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Guo, W.

Publications and source records attributed to Guo, W..

At least 19 recordsLinked to original sources
bioRxiv2026

Endosperm secretion remodels the maternal seed coat

In flowering plants and mammals, maternal tissues must accommodate the growth of the offspring they enclose. The maternal seed coat expands around the developing embryo and endosperm. Endosperm pressure and hormonal signals coordinate seed-coat development1,2, but whether the endosperm directly promotes maternal cell elongation remains unclear. Here we show that the coenocytic Arabidopsis endosperm directly supplies cell-wall-loosening proteins to maternal seed-coat walls. The seed-size-regulating HAIKU-WRKY10 pathway activates an endosperm secretory programme enriched in cell-wall-associated proteins. These proteins spread through a shared extracellular domain across multiple inner seed-coat layers, revealing an extensive functional maternal-filial interface through which the endosperm reaches maternal cells it does not directly contact. Among these proteins, three expansins are necessary and sufficient for maternal cell elongation and seed growth. The endosperm therefore promotes its own growth by enabling expansion of the maternal tissues that enclose it. Paternal DNA methylation and maternal Polycomb activity jointly regulate this programme, with Polycomb also required for timely shutdown of expansin expression. These findings link parental epigenetic states to maternal tissue expansion through proteins supplied by the offspring. This cross-generational control of growth parallels epigenetically regulated signaling from mammalian extraembryonic tissues3, suggesting a shared strategy for adapting the maternal environment to offspring development.

plant biology↗
bioRxiv2026

A molecularly defined recurrent CA3 circuit regulates network dynamics and spatial working memory

The hippocampal CA3 region supports coordinated network activity and memory processes, but how molecularly distinct CA3 neuronal populations contribute to recurrent circuit function remains poorly understood. Here we identify St18 as a molecular marker of a distinct population of deep-layer, burst-firing CA3 pyramidal neurons and generate an St18-Cre mouse line for their selective genetic targeting. In contrast to canonical CA3 pyramidal neurons, St18 neurons preferentially innervate CA3 bilaterally, with only sparse projections to CA1. Moreover, St18 neurons are highly active during endogenous CA3 sharp-wave ripples, and their optogenetic activation evokes local ripple-like activity in CA3 but not in CA1. Furthermore, chemogenetic suppression markedly reduces CA3 ripple occurrence without significantly affecting CA1 ripple occurrence and selectively impairs spatial working memory performance. Together, these findings reveal the functional significance of a molecularly defined CA3 recurrent circuit, linking neuronal heterogeneity to hippocampal network dynamics and spatial working memory.

neuroscience↗
bioRxiv2026

Asymmetric flagellar filaments shape Borreliella burgdorferi morphology and motility

The Lyme disease spirochete Borreliella burgdorferi possesses bipolar periplasmic flagella that are essential for its distinctive flat-wave morphology, motility, and infectivity. However, how the molecular architecture of these flagella contributes to spirochetal morphology and motility remains poorly understood. Here, using in situ single-particle cryo-electron microscopy, we determine near-atomic structures of native periplasmic flagellar filaments and reveal two distinct architectures: half-sheathed and unsheathed. We show that the spirochete-specific protein FlaA forms an asymmetric sheath along the convex surface of the conserved FlaB filament core, with sheath assembly restricted to the proximal filament region near the flagellar motor. Atomic models reveal that FlaA anchors to the FlaB core through specific interactions with two surface-exposed loops, while genetic and motility analyses demonstrate distinct roles for these loops in maintaining cell morphology and motility. Structural comparisons reveal that the FlaB core possesses intrinsic curvature and supercoiling, which are substantially amplified by asymmetric FlaA assembly. These findings support a model in which localized FlaA sheath assembly reinforces the proximal filament and potentially modulates its mechanical properties. Together, our results uncover a previously unrecognized mechanism by which asymmetric sheath assembly enhances flagellar supercoiling, providing a molecular basis for understanding the distinctive morphology and motility of spirochetes.

