Tackling the methylome: recent methodological advances in genome-wide methylation profiling

DNA methylation of promoter CpG islands is strongly associated with gene silencing and is known as a frequent cause of loss of expression of tumor suppressor genes, as well as other genes involved in tumor formation. DNA methylation of driver genes is very likely outnumbered by the number of methylated passenger genes, though these can be useful as tumor markers. Much of what is known about the importance of DNA methylation in cancer was gained through small- and moderate-scale analysis of gene promoters and tumor samples. A much better understanding of the role of DNA methylation in cancer, either as a marker of disease or as an active driver of tumorigenesis, will likely be gained from genome-wide studies of this modification in normal and malignant cells. This goal has become more attainable with the recent introduction of large-scale genome analysis methodologies and these have been modified to allow for investigation of DNA methylation. Several research groups have been formed to coordinate efforts and apply these methodologies to decipher the methylome of healthy and diseased tissues. In this article we review technological advances in genome-wide methylation profiling

Cross-entropy Method In Structural Optimization with Dynamic Constraints

International audienc

Desarrollo de un método activo de medición de oxidantes en el aire

En el presente trabajo se postula que la medición de oxidantes en el aire debido asustancias gaseosas y a la fracción toráxica (MP10) del material particulado podría serun buen indicador de la calidad del aire. Se plantea un método activo para la mediciónde estos oxidantes utilizando una solución captora en base a sulfato ferroso amoniacalen medio ácido (denominada FAA). En esta solución los oxidantes del aire oxidan elFe2+ en Fe3+ que luego es analizado por espectrofotometría. Con una disposición dedos impingers en serie y dos líneas de muestreo, una con un filtro y otra con un ciclónseparador de partículas, fue posible medir los oxidantes gaseosos y los oxidantesasociados al material particulado. Además, la disposición en serie de dos impingers y unanálisis, por separado, de la cantidad recolectada en cada uno de ellos, permite estimarel rendimiento de la captación. Se determinó que el rendimiento de captación delsistema es de 81% en promedio. Con este sistema activo se realizaron dos series demediciones en la ciudad de Cochabamba; una en una zona con poca contaminaciónpor material particulado, pero con elevado nivel de oxidantes y; otra serie en una zonacon elevada contaminación. Los niveles de oxidantes se revelaron ser mucho máselevados en la zona de mayor contaminación, mientras que los niveles de ozono, en losdos sitios estudiados, eran muy similares. El aporte en oxidantes de PM10 está entre un12,3% y 42,5% en relación a los oxidantes totales, el aporte es mayor en las zonas conmayor contaminación por material paniculado. La concentración de oxidantes en elaire que pueden ser asimilados por el organismo (gaseosos y asociados al materialparticulado) puede más que duplicar la concentración de ozono en determinadosepisodios de contaminación. La variación espacial y temporal del nivel de oxidantesestá fuertemente correlacionada con zonas de mayor emisión de contaminantes y conepisodios de baja y alta contaminación. Esto muestra que el nivel de oxidantes en elaire puede ser un buen indicador de la contaminación del aire y el método descrito enel presente trabajo es una buena opción para medirlos cuantitativamente. Esta opciónes sobre todo interesante para los países que no tienen muchos recursos y pocodesarrollo tecnológico ya que el sistema es de tecnología simple, confiable y de bajocosto, tanto en la implementación como en la operación

Steroid-Refractory Acute GVHD: Predictors and Outcomes

Patients with steroid-resistant acute graft versus host disease (aGVHD) have a dismal prognosis, with mortality rates in excess of 90%. We sought to identify a subgroup of patients less likely to benefit from initial therapy with corticosteroids as well as the impact of response on day 14 on outcome. Retrospective evaluation was performed of patients with biopsy-proven aGVHD treated with corticosteroids after allogeneic HSCT at M.D. Anderson Cancer Center from 1998 through 2002 (N = 287). Overall response to first-line therapy on day 14 was 56%. Grade III-IV aGVHD and hyperacute GVHD were the most significant factors predicting failure. Patients who fail to respond to steroids by day 14 should be considered for clinical trials. Severity of aGVHD, hyperacute GVHD, and sex mismatch could be integrated into prognostic scoring systems which may allow for pretreatment identification of patients unlikely to benefit from standard therapy with corticosteroids

