Biology subjects

Kim, C. H.

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

At least 19 recordsLinked to original sources

bioRxiv2026

Macrophage-Derived 25-Hydroxycholesterol Drives Statin-Associated Acute Kidney Injury

Although acute kidney injury (AKI) has been implicated as a potential adverse effect of statin therapy, experimental evidence supporting this association remains limited. Here, we investigated whether elevated levels of 25-hydroxycholesterol (25-HC), an oxysterol produced by activated macrophages and monocytes, increase susceptibility to statin-induced AKI. We found that atorvastatin and fluvastatin induced cell death in proximal tubular cells when combined with 25-HC. Consistently, administration of low-dose lipopolysaccharide triggered AKI in statin-treated mice. Mechanistically, impaired protein prenylation disrupted the autophagosome-lysosome pathway in proximal tubular cells. AKI was attenuated by mevalonate supplementation, which restored protein prenylation, and by macrophage/monocyte depletion, which reduced the cellular sources of 25-HC. Furthermore, combined exposure to fluvastatin and 25-HC increased kidney injury molecule-1 (KIM-1) expression in human induced pluripotent stem cell-derived kidney organoids. Together, these findings suggest that elevated macrophage-derived 25-HC under conditions of infection, inflammation, or major surgery may increase susceptibility to statin-induced AKI. Our study identifies a previously unrecognized interaction between statins and 25-HC and suggests potential strategies to mitigate kidney injury while preserving the therapeutic benefits of statins.

pharmacology and toxicology↗

bioRxiv2026

Chirality-Driven Photonic PCR Enables Label-Free Genetic Amplification

Photonic polymerase chain reaction (PCR) offers a rapid alternative to conventional thermal cycling for genetic amplification, but current platforms are limited by low photothermal conversion efficiencies and a dependence on bulky fluorescent monitoring systems. Here we report a chirality-driven photonic amplification paradigm that achieves both accelerated nucleic acid replication and direct, label-free detection. By leveraging chiral plasmonic nanoparticles, we exploit their elevated absorption cross-sections to achieve exceptional light-to-heat conversion and rapid thermal relaxation, significantly accelerating heating and cooling rates during cycling. We show that localized chiral near-fields generated by these chiral plasmonic nanoparticles optimize DNA polymerase conformational dynamics, lowering the activation energy barrier for synthesis and boosting amplification efficiency. Furthermore, by tracking the reaction with circular dichroism spectroscopy, we directly monitor the intrinsic chiroptical signature of amplifying DNA, completely eliminating the need for external fluorescent dyes or labeled probes. We validate this system using SARS-CoV-2 E-gene plasmid DNA templates, demonstrating rapid, label-free amplification and single-copy detection within clinically relevant timelines. By bridging asymmetric photothermal dynamics with chiral-field-induced enzymatic activation, this work translates chiroplasmonic materials from fundamental physics into high-performance, point-of-care molecular diagnostics.

bioengineering↗

bioRxiv2026

Emergence of tunneling nanotube-like intervesicular connections

Tunneling nanotubes (TNTs) are actin-supported membrane bridges that mediate long-range intercellular communication and direct transfer of signaling molecules, organelles, and pathogenic cargo, yet the physicochemical mechanisms underlying their formation and organization remain poorly understood. Here we show that TNT-like intervesicular connections emerge from minimal physicochemical interactions between actin filaments and lipid membranes. Upon Mg2+ exposure, actin-encapsulating vesicles spontaneously generated actin bundle-embedded lipid nanotubes (AT-LNTs) that formed stable intervesicular networks. Mg2+ simultaneously induced actin polymerization, filament bundling, and electrostatic recruitment of F-actin to phosphatidylcholine membranes, enabling membrane tubulation without actin-binding proteins. Systematic perturbation of membrane phase, membrane tension, Mg2+ concentration, ionic strength, and actin concentration revealed that AT-LNT formation occurs only within a narrow physicochemical regime where membrane deformation and actin-membrane coupling are simultaneously permissive. The resulting AT-LNTs reproduced key structural and dynamic features of cellular TNTs, including bundled organization, helical unwinding, lumenal diffusion, and spontaneous bridging between synthetic vesicles and living cells. These findings establish a minimal biophysical framework for understanding the emergence of intercellular membrane connections in living systems and provide a foundation for engineering communication between synthetic and living cell.