microbiology↗
bioRxiv2026

A molecular clutch governs stator engagement and flagellar torque

Motile bacteria must continuously adjust their motility to navigate and colonize diverse environments, including mammalian hosts, yet the underlying mechanisms remain poorly understood. Here, using in situ single-particle cryo-electron microscopy, we determine near-atomic structures of the flagellar motor in the Lyme disease spirochete Borrelia burgdorferi and uncover a novel mechanism for controlling torque generation. We identify a distinct neutral state in which individual torque-generating MotA5B2 stator complexes remain incorporated in the motor but adopt an extended, tilted conformation disengaged from the rotor. Two conserved flagellar proteins, FliL and FlcA, form a transmembrane scaffold that retains 16 stator complexes, while FapA, a newly identified multidomain flagellar protein, binds the cytoplasmic base of the stator complex and stabilizes its rotor-disengaged conformation. Strikingly, rotor-engaged and rotor-disengaged stators coexist within individual motors, demonstrating that stator retention and torque engagement are separable states. Our findings establish a motor-retained neutral stator state and reveal a molecular-clutch mechanism that independently controls the engagement of individual stator units with the rotor, enabling rapid and precise regulation of flagellar torque and motility.

microbiology↗
bioRxiv2026

In situ cryo-EM reveals how a flagellar motor transmits high torque

Bacterial flagellar motors are diverse rotary machines that require robust mechanical coupling to transmit torque across components with distinct architectures, yet how such coupling is achieved remains poorly understood. Here, we determine near-atomic in situ structures of the periplasmic flagellar motor in the Lyme disease spirochete Borrelia burgdorferi, revealing how an expanded rotor is mechanically coupled to the conserved rod through symmetry breaking and local remodeling of the rotor rod interface. Surprisingly, pentameric FrbA forms a split washer-shaped brace around the rotor rod junction, providing a second layer of mechanical reinforcement. Deletion of frbA destabilizes distal flagellar structures and impairs motility, particularly under increased viscous load. FrbA homologues are broadly distributed across spirochetes, suggesting a conserved mechanism for reinforcing high-torque flagellar motors. Together, these findings reveal how symmetry breaking couples an expanded rotor to a conserved driveshaft, while a molecular split washer reinforces this interface to enable robust torque transmission and motility.

microbiology↗
bioRxiv2026

Carcinogen-induced preinvasive human squamous lung cancer is characterised by a novel atypical basal cell state and presents opportunities for chemoprevention

There are no adequate carcinogen-induced models of the earliest stages of human squamous lung cancer (LUSC), limiting the development of effective chemoprevention strategies. We developed a novel human model of early LUSC by exposing differentiated primary human airway cells to a chemical carcinogen known to cause murine LUSC. Carcinogen exposure induced a phenotype recapitulating the earliest stages of human LUSC and associated with the emergence of a novel population of atypical basal cells (ABCs). ABCs express key cancer hallmark markers but without evidence of either common LUSC-associated mutations or an emergent major clonal/subclonal population. We established the clinical relevance of this model by demonstrating enrichment of the ABC expression profile in independent clinical precancer specimens. We then show that capivasertib, a clinically approved kinase inhibitor, prevented the emergence of the abnormal phenotype and the accumulation of cells with an active DNA damage response. Further, capivasertib reversed the established phenotype; and remained effective when nebulised in vitro, mimicking therapeutic inhalation. Together, these findings establish a tractable human model of carcinogen-induced early LUSC and provide a proof-of-principle for repurposing targeted therapies for the prevention of lung cancer.

cancer biology↗
bioRxiv2026

PromptBio: An Agentic Platform for End-to-End Computational Biomedical Research

Modern biomedical research increasingly depends on complex computational analyses, yet translating a scientific question into a reliable workflow still requires substantial technical expertise and manual coordination. PromptBio is a multi-agent AI platform available through a web portal at https://promptbio.ai that addresses this challenge. Through natural-language interaction, its agent harness, PromptGenie, translates a research objective into an inspectable plan, executes the required research and analysis, and adapts subsequent steps as evidence and results emerge. PromptBio integrates reasoning with managed execution while preserving human oversight and a traceable record of the research process. It can apply validated methods, construct custom analyses, and incorporate external workflows, enabling researchers to move beyond fixed pipelines while supporting reproducibility. We evaluate the platform through benchmarks of end-to-end bioinformatics analysis and biomedical deep research, validation of representative omics and machine-learning skills, and a hypothesis-driven regulatory-genomics case study. PromptGenie achieved higher analytical accuracy and stronger evidence retrieval and synthesis than the comparison agents, while the evaluated domain skills produced results consistent with established methods. The case study further demonstrates how PromptBio can integrate human-specific genomic and epigenomic features to investigate cortical development. Together, these findings show that PromptBio can coordinate complex biomedical analyses under researcher oversight, offering an accessible approach for accelerating scientific iteration and transforming research questions into transparent, reusable computational workflows.

