Bifidobacterium and Lactobacillus Probiotics and Gut Dysbiosis in Preterm Infants: The PRIMAL Randomized Clinical Trial.

Importance: The effects of probiotic interventions on colonization with resistant bacteria and early microbiome development in preterm infants remain to be clarified. Objective: To examine the efficacy of Bifidobacterium longum subsp infantis, Bifidobacterium animalis subsp lactis (BB-12), and Lactobacillus acidophilus (La-5) probiotics to prevent colonization with multidrug-resistant organisms or highly epidemic bacteria (MDRO+) and to shape the microbiome of preterm infants toward the eubiotic state of healthy full-term infants. Design, Setting, and Participants: The multicenter, double-blinded, placebo-controlled, group sequential, phase 3 Priming Immunity at the Beginning of Life (PRIMAL) randomized clinical trial, conducted from April 2018 to June 2020, included infants with gestational age of 28 to 32 weeks at 18 German neonatal units. Data analyses were conducted from March 2020 to August 2023. Intervention: A total of 28 days of multistrain probiotics diluted in human milk/formula starting within the first 72 hours of life. Main Outcomes and Measures: Colonization with MDRO+ at day 30 of life (primary end point), late-onset sepsis and severe gastrointestinal complication (safety end points), and gut dysbiosis, ie, deviations from the microbiome of healthy, term infants (eubiosis score) based on 16-subunit ribosomal RNA and metagenomic sequencing. Results: Among the 643 infants randomized until the stop of recruitment based on interim results, 618 (median [IQR] gestational age, 31.0 [29.7-32.1] weeks; 333 male [53.9%]; mean [SD] birth weight, 1502 [369] g) had follow-up at day 30. The interim analysis with all available data from 219 infants revealed MDRO+ colonization in 43 of 115 infants (37.4%) in the probiotics group and in 39 of 104 infants (37.5%) in the control group (adjusted risk ratio, 0.99; 95% CI, 0.54-1.81; P = .97). Safety outcomes were similar in both groups, ie, late-onset sepsis (probiotics group: 8 of 316 infants [2.5%]; control group: 12 of 322 infants [3.7%]) and severe gastrointestinal complications (probiotics group: 6 of 316 infants [1.9%]; control group: 7 of 322 infants [2.2%]). The probiotics group had higher eubiosis scores than the control group at the genus level (254 vs 258 infants; median scores, 0.47 vs 0.41; odds ratio [OR], 1.07; 95% CI, 1.02-1.13) and species level (96 vs 83 infants; median scores, 0.87 vs 0.59; OR, 1.28; 95% CI, 1.19-1.38). Environmental uptake of the B infantis probiotic strain in the control group was common (41 of 84 [49%]), which was highly variable across sites and particularly occurred in infants with a sibling who was treated with probiotics. Conclusions and Relevance: Multistrain probiotics did not reduce the incidence of MDRO+ colonization at day 30 of life in preterm infants but modulated their microbiome toward eubiosis. Trial Registration: German Clinical Trials Register: DRKS00013197.

Abnormalities of the Eyelashes in Turner's Syndrome.

Turner's syndrome (TS) is a sex chromosome disorder caused by a partial loss, complete absence or structural abnormality of one X chromosome in females. Special ocular features are often found. Some of the abnormalities are only cosmetic, such as the abnormalities of the eyelashes. The present prospective study with 12 TS and 12 control patients demonstrates the higher number of eyelashes as well as the greater vertical distance between the roots of the eyelashes in patients with TS compared with the control group. Increased awareness of this ophthalmological abnormality could be an additional diagnostic tool for early clinical suspicion of TS diagnosis.

Discovery of BI 7446: A Potent Cyclic Dinucleotide STING Agonist with Broad-Spectrum Variant Activity for the Treatment of Cancer.

Activating the stimulator of interferon genes (STING) pathway with STING agonists is an attractive immune oncology concept to treat patients with tumors that are refractory to single-agent anti-PD-1 therapy. For best clinical translatability and broad application to cancer patients, STING agonists with potent cellular activation of all STING variants are desired. Novel cyclic dinucleotide (CDN)-based selective STING agonists were designed and synthesized comprising noncanonical nucleobase, ribose, and phosphorothioate moieties. This strategy led to the discovery of 2',3'-CDN 13 (BI 7446), which features unprecedented potency and activates all five STING variants in cellular assays. ADME profiling revealed that CDN 13 has attractive drug-like properties for development as an intratumoral agent. Injection of low doses of CDN 13 into tumors in mice induced long-lasting, tumor-specific immune-mediated tumor rejection. Based on its compelling preclinical profile, BI 7446 has been advanced to clinical trials (monotherapy and in combination with anti-PD-1 antibody).

