Biology subjects

Park, D.

Publications and source records attributed to Park, D..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Anti-activin treatment increases T cell infiltration in breast and pancreatic tumours and promotes survival in a SMAD4-null mouse pancreatic cancer model

Activin A and B share the same downstream signalling pathway (activation of SMAD2/3) as TGF-{beta} and consequently elicit many of the same functional responses as TGF-{beta}, including immune suppression, activation of cancer-associated fibroblasts (CAFs) and extracellular matrix production and remodelling. However, activins role in tumourigenesis has been relatively overlooked compared to TGF-{beta}s. We generated and characterized a dual specificity human antibody that recognizes both activin A and B and compared its activity in syngeneic mouse models of breast cancer and pancreatic ductal adenocarcinoma (PDAC) with an activin A-specific antibody. We demonstrate that activin A and B are central to the function of CAFs and therapeutic inhibition of activin results in a reduction of collagen rich desmoplastic barriers, enabling the infiltration of cytotoxic T cells. This is correlated with an upregulation of the T cell chemoattractant CXCL10, which is normally repressed by activin signalling. Interestingly, despite greater T cell infiltration, activin A inhibition resulted in poorer survival in the KPC mouse model of PDAC and slightly larger tumours in the breast cancer model, indicating a tumour suppressive role of activin A-rich CAFs. Strikingly, however, treatment with the same anti-activin A antibody of PDAC tumours where SMAD4 is deleted in the tumour cells, resulted in increased survival, which was potentiated with additional treatment with immune checkpoint inhibitors. These results suggest that anti-activin therapy has potential for the cohort of PDAC patients exhibiting inactivation of SMAD4.

cancer biology↗

bioRxiv2025

Transcription factors overcome the repressive impact of Polycomb-associated methylation in tumors

DNA methylation is a key epigenetic regulator often disrupted in cancer, yet how promoter methylation dynamics translate into transcriptional changes during cancer progression remains incompletely understood. Here, we employed targeted bisulfite sequencing and RNA-seq on paired tumor and non-tumor tissues from 80 Korean colorectal cancer (CRC) patients to map promoter methylation and gene expression dynamics. Promoters with high baseline methylation in non-tumor tissues tended to become hypomethylated in tumors, while those with low baseline methylation underwent partial hypermethylation. However, these changes did not consistently correlate with gene silencing or activation. Strikingly, promoters marked by Polycomb (PcG+) in non-tumor tissue were prone to hypermethylation yet often remained transcriptionally active in tumors, a paradox most prominent in transcription factor (TF) genes. In contrast, hypermethylation in PcG- promoters was more consistently associated with transcriptional repression. Our findings suggest that epigenetic plasticity at PcG+ TF gene promoters can override the typically repressive effects of DNA methylation, potentially enabling tumors to maintain or enhance the expression of key regulatory genes. This highlights the importance of PcG occupancy in shaping the functional consequences of methylation changes during colorectal tumorigenesis, warranting deeper investigation into how these epigenetic adaptations drive cancer progression.

bioinformatics↗

bioRxiv2025

Using a "one-strain-many-compounds" (OSMAC) approach to screen a collection of diverse fungi from Aotearoa New Zealand for antibacterial activity against Escherichia coli

There is an urgent need to identify new chemical compounds with novel modes of action to help manage the antimicrobial resistance crisis. Fungi are prolific producers of secondary metabolites, including those with antimicrobial properties, and contain biosynthetic gene clusters that awaken only under certain growth conditions. In recent years, a wealth of novel fungal biosynthetic pathways and compounds have been identified, suggesting fungi remain a viable source for developing new antimicrobials. The International Collection of Microorganisms from Plants (ICMP) contains thousands of fungi and bacteria primarily sourced from Aotearoa New Zealand. Here, we report the results of our efforts to screen 32 fungal ICMP isolates for activity against Escherichia coli, a leading cause of deaths attributable to antimicrobial resistance. We used a one strain-many compounds (OSMAC) approach, growing the ICMP isolates on seven different media with different pH and various carbon and nitrogen sources. We also tested the isolates for activity at various ages. Our results indicate that several of the tested fungi possess anti-E. coli activity and are suitable for further study, including the aero-aquatic Ascomycete Hyaloscypha sp. ICMP 16864. Our results also provide further strong evidence for the impact of media on both fungal growth and bioactivity.

