Biology subjects

Kim, S.-K.

Publications and source records attributed to Kim, S.-K..

15 recordsLinked to original sources

bioRxiv2026

Primary tumor transcriptomic signature is associated with locoregional dissemination in canine mammary carcinoma

Canine mammary carcinoma (CMC) exhibits heterogeneous metastatic behavior, while accurate assessment of locoregional dissemination may be limited by incomplete sampling, occult metastasis, and variable sentinel lymph node anatomy. We investigated whether primary-tumor transcriptomic programs are associated with locoregional dissemination. The training cohort comprised 113 CMC RNA sequencing samples classified by peritumoral lymphatic vessel invasion, and the independent evaluation cohort comprised 27 microarray samples classified by histopathologically confirmed lymph node (LN) metastasis. Expression profiles were mapped to human ortholog gene symbols, and single-sample gene set enrichment analysis (ssGSEA) was performed using Molecular Signatures Database (MSigDB) gene sets. Seven candidate gene sets selected through univariable screening and literature-guided curation were entered into least absolute shrinkage and selection operator (LASSO) logistic regression, yielding a four-gene-set transcriptomic risk score (RS). The RS showed an apparent receiver operating characteristic area under the curve (ROC-AUC) of 0.949 (95% confidence interval, 0.906-0.993) and precision-recall area under the curve (PR-AUC) of 0.725 in the training cohort; bootstrap internal validation yielded an optimism-corrected ROC-AUC of 0.920. In the evaluation cohort, the ROC-AUC was 0.890 (95% confidence interval, 0.766-1.000) and PR-AUC was 0.869. Discrimination was attenuated but retained in histologically restricted sensitivity analyses, and higher RS remained associated with locoregional dissemination after clinicopathologic adjustment. These findings support gene-set-level transcriptomic scoring as a potential complementary approach for characterizing dissemination-associated primary-tumor states in CMC.

cancer biology↗

bioRxiv2026

Identification of Pseudomonas aeruginosa genetic determinants that connect redox metabolism to alginate biosynthesis

Pseudomonas aeruginosa is a well-known human pathogen that contributes significantly to chronic infections, particularly in cystic fibrosis (CF) patients. During this chronic infection, P. aeruginosa undergoes a phenotype change, the inactivation of mucA, which leads to the production of exopolysaccharide alginate, known as mucoid, a key virulence factor associated with biofilm formation. This mucoid phenotype allows the bacterium to persist in the lungs of CF patients for the duration of their lives. Previously, we identified ebselen oxide (EbO) as an inhibitor that suppresses alginate production in P. aeruginosa. In the current study, we synthesized a series of structural analogs based on EbO and ebselen (Eb) and evaluated their ability to inhibit alginate production. These analogs did have similar or lower inhibitory activity than EbO. The mechanism by which EbO inhibits alginate production remains unclear. We employed RNA sequencing analysis of P. aeruginosa treated with inhibitors and identified several candidate genes potentially involved in this inhibitory pathway. Interestingly, we observed that a transposon and in-frame deletion mutants of the candidate genes were defective for alginate production. These findings suggest there are additional requirements for optimal alginate production in conditions that mimic the CF lung beyond the algD-A operon. IMPORTANCEWhen bacteria encounter the correct conditions, they can dedicate their energy toward a specific function to maximize the function. One example is the low calcium response in Yersinia pestis in which the bacteria arrest growth when grown at 37 {degrees}C in the absence of calcium because it uses all its energy for type III secretion. Another example is production of alginate by P. aeruginosa in the lungs of CF patients that can lead to occlusion of the airways. In both cases, the dedicated use of energy toward type III secretion for Y. pestis and alginate biosynthesis for P. aeruginosa reduces the ability of the bacteria to multiply. In the lab, suppressors can be easily identified that restore bacteria growth. The suppressor mutations are often located in the operons that are up-regulated and thereby prevent the execution of the energetically costly process. While these results indicate these processes are energetically costly, we still do not understand how the bacteria dedicate their energy toward these processes over other cellular processes such as growth. Previously, we identified ebselen oxide (EbO) as an inhibitor that suppresses alginate production in P. aeruginosa, but chemical analogues fail to improve the inhibitory activity. We used RNA sequencing analysis of P. aeruginosa treated with inhibitors and identified several candidate genes potentially involved in this inhibitory pathway. Interestingly, we observed that a transposon and in-frame deletion mutants of these genes involved in redox reactions were defective for alginate production. These findings suggest there proteins may shunt energy for optimal alginate production in conditions that mimic the CF lung beyond the algD-A operon. Results from P. aeruginosa alginate production may inform how other bacteria can similarly focus energy toward specific cellular processes.

