Biology subjects

Chang, H.-F.

Publications and source records attributed to Chang, H.-F..

14 recordsLinked to original sources

bioRxiv2026

Interferon-γ promotes SMAP production by cytotoxic T lymphocytes in a thrombospondin 4 dependent manner

Cytotoxic T lymphocytes (CTLs) eliminate infected and cancerous cells by exocytosing cytotoxic granules, either as single-core granules (SCGs) releasing diffusible Granzyme B and Perforin, or as multi-core granules (MCGs) releasing these effectors as thrombospondin-1/4-encapsulated supramolecular attack particles (SMAPs). How CTLs differentially deploy these granule types remains unclear. We demonstrate that prolonged in vitro expansion and restimulation selectively enhance SMAP release, correlating with increased MCG maturation and thrombospondin-4 expression. Using high-resolution imaging, we identify fusion-competent MCG intermediates lacking SMAPs but releasing granzyme B diffusively. Mechanistically, interferon-{gamma} upregulates thrombospondin-4, driving MCG maturation and SMAP biogenesis, enhancing late-phase CTL killing efficiency against resistant targets. Consistent with this, THBS1 and THBS4 transcript levels appear elevated in melanoma-infiltrating CTLs compared with those during acute adenovirus infection. These findings define a stimulus-dependent, interferon-{gamma}-driven pathway tailoring CTL responses to chronic pathology and highlight opportunities for SMAP-targeted immunotherapies.

immunology↗

bioRxiv2026

The missing part of the DMSP cycle in coral holobionts: Endozoicomonas exports acetate derived from DMSP degradation

Endozoicomonas, a dominant symbiotic bacterium in coral holobionts, is noted for its ability to degrade dimethylsulfoniopropionate (DMSP) so as to generate acetate. While acetate is a well-known short-chain fatty acid in metabolic cross-feeding relationships, it remains unclear whether acetate derived from bacterial DMSP degradation is available to corals and their other symbionts. In this study, we employed Endozoicomonas ruthgatesiae strain 8E (herein referred as 8E) as a model to examine availability of DMSP-derived acetate for other symbionts. Using gas chromatography-mass spectrometry (GC-MS), we observed a significant increase in acetate excretion in 8E upon exposure to DMSP. Stable isotope labeling further confirmed that this elevated acetate efflux originated directly from DMSP, suggesting a complete cycle of DMSP-derived carbon among coral symbionts. Transcriptomic analysis revealed that DMSP exposure upregulated dddD expression and triggered a systemic reconfiguration of metabolism, characterized by down-regulation of the TCA cycle and the Pta-AckA pathway, with carbon flux redirected to the glyoxylate shunt. These findings suggest that upon exposure to DMSP, metabolism of 8E shifts from biomass production to DMSP catabolism, resulting in acetate efflux. Notably, we found that elevated temperature diminishes DMSP cleavage activity of 8E, indicating thermal sensitivity of this bacterial metabolic activity. ImportanceEndozoicomonas is known for its dominance in coral holobionts and its ability to degrade DMSP, an important compound in the marine sulfur cycle. Acetate is one resulting product in microbial DMSP metabolism and a common cross-feeding molecule. Whether DMSP-derived acetate in coral-associated DMSP-degrading bacteria is employed for cross-feeding stands a critical step in making a complete carbon cycle of DMSP metabolism within coral holobionts. In this study, we employed GC-MS and RNA-sequencing techniques to offer the first evidence of acetate excretion in Endozoicomonas while metabolizing DMSP, as well as its underlying genetic mechanism. Furthermore, we demonstrate reduced genetic response and DMSP-degrading capability under an elevated temperature in Endozoicomonas ruthgatesiae strain 8E, the model bacterium employed in this study. These findings provide the missing puzzle of DMSP metabolism in coral holobionts and suggest a potential role of DMSP in modulating symbiotic interactions within coral holobionts.

microbiology↗

bioRxiv2025

Bacteriophages of the predominant coral symbiont Endozoicomonas: novel models for coral holobiont interactions

