Can loss-of-function prion-related diseases exist?

Discovery of mutations of the PrnP gene without typical plaque formation and the characterization of two prion receptors led us to postulate a new class of prion-related disease: 'loss of function'.Ludwig Inst Canc Res, BR-01509010 São Paulo, BrazilUNIFESP, Dept Psychiat, BR-01509010 São Paulo, BrazilUNIFESP, Dept Psychiat, BR-01509010 São Paulo, BrazilWeb of Scienc

Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE)

BACKGROUND: An important challenge for transcript counting methods such as Serial Analysis of Gene Expression (SAGE), "Digital Northern" or Massively Parallel Signature Sequencing (MPSS), is to carry out statistical analyses that account for the within-class variability, i.e., variability due to the intrinsic biological differences among sampled individuals of the same class, and not only variability due to technical sampling error. RESULTS: We introduce a Bayesian model that accounts for the within-class variability by means of mixture distribution. We show that the previously available approaches of aggregation in pools ("pseudo-libraries") and the Beta-Binomial model, are particular cases of the mixture model. We illustrate our method with a brain tumor vs. normal comparison using SAGE data from public databases. We show examples of tags regarded as differentially expressed with high significance if the within-class variability is ignored, but clearly not so significant if one accounts for it. CONCLUSION: Using available information about biological replicates, one can transform a list of candidate transcripts showing differential expression to a more reliable one. Our method is freely available, under GPL/GNU copyleft, through a user friendly web-based on-line tool or as R language scripts at supplemental web-site

Tumor slices as a model to evaluate doxorubicin in vitro treatment and expression of trios of genes PRSS11, MTSS1, CLPTM1 and PRSS11, MTSS1, SMYD2 in canine mammary gland cancer

<p>Abstract</p> <p>Background</p> <p>In women with breast cancer submitted to neoadjuvant chemotherapy based in doxorubicin, tumor expression of groups of three genes (PRSS11, MTSS1, CLPTM1 and PRSS11, MTSS1, SMYD2) have classified them as responsive or resistant. We have investigated whether expression of these trios of genes could predict mammary carcinoma response in dogs and whether tumor slices, which maintain epithelial-mesenchymal interactions, could be used to evaluate drug response <it>in vitro</it>.</p> <p>Methods</p> <p>Tumors from 38 dogs were sliced and cultured with or without doxorubicin 1 μM for 24 h. Tumor cells were counted by two observers to establish a percentage variation in cell number, between slices. Based on these results, a reduction in cell number between treated and control samples ≥ 21.7%, arbitrarily classified samples, as drug responsive. Tumor expression of PRSS11, MTSS1, CLPTM1 and SMYD2, was evaluated by real time PCR. Relative expression results were then transformed to their natural logarithm values, which were spatially disposed according to the expression of trios of genes, comprising PRSS11, MTSS1, CLPTM1 and PRSS11, MTSS1, SMYD2. Fisher linear discrimination test was used to generate a separation plane between responsive and non-responsive tumors.</p> <p>Results</p> <p>Culture of tumor slices for 24 h was feasible. Nine samples were considered responsive and 29 non-responsive to doxorubicin, considering the pre-established cut-off value of cell number reduction ≥ 21.7%, between doxorubicin treated and control samples. Relative gene expression was evaluated and tumor samples were then spatially distributed according to the expression of the trios of genes: PRSS11, MTSS1, CLPTM1 and PRSS11, MTSS1, SMYD2. A separation plane was generated. However, no clear separation between responsive and non-responsive samples could be observed.</p> <p>Conclusion</p> <p>Three-dimensional distribution of samples according to the expression of the trios of genes PRSS11, MTSS1, CLPTM1 and PRSS11, MTSS1, SMYD2 could not predict doxorubicin <it>in vitro </it>responsiveness. Short term culture of mammary gland cancer slices may be an interesting model to evaluate chemotherapy activity.</p

Overall and sex-specific associations between fetal adversity and child development at age 1 year : evidence from Brazil

