Biology subjects

Vining, K. H.

Publications and source records attributed to Vining, K. H..

11 recordsLinked to original sources

bioRxiv2026

Nuclear confinement from matrix stiffness drives epigenomic reprogramming of gingival fibroblasts

Periodontal disease is characterized by progressive degradation of the gingival extracellular matrix and loss of the physical confinement it imposes on resident stromal cells. In human periodontal tissue, ECM collagen integrity is inversely correlated with facultative nuclear histone acetylation in stromal cells. We hypothesized that matrix stiffness directly coordinates an epigenomic shift in stromal cells. We use a three-dimensional mechanically tunable hydrogel system to independently tune the storage moduli across the mechanical range of healthy and periodontitis-affected gingival tissue. Matrix stiffness drives a genome-wide response in donor-derived human gingival fibroblasts. Matrix-induced confinement leads to an isotropic nuclear geometry and a folded nuclear envelope architecture compared with more permissive, soft matrices. H3K27Ac is suppressed through a stiffness and actomyosin contractility-dependent mechanism. DNMT inhibition in stiff matrices restores the high-acetylation chromatin state with persistent nuclear envelope folding. At the genomic level, stiff matrix confinement drives global CpG methylation gain concentrated at pericentromeric satellite repeats and repeat-dense regions, while collagen synthesis gene promoters and CTCF binding sites are selectively hypomethylated. Non-canonical NF-{kappa}B inflammatory signaling is attenuated through promoter methylation of MAP3K14, and pharmacological NIK inhibition reduces TLR2-stimulated IL-6 secretion in soft-matrix fibroblasts to levels comparable to the stiff condition. These findings identify the gingival ECM as an active epigenomic regulator of stromal inflammatory competence and provide a mechanistic rationale for targeting matrix mechanics to restore stromal homeostasis in periodontitis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/728299v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@131db0borg.highwire.dtl.DTLVardef@23ba0borg.highwire.dtl.DTLVardef@18b67d9org.highwire.dtl.DTLVardef@14ede81_HPS_FORMAT_FIGEXP M_FIG C_FIG The mechanobiological state of human gingival fibroblasts differs between healthy, stiff extracellular matrices and degraded, soft matrices characteristic of periodontal disease. In a healthy environment, stiff matrices impose physical confinement that enforces an isotropic nuclear geometry, driving dense heterochromatin formation, high global CpG methylation, and reduced histone acetylation. Conversely, the loss of mechanical confinement in soft matrices enables cell spreading and an open euchromatin state, fundamentally rewiring the cellular epigenome to promote non-canonical NF-{kappa}B signaling and chronic inflammation.

bioengineering↗

bioRxiv2026

Mechanical licensing of functional dendritic cell states for enhanced T cell priming

The plasticity of dendritic cell (DC) functional state is a major hurdle in DC therapy, yet how DCs acquire distinct states independent of ontogeny remains poorly understood. Here, we demonstrate that changes in matrix stress relaxation mechanically educate DCs to adopt distinct, persistent functional states even after the removal of mechanical cues. Stem cell-derived DCs cultured in a fast-relaxing environment exhibited enhanced antigen presentation, faster migration, and higher expression of T cell-recruiting chemokines. Slow-relaxing DCs, biased towards pro-inflammatory cytokine secretion, were enriched for gene signatures associated with lipid accumulation and stress response. These mechanical responses were conserved across human and murine DCs. Using ovalbumin (OVA) as the model antigen, fast-relaxing DCs elicited a CD8+-biased response in vitro, with higher antigen-specific CD8+ T cell activation and proliferation. In vivo adoptive cell transfer of mechanically educated DCs demonstrated that the fast-relaxing matrix licensed DCs to induce a potent draining lymph node T cell response with more antigen-specific T cells and higher restimulation potential. We further showed that DCs sensed matrix stress relaxation through PI3K signaling and actin branching, mediated by the concerted signaling of IL-4 and GM-CSF. Together, these findings demonstrate the role of matrix stress relaxation on the functional state of DCs and suggest a novel approach to enhance ex vivo cellular engineering by targeting mechanical signaling. Graphical AbstractStem cell-derived dendritic cells (DCs) generated ex vivo are engineered using biomaterial platform with tunable matrix stress relaxation. Mechanical education of DCs is licensed by cytokine signaling, actin branching, and PI3K signaling. Fast-relaxing DCs exhibit higher antigen presentation and faster migration, which enhances their capacity to prime and activate antigen-specific CD8+ T cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/725170v2_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@19c68aaorg.highwire.dtl.DTLVardef@19ba1f0org.highwire.dtl.DTLVardef@a49ea5org.highwire.dtl.DTLVardef@1ab7153_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Unique mineralization pattern revealed in TBCK syndrome mouse model