bioinformatics↗
bioRxiv2026

Multiplexed Quantification of Variant Abundance in the Globin Gene Family: Integrating Saturation Mutagenesis with Cross-Paralog Prediction

Widespread genetic testing has expanded variant identification, yet functional characterization remains a bottleneck in genome guided medicine. Here, we present a modified Variant Abundance by Massively Parallel Sequencing (VAMP-seq) platform integrating experimental and computational approaches for high-resolution abundance profiling of protein variants. Utilizing a lentiviral integration system, we systematically assessed the stability effects of 2,696 amino acid substitutions in {zeta}-globin (HBZ) via saturation mutagenesis in human cells, achieving complete variant coverage with high reproducibility. Representative variants showed strong concordance with orthogonal low-throughput validation assays. We further developed a deep learning framework leveraging VAMP-seq derived HBZ data to predict variant abundance across thalassemia-associated globin paralogs (HBA, HBB, and HBG1) not experimentally tractable. Our hybrid framework demonstrates how targeted experimental profiling combined with AI-driven extrapolation can accelerate variant interpretation across protein family members.

genetics↗
bioRxiv2026

The HES1-SOD1 Antagonism Shapes Senescence Heterogeneity and Impacts Metastatic Relapse of Circulating Tumor Cells

Circulating tumor cells (CTCs) encounter multiple challenges within the blood microenvironment, including oxidative stress, flow shear forces, and immune surveillance, often leading to anoikis. Recently, a transitional state of CTC senescence has been identified, contributing to metastatic inefficiency. However, the molecular mechanisms linking senescent CTCs to disease relapse remain to be defined. By integrating a genetic model of cortactin knockdown-induced CTC senescence with single-cell multi-omic analyses, we revealed two distinct senescent CTC subpopulations marked by HES1 expression levels. These HES1low and HES1high subpopulations exhibited differential evolutionary trajectory dynamics and unique molecular and metabolic signatures, which were significantly correlated with adverse clinical outcome across several patient cohorts. HES1low senescent CTCs displayed enhanced mitochondrial fitness, oxidative phosphorylation, and ROS-detoxifying capabilities, resulting in more efficient tumor regrowth with a pro-inflammatory and thrombotic phenotype when compared to the HES1high group. Mechanistically, HES1 directly bound to the Sod1 promoter and repressed its expression, leading to redox imbalance and mitochondrial dysfunction that were linked to weakened tumor regrowth capacity. Both senescent CTC subpopulations were broadly resistant to cytotoxic and targeted therapies, yet they showed elevated dependency on anti-apoptosis programs that make them susceptible to dual blockade by SOD1 inhibitor and the anti-senolytic drug ABT737 in vivo. Finally, in a prospective cohort of on-treatment melanoma patients, HES1 senescent CTCs were highly enriched in patients with progressive disease. Thus, the HES1-SOD1 antagonism shapes CTC senescence heterogeneity and contributes to differential tumor relapse, which can be therapeutically explored for eliminating residual metastatic disease.

cancer biology↗
bioRxiv2026

Distinct extracellular matrix states uncouple collagen accumulation from pathological fibrosis in Duchenne muscular dystrophy