Phages are important symbionts in corals that modulate the community and functions of other symbiotic bacteria. Although phages infecting coral pathogens have been reported, no phage targeting beneficial microorganisms in corals has been isolated to date. From seawater near Acropora and Stylophora corals, we isolated the first bacteriophages (designated EmPhiA and EmPhiS) that infect Endozoicomonas montiporae CL-33, a model strain of the coral-prevalent and predominant Endozoicomonas bacteria. Electron microscopic observations of both phages showed Myovirus-like morphology and head sizes characteristic of jumbophages, with cryo-electron microscopy reveals long whiskers unprecedent in known phages. Genetically, these phages shared 99.21% genome similarity and are distant from known prokaryotic viruses, suggesting that they represent a novel viral species, which we name Encorevirus taiwanensis, in a novel family Encoreviridae. The small burst sizes of these phages (13.14 PFU/cell for EmPhiA and 21.4 PFU/cell for EmPhiS) potentially enable continuous coexistence of them with host bacteria within corals, making them putative core members of coral holobionts. Furthermore, host range test showed that EmPhiA and EmPhiS infect both Endozoicomonas bacteria isolated from stony and soft corals, implying their presence in a broad spectrum of host marine invertebrates. Using EmPhiS, we also investigated phage-bacterium interaction during its infection of E. montiporae CL-33. Interestingly, in addition to modulation of host cellular machinery, we found expression of several tellurium resistance proteins by EmPhiS during infection, which may provide the host additional stress resistance. These phages provide a novel model that will greatly advance our understanding of coral-Endozoicomonas-phage interactions.

microbiology↗

bioRxiv2025

Microbial profiling and single-cell transcriptomics reveal probiotic mechanisms of coral thermal resilience

Probiotics hold promise for enhancing coral resilience under climate-driven thermal stress, yet their mechanisms remain poorly understood. Here, we evaluate two Endozoicomonas species as coral probiotics and characterize their effects on microbial communities and host gene expression. We show that E. acroporae Acr-14T enhances thermal tolerance in Stylophora pistillata, suppresses opportunistic pathogens, and promotes beneficial microbes. To facilitate transcriptomic profiling, we assembled a chromosome-level genome of S. pistillata clade 1 (Pacific lineage) and used it to reveal that E. acroporae Acr-14T mitigates heat-induced protein-folding stress and supports host energy homeostasis. Single-cell transcriptomics further uncovered enhanced pro-survival signaling and modulation of the S-adenosylmethionine (SAMe) synthesis pathway. Together, our findings identify E. acroporae Acr-14T as a robust coral probiotic and provide mechanistic insights into host-microbe interactions that promote coral resilience under thermal stress.

microbiology↗

bioRxiv2025

Distinct Flower signaling domains orchestrate cellular fitness via secreted vesicles in Aβ-induced neurodegeneration

Cellular fitness surveillance preserves tissue integrity, yet its regulation within the mammalian brain remains poorly understood. We identify a bifurcated mechanism in the transmembrane protein Flower--encoding both survival-promoting ("win") and apoptosis-inducing ("lose") isoforms. We demonstrate that astrocytes secrete specialized extracellular vesicles (EVs), termed "fitness vesicles," carrying Flower to facilitate competitive selection across distal cell populations. The N-terminal Flower domain acts extrinsically via these EVs to drive the elimination of less-fit neighbors. Conversely, the "win"-specific C-terminal domain functions as a cell-intrinsic module; it translocates to the nucleus under stress to repress Caspase-3 and provide resilience. In Alzheimers disease (AD) models and human AD brains, Flower-positive astrocytes accumulate around amyloid-{beta} (A{beta}) plaques. Under A{beta} stress, the "win" isoform reprograms astrocytes toward a neuroprotective state that enhances plaque clearance while ensuring cell-intrinsic survival. Our findings reveal how Flower couples long-range, EV-mediated cellular selection with cell-autonomous protection to coordinate astrocyte quality control and tissue resilience in neurodegeneration.

