Biology subjects

Zhao, G.

Publications and source records attributed to Zhao, G..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Tryptophan metabolism reprogramming contributes to the prothrombotic milieu in mice and humans infected with SARS-CoV-2

SARS-CoV-2 infection disturbs the coagulation balance in the blood, triggering thrombosis and contributing to organ failure. The role of prothrombotic metabolites in COVID-19-associated coagulopathy remains elusive. Leveraging K18-hACE2 mice infected with SARS-CoV-2, we observed higher levels of the tryptophan metabolite, kynurenine, compared to controls. SARS-CoV-2 infected mice showed a significant upregulation of enzymes controlling Kynurenine biogenesis, such as indoleamine 2,3-dioxygenase (IDO-1) and tryptophan 2,3-dioxygenase levels in kidneys and liver, respectively, as well as changes in the enzymes involved in kynurenine catabolism, including kynurenine monooxygenase and kynurinase. Consistent with the agonistic role of these metabolites in Aryl Hydrocarbon Receptor (AHR) signaling, AHR activation and its downstream mediator, tissue factor (TF), a highly potent procoagulant factor, was observed in endothelial cells (ECs) of lungs and kidneys of infected mice. These findings were validated in humans, where compared to controls, sera of COVID-19 patients showed increased levels of Kynurenine, kynurenic acid, anthranilic acid, and quinolinic acid. Activation of the AHR-TF axis was noted in the kidneys and lungs of COVID-19 patients, and COVID-19 sera showed higher IDO-1 activity than controls. Levels of Kyn in COVID-19 patients correlated strongly with the TF-inducing activity of COVID-19 sera on ECs. A specific IDO-1 inhibitor or AHR inhibitor separately or in combination suppressed COVID-19 sera-induced TF activity in ECs. Together, we identified IDO-1 as upregulated by SARS-CoV-2 infection, resulting in augmented Kyn and its prothrombotic catabolites, thereby suggesting the Kyn-AHR-TF axis as possibly a new diagnostic and/or therapeutic target. Key pointsO_LISARS-CoV-2-infection upregulates kynurenine biogenesis in the liver and diminishes kynurenine catabolism in the lungs and kidneys. C_LIO_LIAn increase in kynurenine stimulates the AHR-TF axis in the microvasculature in COVID-19 patients, which is inhibited by pharmacological manipulation. C_LI

systems biology↗

bioRxiv2025

PD-1 prelimits both the cytotoxic and exhaustion potential in thymic CD8+ T cells and impacts the maintenance of peripheral tumor immunity

Durable T cell immunity against cancer depends on the continual replenishment of effector CD8+ T cells. Thymic output has been correlated with favorable prognosis in cancer patients across a range of ages, suggesting that the thymus is an important source for replenishing T cells capable of controlling cancer progression. However, the effector potential of thymic mature CD8+ T cells and their regulation have not been clearly defined. In this study, we identified the ability of thymic single positive CD8+ T cells to gain effector potential after thymic selection, but they are subject to the regulation of PD-1. We found a previously undisclosed role of PD-1 in limiting both the cytotoxic and exhaustion potential of thymic and peripheral CD8+ T cells. Our results show that although PD-1 inhibition facilitates the expansion of effector CD8+ T cells, effector CD8+ cells gradually lose their antitumor activity within tumor tissues due to advanced exhaustion in the absence of PD-1. Thus, although the preset effector potential in thymic mature CD8+ T cells allows them to rapidly respond to malignant cells in the periphery, PD-1, as a checkpoint, is embedded in the thymic mature CD8+ T cells after positive selection to balance their effector function from exaggeration and exhaustion. Therefore, we propose that a strategy capable of upholding the cytotoxic capacity and avoiding exhaustion of CD8+ T cells during the early stages of PD-1 inhibition therapy is needed to achieve durable antitumor immunity.

immunology↗

bioRxiv2025

An explainable artificial intelligence framework reveals mutations associated with drug resistance in Mycobacterium tuberculosis

