Three-Dimensional MSC Culture:
Why Geometry Is a Biological Variable
The Biology of Three-Dimensional Culture
Where MSCs Actually Reside In Vivo
In native tissue, mesenchymal stem cells occupy perivascular niches within connective tissue. These niches are not flat. MSCs are embedded in a three-dimensional hydrogel-like extracellular matrix, maintain direct cell-cell contacts on all spatial axes, and are subject to oxygen and nutrient gradients that shift from the vessel lumen outward into surrounding parenchyma.[1] This architecture is not incidental. It actively regulates MSC gene expression, paracrine output, and biological identity.
The mismatch between this in vivo context and the flat plastic surface of conventional 2D culture is substantial. When MSCs are plated as a monolayer, the cell geometry, mechanical signaling, oxygen delivery, and intercellular contact patterns all diverge from the native niche. The resulting cell is a 2D-adapted version of an MSC — one that behaves differently at the molecular level than the cell it originated from.
Cytoskeletal Tension and Gene Expression
When MSCs are expanded on rigid, flat plastic surfaces, the geometry forces the cells to spread laterally. The resulting increase in cytoskeletal tension reorganizes focal adhesions and activates mechanotransductive pathways that suppress pluripotency-associated transcription factors, including Nanog, Oct4, and Sox2.[2]
Re-aggregating these same cells into 3D spheroids reverses this suppression. Quantitative PCR and RNA-seq analyses have reported fold-changes ranging from 9.7- to 30.4-fold in stemness gene expression relative to 2D culture, attributed to relaxation of actin stress fibers, reduction in nuclear flattening, and re-establishment of cell-cell junctions.[3] Transcriptome-wide analysis of MSC spheroids identified 1,731 upregulated genes and 1,387 downregulated genes relative to monolayer — a comprehensive rewiring of cellular biology, not a minor adjustment.[4]
"Three-dimensional culture more faithfully recapitulates the biomechanical and biochemical context of MSCs in vivo. By preserving niche-like tension, oxygen gradients, and cell-cell interactions, spheroid systems sustain pluripotency gene networks." — Adapted from PMC5431137 (2017)
The Caspase–IL-1 Mechanism
Beyond transcriptional changes, 3D culture initiates a self-contained paracrine activation cascade absent in monolayer conditions. During spheroid compaction, caspase-dependent activation of interleukin-1 (IL-1) signaling leads to autocrine release of IL-1α and IL-1β. This signal drives synthesis and secretion of several key anti-inflammatory mediators: tumor necrosis factor-stimulated gene-6 (TSG-6), prostaglandin E2 (PGE2), and stanniocalcin-1 (STC1).[5]
These factors modulate macrophage polarization toward an anti-inflammatory M2 phenotype, inhibit neutrophil infiltration, and protect surrounding tissues from oxidative stress. MSCs maintained on 2D substrates produce only basal levels of these molecules. Comparative studies consistently report higher TSG-6, HGF, VEGF, and PGE2 concentrations in spheroid-derived conditioned media versus 2D monolayer media.[6]
NLRP3 Inflammasome Regulation
Three-dimensional culture suppresses NLRP3 inflammasome activation through autophagy and endoplasmic reticulum stress modulation pathways. Spheroid-forming MSCs demonstrate attenuated NLRP3 activity relative to 2D counterparts, resulting in enhanced cell survival under physiological stress and more sustained paracrine output — which is particularly relevant when cells are deployed into inflammatory tissue environments.[7]
The Secretome in Three-Dimensional Culture
Exosome Yield
The secretome — the complete complement of proteins, vesicles, and nucleic acids released by a cell — is the primary mechanism through which MSCs exert biological effects. Multiple independent laboratories have demonstrated that 3D spheroid culture substantially increases extracellular vesicle output per cell.
