Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1 alpha and PKR

Background: Interaction of non-structural protein 5A (NS5A) of Hepatitis C virus (HCV) with human kinases namely, casein kinase 1 alpha (ck1 alpha) and protein kinase R (PKR) have different functional implications such as regulation of viral replication and evasion of interferon induced immune response respectively. Understanding the structural and molecular basis of interactions of the viral protein with two different human kinases can be useful in developing strategies for treatment against HCV. Results: Serine 232 of NS5A is known to be phosphorylated by human ck1 alpha. A structural model of NS5A peptide containing phosphoacceptor residue Serine 232 bound to ck1 alpha has been generated using the known 3-D structures of kinase-peptide complexes. The substrate interacting residues in ck1 alpha has been identified from the model and these are found to be conserved well in the ck1 family. ck1 alpha - substrate peptide complex has also been used to understand the structural basis of association between ck1 alpha and its other viral stress induced substrate, tumour suppressor p53 transactivation domain which has a crystal structure available. Interaction of NS5A with another human kinase PKR is primarily genotype specific. NS5A from genotype 1b has been shown to interact and inhibit PKR whereas NS5A from genotype 2a/3a are unable to bind and inhibit PKR efficiently. This is one of the main reasons for the varied response to interferon therapy in HCV patients across different genotypes. Using PKR crystal structure, sequence alignment and evolutionary trace analysis some of the critical residues responsible for the interaction of NS5A 1b with PKR have been identified. Conclusions: The substrate interacting residues in ck1 alpha have been identified using the structural model of kinase substrate peptide. The PKR interacting NS5A 1b residues have also been predicted using PKR crystal structure, NS5A sequence analysis along with known experimental results. Functional significance and nature of interaction of interferon sensitivity determining region and variable region 3 of NS5A in different genotypes with PKR which was experimentally shown are also supported by the findings of evolutionary trace analysis. Designing inhibitors to prevent this interaction could enable the HCV genotype 1 infected patients respond well to interferon therapy.

Inflammation and cancer stem cells

Cancer stem cells are becoming recognised as being responsible for metastasis and treatment resistance. The complex cellular and molecular network that regulates cancer stem cells and the role that inflammation plays in cancer progression are slowly being elucidated. Cytokines, secreted by tumour associated immune cells, activate the necessary pathways required by cancer stem cells to facilitate cancer stem cells progressing through the epithelial-mesenchymal transition and migrating to distant sites. Once in situ, these cancer stem cells can secrete their own attractants, thus providing an environment whereby these cells can continue to propagate the tumour in a secondary niche. (C) 2013 Elsevier Ireland Ltd. All rights reserved.

Cancer gene signatures in risk stratification: use in personalized medicine

Cancer is a complex disease which arises due to a series of genetic changes related to cell division and growth control. Cancer remains the second leading cause of death in humans next to heart diseases. As a testimony to our progress in understanding the biology of cancer and developments in cancer diagnosis and treatment methods, the overall median survival time of all cancers has increased six fold one year to six years during the last four decades. However, while the median survival time has increased dramatically for some cancers like breast and colon, there has been only little change for other cancers like pancreas and brain. Further, not all patients having a single type of tumour respond to the standard treatment. The differential response is due to genetic heterogeneity which exists not only between tumours, which is called intertumour heterogeneity, but also within individual tumours, which is called intratumoural heterogeneity. Thus it becomes essential to personalize the cancer treatment based on a specific genetic change in a given tumour. It is also possible to stratify cancer patients into low- and high-risk groups based on expression changes or alterations in a group of genes gene signatures and choose a more suitable mode of therapy. It is now possible that each tumour can be analysed using various high-throughput methods like gene expression profiling and next-generation sequencing to identify its unique fingerprint based on which a personalized or tailor-made therapy can be developed. Here, we review the important progress made in the recent years towards personalizing cancer treatment with the use of gene signatures.

Insulin-Like Growth Factor System in Cancer: Novel Targeted Therapies

Insulin-like growth factors (IGFs) are essential for growth and survival that suppress apoptosis and promote cell cycle progression, angiogenesis, and metastatic activities in various cancers. The IGFs actions are mediated through the IGF-1 receptor that is involved in cell transformation induced by tumour. These effects depend on the bioavailability of IGFs, which is regulated by IGF binding proteins (IGFBPs). We describe here the role of the IGF system in cancer, proposing new strategies targeting this system. We have attempted to expand the general viewpoint on IGF-1R, its inhibitors, potential limitations of IGF-1R, antibodies and tyrosine kinase inhibitors, and IGFBP actions. This review discusses the emerging view that blocking IGF via IGFBP is a better option than blocking IGF receptors. This can lead to the development of novel cancer therapies.

