Biology subjects

Wang, P.

Publications and source records attributed to Wang, P..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Germline regulation of tumor evolutionary dynamics shapes multiple myeloma progression

Germline variation shapes cancer risk, yet its influence on the evolutionary dynamics of established tumors remains poorly understood. In multiple myeloma, subclonal diversification drives disease progression and treatment failure, but the heritable factors that modulate this process are unknown. Here, we show that germline variation is associated with tumor evolutionary features, implicating inherited regulation in subclonal expansion. Integrating germline variation with tumor evolutionary parameters identifies variants associated with evolutionary features, with signals enriched in regulatory regions, consistent with a transcriptional basis. We further identify TBKBP1 as a key locus linking germline variation to tumor evolution and clinical outcome. Germline variation at this locus is associated with TBKBP1 expression and subclonal expansion, and TBKBP1 expression correlates with adverse prognosis, consistent across independent cohorts. Functional analyses demonstrate that TBKBP1 promotes proliferation and activates MYC, mTORC1 and non-canonical NF-{kappa}B signaling pathway. Together, these findings establish germline regulatory variation as a determinant of tumor evolutionary dynamics and identify TBKBP1 as a mediator linking inherited variation to subclonal expansion and disease progression in multiple myeloma.

bioinformatics↗

bioRxiv2026

Particle Biology: A Perspective on a First-Principles Theory of Life

This Perspective formally proposes Particle Biology as a unifying theoretical framework to address the critical bottleneck in current life science research. Current life science research has reached a critical bottleneck. While the field has advanced to the study of 3D genomic spatial configurations and chromosomal organization, it remains largely descriptive and confined to the macromolecular level. This approach lacks a first-principles understanding of the underlying physical forces that drive biological processes. This Perspective formally proposes Particle Biology as a unifying theoretical framework. We establish an axiomatic system positing that life phenomena are fundamentally emergent spatiotemporal patterns of electromagnetic forces among atoms, electrons, and nuclei operating far from thermodynamic equilibrium. By defining biological states through the Biological Hamiltonian and mapping biochemical pathways to multidimensional Potential Energy Surfaces (PES), we bridge the gap between descriptive biology and predictive physics. We categorize core research technologies into three modalities--seeing, computing, and controlling particles--facilitated by advancements in Cryo-EM, AlphaFold 3, and Boron Neutron Capture Therapy (BNCT). Ultimately, the trajectory of molecular biology has evolved from cells to DNA and onto the 3D spatial genome, yet it cannot go deeper within current paradigms. The next logical evolution is to move beyond the macromolecular bottleneck to focus on the electromagnetic interactions between atoms and ions--the true Particle Biology level--to redefine disease and intervention.

biophysics↗

bioRxiv2026

Stromal Gasdermin D-mediated Pyroptosis Drives Maladaptive CD4⁺ T-cell Remodeling in Tet2-Deficient Hematopoiesis

An inflammatory bone marrow microenvironment is increasingly recognized as critical in myeloid disease evolution, yet how stromal inflammation interfaces with adaptive immunity remains poorly defined. Here, we show that stromal pyroptosis drives mutation-specific myeloid expansion by coordinating monocytic remodeling and CD4 T-cell activation. Genetic ablation of gasdermin D in the bone marrow stroma suppressed stromal pyroptosis and attenuated Tet2-deficient myeloid expansion. Tet2 deficiency skewed monocyte and macrophage differentiation toward an activated, antigen-presenting state that interacted with pyroptotic stromal cells to promote expansion of a distinct CD4 T-cell population. These cells expressed canonical T follicular helper markers (Bcl6, Cxcr5, Il21, and Cd40l) together with interferon-responsive and tissue-interaction programs, consistent with an inflammation-adapted TFH-like state. CD40L produced by these cells reinforced the expansion of Tet2-deficient monocytes and macrophages, establishing a feed-forward stromal-immune circuit. Disruption of this axis through stromal gasdermin D deficiency or CD40L blockade attenuated myeloid expansion in vivo. Consistent with these findings, patients with isolated TET2 loss-of-function mutations exhibited CD4 T-cell skewing and CD40L+ T-cell-rich tertiary lymphoid structures in the bone marrow. Together, these data identify a pyroptosis-dependent stromal-immune axis that links early myeloid inflammation to maladaptive remodeling of adaptive immunity and reveals a context-dependent therapeutic vulnerability in Tet2-deficient hematopoiesis.

