Biology subjects

Kim, J. H.

Publications and source records attributed to Kim, J. H..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Initial Condition Decision to Ensure Reliable Circadian Phase Estimation with Shorter-Term Wearable Data

Various studies in the medical field highlight the importance of circadian medicine, which optimizes treatment timing based on patients circadian phases. While the circadian phase has been measured using dim light melatonin onset (DLMO), the gold standard marker, its high cost and time-intensive nature have led to the development of alternative estimation methods. Among these, the most promising method is using ordinary differential equation (ODE) models, which simulate the circadian rhythm by using a light exposure profile estimated from sleep data. These ODE models require an initial condition (IC) representing the initial state of the circadian rhythm, which is unknown in real-world settings. However, it is unclear how the uncertainty of IC affects the accuracy of circadian phase estimation. In this study, by using sleep data collected from 28 shift workers using ActiWatch (mean duration = 56 days, range = 34-75 days), we found that [≥]18 days of sleep data are required for the circadian phase to become independent of the subjective IC choice. The result showed that without an accurate IC, circadian phase estimation is dependent on subjective IC choice, meaning that circadian phase estimates in the first 17 days are not reliable. Indeed, these days were reduced to 13 - 15 days on average when previous studies IC estimation methods were used. To further shorten this length, we developed new IC estimation methods--period- and work history-based sleep methods--that incorporate daily variations in sleep history. Notably, the new methods reduced the number of days required for reliable circadian phase estimation to about seven days. Hence, our approach allows a larger portion of circadian phase estimates from given sleep data to be used as reliable information. The superiority of our methods paves the way for improved circadian phase estimation, ultimately enhancing the practicality of chronotherapy applications.

bioinformatics↗

bioRxiv2025

Discrete interneuron subsets participate in GluN1/GluN3A excitatory glycine receptor (eGlyR)-mediated regulation of hippocampal network activity throughout development and evolution.

Decades of studies implicating GluN3A N-methyl-D-aspartate receptor (NMDAR) subunits in physiological and pathological function have largely been interpreted through direct regulation of conventional glutamatergic NMDARs. However, emerging evidence indicates that GluN3A frequently assembles with GluN1 forming unconventional glutamate-insensitive NMDARs that operate as native excitatory glycine receptors (eGlyRs). Here we demonstrate that hippocampal somatostatin and neurogliaform interneurons (Sst-INs and NGFCs) express functional eGlyRs from early postnatal through adult ages. In the developing hippocampus eGlyR-mediated excitation of NGFCs with ambient glycine dramatically increases GABAergic tone, with consequences for the generation of giant depolarizing potentials (GDPs). In the mature hippocampus, eGlyR- mediated excitation of Sst-INs regulates sharp wave ripples (SWRs). Finally, we reveal evolutionary conservation of hippocampal Sst-IN eGlyRs and eGlyR- mediated SWR regulation in non-human primates confirming functional eGlyR availability for therapeutic potential in higher species. Our findings underscore that eGlyR mediated regulation of cell and circuit excitability through both cell autonomous and cell non-autonomous mechanisms must be considered to understand GluN3A roles in brain development, plasticity, and disease.

neuroscience↗

bioRxiv2025

VEGFR2 blockade overcomes acquired KRAS G12D inhibitor resistance driven by PI3Kγ activation

