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Zhou, F.

Publications and source records attributed to Zhou, F..

At least 109 records · Page 6Linked to original sources

Regulated Cleavage and Relocation of FERONIA Control Immunity in Arabidopsis Roots

Plant roots exhibit localized immunity (LI) specifically in the root cap and transition/elongation zone (TZ/EZ). Such immunity relies on receptor-like kinases localized at the plasma membrane (PM), which are essential for plant response to bacteria in the rhizosphere. Here, we identified a new mechanism of action for receptor kinase FERONIA (FER) in LI. In the absence of bacterial stimuli, FER is localized to the PM, maintaining plant growth. When confronted with bacterial colonization, RALF23 peptide hyper-accumulates in TZ/EZ cells and activates a metalloproteinase that cleaves FER and transfer the cytosolic kinase domain into the nucleus. The nucleus-localized kinase domain of FER contributes to LI by reducing bacterial abundance at TZ/EZ. Thus, this work uncovered a unique mechanism by which a single receptor kinase acts in two molecular forms and two distinct subcellular locations to balance growth and immunity. One Sentence SummaryBacteria induces the cleavage of FER via At2-MMP to trigger a localized immunity around TZ and EZ of Arabidopsis roots.

plant biology↗

Transcriptome-wide analysis of the function of Ded1 in translation preinitiation complex assembly in a reconstituted in vitro system

We have developed a deep sequencing-based approach, Rec-Seq, that allows simultaneous monitoring of ribosomal 48S pre-initiation complex (PIC) formation on every mRNA in the translatome in an in vitro reconstituted system. Rec-Seq isolates key early steps in translation initiation in the absence of all other cellular components and processes. Using this approach we show that the DEAD-box ATPase Ded1 promotes 48S PIC formation on the start codons of >1000 native mRNAs, most of which have long, structured 5-untranslated regions (5UTRs). Remarkably, initiation measured in Rec-Seq was enhanced by Ded1 for most mRNAs previously shown to be highly Ded1-dependent by ribosome profiling of ded1 mutants in vivo, demonstrating that the core translation functions of the factor are recapitulated in the purified system. Our data do not support a model in which Ded1acts by reducing initiation at alternative start codons in 5UTRs and instead indicate it functions by directly promoting mRNA recruitment to the 43S PIC and scanning to locate the main start codon. We also provide evidence that eIF4A, another essential DEAD-box initiation factor, is required for efficient PIC assembly on almost all mRNAs, regardless of their structural complexity, in contrast to the preferential stimulation by Ded1 of initiation on mRNAs with long, structured 5UTRs.

biochemistry↗

A neural signature for the subjective experience of threat anticipation under uncertainty

Uncertainty about potential future threats and the associated anxious anticipation represents a key feature of anxiety. However, the neural systems that underlie the subjective experience of threat anticipation under uncertainty remain unclear. Combining a novel uncertain shock anticipation paradigm that allows precise modulation of the level of momentary anxious arousal during functional magnetic resonance imaging (fMRI) with multivariate predictive modeling, we trained a brain model that accurately predicted the intensity of subjective experience of anxious arousal on the population and individual level. In a series of analyses utilizing available fMRI datasets, we further demonstrate that the signature specifically predicted anxious anticipation and was not sensitive in predicting pain, general anticipation or unspecific arousal. The signature was functionally and spatially distinguishable from representations of subjective fear or negative affect. We developed a sensitive, generalizable, and specific neuromarker for subjective anxious arousal experienced during uncertain threat anticipation that can facilitate model development and clinical translation.

neuroscience↗

Prolonging the Delivery of Influenza Virus Vaccine Improves the Quantity and Quality of the Induced Immune Responses in Mice

