Biology subjects

Zhu, J.

Publications and source records attributed to Zhu, J..

At least 397 records · Page 22Linked to original sources

bioRxiv2022

ZmEREB57 regulates OPDA synthesis and enhances salt stress tolerance through two distinct signal pathways in Zea mays

In plants, APETALA2/Ethylene-Responsive Factor (AP2/ERF)-domain transcription factors play important roles in regulating responses to biotic and abiotic types of stress. In this study, a novel AP2/ERF gene in maize, ethylene responsive element binding factor 57 (ZmEREB57), was identified by comparative transcriptomics, which was significantly upregulated under salt treatment; however, its function remained unclear. Our findings revealed that ZmEREB57 is a nuclear protein with transactivation activity, induced by a number of abiotic types of stress. Whats more, two CRISPR/Cas9 knockout lines of ZmEREB57 conferred sensitivity to saline conditions. DNA affinity purification sequencing (DAP-Seq) analysis revealed that ZmEREB57 mainly binds to promoters containing the O-box like motif (CCGGCC) to regulate the expression of its target genes. Further experiments validated that ZmEREB57 directly bind to the promoter of ZmAOC2 involved in the synthesis of 12-oxo-phytodienoic acid (OPDA) and JA. Besides, transcriptome analysis identified a number of genes responded to both OPDA and JA treatment, while a different set of genes specifically responded specifically to OPDA, but not JA. Analysis of mutants deficient in the biosynthesis of OPDA and JA revealed that OPDA functions as a signaling molecule in the salt response. Our results provide evidence for ZmEREB57s involvement in salt tolerance by regulating OPDA and JA signaling, and confirm early observations that OPDA signaling can function independently of JA signaling in maize.

plant biology↗

bioRxiv2022

Zbtb14 regulates monocyte and macrophage development through inhibiting pu.1 expression in zebrafish

Macrophages and their precursor cells, monocytes, are the first line of defense of the body against foreign pathogens and tissue damage. Although the origins of macrophages are diverse, some common transcription factors (such as PU.1) are required to ensure proper development of monocytes/macrophages. Here we report that the deficiency of zbtb14, a transcription repressor gene belonging to ZBTB family, leads to an aberrant expansion of monocyte/macrophage population in zebrafish. Mechanistically, Zbtb14 functions as a negative regulator of pu.1, and SUMOylation on a conserved lysine is essential for the repression activity of Zbtb14. Moreover, a serine to phenylalanine mutation found in an acute myeloid leukemia (AML) patient could target ZBTB14 protein to autophagic degradation. Hence, ZBTB14 is a newly identified gene implicated in both normal and malignant myelopoiesis.

developmental biology↗

bioRxiv2022

Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimers as HIV-1 vaccine candidates

Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 trimeric antigens as multivalent vaccines. Here, we characterized the biophysical, structural, and antigenic properties of 1c-SApNPs that present the BG505 UFO trimer with wildtype and modified glycans. Trimming the glycan shield improved Env recognition by broadly neutralizing antibodies (bNAbs) to the CD4 binding site and other major glycan-containing epitopes. In mice, rabbits, and nonhuman primates, glycan trimming increased the frequency of vaccine responders (FVR) and steered antibody responses away from immunodominant glycan holes and glycan epitopes. The mechanism of vaccine-induced immunity was examined in mice. Compared with the soluble trimer, two large 1c-SApNPs showed 420 times longer retention, 20-32 times greater presentation on follicular dendritic cell dendrites, and up-to-4 times stronger germinal center reactions in lymph node follicles. These findings will inform the next phase of HIV-1 vaccine development. ONE-SENTENCE SUMMARYGlycan trimming of HIV-1 Env immunogens improves the vaccine-induced neutralizing antibody responses in small animals and primates

microbiology↗

bioRxiv2022

Clean-PIE: a novel strategy for efficiently constructing precise circRNA with thoroughly minimized immunogenicity to direct potent and durable protein expression

