Biology subjects

Xiong, Y.

Publications and source records attributed to Xiong, Y..

At least 91 records · Page 5Linked to original sources

bioRxiv2024

WRAD core perturbation impairs DNA replication fidelity promoting immunoediting in pancreatic cancer

It is unclear how cells counteract the potentially harmful effects of uncoordinated DNA replication in the context of oncogenic stress. Here, we identify the WRAD (WDR5/RBBP5/ASH2L/DPY30) core as a modulator of DNA replication in pancreatic ductal adenocarcinoma (PDAC) models. Molecular analyses demonstrated that the WRAD core interacts with the replisome complex, with disruption of DPY30 resulting in DNA re-replication, DNA damage, and chromosomal instability (CIN) without affecting cancer cell proliferation. Consequently, in immunocompetent models, DPY30 loss induced T cell infiltration and immune-mediated clearance of highly proliferating cancer cells with complex karyotypes, thus improving anti-tumor efficacy upon anti-PD-1 treatment. In PDAC patients, DPY30 expression was associated with high tumor grade, worse prognosis, and limited response to immune checkpoint blockade. Together, our findings indicate that the WRAD core sustains genome stability and suggest that low intratumor DPY30 levels may identify PDAC patients who will benefit from immune checkpoint inhibitors.

cancer biology↗

bioRxiv2024

Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology

Cryptococcus neoformans is the most common cause of fungal meningitis and the top-ranked W.H.O. priority fungal pathogen. Only distantly related to model fungi, C. neoformans is also a powerful experimental system for exploring conserved eukaryotic mechanisms lost from specialist model yeast lineages. To decipher its biology globally, we constructed 4328 gene deletions and measured--with exceptional precision--the fitness of each mutant under 141 diverse growth-limiting in vitro conditions and during murine infection. We defined functional modules by clustering genes based on their phenotypic signatures. In-depth studies leveraged these data in two ways. First, we defined and investigated new components of key signaling pathways, which revealed animal-like pathways/components not predicted from studies of model yeasts. Second, we identified environmental adaptation mechanisms repurposed to promote mammalian virulence by C. neoformans, which lacks a known animal reservoir. Our work provides an unprecedented resource for deciphering a deadly human pathogen.

microbiology↗

bioRxiv2024

Structural insights into HIV-2 CA lattice formation and FG-pocket binding revealed by single particle cryo-EM.

One of the most striking features of HIV is the capsid; a fullerene cone comprised of the pleomorphic capsid protein (CA) which shields the viral genome from cellular defense mechanisms and recruits cellular cofactors to the virus. Despite significant advances in understanding the mechanisms of HIV-1 CA assembly and host factor interaction, HIV-2 CA remains poorly understood. By templating the assembly of HIV-2 CA on functionalized liposomes, we were able to determine high resolution structures of the HIV-2 CA lattice, including both CA hexamers and pentamers, alone and in complexes with peptides of host phenylalanine-glycine (FG)-motif proteins Nup153 and CPSF6. While the overall fold and mode of binding the FG-peptides are conserved with HIV-1, this study reveals distinctive structural features that define the HIV-2 CA lattice, potential differences in interactions with other host factors such as CypA, and divergence in the mechanism of formation of hexameric and pentameric CA assemblies. This study extends our understanding of HIV capsids and highlights an approach with significant potential to facilitate the study of lentiviral capsid biology.

biochemistry↗

bioRxiv2024

Structural insights into inhibitor mechanisms on immature HIV-1 Gag lattice revealed by high-resolution in situ single-particle cryo-EM

