Biology subjects

Guo, X.

Publications and source records attributed to Guo, X..

At least 181 records · Page 10Linked to original sources

bioRxiv2023

Enhanced K Na 1.1 Channel Underlies Cortical Hyperexcitability and Seizure Susceptibility after Traumatic Brain Injury

Pathogenic variants of the sodium-activated potassium channel KNa1.1, have been reported in multiple epileptic disorders. However, whether and how KNa1.1 channel is involved in epileptogenesis after traumatic brain injury (TBI) remains unknown. Firstly, we used behavioral monitoring and EEG recording to examine physiological property, spontaneous seizure activity, and seizure susceptibility after TBI. We explored the changes of KNa1.1 channel following TBI, including changes of subcellular distribution and expression pattern. Meanwhile, we performed patch-clamp recording to detect the neuronal excitability. Furthermore, we built TBI model using kcnt1-/- mice and compared seizure activity with those on wild- type mice. We found severity-dependent seizure susceptibility in different degree of injured mice. Meanwhile, increased neuronal expression of KNa1.1 channel, especially in inhibitory neurons, around the lesion was also observed following TBI with increased neuronal excitability including reduced firing rate of interneurons and imbalanced excitation and inhibition (E/I). Although the maximum frequency of action potential of kcnt1-/- neurons was increased, kcnt1-/- mice displayed decreased seizure susceptibility to the pentylenetetrazole (PTZ) after TBI. Taken together, this study suggests that pathologically enhanced expression and abnormally distributed KNa1.1 channel after TBI contribute to disputed E/I and seizure susceptibility, which might provide a potential therapeutic target on the epileptogenesis after TBI.

neuroscience↗

bioRxiv2023

Potential intrahospital dissemination of Pseudomonas aeruginosa carrying the blaIMP-1 gene within a Tn7-like transposon

We aimed to determine the molecular characteristics of carbapenem-resistant Pseudomonas aeruginosa 18081308 and 18083286 isolated from the urine and sputum of two Chinese patients respectively, and analyzed the formation mechanism of the genetic environment in which it carries blaIMP-1. Bacterial genome sequencing was carried out on strains 18081308 and 18083286 to obtain their whole genome sequence. Average nucleotide identity (ANI) was used for their precise species identification. Serotyping and multilocus sequence typing were performed. Furthermore, the acquired resistance genes, and virulence factors of these strains were identified. The carbapenem-resistant P. aeruginosa strains isolated in the present study were of sequence type ST865 and serotype O6. They all carried the same virulence factors (PLC, ExoSTY) and resistance genes (aacC2, tmrB, and blaIMP-1). Tn6411, a Tn7-like transposon carrying blaIMP-1, was found in both strains. Detailed genetic dissection was applied to this transposon to display the genetic environment of blaIMP-1. The aacC2-tmrB region remnant-Tn6411 backbone was the original structure of this type of transposon. A Tn402-like type 1 integron (intl1-aac(6)-II-blaIMP-1) was inserted into it and formed a stable structure, which was localized in the chromosome by TnsD for transmission within P. aeruginosa; the original structure of Tn7-like transposon was localized on the plasmid by TnsE for horizontal transmission between bacterial species. The intrahospital dissemination of P. aeruginosa ST865 isolated in this study was episodic. The blaIMP-1-carrying Tn7-like transposon might enhance their ability to survive under drug selection pressure and aggravate the difficulty in treating infections.

genomics↗

bioRxiv2023

Pan-genome of pear provides insights into the differentiation of fruit quality traits between Asian and European pears

The pear (Pyrus spp.) is a remarkable fruit, well known for its diverse flavors, textures, culinary versatility, and global horticultural importance. However, the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled and annotated the genomes of the maternal (PsbM) and paternal (PsbF) lines of the hybrid Yuluxiang pear and constructed the first pear pangenome of 1.15Gb by combining these two genomes with five previously published pear genomes. Using the constructed pangenome, we identified 21,224 gene PAVs and 1,158,812 SNPs in the non-reference genome that were absent in the PsbM reference genome. Compared with SNP markers, we found that PAV-based analysis provides additional insights into the pear population structure. In addition, we also revealed that some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations. Moreover, our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhances sepal shedding in Xuehuali which is vital for pear quality. This research helps further capture the genetic diversity of pear populations and provides valuable genomic resources for accelerating pear breeding.

genomics↗

bioRxiv2023

Short-term statin treatment reduces, and long-term statin treatment abolishes chronic vascular injury by radiation therapy