TBCK syndrome is a severe degenerative leukoencephalopathy with multisystem involvement. Neurodevelopmental, craniofacial, and pulmonary challenges are among the topmost effects on these children. TBCK has been implicated in endo-lysosomal regulation, RNA transport, and mTOR-associated pathways, all of which are critical for the development of mineralized tissue. Although craniofacial abnormalities can be clinically apparent, conventional imaging approaches may overlook subtle defects in mineral quality. Here, we apply our multimodal framework to investigate the mineralization of enamel, dentin, and alveolar bone in a Tbck knockout mouse model. This is the first time our multimodal framework will be applied to a genetic condition. Using micro-computed tomography (microCT), histology, nanoindentation, energy-dispersive spectroscopy, and Raman spectroscopy, we identify tissue- and stage-dependent mineral effects undetected by microCT alone. Tbck loss resulted in differences in enamel and dentin element compositions as early as secretory and transition stages, while mechanical properties remained undetected until maturation stage. Notably, Tbck knockout enamel exhibited reduced calcium and phosphorus content, along with increased carbon content during early mineralization, consistent with the retained organic matrix. Additionally, marked and opposing alterations in magnesium and iron levels began at the secretory stage. Together, these findings define a previously unrecognized mineralization signature associated with TBCK deficiency and establish multimodal hard-tissue analysis as a sensitive approach for detecting early craniofacial phenotypes in rare genetic disorders.

developmental biology↗

bioRxiv2025

Mechanical cues of an interpenetrating polysaccharide matrix regulate self-assembly of collagen fibers

Collagen molecules self-assemble into supramolecular fibers within a molecularly crowded, polysaccharide-rich extracellular matrix (ECM). The ECM typically has fluid-like, viscoelastic properties that can be quantified rheologically. Here, we determine that the viscoelasticity of a polysaccharide alginate ECM regulates the assembly of type I collagen fibers. The viscoelasticity and shear moduli of the alginate network were tuned by the polymer weight percentage and degree of cooperative ionic and covalent norbornene-tetrazine crosslinking. Stepwise shear strain applied to covalently-crosslinked hydrogels generated higher stress than in ionic hydrogels. Hydrogels with reduced viscoelasticity also showed a reduction in water permeability. Second-harmonic generation confocal imaging revealed that decreasing viscoelasticity significantly suppressed collagen fiber self-assembly. Simulations demonstrated a mechanical coupling of the hydrogel network and the aggregate size of collagen molecules. Increased covalent crosslinking impaired the rate and magnitude of self-assembly in simulations and experimental results. These results suggest that ECM viscoelasticity plays a role in modulating the assembly and structural organization of collagen within the matrix. More broadly, they provide a framework for understanding how ECM mechanical properties can influence the assembly and organization of fibrillar macromolecules.

bioengineering↗

bioRxiv2025

Mineralized Tissue-Targeting Expression System for Local Control of Gene Expression

Targeted control of gene expression in mineralized tissue would enable the use of nucleic acids to modulate the local microenvironment at diseased sites, ultimately promoting bone regeneration. Piperazine-linked bisphosphonate ionizable lipids provide a facile approach to targeting the transfection of mineralized tissue with lipid nanoparticles (LNPs). Here, we develop a Mineralized Tissue-Targeting Expression System (MiTEX) using bisphosphonate LNPs to locally target mineralized tissues by adsorption to mineral surfaces and bone graft materials. MiTEX demonstrated a significant increase in the adsorption of RNA onto hydroxyapatite substrates, which retained the ability to transfect bone mesenchymal cells via the adsorbed layer of mRNA LNPs. Bone graft scaffolds functionalized by adsorbed Cre mRNA-LNP were implanted to genetically label newly formed bone tissues in vivo. The surface affinity and adsorption of bisphosphonate lipids provided a local reservoir in mineralized tissues, sustaining the in vivo delivery of MiTEX. Furthermore, the targeted delivery of RNA therapeutics was demonstrated using STAT3 siRNA to modulate gene expression and proinflammatory cytokine release in ex vivo periodontal tissues. The design of this new RNA-functionalized delivery platform will promote the development of precision nucleic acid therapeutics for local anti-inflammatory treatments and bone regeneration at mineralized tissue interfaces.