Fibrosis severity is routinely inferred from collagen abundance, although whether collagen quantity determines pathological fibrosis remains unclear. In Duchenne muscular dystrophy (DMD), chronic muscle injury and inflammation drive extracellular matrix accumulation, making these processes difficult to disentangle. We exploit sarcospan overexpression in mdx mice, a model of DMD (mdxTG), which improves membrane integrity and muscle function despite persistent matrix remodeling. mdxTG muscle accumulates more collagen than mdx yet lacks its dense macrophage-rich scars. Matrisome proteomics and spatial transcriptomics reveal compositionally and spatially distinct matrix states, while decellularized mdxTG matrix protects myotubes from membrane damage relative to mdx matrix. Despite these differences, both dystrophic matrices remain stiff and induce nuclear YAP in fibro-adipogenic progenitors. Verteporfin suppresses collagen production and reduces fibrosis in vivo, while nuclear YAP is increased in FAPs from patients with DMD. Thus, collagen abundance alone does not define pathological fibrosis; matrix organization, biological activity, and mechanosignaling distinguish functionally distinct fibrotic states.

physiology↗
bioRxiv2026

Evolutionary history and microbial cross-feeding shape lifestyle-stratified dominance of Bifidobacterium longum subspecies in infants

Bifidobacterium longum (Bl.) is a key early-life gut symbiont, yet its evolutionary origin and mechanisms underlying the global biogeographic distribution of its subspecies remain poorly resolved. Here, we compiled a global genomic atlas of >7,000 MAGs/genomes from infants, domesticated animals, non-human primates, and ancient humans. High-resolution phylogenomic and functional analyses expanded infant-associated subspecies to five. Compared with non-human primates, B. longum was more prevalent in domesticated animals and ancient humans dating from 150 to 1,500 years ago. Moreover, human- and livestock-derived lineages from the same geographic regions clustered together, suggesting potential host-associated transmission. Ecologically, Bl. infantis and Bl. longum predominated in non-Western and Western infants, respectively, independent of breastfeeding, delivery mode, or antibiotic exposure. Instead, their distribution was associated with co-occurring microbes and HMO-driven cross-feeding interactions. These findings explain subspecies differentiation in the gut microbiota of Western and non-Western infants and provide a framework for community-mediated interventions in early life.

microbiology↗
bioRxiv2026

A generalizable codesigned platform for solid-state nanopore sensing beyond the capacitive-noise constraints

Solid-state nanopores offer label-free, real-time single-molecule sensing, yet resolving rapidly translocating biomolecules requires high-bandwidth data acquisition, where increased high-frequency noise fundamentally limits reliable recovery of informative events. Here we establish a hardware-software co-designed nanopore sensing platform that overcomes this bandwidth-noise limitation by integrating scalable low-noise device engineering with deep learning-based signal reconstruction. A wafer-scale dielectric-engineering strategy using low-dielectric SU8 photoresist reduces total device capacitance to the picofarad regime and suppresses high-frequency noise by up to fivefold while maintaining facile, controllable and reproducible fabrication. This extends usable acquisition rate to 40 MHz and enables capture of fast molecular features. Combined with a reconstruction neural network trained on synthetic translocation signals embedded in experimentally measured noise, the platform recovers transient blockade sublevels while preserving temporal fidelity. Using engineered DNA molecules carrying dumbbell-like barcodes, we resolve nanometer-scale structural features on sub-microsecond timescales, and experimentally measure translocation velocity within the sub-5 nm regime. Dual-channel measurement on a single nanopore device further demonstrates transferability of the platform by showing robust cross-channel signal reconstruction across distinct baseline noise levels. This platform provides a general route for reliable recovery of previously inaccessible molecular information from high-bandwidth nanopore measurements.

biophysics↗
bioRxiv2026

Asymmetric introgression and thermal advantage jointly drive climate-mediated lineage turnover in a mixed-ploidy reed

Species distribution forecasts commonly overlook intraspecific genetic variation, missing a potentially important mechanism of ecosystem change: climate-driven range shifts among lineages within a species native range. Here we integrate population genomic analysis of 495 individuals, multi-site common garden experiments, and species distribution modeling based on 837 occurrence records for three major genetic lineages of the foundation grass Phragmites australis in China. The octoploid FEAU lineage (haplotype P) exhibits superior heat tolerance (critical temperature Tcrit and T50) and produces significantly greater total biomass in three of four common gardens compared to the cold-adapted CN lineage (tetraploid, haplotypes O/M), which occupies a climatic niche with lower annual mean temperature (Bio1) and mean temperature of the wettest quarter (Bio8). Genomic analyses further reveal bidirectional but asymmetric introgression, with admixed individuals showing a systematic bias toward FEAU ancestry. Under the high-emission scenario (SSP5-8.5) by 2070, projected highly suitable habitat for the FEAU lineage expands by 18.6%, while the CN lineage shows a smaller relative increase. By contrast, the subtropical SW lineage (haplotypes U/I) exhibits limited and stable suitable habitat. These results demonstrate that climate change interacts with intraspecific variation among polyploidy-associated lineages, manifested through differences in thermal tolerance, biomass production, and asymmetric gene flow, to drive potential lineage replacement within a native range, a process already suggested by field observations of FEAU expansion in a plateau lake. Our findings argue for integrating evolutionary history and genetic identity into ecological forecasting to better anticipate ecosystem responses under ongoing climate warming.