cancer biology↗

bioRxiv2026

Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cells

Cohesin is crucial for establishing 3D genome organization and functions. However, the in vivo mechanism of cohesin-mediated extrusion remains unsettled. Here, we investigated extrusion directionality using integrated genome mapping coupled with perturbation in human cells. By defining cohesin loading at NIPBL binding loci and anchoring at CTCF sites, we systematically characterized the aggregated and single-molecule trajectories of extrusion "stripes" and contact "dots" from and between individual cohesin loading and anchoring points. Our analyses delineated two dynamic modes of in vivo mechanism in which NIPBL/cohesin initiates extrusion at its loading sites in a one-sided manner; after encountering CTCF, CTCF/cohesin switches its extrusion direction backward and robustly extrude DNA unidirectionally until completing the convergent CTCF loop. Surprisingly, depleting CTCF resulted substantial increase of NIPBL/cohesin-mediated extrusion activity, which is further validated by in silico perturbation. These findings reveal novel mechanistic insights into how cohesin and CTCF orchestrate cohesin-mediated loop extrusion in vivo.

genomics↗

bioRxiv2026

Autoluminescence characteristics of 25 Phalaenopsis orchids following transient transformation with eFBP2

Engineering autoluminescent plants, especially horticultural crops, has recently emerged as a promising research area, with one current approach involving the transgenic introduction of fungal bioluminescence pathway genes. Although autoluminescent plants such as tobacco and petunia have been created, it remains unclear whether all horticultural plants have the potential to be autoluminescent after genetic modification, especially those having flowers with dark colors and thick cuticles. To understand whether, and what if any, floral traits affect autoluminescence potential, we assess the autoluminescence characteristics of 25 representative Phalaenopsis cultivars after transient transformation of fungal bioluminescence pathway genes, alongside several key morphological and biochemical traits. Our results demonstrate that autoluminescence characteristics are correlated with floral color lightness, organ textures and epidermal cell types. In contrast, the content of the substrates of luciferin--caffeic acid and tyrosine, and the infiltration ease of inoculation solution into floral organs after injection, have limited effects on autoluminescence characteristics. Autoluminescence intensity can be reasonably predicted using five floral traits investigated, as 80.4% of variation can be explained by these traits. Our study not only identifies specific Phalaenopsis cultivars with high potential for developing autoluminescent lines but also provides a selection framework applicable to other horticultural crops.

plant biology↗

bioRxiv2026

Pan-cancer circular genomics identifies intratumoral Staphylococcus lugdunensis as a metabolic driver in bladder cancer

Intratumoral microbiota play key roles in cancer but are challenging to profile due to low biomass. We developed CIRCMIP, an enzymatic pipeline that eliminates linear DNA to enrich bacterial genomes, achieving 100-fold higher sensitivity than standard metagenomics. Applied to 312 pan-cancer specimens, CIRCMIP identified Staphylococcus lugdunensis as a signature bacterium enriched in early-stage bladder cancer (BLCA), where its presence predicts poor survival. Integrated modeling and lipidomics revealed that Staphylococcus lugdunensis colonization drives aberrant lipid metabolism with secretion of LPC14:0. Both Staphylococcus lugdunensis and LPC14:0 drive BLCA progression by promoting fatty acid uptake and {beta}-oxidation. Mechanistically, chemical proteomics revealed LPC14:0 as a direct PPAR{delta} ligand, binding via hydrogen bonds with Thr292/Thr289. This activation upregulates fatty acid transporters (CD36, FABP4) and metabolic enzymes (ACOX2), fueling malignant proliferation. Furthermore, CIRCMIP-derived biomarkers show robust diagnostic accuracy, establishing a new research paradigm and revealing the Staphylococcus lugdunensis-LPC14:0-PPAR{delta} axis as a therapeutic target in bladder cancer. HIGHLIGHTO_LICIRCMIP leverages DNA circularity to achieve 100-fold sensitivity in pan-cancer bacteriome profiling. C_LIO_LIStaphylococcus lugdunensis is a bacterial signature in early-stage bladder cancer that predicts poor patient survival. C_LIO_LIBacteria-derived LPC14:0 acts as a direct ligand for PPAR{delta} to drive host malignant metabolic reprogramming. C_LIO_LITargeting the Staphylococcus lugdunensis-LPC14:0-PPAR{delta} axis abrogates malignant progression in bladder cancer. C_LI

