Biology subjects

Zhang, T.

Publications and source records attributed to Zhang, T..

At least 433 records · Page 24Linked to original sources

bioRxiv2022

Maintaining hypoxia environment of subchondral bone alleviates osteoarthritis progression

Abnormal subchondral bone remodeling featured by over-activated osteoclastogenesis leads to articular cartilage degeneration and osteoarthritis (OA) progression, but the mechanism is still unclear. In this study, we used lymphocyte cytosolic protein 1 (Lcp1) knock-out mice to suppress subchondral osteoclast formation in mice OA model with anterior cruciate ligament transection (ACLT) and Lcp1-/- mice showed decreased bone remodeling and sensory innervation in subchondral bone accompanied by retarded cartilage degeneration. For mechanisms, in wildtype mice with ACLT the activated osteoclasts in subchondral bone induced type-H vessels and elevated oxygen concentration which ubiquitylated hypoxia-inducible factor 1 (HIF-1), vital for maintaining chondrocyte homeostasis in articular chondrocytes and led to cartilage degeneration. Deletion of Lcp1 impeded osteoclast-mediated angiogenesis, which maintained the low levels of oxygen partial pressure (pO2) in subchondral bone as well as the whole joint and delayed the OA progression. Stabilization of HIF-1 delayed cartilage degeneration and knockdown of Hif1a abolished the protective effects of Lcp1 knockout. Notably, we identified a novel subgroup of hypertrophic chondrocytes highly associated with OA by single cell sequencing analysis of human articular chondrocytes. Lastly, we showed that Oroxylin A, an Lcp1-encoded protein L-plastin (LPL) inhibitor, could alleviate OA progression. In conclusion, maintaining hypoxic environment in subchondral bone is an attractive strategy for OA treatment. TeaserInhibiting subchondral osteoclastogenesis alleviates OA progression via maintaining joint hypoxia environment.

biochemistry↗

bioRxiv2022

Minor differences in peptide presentation between chicken MHC class I molecules can explain differences in disease susceptibility

The highly polymorphic classical major histocompatibility complexes (MHCs) can confer resistance or susceptibility to diseases. The chicken MHC is known to confer decisive resistance or susceptibility to various economically-important pathogens, including the iconic oncogenic herpesvirus that causes Mareks disease (MD). Only one classical class I gene, BF2, is expressed at a high level in chickens, so it was relatively easy to discern a hierarchy from well-expressed thermostable fastidious specialist alleles to promiscuous generalist alleles that are less stable and expressed less on the cell surface. The BF2*1901 is more highly expressed and more thermostable than the closely-related BF2*1501, but the data for peptide repertoire available did not obviously correlate as expected. Here, we confirm for newly-developed chicken lines that the chicken haplotype B15 confers resistance to MD compared to B19. Using gas phase sequencing of peptide pools, and using immunopeptidomics involving mass spectroscopy, we find that the BF2*1901 binds a greater variety of amino acids in some anchor positions than BF2*1501. However, by X-ray crystallography, we find that the peptide-binding groove of BF2*1901 is narrower and shallower. Though the self-peptides bound to BF2*1901 may appear more various than those of BF2*1501, the structures show that the wider and deeper peptide-binding groove of BF2*1501 allows it to tightly accept many more peptides overall, correlating with the expected hierarchies for expression level, thermostability and MD resistance. Moreover, the 2 helix of BF2*1901 is higher than BF2*1501, potentially reducing the number of T cell clones that can recognize this fastidious class I molecule. IMPORTANCEDisease susceptibility mechanism is complicated, but chicken infection of Mareks disease (MD) is one of ideal models, considering the only one highly expressed classical MHC class I, BF2. The different susceptibility of the two close alleles BF2*1901 and BF2*1501 with minor difference of expression and thermostability is still unfathomed. Here, we confirm B15 chicken confers resistance to MD compared to B19. But the BF2*1901 binds a broader variety of anchoring peptides than BF2*1501. This mystery was solved by the structural determination of the two molecules with one similar peptide. The wider and deeper peptide-binding groove of BF2*1501 allows it to tightly accept many more peptides overall, which is concordant to the expected hierarchies for expression level, thermostability and MD resistance.

