Biology subjects

Xu, Z.

Publications and source records attributed to Xu, Z..

At least 271 records · Page 15Linked to original sources

bioRxiv2023

MUSTANG: MUlti-sample Spatial Transcriptomics data ANalysis with cross-sample transcriptional similarity Guidance

AO_SCPLOWBSTRACTC_SCPLOWSpatially resolved transcriptomics has revolutionized genome-scale transcriptomic profiling by providing high-resolution characterization of transcriptional patterns. We here present our spatial transcriptomics analysis framework, MUSTANG (MUlti-sample Spatial Transcriptomics data ANalysis with cross-sample transcriptional similarity Guidance), which is capable of performing multi-sample spatial transcriptomics spot cellular deconvolution by allowing both cross-sample expression based similarity information sharing as well as spatial correlation in gene expression patterns within samples. Experiments on two real-world spatial transcriptomics datasets demonstrate the effectiveness of MUSTANG in revealing biological insights inherent in cellular characterization of tissue samples under the study. MUSTANG is publicly available at at https://github.com/namini94/MUSTANG

bioinformatics↗

bioRxiv2023

CD36-Pyruvate Kinase M2 Signaling Promotes Macrophage Phagocytosis Through Mitochondrial Reactive Oxygen Species

Macrophage efferocytosis, the process by which phagocytes engulf and remove apoptotic cells (ACs), plays a critical role in maintaining tissue homeostasis. Efficient efferocytosis prevents secondary necrosis, mitigates chronic inflammation, and impedes atherosclerosis progression. However, the regulatory mechanisms of efferocytosis under atherogenic conditions remain poorly understood. We previously demonstrated that oxidized LDL (oxLDL), an atherogenic lipoprotein, induces mitochondrial reactive oxygen species (mtROS) in macrophages via CD36. In this study, we demonstrate that macrophage mtROS facilitate continual efferocytosis through a positive feedback mechanism. However, oxLDL disrupts continual efferocytosis by dysregulating the internalization of ACs. This disruption is mediated by an overproduction of mtROS. Mechanistically, oxLDL/CD36 signaling promotes the translocation of cytosolic PKM2 to mitochondria, facilitated by the chaperone GRP75. Mitochondrial PKM2 then binds to Complex III of the electron transport chain, inducing mtROS production. This study elucidates a novel regulatory mechanism of efferocytosis in atherosclerosis, providing potential therapeutic targets for intervention. SUMMARYMacrophages clear apoptotic cells through a process called efferocytosis, which involves mitochondrial ROS. However, the atherogenic oxidized LDL overstimulates mitochondrial ROS via the CD36-PKM2 pathway, disrupting continual efferocytosis. This finding elucidates a novel molecular mechanism that explains defects in efferocytosis, driving atherosclerosis progression.

immunology↗

bioRxiv2023

Robust collection and processing for label-free single voxel proteomics

With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk tissues. However, such bulk measurement lacks spatial resolution and obscures important tissue heterogeneity, which make it impossible for proteome mapping of tissue microenvironment. Here we report an integrated wet collection of single tissue voxel and Surfactant-assisted One-Pot voxel processing method termed wcSOP for robust label-free single voxel proteomics. wcSOP capitalizes on buffer droplet-assisted wet collection of single tissue voxel dissected by LCM into the PCR tube cap and MS-compatible surfactant-assisted one-pot voxel processing in the collection cap. This convenient method allows reproducible label-free quantification of [~]900 and [~]4,600 proteins for single voxel from fresh frozen human spleen tissue at 20 m x 20 m x 10 m (close to single cells) and 200 m x 200 m x 10 m ([~]100 cells), respectively. 100s-1000s of protein signatures with differential expression levels were identified to be spatially resolved between spleen red and white pulp regions depending on the voxel size. Region-specific signaling pathways were enriched from single voxel proteomics data. Antibody-based CODEX imaging was used to validate label-free MS quantitation for single voxel analysis. The wcSOP-MS method paves the way for routine robust single voxel proteomics and spatial proteomics.

molecular biology↗

bioRxiv2023

Osteoclast-Cancer Cell Metabolic Symbiosis Renders PARP Inhibitor Therapy Resistance in Bone Metastasis

