Biology subjects

Kim, W.

Publications and source records attributed to Kim, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Pathway impact analysis (PIS) for robust and comprehensive interpretation of differentially expressed genes (DEGs)

In transcriptome analysis, identifying differentially expressed genes (DEGs) is fundamental for understanding cellular responses and elucidating disease mechanisms. However, conventional DEG selection often relies on arbitrary thresholds for fold change and statistical significance, which are sensitive to experimental noise and sample size, thereby affecting reproducibility and biological interpretability. We present the Pathway Impact Score (PIS), a data-adaptive method that optimizes DEG thresholds by maximizing cumulative pathway enrichment. Unlike fixed cut-offs, PIS systematically determines dataset-specific thresholds that yield the most coherent and enriched pathways. Validation using the MAQC2 benchmark and 16 dataset of pulmonary fibrosis model suggested that PIS can improve the recovery of true DEGs, while maintaining stability under varying noise levels and replicate counts, and increasing pathway enrichment strength. PIS also supported high-resolution analysis of dose-dependent transcriptomic responses to phosphodiesterase (PDE) inhibitors, capturing pathway-level perturbations that appeared to align with each compounds potency. Such analyses may facilitate more precise characterization of drug-induced transcriptional changes, highlighting the potential of PIS for integrative transcriptomic studies. Overall, PIS provides a practical, biologically informed framework for adaptive DEG selection, particularly suited for meta-analyses and integrative studies where dataset-specific variability needs careful consideration. It is designed for seamless integration into existing transcriptomic analysis pipelines or as a complementary module, requiring minimal additional parameter tuning beyond standard differential expression workflows.

bioinformatics↗

bioRxiv2025

Elucidation of Radical Degradation in Native Biofilms by EPR Sheds Light on Bacterial Resistance and Efficient DNP Solid-state NMR

Bacterial biofilms exhibit enhanced antimicrobial resistance, yet the mechanisms determining molecular transport and reactivity within these complex communities remain poorly understood. Here, we combine electron paramagnetic resonance (EPR), solid-state NMR (ssNMR), and dynamic nuclear polarization (DNP) ssNMR to determine how native Pseudomonas fluorescens Pf0-1 colony biofilms regulate nitroxide radicals. EPR measurements reveal that radical reduction depends on biofilm morphology, hydration, and composition of extracellular matrix (ECM). Wild-type biofilms exhibit slower nitroxide reduction than planktonic cells, while isolated ECM and dehydrated biofilms show no radical reduction, indicating that bacterial cells primarily drive radical reduction. Complementary ssNMR measurements identify polysaccharides and lipids within the ECM as primary interaction sites for nitroxide radicals. DNP-enhanced ssNMR further reveals compositional differences across biofilm morphologies, with increasingly polysaccharide-rich ECM environments correlating with slower reduction kinetics. These findings support a mechanism in which the ECM acts as a diffusion barrier and selective interaction region for nitroxide radicals to regulate cellular penetration. This work showcases an integrated magnetic resonance approach that provides molecular insight into how biofilm structure determines the fate of toxic redox-active small molecules. We also set the stage for high-sensitivity measurements of structure-function relationships in these medically relevant assemblies.

biophysics↗

bioRxiv2025

Huntington's disease LIG1 modifier variant increases ligase fidelity and suppresses somatic CAG repeat expansion

