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Biology subjects

Kim, K.-H.

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

At least 19 recordsLinked to original sources

Spatial Mapping of the Lung Cancer Ecosystem Reveals Distinct Patterns of Intratumoral and Internodular Heterogeneity

The spatial organization of malignant and non-malignant cells within the tumor microenvironment (TME) critically influences tumor evolution and therapeutic response. However, the architecture of micro-niches remains incompletely understood. Leveraging Xenium-based spatial transcriptomics, we comprehensively mapped the spatial ecosystem of an orthotopic murine lung cancer model, identifying distinct spatial domains that form unique, organized cellular neighborhoods. These domains cluster into three major communities: (1) non-tumoral regions that recapitulate canonical normal lung structures; (2) a heterogeneous peri-tumoral region composed of spatial domains characterized by mesenchymal remodeling, active immune checkpoint signaling, and immunosuppressive myeloid populations; and (3) intra-tumoral regions that reveal marked tumor nodule heterogeneity, with unique tumor-specific domains exhibiting hallmark cancer pathways. Furthermore, our analytic approach was applicable to human lung cancer tissue. Notably, spatial domain analysis allowed us to resolve tumor nodules into multiple biologically distinct subtypes, defined by domain composition, hallmark cancer programs, and intercellular communication patterns within the TME.

cancer biology↗

Diet-Induced Obesity Exacerbates Helicobacter pylori-Associated Precancerous Phenotypes

Stomach infection with the bacterium Helicobacter pylori (Hp) can cause chronic gastric inflammation, metaplasia (transdifferentiation of mature cell types), dysplasia (abnormal cells), and finally cancer. Obesity can also increase gastric cancer risk. However, host-Hp interactions during obesity are poorly understood. Here we investigated the impact of diet-induced obesity in two mouse models of Hp-associated disease. To model chronic gastric inflammation, we used C57BL/6 mice, and to model more severe disease, we used transgenic mice in which tamoxifen induces gastric expression of a constitutively active Kras allele, leading to metaplasia. We fed mice a high-fat diet (60% kilocalories from fat) to induce obesity, or a matched control diet (10% kilocalories from fat), then infected them with Hp or mock-infected them. In mock-infected C57BL/6 mice, high-fat diet had a minimal impact on gastric pathology and gene expression. In Hp-infected C57BL/6 mice, high-fat diet increased inflammation at the junction between the glandular stomach and non-glandular forestomach, a squamous epithelium similar to the human esophagus, and increased gastric expression of the cancer-associated genes Cldn7 and Reg3g. In KRAS+ mice with or without Hp infection, the impact of diet-induced obesity was more apparent, with increased metaplasia and dysplasia (abnormal cells). As well, high-fat diet caused an expansion of metaplastic pit cells, a lineage we previously found to be associated with Hp-driven inflammation. Thus, in these mouse models, diet-induced obesity does not directly drive gastric immunopathology, but enhances the development of pre-cancerous changes under susceptible conditions. IMPORTANCEMost gastric cancers are caused by stomach infection with the bacterium Helicobacter pylori. However, most infected individuals never develop cancer. Therefore, additional risk factors must tip the balance toward gastric cancer development. Obesity, or excessive body fat accumulation that poses a risk to health, is associated with gastric cancer development. However, specific mechanisms for obesity-driven gastric cancer risk are not well defined. Here we tested the hypothesis that obesity would exacerbate Helicobacter pylori-associated disease phenotypes using two clinically relevant mouse models. In wild-type mice, obesity induced by a very high-fat diet had a minimal impact on the stomach in the absence of infection, but increased the expression of some cancer-associated genes during infection. However, in mice with genetically driven pre-cancer, diet-induced obesity exacerbated the disease pathology, especially in infected mice. Therefore, obesitys impact on gastric cancer risk may be more evident in the later stages of the disease.

microbiology↗

Development of a low-dose PBMC humanized mouse model using CD47;Rag2;IL2rγ triple KO mice: Enhanced leukocyte reconstitution and extended experimental window

