Multi-omics insights into bone tissue injury and healing: bridging orthopedic trauma and regenerative medicine

Abstract

To preserve functionality, bone is an active tissue that can constantly reconstruct itself through modeling and remodeling. It plays critical roles in the body, including maintaining mineral homeostasis, serving as the adult human body’s core site of hematopoiesis, and supporting the structures of the body’s soft tissues. It possesses the natural regeneration capacity, but large and complex lesions often require surgical intervention. Multiple omics integrate proteomics, metabolomics, genomics, and transcriptomics to provide a comprehensive understanding of biological processes like bone tissue injury and healing in bone tissue regeneration and engineering. Recently, bone tissue engineering and regenerative medicines have offered promising tools for bone regeneration using a multi-omics approach. Thus, this article will highlight the role of multiple omics in understanding bone tissue injury and healing. It will discuss the role of bone tissue engineering in developing bone substitutes that can replace translational medicine. Lastly, new developments in bone tissue engineering and regenerative medicine, along with multi-omics approaches, offer promising tools for bone regeneration.

Keywords

Multi-omics / Bone tissue healing / Orthopedic trauma / Regenerative medicine

References

[1] Marolt D, Knezevic M, Vunjak-Novakovic G.Bone tissue engineering with human stem cells. Stem Cell Res Ther. 2010; 1: 10. https://doi.org/10.1186/scrt10.

[2] Su X, Wang T, Guo S. Applications of 3D printed bone tissue engineering scaffolds in the stem cell field. Regen Ther. 2021; 16: 63-72. https://doi.org/10.1016/j.reth.2021.01.007.

[3] Tian G, Cheng B, Fu X. Role and prospect of regenerative medicine in early treatment of combat trauma. Chin J Burns Wounds. 2023; 39: 411-6. https://doi.org/10.3760/cma.j.cn501225-20220419-00147.

[4] Subramanian I, Verma S, Kumar S, Jere A, Anamika K. Multi-omics data integration, interpretation, and its application. Bioinforma Biol Insights. 2020; 14: 117793221989905. https://doi.org/10.1177/1177932219899051.

[5] Mohr AE, Ortega-Santos CP, Whisner CM, Klein-Seetharaman J, Jasbi P. Navigating challenges and opportunities in multi-omics integration for personalized healthcare. Biomedicines. 2024; 12: 1496. https://doi.org/10.3390/biomedicines12071496.

[6] Lee S, Baker ME, Clinton M, Taylor SE. Use of omics data in fracture prediction; a scoping and systematic review in horses and humans. Animals. 2021; 11: 959. https://doi.org/10.3390/ani11040959.

[7] Mullin BH, Ribet ABP, Pavlos NJ. Bone trans-omics: integrating omics to unveil mechanistic molecular networks regulating bone biology and disease. Curr Osteoporos Rep. 2023; 21: 493-502. https://doi.org/10.1007/s11914-023-00812-8.

[8] Oryan A, Alidadi S, Moshiri A. Current concerns regarding healing of bone defects. Hard Tissue. 2013; 2: 13. https://doi.org/10.13172/2050-2303-2-2-374.

[9] Hajiali H, Ouyang L, Llopis-Hernandez V, Dobre O, Rose FRAJ. Review of emerging nanotechnology in bone regeneration: progress, challenges, and perspectives. Nanoscale. 2021; 13: 10266-80. https://doi.org/10.1039/D1NR01371H.

[10] Boccaccini AR, Erol M, Stark WJ, Mohn D, Hong Z, Mano JF. Polymer/bioactive glass nanocomposites for biomedical applications: a review. Compos Sci Technol. 2010; 70: 1764-76. https://doi.org/10.1016/j.compscitech.2010.06.002.

[11] Gu W, Chen XY. Nanotechnology in the targeted drug delivery for bone diseases and bone regeneration. Int J Nanomedicine. 2013; 8: 2305-17. https://doi.org/10.2147/IJN.S44393.

[12] Barry M, Pearce H, Cross L, Tatullo M, Gaharwar AK. Advances in nanotechnology for the treatment of osteoporosis. Curr Osteoporos Rep. 2016; 14: 87-94. https://doi.org/10.1007/s11914-016-0306-3.

[13] Wang Q, Yan J, Yang J, Li B. Nanomaterials promise better bone repair. Mater Today. 2016; 19: 451-63. https://doi.org/10.1016/j.mattod.2015.12.003.

[14] Qu H, Fu H, Han Z, Sun Y. Biomaterials for bone tissue engineering scaffolds: a review. RSC Adv. 2019; 9: 26252-62. https://doi.org/10.1039/C9RA05214C.

[15] Sanz M, Dahlin C, Apatzidou D, Artzi Z, Bozic D, Calciolari E, et al. Biomaterials and regenerative technologies used in bone regeneration in the craniomaxillofacial region: consensus report of group 2 of the 15th European workshop on periodontology on bone regeneration. J Clin Periodontol. 2019; 46: 82-91. https://doi.org/10.1111/jcpe.13123.

[16] Calciolari E, Donos N. The use of omics profiling to improve outcomes of bone regeneration and osseointegration. How far are we from personalized medicine in dentistry? J Proteome. 2018; 188: 85-96. https://doi.org/10.1016/j.jprot.2018.01.017.

[17] Phillips AM.Overview of the fracture healing cascade. Injury. 2005; 36: S5-7. https://doi.org/10.1016/j.injury.2005.07.027.

[18] Winkler T, Sass FA, Duda GN, Schmidt-Bleek K. A review of biomaterials in bone defect healing, remaining shortcomings and future opportunities for bone tissue engineering: the unsolved challenge. Bone Jt Res. 2018; 7: 232-43. https://doi.org/10.1302/2046-3758.73.BJR-2017-0270.R1.

[19] Willie BM, Petersen A, Schmidt-Bleek K, Cipitria A, Mehta M, Strube P, et al. Designing biomimetic scaffolds for bone regeneration: why aim for a copy of mature tissue properties if nature uses a different approach? Soft Matter. 2010; 6: 4976. https://doi.org/10.1039/c0sm00262c.

[20] Lim JY, Donahue HJ. Biomaterial characteristics important to skeletal tissue engineering. J Musculoskelet Neuronal Interact. 2004; 4: 396-8.

