Biology subjects

Gee, H. Y.

Publications and source records attributed to Gee, H. Y..

9 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↗

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

A predictive framework for stop-loss variants with C-terminal extensions

Stop codons dictate translation termination, and variants occurring at these sites can result in stop-loss variants, leading to C-terminal extensions with potentially significant functional consequences. Despite their clinical relevance, existing prediction tools--primarily developed for missense variants--lack sufficient accuracy for assessing stop-loss variants, mainly due to their insufficiency in accounting for the sequence features of the extended peptide. To address this gap, we developed TAILVAR (Terminal codon Analysis and Improved prediction of Lengthened VARiants), a machine-learning classifier that integrates multi-omics features spanning transcript- and protein-level properties, along with variant effect annotations. Our analyses showed that transcripts lacking downstream stop codons in the 3 untranslated region exhibit lower evolutionary constraints. Additionally, we observed that deleterious variants exhibit greater C-terminal hydrophobicity, which is associated with reduced protein stability and increased degradation, as well as a higher aggregation propensity. TAILVAR outperformed existing benchmarks, demonstrating the highest correlation with functional experiments and establishing thresholds to classify variants as benign or pathogenic. This work offers a systematic framework for interpreting stop-loss variants, providing precise predictions of elongated protein effects that may aid genetic diagnosis and facilitate the discovery of novel disease-associated genes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/673407v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@1d53baaorg.highwire.dtl.DTLVardef@403289org.highwire.dtl.DTLVardef@b5c8b4org.highwire.dtl.DTLVardef@8bd61a_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

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↗

bioRxiv2024

Adherent-to-suspension transition promotes melanoma metastatic dissemination

Melanoma is a highly metastatic skin cancer that often evades current therapeutic strategies primarily because of the complex mechanisms involved in metastasis. This study investigated the role of adherent-to-suspension transition (AST) in melanoma and its potential to facilitate metastasis by reprogramming cellular anchorage dependency. Using melanoma models, we demonstrated that the AST factors IKZF1, IRF8, and NFE2 are crucial for reprogramming, influencing gene expression related to cell adhesion and survival. Notably, our results highlight that AST factor expression undergoes dynamic changes during metastasis, which can be reversed in circulating tumor cells. Our findings revealed that AST contributes to the increased metastatic potential and invasiveness of melanoma cells and underscores its role independent of the epithelial-to-mesenchymal-like transition pathways. Based on the results, we highlight the potential of targeting AST mechanisms to develop new therapeutic strategies against metastasis.

cancer biology↗

bioRxiv2024

Adherent-suspension plasticity promotes the dissemination and colonization of circulating tumor cells

Cell competition within the primary tumor drives tumor growth by promoting the uncontrolled proliferation of winner cells and eliminating loser cells by sensing cell fitness. However, the mechanism of how cell competition confers the loser cells with the metastatic potential of circulating tumor cells (CTCs) to transit between dissemination and colonization remains elusive. Here we found cell competition gives rise to less fit but viable cells that transformed into CTCs via adherent-to-suspension transition (AST) mechanisms. The induction of hematopoietic transcription factors hijacked by solid tumor cells rendered CTCs competent to reprogram their anchorage dependency and disseminate into the bloodstream, while subsequent suppression of these factors was critical to regain adhesion and colonize metastatic lesions. Disrupting the oscillatory dynamics of AST factors blocked the adherent-suspension plasticity (ASP) of breast cancer CTCs and suppressed lung metastasis. Furthermore, multiregional single-cell transcriptomic analyses of matched primary tumors, CTCs, and metastatic lesions from de novo metastatic breast cancer patients demonstrate the critical role of ASP in metastasis. SignificanceWe demonstrate cell competition-mediated displacement of loser cells manifests dynamic oscillation of AST factors that confer anchorage plasticity to circulating tumor cells critical for their dissemination and colonization in metastasis. These findings highlight the potential of targeting AST factors to develop effective anti-metastatic therapies.

cancer biology↗

bioRxiv2023

Distinct modulation of calcium-activated chloride channel TMEM16A by a novel drug-binding site