BackgroundThe incidental use of statins during radiation therapy has been associated with a reduced long-term risk of developing atherosclerotic cardiovascular disease. ObjectivesDetermine if irradiation causes chronic vascular injury and whether short-term administration of statins during and after irradiation is sufficient to prevent chronic injury compared to long-term administration. MethodsC57Bl/6 mice were pretreated with pravastatin for 72 hours and then exposed to 12 Gy x-ray head-and-neck irradiation. Subsequently, they received pravastatin either for one additional day or for one year. Carotid arteries were tested for vascular reactivity and altered gene expression one year after irradiation. ResultsTreatment with pravastatin for 24 hours reduced the loss of endothelium-dependent vasorelaxation and protected against enhanced vasoconstriction after IR. It reduced the expression of some markers associated with inflammation and oxidative stress and modulated that of subunits of the voltage and Ca2+ activated K+ (BK) channel in the carotid artery one year after irradiation. Treatment with pravastatin for one year completely reversed the changes caused by irradiation. ConclusionsIn mice, short-term administration of pravastatin is sufficient to reduce chronic vascular injury after irradiation. Long-term administration eliminates the effects of irradiation. These findings suggest that a prospective treatment strategy involving statins could be effective in patients undergoing radiation therapy. The optimal duration of treatment in humans has yet to be determined.

pathology↗

bioRxiv2023

Tissue-specific transfer-learning enables retasking of a general comprehensive model to a specific domain

Machine learning (ML) has proven successful in biological data analysis. However, may require massive training data. To allow broader use of ML in the full spectrum of biology and medicine, including sample-sparse domains, re-directing established models to specific tasks by add-on training via a moderate sample may be promising. Transfer learning (TL), a technique migrating pre-trained models to new tasks, fits in this requirement. Here, by TL, we retasked Enformer, a comprehensive model trained by massive data, tailored to breast cancers using breast-specific data. Its performance has been validated through statistical accuracy of predictions, annotation of genetic variants, and mapping of variants associated with breast cancer. By allowing the flexibility of adding dedicated training data, our TL protocol unlocks future discovery within specific domains with moderate add-on samples by standing on the shoulders of giant models.

bioinformatics↗

bioRxiv2023

Genome-wide Perturbation Analysis Screening System for Exosomes-Related Genes Based on the CRISPR/Cas9 Platform

As reported previously, exosomes have significant impacts on the physiological and pathological state in vivo. Exosomes have been extensively studied as a drug delivery carrier and some exosomes drugs have been undergoing clinical research. The mechanisms of exosome production, transport, and secretion remain to be studied in depth. Thus, here, we developed a novel CRISPR-UMI-based gene screening system, with which we can reveal the exosomes biogenesis, transport, and uptake mechanisms on a genome-wide scale. This system consists of two parts: one is a gene knockout component; the other part is a unique molecular identifiers (UMI) labeling component that can label the exosomes produced by the knockout cells, in which each sgRNA corresponds to a specific UMI. In this way, by detecting the UMI loaded in the exosomes, we can trace the knockout gene. In this study, we first verified the function of each component using plasmids and lentiviruses respectively. Next, we simulated the infection of cells with lentiviral libraries using a single lentivirus to validate the functionality of the screening system. Finally, we constructed a CRISPR-UMI-based library targeting 15 genes (genes with clear effects on exosomes biogenesis) to further validate the reliability of the screening system. The development of this screening system is of indispensable importance for the in-depth study of the mechanisms of exosome production and secretion, as well as for the improvement of exosomes production and the advancement of exosomes industrialization.

bioengineering↗

bioRxiv2023

Evolution of a large periplasmic disk in Campylobacterota flagella facilitated efficient motility alongside autoagglutination

Although the bacterial flagella of Escherichia coli and Salmonella enterica are distributed around the cell body, many bacteria instead place their flagella at their poles. This widespread form of flagellar motility is relatively poorly understood, but these polar flagellar motors invariably feature periplasmic disk structures of unknown function. The flagellar motor of Campylobacter jejuni features a 100 nm-wide periplasmic disk associated with scaffolding a wider ring of motor proteins to increase torque, but the size of this disk is excessive for a role solely in scaffolding motor proteins. Here we show that the basal disk in C. jejuni is a flange that braces the motor during disentanglement of the flagellar filament from interactions with the cell body and other filaments, interactions that are otherwise important for host colonization. Our results reveal an entanglement of co-dependencies in the evolution of flagellar motor structure and cell plan in the Campylobacterota (previously epsilonproteobacteria). Note that this manuscript has a sibling manuscript titled Molecular model of a bacterial flagellar motor in situ reveals a "parts-list" of protein adaptations to increase torque that describes a molecular model of the Campylobacter jejuni flagellar motor discussed here.