[21] Parikh SN. Bone graft substitutes: past, present, future. J Postgrad Med. 2002; 48: 142-8.

[22] Parizi AM, Oryan A, Shafiei-Sarvestani Z, Bigham AS. Human platelet rich plasma plus Persian Gulf coral effects on experimental bone healing in rabbit model: radiological, histological, macroscopical and biomechanical evaluation. J Mater Sci Mater Med. 2012; 23: 473-83. https://doi.org/10.1007/s10856-011-4478-1.

[23] Zhang Y, Wu D, Zhao X, Pakvasa M, Tucker AB, Luo H, et al. Stem cell-friendly scaffold biomaterials: applications for bone tissue engineering and regenerative medicine. Front Bioeng Biotechnol. 2020; 8: 598607. https://doi.org/10.3389/fbioe.2020.598607.

[24] Iaquinta MR, Mazzoni E, Bononi I, Rotondo JC, Mazziotta C, Montesi M, et al. Adult stem cells for bone regeneration and repair. Front Cell Dev Biol. 2019; 7: 268. https://doi.org/10.3389/fcell.2019.00268.

[25] Ray S, Thormann U, Sommer U, Khassawna TE, Hundgeburth M, Henß A, et al. Effects of macroporous, strontium loaded xerogel-scaffolds on new bone formation in critical-size metaphyseal fracture defects in ovariectomized rats. Injury. 2016; 47: S52-61. https://doi.org/10.1016/S0020-1383(16)30013-4.

[26] Yang S, Wang L, Feng S, Yang Q, Yu B, Tu M. Enhanced bone formation by strontium modified calcium sulfate hemihydrate in ovariectomized rat critical-size calvarial defects. Biomed Mater. 2017; 12: 035004. https://doi.org/10.1088/1748-605X/aa68bc.

[27] Moshiri A, Oryan A. Role of tissue engineering in tendon reconstructive surgery and regenerative medicine: current concepts, approaches and concerns. Hard Tissue. 2012; 1: 11. https://doi.org/10.13172/2050-2303-1-2-291.

[28] Wong SK, Wong YH, Chin K-Y, Ima-Nirwana S. A review on the enhancement of calcium phosphate cement with biological materials in bone defect healing. Polymers. 2021; 13: 3075. https://doi.org/10.3390/polym13183075.

[29] Bishop ES, Mostafa S, Pakvasa M, Luu HH, Lee MJ, Wolf JM, et al. 3-D bioprinting technologies in tissue engineering and regenerative medicine: current and future trends. Genes Dis. 2017; 4: 185-95. https://doi.org/10.1016/j.gendis.2017.10.002.

[30] Qasim M, Chae DS, Lee NY. Advancements and frontiers in nano-based 3D and 4D scaffolds for bone and cartilage tissue engineering. Int J Nanomedicine. 2019; 14: 4333-51. https://doi.org/10.2147/IJN.S209431.

[31] Bose S, Vahabzadeh S, Bandyopadhyay A. Bone tissue engineering using 3D printing. Mater Today. 2013; 16: 496-504. https://doi.org/10.1016/j.mattod.2013.11.017.

[32] Whiting P, Kerby J, Coffey P, Da Cruz L, McKernan R. Progressing a human embryonic stem-cell-based regenerative medicine therapy towards the clinic. Philos Trans R Soc B Biol Sci. 2015; 370: 20140375. https://doi.org/10.1098/rstb.2014.0375.

[33] Iwata T, Washio K, Yoshida T, Ishikawa I, Ando T, Yamato M, et al. Cell sheet engineering and its application for periodontal regeneration. J Tissue Eng Regen Med. 2015; 9: 343-56. https://doi.org/10.1002/term.1785.

[34] Sharma R, Kumar S, Bhawna, Gupta A, Dheer N, Jain P, et al. An insight of nanomaterials in tissue engineering from fabrication to applications. Tissue Eng Regen Med. 2022; 19: 927-60. https://doi.org/10.1007/s13770-022-00459-z.

[35] Ma Q, Liang M, Wu Y, Luo F, Ma Z, Dong S, Xu J, Dou C. Osteoclast-derived apoptotic bodies couple bone resorption and formation in bone remodeling. Bone Res. 2021; 9: 5. https://doi.org/10.1038/s41413-020-00121-1.

[36] Li J, Qin L, Yang K, Ma Z, Wang Y, Cheng L, et al. Materials evolution of bone plates for internal fixation of bone fractures: a review. J Mater Sci Technol. 2020; 36: 190-208. https://doi.org/10.1016/j.jmst.2019.07.024.

[37] Gruber F, Kremslehner C, Narzt M-S. The impact of recent advances in lipidomics and redox lipidomics on dermatological research. Free Radic Biol Med. 2019; 144: 256-65. https://doi.org/10.1016/j.freeradbiomed.2019.04.019.

[38] Siddiqui JA, Partridge NC. Physiological bone remodeling: systemic regulation and growth factor involvement.Physiology. 2016; 31: 233-45. https://doi.org/10.1152/physiol.00061.2014.

[39] Saska S, Pires LC, Cominotte MA, Mendes LS, De Oliveira MF, Maia IA, et al. Three-dimensional printing and in vitro evaluation of poly(3-hydroxybutyrate) scaffolds functionalized with osteogenic growth peptide for tissue engineering. Mater Sci Eng C. 2018; 89: 265-73. https://doi.org/10.1016/j.msec.2018.04.016.

[40] Shang F, Yu Y, Liu S, Ming L, Zhang Y, Zhou Z, et al. Advancing application of mesenchymal stem cell-based bone tissue regeneration. Bioact Mater. 2021; 6: 666-83. https://doi.org/10.1016/j.bioactmat.2020.08.014.

[41] Huang Y, Chen X, Che J, Zhan Q, Ji J, Fan Y. Shear stress promotes arterial endothelium-oriented differentiation of mouse-induced pluripotent stem cells. Stem Cells Int. 2019; 2019: 1-13. https://doi.org/10.1155/2019/1847098.

[42] Huang J, Zhang Q, Scarpa F, Liu Y, Leng J. Shape memory polymer-based hybrid honeycomb structures with zero Poisson’s ratio and variable stiffness. Compos Struct. 2017; 179: 437-43. https://doi.org/10.1016/j.compstruct.2017.07.091.

