Fuel to fire: developmental niche-empowered ApoEVs unlock adult hierarchical tissue regenerative potential via mitochondrial complex I-driven developmental metabolic profile

Abstract

Organ defects involving hierarchical tissue structures remain a major challenge due to limited regenerative capacity in adulthood. To break this bottleneck, regenerative medicine is undergoing a paradigm shift from simulating the healing process of mature organs to reactivating re-development potential, namely developmental engineering strategy. In this study, we propose a novel paradigm based on developmental niche-empowered stem cell-derived apoptotic extracellular vesicles (DevNiche-ApoEVs), which integrates cues from both parental stem cells and their environmental niches. Using the periodontium as a classical hierarchical model, we identified developmental M2-phenotype macrophages (DevM2φ) as a key niche component that induces a developmental metabolic profile in stem cells, characterized by enhanced energy metabolism, mitochondrial homeostasis, and dominance of oxidative phosphorylation. We subsequently empowered ApoEVs with DevM2φ-mediated developmental niche to generate DevNiche-ApoEVs capable of delivering mitochondrial complex I and recapitulating the developmental metabolic profile. In vitro studies confirmed DevNiche-ApoEVs reactivated the developmental potential of adult periodontal ligament cells (PDLCs), while complex I inhibition abrogated this effect. Consistently, DevNiche-ApoEVs promoted re-development-based hierarchical periodontal regeneration by recapitulating critical developmental events in vivo. This study highlights the pivotal role of the developmental niche in hierarchical tissue regeneration and provides a promising DevNiche-ApoEVs-focused developmental engineering strategy, which offers both a solid theoretical foundation and an effective translational solution to overcome the longstanding bottleneck in adult tissue regeneration.

References

[1] Gomez-Salinero JM, Redmond D, Rafii S. Microenvironmental determinants of endothelial cell heterogeneity. Nat. Rev. Mol. Cell Biol., 2025, 26: 476-495

[2] He L, et al.. Parenchymal and stromal tissue regeneration of tooth organ by pivotal signals reinstated in decellularized matrix. Nat. Mater., 2019, 18: 627-637

[3] Lantz C, et al.. Early-age efferocytosis directs macrophage arachidonic acid metabolism for tissue regeneration. Immunity, 2025, 58: 344-361.e347

[4] Yu M, et al.. A hierarchical bilayer architecture for complex tissue regeneration. Bioact. Mater., 2022, 10: 93-106

[5] Woo HN, Cho YJ, Tarafder S, Lee CH. The recent advances in scaffolds for integrated periodontal regeneration. Bioact. Mater., 2021, 6: 3328-3342

[6] Ono W, Sakagami N, Nishimori S, Ono N, Kronenberg HM. Parathyroid hormone receptor signalling in osterix-expressing mesenchymal progenitors is essential for tooth root formation. Nat. Commun., 2016, 7 Article ID: 11277

[7] Lin JD, Ryder M, Kang M, Ho SP. Biomechanical pathways of dentoalveolar fibrous joints in health and disease. Periodontology 2000, 2020, 82: 238-256

[8] Huang X, et al.. Genetically engineered M2-like macrophage-derived exosomes for P. gingivalis-suppressed cementum regeneration: From mechanism to therapy. Bioact. Mater., 2024, 32: 473-487

[9] Garreta E, et al.. Rethinking organoid technology through bioengineering. Nat. Mater., 2021, 20: 145-155

[10] Kawasumi-Kita A, et al.. hoxc12/c13 as key regulators for rebooting the developmental program in Xenopus limb regeneration. Nat. Commun., 2024, 15 Article ID: 3340

[11] Viragova S, Li D, Klein OD. Activation of fetal-like molecular programs during regeneration in the intestine and beyond. Cell Stem Cell, 2024, 31: 949-960

[12] Liu G, et al.. Inducing the “re-development state” of periodontal ligament cells via tuning macrophage mediated immune microenvironment. J. Adv. Res., 2024, 60: 233-248

[13] Chakraborty J, Chawla S, Ghosh S. Developmental biology-inspired tissue engineering by combining organoids and 3D bioprinting. Curr. Opin. Biotechnol., 2022, 78 Article ID: 102832

[14] Xie C, et al.. High-efficient engineering of osteo-callus organoids for rapid bone regeneration within one month. Biomaterials, 2022, 288 Article ID: 121741

[15] Liu G, et al.. The paradigm shifts of periodontal regeneration strategy: From reparative manipulation to developmental engineering. Bioact. Mater., 2025, 49: 418-436

[16] Amadei G, et al.. Embryo model completes gastrulation to neurulation and organogenesis. Nature, 2022, 610: 143-153

