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Publications and source records attributed to Xu, Y..
Withdrawal StatementThe authors have withdrawn this manuscript because substantial revisions are required and the authorship contributions have changed. Therefore, the authors do not wish this work to be cited as a reference for the project. If you have any questions, please contact the corresponding author.
Multivalency enables nanostructures to bind molecular targets with high affinity. Although IgG antibodies can be generated against a wide range of antigens, their shape and size cannot be tuned to match a given target. DNA nanotechnology provides an attractive approach for designing customized multivalent scaffolds due to the addressability and programmability of the nanostructure shape and size. Here, we use computational simulation to guide the design and synthesis of a DNA nanostructure-based synthetic antibody ("nano-synbody"). The nano-synbody is comprised of a three-helix bundle DNA nanostructure with three identical arms terminating in a mini-binder protein that targets the SARS-CoV-2 spike protein. The structure was designed to match the valence and distance between the three receptor binding domains (RBDs) in the spike trimer, in order to enhance binding through avidity effects. Moreover, the design allowed for the display of one, two, or three protein-displaying arms, thereby systematically probing the effect of multivalency on binding affinity. The binding strength of the nano-synbody increased with the increasing number of arms, yielding 11.2 pM affinity ([~]100-fold enhancement over monovalent binding) for the wild-type spike protein for the three-arm structure. Moreover, the multivalency was able to yield a 95 pM affinity for the Omicron variant, a mutant against which the monovalent protein was ineffective. The nano-synbody could also block infection of a spike protein-bearing pseudovirus, and similarly demonstrated effective inhibition of the Omicron variant when trimerized. The structure of the three-arm nano-synbody bound to the Omicron variant spike trimer was solved by negative-stain transmission electron microscopy reconstruction, and shows the protein-DNA nanostructure with all three arms bound to the RBD domains, confirming the intended trivalent attachment. Finally, nano-synbody binding could be reversed by removing one, two, or three arms in a programmable fashion, via toehold-mediated strand displacement. The ability to tune the size and shape of the nano-synbody, as well as its potential ability to attach (and then remove) two or more different binding ligands, will enable the high-affinity binding of a range of proteins, and pave the way towards their manipulation using DNA-based nano-robotic devices.
Increasing evidences have linked the hippo pathway with the fibroinflammatory diseases. We generated a series of genetic knockout mice for targeting the key components of Hippo pathway to examine the individual effects of YAP1 and TAZ on pancreatic inflammation and evaluated the therapeutic potential of the YAP1/TAZ inhibitor VT-104. Mice with acinar-specific knockout of YAP1/TAZ did not exhibit any histological abnormalities in the pancreas. LATS1/2 deficiency induced acinar-to-ductal metaplasia, immune cell infiltration and fibroblast activation, which were rescued by the homozygous knockout YAP1, but not TAZ. Additionally, treatment with VT-104 also decreased pathological alterations induced by deletions of LATS1 and LATS2 in acinar cells. Our findings highlight the critical role of YAP1 in modulating pancreatic inflammation and demonstrate that VT-104 holds therapeutic potential to mitigate pancreatitis-associated pathological manifestations. Further exploration is necessary to unravel the underlying mechanisms and translate these insights into clinical applications.
BackgroundChronic Obstructive Pulmonary Disease (COPD) is a heterogeneous lung condition associated with RNA methylation and autophagy. However, the specific autophagy-related genes and RNA methylation regulators involved in COPD development remain unknown. MethodsWe analyzed COPD and non-COPD patients datasets obtained from the Gene Expression Omnibus database, including Tissue Sequencing Transcriptome (bulk-seq) and single-cell sequencing (scRNA-seq) data. Differentially expressed genes (DEGs) were identified through differential genetic analysis using non-COPD bulk-seq data as the control group and COPD samples were used as the experimental group. Animal experiments were conducted to validate the expression of key genes. COPD model mice were exposed to smoke for four months, and lung function and histopathological changes were assessed. The mRNA and protein expression levels of FTO, IGF2BP2, DDIT3, DNAJB1, and YTHDF3 were measured using RT-qPCR and Western blotting, respectively. ResultsWe identified FTO, IGF2BP2, and YTHDF3 as key methylation genes, along with autophagy hub genes DDIT3 and DNAJB1. Animal experiments showed significantly increased mRNA and protein levels of FTO, YTHDF3 and DNAJB1 and significantly decreased levels of IGF2BP2 in lung tissue of COPD mice compared to the control group. ConclusionOur findings suggest that DDIT3 and DNAJB1 as autophagy hub genes, along with FTO, IGF2BP2 and YTHDF3 as RNA methylation genes, may play crucial roles in the development of COPD. These findings, supported by bulk-seq and scRNA-seq data, contribute novel genetic evidence for understanding the epigenetics of COPD.