microbiology↗

bioRxiv2023

Highly accurate estimation of cell type abundance in bulk tissues based on single-cell reference and domain adaptive matching

Accurately identifying the cellular composition of complex tissues is critical for understanding disease pathogenesis, early diagnosis, and prevention. However, current methods for deconvoluting bulk RNA sequencing (RNA-seq) typically rely on matched single-cell RNA sequencing (scRNA-seq) as a reference, which can be limiting due to differences in sequencing distribution and the potential for invalid information from single-cell references. To overcome these limitations, we introduced SCROAM, a novel computational method that overcomes these challenges. SCROAM transforms scRNA-seq and bulk RNA-seq into a shared feature space, effectively eliminating distributional differences in the latent space. We then generate cell-type-specific expression matrices from scRNA-seq, enabling accurate identification of cell types in bulk tissues. We evaluated the performance of SCROAM by benchmarking it against simulated datasets and human breast cancer and peripheral blood datasets, demonstrating its accuracy and robustness. To further validate SCROAMs performance, we conducted single-cell and bulk RNA-seq experiments on mouse spinal cord tissue and applied SCROAM to identify bulk tissue cell types. Our results indicate that SCROAM is a highly effective tool for identifying similar cell types, surpassing the performance of existing methods. We then performed an integrated analysis of liver cancer and primary glioblastoma to investigate the relationship between cell type composition and clinical outcomes in various tumor types, highlighting the significance of SCROAM for understanding cellular heterogeneity in complex diseases. Overall, our work presents a novel perspective to accurately infer cellular composition and expression in bulk RNA-seq, offering valuable insights into disease pathogenesis and potential therapeutic strategies.

bioinformatics↗

bioRxiv2023

An expression-directed linear mixed model (edLMM) discovering low-effect genetic variants

Detecting genetic variants with low effect sizes using a moderate sample size is difficult, hindering downstream efforts to learn pathology and estimating heritability. In this work, by utilizing informative weights learned from training genetically predicted gene expression models, we formed an alternative approach to estimate the polygenic term in a linear mixed model (LMM). Our LMM estimates the genetic background by incorporating their relevance to gene expression. Our protocol, expression-directed linear mixed model (edLMM), enables the discovery of subtle signals of low-effect variants using moderate sample size. By applying edLMM to cohorts of around 5,000 individuals with either binary (WTCCC) or quantitative (NFBC1966) traits, we demonstrated its power gain at the low-effect end of the genetic etiology spectrum. In aggregate, the additional low-effect variants detected by edLMM substantially improved estimation of missing heritability. edLMM moves precision medicine forward by accurately detecting the contribution of low-effect genetic variants to human diseases.

genetics↗

bioRxiv2023

Comprehensive Characterization and Global Transcriptome Analyses of Human Fetal Liver Terminal Erythropoiesis

The fetal liver (FL) is the key erythropoietic organ during fetal development, but knowledge on human FL erythropoiesis is very limited. In this study, we sorted primary erythroblasts from FL cells and performed RNA sequencing analyses. We found that temporal gene expression patterns reflected changes in function during primary human FL terminal erythropoiesis. Notably, expression of genes enriched in proteolysis and autophagy was upregulated in orthochromatic erythroblasts (OrthoE), suggesting involvement of these pathways in enucleation. We also performed RNA sequencing of in vitro cultured erythroblasts derived from FL CD34+ cells. Comparison of transcriptomes between the primary and cultured erythroblasts revealed significant differences, indicating impacts of the culture system on gene expression. Notably, lipid metabolism gene expression was increased in cultured erythroblasts. We further immortalized erythroid cell lines from FL and cord blood (CB) CD34+ cells (FL-iEry and CB-iEry, respectively). FL-iEry and CB-iEry are immortalized at the proerythroblast stage and can be induced to differentiate into OrthoE, but their enucleation ability is very low. Comparison of transcriptomes between OrthoE with and without enucleation capability revealed downregulation of pathways involved in chromatin organization and mitophagy in OrthoE without enucleation capacity, indicating that defects in chromatin organization and mitophagy contribute to the inability of OrthoE to enucleate. Additionally, the expression levels of HBE1, HBZ, and HBG2 were upregulated in FL-iEry compared with CB-iEry, and this was accompanied by downregulation of BCL11A and upregulation of LIN28B and IGF2BP1. Our study provides new insights into human FL erythropoiesis and rich resources for future studies.