Huntingtons disease (HD) is a fatal neurodegenerative disorder caused by inheriting an expanded CAG repeat tract in the huntingtin gene (HTT) that further expands in somatic cells over an individuals lifetime. Genome-wide association studies have provided critical insight into factors that modify the course of disease. These include DNA repair genes that alter the rate of somatic expansion and other genes that do not appear to directly influence this process. One modifier gene is DNA ligase 1 (LIG1), in which a variant specifying a lysine to asparagine substitution (K845N) is associated with a profound (7-8 year) delay in the onset of motor signs. Here, we have taken a multifaceted approach to gain insight into the protective nature of this variant in HD. We demonstrate using in vitro ligase assays and enzyme kinetics that K845N enhances discrimination towards mismatched substrates and increases repair fidelity. Consistent with increased ligation fidelity, K845N confers protection against oxidative stress in cell-based assays. Finally, we demonstrate that the mouse LIG1 K843N orthologue suppresses somatic CAG expansion in HD knock-in mice. Overall, our data provide evidence that altered LIG1 function due to the K845N substitution may contribute to HD clinical delay by slowing somatic expansion in the brain and protecting the genome globally against damage. Significantly, our results provide a mechanistic foundation for considering DNA ligase fidelity as a therapeutic target in HD and potentially in other trinucleotide repeat disorders. Significance StatementWe analyzed a missense variant in DNA Ligase 1 (K845N) that is associated with a profound delay in the onset of Huntingtons disease (HD). We find that K845N enhances substrate discrimination towards mismatched substrates, thus increasing repair fidelity, conferring protection against oxidative stress and slows somatic expansion of the HD CAG repeat. Our observations provide insight into underlying mechanisms of disease modification and suggest avenues that can be harnessed for disease-modifying therapeutic intervention. Classification: Biological Sciences, Genetics

genetics↗

bioRxiv2025

A Human Tumor-Immune Organoid Model of Glioblastoma

A major obstacle to identifying effective therapies for the aggressive brain tumor glioblastoma is the lack of human-specific, immunocompetent models that reflect the human tumor microenvironment. To address this, we developed the immune-Human Organoid Tumor Transplantation (iHOTT) model. This is an autologous co-culture platform that integrates patient-derived tumor cells and matched peripheral blood mononuclear cells (PBMCs) within human cortical organoids, enabling the study of the patient-specific immune response to the tumor and tumor-immune interactions. This platform preserves tumor and immune populations, immune signaling, and cell-cell interactions observed in patient tumors. Treatment of iHOTT with pembrolizumab, a checkpoint inhibitor, mirrored cell type shifts and cell interactions observed in patients. TCR sequencing further revealed pembrolizumab-driven expansion of stem-like CD4-T-cell clonotypes exhibiting patient-specific repertoires. These findings establish iHOTT as a physiologically relevant platform for exploring autologous tumor-immune interactions and underscore the critical need for antigen-targeted strategies to enhance immunotherapy in glioblastoma.

cancer biology↗

bioRxiv2025

Siderophores can alter the population dynamics of fungal-bacterial communities by inhibiting specialized metabolism

Siderophores are microbial metabolites with a strong affinity for Fe(III) ions, in addition to other roles beyond iron acquisition. In this study, we propose that bacillibactin, a siderophore produced by the bacterium Bacillus subtilis, provides an advantage to its producer by inhibiting the specialized metabolism of antagonistic Penicillium fungi. Metabolome and transcriptome analyses indicate that iron deficiency caused by bacillibactin plays a critical role in downregulating the specialized metabolism of competing Penicillium species. Since many specialized metabolites of Penicillium spp. have antibacterial properties, we hypothesize that bacillibactin cross-protects other bacteria during fungal-bacterial community interactions. A tripartite coculture model demonstrated that bacillibactin production influences community dynamics by reducing the growth of specialized metabolite-producing Penicillium species, thereby facilitating the colonization of B. subtilis and other co-inhabiting bacterial species.

microbiology↗

bioRxiv2025

EZH1 Q571R-mediated chromatin compaction and its oncogenic potential in thyroid cancer

Dysregulation of Polycomb Repressive Complex 2 (PRC2) is established to contribute to cancer. Of its catalytic subunits, EZH1 and EZH2, EZH2 mutations in cancer have been extensively identified and studied, but the role of EZH1 in cancer remains largely unexplored. The recurrent presence of the EZH1Q571R mutation in follicular thyroid cancer suggests its involvement in tumor progression. Using EZH1 ChIP-seq, ATAC-seq, and H3K27me3 CUT&Tag, we demonstrated that EZH1Q571R enhances chromatin binding and compaction and stimulates PRC2-EZH1 catalytic activity, leading to increased H3K27me3 levels and repression of tumor suppressor genes. Purified PRC2-EZH1Q571R demonstrated a significant increase in histone methyltransferase activity compared to PRC2-EZH1WT via enhanced nucleosome binding and DNA compaction. Notably, this effect is particularly observed with EZH1Q571R but only to a lesser extent with the corresponding EZH2Q570R mutation, highlighting it as an EZH1-specific mechanism. We additionally demonstrated PRC2-EZH1Q571R to efficiently methylate H3K27 in pre-existing H3K36me2/3 nucleosomes, disrupting chromatin homeostasis. Our findings provide key insights into the molecular pathogenesis of EZH1Q571R-driven follicular thyroid cancer.