microbiology↗

bioRxiv2025

ArcDFI: Attention Regularization guided by CYP450 Interactions for Predicting Drug-Food Interactions

CYP450 isoenzymes are known to be deeply involved in the formation of drug-food interactions (DFI). Previously introduced computational approaches for predicting DFIs do not take drug-CYP450 interactions (DCI) into account and have limited generalizability in handling compounds unseen during model training. We introduce ArcDFI, a model that utilizes attention regularization guided by CYP450 interactions to predict drug-food interactions. Experimental results demonstrate ArcDFIs ability to predict DFIs when given unseen food or drug compounds as input. Analysis of its attention mechanism provides insight into its current understanding of DCI and how they are related to its DFI predictions. To the best of our knowledge, ArcDFI is the first DFI prediction model that incorporates the concept of DCI, resulting in improved predictive generalizability and model explainability. ArcDFI is available at https://github.com/KU-MedAI/ArcDFI

pharmacology and toxicology↗

bioRxiv2025

Prenatal DEHP plastic chemical exposure increases the likelihood of child autism and ADHD symptoms through epigenetic programming

Increasing evidence implicates prenatal exposure to di-(2-ethylhexyl) phthalate (DEHP), a common endocrine-disrupting plastic chemical, in autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD). However, the underlying mechanisms are poorly understood. Here we examined whether cord blood DNA methylation, a key epigenetic marker, mediates the association between prenatal DEHP exposure and ASD/ADHD symptoms in 847 children enrolled in the Barwon Infant Study. ASD and ADHD are complex phenotypes characterised by differences at the gene regulatory network and neuronal circuit level, where heterogeneous genetic and environmental risk factors converge. Accordingly, we employed a data-driven computational strategy that helped elucidate broader functional epigenetic signatures of ASD and ADHD elicited by DEHP exposure. This included (1) a methylation profile score for DEHP exposure (MPSDEHP), and (2) an analysis of co-methylated gene networks. Causal mediation analysis demonstrated that both MPSDEHP and a DEHP-associated network of co-methylated genes mediated the effect of DEHP exposure on increased ASD and ADHD symptoms at ages 2 and 4 years (proportion of effect mediated ranged from 0.21 to 0.80). The co-methylation network was enriched for neural cell-type markers, ASD risk genes (including FOXP1, SHANK2, and PLXNB1), and targets of endocrine receptors previously linked to DEHP (including targets of the estrogen receptor ER and the glucocorticoid receptor GR), providing biological plausibility. We validated key results in independent blood (n=66) and postmortem brain (n=40) DNA methylation datasets. These findings provide mechanistic evidence linking DEHP to ASD and ADHD symptoms and reinforce growing concerns regarding the risks of prenatal exposure.\n\nSignificanceExposure to endocrine-disrupting plastic chemicals has been linked to adverse neurodevelopment, but the underlying biological mechanisms remain unclear. We demonstrate that prenatal exposure to di-(2-ethylhexyl) phthalate (DEHP), a common plasticizer, increases autism and ADHD symptoms through alterations in DNA methylation, a key epigenetic regulator of gene activity. Using birth cohort data, we identify epigenetic signatures of prenatal DEHP exposure, including alterations in an endocrine-related co-methylation network enriched for neural cell-type markers and known autism-associated genes. These signatures mediate the effects of DEHP on autism and ADHD symptoms and are also associated with autism in external blood and postmortem-brain datasets, providing independent validation. This causal evidence further underscores concerns regarding the consequences of prenatal plastic-chemical exposure on the developing brain.

neuroscience↗

bioRxiv2024

Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure

Biomolecular condensates play key roles in the spatiotemporal regulation of cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We studied this relationship using the polar organizing protein Z (PopZ) as a model system, revealing how its material properties and cellular function depend on its ultrastructure. We revealed PopZs hierarchical assembly into a filamentous condensate by integrating cryo-electron tomography, biochemistry, single-molecule techniques, and molecular dynamics simulations. The helical domain drives filamentation and condensation, while the disordered domain inhibits them. Phase-dependent conformational changes prevent interfilament contacts in the dilute phase and expose client binding sites in the dense phase. These findings establish a multiscale framework that links molecular interactions and condensate ultrastructure to macroscopic material properties that drive cellular function.

cell biology↗

bioRxiv2024

Co-delivery of neurotrophic factors and a zinc chelator substantially promotes axon regeneration in the optic nerve crush model

