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Kim, K. H.

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

At least 19 recordsLinked to original sources
bioRxiv2026

TCR-FramePose: a local-frame representation for decomposing global docking and CDR3 loop geometry in TCR-pMHC recognition

T cell receptor recognition of peptide-MHC depends on sequence, interface chemistry, and three-dimensional geometry, but docking geometry is often summarized at the whole-receptor level, leaving CDR3-local pose difficult to compare across structures. We introduce TCR-FramePose, a local-frame descriptor set that represents each TCR-pMHC complex as three bodies -- whole TCR, CDR3, and CDR3{beta} -- measured relative to a pMHC groove frame. For each body, FramePose decomposes the native pose into reach, offset direction on S2, and orientation on SO(3); for tangent-space analyses, these components are mapped to six coordinates per body and 18 coordinates per complex. Applied to 378 curated {beta}TCR-pMHC crystal structures, FramePose recovers known class-associated receptor-placement differences and additionally resolved whole-TCR and CDR3{beta} orientation shifts that were not captured by crossing angle. The same orientation coordinates identified reverse-polarity and off-axis outliers as distinct modes. In cross-validated association analyses, FramePose added nonredundant BSA- and affinity-associated information beyond conventional descriptors, and the modest affinity gain was concentrated in CDR3 orientation blocks which were least recoverable from conventional descriptors. Biological grouping analyses showed that shared receptor pose over peptide-MHC was organized primarily by germline V-region framework. TCRs recognizing the same peptide-MHC target favors shared FramePose geometries rather than strong receptor-specific divergence, whereas CDR3 sequence did not detectably reposition the rigid-body pose after antigen context and germline framework were fixed. MHC allele and peptide length contributed smaller adjustments, localized mainly to CDR3{beta} and groove-normal orientation axes. Finally, interface analyses showed that affinity tracked interface burial, with CDR3{beta} reach linking FramePose geometry to binding through buried surface area. Within engineered panels, mutation-level effects were panel-specific, with CDR3{beta} remodeling localizing to a recurrent interface region but varying in direction across receptors. These properties enable FramePose to serve as a geometric filter for in silico TCR-pMHC models and as a feature layer for structure-guided TCR engineering. Together, TCR-FramePose provides a nonredundant geometric layer for structure-guided TCR-pMHC analysis, linking germline-scaffolded recognition, CDR3-local pose, and interface organization without replacing sequence, contact, or energetic descriptors.

bioinformatics↗
bioRxiv2026

Unraveling the Mechanism of HIV-1 Hypersusceptibility to Tenofovir Imparted by Islatravir Resistance Mutations

In response to the newly approved antiretroviral therapy (ART) islatravir (ISL), the M184V and A114S resistance mutations have emerged in the human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT). These mutations markedly hypersensitize RT to the globally administered ART tenofovir disoproxil fumarate (TDF). We have solved six structures - four by X-ray crystallography and two by cryo-EM - that capture the single- and double-mutant RTs during inhibitor incorporation and demonstrate the role of the mutations in altering protein-antiviral interactions. These snapshots reveal that the smaller, more flexible TDF diphosphate (TDF-DP) can better accommodate mutation-induced active site changes than ISL triphosphate (ISL-TP). Structural differences between the two inhibitors are consistent with biochemical determination of inhibitory constants (Kis), highlighting differences at the step of inhibitor incorporation. Virological evaluation of ISL and TDF combinations reveals additive inhibition of HIV-1. Given the converse ISL hypersusceptibility imparted by the TDF-resistant K65R mutation, we propose ISL and TDF as a combination that can inspire future therapeutic options.

biochemistry↗
bioRxiv2025

Chondrolectin regulates the sublaminar localization and regenerative function of muscle satellite cells in mice