immunology↗

bioRxiv2022

ezQTL: A Web Platform for Interactive Visualization and Colocalization of Quantitative Trait Loci and GWAS

Genome-wide association studies (GWASs) have identified thousands of genomic loci associated with complex diseases and traits, including cancer. The vast majority of common trait-associated variants identified via GWAS fall in non-coding regions of the genome, posing a challenge in elucidating the causal variants, genes, and mechanisms involved. Expression quantitative trait locus (eQTL) and other molecular QTL studies have been valuable resources in identifying candidate causal genes from GWAS loci through statistical colocalization methods. While QTL colocalization is becoming a standard analysis in post-GWAS investigation, an easy web tool for users to perform formal colocalization analyses with either user-provided or public GWAS and eQTL datasets has been lacking. Here, we present ezQTL, a web-based bioinformatic application to interactively visualize and analyze genetic association data such as GWAS and molecular QTLs under different linkage disequilibrium (LD) patterns (1000 Genomes Project, UK Biobank, or user-provided data). This application allows users to perform data quality control for variants matched between different datasets, LD visualization, and two-trait colocalization analyses using two state-of-the-art methodologies (eCAVIAR and HyPrColoc), including batch processing. ezQTL is a free and publicly available cross-platform web tool, which can be accessed online at https://analysistools.cancer.gov/ezqtl.

genetics↗

bioRxiv2022

Engineering bacterial blight-resistant plants through CRISPR/Cas9-targeted editing of the MeSWEET10a promoter in cassava

Cassava starch is a widely used raw materials for industrial production. However, cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) results in severe yield losses and is the most destructive bacterial disease in all worldwide cassava planting regions. This study showed that editing of the promoter in the disease-susceptibility gene MeSWEET10a of SC8 cassava confers resistance to CBB. All mutated cassava lines had normal morphological and yield-related traits as the wild type. The results lay a research foundation for breeding cassava resistant to bacterial blight. HighlightsMeSWEET10a gene in SC8 cultivar is hijacked by TALE20 from Xam11 strain. Editing of the MeSWEET10a promoter in SC8 cultivar confers resistance to CBB. All the mutated cassava lines had similar yield-related traits compared to wild-type.

plant biology↗

bioRxiv2022

Genomic analyses identify biological processes and functions between M1 and M2 macrophages

Macrophages can be induced by a variety of factors to change their phenotype and functions. M1 and M2 macrophages play converse roles during inflammation or other diseases. However, the mechanism and function of M1 and M2 macrophages are still not clear. This study aims to identify the different molecules and functions by analyzing the RNA-seq data. The GSE189354 was created by the Illumina HiSeq 4000 (Mus musculus). The KEGG and GO analyses indicated the Phagosome and Hematopoietic cell lineage are the major biological processes between M1 and M2 macrophages. Moreover, we further identified ten molecules including Il6, Il1b, Tlr2, Myc, Fn1, Itgax, Cxcl10, Ccl5, Cxcr4, and Pparg. Therefore, our study may provide novel knowledge of innate immunity.

bioinformatics↗

bioRxiv2022

TraB is a novel component of the ER-Mitochondria contact site (EMCS) with dual roles in ER-Mitochondrial tethering and mitophagy

ER-mitochondria contact sites (EMCSs) are important for mitochondrial function. Here, we have identified a novel eukaryotic EMCS complex, comprising a family of uncharacterised mitochondrial outer-membrane proteins, TraB1 and the ER protein, VAP27-1. In Arabidopsis, there are two TraB1 isoforms and the trab1a/trab1b double mutant exhibits abnormal mitochondrial morphology, strong starch accumulation and impaired energy metabolism, indicating that these proteins are essential for normal mitochondrial function. Moreover, TraB1 proteins also interact with ATG8 in order to regulate mitochondrial degradation (mitophagy). The turnover of depolarised mitochondria is significantly reduced in both trab1a/b and VAP27 mutants (vap27-1/3/4/6) under mitochondrial stress conditions, with an increased population of dysfunctional mitochondria present in the cytoplasm. Consequently, plant recovery after stress is significantly perturbed. A similar phenotype is found in both autophagy mutants (atg5 and atg7), suggesting that TraB1 regulated mitophagy and ER-mitochondrial tethering are two closely related processes, necessary for normal mitochondrial function. Taken together, we ascribe a dual role to TraB1 which is a novel component of the EMCS complex in eukaryotes, regulating both tethering of the mitochondria to the ER and mitophagy.

