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Zhang, W.

Publications and source records attributed to Zhang, W..

At least 685 records · Page 38Linked to original sources

Mex67 paralogs mediate division of labor in trypanosome RNA processing and export.

In opistokhonts (animals and fungi), mRNA export to the cytoplasm is mediated by the Mex67/Mtr2 (NXF1/NXT1) heterodimer via the nuclear pore complex (NPC). In contrast to most nucleocytoplasmic transport, mRNA export requires ATP-dependent remodeling machinery, and in animals and fungi is Ran-independent. While most eukaryotes possess one Mex67 gene, trypanosomes have three distinct Mex67 paralogs, while retaining a single Mtr2 gene. We show here that these paralogs, TbMex67, TbMex67b and TbMex67L, have differing and non-redundant roles in RNA export. Specifically, TbMex67 and TbMex67b retain a canonical role in mRNA export, albeit associating with specific mRNA cohorts, but in contrast, TbMex67L is primarily involved in ribosome biogenesis. Together with the association of all Mex67 paralogs with the Ran machinery, these findings indicate significant departures in RNA export mechanisms in these divergent organisms, with implications for evolutionary origins and diversity in control of gene expression.

cell biology↗

Mouse genomic rewriting and tailoring: synthetic Trp53 and humanized ACE2

Genetically Engineered Mouse Models (GEMMs) aid in understanding human pathologies and developing new therapeutics, yet recapitulating human diseases authentically in mice is challenging to design and execute. Advances in genomics have highlighted the importance of non-coding regulatory genome sequences controlling spatiotemporal gene expression patterns and splicing to human diseases. It is thus apparent that including regulatory genomic regions during the engineering of GEMMs is highly preferable for disease modeling, with the prerequisite of large-scale genome engineering ability. Existing genome engineering methods have limits on the size and efficiency of DNA delivery, hampering routine creation of highly informative GEMMs. Here, we describe mSwAP-In (mammalian Switching Antibiotic resistance markers Progressively for Integration), a method for efficient genome rewriting in mouse embryonic stem cells. We first demonstrated the use of mSwAP-In for iterative genome rewriting of up to 115 kb of the Trp53 locus, as well as for genomic humanization of up to 180 kb ACE2 locus in response to the COVID-19 pandemic. Second, we showed the hACE2 GEMM authentically recapitulated human ACE2 expression patterns and splicing, and importantly, presented milder symptoms without mortality when challenged with SARS-CoV-2 compared to the K18-ACE2 model, thus representing a more authentic model of infection.

genomics↗

Hepatitis Viruses affect the expression of Endogenous Retrovirus and Tumor Microenvironment in HCC

Hepatocellular carcinoma (HCC) is a commonly diagnosed cancer with high mortality rates.Chronic hepatitis B virus (HBV) infection is a major cause of hepatocellular carcinoma (HCC) world-wide. The molecular mechanisms of viral hepatocarcinogenesis are still partially understood. The immune response plays an important role in the progression of HCC. Immunotherapies are becoming an increasingly promising tool for treating cancers. Advancements in scRNA-seq (single-cell RNA sequencing) have allowed us to identify new subsets in the immune microenvironment of HCC. Yet, distribution of these new cell types and their potential prognostic value in bulk samples from large cohorts remained unclear. Here, we use single-cell RNA sequencing analysis to delineate the immune landscape and tumor heterogeneity in a cohort of patients with hepatitis viruses(HBV,HCV,HDV) associated human hepatocellular carcinoma (HCC).We also re-analyze the bulk RNA-seq data for the cohort to include the expression values of human Endogenous Retrovirus (hERV). And found correlations with hepatitis viruses status.

bioinformatics↗

KLF7 Promotes Preadipocyte Proliferation via Activation of the Akt Signaling Pathway by Cis-regulating CDKN3