Skeletal muscle satellite cells (SCs) reside between the myofiber sarcolemma and basal lamina, where extracellular matrix (ECM) interactions are essential for their maintenance and regenerative function. Here, we identify chondrolectin (CHODL), a type I transmembrane protein with a C-type lectin domain, as a critical regulator of SC biology. Single-cell RNA-seq analysis reveals that Chodl is highly enriched in quiescent SCs but downregulated in proliferating myoblasts. Using conditional knockout models, we show that deletion of Chodl in embryonic myoblasts (ChodlMKO) or adult SCs (ChodlPKO) does not affect muscle development but markedly impairs regeneration in both young and aged mice. Chodl-deficient SCs exhibit reduced self-renewal, diminish proliferation, and impair differentiation, leading to defective myofiber repair. In silico network perturbation further predicts disruption of ECM-ligand interactions and Notch signaling, consistent with our observation that a significant fraction of SCs in ChodlPKOmice localize outside the basal lamina and undergo precocious activation. Together, these findings establish CHODL as a key determinant of SC niche localization and regenerative function, uncovering a previously unrecognized mechanism linking ECM interactions to muscle stem cell maintenance and repair.

developmental biology↗
bioRxiv2025

Nutrient-Sensing Nuclear Receptor PPARα Controls Liver Proteostasis

Peroxisome proliferator-activated receptor alpha (PPAR) is a nuclear receptor that orchestrates metabolic adaptation to fasting by regulating hepatic lipid and glucose metabolism. While these functions are well established, its role in protein homeostasis, another energy-intensive process, has remained unclear. Here, we performed multi-omics analyses in wild-type and PPAR knockout mice treated with the PPAR agonist fenofibrate to define its broader role in proteostasis. Interestingly, chronic PPAR activation suppressed hepatic secretory pathways, reducing secretome gene expression and circulating serum proteins, and downregulated genes involved in endoplasmic reticulum (ER) translocation, glycosylation, folding, and trafficking. Concurrently, PPAR activation enhanced proteasome activity, which was associated with selective induction of proteasome 26S subunit non-ATPase (PSMD) family members. In addition, hepatic protein synthesis was strongly attenuated. This was associated with an increase in the inhibitory phosphorylation of the eukaryotic translation initiation factor 2 (eIF2), that in turn was linked to disrupted iron homeostasis. Together, these findings identify PPAR as a regulator of proteostasis, suppressing protein synthesis and secretion while promoting protein degradation pathways. Beyond its canonical role in lipid and glucose metabolism, we conclude that PPAR exerts an additional energy-conserving function by coordinating proteostasis, expanding our understanding of its systemic metabolic role.

physiology↗
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

TCR signaling via NFATc1 constrains IL-15-induced NK-like activation of human memory CD8+ T cells

Here we investigated the regulatory mechanisms of TCR-independent bystander activation and NK-like cytotoxicity of human memory CD8+ T cells. We found that TCR signals suppressed characteristic features of IL-15-induced CD8+ T-cell activation, including increased NKG2D expression and upregulation of genes related to NK cytotoxicity and IFN response. Moreover, ionomycin suppressed IL-15-induced bystander activation and NK-like cytotoxicity, indicating that Ca2+-calcineurin signaling is responsible for TCR-mediated suppression of IL-15-induced bystander activation. In detail, NFATc1 suppressed IL-15-induced bystander activation via binding to AP-1 that is necessary for the IL-15-induced upregulation of NK cytotoxicity-related genes. Consistent with these results, calcineurin inhibitors enhanced IL-15-induced NKG2D expression in the presence of TCR signals. Additionally, we defined genes upregulated by IL-15 and downregulated by concurrent TCR signals as an IL-15-induced bystander activation gene set, and found that this gene signature was upregulated in bystander CD8+ T cells from patients with hepatitis A virus infection. This study paves the way for further investigation of bystander CD8+ T-cell activation in various pathological conditions, and its regulation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/632884v2_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@1e6c320org.highwire.dtl.DTLVardef@114a23eorg.highwire.dtl.DTLVardef@1a7b9edorg.highwire.dtl.DTLVardef@9faccc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITCR signaling downregulates IL-15-induced transcriptomic features related to NK-like bystander activation of human memory CD8+ T cells via the Ca2+-calcineurin pathway. C_LIO_LINFATc1 suppresses IL-15-induced bystander activation via binding to AP-1, which is responsible for IL-15-induced NK-like cytotoxic activity. C_LIO_LICalcineurin inhibitors cannot suppress IL-15-induced bystander CD8+ T-cell activation, and paradoxically increase IL-15-induced NKG2D expression in the presence of TCR signals. C_LIO_LIGenes upregulated by IL-15 and downregulated by concurrent TCR signals define the gene set of bystander CD8+ T-cell activation, which was validated in disease contexts. C_LI

immunology↗
bioRxiv2024

Excitatory Cortical Neurons from CDKL5 Deficiency Disorder Patient-Derived Organoids Show Early Hyperexcitability Not Identified in Neurogenin2 Induced Neurons

