Biology subjects

Bo, Y.

Publications and source records attributed to Bo, Y..

15 recordsLinked to original sources

bioRxiv2026

Live imaging reveals oocyte membrane pre-remodeling forming permissive space for asymmetric division

Abstract Successful oocyte maturation requires first polar body (PB1) extrusion, yet how the oocyte prepares for this asymmetric event remains unclear. Live membrane imaging of mouse oocytes reveals pronounced regional heterogeneity in plasma-membrane dynamics, generating an early polarized pattern across the surface. Whereas most of the oocyte surface and its microvilli remain relatively stable, a discrete membrane domain collapses and retracts around germinal vesicle breakdown (GVBD), separating from the zona pellucida to establish a pre-extrusion space (PES). Transient oocyte comb-like protrusions arise within the PES and subsequently collapse, converting the protrusion-filled region into an open cavity before PB1 extrusion. Mechanistically, early ERK28 dependent dissociation of the cortical scaffold ZO-1 is required for this space to form. ERK2 phosphorylates ZO-1, suppresses its phase separation, and promotes its removal from the cortex. Blocking MEK-ERK signaling prevents ZO-1 dissociation, abolishes pre-extrusion space formation, and impairs PB1 extrusion, whereas ERK activation restores these events in aged oocytes. Together, our findings identify a membrane collapse-based pre-remodeling mechanism that licenses PB1 extrusion and reveal ERK-ZO-1 signaling as a key regulator of oocyte maturation.

cell biology↗

bioRxiv2026

Inhibition of oogenic JNK preserves fertility and ovarian hormones during DNA-damaging cancer therapy

Primary ovarian insufficiency (POI) and related infertility, early menopause, and endocrine disorders due to hormonal deficiency are major side effects in young female cancer patients undergoing cancer therapy. Current strategies preserving the fertility and hormonal functions of the ovary remain imperfect due to concerns of feasibility, efficacy, or safety. Herein, we identified c-Jun N-terminal kinase (JNK) as a pivotal regulator of the DNA damage response (DDR) signaling in oocytes of primordial follicles in response to DNA-damaging cancer therapy. Using pharmacological JNK inhibition and a genetically modified mouse model with oocyte-specific JNK deletion, together with histological, bioinformatic, and molecular approaches, we demonstrated that JNK inhibition prevented chemotherapy-induced oocyte apoptosis and POI, and preserved long-term reproductive cycles and fertility. Mechanistically, JNK was activated in response to chemotherapy-induced DNA damage in oocytes of primordial follicles, causing activation of transcription factor TAp63 and subsequent oocyte apoptosis, ultimately resulting in diminished ovarian reserve and POI. A more clinically relevant breast cancer-bearing mouse model revealed that JNK inhibition preserved the ovarian reserve without compromising anti-cancer efficacy of chemotherapy. Together, our study identifies oocyte-intrinsic JNK as a promising target for developing ovarian protectants and safeguarding reproductive health and fertility in young female cancer survivors.

pharmacology and toxicology↗

bioRxiv2025

Pan-cancer tumor classification by a holistic tumor microenvironment atlas

The tumor microenvironment (TME) heterogeneity presents a major bottleneck to effective cancer immunotherapies. We address this by establishing a pan-cancer tumor classification system based on the holistic TME cellular components. First, using single-cell transcriptomes from 1,271 patients across 26 cancer types, we compile a TME cellular atlas, leading to the identification of recurrent cell states and multicellular modules across cancer types. Among these, we highlight a type I interferon (IFN-I)-related multicellular module, including IFIT1+ tumor-associated macrophages, as a critical contributor to immune-activation TMEs. From a holistic perspective, pan-cancer TMEs exhibit trichotomous patterns predominantly driven by T, myeloid, and stromal compartments. Leveraging fine-grained TME cellular composition, we further stratify all tumors into 10 stable groups. These groups display varying responses to immune checkpoint blockade (ICB), and each rationally selected therapeutic strategy specifically perturbs the corresponding expression signature. Our pan-cancer tumor classification scheme reveals the underlying patterns of TME heterogeneity and provides a framework for stratifying patients, guiding treatment selection, and developing novel therapeutic options.

