2%; G/G = 13.1% and 13.4%, indicating that SNP309 is not a predisposing factor for breast cancer. The 309G/G genotype was associated with high grade tumours (OR = 1.64, 95%CI = 1.06-2.53, p = 0.025) and greater nodal involvement (OR = 2.51, 95%CI = 1.26-4.98, p = 0.009). SNP309 was not associated with an earlier age of cancer diagnosis. No association was observed between genotype and age of breast cancer diagnosis when patients were stratified by menopausal status and estrogen receptor status. Three additional low frequency SNPs were identified: 344T>A, 285G>C and 443G>T, the latter two novel. SNP285 was in complete linkage disequilibrium with SNP309 (D' = 1.0) with the minor alleles being in phase with each other. Moreover, the 285C/C, 309G/G double homozygous genotype was only observed in the breast cancer cohort. CONCLUSION: SNP309G/G is associated with poor prognostic breast cancer features in the Scottish population. Additionally, a novel SNP, SNP285, that is in linkage disequilibrium with SNP309, may also have a role in breast tumorigenesis.


Asunto(s)
Neoplasias de la Mama/genética , Intrones , Desequilibrio de Ligamiento , Polimorfismo de Nucleótido Simple , Proteínas Proto-Oncogénicas c-mdm2/genética , Edad de Inicio , Biomarcadores de Tumor/análisis , Neoplasias de la Mama/química , Neoplasias de la Mama/patología , Estudios de Casos y Controles , Femenino , Predisposición Genética a la Enfermedad , Genotipo , Humanos , Masculino , Menopausia , Pronóstico , Receptores de Estrógenos/análisis , Análisis de Regresión , Escocia
12.
Nat Genet ; 38(12): 1386-96, 2006 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-17099711

RESUMEN

Genetic and epigenetic alterations have been identified that lead to transcriptional deregulation in cancers. Genetic mechanisms may affect single genes or regions containing several neighboring genes, as has been shown for DNA copy number changes. It was recently reported that epigenetic suppression of gene expression can also extend to a whole region; this is known as long-range epigenetic silencing. Various techniques are available for identifying regional genetic alterations, but no large-scale analysis has yet been carried out to obtain an overview of regional epigenetic alterations. We carried out an exhaustive search for regions susceptible to such mechanisms using a combination of transcriptome correlation map analysis and array CGH data for a series of bladder carcinomas. We validated one candidate region experimentally, demonstrating histone methylation leading to the loss of expression of neighboring genes without DNA methylation.


Asunto(s)
Dosificación de Gen , Transcripción Genética , Neoplasias de la Vejiga Urinaria/genética , Línea Celular Tumoral , Cromosomas Humanos Par 3/genética , Metilación de ADN , ADN de Neoplasias/genética , ADN de Neoplasias/metabolismo , Epigénesis Genética , Regulación Neoplásica de la Expresión Génica , Humanos , Análisis de Secuencia por Matrices de Oligonucleótidos
13.
J Invest Dermatol ; 126(8): 1770-5, 2006 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-16810297

RESUMEN

Mutations in the filament aggregating protein (filaggrin) gene have recently been identified as the cause of the common genetic skin disorder ichthyosis vulgaris (IV), the most prevalent inherited disorder of keratinization. The main characteristics of IV are fine-scale on the arms and legs, palmar hyperlinearity, and keratosis pilaris. Here, we have studied six Irish families with IV for mutations in filaggrin. We have identified a new mutation, 3702delG, in addition to further instances of the reported mutations R501X and 2282del4, which are common in people of European origin. A case of a 2282del4 homozygote was also identified. Mutation 3702delG terminates protein translation in filaggrin repeat domain 3, whereas both recurrent mutations occur in repeat 1. These mutations are semidominant: heterozygotes have an intermediate phenotype most readily identified by palmar hyperlinearity and in some cases fine-scale and/or keratosis pilaris, whereas homozygotes or compound heterozygotes generally have more marked ichthyosis. Interestingly, the phenotypes of individuals homozygous for R501X, 2282del4, or compound heterozygous for R501X and 3702delG, were comparable, suggesting that mutations located centrally in the filaggrin repeats are also pathogenic.


