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Zhang, G.

Publications and source records attributed to Zhang, G..

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

Tumor landscape of epithelial ovarian cancer highlights that EGR1 drives tumor invasion at single-cell resolution

Identifying underlying molecular mechanisms and biomarkers of epithelial ovarian carcinoma (EOC) proliferation and metastasis remains challenging. Patients of EOC are usually diagnosed at an advanced stage and the availability of invasion-related targets is limited. Herein, we explored the single-cell RNA sequencing (scRNA-seq) dataset of EOC and defined tumor physiological reprograming compared to bulk RNA-seq. The energy metabolism and anti-apoptotic pathway was found as critical contributors to intratumor heterogeneity. Moreover, hypoxia, oxidative phosphorylation (OXPHOS) and glycolysis were positively correlated, which have biologically activity trajectories during epithelial mesenchymal transition (EMT). The HMGH1, EGR1 and RUNX1 were found to be critical inducers of the EMT process in EOC. Experimental validation revealed that suppressed EGR1 decreased the expression of FAS and HSPG2 and associating with EMT progression in EOC. In tumor microenvironment (TME), CAFs were found have significant contribution to tumor immune infiltration and metastasis and accumulation of CAFs was associated with poorer patient survival. In conclusion, physiological features and molecular mechanisms in the TME of EOC were revealed and provided effective targets for the suppression of tumor metastasis.

bioinformatics↗
bioRxiv2022

Grain filling leads to backflow of surplus water in maize grain via the xylem to the cob and plant

The rapid dehydration rate of maize grain is one of the main characteristics of cultivar selection of mechanical grain harvest, but the dominant driving force and mechanism of grain dehydration before physiological maturity remains disputable and obscure, respectively. This study found that, from grain formation to 5-10 days before physiological maturity of early and middle maturity maize cultivars, the main driving force of grain dehydration is filling and then converts to surface evaporation, by comparing the grain moisture content and dehydration rate between grain coated treatment and control. In the dye movement experiment, xylem-mobile dye movement into grain through pedicel xylem was observed during grain formation period, and declined and gradually not observed after grain formation. Xylem-mobile dye movement out of ear via cob, ear-pedicel and stem xylem was observed after grain formation. In addition, from grain formation to physiological maturity, there was a very significant positive correlation between grain filling rate and dehydration rate. According to these results, it is proposed here that in the grain dehydration phase driven by filling, the surplus water in grain flows back to cob via pedicel xylem, and some of it flows back to plant via cob and ear-pedicel xylem. HighlightThe surplus water in grain driven by grain filling flows back to the cob and plant for recyclingvia the xylem during the development of maize grain.

plant biology↗
bioRxiv2022

Epinephrine inhibits PI3K alpha via the Hippo kinases.

The phosphoinositide 3-kinase, p110, is an essential mediator of insulin signaling and glucose homeostasis. We systematically interrogated the human serine, threonine, and tyrosine kinome to search for novel regulators of p110 and found that the Hippo kinases phosphorylate and completely inhibit its activity. This inhibitory state corresponds to a conformational change of a membrane binding domain on p110, which impairs its ability to engage membranes. In human primary hepatocytes, cancer cell lines, and rodent tissues, activation of the Hippo kinases, MST1/2, using forskolin or epinephrine is associated with phosphorylation and inhibition of p110, impairment of downstream insulin signaling, and suppression of glycolysis and glycogen synthesis. These changes are abrogated when MST1/2 are genetically deleted or inhibited with small molecules. Our study reveals a novel inhibitory pathway of PI3K signaling and a previously unappreciated link between epinephrine and insulin signaling.

physiology↗
bioRxiv2022

Transcellular progression of infection threads in Medicago truncatula roots is controlled by locally confined cell wall modifications

The root nodule symbiosis with its global impact on nitrogen fertilization of soils is characterized by an intracellular colonization of legume roots by rhizo-bacteria. While the symbionts are initially taken up by morphologically adapted root hairs, rhizobia persistently progress within a membrane-confined infection thread through several root cortical and later nodular cell layers. Throughout this transcellular passaging, rhizobia have to repeatedly pass host plasma membranes and cell walls. Here, we genetically dissected this essential process and describe the concerted action of the symbiosis-specific pectin methyl esterase SyPME and the pectate lyase NPL at the infection thread and transcellular passage sites. Their coordinated function mediates spatially confined pectin alterations in the cell-cell interface that result in the establishment of an apoplastic compartment where bacteria are temporarily released into and taken up from the subjacent cell. This process allows successful intracellular progression of infection threads through the entire root cortical tissue.

