Biology subjects

Makkar, H.

Publications and source records attributed to Makkar, H..

5 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↗

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

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

Marginal zone and follicular B cells respond differently to TLR4 and TLR9 stimulation

Marginal zone (MZ) B cells are considered to be innate-like immune cells, and follicular (FO) B cells are considered to be adaptive immune B cells. Yet, the proliferative response of MZ and FO B cells to different innate stimuli remains unclear. Here, we investigated cell growth, division, and death to determine the collective proliferative response of MZ and FO B cells in response to innate stimuli, LPS and CpG. We show that the growth rate of FO B cells is higher than that of MZ B cells in response to CpG, though MZ B cells acquire a higher mass at division, whereas both the growth rate and mass at division for MZ and FO B cells remain similar in response to LPS stimulation. We show that MZ B cells divide faster and induce a higher cRel expression in response to both CpG and LPS stimulation than FO B cells. A higher proportion of MZ B cells enter first division in response to LPS stimulation, not in response to CpG stimulation, than FO B cells. Interestingly, CpG stimulation, not LPS stimulation, leads to higher cell death in MZ B cells than FO B cells. In response to LPS stimulation, MZ B cells show a higher cell number at early time and a reduced/ similar cell number at late time, whereas in response to CpG stimulation, MZ B cells show a lower cell number at both early and late time. Our study suggests that LPS and CpG stimulation impact cell growth, division, and death differently, which in turn regulate different proliferative responses of MZ and FO B cells. Thus, our study offers a new perspective that different innate stimuli regulate different features of proliferative responses.

immunology↗