Xenbase: Facilitating the Use of Xenopus to Model Human Disease

• Main Authors: Mardi J. Nenni, Malcolm E. Fisher, Christina James-Zorn, Troy J. Pells, Virgilio Ponferrada, Stanley Chu, Joshua D. Fortriede, Kevin A. Burns, Ying Wang, Vaneet S. Lotay, Dong Zhou Wang, Erik Segerdell, Praneet Chaturvedi, Kamran Karimi, Peter D. Vize, Aaron M. Zorn
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2019-02-01
• Series: Frontiers in Physiology
• Subjects: Xenopus; Xenbase; model organism database; human disease; ontologies; oocyte
• Online Access: https://www.frontiersin.org/article/10.3389/fphys.2019.00154/full

At a fundamental level most genes, signaling pathways, biological functions and organ systems are highly conserved between man and all vertebrate species. Leveraging this conservation, researchers are increasingly using the experimental advantages of the amphibian Xenopus to model human disease. The online Xenopus resource, Xenbase, enables human disease modeling by curating the Xenopus literature published in PubMed and integrating these Xenopus data with orthologous human genes, anatomy, and more recently with links to the Online Mendelian Inheritance in Man resource (OMIM) and the Human Disease Ontology (DO). Here we review how Xenbase supports disease modeling and report on a meta-analysis of the published Xenopus research providing an overview of the different types of diseases being modeled in Xenopus and the variety of experimental approaches being used. Text mining of over 50,000 Xenopus research articles imported into Xenbase from PubMed identified approximately 1,000 putative disease- modeling articles. These articles were manually assessed and annotated with disease ontologies, which were then used to classify papers based on disease type. We found that Xenopus is being used to study a diverse array of disease with three main experimental approaches: cell-free egg extracts to study fundamental aspects of cellular and molecular biology, oocytes to study ion transport and channel physiology and embryo experiments focused on congenital diseases. We integrated these data into Xenbase Disease Pages to allow easy navigation to disease information on external databases. Results of this analysis will equip Xenopus researchers with a suite of experimental approaches available to model or dissect a pathological process. Ideally clinicians and basic researchers will use this information to foster collaborations necessary to interrogate the development and treatment of human diseases.