CDKL5 deficiency disorder (CDD) is a rare developmental and epileptic encephalopathy resulting from variants in cyclin-dependent kinase-like 5 (CDKL5) that lead to impaired kinase activity or loss of function. CDD is one of the most common genetic etiologies identified in epilepsy cohorts. To study how CDKL5 variants impact human neuronal activity, gene expression and morphology, CDD patient-derived induced pluripotent stem cells and their isogenic controls were differentiated into excitatory neurons using either an NGN2 induction protocol or a guided cortical organoid differentiation. Patient-derived neurons from both differentiation paradigms had decreased phosphorylated EB2, a known molecular target of CDKL5. Induced neurons showed no detectable differences between cases and isogenic controls in network activity using a multielectrode array, or in MAP2+ neurite length, and only two genes were differentially expressed. However, patient-derived neurons from the organoid differentiation showed increased synchrony and weighted mean firing rate on the multielectrode array within the first month of network maturation. CDD patient-derived cortical neurons had lower expression of CDKL5 and HS3ST1, which may change the extracellular matrix around the synapse and contribute to hyperexcitability. Similar to the induced neurons, there were no differences in neurite length across or within patient-control cell lines. Induced neurons have poor cortical specification while the organoid derived neurons expressed cortical markers, suggesting that the changes in neuronal excitability and gene expression are specific to cortical excitatory neurons. Examining molecular mechanisms of early hyperexcitability in cortical neurons is a promising avenue for identification of CDD therapeutics. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/622878v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@9d84b8org.highwire.dtl.DTLVardef@1745073org.highwire.dtl.DTLVardef@14dbd20org.highwire.dtl.DTLVardef@bba058_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗
bioRxiv2024

Mosaic display of stable hemagglutinin monomers induces broad immune responses

The nature of the interplay between immunity and viral variation is infinitely adaptive. Infection frequently induces immune responses against variation-prone epitopes, rather than against spatially hidden conserved epitopes. It thus remains a substantial challenge to elicit the immune responses to the conserved epitopes providing broad-spectrum immunity. We developed an approach of scaffold-mediated mosaic display to present monomeric influenza virus hemagglutinins (HAs), which exposes highly conserved stem and interface epitopes. Stable monomers were rationally engineered from H1 and H3 subtypes and B type HA trimers, with amino acid mutations at the monomer-monomer interface and for disulfide bond formation, and fused to a self-assembling scaffold, to generate a mosaic HA monomer-displaying nanoparticle, 3HA-np. Immunization with 3HA-np induced broadly neutralizing antibodies (bnAbs) in mice and ferrets and protected against challenges with H1N1 and H3N2 viruses. Competitive immunoassays revealed that 3HA-np induced high interface- and stem-binding Ab titers as compared to head Ab titers, indicating that the monomeric and mosaic nature of 3HA-np elicit cross-reactive Abs. Our results suggest that exposure of the hidden conserved epitope by monomer-displaying nanoparticles is a promising approach to generate a universal influenza vaccine.

bioengineering↗
bioRxiv2024

Vaginal lactobacilli produce anti-inflammatory beta-carboline compounds.

The vaginal microbiome is a lactobacilli-dominant, human-adapted community consistently found in people around the world. Presence of lactobacilli-dominant vaginal microbial communities, apart from Lactobacillus iners, is associated with reduced vaginal inflammation and reduced levels of pro-inflammatory cytokines. Loss of lactobacilli-dominance is associated with inflammatory conditions such as bacterial vaginosis. It remains unclear if health-associated lactobacilli actively promote the anti-inflammatory immune homeostasis of the vaginal mucosa and if so, by which mechanisms. We have identified that Lactobacillus crispatus, a key vaginal bacterial species, secretes a family of {beta}-carboline compounds with anti-inflammatory activity. These compounds suppress NF{kappa}B and interferon signaling downstream of multiple pattern recognition receptors in human macrophages and significantly dampen type I interferon receptor activation. Topical vaginal application of an anti-inflammatory {beta}-carboline compound, perlolyrine, was sufficient to significantly reduce vaginal inflammation in a mouse model of genital herpes infection. Together, we identify a key family of compounds by which vaginal lactobacilli mediate host immune homeostasis and could highlight a new therapeutic avenue for vaginal inflammation.