ecology↗
bioRxiv2026

MLL3 adaptor function, not methyltransferase catalytic activity, is essential for breast tumor suppression

MLL3 (Mixed-Lineage Leukemia 3), also known as KMT2C, is one of the most frequently altered epigenetic regulators in breast cancer. MLL3 loss-of-function leads to accelerated tumor onset and growth and increased metastasis. As a large multi-domain protein, MLL3 functions as a histone methyltransferase and a nuclear protein adaptor interacting with other epigenetic proteins. Since breast cancer MLL3 mutations are often truncating mutations that lead to protein degradation, whether the MLL3 tumor suppressor activity depends on its catalytic activity or non-catalytic chromatin adaptor function remains unclear. Here, using CRISPR genetically engineered mouse mammary stem cell organoid-based breast tumor models, we dissected dosage-dependent and domain-specific functions of MLL3 in breast tumor suppression. MLL3 heterozygous loss breast tumor models revealed that MLL3 is haplo-insufficient for breast tumor suppression. Interestingly, homozygous catalytic-dead MLL3-Y4792A mutation did not accelerate tumor onset, growth, or metastasis. By contrast, G367V mutation in the PHD2 domain, which disrupts the BAP1 complex binding without affecting MLL3 protein stability, accelerated tumor onset and growth, phenocopying MLL3 loss. Mechanistically, MLL3 loss impaired chromatin localization of UTX, and genetic depletion of UTX accelerated breast tumor progression in MLL3-wildtype but not MLL3-deficient cells. Integrated RNA-seq, CUT&TAG, and ATAC-seq analyses further showed that transcriptional changes induced by MLL3 loss were more closely associated with promoter-proximal alterations in H3K27Ac, H3K27me3, and chromatin accessibility than with putative MLL3-dependent enhancer regions. Together, these findings reveal that MLL3 suppresses breast tumor initiation through a dosage-sensitive, catalytic-independent adaptor function that regulates promoter-proximal epigenetic states.

cancer biology↗
bioRxiv2026

Mono-ADP-ribosylation-driven immunosuppression and cross-resistance to therapy through cancer cell intrinsic and extrinsic mechanisms

Mono-ADP-ribosylation (MARylation) is emerging as an important regulator of anti-cancer immunity and immunosuppressive tumor microenvironment (TME). Our previous studies showed that PARP11, one of several enzymes that facilitate MARylation, regulates the activities of intratumoral cytotoxic T lymphocytes (CTLs) and regulatory T cells (Tregs). Here, we demonstrate that stimuli such as adenosine, epinephrine, or glucagon-like peptide-1 (GLP1) induced PARP11 in cancer cells. Upregulation of PARP11 in cancer cells led to PARP11-mediated MARylation, ubiquitination, and accelerated degradation of MHC-I through the autophagy-lysosomal pathway. Induction of PARP11 protected cancer cells from killing by specific CTLs and stimulated tumor growth and progression. Genetic ablation of PARP11 attenuated MHC-I MARylation, ubiquitination, and interaction with autophagy receptors. Pharmacologic inhibition of PARP11 in pancreatic ductal adenocarcinoma (PDAC) cells restored their MHC-I levels, sensitized them to killing by CTLs, inhibited tumor growth, and impeded their initial resistance to chemotherapy and their acquired resistance to targeted therapy with RAS inhibitors. Moreover, inhibition of PARP11 prevented hyperprogressive disease in a mouse melanoma model treated with immune checkpoint inhibitors (ICBs), suggesting that PARP11 is a major therapeutically actionable driver of immunosuppression in tumors. SYNOPSISInduction of PARP11 in the tumor microenvironment mediates immunosuppression. This study reports that PARP11-driven MARylation and ubiquitination of MHC-I in cancer cells drives immune evasion, tumor growth and resistance to therapies.

