Dissertation (Ph.D.)--University of South Florida, 2007. / Title from PDF of title page. Document formatted into pages; contains 87 pages. Includes vita. Includes bibliographical references.

Thesis (Ph.D.)--University of Alabama at Birmingham, 2007. / Title from first page of PDF file (viewed on June 24, 2009). Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (leaves 91-100).

Pacientes submetidos por longos períodos à diálise peritoneal (DP) podem evoluir com fibrose e redução da capacidade de ultrafiltração da membrana peritoneal (MP). Essas alterações da MP são desencadeadas pela exposição prolongada às soluções de diálise peritoneal, peritonites de repetição e irritantes químicos que induzem inflamação, neoangiogênese e fibrose da MP. A ativação da via Transforming Growth Factor (TGF-beta)/Smad é um fundamental mecanismo mediador da fibrogênese peritoneal. Sendo assim, drogas que inibam a via TGF-beta/Smad são de especial interesse no tratamento da FP. O ácido valpróico (VPA) é um inibidor das histona desacetilases (iHDAC), enzimas que regulam a conformação da cromatina e a expressão gênica, com atividade anti-inflamatória e antifibrótica. O presente estudo tem como objetivo principal avaliar o efeito do VPA em um modelo experimental de fibrose peritoneal em ratos. Vinte e quatro ratos Wistar machos (peso inicial de 280 - 320g) foram dividos em 3 grupos experimentais: CONTROLE (n=8), animais normais que receberam injeções de salina intraperitoneal (IP); FP (n=8), animais que recereberam injeções IP de gluconato de clorexidina (GC) diariamente por 15 dias para indução de fibrose peritoneal; FP+VPA (n=8), animais com FP e tratados com VPA. O ácido valpróico (300mg/kg) foi administrado por gavage diariamente por 15 dias, simultaneamente à indução de fibrose peritoneal. Ao fim dos experimentos, amostras do tecido peritoneal foram coletadas para realização de histologia, imunho-histoquímica (IH), imunofluorescência (IF) e biologia molecular. A análise da MP dos animais do grupo FP revelou um espessamento significativo da camada submesotelial devido ao acúmulo de matriz extracelular e infiltrado inflamatório. O tratamento com VPA foi capaz de prevenir significativamente o espessamento da MP, mantendo a espessura do peritôneo do grupo FP+VPA similar a do grupo CONTROLE. Com relação à função peritoneal, a administração de VPA evitou a queda da ultrafiltração e aumento do transporte peritoneal de glicose induzidos pelo GC. Além disso, o VPA impediu o aumento da expressão de miofibroblastos e de fatores associados à fibrose (TGF-beta, FSP-1 e fibronectina) induzidos pelo GC. Interessantemente, o VPA reduziu de maneira significativa a expressão da Smad3, mediador intracelular crítico da sinalização TGF-beta/Smad, em relação ao grupo FP. Por outro lado, os animais tratados com VPA apresentaram um aumento da expressão peritoneal de fatores antifibróticos como a BMP-7 e Smad7, proteínas que contrarregulam as ações do TGF-beta. Além de atenuar a fibrose peritoneal, o VPA apresentou efeitos anti-inflamatório e antiangiogênico, demonstrado pela menor expressão de citocinas pró-inflamatórias, fatores quimiotáticos para macrófagos (MCP-1) e VEGF no grupo FP+VPA quando comparado ao grupo FP. Em resumo, o VPA foi capaz de bloquear o espessamento por fibrose da MP e preservar a sua função, além de proteger o peritônio contra a neoangiogênese e inflamação. Além disso, o VPA induziu um aumento da expressão de fatores antifibróticos na MP. Os resultados apresentados neste trabalho chamam a atenção para mecanismos envolvidos nas modificações da MP induzidas pela DP ainda pouco explorados e que podem constiuir potenciais alvos na prevenção do desenvolvimento da fibrose peritoneal associada à DP / Long term peritoneal dialysis (PF) can induce peritoneal fibrosis and loss of ultrafiltration capacity of peritoneal membrane (PM). These peritoneal changes are due to prolonged exposure to peritoneal dialysis solutions, chemical irritants and acute peritonitis episodes that induce inflammation, neoangiogenesis and PM fibrosis. The Transforming Growth Factor (TGF-?) is the main mediator involved in the development of peritoneal fibrosis. Thus, drugs that inhibit the TGF-?/Smad pathway or inflammation are of particular interest in the treatment of PF. Valproic acid (VPA) is an histone deacetylase (HDAC) inhibitor. HDACs are enzymes that regulate chromatin conformation and gene expression. Recent studies have described HDACi as promising drugs in the treatment of inflammatory and fibrotic diseases. The main aim of this study was to evaluate the effect of VPA in an experimental model of peritoneal fibrosis in rats. Twenty four Wistar rats (initial weight of 280-320g) were divided into three experimental groups: CONTROL (n = 8), normal animals that received only saline ip; FP (n = 8), peritoneal fibrosis was induced by daily Gluconate Clorhexedine (GC) intraperitoneal (IP) injections for 15 days; FP+VPA (n = 8), animals with peritoneal fibrosis and treated with VPA. Daily valproic acid (300mg/kg) doses were administered by gavage simultaneously with the induction of peritoneal fibrosis in the FP+VPA group. At the end of experiments, the animals were submitted to euthanasia and samples of peritoneal tissue were collected for histology, immunocytochemistry, immunofluorescence, and molecular biology. Also, a functional peritoneal test was performed. The FP group showed a significant thickening of PM due to the accumulation of extracellular matrix and inflammatory cellular infiltration. VPA treatment was able to significantly prevent PM thickening, maintaining the peritoneal thickness of the VPA group similar to that of the CONTROL group. The VPA administration also preserved peritoneal function in the FP+VPA group, avoiding the reduction of ultrafiltration and increasing of peritoneal glucose transport induced by GC. According to the histological changes mentioned above, the VPA hampered the upregulation of the pro-fibrotic genes (TGF-beta, FSP-1, and fibronectin) and increase in the myofibroblasts expression induced by GC injections. Interestingly, the peritoneal expression of phosphorylated Smad3 detected by immunohistochemistry and Smad3 mRNA was significantly higher in the FP group. However, this effect was attenuated by VPA treatment. On the other hand, VPA was able to induce an increase in the expression of the antifibrotic factors, such as BMP-7 and Smad7, in the peritoneal membrane. Besides its antifibrotic activity, VPA also showed anti-inflammatory and anti-angiogenic effects. Animals of the FP+VPA group showed a significant reduction of the PM expression of pro-inflmmatory cytokines, macrophage chemoattractants and, VEGF expression when compared with FP group. In conclusion, we have shown that VPA inhibits the progression of peritoneal fibrosis in a CG-induced peritoneal fibrosis model in rats. VPA inhibited different and important mechanisms involved in peritoneal membrane modifications induced by PD, as activation of TGF-beta/Smad pathway, inflammation, and angiogenesis. Notably, VPA induced the expression of antifibrotic factors. Our results are very interesting and shed lights on a new perspective for the treatment of peritoneal fibrosis. However, this is an exploratory study and future studies are needed before to translate this experimental finding into clinical application

