Isoform-level gene signature improves prognostic stratification and accurately classifies glioblastoma subtypes.

Molecular stratification of tumors is essential for developing personalized therapies. Although patient stratification strategies have been successful; computational methods to accurately translate the gene-signature from high-throughput platform to a clinically adaptable low-dimensional platform are currently lacking. Here, we describe PIGExClass (platform-independent isoform-level gene-expression based classification-system), a novel computational approach to derive and then transfer gene-signatures from one analytical platform to another. We applied PIGExClass to design a reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) based molecular-subtyping assay for glioblastoma multiforme (GBM), the most aggressive primary brain tumors. Unsupervised clustering of TCGA (the Cancer Genome Altas Consortium) GBM samples, based on isoform-level gene-expression profiles, recaptured the four known molecular subgroups but switched the subtype for 19% of the samples, resulting in significant (P = 0.0103) survival differences among the refined subgroups. PIGExClass derived four-class classifier, which requires only 121 transcript-variants, assigns GBM patients' molecular subtype with 92% accuracy. This classifier was translated to an RT-qPCR assay and validated in an independent cohort of 206 GBM samples. Our results demonstrate the efficacy of PIGExClass in the design of clinically adaptable molecular subtyping assay and have implications for developing robust diagnostic assays for cancer patient stratification

Factors associated with increased survival after surgical resection of glioblastoma in octogenarians.

Elderly patients with glioblastoma represent a clinical challenge for neurosurgeons and oncologists. The data available on outcomes of patients greater than 80 undergoing resection is limited. In this study, factors linked to increased survival in patients over the age of 80 were analyzed. A retrospective chart review of all patients over the age of 80 with a new diagnosis of glioblastoma and who underwent surgical resection with intent for maximal resection were examined. Patients who had only stereotactic biopsies were excluded. Immunohistochemical expression of oncogenic drivers (p53, EGFR, IDH-1) and a marker of cell proliferation (Ki-67 index) performed upon routine neuropathological examination were recorded. Stepwise logistic regression and Kaplan Meier survival curves were plotted to determine correlations to overall survival. Fifty-eight patients fit inclusion criteria with a mean age of 83 (range 80-93 years). The overall median survival was 4.2 months. There was a statistically significant correlation between Karnofsky Performance Status (KPS) and overall survival (P < 0.05). There was a significantly longer survival among patients undergoing either radiation alone or radiation and chemotherapy compared to those who underwent no postoperative adjuvant therapy (p < 0.05). There was also an association between overall survival and lack of p53 expression (p < 0.001) and lack of EGFR expression (p <0.05). In this very elderly population, overall survival advantage was conferred to those with higher preoperative KPS, postoperative adjuvant therapy, and lack of protein expression of EGFR and p53. These findings may be useful in clinical decision analysis for management of patients with glioblastoma who are octogenarians, and also validate the critical role of EGFR and p53 expression in oncogenesis, particularly with advancing age

An Outbreak of Pseudomonas aeruginosa Pneumonia and Bloodstream Infection Associated With Intermittent Otitis Externa in a Healthcare Worker

Arstract Objectives: To investigate an outbreak of Pseudomonas aeruginosa pneumonia and bloodstream infection among four neonates, determine risk factors for infection, and implement preventive strategies. Design: Retrospective case finding; prospective surveillance cultures of patients, personnel, and environmental sites; molecular typing by pulsed-field gel electrophoresis; and a matched case-control study. Patients and Setting: Neonates in the level-III neonatal intensive care unit of a tertiary-care pediatric institution. Interventions: Cohorting of patients with positive results for P. aeruginosa, work restrictions for staff with positive results, implementation of an alcohol-based hand product, review of infection control policies and procedures, and closure of the unit until completion of the investigation. Results: Seven (4%) of 190 environmental cultures and 5 (3%) of 178 cultures of individual healthcare workers' hands grew P. aeruginosa. All four outbreak isolates and one previous bloodstream isolate were genotypically identical, as were the P. aeruginosa isolates from the hands and external auditory canal of a healthcare worker with intermittent otitis externa. Four of 5 case-patients versus 5 of 15 matched control-patients had been cared for by this healthcare worker (P = .05). The healthcare worker was treated and no further cases occurred. Conclusions: These findings suggest that a healthcare worker with intermittent otitis externa may have caused this cluster of fatal P. aeruginosa infections, adding the external ear to the list of colonized body sites that may serve as a source of potentially pathogenic organism

Vascular niche IL-6 induces alternative macrophage activation in glioblastoma through HIF-2α.