cancer biology↗
bioRxiv2026

FlcE latches onto the FliL-stator complex to turbocharge flagellar motility in Borrelia burgdorferi

Periplasmic flagella are essential for the distinctive morphology and motility of the Lyme disease spirochete Borrelia burgdorferi, and motility plays a critical role in its pathogenic lifestyle. These flagella are powered by specialized motors that contain a large spirochete-specific multiprotein collar complex, yet the molecular architecture and mechanisms underlying high-torque motility remain poorly understood. Here, we identify the tetratricopeptide repeat (TPR)-containing protein BB0298 as a previously unrecognized flagellar collar component and rename it FlcE. Loss of flcE results in altered morphology and nearly abolishes the spirochetes motility. Using cryo-electron tomography and biochemical analyses, we show that FlcE occupies a unique position within the collar where it surrounds the FliL-stator complex by binding to FliL and the collar protein FlcA. These findings support a model in which FlcE functions as a molecular "latch" that secures stator assemblies to sustain efficient torque generation. Notably, flcE is conserved across most motile members of the Spirochaetales and is located within the division and cell-wall (dcw) gene cluster. More broadly, the conservation of TPR-containing structural proteins across diverse bacterial flagellar systems suggests a general architectural principle whereby dedicated scaffolds reinforce stator complexes to maximize motor performance under high mechanical loads. ImportanceSpirochetal motility requires the stable engagement of torque-generating stator units, yet the mechanisms that secure these complexes have remained unknown. Here, we identify FlcE as a previously unrecognized collar protein that functions as a molecular latch by restraining the FliL-stator complex. Loss of FlcE destabilizes FliL-stator assemblies and severely impairs motility, demonstrating that peripheral scaffolding is essential for sustaining high torque output in the Lyme disease spirochete Borrelia burgdorferi. The conservation of tetratricopeptide repeat domains in FlcE and other bacterial flagellar proteins further suggests a broader mechanism in which specialized scaffolds anchor and stabilize stator complexes, enabling high torque generation. Because motility is a central virulence determinant in many pathogenic bacteria--including B. burgdorferi during transmission from the tick to the mammalian host and subsequent infection--defining the mechanistic role of FlcE provides important insight into the molecular basis of motility-driven pathogenesis and suggests new strategies for disrupting bacterial infection.

microbiology↗
bioRxiv2026

Chromosome-scale genome assembly of diploid halophyte Thinopyrum bessarabicum excludes J genome from polyploid Thinopyrum ancestry

Wild relatives of wheat harbour genetic diversity essential for improving resilience to climate-driven stresses, yet their deployment is hampered by unresolved evolutionary relationships and the absence of reference genomes. Here we present a chromosome-scale reference genome for Thinopyrum bessarabicum, a diploid halophyte and high-priority donor for wheat salt tolerance breeding. A key unresolved question is whether the diploid J genome contributed directly to the subgenome composition of extant polyploid Thinopyrum species, and which genomic features underpin its exceptional salt tolerance. Using this resource, we show that the diploid J genome of Th. bessarabicum is not represented among the subgenomes of polyploid Thinopyrum species, resolving a long-standing ambiguity in Triticeae genomics. Gene-level resolution of the reciprocal 4/5 chromosomal translocation across six related Triticeae species identifies conserved breakpoint gene pairs, supporting a single ancestral rearrangement. Genome-wide gene content analysis shows that halophytic capacity is underpinned by quantitative expansion of conserved stress-response gene families. Salt tolerance phenotyping validates chromosome 5J as a tolerance locus in both Th. bessarabicum and wheat introgression lines. A physically anchored marker framework and dual-reference skim-sequencing pipeline enable precise megabase-resolution characterisation of Th. bessarabicum introgressions in wheat, providing a genomic foundation for deploying J-genome diversity in crop improvement.

plant biology↗