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Wang, C.

Publications and source records attributed to Wang, C..

At least 235 records · Page 13Linked to original sources

A SARS-CoV-2 entry inhibitor trimerizes to lock the spike protein in a closed conformation

The SARS-CoV-2 spike protein binds its receptor ACE2 to initiate target-cell infection. To engage ACE2, at least one of the three receptor-binding domains (RBDs) of the spike must adopt the up orientation. Here we describe S22, a potent, bioavailable, and non-toxic inhibitor of BA.2 and all subsequent Omicron variants. Cryo-EM analyses showed that S22 assembled as a trimer in a previously uncharacterized pocket of the spike apex, stabilizing all three RBDs in the down orientation, thereby preventing ACE2 association. Binding studies, especially those using mixed S22-sensitive and -resistant spikes, imply a cooperative assembly of three S22 molecules with three RBDs, resulting in an unusually slow S22 off-rate. Consistent with its slow dissociation and favorable pharmacokinetics, S22 suppressed viral replication 100-fold in the lungs of XBB.1.5-infected mice. Thus, S22 potently inhibits Omicron entry through a distinct mechanism whereby a small compound assembles cooperatively as a trimer to stabilize spike in an inactive conformation.

microbiology↗

A Syngeneic Immunocompetent Mouse Model of Gallbladder Cancer Reveals Tumorigenesis and Therapeutic Response

PurposeGallbladder cancer (GBC) is a rare but highly lethal malignancy with one of the poorest prognoses among cancers of the digestive system cancers. However, current experimental models of GBC face critical limitations, particularly their dependence on immunodeficient hosts, which precludes the investigation of the tumor microenvironment. We aimed to establish a novel syngeneic immunocompetent mouse model that recapitulates human GBC and enables the investigation of tumor-immune interactions. Experimental DesignWe engineered a murine cell line (mGBC1-ZH) from normal mouse gallbladder organoids expressing Kras and Trp53 (encoding mouse p53) mutations. Tumorigenic potential of mGBC1-ZH was evaluated by subcutaneous and orthotopic implantation. RNA-Seq and WES was used to demonstrate its characterization and similarity with human GBC. Immunohistochemistry, CCK8, and transwell assays wereused to investigate the role of CXCL5 in GBC. Therapeutic responses to standard first-line chemotherapeutic agents was evaluated in the syngeneic GBC model. ResultsThis model supports both subcutaneous and orthotopic tumor growth in immunocompetent C57BL/6J hosts while preserving hallmark features of human GBC, including biliary epithelial differentiation (CK7+/CK19+), aggressive histopathology, and an immunosuppressive "cold" tumor microenvironment. Genomic characterization revealed recurrent chromosomal instability and copy number alterations mirroring human GBC. Comprehensive transcriptomic profiling revealed profound gene expression changes during the model development, and resembled transcriptional features between mGBC1-ZH and human GBC cell lines and samples. CXCL5 was found to be upregulated in human GBC, and promote proliferation, metastasis, and neutrophils infiltration of GBC in the syngeneic mouse model. Functional validation of the syngeneic GBC model demonstrated therapeutic responsiveness to frontline chemotherapeutics gemcitabine and cisplatin with significant in vivo tumor regression. ConclusionsIn summary, we establised a novel syngeneic GBC mouse model, overcoming the limitations of traditional models by enabling studies in immunocompetent hosts. This model provides valuable insights into the molecular evolution from normal gallbladder cells to transformed cancer cells and establishes a robust platform for both mechanistic studies and therapeutic development.

cancer biology↗

A disease mutation reveals a non-swapped pore and rewired gating cycle of the mechanically activated PIEZO1 channel