Pancreatic ductal adenocarcinoma (PDAC) is a clinically challenging cancer with a dismal overall prognosis. NSD2 is an H3K36-specific di-methyltransferase which has been reported to play a crucial role in promoting tumorigenesis. Here, we demonstrate that NSD2 acts as a putative tumor suppressor in Kras-driven pancreatic tumorigenesis. Low level of NSD2 indicates aggressive feature of PDAC. NSD2 restrains the mice from inflammation and Kras-induced ductal metaplasia, while NSD2 loss facilitates pancreatic tumorigenesis. Mechanistically, NSD2-mediated H3K36me2 promotes the expression of I{kappa}B, which inhibits the phosphorylation of p65 and NF-{kappa}B nuclear translocation. More importantly, NSD2 interacts with the DNA binding domain of p65, attenuating NF-{kappa}B transcriptional activity. Furthermore, inhibition of NF-{kappa}B signaling relieves the symptoms of Nsd2-deficient mice. Together, our study reveals the important tumor suppressor role of NSD2 and multiple mechanisms by which NSD2 suppresses both p65 phosphorylation and downstream transcriptional activity during pancreatic tumorigenesis. This study contributes to understanding the pathogenesis of pancreatic tumorigenesis and identifies a novel negative regulator of NF-{kappa}B signaling.
The lifespan growth of the functional connectome remains unknown. Here, we assemble task-free functional and structural magnetic resonance imaging data from 33,250 individuals aged 32 postmenstrual weeks to 80 years from 132 global sites. We report critical inflection points in the nonlinear growth curves of the global mean and variance of the connectome, peaking in the late fourth and late third decades of life, respectively. After constructing a fine-grained, lifespan-wide suite of system-level brain atlases, we show distinct maturation timelines for functional segregation within different systems. Lifespan growth of regional connectivity is organized along a primary-to-association cortical axis. These connectome-based normative models reveal substantial individual heterogeneities in functional brain networks in patients with autism spectrum disorder, major depressive disorder, and Alzheimers disease. These findings elucidate the lifespan evolution of the functional connectome and can serve as a normative reference for quantifying individual variation in development, aging, and neuropsychiatric disorders.
