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Xu, S.

Publications and source records attributed to Xu, S..

At least 289 records · Page 16Linked to original sources
bioRxiv2022

The Prioritization of Eleven-Nineteen-Leukemia Inhibitors as Potential Drug Candidates to Treat Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is the second most diagnosed and the deadliest subtype of leukemia. Recently genetic loss-of-function studies have demonstrated that a human YEATS domain-containing protein named eleven-nineteen-leukaemia (ENL) functions as a transcriptional coactivator and is essential for the proliferation of AML that harbours oncogenic multiple lineage leukemia (MLL) rearrangements. We previously synthesized a series of small molecule inhibitors (1, 7-9, 11-15 and 24) that displayed significant and specific inhibitory effects against the ENL YEAST domain. In the current work, we report the development of a novel NanoBRET system that allows the analysis of cellular permeability, potency, selectivity, and stability of synthesized ENL inhibitors for their prioritization for further characterizations. Followed by in vitro metabolic stability and cell growth inhibition studies, we narrowed down to a potent and specific ENL YEATS domain inhibitor 13 with both high in vitro metabolic stability and strong anti-proliferation ability on MLL-fusion leukemia cell lines. A mouse pharmacokinetic (PK) analysis showed that at an oral dose of 20 mg/kg compound 13 had 60.9% bioavailability and 2.6 h mean residence time. With these favorable PK characteristics, compound 13 is ready for efficacy studies in an animal model. Cumulatively, the current study has prioritized compound 13 as a promising drug candidate to disrupt the pathogenic functions of ENL for the AML treatment.

biochemistry↗
bioRxiv2022

Induced responses contribute to rapid plant adaptation to herbivory

Herbivory-induced responses in plants are typical examples of phenotypic plasticity, and their evolution is thought to be driven by herbivory. However, direct evidence of the role of induced responses in plant adaptive evolution to herbivores is scarce. Here, we experimentally evolved populations of an aquatic plant (Spirodela polyrhiza, giant duckweed) and its native herbivore (Lymnaea stagnalis, freshwater snail) testing whether herbivory drives rapid adaptive evolution in plant populations using a combination of bioassays, pool-sequencing, metabolite analyses, and amplicon metagenomics. We found that snail herbivory drove rapid phenotypic changes, increased herbivory resistance, and altered genotype frequencies in the plant populations. Additional bioassays suggested that evolutionary changes of induced responses contributed to the rapid increase of plant resistance to herbivory. This study provides direct evidence that herbivory-induced responses in plants can be subjected to selection and have an adaptive role by increasing resistance to herbivores.

evolutionary biology↗
bioRxiv2022

Differential reach vector computations in mIPS and PMd as revealed through HD-tDCS

Recent neural and behavioural findings provide support that the medial intraparietal sulcus (mIPS) and dorsal premotor (PMd) activity reflect aspects of a kinematic plan for reaching movements. However, it is unclear how these two regions differentially contribute to reach planning. Here, we used high-definition transcranial direct current stimulation (HD-tDCS; 4 x 1 electrode placement; 2 mA for 20 min; 3 cm radius) to investigate the functional roles of mIPS and PMd in the left hemisphere of humans. We examined the changes in endpoint error in reaching task with different initial hand positions and different target locations spanning both visual hemi-fields. Participants completed the task with (stimulation, post-stimulation) and without stimulation (pre-stimulation) of individually fMRI-localized cortical areas mIPS and PMd. We found a significant interaction effect between initial hand position (IHP) and target position on the difference in horizontal endpoint error after cathodal left mIPS stimulation and significant IHP and target position main effects after cathodal left PMd stimulation, suggesting that IHP and target position are not yet integrated into a movement vector at the input of the mIPS, but are integrated in the input of PMd. Hence, these findings reveal a distinction between mIPS and PMd in the stages of movement vector formation for reaching movements and indicate that HD-tDCS is a viable method for perturbing localized cortical activity to elucidate localized cortical function.

neuroscience↗
bioRxiv2022

High-Contrast PET imaging with -NT160, a Class-IIa Histone Deacetylase (Class-IIa HDAC) Probe for In Vivo Imaging of Epigenetic Machinery in the Central Nervous System