Significance of Persistent Cytogenetic Abnormalities on Myeloablative Allogeneic Stem Cell Transplantation in First Complete Remission

AbstractRisk stratification is important to identify patients with acute myelogenous leukemia (AML) who might benefit from allogeneic hematopoietic stem cell transplantation (allo-HSCT) in first complete remission. We retrospectively studied 150 patients with AML and diagnostic cytogenetic abnormalities who underwent myeloablative allo-HSCT while in first complete remission to evaluate the prognostic impact of persistent cytogenetic abnormalities at allo-HSCT. Three risk groups were identified. Patients with favorable/intermediate cytogenetics at diagnosis (n = 49) and patients with unfavorable cytogenetics at diagnosis but without a persistent abnormal clone at allo-HSCT (n = 83) had a similar 3-year leukemia-free survival of 58%-60% despite the higher 3-year relapse incidence (RI) in the latter group (32.3%, versus 16.8% in the former group). A third group of patients with unfavorable cytogenetics at diagnosis and a persistent abnormal clone at allo-HSCT (n = 15) had the worst prognosis, with a 3-year RI of 57.5% and 3-year leukemia-free survival of only 29.2%. These data suggest that patients with AML and unfavorable cytogenetics at diagnosis and a persistent abnormal clone at allo-HSCT are at high risk for relapse after allo-HSCT. These patients should be considered for clinical trials designed to optimize conditioning regimens and/or to use preemptive strategies in the posttransplantion setting aimed at decreasing RI

An Sp1/Sp3 Binding Polymorphism Confers Methylation Protection

Hundreds of genes show aberrant DNA hypermethylation in cancer, yet little is known about the causes of this hypermethylation. We identified RIL as a frequent methylation target in cancer. In search for factors that influence RIL hypermethylation, we found a 12-bp polymorphic sequence around its transcription start site that creates a long allele. Pyrosequencing of homozygous tumors revealed a 2.1-fold higher methylation for the short alleles (P<0.001). Bisulfite sequencing of cancers heterozygous for RIL showed that the short alleles are 3.1-fold more methylated than the long (P<0.001). The comparison of expression levels between unmethylated long and short EBV-transformed cell lines showed no difference in expression in vivo. Electrophorectic mobility shift assay showed that the inserted region of the long allele binds Sp1 and Sp3 transcription factors, a binding that is absent in the short allele. Transient transfection of RIL allele-specific transgenes showed no effects of the additional Sp1 site on transcription early on. However, stable transfection of methylation-seeded constructs showed gradually decreasing transcription levels from the short allele with eventual spreading of de novo methylation. In contrast, the long allele showed stable levels of expression over time as measured by luciferase and ∼2–3-fold lower levels of methylation by bisulfite sequencing (P<0.001), suggesting that the polymorphic Sp1 site protects against time-dependent silencing. Our finding demonstrates that, in some genes, hypermethylation in cancer is dictated by protein-DNA interactions at the promoters and provides a novel mechanism by which genetic polymorphisms can influence an epigenetic state

Análisis Sedimentológico y geomorfológico de áreas lacustres en la Península Fildes, Isla Rey Jorge, Antártica Marítima

Geomorphological features and sedimentary characteristics are analized from five sets of shallow sediment cores collected in lakes in the Fildes Peninsula, King George Island. The geomorphology of the area was observed and sediments samples were obtained at field activities during the XXXI Brazilian Antarctic Operation (March-April/2013). Biogeochemical characteristics, physical parameters, mineralogical composition, particle size distribution, macroscopic characteristics of the sediments and satellite images were analized. Preliminary results indicate climatic and environmental changes in north-south transect of the peninsula. The mineralogical composition is associated with geological structure of the area, where basaltic rocks predominate. The particle size variation reflects different sediment source environments. Macroscopic analysis and mineralogical composition variation reflect the action of weathering along the peninsula. The sediments also have potential mineralization and subsequent release of greenhouse gases. A preliminary map of the classification of the lakes is presented. In addition, it was identified that wetland sediment presents methane production rates (CH4) about 40 times larger and more sensitive to the effect of global warming compared to lake sediment. Subpolar aquatic ecosystems sediments from Maritime Antarctica can be a preferential site for the effects of climate variability