molecular biology↗

bioRxiv2025

Single Nuclei-Derived Molecular Subtypes of Gastrointestinal Stromal Tumors Correlate with Clinicopathologic Features and Predict Clinical Outcomes

Historically, gastrointestinal stromal tumor (GIST) has been subtyped by oncogenic driver mutations. However, tumors with the same mutational profile can have variable biology. To further explore the impact of molecular diversity on GIST biology, we performed single nucleus RNA sequencing on 16 primary GIST and utilized an integrated single cell atlas of the normal GI tract composed from multiple publicly available datasets to identify six distinct GIST cell states. We then statistically estimated the relative abundances of these profiles in bulk transcriptomic data. These were used to define six common GIST molecular subtypes based upon one or two predominant tumor cell states. We found that these molecular subtypes correlate with tumor locations, mutational profiles, and patient outcomes, and validated these subtypes in an independent international cohort. These molecular subtypes have the potential to be used for clinical prognostication for patients with GIST, identifying new therapeutic targets, and studying the cell of transformation of GIST.

cancer biology↗

bioRxiv2025

NitrOFF: An engineered fluorescent biosensor to illuminate nitrate transport in living cells

The duality of nitrate is nowhere best exemplified than in human physiology - a detrimental pollutant but also a protective nutrient and signaling ion - particularly as connected to reactive nitrogen oxides. Aside from limited insights into nitrate uptake and storage, foundational nitrate biology has lagged. Genetically encoded fluorescent biosensors can address this gap with real-time imaging. However, imaging technologies for mammalian cell applications remain rare. Here, we set out to design and engineer a two-domain chimera fusing the split green fluorescent protein EGFP and the nitrate recognition domain NreA from Staphylococcus carnosus. Over 7 rounds of directed evolution, 15 mutations were accumulated resulting in the functional biosensor NitrOFF. NitrOFF has a high degree of allosteric communication between the domains reflected in a turn-off intensiometric response (Kd {approx} 9 {micro}M). This was further reinforced by X-ray crystal structures of apo and nitrate bound NitrOFF, which revealed that the two domains undergo a large-scale conformational rearrangement that changes the relative positioning of the EGFP and NreA domains by 68.4{degrees}. Such a dramatic difference was triggered by the formation of a long helix at the engineered linker connecting the two domains, peeling the {beta}7 strand off the EGFP and thus extinguishing the fluorescence upon nitrate binding. Finally, as a proof-of-concept, we highlighted the utility of this first-generation biosensor to monitor exogenous nitrate uptake and modulation in a human embryonic kidney (HEK) 293 cell line. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/644677v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1ba853eorg.highwire.dtl.DTLVardef@81bed9org.highwire.dtl.DTLVardef@18a313org.highwire.dtl.DTLVardef@17a5e80_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Long-term innovative potential of genetic research and its suppression

Long-term innovation depends not only on discovering new elements but also on facilitating new recombination at the time of their co-availability. This notion of combinatorial innovation raises the question about whether scientific exploration and industry research persist over similar time horizons to meet innovative opportunities. Here, we analyze about 20 million papers and US, Chinese, and European patents to compare the courses of scientific and industrial activities in genetic research, a domain of far-reaching societal importance. We observe that research on new genes has declined since the early 2000s, but the exploration of novel gene combinations remains active for biotechnology innovation. Yet, fields of highly practical or commercial focus are less likely to test novel gene combinations. Furthermore, industry R&D on each gene tends to decline earlier than scientific interest in that gene. After this decline of the industrial momentum, continuous scientific research still sustains exploratory and innovative opportunities, involving novel gene combinations, clinical trials, and technologically-impactful work. Based on a hypothetical scenario of over-aligned science and industry, we estimate that up to 42.2-74.4% of the combinational opportunities would be unexplored if scientific research becomes hindered due to industrys retreat. This study suggests the potential complementary roles of scientific and industrial research with different temporal modes in innovation cycles, calling for balanced policies to foster innovation ecosystems.