cancer biology↗

bioRxiv2025

Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell

Macromolecular complexes in the genetically minimized bacterium, JCVI-syn3A, support gene expression (RNA polymerase, ribosome, degradosome), metabolism (ABC transporters, ATP synthase) and chromosome dynamics. In this work, we further incorporate the assembly of 21 unique macromolecular complexes into the existing whole-cell kinetic model of Syn3A. The synthesis and translocation of protein subunits in membrane complexes occur through distinct pathways. A range of 2D association rates for membrane complexes were considered to guarantee a high yield of assembly given the existing time scales of gene expression. By alleviating the undesired kinetically trapped intermediates in ATP synthase assembly, the efficiency was improved. The assembly of RNA polymerase, ribosome, and degradosome influence the speed and efficiency of protein synthesis. Collectively, this model predicted time-dependent cellular behaviors consistent with experiments. A machine learning analysis of the time-dependent metabolomics and metabolic fluxes highlighted the effect of introducing complex assembly into our whole-cell model.

biophysics↗

bioRxiv2025

Intense oocyte competition builds the female reproductive reserve in mice

During the process of ovariogenesis, more than two-thirds of germ cells are sacrificed to enhance the quality of the remaining oocytes. But the detail process of selection is not completely understood in mammals. Here, by creating a high resolution 4- dimensional ovariogenesis imaging system, we recorded the progress of oocyte fate determination in live mouse ovaries, and discovered an oocyte competition mechanism that determines the survival of oocytes. We found that dominant oocytes catch and absorb the cell debris from sacrificed oocytes to enrich their cytoplasm for survival. Single-cell sequencing demonstrated that this competition follows a classic autophagy- driven model. Blocking competition by suppressing autophagy resulted in an enlarged pool of survived oocytes. However, these oocytes lacking competition were unable to fully develop and contribute to fertility. Our study suggests that mammals have evolved a unique intensive competition system to enhance oocyte quality, necessary to support their long reproductive lifespan.

developmental biology↗

bioRxiv2024

Nanoparticles co-delivering siRNA and mRNA for simultaneous restoration and silencing of gene/protein expression in vitro and invivo

RNA-based agents such as siRNA, miRNA, and mRNA can selectively manipulate gene expression/proteins and have the potential to revolutionize the current therapeutic strategies for various diseases, including cancer. To address the poor stability and inherent limitations of RNA agents, nanoparticle (NP) platforms have been developed to deliver functional mRNA or siRNA inside the cells. Recent studies have focused on either siRNA to knock down proteins causing drug resistance or mRNA technology to introduce tumor suppressors. However, complex diseases like cancer need multi-targeted approaches to selectively target multiple gene expressions/proteins. In this proof-of-concept study, we developed co-delivery nanoparticles containing Luc-mRNA and siRNA-GFP as model RNA agents ((M+S)-NPs) and assessed their effects in vitro and in vivo. Our studies show that NPs can effectively deliver both functional mRNA and siRNA together, simultaneously impacting the expression of two genes/proteins in vitro. Additionally, after in vivo administration, co-delivery NPs successfully knocked down GFP while introducing luciferase in a TNBC mouse model, indicating our NPs have the potential to develop RNA-based anticancer therapeutics. These studies pave the way to develop RNA-based, multitargeted, multi-delivery approaches for complex diseases like cancer. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/600196v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1668ae2org.highwire.dtl.DTLVardef@1283491org.highwire.dtl.DTLVardef@9336daorg.highwire.dtl.DTLVardef@f654c5_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Functional marker CAPS-799 of the TaPHT1;9-4B gene is useful for screening phosphorus-efficient wheat cultivars