El viejo, el amor y la hermosa como texto espectacular

Resumen: Inspirada por el Diálogo entre Amor y un viejo, de Rodrigo Cota, Interlocutores senex et amor mulierque pulcra forma es una muy interesante obra concebida para su puesta en escena; sin embargo, no posee acotación autoral alguna, lo que implica que el texto espectacular debe extraerse de la construcción semántica-formal de los signos verbales discursivos en voz de los personajes, que son los que comportan los requisitos necesarios de dramaticidad. A partir de estos signos analizaré varios aspectos contenidos en la estructura, que determino tripartita, de inicio, nudo y desenlace; por ejemplo, la actio (gestus, motus y vultus corporales), la pronuntiatio, la representación de los espacios ficcionales, y elementos obligados de caracterización. Comentaré, también, el espacio para la puesta; habré de aducir condicionantes culturales tanto para la caracterización (corporal y de indumentaria), como para los tipos de gestualidad que deben realizarse en escena (mediante el apoyo de preceptivas retóricas y obras iconográficas). No dejaré del lado la descodificación semántica asociada con todos los elementos referidos.

Osteoblast and monocyte responses to 444 ferritic stainless steel intended for a Magneto-Mechanically Actuated Fibrous Scaffold

The rationale behind this work is to design an implant device, based on a ferromagnetic material, with the potential to deform in vivo promoting osseointegration through the growth of a healthy periprosthetic bone structure. One of the primary requirements for such a device is that the material should be non-inflammatory and non-cytotoxic. In the study described here, we assessed the short-term cellular response to 444 ferritic stainless steel; a steel, with a very low interstitial content and a small amount of strong carbide-forming elements to enhance intergranular corrosion resistance. Two different human cell types were used: (i) foetal osteoblasts and (ii) monocytes. Austenitic stainless steel 316L, currently utilised in many commercially available implant designs, and tissue culture plastic were used as the control surfaces. Cell viability, proliferation and alkaline phosphatase activity were measured. In addition, cells were stained with alizarin red and fluorescently-labelled phalloidin and examined using light, fluorescence and scanning electron microscopy. Results showed that the osteoblast cells exhibited a very similar degree of attachment, growth and osteogenic differentiation on all surfaces. Measurement of lactate dehydrogenase activity and tumour necrosis factor alpha protein released from human monocytes indicated that 444 stainless steel did not cause cytotoxic effects or any significant inflammatory response. Collectively, the results suggest that 444 ferritic stainless steel has the potential to be used in advanced bone implant designs. © 2011 Elsevier Ltd.

Identification of a biomarker panel for colorectal cancer diagnosis

Background: Malignancies arising in the large bowel cause the second largest number of deaths from cancer in the Western World. Despite progresses made during the last decades, colorectal cancer remains one of the most frequent and deadly neoplasias in the western countries. Methods: A genomic study of human colorectal cancer has been carried out on a total of 31 tumoral samples, corresponding to different stages of the disease, and 33 non-tumoral samples. The study was carried out by hybridisation of the tumour samples against a reference pool of non-tumoral samples using Agilent Human 1A 60- mer oligo microarrays. The results obtained were validated by qRT-PCR. In the subsequent bioinformatics analysis, gene networks by means of Bayesian classifiers, variable selection and bootstrap resampling were built. The consensus among all the induced models produced a hierarchy of dependences and, thus, of variables. Results: After an exhaustive process of pre-processing to ensure data quality–lost values imputation, probes quality, data smoothing and intraclass variability filtering–the final dataset comprised a total of 8, 104 probes. Next, a supervised classification approach and data analysis was carried out to obtain the most relevant genes. Two of them are directly involved in cancer progression and in particular in colorectal cancer. Finally, a supervised classifier was induced to classify new unseen samples. Conclusions: We have developed a tentative model for the diagnosis of colorectal cancer based on a biomarker panel. Our results indicate that the gene profile described herein can discriminate between non-cancerous and cancerous samples with 94.45% accuracy using different supervised classifiers (AUC values in the range of 0.997 and 0.955).