| Study | Year | Yield increase (3D vs 2D) | Notes |
|---|---|---|---|
| Tissue Engineering & Regenerative Medicine (PMID 30603566) | 2018 | 18.4× | 150 μm spheroids; smaller size = highest per-cell efficiency |
| Stem Cell Research & Therapy (PMC7251891) | 2020 | 19.4× total; 15.5× supernatant concentration | Hollow fiber bioreactor; GMP-compatible |
| Biomaterials (hepatic fibrosis model) | 2023 | ~20× | PMC11351945; used in 3D liver spheroid co-culture model |
Cargo Composition
Yield alone does not determine therapeutic value. Proteomic and miRNA analyses show the molecular cargo of 3D-derived exosomes differs substantially from 2D-derived vesicles. Comparative studies have identified over 195 distinct miRNAs and proteins differentially expressed between 3D and 2D exosome preparations, including neprilysin, IDE, HSP70, AHSG, and albumin — molecules associated with cellular protection and enhanced endocytosis of vesicles.[8]
Three-dimensional culture consistently enriches exosomes for proangiogenic miRNAs, anti-inflammatory mediators, and matrix remodeling regulators. The miRNA profiles of 3D- and 2D-derived exosomes are reproducibly distinct across cell sources and preparation methods, which indicates culture geometry is a systematic upstream determinant of cargo — not batch variation.[9]
Xenofree and Serum-Free Media
The choice of culture medium interacts with dimensionality. Chemically defined, xenofree, serum-free media combined with 3D conditions optimizes exosome output while reducing batch-to-batch variability and eliminating the risk of bovine serum contaminants in the preparation.[10] Xenofree conditions have been shown to independently enhance the regenerative properties of umbilical cord MSC-derived exosomes.[11] For applications where regulatory compliance matters, both culture dimensionality and xenofree media represent documented quality determinants.
Passage Number
3D culture priming benefits are maintained even after extensive cell expansion.[12] Spheroid size influences cellular senescence and angiogenic vesicle cargo, with optimal size ranges identified for specific applications.[13] Protocols harvesting at passages P2–P4 with 3D spheroid production represent the current evidence-based standard for preserving both yield and functional quality of the secretome.
Clinical and Therapeutic Evidence
A 2017 meta-analysis in Stem Cell Research & Therapy concluded that 3D spheroid culture enhances anti-inflammatory, angiogenic, and overall therapeutic potential relative to monolayer methods.[14] A 2021 systematic review confirmed consistently enhanced stemness, immunomodulation, and therapeutic efficacy in 3D spheroids across disease models.[15]
Immunomodulation
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View →3D UC-MSC extracellular vesicles vs pancreatic islet inflammationPMC9970714 · 20233D hUCB-MSC EVs more effectively suppressed pro-inflammatory cytokines and caspase-1; enhanced M2 macrophage polarization vs 2D-derived EVs.
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View →3D-UC-MSC secretome in rheumatoid arthritis modelsPMC6370626 · 20193D secretome demonstrated superior anti-inflammatory efficacy vs 2D secretome, suppressing synovial inflammation and cartilage degradation markers.
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View →NLRP3 modulation improves MSC spheroid survival and immunomodulationPMID 36566348 · Molecular Therapy · 20233D spheroid culture suppressed NLRP3 inflammasome through autophagy and ER stress modulation, enhancing MSC survival and sustained immunomodulatory function under stress.
Wound Healing and Tissue Repair
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View →3D MSC exosomes in cisplatin-induced acute kidney injuryPMC7251891 · Stem Cell Research & Therapy · 202019.4× exosome yield increase with 3D culture; enhanced therapeutic efficacy vs 2D-derived exosomes in kidney injury models.
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View →3D MSC spheroids for diabetic wound healingAdvanced Functional Materials · 20243D MSC spheroids promoted diabetic wound closure more effectively than 2D suspended cells, with sustained anti-inflammatory secretion and improved tissue repair.
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View →3D MSC-EVs for hepatic fibrosis reversalPMC11351945 · 20233D culture-derived MSC-EVs (~20× yield increase) more effectively suppressed hepatic stellate cell activation and fibrosis vs 2D-derived EVs in liver spheroid models.
Orthopedics and Cartilage
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View →3D spheroid exosomes for osteoarthritis and cartilage repairPMID 35888029 · Life · 20223D spheroid exosomes superior to 2D for chondrocyte protection and cartilage regeneration; smaller 3D-derived exosomes showed improved cellular uptake in target tissue.