Translatable circular RNAs (circRNAs) are emerging as a crucial molecular format for transient protein expression, with high potential to be an alternative for linear mRNA to reshape the landscape of mRNA pharmaceutical industry. Canonical Anabaena permuted intron-exon (Ana PIE) format that developed by ORNA is an efficient method for RNA circularization, and the engineered circRNAs direct supreme protein expression in eukaryotic cells. However, recent studies revealed that this method may unavoidably result in a remain of immunogenicity in the circRNA products, albeit after thorough RNA purification. In the current study, we develop a novel strategy for efficient generation of circRNA, via the permuted T4Td introns mediated autocatalytically ribozymatic reaction mediated ligation of the flanking segment sequences that concealing in ORF or translation initiation sequence (normally equal to IRES). This strategy universally realizes around 90% circularization effectivity, and the circRNA products can be purified to around 90% purity by our new purification method, and presented thoroughly minimized immunogenicity, thus is termed "Clean-PIE". The purified circRNAs are found to direct potent and durable expression of various proteins in vitro and in vivo. The partly purified Fluc circRNA by HPLC-SEC was found to direct Fluc expression in muscle for no less than 20 days. The highly purified circRNA exhibits much stronger protein expression in vitro and in vivo, and presumed a longer duration. Additionally, the scale-up of RNA circularization with the RNA precursors from 1 L transcription revealed high circularization effectivity (around 90%) and a high productivity of the final circRNA products. Collectively, Clean-PIE is a novel circRNA platform that possesses high circularization effectivity, enabled high RNA purity and thoroughly minimized immunogenicity, as well as scaling-up accessibility and directing extreme durability of protein expression, thus has the potential to develop advanced RNA vaccines and therapeutics in pharmaceutical industrial scale.

molecular biology↗

bioRxiv2022

The mechanosensitive ion channel Piezo1 modulates the migration and immune response of microglia

Microglia are the brains resident immune cells, performing surveillance to promote homeostasis and healthy functioning. While chemical signaling in microglia is well-studied, the mechanical cues regulating their function are less well-understood. Here, we investigate the role of the mechanosensitive ion channel Piezo1 in microglia migration, pro-inflammatory cytokine production and stiffness sensing. We demonstrated the functional expression of Piezo1 in microglia and identified genes whose expression was affected by conditional Piezo1 knockout in transgenic mice. Functional assays revealed that Piezo1-deficiency in microglia enhanced migration towards amyloid {beta}-protein, and decreased levels of pro-inflammatory cytokines produced upon stimulation by lipopolysaccharide, both in vitro and in vivo. The phenomenon could be mimicked or reversed using a Piezo1-specific agonist or antagonist. Finally, we also showed that Piezo1 mediated the effect of substrate stiffness-induced migration and cytokine expression. Altogether, we show that Piezo1 is an important molecular mediator for microglia, its activation modulating their migration and immune responses.

neuroscience↗

bioRxiv2022

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↗

bioRxiv2022

Structural bases for blockade and activation of BK channels by Ba2+ ions

Ba2+ increases open probability and blocks the permeation pathway of BK channels. Here we discuss Cryo-EM structures of BK channels with Ba2+. They reveal that Ba2+ occupies site S3 in the selectivity filter, leading to blockade. Ba2+ are also detected at all high affinity Ca2+ binding sites of the gating ring. However, the architectures of this region in these structures represent intermediate transitions between the extreme close and open configurations.

biophysics↗

bioRxiv2022

The Maximum Entropy Principle For Compositional Data

In this work, we provide a general method for inferring the stochastic behavior of compositional systems. Our approach is guided by the principle of maximum entropy, a data-driven modeling technique. In particular, we show that our method can accurately capture stochastic, inter-species relationships with minimal model parameters. We provide two proofs of principle. First, we measure the relative abundances of different bacteria and infer how they interact. Second, we show that our method outperforms a common alternative for the extraction of gene-gene interactions in triple-negative breast cancer. Author summaryCompositional systems, represented as proportions of some whole, are ubiquitous. They encompass the abundances of proteins in a cell, the distribution of organisms in nature, and the stoichiometry of the most basic chemical reactions. Thus, a central goal is to understand how such processes emerge from the behaviors of their components and their pairwise interactions. Such a study, however, is challenging for two key reasons. Firstly, such systems are complex and depend, often stochastically, on their constituent parts. Secondly, the data lie on a simplex which influences their correlations. We provide a general and data-driven modeling tool for compositional systems to resolve both of these issues. We achieve this through the principle of maximum entropy, which requires only minimal assumptions and limited experimental data in contrast to current alternatives. We show that our approach provides novel and biologically-intuitive insights and is promising as a comprehensive quantitative framework for compositional data.

