Biology subjects

Xu, Y.

Publications and source records attributed to Xu, Y..

At least 613 records · Page 34Linked to original sources

bioRxiv2022

Boosting wheat functional genomics via indexed EMS mutant library of KN9204

A better understanding of wheat functional genomics could facilitate the targeted breeding for agronomic traits improvement and environmental adaptation. With the release of reference genomes and extensive re-sequencing data of wheat and relatives, wheat functional genomics enters a new era. However, limited transformation efficiency in wheat hampers in-depth gene functional study and genetic manipulation for breeding. Here, we generated an EMS mutagenesis library of KN9204, a widely grown elite wheat variety in northern China, with available reference genome, transcriptome, and epigenome of various tissues. The library harbors enormous developmental diversity covering important tissues and transition stages. Exome capture sequencing of 2,090 mutant lines, with probes designed by KN9204 genome, revealed that 98.79% of coding genes have mutations and 1,383 EMS-type SNPs per line averagely. Novel allelic variations for important agronomic trait-related genes, such as Rht-D1, Q, TaTB1, and WFZP, were identified. We tested 100 lines with severe mutations in 80 NAC TFs under drought and salinity stresses, and found 13 lines with altered sensitivity. Three lines were further analyzed for the regulation insight of NAC TFs in stress response by combing transcriptome and available chromatin accessibility data. Hundreds of direct targets of NAC with altered transcriptional pattern in mutant lines under salt or drought stress induction were identified, including SNAC1, DREB2B, CML16 and ZFP182, knowing factors in abiotic stresses response. Thus, we have generated and indexed KN9204 EMS mutant library which would facilitate functional genomics study and provide resources for genetic manipulation in wheat.

plant biology↗

bioRxiv2022

SAYSD1 senses UFMylated ribosome to safeguard co-translational protein translocation at the endoplasmic reticulum

Translocon clogging at the endoplasmic reticulum (ER) as a result of translation stalling triggers ribosome UFMylation, activating a Translocation-Associated Quality Control (TAQC) mechanism that degrades clogged substrates. How cells sense ribosome UFMylation to initiate TAQC is unclear. Here we use a genome-wide CRISPR/Cas9 screen to identify an uncharacterized membrane protein named SAYSD1 that facilitates TAQC. SAYSD1 associates with the Sec61 translocon, and also recognizes both ribosome and UFM1 directly, engaging a stalled nascent chain to ensure its transport via the TRAPP complex to lysosomes for degradation. Like UFM1 deficiency, SAYSD1 depletion causes the accumulation of translocation-stalled proteins at the ER and triggers ER stress. Importantly, disrupting UFM1- and SAYSD1-dependent TAQC in Drosophila leads to intracellular accumulation of translocation-stalled collagens, defective collagen deposition, abnormal basement membranes, and reduced stress tolerance. Together, our data support a model that SAYSD1 acts as a UFM1 sensor that collaborates with ribosome UFMylation at the site of clogged translocon, safeguarding ER homeostasis during animal development.

cell biology↗

bioRxiv2022

Pleiotropy of autism-associated chromatin regulators

Gene ontology analyses of high confidence autism spectrum disorder (hcASD) risk genes have historically highlighted chromatin regulation and synaptic function as major contributors to pathobiology. Our recent functional work in vivo has additionally implicated microtubule biology and identified disrupted cellular proliferation as a convergent ASD phenotype. As many chromatin regulators, including ASD risk genes ADNP and CHD3, are known to directly regulate both tubulins and histones, we studied the five chromatin regulators most strongly associated with ASD (ADNP, CHD8, CHD2, POGZ, and SUV420H1/KMT5B) specifically with respect to microtubule biology. We observe that all five localize to microtubules of the mitotic spindle in vitro and in vivo. Further in-depth investigation of CHD2 provides evidence that patient-derived mutations lead to a range of microtubule-related phenotypes, including disrupted localization of the protein at the mitotic spindle, spindle defects, cell cycle stalling, DNA damage, and cell death. Lastly, we observe that ASD genetic risk is significantly enriched among microtubule-associated proteins, suggesting broader relevance. Together, these results provide further evidence that the role of tubulin biology and cellular proliferation in ASD warrant further investigation and highlight the pitfalls of relying solely on annotated gene functions in the search for pathological mechanisms.