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View →WJ-MSC EVs for intervertebral disc degenerationPMC12366443 · 2024WJ-MSC EVs from 3D culture superior for degenerative disc disease via enhanced anti-inflammatory and anabolic effects vs 2D-derived EVs.
Neuroprotection
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View →3D MSC spheroids for ischemic stroke neuroprotectionBiomaterials · 2021Co-cultured 3D MSC spheroids demonstrated superior neuroprotection and vascular regeneration vs cell suspensions in ischemic stroke models.
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View →3D placenta-derived MSC spheroids for spinal cord injuryCell Death & Disease (Nature) · 2021Placenta-derived 3D spheroids demonstrated superior neuroprotection and spinal cord regeneration vs monolayer cells in vivo, with enhanced survival post-injection.
Aesthetic and Cosmetic Evidence
A growing body of clinical research documents the effects of MSC-derived exosomes and secretome in aesthetic medicine. Controlled trials and systematic reviews now exist for skin aging, post-procedure recovery, scar remodeling, and hair restoration.
Skin Aging: Collagen, Fibroblast Renewal, and Matrix Preservation
A 2023 split-face randomized controlled trial (n=28) demonstrated that microneedling combined with topical exosome application produced a statistically significant reduction in wrinkle depth of 12.4–14.4% and an 11.3% increase in cutaneous elasticity compared with control microneedling alone.[16]
Mechanistic in-vitro studies show MSC-derived exosomes upregulate collagen type I and III synthesis in dermal fibroblasts and concurrently downregulate MMP-1, MMP-3, and MMP-9 — shifting the matrix toward preservation over degradation. Exosome exposure has also been shown to reverse fibroblast senescence markers including p16INK4a and SA-β-galactosidase activity.[17] A 2024 study confirmed that combinations of UC-MSC-derived exosomes with collagen oligopeptides enhanced fibroblast proliferation, reduced ROS, and downregulated the full matrix metalloproteinase panel.[18]
Post-Procedure Recovery
A prospective six-month cohort of 100 patients receiving MSC-exosome gel after microneedling reported improvements across multiple outcome parameters: skin texture, firmness, pigmentation uniformity, radiance, pore diameter, and surface moisture content, relative to baseline and to a matched untreated cohort.[19] Quantitative imaging confirmed an approximately 18% increase in dermal hydration and a 14% reduction in erythema scores, consistent with exosome effects on keratinocyte migration and inflammatory resolution.
A 2022 split-face RCT (n=25) demonstrated that adipose MSC-derived exosomes applied after fractional CO2 laser significantly improved acne scar outcomes and accelerated post-procedure recovery versus laser alone.[20]
Scar Remodeling
Adipose-derived MSC exosomes have been shown to correct the collagen III:I ratio in treated scars, shifting from a scar-promoting profile (>1.5) toward an anti-scarring range (<0.8). This is consistent with a fetal wound healing biology. The primary mechanistic mediator identified is ERK/MAPK cascade activation, which modulates fibroblast phenotype toward balanced ECM deposition and reduced hypertrophic scar formation.[21]
Hair Restoration
A 2025 systematic review encompassing 40 interventional studies found that MSC-exosome therapy yields hair coverage improvements ranging from 50% to 99% in alopecic area and increases clinical hair density by 9 to 31 hairs per cm². These effects are attributed to activation of the Wnt/β-catenin pathway, promotion of dermal papilla cell proliferation, and prolongation of anagen phase duration.[22]
Hyperpigmentation
A double-blind, placebo-controlled study in 21 participants (ages 39–55) showed that adipose-derived MSC exosomes significantly reduced melanin index within four weeks in hyperpigmented subjects with no adverse effects.[23] A 2025 non-inferiority trial comparing adipose MSC-derived exosomes versus PRP for photoaging found equivalent or superior outcomes for wrinkling, dyschromia, erythema, and texture, with increased collagen I and glycosaminoglycans confirmed on histology.[24]
| Application | Study type | Key outcome | Source |
|---|---|---|---|
| Skin aging / microneedling | Split-face RCT, n=28 | 12.4–14.4% wrinkle reduction; +11.3% elasticity | DOI → |
| Post-microneedling recovery | Prospective cohort, n=100 | Texture, firmness, pigmentation, hydration all improved; −14% erythema | PubMed → |
| Acne scarring / CO2 laser | Split-face RCT, n=25 | Significantly improved scar outcomes; faster post-laser recovery | PMC → |
| Hyperpigmentation | DB-RCT, n=21 | Significant melanin index reduction at 4 weeks | MDPI → |
| Photoaging vs PRP | Non-inferiority RCT | Exosomes non-inferior or superior to PRP; collagen I increase on histology | PubMed → |
| Alopecia | Systematic review, 40 studies | 50–99% hair coverage; +9 to +31 hairs/cm² | PMC → |
Why Source Culture Conditions Define Exosome Biology
Extracellular vesicles — including exosomes (30–150 nm) — are released constitutively by MSCs and carry proteins, mRNAs, and miRNAs into recipient cells. Their surface proteins determine cellular targeting; their internal cargo determines the biological response.