We utilized positron emission tomography (PET) imaging in vivo to map the spatiotemporal biodistribution/expression (protein density) of class-IIa histone deacetylases (class-IIa HDACs) in the brain. Herein, we report an improved radiosynthesis of [18F]-NT160 using 4-hydroxy-TEMPO which led to a significant improvement in radiochemical yield and molar activity. PET imaging with [18F]-NT160, a highly potent class-IIa HDAC inhibitor with sub-nM affinity for HDAC4 and 5 isoforms, led to high-quality and high-contrast images among various brain regions. [18F]-NT160 displayed excellent pharmacokinetic and imaging characteristics: brain uptake is high in gray matter regions, leading to high-quality PET images; tissue kinetics are appropriate for an 18F tracer and specific binding for class-IIa HDACs is demonstrated by self-blockade. Higher uptake with [18F]-NT160 was observed in the hippocampus, thalamus, and cortex while there was relatively lower uptake in the cerebellum and striatum. Overall, our current studies with [18F]-NT160 will likely facilitate the development and clinical translation of class-IIa HDACs of the next generation of PET tracers for imaging and targeted therapy of cancer and the diseases of the central nervous system (CNS).

neuroscience↗
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

A Fast Solution for Automated Single-Molecule Force Spectroscopy Data Collection and Processing

Force spectroscopy is a sophisticated technology for studying the physical chemistry of polymers at the single-molecule level. Its implication in biomolecules, e.g., proteins, DNA or RNA, yielded tremendous information on their structures, folding, and functions. In a routine procedure, an experimenter pulls the molecule of interest to generate the force-extension (FE) curve using technologies that include atomic force microscopy (AFM), magnetic force spectroscopy (MFS), optical tweezer and acoustic force spectroscopy (AFS), then extract parameters characteristic to the polymer. The latter step requires fitting the FE curve with mathematical models. Although several models have been widely applied for over 20 years, the fitting of the experimental data was not as straightforward. This step can be time-consuming, prone to mistakes, and sometimes cause debate. To lower the technical barriers for users and to reduce the time consumption and errors involved in force spectroscopy data processing, we optimized the fitting procedure for three classical worm-like chain (WLC) models into an automated software package named Single Molecule Force Spectroscopy Toolkit (SMFST). Our MATLAB-based software with a graphical user interface demonstrated robust fitting for three models in a wide range of forces and provided convenient tools for batch data processing to meet future requirements of high-throughput data collection.

biophysics↗
bioRxiv2022

Predestined neutrophil heterogeneity in homeostasis varies in transcriptional and phenotypic response to Candida

Once perceived to be homogenous effector cells, neutrophils have since been shown to exhibit population heterogeneity. Here, we established an experimental model of clonal neutrophil heterogeneity using conditionally immortalized clonal granulocyte monocyte progenitors (GMPs) and their mature neutrophil progeny. Transcriptional and epigenetic profiling showed conserved genome-wide signatures of transcription and chromatin accessibility that were specific to individual GMP clones and their paired neutrophil progeny, suggesting that clone specificity is established as early as the GMP stage. Clone-specific genes in vital regulatory pathways were pre-programmed and exhibited delayed expression in the mature neutrophil stage. The clone-specific gene expression in the mature neutrophils paired to enhancer activation in their parental GMPs. To determine whether transcriptional heterogeneity predicted the response to fungal pathogens, neutrophil clones were functionally profiled. Clones demonstrated heterogeneous responses to fungal pathogens in vitro and revealed neutrophil subsets with evidence for tailored functional responses to Candida spp. as well as specific transcriptional and epigenetic patterns that may explain these differences. Together, this work establishes that heterogenous GMP and neutrophil compartments exist under homeostatic conditions and that these represent predefined clusters that are uniquely adapted to control invasive fungal pathogens. Short SummaryClonal neutrophil progenitors demonstrate heterogeneity in transcription and chromatin accessibility which may inform response to later fungal challenges.

immunology↗
bioRxiv2022

Fast and Accurate Prediction of Intrinsically Disordered Protein by Protein Language Model