Seventy percent of patients with late-stage breast cancer develop distal bone metastases; however, the mechanism by which the metabolic microenvironment affects resistance to therapy remains unknown. We investigated the metabolic bone microenvironment and identified glutathione metabolism as the top pathway in osteoclasts, which provides feedback to tumor cells to help neutralize oxidative stress and generate PARP inhibitor (PARPi) therapy resistance. GPX4, the critical enzyme responsible for glutathione oxidation, was upregulated during PARPi therapy through stress-induced ATF4-dependent transcriptional programming. The increased absorption of glutamine and the upregulation of GPX4 expression work in concert to enhance glutathione metabolism in cancer cells. Human clinical sample analysis of paired primary breast tumor and bone metastasis samples revealed that GPX4 was significantly induced in bone metastases. Combination therapy utilizing PARPi and zoledronate, which blocks osteoclast activity and thereby reduces the microenvironmental glutamine supply, generates a synergistic effect in reducing bone metastasis. Thus, our results identified an essential metabolic symbiosis between bone-resident cells and metastatic cancer cells during PARPi therapy. SIGNIFICANCEOsteoclast-derived glutamine is taken up by tumor cells to synthesize glutathione and neutralize the ROS generated by PARPi. This is the first example of "metabolic symbiosis" in therapeutic resistance of bone metastasis.

cancer biology↗

bioRxiv2023

ERK signaling drives evolutionary expansion of the mammalian cerebral cortex

The molecular basis for cortical expansion during evolution remains largely unknown. Here, we found that FGF-extracellular signal-regulated kinase (ERK) signaling promotes the self-renewal and expansion of cortical radial glial (RG) cells. Furthermore, FGF-ERK signaling induces Bmp7 expression in cortical RG cells, which increases the length of the neurogenic period. We demonstrate that ERK signaling and SHH signaling mutually inhibit each other in cortical RG cells. We also provide evidence that ERK signaling is elevated in cortical RG cells during development and evolution. We conclude that the evolutionary expansion of the mammalian cortex, notably in human, is driven by ERK-BMP7-GLI3R signaling pathway in cortical RG cells, which participates in a positive feedback loop through antagonizing SHH signaling. We also propose that the molecular basis for cortical evolutionary dwarfism, exemplified by the lissencephalic mouse which originated from a larger and gyrencephalic ancestor, is due to mouse cortical RG cells receiving higher SHH signaling that antagonizes ERK signaling.

neuroscience↗

bioRxiv2023

A reverse-central-dogma pathway underlies ribosome-antibiotic efficacy and accelerates resistance evolution

In bacteria, the precise coordination of DNA replication, transcription and translation is mediated by dynamic interactions among the corresponding macromolecular machineries, playing a pivotal role in maintaining cellular homeostasis. Here we show that such coordination is hijacked by ribosome antibiotics to trigger secondary damage that predominantly contributes to their efficacy. Specifically, through developing a transcription dynamics profiling method, complemented by genetic and biochemical approaches, we unveil that translation inhibition disrupts transcription-translation coupling, leading to premature stalling of RNA polymerase (RNAP) at genome scale, which subsequently triggers extensive genomic instability. Moreover, mutagenic repairment of genomic lesions is mediated by heterogenous hyperactivation of SOS response, facilitating an inducible evolutionary path towards genetic resistance characterized by a unique mutation spectrum. Our findings thereby reveal a yet overlooked reverse-central-dogma pathway underlying actions of ribosome inhibitors, and establish a framework to understand antibiotic efficacy and induced mutagenesis through network disorder.

microbiology↗

bioRxiv2023

Unraveling the Pathogenesis of Idiopathic Pulmonary Fibrosis Complicated with Type 2 Diabetes through Microarray Data Analysis

BackgroundIdiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease characterized by excessive scarring of lung tissue. Recent studies have indicated a potential link between IPF and type 2 diabetes (T2D), suggesting that T2D may contribute to the pathogenesis of IPF or vice versa. In this study, we aim to investigate the underlying molecular mechanisms and pathways involved in the development of IPF complicated with T2D using microarray data analysis. MethodsThe datasets for Type 2 Diabetes (T2D) (GSE25724) and Idiopathic Pulmonary Fibrosis (IPF) (GSE110147) were obtained from the Gene Expression Omnibus (GEO) database. Differential expression analysis was conducted using the limma package in R to identify genes that were significantly differentially expressed between T2D and IPF samples. Functional enrichment analysis of these differentially expressed genes was performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG). To explore protein-protein interactions, protein-protein interaction networks were constructed using the Search Tool for the Retrieval of Interacting Genes (STRING) database and visualized using Cytoscape. CytoHubba, a plugin in Cytoscape, was utilized to identify hub genes in the network. The identified hub genes were further validated in independent datasets: GSE166467 for T2D and GSE24206 for IPF. To assess the predictive value of the hub genes, receiver operating characteristic (ROC) curves were generated. Additionally, gene set enrichment analysis was performed to uncover potential biological pathways associated with the hub genes. Finally, an analysis of immune infiltration within the hub gene network was conducted. ResultsA total of 255 differentially expressed genes (DEGs) were found to be commonly dysregulated in both Type 2 Diabetes (T2D) and Idiopathic Pulmonary Fibrosis (IPF). Pathways related to metabolic processes were significantly enriched in the analysis of both T2D and IPF. Through the validation process, RPL30 was identified as a hub gene, exhibiting an area under the curve (AUC) value greater than 0.65 for both T2D and IPF. Additionally, we identified 92 transcription factors (TFs) and 54 microRNAs (miRNAs) that may potentially regulate the expression of RPL30. ConclusionsThis study provides novel insights by highlighting the role of RPL30 in the shared pathogenesis of pulmonary fibrosis and Type 2 diabetes (T2D). The findings suggest that RPL30 has the potential to serve as a biomarker and therapeutic target for these conditions.

bioinformatics↗

bioRxiv2023

Patient-derived organoids assist personalized treatment for a patient with multiple metastatic neuroendocrine carcinoma of the cervix

Neuroendocrine carcinoma of the cervix (NECC) is a rare subtype of cervical cancer with rapid metastasis. Lack of treatment regimens for metastatic NECC highlights the need for preclinical models and personalized treatment. Here, we established two patient-derived NECC organoid lines from lung metastases from the same patient, one of which was drug-free and the other exhibited tolerance to carboplatin plus etoposide (EP). The two organoids recapitulated the histopathology and genomic spectrum of the original tumors. Whole-genome sequencing revealed genomic structural variations (SVs), including HPV16 infection, NEUROD2, and ERBB2 amplification. The sensitivity phenotype of organoids to ERBB2 inhibitors coincides with the genomic features of ERBB2 amplification. In addition, the patient after relapse responded well to the paclitaxel plus carboplatin (TC) regimen as recommended by organoid drug screening, underscoring the utility of organoids as preclinical models. We first provide two NECC organoids of lung metastases with comprehensive molecular characteristics as valuable resources for this rare cancer and give a typical application for personalized treatment based on organoids.

cancer biology↗

bioRxiv2023

Microglia Regulate Sleep via Calcium-Dependent Modulation of Norepinephrine Transmission

Sleep interacts reciprocally with immune system activity, but its specific relationship with microglia - the resident immune cells in the brain - remains poorly understood. Here we show that microglia can regulate sleep through a mechanism involving Gi-coupled GPCRs, intracellular Ca2+ signaling, and suppression of norepinephrine transmission. Chemogenetic activation of microglia Gi signaling strongly promoted sleep, whereas pharmacological blockade of Gi-coupled P2Y12 receptors decreased sleep. Two-photon imaging showed that P2Y12/Gi activation elevated microglia intracellular Ca2+, and blockade of this Ca2+ elevation largely abolished the Gi-induced sleep increase. Microglia Ca2+ level also increased at natural wake-to-sleep transitions, caused partly by reduced norepinephrine. Furthermore, imaging of norepinephrine activity with its biosensor showed that microglia P2Y12/Gi activation significantly reduced norepinephrine, partly by increasing the adenosine concentration. Thus, microglia can regulate sleep through reciprocal interactions with norepinephrine transmission.