A growing body of epigenetic research suggests that in-utero adaptations to environmental changes display important sex-specific variation. We tested this heterogeneous adaptation hypothesis using data from 900 children born at the University Hospital in São Paulo, Brazil, between October 2013 and April 2014. Crude and adjusting linear models were used to quantify the associations between prematurity, being small for gestational age, and children's physical and mental development at 12 months of age. Prematurity was negatively associated with neuropsychological development in final models (z score difference, -0.42, 95% confidence intervals: -0.71, -0.14), but associations did not vary significantly by sex. For being small for gestational age, associations with height-for-age, weight-for-age, and neuropsychological development were also negative, but they were systematically larger for male than for female infants (P &lt; 0.05 for all). These results suggest that male fetuses may be more vulnerable to intrauterine adversity than female fetuses. Further research will be needed to better understand the mechanisms underlying these sex-specific associations

No-match ORESTES explored as tumor markers

Sequencing technologies and new bioinformatics tools have led to the complete sequencing of various genomes. However, information regarding the human transcriptome and its annotation is yet to be completed. The Human Cancer Genome Project, using ORESTES (open reading frame EST sequences) methodology, contributed to this objective by generating data from about 1.2 million expressed sequence tags. Approximately 30% of these sequences did not align to ESTs in the public databases and were considered no-match ORESTES. On the basis that a set of these ESTs could represent new transcripts, we constructed a cDNA microarray. This platform was used to hybridize against 12 different normal or tumor tissues. We identified 3421 transcribed regions not associated with annotated transcripts, representing 83.3% of the platform. The total number of differentially expressed sequences was 1007. Also, 28% of analyzed sequences could represent noncoding RNAs. Our data reinforces the knowledge of the human genome being pervasively transcribed, and point out molecular marker candidates for different cancers. To reinforce our data, we confirmed, by real-time PCR, the differential expression of three out of eight potentially tumor markers in prostate tissues. Lists of 1007 differentially expressed sequences, and the 291 potentially noncoding tumor markers were provided

No-match ORESTES explored as tumor markers

Sequencing technologies and new bioinformatics tools have led to the complete sequencing of various genomes. However, information regarding the human transcriptome and its annotation is yet to be completed. The Human Cancer Genome Project, using ORESTES (open reading frame EST sequences) methodology, contributed to this objective by generating data from about 1.2 million expressed sequence tags. Approximately 30% of these sequences did not align to ESTs in the public databases and were considered no-match ORESTES. On the basis that a set of these ESTs could represent new transcripts, we constructed a cDNA microarray. This platform was used to hybridize against 12 different normal or tumor tissues. We identified 3421 transcribed regions not associated with annotated transcripts, representing 83.3% of the platform. The total number of differentially expressed sequences was 1007. Also, 28% of analyzed sequences could represent noncoding RNAs. Our data reinforces the knowledge of the human genome being pervasively transcribed, and point out molecular marker candidates for different cancers. To reinforce our data, we confirmed, by real-time PCR, the differential expression of three out of eight potentially tumor markers in prostate tissues. Lists of 1007 differentially expressed sequences, and the 291 potentially noncoding tumor markers were provided

Influence of lithium in neuron-glia interaction in hippocampal neurons: preliminary study

