Biology subjects

Liu, H.

Publications and source records attributed to Liu, H..

At least 595 records · Page 33Linked to original sources

bioRxiv2022

Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody to antigenically distinct omicron SARS-CoV-2 subvariants

The rapid evolution of SARS-CoV-2 Omicron variants has emphasized the need to identify antibodies with broad neutralizing capabilities to inform future monoclonal therapies and vaccination strategies. Herein, we identify S728-1157, a broadly neutralizing antibody (bnAb) targeting the receptor-binding site (RBS) and derived from an individual previously infected with SARS-CoV-2 prior to the spread of variants of concern (VOCs). S728-1157 demonstrates broad cross-neutralization of all dominant variants including D614G, Beta, Delta, Kappa, Mu, and Omicron (BA.1/BA.2/BA.2.75/BA.4/BA.5/BL.1). Furthermore, it protected hamsters against in vivo challenges with wildtype, Delta, and BA.1 viruses. Structural analysis reveals that this antibody targets a class 1 epitope via multiple hydrophobic and polar interactions with its CDR-H3, in addition to common class 1 motifs in CDR-H1/CDR-H2. Importantly, this epitope is more readily accessible in the open and prefusion state, or in the hexaproline (6P)-stabilized spike constructs, as compared to diproline (2P) constructs. Overall, S728-1157 demonstrates broad therapeutic potential, and may inform target-driven vaccine design against future SARS-CoV-2 variants.

immunology↗

bioRxiv2022

A new polymodal gating model of the proton-activated chloride channel

The proton-activated chloride (PAC) channel plays critical roles in ischemic neuron death, but its activation mechanisms remain elusive. Here, we interrogated PAC channel gating using its unique bidirectional modulator C77304 as a pharmacological probe. C77304 activated the PAC channel by acting on its proton gating, while simultaneously inhibiting channel activity at higher doses, through interaction with two modulatory sites with different affinities and state-dependence. Excitingly, we revealed that PAC undergoes intrinsic proton gating-independent voltage activation, which was defined by an ion-flux gating mechanism. Scanning-mutagenesis and molecular dynamics simulation confirmed that E181, E257, and E261 in human PAC form the primary proton sensors, as alanine mutations eliminated the channels proton gating while sparing the voltage-dependent gating. This proton sensing mechanism was basically conserved among orthologous PAC channels. Collectively, our data unveils the polymodal gating and proton sensing mechanisms in the PAC channel which may inspire potential drug development.

neuroscience↗

bioRxiv2022

Multiscale Hybrid Fabrication: Volumetric Printing Meets Two-Photon Ablation

The vascular tree spans length scales from centimeter to micrometer. Engineering multiscale vasculature, in particular from millimeter vessels to micrometer-size capillaries, represents an unmet challenge and may require the convergence of two or more printing modalities. Leveraging the great advances in light-based biofabrication, we herein introduce a hybrid strategy to tackle this challenge. By combining volumetric printing (VP) and high-resolution two-photon ablation (2PA), we demonstrate the possibility to create complex multiscale organotypic perfusable models with features ranging from mesoscale (VP) to microscale (2PA). To successfully combine these two methods, we first eliminated micrometer-size defects generated during VP process. Due to optical modulation instability of the laser source and selffocusing phenomenon that occurs when the light triggers the photoresin crosslinking, VP printed constructs feature micrometer-size filaments and channels. By optical tuning the refractive index of the photoresin, we demonstrate defect-free VP that can then be combined with 2PA. To facilitate the 2PA process and meet VP requirements, we introduce a purely protein-based photoclick photoresin combining gelatin-norbornene and gelatin-thiol. By optimizing defect-free VP and 2PA processes, we finally demonstrate the possibility to generate complex 3D vasculature-like constructs with features ranging from ~400 m of VP to ~2 m of 2PA. This hybrid strategy opens new possibilities to better recapitulate microtissues vasculature and complex architectures, with particular potential for microfluidics and organ/tissue-on-a-chip technologies.

bioengineering↗

bioRxiv2022

Spatially resolved human kidney multi-omics single cell atlas highlights the key role of the fibrotic microenvironment in kidney disease progression

