Biology subjects

Chen, T.

Publications and source records attributed to Chen, T..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

Potent and selective repression of SCN9A by engineered zinc finger repressors for the treatment of neuropathic pain

Peripheral neuropathies are estimated to affect several million patients in the US with no long-lasting therapy currently available. In humans, the Nav1.7 sodium channel, encoded by the SCN9A gene, is involved in a spectrum of inherited neuropathies, and has emerged as a promising target for analgesic drug development. The development of a selective Nav1.7 inhibitor has been challenging, in part due to structural similarities among other Nav channels. Here we present preclinical studies for the first genomic medicine approach using engineered zinc finger repressors (ZFRs) specifically targeting human/nonhuman primate (NHP) SCN9A. AAV-mediated delivery of ZFRs in human iPSC-derived neurons resulted in 90% reduction of SCN9A with no detectable off-target activity. To establish proof-of-concept, a ZFR targeting the mouse Scn9a was assessed in the SNI neuropathic pain mouse model, which resulted in up to 70% repression of Scn9a in mouse DRGs and was associated with reduction in pain hypersensitivity as measured by increased mechanical- and cold-induced pain thresholds. AAV-mediated intrathecal delivery of ZFR in NHPs demonstrated up to 60% repression of SCN9A in bulk DRG tissue and on single-cell levels in the nociceptors. The treatment was well tolerated in NHPs, and no dose-limiting findings were observed four weeks after a single intrathecal injection. Taken together, our results demonstrate that AAV-delivered ZFR targeting the SCN9A gene is promising and supports further development as a potential therapy for peripheral neuropathies.

neuroscience↗

bioRxiv2024

The AP2/ERF transcription factor HcERF5 confers drought tolerance via ABA-mediated signaling in kenaf

The APETALA2/ethylene response factor (AP2/ERFs) are pivotal in regulating abiotic stress responses in plants. However, the specific role of ERFs in kenafs response to drought stress remains unclear. In this study, a transcription factors HcERF5 was isolated from kenaf and its role in drought stress tolerance was analyzed. HcERF5 was found to localize in both nucleus and cytoplasm and could be significantly induced by polyethylene glycol-6000 (PEG-6000) and abscisic acid (ABA) in kenaf seedlings. In transgenic Arabidopsis expressing the HcERF5 promoter-driven {beta}-glucuronidase (GUS), strong GUS activity was observed in roots, stems, and leaves. Overexpression of HcERF5 in Arabidopsis enhanced seed germination rates under drought or ABA stress and improved drought tolerance in seedlings by increasing antioxidant enzyme activities, whereas aterf5 knockout lines exhibited the opposite trend. Additionally, HcERF5 overexpressing Arabidopsis showed significantly increased drought tolerance and reduced sensitivity to ABA. Furthermore, virus-induced gene silencing (VIGS) of HcERF5 in kenaf reduced drought tolerance, as evidenced by decreased antioxidant enzyme activity, increased stomatal aperture, and elevated levels of malondialdehyde (MDA), reactive oxygen species (ROS), and proline under drought stress. RNA-seq analysis further revealed that HcERF5 directly regulated ABA signaling pathway. Yeast-two-hybrid (Y2H) assays revealed 29 proteins that interact with HcERF5. Among them, the expression of downstream drought stress-related genes HcPRK, HcRD22, HcMAP2, HcCAB, HcCS, and HcCCoAOMT3 were significantly reduced in HcERF5-silenced plants. Overall, this study highlights the significant potential of HcERF5 in enhancing drought tolerance in kenaf. HighlightO_LIHcERF5 overexpression enhanced drought tolerance in kenaf, however silencing increased drought sensitivity. C_LIO_LIHcERF5 regulates ABA synthesis and increases kenaf stomatal conductance and density under drought stress. C_LIO_LIHcERF5 regulates plant hormone signal transduction, MAPK signalling, and phenylpropanoid biosynthesis in kenaf under drought stress. C_LIO_LIProtein interaction revealed HcERF5 interacts with six stress-response genes. C_LI

molecular biology↗

bioRxiv2024

moPPIt: De Novo Generation of Motif-Specific Binders with Protein Language Models