ContextIn our previous study, TaPHT1;9-4B, one key high-affinity Pi transporter, was found to greatly contribute to Pi acquisition and transportation, and its functional marker CAPS-799 was subsequently developed to identify its Pi-efficient elite haplotype. ObjectiveThe study aimed to screen a varieties of wheat cultivars by using the above CAPS-799, identify its Pi-efficient elite haplotype cultivars, and reveal its physiological mechanism. MethodsSuccessive two-year field experiments without Pi fertilizer supply, and hydroponic experiment with low Pi (10 M) were performed. P concentrations, biomasses, grain yields, yield components, root growth parameters, and TaPHT1;9-4B transcript levels were measured. Total P accumulation and transport efficiency, and the relative growth rates were calculated. ResultsEight Pi-efficient wheat cultivars (Hap3 haplotype) were screened out by using the CAPS-799 from 80 modern major cultivars, and in successive two-year field experiments, their grain yields, spike numbers, P absorption and transport efficiencies were significantly higher than those of Non-Hap3 haplotypes (Hap1, 2 and 4) under no Pi fertilizer supply condition, and therefore, these eight cultivars belonged to Pi-efficient elite haplotype. TaPHT1;9-4B transcript levels in roots at the early stage of grain filling period in field experiment, and the relative growth rates of total root surface areas, volumes and mean root diameters of Hap3 cultivars in hydroponic experiment, were markedly higher than other haplotypes. ConclusionsCAPS-799 was a useful functional marker for screening Pi-efficient wheat cultivars, and its Pi-efficient wheat cultivars were characterized with higher TaPHT1;9-4B transcript levels and more roots. ImplicationsCAPS-799 will be used to screen or develop Pi-efficient wheat cultivars.

plant biology↗

bioRxiv2024

Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission

The continued evolution of SARS-CoV-2 requires persistent monitoring of its subvariants. Omicron subvariants are responsible for the vast majority of SARS-CoV-2 infections worldwide, with XBB and BA.2.86 sublineages representing more than 90% of circulating strains as of January 2024. In this study, we characterized the functional properties of Spike glycoproteins from BA.2.75, CH.1.1, DV.7.1, BA.4/5, BQ.1.1, XBB, XBB.1, XBB.1.16, XBB.1.5, FD.1.1, EG.5.1, HK.3 BA.2.86 and JN.1. We tested their capacity to evade plasma-mediated recognition and neutralization, ACE2 binding, their susceptibility to cold inactivation, Spike processing, as well as the impact of temperature on Spike-ACE2 interaction. We found that compared to the early wild-type (D614G) strain, most Omicron subvariants Spike glycoproteins evolved to escape recognition and neutralization by plasma from individuals who received a fifth dose of bivalent (BA.1 or BA.4/5) mRNA vaccine and improve ACE2 binding, particularly at low temperatures. Moreover, BA.2.86 had the best affinity for ACE2 at all temperatures tested. We found that Omicron subvariants Spike processing is associated with their susceptibility to cold inactivation. Intriguingly, we found that Spike-ACE2 binding at low temperature was significantly associated with growth rates of Omicron subvariants in humans. Overall, we report that Spikes from newly emerged Omicron subvariants are relatively more stable and resistant to plasma-mediated neutralization, present improved affinity for ACE2 which is associated, particularly at low temperatures, with their growth rates.

microbiology↗

bioRxiv2022

Sphingosine kinases promote Ebola virus infection and can be targeted to inhibit filoviruses, coronaviruses, and arenaviruses using late endocytic trafficking to enter cells

Entry of enveloped viruses in host cells requires the fusion of the viral and host cell membranes, a process that is facilitated by viral fusion proteins protruding from the viral envelope. For fusion, viral fusion proteins need to be triggered by host factors and for some viruses, such as Ebola virus (EBOV) and Lassa fever virus, this event occurs inside endosomes and/or lysosomes. Consequently, these late-penetrating viruses must be internalized and delivered to entry-conducive intracellular vesicles. Because endocytosis and vesicular trafficking are tightly regulated cellular processes, late penetrating viruses also depend on specific host factors, such as signaling molecules, for efficient viral delivery to the site of fusion, suggesting that these could be targeted for antiviral therapy. In this study, we investigated a role for sphingosine kinases (SKs) in viral entry and found that chemical inhibition of sphingosine kinase 1 (SK1) and/or SK2 and knockdown of SK1 or SK2, inhibited entry of EBOV into host cells. Mechanistically, inhibition of SK1 and/or SK2 prevented EBOV from reaching late-endosomes and lysosomes that are positive for the EBOV receptor, Niemann Pick C1 (NPC1). Furthermore, we present evidence that suggests the trafficking defect caused by SK1/2 inhibition occurs independently of S1P signaling through cell-surface S1PRs. Lastly, we found that chemical inhibition of SKs prevents entry of other late-penetrating viruses, including arenaviruses and coronaviruses, in addition to inhibiting infection by replication competent EBOV and SARS-CoV-2 in Huh7.5 cells. In sum, our results highlight an important role played by SKs in endocytic trafficking which can be targeted to inhibit entry of late-penetrating viruses. SK inhibitors could serve as a starting point for the development of broad-spectrum antiviral therapeutics.