PIEZO1 is a versatile mechanotranduction channel critical for diverse cellular and physiological processes1-3. Gain-of-function mutations, such as R2482H, which slow channel inactivation, are linked to dehydrated hereditary stomatocytosis (DHS) and iron overload4-7. PIEZO1 forms a gigantic bowl-shaped trimer comprising flattenable peripheral blades and a central pore module with a switchable cap8-12. However, the structural dynamics governing its gating process and pathogenesis remain incompletely understood. Here, we determined distinct conformational states of the DHS-associated PIEZO1-R2482H mutant in both detergents and proteoliposomes. Remarkably, the R2482H mutation in the central pore induces a conformational change that propagates [~]25 nm to the most distal blade, enabling resolution of all 38 transmembrane helices. PIEZO1-R2482H is inherently flatter than PIEZO1, lowering the gating force and energy barrier and thus explaining its heightened mechanosensitivity. While the flattened PIEZO1 has its cap in the up-state adopting an inactivated state, the flattened PIEZO1-R2482H has its cap in the down-state and twisted by [~]75{degrees}, drastically switching the pore module from a swapped to a non-swapped organization. Such twisted conformation of PIEZO1-R2482H might hinder the transition to the inactivated state, instead proceeding through a deactivation-transition state characterized by curved blades and a partially twisted cap, thereby accounting for the slowed inactivation and deactivation kinetics. Taken together, we reveal the full transmembrane topology and a non-swapped pore conformation induced by R2482H, and propose the structural dynamic model that delineates the distinct gating cycle of activation, inactivation, and deactivation for PIEZO1 and PIEZO1-R2482H.

biophysics↗

Decorin promotes nascent proteoglycan retention in cartilage matrix by strengthening collagen II-aggrecan integration

Cartilage extracellular matrix (ECM), a hydrated collagen II-aggrecan composite, undergoes dynamic turnover during both normal homeostasis and disease-associated remodeling. This study elucidates a crucial role for decorin in promoting the retention and stability of nascent aggrecan within this matrix. By applying bio-orthogonal click-labeling, we demonstrate that loss of decorin accelerates the release of nascent aggrecan under both physiological and inflammatory conditions, without affecting its preferred localization to the pericellular matrix. Conversely, supplementation with exogenous decorin mitigates inflammation-induced loss of nascent aggrecan, supporting its potential as a therapeutic target. At the molecular level, decorin exhibits strong binding affinity for aggrecan, and enhances aggrecan-aggrecan and aggrecan-collagen II interactions, reinforcing its direct role in integrating cartilage matrix constituents. Also, by binding to collagen II, decorin stiffens the collagen II fibril network, thereby strengthening the confinement effect that limits the diffusive loss of entrapped aggrecan. Notably, decorin does not alter chondrocyte transcriptomic profiles in vivo, emphasizing its primary role in maintaining matrix integrity through biophysical mechanisms rather than cell signaling. Together, these findings provide a mechanistic foundation for developing decorin-based biomaterials or gene therapies aimed at preserving or regenerating the cartilage matrix for improved outcomes in osteoarthritis.

biophysics↗

HalluDesign: Protein Optimization and de novo Design via Iterative Structure Hallucination and Sequence design

Deep learning has revolutionized biomolecular modeling, enabling the prediction of diverse structures with atomic accuracy. However, leveraging the atomic-level precision of the structure prediction model for de novo design remains challenging. Here, we present HalluDesign, a general all-atom framework for protein optimization and de novo design, which iteratively update protein structure and sequence. HalluDesign harnesses the inherent hallucination capabilities of AlphaFold3-style structure prediction models and enables fine-tune free, forward-pass only sequence-structure co-optimization. Structure conditioning at different noise level in the structure prediction stage allows precise control over the sampling space, facilitating tasks from local and global protein optimization to de novo design. We demonstrate the versatility of this framework by optimizing suboptimal structures, rescuing previously unsuccessful designs, designing new biomolecular interactions and generating new protein structures from scratch. Experimental characterization of a diverse set of proteins--including protein binders for small molecules, a metal ion and proteins; antibody design of phosphorylation-specific peptide; and monomeric proteins--revealed high design success rates and excellent structural accuracy. Together, our comprehensive computational and experimental results highlight the broad utility of this framework. We anticipate that HalluDesign will further unlock the modeling and design potential of AlphaFold3-like models, enabling the robust creation of complex biomolecules for a wide range of biotechnological applications.

