Loss of BAP1 Expression Is Very Rare in Pancreatic Ductal Adenocarcinoma

BACKGROUND: Pancreatic cancer is both common and highly lethal and therefore new biomarkers or potential targets for treatment are needed. Loss of BRCA associated protein-1 (BAP1) expression has been found in up to a quarter of intrahepatic cholangiocarcinomas. Given the close anatomical relationship between intrahepatic cholangiocarcinoma and pancreatic ductal adenocarcinoma, we therefore sought to investigate the frequency of loss of BAP1 expression in pancreatic ductal adenocarcinoma. METHODS: The records of the department of Anatomical Pathology Royal North Shore Hospital, Sydney, Australia, were searched for cases of pancreatic ductal adenocarcinoma diagnosed between 1992 and 2014 with material available in archived formalin fixed paraffin embedded tissue blocks. Immunohistochemistry for BAP1 was performed on tissue microarray sections and if staining was equivocal or negative it was confirmed on whole sections. Negative staining for BAP1 was defined as loss of expression in all neoplastic nuclei, with preserved expression in non-neoplastic cells which acted as an internal positive control. RESULTS: Loss of BAP1 expression was found in only 1 of 306 (0.33%) pancreatic ductal adenocarcinomas. This case was confirmed to demonstrate diffuse loss of expression throughout all neoplastic cells in multiple blocks, consistent with BAP1 loss being an early clonal event. All other cases demonstrated positive expression of BAP1. CONCLUSION: We conclude that, in contrast to intrahepatic cholangiocarcinoma, loss of expression of BAP1 occurs very rarely in pancreatic ductal adenocarcinoma. Therefore BAP1 inactivation is unlikely to be a frequent driver abnormality in pancreatic adenocarcinoma

Microarray analysis of peripheral blood lymphocytes from ALS patients and the SAFE detection of the KEGG ALS pathway

<p>Abstract</p> <p>Background</p> <p>Sporadic amyotrophic lateral sclerosis (sALS) is a motor neuron disease with poorly understood etiology. Results of gene expression profiling studies of whole blood from ALS patients have not been validated and are difficult to relate to ALS pathogenesis because gene expression profiles depend on the relative abundance of the different cell types present in whole blood. We conducted microarray analyses using Agilent Human Whole Genome 4 × 44k Arrays on a more homogeneous cell population, namely purified peripheral blood lymphocytes (PBLs), from ALS patients and healthy controls to identify molecular signatures possibly relevant to ALS pathogenesis.</p> <p>Methods</p> <p>Differentially expressed genes were determined by LIMMA (Linear Models for MicroArray) and SAM (Significance Analysis of Microarrays) analyses. The SAFE (Significance Analysis of Function and Expression) procedure was used to identify molecular pathway perturbations. Proteasome inhibition assays were conducted on cultured peripheral blood mononuclear cells (PBMCs) from ALS patients to confirm alteration of the Ubiquitin/Proteasome System (UPS).</p> <p>Results</p> <p>For the first time, using SAFE in a global gene ontology analysis (gene set size 5-100), we show significant perturbation of the KEGG (Kyoto Encyclopedia of Genes and Genomes) ALS pathway of motor neuron degeneration in PBLs from ALS patients. This was the only KEGG disease pathway significantly upregulated among 25, and contributing genes, including <it>SOD1</it>, represented 54% of the encoded proteins or protein complexes of the KEGG ALS pathway. Further SAFE analysis, including gene set sizes >100, showed that only neurodegenerative diseases (4 out of 34 disease pathways) including ALS were significantly upregulated. Changes in <it>UBR2 </it>expression correlated inversely with time since onset of disease and directly with ALSFRS-R, implying that <it>UBR2 </it>was increased early in the course of ALS. Cultured PBMCs from ALS patients accumulated more ubiquitinated proteins than PBMCs from healthy controls in a serum-dependent manner confirming changes in this pathway.</p> <p>Conclusions</p> <p>Our study indicates that PBLs from sALS patients are strong responders to systemic signals or local signals acquired by cell trafficking, representing changes in gene expression similar to those present in brain and spinal cord of sALS patients. PBLs may provide a useful means to study ALS pathogenesis.</p

Global, regional, and national age-sex specific all-cause and cause-specific mortality for 240 causes of death, 1990-2013: A systematic analysis for the Global Burden of Disease Study 2013