Functional connectome gradients represent fundamental brain organizing principles. Here, we investigate the maturation of the macroscopic connectome gradients in a task-free functional MRI dataset consisting of 39 preterm and term babies aged 31-42 postmenstrual weeks and its connection with postnatal cognitive growth. We show that the principal sensorimotor-to-visual gradient is present in baby connectomes around 35.6 postmenstrual weeks and continuously develops towards a more term-like pattern. The gradients global topographical structure undergoes progressive maturation with age, characterized by increases in explanation ratio, gradient range and gradient variation. The development of focal gradients is mostly localized in primary regions serving sensory, motor and visual functions. Machine learning approaches revealed that the connectome gradient at birth significantly predicts individual cognitive outcomes at 2-y follow-up. These findings highlight the early emerging rules of functional connectome gradients and have implications for understanding how the connectome gradients at birth underlies cognitive growth in later life. HighlightsO_LISensorimotor-to-visual gradient is present around 35.6 postmenstrual weeks C_LIO_LIGlobal gradient structure undergoes substantial changes during the third trimester C_LIO_LIRegional gradient develops mostly in primary sensory, motor, and visual regions C_LIO_LISensorimotor-to-visual gradient at birth predicts cognitive outcomes at age 2 C_LI
Understanding the process of signal communication between pollen and stigma is of significant importance for plant sexual reproduction. In the case of inter-subgeneric hybridization in water lily, there exists a pre-fertilization hybridization barrier, the regulatory mechanism of which remains unclear. In this study, we conducted hormone and transcriptome analyses of unpollinated stigmas (Mock), self-pollinated stigmas (SP), cross-pollinated stigmas within the same subgenus (CP), and inter-subgenus cross-pollination stigmas (ISCP) in water lily to elucidate the formation mechanism of the inter-subgeneric hybridization barrier. Our results indicated that the lack of ABA and BR in ISCP stigmas are key factors contributing to the formation of the inter-subgeneric hybridization barrier in water lily. Exogenous application of ABA and BR can help overcome the barrier between inter-subgeneric water lily crosses. Through transcriptome analysis, we identified nine candidate genes involved in regulating the inter-subgeneric hybridization barrier in water lily. In addition, we further demonstrated the importance of the NCED2-mediated ABA synthesis pathway in the hybridization process through AS-ODN technology. Our study confirms that ABA and BR are critical for breaking the inter-subgeneric hybridization barrier in water lily. The identification of the nine candidate genes provides important clues for further research on the hybridization recognition mechanism in water lily.
Obesity and its detrimental metabolic consequences are commonly recognized as risk factors for impairments in the central nervous system (CNS). However, the direct link between metabolic abnormalities and brain functions during high-fat feeding remains unclear. Here, we show that treatment with probucol, a cholesterol-lowering drug, counteracts the cognitive and social impairments induced by a high-fat diet in mice, while having no effect on mood disorders. Unexpectedly, the beneficial effects of probucol do not result from rectifying obesity or restoring glucose and lipid homeostasis, as evidenced by the lack of change in body weight, blood glucose and serum cholesterol levels. Interestingly, high-fat feeding led to association among the levels of redox factors, including oxidized low-density lipoprotein, glutathione and malondialdehyde, as well as a significant negative correlation between malondialdehyde levels and behavioral performance. Probucol treatment interrupts these linkages and differentially regulates the proteins for the generation of reactive oxygen species and reactive nitrogen species in the brain. These findings prompt a reconsideration of the mechanism of action of probucol, as well as the roles of altered metabolic profiles and free radicals in brain function.
The recently identified SARS-CoV-2 variant, BA.2.86, which carries a substantial number of Spike mutations, has raised a global alarm. An immediate assessment of its antigenic properties and infectivity is necessary. Here, we reveal the distinct antigenicity of BA.2.86 compared with previous variants including XBB.1.5. BA.2.86 significantly evades convalescent plasma from XBB breakthrough infection (BTI) and reinfections. Key mutations that mediate the enhanced resistance include N450D, K356T, L452W, A484K, V483del, and V445H on the RBD, while BA.2.86s NTD mutations and E554K on SD1 also largely contribute. However, we found that BA.2.86 pseudovirus exhibits compromised efficiency of infecting HEK293T-hACE2 cells compared to XBB.1.5 and EG.5, which may be caused by K356T, V483del, and E554K, and could potentially limit BA.2.86s transmissibility. In sum, it appears that BA.2.86 has traded its infectivity for higher immune evasion during long-term host-viral evolution. Close attention should be paid to monitoring additional mutations that could improve BA.2.86s infectivity.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) XBB lineages have achieved dominance worldwide and keep on evolving. Convergent evolution of XBB lineages on the receptor-binding domain (RBD) L455F and F456L is observed, resulting in variants like EG.5, FL.1.5.1, XBB.1.5.70, and HK.3. Here, we show that neutralizing antibody (NAb) evasion drives the convergent evolution of F456L, while the epistatic shift caused by F456L enables the subsequent convergence of L455F through ACE2 binding enhancement and further immune evasion. L455F and F456L evade Class 1 NAbs, reducing the neutralization efficacy of XBB breakthrough infection (BTI) and reinfection convalescent plasma. Importantly, L455F single substitution significantly dampens receptor binding; however, the combination of L455F and F456L forms an adjacent residue flipping, which leads to enhanced NAbs resistance and ACE2 binding affinity. The perturbed receptor-binding mode leads to the exceptional ACE2 binding and NAb evasion, as revealed by structural analyses. Our results indicate the evolution flexibility contributed by epistasis cannot be underestimated, and the evolution potential of SARS-CoV-2 RBD remains high.