synthetic biology↗

bioRxiv2026

Generation of Human Taste Bud Organoids as a Human-Mimetic Platform for Modeling Taste Perception

We established a human taste bud organoid system derived from circumvallate papillae. This model has been highly anticipated in the field of taste research, where feasible approaches for validating taste biology discovered in rodent models have been limited. Through a stepwise exploratory strategy, we systematically identified and optimized the niche factors required to maintain taste bud organoids and promote their differentiation. This human taste bud organoid system comprises Type I-IV taste receptor cells (TRCs) as well as stem/progenitor cells, and its sensory receptor cells exhibit calcium responses to taste stimuli. Using this system, we identified robust Wnt signaling as a requirement for optimal TRC fate progression, uncovered a human-specific transcriptional program in LGR5 cells, and identified previously unrecognized molecular markers for Type I TRCs. By recapitulating native human taste bud cell diversity and function, this organoid provides a tractable platform for studying human taste biology and dysfunction.

developmental biology↗

bioRxiv2025

Figure--ground relationship of voices in musical structure modulates reciprocal frontotemporal connectivity

When listening to polyphonic music, we often perceive a melody as the figure against the ground of accompanying sounds. However, with repeated exposure, this figure-ground relationship may naturally shift, allowing the melody to recede into the ground. In a previous study, we found the consistent pattern of frontotemporal connectivity for the "Twinkle, Twinkle, Little Star" (TTLS) melody in the headings of two variations (II and IV) in Mozarts 12 Variations, K. 265, indicating that the TTLS melody, but not the different lower voices, was the figure. However, the frontotemporal connectivity pattern may change in the same phrases repeating in the two variations. In the current study, we examined how frontotemporal connectivity changes in the repeated phrases. In the results, the frontotemporal connectivity pattern between the two variations changed in the final phrase after repeated passages. This suggests that the shift in the figure-ground relationship persists, with the TTLS melody becoming less prominent while the lower voices become relatively more prominent. Additionally, frontotemporal connectivity was strongly correlated with temporofrontal connectivity in the opposite direction. Finally, our data indicate that TTLS melody-based and sensory-based processes in response to a switched figure-ground relationship, are incorporated into the bidirectional connections between frontotemporal and temporofrontal connectivity. Our study highlights the brains ability to reconfigure figure- ground relationships in the processing of musical voices.

neuroscience↗

bioRxiv2025

Gram-positive bacterial cell wall components inhibit herpes simplex virus infection.

The role of the mucosal microbiome in viral infections remains unclear. Genital herpes, caused by herpes simplex virus 1 and 2 (HSV-1 and HSV-2), is among the most prevalent sexually transmitted infections worldwide. Despite evidence linking vaginal Lactobacillus to protection against sexually transmitted viruses, the specific microbial components and mechanisms that mediate this defense are not well understood. Here, we show that multiple cell wall components from diverse gram-positive bacteria, including lactobacilli, inhibit HSV-1 and HSV-2 infection in cells and in a mouse model of genital herpes infection. Peptidoglycan (PG) and lipoteichoic acid (LTA), both major components of the gram-positive bacterial cell wall, significantly reduced HSV infectivity in vitro and improved survival and disease outcomes in mice. We further showed that Lactobacillus crispatus surface layer proteins SlpA and SlpB bind HSV-1 and inhibit infection. Antiviral effects of cell wall components were dose-dependent, relied on intact PG structure, and, in the case of PG and LTA, were independent of TLR2-mediated host signaling. Collectively, our findings identify a species-independent antiviral function for gram-positive bacterial cell wall components against HSV and suggest that the composition of the mucosal microbiome may play an underappreciated role in suppressing mucosal herpes infection in humans.