KRAS G12D mutation is a key oncogenic driver in many solid tumors, including pancreatic, gastric, and colorectal cancers. While recent studies have characterized features associated with primary and acquired resistance to KRAS inhibitors, strategies to overcome such resistance, particularly in the context of gastrointestinal cancers, remain underexplored. Here, we have generated nine human gastrointestinal cancer models, including three patient-derived organoids (PDOs), with acquired resistance to the KRAS G12D-selective inhibitor MRTX1133. Using single-cell RNA sequencing analysis, we identified the enrichment of angiogenesis, hypoxia, and epithelial-to-mesenchymal transition (EMT) signatures in the resistant model compared to the parental PDO. Across all resistant models, VEGFA expression and VEGFR2 phosphorylation were uniformly elevated, which were driven by AKT activation and SP1 nuclear translocation. Mechanistic investigations uncovered increased PI3K{gamma} activity in MRTX1133-resistant models via complex formation of KRAS with p110{gamma} and p101. This leads to an autocrine VEGFA-VEGFR2 signaling loop formation and EMT induction. Therapeutically, the disruption of VEGFA-VEGFR2 signaling restored MRTX1133 sensitivity and inhibited EMT. Furthermore, cancer-endothelial paracrine signaling amplified angiogenesis, hypoxia, and EMT signatures in cancer cells and simultaneously promoted endothelial cell proliferation, reinforcing an adaptive feedback mechanism. In a mouse model of MRTX1133-resistant tumor xenograft, a combination of anti-VEGFR2 therapy and MRTX1133 more effectively reduced tumor growth, angiogenesis, and proliferation markers than monotherapy without significant body weight change. These findings establish VEGFA-VEGFR2 signaling by PI3K{gamma} activation as a key driver of acquired resistance to KRAS G12D inhibition and provide a rationale for combining VEGFA-VEGFR2 inhibition with KRAS blockade in KRAS-mutant cancers. HighlightO_LIVEGFA-VEGFR2 signaling activation is a common feature of MRTX1133 resistance in KRASG12D cancer cells C_LIO_LINuclear translocation of SP1 by AKT activation promotes VEGFA transcription in MRTX1133-resistant models C_LIO_LIInteraction of p110{gamma}-p101 with KRAS activates PI3K{gamma} in the resistant models C_LIO_LIVEGFA-VEGFR2 inhibition reverses MRTX1133 resistance in vitro and in vivo C_LI

cancer biology↗

bioRxiv2025

Regulatory T cells epigenetically reprogrammed from autoreactive effector T cells mitigate established autoimmunity

Reprogramming autoreactive CD4+ effector T (Teff) cells into immunosuppressive regulatory T (Treg) cells represents a promising strategy for treating established autoimmune diseases. However, the stability and function of such reprogrammed Tregs under inflammatory conditions remain unclear. Here, we show that demethylation of core Treg identity genes in Teff cells yields lineage-stable Effector T cell Reprogrammed Tregs (ER-Tregs). A single adoptive transfer of ER-Tregs not only prevents autoimmune neuroinflammation in mice when given before disease onset but also arrests its progression when administered after onset. Compared to Foxp3-overexpressing Teff cells, induced Tregs from naive precursors, and endogenous Tregs, ER-Tregs provide superior protection against autoimmune neuroinflammation. This enhanced efficacy stems from their inherited autoantigen specificity and selectively preserved effector-cell transcriptional programs, which together bolster their fitness in inflammatory environments and enhance their suppressive capacity. Our results establish epigenetic reprogramming of autoreactive Teff cells as an effective approach to generate potent, stable Tregs for the treatment of refractory autoimmune conditions.

immunology↗

bioRxiv2025

A single extracellular vesicle-based platform supporting both RBD protein and mRNA vaccination against SARS-CoV-2

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syn-drome coronavirus 2 (SARS-CoV-2) has highlighted the need for novel, effective, and safe vaccine platforms. Extracellular vesicles (EVs) facilitate cell-to-cell communication and can modulate immune responses by delivering antigens. Here, we propose a versatile EV-based vaccine plat-form in which immune-stimulating EVs, engineered using acoustic shock waves (SW), are used to deliver either protein or mRNA antigens. Immunostimulatory EVs derived from LPS-activated THP-1 monocytes (aTEVs) were loaded with SARS-CoV-2 receptor-binding domain (RBD) protein or RBD-encoding mRNA via SW post-loading. Both aTEV-RBD-Pro and aTEV-RBD-mRNA elicited robust RBD-specific humoral and cellular immune responses in mice without the need for external adjuvants. Moreover, lyophilized aTEV-RBD-Pro vaccines retained immunogenicity after storage, supporting their chain-independent stability. These results demonstrate that a single EV-based platform can independently support both protein- and mRNA-based vaccination, highlighting its flexibility for next-generation vaccine development.