[43] Kohli N, Ho S, Brown SJ, Sawadkar P, Sharma V, Snow M, et al. Bone remodelling in vitro: where are we headed? Bone. 2018; 110: 38-46. https://doi.org/10.1016/j.bone.2018.01.015.

[44] Pihlström S, Määttä K, Öhman T, Mäkitie RE, Aronen M, Varjosalo M, et al. A multi-omics study to characterize the transdifferentiation of human dermal fibroblasts to osteoblast-like cells. Front Mol Biosci. 2022; 9: 1032026. https://doi.org/10.3389/fmolb.2022.1032026.

[45] Richards J, Rivadeneira F, Inouye M, Pastinen T, Soranzo N, Wilson S, et al. Bone mineral density, osteoporosis, and osteoporotic fractures: a genome-wide association study. Lancet. 2008; 371: 1505-12. https://doi.org/10.1016/S0140-6736(08)60599-1.

[46] Delgado-Calle J, Sañudo C, Bolado A, Fernández AF, Arozamena J, Pascual-Carra MA, et al. DNA methylation contributes to the regulation of sclerostin expression in human osteocytes. J Bone Miner Res. 2012; 27: 926-37. https://doi.org/10.1002/jbmr.1491.

[47] Kersey AL, Nguyen T-U, Nayak B, Singh I, Gaharwar AK. Omics-based approaches to guide the design of biomaterials. Mater Today. 2023; 64: 98-120. https://doi.org/10.1016/j.mattod.2023.01.018.

[48] Hickman TT, Rathan-Kumar S, Peck SH. Development, pathogenesis, and regeneration of the intervertebral disc: current and future insights spanning traditional to omics methods. Front Cell Dev Biol. 2022; 10: 841831. https://doi.org/10.3389/fcell.2022.841831.

[49] Antonelli L, Guarracino MR, Maddalena L, Sangiovanni M. Integrating imaging and omics data: a review. Biomed Signal Process Control. 2019; 52: 264-80. https://doi.org/10.1016/j.bspc.2019.04.032.

[50] Yang J, Wu J. Discovery of potential biomarkers for osteoporosis diagnosis by individual omics and multi-omics technologies. Expert Rev Mol Diagn. 2023; 23: 505-20. https://doi.org/10.1080/14737159.2023.2208750.

[51] Richards JB, Kavvoura FK, Rivadeneira F, Styrkársdóttir U, Estrada K, Halldórsson BV, et al. Collaborative meta-analysis: associations of 150 candidate genes with osteoporosis and osteoporotic fracture. Ann Intern Med. 2009; 151: 528-37. https://doi.org/10.7326/0003-4819-151-8-200910200-00006.

[52] Piunti A, Shilatifard A. Epigenetic balance of gene expression by Polycomb and COMPASS families. Science. 2016; 352: aad9780. https://doi.org/10.1126/science.aad9780.

[53] Ren S, Li J, Dorado J, Sierra A, González-Díaz H, Duardo A, et al. From molecular mechanisms of prostate cancer to translational applications: based on multi-omics fusion analysis and intelligent medicine. Health Inf Sci Syst. 2023; 12: 6. https://doi.org/10.1007/s13755-023-00264-5.

[54] Zhang C, Xie B, Zou Y, Zhu D, Lei L, Zhao D, et al. Zero-dimensional, one-dimensional, two-dimensional and three-dimensional biomaterials for cell fate regulation. Adv Drug Deliv Rev. 2018; 132: 33-56. https://doi.org/10.1016/j.addr.2018.06.020.

[55] Angelidis I, Simon LM, Fernandez IE, Strunz M, Mayr CH, Greiffo FR, et al. An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics. Nat Commun. 2019; 10: 963. https://doi.org/10.1038/s41467-019-08831-9.

[56] Neri S. Genetic stability of mesenchymal stromal cells for regenerative medicine applications: a fundamental biosafety aspect. Int J Mol Sci. 2019; 20: 2406. https://doi.org/10.3390/ijms20102406.

[57] Santos-Moreno J, Schaerli Y. CRISPR-based gene expression control for synthetic gene circuits. Biochem Soc Trans. 2020; 48: 1979-93. https://doi.org/10.1042/BST20200020.

[58] Tewary M, Shakiba N, Zandstra PW. Stem cell bioengineering: building from stem cell biology. Nat Rev Genet. 2018; 19: 595-614. https://doi.org/10.1038/s41576-018-0040-z.

[59] Lowe R, Shirley N, Bleackley M, Dolan S, Shafee T. Transcriptomics technologies. PLoS Comput Biol. 2017; 13: e1005457. https://doi.org/10.1371/journal.pcbi.1005457.

[60] Abazari R, Mahjoub AR, Shariati J. Synthesis of a nanostructured pillar MOF with high adsorption capacity towards antibiotics pollutants from aqueous solution. J Hazard Mater. 2019; 366: 439-51. https://doi.org/10.1016/j.jhazmat.2018.12.030.

[61] Ziegenhain C, Vieth B, Parekh S, Hellmann I, Enard W. Quantitative single-cell transcriptomics. Brief Funct Genomics. 2018; 17: 220-32. https://doi.org/10.1093/bfgp/ely009.

[62] Kinaret PAS, Serra A, Federico A, Kohonen P, Nymark P, Liampa I, et al. Transcriptomics in toxicogenomics, part I: experimental design, technologies, publicly available data, and regulatory aspects. Nano. 2020; 10: 750. https://doi.org/10.3390/nano10040750.

[63] Wu CH, Chen C (eds). Bioinformatics for Comparative Proteomics, Vol. 694. Totowa, NJ: Humana Press, 2011, 10.1007/978-1-60761-977-2.

[64] Lamas A, Regal P, Vázquez B, Miranda JM, Franco CM, Cepeda A. Transcriptomics: a powerful tool to evaluate the behavior of foodborne pathogens in the food production chain. Food Res Int. 2019; 125: 108543. https://doi.org/10.1016/j.foodres.2019.108543.