microbiology↗

bioRxiv2025

A Retinoic Acid Autoregulatory Loop Governing Prefrontal-Motor Arealization

The frontal lobe comprises the prefrontal association cortex (PFC), which supports complex cognition and goal-directed behavior, and the motor cortex (MC), which executes movement. A hallmark of primate brain evolution is PFC expansion accompanied by a posterior displacement of the MC. Retinoic acid (RA) signaling has emerged as a key regulator of PFC specification and expansion. However, the mechanisms that spatially confine RA signaling within the developing PFC, and the downstream RA-responsive gene networks, remain poorly understood. Here we defined an RA-associated gene regulatory network (RA-GRN) in the developing human PFC and identified MEIS2, which encodes a transcription factor linked to intellectual disability and autism spectrum disorder (ASD), as its key hub of this network. Conditional deletion of Meis2 in postmitotic cortical excitatory neurons in mice results in a partial respecification of prospective prefrontal association territories toward motor-like molecular and connectional features, highlighting a critical role of postmitotic neurons in establishing and maintaining cortical areal identities. Concomitant with Meis2 loss, the population of excitatory neurons expressing the RA-synthesizing enzyme ALDH1A3, and consequently RA signaling itself, is markedly reduced in the developing medial prefrontal cortex (mPFC). These findings revealed a conserved autoregulatory loop: RA [->] MEIS2 [->] ALDH1A3 [->] RA that reinforces a PFC-enriched RA gradient and organizes the MC-PFC axis. Together, our findings reveal a postmitotic mechanism by which specific features of neuronal identity reinforce RA signaling to define key features of prefrontal and motor cortical territories, linking a classic morphogen to transcriptional identity, neural circuit formation and function, and potentially to psychiatric disorders.

neuroscience↗

bioRxiv2025

10,239 whole genomes with multiomic and clinical health information as the Korean population multiomic reference dataset

We present Korea10K, the largest genomic dataset of the Korean population, comprising 10,239 high-coverage whole genomes (mean depth 30x) with matched multiomic profiles and phenotype data. Korea10K achieves complete and near-complete discovery of very rare and ultra-rare alleles, respectively, at 9,000 Korean genomes. This dataset provides the high-quality population-specific imputation panel, enabling accurate inference of low-frequency variants. Admixture analyses confirm the genetic homogeneity of the Korean population, despite its diverse Y-chromosomal, mitochondrial, and HLA repertoires. This pattern reflects a long and continuous lineage history characterized by persistent internal admixture and genomic homogenization over thousands of years on the Korean peninsula. We also identified 16.8 million genomic variants that directly modify CG sites by creating or abolishing CG dinucleotides, providing the population-scale evidence of coordinated genomic-epigenomic regulatory mechanism in Koreans.

genomics↗

bioRxiv2025

Human-specific features of the cerebellum and ZP2-regulated synapse development

Understanding the unique features of the human brain compared to non-human primates has long intrigued humankind. The cerebellum refines motor coordination and cognitive functions, contributing to the evolutionary development of human adaptability and dexterity. To identify shared and divergent features across primates, we conducted single-nucleus transcriptomic and chromatin accessibility profiling of the adult cerebellar cortex in humans, chimpanzees, macaques, and marmosets. We revealed human-specific transcriptomic and regulatory features, particularly those involved in synaptogenesis. Notably, we identified an enrichment of the sperm receptor zona pellucida glycoprotein 2 (ZP2) and its potential interactors, known for their roles in gamete interaction, in human granule cells. Experimental data show that ZP2 expression in human granule cells is induced by pontine mossy fibers, reducing synaptic proteins at pontocerebellar glomerular synapses, and decreasing cerebellar neuron electrophysiological activity. This unexpected co-option of ZP2 in human-specific synapse regulation provides insights into the evolutionary specialization of the human cerebellum.

neuroscience↗

bioRxiv2025

Synaptic Ultrastructural Alterations in Human Focal Cortical Dysplasia: Insights from Volume Electron Microscopy