immunology↗

bioRxiv2025

Downregulation of LATS1/2 Drives Endothelial Senescence-Associated Stemness (SAS) and Atherothrombotic Lesion Formation

BackgroundAtherothrombosis, the main event leading to acute coronary syndrome (ACS), is strongly linked to disturbed blood flow (d-flow) regions. Although the involvement of the Hippo pathway and its kinases Large Tumor Suppressor Kinase 1and 2 (LATS 1 and 2) in mechanical stress responses is known, the mechanisms by which d-flow simultaneously induces senescence, proliferation, and atherothrombosis remain unclear. MethodsThe role of endothelial cells (EC)-specific LATS1/2 was examined using EC specific knock-out (EKO) mice in a partial left carotid ligation (PLCL) model. Plaque spatial multi-omics analysis was performed by integrating imaging mass cytometry, sequential immunofluorescence (COMET), and spatial metabolomics at the single-cell level in human and mouse atherosclerotic plaques. ResultsIn tamoxifen-inducible Lats1homo(-/-) /Lats2 homo(-/-) EC-specific knockout (EKO) mice, deletion of LATS1/2 induced by tamoxifen led to fatal outcomes, characterized by severe systemic edema and markedly increased vascular permeability. In contrast, Lats1het(+/-)/Lats2 homo(-/-)-EKO mice survived and developed atherothrombotic plaques exhibiting neovascularization even without further additional dietary or genetic intervention. Spatial proteomics analysis revealed that LATS1/2 depletion in ECs triggered a senescence-associated stemness (SAS) phenotype, primarily driven by CD38 upregulation. Complementary spatial metabolomics profiling demonstrated a significant increase in sulfite and taurine within LATS1/2-deficient plaques, indicating lowered sulfite oxidase (SUOX) activity. Mechanistically, CD38 upregulation was found to suppress SUOX expression, induce the reverse mode of mitochondrial complex V, and increase succinate dehydrogenase (SDH) activity along with ATP consumption. Paradoxically, despite ATP depletion, this metabolic disturbance enhanced glutamate metabolism and the tricarboxylic acid (TCA) cycle, sustaining EC proliferation under energetically stressed conditions. The combined effect of LATS1/2 deletion and CD38 activation established a unique EC phenotype defined by increased SAS, leading to proliferation, senescence, and eventual cell death. These pathological processes culminated in the formation of atherothrombotic plaques, which were attenuated by inhibition of CD38. Notably, a similar phenotype--marked by metabolically active ECs--was observed in human atherothrombotic plaques, suggesting translational relevance. ConclusionLoss of LATS1/2 in ECs induces SAS state that promotes excessive EC proliferation, senescent cell accumulation, and the development of structurally fragile, leaky neo vessels--hallmarks of atherothrombotic lesions. CD38-mediated SUOX deficiency further amplifies this pathological process by inducing mitochondrial dysfunction, depleting ATP, and triggering compensatory upregulation of glutamate and TCA cycle metabolism. These findings identify a novel LATS1/2-CD38-SUOX axis in ECs that orchestrates SAS-driven atherothrombosis. Targeting CD38 may represent a promising therapeutic strategy to mitigate vascular dysfunction and plaque instability in high-risk ACS patients. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/660635v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@149d313org.highwire.dtl.DTLVardef@1c0988borg.highwire.dtl.DTLVardef@15efec9org.highwire.dtl.DTLVardef@1a96e03_HPS_FORMAT_FIGEXP M_FIG C_FIG Under normal physiological conditions, LATS1/2 and Lamin A work together to suppress CD38 expression. Lamin A binds directly to the CD38 promoter to repress transcription, and LATS1/2 interact with Lamin A to reinforce this suppression. This collaboration helps maintain low CD38 activity and preserves cellular NAD levels. However, under disturbed flow (d-flow), both LATS1/2 and Lamin A are downregulated. The loss of this dual repression leads to increased CD38 NADase expression. Elevated CD38 accelerates NAD consumption, causing NAD depletion--a hallmark of cellular senescence. Reduced NAD disrupts key metabolic and stress-response pathways, contributing to the onset of the senescent state. At the same time, CD38 suppresses sulfite oxidase (SUOX), leading to sulfite accumulation and mitochondrial redox imbalance. This shift activates the reverse mode of mitochondrial Complex V, which decreases ATP production and increases mitochondrial ROS, intensifying metabolic and oxidative stress in endothelial cells (ECs). In response, ECs compensate by upregulating succinate dehydrogenase (SDH), enhancing TCA cycle activity and glutamate metabolism. This metabolic adaptation provides the biosynthetic building blocks needed for cell growth and proliferation. As a result, ECs adopt a paradoxical phenotype: they show classical features of stress-induced senescence (such as NAD depletion, oxidative stress, and cell cycle arrest signals), while simultaneously undergoing metabolic activation and proliferation, also mediated by YAP. This defines a non-canonical endothelial program known as senescence-associated stemness (SAS), characterized by the formation of abnormal, proliferative, yet fragile neovessels. These dysfunctional vessels contribute to atherothrombosis, setting this process apart from the more stable lesions typical of conventional atherosclerosis.

