Biology subjects

Zhang, H.

Publications and source records attributed to Zhang, H..

At least 865 records · Page 48Linked to original sources

bioRxiv2023

Protein language model-based end-to-end type II polyketide prediction without sequence alignment

Natural products are important sources for drug development, and the precise prediction of their structures assembled by modular proteins is an area of great interest. In this study, we introduce DeepT2, an end-to-end, cost-effective, and accurate machine learning platform to accelerate the identification of type II polyketides (T2PKs), which represent a significant portion of the natural product world. Our algorithm is based on advanced natural language processing models and utilizes the core biosynthetic enzyme, chain length factor (CLF or KS{beta}), as computing inputs. The process involves sequence embedding, data labeling, classifier development, and novelty detection, which enable precise classification and prediction directly from KS{beta} without sequence alignments. Combined with metagenomics and metabolomics, we evaluated the ability of DeepT2 and found this model could easily detect and classify KS{beta} either as a single sequence or a mixture of bacterial genomes, and subsequently identify the corresponding T2PKs in a labeled categorized class or as novel. Our work highlights deep learning as a promising framework for genome mining and therefore provides a meaningful platform for discovering medically important natural products.

evolutionary biology↗

bioRxiv2023

The cation channel mechanisms of subthreshold inward depolarizing currents in the VTA dopaminergic neurons and their roles in the depression-like behavior

The slow-intrinsic-pacemaker dopaminergic (DA) neurons originating in the ventral tegmental area (VTA) are implicated in various mood- and emotion-related disorders, such as anxiety, fear, stress and depression. Abnormal activity of projection-specific VTA DA neurons is the key factor in the development of these disorders. Here, we describe the crucial role for the NALCN and TRPC6, non-selective cation channels in mediating the subthreshold inward depolarizing current and driving the firing of action potentials of VTA DA neurons in physiological condition. Furthermore, we demonstrate that down-regulation of TRPC6 protein expression in the VTA DA neurons likely contributes to the reduced activity of projection-specific VTA DA neuron in chronic mild unpredictable stress (CMUS) depressive mice. In consistent with these, selective knockdown of TRPC6 channels in the VTA DA neurons conferred mice with depression-like behavior. This current study suggests down-regulation of TRPC6 expression/function is involved in reduced VTA DA neuron firing and chronic stress-induced depression-like behavior of mice.

neuroscience↗

bioRxiv2023

Sterile Soil as Prebiotics Mitigate Intergenerational Loss of Gut Microbial Diversity and Anxiety-Like Behavior Induced by Antibiotics in mice

The decline in gut microbial diversity of modern human is closely associated with the rising prevalence of various diseases. It is imperative to investigate the underlying causes of gut microbial loss and the rescue measures. Although the impact of non-perinatal antibiotic use on gut microbiota has been recognized, its intergenerational effects remain unexplored. Our previous research has highlighted soil in the farm environment as a key prebiotic for gut microbiome health by restoring gut microbial diversity and balance. In this study, we investigated the intergenerational consequences of antibiotic exposure and the therapeutic potential of soil prebiotics. We treated mice with vancomycin and streptomycin for 2 weeks continuously, followed by 4-8 weeks of withdrawal period before breeding. The process was repeated across 3 generations. Half of the mice in each generation received an oral soil prebiotic intervention. We assessed gut microbial diversity, anxiety behavior, microglia reactivity, and gut barrier integrity across generations. The antibiotics exposure led to a decrease in gut microbial diversity over generations, along with aggravated anxiety behavior, microglia abnormalityies, and altered intestinal tight junction protein expression. Notably, the third generation of male mice exhibited impaired reproductive capacity. Oral sterile soil intervention restored gut microbial diversity in adult mice across generations, concomitantly rescuing abnormalities in behavior, microglia activity, and intestinal barrier integrity. In conclusion, this study simulated an important process of the progressive loss gut microbiota diversity in modern human and demonstrated the potential of sterile soil as a prebiotic to reverse this process. The study provides a theoretical and experimental basis for the research and therapeutic interventions targeting multiple modern chronic diseases related to intestinal microorganisms.