Kidneys possess one of the most intricate three-dimensional cellular structures in the body, yet the spatial and molecular principles of kidney health and disease remain inadequately understood. Here, we have generated high-quality datasets for 81 samples, including single cell (sc), single nuclear (sn), spot level (Visium) and single cell resolution (CosMx) spatial (sp)-RNA expression, and sn open chromatin, capturing cells from healthy, diabetic, and hypertensive diseased human kidneys. By combining the snRNA, snATAC and scRNA sequencing we identify cell types and map these cell types to their locations within the tissue. Unbiased deconvolution of the spatial data identifies 4 distinct spatial microenvironments: glomerular, immune, tubule and fibrotic. We describe the complex, heterogenous cellular and spatial organization of human microenvironments in health and disease. Further, we find that the fibrotic microenvironment spatial gene signature is not only able to molecularly classify human kidneys, but it also offers an improved prognosis prediction compared to traditional histopathological analysis. We provide a comprehensive spatially resolved molecular roadmap of the human kidney and the fibrotic process, demonstrating the clinical utility of spatial transcriptomics.

genetics↗

bioRxiv2022

Ratio-based quantitative multiomics profiling using universal reference materials empowers data integration

Multiomics profiling is a powerful tool to characterize the same samples with complementary features orchestrating the genome, epigenome, transcriptome, proteome, and metabolome. However, the lack of ground truth hampers the objective assessment of and subsequent choice from a plethora of measurement and computational methods aiming to integrate diverse and often enigmatically incomparable omics datasets. Here we establish and characterize the first suites of publicly available multiomics reference materials of matched DNA, RNA, proteins, and metabolites derived from immortalized cell lines from a family quartet of parents and monozygotic twin daughters, providing built-in truth defined by family relationship and the central dogma. We demonstrate that the "ratio"-based omics profiling data, i.e., by scaling the absolute feature values of a study sample relative to those of a concurrently measured universal reference sample, were inherently much more reproducible and comparable across batches, labs, platforms, and omics types, thus empower the horizontal (within-omics) and vertical (cross-omics) data integration in multiomics studies. Our study identifies "absolute" feature quantitation as the root cause of irreproducibility in multiomics measurement and data integration, and urges a paradigm shift from "absolute" to "ratio"-based multiomics profiling with universal reference materials.

systems biology↗

bioRxiv2022

Relative enrichment of oral bacteria in feces indicates loss of intestinal commensals with implications for host health

The increased relative abundance of oral bacteria detected in fecal samples has been associated with intestinal diseases and digestive disorders. This observation raises two competing hypotheses: either oral bacteria invade the gut bacterial population and expand in the intestine (the Expansion hypothesis), or oral bacteria transit through and their relative increase in feces marks a depletion of the gut bacterial population (the Marker hypothesis). To address this, we conducted a comprehensive analysis of quantitative microbiome data from mouse experiments and diverse patient cohorts. Our findings consistently support the Marker hypothesis as the primary explanation. We further establish a robust inverse correlation between the total fraction of oral bacteria and decreased total bacterial abundance in feces. This correlation underlies the associations between the oral bacterial fraction and multiple patient outcomes consistent with a depleted gut microbiota. By distinguishing between the two hypotheses, our study guides the interpretation of microbiome compositional data and their links with human health.

microbiology↗

bioRxiv2022

SARS-CoV-2 infected cells sprout actin-rich filopodia that facilitate viral invasion