Background Up-to-date evidence on levels and trends for age-sex-specific all-cause and cause-specific mortality is essential for the formation of global, regional, and national health policies. In the Global Burden of Disease Study 2013 (GBD 2013) we estimated yearly deaths for 188 countries between 1990, and 2013. We used the results to assess whether there is epidemiological convergence across countries. Methods We estimated age-sex-specific all-cause mortality using the GBD 2010 methods with some refinements to improve accuracy applied to an updated database of vital registration, survey, and census data. We generally estimated cause of death as in the GBD 2010. Key improvements included the addition of more recent vital registration data for 72 countries, an updated verbal autopsy literature review, two new and detailed data systems for China, and more detail for Mexico, UK, Turkey, and Russia. We improved statistical models for garbage code redistribution. We used six different modelling strategies across the 240 causes; cause of death ensemble modelling (CODEm) was the dominant strategy for causes with sufficient information. Trends for Alzheimer's disease and other dementias were informed by meta-regression of prevalence studies. For pathogen-specific causes of diarrhoea and lower respiratory infections we used a counterfactual approach. We computed two measures of convergence (inequality) across countries: the average relative difference across all pairs of countries (Gini coefficient) and the average absolute difference across countries. To summarise broad findings, we used multiple decrement life-tables to decompose probabilities of death from birth to exact age 15 years, from exact age 15 years to exact age 50 years, and from exact age 50 years to exact age 75 years, and life expectancy at birth into major causes. For all quantities reported, we computed 95% uncertainty intervals (UIs). We constrained cause-specific fractions within each age-sex-country-year group to sum to all-cause mortality based on draws from the uncertainty distributions. Findings Global life expectancy for both sexes increased from 65·3 years (UI 65·0-65·6) in 1990, to 71·5 years (UI 71·0-71·9) in 2013, while the number of deaths increased from 47·5 million (UI 46·8-48·2) to 54·9 million (UI 53·6-56·3) over the same interval. Global progress masked variation by age and sex: for children, average absolute differences between countries decreased but relative differences increased. For women aged 25-39 years and older than 75 years and for men aged 20-49 years and 65 years and older, both absolute and relative differences increased. Decomposition of global and regional life expectancy showed the prominent role of reductions in age-standardised death rates for cardiovascular diseases and cancers in high-income regions, and reductions in child deaths from diarrhoea, lower respiratory infections, and neonatal causes in low-income regions. HIV/AIDS reduced life expectancy in southern sub-Saharan Africa. For most communicable causes of death both numbers of deaths and age-standardised death rates fell whereas for most non-communicable causes, demographic shifts have increased numbers of deaths but decreased age-standardised death rates. Global deaths from injury increased by 10·7%, from 4·3 million deaths in 1990 to 4·8 million in 2013; but age-standardised rates declined over the same period by 21%. For some causes of more than 100 000 deaths per year in 2013, age-standardised death rates increased between 1990 and 2013, including HIV/AIDS, pancreatic cancer, atrial fibrillation and flutter, drug use disorders, diabetes, chronic kidney disease, and sickle-cell anaemias. Diarrhoeal diseases, lower respiratory infections, neonatal causes, and malaria are still in the top five causes of death in children younger than 5 years. The most important pathogens are rotavirus for diarrhoea and pneumococcus for lower respiratory infections. Country-specific probabilities of death over three phases of life were substantially varied between and within regions. Interpretation For most countries, the general pattern of reductions in age-sex specific mortality has been associated with a progressive shift towards a larger share of the remaining deaths caused by non-communicable disease and injuries. Assessing epidemiological convergence across countries depends on whether an absolute or relative measure of inequality is used. Nevertheless, age-standardised death rates for seven substantial causes are increasing, suggesting the potential for reversals in some countries. Important gaps exist in the empirical data for cause of death estimates for some countries; for example, no national data for India are available for the past decade. Funding Bill &amp; Melinda Gates Foundation

Study of deoxyribonucleic acid (DNA) damage in blood lymphocytes of pedicab drivers using the comet assay

People who are working in an urban setting are more likely to be exposed to numerous environmental toxicants. How much damage these harmful agents can do one\u27s body/health is quite difficult to determine. Recently, a new and sensitive technique called COMET assay has become popular and widely used for biomonitoring and occupational exposure studies. Pedicab drivers are unique workers along the selected streets of Metro Manila. They ply the side streets of the city by pedaling their way on their bicycles for short distances not normally serviced by regular buses jeeps and taxis. These drivers are out on the streets for long hours and are exposed to the polluted atmosphere of the streets typical of any urban setting or metropolis. Twelve pedicab drivers agreed to participate in this study aimed at determining whether exposure to environmental toxic materials will have an effect on the DNA, genetic material. From each driver, 4 ml of blood was extracted and these samples were processed for DNA extraction and consequently for COMET assay. Another 12 non pedicab drivers volunteered as control subjects. DNA damage was measured using three parameters: tail length, % DNA in tail and tail moment. Results showed that the mean values of tail length between the pedicab drivers and reference subjects are 29.05 and 9.04 respectively. For the tail moment the mean values are 6.25 for the drivers and 0.94 for the reference subjects. More so, for the % of DNA in tail, the mean values are 17.56 for the drivers and 6.34 for the reference subjects. These data were analyzed using the Wilcoxon Mann- Whitney test to determine whether the differences in these means are statistically significant. Results of analysis revealed that the DNA damage scored among drivers as seen in these 3 parameters (Tail moment, tail length and % of DNA in tail) were significantly higher than those observed among the reference group. From these data, we may infer that constant exposure of the pedicab drivers to environmental toxicants (e.g. air pollutants) could account for this increased DNA damage in their lymphocytes based on the 3 parameters described

Superhero play in selected Barangay day care centers in NCR: teachers\u27 perception and classroom management techniques

