Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival.

BACKGROUND: Glioblastoma multiforme, the most common type of primary brain tumor in adults, is driven by cells with neural stem (NS) cell characteristics. Using derivation methods developed for NS cells, it is possible to expand tumorigenic stem cells continuously in vitro. Although these glioblastoma-derived neural stem (GNS) cells are highly similar to normal NS cells, they harbor mutations typical of gliomas and initiate authentic tumors following orthotopic xenotransplantation. Here, we analyzed GNS and NS cell transcriptomes to identify gene expression alterations underlying the disease phenotype. METHODS: Sensitive measurements of gene expression were obtained by high-throughput sequencing of transcript tags (Tag-seq) on adherent GNS cell lines from three glioblastoma cases and two normal NS cell lines. Validation by quantitative real-time PCR was performed on 82 differentially expressed genes across a panel of 16 GNS and 6 NS cell lines. The molecular basis and prognostic relevance of expression differences were investigated by genetic characterization of GNS cells and comparison with public data for 867 glioma biopsies. RESULTS: Transcriptome analysis revealed major differences correlated with glioma histological grade, and identified misregulated genes of known significance in glioblastoma as well as novel candidates, including genes associated with other malignancies or glioma-related pathways. This analysis further detected several long non-coding RNAs with expression profiles similar to neighboring genes implicated in cancer. Quantitative PCR validation showed excellent agreement with Tag-seq data (median Pearson r = 0.91) and discerned a gene set robustly distinguishing GNS from NS cells across the 22 lines. These expression alterations include oncogene and tumor suppressor changes not detected by microarray profiling of tumor tissue samples, and facilitated the identification of a GNS expression signature strongly associated with patient survival (P = 1e-6, Cox model). CONCLUSIONS: These results support the utility of GNS cell cultures as a model system for studying the molecular processes driving glioblastoma and the use of NS cells as reference controls. The association between a GNS expression signature and survival is consistent with the hypothesis that a cancer stem cell component drives tumor growth. We anticipate that analysis of normal and malignant stem cells will be an important complement to large-scale profiling of primary tumors.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Ultra High Energy Cosmic Rays from Sequestered X Bursts

Assuming that there is no GZK (Greisen-Zatsepin-Kuzmin) cut-off and that super-GZK cosmic rays correlate with AGN (Active Galactic Nuclei) at cosmological distances, it is speculated that a relic superheavy particle (X) has its lifetime enhanced by sequestration in an extra dimension. This sequestration is assumed to be partially liberated by proximity of merging supermassive black holes in an AGN, temporarily but drastically reducing the lifetime, thus stimulating an X burst. Based on sequestration of the decay products of X, a speculative explanation of the observed $\gamma/N$ ratio is proposed.Comment: 12 pages LaTe

Assessment of transcript reconstruction methods for RNA-seq

We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data

Resetting transcription factor control circuitry toward ground-state pluripotency in human.

Current human pluripotent stem cells lack the transcription factor circuitry that governs the ground state of mouse embryonic stem cells (ESC). Here, we report that short-term expression of two components, NANOG and KLF2, is sufficient to ignite other elements of the network and reset the human pluripotent state. Inhibition of ERK and protein kinase C sustains a transgene-independent rewired state. Reset cells self-renew continuously without ERK signaling, are phenotypically stable, and are karyotypically intact. They differentiate in vitro and form teratomas in vivo. Metabolism is reprogrammed with activation of mitochondrial respiration as in ESC. DNA methylation is dramatically reduced and transcriptome state is globally realigned across multiple cell lines. Depletion of ground-state transcription factors, TFCP2L1 or KLF4, has marginal impact on conventional human pluripotent stem cells but collapses the reset state. These findings demonstrate feasibility of installing and propagating functional control circuitry for ground-state pluripotency in human cells.This research was supported by the UK Medical Research Council, the Japan Science and Technology agency (JST, PRESTO), the Genome Biology Unit of the European Molecular Biology Laboratory, European Commission projects PluriMes, BetaCellTherapy, EpiGeneSys, and Blueprint, and the Wellcome Trust. Y.T. was a University of Cambridge Herchel Smith Fellow. A.S. is a Medical Research Council Professor

StemBond hydrogels control the mechanical microenvironment for pluripotent stem cells.

