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Phylobone: a comprehensive database of bone extracellular matrix proteins in human and model organisms

Bone Research 2023年第3期11卷 617-624页

作者： Margalida Fontcuberta-Rigo Miho Nakamura pere puigbò Medicity Research Laboratory Faculty of MedicineUniversity of TurkuTykistökatu 620520 TurkuFinland Institute of Biomaterials and Bioengineering Tokyo Medical and Dental University2-3-10 Kanda-SurugadaiChiyodaTokyo 1010062Japan Graduate School of Engineering Tohoku University6-6 Aramaki Aza AobaAoba-kuSendaiMiyagi 9808579Japan Department of Biology University of Turku20500 TurkuFinland Eurecat Technology Center of Catalonia.Nutrition and Health UnitReus 43204 CataloniaSpain Department of Biochemistry and Biotechnology University Rovira i Virgili43007 TarragonaCataloniaSpain

The bone extracellular matrix(ECM) contains minerals deposited on highly crosslinked collagen fibrils and hundreds of noncollagenous proteins. Some of these proteins are key to the regulation of bone formation and regeneration via signaling pathways,and play important regulatory and structural roles. However, the complete list of bone extracellular matrix proteins, their roles, and the extent of individual and cross-species variations have not been fully captured in both humans and model organisms. Here, we introduce the most comprehensive resource of bone extracellular matrix(ECM) proteins that can be used in research fields such as bone regeneration, osteoporosis, and mechanobiology. The Phylobone database(available at https://***) includes 255proteins potentially expressed in the bone extracellular matrix(ECM) of humans and 30 species of vertebrates. A bioinformatics pipeline was used to identify the evolutionary relationships of bone ECM proteins. The analysis facilitated the identification of potential model organisms to study the molecular mechanisms of bone regeneration. A network analysis showed high connectivity of bone ECM proteins. A total of 214 functional protein domains were identified, including collagen and the domains involved in bone formation and resorption. Information from public drug repositories was used to identify potential repurposing of existing drugs. The Phylobone database provides a platform to study bone regeneration and osteoporosis in light of(biological) evolution,and will substantially contribute to the identification of molecular mechanisms and drug targets.

关键词： drugs matrix database

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