Asunto(s)
Dermatitis Atópica/genética , Ictiosis Vulgar/genética , Proteínas de Filamentos Intermediarios/genética , Mutación Puntual , Dermatitis Atópica/epidemiología , Salud de la Familia , Femenino , Proteínas Filagrina , Ligamiento Genético , Predisposición Genética a la Enfermedad , Heterocigoto , Homocigoto , Humanos , Ictiosis Vulgar/epidemiología , Irlanda/epidemiología , Masculino , Linaje , Fenotipo , Prevalencia
14.
J Investig Dermatol Symp Proc ; 10(1): 31-6, 2005 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-16250207

RESUMEN

Keratins are the intermediate filament proteins specifically expressed by epithelial cells. The Human Genome Project has uncovered a total of 54 functional keratin genes that are differentially expressed in specific epithelial structures of the body, many of which involve the epidermis and its appendages. Pachyonychia congenita (PC) is a group of autosomal dominant genodermatoses affecting the nails, thick skin and other ectodermal structures, according to specific sub-type. The major clinical variants of the disorder (PC-1 and PC-2) are known to be caused by dominant-negative mutations in one of four differentiation-specific keratins: K6a, K6b, K16, and K17. A total of 20 human keratin genes are currently linked to single-gene disorders or are predisposing factors in complex traits. In addition, a further six intermediate filament genes have been linked to other non-epithelial genetic disorders. We have established a comprehensive mutation database that catalogs all published independent occurrences of intermediate filament mutations (http://www.interfil.org), with details of phenotypes, published papers, patient support groups and other information. Here, we review the genotype-phenotype trends emerging from the spectrum of mutations in these genes and apply these correlations to make predictions about PC phenotypes based on the site of mutation and keratin pair involved.


Asunto(s)
Bases de Datos Genéticas , Displasia Ectodérmica/genética , Queratinas/genética , Queratodermia Palmoplantar/genética , Uñas Malformadas/genética , Edad de Inicio , Enfermedad de Darier/congénito , Enfermedad de Darier/genética , Epidermólisis Ampollosa Simple/genética , Femenino , Genotipo , Humanos , Queratodermia Palmoplantar/congénito , Masculino , Mutación , Uñas Malformadas/congénito , Fenotipo , Polimorfismo Genético
15.
J Investig Dermatol Symp Proc ; 10(1): 21-30, 2005 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-16250206

RESUMEN

In 1994, the molecular basis of pachyonychia congenita (PC) was elucidated. Four keratin genes are associated with the major subtypes of PC: K6a or K16 defects cause PC-1; and mutations in K6b or K17 cause PC-2. Mutations in keratins, the epithelial-specific intermediate filament proteins, result in aberrant cytoskeletal networks which present clinically as a variety of epithelial fragility phenotypes. To date, mutations in 20 keratin genes are associated with human disorders. Here, we review the genetic basis of PC and report 30 new PC mutations. Of these, 25 mutations were found in PC-1 families and five mutations were identified in PC-2 kindreds. All mutations identified were heterozygous amino acid substitutions or small in-frame deletion mutations with the exception of an unusual mutation in a sporadic case of PC-1. The latter carried a 117 bp duplication resulting in a 39 amino acid insertion in the 2B domain of K6a. Also of note was mutation L388P in K17, which is the first genetic defect identified in the helix termination motif of this protein. Understanding the genetic basis of these disorders allows better counseling for patients and paves the way for therapy development.


Asunto(s)
Displasia Ectodérmica/genética , Queratinas/genética , Queratodermia Palmoplantar/genética , Uñas Malformadas/genética , Secuencia de Bases , ADN/genética , Análisis Mutacional de ADN , Enfermedad de Darier/congénito , Enfermedad de Darier/genética , Femenino , Humanos , Queratodermia Palmoplantar/congénito , Masculino , Mutación , Uñas Malformadas/congénito , Linaje , Fenotipo
16.
Cancer Res ; 65(4): 1376-83, 2005 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-15735024

RESUMEN

Completion of the working draft of the human genome has made it possible to analyze the expression of genes according to their position on the chromosomes. Here, we used a transcriptome data analysis approach involving for each gene the calculation of the correlation between its expression profile and those of its neighbors. We used the U133 Affymetrix transcriptome data set for a series of 130 invasive ductal breast carcinomas to construct chromosomal maps of gene expression correlation (transcriptome correlation map). This highlighted nonrandom clusters of genes along the genome with correlated expression in tumors. Some of the gene clusters identified by this method probably arose because of genetic alterations, as most of the chromosomes with the highest percentage of correlated genes (1q, 8p, 8q, 16p, 16q, 17q, and 20q) were also the most frequent sites of genomic alterations in breast cancer. Our analysis showed that several known breast tumor amplicons (at 8p11-p12, 11q13, and 17q12) are located within clusters of genes with correlated expression. Using hierarchical clustering on samples and a Treeview representation of whole chromosome arms, we observed a higher-order organization of correlated genes, sometimes involving very large chromosomal domains that could extend to a whole chromosome arm. Transcription correlation maps are a new way of visualizing transcriptome data. They will help to identify new genes involved in tumor progression and new mechanisms of gene regulation in tumors.


