Xenbase: Facilitating the Use of Xenopus to Model Human Disease

Abstract

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.

A systematic, label-free method for identifying RNA-associated proteinsin vivoprovides insights into vertebrate ciliary beating

“…Two Xenopus laevis protein database were downloaded from Xenbase (http://www.xenbase.org/ ) (Karpinka JB et al, 2015;Nenni et al, 2019): the X. laevis JGI gene model (v9.1) peptide FASTA (http://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.1/1.8.3.2/XL_9.1_v1.8.3.2.primaryTranscripts. pep.fa.gz) and an X. laevis protein sequence file containing GenBank sequences (http://ftp.xenbase.org/pub/Genomics/Sequences/xlaevisProtein.fasta).…”

Blood-Brain Barrier Protein Claudin-5 Expressed in Paired Xenopus laevis Oocytes Mediates Cell-Cell Interaction

“…In the present study, we employed the classic model for transporters and human disease modeling (Tammaro et al, 2009;Nenni et al, 2019), the X. laevis oocytes, for an in-depth analysis of claudin-5 interaction and functional contribution to the junction seal. To this end, a novel approach, introducing a HPI for challenging interaction within the contact area of clustered Xenopus oocytes, was established.…”

Heart Development and Regeneration in Non-mammalian Model Organisms

“…These features make it relatively easy to perform powerful “cut and paste” transplant experiments to study tissue interactions, especially in heart development. Such methods can be used to separate cardiogenic mesoderm from non-cardiogenic mesoderm, to study the progress of cardiac fate decision and the function of inducers/repressors of heart development ( Nenni et al, 2019 ).…”