Understanding the mechanisms of drug resistance in Mycobacterium tuberculosis (MTB) is essential for the rapid detection of resistance and for guiding effective treatment, ultimately contributing to reducing the global burden of tuberculosis (TB). Under anti-TB drugs pressure, MTB continues to accumulate resistance loci. The current repertoire of known resistance-associated mutations requires further refinement, necessitating efficient methods for the timely identification of potential resistance sites. Here, we introduce xAI-MTBDR, an explainable artificial intelligence framework designed to identify new resistance-associated mutations and predict drug resistance in MTB. It outperforms state-of-the-art methods in predicting drug resistance for all first-line drugs, and scoring each mutations contribution to resistance. By leveraging public whole-genome sequencing data from nearly 40,000 MTB isolates, the framework identified 788 candidate resistance-related mutations and revealed 30 potential resistance markers, several of which are structurally located closer to their respective drugs compared to known resistance mutations. Furthermore, these scores enabled the framework to efficiently subgroup isolates with different resistance mechanisms and reflect varying levels of resistance. The framework serves as a valuable tool for accurate detection of drug-resistant MTB and offers new insights into its underlying mechanisms.

microbiology↗

bioRxiv2024

Abnormal eNK cells contribute to endometrial fibrosis in intrauterine adhesions patients

Endometrial natural killer cells (eNK) at the proliferative phase are one of the major lymphocytes in the endometrium, but their phenotype and function remain elucidated. Here, we demonstrated that eNK cells had three subtypes and were different from peripheral blood NK (pbNK) and decidual NK (dNK) cells. They played an important role in maintaining the homeostasis of the endometrium through preventing endometrial stromal cells (ESCs) from the differentiation into myofibroblasts physiologically. However, in the fibrotic endometria of patients with intrauterine adhesions (IUA), eNK cells were significantly decreased and highly negatively correlated with an increase in myofibroblasts. In vitro experiments showed that eNK cells could inhibit the differentiation of ESCs into myofibroblasts and promote the dedifferentiation of myofibroblasts, in which the main effector molecules from eNK cells was Prostaglandin D2 (PGD2). PGD2 downregulated the expression of ZNF521 to decrease profibrotic protein synthesis. Furthermore, we confirmed the anti-endometrial fibrosis effect of eNK cells and its mechanism in an IUA-like murine model. These findings reveal an important role of eNK cells in endometrial homeostasis and provide potential therapeutic approaches for IUA patients.

immunology↗

bioRxiv2024

A CRISPR/SpCas9M-reporting system for efficient and rapid genome editing in Caulobacter crescentus

As members of the -proteobacteria group, Caulobacter crescentus and its relatives are known for their asymmetric life cycle and comprehensive applications in gene delivery, agricultural biotechnology, and the production of high-value compounds. However, genetic manipulations of these bacteria are often time-consuming and labor-intensive due to the lack of efficient genome editing tools. Here, we report a practical CRISPR/SpCas9M-reporting system that overcomes the limitations of SpCas9 expression, enabling efficient, markerless, and rapid genome editing in C. crescentus. As a demonstration, we successfully knocked out two genes encoding the scaffold proteins, achieving apparent editing efficiencies up to 80%. Key components, including the Cas protein, Cas inducer, sgRNA, homologous arms, and reporter, were systematically analyzed and optimized to enhance the editing efficiency or decrease the cell lethality. A nearly zero off-target ratio was observed after the curing of the editor plasmid in editing strains. Furthermore, we applied the CRISPR/SpCas9M-reporting system to two C. crescentus relatives, Agrobacterium fabrum and Sinorhizobium meliloti, establishing it as an efficient and reliable editing strategy. We anticipate that this system could be applied to other hard-to-edit organisms, accelerating both basic and applied research in -proteobacteria.

bioengineering↗

bioRxiv2024

Transcriptomic signatures of host immune responses in aphthous ulcers, the earliest lesions of Crohn's disease, suggest that a bacterial invasive challenge, rather than global dysbiosis, is the initiating factor.