TMEM16A is a calcium-activated chloride channel with significant role in multiple cellular processes. Several TMEM16A inhibitors have been identified; however, their binding sites and inhibitory mechanisms remain unclear. Using magnolol and honokiol, the two regioisomeric inhibitors, as chemical probes, we have identified a novel drug-binding site distinct from the pore region, in TMEM16A, which is described here. With electrophysiology, unbiased molecular docking and clustering, molecular dynamics simulations, and experimental validation with mutant cycle analysis, we show that magnolol and honokiol utilize different drug-binding sites, pore and non-pore pockets. The pore blocker utilizes amino acids crucial for chloride passage, whereas the non-pore blocker allosterically modulates the pore residues to hinder ion permeation. Among 17 inhibitors tested, 11 were pore blockers and six were non-pore blockers, indicating the importance of this newly identified non-pore pocket. Our study provides insights into drug-binding mechanism in TMEM16A together with a rationale for future drug development.

physiology↗

bioRxiv2019

ADCK4 deficiency destabilizes the coenzyme Q complex, which is rescued by 2,4-dihydroxybenzoic acid treatment

ADCK4 mutations usually manifest as steroid-resistant nephrotic syndrome, and cause coenzyme Q10 (CoQ10) deficiency. However, the function of ADCK4 remains obscure. We investigated ADCK4 function using mouse and cell models. Podocyte-specific Adck4 deletion in mice significantly reduced survival and caused severe focal segmental glomerular sclerosis with extensive interstitial fibrosis and tubular atrophy, which were prevented by treatment with 2,4-dihydroxybenzoic acid (2,4-diHB), an analog of CoQ10 precursor molecule. ADCK4 knockout podocytes exhibited significantly decreased CoQ10 level, respiratory chain activity, mitochondrial potential, and dysmorphic mitochondria with loss of cristae formation, which were rescued by 2,4-diHB treatment, thus attributing these phenotypes to decreased CoQ10 levels. ADCK4 interacted with mitochondrial proteins including COQ5, and also cytoplasmic proteins including myosin and heat shock proteins. ADCK4 knockout decreased COQ complex levels, and the COQ5 level was rescued by ADCK4 overexpression in ADCK4 knockout podocytes. Overall, ADCK4 is required for CoQ10 biosynthesis and mitochondrial function in podocytes.

genetics↗

bioRxiv2018

Genetic predisposition to hypouricemia on whole-exome sequencing analysis and its utilities in primary screening purposes

Differentiating between inherited renal hypouricemia and transient hypouricemia is challenging. Here, we aimed to describe the genetic predisposition of hypouricemia patients using whole-exome sequencing (WES) and assess the feasibility for genetic diagnosis in primary screening. WES was performed for the discovery of diagnostic markers in discovery cohorts (N=31). Two known genetic markers SLC22A12 c.774G>A (p.Trp258*) and SLC22A12 c.269G>A (p.Arg90His) were identified, We genotyped for the 2 SLC22A12 SNPs among screened 50 hypouricemia subjects for the replication cohorts; 47 carried known SLC22A12 markers; three unexplained hypouricemic cases were analyzed by using WES. We used 46 healthy internal controls for the variant discovery. Four novel variants of SLC22A12, c.408C>A (p.Asn136Lys), c.674C>A (p.Thr225Lys), c.851G>A (p.Arg284Gln), and c.1285G>A (p.Glu429Lys), and one novel variant of SLC2A9, c. 376A>G (p.Met155Val), were identified. After filtering out known genes (SLC22A12 and SLC2A9), the p.Arg78His variant in ASB12 was overlapped in two unexplained conditions. This is the first attempt to investigate the effectiveness of integrating exome sequencing and genotype into the clinical care for hypouricemia and determine the value of genetic diagnostic screening for hypouricemia in the clinical setting. Screening of just two SNPs (p.Trp258* and p.Arg90His) identified 87.7% (71/81) of patients with hypouricemia. Early identification and intervention of hypouricemia is feasible using genetic screening to prevent acute kidney injury, especially for soldiers and athletics.

genetics↗