Biology subjects

Zhang, A.

Publications and source records attributed to Zhang, A..

At least 109 records · Page 6Linked to original sources

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

Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite

Nucleotide recoding RNA sequencing methods (NR-seq; TimeLapse-seq, SLAM-seq, TUC-seq, etc.) are powerful approaches for assaying transcript population dynamics. In addition, these methods have been extended to probe a host of regulated steps in the RNA life cycle. Current bioinformatic tools significantly constrain analyses of NR-seq data. To address this limitation, we developed EZbakR, an R package to facilitate a more comprehensive set of NR-seq analyses, and fastq2EZbakR, a Snakemake pipeline for flexible preprocessing of NR-seq datasets, collectively referred to as the EZbakR suite. Together, these tools generalize many aspects of the NR-seq analysis workflow. The fastq2EZbakR pipeline can assign reads to a diverse set of genomic features (e.g., genes, exons, splice junctions, etc.), and EZbakR can perform analyses on any combination of these features. EZbakR extends standard NR-seq mutational modeling to support multi-label analyses (e.g., s4U and s6G dual labeling), and implements an improved hierarchical model to better account for transcript-to-transcript variance in metabolic label incorporation. EZbakR also generalizes dynamical systems modeling of NR-seq data to support analyses of premature mRNA processing and flow between subcellular compartments. Finally, EZbakR implements flexible and well-powered comparative analyses of all estimated parameters via design matrix-specified generalized linear modeling. The EZbakR suite will thus allow researchers to make full, effective use of NR-seq data.

bioinformatics↗

bioRxiv2024

Vispro improves imaging analysis for Visium spatial transcriptomics

Spatial transcriptomics (ST) enables the comprehensive analysis of gene expression while preserving the spatial context of tissues. The histological images accompanying ST data provide spatially cohesive information that is often challenging to capture through gene expression alone. However, analyzing such images is challenging due to the presence of fiducial markers and background regions, which can obscure important features and complicate downstream analysis. To address these challenges, we developed Vispro, an end-to-end, fully automated image processing tool tailored for 10x Visium data. Vispro integrates four key modules of fiducial marker detection, fiducial marker removal and image restoration, tissue region detection, and segmentation of disconnected tissue areas. We demonstrated that Vispro enhances the quality of ST images and improves the performance of downstream analyses, including tissue segmentation, cell segmentation, image registration, and histology-based gene imputation.

bioinformatics↗

bioRxiv2024

BEDMS: A metadata standardizer for genomic regionattributes

High-throughput sequencing technologies have generated vast omics data annotating genomic regions. A challenge arises in integrating this data because the associated metadata does not follow a uniform schema. This hinders data management, discovery, interoperability, and reusability. Existing tools that address metadata standardization issues are generally limited in scope and targeted toward specific data sets or types and are not generally applicable to custom schemas. To improve standardization of genomic interval metadata, we have developed BEDMS. We developed and evaluated several model architectures and trained models that achieved high performance on held-out training data. With a trained model, BEDMS provides users with predicted standardized metadata attributes that follow a standardized schema. Furthermore, BEDMS provides the ability to train custom models. To demonstrate, we trained BEDMS on three different schemas, allowing users to choose which schema to standardize into. We also deployed BEDMS on PEPhub, which provides a graphical user interface to allow users to standardize metadata without requiring any local training or software at all. In conclusion, BEDMS offers a practical one-stop solution for metadata management and standardization for genomic interval data.

genomics↗

bioRxiv2024

Network-driven identification of indisulam neo-substrates for targeted protein degradation

Indisulam, a DCAF15-based molecular glue degrader, induces widespread proteome changes with implications for cell division and chromosome segregation. While RBM39 and RBM23 are two well-characterized indisulam neo-substrates, additional targets likely exist. To identify those degradation targets, we applied a network-based approach to prioritize novel neo-substrates from large-scale omics data. Our approach integrates proteome-wide expression measurements with information from publicly accessible databases into a multiplex heterogeneous network. Utilizing a Random Walk with Restart algorithm, we identified a preliminary list of 30 neo-substrates. These proteins are likely interactors with DCAF15 in the presence of indisulam and are subject to subsequent degradation. Experimental validation of RBM5, one of the shortlisted candidates, confirmed its degradation in a proteasome-dependent manner, supporting its identification as a novel indisulam neo-substrate. Our work employs established network resources and analytical methods to effectively identify direct targets of indisulam molecular glue degrader. This approach is readily adaptable for exploring novel targets across other molecular glue systems, enhancing its applicability and value to the drug discovery community. SummaryMolecular glue neo-substrate identification via network analysis and proteomics profiling