cancer biology↗

bioRxiv2026

Mechanism of GPR84 allosteric modulation at a helix 8-proximate site

Allosteric modulators offer opportunities for pathway-selective GPCR signalling, but the structural mechanisms enabling biased allosteric modulation remain unclear. Here we identify a helix 8-proximate allosteric site in the immune-metabolic receptor GPR84 and define how it achieves Gi -biased signalling. Cryo-EM structures of the GPR84-Gi complexes bound to the orthosteric agonist OX04539 alone or in combination with the positive allosteric modulator (PAM) PSB-16671 reveal that PSB-16671 binds at the interface of TM1, TM7, and helix 8, a location distinct from previously characterized GPCR allosteric pockets. Molecular dynamics simulations and mutagenesis uncover a polar interaction network linking orthosteric and allosteric sites through conserved residues including Asp662.50, Asn1043.36, and Asn3627.45. Unexpectedly, disrupting this network enhances allosteric cooperativity, indicating that conformational flexibility within the network is essential for allosteric communication. PSB-16671 stabilizes a receptor conformation with pronounced TM6 displacement that favours Gi coupling while disfavouring {beta}-arrestin recruitment. This Gi-biased profile sustains macrophage phagocytosis of cancer cells without the desensitization induced by balanced agonists. Sequence analysis suggests that helix 8-proximate allosteric sites may be broadly targetable across class A GPCRs, while receptor-specific contacts enable selective modulation. These findings establish structural and mechanistic principles for biased allosteric modulation applicable beyond GPR84.

biochemistry↗

bioRxiv2026

Transition metal-triggered immunity via an Arabidopsis NLR pair

Plants are challenged by multiple biotic (e.g. pathogens) and abiotic (e.g. heavy metals) stressors. Some transition metals can enhance plants defense against pathogens, but the mechanism remains unclear. Here, we demonstrate that an Arabidopsis head-to-head gene pair of intracellular nucleotide-binding leucine-rich repeat (NLR) receptors, both expressed in the endodermis of roots, antagonistically control transition metal-triggered immunity. One NLR, STM2 binds transition metal ions, such as Cd2+, Cu2+ and Zn2+, with its LRR domain to enhance its NAD+ hydrolytic activity and immune responses via the EDS1/PAD4/ADR1 module, triggering enhanced resistance to bacterial wilt Ralstonia solanacearum. The other NLR, STM1 suppresses STM2 to protect plants from transition metal-triggered immunity and growth inhibition in the presence of excess metals. STM1 also dampens resistance to the pathogen. Our study defines an NLR activated by transition metals and reveals a trade-off between susceptibility to pathogens and sensitivity to transition metals that are pervasive in soil.

plant biology↗

bioRxiv2026

PRISM: A High-Throughput Simulation Infrastructure for CADD Agents

Despite rapid progress in AI agents for computer-aided drug design (CADD), protein-ligand simulation workflows remain fragmented across disparate tools, creating a major bottleneck for scalable candidate evaluation. Here, we present PRISM (Protein-Receptor Interaction Simulation Modeler), a Python platform built on GROMACS that unifies ligand parameterization across multiple force fields, automated system construction, enhanced sampling, multi-tier binding free energy estimation, and trajectory analysis within a single workflow. Through the Model Context Protocol (MCP), PRISM further serves as the computational infrastructure for CADD-Agent, an expert-workflow-driven AI agent designed to orchestrate hierarchical drug screening pipelines. As a pilot application, we applied PRISM to riboflavin synthase and demonstrated end-to-end automation from candidate library assembly to binding pocket characterization, identifying a potential allosteric inhibition site at the oligomerization interface. Together, these results establish PRISM as a high-throughput simulation infrastructure for agent-enabled CADD.

biophysics↗

bioRxiv2026

A rugged binding landscape unifies static and dynamic paradigms in protein-protein interactions