microbiology↗

bioRxiv2023

Engineering Nme2Cas9 Adenine Base Editors with Improved Activity and Targeting Scope

Nme2Cas9 has been established as a genome editing platform with compact size, high accuracy, and broad targeting range, including single-AAV-deliverable adenine base editors. Here, we have engineered Nme2Cas9 to further increase the activity and targeting scope of compact Nme2Cas9 base editors. We first used domain insertion to position the deaminase domain nearer the displaced DNA strand in the target-bound complex. These domain-inlaid Nme2Cas9 variants exhibited shifted editing windows and increased activity in comparison to the N-terminally fused Nme2-ABE. We next expanded the editing scope by swapping the Nme2Cas9 PAM-interacting domain with that of SmuCas9, which we had previously defined as recognizing a single-cytidine PAM. We used these enhancements to correct two common MECP2 mutations associated with Rett syndrome with little or no bystander editing. Finally, we validated domain-inlaid Nme2-ABEs for single-AAV delivery in vivo.

molecular biology↗

bioRxiv2023

ME-Bayes SL: Enhanced Bayesian Polygenic Risk Prediction Leveraging Information across Multiple Ancestry Groups

Polygenic risk scores (PRS) are now showing promising predictive performance on a wide variety of complex traits and diseases, but there exists a substantial performance gap across different populations. We propose MUSSEL, a method for ancestry-specific polygenic prediction that borrows information in the summary statistics from genome-wide association studies (GWAS) across multiple ancestry groups. MUSSEL conducts Bayesian hierarchical modeling under a MUltivariate Spike-and-Slab model for effect-size distribution and incorporates an Ensemble Learning step using super learner to combine information across different tuning parameter settings and ancestry groups. In our simulation studies and data analyses of 16 traits across four distinct studies, totaling 5.7 million participants with a substantial ancestral diversity, MUSSEL shows promising performance compared to alternatives. The method, for example, has an average gain in prediction R2 across 11 continuous traits of 40.2% and 49.3% compared to PRS-CSx and CT-SLEB, respectively, in the African Ancestry population. The best-performing method, however, varies by GWAS sample size, target ancestry, underlying trait architecture, and the choice of reference samples for LD estimation, and thus ultimately, a combination of methods may be needed to generate the most robust PRS across diverse populations.

genetics↗

bioRxiv2023

A new tractable method for generating Human Alveolar Macrophage Like cells in vitro to study lung inflammatory processes and diseases

Alveolar macrophages (AMs) are unique lung resident cells that contact airborne pathogens and environmental particulates. The contribution of human AMs (HAM) to pulmonary diseases remains poorly understood due to difficulty in accessing them from human donors and their rapid phenotypic change during in vitro culture. Thus, there remains an unmet need for cost-effective methods for generating and/or differentiating primary cells into a HAM phenotype, particularly important for translational and clinical studies. We developed cell culture conditions that mimic the lung alveolar environment in humans using lung lipids, i.e., Infasurf (calfactant, natural bovine surfactant) and lung-associated cytokines (GM-CSF, TGF-{beta}, and IL-10) that facilitate the conversion of blood-obtained monocytes to an AM-Like (AML) phenotype and function in tissue culture. Similar to HAM, AML cells are particularly susceptible to both Mycobacterium tuberculosis and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. This study reveals the importance of alveolar space components in the development and maintenance of HAM phenotype and function, and provides a readily accessible model to study HAM in infectious and inflammatory disease processes, as well as therapies and vaccines. IMPORTANCEMillions die annually from respiratory disorders. Lower respiratory track gas-exchanging alveoli maintain a precarious balance between fighting invaders and minimizing tissue damage. Key players herein are resident AMs. However, there are no easily accessible in vitro models of HAMs, presenting a huge scientific challenge. Here we present a novel model for generating AML cells based on differentiating blood monocytes in a defined lung component cocktail. This model is non-invasive, significantly less costly than performing a bronchoalveolar lavage, yields more AML cells than HAMs per donor and retains their phenotype in culture. We have applied this model to early studies of M. tuberculosis and SARS-CoV-2. This model will significantly advance respiratory biology research.

immunology↗

bioRxiv2023

HCV E1 influences the fitness landscape of E2 and may enhance escape from E2-specific antibodies