HIV-1 inhibitors, such as Bevirimat (BVM) and Lenacapavir (LEN), block the production and maturation of infectious virions. However, their mechanisms remain unclear due to the absence of high-resolution structures for BVM complexes and LENs structural data being limited to the mature capsid. Utilizing perforated virus-like particles (VLPs) produced from mammalian cells, we developed an approach to determine in situ cryo-electron microscopy (cryo-EM) structures of HIV-1 with inhibitors. This allowed for the first structural determination of the native immature HIV-1 particle with BVM and LEN bound inside the VLPs at high resolutions. Our findings offer a more accurate model of BVM engaging the Gag lattice and, importantly, demonstrate that LEN not only binds the mature capsid but also targets the immature lattice in a distinct manner. The binding of LEN induces a conformational change in the capsid protein (CA) region and alters the architecture of the Gag lattice, which may affect the maturation process. These insights expand our understanding of the inhibitory mechanisms of BVM and LEN on HIV-1 and provide valuable clues for the design of future inhibitors.

biochemistry↗

bioRxiv2024

Global patterns, drivers and impacts of metabolic traits across amniotes

Metabolism and climate are thought to influence species richness and diversification, yet few studies have examined whether global patterns of metabolic traits are linked to climate and diversification rate. Here we investigate the drivers of global metabolic rates and their impacts on biodiversity across 2,633 amniote vertebrates. We found consistent distribution patterns of metabolic rates in terrestrial amniotes and marine birds, with metabolic rates increasing with distance from the equator across latitudes. Temperature is a primary climatic variable affecting metabolic rates in birds and mammals, whereas precipitation dominates in terrestrial reptiles. Furthermore, elevated metabolic rates promote diversification rates and reduce extinction risks in birds and terrestrial mammals. Conversely, high metabolic rates decrease diversification rates and increase extinction risks in reptiles. Our results show that global patterns of metabolic rates are driven by various climate variables and may shape diversification and extinction patterns among amniotes in the context of climate change.

ecology↗

bioRxiv2024

Ultra-Fast Multi-Organ Proteomics Unveils Tissue-Specific Mechanisms of Drug Efficacy and Toxicity

Rapid and comprehensive analysis of complex proteomes across large sample sets is vital for unlocking the potential of systems biology. We present UFP-MS, an ultra-fast mass spectrometry (MS) proteomics method that integrates narrow-window data-independent acquisition (nDIA) with short-gradient micro-flow chromatography, enabling profiling of >240 samples per day. This optimized MS approach identifies 6,201 and 7,466 human proteins with 1- and 2-min gradients, respectively. Our streamlined sample preparation workflow features high-throughput homogenization, adaptive focused acoustics (AFA)-assisted proteolysis, and Evotip-accelerated desalting, allowing for the processing of up to 96 tissue samples in 5 h. As a practical application, we analyzed 507 samples from 13 mouse tissues treated with the enzyme-drug L-asparaginase (ASNase) or its glutaminase-free Q59L mutant, generating a quantitative profile of 11,472 proteins following drug treatment. The MS results confirmed the impact of ASNase on amino acid metabolism in solid tissues. Further analysis revealed broad suppression of anticoagulants and cholesterol metabolism and uncovered numerous tissue-specific dysregulated pathways. In summary, the UFP-MS method greatly accelerates the generation of biological insights and clinically actionable hypotheses into tissue-specific vulnerabilities targeted by ASNase.

systems biology↗

bioRxiv2024

Nodal Modulator (NOMO) is a force-bearing transmembrane protein required for muscle differentiation

The endoplasmic reticulum (ER) relies on specialized membrane-shaping proteins to maintain a continuous network of sheets and tubules that host distinct biological processes. How this intricate structure of the ER membrane system is maintained under conditions of mechanical strain is incompletely understood. NOMO is an ER-resident transmembrane protein that contributes to ER morphology and is highly expressed in striated muscle. In this study, we identify a critical interface between distal Ig domains that enables NOMO to maintain ER morphology and buffer mechanical forces. By incorporating two independent tension sensors in the luminal domain of NOMO, we demonstrate that NOMO assemblies experience forces in the single piconewton (pN) range, with a significant contribution from the identified interface. These newly defined features are important, if not indispensable, for myogenesis, as interface mutations affecting mechanosensing fail to restore the essential role of NOMO during myogenesis in a C2C12 differentiation model. Moreover, NOMO depletion impairs nematode motility, underscoring a broader functional importance in muscle physiology.

