Biology subjects

Yu, M.

Publications and source records attributed to Yu, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Establishment of Rabbit Formative-like Pluripotent Cells by Bidirectional Modulation of WNT Signaling Pathway

The generation of embryonic stem cells (ESCs) with full developmental capacity and robust chimera-forming potential remains a major bottleneck for most non-rodent mammalian species including rabbits, an important animal both for biomedicine and agriculture. Formative pluripotency is a unique intermediate state bridging the naive and primed pluripotent states, which is defined by distinct molecular signatures, intrinsic competence for primordial germ cell (PGC) specification, and unique developmental adaptability to early embryonic microenvironments. Here, we established a novel culture medium termed KFiC, which could bidirectionally and coordinately modulate the WNT/{beta}-catenin signaling pathway via combined treatment of WNT activator CHIR99021 and inhibitor IWR-1. The KFiC culture system enables efficient derivation and stable long-term self-renewal of rbESCs with consistent formative-like pluripotent characteristics. KFiC-cultured rbESCs (KFiC-rbESCs) form compact, undifferentiated colonies, maintain intact genomic stability, and recapitulate the transcriptional landscape of pre-implantation epiblast cells, accompanied by sustained high expression of the core formative pluripotency marker OTX2. Functionally, KFiC-rbESCs possess efficient PGC differentiation competence and extensively contribute to embryonic development after microinjection into rabbit morulae, displaying their superior developmental plasticity. Notably, the KFiC system can stabilize an intermediate formative-like pluripotent state in mouse, human, and porcine pluripotent stem cells, and KFiC-adapted mouse ESCs retain potent chimera-forming ability. Collectively, this study establishes a reliable culture platform for generating and maintaining formative-like rbESCs. This cross-species compatible system provides a promising foundation for further optimizing naive-level pluripotency in rbESCs and facilitates the generation of genetically engineered rabbit disease models.

developmental biology↗

bioRxiv2026

Rac1 and CHK1 Converge on Abi-1 to Regulate DNA Repair Dependency and Treatment Response in Human Cancers

Radiation therapy (RT) resistance remains a major clinical challenge, yet biomarkers guiding precision radiosensitization are lacking. We previously demonstrated that Rac1 promotes RT resistance in glioblastoma (GBM) by inducing Abi-1-S323 dephosphorylation and enhancing non-homologous end joining (NHEJ). Here, we identify Abi-1-S323 as a key regulator of DNA repair states and a determinant of therapeutic efficacy in human cancers. Clinically, loss of Abi-1-S323 phosphorylation was associated with poor outcomes in patients with RT-treated GBM. Bioinformatic analyses revealed that non-small cell lung cancer (NSCLC) and head and neck cancer (HNC) are among the cancers with frequent RAC1 amplification, suggesting that these tumor types may have increased Rac1-Abi-1 signaling activity. Loss of Abi-1-S323 phosphorylation also predicted poor outcomes in patients with RT-treated HNC. Consistent with these clinical observations, high Rac1 activity and low Abi-1-S323 phosphorylation were associated with enhanced DNA double-strand break repair and radioresistance in NSCLC and HNC models, whereas genetic or pharmacological inhibition of this signaling impaired DNA repair and radiosensitized tumors in vitro and in vivo. Mechanistically, we identified CHK1 as a kinase that phosphorylates Abi-1 at S323 and defines an alternative homologous recombination (HR)-dependent repair state. Tumors with high Rac1-Abi-1 signaling exhibited elevated NHEJ capacity and were selectively radiosensitized by Rac1 inhibition, whereas tumors with low Rac1-Abi-1 signaling displayed high CHK1 activity, preferentially relied on HR, and were selectively radiosensitized by CHK1 inhibition. These findings establish Abi-1-S323 as a biomarker defining therapeutically distinct DNA repair states and provide a framework for precision radiosensitization.

