Biology subjects

Kang, C.-Y.

Publications and source records attributed to Kang, C.-Y..

7 recordsLinked to original sources

bioRxiv2026

Elevated procoagulant platelets driven by necroptosis and pyroptosis aggravate pulmonary thrombosis via suppressing monocyte efferocytosis in severe pneumonia

BACKGROUND: Severe influenza pneumonia with secondary bacterial infection is complicated by progressive pulmonary thrombus exacerbation, a key contributor to respiratory failure, yet anticoagulant therapies show limited efficacy and bleeding risks. Although platelet-monocyte crosstalk initiates thrombosis, whether and how it drives thrombus exacerbation via procoagulant platelets and monocyte efferocytosis remains unclear. METHODS: Clinical samples, mouse models, and isolated platelets challenged with influenza A virus followed by methicillin-resistant Staphylococcus aureus (MRSA) were analyzed. Procoagulant platelet, platelet programmed cell death and monocyte efferocytosis were assessed, and pharmacological inhibition, platelet depletion and systemic/platelet-specific Gsdmd knockout were used. Platelet proteomics and exogenous C1qa supplementation identified C1qa as a key mediator. RESULTS: We showed that elevated procoagulant platelet-driven thrombus exacerbation, rather than initial thrombus formation, was a critical driver of disease progression in influenza pneumonia with secondary bacterial infection, whereas influenza alone caused milder illness. Procoagulant platelet formation was induced via MLKL-mediated necroptosis and GSDMD-mediated pyroptosis. These platelets exacerbated pulmonary thrombosis and lung injury by inhibiting monocyte efferocytosis via complement C1qa. Platelet depletion reduced monocyte efferocytosis and worsened pneumonia, while pharmacological inhibition or platelet-specific Gsdmd knockout decreased procoagulant platelet levels, restored monocyte efferocytosis, and alleviated thrombotic and pulmonary injury. Mechanistically, C1qa impaired efferocytosis both by directly suppressing monocyte function and by reducing the proportion of reparative (M2-like) monocytes. Clinical relevance was confirmed by detection of MLKL/GSDMD-dependent procoagulant platelets and reduced efferocytosis receptor levels on monocytes in bronchoalveolar lavage fluid from severe pneumonia patients. CONCLUSIONS: Necroptosis/pyroptosis-driven procoagulant platelets exacerbate pulmonary thrombosis by suppressing monocyte efferocytosis in a C1qa-dependent manner. These findings extend platelet-monocyte crosstalk from thrombus initiation to thrombus exacerbation, identifying modulation of the interaction between procoagulant platelets and monocyte efferocytosis as a potential therapeutic strategy for thrombus-exacerbating diseases, especially in subpopulations of patients with severe pneumonia and progressive pulmonary thrombosis.

cell biology↗

bioRxiv2026

The structural mechanism of eukaryotic fluoride channel activation and inhibition by monovalent cations

Fluoride is an environmentally prevalent inhibitor of fungi, plants, and other eukaryotes. The fluoride exporter (FEX) is the major resistance mechanism that prevents intracellular fluoride accumulation in eukaryotes. FEX activity is sodium-dependent, but the mechanism for Na+ activation and the impact of other cations on FEX function remain poorly understood. Here, we show that sodium and lithium have different effects on channel activity. We leverage these differences to understand how monovalent cations regulate FEX. Functional assays in a reconstituted system show that lithium acts as a competitive antagonist of channel activation by competing with sodium for the central cation binding site. We further demonstrate that FEX inhibition by lithium has consequences in vivo, as lithium markedly reduces fluoride tolerance of yeast. A cryo-EM structure of Candida albicans FEX with Li+, together with molecular dynamics (MD) simulations, reveals the structural mechanism underlying cation-dependent FEX activity. Whereas sodium binding supports a dynamic structure with a broader pore radius, lithium coordination causes a more rigid conformation that is more compact in the channels vestibule. These changes perturb the tilt angle of a pore lining helix, and the alter the rotamer of a key phenylalanine in the pore, which together constrict the permeation pathway. In addition to providing general insight into the mechanism of fluoride channel regulation by monovalent cations, these results identify lithium as a previously unknown environmental antagonist of eukaryotic fluoride export and tie cellular fluoride stress tolerance to the abundance of additional ions in the cellular milieu.