microbiology↗

bioRxiv2022

Molecular basis for antiviral activity of pediatric neutralizing antibodies targeting SARS-CoV-2 Spike receptor binding domain

Neutralizing antibodies (NAbs) hold great promise for clinical interventions against SARS-CoV- 2 variants of concern (VOCs). Understanding NAb epitope-dependent antiviral mechanisms is crucial for developing vaccines and therapeutics against VOCs. Here we characterized two potent NAbs, EH3 and EH8, isolated from an unvaccinated pediatric patient with exceptional plasma neutralization activity. EH3 and EH8 cross-neutralize the early VOCs and mediate strong Fc-dependent effector activity in vitro. Structural analyses of EH3 and EH8 in complex with the receptor-binding domain (RBD) revealed the molecular determinants of the epitope-driven protection and VOC-evasion. While EH3 represents the prevalent IGHV3-53 NAb whose epitope substantially overlaps with the ACE2 binding site, EH8 recognizes a narrow epitope exposed in both RBD-up and RBD-down conformations. When tested in vivo, a single-dose prophylactic administration of EH3 fully protected stringent K18-hACE2 mice from lethal challenge with Delta VOC. Our study demonstrates that protective NAbs responses converge in pediatric and adult SARS-CoV-2 patients.

microbiology↗

bioRxiv2022

Identification of a SARS-CoV-2 host metalloproteinase-dependent entry pathway differentially used by SARS-CoV-2 and variants of concern Alpha, Delta, and Omicron

To infect cells, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) binds to angiotensin converting enzyme 2 (ACE2) via its spike glycoprotein (S), delivering its genome upon S-mediated membrane fusion. SARS-CoV-2 uses two distinct entry pathways: 1) a surface, serine protease-dependent or 2) an endosomal, cysteine protease-dependent pathway. In investigating serine protease-independent cell-cell fusion, we found that the matrix metalloproteinases (MMPs), MMP2/9, can activate SARS-CoV-2 S fusion activity, but not that of SARS-CoV-1. Importantly, metalloproteinase activation of SARS-CoV-2 S represents a third entry pathway in cells expressing high MMP levels. This route of entry required cleavage at the S1/S2 junction in viral producer cells and differential processing of variants of concern S dictated its usage. In addition, metalloproteinase inhibitors reduced replicative Alpha infection and abrogated syncytia formation. Finally, we found that the Omicron S exhibit reduced metalloproteinase-dependent fusion and viral entry. Taken together, we identified a MMP2/9-dependent mode of activation of SARS-CoV-2 S. As MMP2/9 are released during inflammation and severe COVID-19, they may play important roles in SARS-CoV-2 S-mediated cytopathic effects, tropism, and disease outcome.

microbiology↗

bioRxiv2021

SARS-CoV-2 Omicron Spike recognition by plasma from individuals receiving BNT162b2 mRNA vaccination with a 16-weeks interval between doses

Continuous emergence of SARS-CoV-2 variants of concern (VOC) is fueling the COVID-19 pandemic. Omicron (B.1.1.529), is rapidly spreading worldwide. The large number of mutations in its Spike raised concerns about a major antigenic drift that could significantly decrease vaccine efficacy and infection-induced immunity. A long interval between BNT162b2 mRNA doses was shown to elicit antibodies that efficiently recognize Spikes from different VOCs. Here we evaluated the recognition of Omicron Spike by plasma from a cohort of SARS-CoV-2 naive and previously-infected individuals that received their BNT162b2 mRNA vaccine 16-weeks apart. Omicron Spike was recognized less efficiently than D614G, Alpha, Beta, Gamma and Delta Spikes. We compared to plasma activity from participants receiving a short (4-weeks) interval regimen. Plasma from individuals of the long interval cohort recognized and neutralized better the Omicron Spike compared to those that received a short interval. Whether this difference confers any clinical benefit against Omicron remains unknown.