microbiology↗

bioRxiv2025

Cereblon-related mild intellectual disability disrupts response inhibition and uniformity of group--individual strategies

Temporal processing, including duration, is essential for survival and communication across species. Intellectual disability (ID), which has diverse causes, including Cereblon (CRBN), impairs duration discrimination. CRBN-related ID, link to abnormal cognitive behaviors, may disrupt both perception and behavior during duration discrimination. However, cross-species behavioral strategies, their variation with ID, and associated behavioral indices remain unclear. Here, humans and wild-type (WT) mice with typical intelligence, and CRBN knockout (KO) mice with ID, performed an auditory duration discrimination task with Long (10 s) and Short (2 s) cues. All groups distinguished stimulus durations, but latency-based strategies diverged. KO mice showed impulsivity and divergent responses at both individual and group levels, whereas WT mice and humans consistently delayed their responses by [~]2 s to the Short cue length, reflecting inhibition and convergent responses. In typical intelligence models, latencies for both stimuli clustered between 2-5 s, while in ID model depended on stimulus duration. Duration perception is a conserved cross-species capacity, while task-specific cognitive strategies are intrinsically preserved though variation emerges with ID. We suggest that latency indices dissociated inhibition from impulsivity, and convergence from divergence. We further suggest that CRBN-related ID preserves perceptual understanding but disrupts the shared behavioral language of typical intelligence.

neuroscience↗

bioRxiv2025

Exhausted-like effector CD8 T cells mediate immune-stromal interactions at mucosal Chronic Graft-versus-Host Disease onset

Chronic graft-versus-host disease (cGVHD) frequently follows allogeneic hematopoietic stem cell transplantation and impacts the mucosa. This atlas study highlights the role of exhausted-like effector CD8+ T cells (TEXEF) in oral mucosal cGVHD pathogenesis. Biopsies from the oral mucosa were collected at oral cGVHD onset or at six months post-transplant and analyzed using single-cell RNA sequencing and other modalities. At cGVHD onset, in addition to changes in the myeloid compartment, two distinct populations of CD8+T cells with a TEXEF phenotype were prevalent: an inflammatory CD8T cell cluster (CD8T_4) expressing CCL4, CD69, and TNFSF9, and an exhausted CD8T cell cluster (CD8T_5) characterized by the expression of CXCL13, HIF1A, and HLA-DRA, both correlated with clinical disease severity. Pseudo-time analysis suggests a transition from the inflammatory pre-exhausted CD8T_4 cluster to the cytolytic, terminally exhausted CD8T_5 cluster. The CXCL9-CXCR3 interactions among CD8+ T cells, fibroblasts and myeloid cells are implicated in tissue damage. Onset of cGVHD despite frequent oral mucosal FOXP3 regulatory CD4T cells suggests potential impaired Treg function or CD8+T cell dysfunction. These findings highlight TEXEF cells as key contributors to oral cGVHD pathology and potential therapeutic targets for mitigating sustained tissue injury in cGVHD.

immunology↗

bioRxiv2025

A Tonotopic Regulatory Axis Governing Isoform-Specific MYO7A Expression in Cochlear Hair Cells