plant biology↗
bioRxiv2022

Natural variation in C. elegans short tandem repeats

Short tandem repeats (STRs) represent an important class of genetic variation that can contribute to phenotypic differences. Although millions of single nucleotide variants (SNVs) and short indels have been identified among wild Caenorhabditis elegans strains, the natural diversity in STRs remains unknown. Here, we characterized the distribution of 31,991 STRs with motif lengths of 1-6 bp in the reference genome of C. elegans. Of these STRs, 27,636 harbored polymorphisms across 540 wild strains and only 9,691 polymorphic STRs (pSTRs) had complete genotype data for more than 90% of the strains. Compared to the reference genome, the pSTRs showed more contraction than expansion. We found that STRs with different motif lengths were enriched in different genomic features, among which coding regions showed the lowest STR diversity and constrained STR mutations. STR diversity also showed similar genetic divergence and selection signatures among wild strains as in previous studies using single-nucleotide variants. We further identified STR variation in two mutation accumulation line panels that were derived from two wild strains and found background-dependent and fitness-dependent STR mutations. Overall, our results delineate the first large-scale characterization of STR variation in wild C. elegans strains and highlight the effects of selection on STR mutations.

genomics↗
bioRxiv2022

Molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk

We performed the first molecular atlas of natural spider dragline silk production using genome assembly for the golden orb-web spider Trichonephila clavata and multiomics defining for the segmented major ampullate (Ma) gland: Tail, Sac, and Duct. We uncovered a hierarchical biosynthesis of spidroins, organic acids, lipids, and chitin in the sectionalized Ma gland dedicated to fine silk constitution. The ordered secretion of spidroins was achieved by the synergetic regulation of epigenetic and ceRNA signatures for genomic group-distributed spidroin genes. Single-cellular and spatial RNA profiling identified ten cell types with partitioned functional division determining the tri-sectional organization of the Ma gland. Convergent evolution and genetic manipulation analyses further validated that this tri-sectional architecture of the silk gland was analogous in silk-spinning animals and inextricably linked with silk formation. Our study provided multiple levels of data that significantly expand the knowledge of spider dragline silk generation and may eventually benefit spider-inspired fiber innovations.

genomics↗
bioRxiv2022

Metabolomics and transcriptomics reveal the response mechanisms of Mikania micrantha to Puccinia spegazzinii infection

Mikania micrantha is one of the 100 worst invasive species globally and can cause significant negative impacts to agricultural and forestry economics, particularly in Asia and the Pacific region. The rust Puccinia spegazzinii has been used successfully as a biological control agent in several countries to help manage M. micrantha. However, the response mechanisms of M. micrantha to P. spegazzinii infection have never been studied. To investigate the response of M. micrantha to infection by P. spegazzinii, an integrated analysis of metabolomics and transcriptomics was performed. The levels of 101 metabolites, including organic acids, amino acids and secondary metabolites in M. micrantha infected with P. spegazzinii, were significantly different compared to those in plants that were not infected. The relative amounts of L-leucine, L-ioleucine, L-tryptophan, histidine, L-phenylalanine and L-citrulline were increased under P. spegazzinii infection. These may convert to intermediates within the TCA cycle, participating in energy biosynthesis. In addition, phytoalexins, such as maackiain, nobiletin, vasicin, arachidonic acid and JA-Ile, were synthesized and accumulated in M. micrantha in response to P. spegazzinii infection. A total of 4,978 differentially expressed genes were identified in M. micrantha infected by P. spegazzinii. Many key genes of the Mitogen-activated protein kinase (MAPK) signalling pathway, showed significantly higher expression under P. spegazzinii infection. These results not only help us to understand the response of metabolites and gene expression in M. micrantha following infection by P. spegazzinii, but also help us understand the potential for the continuous biological control of M. micrantha using P. spegazzinii.

pathology↗
bioRxiv2022

Distinct Single-cell Immune Ecosystems Distinguish True and De Novo HBV-related Hepatocellular Carcinoma Recurrences