Influenza vaccines play a vital role in protecting individuals from influenza virus infection and severe illness. However, current influenza vaccines have suboptimal efficacy, which is further reduced in cases where the vaccine strains do not match the circulating strains. One strategy to enhance the efficacy of influenza vaccines is by extended antigen delivery, thereby mimicking the antigen kinetics of a natural infection. Prolonging antigen availability was shown to quantitatively enhance influenza virus-specific immune responses but how it affects the quality of the induced immune response is unknown. Therefore, the current study aimed to investigate whether prolongation of the delivery of influenza vaccine improves the quality of the induced immune responses over that induced by prime-boost immunization. To study this, mice were given daily doses of whole inactivated influenza virus vaccine for periods of 14, 21, or 28 days; the control group received prime-boost immunization with a 28 days interval. Our data show that the highest levels of cellular and humoral immune responses were induced by 28 days of extended antigen delivery, followed by 21, and 14 days of delivery, and prime-boost immunization. Moreover, prolonging vaccine delivery also improved the quality of the induced antibody response, as indicated by higher level of high avidity antibodies, a balanced IgG subclass profile, and a higher level of cross-reactive antibodies. Overall, our findings contribute to a better understanding of the immune response to influenza vaccination and have important implications for the design and development of future slow-release influenza vaccines.

immunology↗

Cryo-EM structures of human magnesium channel MRS2 reveal gating and regulatory mechanisms

Magnesium ions (Mg2+) play an essential role in cellular physiology. In mitochondria, protein and ATP synthesis and various metabolic pathways are directly regulated by Mg2+. MRS2, a magnesium channel located in the inner mitochondrial membrane, mediates the influx of Mg2+ into the mitochondrial matrix and regulates Mg2+ homeostasis. Knockdown of MRS2 in human cells leads to reduced uptake of Mg2+ into mitochondria and disruption of the mitochondrial metabolism. Despite the importance of MRS2, the Mg2+ translocation and regulation mechanisms of MRS2 are still unclear. Here, using cryo-EM we determined the structure of human MRS2 in the presence and absence of Mg2+ at 2.8 [A] and 3.3 [A], respectively. From the homo-pentameric structures, we identified R332 and M336 as major gating residues, which were then tested using mutagenesis and two cellular divalent ion uptake assays. A network of hydrogen bonds was found connecting the gating residue R332 to the soluble domain, potentially regulating the gate. Two Mg2+-binding sites were identified in the MRS2 soluble domain, distinct from the two sites previously reported in CorA, a homolog of MRS2 in prokaryotes. Altogether, this study provides the molecular basis for understanding the Mg2+ translocation and regulatory mechanisms of MRS2.

biophysics↗

Capturing dynamic fear experiences in naturalistic contexts: An ecologically valid fMRI signature integrating brain activation and connectivity

Enhancing our understanding of how the brain constructs conscious emotional experiences within dynamic real-life contexts necessitates ecologically valid neural models. Here, we present evidence delineating the constraints of current fMRI activation models in capturing naturalistic fear dynamics. To address this challenge, we fuse naturalistic fMRI with predictive modeling techniques to develop an ecologically valid fear signature that integrates activation and connectivity profiles, allowing for accurate prediction of subjective fear experience under highly dynamic close-to-real-life conditions. This signature arises from insights into the crucial role of distributed brain networks and their interactions in emotion modulation, and the potential of network-level information to improve predictions in dynamic contexts. Across a series of investigations, we demonstrate that this signature predicts stable and dynamic fear experiences across naturalistic scenarios with heightened sensitivity and specificity, surpassing traditional activation- and connectivity-based signatures. Notably, the integration of affective connectivity profiles enables accurate real-time predictions of fear fluctuations in naturalistic settings. Additionally, we unearth a distributed yet redundant brain-wide representation of fear experiences. Subjective fear is encoded not only by distributed cortical and subcortical regions but also by their interactions, with no single brain system conveying substantial unique information. Our study establishes a comprehensive and ecologically valid functional brain architecture for subjective fear in dynamic environments and bridges the gap between experimental neuroscience and real-life emotional experience.

neuroscience↗

Intercellular communication atlas reveals Oprm1 as a neuroprotective factor for retinal ganglion cells