Myo7a, a gene mutated in Usher syndrome and non-syndromic deafness, encodes an unconventional myosin essential for hair cell function. Our previous work revealed that cochlear hair cells express distinct Myo7a isoforms with unique spatial and cell type-specific patterns. The canonical isoform (Myo7a-C) and a novel isoform (Myo7a-N) are co-expressed in outer hair cells (OHCs) but exhibit opposing tonotopic gradients, while inner hair cells (IHCs) primarily express Myo7a-C. These isoforms arise from distinct transcriptional start sites, indicating separate regulatory inputs. Here, we identify an intronic cis-regulatory element, EnhancerA, essential for tonotopically graded Myo7a expression. EnhancerA deletion reduces MYO7A protein levels in a tonotopically varied manner, disrupts hair bundle morphogenesis, alters OHC mechanotransduction, and leads to hair cell degeneration and hearing loss. We further identify SIX2, a tonotopically expressed transcription factor that may interact with EnhancerA to regulate Myo7a-N in OHCs. These findings define a cis-trans regulatory axis critical for isoform-specific Myo7a expression and cochlear function. SignificanceCochlear hair cells rely on the molecular motor MYO7A for mechanosensory function. Our previous study revealed that Myo7a isoforms are differentially expressed in auditory hair cells, however, the mechanisms regulating this isoform-specific expression remain unclear. In this study, we identify a cis-regulatory element, EnhancerA, that governs MYO7A expression in a tonotopically graded manner. Furthermore, we demonstrate that the transcription factor SIX2 plays a role in regulation of MYO7A, and is essential for hair cell maintenance. These findings establish a mechanistic link between cochlear position and protein isoform diversity, highlighting how hair cells adapt to frequency-specific mechanical demands. Importantly, the tonotopic regulatory function of EnhancerA also offers new avenues for targeted gene therapy in auditory disorders.

neuroscience↗

bioRxiv2025

TMEM145 is a key component in stereociliary link structures of outer hair cells

Outer hair cells (OHCs) in the cochlea contain specialized stereociliary structures essential for auditory function. These include horizontal top connectors (HTCs), linking adjacent stereocilia and tectorial membrane-attachment crowns (TM-ACs), anchoring the tallest stereocilia to the tectorial membrane. The known molecular components of these structures, such as stereocilin, otogelin, otogelin-like, and tubby, lack transmembrane domains, suggesting the existence of anchoring proteins. This study identified TMEM145, a transmembrane protein with a Golgi dynamics (GOLD) domain, as a crucial OHC stereocilia component. TMEM145 was expressed in both OHCs and spiral ganglion neurons, with specific localization to TM-ACs and HTCs in OHCs. Tmem145 knockout (KO) mice exhibited profound hearing impairment at three weeks of age, with complete loss of distortion product otoacoustic emissions, indicating OHC dysfunction. Immunostaining and scanning electron microscopy revealed the absence of TM-ACs and HTCs in Tmem145 KO mice. In heterologous cell systems, TMEM145 interacted with stereocilin and tubby, facilitating their extracellular secretion. TMEM145 was undetectable in stereocilin KO and tubby mutant mice, indicating interdependence among these proteins. These findings establish TMEM145 as an essential membrane protein for the structural integrity of OHC stereocilia, providing insights into the molecular architecture of cochlear hair cells and their role in auditory function.

neuroscience↗

bioRxiv2025

Seq-Scope-eXpanded: Spatial Omics Beyond Optical Resolution

Sequencing-based spatial transcriptomics (sST) enables transcriptome-wide gene expression mapping but falls short of reaching the optical resolution (200-300 nm) of imaging-based methods. Here, we present Seq-Scope-X (Seq-Scope-eXpanded), which empowers submicrometer-resolution Seq-Scope with tissue expansion to surpass this limitation. By physically enlarging tissues, Seq-Scope-X minimizes transcript diffusion effects and increases spatial feature density by an additional order of magnitude. In liver tissue, this approach resolves nuclear and cytoplasmic compartments in nearly every single cell, uncovering widespread differences between nuclear and cytoplasmic transcriptome patterns. Independently confirmed by imaging-based methods, these results suggest that individual hepatocytes can dynamically switch their metabolic roles. Seq-Scope-X is also applicable to non-hepatic tissues such as brain and colon, and can be modified to perform spatial proteomic analysis, simultaneously profiling hundreds of barcode-tagged antibody stains at microscopic resolutions in mouse spleens and human tonsils. These findings establish Seq-Scope-X as a transformative tool for ultra-high-resolution whole-transcriptome and proteome profiling, offering unparalleled spatial precision and advancing our understanding of cellular architecture, function, and disease mechanisms.

