Biology subjects

Kim, H.-R.

Publications and source records attributed to Kim, H.-R..

11 recordsLinked to original sources

bioRxiv2026

Staged heavy-chain filtering enables Fab discovery from combinatorially intractable library spaces

BackgroundCombinatorial fragment antigen-binding (Fab) libraries encode an immense heavy-light chain pairing space, often exceeding 10{superscript 1} possible combinations, which far surpasses the diversity that can be experimentally constructed and screened in display systems. As a result, direct Fab screening samples only a small fraction of the theoretical search space, creating a practical bottleneck for functional binder discovery. ResultsHere, we frame Fab discovery as a staged search problem by decoupling heavy-chain (HC) and light-chain (LC) exploration. We implemented a sequential HC preselection-remating workflow in yeast surface display, in which antigen-reactive HC variants are first enriched and subsequently recombined with a diverse LC repertoire to reconstruct a focused Fab library. In a SARS-CoV-2 spike-targeted campaign, HC and LC libraries of 2.05 x 10 and 2.33 x 10 members corresponded to a theoretical pairing space of approximately 4.8 x 10{superscript 1} combinations. Sequential HC enrichment followed by LC remating allowed recovery of multiple functional Fab clones from a tractable library scale of approximately 10, including clones that shared a common HC scaffold but carried distinct LC partners. A representative recombinant IgG output showed broad but heterogeneous spike/RBD binding, measurable pseudovirus neutralization activity (EC = 11.1 nM), and compatibility with standard early biophysical characterization after full-length IgG reformatting. ConclusionsThese results provide proof of principle that combinatorial Fab discovery can be approached as a staged exploration problem under realistic library-size constraints. By focusing downstream Fab reconstruction on an antigen-compatible HC subspace, sequential HC preselection followed by LC remating offers a practical strategy for exploring otherwise intractable antibody pairing landscapes in eukaryotic display systems.

bioengineering↗

bioRxiv2026

Targeting Noncanonical TEAD Axis to Overcome DNA Repair-Driven Chemoresistance

How transcription factors contribute to DNA damage repair (DDR) independent of canonical gene regulation remains poorly understood. Here, we show that DNA double-strand break (DSB) triggers a functional state transition in TEAD, disengaging it from YAP-dependent transcription and translocating it to DNA lesions as a chromatin-associated DDR factor. Upon genotoxic stress, TEAD is rapidly recruited to damaged chromatin through a biphasic mechanism involving early poly(ADP-ribose)-dependent recruitment followed by ATM-driven {gamma}H2AX-mediated retention. At DNA lesions, TEAD constrains chromatin over-relaxation, suppresses excessive end resection, and promotes non-homologous end joining (NHEJ) independent of its canonical function. Conserved residues within the TEA domain mediate this noncanonical chromatin engagement of TEAD and define a druggable N-terminal interface. Pharmacological targeting of this interface impaired TEAD-dependent DSB repair and sensitized tumors to chemotherapy. Together, these findings establish noncanonical TEAD as a critical DNA repair factor and a clinically actionable driver of chemoresistance, while providing a conceptual framework for understanding how broader families of transcription factors may be repurposed as targetable DNA damage regulators in cancer.

cancer biology↗

bioRxiv2025

T-Cell Synaptosomes Orchestrate Long-Term Anti-Tumor Immunity via Proliferative and Metabolic Reprogramming

A defining feature of T-cell activation is its dependence on physical contact with antigen-presenting cells (APCs). During this interaction, activated T cells release microvesicles, known as T-cell immunological synaptosomes (TIS), onto the surface of APCs. While TIS are known to activate APCs, their broader in vivo functions remain largely unexplored. Here, we show that TIS are primarily phagocytosed by macrophages and dendritic cells, persist intracellularly for several days, and reprogram these cells in a manner distinct from LPS. TIS upregulate genes involved in metabolism, proliferation, and anti-inflammatory responses, and promote immune cell recruitment, including eosinophils. Notably, TIS induce minimal immune activation upon initial exposure but trigger a rapid and robust response upon secondary administration, indicating a priming effect reminiscent of adaptive immunity. In an MC38 colon cancer model, TIS treatment resulted in near-complete tumor suppression and durable protection upon rechallenge, highlighting their potential as a potent and long-lasting immunotherapeutic platform.

immunology↗

bioRxiv2024

Chemical tools to define and manipulate interferon-inducible Ubl protease USP18

Ubiquitin-specific protease 18 (USP18) is a multifunctional cysteine protease primarily responsible for deconjugating interferon-inducible ubiquitin-like (Ubl) modifier ISG15 from protein substrates. Here, we report the design and synthesis of activity-based probes (ABPs) capable of selectively detecting USP18 activity over other ISG15 cross-reactive deubiquitinases (DUBs) by incorporating unnatural amino acids into the C-terminal tail of ISG15. Combining with a ubiquitin-based DUB ABP, the selective USP18 ABP is employed in a chemoproteomic screening platform to identify and assess inhibitors of DUBs including USP18. We further demonstrate that USP18 ABPs can be utilized to profile differential activities of USP18 in lung cancer cell lines, providing a strategy that will help define the activity-related landscape of USP18 in different disease states and unravel important (de)ISGylation-dependent biological processes.