Targeting specific functional motifs, whether conserved viral epitopes, intrinsically disordered regions (IDRs), or fusion breakpoints, is essential for modulating protein function and protein-protein interactions (PPIs). Current design methods, however, depend on stable tertiary structures, limiting their utility for disordered or dynamic targets. Here, we present a motif-specific PPI targeting algorithm (moPPIt), a framework for the de novo generation of motif-specific peptide binders derived solely from target sequence data. The core of this approach is BindEvaluator, a transformer architecture that interpolates protein language model embeddings to predict peptide-protein binding site interactions with high accuracy (AUC = 0.97). We integrate this predictor into a novel Multi-Objective-Guided Discrete Flow Matching (MOG-DFM) framework, which steers generative trajectories toward peptides that simultaneously maximize binding affinity and motif specificity. After comprehensive in silico validation of binding and motif-specific targeting, we validate moPPIt in vitro by generating binders that strictly discriminate between the FN3 and IgG domains of NCAM1, confirming domain-level specificity, and further demonstrate precise targeting of IDRs by generating binders to the N-terminal disordered domain of {beta}-catenin. In functional, disease-relevant assays, moPPIt-designed peptides specifically targeting the GM-CSF receptor [a] subunit effectively block human macrophage polarization. Finally, we demonstrate utility in cell engineering, where binders directed against a defined motif on a synthetic cell surface ligand (AGR2t) drive specific chimeric antigen receptor regulatory T cell (CAR Treg) activation and suppressive function, including in the context of human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes. Altogether, moPPIt serves as a theoretically-justified, sequence-based paradigm for controllably targeting the complete proteome with immediate therapeutic applications.

synthetic biology↗

bioRxiv2024

Cholecystokinin modulates age-dependent Thalamocortical Neuroplasticity

The thalamocortical pathways exhibit neuroplasticity not only during the critical period but also in adulthood. In this study, we investigated how cholecystokinin (CCK) modulates age-dependent thalamocortical plasticity. Our findings demonstrated that CCK is expressed in thalamocortical neurons and that high-frequency stimulation (HFS) of the thalamocortical pathway triggers the release of CCK in auditory cortex (ACx), as detected by a CCK sensor. HFS of the medial geniculate body (MGB) induced thalamocortical long-term potentiation (LTP) in wild-type young adult mice. However, knockdown of Cck expression in MGB neurons or blockade of the CCK-B receptor (CCKBR) in the ACx abolished HFS-induced LTP. Interestingly, this LTP could not be elicited in juvenile (3-week-old) or aged mice (over 18-month-old) due to distinct mechanisms: the absence of CCKBR in juveniles and the inability to release CCK in aged mice. Notably, exogenous administration of CCK into the ACx rescued LTP in aged mice and significantly improved frequency discrimination. These findings highlight the potential of CCK as a therapeutic intervention for ameliorating neuroplasticity deficits associated with thalamocortical connectivity.

neuroscience↗

bioRxiv2024

Overcrowding Drives Tumor Invasion by Inducing Nanotopographical Transition of Plasma Membrane

During the progression from epithelial neoplasms to invasive carcinoma, cells are subjected to prolonged confinement. However, the response of cancer cells to such mild yet sustained compressive pressure during the initial stages of tumor invasion remain poorly understood. Here, using a spontaneous crowding model to recapitulate the progressive compressive stress caused by cell proliferation, we demonstrated that prolonged crowding alone is sufficient to induce the acquisition of an invasive phenotype and associated gene expression patterns in cancer cells. This invasiveness persisted even after cells were removed from the crowded environment, a phenomenon mediated by mechanomemory. By combining genetic manipulations, mechanical modeling, and biophysical measurements, we revealed that the disaggregation of membrane domains--driven by a nanoscale smooth-corrugated topography transition of plasma membranes induced by Laplace pressure under crowded conditions--is essential for initiating cancer cell invasion. Inhibiting membrane domains disaggregation through membrane-to-cortex-attachment effectively suppresses cancer cell invasion in both cellular crowding models and mouse xenograft models. This study underscores the critical role of tissue-scale mechanics in regulating the biophysics of mechanosensitive membrane domains during the early stages of tumor invasion.