The progressive death of mature neurons often results in neurodegenerative diseases. While the previous studies have mostly focused on identifying intrinsic mechanisms controlling neuronal survival, the extracellular environment also plays a critical role in regulating cell viability. Here we explore how intercellular communication contributes to the survival of retinal ganglion cells (RGCs) following the optic nerve crush (ONC). Although the direct effect of the ONC is restricted to the RGCs, we observed transcriptomic responses in other retinal cells to the injury based on the single-cell RNA-seq, with astrocytes and Muller glia having the most interactions with RGCs. By comparing the RGC subclasses with distinct resilience to ONC-induced cell death, we found that the high-survival RGCs tend to have more ligand-receptor interactions with other retinal cells, suggesting that these RGCs are intrinsically programmed to foster more communication with their surroundings. Furthermore, we identified the top 47 interactions that are stronger in the high-survival RGCs, likely representing neuroprotective interactions. We performed functional assays on one of the receptors, -opioid receptor (Oprm1), a receptor known to play roles in regulating pain, reward, and addictive behavior. Although Oprm1 is preferentially expressed in intrinsically photosensitive retinal ganglion cells (ipRGC), its neuroprotective effect could be transferred to multiple RGC subclasses by selectively overexpressing Oprm1 in pan-RGCs in ONC, excitotoxicity, and glaucoma models. Lastly, manipulating Oprm1 activity improved visual functions or altered pupillary light response in mice. Our study provides an atlas of cell-cell interactions in intact and post-ONC retina, and a strategy to predict molecular mechanisms controlling neuroprotection, underlying the principal role played by extracellular environment in supporting neuron survival.

neuroscience↗

Leveraging information between multiple population groups and traits improves fine-mapping resolution

Statistical fine-mapping helps to pinpoint likely causal variants underlying genetic association signals. Its resolution can be improved by (i) leveraging information between traits; and (ii) exploiting differences in linkage disequilibrium structure between diverse population groups. Using association summary statistics, MGflashfm jointly fine-maps signals from multiple traits and population groups; MGfm uses an analogous framework to analyse each trait separately. We also provide a practical approach to fine-mapping with out-of-sample reference panels. In simulation studies we show that MGflashfm and MGfm are well-calibrated and that the mean proportion of causal variants with PP>0.80 is above 0.75 (MGflashfm) and 0.70 (MGfm). In our analysis of four lipids traits across five population groups, MGflashfm gives a median 99% credible set reduction of 10.5% over MGfm. MGflashfm and MGfm only require summary level data, making them very useful fine-mapping tools in consortia efforts where individual-level data cannot be shared.

genomics↗

CCR9 overexpression promotes T-ALL progression by enhancing cholesterol biosynthesis

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy of the lymphoid progenitor cells contributing to [~] 20% of the total ALL cases with higher prevalence in adults than the children. Despite the important role of human T-ALL cell lines in understanding the biology and treatment options, a detailed comparison of the tumorigenic potential of two commonly used T-ALL cell lines, MOLT4 and JURKAT cells is still lacking. In the present study, we compared the leukemogenic potentials of the two T-ALL cell lines (MOLT4 and JURKAT) in NOD-PrkdcscidIL2rgdull (NTG) mice and found that MOLT4 cells possessed a relatively higher aggressive phenotype characterized by their enhanced tissue infiltration as compared to the JURKAT cells. Gene expression profiling of the two cell lines revealed numerous differentially expressed genes (DEGs) including CC chemokine receptor 9 (CCR9), which augmented the invasion and metastasis of MOLT4 and JURKAT cells in vitro. The upregulation of CCR9 also promoted the tissue infiltration of JURKAT cells in the NTG mice. CCR9 overexpression increased cholesterol production by upregulating the expression of the core regulatory genes of the cholesterol biosynthesis pathway including MSMO1, MVD, and HMGCS1. Moreover, the upregulated expression of EGR1 was also found with CCR9 overexpression that modulated the expression of MSMO1, MVD, and HMGCS1. Notably, the treatment of the cells with simvastatin and siRNA-EGR1 decreased the aggressiveness of the CCR9 overexpressing JURKAT cells in vitro, suggesting the CCR9-EGR1 axis in T-ALL progression. This study highlights the distinct tumorigenic potentials of two T-ALL cell lines and reveals CCR9-regulated enhanced cholesterol biosynthesis in T-ALL. Simple summaryT-ALL is an aggressive cancer of the blood and bone marrow. In order to understand the biological mechanism of T-ALL, in vitro T-ALL cell lines are commonly employed. However, a comprehensive comparison of two common T-ALL cell lines, MOLT4 and JURKAT cells for T-ALL development is not yet available. We compared MOLT4 and JURKAT cells for T-ALL inducing potential and found that MOLT4 cells exhibited a relatively increased aggressiveness in mice as compared to JURKAT cells. We examined the molecular characteristics of two cell lines that could lead to differences in cancer development. Transcriptional profiling of MOLT4 and JURKAT cells revealed significant changes in the expression of several genes including CCR9. This aberrant expression of CCR9 impacted the migration and invasion of the T-ALL cell lines in vitro. In addition, higher expression levels of CCR9 also promoted T-ALL progression in vivo. Transcriptome analysis and gene ontology analysis of the DEGs of CCR9 over-expressing JURKAT cells indicated the enrichment of the genes in the cholesterol biosynthesis pathway, suggesting this metabolic rewiring mechanism as a strategy to cope with the increased energy demand of the malignant T-ALL cells.