neuroscience↗

bioRxiv2025

Gut miRNA regulates gut microbiome and Alzheimer pathology in App-knock-in mice

Alzheimers disease (AD) alters the gut microbiome. It remains unclear whether manipulation of miRNA could modulate the gut microbiome and AD pathologies. Depletion of gut miRNA in App-knock-in mice by conditional knockout of Dicer1 gene in intestinal epithelial cells: 1) decreased the absolute number and changed the composition of bacteria in both the gut and brain; 2) reduced cerebral A{beta} load by inhibiting {beta}-secretase activity and increasing the expression of LRP1 and ABCB1 at the blood-brain barrier; 3) increased Il-10 transcription and decreased the transcription of Ccl-2 gene, and that of Ndufa2 and Ndufa5 genes encoding mitochondrial respiratory enzymes in the brain; and 4) induced anxiety symptoms without affecting cognitive function in AD mice. Thus, manipulating miRNA in the gut can modify AD pathogenesis. Future studies should focus on identifying AD-specific miRNAs in the gut that can be therapeutically exploited (e.g. by oral administration) to prevent the progression of AD.

neuroscience↗

bioRxiv2025

IFNγ expression correlates with enhanced cytotoxicity in CD8+ T cells

BackgroundCD8+ T lymphocytes (CTLs) act as serial killers of infected or malignant cells by releasing large amounts of interferon-gamma (IFN{gamma}) and granzymes. Although IFN{gamma} is a pleiotropic cytokine with diverse immunomodulatory functions, its precise spatiotemporal regulation and role in CTL-mediated cytotoxicity remain incompletely characterized. MethodsUsing wild-type (WT) and granzyme B-mTFP knock-in mice, we combined in vitro approaches, including T-cell isolation and culture, plate-bound anti-CD3e stimulation, degranulation assays, flow cytometry, immunofluorescence, and structured illumination microscopy, to investigate IFN{gamma} dynamics in CTLs. ResultsIFN{gamma} expression in CTLs was rapid, transient, and strictly dependent on T-cell receptor (TCR) activation. We identified two functionally distinct IFN{gamma}-producing subsets: IFN{gamma}high (IFN{gamma}hi) and IFN{gamma}low (IFN{gamma}lo) CTLs. IFN{gamma}hi CTLs exhibited an effector/effector memory phenotype, significantly elevated CD107a surface expression (a marker of lytic granule exocytosis), and pronounced colocalization with cis-Golgi and granzyme B compared to IFN{gamma}lo CTLs. Furthermore, CRTAM, an early activation marker, correlated with IFN{gamma} expression in naive CTLs. ConclusionOur findings establish a link between elevated IFN{gamma} production and enhanced CTL cytotoxicity, implicating CRTAM as a potential regulator of early CTL activation and IFN{gamma} induction. These insights provide a foundation for optimizing T cell-based immunotherapies against infections and cancers.

molecular biology↗

bioRxiv2025

Lytic IFNγ is stored in granzyme B-containing cytotoxic granules and co-secreted by effector CD8⁺ T cells

Cytotoxic CD8 T cells form immunological synapses with target cells and release effector molecules, including IFN{gamma}, to mediate antitumor immunity. However, the mechanisms by which IFN{gamma} contributes to cytotoxicity remain incompletely understood. Here, we identify a subset of IFN{gamma} stored within GzmB cytotoxic granules (CGs) in activated mouse and human CD8 T cells, termed lytic IFN{gamma}. Lytic IFN{gamma} is polarized to the synapse and co-secreted with GzmB in both soluble and supramolecular attack particle (SMAP)-associated forms. Mouse CD8 T cells lacking the vesicle priming factor Munc13-4 exhibit impaired both CG and early IFN{gamma} release at the immunological synapse, while prolonged synaptic engagement restores IFN{gamma} secretion. Super-resolution imaging demonstrates that sustained synaptic interactions drive IFN{gamma} secretion at distal membrane sites, suggesting the existence of distinct IFN{gamma} populations with potentially diverse functions beyond lytic IFN{gamma}. These findings uncover an unrecognized mechanism of IFN{gamma} storage and release, underscoring its pivotal role in CD8 T cell-mediated tumor elimination.

