{"database":"BioModels","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xml":["https://www.ebi.ac.uk/biomodels/model/download/MODEL2411040001?filename=network_model.xml"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"submitter":["sofia"],"curationStatus":["Non-curated"],"modellingApproach":["fuzzy logic model"],"levelVersion":["L3V1"],"submitter_keywords":["Not Peer Reviewed"],"full_dataset_link":["https://www.ebi.ac.uk/biomodels/MODEL2411040001"],"isPrivate":["false"],"repository":["BioModels"],"modelFormat":["SBML"],"omics_type":["Models"],"tokenised_name":["Nucleus Pulposus Regulatory Network"],"publication_year":["2024"],"submissionId":["MODEL2411040001"],"first_author":["Sofia Tseranidou"],"publication_authors":["Sofia Tseranidou, Maria Segarra-Queralt, Francis Kiptengwer Chemorion, Christine Le Maitre, Janet Piñero, Jérôme Noailly"],"publication":["10.1101/2024.09.18.613636,\n                            Intervertebral disc degeneration (IDD) arises from an intricate imbalance between the anabolic and catabolic processes governing the extracellular matrix (ECM) within the disc. Biochemical processes are complex, redundant and feedback-looped, thus improved integration of knowledge is needed. To address this, a literature-based regulatory network model (RNM) for nucleus pulposus cells (NPC) is proposed, representing the normal state of the intervertebral disc (IVD) cells, in which proteins are represented by nodes that interact with each other through activation and/or inhibition edges. This model includes 33 different proteins and 153 edges by incorporating critical biochemical interactions in IVD regulation, tested in vivo or in vitro in human and animal NPC, alongside non-tissue-specific protein-protein interactions. We used the network to calculate the dynamic regulation of each node through a semi-quantitative method. The basal steady state successfully represented the activity of a normal NPC, and the model was assessed through the published literature, by replicating two independent experimental studies in human normal NPC. Pro-catabolic or pro-anabolic shifts of the network activated by nodal perturbations could be predicted. Sensitivity analysis underscored the significant influence of transforming growth factor beta (TGF-β) and interleukin-1 receptor antagonist (IL-1Ra) on the regulation of structural proteins and degrading enzymes within the system. Given the ongoing challenge of elucidating the mechanisms that drive ECM degradation in IDD, this unique IVD RNM holds promise as a tool for exploring and predicting IDD progression, shedding light on IVD phenotypes and guiding experimental research efforts.. null, null.\n                            1. Department of Engineering, Universitat Pompeu Fabra, Spain; 2. Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom; 3. Hospital del Mar Medical Research Institute, Spain"],"submitter_mail":["sofia.tseranidou@upf.edu"],"publication_doi":["10.1101/2024.09.18.613636"],"additional_accession":[]},"is_claimable":false,"name":"Nucleus Pulposus Regulatory Network","description":"We have added and new protein","dates":{"last_modification":"2024-11-04","publication":"2024-11-04","submission":"2024-11-04"},"accession":"MODEL2411040001","cross_references":{"mamo":["MAMO:0000186"],"biomodels__db":["MODEL2411040001"],"doi":["10.1101/2024.09.18.613636"]}}