Revealing differential tumor immune microenvironment (TIME) characteristics between true versus de novo hepatocellular carcinoma (HCC) recurrence could help optimal development and use of immunotherapies. Here, we studied the TIME of recurrent HBV-related HCCs by 5and VDJ single-cell and bulk RNA-sequencing, flow cytometry, and multiplexed immunofluorescence. Analyses of mutational profiles, evolutionary trajectories, and clonal architecture using whole-exome sequencing identified de novo versus true recurrences, some of which occurred before clinical diagnosis. The TIME of truly recurrent HCCs was characterized by an increased abundance in KLRB1+CD8+ T cells with memory phenotype and low cytotoxicity. In contrast, we found an enrichment in cytotoxic and exhausted CD8+ T cells in the TIME of de novo recurrent HCCs. Transcriptomic and interaction analyses showed an upregulated GDF15 expression level on HCC cells in proximity to dendritic cells, which may have dampened antigen presentation and inhibited anti-tumor immunity in the TIME of truly recurrent lesions. In contrast, we found that myeloid cells crosstalk with T cells mediated T cell exhaustion and immunosuppression in the TIME of de novo recurrent HCC. In conclusion, our results support genomic diagnosis and immune profiling for guiding immunotherapy implementation based on the type of HCC recurrence and TIME. HighlightsO_LITruly recurrent lesions are seeded before primary tumor diagnosis, and that de novo cancer can occur earlier than the clinically used 2-year limit. C_LIO_LIScRNA-seq unravels distinct immune ecosystems in true versus de novo HCC recurrences, highlighting the need for different immunotherapy strategies for two types of HCC recurrence. C_LIO_LICD8+ T cells in de novo recurrence displayed cytotoxic and exhausted phenotypes while those in truly recurrent lesions showed a memory phenotype with weak cytotoxicity. C_LIO_LIHCC cells expressing the inhibitory molecule GDF15 were in the proximity of DCs only in truly recurrent lesions. C_LIO_LIHigh GDF15 expression level was associated with truly recurrent HCC and worse prognosis. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/494526v1_ufig1.gif" ALT="Figure 1"> View larger version (71K): org.highwire.dtl.DTLVardef@1b76bf0org.highwire.dtl.DTLVardef@10f889aorg.highwire.dtl.DTLVardef@d16b52org.highwire.dtl.DTLVardef@dceb7a_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗
bioRxiv2022

vsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data

Virus-encoded small RNAs (vsRNA) have been reported to play an important role in viral infection. Unfortunately, there is still a lack of an effective method for vsRNA identification. Herein, we presented vsRNAfinder, a de novo method for identifying high-confidence vsRNAs from small RNA-Seq (sRNA-Seq) data based on peak calling and Poisson distribution and is public available at https://github.com/ZenaCai/vsRNAfinder. vsRNAfinder outperformed two widely-used methods namely miRDeep2 and ShortStack in identifying viral miRNAs with a significantly improved sensitivity. It can also be used to identify sRNAs in animals and plants with similar performance to miRDeep2 and ShortStack. The study would greatly facilitate effective identification of vsRNAs.

bioinformatics↗
bioRxiv2022

Functional evolution of SARS-COV-2 Spike protein: adaptation on translation and infection via surface charge of spike protein

The SARS-COV-2 virus, which causes the COVID-19, is rapidly accumulating mutations to adapt to the hosts. We collected SARS-COV-2 sequence data from the end of 2019 to April 2022 to analyze for their evolutionary features during the pandemic. We found that most of the SARS-COV-2 genes are undergoing negative purifying selection, while the spike protein gene (S-gene) is undergoing rapid positive selection. From the original strain to the alpha, delta and omicron variant types, the Ka/Ks of the S-gene increases, while the Ka/Ks within one variant type decreases over time. During the evolution, the codon usage did not evolve towards optimal translation and protein expression. In contrast, only S-gene mutations showed a remarkable trend on accumulating more positive charges. This facilitates the infection via binding human ACE2 for cell entry and binding furin for cleavage. Such a functional evolution emphasizes the survival strategy of SARS-COV-2, and indicated new druggable target to contain the viral infection. The nearly fully positively-charged interaction surfaces indicated that the infectivity of SARS-COV-2 virus may approach a limit.

genetics↗
bioRxiv2022

Subtyping evaluation of Salmonella Enteritidis using SNP and core genome MLST with nanopore reads