developmental biology↗

bioRxiv2022

Sleep restores an optimal computational regime in cortical networks

SUMMARYSleep is vitally important for brain function, yet its core restorative process remains an open question. Sleep is assumed to subserve homeostatic processes in the brain because sleep restores functional capacity, and stable function requires compensatory tuning of circuits in the face of experience. However, the set-point around which sleep tunes circuit computation is unknown; for more than four decades, the homeostatic aspect of sleep has been approximated by a heuristic model whose strongest correlate is Slow-wave Activity (SWA). While SWA can indicate sleep pressure, it fails to explain why animals need sleep. In contrast, criticality is a computational regime that optimizes information processing capacity, and is a homeostatically regulated set-point in isocortical circuits. Consistent with the effects of waking, criticality is degraded by experience-dependent plasticity. Whether criticality is the computational set-point of sleep is unknown. To address this question, we evaluated the effects of sleep and wake on emergent dynamics in ensembles of cortical neurons recorded continuously for 10-14 d in freely behaving rats. We show that normal waking experience progressively disrupts criticality, and that sleep functions to restore critical dynamics. Criticality is perturbed in a context-dependent manner depending on behavior and environmental variables, and waking experience is causal in driving these effects. The degree of deviation from criticality is robustly predictive of future sleep/wake behavior, more accurate than SWA, behavioral history, and other neural measures. Our results demonstrate that perturbation and recovery of criticality is a network homeostatic mechanism consistent with the core, restorative function of sleep.

neuroscience↗

bioRxiv2022

Trem2 Promotes Foamy Macrophage Lipid Uptake and Survival in Atherosclerosis

Atherosclerotic plaque formation is driven by the continued expansion of cholesterol loaded foamy macrophages within the arterial intima. Foamy macrophages are primarily derived from newly recruited monocytes, but factors regulating monocyte specification toward foamy macrophage differentiation and prolonged survival in plaque remain poorly understood. We used trajectory analysis of integrated single cell RNA-seq data, along with a genome-wide CRISPR screening approach to identify Triggering Receptor Expressed on Myeloid Cells 2 (Trem2) as a candidate regulator for foamy macrophage specification. Loss of Trem2 led to a reduced ability of foamy macrophages to take up additional oxidized low density lipoprotein (LDL) cholesterol in vitro. Competitive chimera experiments showed that Trem2-deficient macrophages were less competent to form foamy macrophages when competed against Trem2-sufficient macrophages in vivo. In addition, myeloid specific conditional deletion of Trem2 resulted in a dramatic attenuation of plaque progression, even when targeted in established atherosclerotic lesions. This was independent of changes in circulating inflammatory cytokines, monocyte recruitment, or serum cholesterol levels, but due to a reduction in plaque macrophage proliferation and enhanced cell death. Mechanistically, we link Trem2-deficient macrophages with an inability for cells to sense cholesterol loading and failure to upregulate efflux molecules. Accumulation of cholesterol in the endoplasmic reticulum enhanced activation of the ER-stress response that increased susceptibility for cholesterol-toxicity and cell death in foamy Trem2-deficient macrophages. Overall, this study identifies Trem2 as a regulator of foamy macrophage differentiation, atherosclerotic plaque growth, and as a putative therapeutic target for future intervention studies.

immunology↗

bioRxiv2022

MSdb: an integrated expression atlas of human musculoskeletal system

We introduce MSdb (https://www.msdb.org.cn), a database for visualization and integrated analysis of next-generation sequencing data from human musculoskeletal system, along with manually curated patient phenotype data. Systematic categorizing, standardized processing and freely accessible knowledge enables the reuse of public data. MSdb provides various types of analysis, including sample-level browsing of metadata information, gene/miRNA expression, and single-cell RNA-seq dataset. In addition, MSdb also allows integrated analysis for cross-samples and cross-omics analysis, including customized differentially-expressed gene/microRNA analysis, microRNA-gene network, scRNA-seq cross-sample/disease integration, and gene regulatory network analysis.

bioinformatics↗

bioRxiv2022

scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data

In droplet-based single-cell RNA-seq (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) assays, systematic contamination of ambient RNA molecules biases the estimation of genuine transcriptional levels. To correct the contamination, several computational methods have been developed. However, these methods do not distinguish the contamination-causing genes and thus either under- or over-corrected the contamination in our in-house snRNA-seq data of virgin and lactating mammary glands. Hence, we developed scCDC as the first method that specifically detects the contamination-causing genes and only corrects the expression counts of these genes. Benchmarked against existing methods on synthetic and real scRNA-seq and snRNA-seq datasets, scCDC achieved the best contamination correction accuracy with minimal data alteration. Moreover, scCDC applies to processed scRNA-seq and snRNA-seq data with empty droplets removed. In conclusion, scCDC is a flexible, accurate decontamination method that detects the contamination-causing genes, corrects the contamination, and avoids the over-correction of other genes.