Crohns disease is a chronic, transmural inflammatory disease of the human gut. Changes in the faecal microbial composition and a reduction in species diversity (dysbiosis) are consistent features in studies of Crohns disease patients, but whether dysbiosis is a cause or consequence of inflammation remains unresolved. Genetic susceptibility also plays a role in the development of Crohns disease and has been linked to genes involved in recognition of intestinal bacteria by cells of the mononuclear phagocyte system. The earliest visible lesions in Crohns disease are aphthous ulcers, overlying Peyers patches and lymphoid follicles. To identify mechanisms underlying the earliest stages of disease initiation we compared gene expression in aphthous ulcers, Peyers patches, inflamed and endoscopically normal mucosa from patients and controls using total RNA-seq. The resulting data was subjected to network analysis to identify co-regulated gene expression signatures of cell types and processes. These results were compared to recent single cell RNA-seq analysis of intestinal macrophages in normal and diseased mucosa. The analysis of aphthous ulcers revealed signatures of epithelial stress and antimicrobial defence, plasma cell activation and immunoglobulin production, monocyte recruitment, inflammatory gene expression and induction of interferon-{gamma} and downstream target genes. These signatures were not present in the normal appearing mucosa adjacent to aphthous ulcers which were similar to healthy control mucosa. We conclude that the initial lesion in Crohns disease arises from an invasive bacterial challenge leading to intense activation of multiple host defence pathways rather than the breakdown of epithelial barrier integrity and widespread bacterial translocation.

immunology↗

bioRxiv2024

Multimodal Protein-Ligand Contrastive Pretraining for Effective and Efficient Drug Discovery

Recent advancements in genomics and proteomics have identified numerous clinically significant protein targets, with notably 85% categorized as undruggable. These targets present widespread challenges due to their complex structures and dynamics, rendering conventional drug design strategies not always effective. In this study, we introduce Uni-Clip, a contrastive learning framework that incorporates multi-modal features of proteins (structure and residue) and ligands (conformation and graph). Optimized with a specifically designed CF-InfoNCE loss, Uni-Clip enhances the modeling of protein-ligand interactions for both undruggable and druggable proteins. Uni-Clip demonstrates superior performance in benchmark evaluations on widely acknowledged datasets, LIT-PCBA and DUD-E, achieving a 147% and 218% improvements in enrichment factors at 1% compared to baselines. Furthermore, Uni-Clip proves to be a practical tool for various drug discovery applications. In virtual screening for the challenging protein target GPX4 with flat surface, it identified non-covalent inhibitors with an IC50 of 4.17 M, in contrast to the predominantly covalent inhibitors currently known. Through target fishing for benzbromarone, Uni-Clip identified the intrinsically disordered protein c-Myc as a potential target, highlighting benzbromarones potential for repurposing in cancer therapy. Explainable analyses effectively identified binding sites consistent with molecular dynamics and experimental results, even for challenging undruggable targets.

bioinformatics↗

bioRxiv2024

A modular self-assembling and self-adjuvanting multiepitope peptide nanoparticle vaccine platform to improve the efficacy and immunogenicity of BCG

After more than a century since its initial development, Bacille Calmette-Guerin (BCG) remains the only licensed vaccine against tuberculosis (TB). Subunit boosters are considered a viable strategy to enhance BCG efficacy, which often wanes in adolescence. While many studies on booster subunit vaccines have concentrated on recombinant proteins, here we developed a novel modular peptide-based subunit vaccine platform that is flexible, cold-chain independent and customizable to diverse circumstances and populations. Each individual peptide building block consists of a linear arrangement comprising a 15-leucine self-assembly inducer moiety, a Mycobacterium tuberculosis (Mtb) target epitope and an HLA-E binding moiety, with each moiety separated by a triple lysine spacer. The building blocks, in any combination, were able to form a multiepitope nanoparticle. Six Mtb epitopes were selected to produce the self-assembling and self-adjuvanting peptide-based TB nano-vaccine candidate PNx6. In vivo vaccination-challenge experiments demonstrated that subcutaneous boost of parenteral BCG immunization with PNx6 significantly enhanced its immunogenicity and improved its protective efficacy in a murine model of TB by more than 5-fold. Our study present evidence that purely amphiphilic peptides self-assemble into self-adjuvanting nanoparticles with appropriate size and morphology for TB vaccination with great potential for a multitude of other diseases.