Emerging COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a great threat to human health and economics. Although SARS-CoV-2 entry mechanism has been explored, little is known about how SARS-CoV-2 regulates the host cell remodeling to facilitate virus invasion process. Here we unveil that SARS-CoV-2 boosts and repurposes filopodia for entry to the target cells. Using SARS-CoV-2 virus-like particle (VLP), real-time live-cell imaging and simulation of active gel model, we reveal that VLP-induced Cdc42 activation leads to the formation of filopodia, which reinforce the viral entry to host cells. By single-particle tracking and sparse deconvolution algorithm, we uncover that VLP particles utilize filopodia to reach the entry site in two patterns, surfing and grabbing, which are more efficient and faster than entry via flat plasma membrane regions. Furthermore, the entry process via filopodia is dependent on the actin cytoskeleton and actin-associated proteins fascin, formin, and Arp2/3. Importantly, either inhibition the actin cross-linking protein fascin or the active level of Cdc42 could significantly hinders both the VLP and the authentic SARS-CoV-2 entry. Together, our results highlight that the spatial-temporal regulation of the actin cytoskeleton by SARS-CoV-2 infection makes filopodia as a highway for virus entry, which emerges as an antiviral target. Significance StatementRevealing the mechanism of SARS-CoV-2 invasion is of great significance to explain its high pathogenic and rapid transmission in the world. We discovered a previously unknown route of SARS-CoV-2 entry. SARS-CoV-2 virus-like particles boost cellular filopodia formation by activating Cdc42. Using state-of-art-technology, we spatial-temporally described how virus utilize filopodia to enter the target cell in two modes: surfing and grabbing. Filopodia can directly transport the virus to endocytic hot spots to avoid the virus from disorderly searching on the plasma membrane. Our study complements current knowledge of SARS-CoV-2 that filopodia and its components not only play an important role in virus release and cell-cell transmission, but also in the entry process, and provides several potential therapeutic targets for SARS-CoV-2. HighlightsO_LISARS-CoV-2 VLP infection promotes filopodia formation by activating Cdc42 C_LIO_LISARS-CoV-2 VLP utilizes filopodia to enter target cell via two modes, surfing and grabbing C_LIO_LIFilopodia disruption compromises the invasion of both VLP and authentic SARS-CoV-2 C_LI

cell biology↗

bioRxiv2022

Structure of a G protein-coupled receptor with GRK2 and a biased ligand

Phosphorylation of G protein-coupled receptors (GPCR) by GPCR kinases (GRKs) desensitizes G protein signaling and promotes arrestin signaling, which is also modulated by biased ligands1-6. Molecular assembly of GRKs to GPCRs and the basis of GRK-mediated biased signaling remain largely unknown due to the weak GPCR-GRK interactions. Here we report the complex structure of neurotensin receptor 1 (NTSR1) bound to GRK2, Gq, and an arrestin-biased ligand, SBI-5537, at a resolution of 2.92 [A]. The high-quality density map reveals the clear arrangement of the intact GRK2 with the receptor, with the N-terminal helix of GRK2 docking into the open cytoplasmic pocket formed by the outward movement of the receptor TM6, analogous of the binding of G protein to the receptor. Strikingly, the arrestin-biased ligand is found at the interface between GRK2 and NTSR1 to enhance GRK2 binding. The binding mode of the biased ligand is compatible with arrestin binding but is clashed with the binding of a G protein, thus provide an unambiguous mechanism for its arrestin-biased signaling capability. Together, our structure provides a solid model for understanding the details of GPCR-GRK interactions and biased signaling.

cell biology↗

bioRxiv2022

Broad SARS-CoV-2 Neutralization by Monoclonal and Bispecific Antibodies Derived from a Gamma-infected Individual

The worldwide pandemic caused by SARS-CoV-2 has remained a human medical threat due to the continued evolution of multiple variants that acquire resistance to vaccines and prior infection. Therefore, it is imperative to discover monoclonal antibodies (mAbs) that neutralize a broad range of SARS-CoV-2 variants for therapeutic and prophylactic use. A stabilized autologous SARS-CoV-2 spike glycoprotein was used to enrich antigen-specific B cells from an individual with a primary Gamma variant infection. Five mAbs selected from those B cells showed considerable neutralizing potency against multiple variants of concern, with COVA309-35 being the most potent against the autologous virus, as well as against Omicron BA.1 and BA.2. When combining the COVA309 mAbs as cocktails or bispecific antibody formats, the breadth and potency was significantly improved against all tested variants. In addition, the mechanism of cross-neutralization of the COVA309 mAbs was elucidated by structural analysis. Altogether these data indicate that a Gamma-infected individual can develop broadly neutralizing antibodies.

immunology↗

bioRxiv2022

Molecular Recognition of Itching Neuropeptides by Bombesin Receptors.