Humanized mice (hu-mice), which recapitulate the human immune system, have become increasingly important for preclinical immunotherapy studies. Among these models, the human peripheral blood mononuclear cells (PBMC)-engrafted hu-mice model is the simplest and fastest. However, its utility is hindered by the development of lethal graft-versus-host disease (GvHD) and the insufficient reconstitution of human leukocytes. To address these limitations, we developed PBMC hu-mice models using a novel strain, NOD-CD47nullRag2nullIL-2r{gamma}null (RTKO) focusing on the immunological defects of the NOD strain and the immunotolerance provided by CD47 deficiency. Six-week-old female NOD-Rag2nullIL-2r{gamma}null (RID) and RTKO mice were intravenously injected with three different PBMC doses (3x106, 5x106, and 1x107 cells). At standard doses (5x106 and 1x107 cells), RTKO mice exhibited enhanced engraftment of human leukocytes, though GvHD was more severe compared to the RID strain, resulting in a limited experimental window. However, in a subsequent trial using a lower dose of PBMCs (3 x 106 cells), RTKO mice demonstrated notable advantages, including stable reconstitution of human leukocytes, milder GvHD symptoms without life-threatening lesions, and a markedly prolonged experimental window. Considering the difficulties in generating hematopoietic stem cell (HSC)-engrafted hu-mice, the extended experimental window provided by this model, which is comparable to HSC hu-mice, is a significant improvement. Moreover, the radiation tolerance conferred by the Rag gene mutation in this model offers another advantage for radiotherapy research. Consequently, the low-dose PBMC RTKO model serves as a versatile and valuable platform for a broad spectrum of immunotherapy studies, especially in the field of immuno-oncology.

cancer biology↗

Sex- and ketogenesis-dependent effects of intermittent fasting against diet-induced obesity and fatty liver disease

ABSTRACTSIntermittent fasting (IF) improves metabolic health, yet the requirement for hepatic ketogenesis in mediating these benefits remains unclear. Here, we investigated how hepatic ketogenesis contributes to the metabolic and hepatic effects of IF in male and female mice. In the human liver, ketogenesis-associated genes showed sex-dependent correlations with inflammatory and fibrotic pathways. In mice, fasting increased circulating ketone bodies, with females exhibiting a greater rise, indicating intrinsic sex differences in ketone metabolism. IF reduced body weight and adiposity in both sexes, and these systemic benefits persisted despite antisense oligonucleotide (ASO)-mediated knockdown of hepatic Hmgcs2. In contrast, hepatic benefits were sex- and ketogenesis-dependent. IF markedly reduced steatosis and fibrosis in male mice, but these improvements were attenuated or abolished when hepatic ketogenesis was disrupted. Female mice showed minimal hepatic benefit from IF and displayed heightened susceptibility to steatosis, fibrosis, and inflammatory activation under ketogenic insufficiency. Single-cell transcriptomic analyses identified neutrophils and myofibroblasts as key responders to hepatocyte-derived ketone bodies, and IF suppressed neutrophil-driven inflammatory signaling in a ketogenesis-dependent manner in males but not females. Together, these findings demonstrate that while systemic metabolic improvements from IF are largely ketogenesis-independent, the hepatic anti-steatotic and anti-fibrotic effects of IF are sexually dimorphic and require intact hepatic ketogenesis.

physiology↗

Human olfactory organoids as an in vitro model of the olfactory epithelium

Abstract/Key PointsO_LIA novel human olfactory epithelial organoid model has been generated from primary cell culture. C_LIO_LIHuman olfactory organoids exhibit immunostaining and gene expression for olfactory cells. C_LIO_LIOlfactory organoids mobilize Ca2+ in response to odorants, a surrogate for neuronal function. C_LI

cell biology↗

Conservation and divergence of transcriptional heterogeneity in the cardiac conduction system