cancer biology↗

bioRxiv2024

Genomics-FM: Universal Foundation Model for Versatile andData-Efficient Functional Genomic Analysis

Artificial intelligence (AI) plays a crucial role in functional genomic analysis, offering great potential for comprehending biological phenomena such as heredity, development, diseases, and evolution. However, the development of AI models needs substantial labeled data, and these models are typically task-specific with limited generalizability to various applications. Here, we develop Genomics-FM, a genomic vocabulary driven foundation model that enables versatile and label-efficient functional genomic analysis. Specifically, Genomics-FM is first pretrained with ensemble genomic vocabulary on vast unlabelled data to learn comprehensive and generalizable representations and then finetuned with specific genomic vocabulary on limited labeled data to selectively activate and adapt the pretraining knowledge for specific tasks. We show that Genomics-FM significantly reduces the dependence on labeled data, and demonstrates the capability to outperform existing models across a comprehensive suite of tasks including genome annotation, epigenomic and expression profile prediction, and variant effect assessment. Remarkably, Genomics-FM even shows impressive zero-shot predictive capabilities across diverse species and tissues and exhibits noticeable adaptability to RNA-related tasks. With feasibility in data scarcity and even cross-domain biological scenarios, Genomics-FM will promote the broad application of AI and empower researchers to tackle previously insurmountable challenges, paving the way for groundbreaking research and discoveries.

bioinformatics↗

bioRxiv2024

Illuminating microbial phosphorus cycling in deep-sea cold seep sediments using protein language models

Phosphorus is essential for life and critically influences marine productivity. Despite geochemical evidence of active phosphorus cycling in deep-sea cold seep ecosystems, the microbial processes involved remain poorly understood. Traditional sequence-based searches often fail to detect proteins with remote homology. To address this, we developed a protein language model (PLM) named LucaPCycle that integrates sequence and structural information. This PLM-based approach identified 4,606 new phosphorus-cycling protein families based on the non-redundant gene and genome catalogs from global cold seeps, substantially enhancing our understanding of their diversity, ecology, and function. Among previously unannotated sequences, we discovered three novel alkaline phosphatase families (ALP1, ALP2 and ALP3) that feature unique domain organizations and preserved enzymatic capabilities. These results highlight previously overlooked ecological importance of phosphorus cycling within cold seeps, corroborated by data from porewater geochemistry, metatranscriptomics, and metabolomics. We identified a previously unrecognized diversity of archaea contributing to organic phosphorus mineralization and inorganic phosphorus solubilization through various mechanisms. This includes ecologically significant groups such as Asgardarchaeota, anaerobic methanotrophic archaea (ANME), and Thermoproteota. Additionally, viruses can enhance their hosts (e.g., ANME) phosphorus utilization through the PhoR-PhoB regulatory system and PhnCDE transporter, indirectly influencing methane dynamics. Overall, our PLM-based functional predictions are capable of accessing previously hidden sequence spaces for microbial phosphorus cycling, and can be applied to other various ecosystems.

microbiology↗

bioRxiv2024

An applicable and efficient retrograde monosynaptic circuit mapping tool for larval zebrafish

The larval zebrafish is a vertebrate model for in vivo monitoring and manipulation of whole-brain neuronal activity. Tracing its neural circuits remains challenging. Here, we report an applicable methodology tailored for larval zebrafish to achieve efficient retrograde trans-monosynaptic tracing from genetically defined neurons via EnvA-pseudotyped glycoprotein-deleted rabies viruses. By combinatorially optimizing multiple factors involved, we identified the CVS strain trans-complemented with advanced expression of N2cG at 36 {degrees}C as the optimal combination. It yielded a tracing efficiency of up to 20 inputs per starter cell. Its low cytotoxicity enabled the viable labeling and calcium imaging of infected neurons 10 days post-infection, spanning larval ages commonly used for functional examination. Cre-dependent labeling was further developed to enable cell-type-specific input tracing and circuit reconstruction. We mapped cerebellar circuits and uncovered the ipsilateral preference and subtype specificity of granule cell-to-Purkinje cell connections. Our method offers an efficient way for tracing neural circuits in larval zebrafish.