molecular biology↗

bioRxiv2025

Agent-based computational modeling of the stochastic dynamic behavior of actin filaments recapitulates the homeostatic cortical array in plant epidermal cells

The homeostatic cortical actin array in plant cells plays important roles in fundamental processes, including intracellular transport, secretion, cell expansion, and cytoplasmic streaming. In response to diverse chemical and mechanical signals, the cortical array can remodel within minutes to assume new configurations or altered filament abundance. The homeostatic cortical actin array of some plant epidermal cells comprise sparsely distributed individual actin filaments and actin bundles, which enables tracking and quantitative analysis of dynamic properties over many minutes at high spatiotemporal resolution. Previous studies using quantitative live-cell imaging, small molecule inhibitors, and genetic mutations reveal the robust dynamic steady state of the cortical actin array, with individual filaments showing a behavior termed stochastic dynamics. Compared to experimental findings, computational efforts focused on the plant actin cytoskeleton are lacking, although computational models have the potential to define underlying mechanisms of actin array homeostasis and remodeling. Here, we used an agent-based computational model to reproduce the stochastic dynamic behavior of individual actin filaments in epidermal cells with consideration of key governing factors, including the nucleation, polymerization, depolymerization, severing, capping, and branching of filaments. Our model was able to reproduce experimental observations with respect to the abundance and length of filaments as well as the rates or frequencies of dynamic events. This model can be used to study the role of myosin motors and other actin-binding proteins, as well as the effects of signaling events and fluxes in cellular second messengers, on actin dynamics in plant cells.

plant biology↗

bioRxiv2025

Genotypic Characterization of Virulence and Antibiotic-Heavy Metal Resistance in Enterococcus Strains from Vladivostoks Water Bodies