Recentemente, especial atenção foi dada aos possíveis efeitos neuroprotetores do lítio, especialmente pela descoberta de seus efeitos regulatórios sobre proteínas pró e anti-apoptóticas. O lítio aumenta substancialmente a expressão de proteínas citoprotetoras no sistema nervoso central, tanto no córtex de ratos quanto em células humanas de origem neuronal. Além de ações neuroprotetoras, auxilia na regeneração de axônios no sistema nervoso central de mamíferos. O lítio regula negativamente a expressão e a atividade de enzimas que exercem funções importantes na homeostase cerebral: plasticidade sináptica, neurogênese e fosforilação da proteína tau. Microglia é conhecida por sua importância na neuropatologia. No entanto, sob condições fisiológicas, tais células imunes interagem ativamente com os neurônios, sendo capazes de modular o destino e as funções das sinapses. Essa capacidade das células microgliais sugere as conseqüências de mudanças no fenótipo microglial sob condições patológicas, o que torna relevante o entendimento da interação entre micróglia e outras células cerebrais em desenvolvimento e sua influência na formação de redes neuronais e sinápticas. O presente trabalho tem como objetivo identificar a principal via de integração neurônio-glia ativada pelo tratamento crônico com lítio em neurônios, explorando o uso de ferramentas de bioinformática em dados de microarray. O tratamento de neurônios hipocampais com lítio alterou os genes relacionados a diferentes vias de neuroproteção na dose terapêutica mais alta. Houve dissociação entre a dose terapêutica e sub-terapêutica de lítio na neuroproteção. Portanto, o tratamento em doses terapêuticas (2mM) modificou diferentes vias de sinalização quando comparado com as doses sub-terapêuticas (0,02 e 0,2mM).Recently, special attention has been given to the possible neuroprotective effects of lithium, especially by the discovery of its regulatory effects on pro and anti-apoptotic proteins. Lithium substantially increases the cytoprotective proteins expression in the central nervous system, both in rat cortex and in human cells of neuronal origin. In addition to neuroprotective actions, it aids in the regeneration of axons in the central nervous system of mammals. Lithium negatively regulates the expression and activity of enzymes that exert important functions in cerebral homeostasis: synaptic plasticity, neurogenesis, and phosphorylation of tau protein. Microglia is known for its importance in neuropathology. However, under physiological conditions, such immune cells interact actively with neurons, being able to modulate the fate and functions of the synapses. Such ability of microglial cells suggests the consequences of changes in microglial phenotype under pathological conditions, which makes it relevant to understand the interaction between microglial and other developing brain cells and their influence on the formation of neuronal and synaptic networks. The current work aims to identify the main pathway of neuronal-glia integration activated by chronic treatment with lithium in neurons, exploring the use of bioinformatics tools in microarray data. Treatment of primary hippocampal neurons with lithium changed the genes related to different neuroprotection pathways at the highest therapeutic dose. There was dissociation between the therapeutic and sub-therapeutic dose of lithium in neuroprotection. Therefore, treatment at therapeutic doses (2mM) modified different signaling pathways when compared to the sub-therapeutic dose (0.02 and 0.2mM)

A feature selection approach for identification of signature genes from SAGE data

<p>Abstract</p> <p>Background</p> <p>One goal of gene expression profiling is to identify signature genes that robustly distinguish different types or grades of tumors. Several tumor classifiers based on expression profiling have been proposed using microarray technique. Due to important differences in the probabilistic models of microarray and SAGE technologies, it is important to develop suitable techniques to select specific genes from SAGE measurements.</p> <p>Results</p> <p>A new framework to select specific genes that distinguish different biological states based on the analysis of SAGE data is proposed. The new framework applies the bolstered error for the identification of strong genes that separate the biological states in a feature space defined by the gene expression of a training set. Credibility intervals defined from a probabilistic model of SAGE measurements are used to identify the genes that distinguish the different states with more reliability among all gene groups selected by the strong genes method. A score taking into account the credibility and the bolstered error values in order to rank the groups of considered genes is proposed. Results obtained using SAGE data from gliomas are presented, thus corroborating the introduced methodology.</p> <p>Conclusion</p> <p>The model representing counting data, such as SAGE, provides additional statistical information that allows a more robust analysis. The additional statistical information provided by the probabilistic model is incorporated in the methodology described in the paper. The introduced method is suitable to identify signature genes that lead to a good separation of the biological states using SAGE and may be adapted for other counting methods such as Massive Parallel Signature Sequencing (MPSS) or the recent Sequencing-By-Synthesis (SBS) technique. Some of such genes identified by the proposed method may be useful to generate classifiers.</p