bioinformatics↗

bioRxiv2024

Acute Viral Infection Accelerates Neurodegeneration in a Mouse Model of ALS

While several viral infections have been associated with amyotrophic lateral sclerosis (ALS), the mechanism(s) through which they promote disease has remained almost entirely elusive. This study investigated the impact of common, acute viral infections prior to disease onset on ALS progression in the SOD1G93A mouse model. A single sublethal infection prior to onset of ALS clinical signs was associated with markedly accelerated ALS disease progression characterized by rapid loss of hindlimb function. Prior infection resulted in gliosis in the lumbar spine and upregulation of transcriptional pathways involved in inflammatory responses, metabolic dysregulation, and muscular dysfunction. Therapeutic suppression of gliosis with an anti-inflammatory small molecule, or administration of a direct-acting antiviral, was associated with significantly improved ALS clinical signs, akin to what was observed in uninfected animals. This study provides causal and mechanistic evidence that the immune response elicited by acute viral infections may be an important etiological factor that alters ALS disease trajectory, and provides insight into novel therapeutic and preventative strategies for ALS. One Sentence SummaryAcute viral infection with influenza A virus and SARS-CoV-2 accelerates the progression of ALS in SOD1G93A mice.

immunology↗

bioRxiv2024

Decoding multicellular niche formation in the tumour microenvironment from nonspatial single-cell expression data

Accurate inference of granular cell states that co-occur within the tumour microenvironment (TME) is central to defining pro- and anti-tumour environments. Here, we describe how ecosystems of cell populations can be robustly inferred from nonspatial single-cell RNA-seq (scRNA-seq) atlases. Leveraging a unique discovery-validation setup across eight scRNA-seq datasets profiling pancreatic ductal adenocarcinoma (PDAC), we show highly consistent co-occurrence of fine-grained cell states across patients and characterize the positive predictive value of such analyses. Building on this, we develop a novel probabilistic model to quantify multi-cellular ecosystems directly from such atlas-scale scRNA-seq datasets. By mapping these ecosystems to spatial transcriptomics data, we demonstrate that such ecosystems represent bona fide spatial variation within individual tumours despite being learned from nonspatial data. Importantly, through mapping these ecosystems across two large clinical cohorts, we show they are more predictive of therapy response than any individual cell state and are associated with specific tumour somatic mutations. Together, this work lays the foundation for inferring reproducible multicellular ecosystems directly from large nonspatial scRNA-seq atlases.

bioinformatics↗

bioRxiv2024

Water availability determines plant regeneration fates

Wounding and hormones serve as diverse triggers for regeneration in animals and plants but how organisms determine regeneration outcomes remains largely unknown. Here, we demonstrated that wounded Arabidopsis tissues regenerate two distinct fates, wound-induced callus or de novo root formation, that are driven by antagonizing molecular pathways related to cambium and root development. We discovered that local water availability dictated these regeneration outcomes in Arabidopsis and tomato, with high water triggering root fate and low water initiating callus fate. Moreover, distinct spatial distributions of auxin response maxima were critical for fate progression and water availability regulated these auxin maxima through the hormones ethylene and jasmonic acid. We propose that water availability determines environmental control of regeneration plasticity with applied potential for improving regeneration in agriculture.

plant biology↗

bioRxiv2024

PRAME expression in melanoma is negatively regulated by TET2-mediated DNA hydroxymethylation