neuroscience↗

bioRxiv2024

Occurrence, risk assessment of antibiotics and antimicrobial resistance in Escherichia coli in typical rivers of Sichuan

Worldwide interest has been generated by the presence and distribution of antibiotics and antibiotic resistance genes (ARGs) in rivers. However, there was a dearth of research on the contamination of Sichuan provinces typical rivers with antibiotics. In this study, the residual level of antibiotics in 42 national/provincial sites of 9 rivers was analyzed by UPLC-MS/MS, the ecological risk level was evaluated using risk assessment method, and the drug resistance of E. coli in water was evaluated by Kirby-Bauer method. Redundancy analysis demonstrated how residual antibiotics affect the structure of the microbial community in the Minjiang River basin (RDA). Nine rivers all contained antibiotics. Among them, the MinJiang, TuoJiang, and JiaLingJiang rivers were severely contaminated with antibiotic concentrations ranging from 0.29 to 2233.71 ng/L. The Sichuan Basins antibiotic pollution level was significantly higher when compared to other Sichuan zones, which was consistent with the regions high population density. Additionally, it was discovered that 9.77% of the E. coli isolated from 9 rivers had antibiotic resistance, and more than 5.8% of them had multidrug resistance. Moreover, Norfloxacin, amoxicillin, ampicillin, and tetracycline were the main risk factors for high ecological risk in 26 of the 42 monitoring sites. Additionally, there is a strong correlation between the microbial community change and residual antibiotic. These results offered some reference information regarding the distribution of antibiotics and ARGs in typical rivers in the Chinese province of Sichuan, and this study showed that more attention needs to be paid to antibiotic pollution in Sichuans typical rivers.

microbiology↗

bioRxiv2024

Lipid droplets restrict phagosome formation during Candida challenge

Lipid droplets (LDs) are intracellular organelles which can be induced and interact with phagosomes during the process of pathogen phagocytosis in macrophages. However, the function of LDs in the phagocytosis remains elusive. Here, we unveil the role of LDs in modulating phagosome formation using a fungal infection model. Specifically, LDs accumulation restricted the quantity of phagosome formation, and protected macrophages from death. Mechanistically, LDs formation competitively consumed intracellular endoplasmic reticulum membrane and altered RAC1 translocation and its GTPase activity, which resulted in limiting phagosomes formation in macrophages during fungi engulfed. Mice with Hilpda-deficient macrophages were more susceptible to the lethal sequelae of systemic infection with C. albicans. Notably, administration of ATGL inhibitor Atglistatin improved host outcomes in disseminated fungal infections. Taken together, our study elucidates the mechanism of LDs in controlling phagosomes formation to avoid immune cell death, and offers a potential drug target for treatment of C. albicans infections. HighlightsO_LIC. albicans infection induces triglycerides production and LD accumulation in macrophages. C_LIO_LILD restricts the quantity of phagosome formation and protects macrophages from death. C_LIO_LILD consumes intracellular ER membrane components and alters RAC1 translocation and its GTPase activity. C_LIO_LIAdministration of ATGL inhibitor Atglistatin improves host outcomes in disseminated fungal infections. C_LI

microbiology↗

bioRxiv2024

Alarm functions of PD-1+ brain resident memory T cells

Resident memory T cells (TRM) have been described in barrier tissues as having a sensing and alarm function where, upon sensing cognate antigen, they alarm the surrounding tissue and orchestrate local recruitment and activation of immune cells. In the immunologically unique and tightly restricted CNS, it remains unclear if and how brain TRM, which express the inhibitory receptor PD-1, alarm the surrounding tissue during antigen re-encounter. Here, we reveal that TRM are sufficient to drive the rapid remodeling of the brain immune landscape through activation of microglia, DCs, NK cells, and B cells, expansion of Tregs, and recruitment of macrophages and monocytic dendritic cells. Moreover, we report that while PD-1 restrains granzyme B expression by reactivated brain TRM, it has no effect on cytotoxicity or downstream alarm responses. We conclude that TRM are sufficient to trigger rapid immune activation and recruitment in the CNS and may have an unappreciated role in driving neuroinflammation.