cancer biology↗

bioRxiv2026

Multi-Omics analysis provides crucial insights into ecological adaptation to dryland of a dominant grass (Psammochloa villosa, Poaceae) in Northwest China

Desertification exerts dramatic selection pressures on the evolution of plants. Despite the key role of ecological adaptation by natural selection to arid grasslands and subsequent intraspecific divergence, specific mechanisms driving this process remain poorly understood. Psammochloa villosa, a perennial forage grass endemic to the arid grasslands in Northwest China, where it thrives in shifting and semi-fixed sand land due to its exceptional drought tolerance, provides an ideal system to study adaptive evolution to aridity. In our study, we assembled a high-quality, chromosome-scale genome and conducted genomic resequencing of 42 populations across its major distribution. The genome assembly, which is approximately 1.55 Gb in size, has a super-scaffold N50 of 66.79 Mb, with 75.84% of the sequences identified as transposable elements. Coalescent phylogeny and genomic collinearity analyses strongly supported that P. villosa and Neotrinia splendens, as the closest taxa, shared a recent whole-genome duplication (WGD) event occurring approximately 18-20 Mya and followed by their divergence around ~11.2 Mya. Based on ancestral grass karyotype (AGK) reconstruction from synteny analysis, our results suggest that, relative to the AGK after the {rho}-WGD event, P. villosa and N. splendens underwent similar chromosomal restructuring and lineage-specific retention of numerous copies, providing a genomic basis for potential ecological adaptation and intraspecific diversification. The expanded XTH family, which encodes enzymes mediating xyloglucan endotransglucosylation and hydrolysis and thereby regulating xyloglucan remodeling, showed strong transcriptional responses under PEG-6000 treatment, suggesting that retained copies may be associated with xerophytic adaptation in P. villosa. Together, these findings suggest that WGD-derived gene retention created a delayed reservoir of genetic diversity that was later shaped by desertification and Qinghai-Xizang Plateau environmental changes, contributing to climate-associated genomic islands and intraspecific differentiation.

genomics↗

bioRxiv2026

A Tumor-Pituitary-Stromal Axis Promotes Colorectal Cancer Progression

Peripheral tumors can reprogram systemic physiology, yet how they engage central endocrine organs to remodel the local tumor microenvironment is unknown. We found that colorectal cancer (CRC) elevates circulating BMP2, which activates pituitary signaling and enhances endocrine output. Increased pituitary-derived growth hormone acted on growth hormone receptor-expressing cancer-associated fibroblasts (CAFs), inducing a p21-dependent senescence-like state and tumor-promoting secretory program. Disruption of pituitary BMP signaling or fibroblast GHR reduced tumor growth, whereas fibroblast-specific depletion of p21 abrogated GHR-dependent tumor promotion. In patients with CRC, elevated pituitary metabolic activity correlated with stromal p21 expression and tumor burden. Our study reveals a tumor-pituitary-stromal signaling axis through which a peripheral malignancy recruits a central endocrine organ to remotely shape its own microenvironment and promote disease progression.

cancer biology↗

bioRxiv2026

DPF3a couples H3K36me2-dependent chromatin remodeling to genome architecture during myogenesis

Chromatin remodelers are generally thought to regulate gene expression through nucleosome mobilization and modulation of local chromatin accessibility. Whether these complexes can instead control transcription through higher-order chromatin organization remains poorly understood. Here we identify the BAF subunit DPF3a as an essential regulator of skeletal muscle regeneration and myogenic differentiation. DPF3a functions through association with the H3K36me2/3 reader HRP2 and preferentially localizes to a distinctive chromatin state characterized by focal depressions within broad H3K36me2 domains. Biochemical reconstitution demonstrates that H3K36 methylation directly enhances remodeling activity of the DPF3a-containing cBAF complex. Unexpectedly, despite profound transcriptional defects, loss of DPF3a produces minimal changes in local chromatin accessibility. Instead, DPF3a is required for long-range chromatin looping associated with activation of myogenic genes. Together, our findings uncover a non-canonical mechanism whereby a chromatin remodeler regulates transcription primarily through three-dimensional genome organization rather than local accessibility control, and establish histone modification-guided chromatin remodeling as a key principle in gene regulation.

