MicroRNA expression, survival, and response to interferon in liver cancer

BACKGROUND: Hepatocellular carcinoma is a common and aggressive cancer that occurs mainly in men. We examined microRNA expression patterns, survival, and response to interferon alfa in both men and women with the disease. METHODS: We analyzed three independent cohorts that included a total of 455 patients with hepatocellular carcinoma who had undergone radical tumor resection between 1999 and 2003. MicroRNA-expression profiling was performed in a cohort of 241 patients with hepatocellular carcinoma to identify tumor-related microRNAs and determine their association with survival in men and women. In addition, to validate our findings, we used quantitative reverse-transcriptase-polymerase- chain-reaction assays to measure microRNAs and assess their association with survival and response to therapy with interferon alfa in 214 patients from two independent, prospective, randomized, controlled trials of adjuvant interferon therapy. RESULTS: In patients with hepatocellular carcinoma, the expression of miR-26a and miR-26b in nontumor liver tissue was higher in women than in men. Tumors had reduced levels of miR-26 expression, as compared with paired noncancerous tissues, which indicated that the level of miR-26 expression was also associated with hepatocellular carcinoma. Moreover, tumors with reduced miR-26 expression had a distinct transcriptomic pattern, and analyses of gene networks revealed that activation of signaling pathways between nuclear factor κB and interleukin-6 might play a role in tumor development. Patients whose tumors had low miR-26 expression had shorter overall survival but a better response to interferon therapy than did patients whose tumors had high expression of the microRNA. CONCLUSIONS: The expression patterns of microRNAs in liver tissue differ between men and women with hepatocellular carcinoma. The miR-26 expression status of such patients is associated with survival and response to adjuvant therapy with interferon alfa. Copyright © 2009 Massachusetts Medical Society. All rights reserved.published_or_final_versio

Interlobular and intralobular mammary stroma: Genotype may not reflect phenotype

<p>Abstract</p> <p>Background</p> <p>The normal growth and function of mammary epithelial cells depend on interactions with the supportive stroma. Alterations in this communication can lead to the progression or expansion of malignant growth. The human mammary gland contains two distinctive types of fibroblasts within the stroma. The epithelial cells are surrounded by loosely connected intralobular fibroblasts, which are subsequently surrounded by the more compacted interlobular fibroblasts. The different proximity of these fibroblasts to the epithelial cells suggests distinctive functions for these two subtypes. In this report, we compared the gene expression profiles between the two stromal subtypes.</p> <p>Methods</p> <p>Fresh normal breast tissue was collected from reduction mammoplasty patients and immediately placed into embedding medium and frozen on dry ice. Tissue sections were subjected to laser capture microscopy to isolate the interlobular from the intralobular fibroblasts. RNA was prepared and subjected to microarray analysis using the Affymetrix Human Genome U133 GeneChip^®. Data was analyzed using the Affy and Limma packages available from Bioconductor. Findings from the microarray analysis were validated by RT-PCR and immunohistochemistry.</p> <p>Results</p> <p>No statistically significant difference was detected between the gene expression profiles of the interlobular and intralobular fibroblasts by microarray analysis and RT-PCR. However, for some of the genes tested, the protein expression patterns between the two subtypes of fibroblasts were significantly different.</p> <p>Conclusion</p> <p>This study is the first to report the gene expression profiles of the two distinct fibroblast populations within the human mammary gland. While there was no significant difference in the gene expression profiles between the groups, there was an obvious difference in the expression pattern of several proteins tested. This report also highlights the importance of studying gene regulation at both the transcriptional and post-translational level.</p

SMAR1 binds to T(C/G) repeatvand inhibits tumor progression by regulating miR-371-373 cluster

Chromatin architecture and dynamics are regulated by various histone and non-histone proteins. The matrix attachment region binding proteins (MARBPs) play a central role in chromatin organization and function through numerous regulatory proteins. In the present study, we demonstrate that nuclear matrix protein SMAR1 orchestrates global gene regulation as determined by massively parallel ChIPsequencing. The study revealed that SMAR1 binds to T(C/G) repeat and targets genes involved in diverse biological pathways. We observe that SMAR1 binds and targets distinctly different genes based on the availability of p53. Our data suggest that SMAR1 binds and regulates one of the imperative microRNA clusters in cancer and metastasis, miR-371-373. It negatively regulates miR-371-373 transcription as confirmed by SMAR1 overexpression and knockdown studies. Further, deletion studies indicate that a ~200 bp region in the miR-371-373 promoter is necessary for SMAR1 binding and transcriptional repression. Recruitment of HDAC1/mSin3A complex by SMAR1, concomitant with alteration of histone marks results in downregulation of the miRNA cluster. The regulation of miR-371-373 by SMAR1 inhibits breast cancer tumorigenesis and metastasis as determined by in vivo experiments. Overall, our study highlights the binding of SMAR1 to T(C/G) repeat and its role in cancer through miR-371-37

Impact of singlehood during pregnancy on dietary intake and birth outcomes- a study in the Norwegian Mother and Child Cohort Study