Kruppel-like transcription factor 7 (KLF7) promotes preadipocyte proliferation; however, its target gene in this process has not yet been identified. Using KLF7 ChIP-seq analysis, we previously showed that a KLF7-binding peak is present upstream of the cyclin-dependent kinase inhibitor 3 gene (CDKN3) in chicken preadipocytes. In the current study, we identified CDKN3 as a target gene of KLF7 that mediates the effects of KLF7 on preadipocyte proliferation. Furthermore, 5'-truncating mutation analysis showed that the minimal promoter was located between CDKN3 nt -160 and nt -7 (relative to the translation initiation codon ATG). KLF7 overexpression increased CDKN3 promoter activity in the DF-1 and immortalized chicken preadipocyte (ICP1) cell lines. Deletion of the putative binding site of KLF7 abolished the promotive effect of KLF7 overexpression on CDKN3 promoter activity. Moreover, CDKN3-knockdown and -overexpression assays revealed that CDKN3 enhanced ICP1 cell proliferation. Flow cytometry analysis showed that CDKN3 accelerated the G1/S transition. Further, we found that KLF7 promoted ICP1 cell proliferation via Akt phosphorylation by regulating CDKN3. Taken together, these results suggest that KLF7 promotes preadipocyte proliferation via activating the Akt signaling pathway by cis-regulating CDKN3, thus driving the G1/S transition.

molecular biology↗

Identification of cancer-keeping genes as therapeutic targets by finding network control hubs

Finding cancer-driver genes - the genes whose mutations may transform normal cells into cancerous ones - remains a central theme of cancer research. We took a different perspective; instead of considering normal cells, we focused on cancerous cells and genes that maintained abnormal cell growth which we named cancer-keeping genes (CKGs). Intervention in CKGs may rectify aberrant cell growth so that they can be adopted as therapeutic targets for cancer treatment. We developed a novel approach to identifying CKGs by extending the well-established theory of network structural controllability, which aims at finding a control scheme (i.e., a minimal set of non-overlapping control paths covering all nodes) and control nodes (driver genes) that can steer the cell from any state to the designated state. Going beyond driver genes defined by one control scheme, we introduced control-hub genes located in the middle of a control path of every control scheme. Control hubs are essential for maintaining cancerous states and thus can be taken as CKGs. We applied our CKG-based approach to bladder cancer (BLCA) as a case study. All the genes on the cell cycle and p53 pathways in BLCA were identified as CKGs, showing the importance of these genes in cancer and demonstrating the power of our new method. Furthermore, sensitive CKGs that could be easily changed by structural perturbation were better suited as therapeutic targets. Six sensitive CKGs (RPS6KA3, FGFR3, N-cadherin (CDH2), EP300, caspase-1, and FN1) were subjected to small-interferencing-RNA knockdown in two BLCA cell lines to validate their cancer-suppressing effects. Knocking down RPS6KA3 in a mouse model of BLCA significantly inhibited the growth of tumor xenografts in mice. Combined, our results demonstrated the value of CKGs as therapeutic targets for cancer therapy. Key pointsO_LIFocus on genes that maintain aberrant cell growth, named cancer-keeping genes (CKGs). C_LIO_LIDevelop a novel approach for finding CKGs by extending the well-estabilished theory of network structural controllability to total network controllability. C_LIO_LIApply the new method to bladder cancer and experimentally validated the cancer-suppressing function of six CKGs in two bladder cancer cell lines and that of one CKG in bladder cancer mice. C_LI

bioinformatics↗

Stable twin rDNA loci form a single nucleolus in brewer's yeast

The nucleolus is the most prominent membraneless compartment within the nucleus1, 2 - dedicated to the metabolism of ribosomal RNA. Nucleoli are composed of hundreds of ribosomal DNA (rDNA) repeated genes that form large chromosomal clusters3-5, whose high recombination rates can cause nucleolar dysfunction and promote genome instability6-8 related to metabolic and genetic diseases9-13. Intriguingly, the evolving architecture of genomes appears to have favored two strategic rDNA locations in a broad range of species - where a single locus per chromosome is situated either near the centromere or the telomere14, 15. To delve into how organisms may benefit from these nuclear organizations, we used a fused-karyotype strain of Saccharomyces cerevisiae16 to megabase-engineer a chromosome with twin chromosome-collinear rDNA loci. We showed that the twin-rDNA yeast readily adapts exhibiting wild-type growth and maintaining rRNA homeostasis. Using imaging and chromosome conformation capture, we found that the twin loci merge into a single subnuclear compartment throughout the cell cycle. Unexpectedly, we found that rDNA locus size is dependent on its position relative to the centromere, whereby the locus that is centromere-distal undergoes size reduction at a higher frequency compared to the centromere-proximal counterpart. In sum, our work sheds light on the structural evolution of rDNA loci and provides new tools to study the rDNA dosage effect on cellular metabolism.

