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

Abstract

The bone extracellular matrix (ECM) contains minerals deposited on highly crosslinked collagen fibrils and hundreds of non-collagenous 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://phylobone.com) includes 255 proteins 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.

References

[1] Lin X, Patil S, Gao Y-G, Qian A. The bone extracellular matrix in bone formation and regeneration. Front. Pharmacol., 2020, 11: 757

[2] Mansour, A., Mezour, M. A., Badran, Z. & Tamimi, F. *Extracellular matrices for bone regeneration: a literature review. Tissue Eng. Part A 23, 1436–1451 (2017).

[3] Zhao D et al. Osteocytes regulate bone anabolic response to mechanical loading in male mice via activation of integrin α5. Bone Res., 2022, 10: 49

[4] Alford AI, Kozloff KM, Hankenson KD. Extracellular matrix networks in bone remodeling. Int. J. Biochem. Cell Biol., 2015, 65: 20-31

[5] Calciolari E, Donos N. Proteomic and transcriptomic approaches for studying bone regeneration in health and systemically compromised conditions. Proteomics Clin. Appl., 2020, 14: e1900084

[6] Lee J-H, Cho J-Y. Proteomics approaches for the studies of bone metabolism. BMB Rep., 2014, 47: 141-148

[7] Mueller C et al. Unlocking bone for proteomic analysis and FISH. Lab. Invest., 2019, 99: 708-721

[8] Mickleburgh HL et al. Human bone proteomes before and after decomposition: investigating the effects of biological variation and taphonomic alteration on bone protein profiles and the implications for forensic proteomics. J. Proteome Res., 2021, 20: 2533-2546

[9] Reinwald S, Burr D. Review of nonprimate, large animal models for osteoporosis research. J. Bone Miner. Res., 2008, 23: 1353-1368

[10] Borsy A et al. Identifying novel genes involved in both deer physiological and human pathological osteoporosis. Mol. Genet. Genomics, 2009, 281: 301-313

[11] Yao B et al. Comparative transcriptome analysis of the main beam and brow tine of sika deer antler provides insights into the molecular control of rapid antler growth. Cell. Mol. Biol. Lett., 2020, 25: 42

[12] Banks WJ, Epling GP, Kainer RA, Davis RW. Antler growth and osteoporosis. I. Morphological and morphometric changes in the costal compacta during the antler growth cycle. Anat. Rec., 1968, 162: 387-398

[13] Wang D, Landete-Castillejos T. Stem cells drive antler regeneration. Science, 2023, 379: 757-758

[14] Qin T et al. A population of stem cells with strong regenerative potential discovered in deer antlers. Science, 2023, 379: 840-847

[15] Noh J-Y, Yang Y, Jung H. Molecular mechanisms and emerging therapeutics for osteoporosis. Int. J. Mol. Sci., 2020, 21: 7623

[16] UniProt Consortium. UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res., 2021, 49: D480-D489

[17] Kessels MY et al. Proteomics analysis of the zebrafish skeletal extracellular matrix. PLoS One, 2014, 9: e90568

[18] Zhang R, Li Y, Xing X. Comparative antler proteome of sika deer from different developmental stages. Sci. Rep., 2021, 11

[19] Shi G-X et al. Evidence of the role of R-Spondin 1 and its receptor Lgr4 in the transmission of mechanical stimuli to biological signals for bone formation. Int. J. Mol. Sci., 2017, 18: 564

[20] Frasheri I et al. Full-length amelogenin influences the differentiation of human dental pulp stem cells. Stem Cell Res. Ther., 2016, 7: 10

[21] Yu M et al. BMP4 mutations in tooth agenesis and low bone mass. Arch. Oral Biol., 2019, 103: 40-46

[22] Thibaud-Nissen, F., Souvorov, A., Murphy, T., DiCuccio, M. & Kitts, P. Eukaryotic Genome Annotation Pipeline - The NCBI Handbook (NCBI Bookshelf, 2013).

[23] Home - Gene - NCBI (2022). https://www.ncbi.nlm.nih.gov/gene.