molecular biology↗

bioRxiv2026

Tumor control of lysosomal acidification promotes lipoprotein assimilationand ferroptosis resistance

Lysosomes are acidic organelles that fuel cancer progression by facilitating nutrient acquisition and metabolic adaptation, yet the determinants through which cancer cells sustain specialized lysosomal functions are not fully delineated. Notably, assimilation of dietary antioxidants within lipoproteins, a lysosome-dependent process, protects tumors from ferroptosis, an oxidative form of cell death, raising the possibility that tumors evolve mechanisms to enhance this process. Here, we applied genetic screens to identify regulators of lysosome-dependent lipoprotein assimilation and ferroptosis resistance and identified ZNF217, a frequently amplified transcriptional regulator in human cancers, as a driver of tumor lysosomal function and ferroptosis resistance. ZNF217 promoted lipoprotein assimilation through transcriptional maintenance of RAB11FIP4, an endolysosomal protein. Loss of either ZNF217 or RAB11FIP4 impaired lysosomal acidification across multiple cancer types, leading to defective lipoprotein assimilation, increased lipid peroxidation, ferroptosis sensitivity, and impaired tumor growth. Mechanistically, RAB11FIP4 boosts lysosomal acidity through maintenance of RAB7A activity. Finally, disruption of ZNF217 in breast cancer cell lines and patient-derived organoids, a tumor context linked to ZNF217 expression, reduced lysosomal acidity and impaired cancer growth through increased ferroptosis sensitivity. Together, we identify transcriptional regulation of lysosomal acidification as a key metabolic adaptation that enables extracellular antioxidant acquisition and tumor progression.

cancer biology↗

bioRxiv2026

The common evolution of fungicide persistence in cryptococcosis patients

Fungicide persistence, the ability of dormant fungal cells to survive lethal drug exposure, undermines treatment efficacy, yet its clinical evolution remains largely unexplored. We assembled a nationwide collection of clinical Cryptococcus neoformans isolates from China and revealed extensive inter strain variation in amphotericin B (AmB) persistence. This variation can arise from common evolutionary events in patients, generating previously undescribed high persistence cryptococcal variants refractory to AmB clearance. Genome wide fitness landscape analysis shows that persistence associated mutations generally impose minimal fitness costs, facilitating persistence evolution even in fungistatic resistant and hypervirulent genetic backgrounds. Machine learning identified deficient ACO2 expression as a key predictor of high persistence clinical isolates. ACO2 deficiency reproduces the high persistence phenotype by promoting POPC accumulation, which competes with AmB for its target. Moreover, the clinical stage antifungal T-2307 effectively eliminates high persistence strains across diverse genetic backgrounds. Collectively, our findings unveil common evolution of fungicide persistence in cryptococcosis patients, representing a previously overlooked clinical concern.

microbiology↗

bioRxiv2026

FP8 Inference in Genomic Foundation Models: Theoretical vs. Realized Speedups on GenomeOcean