cell biology↗

bioRxiv2022

TFIIB-related factor 1 is a nucleolar protein that promotes RNA polymerase I-directed transcription and tumour cell growth

RNA polymerase I (Pol I) products play pivotal roles in ribosomal assembly, protein synthesis and cell growth. Dysregulation of Pol I product synthesis closely correlates with tumourigenesis. However, the factors and pathways governing Pol I-dependent transcription remain to be identified. Here, we report that TFIIB-related factor 1 (BRF1), a subunit of TFIIIB required for Pol III-mediated transcription, is a nucleolar protein and modulates the rRNA synthesis directed by Pol I. We show that BRF1 can be co-localized with nucleolar protein markers in several human cell types. BRF1 expression positively correlates with Pol I product levels and tumour cell growth in vitro and in vivo. Mechanistically, BRF1 binds to the Pol I transcription machinery factors and is recruited to the rDNA promoter with them. Alteration of BRF1 expression affected the recruitment of Pol I transcription machinery at the rDNA promoter, the rDNA promoter activity and expression of TBP and TAF1A, indicating that BRF1 modulates Pol I-direct transcription by controlling the expression of selective factor 1 subunits. Collectively, we demonstrate that BRF1 acts as a positive factor to regulate Pol I-directed transcription, suggesting that BRF1 can concurrently modulate Pol I and Pol III transcription and acts as a key coordinator between them.

molecular biology↗

bioRxiv2022

DGMP: Identifying Cancer Driver Genes by Jointing DGCN and MLP from Multi-omics Genomic Data

Identification of cancer driver genes plays an important role in precision oncology research, which is helpful to understand the cancer initiation and progression. However, most of existing computational methods mainly used the protein-protein interaction networks (PPIs), or treated the directed gene regulatory networks (GRNs) as the undirected gene-gene association networks to identify the cancer driver genes, which will lose the unique structure regulatory information in the directed GRNs, and then affect the outcome of the cancer driver genes identification. Here, based on the multi-omics pan-cancer data (i.e., gene expression, mutation, copy number variation and DNA methylation), we proposed a novel method (called DGMP) to identify cancer driver genes by jointing Directed Graph Convolution Network (DGCN) and Multilayer Perceptron (MLP). DGMP learns the multi-omics features of genes as well as the topological structure features in GRN with DGCN model, and uses MLP to weight more on gene features for mitigating the bias toward the graph topological features in DGCN learning process. The results on three gene regulation networks show that DGMP outperforms other existing state-of-the-art methods. It can not only identify highly mutated cancer driver genes but also the driver genes harboring other kinds of alterations (e.g., differential expression, aberrant DNA methylation) or genes involved in GRNs with other cancer genes. The source code of DGMP can be freely downloaded from https://github.com/NWPU-903PR/DGMP.

bioinformatics↗

bioRxiv2022

ScRNA-seq Identified the Metabolic Reprogramming of Human Colonic Immune Cells in Different Locations and Disease States

Different regions and states of the human colon are likely to have a distinct influence on immune cell functions. Here we studied the immunometabolic mechanisms for the spatial immune specialization and the dysregulated immune response during ulcerative colitis at single-cell resolution. We revealed that the macrophages and CD8+ T cells in the lamina propria (LP) of the human colon possessed an effector phenotype and were more activated, while their lipid metabolism was suppressed compared with those in the epithelial (Epi). Also, IgA+ plasma cells accumulated in lamina propria of the sigmoid colon were identified to be more metabolically activated versus those in the cecum and transverse colon, and the improved metabolic activity was correlated with the expression of CD27. In addition to the immunometabolic reprogramming caused by spatial localization colon, we found dysregulated cellular metabolism was related to the impaired immune functions of macrophages, dendritic cells, regulatory T cells, and ILCs in patients with ulcerative colitis. The cluster of OSM+ inflammatory monocytes was also identified to play its role in resistance to anti-TNF treatment, and we explored targeted metabolic reactions that could reprogram them to a normal state. Altogether, this study revealed a landscape of metabolic reprogramming of human colonic immune cells in different locations and disease states, and offered new insights into treating ulcerative colitis by immunometabolic modulation.