Pravastatin inhibits cell proliferation and increased MAT1A expression in hepatocarcinoma cells and in vivo models

Background: Statins may have therapeutic effects on hepatocarcinoma (HCC). This type of disorder is the most common malignant primary tumour in the liver. Our objective was to determine whether pravastatin had a therapeutic effect in vitro and in vivo models. Method: We design in vitro and in vivo model. In vitro we used PLC and determine cell proliferation. In vivo, we used and animal model to determined, PCNA and MAT1A expression and transaminases levels. Results: We found that pravastatin decreases cell proliferation in vitro (cell proliferation in pravastatin group was 82%, in sorafenib group 51% and in combined group 40%) and in vivo (in pravastatin group 80%, in sorafenib group 76.4% and in combined group 72.72%). The MAT1A levels, was significantly higher in Pravastatin group (D 62%, P 94%, S 71%, P + S 91%). The transaminases levels, decreased significantly in Pravastatin group (GOT and GPT levels D 619.5 U/L; 271 U/L) (P 117.5 U/L; 43.5 U/L) (S 147 U/L; 59 U/L) (P + S 142 U/L; 59 U/L). Conclusion: The combination of pravastatin + sorafenib were more effective than Sorafenib alone.

Catch-per-unit-effort and biological parameters from the Massachusetts coastal lobster (Homarus americanus) resource: Description and trends

Acomprehensive description of the Massachusetts coastal lobster (Homarus americanus) resou,rce was obtained by sampling commercial catches coastwide at sea and at dealerships between 1981 and 1986. Acommercial lobster sea-sampling program, wherein six coastal regions were sampled monthly, with an areal and temporal data weighting design, was the primary source of data. An improved index of catch per trap haul/set-over-day was generated by modeling the relationship between catch and immersion time and standardizing effort. This 6-year time-series of mean annual catch rates tracked closely the landings trend for territorial waters. During the study period there was a gradual increase in indices of exploitation and total annual mortality which corresponded to a gradual decline in mean carapace length of marketable lobster. The frequency of culls escalated from 10.0% in 1981 to 20.9% in 1986, while the percentage of lobster found dead in traps was consistently less than 1%. The sex ratio (%F:%M) was significantly different from 50:50 and approximated a 60:40 relationship during the study period. Male and female weight-length relationships were significantly different. Females weighed more than males at smaller sizes and less than males at larger sizes. A north-south clinal trend was evident wherein lobster north of Cape Cod weighed less at length than those from regions south of Cape Cod. Functional size-maturity relationships were developed for female lobster by staging cement gland development. Proportions mature at size represent more realistic values than those obtained by analyses of percent of females ovigerous. Regional variation occurred in most of the parameters studied. Three lobster groups, differing in major population descriptors, are defined by our data.(PDF file contains 28 pages.)

Evidence for classification of c.1852_1853AA > GC in MLH1 as a neutral variant for Lynch syndrome

Background: Lynch syndrome (LS) is an autosomal dominant inherited cancer syndrome characterized by early onset cancers of the colorectum, endometrium and other tumours. A significant proportion of DNA variants in LS patients are unclassified. Reports on the pathogenicity of the c.1852_1853AA>GC (p.Lys618Ala) variant of the MLH1 gene are conflicting. In this study, we provide new evidence indicating that this variant has no significant implications for LS. Methods: The following approach was used to assess the clinical significance of the p.Lys618Ala variant: frequency in a control population, case-control comparison, co-occurrence of the p.Lys618Ala variant with a pathogenic mutation, co-segregation with the disease and microsatellite instability in tumours from carriers of the variant. We genotyped p.Lys618Ala in 1034 individuals (373 sporadic colorectal cancer [CRC] patients, 250 index subjects from families suspected of having LS [revised Bethesda guidelines] and 411 controls). Three well-characterized LS families that fulfilled the Amsterdam II Criteria and consisted of members with the p.Lys618Ala variant were included to assess co-occurrence and co-segregation. A subset of colorectal tumour DNA samples from 17 patients carrying the p.Lys618Ala variant was screened for microsatellite instability using five mononucleotide markers. Results: Twenty-seven individuals were heterozygous for the p.Lys618Ala variant; nine had sporadic CRC (2.41%), seven were suspected of having hereditary CRC (2.8%) and 11 were controls (2.68%). There were no significant associations in the case-control and case-case studies. The p.Lys618Ala variant was co-existent with pathogenic mutations in two unrelated LS families. In one family, the allele distribution of the pathogenic and unclassified variant was in trans, in the other family the pathogenic variant was detected in the MSH6 gene and only the deleterious variant co-segregated with the disease in both families. Only two positive cases of microsatellite instability (2/17, 11.8%) were detected in tumours from p.Lys618Ala carriers, indicating that this variant does not play a role in functional inactivation of MLH1 in CRC patients. Conclusions: The p.Lys618Ala variant should be considered a neutral variant for LS. These findings have implications for the clinical management of CRC probands and their relatives.