Cardiovascular diseases are one of the leading causes of mortality. A common denominator across most of the cardiovascular diseases like diabetic cardiomyopathy, hypertrophic cardiomyopathy, myocardial infarction and dilated cardiomyopathy is the pathological remodelling of heart leading to fibrosis. Cardiac fibrosis is characterized by the excessive production and deposition of extracellular matrix components due to unwarranted proliferation of fibroblasts. Under normal conditions, following cardiac remodelling, my fibroblasts undergo programmed cell death. However, this does not happen under pathological conditions ultimately leading to fibrosis. Although the molecular events and signalling pathways that contribute to the development of cardiac fibrosis is well established, there are limited studies which try to understand the mechanisms by which fibroblasts persist and resist programmed cell death. Here we demonstrate that SIRT6, one of the members of sirtuin family of histone deacetylases, plays an important role in regulating my fibroblast cell death. When we analysed the mice hearts and isolated fibroblasts deficient in SIRT6, we observed increased expression of my fibroblast markers, suggesting that SIRT6 deficient hearts might have a high proportion of resident my fibroblasts. Also, when SIRT6 deficient fibroblasts were subjected to genotoxic stress, they showed reduced cell death and impaired mitochondrial to nuclear AIF translocation as compared to WT controls. An important regulator of AIF mediated cell death is the protein PARP-1. When we checked the expression levels of this protein under SIRT6 deficient conditions, it was found to be low. PARP-1 was also found to degrade faster under SIRT6 deficient conditions. Further qPCR analysis revealed that the transcript levels of PARP-1 were unaffected by SIRT6 suggesting that the regulation might not be at the transcriptional level. When we studied the acetylation of PARP-1 under SIRT6 deficient conditions we found the protein to be hypo-acetylated indicating a more complex mechanism of regulation.

