Biology subjects

Zhu, J.

Publications and source records attributed to Zhu, J..

At least 235 records · Page 13Linked to original sources

bioRxiv2024

Covalent adducts formed by the androgen receptor transactivation domain and small molecule drugs remain disordered

Intrinsically disordered proteins are implicated in many human diseases. Small molecules that target the disordered androgen receptor transactivation domain have entered human trials for the treatment of castration-resistant prostate cancer. These molecules have been shown to react with cysteine residues of the androgen receptor transactivation domain and form covalent adducts under physiological conditions. It is currently unclear how covalent attachment of these molecules alters the conformational ensemble of the androgen receptor. Here, we utilize all-atom molecular dynamics computer simulations to simulate covalent adducts of the small molecule ligands EPI-002 and EPI-7170 bound to the disordered androgen receptor transactivation domain. Our simulations reveal that the conformational ensembles of androgen receptor transactivation domain covalent adducts are heterogeneous and disordered. We find that covalent attachment of EPI-002 and EPI-7170 increases the population of collapsed helical transactivation domain conformations relative to the populations observed in non-covalent binding simulations and we identify networks of protein-ligand interactions that stabilize collapsed conformations in covalent adduct ensembles. We compare the populations of protein-ligand interactions observed in covalent adduct ensembles to those observed in non-covalent ligand-bound ensembles and find substantial differences. Our results provide atomically detailed descriptions of covalent adducts formed by small molecules and an intrinsically disordered protein and suggest strategies for developing more potent covalent inhibitors of intrinsically disordered proteins.

biophysics↗

bioRxiv2024

Exploring methanogenic archaea and their thermal responses in the glacier-fed stream sediments of Rongbuk River Basin, Mt. Everest

Glacier-fed streams (GFS) are emergent sources of greenhouse gas methane, and methanogenic archaea in sediments contribute largely to stream methane emissions. However, little is known about the methanogenic communities in GFS sediments and their key environmental driving factors. This study analyzed stream sediments from the Rongbuk River basin on Mount Everest for methanogenic communities and their temperature responses through anaerobic microcosm incubations at 5{degrees}C and 15{degrees}C. Diverse methanogens were identified, including acetoclastic, hydrogenotrophic, and methylotrophic types. Substantial methane and CO2 production were detected across altitudes and increased significantly at 15{degrees}C, with both methane and CO2 production rate negatively correlated with altitude. While temperature sensitivity of CO2 production but not CH4 showed a negative altitude correlation. Methanogens increased substantially over long-term incubation, dominating the archaeal community. At 15{degrees}C, the relative abundance of several methanogenic groups was strongly correlated with altitude, with positive correlations observed for Methanomassiliicoccaceae and Methanoregulaceae, and negative correlations for Methanocellaceae and Methanotrichaceae, respectively. Besides altitude, factors like phosphorus, C-to-N ratio, and pH also affected methanogenic structure, methane and CO2 production, and temperature sensitivities. This study offers new insights into methanogens and methane production in GFS sediments, improving our understanding of GFS carbon cycling and its potential responses to climate change.

ecology↗

bioRxiv2024

Enhancing Gene Set Overrepresentation Analysis with Large Language Models

Gene set overrepresentation analysis is widely used to interpret high-throughput transcriptomics and proteomics data, but traditional methods rely on static, human-curated gene set databases that lack flexibility. We introduce llm2geneset, a framework that leverages large language models (LLMs) to dynamically generate gene set databases tailored to input query genes, such as differentially expressed genes (DEGs) and a biological context specified in natural language. These databases integrate with methods, such as overrepresentation analysis (ORA), to assign biological functions to input genes. Benchmarking against human-curated gene sets demonstrates that LLMs generate gene sets comparable in quality to those curated by humans. llm2geneset also identifies biological processes represented by input gene sets, outperforming traditional ORA and direct LLM prompting. Applying the framework to RNA-seq data from iPSC-derived microglia treated with a TREM2 agonist highlights its potential for flexible, context-aware gene set generation and improved interpretation of high-throughput biological data. llm2geneset is available as open source at https://github.com/Alector-BIO/llm2geneset and via a web interface at https://llm2geneset.streamlit.app.