bioinformatics↗

Bronsted-basic small molecules activate GTP hydrolysis in Ras Q61 mutants

The RAS oncogenes (KRAS, HRAS, NRAS) are among the most frequently mutated genes in human cancer, affecting over three million patients annually. Therapeutic development has largely focused on inhibitors for KRAS codon 12 mutations (G12C/D/V/S/R) which are key drivers in lung, colorectal, and pancreatic cancers. In contrast, mutant-selective inhibitors for Q61 variants remain elusive. A common mechanistic feature of G12 and Q61 mutants is the impaired hydrolysis of GTP, which traps Ras in its active, signaling-competent state. We envisioned that an alternative therapeutic strategy - reactivation of GTP hydrolysis - could address this shared oncogenic mechanism. Here we report small molecules that accelerate GTP hydrolysis in K-Ras Q61 mutants. These compounds compensate for the loss of the catalytic residue Gln61 by introducing a general base into the active site, selectively enhancing hydrolysis of K-Ras Q61X (X = H, L, K, R) mutants by up to 20-fold while sparing the wild-type protein. In mutant cancer cell lines, these compounds reduce GTP-bound Ras levels and suppress downstream signaling. We show that the chemical design principles are generalizable to other Ras isoforms. This work establishes a mechanistic foundation for small-molecule "GTPase activators" and offers a new paradigm for targeting Ras-driven cancers.

cancer biology↗

Vulnerability in the breadth evolution of an influenza broadly neutralizing antibody

The highly conserved influenza hemagglutinin (HA) stem domain is a major target for broadly neutralizing antibodies (bnAbs). However, despite being discovered more than a decade ago, the IGHV1-69-encoded CR9114 remains the only HA stem bnAb that cross-reacts with both influenza A and B viruses. To investigate the constraints on the breadth evolution of CR9114, this study performs four deep mutational scanning experiments to compare the binding affinity landscapes of the germline and somatic CR9114 against H1 HA, H3 HA, and influenza B HA. Many mutations that minimally affect or even improve the H1 HA binding are detrimental for binding to H3 HA and BHA. We further reveal the prevalence of epistasis in IGHV1-69 HA stem bnAbs. Overall, our findings provide a mechanistic explanation for the scarcity of HA stem bnAbs with cross-reactivity against both influenza A and B viruses, and have important implications for developing broadly protective influenza vaccines.

immunology↗

Beyond reference bias: Making pangenomes accessible with PangyPlot

Linear reference genomes have standardized genomics research but remain limited by reference bias, which skews read mapping and variant discovery. This bias can distort the interpretation of genetic variation, particularly for populations that are genetically distant from the reference. Pangenome graphs, such as those generated by the Human Pangenome Reference Consortium (HPRC), mitigate this limitation by integrating diverse haplotypes into a unified representation of human genetic variation. However, the complexity of graph-based data and the lack of intuitive visualization tools have hindered broader adoption. Here we introduce PangyPlot, a genome browser that simplifies exploration of pangenome graphs by retaining linear-style navigation, integrating gene annotations, abstracting complex variation into interpretable structures, and employing a dynamic, physics-based layout optimization engine. We demonstrate its utility by constructing a chromosome 7 graph from 101 individuals with cystic fibrosis (CF), capturing a broad spectrum of genetic variation. Using PangyPlot, we visualized CF-relevant loci and compared results with existing graph viewers, highlighting its ability to display both base-level and large structural variation. With an additional 64 PacBio HiFi assemblies, we fine-mapped a repeat-dense CF modifier locus on chromosome 5, where PangyPlot was used in conjunction with graph-based analysis to identify a repeat expansion in the 5' end of EXOC3 that may promote G-quadruplex formation and affect gene expression. Together, these examples demonstrate PangyPlot s capacity to make populationlevel variation interpretable. To support broader use of graph-based resources, we also released a live public instance of PangyPlot preloaded with HPRC data (https://pangyplot.research.sickkids.ca/).

genomics↗

Rete Ovarii Epithelial Cells as an Unappreciated Cell of Origin for Pelvic and Ovarian High-Grade Serous Carcinoma