genomics↗

bioRxiv2024

Type I interferon signaling enhances kainic acid-induced seizure severity

Epilepsy is a chronic neurological disorder characterized by recurrent seizures, yet the role and mechanisms of type I interferon (IFN) signaling in seizure conditions remain elusive. In this study, we demonstrate that type I IFN signaling exacerbates seizure phenotypes in a kainic acid-induced seizure mouse model. We found that the absence of type I IFN signaling in Ifnar1-/- mice led to decreased neuronal excitability and microglial activation in response to kainic acid stimulation. Conversely, intracerebroventricular injection of IFN-{beta} heightened the severity of kainic acid-induced seizures. In vitro calcium imaging revealed that IFN-{beta} treatment amplified both basal and kainic acid-induced neuronal excitability, though no significant difference was observed in basal neuronal excitability between wild-type and Ifnar1-/- neurons. Furthermore, Ifnar1-/- mice exhibited reduced mTOR activation in the brain following kainic acid administration. Consistent with this finding, IFN-{beta} treatment induced mTOR activation, as indicated by S6 phosphorylation in in vitro mixed glial cultures. Taken together, these results demonstrate the critical role of type I IFN signaling in seizure pathogenesis and suggest that targeting type I IFNs could be a promising therapeutic strategy for reducing seizure severity and mitigating epilepsy.

neuroscience↗

bioRxiv2024

Short-term memory errors are strongly associated with a drift in neural activity in the posterior parietal cortex

Understanding the neural mechanisms behind short-term memory (STM) errors is crucial for unraveling cognitive processes and addressing deficits associated with neuropsychiatric disorders. This study examines whether STM errors arise from misrepresentation of sensory information or decay in these representations over time. Using 2-photon calcium imaging in the posterior parietal cortex (PPC) of mice performing a delayed match-to-sample task, we identified a subset of PPC neurons exhibiting both directional and temporal selectivity. Contrary to the hypothesis that STM errors primarily stem from mis-encoding during the sample phase, our findings reveal that these errors are more strongly associated with a drift in neural activity during the delay period. This drift leads to a gradual divergence away from the correct representation, ultimately leading to incorrect behavioral responses. These results emphasize the importance of maintaining stable neural representations in the PPC for accurate STM. Furthermore, they highlight the potential for therapeutic interventions aimed at stabilizing PPC activity during delay periods as a strategy for mitigating cognitive impairments in conditions like schizophrenia.

animal behavior and cognition↗

bioRxiv2024

Frontotemporal connectivity changes reflect figure-ground reversal in multivoiced music

When listening to multivoiced music, it is possible to perceive distinct voices in differing pitch ranges independently. The melody that one focuses on becomes the figure, and other voices form the background. Shifting focus from one voice to another causes a figure-ground reversal, which may easily occur as a result of anticipation within repeated passages in a musical structure. We previously found that frontotemporal connectivity reflects changes in the melody of "Twinkle, Twinkle, Little Star" (TTLS) in Mozarts 12 Variations K. 265. We hypothesized that if frontotemporal connectivity remains unchanged in repeated passages, the melody of TTLS remains the figure; however, if connectivity changes, the melody shifts toward the background. Our findings show that frontotemporal connectivity only changed during the final, fourth repetition. This was accompanied by a bidirectional correlation in frontotemporal regions, implying both top-down and bottom-up processes. We captured a momentary figure-ground reversal in the multivoiced texture of continuously changing and developing music.

neuroscience↗

bioRxiv2024

Harmonization of the fastest and densest responses embodies human-like reaction time of mice

Reaction time (RT) is important in evaluating delayed latency in behavior. Unlike that of humans, the RT of animals, in which the stimulus-response relationship is not one-to-one due to repeated responses per trial, may exhibit two peaks of the fastest and densest responses in a distribution of responses. We determined whether the two peak latencies are aligned for a single RT by controlling stimulus duration. In delay conditioning with mice using sound cues of 10, 5, and 2s, the 2s group exhibited the strongest positive correlations between the two peaks, as well as responses number and accuracy rate, suggesting coupling of the fastest and densest responses, and a one-to-one relationship between stimulus and response, respectively. We propose the use of harmonization of the two peaks, elicited by stimuli that induce minimal responses, as a criterion for designing animal experiments to mimic humanlike RT.

