CR2Cancer: a database for chromatin regulators in human cancer.

Chromatin regulators (CRs) can dynamically modulate chromatin architecture to epigenetically regulate gene expression in response to intrinsic and extrinsic signalling cues. Somatic alterations or misexpression of CRs might reprogram the epigenomic landscape of chromatin, which in turn lead to a wide range of common diseases, notably cancer. Here, we present CR2Cancer, a comprehensive annotation and visualization database for CRs in human cancer constructed by high throughput data analysis and literature mining. We collected and integrated genomic, transcriptomic, proteomic, clinical and functional information for over 400 CRs across multiple cancer types. We also built diverse types of CR-associated relations, including cancer type dependent (CR-target and miRNA-CR) and independent (protein-protein interaction and drug-target) ones. Furthermore, we manually curated around 6000 items of aberrant molecular alterations and interactions of CRs in cancer development from 5007 publications. CR2Cancer provides a user-friendly web interface to conveniently browse, search and download data of interest. We believe that this database would become a valuable resource for cancer epigenetics investigation and potential clinical application. CR2Cancer is freely available at http://cis.hku.hk/CR2Cancer.

Recent Advances in Enzymatic Complexity Generation: Cyclization Reactions.

Enzymes in biosynthetic pathways, especially in plant and microbial metabolism, generate structural and functional group complexity in small molecules by conversion of acyclic frameworks to cyclic scaffolds via short, efficient routes. The distinct chemical logic used by several distinct classes of cyclases, oxidative and non-oxidative, has recently been elucidated by genome mining, heterologous expression, and genetic and mechanistic analyses. These include enzymes performing pericyclic transformations, pyran synthases, tandem acting epoxygenases, and epoxide "hydrolases", as well as oxygenases and radical S-adenosylmethionine enzymes that involve rearrangements of substrate radicals under aerobic or anaerobic conditions.

Advances in enzyme bioelectrochemistry

ABSTRACT Bioelectrochemistry can be defined as a branch of Chemical Science concerned with electron-proton transfer and transport involving biomolecules, as well as electrode reactions of redox enzymes. The bioelectrochemical reactions and system have direct impact in biotechnological development, in medical devices designing, in the behavior of DNA-protein complexes, in green-energy and bioenergy concepts, and make it possible an understanding of metabolism of all living organisms (e.g. humans) where biomolecules are integral to health and proper functioning. In the last years, many researchers have dedicated itself to study different redox enzymes by using electrochemistry, aiming to understand their mechanisms and to develop promising bioanodes and biocathodes for biofuel cells as well as to develop biosensors and implantable bioelectronics devices. Inside this scope, this review try to introduce and contemplate some relevant topics for enzyme bioelectrochemistry, such as the immobilization of the enzymes at electrode surfaces, the electron transfer, the bioelectrocatalysis, and new techniques conjugated with electrochemistry vising understand the kinetics and thermodynamics of redox proteins. Furthermore, examples of recent approaches in designing biosensors and biofuel developed are presented.

Analysis of the intricate relationship between chronic inflammation and cancer.

Deregulated inflammatory response plays a pivotal role in the initiation, development and progression of tumours. Potential molecular mechanism(s) that drive the establishment of an inflammatory-tumour microenvironment is not entirely understood owing to the complex cross-talk between pro-inflammatory and tumorigenic mediators such as cytokines, chemokines, oncogenes, enzymes, transcription factors and immune cells. These molecular mediators are critical linchpins between inflammation and cancer, and their activation and/or deactivation are influenced by both extrinsic (i.e. environmental and lifestyle) and intrinsic (i.e. hereditary) factors. At present, the research pertaining to inflammation-associated cancers is accumulating at an exponential rate. Interest stems from hope that new therapeutic strategies against molecular mediators can be identified to assist in cancer treatment and patient management. The present review outlines the various molecular and cellular inflammatory mediators responsible for tumour initiation, progression and development, and discusses the critical role of chronic inflammation in tumorigenesis.