scientific communication and education↗

bioRxiv2025

Magnetic activation of electrically active cells

Magnetic control of cell activity has applications ranging from non-invasive neurostimulation to remote activation of cell-based therapies. Unlike other methods of regulating cell activity like heat and light, which are based on known receptors or proteins, no magnetically gated channel has been identified to date. As a result, effective approaches for magnetic control of cell activity are based on strong alternating magnetic fields able to induce electric fields or materials that convert magnetic energy into electrical, thermal, or mechanical energy to stimulate cells. In our investigations of magnetic cell responses, we found that a spiking HEK cell line with no other co-factors responds to a magnetic field that reaches a maximum of 500 mT within 200 ms using a permanent magnet. The response is rare, approximately 1 in 50 cells, but is fast and reproducible, generating an action potential within 200 ms of magnetic field stimulation. The magnetic field stimulation is over 10,000 times slower than the magnetic fields used in transcranial magnetic stimulation (TMS) and the induced electric field is more than an order of magnitude lower than necessary for neuromodulation, suggesting that induced electric currents do not drive the cell response. Instead, our calculation suggests that this response depends on mechanoreception pathways activated by the magnetic torque of TRP-associated lipid rafts. Despite the relatively rare response to magnetic stimulation, when cells form gap junctions, the magnetic stimulation can propagate to nearby cells, causing tissue-level responses. As an example, we co-cultured spiking HEK cells with beta-pancreatic MIN6 cells and found that this co-culture responds to magnetic fields by increasing insulin production. Together, these results point toward a method for the magnetic control of biological activity without the need for a material co-factor such as synthetic nanoparticles. By better understanding this mechanism and enriching for magneto-sensitivity it may be possible to adapt this approach to the rapidly expanding tool kit for wireless cell activity regulation.

biophysics↗

bioRxiv2025

Structural basis for the evolution of a domesticated group II intron-like reverse transcriptase to function in host cell DNA repair

A previous study found that a domesticated bacterial group II intron-like reverse transcriptase (G2L4 RT) functions in double-strand break repair (DSBR) via microhomology-mediated end joining (MMEJ) and that a mobile group II intron-encoded RT has a basal DSBR activity that uses conserved structural features of non-LTR-retroelement RTs. Here, we determined G2L4 RT apoenzyme and snap-back DNA synthesis structures revealing novel structural adaptations that optimized its cellular function in DSBR. These included a unique RT3a structure that stabilizes the apoenzyme in an inactive conformation until encountering an appropriate substrate; a longer N-terminal extension/RT0-loop with conserved residues that together with a modified active site favors strand annealing; and a conserved dimer interface that localizes G2L4 RT homodimers to DSBR sites with both monomers positioned for MMEJ. Our findings reveal how a non-LTR-retroelement RT evolved a dedicated cellular function and suggest new ways of optimizing these RTs for genome engineering applications.

molecular biology↗

bioRxiv2025

Pathobiont-triggered induction of epithelial IDO1 drives regional susceptibility to Inflammatory Bowel Disease

The structure and function of the mammalian gut vary by region, yet why inflammatory diseases manifest in specific regions and not others remains unclear. We use a TNF-overexpressing Crohns disease (CD) model (Tnf{Delta}ARE/+), which typically presents in the terminal ileum (TI), to investigate how environmental factors interact with the hosts immune susceptibility to drive region-specific disease. We identified Chlamydia muridarum, an intracellular bacterium and murine counterpart to the human sexually transmitted C. trachomatis, as necessary and sufficient to trigger disease manifestation in the ascending colon (AC), another common site of human CD. Disease manifestation in the AC depends on indoleamine 2,3-dioxygenase (IDO1) activity induced by hypersensitive surface secretory cells in genetically susceptible hosts. Single-cell and microbial analyses of human specimens also implicates this pathobiont-epithelial IDO1 pathway in patients with a history of CD in the AC. Our findings demonstrate that genetic and microbial factors can independently drive region-specific disease and provide a unique model to study CD specific to the AC.