[65] Rike WA, Stern S. Proteins and transcriptional dysregulation of the brain extracellular matrix in Parkinson’s disease: a systematic review. Int J Mol Sci. 2023; 24: 7435. https://doi.org/10.3390/ijms24087435.

[66] Song Y, Soto J, Chen B, Yang L, Li S. Cell engineering: biophysical regulation of the nucleus. Biomaterials. 2020; 234: 119743. https://doi.org/10.1016/j.biomaterials.2019.119743.

[67] Bastounis EE, Yeh Y-T, Theriot JA. Subendothelial stiffness alters endothelial cell traction force generation while exerting a minimal effect on the transcriptome. Sci Rep. 2019; 9: 18209. https://doi.org/10.1038/s41598-019-54336-2.

[68] Groen N, Guvendiren M, Rabitz H, Welsh WJ, Kohn J, De Boer J. Stepping into the omics era: opportunities and challenges for biomaterials science and engineering.Acta Biomater. 2016; 34: 133-42. https://doi.org/10.1016/j.actbio.2016.02.015.

[69] Gaharwar AK, Singh I, Khademhosseini A. Engineered biomaterials for in situ tissue regeneration. Nat Rev Mater. 2020; 5: 686-705. https://doi.org/10.1038/s41578-020-0209-x.

[70] Tsiridis E, Giannoudis PV. Transcriptomics and proteomics: advancing the understanding of genetic basis of fracture healing. Injury. 2006; 37: S13-9. https://doi.org/10.1016/j.injury.2006.02.036.

[71] Dettmer K, Aronov PA, Hammock BD. Mass spectrometry-based metabolomics. Mass Spectrom Rev. 2007; 26: 51-78. https://doi.org/10.1002/mas.20108.

[72] Gowda GN, Zhang S, Gu H, Asiago V, Shanaiah N, Raftery D. Metabolomics-based methods for early disease diagnostics.Expert Rev Mol Diagn. 2008; 8: 617-33. https://doi.org/10.1586/14737159.8.5.617.

[73] Wang R, Li B, Lam SM, Shui G. Integration of lipidomics and metabolomics for in-depth understanding of cellular mechanism and disease progression. J Genet Genomics. 2020; 47: 69-83. https://doi.org/10.1016/j.jgg.2019.11.009.

[74] Johnson CH, Ivanisevic J, Siuzdak G. Metabolomics: beyond biomarkers and towards mechanisms. Nat Rev Mol Cell Biol. 2016; 17: 451-9. https://doi.org/10.1038/nrm.2016.25.

[75] Gonzalez-Covarrubias V, Martínez-Martínez E, Del Bosque-Plata L. The potential of metabolomics in biomedical applications. Meta. 2022; 12: 194. https://doi.org/10.3390/metabo12020194.

[76] Kogut MH, Lee A, Santin E. Microbiome and pathogen interaction with the immune system. Poult Sci. 2020; 99: 1906-13. https://doi.org/10.1016/j.psj.2019.12.011.

[77] Thaiss CA, Zmora N, Levy M, Elinav E. The microbiome and innate immunity. Nature. 2016; 535: 65-74. https://doi.org/10.1038/nature18847.

[78] Levy M, Blacher E, Elinav E. Microbiome, metabolites and host immunity. Curr Opin Microbiol. 2017; 35: 8-15. https://doi.org/10.1016/j.mib.2016.10.003.

[79] Shi N, Li N, Duan X, Niu H. Interaction between the gut microbiome and mucosal immune system. Mil Med Res. 2017; 4: 14. https://doi.org/10.1186/s40779-017-0122-9.

[80] Sethi S, Brietzke E. Recent advances in lipidomics: analytical and clinical perspectives. Prostaglandins Other Lipid Mediat. 2017; 128-129: 8-16. https://doi.org/10.1016/j.prostaglandins.2016.12.002.

[81] Wu Z, Bagarolo GI, Thoröe-Boveleth S, Jankowski J. “Lipidomics”: mass spectrometric and chemometric analyses of lipids.Adv Drug Deliv Rev. 2020; 159: 294-307. https://doi.org/10.1016/j.addr.2020.06.009.

[82] Vvedenskaya O, Holčapek M, Vogeser M, Ekroos K, Meikle PJ, Bendt AK. Clinical lipidomics-a community-driven roadmap to translate research into clinical applications. J Mass Spectrom Adv Clin Lab. 2022; 24: 1-4. https://doi.org/10.1016/j.jmsacl.2022.02.002.

[83] Serowoky MA, Kuwahara ST, Liu S, Vakhshori V, Lieberman JR, Mariani FV. A murine model of large-scale bone regeneration reveals a selective requirement for Sonic Hedgehog. Npj Regen Med. 2022; 7: 30. https://doi.org/10.1038/s41536-022-00225-8.

[84] Xu J, Li Z, Tower RJ, Negri S, Wang Y, Meyers CA, et al. NGF-p75 signaling coordinates skeletal cell migration during bone repair. Sci Adv. 2022; 8: eabl5716. https://doi.org/10.1126/sciadv.abl5716.

[85] Sivaraj KK, Majev P-G, Jeong H-W, Dharmalingam B, Zeuschner D, Schröder S, et al. Mesenchymal stromal cell-derived septoclasts resorb cartilage during developmental ossification and fracture healing. Nat Commun. 2022; 13: 571. https://doi.org/10.1038/s41467-022-28142-w.

[86] Wang Y, Wang Q, Xu Q, Li J, Zhao F. Single-cell RNA sequencing analysis dissected the osteo-immunology microenvironment and revealed key regulators in osteoporosis. Int Immunopharmacol. 2022; 113: 109302. https://doi.org/10.1016/j.intimp.2022.109302.

[87] Tower RJ, Li Z, Cheng Y-H, Wang X-W, Rajbhandari L, Zhang Q, et al. Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGF-β signaling. Proc Natl Acad Sci. 2021; 118: e2103087118. https://doi.org/10.1073/pnas.2103087118.

[88] Yang Y, Yang M, Shi D, Chen K, Zhao J, He S, et al. Single-cell RNA Seq reveals cellular landscape-specific characteristics and potential etiologies for adolescent idiopathic scoliosis. Jor Spine. 2021; 4: e1184. https://doi.org/10.1002/jsp2.1184.