This study sought to identify the perceptions of teachers in selected Day Care Centers in National Capital Region (NCR) regarding Superhero Play inside the classroom and how it can be managed. The participant day care centers are located in Pasay, Makati, Mandaluyong, Valenzuela, Malabon, Las Pinas, Caloocan. This research made us of purposive sampling method wherein the Day Care Centers that were part of this study had the standards that the researchers were looking for like the number of teachers in the classroom, their years of experience and the location of the Day Care Center should be within NCR. In gathering the data, the 20 respondents were interviewed with the use of a survey/interview form. To validate the data from the survey/interview form, the respondents were observed three (3) times using an observation guide. Basically, this study determined: (a) whether teachers see superhero play as something essential to child development, (b) what teachers perceive as the superheroes that appeal most to children, (c) how the perceptions of teachers vary when grouped according to age, educational background, and years of teaching (d) the techniques used by the teachers to manage superhero play inside the classroom. The results showed that superhero play occurs inside the classroom and the perceptions of the teachers regarding this kind of activity vary. Significant variations, like the teacher\u27s perceived role during superhero play and the skills developed in this kind of play are seen when the perceptions are grouped according to educational background. The findings of the study show that with the continuing popularity of shows about superheroes, children engage more and more on superhero play. It is therefore important that teachers learn how to manage this activity or use it as a tool for learning. It is recommended that replication of the study be done among day care centers in other regions or among private schools in NCR

Do you think you have a good job? Determining the quality of jobs in the Philippines through wage differentials: A quantile regression approach

One of the macroeconomic goals of every country is to pursue low in employment because this would aid in economic development and growth. However, it does not always take into account the quality of jobs. This research paper will determine which jobs are most likely good and bad jobs in terms of wages and what factors define the quality of a job. The researchers obtained their data from the Philippine Labor Force Survey (LFS), 2nd quarter of year 2007. Quantile regression will be used in determining jobs that are more likely to be good in terms of wage differentials

Utility of the succinate: Fumarate ratio for assessing SDH dysfunction in different tumor types

Objective Mutations of genes encoding the four subunits of succinate dehydrogenase (SDH) have been associated with pheochromocytoma and paraganglioma (PPGLs), gastrointestinal stromal tumors (GISTs) and renal cell carcinomas (RCCs). These tumors have not been characterized in a way that reflects severity of SDH dysfunction. Mass spectrometric analysis now allows measurement of metabolites extracted from formalin fixed paraffin embedded (FFPE) specimens. We assess whether SDH deficiency in various tumor types characterized by loss of SDHB protein expression correlates with SDH dysfunction as assessed by the ratio of succinate:fumarate in FFPE specimens. Patients and methods Sections of FFPE tumor specimens from 18 PPGL, 10 GIST and 11 RCC patients with known SDHx mutation status for SDH deficiency were collected for mass spectrometric analysis of succinate and fumarate. Results FFPE samples showed higher succinate:fumarate ratios in SDH-deficient PPGLs compared to SDH-sufficient PPGLs. Similarly, a higher succinate:fumarate ratio was able to distinguish SDH-deficient GISTs and RCCs from their SDH-sufficient counterparts with great selectivity. Interestingly, the cut-off value of the succinate:fumarate ratio was two-folds greater in RCCs than GISTs. Conclusion Analyzing biochemical imbalances preserved in FFPE specimens with mass spectrometry expands the method and sample type repertoire available for characterisation of multiple neoplasias associated with SDH deficiency

Necrosis is an independent predictor of disease-free and overall survival in pancreatic well-differentiated neuroendocrine tumours (NETs): A proposal to include it in grading systems

Pancreatic neuroendocrine tumours (NETs) are currently graded using the World Health Organization (WHO) 2019 system, which is based solely on mitotic count and Ki-67 proliferative index. Although necrosis is a well-recognised adverse prognostic feature that is included in the grading systems of NETs of certain types such as pulmonary carcinoid and medullary thyroid carcinoma, there is currently insufficient evidence to support its inclusion in the grading of pancreatic NETs. Therefore, we sought to investigate the prognostic significance of tumour necrosis in our cohort of resected pancreatic NETs, with a view to providing evidence to support its incorporation into the WHO grading scheme. Under our proposal, pancreatic NETs without necrosis would continue to be graded based solely on mitotic count and Ki-67 index using the established WHO cut-offs, while NETs with tumour necrosis would be classified as grade 3, irrespective of proliferative activity. Using this system in our cohort of 110 resected pancreatic NETs, overall survival (OS) was 250, 198, and 151 months (p=0.039) and disease-free survival (DFS) was 180 months, 117 months, and 38 months (p\u3c0.0001) for grades 1, 2, and 3, respectively. In contrast, there was no significant difference in OS (p=0.231) or DFS (p=0.058) between low grade (grade 1) and intermediate-high grade (grade 2/3) tumours using the current WHO system which does not consider necrosis. Interobserver concordance for assessment of necrosis was excellent. In conclusion, necrosis is an independent predictor of OS and DFS for pancreatic NETs, and our findings strongly support its addition to the grading scheme for this tumour