Over the past two decades, converging clinicopathologic, molecular, and evolutionary evidence has established that pelvic and ovarian high-grade serous carcinoma (HGSC) originates predominantly from tubal-type epithelia rather than the ovarian surface epithelium. Consequently, Fallopian tube secretory epithelial cells are widely recognized as the principal cell of origin for HGSC. However, the female reproductive tract contains additional tubular epithelial networks whose potential contributions to HGSC pathogenesis remain unexplored. Here, we identify the rete ovarii (RO), a complex network of intra- and extra-ovarian tubules located within the ovarian hilus and mesovarium, as an alternative candidate tissue of origin for HGSC. We demonstrate that genetic and genomic alterations in rete ovarii epithelial cells (ROECs) can drive their malignant transformation, giving rise to tumors that closely recapitulate the histologic and molecular characteristics of human HGSC. Spatially resolved single-cell transcriptomic analyses of tumors derived from Brca/Trp53/Pten-deficient ROECs (BTP-RO) reveal distinct invasive and immunosuppressive molecular programs. These findings establish ROECs as a previously unrecognized cell of origin for HGSC, expanding the landscape of potential precursor populations beyond the Fallopian tube. The RO-based HGSC model provides a powerful framework for developing origin-informed prevention strategies, early detection approaches, and targeted therapeutics.

cancer biology↗

Macrophage-secreted Pyrimidine Metabolites Confer Chemotherapy Resistance in Acute Myeloid Leukemia (AML)

The tumor microenvironment (TME) programs cancer cells to influence therapeutic responses. Macrophages residing in TME switch from pro-phagocytic to tumor-promoting and immunosuppressive phenotypes as cancer develops. While these pro-tumor functions of macrophages are associated with poor outcomes, the underlying mechanisms by which bone-marrow (BM)-associated macrophages fuel myeloid malignancy and their precise contribution to relapse remain undissected. Here, we show expansion of monocyte/macrophage population in leukemia patients post-chemotherapy relapse, and spatial proximity of macrophages to leukemia blasts in the BM niche. This proximity proved functionally consequential--depletion of macrophages delayed leukemia relapse post cytarabine (AraC), a frontline chemotherapy, in patient-derived xenografts (PDX) and syngeneic leukemia models. Mechanistically, a pyrimidine metabolite, deoxycytidine (dC), secreted by BM macrophages, is taken up by leukemia cells to directly inhibit deoxycytidine kinase (DCK) to hamper AraC activation and subsequent resistance in a cell non-autonomous manner. Diagnosis AML patients exhibited significantly higher circulating dC levels than healthy donors, and dC levels further increased following chemotherapy. SAMHD1, which catalyzes deoxynucleoside triphosphates (dNTPs) into deoxynucleoside, was highly abundant in macrophages and mediated dC accumulation. Blockade of dC production in mouse and human macrophages via genetic and pharmacological inhibition of SAMHD1 or DHODH, a critical enzyme in pyrimidine synthesis, restored AraC sensitivity. Combination with DHODH inhibitors significantly delayed AraC relapse in human PDX and mouse syngeneic AML models. Collectively, we identify a metabolic immune-leukemia crosstalk in which SAMHD1high macrophages mediates chemoresistance by secreting pyrimidine metabolites and propose macrophage metabolic reprogramming as a tractable strategy to overcome TME-driven chemoresistance in myeloid leukemia.

cancer biology↗

Deciphering the Antigenic Evolution of Seasonal Influenza A Viruses with PREDAC-Transformer: From Antigenic Clustering to Key Site Identification

Seasonal influenza viruses undergo continuous antigenic drift due to mutations in the hemagglutinin (HA) protein, rendering vaccines ineffective and posing a significant global public health challenge. Existing computational models can predict antigenic relationships but generally lack interpretability, making it difficult to reveal the molecular determinants driving antigenic changes. To address this, we developed PREDAC-Transformer, an end-to-end deep learning framework that integrates sequence, physicochemical, and evolutionary features, and employs a self-attention mechanism to capture long-range dependencies relevant to antigenicity. More importantly, we introduce the integrated antigenicity score, which combines attention-based attribution with information-theoretic metrics to provide continuous quantification and ranking of the antigenic contributions of individual amino acid site. Our results demonstrate that PREDAC-Transformer not only significantly improves the accuracy of antigenic relationship prediction but also successfully recapitulates major historical antigenic cluster transitions. Using integrated antigenicity score, we systematically identified two classes of key sites: global key sites with sustained impact on antigenic evolution, and cluster-transition determining sites that drive cluster transitions. These sites include most canonical epitopes and reveal additional functional residues previously overlooked, which may influence immune escape via cooperative effects or glycosylation. Collectively, these findings advance our understanding of influenza antigenic evolution and provide novel insights for refining computational models. PREDAC-Transformer achieves high-precision prediction while attributing antigenic differences to individual residues, thereby linking viral genomic variation, antigenic change, and public health decision-making. This framework has the potential to reduce experimental burdens in influenza surveillance and assist in vaccine strain recommendation, thereby supporting global influenza control efforts.