Asunto(s)
Neoplasias de la Mama/genética , Carcinoma Ductal de Mama/genética , Neoplasias de la Mama/metabolismo , Carcinoma Ductal de Mama/metabolismo , Mapeo Cromosómico , Cromosomas Humanos/genética , Perfilación de la Expresión Génica , Humanos , Análisis de Secuencia por Matrices de Oligonucleótidos , ARN Neoplásico/biosíntesis , ARN Neoplásico/genética
17.
Oncogene ; 23(57): 9201-11, 2004 Dec 09.
Artículo en Inglés | MEDLINE | ID: mdl-15516981

RESUMEN

The b isoform of fibroblast growth factor receptor 2, FGFR2b/FGFR2-IIIb/Ksam-IIC1/KGFR, a tyrosine kinase receptor, is expressed in a wide variety of epithelia and is downregulated in several human carcinomas including prostate, salivary and urothelial cell carcinomas. FGFR2b has been shown to inhibit growth in tumour cell lines derived from these carcinomas. Here, we investigated the molecular mechanisms underlying the inhibition of human urothelial carcinoma cell growth following FGFR2b expression. Using a nylon DNA array, we analysed the gene expression profile of the T24 bladder tumour cell line, transfected or not with a construct encoding FGFR2b. The expression of FGFR2b in T24 cells decreased insulin-like growth factor (IGF)-II mRNA levels. This decrease was correlated with a decrease in IGF-II secretion and may have been responsible for the observed inhibition of cell growth because the addition of exogenous IGF-II restored growth rates to normal levels. Using SU5402, an inhibitor of FGFR tyrosine kinase activity, and a kinase dead mutant of the receptor, FGFR2b Y659F/Y660F, we also demonstrated that the growth inhibition and decrease in IGF-II secretion induced by FGFR2b did not require tyrosine kinase activity. Finally, we demonstrated the involvement of the distal carboxy-terminal domain of the receptor in decreasing IGF-II expression and inhibiting T24 cell growth, as Ksam-IIC3, a variant of FGFR2b carrying a short carboxy-terminus, neither downregulated IGF-II nor inhibited cell proliferation. Our data suggest that FGFR2b inhibits the growth of bladder carcinoma cells by reducing IGF-II levels via its carboxy-terminal domain, independent of its tyrosine kinase activity.


Asunto(s)
División Celular/fisiología , Receptores de Factores de Crecimiento de Fibroblastos/fisiología , Neoplasias de la Vejiga Urinaria/patología , Secuencia de Bases , Línea Celular Tumoral , Cartilla de ADN , Ensayo de Inmunoadsorción Enzimática , Humanos , Factor II del Crecimiento Similar a la Insulina/metabolismo , Receptor Tipo 2 de Factor de Crecimiento de Fibroblastos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Neoplasias de la Vejiga Urinaria/enzimología
18.
J Foot Ankle Surg ; 42(4): 215-20, 2003.
Artículo en Inglés | MEDLINE | ID: mdl-12907932

RESUMEN

Forty-one patients sustaining 49 tears of the peroneal tendons were evaluated prospectively a minimum of 1 year after surgical treatment. Preoperative and postoperative function and activity were assessed by using the American Orthopedic Foot and Ankle (AOFAS) score. Mean age at the time of surgery was 44.0 +/- 11.7 years. Mean follow-up after the index surgery was 35.5 +/- 22.2 months. There were 17 women and 24 men. One woman had bilateral surgery 1 year apart. There were a total of 18 tears of the peroneus longus tendon; 11 of these were isolated, whereas 7 had a combined tear with peroneus brevis. There 31 peroneus brevis tears; 24 of these were isolated and 7 were combined. Using 3-way analysis of variance, there were no significant differences in return to activity or postoperative AOFAS scores among those with a longus, brevis, or combined tear. The mean return to activity for peroneus longus, peroneus brevis, and combined tears were 3.2, 3.6, and 3.7 months, respectively. The mean postoperative AOFAS scores were 90.6, 90.8, and 84.3 respectively. The mean preoperative AOFAS score was 52.0 +/- 16.8. The mean postoperative score was 89.7 +/- 10.3 (P <.00001). Using this scoring system, there were 24 excellent, 12 good, 4 fair, and 2 poor scores. Three patients underwent additional surgery. Fourteen of 16 athletes returned to full sporting level. The average return to activity for the entire group was 3.49 +/- 1.15 months.


Asunto(s)
Pie/cirugía , Recuperación de la Función , Traumatismos de los Tendones/cirugía , Adulto , Anciano , Traumatismos en Atletas/complicaciones , Traumatismos en Atletas/fisiopatología , Traumatismos en Atletas/cirugía , Femenino , Humanos , Masculino , Persona de Mediana Edad , Complicaciones Posoperatorias , Estudios Prospectivos , Rotura , Traumatismos de los Tendones/complicaciones , Traumatismos de los Tendones/fisiopatología
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