[24] Camacho C et al. BLAST+: architecture and applications. BMC Bioinformatics, 2009, 10

[25] Lemoine F et al. NGPhylogeny.fr: new generation phylogenetic services for non-specialists. Nucleic Acids Res., 2019, 47: W260-W265

[26] Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol., 2013, 30: 772-780

[27] Criscuolo A, Gribaldo S. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol., 2010, 10: 210

[28] Guindon S et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol., 2010, 59: 307-321

[29] Schoch CL et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database, 2020, 2020: baaa062

[30] Huerta-Cepas J et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res., 2019, 47: D309-D314

[31] Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science, 1997, 278: 631-637

[32] Galperin MY, Kristensen DM, Makarova KS, Wolf YI, Koonin EV. Microbial genome analysis: the COG approach. Brief. Bioinformatics, 2019, 20: 1063-1070

[33] Mi H, Muruganujan A, Ebert D, Huang X, Thomas PD. PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Res., 2019, 47: D419-D426

[34] Mistry J et al. Pfam: the protein families database in 2021. Nucleic Acids Res., 2021, 49: D412-D419

[35] Blum M et al. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res., 2021, 49: D344-D354

[36] Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res., 2004, 32: W327-W331

[37] Orchard S et al. The MIntAct project - IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res., 2014, 42: D358-D363

[38] Shannon P et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 2003, 13: 2498-2504

[39] Wishart DS et al. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res., 2018, 46: D1074-D1082

[40] Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res., 2017, 45: D353-D361

[41] Diekwisch TGH et al. Amelogenin evolution and tetrapod enamel structure. Front. Oral Biol., 2009, 13: 74-79

[42] Daneault A, Prawitt J. Fabien Soulé, V., Coxam, V. & Wittrant, Y. Biological effect of hydrolyzed collagen on bone metabolism. Crit. Rev. Food Sci. Nutr., 2017, 57: 1922-1937

[43] Stock SR. The mineral-collagen interface in bone. Calcif. Tissue Int., 2015, 97: 262-280

[44] Gu Y-C et al. Laminin isoform-specific promotion of adhesion and migration of human bone marrow progenitor cells. Blood, 2003, 101: 877-885

[45] Mojzisch A, Brehm MA. The manifold cellular functions of von willebrand factor. Cells, 2021, 10: 2351

[46] Siddiqui JA, Partridge NC. Physiological bone remodeling: systemic regulation and growth factor involvement. Physiology, 2016, 31: 233-245

[47] Edwards JR, Mundy GR. Advances in osteoclast biology: old findings and new insights from mouse models. Nat. Rev. Rheumatol., 2011, 7: 235-243

[48] Bergen DJM, Kague E, Hammond CL. Zebrafish as an emerging model for osteoporosis: a primary testing platform for screening new osteo-active compounds. Front. Endocrinol., 2019, 10: 6

[49] Kenkre JS, Bassett J. The bone remodelling cycle. Ann. Clin. Biochem., 2018, 55: 308-327

[50] Hastings JF, Skhinas JN, Fey D, Croucher DR, Cox TR. The extracellular matrix as a key regulator of intracellular signalling networks. Br. J. Pharmacol., 2019, 176: 82-92

[51] Müller UC, Pietrzik CU, Deller T. The physiological functions of the β-amyloid precursor protein APP. Exp. Brain Res., 2012, 217: 325-329

[52] Roos PM. Osteoporosis in neurodegeneration. J. Trace Elem. Med. Biol., 2014, 28: 418-421

[53] Cui S et al. APPswe/Aβ regulation of osteoclast activation and RAGE expression in an age-dependent manner. J. Bone Miner. Res., 2011, 26: 1084-1098

[54] Yang C et al. Fibronectin 1 activates WNT/β-catenin signaling to induce osteogenic differentiation via integrin β1 interaction. Lab. Invest., 2020, 100: 1494-1502

[55] Saunders JT, Schwarzbauer JE. Fibronectin matrix as a scaffold for procollagen proteinase binding and collagen processing. Mol. Biol. Cell, 2019, 30: 2218-2226