Genomic Foundation Models (GFMs) are increasingly used for large-scale sequence analysis and generation. Compared with frontier language models, GFMs are typically smaller and frequently operate on long genomic sequences, with evaluation often requiring preservation of biologically meaningful structure and sequence-level relationships. Although low-precision post-training quantization (PTQ) has shown substantial memory and throughput benefits for general-purpose language models, it remains unclear whether these benefits transfer to GFMs given their distinct model scales, sequence characteristics, and evaluation requirements. We present an empirical case study of FP8 post-training quantization applied to GenomeOcean, a computationally efficient genomic foundation model with strong reported performance across diverse genomics tasks [Zhou et al., 2025]. Its range of model scales, from 100M to 4B parameters, provides a useful setting for examining how quantization effects vary with model size. We evaluate FP8 across two primary GFM inference regimes--embedding extraction and autoregressive generation--and assess its impact along two dimensions: biological fidelity relative to BF16 baselines and system-level efficiency in terms of throughput, memory usage, and energy efficiency. We find that FP8 largely preserves biological fidelity across the evaluated scales and inference regimes, while reducing GPU memory footprint at 4B scale and improving energy efficiency during autoregressive generation. However, realized throughput gains remain substantially below FP8s theoretical 2x hardware ceiling, with a best-case improvement of 19.3% in autoregressive generation and benefits varying strongly by model scale and workload. Autoregressive generation shows the clearest gains, driven largely by KV-cache compression, whereas embedding extraction provides limited or negative throughput benefits at smaller model scales. We attribute this theory-practice gap to the interaction of model-scale effects, memory-system bottlenecks, and software-stack limitations. These findings highlight the need for workload-specific empirical evaluation before adopting low-precision inference in scientific foundation models. Code availabilityhttps://github.com/jgi-genomeocean/genomeocean_efficiency

bioinformatics↗

bioRxiv2026

Spatial multi-omics and single-cell transcriptomics uncover senescence-associated cellular programs during colon adenoma to cancer progression

Colorectal cancer develops through a normal-adenoma-carcinoma sequence, yet only 5-10% of adenomas progress to malignancy, and the cellular programs governing that sequence remain poorly defined. Here we generate a spatial multi-omics atlas of human colon adenomas, combining Visium CytAssist and protein co-detection across 24 nonadvanced and advanced tubular adenomas with single-cell resolution Xenium Prime 5K profiling of 101 patient-matched normal, adenoma, and carcinoma cores from 16 patients. Integrating whole-transcriptome and 31-plex protein data identifies nine spatial clusters and two dysplastic epithelial populations that co-express stemness, proliferation, and senescence programs. These programs occupy a shared, spatially confined epithelial niche that expands from adenoma to carcinoma. Spatial analysis revealed GDF15, a senescence-associated secretory factor, mediated the coupling between senescence and stemness in advanced adenomas, and that GDF15-high epithelium locally excludes CD8+ T cells in adenoma and, more broadly, in carcinoma. These findings position senescence as a spatially instructive rather than merely tumor-suppressive program during colorectal carcinogenesis and suggest GDF15 might be a potential candidate target for cancer prevention and interception in the colon.

cancer biology↗

bioRxiv2026

The anatomical compartment defines distinct immune remodeling within human visceral adipose tissue during aging

Age-associated inflammation varies across tissues, but whether distinct visceral adipose tissue (VAT) depots undergo inflammatory remodeling in a depot-specific manner remains unclear. Here we profiled human peri-organ VAT, comparing kidney-associated fat (KF, from kidney transplantation donors) and gallbladder-associated fat (GBF, from asymptomatic cholecystectomy patients with incidental polyps), using single-cell RNA sequencing, flow cytometry, intracellular protein profiling and in situ analysis. GBF showed broad tissue-residency and granzyme K-associated remodeling across conventional, regulatory and innate-like lymphocyte compartments, whereas KF showed stronger B cell remodeling, greater myeloid representation and more compartmentalized changes within resident effector-like CD8+ T cell states. We further identified age-associated CD20+ T cells with features consistent with local B-T cell interaction and an antigen-experienced, granzyme K-associated inflammatory memory phenotype. In situ analysis revealed age-associated myeloid accumulation and crown-like structure remodeling, accompanied by distinct myeloid inflammatory programs in KF and GBF. Finally, depot-specific immune signatures associated with clinical indices of adjacent kidney and liver function. These findings indicate that age-associated distinct immune programs within peri-organ VAT depots track with local tissue context and the state of the adjacent organ.

