Investigating the role of Hedgehog/GLI1 signaling in glioblastoma cell response to temozolomide.

Resistance to chemotherapy substantially hinders successful glioblastoma (GBM) treatment, contributing to an almost 100% mortality rate. Resistance to the frontline chemotherapy, temozolomide (TMZ), arises from numerous signaling pathways that are deregulated in GBM, including Hedgehog (Hh) signaling. Here, we investigate suppression of Hh signaling as an adjuvant to TMZ using U87-MG and T98G cell lines as in vitro models of GBM. We found that silencing GLI1 with siRNA reduces cell metabolic activity by up to 30% in combination with TMZ and reduces multidrug efflux activity by 2.5-fold. Additionally, pharmacological GLI inhibition modulates nuclear p53 levels and decreases MGMT expression in combination with TMZ. While we surprisingly found that silencing GLI1 does not induce apoptosis in the absence of TMZ co-treatment, we discovered silencing GLI1 without TMZ co-treatment induces senescence as evidenced by a significant 2.3-fold increase in senescence associated β-galactosidase staining, and this occurs in a loss of PTEN-dependent manner. Finally, we show that GLI inhibition increases apoptosis in glioma stem-like cells by up to 6.8-fold in combination with TMZ, and this reduces the size and number of neurospheres grown from glioma stem-like cells. In aggregate, our data warrant the continued investigation of Hh pathway inhibitors as adjuvants to TMZ chemotherapy and highlight the importance of identifying signaling pathways that determine whether co-treatment will be successful

SARS coronavirus replicase proteins in pathogenesis

Much progress has been made in understanding the role of structural and accessory proteins in the pathogenesis of severe acute respiratory syndrome coronavirus (SARS-CoV) infections. The SARS epidemic also brought new attention to the proteins translated from ORF1a and ORF1b of the input genome RNA, also known as the replicase/transcriptase gene. Evidence for change within the ORF1ab coding sequence during the SARS epidemic, as well as evidence from studies with other coronaviruses, indicates that it is likely that the ORF1ab proteins play roles in virus pathogenesis distinct from or in addition to functions directly involved in viral replication. Recent reverse genetic studies have confirmed that proteins of ORF1ab may be involved in cellular signaling and modification of cellular gene expression, as well as virulence by mechanisms yet to be determined. Thus, the evolution of the ORF1ab proteins may be determined as much by issues of host range and virulence as they are by specific requirements for intracellular replication

TraitBank : practical semantics for organism attribute data

© IOS Press and The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Semantic Web 7 (2016): 577-588, doi:10.3233/SW-150190.Encyclopedia of Life (EOL) has developed TraitBank (http://eol.org/traitbank), a new repository for organism attribute (trait) data. TraitBank aggregates, manages and serves attribute data for organisms across the tree of life, including life history characteristics, habitats, distributions, ecological relationships and other data types. We describe how TraitBank ingests and manages these data in a way that leverages EOL’s existing infrastructure and semantic annotations to facilitate reasoning across the TraitBank corpus and interoperability with other resources. We also discuss TraitBank’s impact on users and collaborators and the challenges and benefits of our lightweight, scalable approach to the integration of biodiversity data.Support for TraitBank was provided by the Alfred P. Sloan Foundation, the Smithsonian Institution, the Marine Biological Laboratory, and the John D. and Catherine T. MacArthur Foundation