genomics↗

An engineered xCas12i with high activity, high specificity and broad PAM range

The type-V CRISPR effector Cas12i, with its smaller size, short crRNA guiding, and self-processing features, is a potentially versatile genome editing tool. By screening Cas12i proteins from a metagenomic database, we identified a natural variant with high activity in mammalian cells, named as xCas12i. We further engineered the PAM-interacting, REC, and RuvC domains for enhanced cleavage activity and specificity. This variant, named as high-fidelity Cas12Max, exhibited robust genome editing activity and minimal off-target activity with a broad 5-TN recognition profile. With the fusion of deaminase TadA8e and further optimization of xCas12i, the base editor dCas12i-Tad8e also showed the high editing efficiency. This study provides highly efficient and specific tools for gene therapy.

bioengineering↗

Rapid Development of a Mucosal Nanoparticle Flu Vaccine by Genetic Engineering of Bacteriophage T4 using CRISPR-Cas

Mucosal vaccines that can induce local mucosal immune responses and combat the pathogens at entry sites are considered to be the most effective way to prevent infection. A universal platform that can be customized for development of mucosal vaccines against any given pathogen is therefore highly desired. Here, we demonstrate an efficient approach to develop nasal mucosal vaccines through genetic engineering of T4 phage to generate antigen-decorated nanoparticles. The antigen coding sequence was inserted into T4 genome in-frame at the C terminus of Soc (small outer capsid protein) using the CRISPR-Cas phage editing technology. During the propagation of recombinant T4 phages in E. coli, the Soc-antigen fusion proteins self-assemble on T4 capsids to form antigen-decorated nanoparticles that have intrinsic adjuvant activity and mucosal adhesive property. As a proof of concept, we showed that intranasal immunization with Flu viral M2e-decorated T4 nanoparticles efficiently induced local mucosal as well as systemic immune responses and provided complete protections against divergent influenza viruses in a mouse model. Potentially, our platform can be customized for any respiratory pathogen to rapidly generate mucosal vaccines against future emerging epidemics and pandemics.

immunology↗

Thinking like a structural biologist: A pocket-based 3D molecule generative model fueled by electron density

We report for the first time the use of experimental electron density (ED) as training data for the generation of drug-like three-dimensional molecules based on the structure of a target protein pocket. Similar to a structural biologist building molecules based on their ED, our model functions with two main components: a generative adversarial network (GAN) to generate the ligand ED in the input pocket and an ED interpretation module for molecule generation. The model was tested on three targets including kinase (HPK1), protease (Covid19-3CL), and nuclear receptor (VDR), and evaluated with a reference dataset composed of over 8,000 compounds that have their activities reported in the literature. The evaluation examined the chemical validity, chemical space distribution-based diversity, and similarity with reference active compounds concerning the molecular structure and pocket-binding mode. Our model can reproduce classical active compounds and can also generate novel molecules with similar binding modes as active compounds, making it a promising tool for library generation supporting high-throughput virtual screening. Our model is available as an online service to academic users via https://edmg.stonewise.cn/#/create.

bioinformatics↗

omicsGAT: Graph Attention Network for Cancer Subtype Analyses

MotivationThe use of high-throughput omics technologies is becoming increasingly popular in all facets of biomedical science. The mRNA sequencing (RNA-seq) method reports quantitative measures of more than tens of thousands of biological features. It provides a more comprehensive molecular perspective of studied cancer mechanisms compared to traditional approaches. Graph-based learning models have been proposed to learn important hidden representations from gene expression data and network structure to improve cancer outcome prediction, patient stratification, and cell clustering. However, these graph-based methods cannot rank the importance of the different neighbors for a particular sample in the downstream cancer subtype analyses. In this study, we introduce omicsGAT, a graph attention network (GAT) model to integrate graph-based learning with an attention mechanism for RNA-seq data analysis. The multi-head attention mechanism in omicsGAT can more effectively secure information of a particular sample by assigning different attention coefficients to its neighbors. ResultsComprehensive experiments on The Cancer Genome Atlas (TCGA) breast cancer and bladder cancer bulk RNA-seq data, and primary diffuse gliomas single-cell RNA-seq data validate that (1) the proposed model can effectively integrate neighborhood information of a sample and learn an embedding vector to improve disease phenotype prediction, cancer patient stratification, and cell clustering of the sample. (2) The attention matrix generated from the multi-head attention coefficients provides more useful information compared to the sample correlation-based adjacency matrix. From the results, we can conclude that some neighbors play a more important role than others in cancer subtype analyses of a particular sample based on the attention coefficient. Availability and implementationSource code is available at: https://github.com/CompbioLabUCF/omicsGAT Supplementary informationSupplementary data are available at BioRxiv online.