The Hepatitis C virus (HCV) envelope glycoprotein E1 forms a noncovalent heterodimer with E2, the main target of neutralizing antibodies. How E1-E2 interactions influence viral fitness and contribute to resistance to E2-specific antibodies remains largely unknown. We investigate this problem using a combination of fitness landscape and evolutionary modelling. Our analysis indicates that E1 and E2 proteins collectively mediate viral fitness, and suggests that fitness-compensating E1 mutations may accelerate escape from E2-targeting antibodies. Our analysis also identifies a set of E2-specific human monoclonal antibodies that are predicted to be especially resilient to escape via genetic variation in both E1 and E2, providing directions for robust HCV vaccine development.

bioinformatics↗

bioRxiv2023

Repurposing the Memory-promoting Meclofenoxate Hydrochloride as a Treatment for Parkinson's Disease through Integrative Multi-omics analysis

Parkinson s disease (PD) is a devastating neurodegenerative disorder with growing prevalence worldwide and, as yet, no effective treatment. Drug repurposing promises to be invaluable for the identification of novel therapeutics for the treatment of PD due to the associated shortened drug development time, fewer safety concerns, and reduced costs. Here, we compiled gene expression data from 1,231 healthy human brains and 357 PD patients across ethnicities, brain regions, Braak stages, and disease status. By integrating them with multiple-source PD-associated genomic data, we found a conserved PD-associated gene co-expression module, and its alignment with the CMAP database successfully identified 15 drug candidates. Among these, we selected meclofenoxate hydrochloride (MH) and sodium phenylbutyrate (SP) for experimental validation because they are capable of passing through the blood brain barrier. In primary neurons, MH was found to prevent the neuronal death and synaptic damage associated with PD and to reverse the abnormal mitochondrial metabolism caused by PD. In hippocampal tissues, MH and SP were found to prevent the destruction of mitochondria, to reduce lipid peroxidation and to protect dopamine synthesis by PET-CT examination, malondialdehyde (MAD) testing and glutathione (GSH) testing, and immunohistochemical tests. Finally, MH was found to have the ability to improve gait behavior, and reduce anhedonic and depressive-like behaviors that are characteristics of PD mice. Taken together, our findings support the contention that MH may have the potential to ameliorate PD by improving mitochondrial metabolism and brain function.

biochemistry↗

bioRxiv2023

Using macromolecular electron densities to improve the enrichment of active compounds in virtual screening

The quest for more effective virtual screening algorithms is hindered by the scarcity of training data, calling for innovative approaches. This study presents the first use of experimental electron density (ED) data for improving active compound enrichment in virtual screening, supported by EDs ability to reflect the time-averaged behavior of ligands and solvents in the binding pocket. Experimental ED-based grid matching score (ExptGMS) was developed to score compounds by measuring the degree of matching between their binding conformations and a series of multi-resolution experimental ED grids. The efficiency of ExptGMS was validated using both in-silico tests with the Directory of Useful Decoys-Enhanced dataset and wet-lab tests on Covid-19 3CLpro-inhibitors. ExptGMS improved the active compound enrichment in top-ranked molecules by approximately 20%. Furthermore, ExptGMS helped identify four new and active inhibitors of 3CLpro, with the top showing an IC50 value of 1.9 {micro}M. To facilitate the use of ExptGMS, we developed an online database containing experimental ED grids for over 17,000 proteins.

bioinformatics↗

bioRxiv2023

TTG2 defines trichome cell shape by modulating microtubules and actin cytoskeleton in Arabidopsis