Traumatic optic neuropathies cause the death of retinal ganglion cells (RGCs) and axon degeneration. This is a result of the blockage of neurotrophic factor (NTF) supply from the brain and a vicious cycle of neurotoxicity, possibly mediated by increased levels of retinal Zn2+. Ciliary neurotrophic factor (CNTF) and brain-derived neurotrophic factor (BDNF) are two NTFs that are known to support RGC survival and promote axon regeneration. Dipicolylamine (DPA) has a strong affinity to Zn2+ and can selectively chelate this ion. To continuously supply NTFs and reduce elevated retinal Zn2+, we developed poly(serinol hexamethylene urea)-based sulfonated nanoparticles (S-PSHU NPs), that co-delivers CNTF, BDNF, and DPA. An in vitro release study was performed using the NTF-DPA-loaded S-PSHU NPs, demonstrating a sustained release of CNTF and BDNF for up to 8 weeks, while DPA was released for 4 weeks. In a rat optic nerve crush (ONC) model, DPA-loaded S-PSHU NPs exhibited dose-dependent elimination of retinal Zn2+. Similarly, in vitro primary RGC culture demonstrated that the activity of RGCs and axon growth were dependent on the dosage of CNTF and BDNF. In addition, the NTF-DPA-loaded S-PSHU NPs significantly improved RGC survival and axon regeneration following ONC in rats, with the regenerated axons extending to the distal segment of the brain, including the suprachiasmatic nucleus, lateral geniculate nucleus, and superior colliculus.

bioengineering↗

bioRxiv2024

Creating overlapping genes by alternate-frame insertion

Overlapping genes-wherein two different proteins are translated from alternative frames of the same DNA sequence-provide a means to stabilize an engineered gene by directly linking its evolutionary fate with that of an overlapped gene. However, creating overlapping gene pairs is challenging as it requires redesign of both protein products to accommodate overlap constraints. Here, we present a new "overlapping, alternate-frame insertion" (OAFI) method for creating overlapping genes by insertion of an "inner" gene, encoded in an alternate frame, into a flexible region of an "outer" gene. Using OAFI, we create new overlapping gene pairs of bacterial toxins within an antibiotic resistance gene. We show that both the inner and outer genes retain functionality despite redesign, with translation of the inner gene is influenced by its overlap position in the outer gene. Additionally, we show that selection for the outer gene alters the permitted inactivating mutations in the inner gene and that overlapping toxins can restrict horizontal gene transfer of the antibiotic resistance gene. Overall, OAFI offers a versatile tool for synthetic biology, expanding the applications of overlapping genes in gene stabilization and biocontainment.

synthetic biology↗

bioRxiv2024

In Vivo Optical Clearing of Mammalian Brain

Established methods for imaging the living mammalian brain have, to date, taken the brains optical properties as fixed; we here demonstrate that it is possible to modify the optical properties of the brain itself to significantly enhance at-depth imaging while preserving native physiology. Using a small amount of any of several biocompatible materials to raise the refractive index of solutions superfusing the brain prior to imaging, we could increase several-fold the signals from the deepest cells normally visible and, under both one-photon and two-photon imaging, visualize cells previously too dim to see. The enhancement was observed for both anatomical and functional fluorescent reporters across a broad range of emission wavelengths. Importantly, visual tuning properties of cortical neurons in awake mice, and electrophysiological properties of neurons assessed ex vivo, were not altered by this procedure.

bioengineering↗

bioRxiv2024

MRGM: An enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes

Mouse gut microbiome research is pivotal for understanding the human gut microbiome, providing insights into disease modeling, host-microbe interactions, and the dietary influence on the gut microbiome. To enhance the translational value of mouse gut microbiome studies, we need detailed and high-quality catalogs of mouse gut microbial genomes. We introduce the Mouse Reference Gut Microbiome (MRGM), a comprehensive catalog with 42,245 non-redundant mouse gut bacterial genomes across 1,524 species. MRGM marks a 40% increase in the known taxonomic diversity of mouse gut microbes, capturing previously underrepresented lineages through refined genome quality assessment techniques. MRGM not only broadens the taxonomic landscape but also enriches the functional landscape of the mouse gut microbiome. Using deep learning, we have elevated the Gene Ontology annotation rate for mouse gut microbial proteins from 3.2% with orthology to 60%, marking an over 18-fold increase. MRGM supports both DNA- and marker-based taxonomic profiling by providing custom databases, surpassing previous catalogs in performance. Finally, taxonomic and functional comparisons between human and mouse gut microbiota reveal diet-driven divergences in their taxonomic composition and functional enrichment. Overall, our study highlights the value of high-quality microbial genome catalogs in advancing our understanding of the co-evolution between gut microbes and their host.