bioinformatics↗

bioRxiv2024

Distinct Binding Modes of Inter-Spike Cross-Linking Suggest a Supplementary Mechanism for SARS-CoV-2 Antibody Neutralization

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its Omicron subvariants drastically amplifies transmissibility, infectivity, and immune escape, mainly due to their resistance to most neutralizing antibodies. Thus, exploring the mechanisms underlying antibody evasion is crucial. Although the full-length native form of antibody, immunoglobulin G (IgG), offers valuable insights into the neutralization, structural investigations primarily focus on the fragment of antigen-binding (Fab). Here, we employ single-particle cryo-electron microscopy (cryo-EM) to characterize a W328-6H2 antibody, in its native IgG form complexed with severe acute respiratory syndrome (SARS), severe acute respiratory syndrome coronavirus 2 wild-type (WT) and Omicron variant BA.1 spike protein (S). Three high-resolution structures reveal that the full-length IgG forms a centered head-to-head dimer of trimer when bound fully stoichiometrically with both SARS and WT S, while adopting a distinct offset configuration with Omicron BA.1 S. Combined with functional assays, our results suggest that, beyond the binding affinity between the RBD epitope and Fab, the higher-order architectures of S trimer and full-length IgG play an additional role in neutralization, elucidate a potential molecular basis of Omicron immune escape, and expand our understanding on antibody evasion mechanisms.

immunology↗

bioRxiv2024

An mRNA Display Approach for Covalent Targeting of a Staphylococcus aureus Virulence Factor

Staphylococcus aureus (S. aureus) is an opportunistic human pathogen that causes over one million deaths around the world each year. We recently identified a family of serine hydrolases termed fluorophosphonate binding hydrolases (Fphs) that play important roles in lipid metabolism and colonization of a host. Because many of these enzymes are only expressed in Staphylococcus bacteria, they are valuable targets for diagnostics and therapeutics. Here we developed and screened highly diverse cyclic peptide libraries using mRNA display with a genetically encoded oxadiazolone (Ox) electrophile that was previously shown to potently and covalently inhibit multiple Fph enzymes. By performing multiple rounds of counter selections with WT and catalytic dead FphB, we were able to tune the selectivity of the resulting selected cyclic peptides containing the Ox residue towards the desired target. From our mRNA display hits, we developed potent and selective fluorescent probes that label the active site of FphB at single digit nanomolar concentrations in live S. aureus bacteria. Taken together, this work demonstrates the potential of using direct genetically encoded electrophiles for mRNA display of covalent binding ligands and identifies potent new probes for FphB that have the potential to be used for diagnostic and therapeutic applications.

microbiology↗

bioRxiv2024

Identification of molecular and functional subtypes using chronic pancreatitis patient-derived organoid models

Chronic pancreatitis (CP) affects [~]3 million people worldwide, yet altering the course of disease is challenging. We developed a patient-derived organoid (PDO) platform to investigate the molecular pathogenesis of this disease and identify therapeutic strategies. We generated 36 PDOs from patients with idiopathic, hereditary, and alcohol-related CP with high genetic concordance. PDOs retained inflammation-associated transcriptional and proteomic features. Transcriptomic profiling revealed three molecular subtypes of CP independent of etiology. We discovered widespread dysfunction of the cystic fibrosis transmembrane conductance regulator (CFTR) in half of the CP PDOs, including those with wildtype CFTR. Clinically available CFTR modulators stabilized mutant or wildtype CFTR, restored CFTR function, and decreased mitogenic and inflammatory signaling. This work provides the first comprehensive PDO platform for modeling CP. We demonstrate the utility of this platform for precision therapeutic investigations. Our findings reveal CFTR modulators as a broadly applicable and effective therapeutic strategy.

cell biology↗

bioRxiv2024

Prenatal stress increases corticosterone levels in offspring by impairing placental glucocorticoid barrier function