The Arabidopsis TRANSPARENT TESTA GLABRA2 (TTG2) gene encodes a WRKY transcription factor that regulates a range of development events like trichome, seed coat, and atrichoblasts formation. Loss-of-function of TTG2 was previously shown to reduce or eliminate trichome branching. Here, we report the identification of a new allele of TTG2, ttg2-6. In contrast to the ttg2 mutants described before, ttg2-6 displays unique trichome phenotypes. Some ttg2-6 mutant trichomes are hyperbranched, whereas others are hypobranched, distorted, or clustered. Further, we found that in addition to specifically activating R3 MYB transcription factor TRIPTYCHON (TRY) to promote trichome branching, TTG2 also integrates cytoskeletal signaling to regulate trichome morphogenesis. The ttg2-6 trichomes display aberrant cortical microtubules (cMTs) and cortical actin filaments (F-actin) configurations. Moreover, genetic and biochemical analysis showed that TTG2 could directly bind and regulate the expression of BRICK1 (BRK1), a subunit of the actin nucleation promoting complex SCAR/WAVE. Collectively, taking advantage of ttg2-6, we uncovered new functions for TTG2 in facilitating cMT and F-actin cytoskeleton-dependent trichome development. Our evidence for a direct relationship between TTG2 and cytoskeletal regulators establishes an unprecedented understanding of cellular signaling events downstream of the core transcriptional regulation during trichome development in Arabidopsis.

developmental biology↗

bioRxiv2023

Distinct Myeloid Derived Suppressor Cell Populations Promote Tumor Aggression in Glioblastoma

The diversity of genetic programs and cellular plasticity of glioma-associated myeloid cells, and thus their contribution to tumor growth and immune evasion, is poorly understood. We performed single cell RNA-sequencing of immune and tumor cells from 33 glioma patients of varying tumor grades. We identified two populations characteristic of myeloid derived suppressor cells (MDSC), unique to glioblastoma (GBM) and absent in grades II and III tumors: i) an early progenitor population (E-MDSC) characterized by strong upregulation of multiple catabolic, anabolic, oxidative stress, and hypoxia pathways typically observed within tumor cells themselves, and ii) a monocytic MDSC (M-MDSC) population. The E-MDSCs geographically co-localize with a subset of highly metabolic glioma stem-like tumor cells with a mesenchymal program in the pseudopalisading region, a pathognomonic feature of GBMs associated with poor prognosis. Ligand-receptor interaction analysis revealed symbiotic cross-talk between the stemlike tumor cells and E-MDSCs in GBM, whereby glioma stem cells produce chemokines attracting E-MDSCs, which in turn produce growth and survival factors for the tumor cells. Our large-scale single-cell analysis elucidated unique MDSC populations as key facilitators of GBM progression and mediators of tumor immunosuppression, suggesting that targeting these specific myeloid compartments, including their metabolic programs, may be a promising therapeutic intervention in this deadly cancer. One-Sentence SummaryAggressive glioblastoma harbors two unique myeloid populations capable of promoting stem-like properties of tumor cells and suppressing T cell function in the tumor microenvironment.

immunology↗

bioRxiv2023

SLC15A4 controls endolysosomal TLR7-9 responses by recruiting the innate immune adaptor TASL.

Nucleic acid sensing by endolysosomal Toll-like receptors (TLRs) plays a crucial role in innate immune responses to invading pathogens. In contrast, aberrant activation of these pathways is associated with several autoimmune diseases, such as systemic lupus erythematosus (SLE). The endolysosomal solute carrier family 15 member 4 (SLC15A4) is required for TLR7, TLR8 and TLR9-induced inflammatory responses and for disease development in different SLE models. SLC15A4 has been proposed to affect TLR7-9 activation through its transport activity, as well as by assembling in an IRF5-activating signalling complex with the innate immune adaptor TASL, but the relative contribution of these different functions remains unclear. Here we show that the essential role of SLC15A4 is to recruit TASL to the endolysosomal compartment, while its transport activity is dispensable. Targeting of TASL to the endolysosomal compartment is sufficient to rescue TLR7-9-induced IRF5 activation in SLC15A4-deficient cells. In line with this, lysosomal-localized TASL restored proinflammatory cytokines and type I interferon responses in absence of SLC15A4. Our study reveals that SLC15A4 acts as a signalling scaffold and that this transport-independent function is essential to control TLR7-9-mediated inflammatory responses. These findings further support targeting the SLC15A4-TASL complex as a potential therapeutic strategy for SLE and related diseases.

immunology↗

bioRxiv2023

Distance-dependent reconfiguration of hubs in Alzheimer's disease:a cross-tissue functional network study