bioinformatics↗

bioRxiv2022

Antibody binding reports spatial heterogeneities in cell membrane organization

The spatial organization of cell membrane glycoproteins and glycolipids is critical for mediating the binding of ligands, receptors, and macromolecules on the plasma membrane. However, we currently do not have the methods to quantify the spatial heterogeneities of macromolecular crowding on live cell surfaces. In this work, we combine experiment and simulation to report crowding heterogeneities on reconstituted membranes and live cell membranes with nanometer spatial resolution. By quantifying the effective binding affinity of IgG monoclonal antibodies to engineered antigen sensors, we discovered sharp gradients in crowding within a few nanometers of the crowded membrane surface. Our measurements on human cancer cells support the hypothesis that raft-like membrane domains exclude bulky membrane proteins and glycoproteins. Our facile and high-throughput method to quantify spatial crowding heterogeneities on live cell membranes may facilitate monoclonal antibody design and provide a mechanistic understanding of plasma membrane biophysical organization.

biophysics↗

bioRxiv2022

Supramodal Shape Representation in the Human Brain

We can sense an objects shape by vision or touch. Previous studies suggested that the inferolateral occipitotemporal cortex (ILOTC) implements supramodal shape representations as it responds more to seeing or touching objects than shapeless textures. However, such activation in the anterior portion of the ventral visual pathway could be due to the conceptual representation of an object or visual imagery triggered by touching an object. We addressed these possibilities by directly comparing shape and conceptual representations in early blind (who lack visual experience/imagery) and sighted participants. We found that bilateral ILOTC in both groups showed stronger activation during a shape verification task than during a conceptual verification task made on the names of the same manmade objects. Moreover, the distributed activity in the ILOTC encoded shape similarity but not conceptual association among objects. Besides the ILOTC, we also found shape representation in both groups bilateral ventral premotor cortices and intraparietal sulcus, a frontoparietal circuit relating to object grasping and haptic processing. In contrast, the conceptual verification task activated both groups left perisylvian brain network relating to language processing, and, interestingly, the cuneus in early blind participants only. The ILOTC had stronger functional connectivity to frontoparietal circuit than to the left perisylvian network, forming a modular structure specialized in shape representation. Our results conclusively support that the ILOTC selectively implements shape representation independently of visual experience, and this unique functionality likely comes from its privileged connection to the frontoparietal haptic circuit.

neuroscience↗

bioRxiv2022

Systematic mining and genetic characterization of regulatory factors for wheat spike development

The spike architecture of wheat plays a crucial role in determining grain number, making it a key trait to optimize in wheat breeding programs. In this study, through a multi-omic approach, we analyzed the transcriptome and epigenome profiles of the shoot apex at eight developmental stages, revealing coordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering transition. We constructed a core transcriptional regulatory network (TRN) that drives wheat spike formation, and experimentally validated a multi-layer regulatory module involving TaSPL15, TaAGLG1, and TaFUL2. By integrating the TRN with genome-wide association analysis (GWAS), we identified 227 transcription factors (TFs), including 42 with known functions and 185 with unknown functions. Further investigation of 61 novel TFs using multiple homozygous mutant lines uncovered 36 TFs with altered spike architecture or flowering time, such as TaMYC2-A1, TaMYB30-A1, and TaWRKY37-A1. Of particular interest, TaMYB30-A1, downstream and repressed by WFZP, was found to regulate fertile spikelet number. Notably, during the domestication and breeding process in China, the excellent haplotype of TaMYB30-A1 containing a C allele at the WFZP binding site was enriched, leading to improved agronomic traits. Our study presents novel and high-confidence regulators and offers an effective strategy for understanding the genetic basis of wheat spike development, with practical impact for wheat breeding applications.

plant biology↗

bioRxiv2022

Tumor-specific CD4 T cells instruct monocyte differentiation in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDA) is a lethal malignancy resistant to immunotherapy. The pancreatic tumor microenvironment is shaped and maintained by myeloid cells that outnumber tumor cells. Here, using monocyte fate-mapping PDA mouse models and human tumor tissues, we identify monocytes give rise to most heterogeneous macrophage subpopulations in PDA. We show that monocyte differentiation is governed by the local presence of CD4, but not CD8, T cells. We demonstrate that tumor specific CD4 T cells induce monocyte differentiation into antitumor MHCIIhi proinflammatory macrophages dependent on non-redundant IFN{gamma} and CD40 signaling pathways that suppress tumor growth. Pancreatic tissue-resident macrophages exhibit an immunosuppressive pro-tumor state that is refractory to the modulatory effects of antitumor CD4 T cells. Intratumoral monocytes adopt a pro-tumor fate indistinguishable from tissue-resident macrophages following CD4 T cell depletion. Thus, tumor-specific CD4 T cell governance of monocyte fate promotes immune-mediated control of solid tumors. Highlights{blacksquare} Circulating monocytes are progenitors to most heterogeneous macrophage subsets in PDA {blacksquare}Monocyte-derived macrophage acquisition of an MHCIIhi phenotype is dependent on tumor-specific CD4 T cells {blacksquare}In the absence of CD4 T cells, monocyte-derived macrophages acquire tissue resident macrophage traits and tumors rapidly progress {blacksquare}IFN{gamma} and CD40 signaling are nonredundant and critical determinants of intratumoral monocyte fate