Focal cortical dysplasia (FCD) is a developmental disorder of the cerebral cortex and a leading cause of drug-resistant epilepsy in children and young adults. A disrupted excitation-inhibition (E-I) balance is a hallmark of neuronal hyperexcitability in FCD, yet the underlying synaptic ultrastructural alterations remain poorly understood. Using volume electron microscopy, we performed a detailed morphological assessment of synaptic density, size, and organelle distribution within synapses in the temporal cortical layer III of an FCD patient. Our quantitation revealed a reduced density of inhibitory (symmetric) synapses on pyramidal neuron cell bodies. Notably, the dysplastic region displayed a lower density of excitatory (asymmetric) synapses but contained extra-large excitatory synapses, which contained an increased number of synaptic vesicles. Additionally, inhibitory synapses were located further away from the nearest excitatory synapses along distal dendrites, possibly weakening the effectiveness of shunting inhibition in the dysplastic area. There was also a decrease in presynaptic boutons housing mitochondria and in postsynaptic protrusions containing a spine apparatus, pointing to potential deficits in intracellular calcium handling and synaptic plasticity in the epileptogenic area. Moreover, maladaptive myelination was a prominent feature in the dysplastic region. These findings collectively indicate that synaptic architectural modifications may contribute to the neuronal hyperexcitability associated with epilepsy in FCD.

pathology↗

bioRxiv2024

Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells

The implications of the early phases of human telencephalic development, involving neural stem cells (NSCs), in the etiology of cortical disorders remain elusive. Here, we explored the expression dynamics of cortical and neuropsychiatric disorder-associated genes in datasets generated from human NSCs across telencephalic fate transitions in vitro and in vivo. We identified risk genes expressed in brain organizers and sequential gene regulatory networks across corticogenesis revealing disease-specific critical phases, when NSCs are more vulnerable to gene dysfunctions, and converging signaling across multiple diseases. Moreover, we simulated the impact of risk transcription factor (TF) depletions on different neural cell types spanning the developing human neocortex and observed a spatiotemporal-dependent effect for each perturbation. Finally, single-cell transcriptomics of newly generated autism-affected patient-derived NSCs in vitro revealed recurrent alterations of TFs orchestrating brain patterning and NSC lineage commitment. This work opens new perspectives to explore human brain dysfunctions at the early phases of development. One-sentence summaryThe temporal analysis of gene regulatory networks in human neural stem cells reveals multiple early critical phases associated with cortical disorders and neuropsychiatric traits.

neuroscience↗

bioRxiv2022

Molecular programs of regional specification and neural stem cell fate progression in developing macaque telencephalon

Early telencephalic development involves patterning of the distinct regions and fate specification of the neural stem cells (NSCs). These processes, mainly characterized in rodents, remain elusive in primates and thus our understanding of conserved and species-specific features. Here, we profiled 761,529 single-cell transcriptomes from multiple regions of the prenatal macaque telencephalon. We defined the molecular programs of the early organizing centers and their cross-talk with NSCs, finding primate-biased signaling active in the antero-ventral telencephalon. Regional transcriptomic divergences were evident at early states of neocortical NSC progression and in differentiated neurons and astrocytes, more than in intermediate transitions. Finally, we show that neuropsychiatric disease- and brain cancer-risk genes have putative early roles in the telencephalic organizers activity and across cortical NSC progression. One-Sentence SummarySingle-cell transcriptomics reveals molecular logics of arealization and neural stem cell fate specification in developing macaque brain

neuroscience↗

bioRxiv2021

CHD4 conceals aberrant CTCF-binding sites at TAD interiors by regulating chromatin accessibility in mESCs

CTCF plays a critical role in the 3D chromatin organization by determining the TAD borders. Although CTCF primarily binds at the TAD borders, there also exist putative CTCF-binding sites within TADs, which are spread throughout the genome by retrotransposition. However, the detailed mechanism responsible for masking these putative CTCF-binding sites remains elusive. Here, we show that the ATP-dependent chromatin remodeler, CHD4, regulates chromatin accessibility to conceal aberrant CTCF-binding sites embedded in H3K9me3-enriched heterochromatic B2 SINEs in mouse embryonic stem cells (mESCs). Upon CHD4 depletion, these aberrant CTCF-binding sites become accessible, and aberrant CTCF recruitment occurs at the TAD interiors, resulting in disorganization of the local TADs. Furthermore, RNA-binding intrinsically disordered domains of CHD4 is required to prevent the aberrant CTCF bindings. Lastly, CHD4 is required for the repression of B2 SINE transcripts. These results highlight the CHD4-mediated mechanism that safeguards the appropriate CTCF bindings and associated TAD organizations in mESCs.