[17] Yamanaka S. Induced pluripotent stem cells: past, present, and future. Cell Stem Cell, 2012, 10: 678-684

[18] Ankrum JA, Ong JF, Karp JM. Mesenchymal stem cells: immune evasive, not immune privileged. Nat. Biotechnol., 2014, 32: 252-260

[19] Deuse T, et al.. Hypoimmunogenic derivatives of induced pluripotent stem cells evade immune rejection in fully immunocompetent allogeneic recipients. Nat. Biotechnol., 2019, 37: 252-258

[20] Harding J, et al.. Immune-privileged tissues formed from immunologically cloaked mouse embryonic stem cells survive long-term in allogeneic hosts. Nat. Biomed. Eng., 2024, 8: 427-442

[21] Teng F, Fussenegger M. Shedding light on extracellular vesicle biogenesis and bioengineering. Adv. Sci., 2020, 8 Article ID: 2003505

[22] Kaur G, et al.. Biopotency and surrogate assays to validate the immunomodulatory potency of extracellular vesicles derived from mesenchymal stem/stromal cells for the treatment of experimental autoimmune uveitis. J. Extracell. Vesicles, 2024, 13 Article ID: e12497

[23] Ding Z, et al.. Apoptotic extracellular vesicles derived from hypoxia-preconditioned mesenchymal stem cells within a modified gelatine hydrogel promote osteochondral regeneration by enhancing stem cell activity and regulating immunity. J. Nanobiotechnol., 2024, 22 Article ID: 74

[24] Ma L, et al.. Apoptotic extracellular vesicles are metabolized regulators nurturing the skin and hair. Bioact. Mater., 2023, 19: 626-641

[25] Qin Y, et al.. Lipid metabolism of apoptotic vesicles accelerates cutaneous wound healing by modulating macrophage function. J. Nanobiotechnol., 2025, 23 Article ID: 106

[26] Yung T, et al.. Sufu- and Spop-mediated downregulation of Hedgehog signaling promotes beta cell differentiation through organ-specific niche signals. Nat. Commun., 2019, 10 Article ID: 4647

[27] Sakhneny L, et al.. The postnatal pancreatic microenvironment guides β cell maturation through BMP4 production. Dev. Cell, 2021, 56: 2703-2711.e2705

[28] Gao L, Lee H, Goodman JH, Ding L. Hematopoietic stem cell niche generation and maintenance are distinguishable by an epitranscriptomic program. Cell, 2024, 187: 2801-2816.e2817

[29] Huang P, et al.. Improving hard metal implant and soft tissue integration by modulating the “inflammatory-fibrous complex” response. Bioact. Mater., 2023, 20: 42-52

[30] Cui Y, et al.. Melatonin Engineering M2 Macrophage-Derived Exosomes Mediate Endoplasmic Reticulum Stress and Immune Reprogramming for Periodontitis Therapy. Adv. Sci., 2023, 10 Article ID: e2302029

[31] Zhang X, et al.. Proteomic analysis of MSC-derived apoptotic vesicles identifies Fas inheritance to ameliorate haemophilia a via activating platelet functions. J. Extracell. Vesicles, 2022, 11 Article ID: e12240

[32] Mogilenko DA, Shchukina I, Artyomov MN. Immune ageing at single-cell resolution. Nat. Rev. Immunol., 2022, 22: 484-498

[33] Zhang L, Zhou J, Kong W. Extracellular matrix in vascular homeostasis and disease. Nat. Rev. Cardiol., 2025, 22: 333-353

[34] Stewart KS, et al.. Stem cells tightly regulate dead cell clearance to maintain tissue fitness. Nature, 2024, 633: 407-416

[35] Guilliams M, Thierry GR, Bonnardel J, Bajenoff M. Establishment and maintenance of the macrophage niche. Immunity, 2020, 52: 434-451

[36] Viola MF, Boeckxstaens G. Niche-specific functional heterogeneity of intestinal resident macrophages. Gut, 2021, 70: 1383-1395

[37] Liu S, et al.. Erythropoietin-stimulated macrophage-derived extracellular vesicles in Chitosan Hydrogel Rescue BMSCs Fate by Targeting EGFR to Alleviate Inflammatory Bone Loss in Periodontitis. Adv. Sci., 2025, 12 Article ID: e2500554

[38] Lazure F, et al.. Transcriptional reprogramming of skeletal muscle stem cells by the niche environment. Nat. Commun., 2023, 14 Article ID: 535

[39] Rayagiri SS, et al.. Basal lamina remodeling at the skeletal muscle stem cell niche mediates stem cell self-renewal. Nat. Commun., 2018, 9 Article ID: 1075