1.BackgroundEnterococcus species are Gram-positive, facultative anaerobic bacteria commonly found in soil, water, and the gastrointestinal tracts of humans and animals. Their ability to acquire antibiotic resistance has made them significant opportunistic pathogens in both clinical and environmental settings. The presence of antibiotic-resistant Enterococcus strains in aquatic environments reflects contamination from human activities and poses a potential risk of horizontal gene transfer to other bacterial species. AimsThis study aims to assess the antibiotic and heavy metal resistance patterns of Enterococcus strains isolated from water bodies in Vladivostok and evaluate their potential environmental risks. Study designExperimental study. MethodsWater samples were collected from the Vtoraya Rechka River and Zolotoy Rog Bay in Vladivostok. 30 enterococcus strains were identified by polymerase chain reaction (PCR) technique. The presence of antibiotic and heavy metal resistance genes was determined using specific primers. ResultsGenetic analysis of the isolated Enterococcus strains revealed that 23% of strains carried the tetL gene, 33% harbored the ermB gene, and the heavy metal resistance genes tcrB and cadA were detected in 40% and 27% of strains, respectively. Notably, the ermB and tcrB genes co-occurred in 13.3% of strains, while none of the tetL-positive strains exhibited simultaneous presence of ermB, tcrB, and cadA. ConclusionEnterococcus strains isolated from Vladivostoks water bodies exhibit resistance to multiple antibiotics and heavy metals, with a notable co-occurrence of copper and antibiotic resistance genes. These findings contribute to understanding microbial contamination in aquatic environments and its public health implications, providing valuable insights for future research in clinical and environmental microbiology. 2. IMPORTANCEThe dissemination of antibiotic and heavy metal resistance genes in environmental reservoirs poses a serious public health threat, as these genes may be transferred to clinically relevant pathogens. Enterococcus species, widely present in aquatic ecosystems, serve as both reservoirs and indicators of such resistance. This study identifies patterns of co-occurrence among resistance genes and highlights a potential genetic linkage between macrolide (ermB) and copper (tcrB) resistance in environmental Enterococcus strains. Notably, none of the tetL-positive strains carried all three of ermB, tcrB, and cadA, suggesting a mutually exclusive distribution pattern and a potentially distinct mechanism of acquisition for tetL. These findings reveal novel gene distribution dynamics in environmental Enterococcus populations and underscore the importance of integrated surveillance of antimicrobial and metal resistance in human-impacted ecosystems.

microbiology↗

bioRxiv2025

Data-driven feedback augments ultrasound nanotheranostics in brain tumors

The blood-brain barrier (BBB) renders the delivery of nanomedicine in the brain ineffective and the detection of circulating disease-related DNA from the brain unreliable. Here, we show that the acoustic emission content of focused ultrasound-controlled microbubble dynamics (MB-FUS) incorporates precursor signals that allow large-data models to predict sonication regimens for safe and effective BBB opening. Crucially, closed-loop MB-FUS controller augmented by machine learning (ML-CL) expands the treatment window (4-fold), as compared to conventional controllers, by persistently and proactively maximizing the BBB permeability while preventing tissue damage. By successfully scaling up from mice to rats and from healthy to diseased brains (glioma), ML-CL rendered the BBB permeable to large nanoparticles and markedly improved the release and detection of tumor DNA in plasma. Together, our findings reveal the potential of data-driven feedback to support the development of next-generation AI-powered ultrasound systems for safe, robust, and efficient nanotheranostic targeting of brain diseases.

bioengineering↗

bioRxiv2025

Resolving the molecular niche of pulmonary fibrosis using cryopreserved human precision cut lung slices

Background and methodsPulmonary fibrosis (PF) manifests locally and heterogeneously in the diseased lung. To uncover mechanistic underpinnings, we have utilized cryopreserved fibrotic human precision-cut lung slices (PCLS), and using single-cell spatial transcriptomics, mapped and interpreted the transcriptomic regulation of effector cell types/states. ResultsCryopreserved-thawed fibrotic human PCLS retained canonical molecular and cellular PF hallmarks including fibroblast and myofibroblast accumulation, epithelial depletion, and vascular remodeling. Notably, these cellular changes were spatially co-incident with 1) collagen-rich regions enriched for extracellular matrix (ECM)-related genes (e.g., COL1A1, SPARC), 2) expanded fibroblast-endothelial crosstalk with enhanced chemokine signaling (CXCL12- CXCR4), 3) integrin-driven mesenchymal signaling targets (ANGPTL-integrin), 4) stress-adapted and immune-interacting Alveolar Type 2 cells with impaired surfactant gene expression, and 5) endothelial reprogramming toward a contractile and profibrotic phenotype. At the transcriptomic level, the spatially-defined fibrotic niche was characterized by increased gene expression related to immune responses (IGKC and IGHG1), fibrosis (collagen, fibronectin, and DCN), mechanotransduction (MYH11, TPM2, ACTG2, ACTA2), immune cell recruitment (CCL2, IL6, ICAM1), ECM remodeling (e.g. thrombospondin 1, THBS1), and decreased gene expression related to surfactant production (SFTPB, SFTPC). At the functional level, the fibrotic niches were defined by the activation of three fibroblast mediating signaling pathways: (1) the matricellular glycoprotein, SPARC, (2) Relaxin signaling, and (3) multiple immunoglobulin transcripts, including IGHA1, IGHG1, IGHG3, and IGKC. ConclusionsWe verify model fidelity, identify both known and unanticipated pro-fibrotic genes, and advocate for the expanded use of spatial transcriptomic measurements using cryopreserved human PCLS for disease modeling and drug discovery.