bioinformatics↗

bioRxiv2022

SMAD4 suppresses colitis-associated carcinoma through inhibition of CCL20/CCR6-mediated inflammation

Background & AimsChronic inflammation in the colon is a predisposing factor for colon cancer. We previously reported that colon epithelial cell silencing of Smad4, the central downstream mediator of TGF{beta} family signaling, increased epithelial expression of inflammatory genes, including the chemokine CCL20, and increased susceptibility to colitis-associated cancer. Here, we examine the role of the chemokine/receptor pair CCL20/CCR6 in mediating colitis-associated colon carcinogenesis induced by SMAD4 loss. MethodsMice with conditional, epithelial-specific Smad4 loss with and without germline deletion of the Ccr6 gene were subjected to three rounds of dextran sodium sulfate and followed for up to 3 months. Tumors were quantified histologically, and immune cell populations were analyzed by flow cytometry and immunostaining. ResultsIn humans, SMAD4 expression inversely correlated with CCL20 expression. Smad4 loss in mouse colon epithelium led to enlarged gut-associated lymphoid tissues and recruitment of specific immune cell subsets to the mouse colon epithelium and underlying stroma, particularly Treg, Th17, and dendritic cells. Loss of CCR6 abrogated these immune responses and significantly reduced the incidence of colitis-associated tumors observed with loss of SMAD4 alone. ConclusionsRegulation of mucosal inflammation is a critical role of SMAD4 signaling within the colon epithelium and central to its tumor suppressor function in the colon. A key downstream node in this regulation is suppression of CCL20 signaling by the epithelium to CCR6 in immune cells. Loss of SMAD4 in the colon epithelium increases CCL20 expression and chemoattraction of CCR6+ immune cells, contributing to greater susceptibility to colon cancer.

cancer biology↗

bioRxiv2022

Enhancement of Cell Adhesion by Anaplasma phagocytophilum Nucleolin-interacting Protein AFAP

Anaplasma phagocytophilum, the aetiologic agent of human granulocytic anaplasmosis (HGA) is an obligate intracellular Gram-negative bacterium. During infection, A. phagocytophilum enhances the adhesion of neutrophils to infected endothelial cells. However the bacterial factors contributing to this phenomenon remain unknown. In this study, we characterized a type IV secretion system substrate of A. phagocytophilum, AFAP (an actin filament-associated Anaplasma phagocytophilum protein), and found it enhanced cell adhesion. Tandem affinity purification combined with mass spectrometry identified host nucleolin as an AFAP-binding protein. Further study showed disruption of nucleolin by RNA interference and treatment of a nucleolin-binding DNA aptamer AS1411 attenuated AFAP-mediated cell adhesion. The characterization of AFAP with enhancement effect on cell adhesion and identification of its interaction partner may help understand the mechanism underlying A. phagocytophilum-promoting cell adhesion, facilitating elucidation of HGA pathogenesis. HighlightsO_LIAnaplasma phagocytophilum AFAP localized to cell periphery. C_LIO_LIAFAP enhanced cell adhesion. C_LIO_LIAFAP interacted with host nucleolin. C_LIO_LIDisruption of nucleolin attenuated AFAP-mediated cell adhesion. C_LI

microbiology↗

bioRxiv2022

Delivery of Circular mRNA via Degradable Lipid Nanoparticles against SARS-COV-2 Delta Variant

mRNA vaccines have emerged as a most promising and potent platform in the fight against various diseases including the COVID-19 pandemic. However, the intrinsic instability, varying side effects associated with the delivery systems, and continuous emergence of virus variants highlight the urgent need for the development of stable, safe and efficacious mRNA vaccines. In this study, by screening a panel of proprietary biodegradable ionizable lipidoids, we reported on a novel mRNA vaccine (cmRNA-1130) formed from a biodegradable lipidoid with eight ester bonds in the branched tail (AX4) and synthetic circular mRNA (cmRNA) encoding the trimeric Delta receptor binding domain (RBD) of SARS-CoV-2 spike protein for the induction of robust immune activation. The AX4-based lipid nanoparticles (AX4-LNP) revealed much faster elimination rate from liver and spleen in comparison with commercialized MC3-based LNP (MC3-LNP) and afforded normal level of alanine transferase (ALT), aspartate aminotransferase (AST), and creatinine (CRE) in BALB/c mice. Following intramuscular (IM) administration in BALB/c mice, cmRNA-1130 elicited potent and sustained neutralizing antibodies, RBD-specific CD4+ and CD8+ T effector memory cells (Tem), and Th1-biased T cell activations. cmRNA-1130 vaccine showed excellent stability against 6-month storage at 4 {degrees}C and freezing-thawing cycles. In brief, our study highlights mRNA vaccines based on cmRNA and biodegradable AX4 lipids hold great potential as superb therapeutic platforms for the treatment of varying diseases.