molecular biology↗

bioRxiv2021

Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF

Enhancer RNAs (eRNAs) are long non-coding RNAs that originate from enhancers. Although eRNA transcription is a canonical feature of activated enhancers, the molecular features required for eRNA function and the mechanism of how eRNAs impinge on target gene transcription have not been established. Thus, using eRNA-dependent RNA polymerase II (Pol II) pause release as a model, we examined the requirement of sequence, structure and length of eRNAs for their ability to stimulate Pol II pause release by detaching NELF from paused Pol II. We found eRNA not to exert their function through common structural or sequence motifs. Instead, efficient NELF release requires a single eRNA molecule that must contain unpaired guanosines to make multiple, allosteric contacts with several NELF subunits. By revealing the molecular determinants for eRNA function, our study mechanistically links eRNAs to Pol II pause release and provides new insight into the regulation of metazoan transcription.

biochemistry↗

bioRxiv2019

A Latent Variable Model for Evaluation of Disparate Ratings of Stem Cell Colonies by Two Experts

The visual inspection of pluripotent stem cell colonies by microscopy is widely used as a primary method to assess the quality of the preparations and degree of pluripotency. The lack of ground truth and the possible inconsistency of evaluations from multiple experts within and between stem cell laboratories are sources of uncertainty about the state of the cells, the reproducibility of preparations, and the efficiency of expansion protocols. To examine how to evaluate the level of confidence one has in disparate rating from experts, we explored a statistical method for assessing the differences in ratings of pluripotent stem cells by two different experts. Two experts rated phase contrast microscope images of human embryonic stem cell (hESC) colonies on a scale of 1 (poor) to 5 (maximum pluripotency character) but agreed with one another only 48% of the time. To assess whether experts used similar criteria to rate colonies, we developed custom image feature algorithms based on the stated visual criteria provided by the experts for selection of colonies. These features, plus others, were then used to develop pluripotency scoring algorithms trained to reflect ratings of both experts. We treated expert ratings as inexact indicators of a continuous pluripotency score and considered the inconsistency between expert ratings in developing our models. The model suggests that the two experts use somewhat different scales for discriminating between colony quality. Covariance analysis indicated that both experts use features that are not included in the model. Two image features, colony perimeter and a feature based on texture, were the most important for both experts for predicting the ratings. Interestingly, colony perimeter was not one of the expert-provided criteria for rating colonies, showing that this modeling approach allowed identification of features that the experts were not aware they were using. A linear model based on both experts identified each experts top-rated colonies as well as, or better than, the ratings of the other expert, as indicated by receiver operator characteristic curve analysis. By providing an understanding of the differences and similarities in disparate sets of expert ratings, this analysis helps to establish confidence in the ratings and the criteria for ratings, even when the experts disagree.

bioinformatics↗

bioRxiv2019

BSU1 family phosphatases mediate Flagellin-FLS2 signaling through a specific phosphocode.

Hundreds of leucine-rich repeat receptor kinases (LRR-RKs) have evolved to control diverse processes of growth, development, and immunity in plants; the mechanisms that link LRR-RKs to distinct cellular responses are not understood. Here we show that two LRR-RKs, the brassinosteroid hormone receptor BRI1 (BRASSINOSTEROID INSENSITIVE 1) and the flagellin receptor FLS2 (FLAGELLIN SENSING 2), regulate downstream glycogen synthase kinase 3 (GSK3) and mitogen-activated protein (MAP) kinases, respectively, through phosphocoding of the BRI1-SUPPRESSOR1 (BSU1) phosphatase. BSU1 was previously identified as a component that inactivates GSK3s in the BRI1 pathway. We found surprisingly that loss of the BSU1 family phosphatases activates effector-triggered immunity (ETI) and impairs flagellin-triggered MAP kinase activation and immunity. The flagellin-activated BOTRYTIS-INDUCED KINASE 1 (BIK1) phosphorylates BSU1 at serine-251. Mutation of serine-251 reduces the ability of BSU1 to mediate flagellin-induced MAP kinase activation and immunity, but not its abilities to suppress ETI and interact with GSK3, which is enhanced through the phosphorylation of BSU1 at serine-764 upon brassinosteroid signaling. These results demonstrate that BSU1 plays an essential role in immunity and transduces brassinosteroid-BRI1 and flagellin-FLS2 signals using different phosphorylation sites. Our study illustrates that phosphocoding in shared downstream components provides signaling specificities for diverse plant receptor kinases.