Predicting protein-protein interaction (PPI) affinities from structural data remains a challenge. Although binding funnel theory describes the formation of native complexes, the topography of the funnel bottom and its influence on affinity are often overlooked. Using two well-controlled nanobody-antigen datasets as model systems, we demonstrate that PPI can exist in both static and dynamic binding paradigms. These two nanobody series adopt nearly identical binding poses toward their respective antigens yet exhibit diverse affinities, each representing a distinct paradigm: a static paradigm in which affinity can be ranked by Rosetta scoring of co-crystal structures alone, and a dynamic paradigm in which affinity can only be ranked using molecular dynamics-sampled ensembles. The two paradigms differ in interfacial dynamics. In the dynamic series, the relative motion between binding partners ({Delta}RMSF) is temperature-sensitive, with optimal affinity correlation at 298 K. In the static series, {Delta}RMSF is minimal and insensitive to temperature. Local frustration analysis establishes a mechanistic bridge between interfacial dynamics and landscape topology. Dynamic interfaces exhibit increased frustration upon thermal sampling, facilitating sampling of functionally relevant microstates, whereas static interfaces show minimal frustration changes across temperatures. The temperature-dependent frustration difference mirrors {Delta}RMSF sensitivity, confirming local frustration as a determinant of interfacial dynamics. Furthermore, static interfaces are characterized by a higher density of canonical hotspot residues, while dynamic interfaces utilize interfacial ruggedness to modulate affinity. Together, these results demonstrate that conserved binding modes can encode different energy landscapes and provide a practical framework for determining when ensemble-based sampling is required for accurate affinity prediction.

biophysics↗

bioRxiv2026

Oscillatory sensory stimulation in the delta-band enhancestemporal prediction performance

Predicting the time point when an event will occur is fundamental for adaptive behavior, yet it remains unresolved whether temporal prediction can be influenced by low-frequency rhythmic modulation of sensory stimuli. Here, we tested whether external rhythmic sensory stimulation at a frequency in the delta range (0.5 - 3 Hz) alters performance in a visual temporal prediction task. Participants judged whether a moving visual stimulus reappeared too early or too late after disappearing behind an occluder, while the temporal structure of crossmodal sensory input was manipulated across two behavioral sessions. Results indicated that in the visual-auditory conditions, oscillatory stimulation in either the visual or auditory modality improved performance, whereas decaying sensory intensity over time impaired performance. In visual-tactile conditions, oscillatory visual stimulation also enhanced sensitivity, but rhythmic tactile stimulation did not produce a comparable benefit in performance. Critically, tactile stimulation improved performance only when aligned to the expected disappearance of the visual stimulus, demonstrating that the phase relationship between sensory input and intrinsic delta oscillations is behaviorally relevant. Together, these findings indicate that temporal prediction depends on the temporal structure of sensory input and support the relevance of delta-band oscillations in predictive behavior across and within sensory modalities. Hence, rhythmic modulation of sensory stimuli may provide a tool to enhance temporal prediction accuracy by stimulating oscillatory neural dynamics.

neuroscience↗

bioRxiv2026

Binary-SPA: A Reference-Free Method for Cell Annotation in High-Resolution Spatial Transcriptomics

Accurate cell type annotation remains a major challenge in high-resolution spatial transcriptomics analysis. Current approaches primarily rely on label transfer from single-cell RNA sequencing (scRNA-seq) reference datasets or marker-based annotation of transcriptionally defined clusters. While these methods are widely used, they have critical limitations. Label transfer approaches depend on the availability of a well-matched scRNA-seq reference. Marker-based annotation methods often suffer from accuracy and limited coverage. To address these challenges, we developed Binary-SPA, a computational framework for cell-type annotation of high-resolution spatial transcriptomics data. Binary-SPA performs annotation in two stages. First, a binary classification step identifies high-confidence cells using predefined marker sets. These confidently annotated cells are then used as an internal reference for anchor-based label transfer in the second stage. Binary-SPA outperforms conventional marker-based annotation approaches and existing label transfer methods across multiple high-resolution spatial transcriptomics platforms, preservation methods, and tissue types. While label transfer methods achieve high accuracy only when same-tissue scRNA-seq references are available, and decline substantially when relying on independent datasets, Binary-SPA matches this performance with 100% annotation coverage while eliminating the need for external reference data entirely. Binary-SPA demonstrates robust performance even in challenging specimens such as bone marrow biopsies, and validation against matched COMET protein expression data confirmed strong concordance between transcriptomic- and protein-based cell identities. Binary-SPA thus provides a robust, reference-free solution for spatial transcriptomics annotation with broad applicability to research and clinical specimens.