Because exosome composition mirrors the secretory state of the producing cell, the culture conditions used to maintain that cell are the upstream determinant of what the exosome contains. A cell maintained under mechanical stress on flat plastic — with suppressed stemness genes and minimal anti-inflammatory output — produces exosomes with a correspondingly impoverished profile. A cell maintained in a 3D spheroid with an activated anti-inflammatory secretome produces a measurably different vesicle.
Exosome quality cannot be separated from the biology of the producing cell. The culture environment shapes the cell; the cell shapes the exosome. Three-dimensional culture recovers more of the in vivo cellular state — and the literature documents this produces exosomes with different cargo and, in most studied applications, greater biological potency.
Documented Cargo Differences in 3D-Derived Exosomes
| Molecule / class | Biological function | Clinical relevance |
|---|---|---|
| Proangiogenic miRNAs | Stimulate vascular formation and tissue perfusion | Wound healing, tissue repair, post-procedure recovery |
| TSG-6, PGE2, STC1 | Anti-inflammatory; M2 macrophage polarization | Inflammatory skin conditions, post-treatment recovery, immunomodulation |
| miR-210 | Tissue protection under hypoxic conditions | Ischemic tissue repair; enriched by hypoxic 3D preconditioning[25] |
| Wnt pathway activators | Promote dermal papilla proliferation; anagen induction | Hair restoration[22] |
| Collagen-regulating factors | Upregulate Col I/III; downregulate MMP-1/3/9 | Scar remodeling, skin aging[21] |
| Neprilysin, IDE, HSP70 | Cellular protection, peptide processing, stress response | Neuroprotection; cellular homeostasis[8] |
References
All references link directly to PubMed, PubMed Central, or the original journal. Inline citation numbers in the text above link to the corresponding entry below.
3D Culture Biology and Gene Expression
- The three-dimensional perivascular MSC niche: in vivo architecture, ECM mechanics, and oxygen gradients. MSC niche biology review. Describes the hydrogel-like ECM environment and multi-axis cell contacts that define MSC identity in native tissue — the context that 2D culture eliminates.
- 3D culture increases pluripotent gene expression in mesenchymal stem cells through relaxation of cytoskeleton tension. PMC5431137 · Biomaterials · 2017. View at PMC → Cytoskeletal relaxation in 3D spheroids upregulates pluripotency genes by reversing the mechanical repression imposed by flat 2D substrates.
- Stemness markers (Nanog, Oct4, Sox2) upregulated 9.7–30.4-fold in MSC spheroids. BMC Biotechnology · 2014. View → QRT-PCR showed re-aggregation of MSCs into 3D spheroids restores pluripotency gene expression 9.7–30.4× above 2D baselines within 48 hours.
- Characterization and gene expression profiles of human periodontal MSCs in spheroid cultures: transcriptome analysis. PMC8548127 · 2021. View at PMC → 1,731 genes upregulated and 1,387 downregulated in 3D spheroids vs 2D — a comprehensive biological shift, not an incremental one.
- Dynamic compaction of human mesenchymal stem/precursor cells self-activates caspase-dependent IL-1 signaling to enhance secretion of modulatory factors. PMID 26861485 · Stem Cells · 2016. View at PubMed → Spheroid compaction triggers autocrine IL-1 signaling driving secretion of TSG-6, PGE2, and STC1 — anti-inflammatory factors largely absent in 2D-cultured MSCs.