cell biology↗

bioRxiv2024

Exclusive cataloging of near-complete genomes unveils novel functional insights into the human gut microbiome

Understanding the human gut microbiome requires comprehensive genomic catalogues, yet many lack geographic diversity and contain medium-quality metagenome-assembled genomes (MAGs) missing up to 50% of genomic regions, potentially distorting functional insights. Here, we describe an enhanced Human Reference Gut Microbiome (HRGM2) resource, a catalogue of near-complete MAGs ([≥]90% completeness, [≤]5% contamination) and isolate genomes. HRGM2 comprises 155,211 non-redundant near-complete genomes from 4,824 prokaryotic species across 41 countries, representing a 66% increase in genome count and a 50% boost in species diversity compared to the Unified Human Gastrointestinal Genome catalogue. It enabled improved DNA-based species profiling, resolution of strain heterogeneity, and survey of human gut resistome. The exclusive use of these genomes improved metabolic capacity assessment enabling high-confidence, automated genome-scale metabolic models (GEMs) of the entire microbiota, revealing disease-associated microbial metabolic interactions. This resource will facilitate reliable functional insights into gut microbiomes.

microbiology↗

bioRxiv2024

Diverging repeatomes in holoparasitic Hydnoraceae uncover a playground of genome evolution

O_LIThe nuclear genomes of parasitic plants have undergone unique evolutionary trajectories to adapt to the heterotrophic lifestyle. These adaptations often involve large genomic alterations, potentially driven by repetitive DNAs. Despite the recognized role of repetitive DNAs for shaping plant genomes, their contribution to parasitic plant genome evolution remains largely unexplored. This study presents the first analysis of repetitive DNAs in eleven genomes of Hydnoraceae, a holoparasitic plant family. C_LIO_LIThe repetitive DNAs were identified and annotated de novo. Patterns of abundance and presence-absence were aligned with the phylogenetic relationships, geographical distribution, and host shifts, suggesting repetitive DNAs key role in shaping Hydnoraceae genomes. C_LIO_LIThe two Hydnoraceae genera, Hydnora and Prosopanche, exhibit distinct profiles. Eight Hydnora genomes are largely populated by long terminal repeat retrotransposons, while three Prosopanche genomes vary greatly in repetitive DNA composition, including P. bonacinae with massive amplifications of a single DNA transposon and P. panguanensis with over 15% 5S rDNA, compared to <0.1% in some Hydnoraceae. Both extremely low and very high abundance of 5S rDNA challenges our current understanding on chromosomal stabilization and rDNA transcription. C_LIO_LIThese genome dynamics, while inviting for further investigations, suggest rapidly evolving repeat profiles, potentially accelerated by the adaptation to the parasitic lifestyle. C_LI

evolutionary biology↗

bioRxiv2024

Defining a highly conserved B cell epitope in the receptor binding motif of SARS-CoV-2 spike glycoprotein

SARS-CoV-2 mRNA vaccines induce robust and persistent germinal centre (GC) B cell responses in humans. It remains unclear how the continuous evolution of the virus impacts the breadth of the induced GC B cell response. Using ultrasound-guided fine needle aspiration, we examined draining lymph nodes of nine healthy adults following bivalent booster immunization. We show that 77.8% of the B cell clones in the GC expressed as representative monoclonal antibodies recognized the spike protein, with a third (37.8%) of these targeting the receptor binding domain (RBD). Strikingly, only one RBD-targeting mAb, mAb-52, neutralized all tested SARS- CoV-2 strains, including the recent KP.2 variant. mAb-52 utilizes the IGHV3-66 public clonotype, protects hamsters challenged against the EG.5.1 variant and targets the class I/II RBD epitope, closely mimicking the binding footprint of ACE2. Finally, we show that the remarkable breadth of mAb-52 is due to the somatic hypermutations accumulated within vaccine-induced GC reaction. One Sentence SummaryBooster SARS-CoV-2 mRNA vaccine recruits and broadens GC B cell responses targeting a highly conserved site on receptor binding domain of spike glycoprotein.