immunology↗

bioRxiv2022

A bacteriophage-based, highly efficacious, needle and adjuvant-free, mucosal COVID-19 vaccine

The authorized mRNA- and adenovirus-based SARS-CoV-2 vaccines are intramuscularly injected and effective in preventing COVID-19, but do not induce efficient mucosal immunity, or prevent viral transmission. We developed a bacteriophage T4-based, multicomponent, needle and adjuvant-free, mucosal vaccine by engineering spike trimers on capsid exterior and nucleocapsid protein in the interior. Intranasal administration of T4-COVID vaccine induced higher virus neutralization antibody titers against multiple variants, balanced Th1/Th2 antibody and cytokine responses, stronger CD4+ and CD8+ T cell immunity, and higher secretory IgA titers in sera and bronchoalveolar lavage with no effect on the gut microbiota, compared to vaccination of mice intramuscularly. The vaccine is stable at ambient temperature, induces apparent sterilizing immunity, and provides complete protection against original SARS-CoV-2 strain and its Delta variant with minimal lung histopathology. This mucosal vaccine is an excellent candidate for boosting immunity of immunized and/or as a second-generation vaccine for the unimmunized population.

microbiology↗

bioRxiv2022

Circular mRNA encoded PROTAC (RiboPROTAC) as a new platform for the degradation of intracellular therapeutic targets

Although proteolysis targeting chimera (PROTAC) technology that hijacking the ubiquitin-proteasome system (UPS) to artificially degrade protein is an emerging promising technology for many undruggable targets, it still faces several challenges, such as the difficulty to select high specificity molecule to protein of interest (POI), and only few of the E3-ligase are suitable for PROTAC mediated protein degradation. Protein-based PROTAC, termed BioPROTAC, owns the advantage of specificity but lacks membrane permeability. Here, we develop a new targeted protein degrading platform, which we termed RiboPROTAC, by encoding BioPROTAC protein degraders with circular mRNA (cmRNA) and delivering intracellularly. In this way, intracellular protein GFP and nuclear protein PCNA were successfully degraded. For PCNA targeting, not only the level of target protein is strongly decreased, but also the cell function related is strongly interfered, such as cell proliferation, apoptosis, as well as the cell cycle. What is more, for the first time, we observed that degrading PCNA with RiboPROTAC causes immunogenic cell death (ICD), although not strong, but was verified in vivo. Importantly, our in vivo results demonstrated that cmRNA encoded PCNA degrader exhibited significant tumor suppression effect, thus we provide the first proof of concept for the application of RiboPROTAC as potential mRNA therapeutic. We consider that RiboPROTAC is a new and superior PROTAC technology for targeting the undruggable targets.

molecular biology↗

bioRxiv2022

Trophoblast and blood vessel organoid cultures recapitulate the role of WNT2B in promoting intravillous vascularization in human intrauterine and ectopic pregnancy

Tubal ectopic pregnancy (TEP), a pregnancy complication caused by aberrant implantation in fallopian tubes, accounts for 9-13% pregnancy-related deaths. The lack of models for human TEP hampers the understanding of its pathological mechanisms. Here, we employed multiple models to investigate the crosstalk between human trophoblast development and intravillous vascularization. We found that the severity of TEP, the size of placental villi, and the depth of trophoblast invasion are correlated with the extent of intravillous vascularization. We identified a key pro-angiogenic factor secreted by trophoblasts, WNT2B, that promotes villous vasculogenesis, angiogenesis, and vascular network expansion. In an organoid coculture model consisting of trophoblast organoids and blood vessel organoids, knockdown of WNT2B in trophoblast organoids compromises their pro-angiogenic effect on the development of blood vessel organoids. These organoid-based models reveal an important role for WNT-mediated angiogenesis in pregnancies and could be employed to investigate the commutations between trophoblasts and endothelial/endothelial progenitor cells.