The hubs of the intra-grey matter (GM) network were sensitive to anatomical distance and susceptible to neuropathological damage. However, few studies examined the hubs of cross-tissue distance-dependent networks and their changes in Alzheimers disease (AD). Using resting-state fMRI data of 30 AD patients and 37 normal older adults (NC), we constructed the cross-tissue networks based on functional connectivity (FC) between GM and white matter (WM) voxels. In the full-ranged and distance-dependent networks (characterized by gradually increased Euclidean distances between GM and WM voxels), their hubs were identified with weight degree metrics (frWD and ddWD). We compared these WD metrics between AD and NC; using the resultant abnormal WDs as the seeds, we performed seed-based FC analysis. With increasing distance, the GM hubs of distance-dependent networks moved from the medial to lateral cortices, and the WM hubs spread from the projection fibers to longitudinal fascicles. Abnormal ddWD metrics in AD were primarily located in the hubs of distance-dependent networks around 20-100mm. Decreased ddWDs were located in the left corona radiation (CR), which had decreased FCs with the executive networks GM regions in AD. Increased ddWDs were located in the posterior thalamic radiation (PTR) and the temporal-parietal-occipital junction (TPO), and their FCs were larger in AD. Increased ddWDs were shown in the sagittal striatum, which had larger FCs with the salience networks GM regions in AD. The reconfiguration of cross-tissue distance-dependent networks possibly reflected the disruption in the neural circuit of executive function and the compensatory changes in the neural circuits of visuospatial and social-emotional functions in AD.

neuroscience↗

bioRxiv2023

Neural Mechanism Underlying NEergic Neurons-Modulated The Arousal Associated With Midazolam Anesthesia

The advent of midazolam holds profound implications for modern clinical practice. The hypnotic and sedative effects of midazolam afford it broad clinical applicability. However, the specific mechanisms underlying the modulation of altered consciousness by midazolam remain elusive. Herein, using pharmacology, optogenetics, chemogenetics, fiber photometry, and gene knockdown, we revealed the role of locus coeruleus (LC)-ventrolateral preoptic nucleus (VLPO) noradrenergic neural circuit in regulating midazolam-induced altered consciousness. This effect was mediated by 1 adrenergic receptors. Moreover, gamma-aminobutyric acid receptor type A (GABAA-R) represents a mechanistically crucial binding site in the LC for midazolam. Our findings will provide novel insights into the neural circuit mechanisms underlying the recovery of consciousness after midazolam administration and will help guide the timing of clinical dosing and propose effective intervention targets for timely recovery from midazolam-induced loss of consciousness.

neuroscience↗

bioRxiv2023

DeepBindGCN: Integrating Molecular Vector Representation with Graph Convolutional Neural Networks for Accurate Protein-Ligand Interaction Prediction

The core of large-scale drug virtual screening is to accurately and efficiently select the binders with high affinity from large libraries of small molecules in which nonbinders are usually dominant. The protein pocket, ligand spatial information, and residue types/atom types play a pivotal role in binding affinity. Here we used the pocket residues or ligand atoms as nodes and constructed edges with the neighboring information to comprehensively represent the protein pocket or ligand information. Moreover, we find that the model with pre-trained molecular vectors performs better than the onehot representation. The main advantage of DeepBindGCN is that it is non-dependent on docking conformation and concisely keeps the spatial information and physical-chemical feature. Notably, the DeepBindGCN_BC has high precision in many DUD.E datasets, and DeepBindGCN_RG achieve a very low RMSE value in most DUD.E datasets. Using TIPE3 and PD-L1 dimer as proof-of-concept examples, we proposed a screening pipeline by integrating DeepBindGCN_BC, DeepBindGCN_RG, and other methods to identify strong binding affinity compounds. In addition, a DeepBindGCN_RG_x model has been used for comparing performance with other methods in PDBbind v.2016 and v.2013 core set. It is the first time that a non-complex dependent model achieves an RMSE value of 1.3843 and Pearson-R value of 0.7719 in the PDBbind v.2016 core set, showing comparable prediction power with the state-of-the-art affinity prediction models that rely upon the 3D complex. Our DeepBindGCN provides a powerful tool to predict the protein-ligand interaction and can be used in many important large-scale virtual screening application scenarios.