To investigate the association between prenatal stress (PS) and corticosterone, and its influence on DNA methylation of genes related to the placental glucocorticoid (GC) barrier, including 11{beta}-HSD2, P-gp, NR3C1, and FKBP5. The PS model was established through chronic unpredictable mild stress (CUMS). DNA methylation of GC-related genes was analyzed using reduced representation bisulfite sequencing (RRBS), and the results were confirmed using MethylTarget sequencing. The mRNA and protein expression levels of these genes were detected through qRT-PCR and Western blotting, respectively. Plasma corticosterone levels are elevated in pregnant female rats exposed to PS conditions and their offspring. Compared to the offspring of the prenatal control (OPC) group, the offspring of the prenatal stress (OPS) group showed down-regulation in both mRNA and protein expression of DNMT 3A and DNMT 3B, while up-regulation was observed in the expression of DNMT1. RRBS analyses identified P-gp and FKBP5 as hypermethylated genes, including a total of 43 differentially methylated sites (DMS) and 2 differentially methylated regions (DMR). MethylTarget sequencing revealed that both genes had 15 differentially methylated CpG sites. This study provides preliminary evidence that PS disrupts the placental GC barrier through abnormal gene expression caused by hypermethylation of GC-related genes, resulting in elevated corticosterone levels in offspring and affecting their growth and development.

developmental biology↗

bioRxiv2024

GESIAP3.0: Sensor-based Image Analysis Program for Transmission Visualization In Vivo

Synaptic transmission mediated by various neurotransmitters influences a wide range of behaviors. However, understanding how neuromodulatory transmitters encode diverse behaviors and affect their functions remains challenging. Here, we introduce GESIAP3.0, an advanced, third-generation image analysis program based on genetically encoded sensors. This tool enables precise quantitative analysis of transmission in both awake, freely moving animals and immobilized subjects. GESIAP3.0 incorporates movement correction algorithms that effectively eliminate image displacement in behaving animals while optimizing synaptic information extraction and simplifying computations on commodity computers. Quantitative analysis of cholinergic, dopaminergic, and serotonergic transmission, corrected for tissue movement, revealed synaptic properties consistent with measurements from ex vivo wide-field and in vivo two-photon imaging under stable conditions. This validates the applicability of GESIAP3.0 for analyzing synaptic properties of neuromodulatory transmission in behaving animals.

bioengineering↗

bioRxiv2024

Integration of protein and coding sequences enables mutual augmentation of the language model

Recent language models have significantly accelerated our understanding on the massive biological data, using protein or DNA/RNA sequences as a single-language modality. Here we present a dual-language foundation model, which integrates both protein and coding sequences (CDS) for pre-training. Compared to the benchmark models, it shows a superior performance up to [~]20% on both protein and mRNA-related discriminative tasks, and gains the capacity to de novo generate coding sequences of [~]50% increased protein yield. Moreover, the model also possesses the knowledge transferability from the pre-training data to the upstream 5 untranslated regions. These findings indicate the intrinsic correlations between protein and its CDS, as well as the coding region and beyond. It provides a new paradigm that leverages the multiple-language foundation model to interpret the hidden context of distinct corpora/biological languages, which could be further applied to mine the yet-unknown biological information/correlation beyond the Central Dogma.

bioinformatics↗

bioRxiv2024

ORCO: Ollivier-Ricci Curvature-Omics: an unsupervised method for analyzing robustness in biological systems

Although recent advanced sequencing technologies have improved the resolution of genomic and proteomic data to better characterize molecular phenotypes, efficient computational tools to analyze and interpret the large-scale omic data are still needed. To address this, we have developed a network-based bioinformatic tool called Ollivier-Ricci curvature-omics (ORCO). ORCO incorporates gene interaction information with omic data into a biological network, and computes Ollivier-Ricci curvature (ORC) values for individual interactions. ORC, an edge-based measure, indicates network robustness and captures global gene signaling changes in functional cooperation using a consistent information passing measure, thereby helping identify therapeutic targets and regulatory modules in biological systems. This tool can be applicable to any data that can be represented as a network. ORCO is an open-source Python package and publicly available on GitHub at https://github.com/aksimhal/ORC-Omics.