MotivationIntrinsically disordered proteins (IDPs) play a vital role in various biological processes and have attracted increasing attention in the last decades. Predicting IDPs from primary structures of proteins provides a very useful tool for protein analysis. However, most of the existing prediction methods heavily rely on multiple sequence alignments (MSAs) of homologous sequences which are formed by evolution over billions of years. Obtaining such information requires searching against the whole protein databases to find similar sequences and since this process becomes increasingly time-consuming, especially in large-scale practical applications, the alternative method is needed. ResultsIn this paper, we proposed a novel IDP prediction method named IDP-PLM, based on the protein language model (PLM). The method does not rely on MSAs or MSA-based profiles but leverages only the protein sequences, thereby achieving state-of-the-art performance even compared with predictors using protein profiles. The proposed IDP-PLM is composed of stacked predictors designed for several different protein-related tasks: secondary structure prediction, linker prediction, and binding predictions. In addition, predictors for the single task also achieved the highest accuracy. All these are based on PLMs thus making IDP-PLM not rely on MSA-based profiles. The ablation study reveals that all these stacked predictors contribute positively to the IDP prediction performance of IDP-PLM. AvailabilityThe method is available at http://github.com/xu-shi-jie. Contactakira.onoda@ees.hokudai.ac.jp Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗
bioRxiv2022

On the Origin of Obligate Parthenogenesis in Daphnia pulex.

Despite the presence of obligately parthenogenetic (OP) lineages derived from sexual ancestors in diverse phylogenetic groups, the genetic mechanisms giving rise to the OP lineages remain poorly understood. The freshwater microcrustacean Daphnia pulex typically reproduces via cyclical parthenogenesis. However, some populations of OP D. pulex have emerged due to ancestral hybridization and introgression events between two cyclically parthenogenetic (CP) species D. pulex and D. pulicaria. These OP hybrids produce both subitaneous and resting eggs parthenogenetically, deviating from CP isolates where resting eggs are produced via conventional meiosis and mating. This study examines the genome-wide expression and alternative splicing patterns of early subitaneous versus early resting egg production in OP D. pulex isolates to gain insight into the genes and mechanisms underlying this transition to obligate parthenogenesis. Our differential expression and functional enrichment analyses revealed a downregulation of meiosis and cell cycle genes during early resting egg production, as well as divergent expression patterns of metabolism, biosynthesis, and signaling pathways between the two reproductive modes. These results provide important gene candidates for future experimental verification, including the CDC20 gene that activates the anaphase-promoting complex in meiosis.

evolutionary biology↗
bioRxiv2022

Natural rubber reduces herbivory and alters the microbiome below ground

O_LILaticifers are hypothesized to mediate both plant-herbivore and plant-microbe interactions. However, there is little evidence for the dual function of these secretory structures. C_LIO_LIWe investigated whether the major constituent of natural rubber, cis-1,4-polyisoprene, a phylogenetically widespread and economically important latex polymer, alters plant resistance and the root microbiome of the Russian dandelion (Taraxacum koksaghyz) under attack of a root herbivore, the larva of the May cockchafer (Melolontha melolontha). C_LIO_LIRubber-depleted transgenic plants lost more shoot and root biomass upon herbivory than normal rubber content near-isogenic lines. M. melolontha preferred to feed on artificial diet supplemented with rubber-depleted rather than normal rubber content latex. Likewise, adding purified cis-1,4-polyisoprene in ecologically relevant concentrations to diet deterred larval feeding and reduced larval weight gain. Metagenomics and metabarcoding revealed that abolishing biosynthesis of natural rubber alters the structure but not the diversity of the rhizosphere and root microbiota in a herbivore-dependent manner. Roots from rubber-depleted plants, however, did not exhibit a higher pathogen load compared to normal rubber content roots. C_LIO_LITaken together, our data demonstrate that natural rubber biosynthesis reduces herbivory and alters the plant microbiota in a herbivore-dependent manner, which highlights the role of plant specialized metabolites and secretory structures in shaping multitrophic interactions. C_LI

plant biology↗
bioRxiv2022

Phage-Assisted, Active Site-Directed Ligand Evolution of a Potent and Selective Histone Deacetylase 8 Inhibitor

