Biology subjects

Zhang, L.

Publications and source records attributed to Zhang, L..

At least 919 records · Page 51Linked to original sources

bioRxiv2022

Fortuitous Somatic Mutations during Antibody Evolution Endow Broad Neutralization against SARS-CoV-2 Omicron Variants

Striking antibody evasion by emerging circulating SARS-CoV-2 variants drives the identification of broadly neutralizing antibodies (bNAbs). However, how a bNAb acquires increased neutralization breadth during antibody evolution is still elusive. Here, we identified a clonally-related antibody family from a convalescent individual. One of the members, XG005, exhibited potent and broad neutralizing activities against SARS-CoV-2 variants, while the other members showed significant reductions in neutralization breadth and potency, especially against the Omicron sublineages. Structural analysis visualizing the XG005-Omicron spike binding interface revealed how crucial somatic mutations endowed XG005 with greater neutralization potency and breadth. A single administration of XG005 with extended half-life, reduced antibody-dependent enhancement (ADE) effect, and increased antibody product quality, exhibited a high therapeutic efficacy in BA.2- and BA.5-challenged mice. Our results provided a natural example to show the importance of somatic hypermutation during antibody evolution for SARS-CoV-2 neutralization breadth and potency.

immunology↗

bioRxiv2022

Leptospermum extract (QV0) suppresses pleural mesothelioma tumour growth in vitro and in vivo by mitochondrial dysfunction associated apoptosis

Pleural mesothelioma (PM) is a highly aggressive, fast-growing asbestos-induced cancer with limited effective treatments. There has been an interest in using naturally occurring anticancer agents derived from plant materials for the treatment of PM. However, it is unclear if aqueous extract from the Leptospermum polygalifolium (QV0) has activity against PM. Here we investigated the anti-cancer property of QV0 in vitro and in vivo. Animals treated with Defender(R) (QV0 dietary supply) exhibited a reduced tumour size over 30 days, which was associated with an average extended of seven days mouse life. There was no liver toxicity, nor increased blood glucose post-treatment in animals treated with Defender(R). Moreover, QV0 suppressed the growth of 13 cancer cell lines in a dose-dependent manner, effective at concentrations as low as 0.02% w/v. This response was found to be associated with inhibited cell migration, proliferation, and colony formation, but without evident cell cycle alteration. We observed mitochondrial dysfunction post QV0 treatment, as evidenced by significantly decreased basal and maximal oxygen consumption rates. Significantly enhanced tumour apoptosis was observed in the Defender(R)-treated animals, correlating with mitochondrial dysfunction. To the best of our knowledge, this study constitutes the first demonstration of an improved host survival (without adverse effects) response in a QV0-treated PM mouse model, associated with an evident inhibition of PM cell growth and mitochondrial dysfunction-related enhancement of tumour apoptosis. ImportanceA major problem with cancer chemotherapy or immunotherapy is the severe adverse effects associated with normal tissue damage. PM is known to be treatment resistant and has poor a prognosis, therefore new therapeutic treatment options are urgently needed. In the present study, we explored the potential utility of a Leptospermum extract (QV0) as a treatment option for mesothelioma. We demonstrated for the first time that QV0 exhibits an anti-tumour response in mesothelioma, without any associated adverse effects observed in the PM mouse model. These findings provide a rationale for early-stage clinical trials. We anticipate that prospective translational research will lead to the clinical implementation of a novel QV0-based treatment strategy that will ultimately benefit PM patients.

cancer biology↗

bioRxiv2022

Discovering Haematoma-Stimulated Circuits for Secondary Brain Injury after Intraventricular Haemorrhage by Spatial Transcriptome Analysis

Central nervous system (CNS) diseases, such as neurodegenerative disorders and brain diseases caused by acute injuries, are important yet challenging to study due to disease leisions locations and other complexities. Utilizing the powerful spatial transcriptome analysis together with novel algorithms we developed for the study, we report here for the first time a 3D trajectory map of gene expression changes in the brain following acute neural injury using a mouse model of intraventricular haemorrhage (IVH). IVH is a common and representative complication after various acute brain injuries with severe mortality and mobility implications. Our data identified three main 3D global pseudospace-time trajectory bundles which represent the main neural circuits from the lateral ventricle to the hippocampus and primary cortex induced by experimental intraventricular haematoma stimulation. Further analysis indicated a rapid response in the primary cortex, as well as a direct and integrated effect on the hippocampus after IVH. These results are informative in understanding the pathophysiological changes, including the spatial and temporal patterns of gene expression changes, in IVH patients after acute brain injuries and strategizing more effective clinical management regimens. The bioinformatics strategies will also be useful for the study of other CNS diseases.