- 3D spheroid culture enhances survival and therapeutic capacities of MSCs: VEGF, HGF, and anti-apoptotic factor secretion. PMC4929304 · 2016. View at PMC → 3D spheroid-cultured MSCs showed significantly enhanced VEGF, HGF, and anti-apoptotic factor secretion compared to 2D cells; correlated with superior in vivo outcomes.
- Modulation of NLRP3 inflammasome activation contributes to improved survival and function of mesenchymal stromal cell spheroids. PMID 36566348 · Molecular Therapy · 2023. View at PubMed → 3D spheroid culture suppressed NLRP3 inflammasome via autophagy and ER stress modulation, enhancing MSC survival and immunomodulatory function under physiological stress.
Exosome Yield and Secretome Quality
- Differential proteomic and miRNA cargo analysis of 3D vs 2D MSC-derived exosomes: 195+ distinct molecules identified. Molecular Therapy · 2018. View → 195+ distinct miRNAs and proteins differentially enriched between 3D and 2D exosomes, including neprilysin, IDE, HSP70, and albumin.
- Engineering three-dimensional spheroid culture for enrichment of proangiogenic miRNAs in umbilical cord mesenchymal stem cells. ACS Omega · 2024. View → 3D culture consistently enriched proangiogenic miRNAs; miRNA profiles of 3D and 2D exosomes are reproducibly distinct across cell sources.
- A chemically defined, xeno- and blood-free culture medium sustains increased production of small extracellular vesicles from MSCs. PMC8187876 · 2021. View at PMC → Xenofree serum-free media combined with 3D conditions optimized exosome output, reduced batch variability, and improved GMP compliance.
- Diverse impact of xeno-free conditions on biological and regenerative properties of hUC-MSCs and their extracellular vesicles. PMC5239805 · 2017. View at PMC → Xeno-free conditions enhanced regenerative properties of UC-MSC exosomes in 3D culture vs FBS-supplemented media.
- Efficacy of 3D culture priming is maintained in human MSCs after extensive expansion. PMC6770505 · 2019. View at PMC → 3D culture priming benefits retained even after extensive passage expansion — supporting scalable manufacturing of biologically potent preparations.
- Spheroid size influences cellular senescence and angiogenic potential of MSC-derived extracellular vesicles. Frontiers in Bioengineering and Biotechnology · 2023. View → Spheroid size critically modulates senescence markers and angiogenic EV cargo; optimal size ranges identified for therapeutic applications.
Systematic Reviews and Meta-Analyses
- The therapeutic potential of three-dimensional multipotent mesenchymal stromal cell spheroids. PMC5406927 · Stem Cell Research & Therapy · 2017. View → Meta-analysis: 3D spheroid culture enhances anti-inflammatory, angiogenic, and overall therapeutic potential; superior in vivo outcomes across multiple disease models.
- Functional properties of human-derived mesenchymal stem cell spheroids: a meta-analysis and systematic review. PMC8041538 · 2021. View at PMC → Systematic review: 3D spheroids display consistently enhanced stemness, immunomodulation, and therapeutic efficacy across regenerative medicine applications.
Cosmetic and Aesthetic Dermatology
- Efficacy of combined treatment with human adipose tissue stem cell-derived exosome-containing solution and microneedling for facial skin aging. Park et al. · Journal of Cosmetic Dermatology · DOI 10.1111/jocd.15872 · 2023. View → 28-patient split-face RCT: 12.4–14.4% wrinkle reduction, +11.3% elasticity, +9.9% pigmentation improvement vs control microneedling.
- The antisenescence effect of exosomes from human adipose-derived stem cells on skin fibroblasts. PMC9259368 · BioMed Research International · 2022. View at PMC → ADSC exosomes increased type I collagen, reduced ROS and SA-β-gal, and inhibited p53/p21/p16 in aged human dermal fibroblasts.
- The combined anti-aging effect of hydrolyzed collagen oligopeptides and exosomes from HucMSCs on skin fibroblasts. PMID 38611748 · Molecules · 2024. View at PubMed → HucMSC-exosome combination enhanced fibroblast proliferation, reduced ROS and senescence, increased collagen I/III, and downregulated MMP-1/3/9.