[89] Mundy C, Yao L, Sinha S, Chung J, Rux D, Catheline SE, et al. Activin A promotes the development of acquired heterotopic ossification and is an effective target for disease attenuation in mice. Sci Signal. 2021; 14: eabd0536. https://doi.org/10.1126/scisignal.abd0536.

[90] Tachibana N, Chijimatsu R, Okada H, Oichi T, Taniguchi Y, Maenohara Y, et al. RSPO2 defines a distinct undifferentiated progenitor in the tendon/ligament and suppresses ectopic ossification. Sci Adv. 2022; 8: eabn2138. https://doi.org/10.1126/sciadv.abn2138.

[91] Wang H, Zheng C, Lu W, He T, Fan J, Wang C, et al. Hedgehog signaling orchestrates cartilage-to-bone transition independently of Smoothened. Matrix Biol. 2022; 110: 76-90. https://doi.org/10.1016/j.matbio.2022.04.006.

[92] Luginbuehl V, Meinel L, Merkle HP, Gander B. Localized delivery of growth factors for bone repair. Eur J Pharm Biopharm. 2004; 58: 197-208. https://doi.org/10.1016/j.ejpb.2004.03.004.

[93] Thomson DD.Introduction-Mechanisms of fracture healing and pharmacologic control. J Musculoskelet Neuronal Interact. 2003; 3: 295-6.

[94] Tsiridis E, Upadhyay N, Giannoudis P. Molecular aspects of fracture healing: which are the important molecules? Injury. 2007; 38: S11-25. https://doi.org/10.1016/j.injury.2007.02.006.

[95] Marsell R, Einhorn TA. The biology of fracture healing. Injury. 2011; 42: 551-5. https://doi.org/10.1016/j.injury.2011.03.031.

[96] Calciolari E, Donos N. Proteomic and transcriptomic approaches for studying bone regeneration in health and systemically compromised conditions. PROTEOMICS-Clin Appl. 2020; 14: e1900084. https://doi.org/10.1002/prca.201900084.

[97] Wagar LE, DiFazio RM, Davis MM. Advanced model systems and tools for basic and translational human immunology. Genome Med. 2018; 10: 73. https://doi.org/10.1186/s13073-018-0584-8.

[98] Feng K, Yu M, Lou X, Wang D, Wang L, Ren W. Multi-omics analysis of bone marrow mesenchymal stem cell differentiation differences in osteoporosis. Genomics. 2023; 115: 110668. https://doi.org/10.1016/j.ygeno.2023.110668.

[99] Bonnarens F, Einhorn TA. Production of a standard closed fracture in laboratory animal bone. J Orthop Res. 1984; 2: 97-101. https://doi.org/10.1002/jor.1100020115.

[100] Schindeler A, Mills RJ, Bobyn JD, Little DG. Preclinical models for orthopedic research and bone tissue engineering. J Orthop Res. 2018; 36: 832-40. https://doi.org/10.1002/jor.23824.

[101] Mills LA, Simpson AHRW. In vivo models of bone repair. J Bone Joint Surg Br. 2012; 94-B: 865-74. https://doi.org/10.1302/0301-620X.94B7.27370.

[102] Reinke S, Geissler S, Taylor WR, Schmidt-Bleek K, Juelke K, Schwachmeyer V, et al. Terminally differentiated CD8+ T cells negatively affect bone regeneration in humans. Sci Transl Med. 2013; 5: 177ra36. https://doi.org/10.1126/scitranslmed.3004754.

[103] Ribitsch I, Baptista PM, Lange-Consiglio A, Melotti L, Patruno M, Jenner F, et al. Large animal models in regenerative medicine and tissue engineering: to do or not to do. Front Bioeng Biotechnol. 2020; 8: 972. https://doi.org/10.3389/fbioe.2020.00972.

[104] Sparks DS, Saifzadeh S, Savi FM, Dlaska CE, Berner A, Henkel J, et al. A preclinical large-animal model for the assessment of critical-size load-bearing bone defect reconstruction. Nat Protoc. 2020; 15: 877-924. https://doi.org/10.1038/s41596-019-0271-2.

[105] Horst K, Eschbach D, Pfeifer R, Hübenthal S, Sassen M, Steinfeldt T, et al. Local inflammation in fracture hematoma: results from a combined trauma model in pigs. Mediat Inflamm. 2015; 2015: 126060. https://doi.org/10.1155/2015/126060.

[106] Schmidt-Bleek K, Marcucio R, Duda G. Future treatment strategies for delayed bone healing: an osteoimmunologic approach. J Am Acad Orthop Surg. 2016; 24: e134-5. https://doi.org/10.5435/JAAOS-D-16-00513.

[107] Amini AR, Laurencin CT, Nukavarapu SP. Bone tissue engineering: recent advances and challenges. Crit Rev Biomed Eng. 2012; 40: 363-408. https://doi.org/10.1615/CritRevBiomedEng.v40.i5.10.

[108] Barradas A, Yuan H, Van Blitterswijk C, Habibovic P. Osteoinductive biomaterials: current knowledge of properties, experimental models and biological mechanisms. Eur Cell Mater. 2011; 21: 407-29. https://doi.org/10.22203/ecm.v021a31.

[109] Koons GL, Diba M, Mikos AG. Materials design for bone-tissue engineering. Nat Rev Mater. 2020; 5: 584-603. https://doi.org/10.1038/s41578-020-0204-2.

[110] Skou ST, Juhl CB, Hare KB, Lohmander LS, Roos EM. Surgical or non-surgical treatment of traumatic skeletal fractures in adults: systematic review and meta-analysis of benefits and harms. Syst Rev. 2020; 9: 179. https://doi.org/10.1186/s13643-020-01424-4.

[111] Fang J, Wang X, Jiang W, Zhu Y, Hu Y, Zhao Y, et al. Platelet-rich plasma therapy in the treatment of diseases associated with orthopedic injuries. Tissue Eng Part B Rev. 2020; 26: 571-85. https://doi.org/10.1089/ten.teb.2019.0292.

[112] Cao S, Zhao Y, Hu Y, Zou L, Chen J. New perspectives: In-situ tissue engineering for bone repair scaffold.Compos Part B Eng. 2020; 202: 108445. https://doi.org/10.1016/j.compositesb.2020.108445.