Prioritization of candidate cancer genes-an aid to oncogenomic studies

The development of techniques for oncogenomic analyses such as array comparative genomic hybridization, messenger RNA expression arrays and mutational screens have come to the fore in modern cancer research. Studies utilizing these techniques are able to highlight panels of genes that are altered in cancer. However, these candidate cancer genes must then be scrutinized to reveal whether they contribute to oncogenesis or are coincidental and non-causative. We present a computational method for the prioritization of candidate (i) proto-oncogenes and (ii) tumour suppressor genes from oncogenomic experiments. We constructed computational classifiers using different combinations of sequence and functional data including sequence conservation, protein domains and interactions, and regulatory data. We found that these classifiers are able to distinguish between known cancer genes and other human genes. Furthermore, the classifiers also discriminate candidate cancer genes from a recent mutational screen from other human genes. We provide a web-based facility through which cancer biologists may access our results and we propose computational cancer gene classification as a useful method of prioritizing candidate cancer genes identified in oncogenomic studies.

Design and synthesis of biofunctional magnetic/fluorescent glyco-nanoparticles and quantum dots and their application as specific molecular imaging probes

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Humor y puesta en escena en la comedia de Aristófanes

Presentado en las Jornadas sobre "El humor (y los humores) en el mundo antiguo", organizado por el Departamento de Estudios Clásicos y el Instituto de Ciencias de la Antigüedad de la UPV y celebrado en Vitoria-Gasteiz los días 16 y 17 de octubre de 2007.

Sobrevida em pacientes mulheres com câncer de pulmão em clínica especializada no Rio de Janeiro, 2000-2009

O câncer de pulmão é atualmente a neoplasia mais frequentemente diagnosticada, considerando ambos os sexos, e a principal causa de óbito por câncer em todo o mundo. A incidência e a mortalidade do câncer de pulmão vêm sendo influenciadas ao longo do tempo pela história do tabagismo e seus aspectos sócio-demográficos. Este estudo tem como objetivo analisar a sobrevida e fatores prognósticos em mulheres com câncer de pulmão assistidas em uma clínica especializada no Rio de Janeiro no período de 2000 a 2009. Foram analisadas 193 mulheres com diagnóstico de câncer de pulmão confirmado por exame histopatológico. Os dados foram obtidos diretamente do sistema informatizado de registros médicos do referido serviço. A idade do diagnóstico foi categorizada em quatro faixas etárias: até 49 anos, 50 a 59 anos, 60 a 69 anos e maior de 70anos. O tabagismo foi categorizado como não fumante, ex-fumante, fumante e fumante passiva. O estado nutricional foi avaliado pelo Índice de Massa Corpórea (IMC). A classificação histológica seguiu a divisão entre tumores de células não-pequenas (CPCNP) e tumores de pequenas células (CPCP). O estadiamento clínico se baseou na classificação do American Joint Committee on Cancer (AJCC) e Veterans Administration Lung Cancer Study Group (VALCSG) para os tumores de células não-pequenas e tumores de células pequenas, respectivamente. A modalidade de tratamento foi categorizada pela intenção da abordagem terapêutica em quatro grupos: controle, neoadjuvância, adjuvância e paliativa. Foram calculadas funções de sobrevida pelo método de Kaplan-Meier. Para os fatores prognósticos de risco, foram calculados os hazards ratios brutos e ajustados com intervalos de confiança de 95%, através do modelo de riscos proporcionais de Cox. A idade média das pacientes foi de 63 anos. Destas, 47,7% eram fumantes, 26,9% não fumantes, 19,7% ex-fumantes e 3,6% fumantes passivas. Em relação ao estado nutricional, 2,6% das pacientes apresentavam IMC baixo peso, 52,8% normal, 29,5% sobrepeso e 15% obesidade. A maioria dos casos, 169 (87,6%) pacientes, foi classificado como câncer de pulmão de células não-pequenas (CPCNP). Apenas 24 casos (12,4%) foram de câncer de pequenas células (CPCP). Durante o período estudado ocorreram 132 óbitos; 114 por CPCNP e 18 por CPCP. O tempo mediano de sobrevida para toda a coorte foi de 23,2 meses (IC95%: 16,9-33,5). Quando os dados foram estratificados por classificação tumoral, a sobrevida mediana nas pacientes com diagnóstico de CPCNP foi de 18,2 meses (IC95%: 15,6-25,5) e para aquelas com CPCP foi de 10,3 meses (IC95%: 8,4-19,3). A sobrevida encontrada em 24 meses foi de 49% (IC95%: 42,25-56,9), sendo 22,95 (IC95%: 0,6-49,3) para os tumores de pequenas células e 50,29% (IC95%: 43,1-58,7) para os tumores de células não- pequenas. Para o total das pacientes, as curvas de sobrevida estratificadas pelas variáveis selecionadas mostraram diferenças em relação à idade do diagnóstico (p=0,0023) nas faixas etárias intermediárias de 50-59 anos e 60-69 anos, se comparadas com os limites extremos (as mais idosas e as mais jovens). Não houve diferenças para o status de tabagismo (p=0,1484) nem para o IMC (p=0,6230). Na análise multivariada para todos os tumores, nenhum fator prognóstico influenciou no risco de morte. A idade nas categorias intermediárias (50-59 anos e 60-69 anos) e o IMC na categoria sobrepeso mostraram uma tendência à proteção, porém, não houve significância estatística. Para o grupo de mulheres com CPCNP, o modelo de riscos proporcionais apontou diferença em relação ao estadiamento clínico, especificamente o estádio IV (HR=3,36, IC95%: 1,66-6,8; p=0,001). As pacientes com idade entre 50-59 anos e sobrepeso mostraram uma tendência à diminuição do risco, embora sem significância estatística. Esses resultados mostram a necessidade de conhecer melhor o perfil das mulheres que desenvolvem câncer de pulmão e de realizar pesquisas que investiguem de forma mais aprofundada as condições que influenciam a evolução clínica dos casos e assim contribuir para o aprimoramento da abordagem terapêutica.