immunology↗

bioRxiv2026

Multitrophic interaction networks mediate biodiversity effects on ecosystem multifunctionality

Biodiversity loss threatens the multifunctionality of ecosystems on which human well-being ultimately depends. Changes in multitrophic species interactions may be key to explaining the ecological consequences of biodiversity loss, but research explicitly linking species interactions and ecosystem multifunctionality remains rare. To assess interaction-mediated biodiversity effects and underlying mechanisms, characterizing the structure of species interaction networks is invaluable. Using comprehensive species interaction and ecosystem functioning data from a large-scale tree biodiversity experiment, we find consistent effects of the structure of species interaction networks on ecosystem multifunctionality across multiple types of antagonistic and mutualistic interactions. While positive effects of network size align with expected positive effects of multitrophic species diversity, positive effects of niche overlap among interacting species and negative effects of highly connected species (i.e. high linkage density) reveal additional, interaction-mediated drivers of multifunctionality. Specifically, the effects of niche overlap suggest benefits of functionally similar species, and the effects of linkage density underscore the importance of specialized interactions in promoting ecosystem multifunctionality. These findings emphasize that to effectively safeguard ecosystem service provisioning, ecosystem management and biodiversity conservation not only need to account for biodiversity changes at multiple trophic levels, but also explicitly for how species interact among each other.

ecology↗

bioRxiv2026

VFUSE: Virulent Feature Understanding with Sparse autoEncoders

Generative models have shown remarkable progress in a variety of domains such as protein design, but such power enables the opaque generation of hazardous proteins. In this work, we introduce VFUSE (Virulent Feature Understanding with Sparse autoEncoders), a mechanistic interpretability approach that trains SAEs on diffusiontransformer activations to audit protein models for hazard-aware features. We apply VFUSE to RoseTTAFold3 and RFDiffusion3, popular openweight models for protein folding and synthesis. We find that for certain blocks, linear probes detect hazardous designs significantly better when fit in the SAE latent space over the original models representations: improving interpretability without sacrificing model performance. Furthermore, we identify monosemantic features from the SAE that fire only on hazardous designs at up to AUROC 0.84 (q < 10-13). To our knowledge this is the first SAE trained on an all-atom diffusion model and the first feature-level virulence audit of a protein design model, paving the way towards safe and interpretable protein design.

bioinformatics↗

bioRxiv2026

Cross-linked volumetric DNA microscopy for dense molecular-network phenotyping in intact tissue

Resolving cellular phenotypes in full tissue context requires methods that can retain those cells physical neighborhoods, together with the identities of individual biomolecules, in intact three-dimensional specimens. We introduce cross-linked volumetric DNA microscopy (xVDM), in which unique molecular identifiers are seeded directly into the tissues protein matrix and linked by uniquely labeled DNA bridges to create a dense, DNA-encoded proximity network. Cell-scale molecular communities are then reconstructed directly from this network. xVDM produces denser molecular networks and broader transcriptome recovery than when these networks are nucleated by transcripts alone. xVDM maps out genetically annotated three-dimensional networks that map onto cell states and tissue regions in intact zebrafish embryos at 12, 18, and 24 hpf. Antibody-oligonucleotide conjugates extend the same framework to protein targets in human tonsil. xVDM provides a route to three-dimensional molecular phenotyping in intact specimens using only standard bench reagents and a DNA sequencer.

bioengineering↗

bioRxiv2026

Novel Muscle-Tropic AAV Capsids with Dramatically Enhanced Transduction and Safety Profiles in Non-Human Primates