microbiology↗

bioRxiv2024

The tubule-sheet continuum model links the pattern of nuclear envelope assembly to nuclear envelope integrity

Nuclear envelope (NE) fragility is associated with a variety of human diseases. However, major questions about the causes of NE fragility are unresolved. In particular, the relationship between NE fragility and NE assembly is unclear. Here, using a panel of 13 mammalian cell lines, we show that normal cells and some cancer cells assemble the NE using distinct patterns from opposite ends of the "tubule-sheet continuum", and that the NE assembly pattern more utilised in cancer cells is a source of NE fragility. In normal cells, the mitotic endoplasmic reticulum (ER) morphology is dominated by ER tubules or small sheets and the NE assembles by "membrane infiltration". By contrast, in some cancer cells, the mitotic ER morphology is dominated by large ER sheets and the NE assembles by "lateral sheet expansion". Experimental manipulations that promote mitotic ER sheet formation and NE assembly by lateral sheet expansion in normal cells result in NE fragility. Thus, we propose that NE assembly by lateral sheet expansion is a source of NE fragility in cancer cells.

cell biology↗

bioRxiv2024

Fructose consumption in pregnancy and associations with maternal and offspring hepatic and whole-body adiposity: a scoping review.

BackgroundFructose is a major component in the Western diet, and its increased intake has been linked to adverse metabolic health, including impaired hepatic function and increased adiposity. The early life period, including preconceptionally, pregnancy and the newborn period, are critical periods in determining later metabolic health. However, the impact of excess fructose intake during this time on maternal, fetal, and offspring hepatic and whole-body adiposity, are ill defined. ObjectivesTo understand the effects of maternal fructose consumption pre- and during pregnancy on maternal, fetal and offspring hepatic and whole-body adiposity. MethodsA systematic search of MEDLINE, EMBASE, and CENTRAL was performed up to August 23, 2022, to identify studies that focused on maternal fructose consumption pre- and during pregnancy on hepatic and whole-body adiposity in the mother, fetus, and offspring. Citations, abstracts, and full texts were screened in duplicate. Hepatic adiposity was defined as elevated hepatic triglycerides or overall hepatic fat accumulation. Whole-body adiposity was defined as increased adipose tissue or adipocyte hypertrophy. ResultsAfter screening 2334 citations, 33 experimental studies reporting maternal fructose consumption pre- and during pregnancy in rodents were included. Prenatal fructose exposure was associated with maternal (9 out of 12) and offspring (6 out of 10) whole-body adiposity. A high proportion of studies (13 out of 14) supported the association between fructose during pregnancy and increased maternal hepatic adiposity. Fetal hepatic adiposity and elevated expression of hepatic lipogenic proteins were noted in four studies. Offspring hepatic adiposity was supported in 14 of the 17 articles that discussed hepatic results, with five studies demonstrating more severe effects in female offspring. ConclusionsFructose consumption during pregnancy in rodent models is associated with maternal, fetal, and offspring hepatic, whole-body adiposity and underlying sex-specific effects. There are no human fructose studies and its effects in the early life period. Registration numberH8F26 on Open Science Framework

developmental biology↗

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

Disruption of Immune Responses By Type I Diabetes Exacerbates SARS-CoV-2 Mediated Lung Injury