The phage-assisted, active site-directed ligand evolution (PADLE) is a recently developed technique that uses an amber codon-encoded noncanonical amino acid (ncAA) as an anchor to direct phage-displayed peptides to a target for an enhanced ligand identification process. 2-Amino-8-oxodecanoic acid (Aoda) is a ketone-containing ncAA residue in the macrocyclic peptide natural product apicidin that is a pan-inhibitor of Zn2+-dependent histone deacetylases (HDACs). Its ketone serves as an anchoring point to chelate the catalytic zinc ion in HDACs. Using a previously evolved N{varepsilon}-acetyl-lysyl-tRNA synthetase in combination with tRNAPyl, we showed that Aoda was efficiently incorporated into proteins in Escherichia coli by amber suppression. By propagating an amber codon-obligate phagemid library in E. coli encoding Aoda, we generated an Aoda-containing phage-displayed peptide library. Using this library to conduct PADLE against HDAC8 revealed a 7-mer peptide GH8P01F1 with Aoda-flanking amino acid residues that match existing peptide sequences in identified HDAC8 substrates. Switching Aoda in GH8P01F1 to a more Zn2+-chelating ncAA S-2-amino-8-hydroxyamino-8-oxooctanoic acid (Asuha) led to an extremely potent GH8HA01 that has an HDAC8-inhibition Ki value as 0.67 nM. GH8HA01 and its 5-mer truncation analogue Ac-GH8HA01{Delta}1{Delta}7 that has an HDAC8-inhibition Ki value as 0.31 nM represent two most potent HDAC8 inhibitors that have been developed so far and both are highly selective against HDAC8 over the other three tested HDACs, demonstrating the great potential of using PADLE to identify highly potent and selective ligands for targets.

biochemistry↗
bioRxiv2022

A microglia-CD4+ T cell partnership generates protective anti-tumor immunity to glioblastoma

The limited efficacy of immunotherapies against glioblastoma illustrates the urgent need to better understand the interactions between the central nervous system and the immune system. Here, we showed that a protective response to CTLA-4 therapy depended on a mutualistic relationship between microglia and CD4+ T cells. Suppression of gliomas by CD4+ T cells did not require tumor-intrinsic MHC-II expression, but rather was dependent on the selective expression of MHC-II and antigen presentation by local microglia that in turn, sustained CD4+ T cell tumoricidal effector functions. CD4+ T cell secretion of IFN{gamma} made the glioma cells vulnerable to enhanced tumor surveillance and phagocytosis by microglia via the AXL/MER tyrosine kinase receptors that were necessary for tumor suppression. This work illustrates a novel partnership between CD4+ T cells and microglia that unleashes the tumoricidal properties of microglia that can be harnessed to improve immunotherapies for glioblastoma.

immunology↗
bioRxiv2022

CRIC-seq reveals positional rule of PTBP1-mediated long-range RNA looping in splicing regulation

RNA-binding proteins bind at different positions of pre-mRNA molecules to promote or reduce the usage of a particular exon. Seeking to understand the working principle of these positional effects, we develop a CRIC-seq method to enrich single RBP-mediated in situ RNA-RNA spatial interacting fragments for deep sequencing. We determine hnRNPA1- and PTBP1-mediated RNA-RNA interactions and regulatory mechanisms in HeLa cells. Unexpectedly, 3D RNA map analysis shows that PTBP1-mediated loops in introns preferably promote cassette exon splicing by accelerating asymmetric intron removal, whereas the loops spanning across cassette exon primarily repress splicing. This "positional rule" can faithfully predict PTBP1-regulated splicing outcomes. We further demonstrate that cancer-related splicing quantitative trait loci can disrupt RNA loops by reducing PTBP1 binding on pre-mRNAs to cause aberrant splicing in tumors. Our study presents a powerful method for exploring the functions of RBP-mediated RNA-RNA interactions in gene regulation and disease.

molecular biology↗
bioRxiv2022

Enhanced Single RNA Imaging Reveals Dynamic Gene Expression in Live Animals

Imaging endogenous mRNAs in live animals is technically challenging. Here we describe an MS2 based signal Amplification with Suntag System that enables live-cell RNA imaging of high temporal resolution and with 8xMS2 stem-loops, which overcomes the obstacle of inserting a 1,300 nt 24xMS2 into the genome for the imaging of endogenous mRNAs. Using this tool we were able to image the activation of gene expression and the dynamics of endogenous mRNAs in the epidermis of live C. elegans.