cancer biology↗

Optimized design and in vivo application of optogenetically functionalized Drosophila dopamine receptors

Neuromodulatory signaling via G protein-coupled receptor (GPCRs) plays a pivotal role in regulating neural network function and animal behavior. Recent efforts have led to the development of optogenetic tools to induce G protein-mediated signaling, with the promise of acute and cell type-specific manipulation of neuromodulatory signals. However, designing and deploying optogenetically functionalized GPCRs (optoXRs) with accurate specificity and activity to mimic endogenous signaling in vivo remains challenging. Here we optimized the design of optoXRs by considering evolutionary conserved GPCR-G protein interactions and demonstrate the feasibility of this approach using two Drosophila Dopamine receptors (optoDopRs). We validated these optoDopRs showing that they exhibit high signaling specificity and light sensitivity in vitro. In vivo we detected receptor and cell type-specific effects of dopaminergic signaling in various behaviors including the ability of optoDopRs to rescue loss of the endogenous receptors. This work demonstrates that OptoXRs can enable optical control of neuromodulatory receptor specific signaling in functional and behavioral studies.

neuroscience↗

Rotten to the core - a neurofunctional signature of subjective core disgust generalizes to socio-moral contexts

While disgust originates in the hard-wired mammalian distaste response, the conscious experience of disgust in humans strongly depends on subjective appraisal and may even extend to sociomoral contexts. In a series of studies, we combined functional magnetic resonance imaging (fMRI) with machine-learning based predictive modeling to establish a comprehensive neurobiological model of subjective disgust. The developed neurofunctional signature accurately predicted momentary self-reported subjective disgust across discovery (n=78) and pre-registered validation (n=30) cohorts and generalized across core disgust (n=34 and n=26), gustatory distaste (n=30), and sociomoral (unfair offers; n=43) contexts. Disgust experience was encoded in distributed cortical and subcortical systems, and exhibited distinct and shared neural representations with subjective fear or negative affect in interoceptive-emotional awareness and conscious appraisal systems while the signatures most accurately predicted the respective target experience. We provide an accurate fMRI-signature for disgust with a high potential to resolve ongoing evolutionary debates.

neuroscience↗

Structure-function Analyses Reveal Key Molecular Determinants of HIV-1 CRF01_AE Resistance to the Entry Inhibitor Temsavir

The HIV-1 entry inhibitor temsavir prevents CD4 from interacting with the envelope glycoprotein (Env) and blocks its conformational changes. To do this temsavir relies on the presence of a residue with small side chain at position 375 in Env and is unable to neutralize viral strains like CRF01_AE carrying His375. Here we investigate the mechanism of temsavir-resistance and show that residue 375 is not the sole determinant of resistance. At least six additional residues within the gp120 inner domain layers, including five distant from the drug-binding pocket, contribute to resistance. A detailed structure-function analysis using engineered viruses and soluble trimer variants reveal that the molecular basis of resistance is mediated by crosstalk between His375 and the inner domain layers. Furthermore, our data confirm that temsavir can adjust its binding mode to accommodate changes in Env conformation, a property that likely contributes to its broad-antiviral activity.

molecular biology↗

Single-cell phenomics reveals behavioural and mechanical heterogeneities underpinning collective migration during mouse anterior patterning

