Genetic And Epigenetic Determinants In Autoinflammatory Diseases

The concept of autoinflammation has evolved over the past 20 years, beginning with the discovery that mutations in the Mediterranean Fever (MEFV) gene were causative of Familial Mediterranean Fever. Currently, autoinflammatory diseases comprise a wide range of disorders with the common features of recurrent fever attacks, prevalence of hyperreactive innate immune cells, and signs of inflammation that can be systemic or organ specific in the absence of pathogenic infection of autoimmunity. Innate immune cells from the myeloid compartment are the main effectors of uncontrolled inflammation that is caused in great extent by the overproduction of inflammatory cytokines such as IL-1 beta and IL-18. Defects in several signaling pathways that control innate immune defense, particularly the hyperreactivity of one or more inflammasomes, are at the core of pathologic autoinflammatory phenotypes. Although many of the autoinflammatory syndromes are known to be monogenic, some of them are genetically complex and are impacted by environmental factors. Recently, epigenetic dysregulation has surfaced as an additional contributor to pathogenesis. In the present review, we discuss data that are currently available to describe the contribution of epigenetic mechanisms in autoinflammatory diseases

A Role for Methyl-CpG Binding Domain Protein 2 in the Modulation of the Estrogen Response of pS2/TFF1 Gene

Background: In human Estrogen Receptor alpha (ER alpha)-positive breast cancers, 59 end dense methylation of the estrogen-regulated pS2/TFF1 gene correlates with its transcriptional inhibition. However, in some ER alpha-rich biopsies, pS2 expression is observed despite the methylation of its TATA-box region. Herein, we investigated the methylation-dependent mechanism of pS2 regulation. Methodology/Principal Findings: We observed interplay between Methyl-CpG Binding Domain protein 2 (MBD2) transcriptional repressor and ER alpha transactivator: (i) the pS2 gene is poised for transcription upon demethylation limited to the enhancer region containing the estrogen responsive element (ERE); (ii) MBD2-binding sites overlapped with the methylation status of the pS2 59 end; (iii) MBD2 depletion elevated pS2 expression and ectopic expression of ER alpha partially overcame the inhibitory effect of MBD2 when the ERE is unmethylated. Furthermore, serial chromatin immunoprecipitation assays indicated that MBD2 and ER alpha could simultaneously occupy the same pS2 DNA molecule; (iv) concomitant ectopic ER alpha expression and MBD2 depletion resulted in synergistic transcriptional stimulation, while the pS2 promoter remains methylated. Conclusions/Significance: MBD2 and ER alpha drive opposite effects on pS2 expression, which are associated with specific steady state levels of histone H3 acetylation and methylation marks. Thus, epigenetic silencing of pS2 could be dependent on balance of the relative intracellular concentrations of ER alpha and MBD2

The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties

The methyl-CpG binding domain (MBD) family of proteins was defined based on sequence similarity in their DNA binding domains. In light of their high degree of conservation, it is of inherent interest to determine the genomic distribution of these proteins, and their associated co-repressor complexes. One potential determinant of specificity resides in differences in the intrinsic DNA binding properties of the various MBD proteins. In this report, we use a capillary electrophoretic mobility shift assay (CEMSA) with laser-induced fluorescence (LIF) and neutral capillaries to calculate MBD-DNA binding affinities. MBD proteins were assayed on pairs of methylated and unmethylated duplex oligos corresponding to the promoter regions of the BRCA1, MLH1, GSTP1 and p16(INK4a) genes, and binding affinities for each case were calculated by Scatchard analyses. With the exception of mammalian MBD3 and Xenopus MBD3 LF, all the MBD proteins showed higher affinity for methylated DNA (in the nanomolar range) than for unmethylated DNA (in the micromolar range). Significant differences between MBD proteins in the affinity for methylated DNA were observed, ranging within two orders of magnitude. By mutational analysis of MBD3 and using CEMSA, we demonstrate the critical role of specific residues within the MBD in conferring selectivity for methylated DNA. Interestingly, the binding affinity of specific MBD proteins for methylated DNA fragments from naturally occurring sequences are affected by local methyl-CpG spacing

La justicia en el tráfico: Conocimiento y valoración de la población española.