cell biology↗

bioRxiv2023

Lipid-anchored Proteasomes Control Membrane Protein Homeostasis

Protein degradation in eukaryotic cells is mainly carried out by the 26S proteasome, a macromolecular complex not only present in the cytosol and nucleus but also associated with various membranes. How proteasomes are anchored to the membrane and the biological meaning thereof have been largely unknown in higher organisms. Here we show that N-myristoylation of the Rpt2 subunit is a general mechanism for proteasome-membrane interaction. Loss of this modification in the Rpt2-G2A mutant cells leads to profound changes in the membrane-associated proteome, perturbs the endomembrane system and undermines critical cellular processes such as cell adhesion, endoplasmic reticulum-associated degradation (ERAD) and membrane protein trafficking. Rpt2G2A/G2A homozygous mutation is embryonic lethal in mice and is sufficient to abolish tumor growth in a nude mice xenograft model. These findings have defined an evolutionarily conserved mechanism for maintaining membrane protein homeostasis and underscored the significance of compartmentalized protein degradation by myristoyl-anchored proteasomes (MAPs) in health and disease.

biochemistry↗

bioRxiv2023

Plasma-free samples for transcriptomic analysis: a potential alternative to whole blood samples

RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring immune cell composition. Human peripheral blood samples are widely used for RNAseq, providing valuable insights into individual biomolecular information. Blood samples can be classified as whole blood (WB), plasma, serum, and remaining sediment samples, including plasma-free blood (PFB) and serum-free blood (SFB) samples. However, the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear. In this study, we aimed to assess the viability of employing PFB or SFB samples as substitute RNA sources in transcriptomic analysis and performed a comparative analysis of WB, PFB, and SFB samples for different applications. Our results revealed that PFB samples exhibit greater similarity to WB samples in terms of protein-coding gene expression patterns, differential expression gene profiling, and immunological characterizations, suggesting that PFB can be a viable alternative for transcriptomic analysis. This contributes to the optimization of blood sample utilization and the advancement of precision medicine research.

bioinformatics↗

bioRxiv2023

MORE IS DIFFERENT: DRUG PROPERTY ANALYSIS ON CELLULAR HIGH-CONTENT IMAGES USING DEEP LEARNING

High-content analysis (HCA) holds enormous potential for drug discovery and research, but widely used methods can be cumbersome and yield inaccurate results. Noise and high similarity in cell images impede the accuracy of deep learning-based image analysis. To address these issues, we introduce More Is Different (MID), a novel HCA method that combines cellular experiments, image processing, and deep learning modeling. MID effectively combines the convolutional neural network and Transformer to encode high-content images, effectively filtering out noisy signals and characterizing cell phenotypes with high precision. In comparative tests on drug-induced cardiotoxicity and mitochondrial toxicity classification, as well as compound classification, MID outperformed both DeepProfiler and CellProfiler, which are two highly recognized methods in HCA. We believe that our results demonstrate the utility and versatility of MID and anticipate its widespread adoption in HCA for advancing drug development and disease research.

pharmacology and toxicology↗

bioRxiv2023

Pharmacologic Activation of an Integrated Stress Response Kinase Promotes Mitochondrial Remodeling

The integrated stress response (ISR) comprises the eIF2 kinases PERK, GCN2, HRI, and PKR, which induce translational and transcriptional signaling in response to diverse insults. Deficiencies in PERK signaling lead to mitochondrial dysfunction and contribute to the pathogenesis of numerous diseases. We define the potential for pharmacologic activation of compensatory eIF2 kinases to rescue ISR signaling and promote mitochondrial adaptation in PERK-deficient cells. We show that the HRI activator BtdCPU and GCN2 activator halofuginone promote ISR signaling and rescue ER stress sensitivity in PERK-deficient cells. However, BtdCPU induces mitochondrial depolarization, leading to mitochondrial fragmentation and activation of the OMA1-DELE1-HRI signaling axis. In contrast, halofuginone promotes mitochondrial elongation and adaptive mitochondrial respiration, mimicking regulation induced by PERK. This shows halofuginone can compensate for deficiencies in PERK signaling and promote adaptive mitochondrial remodeling, highlighting the potential for pharmacologic ISR activation to mitigate mitochondrial dysfunction and motivating the pursuit of highly-selective ISR activators.

cell biology↗

bioRxiv2023

Multi-omics of the gut microbial ecosystem in the immunotherapy resistance in microsatellite instability-high gastrointestinal cancer patients