Neuromedin B (NMB) and gastrin-releasing peptide (GRP), two bombesin analogs, are endogenous itch-specific neuropeptides that induce histaminergic and nonhistaminergic itch, respectively. Their functions are mediated by two G protein-coupled bombesin receptors, NMBR and GRPR. Here we present cryo-electron microscopy(cryo-EM) structures of G protein coupled NMBR and GRPR bound to NMB and GRP, respectively. The structures reveal that both bombesin receptors contain an extended and deep pocket to adopt NMB and GRP, with the conserved C-terminal motif of GH(F/L)M from both peptides to contact the toggle switch residues for the receptor activation. Together with mutational and functional data, our structures reveal the mechanism of ligand selectivity and specific activation of the bombesin receptors. These findings also pave the way to facilitate rational design of therapies targeting bombesin receptors for the treatment of pruritus.

biophysics↗

bioRxiv2022

PTH regulates osteogenesis and suppresses adipogenesis through Zfp 467 in a feed-forward, cyclic AMP-dependent manner

Conditional deletion of the PTH1R in mesenchymal progenitors reduces osteoblast differentiation, enhances marrow adipogenesis and increases zinc finger protein 467 (Zfp467) expression. In contrast, genetic loss of Zfp467 increased Pth1r expression and shifts mesenchymal progenitor cell fate towards osteogenesis and higher bone mass. In this study we hypothesized that PTH1R and ZFP467 could constitute a feedback loop that facilitates PTH-induced osteogenesis and that conditional deletion of Zfp467 in osteogenic precursors would lead to high bone mass. We report that PrrxCre Zfp467 but not AdipoCre Zfp467 mice exhibit an identical phenotype to the Zfp467-/-mice with high bone mass and greater osteogenic differentiation We also found that PTH suppressed Zfp467 expression primarily via the cyclic AMP/PKA pathway. Not surprisingly, PKA activation inhibited the expression of Zfp467 and gene silencing of Pth1r caused an increase in Zfp467 mRNA transcription. Dual fluorescence reporter assays and confocal immunofluorescence demonstrated that genetic deletion of Zfp467 resulted in higher nuclear translocation of p50 that binds to the P2 promoter of the Pth1r and increased its transcription. As expected, Zfp467-/- cells had enhanced production of cyclic AMP and increased glycolysis in response to exogenous PTH. Additionally, the osteogenic response to PTH was also enhanced in Zfp467 -/-calvarial osteoblasts, and the pro-osteogenic effect of Zfp467 deletion was blocked by gene silencing of Pth1r or a PKA inhibitor. In conclusion, our findings suggest that loss or PTH1R-mediated repression of Zfp467 results in a pathway that increases Pth1r transcription via p50 and thus cellular responsiveness to PTH, ultimately leading to enhanced bone formation.

cell biology↗

bioRxiv2022

Causal Epigenetic Age Uncouples Damage and Adaptation

Machine learning models based on DNA methylation data can predict biological age but often lack causal insights. By harnessing large-scale genetic data through epigenome-wide Mendelian Randomization, we identified CpG sites potentially causal for aging-related traits. Neither the existing epigenetic clocks nor age-related differential DNA methylation are enriched in these sites. These CpGs include sites that contribute to aging and protect against it, yet their combined contribution negatively affects age-related traits. We established a novel framework to introduce causal information into epigenetic clocks, resulting in DamAge and AdaptAge--clocks that track detrimental and adaptive methylation changes, respectively. DamAge correlates with adverse outcomes, including mortality, while AdaptAge is associated with beneficial adaptations. These causality-enriched clocks exhibit sensitivity to short-term interventions. Our findings provide a detailed land-scape of CpG sites with putative causal links to lifespan and healthspan, facilitating the development of aging biomarkers, assessing interventions, and studying reversibility of age-associated changes.

genetics↗

bioRxiv2022

Hybrid Synthesis of bioplastics polyhydroxybutyrate from carbon dioxide

The accelerating environmental crisis has intensified the demand for switching from traditional economy to a renewable one with a reduced carbon footprint. Here we reported a hybrid system, coupling chemical process of CO2 hydrogen reduction and biological process for polyhydroxybutyrate (PHB) synthesis, that utilized CO2 as a raw material to produce PHB in vitro. The synthetic pathway of PHB was optimized by screening more efficient methanol oxidases, high activity mutants of glycolaldehyde synthase and coordinating enzyme dosages in the pathway, which achieved the carbon yield of 93.6% for producing PHB from methanol. Finally, by combining with the chemical process from CO2 to methanol, a scaling-up bio-system was performed to convert CO2 into PHB, yielding 5.8 g/L with the productivity of 1.06 g-1L-1h-1. This approach represents a promising carbon-neutral way to produce biodegradable plastics.