[113] Battafarano G, Rossi M, De Martino V, Marampon F, Borro L, Secinaro A, et al. Strategies for bone regeneration: from graft to tissue engineering. Int J Mol Sci. 2021; 22: 1128. https://doi.org/10.3390/ijms22031128.

[114] Kanczler JM, Wells JA, Gibbs DMR, Marshall KM, Tang DKO, Oreffo ROC. Bone tissue engineering and bone regeneration. Princ Tissue Eng Elsevier. 2020; 50: 917-35. https://doi.org/10.1016/B978-0-12-818422-6.00052-6.

[115] Zadpoor AA. Bone tissue regeneration: the role of scaffold geometry. Biomater Sci. 2015; 3: 231-45. https://doi.org/10.1039/C4BM00291A.

[116] Santiesteban DY, Kubelick K, Dhada KS, Dumani D, Suggs L, Emelianov S. Monitoring/imaging and regenerative agents for enhancing tissue engineering characterization and therapies. Ann Biomed Eng. 2016; 44: 750-72. https://doi.org/10.1007/s10439-015-1509-y.

[117] Tang D, Tare RS, Yang L-Y, Williams DF, Ou K-L, Oreffo ROC. Biofabrication of bone tissue: approaches, challenges and translation for bone regeneration. Biomaterials. 2016; 83: 363-82. https://doi.org/10.1016/j.biomaterials.2016.01.024.

[118] Uth N, Mueller J, Smucker B, Yousefi A-M. Validation of scaffold design optimization in bone tissue engineering: finite element modeling versus designed experiments. Biofabrication. 2017; 9: 15023. https://doi.org/10.1088/1758-5090/9/1/015023.

[119] Mende W, Götzl R, Kubo Y, Pufe T, Ruhl T, Beier JP. The role of adipose stem cells in bone regeneration and bone tissue engineering. Cells. 2021; 10: 975. https://doi.org/10.3390/cells10050975.

[120] Tsakiris V, Tardei C, Clicinschi FM. Biodegradable Mg alloys for orthopedic implants-a review. J Magnes Alloys. 2021; 9: 1884-905. https://doi.org/10.1016/j.jma.2021.06.024.

[121] Kanczler J, Oreffo R. Osteogenesis and angiogenesis: the potential for engineering bone. Eur Cell Mater. 2008; 15: 100-14. https://doi.org/10.22203/eCM.v015a08.

[122] Gothard D, Smith E, Kanczler J, Rashidi H, Qutachi O, Henstock J, et al. Tissue engineered bone using select growth factors: a comprehensive review of animal studies and clinical translation studies in man. Eur Cell Mater. 2014; 28: 166-208. https://doi.org/10.22203/eCM.v028a13.

[123] Abdollahi F, Saghatchi M, Paryab A, Malek Khachatourian A, Stephens ED, Toprak MS, et al. Angiogenesis in bone tissue engineering via ceramic scaffolds: a review of concepts and recent advancements. Biomater Adv. 2024; 159: 213828. https://doi.org/10.1016/j.bioadv.2024.213828.

[124] Kesireddy V, Kasper FK. Approaches for building bioactive elements into synthetic scaffolds for bone tissue engineering. J Mater Chem B. 2016; 4: 6773-86. https://doi.org/10.1039/C6TB00783J.

[125] Perić Kačarević Ž, Rider P, Alkildani S, Retnasingh S, Pejakić M, Schnettler R, et al. An introduction to bone tissue engineering. Int J Artif Organs. 2020; 43: 69-86. https://doi.org/10.1177/0391398819876286.

[126] Diomede F, Marconi GD, Fonticoli L, Pizzicanella J, Merciaro I, Bramanti P, et al. Functional relationship between osteogenesis and angiogenesis in tissue regeneration. Int J Mol Sci. 2020; 21: 3242. https://doi.org/10.3390/ijms21093242.

[127] Huang J, Han Q, Cai M, Zhu J, Li L, Yu L, et al. Effect of angiogenesis in bone tissue engineering. Ann Biomed Eng. 2022; 50: 898-913. https://doi.org/10.1007/s10439-022-02970-9.

[128] Federici S, Nobs SP, Elinav E. Phages and their potential to modulate the microbiome and immunity. Cell Mol Immunol. 2021; 18: 889-904. https://doi.org/10.1038/s41423-020-00532-4.

[129] Peng Y, Wu S, Li Y, Crane JL. Type H blood vessels in bone modeling and remodeling. Theranostics. 2020; 10: 426-36. https://doi.org/10.7150/thno.34126.

[130] Abdelaziz AG, Nageh H, Abdo SM, Abdalla MS, Amer AA, Abdal-hay A, et al. A review of 3D polymeric scaffolds for bone tissue engineering: principles, fabrication techniques, immunomodulatory roles, and challenges. Bioengineering. 2023; 10: 204. https://doi.org/10.3390/bioengineering10020204.

[131] Yue S, He H, Li B, Hou T. Hydrogel as a biomaterial for bone tissue engineering: a review.Nano. 2020; 10: 1511. https://doi.org/10.3390/nano10081511.

[132] Jahani B, Wang X, Brooks A. Additive manufacturing techniques for fabrication of bone scaffolds for tissue engineering applications. Recent Prog Mater. 2020; 2: 1-41. https://doi.org/10.21926/rpm.2003021.

[133] Liu L, Ma F, Kang B, Liu P, Qi S, Li W, et al. Preparation and mechanical and biological performance of the Sr-containing microarc oxidation layer on titanium implants. Surf Coat Technol. 2023; 463: 129530. https://doi.org/10.1016/j.surfcoat.2023.129530.

[134] Wassif RK, Elkayal M, Shamma RN, Elkheshen SA. Recent advances in the local antibiotics delivery systems for management of osteomyelitis. Drug Deliv. 2021; 28: 2392-414. https://doi.org/10.1080/10717544.2021.1998246.

[135] On behalf of the Fracture-Related Infection (FRI) group, Metsmakers W-J, Morgenstern M, Senneville E, Borens O, Govaert GAM, et al. General treatment principles for fracture-related infection: recommendations from an international expert group. Arch Orthop Trauma Surg. 2020; 140: 1013-27. https://doi.org/10.1007/s00402-019-03287-4.