cell biology↗
bioRxiv2022

Multi-environmental population phenotyping suggest the higher risks of wheat Rht-B1b and Rht-D1b cultivars in global warming scenarios

After six decades practice, the semi-dwarf alleles Rht-B1b and Rht-D1b (also called Rht-1 and Rht-2) had been applied into around 70% current wheat cultivars, laid the foundation for the worldwide wheat production supply, then the agronomic traits controlled by the two alleles still keep unclear except dwarfing wheat. Here 13 agronomic traits were investigated in 400 wheat accessions with seven environments, uncovered the genetic effects of Rht-B1b and Rht-D1b on wheat structure and yield traits in different genetic backgrounds and environments, and the distinct genetic effects between Rht-B1b and Rht-D1b, suggesting that the introduction of green revolution alleles profoundly shaped the agronomy traits of modern wheat cultivars. The late-sowing assays and regression analysis based on the phenotypic and their meteorological data showed the accessions containing Rht-B1b and Rht-D1b are more sensitive to the temperature increase, and the Rht-D1b may lost additional 8% yield compared the cultivars without the green revolution alleles if the average temperature increases 1 {degrees}C. These results suggest the application of green revolution are facing more challenges to maintain the futural wheat production supply in global warming scenarios.

molecular biology↗
bioRxiv2022

Evidence of active oviposition avoidance to systemically applied imidacloprid in the Colorado Potato Beetle (Leptinotarsa decemlineata)

Agricultural pests can develop behavioral resistance to insecticides via choosing to feed or oviposit on non-toxic hosts. As young larvae have relatively low mobility, oviposition preferences from female adults may play a critical role in shaping the evolutionary trajectory of pest populations. While oviposition avoidance of toxic hosts was found in different agriculture pests, it remains unclear whether such preferences can be learned from female adults. To address this question, we investigated feeding and oviposition preferences to imidacloprid in the Colorado Potato Beetle (CPB, Leptinotarsa decemlineata), a major potato pest. We first identified two CPB strains that have different levels of resistance to imidacloprid. Then, we performed choice assays in the two strains and found that both strains did not have an innate feeding avoidance to systemically applied imidacloprid at both larval and adult stages. Further oviposition choice assays showed that the susceptible strain preferred to lay eggs on insecticide-free plants while the resistant strain did not. Analysing moving patterns of the two strains suggested that the oviposition preference is likely due to active learning by the female adults. Together, these results indicate that CPB can have active oviposition avoidance, which might have contributed to the rapid global invasion of this agricultural pest.

animal behavior and cognition↗
bioRxiv2022

A Novel Regioselective Approach to Cyclize Phage-Displayed Peptides in Combination with Epitope-Directed Selection to Identify a Potent Neutralizing Macrocyclic Peptide for SARS-CoV-2

Using the regioselective cyanobenzothiazole condensation reaction with the N-terminal cysteine and the chloroacetamide reaction with an internal cysteine, a phage-displayed macrocyclic 12-mer peptide library was constructed and subsequently validated. Using this library in combination with iterative selections against two epitopes from the receptor binding domain (RBD) of the SARS-CoV-2 Spike protein, macrocyclic peptides that strongly inhibit the interaction between the Spike RBD and ACE2, the human host receptor of SARS-CoV-2, were identified. The two epitopes were used instead of the Spike RBD to avoid selection of nonproductive macrocyclic peptides that bind RBD but do not directly inhibit its interactions with ACE2. Antiviral tests against SARS-CoV-2 showed that one macrocyclic peptide is highly potent against viral reproduction in Vero E6 cells with an EC50 value of 3.1 M. The AlphaLISA-detected IC50 value for this macrocyclic peptide was 0.3 M. The current study demonstrates that two kinetically-controlled reactions toward N-terminal and internal cysteines, respectively, are highly effective in the construction of phage-displayed macrocyclic peptides, and the selection based on the SARS-CoV-2 Spike epitopes is a promising methodology in the identification of peptidyl antivirals.

biochemistry↗