genomics↗

bioRxiv2026

Ubiquitination-mediated mitochondrial protein degradation ensures seedling emergence by regulating ER-mitochondrial interaction and mitophagy

Seedling emergence is a pivotal step of plant survival, requiring rapid hypocotyl elongation for soil penetration. This energy-demanding process necessitates active mitochondrial respiration, which inevitably induces oxidative damage. Therefore, plants evolved a quality control mechanism that selectively removes dysfunctional mitochondria through the mitophagy pathway. Here, we identified SPL2, a mitochondrial E3 ligase which is essential for hypocotyl elongation and seedling emergence through degrading mitochondrial outer membrane proteins, such as TRB1 and FIS1A. Intriguingly, these proteins also interact with an ER protein, VAP27-1, forming a complex at the ER-mitochondria contact sites, which is essential for mitophagy initiation. The spl2 mutant exhibits enhanced ER-mitochondrial tethering and mitophagy activation, whereas its overexpression has the opposite effects. The expression of SPL2 increases after light perception, in agreement with the reduced mitophagy. Collectively, our findings reveal novel mechanistic insights into seedling emergence, which are coordinated through protein ubiquitination, ER-mitochondrial interaction, and mitophagy.

plant biology↗

bioRxiv2026

Deep Invaginations of Nuclear Envelope Coordinate Spatial Organization of Chromatin in Epithelium

Cell nuclei are often used to assess cell health, but how their shapes vary in normal tissues and how they respond to mechanical forces is not well understood. Here, we describe deep invaginations of the nuclear envelope (DINEs) as common features of epithelial cell nuclei. After their formation, DINEs exist independently of the cytoskeleton, depend on A-type lamins, and emerge in response to cell crowding, contact inhibition, and tissue maturation. High-resolution imaging shows that, in contrast to the peripheral nuclear lamina, DINEs contain densely packed chromatin with regions of active gene transcription. They also remodel dynamically during confined migration, allowing nuclei to adapt to physical constraints. Mechanistically, DINE formation is linked to suppression of MAPK signaling, while activation of growth-promoting pathways reduces their occurrence. These findings reveal DINEs as intrinsic, mechanosensitive structures that coordinate nuclear shape, chromatin organization, and gene activity, providing new insight into how epithelial cells integrate mechanical and biochemical cues to maintain tissue homeostasis. TeaserDeep nuclear envelope invaginations organize chromatin and gene activity in response to epithelial crowding.

cell biology↗

bioRxiv2026

ATP-independent unfolding of ubiquitin by Ufd1 initiates Cdc48/p97-mediated substrate processing

The Cdc48 ATPase (p97 or VCP in mammals) cooperates with its cofactors Ufd1 and Npl4 to extract polyubiquitinated proteins from membranes or multi-subunit complexes, promoting their proteasomal degradation. A ubiquitin molecule in the chain is unfolded in an ATP-independent manner and initiates substrate translocation through the central pore of the ATPase. How ubiquitin is unfolded remains unclear. Here, we demonstrate that the UT3 domain of Ufd1 interacts simultaneously with two Lys48-linked ubiquitins and unfolds one of the ubiquitins by binding its C-termianl {beta}-strand into a cleft. This unfolded ubiquitin is subsequently captured by Npl4 and Cdc48/p97. Experiments in vitro and in cells show that unfolding-defective mutants of Ufd1 indeed compromise Cdc48/p97 function. Our results explain how simple protein-protein interactions cause the unfolding of the remarkably stable ubiquitin. We also establish a linkage-specific recognition that involves ubiquitin unfolding.

biophysics↗

bioRxiv2026

MetaSAG: A Tool for Multi-level Exploration and Taxonomic Analysis of Microbial Single-Amplified Genomes