Antioxidant enzymes as redox-based biomarkers: a brief review.

The field of redox proteomics focuses to a large extent on analyzing cysteine oxidation in proteins under different experimental conditions and states of diseases. The identification and localization of oxidized cysteines within the cellular milieu is critical for understanding the redox regulation of proteins under physiological and pathophysiological conditions, and it will in turn provide important information that are potentially useful for the development of novel strategies in the treatment and prevention of diseases associated with oxidative stress. Antioxidant enzymes that catalyze oxidation/reduction processes are able to serve as redox biomarkers in various human diseases, and they are key regulators controlling the redox state of functional proteins. Redox regulators with antioxidant properties related to active mediators, cellular organelles, and the surrounding environments are all connected within a network and are involved in diseases related to redox imbalance including cancer, ischemia/reperfusion injury, neurodegenerative diseases, as well as normal aging. In this review, we will briefly look at the selected aspects of oxidative thiol modification in antioxidant enzymes and thiol oxidation in proteins affected by redox control of antioxidant enzymes and their relation to disease.

Vascular targeting of nanocarriers: perplexing aspects of the seemingly straightforward paradigm.

Targeted nanomedicine holds promise to find clinical use in many medical areas. Endothelial cells that line the luminal surface of blood vessels represent a key target for treatment of inflammation, ischemia, thrombosis, stroke, and other neurological, cardiovascular, pulmonary, and oncological conditions. In other cases, the endothelium is a barrier for tissue penetration or a victim of adverse effects. Several endothelial surface markers including peptidases (e.g., ACE, APP, and APN) and adhesion molecules (e.g., ICAM-1 and PECAM) have been identified as key targets. Binding of nanocarriers to these molecules enables drug targeting and subsequent penetration into or across the endothelium, offering therapeutic effects that are unattainable by their nontargeted counterparts. We analyze diverse aspects of endothelial nanomedicine including (i) circulation and targeting of carriers with diverse geometries, (ii) multivalent interactions of carrier with endothelium, (iii) anchoring to multiple determinants, (iv) accessibility of binding sites and cellular response to their engagement, (v) role of cell phenotype and microenvironment in targeting, (vi) optimization of targeting by lowering carrier avidity, (vii) endocytosis of multivalent carriers via molecules not implicated in internalization of their ligands, and (viii) modulation of cellular uptake and trafficking by selection of specific epitopes on the target determinant, carrier geometry, and hydrodynamic factors. Refinement of these aspects and improving our understanding of vascular biology and pathology is likely to enable the clinical translation of vascular endothelial targeting of nanocarriers.

[Using peptide strategy for study functions and structure of signal proteins with enzymatic activity].

The peptide strategy, a new direction of molecular endocrinology, includes the synthesis of peptides corresponding to functional regions of signal proteins, the use of the peptides for study of the molecular mechanisms of transduction of hormonal signal into cell ant the development of selective regulators of hormonal signaling systems on the basis of these peptides. The peptide strategy is used for study a wide spectrum of the proteins, components of signal systems, the proteins possessing the catalytic activity in particular, such as tyrosine kinases receptors, the enzymes generating the second messengers, serine/threonine protein kinase, phosphatases. In the first time in the review the data concerning the synthetic peptides, derivatives of the primary structure of proteins with the enzymatic activity, their application for study of the structural-functional organization and the molecular mechanisms of action of signal proteins, and the construction of regulators of fundamental cell processes on the basis of these peptides are analyzed and summarized.

Epigenetics of prostate cancer and the prospect of identification of novel drug targets by RNAi screening of epigenetic enzymes.