Adeno-associated virus (AAV) gene therapy holds immense promise for treating muscular dystrophies, yet its efficacy and safety are constrained by the suboptimal tissue tropism of natural serotypes. Here, we employed the REACH platform, which combines rational design and directed evolution, to engineer muscle targeting vectors. Systemic administration in non-human primates (NHPs) revealed that lead candidate M1 mediates a >10-fold increase in skeletal muscle transduction compared to the AAV9 and 2-3 fold higher than MyoAAV, while concurrently achieving a remarkable 183-fold reduction in liver distribution. Furthermore, M1 exhibited significant de-targeting from key off-target tissues, including dorsal root ganglia (11 fold), lung (27 fold), spleen (2 fold), and kidney (2 fold). These findings demonstrate that the REACH platform can generate AAV capsids with simultaneously enhanced muscle tropism and favorable safety profiles, addressing a critical bottleneck in muscle-directed gene therapy.

bioengineering↗

bioRxiv2026

Beyond Capture Efficiency: A Multidimensional Framework for Benchmarking Circulating Tumor Cell Isolation Technologies

Metastasis remains the major cause of cancer-related mortality, and circulating tumor cells (CTCs) are both candidate liquid-biopsy biomarkers and plausible intermediates of metastatic dissemination. Because CTCs are extremely rare in peripheral blood, platform comparisons have often focused solely on recovery. That focus is insufficient for applications that depend on the quality of the recovered material, including single-cell profiling, short-term culture, and functional testing. Here, we compared four CTC isolation approaches: TellDx CTC System, Genesis System, RosetteSep, and flow cytometry, using spike-in experiments in human blood. Capture efficiency was evaluated across all four platforms; purity was assessed for TellDx, Genesis, and RosetteSep; and post-isolation GFP signal persistence in culture was assessed for TellDx and Genesis as an exploratory proxy for short-term post-isolation preservation. Under the conditions tested, TellDx showed the highest recovery (88.1% {+/-} 3.7%), followed by Genesis (40.6% {+/-} 12.1%), RosetteSep (36.5% {+/-} 9.0%), and flow cytometry (7.6% {+/-} 4.5%). TellDx also showed the highest purity score (3.76), whereas Genesis (2.25) and RosetteSep (2.09) did not differ substantially. In the short-term culture assay, TellDx-derived samples retained a higher normalized GFP signal than Genesis-derived samples at 48 h and 72 h. To synthesize these readouts, we propose the Recovery Performance Index (RPI), a composite score integrating recovery, purity, and post-isolation signal persistence. Within this experimental framework, TellDx achieved the highest RPI. These data support two conclusions. First, platform benchmarking for CTC workflows benefits from multidimensional evaluation rather than recovery alone. Second, under this spike-in model and within the specific workflows used here, TellDx performed best among the platforms tested. The principal contribution of this study is therefore the establishment of a practical benchmarking framework that can be expanded in future work using clinical samples, multiple CTC phenotypes, and orthogonal viability assays.

cancer biology↗

bioRxiv2026

Sphk1-S1P signaling drives blood-brain barrier breakdown after intracerebral hemorrhage via HIF-1α-dependent upregulation of Bsg-MMP-9

Blood-brain barrier (BBB) breakdown is a critical pathological event driving secondary brain injury and poor outcomes following intracerebral hemorrhage (ICH). However, the mechanisms governing acute BBB breakdown after ICH remain incompletely understood. Here we demonstrate that the Sphk1-S1P-S1PR3 signaling plays a pivotal role in this process. Sphk1 expression was significantly upregulated in the perihematomal endothelial cells of both ICH patients and mice, with levels positively correlating with BBB dysfunction severity and poor clinical outcomes. Using endothelial-specific genetic gain- and loss-of-function approaches, we found that Sphk1 knockdown attenuated BBB leakage, reduced hematoma volume and brain edema, preserved tight junction integrity, and improved neurological function at 1-day post-ICH, whereas Sphk1 overexpression exacerbated these pathological features. Mechanistically, transcriptomic profiling of perihematomal endothelial cells revealed that prior to its established role in Nlrp3-mediated pyroptosis, Sphk1 promotes early BBB breakdown by regulating the Bsg-MMP-9 axis. Endothelial-specific Bsg deletion completely abrogated the deleterious effects of Sphk1, confirming Bsg as an indispensable intermediary through which Sphk1 signals to MMP-9. ATAC-seq and dual-luciferase assays further demonstrated that Sphk1-generated S1P signals through S1PR3 to activate HIF-1, which directly binds the Bsg promoter to drive its transcription, ultimately promoting MMP-9-mediated tight junction degradation. These findings delineate a complete hierarchical signaling cascade from metabolic enzyme to transcriptional regulation and subsequent barrier injury, establishing the Sphk1-Bsg-MMP-9 axis as a promising therapeutic target for ICH. One sentence summaryThis work identifies an early and pivotal mechanism of blood-brain barrier breakdown after intracerebral hemorrhage, demonstrating that Sphk1-generated S1P signals through S1PR3 to activate HIF-1, which directly transactivates Bsg expression, leading to MMP-9-mediated tight junction degradation, thereby establishing a novel hierarchical axis with therapeutic potential.