immunology↗

bioRxiv2022

Single-cell transcriptional profiling reveals cellular and molecular divergence in human maternal-fetal interface

Placenta play essential role in successful pregnancy, as the most important organ connecting and interplaying between mother and fetus. However, the cellular and molecular characteristics of fetal origin and maternal origin cell populations within the fetomaternal interface still is poorly understood. Here, we profiled the transcriptomes of single cells with well-defined maternal-fetal origin that consecutively localized from fetal section (FS), middle section (Mid_S) to maternal section (Mat_S) within the human full-term placenta. Then, we initially identified the cellular and molecular heterogeneity of cytotrophoblast cell (CTB) and stromal cell (STR) with the spatial location and fetal/maternal origin, also highlighted STR cells from fetal origins showed greater proliferation ability in Mat_S compared to cells from FS or Mid_S. Further, by integrating analysis with the first-trimester placental single cell transcriptome data, we revealed that a subpopulation of trophoblast progenitor-like cells (TPLCs) existed in the full-term placenta and mainly distributed in Mid_S, with high expression of pool of putative cell surface makers and unique molecular features. Moreover, through the extravillous cytotrophoblast (EVT) subsets differentiation trajectory and regulation network analysis, we proposed a putative key transcription factor PRDM6 that promoted the differentiation of endovascular extravillous trophoblast cells (enEVT). Finally, based on the integrated analyses of single cell transcriptional profiling of preeclampsia (PE) and match-trimester normal placenta, we highlighted the defective EVT subgroup composition and down-regulation of PRDM6 may lead to an abnormal enEVT differentiation process in PE. Together, our study offers important resources for better understanding of human placenta, stem cell-based therapy as well as PE, and provides new insights on the study of tissue heterogeneity, the clinical prevention and control of PE as well as the maternal-fetal interface.

developmental biology↗

bioRxiv2022

Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice

PAM-relaxed Cas9 nucleases, cytosine base editors and adenine base editors are promising tools for precise genome editing in plants. However, their genome-wide off-target effects are largely undetermined. Here, we conduct whole-genome sequencing (WGS) analyses of transgenic plants edited by xCas9, Cas9-NGv1, Cas9-NG, SpRY, nCas9-NG-PmCDA1, nSpRY-PmCDA1 and nSpRY-ABE8e in rice. Our results reveal different guide RNA (gRNA)-dependent off-target effects with different editors. De novo generated new gRNAs by SpRY editors lead to additional but not substantial off-target mutations. Strikingly, ABE8e results in ~500 genome-wide A-to-G off-target mutations at TA motif sites per transgenic plant. The preference of the TA motif by ABE8e is also observed at the target sites. Finally, we investigate the timeline and mechanism of somaclonal variation due to tissue culture, which chiefly contributes to the background mutations. This study provides a comprehensive understanding on the scales and mechanisms of off-target and background mutations during PAM-relaxed genome editing in plants.

genetics↗

bioRxiv2022

Generating Functional Cells Through Enhanced Interspecies Chimerism with Human Pluripotent Stem Cells

Obtaining functional human cells through interspecies chimerism with human pluripotent stem cells (hPSCs) remains unsuccessful due to its extreamly low efficiency. Here, we show that hPSCs failed to differentiate and contribute teratoma in presence of mouse PSCs (mPSCs). While, MYCN, a pro-growth factor dramatically promotes hPSC contribution in teratoma co-formation by hPSCs/mPSCs. MYCN combined with BCL2 (M/B) greatly enhanced conventional hPSCs to integrate into preimplantation embryos of different species, such as mice, rabbits and pigs and substrantially contributed to mouse post-implantation chimera in embryonic and extra-embyonic tissues. Strikingly, M/B-hPSCs injected into preimplantation Flk-1+/- mouse embryos show further enhanced chimerism that allows obtaining live human CD34+ blood progenitor cells from chimeras through cell sorting. The chimera derived human CD34+ cells further gave rise to various subtype blood cells in typical colony forming unit(CFU) assay. Thus, we proof the concept to obtain functional human cells through enchanced interspecies chimerism with hPSCs.