Alterations in epigenetic processes probably underlie most human malignancies. Novel genome-wide techniques, such as chromatin immunoprecipitation and high-throughput sequencing, have become state-of-the-art methods to map the epigenomic landscape of development and disease, such as in cancers. Despite these advances, the functional significance of epigenetic enzymes in cancer progression, such as prostate cancer, remain incompletely understood. A comprehensive mapping and functional understanding of the cancer epigenome will hopefully help to facilitate development of novel cancer therapy targets and improve future diagnostics. The authors have developed a novel cell microarray-based high-content siRNA screening technique suitable to address the putative functional role and impact of all known putative and novel epigenetic enzymes in cancer, including prostate cancer.

Efeito do processamento do alho (Allium sativum L. ) sobre os seus compostos bioativos e potencial antioxidante in vitro e in vivo / Effect of processing of garlic (Allium sativum L. ) on their bioactive compounds and antioxidant potential in vitro and in vivo

Introdução: O aumento do consumo de frutas e hortaliças está associado à redução do risco de ocorrência de doenças crônicas não transmissíveis. Este efeito protetor tem sido atribuído particularmente à presença de vários compostos bioativos como compostos fenólicos e organosulfurados, além de fitosteróis presentes no alho que podem contribuir com os efeitos antioxidante e hipolipemiante. Porém, o processamento do alho pode acarretar mudanças na quantidade e na efetividade dos compostos bioativos. Este trabalho teve como objetivo avaliar se a cocção e a fritura do alho reduziram as concentrações de compostos bioativos, o potencial antioxidante in vitro e in vivo em hamsters hipercolesterolemizados. Métodos: In vitro - foram determinados nos alhos cru, frito e cozido: a) composição centesimal (proteínas, lipídios, cinzas, carboidratos, fibra alimentar solúvel e insolúvel); b) perfil de ácidos graxos; c) teor de fenólicos totais; d) teor de quercetina, miricetina e apigenina; e) fitosteróis; f) alicina; g) teor de cobre, zinco e selênio; h) produtos intermediários da reação de Maillard; i) potencial antioxidante utilizando os testes ORAC (Oxygen radical absorbance capacity), Rancimat® e o sistema -caroteno/ácido linoléico. In vivo - hamsters machos foram distribuidos em 5 grupos com 10 animais em cada grupo. 1 - controle; 2 - hipercolesterolêmico; 3- hipercolesterolêmico e alho cru; grupo 4 - hipercolesterolêmico e alho cozido; grupo 5 - hipercolesterolêmico e alho frito. Os animais foram eutanasiados após 4 semanas de estudo para análises do plasma e do tecido hepático. No plasma foi determinado o potencial antioxidante pelo teste ORAC, o perfil lipídico (colesterol total e frações e triacilgliceróis) e verificado a atividade das enzimas aspartato aminotransferase (AST) e alanina aminotransferase (ALT). No tecido hepático foram avaliadas a atividade das enzimas hepáticas (glutationa peroxidase, catalase e superóxido dismutase) e o potencial antioxidante utilizando dois métodos, ORAC e ensaio cometa. Resultados: In vitro - O teor de fibras totais para o alho cru foi de 10,0por cento (71,6por cento é solúvel e 28,4por cento é insolúvel). O alto conteúdo de ácidos graxos trans no alho frito (14,9por cento ) é devido ao processo de fritura com 50por cento de gordura vegetal hidrogenada. A cocção não alterou o teor dos minerais analisados.

The role of antioxidants and antioxidant-related enzymes in protective responses to environmentally induced oxidative stress.

In aerobic organisms, oxygen is essential for efficient energy production but paradoxically, produces chronic toxic stress in cells. Diverse protective systems must exist to enable adaptation to oxidative environments. Oxidative stress (OS) results when production of reactive oxidative species (ROS) exceeds the capacity of cellular antioxidant defenses to remove these toxic species. Epidemiological and clinical studies have linked environmental factors such as diet and lifestyle to cancer, diabetes, atherosclerosis, and neurodegenerative disorders. All of these conditions, as well as the aging process, are associated with OS due to elevation of ROS or insufficient ROS detoxification. Many environmental pollutants engage signaling pathways that are activated in response to OS. The same sequences of events are also associated with the etiology and early pathology of many chronic diseases. Investigations of oxidative responses in different in vivo models suggest that, in complex organisms such as mammals, organs and tissues contain distinct antioxidant systems, and this may form the basis for differential susceptibility to environmental toxic agents Thus, understanding the pathways leading to the induction of antioxidant responses will enable development of strategies to protect against oxidative damage. We shall review evidence of organ-specific antioxidant responses elicited by environmental pollutants in humans and animal models.