The cardiac conduction system (CCS) consists of specialized cardiomyocytes that initiate and propagate electrical activity through the heart. While the transcriptional programs underlying CCS development and function have been studied within individual species, how these programs compare across species and developmental stages remains unclear. Here, we present a comprehensive cross-species and cross-stage analysis of the CCS transcriptome using single-cell/single-nucleus RNA sequencing and spatial transcriptomic datasets from human, mouse, rat, zebrafish, and medaka hearts. We identify shared and species-or stage-specific gene expression patterns, spanning CCS-wide, zonal-, and component-level features, as well as conserved gene regulatory networks across the species. Many conserved genes are associated with human CCS function and related disorders, highlighting their translational relevance for conduction disease. This work refines the molecular characterization of CCS cell types across vertebrates and provides a resource for advancing our understanding of CCS development, function, and pathology.

genomics↗

Prediction of bacterial protein-compound interactions with only positive samples

Prediction of Compound-Protein Interactions (CPI) in bacteria is crucial to advance various pharmaceutical and chemical engineering fields, including bio-catalysis, drug discovery, and industrial processing. However, current CPI models cannot be applied for bacterial CPI prediction due to the lack of curated negative interaction samples. This paper introduces a novel Positive-Unlabeled (PU) learning framework, named BIN-PU, to address this limitation. BIN-PU generates pseudo positive and negative labels from known positive interaction data, enabling effective training of deep learning models for CPI prediction. We also propose a weighted positive loss function that weights to truly positive samples. We have validated BIN-PU with multiple CPI backbone models, comparing the performance with the existing PU model using bacterial cytochrome P450 (CYP) data. Extensive experiments demonstrate the superiority of BIN-PU over the benchmark model in predicting CPIs with only truly positive samples. Furthermore, we have validated BIN-PU on additional bacterial proteins obtained from literature review, human CYP datasets, and uncurated data for its reproducibility. We have also validated the CPI prediction for the uncurated CYP data with biological and biophysical experiments. BIN-PU represents a significant advancement in CPI prediction for bacterial proteins, opening new possibilities for improving predictive models in related biological interaction tasks.

bioinformatics↗

Genetic modifiers of somatic expansion and clinical phenotypes in Huntington's disease reveal shared and tissue-specific effects

Huntingtons disease (HD), due to expansion of a CAG repeat in HTT, is representative of a growing number of disorders involving somatically unstable short tandem repeats. We find that overlapping and distinct genetic modifiers of clinical landmarks and somatic expansion in blood DNA reveal an underlying complexity and cell-type specificity to the mismatch repair-related processes that influence disease timing. Differential capture of non-DNA-repair gene modifiers by multiple measures of cognitive and motor dysfunction argues additionally for cell-type specificity of pathogenic processes. Beyond trans modifiers, differential effects are also illustrated at HTT by a 5-UTR variant that promotes somatic expansion in blood without influencing clinical HD, while, even after correcting for uninterrupted CAG length, a synonymous sequence change at the end of the CAG repeat dramatically hastens onset of motor signs without increasing somatic expansion. Our findings are directly relevant to therapeutic suppression of somatic expansion in HD and related disorders and provide a route to define the individual neuronal cell types that contribute to different HD clinical phenotypes.

genetics↗

Loss-of-SIRT7 sensitizes hepatocellular carcinoma to sorafenib through the regulation of ERK Phosphorylation

The FDA-approved oral multi-kinase inhibitor, sorafenib (BAY 43-9006, Nexavar), is the first approved systemic therapy for patients with unresectable hepatocellular carcinoma (HCC). Although it has been shown to significantly improve the overall survival of patients with HCC, drug resistance limits the response rate to this therapeutic. Here, we report that acquired sorafenib resistance is associated with overexpression of the deacetylase, SIRT7, and a high level of ERK phosphorylation. Further, we identify that the hyperactivation of ERK is controlled by SIRT7-mediated deacetylation of DDX3X. The inhibition of SIRT7 combined with sorafenib resulted in a marked reduction of cell viability in vitro and of tumor growth in vivo. It seems plausible that SIRT7 is responsible for the acquired sorafenib resistance and its inhibition is most likely beneficial together in conjunction with sorafenib by suppressing ERK signaling. HighlightsO_LISorafenib resistance in HCC is associated with SIRT7 and ERK hyperactivation. C_LIO_LISuppression of SIRT7 combined with sorafenib restores sensitivity to sorafenib. C_LIO_LISIRT7 controls sorafenib resistance through ERK activation by mediating DDX3X deacetylation. C_LI

cancer biology↗

Circadian reprogramming of adipose progenitor cells regulates intermittent fasting-mediated adipose tissue remodeling and metabolic improvement