Tumor-associated T cell receptor repertoires in low- and high-grade gliomas

Glioblastoma (GBM) remains prognostically dismal, with care centered on resection, motivating research into novel therapies. Although inducing anti-tumor immunity remains an attractive target for therapeutic and preventative intervention, the interplay between evolving dysregulation of the glioma microenvironment and T cell inefficacy remains poorly understood. In our murine model of proneural glioma, retroviral delivery of PDGF and cre-mediated knockout of PTEN in glial progenitors of adult C57BL/6 gives rise to slow-growing tumors, which were harvested at early- mid- and late-stage progression timepoints following induction, along with peripheral blood. From human patients, tissue from low- and high-grade glioma resections and corresponding peripheral lymphocytes were cryofrozen during surgery at New York Presbyterian-CUMC. For both species, we employed a commercially available primer set (iRepertoire) for nested PCR of the complementarity-determining region 3 (CDR3) of the TCR-alpha and TCR-beta chains from the T cell RNA, followed by next-generation sequencing on an Illumina MiSeq. We developed a computational pipeline for mapping TCR cassettes, in silico translation, pairwise analysis of tissue/periphery per subject, and error analysis. In the murine model, we observe that at late-stage, the intratumoral TCR repertoire diverges significantly from the peripheral, including dramatic expansion of single tumor-associated CDR3s, while the peripheral repertoire itself diverges from those of healthy mice. In both human patients and mice, we observed tumor-associated CDR3s, disproportionately abundant in tumor tissue compared to the corresponding peripheral blood, at both the amino acid and nucleotide level. In human samples we observed tumor-specific TCR expansions that were associated with particular functional subsets (CD8+, CD4+, Treg, NKT). Sequence-level study of the TCR repertoire promises new insight into the scope of glioma immunosuppression, especially systemic effects which remain elusive and the origins of intratumoral suppressive populations, and holds the potential for immunotherapeutic interventions, non-invasive diagnostics, and direct assessment of global responses to immunotherapy

TCR repertoire divergence reflects micro-environmental immune phenotypes in glioma

Background & significance: Glioblastoma (GBM) remains prognostically dismal, with only modest gains in mean survival time with chemo- and radiotherapy motivating research into reversing its characteristic local and systemic immunosuppression with precision in this high-risk tissue. While whole-repertoire amplification of the TCR repertoire allows unprecedented depth regarding the potentiation of anti-tumor responses, most studies utilize TCRseq for monitoring reactivity to specific tumor antigens, or the identities of particular TCRs as biomarkers. In this study, we have utilized whole-repertoire analysis to describe the relationship between intra-tumoral T cells and peripheral circulation, and leverage mutual information between gene expression and the behavior of the T cell population to characterize glioma-reactive states, driven by the gene expression of the principal resident monocyte population, and perturbable by immunological interventions. Methods & results: From resected tumor tissue and peripheral lymphocytes of low- and high-grade human glioma patients, TCRseq libraries were generated using reverse transcription and nested PCR (iRepertoire 1) of the complementarity-determining region 3 (CDR3) of the TCR-alpha and TCR-beta chains, then sequenced on an Illumina MiSeq. We developed a computational pipeline for mapping TCR cassettes, in silico translation, and sequence error correction from these libraries, enabling sensitive calculation of tumor-infiltrating lymphocyte (TIL) and peripheral TCR diversity (Shannon entropy) 2, as well as the divergence (Jensen-Shannon divergence metric) between the two T cell populations. By integrating amino acid identity and V-J cassette combination, we observed varying levels of divergence between the TIL and peripheral lymphocytes of glioma patients, and changes in this divergence over tumor progression in a PDGF-driven murine model. Correlation of these properties with tumor tissue RNA profiling, by differential gene expression and mutual-information gene ontology, revealed an association between tumor growth and high blood-brain TCR divergence - particularly in amino-acid sequence, suggesting antigen-driven selection - while high expression of inflammatory and certain immune pathway markers computationally attributed to microglia 3 were anti-correlated with divergence. Preliminary murine experiments suggest that TCR divergence can be altered by induction and blockade of cytokine-mediated activation of these pathways. Conclusion: The expression of a subset of microglia-associated genes appears to describe micro-environmental states which are strongly tied to the tumor-specificity of the intra-tumoral TCR repertoire, complementary to the tumor-centric classifications of TCGA. TCRseq-based profiling not only promises to inform tailoring of local and systemic immunotherapy to target the most relevant immunosuppressive mechanisms, but may also provide non-invasive assessment of the intra-tumoral environment for refined diagnosis and monitoring during clinical trials