Influência da variabilidade genética humana dos genes NAT2, CYP2E1, GSTM1 e GSTT1 na ocorrência de reações adversas hepáticas induzidas pela isoniazida em pacientes com tuberculose ativa / Influence of human genetic variability of genes NAT2, CYP2E1, GSTM1 and GSTT1 in the occurrence of hepatic adverse reactions induced by isoniazid in patients with active tuberculosis

A isoniazida (INH), uma das principais drogas usadas no esquema de tratamento de primeira linha anti-tuberculose (anti-TB), tem sido associada à intensificação de efeitos adversos principalmente hepáticos. Sabe-se hoje, que variações polimórficas em genes humanos codificando enzimas envolvidas na biotransformação de diferentes fármacos podem contribuir para diferenças interindividuais na resposta farmacológica ou toxicológica de várias drogas estando diretamente relacionadas aos desfechos de falha terapêutica e reações adversas a drogas (ADRs). A INH é geralmente administrada de forma oral sendo metabolizada por enzimas hepáticas. O mecanismo de lesão hepatocelular induzido pela isoniazida envolve as enzimas de biotransformação N-acetiltransferase 2 e a mono-oxigenase CYP450 2E1. Mutações pontuais na região codificante de NAT2 são capazes de alterar a atividade de acetilação da enzima gerando três possíveis fenótipos: acetiladores lentos, intermediários e rápidos. Os indivíduos que apresentam uma acetilação lenta acumulam intermediários hepatotóxicos levando a ocorrência de ADRs. Outra classe de enzimas cuja participação na biotransformação da isoniazida vem sendo especulada é a glutationa S-transferase (GST). Considerando a importância das variantes alélicas dos genes envolvidos na metabolização da isoniazida e que suas frequências variam entre as diferentes etnias este trabalho teve como objetivos principais: (i) análise descritiva da distribuição dos alelos de NAT2 em duas regiões diferentes do Brasil: (ii) identificação de novas mutações e caracterização haplotípica de novos alelos de NAT2 bem como análise estrutural da influência dessas alterações na estrutura protéica de NAT2 e (iii) estudo de associação, caso-controle, entre as variáveis genéticas presentes nos genes que codificam para NAT2, CYP2E1 e GSTs humanas, com a ocorrência de reações adversas em pacientes com TB em tratamento com esquemas contendo isoniazida. Dezessete SNPs previamente descritos foram identificados na população estudada, dos quais, sete: 191G maior que A; 282C maior que T; 341T maior que C; 481C maior que T; 590G maior que A; 803 maior que G e 857G maior que A são os mais frequentes na população mundial. Adicionalmente, seis mutações novas foram identificadas e sete novos alelos de NAT2 circulantes no Rio de Janeiro e/ou Goiás foram caracterizados através de clonagem e resequenciamento e experimentos de modelagem molecular. Nossos resultados mostraram a predominância de alelos de NAT2 associados com o fenótipo de acetilação lenta em indivíduos brasileiros e que a distribuição desses alelos varia significativamente de acordo com a região brasileira estudada. Além disso, fomos capazes de constatar que os acetiladores lentos apresentaram um risco significativamente maior em desenvolver hepatotoxicidade (OR: 2,62; IC 95por cento: 1,75-3.49; p igual 0.03) ou hepatite medicamentosa (OR: 3,59; IC 95por cento: 2,53-4.64; p igual 0,02) quando comparados aos acetiladores intermediários/rápidos. Por outro lado, não observamos qualquer relação entre polimorfismos nos genes CYP2E1, GSTM1 e GSTT1 com a ocorrência de ADRs durante tratamento anti-TB. Sendo assim, nossos resultados sugerem...colaterais.