bioengineering↗

bioRxiv2025

Feeder-free generation of functional dendritic cells from human pluripotent stem cells

The scarcity of primary conventional dendritic cells (cDCs) and the limited effectiveness of monocyte-derived dendritic cells (moDCs) have long hindered progress in human dendritic cell research and immunotherapy. We developed a feeder-free differentiation platform that generates CD1c+CD141+ hPSC-cDCs phenotypically aligned with CD141+ tissue-resident cDC2 subsets found in human tissues. We further optimized the differentiation process using a Design-of-Experiments framework to refine cytokine and serum conditions, enhancing differentiation efficiency while reducing cytokine demand. These hPSC-cDCs exhibit efficient antigen uptake, defined cytokine responses, and robust priming of antigen-specific CD8+ T cell proliferation and effector differentiation, outperforming moDCs in direct comparison. Together, this work establishes a robust, and generalizable platform for mechanistic studies and translational development of dendritic cell-based vaccines and standardized ex vivo T cell expansion.

immunology↗

bioRxiv2025

Matrix Stiffness Governs Fibroblast-Driven Immune Homeostasis in Gingival Tissues

Periodontal disease is associated with inflamed gingival tissues and degradation of the gingival extracellular matrix (ECM), yet the role of mechanical cues is poorly understood. Gingival ECM in periodontal disease showed a loss of fibrillar collagen compared to healthy samples. We hypothesized that ECM softening in periodontal disease contributes to inflammation due to dysregulated gingival fibroblasts (GFs). A mechanically tunable hydrogel model of the gingival ECM was developed to investigate the mechano-immune crosstalk. Stiff collagen-alginate hydrogels matched the rheological properties of gingival biopsies. Human donor GFs encapsulated in these stiff hydrogels showed significantly suppressed toll-like receptor inflammatory responses compared to soft. Stiffness-dependent inflammatory responses of GFs were directed by the non-canonical NF{kappa}B pathway and epigenetic nuclear organization. The direct impact of mechanical cues on immune responses was investigated with human donor cells ex vivo by co-culture of human GFs with myeloid cells and in human gingival explants. Myeloid progenitors co-cultured with GFs in stiff hydrogels differentiated into immunomodulatory dendritic cells. Ex vivo crosslinking of human gingival tissue increased stiffness and reduced inflammatory cytokines. Gingival mechano-immune regulation provides a new avenue for biomaterials-based treatments in periodontitis.

bioengineering↗

bioRxiv2025

Modeling tumor transport and growth with poroelastic biopolymer networks

The mechanical properties of the extracellular matrix (ECM) regulate tumor growth and invasion in the tumor microenvironment. Models of biopolymer networks have been used to investigate the impact of elasticity and viscoelasticity of ECM on tumor behavior. Under tumor compression, these networks also show poroelastic behavior that is governed by the resistance to water flow through their pores. This work investigates the hypothesis that poroelastic properties regulate tumor growth. Here, alginate hydrogels with tunable ionic and hybrid ionic/covalent crosslinking are used as a model biopolymer system. Hydrogel stiffness, viscoelasticity, and stress relaxation behavior were characterized using stepwise axial compression. Among these properties, we find poroelastic fluid outflow dominates ECM stress relaxation, as the measured water flux was significantly affected under compression. Continuum mechanics-based modeling was developed to formulate and calculate the chemical potential gradients of water (solvent) in the hydrogels under compression. This framework was extended into an advection-diffusion framework to quantify growth factor (solute) distribution under varying strengths of stress and diffusion indexed by the relative strength of convective to diffusive transport, characterized by the Peclet number. An agent-based computational simulation showed that tumor growth was affected by Peclet number. Together, these results highlight the role of the poroelastic properties of ECM on water flux and transport in the tumor microenvironment.