neuroscience↗

bioRxiv2023

Degradation and release of dissolved environmental RNAs from zebrafish cells

Environmental RNAs in water are gradually being applied in aquatic ecological surveys, water pollution monitoring, etc., but the current methods to detect environmental RNAs in water can mainly measure the RNAs in the filters that are used for filtering water samples, neglecting dissolved environmental RNAs in water. The sources and degradation profiles of dissolved environmental RNAs in water remain unknown. The present study was conducted to measure the permeability of extracted RNAs from zebrafish cells through filters, the degradation of extracted RNAs from zebrafish cells in tubes, and the release rate and degradation of dissolved environmental RNAs from living zebrafish cells and dying zebrafish cells, aiming to provide dynamic information from dissolved environmental RNAs in water. The results showed that there were no significant differences between the levels of extracted RNAs from zebrafish cells before filtration with 0.45 {micro}m filters and those in the filtrates. The extracted RNAs from zebrafish cells degraded in water in the tubes, and after 2 months, more than 15% of RNAs in the groups of RNAs in water were still detected. The half-life of all the RNAs in the tubes was approximately 20[~]43 days. During the 6-day experiment of the release and degradation of dissolved RNAs from living cells, an average of 4.1x10-4 [~] 1.7x10-3 pg dissolved RNAs (7.6x105 [~] 3.2x106 RNA bases) were secreted per cell per day into the liquid environment. During the 6-day experiment of the release and degradation of dissolved RNAs from dying cells, approximately 4.2 pg of dissolved RNAs released by a dying zebrafish cell in water could be detected. The dissolved environmental RNAs in water from zebrafish cells degraded faster in the presence of zebrafish cells: under the conditions without zebrafish cells, the average survival rate of the dissolved environmental RNAs in water per day was 98.4%/day; under the conditions with living zebrafish cells, the average survival rate per day was 49.7%/day; and under the conditions with dying zebrafish cells, the average survival rate per day was 34.9%/day. The estimated levels of dissolved environmental RNAs in water in fish tanks were too low to be detected by the current techniques. Although the methods in the present study need to be improved, this study may provide information to develop new ways to measure the dynamics of dissolved environmental RNAs in water and quantitatively analyze RNAs released into liquid environments of living and dying cells.

ecology↗

bioRxiv2023

Optogenetic Stimulation of Single Ganglion Cells in the Living Primate Fovea

Though the responses of the rich variety of retinal ganglion cells (RGCs) reflect the totality of visual processing in the retina and provide the sole conduit for those processed responses to the brain, we have much to learn about how the brain uses these signals to guide behavior. An impediment to developing a comprehensive understanding of the role of retinal circuits in behavior is the paucity of causal studies in the intact primate visual system. Here we demonstrate the ability to optogenetically activate individual RGCs with flashes of light focused on single RGC somas in vivo, with no evidence for activation of neighboring cells. The ability to selectively activate specific cells is the first step toward causal experiments that directly link retinal circuits to visual experience and behavior.

neuroscience↗

bioRxiv2023

Identification of five characteristic ferroptosis-related genes as novel biomarkers for ischemic stroke using bioinformatic and machine learning strategies

Ferroptosis is crucial in neuronal cell death, associated with various neurological disorders. However, the role of ferroptosis-related genes (FRGs) in ischaemic stroke (IS) has yet to be well elucidated. We downloaded IS-related gene information and FRGs from the Gene Expression Omnibus (GEO) and Ferritin databases (FerrDb). 22 IS-related DE-FRGs were obtained. Functional enrichment analysis showed that these genes involve multiple regulatory pathways related to IS pathogenesis, including redox, amino acid metabolism, and cell cycle. Subsequently, DUOX2, MDM2, EGFR, MAP3K14, and TRIM46 were identified as core marker genes among the 22 DE-FRGs by lasso and SVM-RFE algorithms. The construction of the nomogram using the five marker genes had excellent diagnostic value. In addition, CIBERSORT analysis showed that changes in the immune microenvironment of IS patients might be associated with TRIM46, MDM2, and DUOX2. In addition, a total of 66 drugs targeting two characteristic FRGs were obtained. The ceRNA networks revealed complex regulatory relationships based on characteristic FRGs. These findings provide new insights into the diagnosis and treatment of IS.