bioinformatics↗

bioRxiv2022

New gene evolution with subcellular expression patterns detected in PacBio-sequenced genomes of Drosophila genus

Previous studies described gene age distributions in the focal species of Drosophila melanogaster. Using third-generation PacBio technology to sequence Drosophila species we investigated gene age distribution in the two subgenera of Drosophila. Our work resulted in several discoveries. First, our data detected abundant new genes in entire Drosophila genus. Second, in analysis of subcellular expression, we found that new genes tend to secret into extracellular matrix and are involved in regulation, environmental adaption, and reproductive functions. We also found that extracellular localization for new genes provides a possible environment to promote their fast evolution. Third, old genes tend to be enriched in mitochondrion and the plasma membrane compared with young genes which may support the endosymbiotic theory that mitochondria originate from bacteria that once lived in primitive eukaryotic cells. Fourth, as gene age becomes older the subcellular compartments in which their products reside broadens suggesting that the evolution of new genes in subcellular location drives functional evolution and diversity in Drosophila species. Additionally, based on the analysis of RNA-Seq of two D. melanogaster populations, we determined a universal paradigm of "from specific to constitutive" expression pattern during the evolutionary process of new genes.

evolutionary biology↗

bioRxiv2022

Repurposing antihypertensive, lipid-lowering and antidiabetic drugs for lacunar stroke

BackgroundTo estimate the causal associations of modifiable risk factors with lacunar stroke (LS) and repurposing of common antihypertensive, lipid-lowering and antidiabetic drugs to prevent LS. MethodsThe effects of common antihypertensive, lipid-lowering and antidiabetic drugs on LS were estimated using a drug-target Mendelian randomization (MR) approach. LS data for the transethnic analysis were derived from meta-analyses comprising 7,338 cases and 254,798 controls. FindingsGenetically predicted hypertension and type 2 diabetes significantly increased LS risk. Elevated triglyceride and apolipoprotein B levels caused a 14% increased LS risk, while elevated apolipoprotein A-I and high-density lipoprotein levels caused a 12% decreased risk. Elevated triglyceride levels remained significantly associated with a higher LS risk in multivariable MR analysis (OR, 1.21; 95% CI, 1.06-1.40, P =0.005). Drug-target MR demonstrated that genetic variants mimicking calcium channel blockers most stably prevented LS (OR, 0.75; 95% CI, 0.61-0.92, P =0.006). The genetic variants at or near HMGCR (i.e., mimicking the effect of statins), NPC1L1 (mimicking the effects of ezetimibe) and APOC3 (mimicking antisense anti-apoC3 agents) were predicted to decrease LS incidence. Genetically proxied GLP1R agonism showed a marginal effect on LS, while a genetically proxied improvement in overall glycemic control was associated with a reduced LS risk (OR, 0.94; 95% CI, 0.92-0.96; P=4.58x10-7). InterpretationRepurposing several drugs with well-established safety and low costs for LS prevention in clinical practice may contribute to healthier brain aging. FundingThis study was supported by National Natural Science Foundation of China (grant numbers 8210051863).

genetics↗

bioRxiv2022

NanoTrans: an integrated computational framework for comprehensive transcriptome analyses with Nanopore direct-RNA sequencing

Nanopore direct RNA sequencing (DRS) provides the direct access to native RNA strands with full-length information, shedding light on rich qualitative and quantitative properties of gene expression profiles. Here with NanoTrans, we present an integrated computational framework that comprehensively covers all major DRS-based application scopes, including isoform clustering and quantification, poly(A) tail length estimation, RNA modification profiling, and fusion gene detection. In addition to its merit in providing such a streamlined one-stop solution, NanoTrans also shines in its workflow-orientated modular design, batch processing capability, all-in-one tabular and graphic report output, as well as automatic installation and configuration supports. Finally, by applying NanoTrans to real DRS datasets of yeast, Arabidopsis, as well as human embryonic kidney and cancer cell lines, we further demonstrated its utility, effectiveness, and efficacy across a wide range of DRS-based application settings.