biochemistry↗

bioRxiv2025

The molecular basis of sodium-dependent fluoride export by the eukaryotic fluoride channel FEX

Much of life on Earth, including plants, fungi, and bacteria, evolved to resist toxic environmental fluoride. In eukaryotes, the major resistance mechanism is fluoride export by FEX proteins. Using electrophysiology and transport assays, we establish that FEX from plants and yeasts are fluoride channels whose activity depends on reversible sodium ion binding. A cryo-EM structure of FEX from Candida albicans, together with mutagenesis studies, reveals a fluoride permeation route through a single phenylalanine-lined pore. Molecular dynamics simulations demonstrate that a cation binding motif adjacent to the pore provides a stable sodium binding site that is accessible from the external aqueous solution. We propose that sodium gating resolves a major conundrum of channel-based fluoride efflux by preventing fluoride permeation under conditions of membrane depolarization. Comparison to bacterial fluoride channels (Flucs) provides a unique glimpse of the evolution of structural and mechanistic complexity in a membrane protein family with inverted repeat architecture.

biophysics↗

bioRxiv2024

Rewiring oncogenic signaling to RNA vector replication for the treatment of metastatic cancer

Despite recent advances, improvements to long-term survival in metastatic carcinomas, such as pancreatic or ovarian cancer, remain limited. Current therapies suppress growth-promoting biochemical signals, ablate cells expressing tumor-associated antigens, or promote adaptive immunity to tumor neoantigens. However, these approaches are limited by toxicity to normal cells using the same signaling pathways or expressing the same antigens, or by the low frequency of neoantigens in most carcinomas. Here, we report a fundamentally different strategy for designing safer and more effective anti-cancer therapies through the sensing of cancer-driving biochemical signals and their rewiring to virotherapeutic activation. Specifically, we rationally engineer a RNA vector to self-replicate and cause cytotoxicity in cancer cells exhibiting hyperactive HER2 (ErbB2), but not in normal cells with normal HER2 signaling. Compared to a widely tested virotherapeutic from the same vector family, our hyperactive ErbB2-restricted RNA vector (HERV) exhibits lower toxicity and greater activity against metastatic HER2-positive ovarian cancer in mice, extending survival independently of tumor antigenicity. Most importantly, HERV synergizes with standard-of-care chemotherapy against ovarian cancer metastases in vivo, with 43% of combination-treated subjects surviving for months beyond subjects treated with either therapy alone. Taken together, these results introduce rewiring of cancer-driving signaling pathways to virotherapeutic activation as a strategy for more specific and effective cancer treatment.

synthetic biology↗

bioRxiv2024

Fluoride export is required for competitive fitness of pathogenic microorganisms in dental biofilm models