Brain somatic mutations in various components of the mTOR complex 1 (mTORC1) pathway have emerged as major causes of focal malformations of cortical development and intractable epilepsy. While these distinct gene mutations converge on excessive mTORC1 signaling and lead to common clinical manifestations, it remains unclear whether they cause similar cellular and synaptic disruptions underlying cortical network hyperexcitability. Here, we show that in utero activation of the mTORC1 activators, Rheb or mTOR, or biallelic inactivation of the mTORC1 repressors, Depdc5, Tsc1, or Pten in mouse medial prefrontal cortex leads to shared alterations in pyramidal neuron morphology, positioning, and membrane excitability but different changes in excitatory synaptic transmission. Our findings suggest that, despite converging on mTORC1 signaling, mutations in different mTORC1 pathway genes differentially impact cortical excitatory synaptic activity, which may confer gene-specific mechanisms of hyperexcitability and responses to therapeutic intervention.
Nascent pre-mRNA undergoes 5' end capping as the first step of processing. Early evidences demonstrated the guanosine addition and 2'-O-ribose methylation spatiotemporally correlated with transcription machinery at the early stage of transcription. Here, we determined cryo-EM structures of PEC (paused elongation complex)-RNGTT (RNA guanylyltransferase and 5' phosphatase) and PEC-RNGTT-CMTR1 (cap-specific mRNA (nucleoside-2'-O-)-methyltransferase). The structures show that RNGTT docks to the root of Pol II stalk through its OB fold. Within RNGTT, the OB fold binds N-terminal of triphosphatase domain and facilitates positioning its catalytic cavity facing towards the RNA exit tunnel. RNGTT dephosphorylates and guanylates PEC-bound RNAs of 17nt, 19nt, 20nt, but not 22nt, in length. CMTR1 arrayed with RNGTT on the Pol II surface through distinct interfaces. Our structures unravel that capping enzymes RNGTT and CMTR1 directly docks to paused elongation complex, and shed light on how pre-mRNA capping couples with Pol II at the specific transcription stage.
BackgroundArchipelagos and oceanic islands often present high percentage of endemism due to rapid speciation. The Malayan pangolin is a species distributing at both mainland (southern Yunnan, China) and oceanic islands via Malayan peninsula, which may result in deep differentiation among populations. In-depth investigation of population structure and genetic consequences for such species is of vital importance for their protection and conservation, practically for the critically endangered Malayan pangolin that is suffering from poaching, illegal trade, and habitat loss. ResultsHere we carried out a large-scale population genomic analysis for Malayan pangolins, and revealed three highly distinct genetic populations in this species, two of which are now being reported for the first time. Based on multiple lines of genomic and morphological evidence, we postulate the existence of a new pangolin species (Manis_1). Genetic diversity and recent inbreeding were both at a moderate level for both Malayan pangolins and Manis_1, but mainland Malayan pangolins presented relatively lower genetic diversity, higher inbreeding and fitness cost than island populations. ConclusionsWe found extremely deep and graded differentiation in Malayan pangolins, with two newly discovered genetic populations and a new pangolin species that is closely related to the Philippine pangolin than the typical Malayan pangolin, but a distant relative of the Indian pangolin. Anthropogenic factors did not significantly weaken the basis of genetic sustainability for Malayan pangolins, but mainland Malayan pangolins should be paid more attention for conservation due to higher genetic risks than island populations.