cell biology↗

bioRxiv2026

Prevotella copri alleviates hyperuricemia via uricolysis and gut microbiota reconstruction

Despite the therapeutic promise of uric acid-metabolizing microbes for hyperuricemia, their application is hindered by the scarcity of highly efficacious strains. To identify uric acid-metabolizing microbes, we enriched gut microbiota from cynomolgus monkeys under uric acid-supplemented conditions. This selection increased the abundance of Prevotellaceae_UCG-001 and norank_f_Prevotellaceae, implicating Prevotella species as key uric acid degraders. In vitro validation confirmed efficient uric acid consumption by two new Prevotella isolates and the reference strain Prevotella copri DSM 18205 (P. copri). Oral administration of P. copri in hyperuricemic mice reduced uric acid levels in serum and kidney tissues and alleviated renal fibrosis by suppressing the TGF-{beta}/Smad pathway and downstream fibrogenic genes. Moreover, P. copri administration restored the depleted population of Faecalibaculum, and further assays demonstrated that Faecalibaculum rodentium directly metabolizes uric acid. Collectively, P. copri alleviates hyperuricemia via a dual mechanism: direct uric acid catabolism and enrichment of commensal uric acid-consuming bacteria. These findings establish P. copri as a promising live biotherapeutic agent for hyperuricemia and highlight microbial collaboration as a therapeutic strategy for metabolic diseases.

microbiology↗

bioRxiv2026

Capsular K-antigen Coats Outer Membrane Vesicles of Porphyromonas gingivalis

Periodontal disease is an inflammatory disorder that arises from dysbiosis of the subgingival microbiota, with Porphyromonas gingivalis acting as a keystone pathogen in the shift from health to disease. P. gingivalis employs multiple strategies to subvert host immune defenses, and its capsular K-antigen serves as a key virulence determinant. Here, a pre-adsorbed antiserum (pAds106) was generated by removing nonspecific antibodies using cells from a K-antigen-null mutant (W83{Delta}PG0106), resulting in exceptional specificity for the P. gingivalis K1-antigen. Immunofluorescence analysis revealed that the K-antigen preferentially coats outer membrane vesicles (OMVs), rather than attaching to the bacterial cell surface. This localization was further confirmed by ELISAs of density gradient ultracentrifuge-purified OMVs, with background signal detected in OMVs derived from K-antigen-deficient strains, non-K1-strains, and other oral Bacteroidetes. K-antigen-coated OMVs exhibited higher hydrophilicity and elicited weaker inflammatory responses compared to K-antigen-deficient OMVs, consistent with previously reported properties of encapsulated strains. Importantly, the antiserum detected K-antigen-coated OMVs in subgingival plaque from periodontal patients, suggesting that K-antigen is actively produced at diseased sites. These findings revise the prevailing view that K-antigen solely encapsulates the bacterial cell body and suggest that K-antigen-coated OMVs produced by P. gingivalis play distinct roles in immune evasion during periodontal disease.

microbiology↗