bioinformatics↗

The trifecta of disease avoidance, silique shattering resistance and flowering period elongation achieved by the BnaIDA editing in Brassica napus

Rapeseed (Brassica napus) oil is a main vegetable oil source in the world. The devastating disease of stem rot caused by the necrotrophic fungus Sclerotinia sclerotiorum and pod shattering led to a great yield loss in Brassica napus. S.sclerotiorum infects the rapeseed by the detached floral petals, in which the released ascospores land and germinate as mycelium, then the petals fall on the leaves at lower part of the rapeseed and heavily attacks the leaves and stems. The prevention of petal-shedding is a promising approach to avoid the stem rot damage, moreover, longer period of flowering time will bring rapeseed flower tourism a huge economic benefit. Notably, IDA (INFLORESCENCE DEFICIENT IN ABSCISSION) and IDA-LIKE(IDL) protein control floral organ abscission in Arabidopsis thaliana. In our study, the precisely editing of two IDA homologues genes using CRISPR/Cas9 system in Brassica napus caused the petal attaching to the flower till pod mature and enhancing the silique dehiscence resistance. Incubating the S.sclerotiorum to petal showed the edited rapeseed avoiding the infection of S.sclerotiorum RNA-Seq analysis demonstrated that in the editted plant, the genes involed in IDA pathway were regulated, while other genes keep unaltered. Investigation of agronomic traits showed that no positive the agronimic traits was introduced in editted plant. Our study demonstrated that mutation of two BnaIDAs creating a promising germplasm for disease avoidance, siliques shattering resistance and flowering period elongation which will contribute great to rapeseed industry.

plant biology↗

Cis-membrane association of human ATG8 proteins N-terminus mediates autophagy

Autophagy is an essential catabolic pathway which sequesters and engulfs cytosolic substrates via autophagosomes, unique double-membraned structures. ATG8 proteins are ubiquitin-like proteins recruited to autophagosome membranes by lipidation at the C-terminus. ATG8s recruit substrates, such as p62, and play an important role in mediating autophagosome membrane expansion. However, the precise function of lipidated ATG8 in expansion remains obscure. Using a real-time in vitro lipidation assay, we revealed that the N-termini of lipidated human ATG8s (LC3B and GABARAP) are highly dynamic and interact with the membrane. Moreover, atomistic MD simulation and FRET assays indicate that N-termini of LC3B and GABARAP associate in cis on the membrane. The cis-membrane association of the N-terminus is critical to maintain membrane expansion and the size of autophagosomes in cells, consequently, mediating the efficient degradation of p62. Our study provides fundamental molecular insights into autophagosome membrane expansion, revealing the critical and unique function of lipidated ATG8.

cell biology↗

Structural conversion of α-synuclein at the mitochondria induces neuronal toxicity

Aggregation of -Synuclein (-Syn) drives Parkinsons disease, although the initial stages of self-assembly and structural conversion have not been captured inside neurons. We track the intracellular conformational states of -Syn utilizing a single-molecule FRET biosensor, and show that -Syn converts from its monomeric state to form two distinct oligomeric states in neurons in a concentration dependent, and sequence specific manner. 3D FRET-CLEM reveals the structural organization, and location of aggregation hotspots inside the cell. Notably multiple intracellular seeding events occur preferentially on membrane surfaces, especially mitochondrial membranes. The mitochondrial lipid, cardiolipin triggers rapid oligomerization of A53T -Syn, and cardiolipin is sequestered within aggregating lipid-protein complexes. Mitochondrial aggregates impair complex I activity and increase mitochondrial ROS generation, which accelerates the oligomerization of A53T -Syn, and ultimately causes permeabilization of mitochondrial membranes, and cell death. Patient iPSC derived neurons harboring A53T mutations exhibit accelerated oligomerization that is dependent on mitochondrial ROS, early mitochondrial permeabilization and neuronal death. Our study highlights a mechanism of de novo oligomerization at the mitochondria and its induction of neuronal toxicity.