bioinformatics↗

bioRxiv2022

A Brain-Wide Genome-Wide Association Study of Candidate Quantitative Trait Loci Associated with Structural and Functional Phenotypes of Pain Sensitivity

Individual pain sensitivity is influenced by many factors, such as the differentiation of brain regional features and genetic variations. However, its heritability remains largely unclear. The present study conducted a brain-wide genome-wide association study (GWAS) to explore the genetic bases of structural and functional neuroimage phenotypes of pain sensitivity. In total 432 normal participants were firstly divided into high and low pain sensitivity groups according to laser quantitative test threshold and related brain regions gray matter density (GMD) features were identified. Consequently, GWAS was performed on each GMD phenotype using quality-controlled genotypes. Based on the heatmap and hierarchical clustering results from GWAS, the right insula was selected for further refined analysis in terms of sub-regions GMD and resting-state functional connectivity (rs-FC) phenotypes. The results indicate that the right insula GMD in the high sensitivity group is significantly lower than the low sensitivity group. Also, the TT/TC group at locus rs187974 may lead to a lower GMD in the right insula than the CC group. Meanwhile, loci at gene CYP2D6 may lead to a variation of rs-FC between the right insula and left putamen. In conclusion, our study suggests multiple candidate loci associated with pain sensitivity that may influence brain phenotypes.

genomics↗

bioRxiv2022

The direct interaction with transcriptional factor TEAD4 implied a straightforward regulation mechanism of tumor suppressor NF2

As an output effecter of Hippo signaling pathway, the transcription factor TEAD and co-activator YAP play crucial functions in promoting cell proliferation and organ size. The tumor suppressor NF2 has been shown to activate LATS1/2 kinases and interplay with Hippo pathway to suppress YAP-TEAD complex. But, whether and how NF2 could directly regulate TEAD remains unknown. We identified a direct link and physical interaction between NF2 and TEAD4. NF2 interacted with TEAD4 through its FERM domain and the C-terminal tail, and decreased protein stability of TEAD4 independently of LATS1/2 and YAP. Furthermore, NF2 inhibited TEAD4 palmitoylation and retained the cytoplasmic translocation of TEAD4, resulting in ubiquitination and dysfunction of TEAD4. Moreover, the interaction with TEAD4 is required for NF2 function to suppress cell proliferation. These findings revealed a new role of NF2 as a binding partner and inhibitor of the transcription factor TEAD, and would shed light on an alternative mechanism of how NF2 functions as a tumor suppressor through the Hippo signaling cascade.

cell biology↗

bioRxiv2022

Stress-associated purinergic receptors code for fatal suicidality in the hippocampal-hypothalamic-prefrontal circuit

Imbalanced purine metabolism is a key neurological basis for suicide and mood disorders (MD), wherein purinergic receptors in stress-sensitive cerebral regions are thought to be differentially activated. A hippocampal network that links the hypothalamus and prefrontal cortex implements an affective sensation of stress. We discovered that the hippocampus encoded fatal suicidal ideations in the dentate gyrus (DG) by a considerable amount of the granule cell nuclei with P2X purinoceptor 7 (P2RX7) expression, irrespective of the underlying MD. Compared to controls, patients with MD showed microglial dyshomeostasis throughout the hippocampal formation. Strikingly, P2Y purinoceptor 12 (P2RY12)-expressing microglia with segmented processes were remarkably present in the superficial layers of the medial entorhinal cortex (mEnt) in individuals with fatal suicidality. In the hypothalamic stress-sensitive nuclei, P2RY12+ microglia were more expressed in the supraoptic nucleus in MD and even higher when fatal suicidality was present. In the prefrontal cortex, P2RX7 transcripts sharply dropped in suicidal individuals, possibly removing the prefrontal inhibition of the hippocampus and hypothalamus. Confounder analysis showed that the suicide-specific molecular features faded when the postmortem delay was prolonged. Our findings imply that fatal suicidality presents with unique neuropathological alterations. The DG and mEnt are two crucial areas for deciphering the suicidal consequences. By including brain samples from legal euthanasia donors, suicide-specific biosignatures can be maximally retained. Decoding the bioactive framework through key genes, brain regions and neurological processes involved in suicide neuropathology may provide novel therapeutic strategies for suicidal individuals who are beyond the reach of mental health care.