immunology↗

bioRxiv2024

Strong Protection by Bazedoxifene Against Chemically-Induced Ferroptotic Neuronal Death In Vitro and In Vivo

Ferroptosis is a form of regulated cell death characterized by excessive iron-dependent lipid peroxidation. Ferroptosis can be induced in cultured cells by exposure to certain chemicals (e.g., erastin and RSL3). Recently it was shown that protein disulfide isomerase (PDI) is a mediator of chemically-induced ferroptosis and also a target for ferroptosis protection. In this study, we find that bazedoxifene (BAZ), a selective estrogen receptor modulator with reported neuroprotective actions in humans, can inhibit PDI function and also strongly protect against chemically-induced ferroptosis in cultured neuronal cells. We find that BAZ can directly bind to PDI in vitro and in intact neuronal cells, and also can inhibit PDIs catalytic activity. Computational modeling analysis reveals that BAZ forms a hydrogen bond with PDI-His256. Inhibition of PDI by BAZ markedly reduces nNOS and iNOS dimerization and NO accumulation, which have recently been shown to play a crucial role in mediating chemically-induced ferroptosis. In addition, the direct antioxidant activity of BAZ may also partially contribute to its protective effect against chemically-induced ferroptosis. Behavioral analysis shows that mice treated with BAZ are strongly protected against kainic acid-induced memory deficits and hippocampal neuronal damage in vivo. In conclusion, the results of this study demonstrate that BAZ is an inhibitor of PDI and can strongly prevent chemically-induced ferroptosis in hippocampal neurons both in vitro and in vivo. These observations offer a novel, estrogen receptor-independent mechanism for the recently-reported neuroprotective actions of BAZ in humans. SIGNIFICANCE STATEMENTFerroptosis is an iron- and lipid peroxidation-dependent form of regulated cell death. Recent evidence has shown that protein disulfide isomerase (PDI) is an important mediator of chemically-induced ferroptosis and also a new target for ferroptosis protection. We find that bazedoxifene is an inhibitor of PDI, which can strongly protect against chemically-induced ferroptotic neuronal death in vitro and in vivo. Additionally, the molecular mechanism of PDI{square}bazedoxifene binding interaction is defined. This work provides evidence for an estrogen receptor-independent, PDI-mediated mechanism of neuroprotection by bazedoxifene.

neuroscience↗

bioRxiv2024

Bone morphogenetic protein (BMP) signaling determines neuroblastoma cell fate and sensitivity to retinoic acid.

Retinoic acid (RA) is a standard-of-care neuroblastoma drug thought to be effective by inducing differentiation. Curiously, RA has little effect on primary human tumors during upfront treatment but can eliminate neuroblastoma cells from the bone marrow during post-chemo consolidation therapy--a discrepancy that has never been explained. To investigate this, we treated a large cohort of neuroblastoma cell lines with RA and observed that the most RA-sensitive cells predominantly undergo apoptosis or senescence, rather than differentiation. We conducted genome-wide CRISPR knockout screens under RA treatment, which identified BMP signaling as controlling the apoptosis/senescence vs differentiation cell fate decision and determining RAs overall potency. We then discovered that BMP signaling activity is markedly higher in neuroblastoma patient samples at bone marrow metastatic sites, providing a plausible explanation for RAs ability to clear neuroblastoma cells specifically from the bone marrow, seemingly mimicking interactions between BMP and RA during normal development.