Preferentially Expressed Antigen in Melanoma (PRAME) and Ten-Eleven Translocation (TET) dioxygenase-mediated 5-hydroxymethylcytosine (5hmC) are emerging melanoma biomarkers. We observed an inverse correlation between PRAME expression and 5hmC levels in benign nevi, melanoma in situ, primary invasive melanoma, and metastatic melanomas via immunohistochemistry and multiplex immunofluorescence: nevi exhibited high 5hmC and low PRAME, whereas melanomas showed the opposite pattern. Single-cell multiplex imaging of melanoma precursors revealed that diminished 5hmC coincides with PRAME upregulation in premalignant cells. Analysis of TCGA and GTEx databases confirmed a negative relationship between TET2 and PRAME mRNA expression in melanoma. Additionally, 5hmC levels were reduced at the PRAME 5 promoter in melanoma compared to nevi, suggesting a role for 5hmC in PRAME transcription. Restoring 5hmC levels via TET2 overexpression notably reduced PRAME expression in melanoma cell lines. These findings establish a function of TET2-mediated DNA hydroxymethylation in regulating PRAME expression and demonstrate epigenetic reprogramming as pivotal in melanoma tumorigenesis. TeaserMelanoma biomarker PRAME expression is negatively regulated epigenetically by TET2-mediated DNA hydroxymethylation

cancer biology↗

bioRxiv2024

Deep Learning-based Modeling for Preclinical Drug Safety Assessment

In drug development, assessing the toxicity of candidate compounds is crucial for successfully transitioning from preclinical research to early-stage clinical trials. Drug safety is typically assessed using animal models with a manual histopathological examination of tissue sections to characterize the dose-response relationship of the compound - a timeintensive process prone to inter-observer variability and predominantly involving tedious review of cases without abnormalities. Artificial intelligence (AI) methods in pathology hold promise to accelerate this assessment and enhance reproducibility and objectivity. Here, we introduce TRACE, a model designed for toxicologic liver histopathology assessment capable of tackling a range of diagnostic tasks across multiple scales, including situations where labeled data is limited. TRACE was trained on 15 million histopathology images extracted from 46,734 digitized tissue sections from 157 preclinical studies conducted on Rattus norvegicus. We show that TRACE can perform various downstream toxicology tasks spanning histopathological response assessment, lesion severity scoring, morphological retrieval, and automatic dose-response characterization. In an independent reader study, TRACE was evaluated alongside ten board-certified veterinary pathologists and achieved higher concordance with the consensus opinion than the average of the pathologists. Our study represents a substantial leap over existing computational models in toxicology by offering the first framework for accelerating and automating toxicological pathology assessment, promoting significant progress with faster, more consistent, and reliable diagnostic processes. Live Demo: https://mahmoodlab.github.io/tox-foundation-ui/

bioinformatics↗

bioRxiv2024

Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip

As genome sequencing technologies advance, the accumulation of sequencing data in public databases necessitates more robust and adaptable data analysis workflows. Here, we present Rocketchip, which aims to offer a solution to this problem by allowing researchers to easily compare and swap out different components of ChIP-seq, CUT&RUN, and CUT&Tag data analysis, thereby facilitating the identification of reliable analysis methodologies. Rocketchip enables researchers to efficiently process large datasets while ensuring reproducibility and allowing for the reanalysis of existing data. By supporting comparative analyses across different datasets and methodologies, Rocketchip contributes to the rigor and reproducibility of scientific findings. Furthermore, Rocketchip serves as a platform for benchmarking algorithms, allowing researchers to identify the most accurate and efficient analytical approaches to be applied to their data. In emphasizing reproducibility and adaptability, Rocketchip represents a significant step towards fostering robust scientific research practices.

bioinformatics↗

bioRxiv2024

Glutamate, GABA, and dense-core vesicle secretion regulate predatory feeding in the nematode Pristionchus pacificus

Nematodes are one of the most diverse groups of organisms, found in various environments, and exhibit various feeding behaviours. Pristionchus pacificus displays two types of feeding behaviours: predatory and bacterial feeding. Previously, we showed that the neurotransmitter serotonin plays important roles in regulating predatory feeding in P. pacificus. However, the role of other neurotransmitters in predatory feeding remains unclear. Using the CRISPR/Cas9 system, we generated mutants of the dense-core vesicle (DCV)-based neuropeptide secretion system and genes related to seven neurotransmitters. Predatory assays revealed that the vesicular glutamate transporter Ppa-EAT-4, glutamic acid decarboxylase Ppa-UNC-25 which is involved in GABA synthesis, and the calcium-dependent activator protein for DCV secretion Ppa-UNC-31, play roles in predatory feeding behaviour. We assessed the pharyngeal movement necessary for predation as well as locomotion rate in these mutants. While the Ppa-eat-4 and Ppa-unc-31 mutants decreased predation movement, the Ppa-unc-25 mutant showed a reduction only in bacterial events compared to wild type animals. Additionally, Ppa-unc-25 and Ppa-unc-31 decreased in motor movement, potentially reducing predation efficiency. Together, these results suggest that glutamate, GABA and DCV secretion modulate feeding behaviours in P. pacificus. Our mutant collection of neurotransmitter-related genes will be useful for future analysis of neurobiology and behavioural evolution.

animal behavior and cognition↗

bioRxiv2024

The effect of circulating neutralizing antibodies on the replication of SARS-CoV-2 variants following post-vaccination infections.