molecular biology↗

bioRxiv2024

In-situ microscopy-assisted meniscus-guided coating for highly sensitive reduced graphene oxide-based nanocomposite biosensor

Meniscus-guided coating provides great potential for fabricating the nanomaterial-based thin film into high-performance biomedical devices due to the strong relationship between its experimental parameters and the resulting structural properties. However, the complex leverages of various fluid dynamics phenomena hamper optimization of structural properties and device performances. This is due to the absence of in-depth analytical techniques to observe, interpret, and control the solidification process. In this work, we propose an analytical strategy based on the rheological properties of a rGO-based solution using computational fluid dynamics modeling and in situ high-speed microscopy. Through this, we reveal the principles of the solidification mechanism that creates a rGO-based nanocomposite in the form of highly- and evenly-wrinkled thin film and the experimental condition at which this mechanism occurs. The optimized thin film presents high electroconductivity, low chip-to-chip signal variation, and multiplexed electrochemical biosensing performance for three classes of antibodies related to the excessive enrichment of endoplasmic reticulum stress, with detection limits of picomolar levels. This optimizing technique can be universally applied to understanding various solution-based coating systems, and can streamline the production of large-area and high-quality nanocomposite biosensors.

bioengineering↗

bioRxiv2023

Mitochondrial thermogenesis regulates heat-shock response in the nucleus

Mitochondrial thermogenesis is a process in which heat is generated by mitochondrial respiration. In living organisms, the thermogenic mechanisms that maintain body temperature have been studied extensively in fat cells, with little knowledge on how mitochondrial heat may act beyond energy expenditure. Here, we highlighted exothermic oxygen reduction reaction ({Delta}Hf{degrees} = -285 kJ/mol) is the main source of the protonophore-induced mitochondrial thermogenesis and this heat was conducted to other cellular organelles, including the nuclei. As a result, mitochondrial heat that reached the nucleus initiated the classical heat shock response, including the formation of nuclear stress granules and localization of heat shock factor 1 to chromatin. Consequently, activated HSF1 increases gene expression associated with the response to thermal stress in mammalian cells. Our results illustrate heat generated within the cells as a potential source of mitochondrial-nucleus communication and expand our understanding of the biological functions of mitochondria in cell physiology.

cell biology↗

bioRxiv2023

Stitching flexible electronics into the brain

Understanding complex neuronal networks requires monitoring long-term neuronal activity in various regions of the brain. Significant progress has been made in multi-site implantations of well-designed probes, such as multi-site implantation of Si-based and polymer-based probes. However, these multi-probe strategies have been limited by the sizes and weights of interfaces to the multiple probes and the inability to track the activity of the same neurons and changes in neuronal activity over longer time periods. Here, we report a long single flexible probe that can be implanted by stitching into multiple regions of the mouse brain and subsequently transmit chronically-stable neuronal signals from the multiple sites via a single low-mass interface. We implanted the probe at four different sites using a glass capillary needle or two sites using an ultrathin metal needle. In-vitro tests in brain-mimicking hydrogel showed that multi-site probe implantations achieved a high connection yield of >86%. In-vivo histological images at each site of probes, implanted by stitching using either glass capillary or ultrathin metal insertion needles exhibit seamless tissue-probe interfaces with negligible chronic immune response. In addition, electrophysiology studies demonstrated the ability to track single neuron activities at every injection site with chronic stability over at least one month. Notably, the measured spike amplitudes and signal-to-noise ratios at different implantation sites showed no statistically significant differences. Multi-site stitching implantation of flexible electronics in the brain opens up new opportunities for both fundamental neuroscience research and electrotherapeutic applications.

bioengineering↗

bioRxiv2023

Partial in vivo reprogramming enables injury-free intestinal regeneration via autonomous Ptgs1 induction

Tissue regeneration after injury involves the dedifferentiation of somatic cells, a natural adaptive reprogramming process that leads to the emergence of injury-responsive cells with fetal-like characteristics in the intestinal epithelium. However, there is no direct evidence that adaptive reprogramming involves a shared molecular mechanism with direct cellular reprogramming. Here, we induced dedifferentiation of intestinal epithelial cells through forced partial reprogramming in vivo using "Yamanaka factors" (Oct4, Sox2, Klf4, and c-Myc: OSKM). The OSKM-induced dedifferentiation showed similar molecular features of intestinal regeneration, including a rapid transition from homeostatic cell types to injury-responsive-like cell types. These injury-responsive-like cells, sharing a gene signature of revival stem cells and atrophy-induced villus epithelial cells, actively assisted tissue regeneration following ionizing radiation-induced acute tissue damage. In contrast to normal intestinal regeneration, which involves epi-mesenchymal crosstalk through induction of Ptgs2 (encoding Cox2) upon injury, the OSKM expression promotes the autonomous production of prostaglandin E2 via epithelial Ptgs1 (encoding Cox1) expression. These results indicate that prostaglandin synthesis is a common mechanism for intestine epithelial regeneration but involves a different enzyme (Ptgs1 for Cox1) when partial reprogramming is directly applied to the intestinal epithelium.