cell biology↗

bioRxiv2024

Simplified and Rapid Workflow Enhances Throughput of De Novo Sequencing of COVID-19 Neutralizing Antibodies

During the current COVID-19 pandemic, precise antibody sequencing is crucial for the rapid development of broad-spectrum or pan-{beta}-coronavirus neutralizing antibodies (NAbs) to prevent new variants of the coronavirus and other highly pathogenic {beta}-coronaviruses. However, mass spectrometry-based de novo sequencing remains challenging due to its high cost, low throughput, and unexpected missing of certain ion information. We developed an innovative approach using solely bottom-up to provide a rapid, robust, and refined solution for the current de novo sequencing challenges. The methodology, referred to as SP-MEGD for Single-Pot and Multi-Enzymatic Gradient Digestion, capitalizes on a five-protease gradient digestion by sampling every two hours for a total of 6 hours in an integrative reactor. The SP-MEGD method could engender numerous missed cleavage events and produce various peptide products of diverse lengths with overlapping stretches of residues, enabling efficient database-free de novo sequencing. Antibody assembly for single or mixed COVID-19-NAbs with publicly available sequences and commercial antibodies with unknown sequences was efficiently deciphered using our previously proposed optimization method, Fusion assembler. Our innovative study represents the first successful simultaneous discrimination and achieving over 99% accurate sequence coverage of a mixture containing three humanized COVID-19-NAbs (S2P6LH, BD5514LH, and BD5840LH). Furthermore, we utilized SP-MEGD and Fusion to sequence commonly used anti-CD8 and anti-CD4, and successfully confirmed their impact on immune cell clearance through in vivo experiments. Overall, our developed workflow demonstrates promise in facilitating the discovery and development of vaccines and antibody therapeutics while providing deeper insights into monoclonal antibodies (mAbs).

bioengineering↗

bioRxiv2024

Comprehensive assembly of monoclonal and mixed antibody sequences

The elucidation of antibody sequence information is crucial for understanding antigen binding and advancing therapeutic and research applications. However, complete de novo assembly of monoclonal antibody sequences remains challenging due to accuracy and robustness limitations. To address this issue, we introduce Fusion, an innovative de novo assembler that integrates overlapping peptides and template information into complete sequences using a beam search strategy. We demonstrate Fusions performance by reconstructing multiple human and murine antibodies with highest accuracy (100% and over 99%, respectively). Biological validation of the recombinantly expressed AFS98 antibody with unknown sequences further supports its effectiveness. Furthermore, current methods are applicable only to traditional monoclonal antibody sequencing assembly, presenting a significant bottleneck in achieving higher throughput. In contrast, Fusion can assemble peptide sequences from mixtures of two or three monoclonal antibodies into complete individual sequences with the same accuracy as traditional sequencing, significantly enhancing throughput. To our knowledge, this is the first study enabling high-throughput sequencing of multiple antibodies using only bottom-up mass spectrometry. The duration, expense, and reagent consumption of mass spectrometry detection are comparable to those required for sequencing a single monoclonal antibody. In summary, Fusions superior performance in handling the complex antibody sequencing represents a significant advancement in antibody research.

bioinformatics↗

bioRxiv2024

A causative SNP in the promoter of myogenin is essential for myogenic differentiation

Single nucleotide polymorphisms (SNPs) widely existing in different breeds genome represent population-specific. Under the influence of long-term evolution and artificial selection, there are a large number of SNPs between western lean-type pig breeds and Chinese indigenous pig breeds, but until now, little is known about their roles in inter-breed differences. Our study revealed SNP rs3471653254 C>T generated from the two types of pigs mentioned above, located in the promoter shared by MyoG and Myoparr, played an important role in the differentiation of myoblast by influencing the enrichment of HOXA5 to regulate the transcription of MyoG and Myoparr. Meanwhile, Myoparr could be used as the sponge of mir-30b-3p which repressed myogenic differentiation and muscle regeneration through targeting MyoD. Our results indicated that SNP rs3471653254 C>T is essential for myogenic differentiation and regeneration and could be used as an ideal site for increasing lean meat production in pigs.