The impact of pre-existing neutralizing antibodies (NAbs) titers on SARS-CoV-2 viral shedding dynamics in post-vaccination infection (PVI) are not well understood. We characterized viral shedding longitudinally in nasal specimens in relation to baseline (pre/peri-infection) serum neutralizing antibody titers in 125 participants infected with distinct SARS-CoV-2 variants. Among 68 participants who had received vaccinations, we quantified the effect of baseline serum NAb titers on maximum viral RNA titers and on the duration of infectivity. Baseline NAb titers were higher and efficiently targeted a broader range of variants in participants who received one or two monovalent ancestral booster vaccinations compared to those with a full primary vaccine series. In participants with Delta variant infections, baseline NAb titers targeting Delta were negatively correlated with maximum viral RNA copies. Per log10 increase in baseline NAb IC50, maximum viral load was reduced -2.43 (95% confidence interval [CI] -3.76, -1.11) log10 N copies and days of infectious viral shedding were reduced -2.79 [95% CI: -4.99, -0.60] days. By contrast, in those with Omicron infections (BA.1, BA.2, BA.4 or BA.5 lineages) baseline NAb responses against Omicron lineages did not predict viral outcomes. Our results provide robust estimates of the effect of baseline NAbs on the magnitude and duration of nasal viral replication after PVI (albeit with an unclear effect on transmission) and show how immune escape variants efficiently evade these modulating effects.

immunology↗

bioRxiv2024

Weighted variance component test for the integrative multi-omics analysis of microbiome data

Metabolic dysregulation and alterations have been linked to various diseases and conditions. Innovations in high-throughput technology now allow rapid profiling of the metabolome and metagenome -- often the gene content of bacterial populations -- for characterizing metabolism. Due to the small sample sizes and high dimensionality of the data, pathway analysis (wherein the effect of multiple genes or metabolites on an outcome is cumulatively assessed) of metabolomic data is commonly conducted and also represents a standard for metagenomic analysis. However, how to integrate both data types remains unclear. Recognizing that a metabolic pathway can be complementarily characterized by both metagenomics and metabolomics, we propose a weighted variance components framework to test if the joint effect of genes and metabolites in a biological pathway is associated with outcomes. The approach allows analytic p-value calculation, correlation between data types, and optimal weighting. Power simulations show that our approach often outperforms other strategies while maintaining type I error. The approach is illustrated on real data.

bioinformatics↗

bioRxiv2024

SLO2.1/NALCN Functional Complex Activity in Mouse Myometrial Smooth Muscle Cells During Pregnancy.

At the end of pregnancy, the uterus transitions from a quiescent to a highly contractile state. This is partly due to depolarization of the resting membrane potential in uterine (myometrial) smooth muscle cells (MSMCs). In human MSMCs, the membrane potential is regulated by a functional complex between the sodium (Na+)-activated potassium (K+) channel SLO2.1 and the Na+ Leak Channel Non-Selective (NALCN). Na+ entering through NALCN activates SLO2.1, leading to K+ efflux, membrane hyperpolarization (cells become more negative inside), and reduced contractility. Decreased SLO2.1/NALCN activity results in reduced K+ efflux, leading to membrane depolarization, Ca2+ influx via voltage-dependent calcium channels, and increased MSMC contractility. However, all of these data are from MSMCs isolated from women at term, so the role of the SLO2.1/NALCN complex early in pregnancy was speculative. To address this question here, we examined the role of the SLO2.1/NALCN complex in regulating mouse MSMC membrane potential across pregnancy. We report that Slo2.1 and Nalcn are more highly expressed in MSMCs from non-pregnant and early pregnant mice than in those from late-pregnant mice. Functional studies revealed that SLO2.1 channels mediate a significant portion of the K+ current in mouse MSMCs, particularly in cells from non-pregnant and early pregnant mice. Activation of SLO2.1 by Na+ influx through NALCN led to membrane hyperpolarization in MSMCs from early pregnancy but not in MSMCs from later pregnancy. Moreover, the NALCN/SLO2.1 complex regulates intracellular Ca2+ responses more in MSMCs from non-pregnant and early pregnancy mice than in MSMCs from late pregnancy. Together, these findings reveal that the SLO2.1/NALCN functional complex is conserved between mouse and humans and functions throughout pregnancy. This work could open avenues for targeted pharmacological interventions for pregnancy-related complications.