neuroscience↗

bioRxiv2022

An HBV mRNA vaccine with favorable virological suppression and superior immunity

BRIEF ABSTRACTHere we report on the development and comprehensive evaluations of an mRNA vaccine for chronic hepatitis B (CHB) treatment. In two different HBV carrier mouse models generated by viral vector-mediated HBV transfection (pAAV-HBV1.2 and rAAV8-HBV1.3), this vaccine demonstrates sufficient and persistent virological suppression, and robust immunogenicity in terms of induction of strong innate immune activation, high-level virus-specific antibodies, memory B cells and T cells. mRNA platform therefore holds prospects for therapeutic vaccine development to combat CHB.

immunology↗

bioRxiv2022

Cas9-mediated tagging of endogenous loci using HITAG

To facilitate the interrogation of protein function at scale, we have developed High-throughput Insertion of Tags Across the Genome (HITAG). HITAG enables users to rapidly produce libraries of cells, each with a different protein of interest C-terminally tagged is based on a modified strategy for performing Cas9-based targeted insertions, coupled with an improved approach for selecting properly tagged lines. Analysis of the resulting clones generated by HITAG reveals high tagging specificity with the majority of tagging events being indel free. Using HITAG, we fuse mCherry to a set of 167 stress granule-associated proteins and elucidate the features which drive a subset of proteins to strongly accumulate within these transient RNA-protein granules.

cell biology↗

bioRxiv2022

Long-read genome assemblies reveals a cis-regulatory landscape associated with phenotypic divergence in two sister Siniperca fishes

BackgroundDissecting the genetic basis of variation in the regulation of gene expression is essential for understanding phenotypic evolution. Structural variants intersecting the cis-regulatory elements are found to cause gene expression variation in several developmental genes, resulting in morphological divergence between species. Due to the difficulty of identifying structural variants accurately across the genome, a comprehensive study of impacts of structural variants in cis-regulatory divergence of closely related species, especially fish species, is still scarce. Recently identified broad H3K4me3 domains are essential for the regulation of genes involved in several biological processes. However, the role of broad H3K4me3 domains in phenotypic divergence remain poorly understood. Siniperca chuatsi and S. scherzeri are two closely related fish species diverge in several phenotypic traits, making them an ideal model to study cis-regulatory evolution in closely related species. ResultsWe generated chromosome-level genomes of S. chuatsi and S. scherzeri. The evolutionary histories of S. chuatsi and S. scherzeri were studied by inferring the dynamic changes in the ancestral population sizes. The genetic basis of adaptation in S. chuatsi and S. scherzeri was dissected by performing gene family expansion and contraction analysis and identifying positively selected genes (PSGs). To investigate the role of SVs in cis-regulatory divergence of closely related fish species, we identified high-quality SVs between S. chuatsi and S. scherzeri, as well as H3K27ac and H3K4me3 domains. Integrated analysis revealed that cis-regulatory divergence caused by SVs played an essential role in the differentiation of metabolism, skin pigmentation, and immunity between S. chuatsi and S. scherzeri. Additionally, divergent broad H3K4me3 domains were found to mostly associate with cancer-related genes in S. chuatsi and S. scherzeri and contribute to their phenotypic divergence. ConclusionsOur analysis reveals SVs play an essential role in cis-regulatory variation between the two sister fish species, which in turn contributes to their phenotypic divergence. The divergence of broad H3K4me3 domains contributes to phenotypic divergence between closely related species. Additionally, the association of broad H3K4me3 domains and cancer-related genes has an ancient origin.

genomics↗

bioRxiv2022

Whole-Brain fMRI Functional Connectivity Signatures Predict Sustained Emotional Experience in Naturalistic Contexts