genetics↗

bioRxiv2024

GRATCR: epitope-specific T cell receptor sequence generation with data-efficient pre-trained models

T cell receptors (TCRs) play a crucial role in numerous immunotherapies targeting tumor cells. However, their acquisition and optimization present significant challenges, involving laborious and time-consuming wet lab experimental resource. Deep generative model has demonstrated remarkable capabilities in functional protein sequence generation, offering a promising solution for enhancing the acquisition of specific TCR sequences. Here, we propose GRATCR, a framework incorporates two pre-trained modules through a novel "grafting" strategy, to de-novo generate TCR sequences targeting specific epitopes. Experimental results demonstrate that TCRs generated by GRATCR exhibit higher specificity toward desired epitopes and are more biologically functional compared with state-of-the-art model, by using significantly fewer training data. Additionally, the generated sequences display novelty compared to natural sequences, and the interpretability evaluation further confirmed that the model is capable of capturing important binding patterns. GRATCR is freely available at https://github.com/zhzhou23/GRATCR.

bioinformatics↗

bioRxiv2024

Identifying Artifacts from Large Library Docking

While large library docking has discovered potent ligands for multiple targets, as the libraries have grown, the very top of the hit-lists can become populated with artifacts that cheat our scoring functions. Though these cheating molecules are rare, they become ever-more dominant with library growth. Here, we investigate rescoring top-ranked molecules from docking screens with orthogonal methods to identify these artifacts, exploring implicit solvent models and absolute binding free energy perturbation (AB-FEP) as cross-filters. In retrospective studies, this approach deprioritized high-ranking non-binders for nine targets while leaving true ligands relatively unaffected. We tested the method prospectively against results from large library docking AmpC {beta}-lactamase. From the very top of the docking hit lists, we prioritized 128 molecules for synthesis and experimental testing, a mixture of 39 molecules that rescoring flagged as likely cheaters and another 89 that were plausible true actives. None of the 39 predicted cheating compounds inhibited AmpC up to 200{micro}M in enzyme assays, while 57% of the 89 plausible true actives did do so, with 19 of them inhibiting the enzyme with apparent Ki values better than 50{micro}M. As our libraries continue to grow, a strategy of catching docking artifacts by rescoring with orthogonal methods may find wide use in the field. Graphical TOC Entry O_FIG O_LINKSMALLFIG WIDTH=166 HEIGHT=200 SRC="FIGDIR/small/603966v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@c2f1a5org.highwire.dtl.DTLVardef@86bc58org.highwire.dtl.DTLVardef@1b739c7org.highwire.dtl.DTLVardef@325b93_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

NSP4 mutation T492I drives rapid evolution of SARS-CoV-2 toward Omicron

T492I, a mutation encountered in SARS-CoV-2 nonstructural protein 4 (NSP4), enhances viral replication and alters nonstructural protein cleavage, causing potential evolutionary impacts. Through comprehensive comparative analyses based on evolve-and-resequence experiments of SARS-CoV-2 wild-type and Delta strains with or without T492I, we demonstrate that NSP4 T492I not only increases the mutation rate, but also accelerates the emergence of many mutations characteristic for Omicron variants. Accordingly, viral populations that evolved from ancestors with T492I, show Omicron-biased selective forces and increases in viral replication, infectivity, immune evasion capacity, potentials for cross-species transmission and receptor-binding affinity. Aside from enhanced replication, we observed stronger epistasis regarding viral replication and infectivity in T492I than in S N501Y and NSP6 {Delta}SGF; this facilitates the regulation of mutation types, which can drive fast evolution of Omicron specific mutations. Our results highlight the role of an important replication-enhancing mutation in regulating the evolutionary rates and mutational trends of SARS-CoV-2.