cell biology↗

bioRxiv2022

Disrupting ACE2 Dimerization Mitigates the Infection by SARS-COV-2

The coronavirus disease 2019 (COVID-19) pandemic has caused over 6 million death and 460 million reported cases globally. More effective antiviral medications are needed to curb the continued spread of this disease. The infection by SARS-COV-2 virus is initiated via the interaction between the receptor binding domain (RBD) of the viral glycoprotein Spike (S protein) and the N-term peptidase domain (PD) of the angiotensin-converting enzyme 2 (ACE2) expressed on host cell membrane. ACE2 forms protein homodimer primarily through its ferredoxin-like fold domain (aka. Neck-domain). We investigated whether the dimerization of ACE2 receptor plays a role in SARS-COV-2 virus infection. We report here that the ACE2 receptor dimerization enhances the recognition of SARS-COV-2 S protein. A 43 amino acid peptide based on the N-term of Neck-domain could block the ACE2 dimerization and the interaction between RBD and ACE2, and mitigate the SARS-COV-2/host cell interaction. Our study illustrated a new route to develop potential therapeutics for the prevention and treatment of SARS-COV-2 viral infection.

molecular biology↗

bioRxiv2022

Contrasting effects of reduced phosphatidylcholine synthesis in absence of seipin: embryonic lethality goes down while lipid droplets get even larger

Seipin plays a vital role in lipid droplet homeostasis and its deficiency causes congenital generalized lipodystrophy type II in humans. It is not known whether the physiological defects are all caused by cellular lipid droplet defects. Loss-of-function mutation of seip-1, the C. elegans seipin ortholog, causes embryonic lethality and lipid droplet abnormality. We uncover nhr-114 and spin-4 as two suppressors of seip-1 embryonic lethality. Mechanistically, nhr-114 and spin-4 act in the "B12-one-carbon cycle-phosphatidylcholine (PC)" axis and reducing PC synthesis suppresses the embryonic lethality of seip-1 mutants. Conversely, PC deficiency enhances the lipid droplet abnormality of seip-1 mutants. The suppression of seip-1 embryonic lethality by PC reduction requires polyunsaturated fatty acid (PUFA). Therefore, seipin and phosphatidylcholine exhibit opposite actions in embryogenesis, while they function similarly in lipid droplet homeostasis. Our results demonstrate that seipin-mediated embryogenesis is independent of lipid droplet homeostasis. HighlightsO_LIseip-1 suppressors act in the "B12-one-carbon cycle-PC" pathway. C_LIO_LIReducing PC synthesis suppresses the embryonic lethality of seip-1 mutants. C_LIO_LISuppression of the embryonic lethality by PC reduction requires PUFA. C_LIO_LIReduced PC synthesis enhances the large lipid droplet of seip-1 mutants. C_LI

developmental biology↗

bioRxiv2022

Tuberculosis treatment failure associated with evolution of antibiotic resilience

Antibiotics are a cornerstone of medicine, placing bacterial pathogens under intense pressure to evolve new survival mechanisms. Analysis of 51,229 Mycobacterium tuberculosis (Mtb) clinical isolates identified an essential transcriptional regulator, Rv1830 (here named resR) as a frequent target of positive (adaptive) selection. resR mutants do not demonstrate canonical drug resistance or drug tolerance but instead have significantly faster recovery after drug treatment across all antibiotics and combinations tested, a phenotype which we term antibiotic resilience. ResR acts in a regulatory cascade with other growth-controlling transcriptional regulators WhiB2 and WhiA, which are also under positive selection in Mtb clinical isolates. Mutations of these genes are associated with treatment failure and the acquisition of canonical drug resistance.

microbiology↗

bioRxiv2022

Mult-iomic integrated curvature study on pan-cancer genomic data

In this work, we introduce a new mathematical framework based on network curvature to extract significant cancer subtypes from multi-omics data. This extends our previous work that was based on analyzing a fixed single-omics data class (e,g, CNA, gene expression, etc.). Notably, we are able to show that this new methodology provided us with significant survival differences on Kaplan-Meier curves across almost every cancer that we considered. Moreover, the variances in Ollivier-Ricci curvature was explored to investigate its usefulness in network topology analysis as this curvature may be capturing subtle functional changes between various cancer subtypes.

bioinformatics↗