Biology of childhood germ cell tumours, focussing on the significance of microRNAs.

Genomic and protein-coding transcriptomic data have suggested that germ cell tumours (GCTs) of childhood are biologically distinct from those of adulthood. Global messenger RNA profiles segregate malignant GCTs primarily by histology, but then also by age, with numerous transcripts showing age-related differential expression. Such differences are likely to account for the heterogeneous clinico-pathological behaviour of paediatric and adult malignant GCTs. In contrast, as global microRNA signatures of human tumours reflect their developmental lineage, we hypothesized that microRNA profiles would identify common biological abnormalities in all malignant GCTs owing to their presumed shared origin from primordial germ cells. MicroRNAs are short, non-protein-coding RNAs that regulate gene expression via translational repression and/or mRNA degradation. We showed that all malignant GCTs over-express the miR-371-373 and miR-302/367 clusters, regardless of patient age, histological subtype or anatomical tumour site. Furthermore, bioinformatic approaches and subsequent Gene Ontology analysis revealed that these two over-expressed microRNAs clusters co-ordinately down-regulated genes involved in biologically significant pathways in malignant GCTs. The translational potential of this finding has been demonstrated with the detection of elevated serum levels of miR-371-373 and miR-302/367 microRNAs at the time of malignant GCT diagnosis, with levels falling after treatment. The tumour-suppressor let-7 microRNA family has also been shown to be universally down-regulated in malignant GCTs, because of abundant expression of the regulatory gene LIN28. Low let-7 levels resulted in up-regulation of oncogenes including MYCN, AURKB and LIN28 itself, the latter through a direct feedback mechanism. Targeting LIN28, or restoring let-7 levels, both led to effective inhibition of this pathway. In summary, paediatric malignant GCTs show biological differences from their adult counterparts at a genomic and protein-coding transcriptome level, whereas they both display very similar microRNA expression profiles. These similarities and differences may be exploited for diagnostic and/or therapeutic purposes.This is the final version. It was first published by Wiley in Andrology at http://onlinelibrary.wiley.com/doi/10.1111/andr.277/full

Status of Zero Degree Calorimeter for CMS Experiment

The Zero Degree Calorimeter (ZDC) is integral part of the CMS experiment, especially, for heavy ion studies. The design of the ZDC includes two independent calorimeter sections: an electromagnetic section and a hadronic section. Sampling calorimeters using tungsten and quartz fibers have been chosen for the energy measurements. An overview of the ZDC is presented along with a current status of calorimeter's preparation for Day 1 of LHC.Comment: 8 pages, 5 figures, 1 table, to appear in the proceedings of CALOR06, June 5-9, 2006 Chicago, US

A pipeline to quantify serum and cerebrospinal fluid microRNAs for diagnosis and detection of relapse in paediatric malignant germ-cell tumours

Background:The current biomarkers alpha-fetoprotein and human chorionic gonadotropin have limited sensitivity and specificity for diagnosing malignant germ-cell tumours (GCTs). MicroRNAs (miRNAs) from the miR-371-373 and miR-302/367 clusters are overexpressed in all malignant GCTs, and some of these miRNAs show elevated serum levels at diagnosis. Here, we developed a robust technical pipeline to quantify these miRNAs in the serum and cerebrospinal fluid (CSF). The pipeline was used in samples from a cohort of exclusively paediatric patients with gonadal and extragonadal malignant GCTs, compared with appropriate tumour and non-tumour control groups.Methods:We developed a method for miRNA quantification that enabled sample adequacy assessment and reliable data normalisation. We performed qRT-PCR profiling for miR-371-373 and miR-302/367 cluster miRNAs in a total of 45 serum and CSF samples, obtained from 25 paediatric patients.Results:The exogenous non-human spike-in cel-miR-39-3p and the endogenous housekeeper miR-30b-5p were optimal for obtaining robust serum and CSF qRT-PCR quantification. A four-serum miRNA panel (miR-371a-3p, miR-372-3p, miR-373-3p and miR-367-3p): (i) showed high sensitivity/specificity for diagnosing paediatric extracranial malignant GCT; (ii) allowed early detection of relapse of a testicular mixed malignant GCT; and (iii) distinguished intracranial malignant GCT from intracranial non-GCT tumours at diagnosis, using CSF and serum samples.Conclusions:The pipeline we have developed is robust, scalable and transferable. It potentially promises to improve clinical management of paediatric (and adult) malignant GCTs

Tissue resolved, gene structure refined equine transcriptome.

BackgroundTranscriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome.ResultsThis equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome.ConclusionsWe have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. We encourage the integration of further equine transcriptomes with our annotation pipeline to continue and improve the equine transcriptome

Outcome of patients with intracranial non-germinomatous germ cell tumors – lessons from the SIOP-CNS-GCT-96 trial.