Beyond transcription factors: the role of chromatin modifying enzymes in regulating transcription required for memory.

One of the alluring aspects of examining chromatin modifications in the role of modulating transcription required for long-term memory processes is that these modifications may provide transient and potentially stable epigenetic marks in the service of activating and/or maintaining transcriptional processes. These, in turn, may ultimately participate in the molecular mechanisms required for neuronal changes subserving long-lasting changes in behavior. As an epigenetic mechanism of transcriptional control, chromatin modification has been shown to participate in maintaining cellular memory (e.g., cell fate) and may underlie the strengthening and maintenance of synaptic connections required for long-term changes in behavior. Epigenetics has become central to several fields of neurobiology, where researchers have found that regulation of chromatin modification has a significant role in epilepsy, drug addiction, depression, neurodegenerative diseases, and memory. In this review, we will discuss the role of chromatin modifying enzymes in memory processes, as well as how recent studies in yeast genetics and cancer biology may impact the way we think about how chromatin modification and chromatin remodeling regulate neuronal function.

Adrenal androgens in humans and nonhuman primates: production, zonation and regulation.

The synthesis and secretion of large quantities of the adrenal androgens, dehydroepiandrosterone (DHEA) and its sulfoconjugate DHEA sulfate (DS), is a phenomenon that appears limited to humans and some nonhuman primates. Both hydroxylase and lyase activities of the enzyme 17alpha-hydroxylase/17,20-lyase cytochrome P450 (P450c17) are necessary for DHEA production and are differentially regulated during adrenal development. Production of DHEA and DS occurs in the zona reticularis (ZR) of adults and the fetal zone of fetal primate adrenal glands, which is the primary substrate for maternal estrogen production during pregnancy. The onset of adrenal androgen production in childhood, referred to as adrenarche, corresponds with the establishment of the ZR: but the process is poorly understood, largely due to the lack of accessible animal models. Several nonhuman primates have been used to study adrenal function and remodeling, though none completely recapitulates human adrenarche, developmentally, functionally or temporally. This review will summarize the variations in adrenal androgen production and adrenal zonation in humans and nonhuman primates throughout life. It is hoped that recent studies demonstrating adrenarche in the rhesus will put in proper context the significance of adrenal zonation in nonhuman primates as valid models for human adrenal development and function.

Vitamins: not just for enzymes.

Vitamins have traditionally played the role of coenzymes, organic molecules that facilitate the chemical reactions catalyzed by enzymes. However, several vitamins assume additional endocrine-like actions; this review will discuss four such vitamins. Vitamin K2 is involved in the gamma-carboxylation of coagulation factors and bone proteins, but it can also bind and activate the steroid and xenobiotic receptor in order to mediate transcription in bone tissue, and has been used to treat osteoporosis. Biotin is critical for some carboxylation reactions, but it also induces epidermal differentiation and has been used to treat lameness in animals and brittle nails in humans. Pyridoxal phosphate (the active form of vitamin B6) is involved in a multitude of reactions, including decarboxylation and transamination; it can also inhibit DNA polymerases and several steroid receptors and may prove useful as an adjunct in cancer chemotherapy. Finally, nicotinic acid is converted to NAD+ and NADP+, which are used as hydrogen/electron carriers in redox reactions. However, it also possesses vasodilatory and antilipolytic activities.

PlyC: a multimeric bacteriophage lysin.