[56] Compston JE, McClung MR, Leslie WD. Osteoporosis. Lancet, 2019, 393: 364-376

[57] Srivastava M, Deal C. Osteoporosis in elderly: prevention and treatment. Clin. Geriatr. Med., 2002, 18: 529-555

[58] Sun Z et al. Simulated microgravity inhibits L-type calcium channel currents partially by the up-regulation of miR-103 in MC3T3-E1 osteoblasts. Sci. Rep., 2015, 5

[59] Leblanc AD, Schneider VS, Evans HJ, Engelbretson DA, Krebs JM. Bone mineral loss and recovery after 17 weeks of bed rest. J. Bone Miner. Res., 1990, 5: 843-850

[60] Nakamura M, Hiratai R, Yamashita K. Bone mineral as an electrical energy reservoir. J. Biomed. Mater. Res. A, 2012, 100: 1368-1374

[61] Buckwalter JA, Glimcher MJ, Cooper RR, Recker R. Bone biology. I: structure, blood supply, cells, matrix, and mineralization. Instr. Course Lect., 1996, 45: 371-386

[62] Jikko A, Harris SE, Chen D, Mendrick DL, Damsky CH. Collagen integrin receptors regulate early osteoblast differentiation induced by BMP-2. J. Bone Miner. Res., 1999, 14: 1075-1083

[63] Alcorta-Sevillano N, Macías I, Infante A, Rodríguez CI. Deciphering the relevance of bone ECM signaling. Cells, 2020, 9: 2630

[64] Fujihara S et al. Function and regulation of osteopontin in response to mechanical stress. J. Bone Miner. Res., 2006, 21: 956-964

[65] Merry K, Dodds R, Littlewood A, Gowen M. Expression of osteopontin mRNA by osteoclasts and osteoblasts in modelling adult human bone. J. Cell Sci., 1993, 104: 1013-1020

[66] Singh A, Gill G, Kaur H, Amhmed M, Jakhu H. Role of osteopontin in bone remodeling and orthodontic tooth movement: a review. Prog. Orthod., 2018, 19

[67] Sánchez-Duffhues G, Hiepen C, Knaus P, Ten Dijke P. Bone morphogenetic protein signaling in bone homeostasis. Bone, 2015, 80: 43-59

[68] Yan Y, Wang L, Ge L, Pathak JL. Osteocyte-mediated translation of mechanical stimuli to cellular signaling and its role in bone and non-bone-related clinical complications. Curr. Osteoporos. Rep., 2020, 18: 67-80

[69] Wang L et al. Mechanical sensing protein PIEZO1 regulates bone homeostasis via osteoblast-osteoclast crosstalk. Nat. Commun., 2020, 11

[70] The Nobel Prize in Physiology or Medicine, Advanced information, NobelPrize.org (2021). https://www.nobelprize.org/prizes/medicine/2021/advanced-information/.

[71] Qin L, Liu W, Cao H, Xiao G. Molecular mechanosensors in osteocytes. Bone Res., 2020, 8: 23

[72] LeBoff MS et al. The clinician’s guide to prevention and treatment of osteoporosis. Osteoporos. Int., 2022, 33: 2049-2102

[73] Gao Y, Patil S, Jia J. The development of molecular biology of osteoporosis. Int. J. Mol. Sci., 2021, 22: 8182

[74] Wang M, Wu Y-F, Girgis CM. Bisphosphonate drug holidays: evidence from clinical trials and real-world studies. JBMR Plus, 2022, 6: e10629

[75] Zhang N et al. Pros and cons of denosumab treatment for osteoporosis and implication for RANKL aptamer therapy. Front. Cell Dev. Biol., 2020, 8: 325

[76] Uhlén M et al. The human secretome. Sci. Signal., 2019, 12: eaaz0274

[77] Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res., 2021, 49: W293-W296

Funding

Sigrid Juséliuksen Säätiö (Sigrid Jusélius Foundation)(230131)