White adipose tissue (WAT) fibrosis is a hallmark of dysfunctional WAT that is directly linked to metabolic abnormalities. Recent studies have highlighted the role of dysfunctional adipose progenitor cells (APCs) in WAT fibrosis and impaired adaptive tissue plasticity, leading to systemic insulin resistance. However, therapeutic options for WAT fibrosis are limited. Intermittent fasting (IF) is an effective dietary regimen for weight control and metabolic improvement through various mechanisms, including healthy remodeling of WAT. However, whether IF is effective in improving age-associated WAT fibrosis and metabolic homeostasis is unknown. Here, we show that IF confers therapeutic benefits in aged and obese mice through reduction of WAT fibrosis. Single-cell analyses revealed that IF significantly reduces pro-fibrotic signatures within APCs along with upregulation of the circadian pathways, suggesting that the circadian clock of APCs mediates IF-induced WAT remodeling. Importantly, mice lacking core circadian gene exhibited increased fibrotic signatures in WAT and diminished beneficial response to IF, further supporting the importance of circadian rhythm in IF-mediated metabolic benefits. Lastly, insulin resistance in humans also presented with dysregulated circadian rhythm signatures in APC populations. Collectively, our findings highlight the novel role of the APC circadian rhythm in plasticity of WAT and metabolic response to IF.

molecular biology↗

Irx1 and Irx2 play dose-dependent cooperative functions in mammalian development

Irx1 and Irx2 (Irx1/2) are two closely linked and widely expressed members of the conserved Iroquois homeobox family of transcription factors. Despite mounting evidence suggesting the importance of homologs of these genes in many aspects of vertebrate development and function, the role of Irx1/2 in mammals has remained largely unknown. Here, we used mice carrying our newly generated Irx1flox and Irx1floxIrx2del mutant alleles to perform a stepwise genetic ablation of Irx1 and Irx2 levels. Our analysis revealed reduced postnatal growth and viability of Irx1KO mice with gross histological defects in the lung and gut and demonstrated that ablation of one copy of Irx2 in these mice results in neonatal lethality with exacerbated phenotypic defects. Conversely, while Irx2KO mice appear normal, ablation of one copy of Irx1 in these mutants leads to lethality at weaning. Furthermore, we found that homozygous deletion of both Irx1 and Irx2 results in embryonic lethality by mid-gestation with defective extraembryonic vasculature. Our results illustrate that Irx1 and Irx2 play distinct dose-dependent cooperative functions during both the early and late stages of mouse development.

developmental biology↗

Multi-omics approach reveals dysregulation of protein phosphorylation correlated with lipid metabolism in mouse fatty liver

Obesity caused by overnutrition is a major risk factor for non-alcoholic fatty liver disease (NAFLD). Several lipid intermediates such as fatty acids, glycerophospholipids and sphingolipids are implicated in NAFLD, but detailed characterization of lipids and their functional links to proteome and phosphoproteome remain to be elucidated. To characterize this complex molecular relationship, we used multi-omics approach by conducting comparative proteomic, phoshoproteomic and lipidomic analyses of high fat (HFD) and low fat (LFD) diet fed mice livers. We quantified 2447 proteins and 1339 phosphoproteins containing 1650 class I phosphosites (with localization probability > 0.75), of which 669 phosphosites were significantly different between HFD and LFD mice livers. We detected alterations of proteins associated with cellular metabolic processes such as small molecule catabolic process, monocarboxylic acid, long- and medium-chain fatty acid, and ketone body metabolic processes, and peroxisome organization. We observed significant downregulation of protein phosphorylation in HFD fed mice liver in general. Untargeted lipidomics identified upregulation of triacylglycerols, glycerolipids and ether glycerophosphocholines and downregulation of glycerophospholipids such as lysoglycerophospholipids, as well as ceramides and acylcarnitines. Analysis of differentially regulated phosphosites revealed phosphorylation dependent deregulation of insulin signaling as well as lipogenic and lipolytic pathways during HFD induced obesity. Thus, this study reveals a molecular connection between decreased protein phosphorylation and lipolysis, as well as lipid-mediated signaling in diet-induced obesity.

