Evaluation of a short RNA within Prostate Cancer Gene 3 in the predictive role for future cancer using non-malignant prostate biopsies.

BACKGROUND: Prostate Cancer 3 (PCA3) is a long non-coding RNA (ncRNA) upregulated in prostate cancer (PCa). We recently identified a short ncRNA expressed from intron 1 of PCA3. Here we test the ability of this ncRNA to predict the presence of cancer in men with a biopsy without PCa. METHODS: We selected men whose initial biopsy did not identify PCa and selected matched cohorts whose subsequent biopsies revealed PCa or benign tissue. We extracted RNA from the initial biopsy and measured PCA3-shRNA2, PCA3 and PSA (qRT-PCR). RESULTS: We identified 116 men with and 94 men without an eventual diagnosis of PCa in 2-5 biopsies (mean 26 months), collected from 2002-2008. The cohorts were similar for age, PSA and surveillance period. We detected PSA and PCA3-shRNA2 RNA in all samples, and PCA3 RNA in 90% of biopsies. The expression of PCA3 and PCA3-shRNA2 were correlated (Pearson's r = 0.37, p<0.01). There was upregulation of PCA3 (2.1-fold, t-test p = 0.02) and PCA3-shRNA2 (1.5-fold) in men with PCa on subsequent biopsy, although this was not significant for the latter RNA (p = 0.2). PCA3 was associated with the future detection of PCa (C-index 0.61, p = 0.01). This was not the case for PCA3-shRNA2 (C-index 0.55, p = 0.2). CONCLUSIONS: PCA3 and PCA3-shRNA2 expression are detectable in historic biopsies and their expression is correlated suggesting co-expression. PCA3 expression was upregulated in men with PCa diagnosed at a future date, the same did not hold for PCA3-shRNA2. Futures studies should explore expression in urine and look at a time course between biopsy and PCa detection

Levantamento qualitativo de gêneros de parasitos em amostras fecais de jacarés criados comercialmente em sistema fechado no estado do Rio de Janeiro

O objetivo desta pesquisa foi realizar um diagnóstico qualitativo dos gêneros de parasitos encontrados em amostras fecais ambientais de jacarés (Caiman latirostris Daudin, 1802), criados comercialmente em sistema fechado, no período de 2008 a 2009, no estado do Rio de Janeiro. Um total de 300 amostras foi coletado de 150 filhotes, 80 de animais de engorda e 70 de reprodução, e submetido a análises coproparasitológicas, de flutuação (método de Willis-Mollay) e sedimentação simples (método de Lutz), de acordo com Hoffmann (1987). As amostras foram visualizadas à luz da microscopia óptica. Os resultados obtidos evidenciaram a presença de oocistos de Eimeria e Isospora, cistos de Balantidium e ovos de Acanthostomum e Dujardinascaris

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Ação anti-helmíntica de diferentes formulações de lactonas macrocíclicas em cepas resistentes de nematódeos de bovinos