evolutionary biology↗

bioRxiv2024

Visualizing the translation landscape in human cells at high resolution

Obtaining comprehensive structural descriptions of macromolecules within their natural cellular context holds immense potential for understanding fundamental biology and improving health. Here, we present the landscape of protein synthesis inside human cells in unprecedented detail obtained using an approach which combines automated cryo-focused ion beam (FIB) milling and in situ single-particle cryo-electron microscopy (cryo-EM). With this in situ cryo-EM approach we resolved a 2.19 [A] consensus structure of the human 80S ribosome and unveiled its 21 distinct functional states, nearly all higher than 3 [A] resolution. In contrast to in vitro studies, we identified protein factors, including SERBP1, EDF1 and NAC/3, not enriched on purified ribosomes. Most strikingly, we observed that SERBP1 binds to the ribosome in almost all translating and non-translating states to bridge the 60S and 40S ribosomal subunits. These newly observed binding sites suggest that SERBP1 may serve an important regulatory role in translation. We also uncovered a detailed interface between adjacent translating ribosomes which can form the helical polysome structure. Finally, we resolved high-resolution structures from cells treated with homoharringtonine and cycloheximide, and identified numerous polyamines bound to the ribosome, including a spermidine that interacts with cycloheximide bound at the E site of the ribosome, underscoring the importance of high-resolution in situ studies in the complex native environment. Collectively, our work represents a significant advancement in detailed structural studies within cellular contexts.

molecular biology↗

bioRxiv2024

Channel width modulates the permeability of DNA origami based nuclear pore mimics

Nucleoporins (nups) in the central channel of nuclear pore complexes (NPCs) form a selective barrier that suppresses the diffusion of most macromolecules while enabling rapid transport of nuclear transport receptors (NTRs) with bound cargos. The complex molecular interactions between nups and NTRs have been thought to underlie the gatekeeping function of the NPC. Recent studies have shown considerable variation in NPC diameter but how altering NPC diameter might impact the selective barrier properties remains unclear. Here, we build DNA nanopores with programmable diameters and nup arrangement to mimic NPCs of different diameters. We use hepatitis B virus (HBV) capsids as a model for large-size cargos. We find that Nup62 proteins form a dynamic cross-channel meshwork impermeable to HBV capsids when grafted on the interior of 60-nm wide nanopores but not in 79-nm pores, where Nup62 cluster locally. Furthermore, importin-{beta}1 substantially changes the dynamics of Nup62 assemblies and facilitates the passage of HBV capsids through NPC mimics containing Nup62 and Nup153. Our study shows the transport channel width is critical to the permeability of nup barriers and underscores the role of NTRs in dynamically remodeling nup assemblies and mediating the nuclear entry of viruses.

biophysics↗

bioRxiv2024

Paralogue-selective degradation of the lysine acetyltransferase EP300

The transcriptional coactivators EP300 and CREBBP are critical regulators of gene expression that share high sequence identity but exhibit non-redundant functions in basal and pathological contexts. Here, we report the development of a bifunctional small molecule, MC-1, capable of selectively degrading EP300 over CREBBP. Using a potent aminopyridine-based inhibitor of the EP300/CREBBP catalytic domain in combination with a VHL ligand, we demonstrate that MC-1 preferentially degrades EP300 in a proteasome-dependent manner. Mechanistic studies reveal that selective degradation cannot be predicted solely by target engagement or ternary complex formation, suggesting additional factors govern paralogue-specific degradation. MC-1 inhibits cell proliferation in a subset of cancer cell lines and provides a new tool to investigate the non-catalytic functions of EP300 and CREBBP. Our findings expand the repertoire of EP300/CREBBP-targeting chemical probes and offer insights into the determinants of selective degradation of highly homologous proteins.

