Biology subjects

Wagner, J.

Publications and source records attributed to Wagner, J..

7 recordsLinked to original sources

bioRxiv2018

Combinatorial recognition of clustered RNA elementsby a multidomain RNA-binding protein, IMP3

How multidomain RNA-binding proteins recognize their specific target sequences, based on a combinatorial code, represents a fundamental unsolved question and has not been studied systematically so far. Here we focus on a prototypical multidomain RNA-binding protein, IMP3 (also called IGF2BP3), which contains six RNA-binding domains (RBDs): four KH and two RRM domains. We have established an integrative systematic strategy, combining single-domain-resolved SELEX-seq, motif-spacing analyses, in vivo iCLIP, functional validation assays, and structural biology. This approach identifies the RNA-binding specificity and RNP topology of IMP3, involving all six RBDs and a cluster of up to five distinct and appropriately spaced CA-rich and GGC-core RNA elements, covering a >100 nucleotide-long target RNA region. Our generally applicable approach explains both specificity and flexibility of IMP3-RNA recognition, providing a paradigm for the function of multivalent interactions with multidomain RNA-binding proteins in gene regulation.

molecular biology↗

bioRxiv2018

metagenomeFeatures: An R package for working with 16S rRNA reference databases and marker-gene survey feature data.

We developed the metagenomeFeatures R Bioconductor package along with annotation packages for the three primary 16S rRNA databases (Greengenes, RDP, and SILVA) to facilitate working with 16S rRNA sequence databases and marker-gene survey feature data. The metagenomeFeatures package defines two classes, MgDb for working with 16S rRNA sequence databases, and mgFeatures for working with marker-gene survey feature data. The associated annotation packages provide a consistent interface to the different 16S rRNA databases facilitating database comparison and exploration. The mgFeatures represents a crucial step in the development of a common data structure for working with 16S marker-gene survey data in R.\n\nAvailabilityhttps://bioconductor.org/packages/release/bioc/html/metagenomeFeatures.html\n\nContactnolson@nist.gov

bioinformatics↗

bioRxiv2018

NetrinG1/NGL-1 Axis promotes pancreatictumorigenesis through cancer associated fibroblastderived nutritional supply and immunosuppression

Pancreatic ductal adenocarcinoma (PDAC) has a poor 5-year survival rate and lacks effective therapeutics. Therefore, it is of paramount importance to identify new targets. Using multi-plex data from patient tissue, three-dimensional co-culturing in vitro assays, and orthotopic murine models, we identified Netrin G1 (NetG1) as a promoter of PDAC tumorigenesis. NetG1+ cancer-associated fibroblasts (CAFs) supported PDAC survival, through a NetG1 mediated effect on glutamate/glutamine metabolism. NetG1+ CAFs were intrinsically immunosuppressive and inhibited NK cell mediated killing of tumor cells. These pro-tumor functions were controlled by a signaling circuit downstream to NetG1, which was comprised of AKT/4E-BP1, p38/FRA1, vesicular glutamate transporter 1, and glutamine synthetase. Finally blocking NetG1 with a neutralizing antibody stunted in vivo tumorigenesis, suggesting NetG1 as potential target in PDAC. SignificancePDAC is a devastating disease lacking effective therapies. A major hallmark of PDAC is desmoplasia, characterized by the expansion of CAFs and their extracellular matrix, creating a unique microenvironment that limits blood-supplied nutrition and is highly immunosuppressive. A better understanding of the role of CAFs in PDAC may lead to the identification of new targets for therapeutic intervention. Here, we uncovered roles for NetG1 in CAFs to promote tumorigenesis. NetG1 was important for two major CAF functions: the metabolic support of PDAC cells and the intrinsic immunosuppressive capacity of CAFs. Our results helped clarify the role that CAFs play in PDAC, by defining CAF phenotypes through NetG1 expression. Moreover, we established a link between CAF driven metabolism and their intrinsic immunosuppressive capacity, and identified a signaling circuit that governs NetG1 functions. Finally, we demonstrated the therapeutic potential of inhibiting NetG1 in vivo by limiting tumorigenesis in mice with a neutralizing antibody, illustrating that targeting stromal NetG1 could be an attractive therapeutic approach.

cancer biology↗

bioRxiv2018

Mouse models of hereditary hemochromatosis do not develop early liver fibrosis in response to a high fat diet

