BackgroundTumor-infiltrating immune cells have been linked to prognosis and response to immunotherapy; however, the levels of distinct immune cell subsets and the signals that draw them into a tumor, such as the expression of antigen presenting machinery genes, remain poorly characterized. Here, we employ a gene expression-based computational method to profile the infiltration levels of 24 immune cell populations in 19 cancer types.ResultsWe compare cancer types using an immune infiltration score and a T cell infiltration score and find that clear cell renal cell carcinoma (ccRCC) is among the highest for both scores. Using immune infiltration profiles as well as transcriptomic and proteomic datasets, we characterize three groups of ccRCC tumors: T cell enriched, heterogeneously infiltrated, and non-infiltrated. We observe that the immunogenicity of ccRCC tumors cannot be explained by mutation load or neo-antigen load, but is highly correlated with MHC class I antigen presenting machinery expression (APM). We explore the prognostic value of distinct T cell subsets and show in two cohorts that Th17 cells and CD8+ T/Treg ratio are associated with improved survival, whereas Th2 cells and Tregs are associated with negative outcomes. Investigation of the association of immune infiltration patterns with the subclonal architecture of tumors shows that both APM and T cell levels are negatively associated with subclone number.ConclusionsOur analysis sheds light on the immune infiltration patterns of 19 human cancers and unravels mRNA signatures with prognostic utility and immunotherapeutic biomarker potential in ccRCC.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1092-z) contains supplementary material, which is available to authorized users.

Molecular mechanisms associated with tumor metastasis remain poorly understood. Here we report that acquired expression of periostin by colon cancer cells greatly promoted metastatic development of colon tumors. Periostin is overexpressed in more than 80% of human colon cancers examined with highest expression in metastatic tumors. Periostin expression dramatically enhanced metastatic growth of colon cancer by both preventing stress-induced apoptosis in the cancer cells and augmenting endothelial cell survival to promote angiogenesis. At the molecular level, periostin activated the Akt/PKB signaling pathway through the alpha(v)beta(3) integrins to increase cellular survival. These data demonstrated that the survival-promoting function is crucial for periostin to promote tumor metastasis of colon cancer.

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Evolution of growth/dissolution conductive filaments (CFs) in oxide-electrolyte-based resistive switching memories are studied by in situ transmission electron microscopy. Contrary to what is commonly believed, CFs are found to start growing from the anode (Ag or Cu) rather than having to reach the cathode (Pt) and grow backwards. A new mechanism based on local redox reactions inside the oxide-electrolyte is proposed.

OBJECTIVEZinc ions are essential for the formation of hexameric insulin and hormone crystallization. A nonsynonymous single nucleotide polymorphism rs13266634 in the SLC30A8 gene, encoding the secretory granule zinc transporter ZnT8, is associated with type 2 diabetes. We describe the effects of deleting the ZnT8 gene in mice and explore the action of the at-risk allele.RESEARCH DESIGN AND METHODSSlc30a8 null mice were generated and backcrossed at least twice onto a C57BL/6J background. Glucose and insulin tolerance were measured by intraperitoneal injection or euglycemic clamp, respectively. Insulin secretion, electrophysiology, imaging, and the generation of adenoviruses encoding the low- (W325) or elevated- (R325) risk ZnT8 alleles were undertaken using standard protocols.RESULTSZnT8−/− mice displayed age-, sex-, and diet-dependent abnormalities in glucose tolerance, insulin secretion, and body weight. Islets isolated from null mice had reduced granule zinc content and showed age-dependent changes in granule morphology, with markedly fewer dense cores but more rod-like crystals. Glucose-stimulated insulin secretion, granule fusion, and insulin crystal dissolution, assessed by total internal reflection fluorescence microscopy, were unchanged or enhanced in ZnT8−/− islets. Insulin processing was normal. Molecular modeling revealed that residue-325 was located at the interface between ZnT8 monomers. Correspondingly, the R325 variant displayed lower apparent Zn2+ transport activity than W325 ZnT8 by fluorescence-based assay.CONCLUSIONSZnT8 is required for normal insulin crystallization and insulin release in vivo but not, remarkably, in vitro. Defects in the former processes in carriers of the R allele may increase type 2 diabetes risks.

The organic-inorganic hybrid lead halide perovskites have emerged as a series of star materials for solar cells, lasers and detectors. However, the issues raised by the toxic lead element and marginal stability due to the volatile organic components have severely limited their potential applications. In this work, we develop a nucleation-controlled solution method to grow large size high-quality Cs3Bi2I9 perovskite single crystals (PSCs). Using the technique, we harvest some centimeter-sized single crystals and achieved high device performance. We find that X-ray detectors based on PSCs exhibit high sensitivity of 1652.3 μC Gyair−1 cm−2 and very low detectable dose rate of 130 nGyair s−1, both desired in medical diagnostics. In addition, its outstanding thermal stability inspires us to develop a high temperature X-ray detector with stable response at up to 100 °C. Furthermore, PSCs exhibit high X-ray imaging capability thanks to its negligible signal drifting and extremely high stability.

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Resistive switching (RS) is an interesting property shown by some materials systems that, especially during the last decade, has gained a lot of interest for the fabrication of electronic devices, with electronic nonvolatile memories being those that have received the most attention. The presence and quality of the RS phenomenon in a materials system can be studied using different prototype cells, performing different experiments, displaying different figures of merit, and developing different computational analyses. Therefore, the real usefulness and impact of the findings presented in each study for the RS technology will be also different. This manuscript describes the most recommendable methodologies for the fabrication, characterization, and simulation of RS devices, as well as the proper methods to display the data obtained. The idea is to help the scientific community to evaluate the real usefulness and impact of an RS study for the development of RS technology.