Microbial single-amplified genome (SAG) sequencing technologies have elevated microbial research resolution to the single-cell level. However, neither upstream data processing nor downstream analysis has been fully developed, greatly limiting the research in strain level. Herein, we developed MetaSAG (Multi-level Exploration and Taxonomic Analysis of microbial Single-Amplified Genomes), which enables accurate and rapid taxonomic classification of microbial SAGs. MetaSAG outperforms existing method in species classification certainty, computational efficiency, and sensitivity of low abundance species identification. In addition, MetaSAG enables species-level functional analysis, as well as strain-level evolutionary analysis. With the help of MetaSAG, we discovered the parasitic relationship between phages and bacteria, identifying multiple susceptible bacteria and a broad spectrum of phages. Furthermore, we developed MetaK-Lytic (k-mer-based meta-learning framework to predict phage lytic ability) to achieve accurate prediction of phage lytic activity based on 31-mer short sequences, which is well adapted to the characteristics of incomplete SAG sequences. Overall, we offer a comprehensive integrated tool that can parse microbial SAG data from raw data to the strain level to decipher the functional ecology of microbial dark matter, with broad implications for microbial ecology and phage therapy (https://github.com/liangcheng-hrbmu/MetaSAG). Significance StatementThis work provides a comprehensive framework for high-resolution SAG data analysis. The developed pipeline improves taxonomic annotation sensitivity and speed. Strain-level tracking enables dynamic evolutionary and functional insights, while single-cell bacterial-virus network reconstruction reveals precise interaction patterns. The novel annotation-free short sequence-based MetaK-Lytic facilitates functional prediction of uncharacterized phage sequences. Integrated into the MetaSAG platform, these tools deliver a streamlined, multi-level solution for interpreting SAG data, advancing studies in microbial ecology, evolution, and virology.

microbiology↗

bioRxiv2026

Myristoylation licenses disordered viral VP4 protein to anchor to and perforate the membrane through phase separation

The VP4 protein of enteroviruses, such as Coxsackievirus B3, is a small, intrinsically disordered protein essential for perforating the host cell membrane during viral entry. A key feature of VP4 is its N-terminal myristoylation, which is required for infectivity in some enteroviruses but dispensable in others, suggesting a complex and context-dependent role that is not fully understood. The precise biophysical mechanisms by which this lipid anchor enables a disordered protein to breach a membrane remain unresolved. Here, using Coxsackievirus B3 VP4 as a model system and integrating multi-scale molecular dynamics simulations with confocal microscopy, we demonstrate that myristoylation is not a simple membrane tether but a multi-functional regulator that orchestrates VP4 activity through distinct, hierarchical roles. First, it provides the necessary hydrophobic anchor to recruit the disordered VP4 to the membrane interface. Second, the myristoyl group acts as a key molecular driver that promotes the liquid-liquid phase separation of VP4, leading to the formation of dynamic condensates on the membrane surface. These condensates actively remodel the membrane, generating substantial curvature that, in turn, lowers the free energy barrier for VP4 penetration. Furthermore, we find evidence that the myristoyl group plays a third role in stabilizing the final transmembrane pore. Our findings establish a novel paradigm where a single lipid modification empowers a disordered viral protein to form a functionally potent condensate that mechanically primes and physically breaches the target membrane, a mechanism that may explain the conditional myristoylation requirement across enteroviruses.

biophysics↗

bioRxiv2026

The genome of an aneuploid cultivar facilitates elucidating the genetic bases of trait polymorphisms in Phalaenopsis orchids

As an important ornamental crop, Phalaenopsis orchids exhibit extraordinary trait diversity with unclear genetic bases. Here, we present a haplotype-resolved, chromosome-level genome for an aneuploid cultivar Santiago. We reveal pervasive variation in the number and sequence among homoeologous genes. When serving as a reference, this genome facilitates the genetic understanding of trait variation in a hybrid population that is highly representative in trait polymorphisms. Specifically, nucleotide polymorphisms in a potential long-distance enhancer and the consequential expression variation of PsAGL6-2, presence/absence of PsMYB12 and b-type homoeologous gene of PsMYB2 determine lip morphology variation, presence/absence of venation-associated stripes and background pink color, respectively. Diverse functions of PsMYBx1 in repressing anthocyanin accumulation across different cultivars further enhances the color patterning diversity in Phalaenopsis. Our study provides a practical framework for using a highly heterogeneous, haplotype-resolved genome to decode phenotypic diversity and has the potential to promote marker-assisted breeding in Phalaenopsis.

genomics↗