microbiology↗
bioRxiv2023

Open-top Bessel beam two-photon light sheet microscopy for three-dimensional pathology

Nondestructive pathology based on three-dimensional (3D) optical microscopy holds promise as a complement to traditional destructive hematoxylin and eosin (H&E) stained slide-based pathology by providing cellular information in high throughput manner. However, conventional techniques provided superficial information only due to shallow imaging depths. Herein, we developed open-top two-photon light sheet microscopy (OT-TP-LSM) for intraoperative 3D pathology. An extended depth of field two-photon excitation light sheet was generated by scanning a nondiffractive Bessel beam, and selective planar imaging was conducted with cameras at 400 frames/s max during the lateral translation of tissue specimens. Intrinsic second harmonic generation was collected for additional extracellular matrix (ECM) visualization. OT-TP-LSM was tested in various human cancer specimens including skin, pancreas, and prostate. High imaging depths were achieved owing to long excitation wavelengths and long wavelength fluorophores. 3D visualization of both cells and ECM enhanced the ability of cancer detection. Furthermore, an unsupervised deep learning network was employed for the style transfer of OT-TP-LSM images to virtual H&E images. The virtual H&E images exhibited comparable histological characteristics to real ones. OT-TP-LSM may have the potential for histopathological examination in surgical and biopsy applications by rapidly providing 3D information.

pathology↗
bioRxiv2023

FAM210A mediates an inter-organelle crosstalk essential for protein synthesis and muscle growth in mouse

Mitochondria are not only essential for energy production in eukaryocytes but also a key regulator of intracellular signaling. Here, we report an unappreciated role of mitochondria in regulating cytosolic protein translation in skeletal muscle cells (myofibers). We show that the expression of mitochondrial protein FAM210A (Family With Sequence Similarity 210 Member A) is positively associated with muscle mass in mice and humans. Muscle-specific Myl1Cre-driven Fam210a knockout (Fam210aMKO) in mice reduces mitochondrial density and function, leading to progressive muscle atrophy and premature death. Metabolomic and biochemical analyses reveal that Fam210aMKO reverses the oxidative TCA cycle towards the reductive direction, resulting in acetyl-CoA accumulation and hyperacetylation of cytosolic proteins. Specifically, hyperacetylation of several ribosomal proteins leads to disassembly of ribosomes and translational defects. Transplantation of Fam210aMKO mitochondria into wildtype myoblasts is sufficient to elevate protein acetylation in recipient cells. These findings reveal a novel crosstalk between the mitochondrion and ribosome mediated by FAM210A.

cell biology↗
bioRxiv2023

Lipid Bilayer Strengthens the Cooperative Network of a Membrane-Integral Enzyme

Although membrane proteins fold and function in a lipid bilayer constituting cell membranes, their structure and functionality can be recapitulated in diverse amphiphilic assemblies whose compositions deviate from native membranes. It remains unclear how various hydrophobic environments can stabilize membrane proteins and whether lipids play any role therein. Here, using the evolutionary unrelated -helical and {beta}-barrel membrane proteins of Escherichia coli, we find that the hydrophobic thickness and the strength of amphiphile- amphiphile packing are critical environmental determinants of membrane protein stability. Lipid solvation enhances stability by facilitating residue burial in the protein interior and strengthens the cooperative network by promoting the propagation of local structural perturbations. This study demonstrates that lipids not only modulate membrane proteins stability but also their response to external stimuli.

biophysics↗
bioRxiv2023

An interpretable ML model to characterize patient-specific HLA-I antigen presentation

Personalized immunotherapy holds the promise of revolutionizing cancer prevention and treatment. However, selecting HLA-bound peptide targets that are specific to patient tumors has been challenging due to a lack of patient-specific antigen presentation models. Here, we present epiNB, a white-box, positive-example-only, semi-supervised method based on Naive Bayes formulation, with information content-based feature selection, to achieve accurate modeling using Mass Spectrometry data eluted from mono-allelic cell lines and patient-derived cell lines. In addition to achieving state-of-the-art accuracy, epiNB yields novel insights into the structural properties, such as interactions of peptide positions, that appear important for modeling personalized, tumor-specific antigen presentation. epiNB uses substantially less parameters than neural networks, does not require hyperparameter tweaking and can efficiently train and run on our web portal (https://epinbweb.streamlit.app/) or a regular PC/laptop, making it easily applicable in translational settings.