Long-Term Survival, Toxicity Profile, and role of F-18 FDG PET/CT scan in Patients with Progressive Neuroendocrine Tumors Following Peptide Receptor Radionuclide Therapy with High Activity In-111 Pentetreotide

Aim: To study the long term benefits, toxicity and survival rate in patients with neuroendocrine tumors receiving multiple cycles of high activity In-111 Pentetreotide therapy. Moreover, our secondary aim was to evaluate the value of F-18 FDG PET-CT scan as prognostic indicator in this group of patients

A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs

Background: Mounting evidence suggests a major role for epigenetic feedback in Plasmodium falciparum transcriptional regulation. Long non-coding RNAs (lncRNAs) have recently emerged as a new paradigm in epigenetic remodeling. We therefore set out to investigate putative roles for lncRNAs in P. falciparum transcriptional regulation. Results: We used a high-resolution DNA tiling microarray to survey transcriptional activity across 22.6% of the P. falciparum strain 3D7 genome. We identified 872 protein-coding genes and 60 putative P. falciparum lncRNAs under developmental regulation during the parasite's pathogenic human blood stage. Further characterization of lncRNA candidates led to the discovery of an intriguing family of lncRNA telomere-associated repetitive element transcripts, termed lncRNA-TARE. We have quantified lncRNA-TARE expression at 15 distinct chromosome ends and mapped putative transcriptional start and termination sites of lncRNA-TARE loci. Remarkably, we observed coordinated and stage-specific expression of lncRNA-TARE on all chromosome ends tested, and two dominant transcripts of approximately 1.5 kb and 3.1 kb transcribed towards the telomere. Conclusions: We have characterized a family of 22 telomere-associated lncRNAs in P. falciparum. Homologous lncRNA-TARE loci are coordinately expressed after parasite DNA replication, and are poised to play an important role in P. falciparum telomere maintenance, virulence gene regulation, and potentially other processes of parasite chromosome end biology. Further study of lncRNA-TARE and other promising lncRNA candidates may provide mechanistic insight into P. falciparum transcriptional regulation.Organismic and Evolutionary BiologyStem Cell and Regenerative BiologyOther Research Uni

ENVIRONMENTS and EOL : identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bioinformatics 31 (2015): 1872-1874, doi:10.1093/bioinformatics/btv045.The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary-based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users.The Encyclopedia Of Life Rubenstein Fellows Program [CRDF EOL-33066-13/E33066], the LifeWatchGreece Research Infrastructure [384676-94/GSRT/ NSRF(C&E)] and the Novo Nordisk Foundation Center for Protein Research [NNF14CC0001]

MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma

Glioblastomas (GBMs) diffusely infiltrate the brain, making complete removal by surgical resection impossible. The mixture of neoplastic and nonneoplastic cells that remain after surgery form the biological context for adjuvant therapeutic intervention and recurrence. We performed RNA-sequencing (RNA-seq) and histological analysis on radiographically guided biopsies taken from different regions of GBM and showed that the tissue contained within the contrast-enhancing (CE) core of tumors have different cellular and molecular compositions compared with tissue from the nonenhancing (NE) margins of tumors. Comparisons with the The Cancer Genome Atlas dataset showed that the samples from CE regions resembled the proneural, classical, or mesenchymal subtypes of GBM, whereas the samples from the NE regions predominantly resembled the neural subtype. Computational deconvolution of the RNA-seq data revealed that contributions from nonneoplastic brain cells significantly influence the expression pattern in the NE samples. Gene ontology analysis showed that the cell type-specific expression patterns were functionally distinct and highly enriched in genes associated with the corresponding cell phenotypes. Comparing the RNA-seq data from the GBM samples to that of nonneoplastic brain revealed that the differentially expressed genes are distributed across multiple cell types. Notably, the patterns of cell type-specific alterations varied between the different GBM subtypes: the NE regions of proneural tumors were enriched in oligodendrocyte progenitor genes, whereas the NE regions of mesenchymal GBM were enriched in astrocytic and microglial genes. These subtypespecific patterns provide new insights into molecular and cellular composition of the infiltrative margins of GBM