synthetic biology↗

bioRxiv2022

Loss of ZNF251 stimulates NHEJ resulting in PARP inhibitor resistance in BRCA1-mutated cancer cells

Poly (ADP-ribose) polymerase inhibitors (PARPis) represent a promising new class of agents that have demonstrated efficacy in treating various cancers, particularly those with BRCA1/2 mutations. Cancer-associated BRCA1/2 mutations disrupt DNA double-strand break (DSB) repair by homologous recombination (HR). PARP inhibitors (PARPis) have been used to trigger synthetic lethality in BRCA1/2-mutated cancer cells by promoting the accumulation of toxic DSBs. Unfortunately, resistance to PARPis is common and can occur through multiple mechanisms, including the restoration of HR and/or stabilization of replication forks. To gain a better understanding of the mechanisms underlying PARPis resistance, we conducted an unbiased CRISPR-pooled genome-wide library screen to identify new genes whose deficiency confers resistance to the PARPi olaparib. Our research revealed that haploinsufficiency of the ZNF251 gene, which encodes zinc finger protein 251, is associated with resistance to PARPis in various breast and ovarian cancer cell lines carrying BRCA1 mutations. Mechanistically, we discovered that ZNF251 haploinsufficiency leads to stimulation of RAD51-mediated HR repair of DSBs in olaparib-treated BRCA1-mutated cancer cells. Moreover, we demonstrated that a RAD51 inhibitor reversed PARPi resistance in ZNF251 haploinsufficient cancer cells harboring BRCA1 mutations. Our findings provide important insights into the mechanisms underlying PARPis resistance by highlighting the role of RAD51 in this phenomenon.

cancer biology↗

bioRxiv2022

CorA gene rearrangement triggered the salinity-driven speciation of Poseidoniales

Land-ocean interactions greatly impacted the evolution of coastal life on Earth. However, the geological forces and genetic mechanisms that shaped evolutionary adaptations and allowed microorganisms to inhabit coastal brackish waters remain largely unexplored. Here, we infer the evolutionary trajectory of the ubiquitous heterotrophic archaea Poseidoniales (Marine Group II archaea) across global aquatic habitats. Our results show that their brackish subgroups have evolved through the rearrangement of the magnesium transport gene corA that conferred osmotic-stress tolerance dated to over 600 million years ago. The coastal family of Poseidoniales showed a rapid increase in the evolutionary rate during and in the aftermath of the Cryogenian Snowball Earth (~700 million years ago), possibly in response to the enhanced phosphorus supply and the rise of algae. Our study highlights the close interplay between genetic changes and ecosystem transformations that boosted microbial diversification in the Neoproterozoic continental margins.

evolutionary biology↗

bioRxiv2022

Cancer-associated SMARCAL1 loss-of-function mutations promote alternative lengthening of telomeres and tumorigenesis in telomerase-negative glioblastoma cells