biophysics↗

bioRxiv2025

Human progenitor T-cell differentiation regulated by the mechanical resistance of thymus-mimetic extracellular matrices

Therapeutic T-cell engineering ex vivo from human hematopoietic stem cells (HSCs) focuses on recapitulating notch1-signaling and 4{beta}1-integrin-mediated adhesion within the thymic niche with supportive stromal cell feeder-layers or surface-immobilized recombinant protein-based engineered thymic niches (ETNs). The relevant Notch1-DLL-4 and 4{beta}1-integrin-VCAM-1 interactions are known to respond to mechanical forces that regulate their bond dissociation behaviors and downstream signal transduction, yet manipulating the mechanosensitive features of these key receptor-ligand interactions in thymopoiesis has been largely ignored in current ETN designs. Here, we demonstrate that human T-cell development from cord blood-derived CD34+ HSCs is regulated via molecular cooperativity in notch1 and integrin-mediated mechanotransduction. Mechanically confining interpenetrating network (IPN) hydrogel-based 3D cell culture comprised of collagen type I and alginate polysaccharides functionalized with DLL-4 and VCAM-1 is used as a model viscoelastic 3D ETN to manipulate human progenitor (pro)T-cell differentiation. This ETN enables orthogonal control of the mechanical and biomolecular features of the thymic niche, including thymopoietic ligand density, modulus, and viscoelastic properties (e.g., stress relaxation kinetics). We identify that soft, viscous matrices that enhance activation of the notch1-pathway, and subsequently notch1 intracellular domain (NICD) nuclear import sustain the T-cell development gene regulatory network during proT-cell differentiation. Conversely, stiff, elastic matrices inhibit HSC commitment to the T-lineage, and rather promotes Myeloid-cell differentiation. Our observations indicate mechanical reciprocity in signaling pathways indispensable to thymopoiesis, and highlights extracellular matrix mechanics as a variable in controlling hematopoietic stem cell fate decisions.

bioengineering↗

bioRxiv2025

Biocompatible Multi-functional Polymeric Material for Mineralized Tissue Adhesion

This study developed a biocompatible multifunctional thiol-ene resin system for adhesion to dentin mineralized tissue. Adhesive resins maintain the strength and longevity of dental composite restorations through chemophysical bonding to exposed dentin surfaces after cavity preparations. Dental pulp cells are exposed to residual monomers transported through dentinal tubules. Monomers of conventional adhesive systems may result in inhomogeneous polymer networks and the release of residual monomers that cause cytotoxicity. In this study, we develop a one-step multi-functional polymeric resin system by incorporating trimethylolpropane triacrylate (TMPTA) and bis[2-(methacryloyloxy)ethyl] phosphate (BMEP) to enhance both mechanical properties and adhesion to dentin. Molecular dynamics simulations identified an optimal triacylate:trithiol ratio of 2.5:1, which was consistent with rheological and mechanical tests that yielded a storage modulus of ~30 MPa with or without BMEP. Shear bond tests demonstrated that the addition of BMEP significantly improved dentin adhesion, achieving a shear bond strength of 10.8 MPa, comparable to the commercial primer Clearfil SE Bond. Nanoindentation modulus mapping characterized the hybrid layer and mechanical gradient of the adhesive resin system. Further, the triacrylate-BMEP resin showed biocompatibility with fibroblasts in vitro. These findings suggest the triacrylate-trithiol crosslinking and chemophysical bonding of BMEP provide enhanced bond strength and biocompatibility for dental applications.

bioengineering↗

bioRxiv2024

Multi-modal characterization of rodent tooth development

Craniofacial tissues undergo hard tissue development through mineralization and changes in physicochemical properties. This study investigates the mechanical and chemical properties of developing enamel, dentin, and bone in the mouse mandible. We employ a multi-modal, multi-scale analysis of the developing incisor and first molar at postnatal day 12 by integrating micro-computed tomography (microCT), nanoindentation (NI), energy dispersive spectroscopy (EDS), and Raman spectroscopy. Our findings demonstrate distinct patterns of mechanical, elemental, and chemical changes across mineralized tissues. These results suggest that mineral composition drives mechanical properties across different craniofacial hard tissues. Integrating multi-modal characterization of mineralized tissues opens new opportunities for investigating structure-function relationships in craniofacial biology and genetics.

developmental biology↗