Despite the encouraging efficacy of anti-PD-1/PD-L1 immunotherapy in microsatellite instability-high/deficient mismatch repair (MSI-H/dMMR) advanced gastrointestinal cancer, many patients exhibit primary or acquired resistance. Using multi-omics approaches, we interrogated gut microbiome, blood metabolome and cytokines/chemokines of MSI-H/dMMR advanced gastrointestinal cancer patients (N=77) and identified a number of microbes (e.g. Alistipes putredinis) and metabolites (e.g. arginine and SCFA) highly associated with primary resistance. Fecal microbiota transplantation of patients stool replicated the clinical responsiveness as well as certain molecular signatures. Based on the clinical microbiome data, we developed a predictive machine learning model for primary resistance and achieved accuracy at 0.83 on an external validation set. Furthermore, several microbes were pinpointed which gradually changed during the process of acquired resistance. In summary, our study demonstrated the essential role of gut microbiome in drug resistance, and this could be utilized as a preventative diagnosis tool as well as therapeutic targets in the future.

cancer biology↗

bioRxiv2023

A MSTNDel273C mutation with FGF5 knockout sheep by CRISPR/Cas9 promotes skeletal muscle myofiber hyperplasia via MEK-ERK-FOSL1 axis

Mutations in the well-known Myostatin (MSTN) produce a "double-muscle" phenotype, which makes it commercially invaluable for improving livestock meat production and providing high-quality protein for humans. However, mutations at different loci of the MSTN often produce a variety of different phenotypes. In the current study, we increased the delivery ratio of Cas9 mRNA to sgRNA from the traditional 1:2 to 1:10, which improves the efficiency of the homozygous mutation of biallelic gene. Here, a MSTNDel273C mutation with FGF5 knockout sheep, in which the MSTN and FGF5 dual-gene biallelic homozygous mutations were produced via the deletion of 3-base pairs of AGC in the third exon of MSTN, resulting in cysteine-depleted at amino acid position 273, and the FGF5 double allele mutation led to inactivation of FGF5 gene. The MSTNDel273C mutation with FGF5 knockout sheep highlights a dominant "double-muscle" phenotype, which can be stably inherited. Both F0 and F1 generation mutants highlight the excellent trait of high-yield meat with a smaller cross-sectional area and higher number of muscle fibers per unit area. Mechanistically, the MSTNDel273C mutation with FGF5 knockout mediated the activation of FOSL1 via the MEK-ERK-FOSL1 axis. The activated FOSL1 promotes skeletal muscle satellite cell proliferation and inhibits myogenic differentiation by inhibiting the expression of MyoD1, and resulting in smaller myotubes. In addition, activated ERK1/2 may inhibit the secondary fusion of myotubes by Ca2+-dependent CaMKII activation pathway, leading to myoblasts fusion to form smaller myotubes.

cell biology↗

bioRxiv2022

Children Develop Adult-Like Visual Sensitivity to Image Memorability by the Age of Four

Adults have been shown to consistently remember and forget certain images despite large individual differences, suggesting a population-wide sensitivity to an images intrinsic memorability--a measure of how successfully an image is remembered. While a decade of research has focused on image memorability among adults, the developmental trajectory of these consistencies in memory is understudied. Here, we investigate by what age children gain adultlike sensitivity to the image memorability effect. We utilized data from Saragosa-Harris et al. (2021), where 137 children aged between 3 and 5 years old encoded animal-scene image pairs and then after a 5-minute, 24-hour, or 1-week delay performed a cued recognition task for each scene target given its animal cue. We tested adults memory of the same scene images using ResMem (Needell & Bainbridge, 2022), a pre-trained deep neural network that predicts adult image memorability scores, and using an online behavioral continuous recognition task (N = 116). Results showed that ResMem predictions, as a proxy of adults memory, predicted scene memory of children by the age of 4 and were the most predictive of childrens memory across ages after a long, 1-week delay. Children at age 3 show non-adult-like consistent memory patterns, implying that the non-adult-like memory patterns were not due to poor memory performance. Instead, 3-year-olds may have consistently used certain visual memory strategies that become less optimal as they age. Our results suggest that adult-like sensitivity to image memorability emerges by the age of 4 through experience. Public Significance StatementThis study strongly suggests that children older than 4 years old tend to remember and forget the same images as adults. We recommend teachers and caregivers to utilize the ResMem DNN to select memorable images to be used in educational settings.

neuroscience↗

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↗