immunology↗

bioRxiv2025

Plant nutritional and metabolic responses to drought and elevated CO2 revealed by machine learning-enabled non-targeted metabolomics

Projected atmospheric CO2 rise, coupled with intensification of drought in many regions, impacts the physiology of C3 plants beyond photosynthesis and carbon metabolism. The interaction between CO2 and drought affects the concentrations of many nutrients in crops, often resulting in excessive agrochemical use and less nutritious food production. To address these challenges, we investigated nutrient dynamics in Brachypodium distachyon, a model crop plant, under ambient and elevated CO2, factorially combined with well-watered or drought treatments. Integrative analyses of plant physiology, transcriptomics, and machine learning-enabled non-targeted metabolomics revealed that plant elemental composition and metabolomic responses to elevated CO2 strongly depend on water availability and differ between shoots and roots. Elevated CO2 and drought significantly impaired nitrogen status, with root nitrate uptake being more negatively affected than ammonium uptake. However, elevated CO2 increased iron partitioning in shoots under drought, potentially driven by enhanced carbon availability facilitating chelator synthesis for iron translocation. The high accumulation of sphingolipids in roots under combined stresses suggests a protective role against ionome imbalances. These findings highlight how climate stressors interact to shape plant nutrient dynamics, providing insights that can guide agricultural practices and breeding strategies to optimize nutrient management and foster sustainable agriculture under changing climate.

plant biology↗

bioRxiv2024

Highly adaptable deep-learning platform for automated detection and analysis of vesicle exocytosis

Vesicle exocytosis is a fundamental component of intercellular communication, in all organisms. It has been studied for decades, using various imaging tools. Nevertheless, exocytosis research is still limited by the lack of reliable automated analysis procedures. To address this, we developed the Intelligent Vesicle Exocytosis Analysis Platform (IVEA), a nearly universal solution for analyzing exocytosis acquired with live cell imaging. IVEA is applicable to a wide variety of experimental model systems, microscopes and reporter fluorophores. IVEA combines state-of-the-art deep-learning and computer vision regimes to enable fully automated analysis of large data. IVEA runs as a FIJI plugin and does not require prior training or human intervention. IVEA is 60 times faster than manual analysis and is able to detect rare events often missed by the human eye. Overall, IVEA represents a breakthrough in the analysis of cellular secretory mechanisms and has a transformative potential for the exocytosis imaging field.

bioengineering↗

bioRxiv2024

Thrombospondins 1 and 4 undergo coordinated transport to multicore cytotoxic granules to regulate SMAP biogenesis and function in CTL-mediatedcytotoxicity

Supramolecular Attack Particles (SMAPs) are particulate entities, characterized by a cytotoxic core enriched in granzymes and perforin surrounded by a glycoproteic shell, released by CTLs and NK cells. Prior proteomic analysis identified thrombospondin-1 (TSP-1) and thrombospondin-4 (TSP-4) as putative components of SMAPs. While TSP-1 has been validated as a component of the SMAP shell and shown to contribute significantly to CTL-mediated killing, the expression and function of TSP-4 in CTLs, and its interplay with TSP-1 in SMAP biogenesis and function, has not been investigated as yet. Here we demonstrate that TSP-4 and TSP-1 have a complementary expression profile during in vitro human CD8+ T cell differentiation to CTLs and sequentially localize to lytic granules (LG), with TSP-4 being required for TSP-1 association with LGs. Correlative light microscopy identified the TSP-enriched LGs as the SMAP-containing multicore granules. We show by STED microscopy a heterogeneity among TSP-enriched LGs, the most abundant population being positive for both TSP-4 and TSP-1. We also show that TSP-1 and TSP-4 are co-released in association with SMAPs at immune synapses formed on planar supported lipid bilayers, as assessed by dSTORM imaging. Finally, we provide evidence that TSP-4 is required for CTL- and SMAP-mediated cell killing. Of note, we found that chronic lymphocytic leukemia (CLL) cell supernatants, which suppress CTL mediated killing, also suppress expression of TSP-4 as well as of cytolytic effectors and impair SMAP biogenesis. These results identify TSP-4 as a key player in SMAP structure and activity and suggest that SMAPs may be a new target for immune suppression by CLL.