Identification of Highly Selective Orexin 1 Receptor Antagonists Driven by Structure-Based Design.

OX1 receptor antagonists are of interest to treat, for example, substance abuse disorders, personality disorders, eating disorders, or anxiety-related disorders. However, known dual OX1/OX2 receptor antagonists are not suitable due to their sleep-inducing effects; therefore, we were interested in identifying a highly OX1 selective antagonist with a sufficient window to OX2-mediated effects. Herein, we describe the design of highly selective OX1 receptor antagonists driven by the X-ray structure of OX1 with suvorexant, a dual OX1/OX2 receptor antagonist. Moderately selective OX1 antagonists comprising a [2.2.1]-bicyclic scaffold served as our starting point. Based on our binding mode hypothesis, we postulated which part of the scaffold points toward one of the regions where the two binding pockets differ. Structural changes in this part resulted in a modified core with higher inherent selectivity compared to the [2.2.1]-bicyclic template. The structure-based design, synthesis, and hit-to-lead evaluation of this novel OX1 receptor-selective scaffold are discussed herein.

MAGICPL: A Generic Process Description Language for Distributed Pseudonymization Scenarios.

OBJECTIVES: Pseudonymization is an important aspect of projects dealing with sensitive patient data. Most projects build their own specialized, hard-coded, solutions. However, these overlap in many aspects of their functionality. As any re-implementation binds resources, we would like to propose a solution that facilitates and encourages the reuse of existing components. METHODS: We analyzed already-established data protection concepts to gain an insight into their common features and the ways in which their components were linked together. We found that we could represent these pseudonymization processes with a simple descriptive language, which we have called MAGICPL, plus a relatively small set of components. We designed MAGICPL as an XML-based language, to make it human-readable and accessible to nonprogrammers. Additionally, a prototype implementation of the components was written in Java. MAGICPL makes it possible to reference the components using their class names, making it easy to extend or exchange the component set. Furthermore, there is a simple HTTP application programming interface (API) that runs the tasks and allows other systems to communicate with the pseudonymization process. RESULTS: MAGICPL has been used in at least three projects, including the re-implementation of the pseudonymization process of the German Cancer Consortium, clinical data flows in a large-scale translational research network (National Network Genomic Medicine), and for our own institute's pseudonymization service. CONCLUSIONS: Putting our solution into productive use at both our own institute and at our partner sites facilitated a reduction in the time and effort required to build pseudonymization pipelines in medical research.

Automated Reports for Monitoring and Improving Data Quality in a Translational Research Network.

Standardised, automated quality reports were generated at three pilot locations of the decentralized translational research network DKTK with separated local data warehouses (LDW), for assessing syntactic conformity against common data element definitions deposited in a central metadata repository (MDR). Deviations in the LDW were categorised, and locally corrected. Comparisons of reports from two time points confirm a major improvement in data quality in terms of syntactic conformity, an essential prerequisite for network-wide data integration.

A Method to Use Metadata in Legacy Web Applications: The Samply.MDR.Injector.

Whenever medical data is integrated from multiple sources, it is regarded good practice to separate data from information about its meaning, such as designations, definitions or permissible values (in short: metadata). However, the ways in which applications work with metadata are imperfect: Many applications do not support fetching metadata from externalized sources such as metadata repositories. In order to display human-readable metadata in any application, we propose not to change the application, but to provide a library that makes a change to the user interface. The goal of this work is to provide a way to "inject" the meaning of metadata keys into the web-based frontend of an application to make it "metadata aware".

Multiple Binding Sites Contribute to the Mechanism of Mixed Agonistic and Positive Allosteric Modulators of the Cannabinoid CB1 Receptor.