genomics↗

bioRxiv2025

YPEL controls synapse development through p62-Nrf2 antioxidant pathway in Drosophila neuromuscular junction

The Yippee-like (YPEL) genes are highly conserved among all eukaryotic species, yet the molecular and cellular pathways that YPEL regulate are poorly understood. Human and animal studies suggest that YPEL is involved in nervous system functions. Here we report that YPEL is necessary for synapse development in neuromuscular junction and motor functions in Drosophila. YPEL interacts with the Drosophila p62, Refractory to sigma P, which forms cytoplasmic proteinaceous bodies for selective autophagy and signaling. YPEL overexpression decreased p62 bodies, while increased p62 bodies were observed in YPEL mutant neurons. Suppressing p62 bodies by reducing p62 gene dosage significantly alleviated both synaptic and locomotion defects in YPEL mutants, suggesting that YPEL acts through p62 for synapse development. On the other hand, suppressing p62 bodies via autophagy did not restore synapse development in YPEL mutants. Interestingly, reduced levels of reactive oxygen species were found in YPEL mutants, which is consistent with the role of p62 in promoting the nuclear factor erythroid 2-related factor 2 (Nrf2) antioxidant pathway. Overexpressing Drosophila Nrf2, Cap n collar (Cnc), phenocopied the synaptic and locomotion deficits in YPEL mutants. Importantly, both synaptic and locomotion defects were completely rescued by knocking down Cnc in YPEL mutant motor neurons. Taken together, our study demonstrates that YPEL negatively controls p62 - Nrf2 antioxidant pathway for neuromuscular synapse development and locomotion.

neuroscience↗

bioRxiv2025

Mosaic H3K9me3 at BREACHes predicts synaptic gene expression associated with fragile X syndrome cognitive severity

Diseases vary in clinical presentation across individuals despite the same molecular diagnosis. In fragile X syndrome (FXS), mutation-length expansion of a CGG short tandem repeat (STR) in FMR1 causes reduced gene expression and FMRP loss. Nevertheless, FMR1 and FMRP are limited predictors of adaptive functioning and cognition in FXS patients, suggesting that molecular correlates of clinical measures would add diagnostic value. We recently uncovered Megabase-scale domains of heterochromatin (BREACHes) in FXS patient-derived iPSCs. Here, we identify BREACHes in FXS brain tissue (N=4) and absent from sex/age-matched neurotypical controls (N=4). BREACHes span >250 genes and exhibit patient-specific H3K9me3 variation. Using N=4 FXS iPSC lines and N=7 single-cell isogenic FXS iPSC subclones, we observe a strong correlation between inter-sample H3K9me3 variation and heterogeneous BREACH gene repression. We demonstrate improved prediction of cognitive metrics in FXS patients with an additive model of blood FMRP and mRNA levels of H3K9me3-mosaic, but not H3K9me3-invariant, BREACH genes. Our results highlight the utility of H3K9me3 variation at BREACHes for identifying genes associated with FXS clinical metrics.

genomics↗

bioRxiv2025

Phytoplankton recruitment of specific microbial assemblages and phylosymbiotic patterns

