Biology subjects

Ke, Z.

Publications and source records attributed to Ke, Z..

At least 19 recordsLinked to original sources

bioRxiv2026

Serum IgM crosslinks hepatitis B subviral particles into supramolecular immune complexes

Hepatitis B virus (HBV)-infected cells release hepatitis B surface antigen (HBsAg)-rich subviral particles (SVPs) in large excess over infectious virions. SVPs bind antibodies against HBsAg (anti-HBs), including neutralizing antibodies, but the physical products of antibody capture in human blood are uncharacterized. Here we used cryo-electron tomography (cryo-ET) to image HBsAg-enriched serum from a patient with severe acute Hepatitis B and observed three-dimensional assemblies of intact IgM-SVP immune complexes. These associations persisted at a lower particle density and were validated by a spatial-randomization null model. Subtomogram averaging and single-particle cryo-electron microscopy (cryo-EM) identified three serum IgM Fc-core assemblies, IgM-J-CD5L, IgM-J and IgM-J-SC, with cryo-EM maps reaching 2.8 angstrom resolution. Mapping these Fc core assemblies into tomograms revealed full-length IgM engaging individual SVPs through several Fab arms and bridging neighboring particles into immune complex networks containing multiple IgM molecules and SVPs. Thus, serum IgM uses multivalent Fab interactions to crosslink HBsAg-rich SVPs into supramolecular immune complexes. This observation extends the SVP decoy model from passive antibody sequestration to higher-order particle organization.

molecular biology↗

bioRxiv2026

Division state reveals hidden genetic regulation during T cell activation and identifies immune disease-linked gene programmes

A major challenge in human genetics is to connect disease-associated variants to the cellular functions they perturb. Variants associated with immune-mediated disease have implicated CD4 T-cell activation as a disease-causal process; however, it remains unresolved whether these variants act on pathways initiating cell division, driving effector differentiation, or maintaining proliferative capacity. Activated T cells comprise mixtures of cells that have undergone different numbers of divisions, potentially obscuring genetic effects that act at specific stages of this process. Here, we study CD4 T-cell activation through cell division using division-resolved single-cell transcriptomics of naive, memory and regulatory T cells. We show that division state constitutes an important axis of transcriptional organisation, with approximately one third of genes exhibiting division-dependent regulation across shared and subset-specific programmes. We develop CellDivider, a machine-learning model that accurately infers proliferative state directly from single-cell transcriptomes, enabling a scalable approach for cohort level mapping of variant effects on cell proliferation phenotypes. Incorporating inferred division state into single-cell eQTL models reveals regulatory effects that are attenuated or missed when cells are analysed by activation time alone. Finally, we resolve gene expression programmes that govern distinct stages of T cell activation and proliferation. We show that polygenic immune disease risk preferentially converges on early activation and differentiation modules, rather than on proliferative capacity itself. Consistent with this model, division-resolved analysis of the pleiotropic immune risk gene RPS26 localises its genetic effects to early division states, providing mechanistic insight into its broad disease associations. Together, these findings illustrate how resolving dynamic cellular consequences of activation sharpens variant-to-function inference in immune disease genetics.

genetics↗

bioRxiv2026

Dietary Non-protein Amino Acid AZE as an Environmental Trigger Activating Latent Genetic Susceptibility in C9orf72-ALS Pathogenesis

In human disease, clinical manifestations are not always tightly correlated with genetic etiology. While the GGGGCC (G4C2) hexanucleotide repeat expansion in the C9orf72 gene is the most prevalent genetic cause of ALS, a subset of mutation carriers stays asymptomatic. The molecular mechanisms underlying this incomplete penetrance remain elusive. Here, we identify L-azetidine-2-carboxylic acid (AZE), a dietary non-protein amino acid, as a critical environmental risk factor capable of unmasking latent genetic susceptibility in C9orf72-ALS pathogenesis. Specifically, AZE disrupts the proteasome-mediated clearance of toxic poly-GA dipeptide repeats derived from G4C2 repeats, triggering pronounced neuroinflammation and motor defects in a C9orf72-ALS mouse model that otherwise exhibits minimal phenotypes. Notably, AZE is widely present in the food chain (particularly in sugar beet) and consistently detectable in the postmortem human brains. A significant positive correlation was observed between sugar beet consumption and the incidence of sporadic C9-ALS cases in European nations. Critically, dietary intake of sugar beet juice is sufficient to activate subclinical genetic susceptibility in C9orf72-ALS mice. These findings reveal a direct diet-gene interplay in governing C9orf72-ALS penetrance, and propose dietary restriction of AZE-rich foods as a tangible strategy for genetically susceptible individuals to potentially delay or mitigate this currently incurable disorder.

neuroscience↗

bioRxiv2025

Structures of Naked Mole-Rat, Tuco-Tuco, and Guinea Pig Ribosomes: Is rRNA Fragmentation Linked to Translational Fidelity?