immunology↗

bioRxiv2024

High-Sensitivity Analysis of Native Bacterial Biofilms Using Dynamic Nuclear Polarization-Enhanced Solid-State NMR

Bacterial biofilms cause persistent infections that are difficult to treat and contribute greatly to antimicrobial resistance. However, high-resolution structural information on native bacterial biofilms remain very limited. This limitation is primarily due to methodological constraints associated with analyzing complex native samples. Although solid-state NMR (ssNMR) is a promising method in this regard, its conventional applications typically suffer from sensitivity limitations, particularly for unlabeled native samples. Through the use of Dynamic Nuclear Polarization (DNP), we applied sensitivity enhanced ssNMR to characterize native Pseudomonas fluorescens colony biofilms. The increased ssNMR sensitivity by DNP enabled ultrafast structural characterization of the biofilm samples without isotope-labelling, and chemical or physical modification. We collected 1D 13C and 15N, and 2D 1H-13C, 1H-15N and 13C-13C ssNMR spectra within seconds/minutes or hours, respectively which enabled us to identify biofilm components as polysaccharides, proteins, and eDNA effectively. This study represents the first application of ultrasensitive DNP ssNMR to characterize a native bacterial biofilm and expands the technical scope of ssNMR towards obtaining insights into the composition and structure of a wide array of in vitro and ex vivo biofilm applications. Such versatility should greatly boost efforts to develop structure-guided approaches for combating infections caused by biofilm-forming microbes.

microbiology↗

bioRxiv2024

Identification of genes conferring individual-level variation responsible for metabolic dysfunction-associated steatohepatitis using single-cell eQTL analysis

Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly recognized for its medical and socioeconomic impacts, driven by diverse genetic and environmental factors. To address the urgent need for individually tailored therapies, we performed single-cell expression quantitative trait loci (sc-eQTL) analysis on liver biopsies from 25 MASLD patients and 23 controls. This approach identified over 3,500 sc-eQTLs across major liver cell types and cell state-interacting eQTLs (ieQTLs) with significant enrichment for disease heritability (for MASLD trait, ieQTL enrichment odds ratio = 10.27). We integrated transcription factors (TFs) as upstream regulators of ieQTLs, revealing 601 functional units ("quartets") composed of TFs, cell states, ieSNPs, and ieGenes. From these results, we pinpoint the loss of an eQTL in EFHD1 during hepatocyte maladaptation associated with genotype-specific regulation by FOXO1, further contributing to the risk of MASLD. Our approach underscores the role of eQTL analysis in capturing crucial genetic variations that influence gene expression and clinical outcomes in complex diseases.

genetics↗

bioRxiv2024

Elucidating Interactome Dynamics of the A2A Adenosine Receptor

Polydeoxyribonucleotide (PDRN) is a tissue regeneration substance that resembles human DNA and is present in human cells, mullets, salmons, and flatfish. It stimulates physiological regeneration and metabolic activity. The regenerative and metabolic effects of PDRN are attributed to the activation of Adenosine A2A receptors (ADORA2A), which increases the production of angiogenesis factors and growth factors. Activation of ADORA2A leads to the activation of ADORA2A-interacting proteins with similar functions. To investigate the changes and dynamics of proteins in the presence of PDRN, we conducted selected reaction monitoring-mass spectrometry (SRM-MS) to quantify 491 proteins, 3,852 peptides. Through peptide-level analysis, we founded 374 proteins and 1,193 peptides demonstrating both up-regulation and down-regulation in expression. We conducted gene ontology (GO) analysis and physical network analysis and discovered a novel network of proteins related to neuronal differentiation among the ADORA2A-interacting protein. Based on network analysis, we found indirect interactions with MAPK1 and MP2K1, which are known to influence neuronal cell differentiation and suggest the formation of a network involving MAPK signaling transduction. Finally, using AlphaFold multimer, we were able to predict interaction sites among ADORA2A-interacting proteins in the network associated with neuronal cell differentiation. Specifically, we predicted five interaction sites between ADORA2A and NTRK1 (which interacts with ADORA2A), forming the edge. Thus, we provided indicators for further research using ADORA2A present in robust network and highlighted the potential of PDRN to impact neuronal differentiation.

systems biology↗