Semantic text mining in early drug discovery for type 2 diabetes.

BACKGROUND: Surveying the scientific literature is an important part of early drug discovery; and with the ever-increasing amount of biomedical publications it is imperative to focus on the most interesting articles. Here we present a project that highlights new understanding (e.g. recently discovered modes of action) and identifies potential drug targets, via a novel, data-driven text mining approach to score type 2 diabetes (T2D) relevance. We focused on monitoring trends and jumps in T2D relevance to help us be timely informed of important breakthroughs. METHODS: We extracted over 7 million n-grams from PubMed abstracts and then clustered around 240,000 linked to T2D into almost 50,000 T2D relevant 'semantic concepts'. To score papers, we weighted the concepts based on co-mentioning with core T2D proteins. A protein's T2D relevance was determined by combining the scores of the papers mentioning it in the five preceding years. Each week all proteins were ranked according to their T2D relevance. Furthermore, the historical distribution of changes in rank from one week to the next was used to calculate the significance of a change in rank by T2D relevance for each protein. RESULTS: We show that T2D relevant papers, even those not mentioning T2D explicitly, were prioritised by relevant semantic concepts. Well known T2D proteins were therefore enriched among the top scoring proteins. Our 'high jumpers' identified important past developments in the apprehension of how certain key proteins relate to T2D, indicating that our method will make us aware of future breakthroughs. In summary, this project facilitated keeping up with current T2D research by repeatedly providing short lists of potential novel targets into our early drug discovery pipeline.

The EndoC-ßH1 cell line is a valid model of human beta cells and applicable for screenings to identify novel drug target candidates.

OBJECTIVE: To characterize the EndoC-ßH1 cell line as a model for human beta cells and evaluate its beta cell functionality, focusing on insulin secretion, proliferation, apoptosis and ER stress, with the objective to assess its potential as a screening platform for identification of novel anti-diabetic drug candidates. METHODS: EndoC-ßH1 was transplanted into mice for validation of in vivo functionality. Insulin secretion was evaluated in cells cultured as monolayer and as pseudoislets, as well as in diabetic mice. Cytokine induced apoptosis, glucolipotoxicity, and ER stress responses were assessed. Beta cell relevant mRNA and protein expression were investigated by qPCR and antibody staining. Hundreds of proteins or peptides were tested for their effect on insulin secretion and proliferation. RESULTS: Transplantation of EndoC-ßH1 cells restored normoglycemia in streptozotocin induced diabetic mice. Both in vitro and in vivo, we observed a clear insulin response to glucose, and, in vitro, we found a significant increase in insulin secretion from EndoC-ßH1 pseudoislets compared to monolayer cultures for both glucose and incretins. Apoptosis and ER stress were inducible in the cells and caspase 3/7 activity was elevated in response to cytokines, but not affected by the saturated fatty acid palmitate. By screening of various proteins and peptides, we found Bombesin (BB) receptor agonists and Pituitary Adenylate Cyclase-Activating Polypeptides (PACAP) to significantly induce insulin secretion and the proteins SerpinA6, STC1, and APOH to significantly stimulate proliferation. ER stress was readily induced by Tunicamycin and resulted in a reduction of insulin mRNA. Somatostatin (SST) was found to be expressed by 1% of the cells and manipulation of the SST receptors was found to significantly affect insulin secretion. CONCLUSIONS: Overall, the EndoC-ßH1 cells strongly resemble human islet beta cells in terms of glucose and incretin stimulated insulin secretion capabilities. The cell line has an active cytokine induced caspase 3/7 apoptotic pathway and is responsive to ER stress initiation factors. The cells' ability to proliferate can be further increased by already known compounds as well as by novel peptides and proteins. Based on its robust performance during the functionality assessment assays, the EndoC-ßH1 cell line was successfully used as a screening platform for identification of novel anti-diabetic drug candidates.

Identification of a conserved cis-acting region driving expression of mouse Eomesodermin to the primitive streak, node, and definitive endoderm.

The cis-acting elements that regulate Eomes transcription during embryonic development are largely unknown. Here we identify a conserved cis-acting region (EoIV) located ~20kb upstream of the Eomes coding region that faithfully drives reporter expression to sites of Eomes expression during gastrulation. Transgenic EoIV-hsp68-GFP expression was evident in the epiblast of early-streak stage mouse embryos at the site where the primitive streak is initiated. At the mid- and late-streak stages, EoIV-hsp68-GFP expression was found in the streak, node region and definitive endoderm with a particular intensive GFP expression in the node region. At the early head fold stage, GFP was expressed in the node region and the surrounding endoderm. In contrast to earlier reports of Eomes mRNA expression, we confirmed Eomes protein expression in the node of early head fold embryos by immunohistochemistry. In vitro, EoIV-hsp68-GFP expression was activated ES cells differentiating into primitive streak-like progeny in response to Bmp and activin treatment.

Three-dimensional immunohistochemical characterization of lineage commitment by localization of T and FOXA2 in porcine peri-implantation embryos.

Gene expression during gastrulation in porcine embryos has been sparsely studied, but there are indications that species-specific patterns exist. Here, we investigated the three-dimensional (3D) expression of the T-box transcription factor Brachyury (T) and the forkhead box transcription factor FOXA2 by immunocytochemistry in porcine peri-gastrulation embryos. The first T(+) cells were detected in posterior epiblast of ovoid blastocysts. Later T(+) FOXA2(-) cells were found in the posterior primitive streak (PS) and nascent mesoderm, T(+) FOXA2(+) cells in the anterior PS, probably identifying the organizer region, and T(-) FOXA2(+) cells anterior to this region. In embryos with a neural groove, T and FOXA2 were co-expressed in the node and notochord, FOXA2 was expressed in the floor plate and posteriorly T was expressed in the streak. In all developmental stages, FOXA2 was expressed in the entire hypoblast/definitive endoderm. We conclude that the expression pattern of T and FOXA2 is largely conserved between pig and mouse.

Three-dimensional localisation of NANOG, OCT4, and E-CADHERIN in porcine pre- and peri-implantation embryos.

The expression patterns of NANOG and OCT4 have previously been reported to differ markedly between mammalian species indicating distinct species-specific roles during development. We investigate the three-dimensional expression pattern of NANOG and OCT4 in porcine pre- and peri-implantation embryos. The expression of NANOG differed remarkably from that reported in other species. NANOG was not detected in the inner cell mass of hatched porcine blastocysts, but later appeared in the epiblast and hypoblast of spherical blastocysts where Rauber's layer had disintegrated. In pre-gastrulating, filamentous embryos NANOG was localised to nuclei in a minor portion of the epiblast cells in which E-CADHERIN seemed to be up-regulated and OCT4 down-regulated. Later NANOG was restricted to the potential PGCs. OCT4 was detected in inner cell mass, epiblast, and mesoderm, and we found that OCT4 expression, in contrast to earlier speculations, at least in hatched blastocysts, resembles the expression pattern in the mouse embryo.