Microorganisms resist fluoride toxicity using fluoride export proteins from one of several different molecular families. Cariogenic species Streptococcus mutans and Candida albicans extrude intracellular fluoride using a CLCF F-/H+ antiporter and FEX fluoride channel, respectively, whereas commensal eubacteria, such as Streptococcus gordonii, export fluoride using a Fluc fluoride channel. In this work, we examine how genetic knockout of fluoride export impacts pathogen fitness in single-species and three-species dental biofilm models. For biofilms generated using S. mutans with genetic knockout of the CLCF transporter, exposure to low fluoride concentrations decreased S. mutans counts, synergistically reduced the populations of C. albicans, increased the relative proportion of commensal S. gordonii, and reduced properties associated with biofilm pathogenicity, including acid production and hydroxyapatite dissolution. Biofilms prepared with C. albicans with genetic knockout of the FEX channel also exhibited reduced fitness in the presence of fluoride, but to a lesser degree. Imaging studies indicate that S. mutans is highly sensitive to fluoride, with the knockout strain undergoing complete lysis when exposed to low fluoride for a moderate amount of time, and biochemical purification the S. mutans CLCF transporter and functional reconstitution establishes that the functional protein is a dimer encoded by a single gene. Together, these findings suggest that fluoride export by oral pathogens can be targeted by specific inhibitors to restore biofilm symbiosis in dental biofilms, and that S. mutans is especially susceptible to fluoride toxicity. ImportanceDental caries is a globally prevalent condition that occurs when pathogenic species, including Streptococcus mutans and Candida albicans, outcompete beneficial species, such as Streptococcus gordonii, in the dental biofilm. Fluoride is routinely used in oral hygiene to prevent dental caries. Fluoride also has antimicrobial properties, although most microbes possess fluoride exporters to resist its toxicity. This work shows that sensitization of cariogenic species Streptococcus mutans and Candida albicans to fluoride by genetic knockout of fluoride exporters alters the microbial composition and pathogenic properties of dental biofilms. These results suggest that the development of drugs that inhibit fluoride exporters could potentiate the anticaries effect of fluoride in over-the-counter products like toothpastes and mouth rinses. This is a novel strategy to treat dental caries.

microbiology↗

bioRxiv2018

A multi-omics data simulator for complex disease studies and its application to evaluate multi-omics data analysis methods for disease classification

An integrative multi-omics analysis approach that combines multiple types of omics data including genomics, epigenomics, transcriptomics, proteomics, metabolomics, and microbiomics, has become increasing popular for understanding the pathophysiology of complex diseases. Although many multi-omics analysis methods have been developed for complex disease studies, there is no simulation tool that simulates multiple types of omics data and models their relationships with disease status. Without such a tool, it is difficult to evaluate the multi-omics analysis methods on the same scale and to estimate the sample size or power when planning a new multi-omics disease study. We developed a multi-omics data simulator OmicsSIMLA, which simulates genomics (i.e., SNPs and copy number variations), epigenomics (i.e., whole-genome bisulphite sequencing), transcriptomics (i.e., RNA-seq), and proteomics (i.e., normalized reverse phase protein array) data at the whole-genome level. Furthermore, the relationships between different types of omics data, such as meQTLs (SNPs influencing methylation), eQTLs (SNPs influencing gene expression), and eQTM (methylation influencing gene expression), were modeled. More importantly, the relationships between these multi-omics data and the disease status were modeled as well. We used OmicsSIMLA to simulate a multi-omics dataset for breast cancer under a hypothetical disease model, and used the data to compare the performance among existing multi-omics analysis methods in terms of disease classification accuracy and run time. Our results demonstrated that complex disease mechanisms can be simulated by OmicsSIMLA, and a random forest-based method showed the highest prediction accuracy when the multi-omics data were properly normalized.

bioinformatics↗

bioRxiv2018

pWGBSSimla: a profile-based whole-genome bisulphite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions

MotivationDNA methylation plays an important role in regulating gene expression. There has been growing interest in investigating the roles that genetic variants play in changing the methylation levels (i.e., methylation quantitative trait loci or meQTLs), how methylation regulates the imprinting of gene expression (i.e., allele-specific methylation or ASM), and the differentially methylated regions (DMRs) among different cell types. However, none of the current simulation tools can generate whole-genome bisulphite sequencing (WGBS) data while modeling meQTLs, ASM, and DMRs.\n\nResultsWe developed pWGBSSimla, a profile-based WGBS data simulator, which simulates WGBS data for 29 cell types based on real data. meQTLs and ASM are modeled based on the block structures of methylation status at CpGs, and DMRs are simulated based on observations of methylation rates in real data.\n\nAvailabilitypWGBSSimla is available at http://omicssimla.sourceforge.io.

bioinformatics↗