biochemistry↗

bioRxiv2024

The tricellular junctional protein Ildr2 helps maintain glomerular podocyte architecture

Podocytes are highly specialized epithelial cells of the glomerular filtration barrier essential for maintaining proper kidney function. Their intricate cellular projections, called foot processes, wrap around the capillary endothelium, interdigitate, and connect to one another via slit diaphragm intercellular junctions to form a sieve-like barrier. Compromise to this unique podocyte architecture can lead to altered glomerular function and eventual kidney disease. We previously identified Immunoglobulin-like domain containing receptor 2 (Ildr2) as a component of the podocyte foot process through proteomic analyses. Ildr2 is a tricellular tight junction constituent and localizes to distinct puncta in podocytes that likely represent these specialized junctions. However, the significance of tricellular tight junctions and Ildr2 to podocyte integrity is unknown. To this end, we generated a conditional knockout mouse with podocyte-specific deletion of Ildr2 (Podocin-Cretg/+;Ildr2fl/flor Ildr2PodKO). Kidneys from Ildr2PodKO adult animals show disruptions to podocyte foot process architecture including effacement and the unique formation of electron dense strands connecting subsets of processes. Additionally, the glomerular basement membrane was significantly thicker in conditional knockouts and histological analyses revealed glomerular collagen and glycoprotein accumulation. Surprisingly, Ildr2PodKO animals displayed no significant albuminuria. When Ildr2PodKO mice were challenged with a stress to kidney function, immunohistochemistry revealed podocyte loss from a subset of glomeruli with concomitant detection of podocytes in urine, although function was still preserved. Collectively, our data provide novel insights into the function of Ildr2 and suggest tricellular junctions help preserve podocyte architecture but are likely not necessary to maintain proper filtration in no or low stress physiological states.

physiology↗

bioRxiv2024

Resource competition affects the developmental outcome of the acoustic parasitoid fly Ormia ochracea

Ormia ochracea is an acoustic parasitoid fly where the adults are free-living, but their larval young depend on nutritional resources within host crickets for growth and development. In nature, gravid female flies rely on their ability to recognize and localize cricket calling songs to find suitable host species to parasitize. In depth investigations of fly behavior and the mechanistic bases of auditory perception require a reliable approach to propagate stable fly colonies in the laboratory. Previous work has demonstrated that flies can be propagated using a number of natural host cricket species, as well as cricket species that flies do not parasitize in nature. However, we lack a complete understanding of fly developmental outcomes when non-host cricket species are utilized to propagate fly colonies. In this study, we document the feasibility of using commercially supplied Acheta domesticus as a host species. We specifically test the hypothesis that host size and resource competition can affect developmental outcomes of O. ochracea. We performed manual parasitizations on crickets that varied in size, and resource competition was varied by manipulating the number of larvae used to parasitize a host cricket. A series of morphometric analyses were conducted on host crickets, and developmental outcomes were measured in terms of pupation success and eclosion success, pupal width, and eclosed adult fly size. In the absence of resource competition, we found that host cricket size did not affect pupation or eclosion success. In the presence of resource competition between two developing larvae within a host cricket, pupation and eclosion successes were impacted negatively, and the developing pupae were more likely to be smaller. These results confirm that resource competition among developing parasitoids can negatively affect developmental outcomes, and Acheta domesticus can be used effectively to propagate colonies of O. ochracea in the laboratory. HighlightsO_LIThe acoustic parasitoid fly Ormia ochracea can successfully develop within the house cricket Acheta domesticus. C_LIO_LIPupal size and eclosed adult fly size varies positively with the size of host cricket. C_LIO_LIResource competition negatively affects pupation and eclosion success. C_LIO_LIResource competition resulted in smaller fly pupae that were less likely to eclose. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/590943v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@b86e19org.highwire.dtl.DTLVardef@44444corg.highwire.dtl.DTLVardef@1dfe813org.highwire.dtl.DTLVardef@fd5b3b_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