neuroscience↗

Development and application of an uncapped mRNA platform

A novel uncapped mRNA platform was developed. Five lipid nanoparticle (LNP)-encapsulated mRNA constructs were made to evaluate several aspects of our platform, including transfection efficiency and durability in vitro and in vivo and the activation of humoral and cellular immunity in several animal models. The constructs were eGFP-mRNA-LNP (for enhanced green fluorescence mRNA), Fluc-mRNA-LNP (for firefly luciferase mRNA), S{delta}T-mRNA-LNP (for Delta strain SARS-CoV-2 spike protein trimer mRNA), gDED-mRNA-LNP (for truncated glycoprotein D mRNA coding ectodomain from herpes simplex virus type 2 (HSV2)) and gDFR-mRNA-LNP (for truncated HSV2 glycoprotein D mRNA coding amino acids 1[~]400). Quantifiable target protein expression was achieved in vitro and in vivo with eGFP-and Fluc-mRNA-LNP. S{delta}T-mRNA-LNP, gDED-mRNA-LNP and gDFR-mRNA-LNP induced both humoral and cellular immune responses comparable to those obtained by previously reported capped mRNA-LNP constructs. Notably, S{delta}T-mRNA-LNP elicited neutralizing antibodies in hamsters against the Omicron and Delta strains. Additionally, gDED-mRNA-LNP and gDFR-mRNA-LNP induced potent neutralizing antibodies in rabbits and mice. The mRNA constructs with uridine triphosphate (UTP) outperformed those with N1-methylpseudouridine triphosphate (N1m{psi}TP) in the induction of antibodies via S{delta}T-mRNA-LNP. Our uncapped, process-simplified, and economical mRNA platform may have broad utility in vaccines and protein replacement drugs.

bioengineering↗

Spatiotemporal dynamics of zygotic genome activation in basal chordates revealed by interspecific hybrids

Zygotic genome activation (ZGA), a universal process in early embryogenesis that occurs during the maternal-to-zygotic transition, involves reprogramming in the zygotic nucleus that initiates global transcription. In recent decades, knowledge of this process has been acquired from research on various model organisms; however, a consensus explanation of the mechanism underlying the process, especially in relation to housekeeping gene reactivation, is lacking. Here, we used hybrids derived from two ascidian species (Ciona robusta and C. savignyi), which diverged >120 Mya with significant divergence among most orthologous genes, to symmetrically document the unique dynamics of ZGA in urochordates. We found two co-ordinated waves of ZGA, representing early developmental and housekeeping gene reactivation, during the 8-cell to 110-cell stage. Comparative analysis revealed the regulatory connection between maternal and zygotic genes as well as allelic-specific expression in a species-rather than parental-related manner, which was attributed to the divergence of cis-regulatory elements. Single-cell RNA sequencing revealed that spatial differential reactivation of paternal housekeeping genes was significantly correlated with the mechanical property of each cell type. These findings potentially provide a new system for understanding the evolution and adaptation of strategies regulating ZGA in basal chordates.

developmental biology↗

Respiratory mucosal vaccination of peptide-poloxamine-DNA nanoparticles provides complete protection against lethal SARS-CoV-2 challenge