bioinformatics↗

bioRxiv2023

AMPK targets PDZD8 to trigger carbon source shift to glutamine

The shift of carbon utilisation from glucose to other nutrients is a fundamental metabolic adaptation to cope with the decreased glucose oxidation during fasting or starvation1. AMP-activated protein kinase (AMPK) plays crucial roles in manifesting physiological benefits accompanying glucose starvation or calorie restriction2. However, the underlying mechanisms are unclear. Here, we show that low glucose-induced activation of AMPK plays a decisive role in the shift of carbon utilisation from glucose to glutamine. We demonstrate that endoplasmic reticulum (ER)-localised PDZD8, which we identify to be a new substrate of AMPK, is required for the glucose starvation-promoted glutaminolysis. AMPK phosphorylates PDZD8 at threonine 527 (T527), and promotes it to interact with and activate the mitochondrial glutaminase 1 (GLS1), a rate-limiting enzyme of glutaminolysis3-5, and as a result the ER-mitochondria contact is strengthened. In vivo, PDZD8 enhances glutaminolysis, and triggers mitohormesis that is required for extension of lifespan and healthspan in Caenorhabditis elegans subjected to glucose starvation or caloric restriction. Muscle-specific re-introduction of wildtype PDZD8, but not the AMPK-unphosphorylable PDZD8-T527A mutant, to PDZD8-/- mice is able to rescue the increase of glutaminolysis, and the rejuvenating effects of caloric restriction in aged mice, including grip strength and running capacity. Together, these findings reveal an AMPK-PDZD8-GLS1 axis that promotes glutaminolysis and executes the anti-ageing effects of calorie restriction by promoting inter-organelle crosstalk between ER and mitochondria.

cell biology↗

bioRxiv2023

Replication stress inducing ELF3 upregulation promotes BRCA1-deficient breast tumorigenesis in luminal progenitors

BRCA1 is a critical tumor suppressor, mutations in which greatly increase risks for many tumors in carriers, most notably breast cancer. Luminal progenitor cells (LPs) are the currently recognized cells origin of BRCA1-deficient breast cancers. However, the reason why LPs are prone to transform with BRCA1 deficiency has not been elucidated. Here, using single-cell sequencing of human BRCA1 mutant breast cancers and RNA sequencing (RNA-seq) of BRCA1-deficient normal mammary cells, we reveal that replication stress is a feature of LPs and a driving factor during BRCA1-associated tumorigenesis. Mechanistically, replication stress and BRCA1 deficiency lead to significant upregulation of ELF3 expression. ELF3 can help suppress excessive genomic instability and promote LP transformation with BRCA1 deficiency. Moreover, ELF3 emerged as a core transcription factor regulating LP genes, leading to LP expansion. Our findings suggest that replication stress is a driving factor during BRCA1-associated tumorigenesis in luminal progenitor cells and elucidates the key role of ELF3 during this process.

cancer biology↗

bioRxiv2023

A Cryptic Basic Groove formed by Ubiquitin and Histone H3 Mediates the Selective Recognition of H2AK119Ub Nucleosomes by Synovial Sarcoma X Breakpoint 1 Protein

The cancer-specific fusion oncoprotein SS18-SSX1 disturbs chromatin accessibility by hijacking the BAF complex from the promoters and enhancers to the polycomb-repressed chromatin regions. This process relies on the selective recognition of H2AK119Ub nucleosomes by SSX1. However, the mechanism by which SSX1 selective recognition of H2AK119Ub nucleosomes in the absence of ubiquitin (Ub)-binding capacity remains unknown. Here we report the cryo-EM structure of SSX1 bound to H2AK119Ub nucleosomes at 3.1 [A] resolution. Combined in vitro biochemical and cellular assays revealed that the Ub recognition by SSX1 is unique and depends on a cryptic basic groove formed by H3 and the Ub motif on the H2AK119 site. Moreover, this unorthodox binding mode of SSX1 induces DNA unwrapping at the entry/exit sites. Together, our results describe a unique mode of site-specific ubiquitinated nucleosome recognition that underlies the specific hijacking of the BAF complex to polycomb regions by SS18-SSX1 in synovial sarcoma.