Determining and decoding emotional brain processes under ecologically valid conditions remains a key challenge in affective neuroscience. The current functional magnetic resonance imaging (fMRI) based emotion decoding studies are mainly based on brief and isolated episodes of emotion induction, while sustained emotional experience in naturalistic environments that mirror daily life experiences are scarce. Here we use 10-minute movie clips as ecologically valid emotion-evoking procedures in n=52 individuals to explore emotion-specific fMRI functional connectivity (FC) profiles on the whole-brain level at high spatial resolution (400 atlas based parcels). Employing machine-learning based decoding and cross validation procedures allowed to develop predictive FC profiles that can accurately distinguish sustained happiness and sadness and that generalize across movies and subjects. Both functional brain network-based and subnetwork-based emotion prediction results suggest that emotion manifests as distributed representation of multiple networks, rather than a single functional network or subnetwork. Further, the results show that the Visual Network (VN) and Default Mode Network (DMN) associated functional networks, especially VN-DMN, exhibit a strong contribution to emotion prediction. To further estimate the cumulative effect of naturalistic long-term movie-based video-evoking emotions, we divide the 10-min episode into three stages: early stimulation (1 ~ 200 s), middle stimulation (201 ~ 400 s), and late stimulation (401 ~ 600 s) and examine the emotion prediction performance at different stimulation stages. We found that the late stimulation has a stronger predictive ability (accuracy=85.32%, F1-score=85.62%) compared to early and middle stimulation stages, implying that continuous exposure to emotional stimulation can lead to more intense emotions and further enhance emotion-specific distinguishable representations. The present work demonstrates that sustained sadness and happiness under naturalistic conditions are presented in emotion-specific network profiles and these expressions may play different roles in the generation and modulation of emotions. These findings elucidate the importance of network level adaptations for sustained emotional experiences during naturalistic contexts and open new venues for imaging network level contributions under naturalistic conditions.

neuroscience↗

bioRxiv2022

Hydrodynamic and anthropogenic disturbances co-shape microbiota rhythmicity and community assembly within intertidal groundwater-surface water continuum

Tidal hydrodynamics drive the groundwater-seawater exchange and shifts in microbiota structure in the coastal zone. However, how the coastal water microbiota structure and assembly patterns respond to periodic tidal fluctuations and anthropogenic disturbance remain unexplored in the intertidal groundwater-surface water (GW-SW) continuum, although it affects biogeochemical cycles and coastal water quality therein. Here, through hourly time-series sampling in the saltmarsh tidal creek, rhythmic patterns of microbiota structure in response to daily and monthly tidal fluctuations in intertidal surface water are disentangled for the first time. The similarity in archaeal community structures between groundwater and ebb-tide surface water (R2=0.06, p=0.2) demonstrated archaeal transport through groundwater discharge, whereas multi-source transport mechanisms led to unique bacterial biota in ebb-tide water. Homogeneous selection (58.6%-69.3%) dominated microbiota assembly in the natural intertidal GW-SW continuum and the presence of 157 rhythmic ASVs identified at ebb tide and 141 at flood tide could be attributed to different environmental selection between groundwater and seawater. For intertidal groundwater in the tidal creek affected by anthropogenically contaminated riverine inputs, higher microbial diversity and shift in community structure were primarily controlled by increased co-contribution of dispersal limitation and drift (jointly 57.8%) and enhanced microbial interactions. Overall, this study fills the knowledge gaps in the tide-driven water microbial dynamics in coastal transition zone and the response of intertidal groundwater microbiota to anthropogenic pollution of overlying waters. It also highlights the potential of microbiome analysis in enhancing coastal water quality monitoring and identifying anthropogenic pollution sources (e.g., aquaculture pathogenic Vibrio) through the detection of rhythmic microbial variances associated with intertidal groundwater discharge and seawater intrusion.

ecology↗

bioRxiv2022

Musical expertise enhances neural alignment-to-young in sensorimotor regions that predicts older adults' audiovisual speech-in-noise perception