bioinformatics↗

bioRxiv2024

A Modular Bacteriophage T4 Nanoparticle Platform Enables Rapid Design of Completely Protective Multivalent Mucosal Dual Vaccine Against COVID-19 and Flu

A multivalent, rapidly deployable, mucosal vaccine platform is desperately needed to prevent the acquisition and transmission of respiratory infections during epidemics and pandemics. We present one such bacteriophage T4-based platform, and design of dual COVID-19-Flu mucosal vaccines by exploiting its unique architecture. These include: T4s natural affinity for nasal mucosa, flexible engineering to incorporate multiple antigens, and repeat and symmetric epitope presentation for enhanced B cell responses. Hundreds of SARS-CoV-2 spike trimers and nucleocapsid proteins, and influenza hemagglutinin trimers and M2e peptides, were incorporated into a single phage, creating the highest density nanoparticle presentation yet reported. Intranasal administration of adjuvant-free vaccine induced robust mucosal immunity in mice including, neutralizing antibody and secretory IgA, lung-resident CD4+/CD8+ T cells, diverse memory B cells, and complete protection against SARS-CoV-2 and influenza challenges. The noninfectious T4 phage offers an extraordinary platform to rapidly design potent mucosal vaccines against emerging bacterial and viral threats.

microbiology↗

bioRxiv2024

A Wearable Mindfulness Brain-Computer Interface for Alleviating Car Sickness

Car sickness, an enormous vehicular travel challenge, affects a significant proportion of the population. Pharmacological interventions are limited by adverse side effects, and effective nonpharmacological alternatives remain to be identified. Here, we introduce a novel attention shifting method based on a closed-loop, artificial intelligence (AI)-driven, wearable mindfulness brain-computer interface (BCI) to alleviate car sickness. As the user performs an attentional task, i.e., focusing on breathing as in mindfulness, with a wearable headband, the BCI collects and analyses electroencephalography (EEG) data via a convolutional neural network to assess the users mindfulness state and provide real-time audiovisual feedback. This approach might sustainedly shift the users attention from physiological discomfort towards the BCI-based mindfulness practices, thereby mitigating car sickness symptoms. The efficacy of the proposed method was rigorously evaluated in two real-world experiments, namely, short and long car rides, with a large cohort of more than 100 participants susceptible to car sickness. Remarkably, over 83% of the participants rated the BCI-based attention shifting as effective, with significant reductions in car sickness severity, particularly in individuals with severe symptoms. Furthermore, EEG data analysis revealed a neurobiological signature of car sickness, which provided mechanistic insights into the efficacy of the BCI-based attention shifting for alleviating car sickness. This study proposed the first large-scale validated, nonpharmacological and wearable intervention method and system for car sickness, with the potential to transform the travel experiences of hundreds of millions of people suffering from car sickness, which also represents a new application of BCI technology.

bioengineering↗

bioRxiv2024

De novo design of proteins that bind naphthalenediimides, powerful photooxidants with tunable photophysical properties

De novo protein design provides a framework to test our understanding of protein function and to build proteins with cofactors and functions not found in nature. Here, we report the design of proteins designed to bind powerful photooxidants and the evaluation of the use of these proteins to generate diffusible small molecule reactive species for applications in proximity labeling. Because excited state dynamics are influenced by the dynamics and hydration of a photo-oxidants environment, it was important to not only design a binding site, but also to evaluate its dynamic properties. Thus, we used computational design in conjunction with molecular dynamics (MD) simulations to design a protein, designated NBP (NDI Binding Protein) that held a naphthalenediimide (NDI), a powerful photooxidant, in a programable molecular environment. Solution NMR confirmed the structure of the complex. We evaluated two NDI cofactors in this de novo protein, using ultra-fast pump-probe spectroscopy to evaluate light-triggered intra- and intermolecular electron transfer function. Moreover, we demonstrated the utility of this platform to activate multiple molecular probes for protein proximity labeling.

biophysics↗

bioRxiv2024

Change in brain molecular landscapes following electrical stimulation of the nucleus accumbens