immunology↗

bioRxiv2022

The in-tissue molecular architecture of β-amyloid pathology in the mammalian brain.

Amyloid plaques composed of extracellular focal deposition of A{beta} fibrils are a hallmark of Alzheimers disease (AD). Cryo-EM structures of A{beta} fibrils purified from human AD brain tissue post mortem have recently been determined. However, the molecular architecture of amyloid plaques in the context of fresh, unfixed mammalian brain tissue is unknown. Here, using cryogenic correlated light and electron tomography we report the native, in situ molecular architecture of A{beta} fibrils in the brain of a mouse model containing the Arctic familial AD mutation (AppNL-G-F) and an atomic model of Arctic A{beta} fibril purified from the brains of these animals. We show that in-tissue A{beta} fibrils are arranged in a lattice or in parallel bundles within a plaque, and are interdigitated by subcellular compartments, exosomes, extracellular droplets and extracellular multilamellar bodies. At the atomic level, the Arctic A{beta} fibril differs significantly from earlier structures of A{beta} amyloid extracted from AppNL-F mice models and human AD brain tissue, showing a striking effect of the Arctic mutation (E22G) on fibril structure. Cryo-electron tomography of ex vivo purified and in-tissue amyloid revealed an ensemble of additional fibrillar species, including thin protofilament-like rods and branched fibrils. Together, these results provide a structural model for the dense network architecture that characterises {beta}-amyloid plaque pathology.

neuroscience↗

bioRxiv2022

A compound PCP scheme underlies sequential rosettes-based cell intercalation

Sequential rosettes are a type of collective cell behavior recently discovered in the C. elegans embryo to mediate directional cell migration through sequential formation and resolution of multicellular rosettes involving the migrating cell and its neighboring cells along the way. Here we show that a Planar Cell Polarity (PCP)-related polarity scheme regulates sequential rosettes, which is distinct from the known mode of how PCP regulates multicellular rosettes in the process of convergent extension. Specifically, non-muscle myosin (NMY) localization and edge contraction are perpendicular to that of Van Gogh as opposed to colocalizing with Van Gogh. Further analyses suggest a two-component polarity scheme: one being the canonical PCP pathway with MIG-1/Frizzled and VANG-1/Van Gogh localized to the vertical edges, the other being MIG-1/Frizzled and NMY-2 localized to the midline/contracting edges. Both MIG-1/Frizzled and VANG-1/Van Gogh are required for NMY-2 localization and contraction of the midline edges, but in redundancy with LAT-1/Latrophilin, an adhesion GPCR which has not been shown to regulate multicellular rosettes. Our results establish a distinct mode of PCP-mediated cell intercalation and shed light on the versatile nature of PCP pathway.

developmental biology↗

bioRxiv2022

Learning predictive models of tissue cellular neighborhoods from cell phenotypes with graph pooling

It remains poorly understood how different cell types organize and coordinate with each other to support tissue functions. We describe CytoCommunity for identification of tissue cellular neighborhoods (TCNs) based on cell phenotypes and their spatial distributions. CytoCommunity learns a mapping directly from cell phenotype space to TCN space by a graph neural network model without using additional gene or protein expression features and is thus applicable to tissue imaging data with a small number of measured features. By leveraging graph pooling, CytoCommunity enables de novo identification of condition-specific TCNs under the supervision of image labels. Using various types of single-cell-resolution spatial proteomics and transcriptomics images, we demonstrate that CytoCommunity can identify TCNs of variable sizes with substantial improvement over existing methods. To further evaluate the ability of CytoCommunity for discovering condition-specific TCNs by supervised learning, we apply it to colorectal and breast cancer tissue images with clinical outcome information. Our analysis reveals novel granulocyte- and cancer associated fibroblast-enriched TCNs specific to high-risk tumors as well as altered tumor-immune and tumor-stromal interactions within and between TCNs compared to low-risk tumors. CytoCommunity represents the first computational tool for end-to-end unsupervised and supervised analyses of single-cell spatial maps and enables direct discovery of conditional-specific cell-cell communication patterns across variable spatial scales.