The cannabinoid CB1 receptor (CB1R) is an abundant metabotropic G-protein-coupled receptor that has been difficult to address therapeutically because of CNS side effects exerted by orthosteric drug candidates. Recent efforts have focused on developing allosteric modulators that target CB1R. Compounds from the recently discovered class of mixed agonistic and positive allosteric modulators (Ago-PAMs) based on 2-phenylindoles have shown promising functional and binding properties as CB1R ligands. Here, we identify binding modes of both the CP 55,940 agonist and GAT228, a 2-phenylindole allosteric modulator, by using our metadynamics simulation protocol, and quantify their affinity and cooperativity by atomistic simulations. We demonstrate the involvement of multiple adjunct binding sites in the Ago-PAM characteristics of the 2-phenylindole modulators and explain their ability to compete with orthosteric agonists at higher concentrations. We validate these results experimentally by showing the contribution of multiple sites on the allosteric binding of ZCZ011, another homologous member of the class, together with the orthosteric agonist.

An Architecture for Translational Cancer Research As Exemplified by the German Cancer Consortium.

Networking of medical institutions by means of a capable data infrastructure has the potential to open up vast amounts of routine data to translational cancer research. However, the secondary use of information collected independently in several institutions is a challenging task of data integration. In this review, we discuss the requirements and common challenges involved in the establishment of such a platform. We present methods and tools from the field of medical informatics as solutions to semantic and technical heterogeneity, questions of data protection and record linkage, as well as issues of trust and data ownership. We also describe the architecture of an existing cancer research network as an exemplary application of these methods.

GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update.

RNA interference (RNAi) represents a powerful method to systematically study loss-of-function phenotypes on a large scale with a wide variety of biological assays, constituting a rich source for the assignment of gene function. The GenomeRNAi database (http://www.genomernai.org) makes available RNAi phenotype data extracted from the literature for human and Drosophila. It also provides RNAi reagent information, along with an assessment as to their efficiency and specificity. This manuscript describes an update of the database previously featured in the NAR Database Issue. The new version has undergone a complete re-design of the user interface, providing an intuitive, flexible framework for additional functionalities. Screen information and gene-reagent-phenotype associations are now available for download. The integration with other resources has been improved by allowing in-links via GenomeRNAi screen IDs, or external gene or reagent identifiers. A distributed annotation system (DAS) server enables the visualization of the phenotypes and reagents in the context of a genome browser. We have added a page listing 'frequent hitters', i.e. genes that show a phenotype in many screens, which might guide on-going RNAi studies. Structured annotation guidelines have been established to facilitate consistent curation, and a submission template for direct submission by data producers is available for download.

Reactome: a database of reactions, pathways and biological processes.

Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice.

R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases.

R spider is a web-based tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions in human biology accumulated in the Reactome and KEGG databases. R spider implements a network-based statistical framework, which provides a global understanding of gene relations in the supplied gene list, and fully exploits the Reactome and KEGG knowledge bases. R spider provides a user-friendly dialog-driven web interface for several model organisms and supports most available gene identifiers. R spider is freely available at http://mips.helmholtz-muenchen.de/proj/rspider.

The Systems Biology Graphical Notation.

Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.

Reactome knowledgebase of human biological pathways and processes.

Reactome (http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets. Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome's data content and software can all be freely used and redistributed under open source terms.

Patterns of somatic mutation in human cancer genomes.

Cancers arise owing to mutations in a subset of genes that confer growth advantage. The availability of the human genome sequence led us to propose that systematic resequencing of cancer genomes for mutations would lead to the discovery of many additional cancer genes. Here we report more than 1,000 somatic mutations found in 274 megabases (Mb) of DNA corresponding to the coding exons of 518 protein kinase genes in 210 diverse human cancers. There was substantial variation in the number and pattern of mutations in individual cancers reflecting different exposures, DNA repair defects and cellular origins. Most somatic mutations are likely to be 'passengers' that do not contribute to oncogenesis. However, there was evidence for 'driver' mutations contributing to the development of the cancers studied in approximately 120 genes. Systematic sequencing of cancer genomes therefore reveals the evolutionary diversity of cancers and implicates a larger repertoire of cancer genes than previously anticipated.

Reactome: a knowledge base of biologic pathways and processes.

Reactome http://www.reactome.org, an online curated resource for human pathway data, provides infrastructure for computation across the biologic reaction network. We use Reactome to infer equivalent reactions in multiple nonhuman species, and present data on the reliability of these inferred reactions for the distantly related eukaryote Saccharomyces cerevisiae. Finally, we describe the use of Reactome both as a learning resource and as a computational tool to aid in the interpretation of microarrays and similar large-scale datasets.