La norma existe sea cual sea su manifestación, porque es producto y necesidad de la interacción entre las personas. Pero no tiene sentido si nadie controla que ésta se cumpla. Necesitamos a alguien que administre finalmente las sanciones cuando no se cumpla la norma. Necesitamos algo/alguien que administre la veracidad de que los comportamientos realmente se han producido, de la intención de los mismos, que evalúe la gravedad, que los ponga en relación con lo que las normas dicen, sus excepciones… Necesitamos juzgar antes de sancionar. Es necesario aplicar la justicia. Cada uno de nosotros en algún momento asumimos alguno o todos estos roles a la vez. En efecto, en muchas de nuestras actuaciones diarias, ya sean laborales, familiares…, dictamos normas, controlamos que éstas se cumplan y si se nos permite decirlo, dictamos sentencias para los individuos sobre los que tenemos influencias. En el tema del tráfico, de los accidentes e incidentes, como en toda conducta que se lleva a cabo en un sistema interactivo, hay víctimas y culpables/responsables. En nuestro país existe una tendencia abrumadora en los últimos tiempos, de “intensificar temporalmente los controles”, a intentar establecer nuevas fórmulas sancionadoras e incluso aumentar la calificación de gravedad de la infracción, así como su cuantía. Una de las preguntas que surgen a colación de esto sería ¿se justifica este empeño en detrimento de otras medidas?, ¿se atiende a las variables que, al menos teóricamente aumentarán la eficacia de estas medidas? Hemos constatado que realizando un estudio poblacional facilitamos los posicionamientos de las personas e incrementamos la riqueza en las discusiones a través de todas las variables que hemos podido tratar. Conocer los pensamientos de la población española nos va a permitir, sin lugar a dudas, analizar el problema con mayor rigor, así como proponer soluciones (medidas y contramedidas) más ajustadas a la realidad social sobre la que se va a aplicar. Con ello, pretendemos convertir este libro en manual de consulta para aquellos que intervienen en el marco de la seguridad vial tanto a nivel general como a nivel de los que participan más activamente en el tema más especifico que aquí trabajamos. El libro se ha estructurado en tres grandes partes: En la primera de ellas, para permitir una composición mejor acerca de las circunstancias de las que se han extraído los datos del estudio, se describe la metodología del mismo. En una segunda parte presentamos los más relevantes y significativos resultados del estudio, capítulo que está dividido en diferentes bloques: Normativa, Supervisión Policial, Sanciones, Justicia, Modelos de Respuesta y Medidas. Los cuatro primeros bloques aunque son independientes, puesto que tratan aspectos distintos de un proceso que tiene una cronología relativamente clara, tienen un cierto grado de relación que indudablemente va a quedar reflejado en un análisis que cruza algunas de estas variables con el quinto bloque. Además, este quinto bloque que aborda una serie de conductas, de las cuales algunas son sancionables y otras no lo son, tiene un análisis autónomo que trata de reflejar las relaciones que tiene el continuo con las conductas, las creencias, los conocimientos, las actitudes, etc. En el sexto bloque se analizan, también desde el doble enfoque: de forma autónoma y en relación con los otros, las medidas que se llevan o se pueden llevar a cabo y que tienen relación con la temática que estamos trabajando. En realidad, “medidas” son todos los puntos tratados, pero en este bloque analizamos algunas características diferenciales de las mismas tal y como existen y tal y como podrían ser que, nos parece, tienen una implicación diferencial En una tercera parte, realizamos un recorrido sobre algunos de los resultados que, siendo significativos, puedan ofrecer un panorama general de los conocimientos obtenidos mediante esta investigación. Y lo hacemos desde la óptica, que nunca debemos perder, de las implicaciones que los mismos pueden tener desde un punto de vista aplicado. Recogemos en este libro “análisis complementarios” y conclusiones que nos ayuden a encontrar respuestas en la búsqueda de la máxima eficacia y eficiencia del sistema, considerando sus posibles alternativas