microbiology↗

bioRxiv2024

Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes

Characterizing shared patterns of RNA expression between genes across conditions has led to the discovery of regulatory networks and novel biological functions. However, it is unclear if such coordination extends to translation. Here, we uniformly analyzed 3,819 ribosome profiling datasets from 117 human and 94 mouse tissues and cell lines. We introduce the concept of translation efficiency covariation (TEC), identifying coordinated translation patterns across cell types. We nominate candidate mechanisms driving shared patterns of translation regulation. TEC is conserved across human and mouse cells and uncovers gene functions that are not evident from RNA or protein co-expression. Moreover, our observations indicate that proteins that physically interact are highly enriched for positive covariation at both translational and transcriptional levels. Our findings establish TEC as a conserved organizing principle of mammalian transcriptomes.

bioinformatics↗

bioRxiv2024

Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications

Long-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights into the effects of genetic variation on splicing and RNA abundance. Furthermore, the ability to directly sequence RNA promises the detection of RNA modifications in tandem with ascertaining the allelic origin of each molecule. Here, we leverage these advantages to determine allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNA. We utilized human and mouse cells with known genetic variants to assign allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses revealed the importance of sequences adjacent to the DRACH- motif in determining m6A deposition, in addition to allelic differences that directly alter the motif. Moreover, we discovered allele-specific m6A modification (ASM) events with no genetic variants in close proximity to the differentially modified nucleotide, demonstrating the unique advantage of using long reads and surpassing the capabilities of antibody-based short-read approaches. This technological advancement promises to advance our understanding of the role of genetics in determining mRNA modifications.

molecular biology↗

bioRxiv2024

Elevated phagocytic capacity directs innate spinal cord repair

Immune cells elicit a continuum of transcriptional and functional states after spinal cord injury (SCI). In mammals, inefficient debris clearance and chronic inflammation impede recovery and overshadow pro-regenerative immune functions. We found that, unlike mammals, zebrafish SCI elicits transient immune activation and efficient debris clearance, without causing chronic inflammation. Single-cell transcriptomics and inducible genetic ablation showed zebrafish macrophages are highly phagocytic and required for regeneration. Cross-species comparisons between zebrafish and mammalian macrophages identified transcription and immune response regulator (tcim) as a macrophage-enriched zebrafish gene. Genetic deletion of zebrafish tcim impairs phagocytosis and regeneration, causes aberrant and chronic immune activation, and can be rescued by transplanting wild-type immune precursors into tcim mutants. Conversely, genetic expression of human TCIM accelerates debris clearance and regeneration by reprogramming myeloid precursors into activated phagocytes. This study establishes a central requirement for elevated phagocytic capacity to achieve innate spinal cord repair.

neuroscience↗

bioRxiv2024

Molecular tension authenticates apoptotic cells being phagocytosed.

Profound cytoskeletal reorganization and plasma membrane deformation in phagocytes is indispensable for phagocytosis of massive apoptotic cells, but whether these dynamics accompany a mechanical signal modulating signaling during efferocytosis remains largely unexplored. Here, we report that tension between phosphatidylserine (PS) and PS receptors (PSR) generated at the phagocytic synapse serves as a signal to determine whether PS-exposing cells should be phagocytosed. Mechanistically, increased membrane tension of phagocytes via Rac1-dependent actin polymerization and membrane stiffness of apoptotic cells caused tension between PS and PSRs, leading to phosphoinositide 3-kinase recruitment to PSRs, which resulted in Rac1 inactivation and myosin II phosphorylation required for phagocytic cup closure. Our observations imply that tension between PS and PSRs acts as a mechanical fail-safe to prevent removal of all PS-exposing cells for the integrity of efferocytosis. One-Sentence SummaryTension between phosphatidylserine and its receptors acts as a final decision-maker determining phagocytosis of apoptotic cells.

cell biology↗

bioRxiv2024

Overlapping role of synaptophysin and synaptogyrin family proteins in determining the small size of synaptic vesicles