Ribosomes are central to protein synthesis in all organisms. Among mammals, the ribosome functional core is highly conserved. Remarkably, two rodent species, the naked mole-rat (NMR) and tuco-tuco display fragmented 28S rRNA, coupled with high translational fidelity and long lifespan. The unusual ribosomal architecture in the NMR and tuco-tuco has been speculated to be linked to high translational fidelity. Here we show, by single-particle cryo-electron microscopy (cryo-EM), that despite the fragmentation of their rRNA, NMR and tuco-tuco ribosomes retain their core functional architecture. Compared to ribosomes of the guinea pig, a phylogenetically related rodent without 28S rRNA fragmentation, ribosomes of NMR and tuco-tuco exhibit poorly resolved, certain expansion segments. In contrast, the structure of the guinea pig ribosome shows high similarity to human ribosome. Enhanced translational fidelity in the NMR and tuco-tuco may stem from subtle, allosteric effects in dynamics, linked to rRNA fragmentation.

biochemistry↗

bioRxiv2025

High-resolution in situ structures of hantavirus glycoprotein tetramers

SUMMARY/ABSTRACTNew World hantaviruses cause severe infections in humans, with case fatality rates approaching 40%. Previous structural studies have advanced our understanding of hantavirus glycoprotein architecture and function, however, the lack of high-resolution in situ structures of the glycoprotein tetramer and its lattice organization has limited mechanistic insights into viral assembly, entry, and antigenicity. Here, we leveraged a virus-like particle (VLP) system to establish a cryo-electron microscopy workflow for lattice-forming viral glycoproteins. This enabled the determination of a 2.35 [A] resolution structure of the membrane-embedded Andes virus (ANDV) glycoprotein tetramer, as well as structures of dimers of tetramers and a complex with antibody ADI-65534. These structures reveal previously uncharacterized features of glycoprotein organization, stability, and pH-sensing. Immunization of mice with self-amplifying replicon RNA (repRNA) encoding ANDV-VLPs elicited high levels of glycoprotein-binding antibodies but equivalent titers of neutralizing antibodies compared to repRNA-encoded native ANDV glycoprotein complex. Collectively, these findings advance our understanding of hantavirus glycoprotein assemblies and their function, laying a foundation for structure-based vaccine design efforts.

microbiology↗

bioRxiv2024

Structure and organization of full-length Epidermal Growth Factor Receptor in extracellular vesicles by cryo-electron tomography

We report here transport of the Epidermal Growth Factor Receptor (EGFR), Insulin Receptor, 7-pass transmembrane receptor Smoothened, and 13-pass Sodium-iodide symporter to extracellular vesicles (EVs) for structural and functional studies. Mass spectrometry confirmed the transported proteins as the most abundant in EV membranes, and the presence of many receptor-interacting proteins demonstrates the utility of EVs for characterizing membrane protein interactomes. Cryo-electron tomography of EGFR-containing EVs reveals that EGFR forms clusters in the presence of EGF with a [~]3 nm gap between the inner membrane and cytoplasmic density. EGFR extracellular regions do not form regular arrays, suggesting that clustering is mediated by the intracellular region. Subtomogram averaging of the EGFR extracellular region (ECR) yielded a 15 [A] map into which the crystal structure of the ligand-bound EGFR ECR dimer fits well. These findings refine our understanding of EGFR activation, clustering, and signaling, and they establish EVs as a versatile platform for structural and functional characterization of human membrane proteins in a native-like environment. Significance StatementAtomic or near-atomic resolution structural studies of proteins embedded in cell membranes have proven challenging. We show that transporting integral membrane proteins to cell-derived extracellular vesicles enables structural and functional studies of human membrane proteins in a native membrane environment. We have used this approach to visualize an active form of full-length Epidermal Growth Factor Receptor (EGFR) and show that it forms clusters in the membrane and projects its cytoplasmic signaling domains [~]3 nm away from the membrane surface. EGFR is essential for normal development, but abnormal EGFR activity is associated with several human cancers and is the target of many anticancer therapies. Our studies refine current models of how ligand binding to EGFR transmits signals across cell membranes.