Whole genome sequencing (WGS) for public health surveillance and epidemiological investigation of foodborne pathogens predominantly relies on sequencing platforms that generate short reads. Continuous improvement of long-read nanopore sequencing such as Oxford Nanopore Technologies (ONT) presents a potential for leveraging multiple advantages of the technology in public health and food industry settings, including rapid turnaround and onsite applicability in addition to superior read length. However, evaluation, standardization and implementation of the ONT approach to WGS-based, strain-level subtyping is challenging, in part due to its relatively high base-calling error rates and frequent iterations of sequencing chemistry and bioinformatic analytics. Using an established cohort of Salmonella Enteritidis isolates for subtyping evaluation, we assessed the technical readiness of ONT for single nucleotide polymorphism (SNP) analysis and core-genome multilocus sequence typing (cgMLST) of a major foodborne pathogen. By multiplexing three isolates per flow cell, we generated sufficient sequencing depths under seven hours of sequencing for robust subtyping. SNP calls by ONT and Illumina reads were highly concordant despite homopolymer errors in ONT reads (R9.4.1 chemistry). In silico correction of such errors allowed accurate allelic calling for cgMLST and allelic difference measurements to facilitate heuristic detection of outbreak isolates. Our study established a baseline for the continuously evolving nanopore technology as a viable solution to high quality subtyping of Salmonella, delivering comparable subtyping performance when used standalone or together with short-read platforms.

microbiology↗
bioRxiv2022

Selection and validation of reference genes for quantitative real-time polymerase chain reaction in Serratia ureilytica DW2

Serratia ureilytica DW2 is a highly efficient phosphate-solubilizing bacterium isolated from Codonopsis pilosula rhizosphere soil that can promote the growth of C. pilosula. However, no validated reference genes from the genus Serratia for use in quantitative real-time polymerase chain reaction (RT-qPCR) normalization have been reported. To screen stable reference genes in S. ureilytica DW2, the expression of eight candidate reference genes (16S rRNA, ftsZ, ftsA, mreB, recA, slyD, thiC, and zipA) under different treatment conditions (pH, temperature, culture time, and salt content) was assayed by RT-qPCR. The expression stability of these genes was analyzed with different algorithms (geNorm, NormFinder, and BestKeeper). To verify the reliability of the data, the most stably expressed reference gene was used to quantify expression of the glucose dehydrogenase (gdh) gene under different soluble phosphate levels. The results showed that the zipA and 16S rRNA genes were the most stable reference genes, and the least stable were thiC and recA. The expression of gdh was consistent with the phosphate solubilization ability on plates containing National Botanical Research Institute phosphate (NBRIP) growth medium. Therefore, this study provides a stable and reliable reference gene for Serratia, which is vital for the accurate quantification of functional gene expression in future studies.

microbiology↗
bioRxiv2022

Polio Virotherapy of Malignant Glioma Engages the Tumor Myeloid Infiltrate and Induces Diffuse Microglia Activation

Malignant gliomas commandeer abundant inflammatory infiltrates with glioma-associated macrophages and microglia (GAMM) actively promoting tumor progression. Like all cells in the mononuclear phagocytic system, macrophages and microglia constitutively express the poliovirus receptor, CD155. Besides myeloid cells, CD155 is widely upregulated ectopically in the neoplastic compartment of malignant gliomas (and solid cancers in general). Intratumor treatment with the highly attenuated rhino:poliovirus chimera, PVSRIPO, yielded long-term survival with durable radiographic responses in patients with recurrent glioblastoma (Desjardins et al. New England Journal of Medicine, 2018). Here, we studied mechanisms of PVSRIPO immunotherapy in mouse brain tumor models to decipher contributions of myeloid vs. malignant cells to antitumor efficacy. PVSRIPO treatment caused intense engagement of the GAMM infiltrate associated with substantial, but transient tumor regression. This was accompanied by diffuse microglia activation and proliferation in the normal central nervous system (CNS) surrounding the tumor, extending to the ipsilateral and even the contralateral hemispheres. PVSRIPO-instigated microglia activation occurred against a backdrop of sustained innate antiviral inflammation, associated with induction of the PD-L1 immune checkpoint on GAMM. Combining PVSRIPO with PD1/PD-L1 blockade led to durable remissions. Our work implicates GAMM as active drivers of PVSRIPO-induced antitumor inflammation and reveals profound and widespread neuroinflammatory activation of the CNS-resident myeloid compartment by PVSRIPO.

cancer biology↗
bioRxiv2022

Separation of phosphatase and kinase activity within the Bub complex is required for proper mitosis

The Bub1 and BubR1 kinetochore proteins support proper chromosome segregation and mitotic checkpoint activity. Bub1 and BubR1 are paralogues with Bub1 being a kinase while BubR1 localizes the PP2A-B56 protein phosphatase to kinetochores in humans. Whether this separation of kinase and phosphatase activity is important is unclear as some organisms integrate both activities into one Bub protein. Here we engineer human Bub1 and BubR1 proteins integrating kinase and phosphatase activities into one protein and show that these do not support normal mitotic progression. A Bub1-PP2A-B56 complex can supports chromosome alignment but results in impairment of the checkpoint due to dephosphorylation of the Mad1 binding site in Bub1. Furthermore, a chimeric BubR1 protein containing the Bub1 kinase domain induces delocalized H2ApT120 phosphorylation resulting in reduction of centromeric hSgo2 and chromosome segregation errors. Collectively, these results argue that the separation of kinase and phosphatase activities within the Bub complex is required for balancing its functions in the checkpoint and chromosome alignment.