Phytoplankton and bacteria represent two major pillars of the carbon cycle in marine ecosystems. While their interactions are known to be tightly linked, the specific mechanisms underlying these interactions remain largely unexplored. Evidence of host-specific microbial assemblages could serve as a foundation for studies of detailed host-microbe interactions, yet such research remains limited in phytoplankton. Here, we not only investigate the microbial assemblages of six phytoplankton species, including multiple strains of dinoflagellates and diatoms, but also samples of phytoplankton blooms from the field. Our results reveal the presence of host-specific microbial assemblages in phytoplankton, with members of the core microbial lineages (MCGs) playing pivotal roles in shaping host-specific microbial assemblages and contributing to network structures. Deterministic processes, particularly host genotypes, were the dominant factors shaping microbial assemblages, overriding environmental influences. Consequently, microbial composition reflected the evolutionary relationships of the host species, demonstrating phylosymbiotic patterns. These findings suggest that studying MCGs will be a crucial foundation for investigating specific phytoplankton-microbe interactions and highlight the ecological and evolutionary importance of host-microbial specificity in phytoplankton.

ecology↗

bioRxiv2025

RNA sequencing reveals key factors modulating TNFa-stimulated odontoblast-like differentiation of dental pulp stem cells

Inflammation is a complex host response to harmful infections or injuries, playing both beneficial and detrimental roles in tissue regeneration. Notably, clinical dentinogenesis associated with caries development occurs within an inflammatory environment. Reparative dentinogenesis is closely linked to intense inflammation, which triggers the recruitment and differentiation of dental pulp stem cells (DPSCs) into the dentin lineage. Understanding how inflammatory responses influence DPSCs is essential for elucidating the mechanisms underlying dentin and pulp regeneration. Given the limited data on this process, a broad approach is employed here to gain a deeper understanding of the complex mechanisms involved and to identify downstream signaling targets. This study aims to investigate the role of inflammation and the complement receptor C5L2 in the odontoblastic differentiation of DPSCs and the associated transcriptomic changes using poly-A RNA sequencing (RNA-seq). RNA-seq techniques provide insight into the transcriptome of a cell, offering higher coverage and greater resolution of its dynamic nature. Following inflammatory stimulation, DPSCs exhibit significantly altered gene profiles, including marked upregulation of key odontogenic genes, highlighting the critical role of inflammation in dentinogenesis. We demonstrate that TNF-treated odontoblast-like differentiating DPSCs, under C5L2 modulation, exhibit significant differential gene expression and transcriptomic changes. The data presented may provide new avenues for experimental approaches to uncover pathways in dentinogenesis by identifying specific transcription factors and gene profiles.

bioinformatics↗

bioRxiv2025

The N-terminal order-disorder transition is a critical determinant for a metamorphosis of IscU

IscU, a key scaffold protein mediating the biogenesis of iron-sulfur (Fe-S) clusters, exhibits metamorphic characteristics crucial for its versatile and efficient function. Previous studies have demonstrated that IscU has two interconverting conformations: the structured state (S-state) and the disordered state (D-state), each contributing to its distinct functionality and interaction network. Despite its physiological importance, the precise mechanism underpinning the maintenance of IscUs unique structural heterogeneity has remained elusive. In this study, we used computational and experimental approaches to reveal that the N-terminal order-disorder plays a critical role in the metamorphic modulation of IscU. We found that the N-terminal region displays greater structural plasticity, which is linked to other regions of IscU through coevolutionary relationships. Moreover, we demonstrated that the degree of orderliness in the N-terminal region correlates positively with the stabilization of IscUs S-state and negatively with its affinity for HscA. This indicates that the flexibility in the N-terminal region is finely tuned to optimize IscUs physiological efficiency and efficacy. Finally, our data suggest that a peptide mimicking the N-terminal motif can modulate IscUs metamorphic properties, suggesting a novel therapeutic potential for related pathogenic processes.

biochemistry↗

bioRxiv2024

CRISPR-Edited DPSCs, Constitutively Expressing BDNF Enhance Dentin Regeneration in Injured Teeth