COVID-19 commonly presents as pneumonia, with those most severely affected progressing to respiratory failure. Patient responses to SARS-CoV-2 infection are varied, with comorbidities acting as major contributors to varied outcomes. Focusing on one such major comorbidity, we assessed whether pharmacological induction of Type I Diabetes Mellitus (T1DM) would increase the severity of lung injury in a murine model of COVID-19 pneumonia utilizing wild type mice infected with mouse-adapted SARS-CoV-2. Hyperglycemic mice exhibited increased weight loss and reduced blood oxygen saturation in comparison to their euglycemic counterparts, suggesting that these animals indeed experienced more severe lung injury. Transcriptomic analysis revealed a significant impairment of the adaptive immune response in the lungs of diabetic mice compared to those of control. In order to expand the limited options available for tissue analysis due to biosafety restrictions, we also employed a novel technique to digest highly fixed tissue into a single cell suspension, which allowed for flow cytometric analysis as well as single cell RNA sequencing. Flow immunophenotyping and scRNA-Seq confirmed impaired recruitment of T cells into the lungs of T1DM animals. Additionally, scRNA-Seq revealed a distinct, highly inflammatory macrophage profile in the diabetic cohort that correlates with the more severe infection these mice experienced clinically, allowing insight into a possible mechanism for this phenomenon. Recognizing the near certainty that respiratory viruses will continue to present significant public health concerns for the foreseeable future, our study provides key insights into how T1DM results in a much more severe infection and identifies possible targets to ameliorate comorbidity-associated severe disease. NEW AND NOTEWORTHYWe define the exacerbating effects of Type I Diabetes Mellitus (T1DM) on COVID-19 pneumonia severity in mice. Hyperglycemic mice experienced increased weight loss and reduced oxygen saturation. Transcriptomic analysis revealed impaired immune responses in diabetic mice, while flow cytometry and single-cell RNA sequencing confirmed reduced T cell recruitment and an inflammatory macrophage profile. Additionally, we introduced a novel technique for tissue analysis, enabling flow cytometric analysis and single-cell RNA sequencing on highly fixed tissue samples.

immunology↗

bioRxiv2024

Development of the overlapping network modules in the human brain

Developmental connectomic studies have shown that the modular organization of functional networks in the human brain undergoes substantial reorganization with age to support cognitive growth. However, these studies implicitly assume that each brain region belongs to one and only one specific network module, ignoring the potential spatial overlap between functional modules. How the overlapping functional modular architecture develops and whether this development is related to structural signatures remain unknown. Using longitudinal multimodal structural, functional, and diffusion MRI data from 305 children (aged 6-14 years), we investigated the development of the overlapping modular architecture of functional networks, and further explored their structural associations. Specifically, an edge-centric network model was used to identify the overlapping functional modules, and the nodal overlap in module affiliations was quantified using the entropy measure. We showed a remarkable regional inhomogeneity in module overlap in children, with higher entropy in the ventral attention, somatomotor, and subcortical networks and lower entropy in the visual and default-mode networks. Furthermore, the overlapping modules developed in a linear, spatially dissociable manner from childhood to adolescence, with significantly reduced entropy in the prefrontal cortex and putamen and increased entropy in the parietal lobules. Personalized overlapping modular patterns capture individual brain maturity as characterized by brain age. Finally, the overlapping functional modules can be significantly predicted by integrating gray matter morphology and white matter network properties. Our findings highlight the maturation of overlapping network modules and their structural substrates, thereby advancing our understanding of the principles of connectome development.

neuroscience↗

bioRxiv2024

Normative growth modeling of brain morphology reveals neuroanatomical heterogeneity and biological subtypes in children with ADHD