biophysics↗

bioRxiv2023

Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants

The evolution of SARS-CoV-2 variants with increased fitness has been accompanied by structural changes in the spike (S) proteins that are the major target for the adaptive immune response. Single-particle cryo-EM analysis of soluble S from SARS-CoV-2 variants has revealed this structural adaptation at high-resolution. The analysis of S trimers in situ on intact virions has the potential to provide more functionally relevant insights into S structure and virion morphology. Here, we characterized B.1, Alpha, Beta, Gamma, Delta, Kappa, and Mu variants by cryo-electron microscopy and tomography, assessing S cleavage, virion morphology, S incorporation, "in-situ" high-resolution S structures and the range of S conformational states. We found no evidence for adaptive changes in virion morphology, but describe multiple different positions in the S protein where amino acid changes alter local protein structure. Considered together, our data is consistent with a model where amino acid changes at multiple positions from the top to the base of the spike cause structural changes that can modulate the conformational dynamics of S.

microbiology↗

bioRxiv2023

Vampyroteuthis southchinaseais sp. nov.,a second Recent widely distributed species of Vampyromorpha (Cephalopoda, Coleoidea)

The vampire squid, Vampyroteuthis infernalis Chun, 1903, is currently the only extant species in the family Vampyroteuthidae Chun, 1903. However, specimens from the Gulf of Guinea, Africa, and California suggested the possibility of additional taxa. Here, we report the second species of Vampyroteuthis, collected from the South China Sea, China, which differs from V. infernalis by the tail shape, the lower beak, and the phylogenetic analysis of mitochondrial COI and nuclear large subunit ribosomal DNA (LSU) sequences: V. infernalis present by the lacking of the tail, photophores located approximately one-third of the points between the fins and end, and the lower beak with a broad, short wing; V. pseudoinfernalis Qiu, Liu & Huang, sp. nov. present by an acuate tail, a pair of photophores located at the midpoints between the fins and tail, and a lower beak with a broad, elongate wing.

zoology↗

bioRxiv2022

Graph-Based Reconstruction and Analysis of Disease Transmission Networks using Viral Genomic Data

Understanding the patterns of viral disease transmissions helps establish public health policies and aids in controlling and ending a disease outbreak. Classical methods for studying disease transmission dynamics that rely on epidemiological data, such as times of sample collection and duration of exposure intervals, struggle to provide desired insight due to limited informativeness of such data. A more precise characterization of disease transmissions may be acquired from sequencing data that reveals genetic distance between viral populations in patient samples. Indeed, genetic distance between viral strains present in hosts contains valuable information about transmission history, thus motivating the design of methods that rely on genomic data to reconstruct a directed disease transmission network, detect transmission clusters, and identify significant network nodes (e.g., super-spreaders). In this paper, we present a novel end-to-end framework for the analysis of viral transmissions utilizing viral genomic (sequencing) data. The proposed framework groups infected hosts into transmission clusters based on reconstructed viral quasispecies; the genetic distance between a pair of hosts is calculated using Earth Movers Distance, and further used to infer transmission direction between the hosts. To quantify the significance of a host in the transmission network, the importance score is calculated by a graph convolutional auto-encoder. The viral transmission network is represented by a directed minimum spanning tree utilizing the Edmonds algorithm modified to incorporate constraints on the importance scores of the hosts. Results on realistic synthetic as well as experimental data demonstrate that the proposed framework outperforms state-of-the-art techniques for the analysis of viral transmission dynamics. CCS CONCEPTSO_LIApplied computing [->] Bioinformatics. C_LI ACM Reference FormatZiqi Ke and Haris Vikalo. 2022. Graph-Based Reconstruction and Analysis of Disease Transmission Networks using Viral Genomic Data. In Proceedings of The Seventh International Workshop on Computational Network Biology (CNB-MAC 2022). ACM, New York, NY, USA, 10 pages. https://doi.org/XXXXXXX.XXXXXXX

