Research resource: Gonadotropin-releasing hormone receptor-mediated signaling network in LbetaT2 cells: a pathway-based web-accessible knowledgebase

Abstract

The GnRH receptor (GnRHR), expressed at the cell surface of the anterior pituitary gonadotrope, is critical for normal secretion of gonadotropins LH and FSH, pubertal development, and reproduction. The signaling network downstream of the GnRHR and the molecular bases of the regulation of gonadotropin expression have been the subject of intense research. The murine LbetaT2 cell line represents a mature gonadotrope and therefore is an important model for the study of GnRHR-signaling pathways and modulation of the gonadotrope cell by physiological regulators. In order to facilitate access to the information contained in this complex and evolving literature, we have developed a pathway-based knowledgebase that is web hosted. At present, using 106 relevant primary publications, we curated a comprehensive knowledgebase of the GnRHR signaling in the LbetaT2 cell in the form of a process diagram. Positive and negative controls of gonadotropin gene expression, which included GnRH itself, hypothalamic factors, gonadal steroids and peptides, as well as other hormones, were illustrated. The knowledgebase contains 187 entities and 206 reactions. It was assembled using CellDesigner software, which provides an annotated graphic representation of interactions, stored in Systems Biology Mark-up Language. We then utilized Biological Pathway Publisher, a software suite previously developed in our laboratory, to host the knowledgebase in a web-accessible format as a public resource. In addition, the network entities were linked to a public wiki, providing a forum for discussion, updating, and error correction. The GnRHR-signaling network is openly accessible at http://tsb.mssm.edu/pathwayPublisher/GnRHR_Pathway/GnRHR_Pathway_ index.html.

Figure 1

Pathway construction workflow. A workflow diagram summarizes the main stages of pathway assembly from literature mining to pathway update. Boxes represent the pathway construction steps, which are connected by orange arrows. The red arrow indicates feedback to a previous construction step. In the initial phase of literature mining, more specific terms include: LbetaT2 AND PACAP, or searches by authors’ names.

Figure 2

Snapshot of the GnRHR-signaling pathway map. This map was created using CellDesigner version 4.0.1 and version 4.0.α (http://celldesigner.org/). A total of 187 species and 206 reactions were included. The main symbols are those implemented by CellDesigner version 4.0.1 and version 4.0.α. Interactions are color coded: black solid arrows, stimulatory reactions; red bar-headed lines, inhibitory reactions; black solid and white solid arrows with a bar, transport and trigger reactions, respectively; round-headed lines, catalysis reactions. The presence of a question mark or a dashed line denotes that, whether the reactions are direct or indirect, is unknown. Transcription reactions are represented by dashed and double-dotted lines, whereas translation reactions are symbolized by dashed and single-dotted lines. The following cellular compartments are illustrated on the diagram, as indicated: cytoplasm, endoplasmic reticulum, and nucleus. The size and color of each module were configured by us. Briefly, round angle green squares signify cell-signaling proteins, whereas green and yellow circles represent small molecules and ions, respectively; round angle blue squares symbolize transcription factors, and round angle purple squares strictly correspond to nuclear receptors; yellow/green rectangles designate genes, on which some regulatory regions or response elements are depicted as small white squares. The area of the signaling pathway map that is framed in black is shown in more detail in Fig. 3. The map can be best viewed on the web at http://tsb.mssm.edu/pathwayPublisher/GnRHR_Pathway/GnRHR_Pathway_index.html.

Figure 3

Web-accessible GnRHR pathway navigator. This selected part of the GnRHR-signaling pathway map notably displays the promoters of the gonadotropin β-subunit genes (FSHβ and LHβ subunits), their response elements, and transcription factors that bind to them and regulate gene transcription. Indirect regulators of gene transcription are also illustrated. Entities are clickable, such that corresponding annotations, namely the interactions in which those entities are involved, and the related PubMed references are displayed in the bottom left-hand frame. Additionally, other frames include an interaction list, a protein list, a gene list, and an RNA list. Hyperlinks to the relevant NCBI Entrez Gene page(s) and GnRH wiki pages are also provided. A zoom rectangle located in the upper left corner of the image facilitates navigation through the pathway (16).