Studies of mechanical signalling are typically performed by comparing cells cultured on soft and stiff hydrogel-based substrates. However, it is challenging to independently and robustly control both substrate stiffness and extracellular matrix tethering to substrates, making matrix tethering a potentially confounding variable in mechanical signalling investigations. Moreover, unstable matrix tethering can lead to poor cell attachment and weak engagement of cell adhesions. To address this, we developed StemBond hydrogels, a hydrogel in which matrix tethering is robust and can be varied independently of stiffness. We validate StemBond hydrogels by showing that they provide an optimal system for culturing mouse and human pluripotent stem cells. We further show how soft StemBond hydrogels modulate stem cell function, partly through stiffness-sensitive ERK signalling. Our findings underline how substrate mechanics impact mechanosensitive signalling pathways regulating self-renewal and differentiation, indicating that optimising the complete mechanical microenvironment will offer greater control over stem cell fate specification

Political economy analysis of Universal health coverage and health financing reforms in low- and middle-income countries: The role of stakeholder engagement in the research process

Sophie Witter - ORCID: 0000-0002-7656-6188 https://orcid.org/0000-0002-7656-6188Maria Paola Bertone - ORCID: 0000-0001-8890-583X https://orcid.org/0000-0001-8890-583XAM replaced with VoR 2021-12-13.Background: Progress towards Universal Health Coverage (UHC) is an inherently political process. Political economy analysis (PEA) is gaining momentum as a tool to better understand the role of the political and economic dimensions in shaping and achieving UHC in different contexts. Despite the acknowledged importance of actors and stakeholders in political economy considerations, their role in the PEA research process beyond ‘study subjects’ as potential co-creators of knowledge and knowledge users has been overlooked so far. We therefore aimed to review the approaches with reference to stakeholder engagement during the research process adopted in the current published research on the political economy of UHC and health financing reforms, and the factors favouring (or hindering) uptake and usability of PEA work. Methods: We reviewed the literature to describe if, when and how stakeholders were involved in the research process of studies looking at the political economy of UHC and health financing reforms, and to identify challenges and lessons learned on effective stakeholder engagement and research uptake. We used a standardised search strategy with key terms across several databases; we screened and included articles that focused on PEA and UHC. Additionally, we conducted a short survey of authors of the included studies to complement the information retrieved. Results: 50 articles met the inclusion criteria and were included in the analysis. We found overall little evidence of systematic engagement of stakeholders in the research process, which focused mostly on the data collection phase of the research (i.e., key informant interviews). Our study identifies some reasons for the varying stakeholder engagement. Challenges include PEA requiring specific skills, focusing on sensitive issues and the blurriness in researchers’ and stakeholders’ roles and the multiple roles of stakeholders as research participants, study subjects and research users. Among the approaches that might favour usability of PEA work, we identified early engagement, co-production of research questions, local partners and personal contact, political willingness, and trust and use of prospective analysis. Conclusions: Stakeholder engagement and research uptake are multifaceted concepts and complex processes, particularly when applied to PEA. As such, stakeholder engagement in the research process of PEA of UHC and health financing reforms is limited and underreported. Despite the challenges, however, stakeholder engagement remains key to ensure relevance, usability, and research uptake of PEA studies. More efforts are required to ensure engagement at different stages of the research process and better reporting in published articles.This research was funded by the National Institute for Health Research (NIHR) through a Development Award of the NIHR Global Health Policy and Systems Research Programme (project reference: 130266), using UK aid from the UK Government to support global health research. The views expressed in this publication are those of the authors and not necessarily those of the NIHR or the UK Department of Health and Social Care.https://doi.org/10.1186/s12961-021-00788-w19pubpu

Fusion reactions with the one-neutron halo nucleus C15

The structure of C15, with an s1/2 neutron weakly bound to a closed-neutron shell nucleus C14, makes it a prime candidate for a one-neutron halo nucleus. We have for the first time studied the cross section for the fusion-fission reaction C15+Th232 at energies in the vicinity of the Coulomb barrier and compared it to the yield of the neighboring C14+Th232 system measured in the same experiment. At sub-barrier energies, an enhancement of the fusion yield by factors of 2-5 was observed for C15, while the cross sections for C14 match the trends measured for C12,13. © 2011 American Physical Society