molecular biology↗

bioRxiv2023

Neuromorphic Cytometry: Implementation on cell counting and size estimation

Flow cytometry is a widespread and high-throughput technology that can measure the features of cells and can be combined with fluorescence analysis for additional phenotypical characterisations but only provide low-dimensional output and spatial resolution. Imaging flow cytometry is another technology that offers rich spatial information, allowing more profound insight into single-cell analysis. However, offering such high-resolution, full-frame feedback can compromise speed and has become a significant trade-off challenge to tackle during development. In addition, the current dynamic range offered by conventional photosensors can only capture limited fluorescence signals, exacerbating the difficulties in elevating performance speed. Neuromorphic photo-sensing architecture focuses on the events of interest via individual-firing pixels to reduce data redundancy and provide low latency in data processing. With the inherent high dynamic range, this architecture has the potential to drastically elevate the performance in throughput by incorporating motion-activated spatial resolution. Herein, we presented an early demonstration of neuromorphic cytometry with the implementation of object counting and size estimation to measure 8 m and 15 m polystyrene-based microparticles and human monocytic cell line (THP-1). In this work, our platform has achieved highly consistent outputs with a widely adopted flow cytometer (CytoFLEX) in detecting the total number and size of the microparticles. Although the current platform cannot deliver multiparametric measurements on cells, future endeavours will include further functionalities and increase the measurement parameters (granularity, cell condition, fluorescence analysis) to enrich cell interpretation.

cell biology↗

bioRxiv2023

Shape-changing electrode array for minimally invasive large-scale intracranial brain activity mapping

Large-scale brain activity mapping is important for understanding the neural basis of behaviour. Electrocorticograms (ECoGs) have high spatiotemporal resolution, bandwidth, and signal quality. However, the invasiveness and surgical risks of electrode array implantation limit its application scope. We developed an ultrathin, flexible shape-changing electrode array (SCEA) for large-scale ECoG mapping with minimal invasiveness. SCEAs were inserted into cortical surfaces in compressed states through small openings in the skull or dura and fully expanded to cover large cortical areas. MRI and histological studies on rats proved the minimal invasiveness of the implantation process and the high chronic biocompatibility of the SCEAs. High-quality micro-ECoG activities mapped with SCEAs from rodent brains during seizures and canine brains during the emergence period revealed the spatiotemporal organization of different brain states with resolution and bandwidth that cannot be achieved using existing noninvasive techniques. The biocompatibility and ability to map large-scale physiological and pathological cortical activities with high spatiotemporal resolution, bandwidth, and signal quality in a minimally invasive manner offer SCEAs as a superior tool for applications ranging from fundamental brain research to brain-machine interfaces.

neuroscience↗

bioRxiv2023

The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues

Chicken is a valuable model for understanding fundamental biology, vertebrate evolution and diseases, as well as a major source of nutrient-dense and lean-protein-enriched food globally. Although it is the first non-mammalian amniote genome to be sequenced, the chicken genome still lacks a systematic characterization of functional impacts of genetic variants. Here, through integrating 7,015 RNA-Seq and 2,869 whole-genome sequence data, the Chicken Genotype- Tissue Expression (ChickenGTEx) project presents the pilot reference of regulatory variants in 28 chicken tissue transcriptomes, including millions of regulatory effects on primary expression (including protein-coding genes, lncRNA and exon) and post-transcriptional modifications (alternative splicing and 3 untranslated region alternative polyadenylation). We explored the tissue-sharing and context-specificity of these regulatory variants, their underlying molecular mechanisms of action, and their utility in interpreting adaptation and genome-wide associations of 108 chicken complex traits. Finally, we illustrated shared and lineage-specific features of gene regulation between chickens and mammals, and demonstrated how the ChickenGTEx resource can further assist with translating genetic findings across species. One-Sentence SummaryThe ChickenGTEx provides a multi-tissue reference of regulatory variants for chicken genetics and genomics, functional genomics, precision breeding, veterinary medicine, vertebrate evolution and even human biomedicine.

genetics↗