physiology↗

bioRxiv2024

Channel width modulates the permeability of DNA origami based nuclear pore mimics

Nucleoporins (nups) in the central channel of nuclear pore complexes (NPCs) form a selective barrier that suppresses the diffusion of most macromolecules while enabling rapid transport of nuclear transport receptors (NTRs) with bound cargos. The complex molecular interactions between nups and NTRs have been thought to underlie the gatekeeping function of the NPC. Recent studies have shown considerable variation in NPC diameter but how altering NPC diameter might impact the selective barrier properties remains unclear. Here, we build DNA nanopores with programmable diameters and nup arrangement to mimic NPCs of different diameters. We use hepatitis B virus (HBV) capsids as a model for large-size cargos. We find that Nup62 proteins form a dynamic cross-channel meshwork impermeable to HBV capsids when grafted on the interior of 60-nm wide nanopores but not in 79-nm pores, where Nup62 cluster locally. Furthermore, importin-{beta}1 substantially changes the dynamics of Nup62 assemblies and facilitates the passage of HBV capsids through NPC mimics containing Nup62 and Nup153. Our study shows the transport channel width is critical to the permeability of nup barriers and underscores the role of NTRs in dynamically remodeling nup assemblies and mediating the nuclear entry of viruses.

biophysics↗

bioRxiv2024

Deep Lineage: Single-Cell Lineage Tracing and Fate Inference Using Deep Learning

Recent advances in single-cell RNA-sequencing and lineage tracing techniques have provided valuable insights into the temporal changes in gene expression during development, tumour progression, and disease onset. However, there are few computational methods available to analyze this information to help understand multicellular dynamics. We introduce Deep Lineage, a novel deep-learning method for analyzing time-series single-cell RNA-sequencing with matched lineage-tracing data. Our method accurately predicts early cell fate biases and gene expression profiles at different time points within a clone, surpassing current state-of-the-art methods in fate prediction accuracy. Additionally, through in silico perturbations in cellular reprogramming and hematopoiesis development data, we show that Deep Lineage can accurately model dynamic multicellular responses while identifying key genes and pathways associated with cell fate determination.

bioinformatics↗

bioRxiv2024

MetaX: A peptide centric metaproteomic data analysis platform using Operational Taxa-Functions (OTF)

Metaproteomics analyzes the functional dynamics of microbial communities by identifying peptides and mapping them to the most likely proteins and taxa. The challenge in this field lies in seamlessly integrating taxonomic and functional annotations to accurately represent the contributions of individual microbial taxa to functional diversity. We introduce MetaX, a comprehensive tool for analyzing taxa-function relationships in metaproteomics by mapping peptides to their lowest common ancestors and assigning functions based on proportional thresholds, ensuring accurate peptide-level mappings. Importantly, MetaX introduces the Operational Taxa-Functions (OTF), a new conceptual unit for exploring microbial roles and interactions within ecosystems. Additionally, MetaX extends traditional taxonomic classification by adding a genome level below the species level, enhancing the accuracy of function attribution to specific genomes. We demonstrated MetaX by reanalyzing metaproteomic data from gut microbiomes exposed to various sweeteners, achieving results similar to traditional protein analysis. Furthermore, using the peptide-centric approach and OTF, we observed that Parabacteroides distasonis significantly responds to certain sweeteners, highlighting its role in modifying specific metabolic functions. With its intuitive, user-friendly interface, MetaX facilitates detailed study of the complex interactions between microbial taxa and their functions in metaproteomics. It enhances our understanding of microbial roles in ecosystems and health.

bioinformatics↗