immunology↗

bioRxiv2024

Neuronal lysosome transfer to oligodendrocyte precursor cells: a novel mechanism of neuron-glia communication and its role in neurodegenerative disease

Oligodendrocyte precursor cells (OPCs) shape brain function through intricate regulatory mechanisms. Here, we observed that OPC processes establish connections with neuronal somata, with smaller lysosomes positioned near these contact sites. Tracking lysosomes demonstrated neuronal lysosomes were attracted to and released at these contact points, eventually becoming incorporated into OPC processes, suggesting a selective, OPC-evoked release of lysosomes from neuronal soma and their ingestion by OPCs, highlighting a unique lysosome-mediated communication between neurons and OPCs. Diminished branching of OPC processes resulted in fewer neuron-OPC contacts, fostering larger lysosome accumulation in neurons, altered neuronal activity and escalated prevalence of senescent neurons during aging. A similar reduction in OPC branching and neuronal lysosome accumulation was evident in an early-stage Alzheimers disease mouse model. Together, these findings underscore the pivotal role of OPC processes in modulating neuronal activity through direct somatic contact and lysosome ingestion, presenting a prospective therapeutic avenue for addressing neurodegenerative diseases.

neuroscience↗

bioRxiv2021

Impaired bidirectional communication between interneurons and oligodendrocyte precursor cells affects cognitive behavior

Cortical neural circuits are complex but very precise networks of balanced excitation and inhibition (E/I). Yet, the molecular and cellular mechanisms that form the E/I balance are just beginning to emerge. Here, using conditional GABAB receptor-deficient mice we identified a GABA/TNF-related cytokine (TNFSF12)-mediated bidirectional communication pathway between Parvalbumin-positive (PV+) fast spiking interneurons and oligodendrocyte precursor cells (OPCs) that determines the density and function of interneurons in the developing medial prefrontal cortex (mPFC). Interruption of the GABAergic signaling to OPCs resulted in reduced myelination and hypoactivity of interneurons, strong changes of cortical network activities and impaired cognitive behavior. In conclusion, glial transmitter receptors are pivotal elements in finetuning distinct brain functions.

neuroscience↗

bioRxiv2017

Drug discovery to counteract antinociceptive tolerance with mu-opioid receptor endocytosis

Morphine antinociceptive tolerance is highly correlated with its poor ability to promote mu-opioid- receptor (MOR) endocytosis. Our objective was to discover a novel positive allosteric modulator of MOR to enhance morphine-induced MOR endocytosis. We used high-throughput screening to identify several cardiotonic steroids as positive allosteric modulators of morphine-induced MOR endocytosis having high potency and efficacy, independently of Na+/K+-ATPase inhibition. Convallatoxin was found to enhance morphine-induced MOR endocytosis through an adaptor protein 2/clathrin-dependent mechanism without regulating G protein- or {beta}-arrestin-mediated pathways. Both F243 and I292 residues of MOR were essential to the effect of convallatoxin on MOR endocytosis. Co-treatment with chronic morphine and convallatoxin reduced morphine tolerance in animal models of acute thermal pain and chronic inflammatory pain. Acute convallatoxin administration reversed morphine tolerance in morphine-tolerant mice. These findings suggest that cardiotonic steroids are potentially therapeutic for morphine side effects and open a new avenue for the study of MOR trafficking.

neuroscience↗