A rapid cascade of regulatory events defines the differentiated fates of embryonic cells, however, once established, these differentiated fates and the underlying transcriptional programs can be remarkably stable. Here, we describe two proteins, MEP-1, a novel protein, and LET-418/Mi-2, both of which are required for the maintenance of somatic differentiation in C. elegans. MEP-1 was identified as an interactor of PIE-1, a germ-specific protein required for germ cell specification, while LET-418 is a protein homologous to Mi-2, a core component of the nuc1eosome remodeling/histone deacetylase (NuRD) complex. In animals lacking MEP-1 and LET-418, germline-specific genes become derepressed in somatic cells, and Polycomb group (PcG) and SET domain-related proteins promote this ectopic expression. We demonstrate that PIE-1 forms a complex with MEP-1, LET-418, and HDA-1. Furthermore, we show that the overexpression of PIE-1 can mimic the mep-1/let-418 phenotype, and that PIE-1 can inhibit the Histone deacetylase activity of the HDA-1 complex in COS cells. Our findings support a model in which PIE-1 transiently inhibits MEP-1 and associated factors to maintain the pluripotency of germ cells, while at later times MEP-1 and LET-418 remodel chromatin to establish new stage- or cell-type-specific differentiation potential.

Coronary vessel development is a crucial part of heart development requiring the interplay of the epicardial, myocardial and endocardial layers of the heart for proper formation. Coronary vascularization is regulated by a host of transcription factors further regulated by chromatin remodeling enzymes, including Histone Deacetylases (HDACs). To investigate the functions of HDACs in coronary vascular development, we have deleted Hdac3 in endocardial cells using Cre LoxP technology. Endocardial cell-­‐specific deletion of Hdac3 results in aberrant coronary vessel formation and complete postnatal lethality. We have thus shown that Hdac3 is a critical regulator of the coronary vascular development pathway.

No description available.

No description available.