BackgroundNeuroimaging studies suggest substantial individual heterogeneity in brain phenotypes in attention-deficit/hyperactivity disorder (ADHD). However, how these individual-level brain phenotypes contribute to the identification of ADHD biotypes and whether these biotypes have different treatment outcomes and neurobiological underpinnings remain largely unknown. MethodsWe collected multisite, high-quality structural magnetic resonance imaging data from 1,006 children aged 6-14 years, including 351 children with ADHD and 655 typically developing children. Normative growth models of cortical thickness were established for 219 regions in the typically developing children. Individual-level deviations from these normal references were quantified and clustered to identify ADHD biotypes. We validated the replicability and generalizability of the ADHD biotypes using two independent datasets and evaluated the associations of the biotypes with symptomatic, cognitive, and gene expression profiles, as well as follow-up treatment outcomes. FindingsNo more than 10% of children with ADHD had extreme deviations in cortical thickness in a single region, suggesting high heterogeneity among individuals with ADHD. On the basis of the brain deviation maps, we discovered two robust ADHD biotypes, an infra-normal subtype with cortical thinning associated with ADHD symptoms and a supranormal subtype with cortical thickening associated with cognition. Patients with the infra-normal subtype responded better to methylphenidate than to atomoxetine, although both subtypes showed treatment efficacy. Brain deviations in the infra-normal subtype were explained by the expression levels of genes enriched in presynaptic and axonal development and polygenic risk of ADHD. InterpretationWe identified anatomically distinct, clinically valuable, and biologically informed ADHD subtypes, providing insight into the neurobiological basis of clinical heterogeneity and facilitating a personalized medication strategy for ADHD patients. Panel: Research in contextO_ST_ABSEvidence before this studyC_ST_ABSSubstantial individual heterogeneity in brain phenotypes in attention-deficit/hyperactivity disorder (ADHD) motivates the need to discover homogeneous biotypes. We searched PubMed for research articles on ADHD biotypes using brain MRI published before December 1, 2023, using the search terms ((attention deficit hyperactivity disorder [Title/Abstract]) OR (ADHD [Title/Abstract])) AND ((subtypes [Title/Abstract]) OR (subgroups [Title/Abstract]) OR (subtyping [Title/Abstract])) AND ((MRI [Title/Abstract]) OR (neuroimaging [Title/Abstract]) OR (brain [Title/Abstract])) without language restrictions. Of the eight included studies, two identified ADHD biotypes using structural morphology, four used functional activity, and two used multimodal features. However, none of these studies considered the developmental effect of the brain phenotypes, examined treatment response, or investigated the genetic correlates of the biotypes. Added value of this studyThis study is the first to use individualized brain measures extracted from normative models to investigate ADHD biotypes in a large sample of more than 1,000 children. We identified two reproducible ADHD biotypes, characterized by distinct symptomatic, cognitive, and gene expression profiles, as well as differential treatment responses. This study advances our understanding of the neurobiological basis underlying the clinical heterogeneity of ADHD and highlights the critical need to discover ADHD biotypes using an unbiased and individualized approach. Implications of all the available evidenceThis study revealed remarkable neuroanatomical heterogeneity in ADHD patients and identified anatomically distinct, clinically valuable, and biologically informed ADHD biotypes. Our findings have potential value for the investigation of data-driven biotypes to evaluate treatment efficacy and facilitate personalized treatment. We also highlight the need for future studies to move beyond the understanding of ADHD solely based on the "average patient" perspective.

neuroscience↗

bioRxiv2024

CyanoTag: Discovery of protein function facilitated by high-throughput endogenous tagging in a photosynthetic prokaryote

Despite their fundamental importance to aquatic ecosystems, global carbon cycling and exciting potential in sustainable bioindustries, the genomes of photosynthetic prokaryotes still contain large numbers of uncharacterised protein-coding genes. Here we present a high-throughput approach for scarless endogenous fluorescent protein tagging in the model cyanobacterium Synechococcus elongatus PCC7942. From 400 targets we successfully endogenously tag over 330 proteins corresponding to >10% of the proteome. We demonstrate how this resource can be used at scale to determine subcellular localisation, track relative protein abundances and to elucidate protein-protein interaction networks. Our data has provided biological insights into a diverse range of processes - from photosynthesis to cell division. Of particular interest, our CyanoTag lines enabled us to visualise in real time the rapid condensation of Calvin Cycle proteins Prk and Gap2 within seconds of withdrawal of light, effectively switching off photosynthesis in the dark. These insights, CyanoTag cell lines, associated data and optimised methods are intended to be shared as a resource to facilitate further discoveries relevant to cyanobacteria and more broadly to all photosynthetic life.