The ongoing SARS-CoV-2 pandemic represents a brutal reminder of the continual threat of mucosal infectious diseases. Mucosal immunity may provide robust protection at the predominant sites of SARS-CoV-2 infection. However, it remains unclear whether respiratory mucosal administration of DNA vaccines could confer protective immune responses against SARS-CoV-2 challenge due to the insurmountable barriers posed by the airway. Here, we applied self-assembled peptide-poloxamine nanoparticles with mucus-penetrating properties for pulmonary inoculation of a COVID-19 DNA vaccine (pSpike/PP-sNp). Not only displays the pSpike/PP-sNp superior gene-transfection and favorable biocompatibility in the mouse airway, but pSpike/PP-sNp promotes a tripartite immunity consisting of systemic, cellular and mucosal immune responses that are characterized by mucosal IgA secretion, high levels of neutralizing antibodies, and resident memory phenotype T-cell responses in the lungs of mice. Most importantly, pSpike/PP-sNp completely eliminates SARS-CoV-2 infection in both upper and lower respiratory tracts and enables 100% survival rate of mice following lethal SARS-CoV-2 challenge. Our findings indicate PP-sNp might be a promising platform in mediating DNA vaccines to elicit all-around mucosal immunity against SARS-CoV-2.

immunology↗

eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways

Cancer is driven by both genetic and epigenetic changes that impact on gene expression profiles and the resulting tumourigenic phenotype. Enhancers are transcriptional regulatory elements that are key to our understanding of how this rewiring of gene expression is achieved in cancer cells. Here we have harnessed the power of RNA-seq data from hundreds of patients with oesophageal adenocarcinoma (OAC) or its precursor state Barretts oesophagus (BO) coupled with open chromatin maps to identify potential enhancer RNAs (eRNAs) and their associated enhancer regions in this cancer. We identify [~]1000 OAC-specific enhancers and use this data to uncover new cellular pathways that are operational in OAC. Among these are enhancers for JUP, MYBL2 and CCNE1, and we show that their activity is required for cancer cell viability. We also demonstrate the clinical utility of our dataset for identifying disease stage and patient prognosis. Our data therefore identify an important set of regulatory elements that enhance our molecular understanding of OAC and point to potential new therapeutic directions.

cancer biology↗

Senescent Preosteoclast Secretome Promotes Metabolic Syndrome Associated Osteoarthritis through Cyclooxygenase 2

BackgroundMetabolic syndrome-associated osteoarthritis (MetS-OA) is a distinct osteoarthritis phenotype defined by the coexistence of MetS or its individual components. Despite the high prevalence of MetS-OA, its pathogenic mechanisms are unclear. The aim of this study was to determine the role of cellular senescence in the development of MetS-OA. MethodsAnalysis of the human osteoarthritis initiative (OAI) dataset was conducted to investigate the MRI subchondral bone features of MetS-human OA participants. Joint phenotype and senescent cells were evaluated in two MetS-OA mouse models: high-fat diet (HFD)-challenged mice and STR/Ort mice. In addition, the molecular mechanisms by which preosteoclasts become senescent as well as how the senescent preosteoclasts impair subchondral bone microenvironment were characterized using in vitro preosteoclast culture system. ResultsHumans and mice with MetS are more likely to develop osteoarthritis-related subchondral bone alterations than those without MetS. MetS-OA mice exhibited a rapid increase in joint subchondral bone plate and trabecular thickness before articular cartilage degeneration. Subchondral preosteoclasts undergo senescence at the pre- or early-osteoarthritis stage and acquire a unique secretome to stimulate osteoblast differentiation and inhibit osteoclast differentiation. Antagonizing preosteoclast senescence markedly mitigates pathological subchondral alterations and osteoarthritis progression in MetS-OA mice. At the molecular level, preosteoclast secretome activates COX2-PGE2, resulting in stimulated differentiation of osteoblast progenitors for subchondral bone formation. Administration of a selective COX2 inhibitor attenuated subchondral bone alteration and osteoarthritis progression in MetS-OA mice. Longitudinal analyses of the human Osteoarthritis Initiative (OAI) cohort dataset also revealed that COX2 inhibitor use, relative to non-selective nonsteroidal anti-inflammatory drug use, is associated with less progression of osteoarthritis and subchondral bone marrow lesion worsening in participants with MetS-OA. ConclusionsOur findings suggest a central role of a senescent preosteoclast secretome-COX2/PGE2 axis in the pathogenesis of MetS-OA, in which selective COX2 inhibitors may have disease-modifying potential. FundingThis work was supported by the National Institutes of Health grant R01AG068226 and R01AG072090 to M.W., R01AR079620 to S.D., and P01AG066603 to X.C.

cell biology↗