Distal Visceral Endoderm (DVE) cells show a stereotypic unidirectional migration essential for correct orientation of the anterior-posterior axis. They migrate within a simple epithelium, the Visceral Endoderm (VE). It is unknown how DVE cells negotiate their way amongst the surrounding VE cells, what determines the bounds of DVE migration within the VE, and the relative contributions of different cell behaviours to this migration. To address these questions, we used lightsheet microscopy to generate a multi-embryo, singlecell resolution, longitudinal dataset of cell behaviour and morphology. We developed a machine learning based pipeline to segment cells and a data-informed systematic computational framework to extract and compare select morphological, behavioural and molecular parameters of all VE cells in a unified coordinate space. Unbiased clustering of this single-cell phenomic dataset reveals considerable patterned phenotypic heterogeneity within the VE and a previously unknown sub-grouping within the DVE. While migrating, DVE cells retain regular morphology, do not exchange neighbours and are crowded, all hallmarks of the jammed state. In contrast, VE cells immediately ahead of them deform and undergo neighbour exchange. We show that DVE cells are characterised by higher levels of apical F-actin and elevated tension relative to the VE cells immediately ahead of them through which they migrate, but stop migrating upon reaching a region of the VE with matching elevated tension. Lefty1 mutants, known to show abnormal over-migration of DVE cells, show disruption to this patterned tension in the VE. Our findings provide novel insights into the control of cell behaviour during the remodelling of curved epithelia, indicating that the collective migration of sub-sets of cells can be circumscribed by modulating the mechanical properties of surrounding cells and that migrating cells in this context remain as a jammed solid flock, with surrounding cells facilitating their movement by becoming unjammed. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/534937v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@10a7153org.highwire.dtl.DTLVardef@963a1forg.highwire.dtl.DTLVardef@c1fcd0org.highwire.dtl.DTLVardef@1bcdded_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

flashfmZoom: a tool for joint fine-mapping and exploration of GWAS results in the UK Biobank

SummaryflashfmZoom is an all-in-one tool for analysis and interactive visualisation of potential causal genetic variants that underlie associations with quantitative traits from the UK Biobank. It offers a user-friendly interface and guides users in the selection of pleiotropic regions among subsets of 134 quantitative traits, such as cardiometabolic, hematologic, and respiratory traits. Users may then run single-trait fine-mapping, allowing for multiple causal variants, and leverage information between the traits using multi-trait fine-mapping to improve resolution. A series of interactive plots and downloadable tables are generated within flashfmZoom to identify potential causal variants that are shared or distinct between the traits; it also lists relevant literature for the traits and/or variants. Besides exploring traits that are well-known to be related, flashfmZoom encourages interactive exploration for the joint analysis of traits that may not often be considered together. This may reveal common aetiological pathways between traits related to different disorders. Availability and ImplementationflashfmZoom is an interactive open-source R shiny app software available online directly at https://mrc-bsu.shinyapps.io/flashfmZoomOnline/, with source code in GitHub under the MIT license https://github.com/fz-cambridge/flashfmZoom and at https://doi.org/10.5281/zenodo.7756205. Contactfeng.zhou@mrc-bsu.cam.ac.uk or jennifer.asimit@mrc-bsu.cam.ac.uk

genetics↗

The central renin angiotensin II system: a genetic pathway, functional decoding and selective target engagement characterization in humans

The brain renin angiotensin II system plays a pivotal role in cognition and neuropathology via the central angiotensin II type 1 receptor (AT1R), yet the lack of a biologically informed framework currently impedes translational and therapeutic progress. We combined imaging transcriptomic and meta-analyses with pharmaco-resting state fMRI employing a selective AT1R antagonist in a discovery-replication design (n=132 individuals). The AT1R was densely expressed in subcortical systems engaged in reward, motivation, stress, and memory. Pharmacological target engagement suppressed spontaneous neural activity in subcortical systems with high AT1R expression and enhanced functional network integration in cortico-basal ganglia-thalamo-cortical circuits. AT1R-regulation on functional network integration was further mediated by dopaminergic, opioid and corticotrophin-releasing hormone pathways. Overall, this work provides the first comprehensive characterization of the architecture and function of the brain renin angiotensin II system indicating that the central AT1R-mediates human cognition and behavior via regulating specific circuits and interacting with classical transmitter systems.