cell biology↗

bioRxiv2023

Covalent inhibition by a natural product-inspired latent electrophile

Strategies to target specific protein cysteines are critical to covalent probe and drug discovery. 3-bromo-4,5-dihy-droxazole is a natural product-inspired, synthetically accessible electrophilic moiety that has previously been shown to react with nucleophilic cysteines in the active site of purified enzymes. Here we define the global cysteine reactivity and selectivity of a set of 3-bromo-4,5-dihydroxazole-functionalized chemical fragments using competitive chemoproteomic profiling methods. Our study demonstrates that 3-bromo-4,5-dihydroxazoles capably engage reactive cysteine residues in the human proteome and the selectivity landscape of cysteines liganded by 3-bromo-4,5-dihydroxazoles is distinct from that of haloacetamide electrophiles. Given its tem-pered reactivity, 3-bromo-4,5-dihydroxazoles showed restricted, selective engagement with proteins driven by interactions between a tunable binding element and the complementary protein sites. We further validate that 3-bromo-4,5-dihydroxazoles form covalent conjugates with glutathione S-transferase Pi (GSTP1) and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1), emerging anti-cancer targets. Together, this study expands the spectrum of optimizable chemical tools for covalent ligand discovery and high-lights the utility of 3-bromo-4,5-dihydroxazole as a cysteine-reactive electrophile. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=57 SRC="FIGDIR/small/524242v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@13b987eorg.highwire.dtl.DTLVardef@1987ae1org.highwire.dtl.DTLVardef@1ab4fb9org.highwire.dtl.DTLVardef@1ff1f71_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2022

Trogocytic-molting of T-cell microvilli controls T-cell clonal expansion

Internalization of the T-cell antigen receptor (TCR) is intimately linked to T-cell activation: a phenomenon thought to be related to the "exhaustion" of T-cell responses. To date, however, no report has considered that during physical interaction with cognate antigen-presenting cells, T cells release many TCRs via T-cell microvilli particles, which are derived from finger-like membrane structures (microvilli) in a combined process of trogocytosis and enzymatic vesiculation and correspond with the loss of membrane TCRs and many external membrane components. Surprisingly, in contrast to TCR internalization, this event leads to rapid upregulation of surface TCRs and remarkable metabolic reprogramming of cholesterol and fatty acids synthesis to meet the demands of clonal expansion, which drives multiple rounds of division and cell survival. We called this event "trogocytic-molting," which represents an intrinsic molecular basis of T-cell clonal expansion by which T cells gain increased sensitivity to low antigen concentrations. TEASER"Trogocytic-molting," led to the rapid upregulation of surface TCRs and tremendous metabolic reprogramming to meet the demands of clonal expansion.

immunology↗

bioRxiv2018

Attenuation of obesity and related metabolic disorders by the individual or combination treatment with IL-2/anti-IL-2 complex and hyperbaric oxygen

Obesity is the disease accumulating excessive fat in the body. The prevalence of obesity and related metabolic disorders is increasing every year worldwide. Immunologically, obesity is a chronic low-grade inflammatory state with the increase of M1 macrophages and decrease of regulatory T cells (Tregs). IL-2/anti-IL-2 complex (IL-2C) and hyperbaric oxygen (HBO) are known to expand Tregs in vivo and suppress inflammation. Therefore, in this study, IL-2C and HBO were investigated for the preventive effect of obesity and related metabolic disorders. Male C57BL/6 mice were fed with a high-fat diet (HFD) for 16 weeks, and counterparts were fed with a low-fat diet (LFD). At the end of the experiment, the body weight gain and impaired glucose metabolism, elevated levels of insulin and total cholesterol induced by HFD were improved by the individual or combination treatment with Il-2C and HBO. Histological examination of the epididymal white adipose tissue showed adipocyte hypertrophy and many crown-like structures in the HFD control groups. In addition, the liver showed the progression of non-alcoholic fatty liver disease (NAFLD) in the HFD control groups, but it was significantly improved by the individual or combination treatment with IL-2C and HBO.\n\nAs for the underlying mechanism, inflammation induced by obesity was decreased, and HIF-1 expression by adipocyte hypertrophy was also reduced by the individual or combination treatment with IL-2C and HBO. In addition, adipose tissue browning was activated in brown and inguinal adipose tissue, and the expression of UCP-1 involved in the thermogenesis was increased by the individual or combination treatment with IL-2C and HBO. Overall, these results suggested that IL-2C and HBO might be a new promising immunotherapy for the treatment of obesity and related metabolic disorders by regulation of inflammation and activation of adipose tissue browning.

immunology↗