A Targeted Multiomics Approach to Identify Biomarkers Associated with Rapid eGFR Decline in Type 1 Diabetes

Background: Individuals with type 1 diabetes (T1D) demonstrate varied trajectories of estimated glomerular filtration rate (eGFR) decline. The molecular pathways underlying rapid eGFR decline in T1D are poorly understood, and individual-level risk of rapid eGFR decline is difficult to predict. Methods: We designed a case-control study with multiple exposure measurements nested within 4 well-characterized T1D cohorts (FinnDiane, Steno, EDC, and CACTI) to identify biomarkers associated with rapid eGFR decline. Here, we report the rationale for and design of these studies as well as results of models testing associations of clinical characteristics with rapid eGFR decline in the study population, upon which "omics" studies will be built. Cases (n = 535) and controls (n = 895) were defined as having an annual eGFR decline of >= 3 andPeer reviewe

Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response

The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (D500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-beta levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-beta responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.Peer reviewe

Superplastic Deformation Mechanisms in Fine-Grained 2050 Al-Cu-Li Alloys

The deformation behavior and microstructural evolution of fine-grained 2050 alloys at elevated temperatures and slow strain rates were investigated. The results showed that significant dynamic anisotropic grain growth occurred at the primary stage of deformation. Insignificant dislocation activity, particle-free zones, and the complete progress of grain neighbor switching based on diffusion creep were observed during superplastic deformation. Quantitative calculation showed that diffusion creep was the dominant mechanism in the superplastic deformation process, and that grain boundary sliding was involved as a coordination mechanism. Surface studies indicated that the diffusional transport of materials was accomplished mostly through the grain boundary, and that the effect of the bulk diffusion was not significant

Microwave-Assisted Synthesis of Fe3O4 Nanocrystals with Predominantly Exposed Facets and Their Heterogeneous UVA/Fenton Catalytic Activity

Fe3O4 nanocrystals with five different morphologies (i.e., nanospheres, nanorods, nanocubes, nano-octahedrons, and nanoplates) were acquired using a simple, efficient, and economic microwave-assisted oxidation technique. The microstructure, morphology, predominant exposed facets; and iron atom local environment of Fe3O4 were revealed by powder X-ray diffraction (PXRD); scanning transmission electron microscopy (SEM), high-resolution transmission electron microscopy (HRTEM), X-ray photoelectron spectrometer (XPS), and Mossbauer spectrum: We demonstrated that the heterogeneous UVA/Fenton catalytic activities of Fe3O4 nanocrystals are morphology/facets dependent Under UVA irradiation, the catalytic activity of the as-prepared Fe3O4 was in the sequence of nanospheres > nanoplates > nano-octahedrons approximate to nanocubes > nanorods > nano-octahedrons (by coprecipitation). The dominating factor for the catalytic performance was the particle size and BET specific surface area; moreover, the exposed {111} facets, which contained more Fe2+ species, on the nanocrystal surface led to a stronger UVA/Fenton catalytic activity. Both (OH)-O-center dot and O-2(center dot-) radicals participated in the UVA/Fenton degradation process, and (OH)-O-center dot played the dominant role. These morphology-controlled nanomagnetites showed great potential in applications as heterogeneous UVA/Fenton catalysts for effectively treating nonbiodegradable organic pollutants

IL-6/JAK2-dependent G6PD phosphorylation promotes nucleotide synthesis and supports tumor growth

Objective: Tumor cells hijack inflammatory mechanisms to promote their own growth. IL-6 is one of the major cytokines, and is frequently upregulated in tumors. The pentose phosphate pathway (PPP) generates the indispensable building blocks to produce various nucleotides. Here we aimed to determine whether and how PPP is timely tuned in response to IL-6 to support tumor growth. Methods: Protein expression was examined by immunoblot. Protein interaction was examined by immunoprecipitation. Tumor cell proliferation in in vitro culture was examined by BrdU assay and colony formation assay. Tumor cell proliferation in mouse xenograft model was examined by Ki-67 staining. Results: Here we show that the metabolic flux of PPP and enzymatic activity of glucose-6-phosphate dehydrogenase (G6PD) is rapidly induced under IL-6 treatment, without obvious changes in G6PD expression level. Mechanistically, Janus kinase 2 (JAK2) phosphorylates G6PD Y437 under IL-6 treatment, which accentuates G6PD enzymatic activity by promoting G6PD binding with its substrate G6P. Further, JAK2-dependent G6PD Y437 phosphorylation is required for IL-6-induced nucleotide biosynthesis and tumor cell proliferation, and is associated with the progression of oral squamous cell carcinoma. Conclusions: Our findings report a new mechanism implicated in the crosstalk between tumor cells and inflammatory microenvironment, by which JAK2-dependent activation of G6PD governs nucleotide synthesis to support tumor cell proliferation, thereby highlighting its value as a potential anti-tumor target

Direct Approach for Qualitative and Quantitative Characterization of Glycoproteins Using Tandem Mass Tags and an LTQ Orbitrap XL Electron Transfer Dissociation Hybrid Mass Spectrometer

The application of multiplexed isobaric tandem mass tag (TMT) labeling and an LTQ Orbitrap XL ETD (electron transfer dissociation) hybrid mass spectrometer as a direct approach for qualitative and quantitative characterization of glycoproteins is reported. Bovine fetuin was used as a model glycoprotein in this study. For online liquid chromatography–mass spectrometry (LC–MS) analysis, high-resolution, mass accurate full scan MS spectra were acquired in the Orbitrap mass analyzer followed by data-dependent tandem mass spectrometry (MS/MS) with alternating collision-induced dissociation (CID), ETD, and higher-energy collisional dissociation (HCD) scans. An additional in-source dissociation scan was used as a highly sensitive and selective detection method for eluting glycosylated peptides. By alternatively using three different dissociation methods, 23 glycoforms from all 5 corresponding glycopeptides were identified from a trypsin digest of bovine fetuin. With ETD, labile glycans were retained without any signs of carbohydrate cleavage with concurrent fragmentation of the peptide backbone. Glycosylation sites were clearly localized from the ETD fragmentation data. Glycan structure elucidation was accomplished using CID. The CID experiments generated fragment ions predominantly from cleavage of glycosidic bonds without breaking the peptide bond. Novel to this method, the TMT labeling protocol was modified and adapted for higher labeling efficiency, and a TriVersa NanoMate was used to reinfuse samples to improve ETD and HCD spectra of glycopeptides. Quantification with TMT was verified based on the HCD spectra from multiple nonglycopeptides and glycopeptides. This method can be used as a qualitative and quantitative technique for direct characterization of glycoproteins and has applicability for detection of counterfeit glycoprotein drug products