Background. Following promising results to increase survival and reduce treatment burden in intracranial non-germinomatous germ-cell-tumors (NGGCT), we conducted a European study using dose-intense chemotherapy followed by risk-adapted radiotherapy. Methods. All patients received four courses of Cisplatin/Etoposide/Ifosfamide. Non-metastatic patients then received focal radiotherapy only (54Gy); metastatic patients received 30Gy craniospinal radiotherapy with 24Gy boost to primary tumor and macroscopic metastatic sites. Results. Patients with localized malignant NGGCT (n=116) demonstrated five-year progression-free-survival (PFS) and overall-survival (OS) of 0.72±0.04 and 0.82±0.04, respectively. Primary tumor sites were: 67 pineal, 35 suprasellar, five bifocal, nine others. One patient died post-surgery in clinical remission; three patients progressed during treatment and 27 (23%) relapsed afterwards. Fourteen were local, six combined and seven distant relapses (outside radiation field). Seventeen of the 27 relapsed patients died of disease. Patients with metastatic disease (n=33) demonstrated five-year PFS and OS of 0.68±0.09 and 0.75±0.08, respectively; one patient died following progression on treatment and nine (27%) relapsed afterwards (five local, one combined, three distant). Only one metastatic patient with recurrence was salvaged. Multivariate analysis identified diagnostic alpha-fetoprotein level (serum and/or cerebrospinal fluid) (>1000ng/ml, 19/149 patients, of whom 11 relapsed; p<0.0003) and residual disease following treatment, including after second–look surgery (n=52/145 evaluable patients, 26 relapsed; p=0.0002), as significant prognostic indicators in this cohort. Conclusion. In localized malignant NGGCT craniospinal radiotherapy could be avoided without increased relapses outside the radiotherapy field. Chemotherapy and craniospinal radiotherapy remains the gold standard for metastatic disease.The work was supported in part by Deutsche Krebshilfe e. V., Bonn, Germany and Elisabeth Dreves Stiftung, Germany

How hosts control worms

No abstract available

High Throughput Screening of a GlaxoSmithKline Protein Kinase Inhibitor Set Identifies an Inhibitor of Human Cytomegalovirus Replication that Prevents CREB and Histone H3 Post-Translational Modification.

To identify new compounds with anti-human cytomegalovirus (HCMV) activity and new anti-HCMV targets, we developed a high throughput strategy to screen a GlaxoSmithKline (GSK) Published Kinase Inhibitor Set (PKIS). This collection contains a range of extensively characterized compounds grouped into chemical families (chemotypes). From our screen we identified compounds within chemotypes that impede HCMV replication and identified kinase proteins associated with inhibition of HCMV replication that are potential novel anti-HCMV targets. We focused our study on a top "hit" in our screen, SB-734117, which we found inhibits productive replication of several HCMV strains. Kinase selectivity data indicated that SB-734117 exhibits polypharmacology and is an inhibitor of several proteins from the AGC and CMCG kinase groups. Using western blotting we found that SB-734711 inhibited accumulation of HCMV immediate-early proteins, phosphorylation of cellular proteins involved in immediate-early protein production (CREB and histone H3) and histone H3 lysine 36 trimethylation (H3K36me3). Therefore, we identify SB-734117 as a novel anti-HCMV compound and find that inhibition of AGC and CMCG kinase proteins during productive HCMV replication is associated with inhibition of viral protein production and prevents post-translational modification of cellular factors associated with viral protein production

Evaluation of cost-effective strategies for rabies post-exposure vaccination in low-income countries

&lt;b&gt;Background:&lt;/b&gt; Prompt post-exposure prophylaxis (PEP) is essential in preventing the fatal onset of disease in persons exposed to rabies. Unfortunately, life-saving rabies vaccines and biologicals are often neither accessible nor affordable, particularly to the poorest sectors of society who are most at risk and upon whom the largest burden of rabies falls. Increasing accessibility, reducing costs and preventing delays in delivery of PEP should therefore be prioritized.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Methodology/Principal Findings:&lt;/b&gt; We analyzed different PEP vaccination regimens and evaluated their relative costs and benefits to bite victims and healthcare providers. We found PEP vaccination to be an extremely cost-effective intervention (from $200 to less than$60/death averted). Switching from intramuscular (IM) administration of PEP to equally efficacious intradermal (ID) regimens was shown to result in significant savings in the volume of vaccine required to treat the same number of patients, which could mitigate vaccine shortages, and would dramatically reduce the costs of implementing PEP. We present financing mechanisms that would make PEP more affordable and accessible, could help subsidize the cost for those most in need, and could even support new and existing rabies control and prevention programs.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusions/Significance:&lt;/b&gt; We conclude that a universal switch to ID delivery would improve the affordability and accessibility of PEP for bite victims, leading to a likely reduction in human rabies deaths, as well as being economical for healthcare providers.&lt;p&gt;&lt;/p&gt