Los jóvenes en el tráfico: Una visión en primera persona

Los accidentes de tráfico de los conductores jóvenes son un problema de salud y consecuentemente es importante intentar comprender qué está pasando. Los jóvenes constituyen un grupo ampliamente declarado de alto riesgo, donde se conjuga la juventud con la inexperiencia, es y ha de ser, por su inminente o reciente participación en el sistema de tráfico, un grupo objeto de la educación y la formación vial. Los jóvenes, los jóvenes que exhiben conductas de riesgo, los jóvenes que exhiben una conducción arriesgada, han sido objeto de una extensa investigación. Hay muchos factores que contribuyen a la formación de estas actitudes, creencias y comportamientos. Los medios de comunicación, especialmente la televisión, los padres y los "iguales" son centros de influencia que a menudo actúan mediante la potenciación de las actitudes y comportamientos negativos. Es por ello que no podemos responsabilizar en mayor medida a los jóvenes sin que paralelamente nos responsabilicemos más nosotros en lo que se refiere a nuestros comportamientos en general y en los que tenemos con respecto a ellos, al menos en lo que se refiere al tráfico y la seguridad vial. Hemos considerado necesario realizar un análisis de lo que opina la población española, de lo que opinan los jóvenes, toda vez que indagamos en otras cuestiones como sus actitudes, la relación con sus padres, en relación siempre con la seguridad vial. Sin habernos olvidado de abordar aspectos que tienen que ver con las creencias, las actitudes y los conocimientos, nos vamos a centrar en averiguar otros aspectos como son: los jóvenes en su relación con el tráfico y con sus vehículos (ambos hechos objetivos), el historial de accidentes y la tasa de infracciones que suelen cometer (restringidas a unas infracciones específicas), y en su defensa, cómo no, la relación que tienen estas infracciones y accidentes con las de sus padres en lo que hemos venido a titular “padres y jóvenes unidos por el tráfico”, amén de tratar de establecer qué relación tiene todo esto con sus estilos de vida. Y para ello, el libro se ha estructurado en tres grandes apartados: En el primero de ellos, para permitir una composición mejor acerca de las circunstancias de dónde se han extraído los datos del estudio, se describe la metodología del mismo. En un segundo apartado presentamos los más relevantes y significativos resultados del estudio. En un tercer apartado, realizamos un recorrido sobre algunos de los resultados que, siendo significativos, puedan ofrecer un panorama general de los conocimientos obtenidos mediante esta investigación. Y lo hacemos desde la óptica, que nunca debemos perder, de las implicaciones que los mismos pueden tener desde un punto de vista aplicado

DNA methylation polymorphisms precede any histological sign of atherosclerosis in mice lacking apolipoprotein E

The present work investigates the occurrence and significance of aberrant DNA methylation patterns during early stages of atherosclerosis. To this end, we asked whether the genetically atherosclerosis-prone APOE-null mice show any changes in DNA methylation patterns before the appearance of histologically detectable vascular lesion. We exploited a combination of various techniques: DNA fingerprinting, in vitro methyl-accepting assay, 5-methylcytosine quantitation, histone post-translational modification analysis, Southern blotting, and PCR. Our results show that alterations in DNA methylation profiles, including both hyper- and hypomethylation, were present in aortas and PBMC of 4-week-old mutant mice with no detectable atherosclerotic lesion. Sequencing and expression analysis of 60 leukocytic polymorphisms revealed that epigenetic changes involve transcribed genic sequences, as well as repeated interspersed elements. Furthermore, we showed for the first time that atherogenic lipoproteins promote global DNA hypermethylation in a human monocyte cell line. Taken together, our results unequivocally show that alterations in DNA methylation profiles are early markers of atherosclerosis in a mouse model and may play a causative role in atherogenesis

SIRT1/2 orchestrate acquisition of DNA methylation and loss of histone H3 activating marks to prevent premature activation of inflammatory genes in macrophages

Sirtuins 1 and 2 (SIRT1/2) are two NAD-dependent deacetylases with major roles in inflammation. In addition to deacetylating histones and other proteins, SIRT1/2-mediated regulation is coupled with other epigenetic enzymes. Here, we investigate the links between SIRT1/2 activity and DNA methylation in macrophage differentiation due to their relevance in myeloid cells. SIRT1/2 display drastic upregulation during macrophage differentiation and their inhibition impacts the expression of many inflammation-related genes. In this context, SIRT1/2 inhibition abrogates DNA methylation gains, but does not affect demethylation. Inhibition of hypermethylation occurs at many inflammatory loci, which results in more drastic upregulation of their expression upon macrophage polarization following bacterial lipopolysaccharide (LPS) challenge. SIRT1/2-mediated gains of methylation concur with decreases in activating histone marks, and their inhibition revert these histone marks to resemble an open chromatin. Remarkably, specific inhibition of DNA methyltransferases is sufficient to upregulate inflammatory genes that are maintained in a silent state by SIRT1/2. Both SIRT1 and SIRT2 directly interact with DNMT3B, and their binding to proinflammatory genes is lost upon exposure to LPS or through pharmacological inhibition of their activity. In all, we describe a novel role for SIRT1/2 to restrict premature activation of proinflammatory genes