Musical training can offset age-related decline in speech-in-noise perception. However, how lifelong musical expertise affects the functional reorganization of older brain in speech-in-noise perception has not yet been systematically investigated. Here, we address this issue by analyzing fMRI responses of older musicians, older non-musicians and, young non-musicians identifying noise-masked audiovisual syllables. First, we confirmed that older musicians outperformed older non-musicians and even equaled young non-musicians. Then, we showed that both older groups showed decreased auditory activation and increased visual activation compared to young non-musicians, while older musicians showed higher activation in speech motor regions and greater deactivation of default mode network (DMN) regions than older non-musicians. Next, we revealed that musical expertise counteracted the age-related neural dedifferentiation of speech representation, making older musicians exhibit higher neural alignment-to-young in bilateral sensorimotor areas. Finally, we disentangled that greater activation in speech motor areas and stronger deactivation in DMN regions were correlated with higher neural alignment in sensorimotor areas, which strongly predicted better performance in older adults. Together, long-term musical expertise mitigates age-related deficits in audiovisual speech-in-noise processing through enhanced compensatory scaffolding that reserves youth-like representation in sensorimotor areas. Our findings provide a comprehensive perspective on understanding age- and experience-related brain reorganization during speech perception.

neuroscience↗

bioRxiv2022

The Effect of Node Features on GCN-based Brain Network Classification: An Empirical Study

Brain functional network (BFN) analysis has become a popular technique for identifying neurological/mental diseases. Due to the fact that BFN is a graph, graph convolutional network (GCN) can be naturally used in the classification of BFN. Different from traditional methods that directly use the adjacency matrices of BFNs to train a classifier, GCN requires an additional input -- node features. To our best knowledge, however, there is no systematic study to analyze their influence on the performance of GCN-based brain disorder classification. Therefore, in this per, we conduct an empirical study on various node feature measures, including 1) original fMRI signals, 2) one-hot encoding, 3) node statistics, 4) node correlation, and 5) their combination. Experimental results on two benchmark databases show that different node feature inputs to GCN significantly affect the brain disease classification performance, and node correlation usually contributes higher accuracy compared to original signals and manually extracted statistical features.

neuroscience↗

bioRxiv2022

Molecular Mechanism for Bacterial Degradation of Plant Hormone Auxin

Plant-associated bacteria play important regulatory roles in modulating plant hormone auxin levels, affecting the growth and yields of crops. A conserved auxin-degradation (adg) operon was recently identified in the Variovorax genomes, which is responsible for root growth inhibition (RGI) reversion, promoting rhizosphere colonization and root growth. However, the molecular mechanism underlying auxin degradation by Variovorax remains unclear. Here, we systematically screened Variovorax adg operon products and identified two proteins, AdgB and AdgI, that directly associate with auxin indole-3-acetic acid (IAA). Further biochemical and structural studies revealed that AdgB is a highly IAA-specific ABC transporter solute binding protein, likely involved in IAA uptake. AdgI interacts with AdgH to form a functional Rieske non-heme dioxygenase, which works in concert with a FMN-type reductase encoded by gene adgJ to transform IAA into the biologically inactive 2-oxindole-3-acetic acid (oxIAA), representing a new bacterial pathway for IAA inactivation/degradation. Importantly, incorporation of a minimum set of adgH/I/J genes could enable IAA degradation by E. coli, suggesting a promising strategy for repurposing the adg operon for IAA regulation. Together, our study identifies the key components and underlying mechanisms involved in IAA transformation by Variovorax and brings new insights into the bacterial turnover of plant hormones, which would provide the basis for potential applications in rhizosphere optimization and ecological agriculture.

microbiology↗

bioRxiv2022

Ubiquitination steers SRF3 plasma membrane nano-organization to specify signaling outputs

Organisms cope with myriads of competing and conflicting environmental signals. These signals are often perceived by cell surface receptor kinases to mount appropriate adaptive responses. However, it is not well understood by which mechanism single receptor kinases can transduce different signals. The plant receptor kinase SRF3 transduces low iron and bacteria-derived signals. We found that upon these signals, ubiquitinated SRF3 is recognized by clathrin-mediated endocytosis for vacuolar targeting. Live super resolution microscopy revealed that cell surface SRF3 is present in a fast diffusible fraction, which is sustained by ubiquitination, and that non-ubiquitinated SRF3 is present in immobile nanodomains. Ubiquitination-mediated degradation of SRF3 is required for signaling only under low iron but not upon flg22 perception. Flg22-triggered SRF3 phosphorylation leads to SRF3 accumulation in the immobile fraction in which degradation is restricted, thereby preventing low iron signaling. We therefore propose that ubiquitination-dependent plasma membrane nano-organization of SRF3 specifies its signal transduction pathways.

plant biology↗