As lactonas macrocíclicas (LMs) (avermectinas e milbemicinas) são endectocidas amplamente utilizados em animais e em algumas parasitoses humanas. Em bovinos, a resistência parasitária às LMs é emergente, e o surgimento de formulações que diferem nas suas propriedades farmacológicas tornou complexa a escolha da droga mais indicada a cada caso. Com o objetivo de avaliar possíveis alternativas para recuperar a eficácia de LMs sobre cepas resistentes de nematódeos gastrintestinais, testaram-se, neste estudo, dez diferentes tratamentos a base de LMs sobre uma população de nematódeos gastrintestinais de bovinos a qual, sabidamente, sofrera pressão de seleção por avermectinas a 1%. Adicionalmente, testou-se um benzimidazol. A eficácia das drogas foi calculada com base na redução de ovos por grama de fezes (OPG) dos bovinos. A resistência de cada gênero foi avaliada por meio de identificação de larvas, obtidas de cultivos nas fezes, pré- e pós-tratamentos. Não se obteve a eficácia desejada com o emprego de avermectinas de longa ação - com alta concentração e em associação - ou mesmo, com a aplicação de superdoses. Os gêneros Cooperia spp., Haemonchus spp. e Trichostrongylus spp. foram resistentes às avermectinas, e Ostertagia spp. à ivermectina. Observou-se que, uma vez estabelecida a resistência parasitária a LMs a 1%, a aplicação de fármacos, deste mesmo grupo químico, ainda que em formulações mais concentradas, asso-ciações ou superdoses, pode não resultar na eficácia esperada.The macrocyclic lactones (MLs) (avermectins and milbemycins) are endectocides broadly used in livestock and in some parasitic diseases of humans. In cattle, parasite resistance to MLs is emerging, and the appearance of formulations that differ in their pharmacological properties become complex the choice of the most appropriate drug to each case. In order to evaluate possible alternatives to restore the effectiveness of MLs on resistant strains of gastrointestinal nematodes, were tested, in this study, ten different treatments based on the MLs on a population of gastrointestinal nematodes of cattle which, known, was under pressure of selection by 1% avermectins. Additionally, was tested a benzimidazole. The efficacy of the drugs was calculated with basis on the reduction of eggs per gram of feces (EPG) of cattle. The resistance of each genus was evaluated by identification of the larvae, obtained from culture in the feces, pre- and post-treatments. The desired efficacy was not obtained using long action avermectins - with high concentration and in association - even with the application of high doses. The genera Cooperia spp., Haemonchus spp. and Trichostrongylus spp. were resistant to avermectins, and Ostertagia spp. to ivermectin. It was observed that, once established parasite resistance to the 1% MLs, the application of drugs, of this same chemical group, even in formulations of high concentration, association or in high doses, may not result in the expected efficacy

Atividade biológica de extratos acetato de etila, etanólico e aquoso de timbó (Lonchocarpus floribundus) sobre carrapato bovino

Os extratos acetato de etila, etanólico e aquoso de raízes de Lonchocarpus floribundus foram utilizados, a fim de avaliar a atividade biológica sobre carrapato bovino. Carrapatos adultos foram coletados em bovinos infestados artificialmente, separados em grupos de dez indivíduos, pesados e imersos, separadamente, nos extratos de raízes de L. Floribundus, nas concentrações de 5, 25, 50, 75 e 100 mg mL-1. Para a avaliação em larvas, foram utilizados indivíduos de 14 a 21 dias, os quais foram imersos nos extratos nas concentrações de 1, 5, 10, 15 e 20 mg mL-1. Após o tratamento, cada grupo foi colocado em placa de Petri e incubado a 27 ± 1 ºC e umidade relativa de 80 ± 5%. Os extratos avaliados não foram eficazes para induzir, acima de 50%, a mortalidade de fêmeas ingurgitadas. Os extratos acetato de etila e etanólico induziram 100% de mortalidade de larvas. Entretanto, quanto aos valores de concentração letal mediana (CL50), o extrato etanólico (CL50 = 2,1 mg mL-1) foi mais tóxico que o extrato acetato de etila (CL50 = 4,1 mg mL-1). O extrato etanólico estimou concentração inibitória mediana (CI50) de 3,0 mg mL-1 e foi mais tóxico que os demais extratos quanto a este parâmetro de avaliação. Entre os três extratos avaliados, os extratos acetato de etila e etanólico apresentaram os melhores resultados quanto ao controle de reprodução de R. (B.) microplus, atingindo 100% na concentração de 5 mg mL-1. Os extratos de raízes de L. Floribundus apresentaram atividade biológica sobre carrapato bovino

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA), and we identified 119 splicing factor genes with significant non-silent mutation patterns, including mutation over-representation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). Furthermore, RNA sequencing analysis revealed altered splicing events associated with selected splicing factor mutations. In addition, we were able to identify common gene pathway profiles associated with the presence of these mutations. Our analysis suggests that somatic alteration of genes involved in the RNA-splicing process is common in cancer and may represent an underappreciated hallmark of tumorigenesis