[40] Hou R, Denisenko E, Ong HT, Ramilowski JA, Forrest ARR. Predicting cell-to-cell communication networks using NATMI. Nat. Commun., 2020, 11 Article ID: 5011

[41] Davidson CD, et al.. Mechanical Intercellular Communication via Matrix-Borne Cell Force Transmission During Vascular Network Formation. Adv. Sci., 2024, 11 Article ID: e2306210

[42] Shaya O, et al.. Cell-Cell Contact Area Affects Notch Signaling and Notch-Dependent Patterning. Dev. Cell, 2017, 40: 505-511.e506

[43] Yan J, et al.. Macrophage-derived mitochondria-rich extracellular vesicles aggravate bone loss in periodontitis by disrupting the mitochondrial dynamics of BMSCs. J. Nanobiotechnol., 2025, 23 Article ID: 208

[44] Wong YC, Ysselstein D, Krainc D. Mitochondria-lysosome contacts regulate mitochondrial fission via RAB7 GTP hydrolysis. Nature, 2018, 554: 382-386

[45] Wang Y, Jin S, Guo Y, Lu Y, Deng X. Adhesive and injectable hydrogel microspheres for NRF2-mediated periodontal bone regeneration. Int. J. Oral. Sci., 2025, 17: 7

[46] Liu H, et al.. Energy metabolism in health and diseases. Signal Transduct. Target. Ther., 2025, 10: 69

[47] Glancy B, Balaban RS. Energy metabolism design of the striated muscle cell. Physiol. Rev., 2021, 101: 1561-1607

[48] Schell JC, et al.. Control of intestinal stem cell function and proliferation by mitochondrial pyruvate metabolism. Nat. Cell Biol., 2017, 19: 1027-1036

[49] Wu YQ, et al.. Low glucose metabolite 3-phosphoglycerate switches PHGDH from serine synthesis to p53 activation to control cell fate. Cell Res., 2023, 33: 835-850

[50] Denans N, et al.. An anti-inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish. Nat. Commun., 2022, 13 Article ID: 5356

[51] Nicholls SE, et al.. IL-4 promotes macrophage development by rapidly stimulating lineage restriction of bipotent granulocyte-macrophage colony-forming cells. J. Immunol., 1995, 155: 845-853

[52] Chaudhry A, Shi R, Luciani DS. A pipeline for multidimensional confocal analysis of mitochondrial morphology, function, and dynamics in pancreatic β-cells. Am. J. Physiol. Endocrinol. Metab., 2020, 318: E87-e101

[53] Rudokas MW, et al.. Mitochondrial network remodeling of the diabetic heart: implications to ischemia related cardiac dysfunction. Cardiovasc. Diabetol., 2024, 23 Article ID: 261

[54] Cabrera-Orefice A, et al.. Locking loop movement in the ubiquinone pocket of complex I disengages the proton pumps. Nat. Commun., 2018, 9 Article ID: 4500

[55] Padial-Molina M, Rodriguez JC, Volk SL, Rios HF. Standardized in vivo model for studying novel regenerative approaches for multitissue bone-ligament interfaces. Nat. Protoc., 2015, 10: 1038-1049

[56] Liang Y, Luan X, Liu X. Recent advances in periodontal regeneration: A biomaterial perspective. Bioact. Mater., 2020, 5: 297-308

[57] Yang X, et al.. A 3D-Bioprinted Functional Module Based on Decellularized Extracellular Matrix Bioink for Periodontal Regeneration. Adv. Sci., 2023, 10 Article ID: e2205041

[58] Capella-Monsonís H, Coentro JQ, Graceffa V, Wu Z, Zeugolis DI. An experimental toolbox for characterization of mammalian collagen type I in biological specimens. Nat. Protoc., 2018, 13: 507-529

[59] Wen Y, et al.. COL4A2 in the tissue-specific extracellular matrix plays important role on osteogenic differentiation of periodontal ligament stem cells. Theranostics, 2019, 9: 4265-4286

[60] Ou Q, et al.. Electrostatic Charge-Mediated Apoptotic Vesicle Biodistribution Attenuates Sepsis by Switching Neutrophil NETosis to Apoptosis. Small, 2022, 18 Article ID: e2200306

[61] Li X, Li S, Fu X, Wang Y. Apoptotic extracellular vesicles restore homeostasis of the articular microenvironment for the treatment of rheumatoid arthritis. Bioact. Mater., 2024, 35: 564-576

[62] Gregory CD, Rimmer MP. Extracellular vesicles arising from apoptosis: forms, functions, and applications. J. Pathol., 2023, 260: 592-608