Spatiotemporal regulation of tumor immunity remains largely unexplored. Here we identify a vascular niche that controls alternative macrophage activation in glioblastoma (GBM). We show that tumor-promoting macrophages are spatially proximate to GBM-associated endothelial cells (ECs), permissive for angiocrine-induced macrophage polarization. We identify ECs as one of the major sources for interleukin-6 (IL-6) expression in GBM microenvironment. Furthermore, we reveal that colony-stimulating factor-1 and angiocrine IL-6 induce robust arginase-1 expression and macrophage alternative activation, mediated through peroxisome proliferator-activated receptor-γ-dependent transcriptional activation of hypoxia-inducible factor-2α. Finally, utilizing a genetic murine GBM model, we show that EC-specific knockout of IL-6 inhibits macrophage alternative activation and improves survival in the GBM-bearing mice. These findings illustrate a vascular niche-dependent mechanism for alternative macrophage activation and cancer progression, and suggest that targeting endothelial IL-6 may offer a selective and efficient therapeutic strategy for GBM, and possibly other solid malignant tumors

IKK phosphorylates Huntingtin and targets it for degradation by the proteasome and lysosome

Expansion of the polyglutamine repeat within the protein Huntingtin (Htt) causes Huntington's disease, a neurodegenerative disease associated with aging and the accumulation of mutant Htt in diseased neurons. Understanding the mechanisms that influence Htt cellular degradation may target treatments designed to activate mutant Htt clearance pathways. We find that Htt is phosphorylated by the inflammatory kinase IKK, enhancing its normal clearance by the proteasome and lysosome. Phosphorylation of Htt regulates additional post-translational modifications, including Htt ubiquitination, SUMOylation, and acetylation, and increases Htt nuclear localization, cleavage, and clearance mediated by lysosomal-associated membrane protein 2A and Hsc70. We propose that IKK activates mutant Htt clearance until an age-related loss of proteasome/lysosome function promotes accumulation of toxic post-translationally modified mutant Htt. Thus, IKK activation may modulate mutant Htt neurotoxicity depending on the cell's ability to degrade the modified species

A pan-Arctic initiative on the spatial and temporal dynamics of Arctic coasts

Permafrost coasts make up roughly one third of all coasts worldwide. Their erosion leads to the release of previously locked organic carbon, changes in ecosystems and the destruction of cultural heritage, infrastructure and whole communities. Since rapid environmental changes lead to an intensification of Arctic coastal dynamics, it is of great importance to adequately quantify current and future coastal changes. However, the remoteness of the Arctic and scarcity of data limit our understanding of coastal dynamics at a pan-Arctic scale and prohibit us from getting a complete picture of the diversity of impacts on the human and natural environment. In a joint effort of the EU project NUNATARYUK and the NSF project PerCS-Net, we seek to close this knowledge gap by collecting and analyzing all accessible high-resolution shoreline position data for the Arctic coastline. These datasets include geographical coordinates combined with coastal positions derived from archived data, surveying data, air and space born remote sensing products, or LiDAR products. The compilation of this unique dataset will enable us to reach unprecedented data coverage and will allow us a first insight into the magnitude and trends of shoreline changes on a pan-Arctic scale with locally highly resolved temporal and spatial changes in shoreline dynamics. By comparing consistently derived shoreline change data from all over the Arctic we expect that the trajectory of coastal change in the Arctic becomes evident. A synthesis of some initial results will be presented in the 2020 Arctic Report Card on Arctic Coastal Dynamics. This initiative is an ongoing effort – new data contributions are welcome

Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics

The white-tailed deer (Odocoileus virginianus) represents one of the most successful and widely distributed large mammal species within North America, yet very little nucleotide sequence information is available. We utilized massively parallel pyrosequencing of a reduced representation library (RRL) and a random shotgun library (RSL) to generate a complete mitochondrial genome sequence and identify a large number of putative single nucleotide polymorphisms (SNPs) distributed throughout the white-tailed deer nuclear and mitochondrial genomes. A SNP validation study designed to test specific classes of putative SNPs provides evidence for as many as 10,476 genome-wide SNPs in the current dataset. Based on cytogenetic evidence for homology between cow (Bos taurus) and white-tailed deer chromosomes, we demonstrate that a divergent genome may be used for estimating the relative distribution and density of de novo sequence contigs as well as putative SNPs for species without draft genome assemblies. Our approach demonstrates that bioinformatic tools developed for model or agriculturally important species may be leveraged to support next-generation research programs for species of biological, ecological and evolutionary importance. We also provide a functional annotation analysis for the de novo sequence contigs assembled from white-tailed deer pyrosequencing reads, a mitochondrial phylogeny involving 13,722 nucleotide positions for 10 unique species of Cervidae, and a median joining haplotype network as a putative representation of mitochondrial evolution in O. virginianus. The results of this study are expected to provide a detailed template enabling genome-wide sequence-based studies of threatened, endangered or conservationally important non-model organisms