systems biology↗

Influenza virus-like particle-based hybrid vaccine containing RBD induces immunity against influenza and SARS-CoV-2 viruses

Several approaches have produced an effective vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the influence of immune responses induced by other vaccinations on the durability and efficacy of the immune response to SARS-CoV-2 vaccine is still unknown. We have developed a hybrid vaccine for SARS-CoV-2 and influenza viruses using influenza virus-like particles (VLP) incorporated by protein transfer with glycosylphosphatidylinositol (GPI)-anchored SARS-CoV-2 S1 RBD fused to GM-CSF as an adjuvant. GPI-RBD-GM-CSF fusion protein was expressed in CHO-S cells, purified and incorporated onto influenza VLPs to develop the hybrid vaccine. Our results show that the hybrid vaccine induced a strong antibody response and protected mice from both influenza virus and mouse-adapted SARS-CoV-2 challenges, with vaccinated mice having significantly lower lung viral titers compared to naive mice. These results suggest that the hybrid vaccine strategy is a promising approach for developing multivalent vaccines to prevent influenza A and SARS-CoV-2 infections.

immunology↗

Highly efficient, all-organic bioluminescence-photosensitizer conjugate eradicates early-stagetumors and prevents metastasis in mice

Photodynamic therapy (PDT) is an established treatment modality using light-activatable drugs. Despite its unique cytotoxic mechanism, the shallow penetration of light has been a serious drawback limiting the applications of PDT. Here, we report bioluminescence-activated PDT (BL-PDT) using efficient bioluminescence resonance energy transfer (BRET) conjugates of clinically approved photosensitizers, Ce6, and luciferase proteins. A high photon-to-Ce6 conversion efficiency (80%), along with intracellular delivery by membrane-fusion liposomes, enabled effective cancer cell killing in vitro. In a syngeneic mouse model of aggressive 4T1 triple-negative breast cancer, as well as a xenograft model of MDA-MB-231 tumors, BL-PDT resulted in complete tumor remission and prevention of metastasis, as well as neo-adjuvant effects. Our result shows the promise of molecularly activable, clinically viable, depth-unlimited phototherapy.

cancer biology↗

Synthetic glabridin derivatives mitigate steatohepatitis in a diet-induced biopsy-confirmed non-alcoholic steatosis hepatitis mouse model through paraoxonase-2

Limited therapeutic agents have been developed for non-alcoholic steatohepatitis (NASH), a common immunometabolic disease that can progress to hepatic cirrhosis and cancer. Glabridin and its derivatives are potential therapeutics for some metabolic diseases. However, the therapeutic effects of glabridin and its derivatives on NASH and their biological functions are unclear. This study demonstrated the role of synthetic glabridin derivatives (SGDs) in alleviating hepatic steatosis and inflammation in a biopsy-confirmed rodent NASH model. SGDs exerted therapeutic effects by activating autophagy and the antioxidant defense system, which mitigate NASH pathogenesis. The cellular target of HSG4112, an SGD, was paraoxonase 2. These findings will enable the development of novel therapeutics for NASH in the future.

pharmacology and toxicology↗

Deficiency of Irx5 protects mice from diet-induced obesity and associated metabolic abnormalities