Hepatic iron overload, a hallmark of hereditary hemochromatosis (HH), triggers progressive liver disease. There is also increasing evidence for a pathogenic role of iron in non-alcoholic fatty liver disease (NAFLD), which may progress to non-alcoholic steatohepatitis (NASH), fibrosis, cirrhosis and hepatocellular cancer. Mouse models of HH and NAFLD can be used to explore potential interactions between iron and lipid metabolic pathways. Hfe-/- mice, a model of moderate iron overload, were reported to develop early liver fibrosis in response to a high fat diet. However, this was not the case with Hjv-/- mice, a model of severe iron overload. These data raised the possibility that the Hfe gene may protect against liver injury independently of its iron regulatory function. Herein, we addressed this hypothesis in a comparative study utilizing wild type, Hfe-/-, Hjv-/- and double Hfe-/-Hjv-/- mice. The animals, all in C57/BL6 background, were fed with a high fat diet for 14 weeks and developed hepatic steatosis, associated with mild iron overload. Hfe co-ablation did not sensitize steatotic Hjv-deficient mice to liver injury. Moreover, we did not observe any signs of liver inflammation or fibrosis even in single steatotic Hfe-/- mice. Ultrastructural studies revealed a reduced lipid and glycogen content in Hjv-/- hepatocytes, indicative of a metabolic defect. Interestingly, glycogen levels were restored in double Hfe-/-Hjv-/- mice, which is consistent with a metabolic function of Hfe. We conclude that hepatocellular iron excess does not aggravate diet-induced steatosis to steatohepatitis or early liver fibrosis in mouse models of HH, irrespectively of the presence or lack of Hfe.

pathology↗

bioRxiv2018

Sidewall cell envelope synthesis and remodeling in pole-growing mycobacteria

O_SCPLOWDC_SCPLOW-amino acid probes label cell wall peptidoglycan at both the poles and sidewall of pole-growing mycobacteria. Since peptidoglycan assembly along the cell periphery could provide a rapid, growth-independent means by which to edit the cell wall, we sought to clarify the precise metabolic fates of these probes. O_SCPLOWDC_SCPLOW-amino acid monopeptides were incorporated into peptidoglycan by O_SCPLOWLC_SCPLOWO_SCPCAP,C_SCPCAPO_SCPLOWDC_SCPLOW-transpeptidase remodeling enzymes to varying extents. Dipeptides were incorporated into cytoplasmic precursors. While dipeptide-marked peptidoglycan synthesis at the poles was associated with cell elongation, synthesis along the periphery was highly responsive to cell wall damage. Our observations suggest a post-expansion role for peptidoglycan assembly along the mycobacterial sidewall and provide a conceptual framework for understanding cell wall robustness in the face of polar growth.

microbiology↗

bioRxiv2017

Forgot what you like? Evidence for hippocampal dependence of value-based decisions

Consistent decisions are intuitively desirable and theoretically important for utility maximization. Neuroeconomics has established the neurobiological substrate of value representation, but brain regions that provide input to the value-processing network is less explored. The constructed-preference tradition within behavioral decision research gives a critical role to cognitive processes that rely on associations, suggesting a role for the hippocampus in making decisions and to do so consistently. We compared the performance of 31 patients with mediotemporal lobe (MTL) epilepsy and hippocampal lesions, 30 patients with extratemporal lobe epilepsy, and 30 healthy controls on two tasks: binary choices between candy bars based on their preferences and a number-comparison control task where the larger number is chosen. MTL patients make more inconsistent choices than the other two groups for the value-based choice but not the number-comparison task. These inconsistencies increase with the volume of compromised hippocampal tissue. These results suggest a critical involvement of the MTL in preference construction and value-based choices.\n\nSignificanceOur days are full of choices that reflect our preferences. Economics lays out models of how to optimally make these decisions. Neuroeconomics has identified a cortical value-processing network whose activity correlates with constructs related to valuation and choice in economic models. However open questions remain: How are these value signals formed, and what regions might be necessary for retrieving and computing these value signals? Inspired by cognitive models calling on associative processes in value-based decisions, this paper uses unique neuropsychological data to establish the critical role of the medial temporal lobe in making consistent choices and further informs our understanding of the value-processing network.

animal behavior and cognition↗

bioRxiv2017

Metaviz: interactive statistical and visual analysis of metagenomic data

Along with the survey techniques of 16S rRNA amplicon and whole-metagenome shotgun sequencing, an array of tools exists for clustering, taxonomic annotation, normalization, and statistical analysis of microbiome sequencing results. Integrative and interactive visualization that enables researchers to perform exploratory analysis in this feature rich hierarchical data is an area of need. In this work, we present Metaviz, a web browser-based tool for interactive exploratory metagenomic data analysis. Metaviz can visualize abundance data served from an R session or a Python web service that queries a graph database. As metagenomic sequencing features have a hierarchy, we designed a novel navigation mechanism to explore this feature space. We visualize abundance counts with heatmaps and stacked bar plots that are dynamically updated as a user selects taxonomic features to inspect. Metaviz also supports common data exploration techniques, including PCA scatter plots to interpret variability in the dataset and alpha diversity boxplots for examining ecological community composition. The Metaviz application and documentation is hosted at http://www.metaviz.org.

bioinformatics↗