[63] Joshi BS, de Beer MA, Giepmans BNG, Zuhorn IS. Endocytosis of extracellular vesicles and release of their cargo from endosomes. ACS Nano, 2020, 14: 4444-4455

[64] Hagedorn L, Jürgens DC, Merkel OM, Winkeljann B. Endosomal escape mechanisms of extracellular vesicle-based drug carriers: lessons for lipid nanoparticle design. Extracell. Vesicles Circ. Nucleic Acids, 2024, 5: 344-357

[65] Ribovski L, Joshi B, Gao J, Zuhorn I. Breaking free: endocytosis and endosomal escape of extracellular vesicles. Extracell. Vesicles Circ. Nucl. Acids, 2023, 4: 283-305

[66] Shahannaz D. C., Sugiura T., Yoshida T. Mitochondria-Enriched Extracellular Vesicles (EVs) for cardiac bioenergetics restoration: a scoping review of preclinical mechanisms and source-specific strategies. Int. J. Mol. Sci.26, (2025).

[67] Wu S, et al.. Extracellular vesicles meet mitochondria: Potential roles in regenerative medicine. Pharmacol. Res., 2024, 206 Article ID: 107307

[68] Zhou X, et al.. MitoEVs: A new player in multiple disease pathology and treatment. J. Extracell. Vesicles, 2023, 12 Article ID: e12320

[69] Jiang Y, et al.. Lyophilized apoptotic vesicles improve hemostasis and bone regeneration in traumatic patients with impacted third molar extraction. Mol. Ther. : J. Am. Soc. Gene Ther., 2025, 33: 2931-2944

[70] Fu Y, et al.. Apoptotic vesicles: emerging concepts and research progress in physiology and therapy. Life Med., 2023, 2 Article ID: lnad013

[71] Lei F, et al.. Apoptotic vesicles rejuvenate mesenchymal stem cells via Rab7-mediated autolysosome formation and alleviate bone loss in aging mice. Nano Res., 2023, 16: 822-833

[72] Zhang S, Zhang ZY, Sui BD, Zheng CX, Fu Y. The epigenetic landscape of mesenchymal stem cell and extracellular vesicle therapy. Trends Cell Biol., 2026, 36: 42-56

[73] Liu Z, et al.. Nanofibrous spongy microspheres to distinctly release mirna and growth factors to enrich regulatory T cells and rescue periodontal bone loss. ACS Nano, 2018, 12: 9785-9799

[74] Zhang Q, et al.. Regeneration of immunocompetent B lymphopoiesis from pluripotent stem cells guided by transcription factors. Cell. Mol. Immunol., 2022, 19: 492-503

[75] Zhu M, et al.. In vivo engineered extracellular matrix scaffolds with instructive niches for oriented tissue regeneration. Nat. Commun., 2019, 10 Article ID: 4620

[76] Tian J, et al.. Autophagy controls mesenchymal stem cell therapy in psychological stress colitis mice. Autophagy, 2021, 17: 2586-2603

[77] Lungová V, et al.. Tooth-bone morphogenesis during postnatal stages of mouse first molar development. J. Anat., 2011, 218: 699-716

[78] Liu G, et al.. Cell-free immunomodulatory biomaterials mediated in situ periodontal multi-tissue regeneration and their immunopathophysiological processes. Mater. Today Bio, 2022, 16 Article ID: 100432

[79] Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinforma, 2018, 34: i884-i890

[80] Ou Q, et al.. Apoptosis releases hydrogen sulfide to inhibit Th17 cell differentiation. Cell Metab., 2024, 36: 78-89.e75

[81] Huang Z, et al.. Apoptotic vesicles are required to repair DNA damage and suppress premature cellular senescence. J. Extracell. Vesic., 2024, 13 Article ID: e12428

[82] Fu Y, et al.. Mesenchymal stem cell-derived apoptotic vesicles ameliorate impaired ovarian folliculogenesis in polycystic ovary syndrome and ovarian aging by targeting WNT signaling. Theranostics, 2024, 14: 3385-3403

[83] Sui B. et al. Apoptotic Extracellular Vesicles (ApoEVs) Safeguard Liver Homeostasis and Regeneration via Assembling an ApoEV-Golgi Organelle. bioRxiv 2021. https://doi.org/10.1101/2021.02.24.432630 2021.2002.2024.432630

Funding

the National Key R&D Program of China (2022YFA1104400), Science and Technology Program of Guangdong Province, China (2023A0505050138), Guangzhou Basic and Applied Basic Research Foundation (2024A04J6323).

National Natural Science Foundation of China (National Science Foundation of China)(82201012)

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