plant biology↗

bioRxiv2019

M. leprae infects human keratinocytes via the interaction of laminin-5 with α-dystroglycan, integrin-β1, or -β4.

Although Mycobacterium leprae (M. leprae) is usually found in macrophages and nerves of the dermis of patients with multibacillary leprosy, it is also present in all layers of the epidermis, basal, suprabasal, prickle cells, and keratin layers. However, the mechanism by which M.leprae invades the dermis remains unknown, whereas the underlying mechanism by which M.leprae invades peripheral nerves, especially Schwann cells, is well defined. M. leprae binds to the -dystroglycan (DG) of Schwann cells via the interaction of -DG and laminin (LN)-2 in the basal lamina, thus permitting it to become attached to and invade peripheral nerves. In the current study, we investigated the issue of how M.leprae infects keratinocytes. LN-5 is the predominant form of laminin in the epidermis and allows the epidermis to be stably attached to the dermis via its interaction with /{beta}-DG as well as integrins that are produced by keratinocytes. We therefore focused on the role of LN-5 in when M. leprae invades keratinocytes. Our results show that M.leprae preferentially binds to LN-5-coated slides and this binding to LN-5 enhances its binding to human epidermal keratinocytes, neonatal (HEKn). The findings also show that pre-treatment with an antibody against -DG, integrin-{beta}1, or -{beta}4 inhibited the binding of LN-5-coated M.leprae to HEKn cells. These results suggest that M. leprae infects keratinocytes by taking advantage of the interaction of LN-5 in the basal lamina of the epidermis and a surface receptor of keratinocytes, such as -DG, integrin-{beta}1, or -{beta}4.\n\nAuthor summaryIn the current study, we investigated the issue of how M.leprae infects keratinocytes. We focused on the role of LN-5, a predominant form of laminin of the epidermis, in the invasion of M. leprae in keratinocytes. Our results show that M. leprae preferentially binds to LN-5-coated slides and coating M.leprae with LN-5 enhanced its binding to human epidermal keratinocytes, neonatal (HEKn). In addition, a pre-treatment with an antibody against -DG, integrin-{beta}1 or -{beta}4 inhibited the binding of LN-5-coated M. leprae to HEKn cells. These results suggest that M. leprae invades keratinocytes by taking advantage of the interaction of LN-5 in the basal lamina of the epidermis and a surface receptor of keratinocytes, such as -DG, integrin-{beta}1, or -{beta}4

microbiology↗

bioRxiv2019

Human cortical neural stem cells generate regional organizer states in vitro before committing to excitatory neuronal fates

Better understanding the progression of neural stem cells (NSCs) in the developing cerebral cortex is important for modeling neurogenesis and defining the pathogenesis of neuropsychiatric disorders. Here we used RNA-sequencing, cell imaging and lineage tracing of mouse and human in vitro NSCs to model the generation of cortical neuronal fates. We show that conserved signaling mechanisms regulate the acute transition from proliferative NSCs to committed glutamatergic excitatory neurons. As human telencephalic NSCs developed from pluripotency in vitro, they first transitioned through organizer states that spatially pattern the cortex before generating glutamatergic precursor fates. NSCs derived from multiple human pluripotent lines varied in these early patterning states leading differentially to dorsal or ventral telencephalic fates. This work furthers systematic analysis of the earliest patterning events that generate the major neuronal trajectories of the human telencephalon.

neuroscience↗

bioRxiv2019

Oligoribonuclease functions as a diribonucleotidase to bypass a key bottleneck in RNA degradation

Degradation of RNA polymers is a multistep process catalyzed by specific subsets of RNases. In all cases, degradation is completed by exoribonucleases that recycle RNA fragments into nucleotide monophosphate. In {gamma}-proteobacteria, a group of up to eight 3-5 exoribonucleases have been implicated in RNA degradation. Oligoribonuclease (Orn) is unique among them as its activity is required for clearing short RNA fragments, a function important for cellular fitness. However, the mechanistic basis for this substrate selectivity remained unclear. Here we show that Orns activity as a general exoribonuclease has been vastly overestimated by demonstrating that the enzyme exhibits a much narrower substrate preference for diribonucleotides. Co-crystal structures of Orn with substrates reveal an active site optimized for diribonucleotides that does not accommodate longer substrates. While other cellular RNases process oligoribonucleotides down to diribonucleotide entities, our functional studies demonstrate that Orn is the one and only diribonucleotidase that completes the final stage of the RNA degradation pathway. Together, these results indicate that Orn is a dedicated diribonucleotidase that clears the diribonucleotide pool that otherwise affects cellular physiology and viability.

microbiology↗