cell biology↗

bioRxiv2022

cir-DNA sequencing revealed the landscape of extrachromosomal circular DNA in articular cartilage and the potential roles in osteoarthritis

ObjectiveExtrachromosomal circular DNA (eccDNA) has been shown to be involved in several physiological and pathological processes including immunity, inflammation, aging and tumor. However, the expression of eccDNA in cartilage has been not reported until now. In this study, we aimed to investigate the landscape of eccDNA in articular cartilage and analyze the potential roles in Osteoarthritis (OA). MethodsThe samples of articular cartilage were obtained from total knee arthroplasty (TKA) donors with OA. The mtDNAs (mitochondrial DNA) and the linear DNAs from chondrocytes of articular cartilage were removed. Then the eccDNAs were enriched for cir-DNA sequencing. After quality control evaluation, we systematically revealed the identified eccDNA data including size distribution, the size range and sequence pattern. Moreover, we explored and disscussed the potential roles of eccDNA in OA via motif analysis and GO/KEGG pathways analysis. ResultsThe chondrocytes from OA cartilage contained an abundance of eccDNAs, which was termed as OC-eccDNAs (OA Cartilage-derived eccDNA). The characteristics of OC-eccDNAs were tissue specific, including the distribution, the size range and sequence pattern. Moreover, the functional analysis indicated that eccDNA may be involved in the homeostasis maintenance of chondrocytes and participated in the process of OA. ConclutionsOur data firstly showed the landscape of eccDNA in articular cartilage, and preliminarily indicated the potential roles of eccDNA in OA.

molecular biology↗

bioRxiv2022

Lineage-mosaic and mutation-patched spike proteins for broad-spectrum COVID-19 vaccine

The widespread SARS-CoV-2 in humans results in the continuous emergence of new variants. Recently emerged Omicron variant with multiple spike mutations sharply increases the risk of breakthrough infection or reinfection, highlighting the urgent need for new vaccines with broad-spectrum antigenic coverage. Using inter-lineage chimera and mutation patch strategies, we engineered a recombinant monomeric spike variant (STFK1628x), which showed high immunogenicity and mutually complementary antigenicity to its prototypic form (STFK). In hamsters, a bivalent vaccine comprised of STFK and STFK1628x elicited high titers of broad-spectrum antibodies to neutralize all 14 circulating SARS-CoV-2 variants, including Omicron; and fully protected vaccinees from intranasal SARS-CoV-2 challenges of either the ancestral strain or immune-evasive Beta variant. Strikingly, the vaccination of hamsters with the bivalent vaccine completely blocked the within-cage virus transmission to unvaccinated sentinels, for either the ancestral SARS-CoV-2 or Beta variant. Thus, our study provides new insights and antigen candidates for developing next-generation COVID-19 vaccines.

microbiology↗

bioRxiv2022

Harringtonine has the effects of double blocking SARS-CoV-2 membrane fusion

Fusion with host cell membrane is the main mechanism of infection of SARS-CoV-2. Here, we propose a new strategy to double block SARS-CoV-2 membrane fusion by using Harringtonine (HT), a small-molecule antagonist. By using cell membrane chromatography (CMC), we found that HT specifically targeted the SARS-CoV-2 S protein and host cell TMPRSS2, and then confirmed that HT can inhibit pseudotyped virus membrane fusion. Furthermore, HT successfully blocked SARS-CoV-2 infection, especially in the delta and Omicron mutant. Since HT is a small-molecule antagonist, it is minimally affected by the continuous variation of SARS-CoV-2. Our findings show that HT is a potential small-molecule antagonist with a new mechanism of action against SARS-CoV-2 infection, and thus HT mainly targets the S protein, and thus, greatly reduces the damage of the S proteins autotoxicity to the organ system, has promising advantages in the clinical treatment of COVID-19.