bioinformatics↗

bioRxiv2023

Self-delivering CRISPR RNAs for AAV Co-delivery and Genome Editing in vivo

Guide RNAs offer programmability for CRISPR-Cas9 genome editing but also add challenges for delivery. Chemical modification, which has been key to the success of oligonucleotide therapeutics, can enhance the stability, distribution, cellular uptake, and safety of nucleic acids. Previously, we engineered heavily and fully modified SpyCas9 crRNA and tracrRNA, which showed enhanced stability and retained activity when delivered to cultured cells in the form of the ribonucleoprotein complex. In this study, we report that a short, fully stabilized oligonucleotide (a "protecting oligo"), which can be displaced by tracrRNA annealing, can significantly enhance the potency and stability of a heavily modified crRNA. Furthermore, protecting oligos allow various bioconjugates to be appended, thereby improving cellular uptake and biodistribution of crRNA in vivo. Finally, we achieved in vivo genome editing in adult mouse liver and central nervous system via co-delivery of unformulated, chemically modified crRNAs with protecting oligos and AAV vectors that express tracrRNA and either SpyCas9 or a base editor derivative. Our proof-of-concept establishment of AAV/crRNA co-delivery offers a route towards transient editing activity, target multiplexing, guide redosing, and vector inactivation.

molecular biology↗

bioRxiv2023

Coupling of Slack and NaV1.6 sensitizes Slack to quinidine blockade and guides anti-seizure strategy development

Quinidine has been used as an anticonvulsant to treat patients with KCNT1-related epilepsy by targeting gain-of-function KCNT1 pathogenic mutant variants. However, the detailed mechanism underlying quinidines blockade against KCNT1 (Slack) remains elusive. Here, we report a functional and physical coupling of the voltage-gated sodium channel NaV1.6 and Slack. NaV1.6 binds to and highly sensitizes Slack to quinidine blockade. Homozygous knockout of NaV1.6 reduces the sensitivity of native sodium-activated potassium currents to quinidine blockade. NaV1.6-mediated sensitization requires the involvement of NaV1.6s N-and C-termini binding to Slacks C-terminus, and is enhanced by transient sodium influx through NaV1.6. Moreover, disrupting the Slack-NaV1.6 interaction by viral expression of Slacks C-terminus can protect against SlackG269S-induced seizures in mice. These insights about a Slack-NaV1.6 complex challenge the traditional view of "Slack as an isolated target" for anti-epileptic drug discovery efforts, and can guide the development of innovative therapeutic strategies for KCNT1-related epilepsy. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/532982v3_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1127858org.highwire.dtl.DTLVardef@19ad9f4org.highwire.dtl.DTLVardef@15b5542org.highwire.dtl.DTLVardef@13a86b4_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

An Ensemble Penalized Regression Method for Multi-ancestry Polygenic Risk Prediction

Great efforts are being made to develop advanced polygenic risk scores (PRS) to improve the prediction of complex traits and diseases. However, most existing PRS are primarily trained on European ancestry populations, limiting their transferability to non-European populations. In this article, we propose a novel method for generating multi-ancestry Polygenic Risk scOres based on enSemble of PEnalized Regression models (PROSPER). PROSPER integrates genome-wide association studies (GWAS) summary statistics from diverse populations to develop ancestry-specific PRS with improved predictive power for minority populations. The method uses a combination of [L]1 (lasso) and [L]2 (ridge) penalty functions, a parsimonious specification of the penalty parameters across populations, and an ensemble step to combine PRS generated across different penalty parameters. We evaluate the performance of PROSPER and other existing methods on large-scale simulated and real datasets, including those from 23andMe Inc., the Global Lipids Genetics Consortium, and All of Us. Results show that PROSPER can substantially improve multi-ancestry polygenic prediction compared to alternative methods across a wide variety of genetic architectures. In real data analyses, for example, PROSPER increased out-of-sample prediction R2 for continuous traits by an average of 70% compared to a state-of-the-art Bayesian method (PRS-CSx) in the African ancestry population. Further, PROSPER is computationally highly scalable for the analysis of large SNP contents and many diverse populations.

genetics↗