animal behavior and cognition↗

bioRxiv2024

Correspondence of fentanyl brain pharmacokinetics and behavior measured via engineering opioids biosensors and computational ethology

Despite the ongoing epidemic of opioid use disorder and death by fentanyl overdose, opioids remain the gold standard for analgesics. Pharmacokinetics (PK) dictates the individuals experience and utility of drugs; however, PK and behavioral outcomes have been conventionally studied in separate groups, even in preclinical models. To bridge this gap, we developed the first class of sensitive, selective, and genetically encodable fluorescent opioid biosensors, iOpioidSnFRs, including the fentanyl sensor, iFentanylSnFR. We expressed iFentanylSnFR in the ventral tegmental area of mice and recorded [fentanyl] alongside videos of behaviors before and after administration. We developed a machine vision routine to quantify the effects of the behavior on locomotor activity. We found that mice receiving fentanyl exhibited a repetitive locomotor pattern that paralleled the [fentanyl] time course. In a separate experiment, mice navigating a complex maze for water showed a dose-dependent impairment in navigation, in which animals repeated incorrect paths to the exclusion of most of the unexplored maze for the duration of the average fentanyl time course. This approach complements classical operant conditioning experiments and introduces a key feature of human addiction, the ability to carry out an ethologically relevant survival task, only now quantified in rodents. Finally, we demonstrate the utility of iFentanylSnFR in detecting fentanyl spiked into human biofluids and the generalizability of engineering methods to evolve selective biosensors of other opioids, such as tapentadol and levorphanol. These results encourage diagnostic and continuous monitoring approaches to personalizing opioid regimens for humans.

neuroscience↗

bioRxiv2024

Detailed mechanisms for unintended large DNA deletions with CRISPR, base editors, and prime editors

CRISPR-Cas9 nucleases are versatile tools for genetic engineering cells and function by producing targeted double-strand breaks (DSBs) in the DNA sequence. However, the unintended production of large deletions (>100 bp) represents a challenge to the effective application of this genome-editing system. We optimized a long-range amplicon sequencing system and developed a k-mer sequence-alignment algorithm to simultaneously detect small DNA alteration events and large DNA deletions. With this workflow, we determined that CRISPR-Cas9 induced large deletions at varying frequencies in cancer cell lines, stem cells, and primary T cells. With CRISPR interference screening, we determined that end resection and the subsequent TMEJ [DNA polymerase theta-mediated end joining] repair process produce most large deletions. Furthermore, base editors and prime editors also generated large deletions despite employing mutated Cas9 "nickases" that produce single-strand breaks. Our findings reveal an important limitation of current genome-editing tools and identify strategies for mitigating unwanted large deletion events.

genetics↗

bioRxiv2023

Serum albumin maintains Wnt water-solubility and activity

Wnt proteins regulate adult tissue homeostasis and repair by driving stem cell self-renewal and differentiation. High-performance Wnt preparations have enormous therapeutic potential, especially alongside various stem cell technologies. Currently, most of these Wnt preparations contain FBS or the detergent CHAPS to maintain Wnt solubility and activity. Recently, afamin was identified as a serum factor that solubilizes Wnt3a in conditioned media (CM), obviating the requirement for animal sera. Here, we report serum albumin (SA) is required for afamin-mediated solubilization of Wnt3a in CM. Moreover, SA-mediated solubilization of purified Wnt3a in tubes does not require afamin. This means conventional CHAPS-Wnt3a preparations can be modified into SA-purified Wnt3a (SA-pWnt3a) preparations by exchanging CHAPS for SA through dialysis. SA-pWnt3a preparations effectively promote the growth of human stem cell organoids. These data suggest SA as a physiological factor for maintaining Wnt3a activity in therapeutic applications.

biochemistry↗