Members of the synaptophysin and synaptogyrin family are vesicle proteins with four transmembrane domains. In spite of their abundance in synaptic vesicle (SV) membranes, their role remains elusive and only mild defects at the cellular and organismal level are observed in mice lacking one or more family members. Here, we show that co-expression with synapsin of each of the four brain-enriched members of this family - synaptophysin, synaptoporin, synaptogyrin1 and synaptogyrin3 - in fibroblasts is sufficient to generate clusters of small vesicles in the same size range of SVs. Moreover, mice lacking all these four proteins have larger SVs. We conclude that synaptophysin and synaptogyrin family proteins play an overlapping function in the biogenesis of SVs and in determining their small size.

neuroscience↗

bioRxiv2024

Mx1-labeled pulp progenitor cells are main contributors to postnatal odontoblasts and pulp cells in murine molars

Regeneration of dentin and odontoblasts from dental pulp stem cells (DPSCs) is essential for permanent tooth maintenance. However, the in vivo identity and role of endogenous DPSCs in reparative dentinogenesis are elusive. Here, using pulp single-cell analysis before and after molar eruption, we revealed that endogenous DPSCs are enriched in Cxcl12-GFP+ coronal papilla-like cells with Mx1-Cre labeling. These Mx1+Cxcl12-GFP+ cells are long-term repopulating cells that contribute to the majority of pulp cells and new odontoblasts after eruption. Upon molar injury, Mx1+ DPSCs localize into the injury site and differentiate into new odontoblasts, forming scleraxis-GFP+ and osteocalcin-GFP+ dentinal tubules and reparative dentin. Single-cell and FACS analysis showed that Mx1+Cxcl12-GFP+ DPSCs are the most primitive cells with stem cell marker expression and odontoblast differentiation. Taken together, our findings demonstrate that Mx1 labels postnatal DSPCs, which are the main source of pulp cells and new odontoblasts with reparative dentinogenesis in vivo.

cell biology↗

bioRxiv2024

An inappropriate decline in ribosome levels drives a diverse set of neurodevelopmental disorders

Many neurodevelopmental defects are linked to perturbations in genes involved in housekeeping functions, such as those encoding ribosome biogenesis factors. However, how reductions in ribosome biogenesis can result in tissue and developmental specific defects remains a mystery. Here we describe new allelic variants in the ribosome biogenesis factor AIRIM primarily associated with neurodevelopmental disorders. Using human cerebral organoids in combination with proteomic analysis, single-cell transcriptome analysis across multiple developmental stages, and single organoid translatome analysis, we identify a previously unappreciated mechanism linking changes in ribosome levels and the timing of cell fate specification during early brain development. We find ribosome levels decrease during neuroepithelial differentiation, making differentiating cells particularly vulnerable to perturbations in ribosome biogenesis during this time. Reduced ribosome availability more profoundly impacts the translation of specific transcripts, disrupting both survival and cell fate commitment of transitioning neuroepithelia. Enhancing mTOR activity by both genetic and pharmacologic approaches ameliorates the growth and developmental defects associated with intellectual disability linked variants, identifying potential treatment options for specific brain ribosomopathies. This work reveals the cellular and molecular origins of protein synthesis defect-related disorders of human brain development. HighlightsO_LIAIRIM variants reduce ribosome levels specifically in neural progenitor cells. C_LIO_LIInappropriately low ribosome levels cause a transient delay in radial glia fate commitment. C_LIO_LIReduced ribosome levels impair translation of a selected subset of mRNAs. C_LIO_LIGenetic and pharmacologic activation of mTORC1 suppresses AIRIM-linked phenotypes. C_LI

developmental biology↗

bioRxiv2024

Efficient value encoding through convergence of tactile and visual value information in the primate putamen

The processing of diverse sensory values by a limited number of basal ganglia neurons raises the question of whether each value is processed independently or combined as the number of neurons decreases from the cortex to downstream structures. Here, we discovered that tactile and visual values were partially converged in the primate putamen, enhancing its efficiency in encoding values while preserving modality information. Humans and monkeys performed tactile and visual value discrimination tasks. Notably, the human putamen selectively represented both tactile and visual values in fMRI scans. Single-unit electrophysiology further revealed that half of the individual neurons in the macaque putamen encoded both tactile and visual values, and the other half encoded each value separately. The bimodal value neurons enable more efficient value encoding using fewer neurons than the modality-selective value neurons. Our data suggest that the basal ganglia system uses modality convergence to efficiently encode values with limited resources.

neuroscience↗