Genome-scale metabolic network reconstruction of model animals as a platform for translational research.

Genome-scale metabolic models (GEMs) are used extensively for analysis of mechanisms underlying human diseases and metabolic malfunctions. However, the lack of comprehensive and high-quality GEMs for model organisms restricts translational utilization of omics data accumulating from the use of various disease models. Here we present a unified platform of GEMs that covers five major model animals, including Mouse1 (Mus musculus), Rat1 (Rattus norvegicus), Zebrafish1 (Danio rerio), Fruitfly1 (Drosophila melanogaster), and Worm1 (Caenorhabditis elegans). These GEMs represent the most comprehensive coverage of the metabolic network by considering both orthology-based pathways and species-specific reactions. All GEMs can be interactively queried via the accompanying web portal Metabolic Atlas. Specifically, through integrative analysis of Mouse1 with RNA-sequencing data from brain tissues of transgenic mice we identified a coordinated up-regulation of lysosomal GM2 ganglioside and peptide degradation pathways which appears to be a signature metabolic alteration in Alzheimer's disease (AD) mouse models with a phenotype of amyloid precursor protein overexpression. This metabolic shift was further validated with proteomics data from transgenic mice and cerebrospinal fluid samples from human patients. The elevated lysosomal enzymes thus hold potential to be used as a biomarker for early diagnosis of AD. Taken together, we foresee that this evolving open-source platform will serve as an important resource to facilitate the development of systems medicines and translational biomedical applications.

Molecular profiling using tissue microarrays as a tool to identify predictive biomarkers in laryngeal cancer treated with radiotherapy.

AIM: To explore the usefulness of the expression of five potential cancer biomarkers in predicting outcome in patients with laryngeal cancer. MATERIALS AND METHODS: In the present study, the Swedish National Cancer Registry databases were used to identify patients with laryngeal cancer diagnosed during the years 1978-2004 in the Uppsala-Orebro region and treated with radiotherapy. The expression of Ki-67, MutS homolog 2, (MSH2), p53, B-cell CLL/lymphoma 2 (Bcl-2) and cyclin D1 in the cancer cells was assessed immunohistochemically using tissue microarrays (TMAs) and its predicitve value on survival and relapse was analyzed using Cox regression models. RESULTS: A total of 39 patients were included in the present study. Nuclear MSH2 staining was statistically significantly correlated to Ki-67 expression (p=0.022). However, univariate and multivariate Cox analyses showed no statistically significant association between the expression of the investigated biomarkers and overall survival or relapse. CONCLUSION: The present exploratory study does not show any significant predictive value of the biomarkers examined with respect to survival or relapse. However, with larger patient cohorts, we believe that protein profiling using TMAs and immunohistochemistry is a feasible strategy for prognostic and predictive biomarker screening in laryngeal cancer.

Midgut Carcinoids and Solid Carcinomas of the Intestine: Differences in Endocrine Markers and p53 Mutations.

Fifteen midgut carcinoid tumors and 5 solid carcinomas of the intestine with carcinoid-like morphological features were evaluated histochemically and immunohistochemically with respect to various endocrine markers and expression of mutant p53 protein. Direct sequencing of the p53 gene after PCR amplification was carried out on microdissected cells from all tumors. All investigated carcinoid tumors showed chromogranin and argentaffin reaction, but lacked nuclear immunostaining with p53 antibodies. In 14 immunohistochemically negative midgut carcinoid tumors, no mutations were identified. One carcinoid tumor devoid of p53 staining was, however, found to contain mutation in exon 6 of the p53 gene. In contrast, the solid carcinomas were essentially chromogranin negative but all displayed clearly positive p53 staining in a variable number of cell nuclei. Sequence analysis of exons 5-8 of the p53 gene in the 5 carcinomas showed mutations in exons 6 and 7 in 2 tumors and in exon 8 in 2 other tumors, while no mutation was detected in the fifth tumor. The carcinoid tumors and the solid carcinomas of the small intestine are thought to derive histogenetically from endocrine cells and enterocytes, respectively. The present results substantiate that divergent mechanisms operate in the development of the two tumor types.