Dental caries, a prevalent global health issue, results from complex bacterial interactions. In response to harmful stimuli, a desirable outcome for the tooth is the formation of tertiary dentin, a protective reparative process that generates new hard tissue. This reparative dentinogenesis is associated with significant inflammation, which triggers the recruitment and differentiation of dental pulp stem cells (DPSCs). Previously, we have demonstrated that brain-derived neurotrophic factor (BDNF) and its receptor TrkB, key mediators of neural functions, are activated during the DPSC-mediated dentin regeneration process. In this study, we further define the role of inflammation in this process and apply stem cell engineering to enhance dentin regeneration in injured teeth. Our data show that TrkB expression and activation in DPSCs rapidly increase during odontogenic differentiation, further amplified by inflammatory inducers and mediators such as TNF, LTA, and LPS. An in vivo dentin formation assessment was conducted using a mouse pulp-capping/caries model, where CRISPR-engineered DPSCs overexpressing BDNF were transplanted into inflamed pulp tissue. This transplantation significantly enhanced dentin regeneration in injured teeth. To further explore potential downstream pathways, we conducted transcriptomic profiling of TNF-treated DPSCs, both with and without TrkB antagonist CTX-B. The results revealed significant changes in gene expression related to immune response, cytokine signaling, and extracellular matrix interactions. Taken together, our study advances our understanding of the role of BDNF in dental tissue engineering using DPSCs and identifies potential therapeutic avenues for improving dental tissue repair and regeneration strategies.

bioengineering↗

bioRxiv2024

Multi-omic profiling identifies malignant subpopulations and a hypoxia-driven angiogenic axis as therapeutic vulnerabilities in sinonasal squamous cell carcinoma

Sinonasal squamous cell carcinoma (SNSCC) is a rare and aggressive malignancy with limited treatment options, necessitating comprehensive molecular characterization to uncover actionable therapeutic targets. Here, we integrate bulk and single-cell transcriptomics, epigenomics, and DNA methylation profiling to construct a detailed molecular and cellular landscape of SNSCC. Our analysis identifies five transcriptionally and epigenetically distinct malignant subpopulations, including hypoxic (TC1) and proliferative (TC2) clusters, with TC1 showing significant association with poor clinical outcomes. We uncover a hypoxia-driven angiogenic axis, wherein TC1 cells secrete adrenomedullin (ADM), MIF, and VEGFA to activate endothelial tip cells, fostering tumor angiogenesis. Epigenetic reprogramming, characterized by alterations in DNA methylation and chromatin accessibility, underpins these transcriptional programs, with AP-1 transcription factors emerging as key regulators. Notably, ADM expression is epigenetically controlled, correlates with advanced clinical stage, and predicts reduced survival in head and neck cancer patients. This multi-omic study highlights the tumor heterogeneity and microenvironmental interactions driving SNSCC progression, revealing epigenetically regulated pathways as promising therapeutic targets for future intervention.

cancer biology↗

bioRxiv2024

Adherent-suspension plasticity promotes the dissemination and colonization of circulating tumor cells

Cell competition within the primary tumor drives tumor growth by promoting the uncontrolled proliferation of winner cells and eliminating loser cells by sensing cell fitness. However, the mechanism of how cell competition confers the loser cells with the metastatic potential of circulating tumor cells (CTCs) to transit between dissemination and colonization remains elusive. Here we found cell competition gives rise to less fit but viable cells that transformed into CTCs via adherent-to-suspension transition (AST) mechanisms. The induction of hematopoietic transcription factors hijacked by solid tumor cells rendered CTCs competent to reprogram their anchorage dependency and disseminate into the bloodstream, while subsequent suppression of these factors was critical to regain adhesion and colonize metastatic lesions. Disrupting the oscillatory dynamics of AST factors blocked the adherent-suspension plasticity (ASP) of breast cancer CTCs and suppressed lung metastasis. Furthermore, multiregional single-cell transcriptomic analyses of matched primary tumors, CTCs, and metastatic lesions from de novo metastatic breast cancer patients demonstrate the critical role of ASP in metastasis. SignificanceWe demonstrate cell competition-mediated displacement of loser cells manifests dynamic oscillation of AST factors that confer anchorage plasticity to circulating tumor cells critical for their dissemination and colonization in metastasis. These findings highlight the potential of targeting AST factors to develop effective anti-metastatic therapies.

cancer biology↗