Telomere maintenance mechanisms are a hallmark of cancer and are required to enable the replicative immortality of malignant cells. While most cancers activate the enzyme telomerase for telomere maintenance, a subset of cancers (~10-15%) use telomerase-independent mechanisms termed alternative lengthening of telomeres (ALT). ALT is characterized by elevated replication stress at telomeres, telomere synthesis via homology directed-repair mechanisms, and is frequently associated with mutations in the ATRX gene. Because ALT is absent in non-malignant proliferating cells, therapeutic strategies targeting ALT-mediated telomere synthesis is an area of significant translational and clinical interest. We previously showed that a subset of adult GBM patients with ATRX-expressing ALT-positive tumors harbored loss-of-function mutations in the SMARCAL1 gene. SMARCAL1 is an annealing helicase involved in replication fork remodeling and the resolution of replication stress. In this study, we used a patient-derived ALT-positive GBM cell line with native SMARCAL1 deficiency to investigate the role of SMARCAL1 in ALT-mediated telomere synthesis and gliomagenesis in vivo. Our results show that inducible rescue of SMARCAL1 expression suppresses ALT indicators and inhibits de novo telomere synthesis in GBM and osteosarcoma cells, suggesting that SMARCAL1 deficiency plays a functional role in ALT induction in cancers that natively lack SMARCAL1 function. Further, SMARCAL1-deficient ALT-positive cells can be serially propagated in vivo in the absence of detectable telomerase activity, suggesting that the SMARCAL1-deficient ALT phenotype maintains telomeres in a manner that promotes tumorigenesis. In summary, we show that SMARCAL1 loss-of-function mutations are permissive to ALT and promote gliomagenesis. We also established isogenic model systems that permit the dynamic modulation of ALT activity, which will be valuable for future studies aimed at understanding the molecular mechanisms of ALT and for identifying novel anti-cancer therapeutics that target the ALT phenotype.

cancer biology↗

bioRxiv2022

The Slingshot phosphatase 2 is required for acrosome biogenesis during spermatogenesis in mice

The acrosome is a membranous organelle positioned in the anterior portion of sperm head and is essential for male fertility. Acrosome biogenesis requires the dynamic cytoskeletal shuttling of vesicles towards nascent acrosome which is regulated by a series of accessory proteins. However, much remains unknown about the molecular basis underlying this process. Here, we generated Ssh2 knock-out (KO) mice and show that Slingshot phosphatase 2 (SSH2), a regulator of actin remodeling, is essential for acrosome biogenesis and male fertility. In Ssh2 KO males, spermatogenesis was arrested at the early spermatid stage with enhanced germ cell apoptosis and the impaired acrosome biogenesis was characterized by defective transport/fusion of proacrosomal vesicles. Moreover, disorganized F-actin structures accompanied by excessive phosphorylation of COFILIN were observed in testes of Ssh2 KO mice. Collectively, our data reveal a modulatory role for SSH2 in acrosome biogenesis through COFILIN-mediated actin remodeling and the indispensability of this phosphatase in male fertility in mice.

developmental biology↗

bioRxiv2022

Dynamic modelling and analysis of autophagy in the clearance of aggregated α-synuclein in Parkinson's disease

The widely-accepted hallmark pathology of Parkinsons disease (PD) is the presence of Lewy bodies (LB) with characteristic abnormal aggregated -synuclein (Syn). Growing physiological evidences suggest that there is a pivotal role for the autophagy-lysosome pathway in the clearance of misfolded Syn (Syn*) for maintaining homeostasis and neural cell function. In this work, we establish a new mathematical model for Syn* degradation through the autophagy pathway. The qualitative simulations discover the tri-stability phenomena and dynamical behaviors of Syn*, i.e., the coexistence of three stable steady states, in which the lower, medium and upper steady states correspond to the healthy, critical and diseased stages of pathological mechanism of PD, respectively. Diverse analyses on codimension-1 and -2 bifurcations suggest that autophagy can control the switches among the stable steady states for the aggregation of Syn*. It is also found that the double negative crosstalk feedback between autophagy and apoptosis is important to the robustness of tri-stability of Syn* for this biodynamic system. Our novel results may be valuable for making further therapeutic strategies in prevention and treatment for PD. Author summarySyn* is one of the most and primary remarkable targets for the universal neurodegenerative disease of PD. Efficient clearance mechanism of autophagy, contains a lot of molecular components to maintain the cellular homeostasis and cell renewal, could be the possible therapy for PD. Understand the complexity of autophagy in degrading Syn* requires the integration of both theoretical and experimental points of view. Here, we have proposed a novel mathematical model that analyses the temporal and dynamic behaviors of the biosystem for autophagy degrades Syn* to access PD states. The model explains that the tri-stability is of particularly relevance to this biosystem that switch among the healthy, critical and disease states, and captures that the critical intermedium state exits for preventing the system transform healthy to disease state directly, and further illustrates that the molecular signaling feedback loops of autophagy may be important for the robustness of tri-stability. Our work deepens the researches of PD by uncovering the important buffering medium state and providing promising potential therapeutic insights.

systems biology↗