Deep brain stimulation (DBS) targeting the nucleus accumbens (NAc) is a promising therapeutic intervention for treatment-resistant neuropsychiatric disorders such as depression, anxiety, and addiction. However, the molecular mechanisms underlying the clinical efficacy of NAc DBS remain largely unknown. One approach to address this question is by performing spatial gene expression analysis on cells located in different regions of the same circuit following NAc DBS. In this study, we utilized high-resolution spatial transcriptomics (Stereo-seq) to investigate gene expression changes induced by NAc DBS in the mouse brain. Mice were randomly allocated to received continuous electrical stimulation (0.1 mA, 130 Hz) or sham treatment (electrode implanted, no electrical stimulation given) for one week, and subsequent Stereo-seq analysis identified differentially expressed genes (DEGs) across various brain regions. Our findings reveal widespread alterations in synaptic function and neuronal connectivity, particularly in glutamate receptor-expressing neurons in the NAc, which play a key role in the reward circuitry. Functional enrichment analysis highlighted changes in transporter activity and glutamate receptor binding in brain regions such as the anterior cingulate cortex and lateral septal nucleus. Single-cell resolution mapping further identified key molecular players, including Nlgn1, Snca, PDE10a, and Syt1, which are critical for synaptic plasticity and neurotransmitter release, and have been implicated in various psychiatric disorders. These findings shed light on the molecular underpinnings of NAc DBS and provide insights into its therapeutic potential in modulating neural circuits associated with neuropsychiatric disorders.

molecular biology↗

bioRxiv2024

MDA5 ISGylation is crucial for immune signaling to control viral replication and pathogenesis

The posttranslational modification (PTM) of innate immune sensor proteins by ubiquitin or ubiquitin-like proteins is crucial for regulating antiviral host responses. The cytoplasmic dsRNA receptor melanoma differentiation-associated protein 5 (MDA5) undergoes several PTMs including ISGylation within its first caspase activation and recruitment domain (CARD), which promotes MDA5 signaling. However, the relevance of MDA5 ISGylation for antiviral immunity in an infected organism has been elusive. Here, we generated knock-in mice (MDA5K23R/K43R) in which the two major ISGylation sites, K23 and K43, in MDA5 were mutated. Primary cells derived from MDA5K23R/K43R mice exhibited abrogated endogenous MDA5 ISGylation and an impaired ability of MDA5 to form oligomeric assemblies leading to blunted cytokine responses to MDA5 RNA-agonist stimulation or infection with encephalomyocarditis virus (EMCV) or West Nile virus. Phenocopying MDA5-/- mice, the MDA5K23R/K43R mice infected with EMCV displayed increased mortality, elevated viral titers, and an ablated induction of cytokines and chemokines compared to WT mice. Molecular studies identified human HERC5 (and its functional murine homolog HERC6) as the primary E3 ligases responsible for MDA5 ISGylation and activation. Taken together, these findings establish the importance of CARD ISGylation for MDA5-mediated RNA virus restriction, promoting potential avenues for immunomodulatory drug design for antiviral or anti-inflammatory applications. Significance StatementThe work by many groups demonstrated the important role of ubiquitination in modulating the activity of innate immune sensors. In contrast, little is still known about the significance of ISGylation in immune receptor regulation. In this study, we generated knock-in mice in which the two major ISGylation sites of the RNA sensor MDA5 were mutated. Cells from these MDA5-ISGylation-defective mice showed impaired MDA5 oligomerization and antiviral signaling as compared to WT mice. Virus-infected MDA5 knock-in mice displayed ablated antiviral responses, uncontrolled viral replication, and higher mortality. Our study identified HERC5 as the E3 ligase responsible for MDA5 ISGylation and activation. These data may offer opportunities for immune-based antiviral design or ways to alleviate inflammatory diseases associated with overzealous MDA5 activation.

immunology↗

bioRxiv2024

BRD4 expression in microglia supports recruitment of T cells into the CNS and exacerbates EAE