[136] Peppas NA, Langer R. New challenges in biomaterials. Science. 1994; 263: 1715-20. https://doi.org/10.1126/science.8134835.

[137] Tanvir MAH, Khaleque MA, Kim G-H, Yoo W-Y, Kim Y-Y. The role of bioceramics for bone regeneration: history, mechanisms, and future perspectives.Biomimetics. 2024; 9: 230. https://doi.org/10.3390/biomimetics9040230.

[138] Garot C, Bettega G, Picart C. Additive manufacturing of material scaffolds for bone regeneration: toward application in the clinics. Adv Funct Mater. 2021; 31: 2006967. https://doi.org/10.1002/adfm.202006967.

[139] Rasperini G, Pilipchuk SP, Flanagan CL, Park CH, Pagni G, Hollister SJ, et al. 3D-printed bioresorbable scaffold for periodontal repair. J Dent Res. 2015; 94: 153S-7. https://doi.org/10.1177/0022034515588303.

[140] Smith MH, Flanagan CL, Kemppainen JM, Sack JA, Chung H, Das S, et al. Computed tomography-based tissue-engineered scaffolds in craniomaxillofacial surgery. Int J Med Robot. 2007; 3: 207-16. https://doi.org/10.1002/rcs.143.

[141] Xu S, Xu S, Zhou P, Cheng X, Xie Y, Liang C, et al. Selective laser sintering fabrication of nano-hydroxyapatite/poly-ε-caprolactone scaffolds for bone tissue engineering applications. Int J Nanomedicine. 2013; 8: 4197-213. https://doi.org/10.2147/IJN.S50685.

[142] Liang X, Gao J, Xu W, Wang X, Shen Y, Tang J, et al. Structural mechanics of 3D-printed poly(lactic acid) scaffolds with tetragonal, hexagonal and wheel-like designs. Biofabrication. 2019; 11: 035009. https://doi.org/10.1088/1758-5090/ab0f59.

[143] Ge Z, Tian X, Heng BC, Fan V, Yeo JF, Cao T. Histological evaluation of osteogenesis of 3D-printed poly-lactic-co-glycolic acid (PLGA) scaffolds in a rabbit model. Biomed Mater. 2009; 4: 021001. https://doi.org/10.1088/1748-6041/4/2/021001.

[144] Park SH, Park DS, Shin JW, Kang YG, Kim HK, Yoon TR, et al. Scaffolds for bone tissue engineering fabricated from two different materials by the rapid prototyping technique: PCL versus PLGA. J Mater Sci Mater Med. 2012; 23: 2671-8. https://doi.org/10.1007/s10856-012-4738-8.

[145] Haberstroh K, Ritter K, Kuschnierz J, Bormann K, Kaps C, Carvalho C, et al. Bone repair by cell-seeded 3D-bioplotted composite scaffolds made of collagen treated tricalciumphosphate or tricalciumphosphate-chitosan-collagen hydrogel or PLGA in ovine critical-sized calvarial defects. J Biomed Mater Res B Appl Biomater. 2010; 93B: 520-30. https://doi.org/10.1002/jbm.b.31611.

[146] Saijo H, Igawa K, Kanno Y, Mori Y, Kondo K, Shimizu K, et al. Maxillofacial reconstruction using custom-made artificial bones fabricated by inkjet printing technology. J Artif Organs. 2009; 12: 200-5. https://doi.org/10.1007/s10047-009-0462-7.

[147] Kanno Y, Nakatsuka T, Saijo H, Fujihara Y, Atsuhiko H, Chung U, et al. Computed tomographic evaluation of novel custom-made artificial bones, “CT-bone”, applied for maxillofacial reconstruction. Regen Ther. 2016; 5: 1-8. https://doi.org/10.1016/j.reth.2016.05.002.

[148] Igawa K, Mochizuki M, Sugimori O, Shimizu K, Yamazawa K, Kawaguchi H, et al. Tailor-made tricalcium phosphate bone implant directly fabricated by a three-dimensional ink-jet printer. J Artif Organs. 2006; 9: 234-40. https://doi.org/10.1007/s10047-006-0347-y.

[149] Lopez CD, Diaz-Siso JR, Witek L, Bekisz JM, Cronstein BN, Torroni A, et al. Three dimensionally printed bioactive ceramic scaffold osseoconduction across critical-sized mandibular defects. J Surg Res. 2018; 223: 115-22. https://doi.org/10.1016/j.jss.2017.10.027.

[150] Habibovic P, Gbureck U, Doillon CJ, Bassett DC, van Blitterswijk CA, Barralet JE. Osteoconduction and osteoinduction of low-temperature 3D printed bioceramic implants. Biomaterials. 2008; 29: 944-53. https://doi.org/10.1016/j.biomaterials.2007.10.023.

[151] Shim J-H, Kim SE, Park JY, Kundu J, Kim SW, Kang SS, et al. Three-dimensional printing of rhBMP-2-loaded scaffolds with long-term delivery for enhanced bone regeneration in a rabbit diaphyseal defect. Tissue Eng Part A. 2014; 20: 1980-92. https://doi.org/10.1089/ten.tea.2013.0513.

[152] Cao S, Han J, Sharma N, Msallem B, Jeong W, Son J, et al. In vitro mechanical and biological properties of 3D printed polymer composite and β-tricalcium phosphate scaffold on human dental pulp stem cells. Materials. 2020; 13: 3057. https://doi.org/10.3390/ma13143057.

[153] Nibali L, Sultan D, Arena C, Pelekos G, Lin G, Tonetti M. Periodontal infrabony defects: systematic review of healing by defect morphology following regenerative surgery. J Clin Periodontol. 2021; 48: 101-14. https://doi.org/10.1111/jcpe.13381.

[154] Schriber M, Yeung AWK, Suter VGA, Buser D, Leung YY, Bornstein MM. Cone beam computed tomography artefacts around dental implants with different materials influencing the detection of peri-implant bone defects. Clin Oral Implants Res. 2020; 31: 595-606. https://doi.org/10.1111/clr.13596.