cancer biology↗

bioRxiv2024

Uncovering the roles of the scaffolding protein CsoS2 in mediating the assembly and shape of the α-carboxysome shell

Carboxysomes are proteinaceous organelles featuring icosahedral protein shells that enclose the carbon-fixing enzymes, Rubisco, alone with carbonic anhydrase. The intrinsically disordered scaffolding protein CsoS2 plays a vital role in the construction of -carboxysomes through bridging the shell and cargo enzymes. The N-terminal domain of CsoS2 binds Rubisco and facilitates Rubisco packaging within the -carboxysome, whereas the C-terminal domain of CsoS2 (CsoS2-C) anchors to the shell and promotes shell assembly. However, the role of the middle region of CsoS2 (CsoS2-M) has remained elusive. Here, we conducted indepth examinations on the function of CsoS2-M in the assembly of the -carboxysome shell by generating a series of recombinant shell variants in the absence of cargos. Our results reveal that CsoS2-M assists CsoS2-C in the assembly of the -carboxysome shell and plays an important role in shaping the -carboxysome shell through enhancing the association of shell proteins on both the facet-facet interfaces and flat shell facets. Moreover, CsoS2-M is responsible for recruiting the C-terminal truncated isoform of CsoS2, CsoS2A, into -carboxysomes, which is crucial for Rubisco encapsulation and packaging. This study not only deepens our knowledge of how the carboxysome shell is constructed and regulated but also lays the groundwork for engineering and repurposing carboxysome-based nanostructures for diverse biotechnological purposes.

synthetic biology↗

bioRxiv2024

Genome-Wide Identification and Expression Pattern of the N-acetylserotonin deacetylase (ASDAC) Gene Family in Orchidaceae

Orchids are a kind of horticultural plant with highly ornamental and medical value. N-acetylserotonin deacetylase (ASDAC) is the only reverse enzyme of the melatonin biosynthesis pathway, and plays an important role in regulating the balance of melatonin. Melatonin as a multifunctional molecule, is typically involved in plant growth and development regulation, as well as abiotic stress tolerance. Here, we aimed at identifying ASDAC genes from the orchid genome to provide valuable information for further study of the role of melatonin in orchids. In this study, a total of 7 ASDAC genes were identified from the 7 orchid genome with one member in each species. The 7 orchid ASDACs have an HDAC functional domain, and cluster together with functionally confirmed OsHDAC10 and AtHDAC14, it shows that these members may have function of N-acetylserotonin deacetylase. Furthermore, based on the phylogenetic, motif, and gene structure analysis, the same clusters orchid ASDAC or ASDAC-like genes generally contained similar introns and motifs, suggesting the distribution pattern of exons/introns and motifs were strongly related to phylogeny on an evolutionary basis. Interestingly, homologous genes of OsHDAC10 and AtHDAC14 in Gastrodia elata have low homology and not cluster together with rice and A.thaliana ASDACs, showing that ASDAC gene family may lost in the holomycoheterotrophic orchids. The Ka/Ks ratios of ASDAC gene pairs from lower plant to higher plant were less than one, suggested that ASDAC genes have undergone purifying selection during the evolution process. Cis-acting element analysis results showed that the promoter regions of orchid ASDAC genes contained plant growth and development, phytohormone, and stress-responsive elements. Moreover, most orchid ASDACs were expressed in the roots, stems, leaves, flowers, and seeds. Combined cis-acting element and tissue expression analysis, indicating orchid ASDAC genes are involved in melatonin regulation of growth and development, as well as melatonin responding to various stresses in orchids. These findings of orchid ASDAC genes may provide valuable information for further study of the role of melatonin in orchids.

bioinformatics↗

bioRxiv2024

Oseltamivir (Tamiflu), a Commonly Prescribed Antiviral Drug, Mitigates Hearing Loss in Mice