Serum folic acid is reduced in patients with Alzheimer's disease

CONTEXTO: Deficiência de vitaminas do complexo B tem sido associada a deterioração cognitiva e quadros demenciais em idosos. OBJETIVO: Neste trabalho, foi avaliado se pacientes com doença de Alzheimer (DA) e com comprometimento cognitivo leve (CCL) apresentam níveis séricos de ácido fólico e cobalamina (vitamina B12) menores que idosos controles. MÉTODOS: Foram recrutados 146 idosos (40 com DA, 56 com CCL e 49 idosos controles) para este estudo. Os níveis séricos de ácido fólico e vitamina B12 foram avaliados pelo método de eletroquimioluminescência. RESULTADOS: Os pacientes com DA apresentaram redução estatisticamente significativa nos níveis de ácido fólico em relação aos idosos com CCL e controles (p = 0,02). Esses resultados mantiveram-se estatisticamente significativos após controlar por variáveis sociodemográficas e desempenho cognitivo. Não se observaram diferenças estatisticamente significativas nos níveis de vitamina B12 nem em variáveis hematológicas entre os grupos. CONCLUSÃO: Esses resultados reforçam a importância de anormalidades em aspectos nutricionais, em particular do metabolismo de um-carbono, na fisiopatologia da DA.BACKGROUND: Complex B vitamin deficiency has been associated to cognitive impairment and dementing disorders in the elderly. OBJECTIVE: This work aims to assess whether patients with Alzheimer's disease (AD) and mild cognitive impairment (MCI) have lower levels of folic acid and cobalamin (vitamin B12) compared to age and gender-matched controls. METHODS: One hundred and forty six elderly subjects (40 AD, 56 MCI and 49 healthy older adults) were recruited for this study. Serum folic acid and vitamin B12 levels were measured by electrochemoluminescence. RESULTS: Compared to MCI and healthy controls a statistically significant reduction in serum concentrations of folic acid in AD patients was found (p = 0.02). This result remained statistically significant after controlling for socio-demographic and cognitive performance variables (p = 0.01). No significant differences were found in serum concentrations of vitamin B12 in patients with AD, MCI and healthy controls. No significant changes in hematologic parameters were observed across these diagnostic groups. DISCUSSION: The present study provides additional evidence that folic acid is reduced in patients with AD and reinforces the importance of nutritional changes, in particular the one-carbon metabolism, in the physiopathology of AD

No Association between Low Birth Weight and Cardiovascular Risk Factors in Early Adulthood: Evidence from São Paulo, Brazil

Background: A growing literature suggests that low birth weight increases the risk of poor health outcomes in adulthood. We tested this hypothesis among young adults living in São Paulo State, Brazil. Methods and Findings: To identify the effects of low birth weight on young adulthood outcomes, a medical assessment of 297 individuals born between 1977 and 1989 was conducted at a primary care unit in São Paulo State, Brazil. We analyzed body mass index (BMI), waist-hip ratio, blood pressure, fasting glucose and total cholesterol levels using linear and logistic regressions. Low birth was negatively associated with BMI (β = −2.0, 95% CI: −3.69, −0.27, p = 0.02), fasting glucose levels (β = −1.9, 95% CI: −3.9, −0.07, p = 0.05), waist-hip ratio (β = −0.03, 95% CI: −0.07, −0.01, p = 0.10), systolic blood pressure (β = −3.32, 95% CI: −7.60, 0.96, p = 0.12), and total cholesterol levels (β = −3.19, 95% CI: −16.43, 10.05, p = 0.636). Low birth weight was also associated with lower odds of young adults being overweight and obese, but neither association was statistically significant. Weight gain in the first 12 months of life was associated with higher adult BMI (β = 0.79, 95% CI: −0.0455, 1.623, p = 0.064) and blood pressure (β = 2.79, 95% CI: 0.22, 5.35, p = 0.034). No associations were found between low birth weight and early life (catch-up) growth. Conclusions: Low birth weight was not associated with poor health outcomes among young adults in Brazil. These results appear inconsistent with the original Barker hypothesis, but will need to be corroborated in larger samples with longer follow-ups to allow a more general evaluation of the validity of the hypothesis in low and middle income countries