bioinformatics↗

A late cytoplasmic surveillance pathway ensures ribosome integrity

Errors in ribosome assembly can produce defective subunits that can lead to aberrant translation events. How faulty ribosomes are recognized and whether they are recognized during assembly or translation remains poorly understood. We utilized a mutation in the ribosomal protein uL16 to track defective 60S subunits through the biogenesis and translation pathways. This mutation deletes a critical loop in the P site and arrests pre- 60S particles during late cytoplasmic maturation. However, simultaneous mutations in the late biogenesis factors Nmd3 and Tif6 bypass this block, releasing defective ribosomes into the translational pool. Cryo-EM and selective ribosome profiling reveal that these ribosomes can form peptide bonds, but stall predominantly at the first few codons. We show that the uL16 mutant ribosomes are detected and targeted for degradation during biogenesis and that they escape degradation if they enter translation. We identify Reh1 as a non-canonical ribosome assembly factor that is required for this surveillance pathway.

molecular biology↗

End-to-end automation of repeat-target cryo-EM structure determination in CryoSPARC

Single particle cryo-EM is a valuable and growing technique for life science and drug discovery. Currently, obtaining state-of-the-art results from cryo-EM data analysis requires a human in the loop to analyze intermediate results and make image processing decisions. This bottleneck limits the achievable throughput of structure determination, especially in high-throughput settings such as structure-based drug design. In this work, we develop an end-to-end automation strategy for repeat-target structure determination using new tools in CryoSPARC. We demonstrate completely hands-off processing of 21 challenging G protein-coupled receptor (GPCR) datasets. In 17 of 21 cases, automated processing meets or exceeds published resolution and map quality and, in several cases, provides significant improvement in receptor and ligand density that allows improved model building. Our results on both active and inactive state GPCRs show that our automation strategy generalizes easily to new target classes, and that complete automation of data processing is straightforward to achieve in CryoSPARC. We provide downloadable CryoSPARC Workflow files so that users can import, replicate, adapt and extend our automated workflow for their own targets, enabling cryo-EM to be applied at larger scales and to answer larger biological questions.

biophysics↗

Igniting full-length isoform analysis in single-cell and spatial RNA-seq data with FLAMESv2

Long-read single-cell RNA-sequencing enables the profiling of RNA isoform expression and alternative splicing at single cell resolution. However, diverse single-cell technologies and sparse isoform data demand flexible and accurate analysis tools. We introduce FLAMESv2, a highly modular and protocol-agnostic R/Bioconductor package for long-read single-cell RNA-seq data analysis. FLAMESv2 supports a wide range of single-cell and spatial protocols, is highly configurable, scales to allow multi-sample analysis and provides versatile visualisation and analysis outputs. We demonstrate its compatibility with both droplet-based and combinatorial barcoding single-cell methods, as well as spatial transcriptomics workflows. Benchmarking confirms FLAMESv2 achieves field-leading performance across key analysis tasks. Applying FLAMESv2 to in vitro differentiation of stem cells into neurons, we identify cell-types, differentiation trajectories, expression of annotated and novel isoforms and isoform expression diversity and heterogeneity within individual cells. FLAMESv2 provides a comprehensive, flexible approach to analysing long-read single-cell RNA-sequencing, unlocking this powerful methodology for RNA isoform characterisation.

bioinformatics↗

HLA-DQ2/8 genotype imprints strain-level gut microbiome and constrains pantothenate availability in healthy adults