cell biology↗
bioRxiv2022

Using Culture-Enriched Phenotypic Metagenomics for Targeted High-Throughput Monitoring of Clinically-Important Fraction of Beta-Lactam Resistome

The high bacterial community complexity greatly hinders the monitoring of clinically prevalent extended-spectrum beta-lactam resistant bacteria, which are usually present as rare but key populations involving in the environmental dissemination of clinical resistance. Here, we introduce culture-enriched phenotypic metagenomics that integrates culture enrichment, phenotypic screening and metagenomic analyses as an emerging methodology to profile beta-lactam resistome in a municipal wastewater treatment plant (WWTP) and its receiving river. The results showed that clinically prevalent carbapenemase genes (e.g., NDM and KPC family) and extended-spectrum beta-lactamase genes (e.g., CTX-M, TEM and OXA family) considerably existed in the WWTP and showed prominent potential in horizontal dissemination. Strikingly, carbapenem and polymyxin resistance genes co-occurred in highly virulent Enterobacter kobei (MCR-1 and NDM-6) and Citrobacter freundii (ArnA and NDM-16) genomes. Overall, this study exemplifies phenotypic metagenomics for high-throughput surveillance of targeted fraction of clinically-important resistome and substantially expands current knowledge on extended-spectrum beta-lactam resistance in WWTPs.

microbiology↗
bioRxiv2022

Efficient rescue of a newly classified Ebinur lake orthobunyavirus with GFP reporter and its application in rapid antiviral screening

Orthobunyaviruses have been reported to cause severe diseases in humans or animals, posing a threat to human health and social economy. Ebinur lake virus (EBIV) is a newly classified orthobunyavirus, which needs further intensive study and therapies to cope with its potential infection risk to human and animals. Here, through the reverse genetics system, the recombinant EBIV of wild type (rEBIV/WT) and NP-conjugated-eGFP (rEBIV/eGFP/S) were rescued for the application of the rapid antiviral drug screening. The eGFP fluorescence signal of the rEBIV/eGFP/S was stable in the process of successive passage in BHK-21 cells (over 10 passages) and this recombinant virus could replicate in various cell lines. Compared to the wild type EBIV, the rEBIV/eGFP/S caused the smaller plaques and its peak titers were lower, suggesting attenuation due to the eGFP insertion. Through the high-content screening (HCS) system, ribavirin showed an inhibitory effect on the rEBIV/eGFP/S with an EC50 of 21.91 M, while favipiravir did not inhibit, even at high concentrations. In addition, five of ninety-six natural compounds had antiviral against EBIV. The robust reverse genetics system for EBIV will facilitate investigation into replication and assembly mechanisms and assist drug and vaccine development.

molecular biology↗
bioRxiv2022

Real-time denoising of fluorescence time-lapse imaging enables high-sensitivity observations of biological dynamics beyond the shot-noise limit

A fundamental challenge in fluorescence microscopy is the inherent photon shot noise caused by the inevitable stochasticity of photon detection. Noise increases measurement uncertainty, degrades image quality, and limits imaging resolution, speed, and sensitivity. To achieve high-sensitivity imaging beyond the shot-noise limit, we provide DeepCAD-RT, a versatile self-supervised method for effective noise suppression of fluorescence time-lapse imaging. We made comprehensive optimizations to reduce its data dependency, processing time, and memory consumption, finally allowing real-time processing on a two-photon microscope. High imaging signal-to-noise ratio (SNR) can be acquired with 10-fold fewer fluorescence photons. Meanwhile, the self-supervised superiority makes it a practical tool in fluorescence microscopy where ground-truth images for training are hard to obtain. We demonstrated the utility of DeepCAD-RT in extensive experiments, including in vivo calcium imaging of various model organisms (mouse, zebrafish larva, fruit fly), 3D migration of neutrophils after acute brain injury, and 3D dynamics of cortical ATP (adenosine 5-triphosphate) release. DeepCAD-RT will facilitate the morphological and functional interrogation of biological dynamics with minimal photon budget.

biophysics↗