BACKGROUND: Little attention has been given to the impact of singlehood during pregnancy. The aim of this study was to examine the impact of marital status on diet during pregnancy and pregnancy outcome. METHODS: The study population comprised 62,773 women participating in the Norwegian Mother and Child Cohort Study. Marital status was categorised into singles living alone, singles living with parents and married/cohabiting (reference group). Participants answered a general health questionnaire in gestational week 15–17 and a food frequency questionnaire in gestational week 22. We used nonparametric tests to compare dietary intakes by marital status, and multiple logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) for infants being small for gestational age (SGA), large for gestational age (LGA), and preterm delivery (defined as delivery before gestational week 37). RESULTS: Single women living with parents had lower intakes of fruits and vegetables, higher intake of total energy, higher proportion of energy from added sugar, and lower intake of fibre than the reference group. Singles living alone also had a higher intake of added sugar. In both of the single groups, daily smoking was more prevalent than in women living with a partner. In analyses adjusted for maternal age, pre-pregnancy BMI, energy intake, energy contributed by protein, education, income, parity and nausea, single women living alone had increased risk of SGA with OR = 1.27 (95% CI: 1.05, 1.55). When smoking was included among the confounding variables, the association was no longer significant. Likewise, singles living alone had increased risk of preterm delivery, with OR = 1.32 (95% CI: 1.01, 1.72) in a partly adjusted model, but the association did not remain significant in a model fully adjusted for confounding variables. CONCLUSIONS: Single mothers had lower dietary quality and included more smokers than women who lived with a partner. Single mothers living alone had higher prevalence of SGA and preterm delivery, but the associations with adverse pregnancy outcomes were confounded by other variables. This study shows that single mothers should be given special attention during antenatal care and counselling

Assessing the diagnostic accuracy of the identification of hyperkinetic disorders following the introduction of government guidelines in England

<p>Abstract</p> <p>Background</p> <p>Previous studies have suggested that both underdiagnosis and overdiagnosis routinely occur in ADHD and hyperkinesis (hyperkinetic disorders). England has introduced governmental guidelines for these disorders' detection and treatment, but there has been no study on clinical diagnostic accuracy under such a regime.</p> <p>Methods</p> <p>All open cases in three Child and Adolescent Mental Health Services (CAMHS) in the South East of England were assessed for accuracy in the detection of hyperkinetic disorders, using a two-stage process employing the Strengths and Difficulties Questionnaire (SDQ) for screening, with the cut-off between "unlikely" and "possible" as the threshold for identification, and the Development And Well-Being Assessment (DAWBA) as a valid and reliable standard.</p> <p>Results</p> <p>502 cases were collected. Their mean age 11 years (std dev 3 y); 59% were clinically diagnosed as having a hyperkinetic disorder including ADHD. Clinicians had missed two diagnoses of hyperkinesis and six of ADHD. The only 'false positive' case was one that had become asymptomatic on appropriate treatment.</p> <p>Conclusion</p> <p>The identification of children with hyperkinetic disorders by three ordinary English CAMHS teams appears now to be generally consistent with that of a validated, standardised assessment. It seems likely that this reflects the impact of Governmental guidelines, which could therefore be an appropriate tool to ensure consistent accurate diagnosis internationally.</p

Immuno-transcriptomic profiling of extracranial pediatric solid malignancies.

We perform an immunogenomics analysis utilizing whole-transcriptome sequencing of 657 pediatric extracranial solid cancer samples representing 14 diagnoses, and additionally utilize transcriptomes of 131 pediatric cancer cell lines and 147 normal tissue samples for comparison. We describe patterns of infiltrating immune cells, T cell receptor (TCR) clonal expansion, and translationally relevant immune checkpoints. We find that tumor-infiltrating lymphocytes and TCR counts vary widely across cancer types and within each diagnosis, and notably are significantly predictive of survival in osteosarcoma patients. We identify potential cancer-specific immunotherapeutic targets for adoptive cell therapies including cell-surface proteins, tumor germline antigens, and lineage-specific transcription factors. Using an orthogonal immunopeptidomics approach, we find several potential immunotherapeutic targets in osteosarcoma and Ewing sarcoma and validated PRAME as a bona fide multi-pediatric cancer target. Importantly, this work provides a critical framework for immune targeting of extracranial solid tumors using parallel immuno-transcriptomic and -peptidomic approaches

Qualitative thematic analysis of consent forms used in cancer genome sequencing

<p>Abstract</p> <p>Background</p> <p>Large-scale whole genome sequencing (WGS) studies promise to revolutionize cancer research by identifying targets for therapy and by discovering molecular biomarkers to aid early diagnosis, to better determine prognosis and to improve treatment response prediction. Such projects raise a number of ethical, legal, and social (ELS) issues that should be considered. In this study, we set out to discover how these issues are being handled across different jurisdictions.</p> <p>Methods</p> <p>We examined informed consent (IC) forms from 30 cancer genome sequencing studies to assess (1) stated purpose of sample collection, (2) scope of consent requested, (3) data sharing protocols (4) privacy protection measures, (5) described risks of participation, (6) subject re-contacting, and (7) protocol for withdrawal.</p> <p>Results</p> <p>There is a high degree of similarity in how cancer researchers engaged in WGS are protecting participant privacy. We observed a strong trend towards both using samples for additional, unspecified research and sharing data with other investigators. IC forms were varied in terms of how they discussed re-contacting participants, returning results and facilitating participant withdrawal. Contrary to expectation, there were no consistent trends that emerged over the eight year period from which forms were collected.</p> <p>Conclusion</p> <p>Examining IC forms from WGS studies elucidates how investigators are handling ELS challenges posed by this research. This information is important for ensuring that while the public benefits of research are maximized, the rights of participants are also being appropriately respected.</p

Kinase inhibitors for the treatment of inflammatory and autoimmune disorders

Drugs targeting inhibition of kinases for the treatment of inflammation and autoimmune disorders have become a major focus in the pharmaceutical and biotech industry. Multiple kinases from different pathways have been the targets of interest in this endeavor. This review describes some of the recent developments in the search for inhibitors of IKK2, Syk, Lck, and JAK3 kinases. It is anticipated that some of these compounds or newer inhibitors of these kinases will be approved for the treatment of rheumatoid arthritis, psoriasis, organ transplantation, and other autoimmune diseases