Desenvolvimento de técnica de análise de imagens digitais para avaliação do estágio da fibrose em biópsias hepáticas de pacientes portadores de hepatite crônica por vírus da hepatite B e C

As hepatites crônicas por vírus são as mais frequentes, destacando-se os vírus das hepatites B (VHB) e C (VHC). O estudo anatomopatológico da biópsia hepática é considerado o padrão ouro para avaliar com precisão a distorção arquitetural e o grau de fibrose do parênquima do fígado, importantes fatores prognósticos para os pacientes portadores de hepatites crônicas virais. Na avaliação histopatológica atual, em adição aos relatos subjetivos das alterações histológicas, escores semiquantitativos que correlacionam achados morfológicos com graus numéricos são usados, tais como os reconhecidos escores de Ishak e METAVIR. Entretanto, em todos estes sistemas há a desvantagem da subjetividade do examinador e da incorporação de alterações categóricas, sem referências às mudanças quantitativas do colágeno hepático. Técnicas de análise de imagens digitais (AID) que fornecem quantificação objetiva dos graus de fibrose em amostras histológicas têm sido desenvolvidas. Todavia, o alto custo e dificuldade ao acesso das tecnologias descritas restringem seu uso a poucos centros especializados. Este estudo visa o desenvolvimento de uma técnica de custo acessível para a análise de imagens digitais da fibrose hepática em hepatites crônicas virais. Foram estudadas 304 biópsias de pacientes com hepatite crônica por vírus B e C, obtidas através de agulhas Menghini. Todas as amostras tinham pelo menos 15 mm de comprimento ou cinco espaços-porta completos e foram coradas pelo método Tricrômico de Masson. O estadiamento foi feito por um único hepatopatologista experiente, sem o conhecimento dos dados clínicos dos pacientes. Os escores de Ishak e METAVIR foram aplicados. As imagens microscópicas foram digitalizadas. Os índices de fibrose foram determinados de forma automatizada, em técnica desenvolvida no programa Adobe Photoshop. Para o escore de Ishak, observamos os seguintes índices de Fibrose (IF) médios: 0,8% 0,0 (estágio 0), 2.4% 0,6 (estágio 1), 4,7% 1,6 (estágio 2), 7,4% 1,4 (estágio 3), 14,9% 3,7 (estágio 4), 23,4% 2,9 (estágio 5) e 34,5% 1,5 (estágio 6). Para a classificação METAVIR: 0,8% 0,1 (estágio F0), 3,8% 1,8 (estágio F1), 7,4% 1,4 (estágio F2), 20,4% 5,2 (estágio F3) e 34,5% 1,5 (estágio F4). Observamos uma excelente correlação entre os índices de fibrose da AID e os escores de Ishak (r=0,94; p<0,001) e METAVIR (r=0,92; p<0,001). Em relação à indicação de tratamento antiviral, foi observado IF médio de 16,4%. Em relação ao diagnóstico de cirrose, foi observado IF médio de 26,9%, para o escore de Ishak, e 34,5% para a classificação METAVIR. A reprodutibilidade intra-observador foi excelente. Este novo método de análise de imagens digitais para a quantificação de fibrose hepática tem custo acessível e foi desenvolvido com tecnologia que está disponível em todo o mundo, permitindo identificar com precisão todos os estágios de fibrose, com excelente reprodutibilidade intra-observador.