bioinformatics↗

bioRxiv2022

A contamination focused approach for optimizing thesingle-cell RNA-seq experiment

Achieving high data quality in single-cell RNA-seq (scRNA-seq) experiments has always been a significant challenge stemming from minute signal that can be detected in individual cells. Droplet-based scRNA-seq additionally suffers from ambient contamination, comprising nucleic acid materials released by dead cells into the loading buffer and co-encapsulated with real cells, which further washes out real biological signals. Here, we developed quantitative, ambient contamination-based metrics and an associated software package that can both evaluate current datasets and guide new experimental optimizations. We performed a series of experimental optimizations using the inDrops platform to address the mechanical and microfluidic cell encapsulation aspect of an scRNA-seq experiment, with a focus on minimizing ambient contamination. We report improvements that can be achieved via cell fixation, microfluidic loading, microfluidic dilution, and nuclei versus cell preparation; many of these parameters are inaccessible on commercial platforms. We provide insights into previously obscured factors that can affect scRNA-seq data quality and suggest mitigation strategies that can guide future experiments.

genomics↗

bioRxiv2022

Molecular Recognition of Itching Neuropeptides by Bombesin Receptors.

Neuromedin B (NMB) and gastrin-releasing peptide (GRP), two bombesin analogs, are endogenous itch-specific neuropeptides that induce histaminergic and nonhistaminergic itch, respectively. Their functions are mediated by two G protein-coupled bombesin receptors, NMBR and GRPR. Here we present cryo-electron microscopy(cryo-EM) structures of G protein coupled NMBR and GRPR bound to NMB and GRP, respectively. The structures reveal that both bombesin receptors contain an extended and deep pocket to adopt NMB and GRP, with the conserved C-terminal motif of GH(F/L)M from both peptides to contact the toggle switch residues for the receptor activation. Together with mutational and functional data, our structures reveal the mechanism of ligand selectivity and specific activation of the bombesin receptors. These findings also pave the way to facilitate rational design of therapies targeting bombesin receptors for the treatment of pruritus.

biophysics↗

bioRxiv2022

DeepCIP: a multimodal deep learning method for the prediction of internal ribosome entry sites of circRNAs

MotivationCircular RNAs (circRNAs) have been found to have the potential to code proteins. Internal ribosome entry sites (IRESs) are key RNA regulatory elements for the translation of proteins by circRNAs through a cap-independent mechanism. IRES can be identified by bicistronic assay, but the method is time-consuming and laborious. Therefore, it is important to develop computational methods for facilitating IRES identification, evaluation, and design in circRNAs. ResultsIn this study, we proposed DeepCIP, a multimodal deep learning approach for circRNA IRES prediction, by exploiting both sequence and structure information. As far as we know, DeepCIP is the first predictor for circRNA IRESs, which consists of an RNA processing module, an S-LSTM module, a GCN module, a feature fusion module, and an ensemble module. The comparative studies show that DeepCIP outperforms other comparative methods and justify the effectiveness of the sequence model and structure model of DeepCIP for extracting features. We found that the integration of structural information on the basis of sequence information effectively improves predictive performance. For the real circRNA IRES prediction, DeepCIP also outperforms other methods. DeepCIP may facilitate the study of the coding potential of circRNAs as well as the design of circRNA drugs. DeepCIP as a standalone program is freely available at https://github.org/zjupgx/DeepCIP.

bioinformatics↗

bioRxiv2022

Molecular recognition of two endogenous hormones by the human parathyroid hormone receptor-1

Parathyroid hormone (PTH) and PTH-related peptide (PTHrP) are two endogenous hormones recognized by PTH receptor -1 (PTH1R), a member of class B G protein couple receptors (GPCRs). Both PTH and PTHrP analogs including teriparatide and abaloparatide, are approved drugs for osteoporosis, but they exhibit distinct pharmacology. Here we report two cryo-EM structures of human PTH1R bound to PTH and PTHrP in the G protein-bound state at resolutions of 2.6 and 3.2 [A], respectively. Detailed analysis of these structures uncovers both common and unique features for the agonism of PTH and PTHrP. Molecular dynamics (MD) simulation and together with site-directed mutagenesis studies reveal the molecular basis of endogenous hormones recognition specificity and selectivity to PTH1R. These results provide a rational template for the clinical use of PTH and PTHrP analogs as an anabolic therapy for osteoporosis and other disorders.

biochemistry↗