Structural polarity and dynamics of male germline stem cells in the milkweed bug (Oncopeltus fasciatus).

The male germline stem cells (GSCs) of the milkweed bug present an extraordinary structural polarity that is, to our knowledge, unequalled by any other type of stem cells. They consist of a perikaryon and numerous projections arising from the cell pole directed toward the apical cells, the proposed niche of the GSCs. The projections can traverse a considerable distance until their terminals touch the apical cells. From hatching until death, the GSC projections undergo conspicuous changes, the sequence of which has been deduced from observations of all developmental stages. Projection formation starts from lobular cell protrusions showing trabecular ingrowths of the cell membrane. Finger-like projections result from a process of growth and "carving out". The newly formed projections contain mostly only free ribosomes other than a few mitochondria. A stereotyped degradation process commences in the projection terminals: profiles of circular, often concentric, cisternae of rough endoplasmic reticulum appear and turn into myelin bodies, whereas mitochondria become more numerous. The cytoplasm vesiculates, lysosomal bodies appear, and mitochondria become swollen. At the same time, the projection terminals are segregated by transverse ingrowths of the cell membrane. Finally, autophagic vacuoles and myelin bodies fill the segregated terminals, which then rupture. Simultaneously, new projections seem to sprout from the perikaryon of the GSCs. These dynamics, which are not synchronized among the GSCs, indicate that a novel type of signal exchange and transduction between the stem cells and their niche is involved in the regulation of asymmetric versus symmetric division of GSCs.

Fabry disease: reduced activities of respiratory chain enzymes with decreased levels of energy-rich phosphates in fibroblasts.

UNLABELLED: Fabry disease (FD, MIM 301500) caused by a deficient activity of alpha-galactosidase A is characterized by intralysosomal storage of glycosphingolipids. Main clinical features are paresthesia, hypohidrosis, angiokeratoma, renal insufficiency, and cardiovascular or cerebral complications. The exact pathogenesis is unclear. Beside mechanical storage biochemical factors might play a role. As FD is a multisystemic disorder and mitochondrial dysfunction has been described in patients with neuronal ceroidlipofuscinosis (another lysosomal storage disease) we examined mitochondrial function in fibroblasts from patients with FD. RESULTS: Activities of respiratory chain enzymes I, IV, and V were significantly (p < 0.01) lower in FD-cells. Mitochondrial recovery was unchanged as judged by the activity of the mitochondrial marker enzyme citratesynthase, cellular protein content was not significantly different. CP, ADP, and AMP concentrations were significantly (p < 0.01) lower in FD-cells. ATP was slightly, but not significantly reduced (p = 0.045). CONCLUSION: Organ dysfunction in FD may not only be explained by mechanical storage of glycosphingolipids. As in NCL, lysosomal storage material may lead to mitochondrial dysfunction with a reduction of respiratory chain enzyme activities and a subsequent drop in cellular levels of energy-rich phosphates.

Short postoperative survival for glioblastoma patients with a dysfunctional Rb1 pathway in combination with no wild-type PTEN.

PURPOSE: Glioblastoma (GB, WHO grade IV) is the most common primary brain tumor in adults. Survival is typically <1 year but varies between a few months and a couple of years. The aim of the study was to find novel genetic prognostic factors in a well-defined GB series. EXPERIMENTAL DESIGN: The survival data on 129 GBs were correlated with the results of a detailed analysis of 9 genes. These included 3 genes coding for proteins in the p53 pathway (i.e., TP53, p14(ARF), and MDM2), 4 in the Rb1 pathway (i.e., CDKN2A, CDKN2B, RB1, and CDK4), as well as PTEN and epidermal growth factor receptor. RESULTS: We found that abnormalities in any of the four genes (CDKN2A, CDKN2B, RB1, and CDK4) coding for components of the Rb1 pathway were associated with shorter survival (P = 0.002). In combination with loss of wild-type PTEN, the association was even stronger (P < 0.001), the median survival being 166 days as compared with the group without these abnormalities where the median postoperative survival was 437 days. The survival difference remained statistically significant in Cox' regression analysis adjusting for age (P = 0.012). CONCLUSIONS: The findings indicate that knowledge of the molecular genetic abnormalities in GBs provides important data in assessing individual patients. As additional advances in our understanding of the molecular genetics and cell biology of gliomas are made, in addition to providing prognostic information, such data may also provide targets for innovative therapy in the individual case.