Obesity, a leading cause of several metabolic abnormalities, is mainly due to an imbalance of energy homeostasis. IRX3 and IRX5 have been suggested as determinants of obesity in connection with the intronic variants of FTO, the strongest genetic risk factor of polygenic obesity in humans. Although the causal effects of Irx3 on obesity and its related metabolic consequences have been demonstrated in vivo, the metabolic function of Irx5 remains unclear. In this study, using mice homozygous for an Irx5-knockout (Irx5KO) allele, we show a direct link between Irx5 expression and regulation of body mass/composition and energy homeostasis. Irx5KO mice are leaner and resistant to diet-induced obesity and associated metabolic abnormalities, primarily through the loss of adiposity with an increase in basal metabolic rate with adipose thermogenesis and lower food intake. Furthermore, our long-term feeding analysis found that Irx3 mutant mouse lines also have less food intake, indicating that lower caloric intake also contributes to their lean phenotype. Together, these results demonstrate that Irx5 is critical for energy homeostasis and regulation of body mass/composition and suggest that it likely acts in other tissues beyond adipocytes.

genetics↗

The first finding of lichen Solorina saccata at an algific talus slope in Korea

An algific talus slope is composed of broken rocks with vents connected to an ice cave, releasing cool air in summer and relatively warmer air in winter to maintain a more stable microclimate all year round. Such geological features create a very unusual and delicate ecosystem. Although there are around 25 algific talus slopes in Korea, lichen ecology of these areas had not been investigated to date. In this study, we report the first exploration of lichen ecology at an algific talus slope, Jangyeol-ri, in Korea. A total of 37 specimens were collected over 2017-2018. Morphological and sequencing analysis revealed 27 species belonging to 18 genera present in the area. Of particular interest among these species was Solorina saccata, as it has previously not been reported in Korea and most members of genus Solorina are known to inhabit alpine regions of the Northern Hemisphere. We provide here a taxonomic key for S. saccata alongside molecular phylogenetic analyses and prediction of potential habitats in South Korea. Sequences were generated from all S. saccata specimens collected in this study, together with three S. saccata specimens from China for comparison. Phylogenetic analysis based on nuclear small subunit (nuSSU) showed that all the S. saccata specimens are tightly grouped into one clade with high support values (P=0.99) and showed close relatedness to S. spongiosa than S. crocea. Additional analyses were carried out using concatenated sequences: 65 sequences of mitochondrial small subunit (mtSSU) combined with nuLSU and 66 sequences of RPB1 with nuLSU. In these analyses, genus Peltigera was found to be the closest genus to S. saccata. Furthermore, regions in South Korea potentially suitable for Solorina spp. were predicted based on climatic features of known habitats around the globe. Our results showed that the suitable areas are mostly at high altitudes in mountainous areas where the annual temperature range doesnt exceed 26.6{degrees}C. Further survey of other environmental conditions determining the suitability of Solorina spp. should lead to a more precise prediction of suitable habitats and trace the origin of Solorina spp. in Korea.

ecology↗

Genetic overlap between psychiatric disorders and neuropsychiatric symptoms in HD

Huntingtons disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the HTT gene. It is diagnosed following a standardized exam of motor control and often presents with cognitive decline and psychiatric symptoms. Recent studies have detected genetic loci modifying the age at onset of motor symptoms in HD, but genetic factors influencing cognitive and psychiatric presentations are unknown. We tested the hypothesis that psychiatric and cognitive symptoms in HD are influenced by the same common genetic variation as in the general population by constructing polygenic risk scores from large genome-wide association studies of psychiatric and neurodegenerative disorders, and of intelligence, and testing for correlation with the presence of psychiatric and cognitive symptoms in a large sample (n=5160) of HD patients. Polygenic risk score for major depression was associated specifically with increased risk of depression in HD, as was schizophrenia risk score with psychosis and irritability. Cognitive impairment and apathy were associated with reduced polygenic risk score for intelligence. In general, polygenic risk scores for psychiatric disorders, particularly depression and schizophrenia, are associated with increased risk of the corresponding psychiatric symptoms in HD, suggesting a common genetic liability. However, the genetic liability to cognitive impairment and apathy appears to be distinct from other psychiatric symptoms in HD. No associations were observed between HD symptoms and risk scores for other neurodegenerative disorders. These data provide a rationale for treatments effective in depression and schizophrenia to be used to treat depression and psychotic symptoms in HD.

genetics↗