pharmacology and toxicology↗

bioRxiv2022

Explainable t-SNE for single-cell RNA-seq data analysis

BackgroundSingle-cell RNA (scRNA-seq) sequencing technologies trigger the study of individual cell gene expression and reveal the diversity within cell populations. To measure cell-to-cell similarity based on their transcription and gene expression, many dimension reduction methods are employed to retrieve corresponding low-dimensional embeddings of input scRNA-seq data to conduct clustering. However, the methods lack explainability and may not perform well with scRNA-seq data because they are not customized for high-dimensional sparse scRNA-seq data. ResultsIn this study, we propose an explainable t-SNE: cell-driven t-SNE (c-TSNE) that fuses cell differences reflected from biologically meaningful distance metrics for input data. Our study shows that the proposed method not only enhances the interpretation of the original t-SNE visualization but also demonstrates favorable single cell segregation performance on benchmark datasets compared to state-of-the-art peers. The robustness analysis shows that the proposed cell-driven t-SNE demonstrates robustness to dropout and noise in clustering. It provides a novel and practical way to investigate the interpretability of t-SNE in scRNA-seq data analysis. Unlike the general assumption that the explainability of a machine learning method may need to compromise with learning efficiency, the proposed explainable t-SNE improves both clustering efficiency and explainability. More importantly, our work suggests that widely used t-SNE can be easily misused in existing scRNA-seq analysis, because its default Euclidean distance can bring biases or meaningless results in cell difference evaluation for high-dimensional sparse scRNA-seq data. To the best of our knowledge, it is the first explainable t-SNE proposed in scRNA-seq analysis and will inspire other explainable machine learning method development in the field. ConclusionThe proposed explainable t-SNE outperforms classic t-SNE and its peers in meaningful visualization and segregation. The poor performance of the classic t-SNE highlights the importance of developing explainable machine learning methods in scRNA-seq analysis. The explainable t-SNE is a data-centric customized ML enhance efficiency in data analysis through bringing more biological insights and interpretations.

bioinformatics↗

bioRxiv2022

Control of Leaf Width by the APC/CTAD1-WL1-NAL1 Pathway in Rice

Leaf morphology is one of the most important features of the ideal plant architecture. However, the genetic and molecular mechanisms controlling leaf morphology in crops remain largely unknown, despite their central importance. Here we demonstrate that the APC/CTAD1-WL1-NAL1 pathway regulates leaf width in rice, and mutation of WL1 leads to width leaf variation. WL1 interacts with TAD1 and is degraded by APC/CTAD1, with the loss of TAD1 function resulting in narrow leaves. The WL1 protein directly binds to the regulatory region of NAL1 and recruits the corepressor TOPLESS-RELATED PROTEIN to inhibit NAL1 expression by down-regulating the level of histone acetylation of chromatin. Furthermore, biochemical and genetic analyses revealed that TAD1, WL1, and NAL1 function in a common pathway to control leaf width. Our study establishes an important framework for the APC/CTAD1-WL1-NAL1 pathway-mediated control of leaf width in rice and introduces novel perspectives for using this regulatory pathway for improving crop plant architecture.

plant biology↗

bioRxiv2022

Time-resolved proximity labeling of protein networks associated with ligand-activated EGFR

Ligand binding to the EGF receptor (EGFR) triggers multiple signal transduction processes and promotes endocytosis of the receptor. The mechanisms of EGFR endocytosis and its crosstalk with signaling are poorly understood. Here, we combined peroxidase-catalyzed proximity labeling, isobaric peptide tagging and quantitative mass-spectrometry to define the dynamics of the proximity proteome of ligand-activated EGFR. Using this approach, we identified a network of signaling proteins, which remain associated with the receptor during its internalization and trafficking through the endosomal system. We showed that Trk-fused gene (TFG), a protein known to function at the endoplasmic reticulum exit sites, was enriched in the proximity proteome of EGFR in early/sorting endosomes and localized in these endosomes, and demonstrated that TFG regulates endosomal sorting of EGFR. This study provides a comprehensive resource of time-dependent nanoscale environment of EGFR, thus opening avenues to discovering new regulatory mechanisms of signaling and intracellular trafficking of receptor tyrosine kinases.

systems biology↗