genomics↗

bioRxiv2022

Development and application of an uncapped mRNA platform

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

bioengineering↗

bioRxiv2022

A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0

We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a regularised likelihood target that approximates a function of the 2D experimental images. In addition, analogous to Bayesian polishing and contrast transfer function (CTF) refinement in single-particle analysis, we describe approaches that exploit the increased signal-to-noise ratio in the averaged structure to optimise tilt series alignments, beam-induced motions of the particles throughout the tilt series acquisition, defoci of the individual particles, as well as higher-order optical aberrations of the microscope. Implementation of our approaches in the open-source software package RELION aims to facilitate their general use, in particular for those researchers who are already familiar with its single-particle analysis tools. We illustrate for three applications that our approaches allow structure determination from cryo-ET data to resolutions sufficient for de novo atomic modelling.

biophysics↗

bioRxiv2021

Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation

During activation, T cells undergo extensive changes in gene expression which shape the properties of cells to exert their effector function. Therefore, understanding the genetic regulation of gene expression during T cell activation provides essential insights into how genetic variants influence the response to infections and immune diseases. We generated a single-cell map of expression quantitative trait loci (eQTL) across a T cell activation time-course. We profiled 655,349 CD4+ naive and memory T cells, capturing transcriptional states of unstimulated cells and three time points of cell activation in 119 healthy individuals. We identified 38 cell clusters, including stable clusters such as central and effector memory T cells and transient clusters that were only present at individual time points of activation, such as interferon-responding cells. We mapped eQTLs using a T cell activation trajectory and identified 6,407 eQTL genes, of which a third (2,265 genes) were dynamically regulated during T cell activation. We integrated this information with GWAS variants for immune-mediated diseases and observed 127 colocalizations, with significant enrichment in dynamic eQTLs. Immune disease loci colocalized with genes that are involved in the regulation of T cell activation, and genes with similar functions tended to be perturbed in the same direction by disease risk alleles. Our results emphasize the importance of mapping context-specific gene expression regulation, provide insights into the mechanisms of genetic susceptibility of immune diseases, and help prioritize new therapeutic targets.

genomics↗

bioRxiv2021

Respiratory syncytial virus matrix protein assembles as a lattice with local and extended order that coordinates the position of the fusion glycoprotein

Respiratory syncytial virus (RSV) is a significant cause of respiratory illness in young children and adults worldwide. There is currently no vaccine or targeted antiviral for RSV. RSV is an enveloped, filamentous, negative-strand RNA virus. Individual virions vary in both diameter and length, with an average diameter of [~]130 nm and ranging from [~]500 nm to over 10 m in length. The RSV matrix (M) protein is peripherally associated with the interior of the viral membrane. Though the general arrangement of structural proteins within the virion is known, the molecular organization of M and other structural proteins was previously unknown. Here, using whole-cell cryo-electron tomography and sub-tomogram averaging, we show that M is arranged in a packed helical-like lattice of M-dimers ordered at an angle of [~]47{degrees} to the viral long axis. Sub-tomogram averages including F and M indicate that the position of F on the viral surface is correlated with the underlying M lattice. Finally, we report that RSV F is frequently observed as pairs, with the F trimers oriented in an anti-parallel conformation to support potential interaction between trimers. These results provide insight into RSV assembly and virion organization and may aid in the identification and development of RSV vaccines and anti-viral targets.

biophysics↗

bioRxiv2021

Naked mole-rat hematopoietic stem and progenitors are highly quiescent with an inherent myeloid bias

Naked mole-rats (NMRs) are the longest-lived rodents yet their stem cell characteristics remain enigmatic. Here we comprehensively mapped the NMR hematopoietic landscape and identified unique features likely contributing to longevity. Adult NMRs form red blood cells in spleen and marrow, which is a neotenic trait. A myeloid bias towards granulopoiesis in concert with decreased B-lymphopoiesis defines the marrow composition, resembling fetal leukopoiesis. Very similar to primates, the primitive stem cell compartment is marked by CD34 and THY1. Remarkably, stem and progenitor respiration rates are as low as in human cells, while NMR cells show a strong expression signature for fatty acid metabolism. The pool of quiescent stem cells is higher than in mice, and the cell cycle of hematopoietic cells is prolonged. Our work provides a platform to study immunology and stem cell biology in an animal model of exceptional longevity. TeaserJuvenile features of hematopoiesis shape the blood system of the longest-lived rodent.