Lysins are murein hydrolases produced by bacteriophage that act on the bacterial host cell wall to release progeny phage. When added extrinsically in their purified form, these enzymes produce total lysis of susceptible Gram-positive bacteria within seconds, suggesting a unique antimicrobial strategy. All known Gram-positive lysins are produced as a single polypeptide containing a catalytic activity domain, which cleaves one of the four major peptidoglycan bonds, and a cell-wall-binding domain, which may bind a species-specific carbohydrate epitope in the cell wall. Here, we have cloned and expressed a unique lysin from the streptococcal bacteriophage C(1), termed PlyC. Molecular characterization of the plyC operon reveals that PlyC is, surprisingly, composed of two separate gene products, PlyCA and PlyCB. Based on biochemical and biophysical studies, the catalytically active PlyC holoenzyme is composed of eight PlyCB subunits for each PlyCA. Inhibitor studies predicted the presence of an active-site cysteine, and bioinformatic analysis revealed a cysteine, histidine-dependent amidohydrolase/peptidase domain within PlyCA. Point mutagenesis confirmed that PlyCA is responsible for the observed catalytic activity, and Cys-333 and His-420 are the active-site residues. PlyCB was found to self-assemble into an octamer, and this complex alone was able to direct streptococcal cell-wall-specific binding. Similar to no other proteins in sequence databases, PlyC defines a previously uncharacterized structural family of cell-wall hydrolases.

A review of biological factors implicated in abdominal aortic aneurysm rupture.

Abdominal aortic aneurysm (AAA) rupture is the 13th commonest cause of death in the Western World. Although considerable research has been applied to the aetiology and mechanism of aneurysm expansion, little is known about the mechanism of rupture. Aneurysm rupture was historically considered to be a simple physical process that occurred when the aortic wall could no longer contain the haemodynamic stress of the circulation. However, AAAs do not conform to the law of Laplace and there is growing evidence that aneurysm rupture involves a complex series of biological changes in the aortic wall. This paper reviews the available data on patient variables associated with aneurysm rupture and presents the evidence implicating biological factors in AAA rupture.

Role of COX-2, thromboxane A2 synthase, and prostaglandin I2 synthase in papillary thyroid carcinoma growth.

The development of papillary thyroid carcinoma is influenced by many factors including genetic alterations, growth factors, and physical agents such as radiation. Arachidonic acid and its derivatives including prostaglandins (PG) and thromboxane along with the enzymes involved in their synthesis have been shown to influence the growth of various tumors. We analyzed the immunoreactivity for cyclooxygenase-2 (COX-2) and mRNA expression levels of the enzymes COX-2, thromboxane A(2) (TXA(2)) synthase, and PGI(2) synthase by RT-PCR in papillary carcinomas and matching normal tissues to determine the role of these enzymes in the development of papillary thyroid carcinomas. A papillary thyroid carcinoma cell line TPC-1 was also studied in vitro to determine the role of the specific COX-2 inhibitor NS-398 on COX-2 and vascular endothelial growth factor-A, since COX-2 also has a role in regulating tumor angiogenesis. RT-PCR analysis showed significant increases in TXA(2) synthase mRNA levels in papillary thyroid carcinomas compared to normal thyroid tissues. Although COX-2 mRNA levels were generally increased in papillary carcinomas, the differences were not statistically significant. There were no significant differences in PGI(2) synthase mRNA levels. COX-2 protein expression was greater in papillary carcinoma compared to normal thyroid tissues; however, the levels were quite variable. In vitro studies with a COX-2 inhibitor, NS-398, showed inhibition of tumor growth along with increased levels of COX-2 and vascular endothelial growth factor-A mRNA expression. These results indicate that specific enzyme levels in the PG synthesis pathway such as TXA(2) synthase are increased in papillary thyroid carcinomas. COX-2 also has a role in papillary thyroid growth, since a specific inhibitor of COX-2 regulates papillary thyroid carcinoma cell proliferation. These results implicate several enzymes in the synthesis of prostanoids as regulators of thyroid papillary carcinoma proliferation and suggest that increased levels of expression of these enzymes may play a role in the pathogenesis of these tumors.