neuroscience↗

A critical role of VEGFR2 in lymphatic tumor metastasis

Vascular endothelial growth factor receptor-2 (VEGFR2) transduces crucial signals for blood vessel growth but its role in the lymphatic system remains incompletely elucidated. By employing genetic mouse models targeting Vegfr2 in either pan-endothelial cells (ECs) or lymphatic endothelial cells (LECs), we examined roles of VEGFR2 in lymphangiogenesis and in tumor progression. VEGFR2 was differentially expressed in the murine lymphatic system and particularly marked in valves of collecting vessels. The pan-endothelial Vegfr2 deletion (Vegfr2iECKO) reduced the dermal lymphatic growth, and a significant decrease in lymphatic valves of pre-collectors was observed in mice with the LEC-specific attenuation of VEGFR2 (Vegfr2iLECKO). Furthermore, while the primary growth of subcutaneously implanted Lewis lung carcinoma was unaffected in the Vegfr2iLECKO mouse model, the tumor metastasis to sentinel lymph nodes was efficiently suppressed. In accordance, the tumor-associated lymphangiogenesis was decreased in the Vegfr2iLECKO mice compared with the control. Findings from this study imply that the lymphatic VEGFR2 regulates valve morphogenesis and promotes lymph node metastasis by regulating the tumor-associated lymphatic formation.

cancer biology↗

Structure of human NaV1.6 channel reveals Na+ selectivity and pore blockade by 4,9-anhydro-tetrodotoxin

The sodium channel NaV1.6 is widely expressed in neurons of the central and peripheral nervous systems, which plays a critical role in regulating neuronal excitability. Dysfunction of NaV1.6 has been linked to epileptic encephalopathy, intellectual disability and movement disorders. Here we present cryo-EM structures of human NaV1.6/{beta}1/{beta}2 alone and complexed with a guanidinium neurotoxin 4,9-anhydro-tetrodotoxin (4,9-ah-TTX), revealing molecular mechanism of NaV1.6 inhibition by the blocker. In the apo-form structure, two potential Na+ binding sites were revealed in the selectivity filter, suggesting a possible mechanism for Na+ selectivity and conductance. In the 4,9-ah-TTX-bound structure, 4,9-ah-TTX binds to a pocket similar to the tetrodotoxin (TTX) binding site, which occupies the Na+ binding sites and completely blocks the channel. Molecular dynamics simulation results show that subtle conformational differences in the selectivity filter affect the affinity of TTX analogues. Taken together, our results provide important insights into NaV1.6 structure, ion conductance, and inhibition.

biophysics↗

Structure-Kinetic Relationship for Drug Design Revealed by PLS Model with Retrosynthesis-Based Pre-trained Molecular Representation and Molecular Dynamics Simulation

Drug design based on their molecular kinetic properties is growing in application. Pre-trained molecular representation based on retrosynthesis prediction model (PMRRP) was trained from 501 inhibitors of 55 proteins and successfully predicted the koff values of 38 inhibitors for HSP90 protein from an independent dataset. Our PMRRP molecular representation outperforms others such as GEM, MPG, and common molecular descriptors from RDKit. Furthermore, we optimized the accelerated molecular dynamics to calculate relative retention times for 128 inhibitors of HSP90. We observed high correlation between the simulated, predicted, and experimental -log(koff) scores. Combining machine learning (ML) and molecular dynamics (MD) simulation help design a drug with specific selectivity to the target of interest. Protein-ligand interaction fingerprints (IFPs) derived from accelerated MD further expedite the design of new drugs with the desired kinetic properties. To further validate our koff ML model, from the set of potential HSP90 inhibitors obtained by similarity search of commercial databases, we identified two novel molecules with better predicted koff values and longer simulated retention time than the reference molecules. The IFPs of the novel molecules with the newly discovered interacting residues along the dissociation pathways of HSP90 shed light on the nature of the selectivity of HSP90 protein. We believe the ML model described here is transferable to predict koff of other proteins and enhance the kinetics-based drug design endeavor.

biophysics↗