bioinformatics↗
bioRxiv2022

novoRNABreak: local assembly for novel splice junction and fusion transcript detection from RNA-seq data

We present novoRNABreak, a unified framework for cancer specific novel splice junction and fusion transcript detection in RNA-seq data obtained from human cancer samples. novoRNABreak is based on a local assembly model, which offers a tradeoff between the alignment-based and de novo whole transcriptome assembly (WTA) approaches, namely, being more sensitive in assembling novel junctions that cannot be directly aligned, and more efficient due to the strategy that focuses on junctions rather than full-length transcripts. The performance of novoRNABreak is demonstrated by a comprehensive set of experiments using synthetic data generated based on genome reference, as well as real RNA-seq data from breast cancer and prostate cancer samples. The results show that novoRNABreak can detect novel splice junctions and fusion transcripts efficiently with high sensitivity and reasonable specificity.

bioinformatics↗
bioRxiv2022

PRMT5 links lipid metabolism to contractile function of skeletal muscles

The skeletal muscle plays a key role in systemic energy homeostasis besides its canonical contractile function, but what couples these functions is poorly defined. Protein Arginine MethylTransferase 5 (PRMT5) is a well-known oncoprotein but also expressed in healthy tissues with unclear physiological functions. As adult muscles express high levels of Prmt5, we generated myocyte-specific Prmt5 knockout (Prmt5MKO) mice. We observed reduced muscle mass, oxidative capacity, force production and exercise performance in Prmt5MKO mice. The motor deficiency is associated with scarce lipid droplets in myofibers due to defects in lipid biosynthesis and degradation. First, Prmt5MKO reduced demethylation and stability of Sterol Regulatory Element-Binding Transcription Factor 1a (SREBP1a), a master regulator of de novo lipogenesis. Second, Prmt5MKO impaired the repressive H4R3Me2s (histone H4 arginine-3 symmetric demethylation) at the Pnpla2 gene, elevating the level of its encoded protein ATGL, the rate-limiting enzyme catalyzing lipolysis. Accordingly, myocyte-specific double knockout of Pnpla2 and Prmt5 normalized muscle mass and function. Together, our findings delineate a physiological function of PRMT5 in linking lipid metabolism to contractile function of myofibers.

molecular biology↗
bioRxiv2022

Vitamin B2 enables peroxisome proliferator-activated receptor α regulation of fasting glucose availability

Flavin adenine dinucleotide (FAD) interacts with flavoproteins to mediate oxidation-reduction reactions required for cellular energy demands. Not surprisingly, mutations that alter FAD binding to flavoproteins cause rare inborn errors of metabolism (IEMs) that disrupt liver function and render fasting intolerance, hepatic steatosis, and lipodystrophy. In our study, depleting FAD pools in mice with a vitamin B2 deficient diet (B2D) caused phenotypes associated with organic acidemias and other IEMs, including reduced body weight, hypoglycemia, and fatty liver disease. Integrated discovery approaches revealed B2D tempered fasting activation of target genes for the nuclear receptor PPAR, including those required for gluconeogenesis. Treatment with the PPAR agonist fenofibrate activated the integrated stress response and refilled amino acid substrates to rescue fasting glucose availability and overcome B2D phenotypes. Overall, these findings reveal PPAR governs metabolic responses to FAD availability and nominate its pharmacologic activation as strategies for organic acidemias.

physiology↗
bioRxiv2022

Computational conjugate adaptive optics for longitudinal through-skull imaging of cortical myelin

We present a 1.3-m reflection matrix microscope and computational conjugate adaptive optics algorithm for label-free longitudinal imaging of cortical myelin through an intact mouse skull. The myelination processes of the same mice were observed from 3 to 10 postnatal weeks down to cortical layer 4 with a near-diffraction-limited resolution of 0.79 {micro}m. Our system will expedite the investigations on the role of myelination in learning, memory, and brain disorders.

neuroscience↗