microbiology↗

bioRxiv2021

Contribution of single mutations to selected SARS-CoV-2 emerging variants Spike antigenicity

Towards the end of 2020, multiple variants of concern (VOCs) and variants of interest (VOIs) have arisen from the original SARS-CoV-2 Wuhan-Hu-1 strain. Mutations in the Spike protein are highly scrutinized for their impact on transmissibility, pathogenesis and vaccine efficacy. Here, we contribute to the growing body of literature on emerging variants by evaluating the impact of single mutations on the overall antigenicity of selected variants and their binding to the ACE2 receptor. We observe a differential contribution of single mutants to the global variants phenotype related to ACE2 interaction and antigenicity. Using biolayer interferometry, we observe that enhanced ACE2 interaction is mostly modulated by a decrease in off-rate. Finally, we made the interesting observation that the Spikes from tested emerging variants bind better to ACE2 at 37{degrees}C compared to the D614G variant. Whether improved ACE2 binding at higher temperature facilitates emerging variants transmission remain to be demonstrated.

microbiology↗

bioRxiv2021

Structural Basis and Mode of Action for Two Broadly Neutralizing Antibodies Against SARS-CoV-2 Emerging Variants of Concern

Emerging variants of concern for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transmit more efficiently and partially evade protective immune responses, thus necessitating continued refinement of antibody therapies and immunogen design. Here we elucidate the structural basis and mode of action for two potent SARS-CoV-2 Spike (S) neutralizing monoclonal antibodies CV3-1 and CV3-25 that remained effective against emerging variants of concern in vitro and in vivo. CV3-1 bound to the (485-GFN-487) loop within the receptor-binding domain (RBD) in the "RBD-up" position and triggered potent shedding of the S1 subunit. In contrast, CV3-25 inhibited membrane fusion by binding to an epitope in the stem helix region of the S2 subunit that is highly conserved among {beta}-coronaviruses. Thus, vaccine immunogen designs that incorporate the conserved regions in RBD and stem helix region are candidates to elicit pan-coronavirus protective immune responses.

microbiology↗

bioRxiv2017

Characterization of a Novel Model of Overuse-Induced Calcific Achilles Tendinopathy in Mice: Contralateral Tendinopathy Following Unilateral Tenotomy

ObjectiveTo develop a simple but reproducible overuse induced animal model of Achilles tendinopathy in mice for better understanding the underlying mechanism and prevention of calcific Achilles tendinopathy.\n\nMethods80 C57/B6 mice (8-9 weeks old) were employed and randomly divided into control group and experimental group. Unilateral Achilles tenotomy was performed on the right hindlimb of experiment group. After 12 weeks, the onset of Achilles tedinopathy in the contralateral Achilles tendon was determined by radiological assessment, histological analysis, electron microscopy observation and biomechanical test.\n\nResultsThe onset of calcific Achilles tendinopathy in contralateral Achilles tendon was confirmed after 12 weeks unilateral tenotomy. The contralateral Achilles tendon of experimental group was characterized as hypercelluarity, neovascularization and fused collagen fiber disarrangement, compared to the control group. Importantly, intratendon endochondral ossification and calcaneus deformity was featured in contralateral Achilles tendon. Additionally, poor biomechanical properties in the contralateral Achilles tendon revealed the incidence of Achilles tedinopathy.\n\nConclusionWe hereby introduce a novel simple but reproducible spontaneous contralateral calcific Achilles tendinopathy model in mice, which represents the overuse conditions during the tendinopathy development in human-beings. It should be a useful tool to further study the underlying pathogenesis of calcific Achilles tendinopathy.

animal behavior and cognition↗