microbiology↗

bioRxiv2024

Exploring the repository of de novo designed bifunctional antimicrobial peptides through deep learning

Antimicrobial peptides (AMPs) are attractive candidates to combat antibiotic resistance for their capability to target bio-membranes and restrict a wide range of pathogens. It is a daunting challenge to discover novel AMPs due to their sparse distributions in a vast peptide universe, especially for peptides that demonstrate potencies for both bacterial membranes and viral envelopes. Here we establish a de novo AMP design framework by bridging a deep generative module and a graph-encoding activity regressor. The generative module learns hidden grammars of AMP features and produces candidates sequentially pass antimicrobial predictor and antiviral classifiers. We discover 16 bifunctional AMPs and experimentally validated their abilities to inhibit a spectrum of pathogens in vitro and in animal models. Notably, P076 is a highly potent bactericide with the minimal inhibitory concentration of 0.21 M against multidrug-resistant A. baumannii, while P002 broadly inhibits five enveloped viruses. Our study provides feasible means to uncover sequences that simultaneously encode antimicrobial and antiviral activities, thus bolstering the function spectra of AMPs to combat a wide range of drug-resistant infections.

microbiology↗

bioRxiv2024

Bacterial exonuclease III expands its enzymatic activities on single-stranded DNA

Bacterial exonuclease III (ExoIII), widely acknowledged for specifically targeting double-stranded DNA (dsDNA), has been documented as a DNA repair-associated nuclease with apurinic/apyrimidinic (AP)-endonuclease and 3'[->]5' exonuclease activities. Due to these enzymatic properties, ExoIII has been broadly applied in molecular biosensors. Here, we demonstrate that ExoIII (Escherichia coli) possesses highly active enzymatic activities on ssDNA. By using a range of ssDNA fluorescence-quenching reporters and fluorophore-labelled probes coupled with mass spectrometry analysis, we found ExoIII cleaved the ssDNA at 5'-bond of phosphodiester from 3' to 5' end by both exonuclease and endonuclease activities. Additional point mutation analysis identified the critical residues for the ssDNase action of ExoIII and suggested the activity shared the same active center with the dsDNA-targeted activities of ExoIII. Notably, ExoIII could also digest the dsDNA structures containing 3'-end ssDNA. Considering most ExoIII-assisted molecular biosensors require the involvement of single-stranded DNA (ssDNA) or nucleic acid aptamer containing ssDNA, the activity will lead to low efficiency or false positive outcome. Our study revealed the multi-enzymatic activity and the underlying molecular mechanism of ExoIII on ssDNA, illuminating novel insights for understanding its biological roles in DNA repair and the rational design of ExoIII-ssDNA involved diagnostics.

biochemistry↗

bioRxiv2023

Mechano-signaling of prostate tumor initiating cells facilitates their tropism to stiff metastatic niche

Analysis of clinical datasets indicate that cancer stem-like cells/tumor-initiating cells (CSCs/TICs) derived from prostate cancer (PCa) patients display an elevated expression of genes for cell-matrix interactions, cell adhesion proteins and of the putative mechanotransducer TAZ. Here we combined measurements on the cellular mechano-responses to matrix stiffness, including cell-generated forces, zebrafish and PDX-derived organoid models, to show that mechanotransduction serves as a key determinant for PCa CSC maintenance during metastatic onset. The {beta}1-integrin-ILK-CDC42-N-Wasp dependent cytoskeletal tension and TAZ nucleus-translocation mediate this mechano-signaling axis. As a result, expression of the stemness genes NANOG and OCT4 are induced, leading to metastatic tumor initiation. It is further demonstrated that pharmaceutical perturbation of this mechano-signaling using a novel YAP/TAZ inhibitor K975 constrains PCa metastasis in zebrafish, and development of PDX-derived organoids. Our data highlights the essential role of mechanotransduction in PCa aggressiveness, thereby underlying this pathway as a therapeutic target for future studies.

cancer biology↗