[155] Hagelstein S, Zankovic S, Kovacs A, Barkhoff R, Seidenstuecker M. Mechanical analysis and corrosion analysis of zinc alloys for bioabsorbable implants for osteosynthesis. Materials. 2022; 15: 421. https://doi.org/10.3390/ma15020421.

[156] Sun H, Wang Y, Sun C, Yu H, Xi Z, Liu N, et al. In vivo comparison of the degradation and osteointegration properties of micro-arc oxidation-coated Mg-Sr and Mg-Ca alloy scaffolds. Biomed Mater Eng. 2022; 33: 209-19. https://doi.org/10.3233/BME-211300.

[157] Negi P, Kaur N, Kumar P. Experimental and numerical investigation of the bonding conditions of piezoelectric sensors under high compressive strains on structures. J Intell Mater Syst Struct. 2024; 35: 587-604. https://doi.org/10.1177/1045389X231221128.

[158] Tortelli F, Cancedda R. Three-dimensional cultures of osteogenic and chondrogenic cells: a tissue engineering approach to mimic bone and cartilage in vitro. Eur Cell Mater. 2009; 17: 1-14. https://doi.org/10.22203/eCM.v017a01.

[159] Wilson J, Pigott GH, Schoen FJ, Hench LL. Toxicology and biocompatibility of bioglasses. J Biomed Mater Res. 1981; 15: 805-17. https://doi.org/10.1002/jbm.820150605.

[160] Neo M, Nakamura T, Ohtsuki C, Kokubo T, Yamamuro T.Apatite formation on three kinds of bioactive material at an early stage in vivo: a comparative study by transmission electron microscopy. J Biomed Mater Res. 1993; 27: 999-1006. https://doi.org/10.1002/jbm.820270805.

[161] GBD 2019 Lip, Oral, and Pharyngeal Cancer Collaborators, ARDC, Compton K, Xu R, Mishra R, Drangsholt MT, et al. The global, regional, and national burden of adult lip, oral, and pharyngeal cancer in 204 countries and territories: a systematic analysis for the global burden of disease study 2019. JAMA Oncol. 2023; 9: 1401-16. https://doi.org/10.1001/jamaoncol.2023.2960.

[162] Ogay V, Mun EA, Kudaibergen G, Baidarbekov M, Kassymbek K, Zharkinbekov Z, et al. Progress and prospects of polymer-based drug delivery systems for bone tissue regeneration. Polymers. 2020; 12: 2881. https://doi.org/10.3390/polym12122881.

[163] Borciani G, Ciapetti G, Vitale-Brovarone C, Baldini N. Strontium functionalization of biomaterials for bone tissue engineering purposes: a biological point of view. Materials. 2022; 15: 1724. https://doi.org/10.3390/ma15051724.

[164] Sharma S, Sudhakara P, Singh J, Ilyas RA, Asyraf MRM, Razman MR.Critical review of biodegradable and bioactive polymer composites for bone tissue engineering and drug delivery applications. Polymers. 2021; 13: 2623. https://doi.org/10.3390/polym13162623.

[165] Cranford SW, De Boer J, Van Blitterswijk C, Buehler MJ. Materiomics: an-omics approach to biomaterials research. Adv Mater. 2013; 25: 802-24. https://doi.org/10.1002/adma.201202553.

[166] Matsushita Y, Noguchi A, Ono W, Ono N. Multi-omics analysis in developmental bone biology. Jpn Dent Sci Rev. 2023; 59: 412-20. https://doi.org/10.1016/j.jdsr.2023.10.006.

[167] Scheuren A, Wehrle E, Flohr F, Müller R. Bone mechanobiology in mice: toward single-cell in vivo mechanomics. Biomech Model Mechanobiol. 2017; 16: 2017-34. https://doi.org/10.1007/s10237-017-0935-1.

[168] Junker JP, van Oudenaarden A. Every cell is special: genome-wide studies add a new dimension to single-cell biology. Cell. 2014; 157: 8-11. https://doi.org/10.1016/j.cell.2014.02.010.

[169] Hench LL, Polak JM. Third-generation biomedical materials. Science. 2002; 295: 1014-7. https://doi.org/10.1126/science.1067404.

[170] Baik AD, Qiu J, Hillman EMC, Dong C, Guo XE. Simultaneous tracking of 3D actin and microtubule strains in individual MLO-Y4 osteocytes under oscillatory flow. Biochem Biophys Res Commun. 2013; 431: 718-23. https://doi.org/10.1016/j.bbrc.2013.01.052.

[171] Hasin Y, Seldin M, Lusis A. Multi-omics approaches to disease. Genome Biol. 2017; 18: 83. https://doi.org/10.1186/s13059-017-1215-1.

[172] Pinu FR, Beale DJ, Paten AM, Kouremenos K, Swarup S, Schirra HJ, et al. Systems biology and multi-omics integration: viewpoints from the metabolomics research community. Meta. 2019; 9: 76. https://doi.org/10.3390/metabo9040076.

[173] Cushman SA. Grand challenges in evolutionary and population genetics: the importance of integrating epigenetics, genomics, modeling, and experimentation. Front Genet. 2014; 5: 197. https://doi.org/10.3389/fgene.2014.00197.

[174] Savage N.Bioinformatics: big data versus the big C. Nature. 2014; 509: S66-7. https://doi.org/10.1038/509S66a.

[175] Sarmiento P, Little D. Tendon and multiomics: advantages, advances, and opportunities. Npj Regen Med. 2021; 6: 61. https://doi.org/10.1038/s41536-021-00168-6.

[176] Lutolf MP, Weber FE, Schmoekel HG, Schense JC, Kohler T, Müller R, et al. Repair of bone defects using synthetic mimetics of collagenous extracellular matrices. Nat Biotechnol. 2003; 21: 513-8. https://doi.org/10.1038/nbt818.

[177] Silva GA, Czeisler C, Niece KL, Beniash E, Harrington DA, Kessler JA, et al. Selective differentiation of neural progenitor cells by high-epitope density nanofibers. Science. 2004; 303: 1352-5. https://doi.org/10.1126/science.1093783.

[178] Wang X. Clinical trans-omics: an integration of clinical phenomes with molecular multiomics. Cell Biol Toxicol. 2018; 34: 163-6. https://doi.org/10.1007/s10565-018-9431-3.