Epstein–Barr virus-mediated transformation of B cells induces global chromatin changes independent to the acquisition of proliferation

Epstein-Barr virus (EBV) infects and transforms human primary B cells inducing indefinite proliferation. To investigate the potential participation of chromatin mechanisms during the EBV-mediated transformation of resting B cells we performed an analysis of global changes in histone modifications. We observed a remarkable decrease and redistribution of heterochromatin marks including H4K20me3, H3K27me3 and H3K9me3. Loss of H4K20me3 and H3K9me3 occurred at constitutive heterochromatin repeats. For H3K27me3 and H3K9me3, comparison of ChIP-seq data revealed a decrease in these marks in thousands of genes, including clusters of HOX and ZNF genes, respectively. Moreover, DNase-seq data comparison between resting and EBV-transformed B cells revealed increased endonuclease accessibility in thousands of genomic sites. We observed that both loss of H3K27me3 and increased accessibility are associated with transcriptional activation. These changes only occurred in B cells transformed with EBV and not in those stimulated to proliferate with CD40L/IL-4, despite their similarities in the cell pathways involved and proliferation rates. In fact, B cells infected with EBNA-2 deficient EBV, which have much lower proliferation rates, displayed similar decreases for heterochromatic histone marks. Our study describes a novel phenomenon related to transformation of B cells, and highlights its independence of the pure acquisition of proliferation

Data integration in the era of omics: current and future challenges

To integrate heterogeneous and large omics data constitutes not only a conceptual challenge but a practical hurdle in the daily analysis of omics data. With the rise of novel omics technologies and through large-scale consortia projects, biological systems are being further investigated at an unprecedented scale generating heterogeneous and often large data sets. These data-sets encourage researchers to develop novel data integration methodologies. In this introduction we review the definition and characterize current efforts on data integration in the life sciences. We have used a web-survey to assess current research projects on data-integration to tap into the views, needs and challenges as currently perceived by parts of the research community

Epigenome-Wide Comparative Study Reveals Key Differences Between Mixed Connective Tissue Disease and Related Systemic Autoimmune Diseases

Mixed Connective Tissue Disease (MCTD) is a rare complex systemic autoimmune disease (SAD) characterized by the presence of increased levels of anti-U1 ribonucleoprotein autoantibodies and signs and symptoms that resemble other SADs such as systemic sclerosis (SSc), rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE). Due to its low prevalence, this disease has been very poorly studied at the molecular level. We performed for the first time an epigenome-wide association study interrogating DNA methylation data obtained with the Infinium MethylationEPIC array from whole blood samples in 31 patients diagnosed with MCTD and 255 healthy subjects. We observed a pervasive hypomethylation involving 170 genes enriched for immune-related function such as those involved in type I interferon signaling pathways or in negative regulation of viral genome replication. We mostly identified epigenetic signals at genes previously implicated in other SADs, for example MX1, PARP9, DDX60, or IFI44L, for which we also observed that MCTD patients exhibit higher DNA methylation variability compared with controls, suggesting that these sites might be involved in plastic immune responses that are relevant to the disease. Through methylation quantitative trait locus (meQTL) analysis we identified widespread local genetic effects influencing DNA methylation variability at MCTD-associated sites. Interestingly, for IRF7, IFI44 genes, and the HLA region we have evidence that they could be exerting a genetic risk on MCTD mediated through DNA methylation changes. Comparison of MCTD-associated epigenome with patients diagnosed with SLE, or Sjogren's Syndrome, reveals a common interferon-related epigenetic signature, however we find substantial epigenetic differences when compared with patients diagnosed with rheumatoid arthritis and systemic sclerosis. Furthermore, we show that MCTD-associated CpGs are potential epigenetic biomarkers with high diagnostic value. Our study serves to reveal new genes and pathways involved in MCTD, to illustrate the important role of epigenetic modifications in MCTD pathology, in mediating the interaction between different genetic and environmental MCTD risk factors, and as potential biomarkers of SADs