- Topical Wharton's Jelly MSC-derived exosome treatments after micro-needling for skin rejuvenation. PMID 39367640 · Journal of Cosmetic Dermatology · 2024. View at PubMed → 100-patient 6-month study: improvements in wrinkles, texture, firmness, pigmentation, radiance, pore size, moisture, and redness post-microneedling.
- Combination treatment with ADSC-derived exosomes and fractional CO2 laser for acne scars: a 12-week RCT. PMC9309822 · Acta Dermato-Venereologica · 2022. View at PMC → Split-face RCT (n=25): exosomes significantly enhanced CO2 laser efficacy for acne scar improvement with faster post-procedure recovery.
- Exosomes secreted by human adipose MSCs promote scarless cutaneous repair by regulating ECM remodelling. PMID 29042658 · Scientific Reports · 2017. View at PubMed → ASC exosomes corrected collagen III:I ratio to anti-scarring profile and reduced scar extent via ERK/MAPK pathway — similar to fetal wound healing biology.
- Exosome-based therapies for alopecia areata: a systematic review of clinical and experimental evidence. PMC12785886 · International Journal of Molecular Sciences · 2025. View at PMC → 40-study systematic review: 50–99% experimental hair coverage improvement; +9 to +31 hairs/cm² clinical density via Wnt/β-catenin activation.
- Skin brightening efficacy of exosomes from adipose-derived stem cells: a split-face, randomized placebo-controlled study. Cosmetics · MDPI · 2020. View → DB-RCT (n=21, ages 39–55): ADSC exosomes significantly reduced melanin index at 4 weeks in hyperpigmented subjects; no adverse effects.
- Adipose MSC-derived exosomes vs platelet-rich plasma for photoaged skin: a non-inferiority trial. PMID 40414798 · Journal of Cosmetic Dermatology · 2025. View at PubMed → Non-inferiority trial: exosomes non-inferior or superior to PRP for photoaging; improved wrinkling, dyschromia, erythema, texture; collagen I increase on histology.
- Hypoxic-preconditioned WJ-MSC spheroid-derived exosomes delivering miR-210 for tissue protection. Stem Cell Research & Therapy · 2024. View → 3D spheroid culture combined with hypoxic preconditioning enriched therapeutic miR-210 cargo; superior protection vs normoxic 2D or 3D culture.
Additional References
- Increased paracrine immunomodulatory potential of MSCs in three-dimensional culture. PMC · 2015. View →
- Three-dimensional culture of MSCs produces exosomes with improved yield and enhanced therapeutic efficacy for AKI. PMC7251891 · 2020. View →
- Comparison of immunosuppressive and angiogenic properties of amnion-derived MSCs between 2D and 3D culture systems. PMC6397962 · 2019. View →
- The secretome from 3D-cultured UC-MSCs counteracts manifestations of rheumatoid arthritis. PMC6370626 · 2019. View →
- 3D spheroid cultures of stem cells and exosome applications for cartilage repair. PMID 35888029 · 2022. View →
- 3D spheroids of placenta-derived MSCs attenuate spinal cord injury in mice. Cell Death & Disease · 2021. View →
- MSC-derived extracellular vesicles for reversing hepatic fibrosis in 3D liver spheroids. PMC11351945 · 2023. View →
- Bioengineered MSC-derived exosomes in skin wound repair and regeneration. PMC10009159 · 2023. View →
- Exosomes from hiPSC-derived MSCs facilitate wound healing by promoting collagen synthesis and angiogenesis. PMID 25638205 · 2015. View →
- Insights into the role of MSCs in cutaneous medical aesthetics: from basics to clinics. PMID 38886773 · 2024. View →
- Clinical applications of exosomes in cosmetic dermatology. PMID 39624733 · 2024. View →
- Exosomes in dermatology: a comprehensive review of current applications, clinical evidence, and future directions. PMID 40533901 · 2025. View →
- Increased MSC functionalization in 3D manufacturing settings for enhanced therapeutic applications. Frontiers in Bioengineering · 2021. View →
- Exosome-based therapies for alopecia areata: systematic review. PMC12785886 · 2025. View →