Hearing loss affects up to 10% of all people worldwide, but currently there is only one FDA-approved drug for its prevention in a subgroup of cisplatin-treated pediatric patients. Here, we performed an unbiased screen of 1,300 FDA-approved drugs for protection against cisplatin-induced cell death in an inner ear cell line, and identified oseltamivir phosphate (brand name Tamiflu), a common influenza antiviral drug, as a top candidate. Oseltamivir phosphate was found to be otoprotective by oral delivery in multiple established cisplatin and noise exposure mouse models. The drug conferred permanent hearing protection of 15-25 dB SPL for both female and male mice. Oseltamivir treatment reduced in mice outer hair cells death after cisplatin treatment and mitigated cochlear synaptopathy after noise exposure. A potential binding protein, ERK1/2, associated with inflammation, was shown to be activated with cisplatin treatment and reduced by oseltamivir cotreatment in cochlear explants. Importantly, the number of infiltrating immune cells to the cochleae in mice post noise exposure, were significantly reduced with oseltamivir treatment, suggesting an anti-inflammatory mechanism of action. Our results support oseltamivir, a widespread drug for influenza with low side effects, as a promising otoprotective therapeutic candidate in both cisplatin chemotherapy and traumatic noise exposure.

neuroscience↗

bioRxiv2024

Bispecific antibodies with broad neutralization potency against SARS-CoV-2 variants of concern

The ongoing emergence of SARS-CoV-2 variants of concern (VOCs) that reduce the effectiveness of antibody therapeutics necessitates development of next-generation antibody modalities that are resilient to viral evolution. Here, we characterized N-terminal domain (NTD) and receptor binding domain (RBD)-specific monoclonal antibodies previously isolated from COVID-19 convalescent donors for their activity against emergent SARS-CoV-2 VOCs. Among these, the NTD-specific antibody C1596 displayed the greatest breadth of binding to VOCs, with cryo-EM structural analysis revealing recognition of a distinct NTD epitope outside of the site i antigenic supersite. Given C1596s favorable binding profile, we designed a series of bispecific antibodies (bsAbs) termed CoV2-biRNs, that featured both NTD and RBD specificities. Notably, two of the C1596-inclusive bsAbs, CoV2-biRN5 and CoV2-biRN7, retained potent in vitro neutralization activity against all Omicron variants tested, including XBB.1.5, EG.5.1, and BA.2.86, contrasting the diminished potency of parental antibodies delivered as monotherapies or as a cocktail. Furthermore, prophylactic delivery of CoV2-biRN5 significantly reduced the viral load within the lungs of K18-hACE2 mice following challenge with SARS-CoV-2 XBB.1.5. In conclusion, our NTD-RBD bsAbs offer promising potential for the design of resilient, next-generation antibody therapeutics against SARS-CoV-2 VOCs. One Sentence SummaryBispecific antibodies with a highly cross-reactive NTD antibody demonstrate resilience to SARS-CoV-2 variants of concern.

immunology↗

bioRxiv2024

PhaSeDis: A Manually Curated Database of Phase Separation-Disease Associations and Corresponding Small Molecules

Biomacromolecules form membraneless organelles through liquid-liquid phase separation in order to regulate the efficiency of particular biochemical reactions. Dysregulation of phase separation might result in pathological condensation or sequestration of biomolecules, leading to diseases. Thus, phase separation and phase separating factors may serve as drug targets for disease treatment. Nevertheless, such associations have not yet been integrated into phase separation related databases. Therefore, based on MloDisDB, a database for membraneless organelle factor-disease association previously developed by our lab, we constructed PhaSeDis, the phase separation-disease association database. We increased the number of phase separation entries from 52 to 185, and supplemented the evidence provided by the original article verifying the phase separation nature of the factors. Moreover, we included the information of interacting small molecules with low or high-throughput evidence that might serve as potential drugs for phase separation entries. PhaSeDis strives to offer comprehensive descriptions of each entry, elucidating how phase separating factors induce pathological conditions via phase separation and the mechanisms by which small molecules intervene. We believe that PhaSeDis would be very important in the application of phase separation regulation in treating related diseases. PhaSeDis is available at http://mlodis.phasep.pro.

bioinformatics↗