cell biology↗

bioRxiv2021

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind, fuse, and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes the preparation of the fusion machinery by dissociation of the S1 domains. We report the development of bottom-up coarse-grained (CG) models validated with cryo-electron tomography (cryo-ET) data, and the use of CG molecular dynamics simulations to investigate the dynamical mechanisms involved in viral binding and exposure of the S2 trimeric core. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces. The multivalent interaction cyclically and processively induces S1 dissociation, thereby exposing the S2 core containing the fusion machinery. Our simulations thus reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.

biophysics↗

bioRxiv2020

A Convolutional Auto-Encoder for Haplotype Assembly and Viral Quasispecies Reconstruction

Haplotype assembly and viral quasispecies reconstruction are challenging tasks concerned with analysis of genomic mixtures using sequencing data. High-throughput sequencing technologies generate enormous amounts of short fragments (reads) which essentially oversample components of a mixture; the representation redundancy enables reconstruction of the components (haplotypes, viral strains). The reconstruction problem, known to be NP-hard, boils down to grouping together reads originating from the same component in a mixture. Existing methods struggle to solve this problem with required level of accuracy and low runtimes; the problem is becoming increasingly more challenging as the number and length of the components increase. This paper proposes a read clustering method based on a convolutional auto-encoder designed to first project sequenced fragments to a low-dimensional space and then estimate the probability of the read origin using learned embedded features. The components are reconstructed by finding consensus sequences that agglomerate reads from the same origin. Mini-batch stochastic gradient descent and dimension reduction of reads allow the proposed method to efficiently deal with massive numbers of long reads. Experiments on simulated, semi-experimental and experimental data demonstrate the ability of the proposed method to accurately reconstruct haplotypes and viral quasispecies, often demonstrating superior performance compared to state-of-the-art methods.

bioinformatics↗

bioRxiv2020

Maturation of the matrix and viral membrane of HIV-1

Gag - the main structural protein of HIV-1 - is recruited to the plasma membrane for virus assembly by its matrix (MA) domain. Gag is subsequently cleaved into its component domains, causing structural maturation to repurpose the virion for cell entry. We determined the structure and arrangement of MA within immature and mature HIV-1, providing a basis to understand MAs role in virus assembly. Unexpectedly, we found that MA rearranges during maturation, to form a new, hexameric lattice in which the acyl chain of a phospholipid extends out of the membrane to bind a pocket in MA. Our data suggest that proteolytic maturation of HIV-1 not only achieves assembly of the viral capsid surrounding the genome, but extends to repurpose the membrane-bound MA lattice for an entry or post-entry function, and causes partial removal of 2,500 acyl chains from the viral membrane.

microbiology↗

bioRxiv2020

Flagellar structures from the bacterium Caulobacter crescentus and implications for phage {Phi}CbK predation of multi-flagellin bacteria

Caulobacter crescentus is a gram-negative alpha-proteobacterium that commonly lives in oligotrophic fresh and salt-water environments. C. crescentus is a host to many bacteriophages, including {phi}CbK and {phi}CbK-like bacteriophages, which first adsorb to cells by interaction with the bacterial flagellum. It is commonly thought that the six paralogs of the flagellin gene present in C. crescentus are important for bacteriophage evasion. Here, we show that deletion of specific flagellins in C. crescentus can indeed attenuate {phi}CbK adsorption efficiency, although no single deletion completely ablates {phi}CbK adsorption. Thus, bacteriophage {phi}CbK likely recognizes a common motif amongst the six known flagellins in C. crescentus with varying degrees of efficiency. Interestingly, we observe that most deletion strains still generate flagellar filaments, with the exception of a strain that contains only the most divergent flagellin, FljJ, or a strain that contains only FljN and FljO. To visualize the surface residues that are likely recognized by {phi}CbK, we determined two high-resolution structures of the FljK filament, with and without an amino acid substitution that induces straightening of the filament. We observe post-translational modifications on conserved surface threonine residues of FljK that are likely O-linked glycans. The possibility of interplay between these modifications and {phi}CbK adsorption is discussed. We also determined the structure of a filament composed of a heterogeneous mixture of FljK and FljL, the final resolution of which was limited to approximately 4.6 [A]. Altogether, this work builds a platform for future investigation of how phage {phi}CbK infects C. crescentus at the molecular level.

microbiology↗