The functional connectome of the human brain comprises time-varying network structure that facilitates efficient inter-module communication and support flexible cognitive functions. However, little is known about how the connectome dynamics of the brain emerges and develops at very early stages of human life and whether this dynamics is predictive of neurocognitive outcomes later in life. Here, we employed resting-state functional MRI data from 39 infants (31 to 42 postmenstrual weeks) and a multilayer network model to characterize the development of connectome dynamics during the third trimester and its critical role in predicting future neurocognitive outcomes at 2 years of age. We observed that the modular architecture of baby functional connectomes spontaneously reconfigures over time, with lower network module switching across time primarily in the primary regions and higher module switching mainly in the association areas. With development, the dynamic switching between the brain modules was significantly decreased, primarily located in the lateral precentral gyrus, medial temporal lobe, and subcortical areas. The clustering analysis further revealed that the primary areas displayed a higher developmental rate than the higher-order systems. Using the support vector regression approach, we found that brain connectome dynamics at birth significantly predicted cognitive and language performance at 2 years of age. Our findings highlight the emergence and spatially inhomogeneous maturation of the neonate connectome dynamics, laying a critical neural foundation for the development of cognitive and language skills later in life.
The development of methods to synthesize protein oligomers with precisely controlled number and configuration of components will enable artificial protein complexes and nanostructures with diverse biological and medical applications. Using DNA hybridization to link protein-DNA conjugates provides for a programmability that can be difficult to achieve with other methods, such as engineering multiple orthogonal protein-protein interfaces. However, it is still difficult to construct well-defined protein assemblies, and the challenge is magnified if only a single type of building block is used. To overcome this hurdle, we use a DNA origami as an "assembler" to guide the linking of protein-DNA conjugates using a series of oligonucleotide hybridization and displacement operations. We constructed several isomeric protein nanostructures on a DNA origami platform by using a C3-symmetric building block comprised of a protein trimer modified with DNA handles. By changing the number of protein-DNA building blocks attached to the origami, and the sequence of the linking and displacement strands added, we were able to produce dimers, two types of trimer structures, and three types of tetramer assemblies. Our approach expands the scope for the precise design and assembly of protein-based nanostructures, and will enable the formulation of functional protein complexes with stoichiometric and geometric control.
High-performance biosensors play a crucial role in elucidating the intricate spatiotemporal regulatory roles and dynamics of membrane lipids. However, enhancing their sensitivity and substrate-detecting capabilities remains a significant challenge. Here, we presented optogenetic-based strategies to optimize phospholipid biosensors. These strategies involved pre-sequestering unbound probes in the cell nucleus to minimize background signals in the cytoplasm. These stored probes could be released from the nucleus in response to blue light according to experimental requirements. Furthermore, we employed optically-controlled phase separation to generate punctate probes that amplified signals and facilitated the visualization of phospholipids in cells. These improved phospholipid biosensors hold great potential for enhancing our understanding of the spatiotemporal dynamics and regulatory roles of membrane lipids in live cells and this methodological insights might be valuable for developing other high-performance biosensors.
TRAIL (TNF-related apoptosis-inducing ligand) is a potent inducer of tumor cell apoptosis through TRAIL receptors. While it has been previously pursued as a potential anti-tumor therapy, the enthusiasm subsided due to unsuccessful clinical trials and the fact that many tumors are resistant to TRAIL. In this report we identified heparan sulfate (HS) as an important regulator of TRAIL-induced apoptosis. TRAIL binds HS with high affinity (KD = 73 nM) and HS induces TRAIL to form higher-order oligomers. The HS-binding site of TRAIL is located at the N-terminus of soluble TRAIL, which includes three basic residues. Binding to cell surface HS plays an essential role in promoting the apoptotic activity of TRAIL in both breast cancer and myeloma cells, and this promoting effect can be blocked by heparin, which is commonly administered to cancer patients. We also quantified HS content in several lines of myeloma cells and found that the cell line showing the most resistance to TRAIL has the least expression of HS, which suggests that HS expression in tumor cells could play a role in regulating sensitivity towards TRAIL. We also discovered that death receptor 5 (DR5), TRAIL and HS can form a ternary complex and that cell surface HS plays an active role in promoting TRAIL-induced cellular internalization of DR5. Combined, our study suggests that TRAIL-HS interactions could play multiple roles in regulating the apoptotic potency of TRAIL and might be an important point of consideration when designing future TRAIL-based anti-tumor therapy.