In EAE, a mouse model of multiple sclerosis, immunization with MOG autoantigen results in the generation of Th1/Th17 T cells in the periphery. MOG-specific T cells then invade into the central nervous system (CNS), resulting in neuronal demyelination. Microglia, innate immune cells in the CNS are known to regulate various neuronal diseases. However, the role of microglia in EAE has remained elusive. BRD4 is a BET protein expressed in microglia, whether BRD4 in microglia contributes to EAE has not been determined. We show that EAE pathology was markedly reduced with microglia-specific Brd4 conditional knockout (cKO). In these mice, microglia- T cell interactions were greatly reduced, leading to the lack of T cell reactivation. Microglia specific transcriptome data showed downregulation of genes required for interaction with and reactivation of T cells in Brd4 cKO samples. In summary, BRD4 plays a critical role in regulating microglia function in normal and EAE CNS. SummaryThis study demonstrates that in a EAE model, microglia-specific Brd4 conditional knockout mice were defective in expressing genes required for microglia- T cells interaction and those involved in neuroinflammation, and demyelination resulting in fewer CNS T cell invasion and display marked reduction in EAE pathology.

neuroscience↗

bioRxiv2024

ElixirSeeker: A Machine Learning Framework Utilizing Attention-Driven Fusion of Molecular Fingerprints for the Discovery of Anti-Aging Compounds

Despite the growing interest in anti-aging drug development, high cost and low success rate pose a significant challenge. We present ElixirSeeker, a new machine-learning framework designed to help speed up the discovery of potential anti-aging compounds by utilizing the attention-driven fusion of molecular fingerprints. Our approach integrates molecular fingerprints generated by different algorithms and utilizes XGBoost to select optimal fingerprint lengths. Subsequently, we assign weights to the molecular fingerprints and employ Kernel Principal Component Analysis (KPCA) to reduce dimensionality, integrating different attention-driven methods. We trained the algorithm using DrugAge database. Our comprehensive analyses demonstrate that 64-bit Attention-ElixirFP maintains high predictive accuracy and F1 score while minimizing computational cost. Using ElixirSeeker to screen external compound databases, we identified a number of promising candidate anti-aging drugs. We tested top 6 hits and found that 4 of these compounds extend the lifespan of Caenorhabditis elegans, including Polyphyllin , Medrysone, Thymoquinone and Medrysone. This study illustrates that attention-driven fusion of fingerprints maximizes the learning of molecular activity features, providing a novel approach for high-throughput machine learning discovery of anti-aging molecules.

systems biology↗

bioRxiv2024

G3BP1 Maintains Vascular Endothelial Barrier Integrity by Negatively Regulating the MYD88-ARNO-ARF6 Signaling Pathway

Endothelial permeability is essential for vascular function. This process is regulated by intercellular junctions, including adherens junctions (AJs) and tight junctions (TJs), which form the endothelial barrier and dynamically connect adjacent cells. However, the mechanisms that control endothelial permeability are not fully understood. We investigated the role of the RNA-binding protein G3BP1 in regulating endothelial permeability. We examined the effects of Loss of g3bp1 in conditional knockout mice and primary human HUVEC cells. We analyzed endothelial barrier integrity and permeability, focusing on AJ and TJ expression, under both normal and LPS-induced inflammatory conditions. Loss of g3bp1 in vascular endothelial cells decreased AJ and TJ expression, compromised barrier integrity, and increased permeability. These effects were exacerbated under LPS-induced inflammatory conditions. Loss of g3bp1 also increased the expression of MYD88, ARNO, and ARF6, and enhanced ARF6 activity. Mechanistically, G3BP1 bound to and stabilized MYD88 mRNA, negatively regulating the MYD88-ARNO-ARF6 signaling pathway. Inhibiting this pathway by reducing MYD88 or ARF6 expression, or inhibiting ARNO activity, restored AJ/TJ expression and barrier function in G3BP1-deficient models. Our findings identify G3BP1 as a novel regulator of vascular endothelial permeability. G3BP1 acts by negatively regulating the MYD88-ARNO-ARF6 signaling pathway. Targeting G3BP1 may be a potential therapeutic strategy for diseases associated with endothelial barrier dysfunction.

physiology↗