HLA-DQ2/8 haplotypes are established genetic risk factors for autoimmune diseases and are known to influence gut microbiota assembly in early life. However, their impact on the adult microbiome and functional consequences for host physiology remain unclear. Here, we performed a genotype-stratified multi-omics analysis of 60 healthy adults, including 28 HLA-DQ2/8 carriers and 32 non-carriers. We found that host HLA-DQ2/8 genotype was significantly associated with gut microbiome composition, with an effect size exceeding that of sex and BMI. HLA-DQ2/8 carriers exhibited higher gut microbial alpha-diversity, lower virulence factor abundance, and a distinct species profile enriched in butyrate-producing taxa. We identified pervasive intra-species phylogenetic and functional divergence linked to the DQ2/8 genotype. This diversification reflects predicted HLA-restricted microbial peptide-binding specificities, suggesting a possible role for antigen presentation-mediated immune selection, a mechanism further supported by AlphaFold3 structural modeling. We found an enrichment of microbial pathways for pantothenate and coenzyme A (CoA) biosynthesis in carriers, primarily driven by functionally divergent Blautia obeum strains. This functional shift paralleled lower levels of serum pantothenate and HDL-cholesterol in the host. Our findings suggest a potential genotype-microbiome-host axis where antigen presentation-mediated immune selection may modulate microbial adaptation, with possible implications for the host availability of essential cofactor precursors and lipid metabolism.

microbiology↗

Activation of the noncanonical inflammasome-GSDMD pathway triggers pyroptosis in bone marrow and promotes periosteal bone formation

Evidence indicating that inflammation is commonly associated with ectopic osteogenesis in certain autoimmune and infectious conditions challenges the dogma that inflammatory responses always suppress bone formation. In this study, we find that systemic administration of lipopolysaccharide (LPS) to mice causes not only inflammation in bone marrow, as expected, but also stimulates periosteal bone formation. This response can be reproduced in vitro as bone marrow supernatants from LPS-treated mice induce robust osteogenesis of skeletal stem cells (SSCs) compared to supernatants from PBS-treated counterparts. Periosteal bone accrual is partly dependent on periosteal leptin receptor-positive (LepR)+ SSCs but not bone marrow LepR+ or adiponectin (Adq)+ SSCs and correlates with pyroptosis within bone marrow. Consistent with the dependence of periosteal osteogenesis on pyroptosis, this response is slightly attenuated in Nlrp3-/- or caspase-1-/-mice but significantly inhibited in caspase-11-/-, caspase-1-/-;caspase-11-/-, or Gsdmd-/-mice. Our study reveals a novel role for pyroptosis in which lysed cells release intracellular contents that stimulate osteoprogenitors and promote osteogenic differentiation within the periosteal compartment.

cell biology↗

ACE2 Phosphorylation Modulates Angiogenesis via the Activator Protein-1

BackgroundAngiogenesis plays a crucial role in organ development. However, aberrant blood vessel growth is involved in various diseases, including tumors and neovascular eye diseases. Angiotensin-converting enzyme 2 (ACE2) is a critical enzyme regulating the health of cardiovascular system, and its post-translational modifications (PTMs) are crucial to determine ACE2 expression level and activity. Here, we studied how the PTM of ACE2 in vascular endothelial cells (ECs) affect pathological retinal neovascularization and tumor angiogenesis. MethodsThe angiogenic capabilities of ECs were assessed by tube formation, sprouting assays, and 5-ethynyl-2-deoxyuridine (EdU) and filopodia staining. EC angiogenesis was examined by poteome profiler array and aortic ring assays in vitro and by the oxygen-induced retinopathy (OIR) and tumor angiogenesis models in vivo. High-throughput screening involving data from RNA-seq, ATAC-seq, and ChIP-seq were used to explore the epigenetic and transcriptional regulations of pro-angiogenic genes regualtged by ACE2 PTMs. ResultsACE2 Ser-680 dephosphorylation in connection with Lys-788 ubiquitination increased EC angiogenic phenotype, which were manifested by aberrant vascularization in mouse OIR and tumor models. ACE2 Ser-680 dephosphorylation led to the activation of activator protein-1 (AP-1), which transactivated multiple genes involved in angiogenesis. AP- 1 inhibition mitigated such angiogenesis in vivo. ConclusionOur findings show a novel PTM mechanism of ACE2 involved in pathological angiogeneis. Specifically, ACE2 Ser-680 dephosphorylation facilitated AP-1 transactivation of the downstream pro-angiogenic genes in ECs.

cell biology↗

A Druggable Tumor Suppressor and Leukemic Stem Cell Marker

Withdrawal StatementThe authors have withdrawn this preprint because the co-authors were not in agreement about posting the work in its current form. The authors request that this work not be cited. Please contact the corresponding author (Dr. Xunlei Kang, kangxu@health.missouri.edu) with questions.

cancer biology↗