Les histones sont des protéines nucléaires hautement conservées chez les cellules des eucaryotes. Elles permettent d’organiser et de compacter l’ADN sous la forme de nucléosomes, ceux-ci representant les sous unités de base de la chromatine. Les histones peuvent être modifiées par de nombreuses modifications post-traductionnelles (PTMs) telles que l’acétylation, la méthylation et la phosphorylation. Ces modifications jouent un rôle essentiel dans la réplication de l’ADN, la transcription et l’assemblage de la chromatine. L’abondance de ces modifications peut varier de facon significative lors du developpement des maladies incluant plusieurs types de cancer. Par exemple, la perte totale de la triméthylation sur H4K20 ainsi que l’acétylation sur H4K16 sont des marqueurs tumoraux spécifiques a certains types de cancer chez l’humain. Par conséquent, l’étude de ces modifications et des événements determinant la dynamique des leurs changements d’abondance sont des atouts importants pour mieux comprendre les fonctions cellulaires et moléculaires lors du développement de la maladie. De manière générale, les modifications des histones sont étudiées par des approches biochimiques telles que les immuno-buvardage de type Western ou les méthodes d’immunoprécipitation de la chromatine (ChIP). Cependant, ces approches présentent plusieurs inconvénients telles que le manque de spécificité ou la disponibilité des anticorps, leur coût ou encore la difficulté de les produire et de les valider. Au cours des dernières décennies, la spectrométrie de masse (MS) s’est avérée être une méthode performante pour la caractérisation et la quantification des modifications d’histones. La MS offre de nombreux avantages par rapport aux techniques traditionnelles. Entre autre, elle permet d’effectuer des analyses reproductibles, spécifiques et facilite l’etude d’un large spectre de PTMs en une seule analyse. Dans cette thèse, nous présenterons le développement et l’application de nouveaux outils analytiques pour l’identification et à la quantification des PTMs modifiant les histones. Dans un premier temps, une méthode a été développée pour mesurer les changements d’acétylation spécifiques à certains sites des histones. Cette méthode combine l’analyse des histones intactes et les méthodes de séquençage peptidique afin de déterminer les changements d’acétylation suite à la réaction in vitro par l’histone acétyltransférase (HAT) de levure Rtt109 en présence de ses chaperonnes (Asf1 ou Vps75). Dans un second temps, nous avons développé une méthode d’analyse des peptides isomériques des histones. Cette méthode combine la LC-MS/MS à haute résolution et un nouvel outil informatique appelé Iso-PeptidAce qui permet de déconvoluer les spectres mixtes de peptides isomériques. Nous avons évalué Iso-PeptidAce avec un mélange de peptides synthétiques isomériques. Nous avons également validé les performances de cette approche avec des histones isolées de cellules humaines érythroleucémiques (K562) traitées avec des inhibiteurs d’histones désacétylases (HDACi) utilisés en clinique, et des histones de Saccharomyces cerevisiae liées au facteur d’assemblage de la chromatine (CAF-1) purifiées par chromatographie d’affinité. Enfin, en utilisant la méthode présentée précédemment, nous avons fait une analyse approfondie de la spécificité de plusieurs HATs et HDACs chez Schizosaccharomyces pombe. Nous avons donc déterminé les niveaux d’acétylation d’histones purifiées à partir de cellules contrôles ou de souches mutantes auxquelles il manque une HAT ou HDAC. Notre analyse nous a permis de valider plusieurs cibles connues des HATs et HDACs et d’en identifier de nouvelles. Nos données ont également permis de définir le rôle des différentes HATs et HDACs dans le maintien de l’équilibre d’acétylation des histones. Dans l’ensemble, nous anticipons que les méthodes décrites dans cette thèse permettront de résoudre certains défis rencontrés dans l’étude de la chromatine. De plus, ces données apportent de nouvelles connaissances pour l’élaboration d’études génétiques et biochimiques utilisant S. pombe. / Histones are highly conserved, basic proteins found in eukaryotic cell nuclei. They organize and package DNA strands into nucleosome core particles (NCPs), the fundamental repeating units of eukaryotic chromatin. The histones are subject to a wide variety of posttranslational modifications (PTMs) including acetylation, methylation and phosphorylation. These PTMs play an essential role in DNA-replication, transcription, and chromatin assembly. Alterations in histone PTM abundances have been implicated in several types of cancer. For example, the global loss of trimethylation at H4K20 and acetylation at H4K16 is a hallmark of human cancers. Thus, characterization of histone PTMs and their dynamics is extremely useful for elucidating normal cellular functions and molecular pathways that lead to diseases. Traditionally, histone PTMs are analyzed using antibody-based approaches such as western blot and chromatin immunoprecipitation (ChIP) assays. These methods, however, suffer from several limitations including antibody cross-reactivity, epitope occlusion, and the cost and difficulty in producing and validating antibodies. Over the last decade, mass spectrometry (MS) has emerged as a powerful technique for the characterization and quantification of histone PTMs. MS offers several advantages over the traditional approaches including reproducibility, specificity, and ability to rapidly analyze numerous PTMs in a single experiment. In this thesis, the development and applications of novel analytical tools for the identification and quantification of histone PTMs are presented. First, a method useful for measuring the global and site specific changes in histone acetylation is described. This method combines intact mass analysis and peptide sequencing approaches to study the global and site specific changes in histone acetylation during in vitro assays with yeast Rtt109 and its chaperone (Asf1 or Vps75). Second, a method for analysis of isomeric histone peptides is presented. This method combines a high resolution LC-MS/MS with a novel bioinformatics tool called Iso-PeptidAce to deconvolute mixed spectra of co-eluting isomeric peptides. We benchmarked Iso-PeptidAce using mixtures of synthetic isomeric peptides. We demonstrated its capability in histones isolated from human erythroleukemic (K562) cells treated with clinically relevant histone deacetylase inhibitors (HDACi) and in affinity-purified S. cerevisiae histones bound to chromatin assembly factor-1 (CAF-1). Third, by employing the above methods, an in-depth quantitative analysis of the substrate specificities of several fission yeast HATs and HDACs was assessed. We determined the acetylation site occupancy of multiple lysines in histones isolated from a control or mutant strains lacking specific HAT or HDAC activities. Our analysis identified several known and novel HAT and HDAC target sites. Our data also defined the division of labor between the different HATs and HDACs in maintaining the steady-state level of histone acetylation. Overall, we anticipate that the methods described in this thesis will address some of the existing challenges facing the chromatin field. Moreover, the data presented will provide valuable insights for future genetic and biochemical studies involving the fission yeast.