Biology subjects

Wu, W.

Publications and source records attributed to Wu, W..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

Ultra-high temporal resolution 4D angiography using arterial spin labeling with subspace reconstruction

PurposeTo achieve ultra-high temporal resolution non-contrast 4D angiography with improved spatiotemporal fidelity. MethodsContinuous data acquisition using 3D golden-angle sampling following an arterial spin labeling preparation allows for flexibly reconstructing 4D dynamic angiograms at arbitrary temporal resolutions. However, k-space data is often temporally "binned" before image reconstruction, negatively affecting spatiotemporal fidelity and limiting temporal resolution. In this work, a subspace was extracted by linearly compressing a dictionary constructed from simulated curves of an angiographic kinetic model. The subspace was used to represent and reconstruct the voxelwise signal timecourse at the same temporal resolution as the data acquisition without temporal binning. Physiological parameters were estimated from the resulting images using a Bayesian fitting approach. A group of 8 healthy subjects were scanned and the in-vivo results reconstructed by different methods were compared. Due to the difficulty of obtaining ground truth 4D angiograms with ultra-high temporal resolution, the in-vivo results were cross-validated with numerical simulations. ResultsThe proposed method enables 4D time-resolved angiography with much higher temporal resolution (14.7 ms) than previously reported ([~]50 ms) whilst maintaining high spatial resolution (1.1 mm isotropic). Blood flow dynamics were depicted in greater detail, thin vessel visibility was improved, and the estimated physiological parameters also exhibited more realistic spatial patterns with the proposed method. ConclusionIncorporating a subspace compressed kinetic model into the reconstruction of 4D ASL angiograms notably improved the temporal resolution and spatiotemporal fidelity, which was subsequently beneficial for accurate physiological modeling.

neuroscience↗

bioRxiv2024

Constant surface area-to-volume ratio during cell growth as a design principle in mammalian cells

All cells are subject to geometric constraints, including the surface area-to-volume (SA/V) ratio, which can limit nutrient uptake, maximum cell size, and cell shape changes. Like the SA/V ratio of a sphere, it is generally assumed that the SA/V ratio of cells decreases as cell size increases. However, the structural complexity of the plasma membrane makes studies of the surface area challenging in cells that lack a cell wall. Here, we investigate near-spherical mammalian cells using single-cell measurements of cell mass and plasma membrane proteins and lipids, which allows us to examine the cell size scaling of cell surface components as a proxy for the SA/V ratio. Surprisingly, in various proliferating cell lines, cell surface components scale proportionally with cell size, indicating a nearly constant SA/V ratio as cells grow larger. This behavior is largely independent of the cell cycle stage and is also observed in quiescent cells, including primary human monocytes. Moreover, the constant SA/V ratio persists when cell size increases excessively during polyploidization. This is enabled by increased plasma membrane folding in larger cells, as verified by electron microscopy. We also observe that specific cell surface proteins and cholesterol can deviate from the proportional size scaling. Overall, maintaining a constant SA/V ratio ensures sufficient plasma membrane area for critical functions such as cell division, nutrient uptake, growth, and deformation across a wide range of cell sizes.

cell biology↗

bioRxiv2024

Nanopore Direct RNA Sequencing Reveals Virus-Induced Changes in the Transcriptional Landscape in Human Bronchial Epithelial Cells

Direct RNA nanopore sequencing data reveals changes in gene expression, polyadenylation, splicing, m6A methylation, and pseudouridylation in response to influenza virus exposure of primary human bronchial epithelial cells. This study focuses on the epitranscriptomic profile of genes in the host immune response. In addition to polyadenylated noncoding RNA, we purified and sequenced nonpolyadenylated noncoding RNA and observed changes in expression, N6-methyl-adenosine (m6A), and pseudouridylation ({Psi}) in these novel RNA. Two recently discovered lincRNA with roles in immune response, Chaserr and LEADR, are predicted in the analysis of the sequencing data to be highly methylated in response to influenza exposure. Several H/ACA type snoRNAs that guide pseudouridylation are decreased in expression in response to influenza, and there is a corresponding predicted decrease in the pseudouridylation of two novel lncRNA. Thus, novel epitranscriptomic changes revealed by direct RNA sequencing with nanopore technology provide unique insights into the host epitranscriptomic changes in epithelial gene networks that respond to influenza virus exposure.

bioinformatics↗

bioRxiv2024

Densely sampled stimulus-response map of human cortex with single pulse TMS-EEG and its relation to whole brain neuroimaging measures

Large-scale networks underpin brain functions. How such networks respond to focal stimulation can help decipher complex brain processes and optimize brain stimulation treatments. To map such stimulation-response patterns across the brain non-invasively, we recorded concurrent EEG responses from single-pulse transcranial magnetic stimulation (i.e., TMS-EEG) from over 100 cortical regions with two orthogonal coil orientations from one densely-sampled individual. We also acquired Human Connectome Project (HCP)-styled diffusion imaging scans (six), resting-state functional Magnetic Resonance Imaging (fMRI) scans (120 mins), resting-state EEG scans (108 mins), and structural MR scans (T1- and T2-weighted). Using the TMS-EEG data, we applied network science-based community detection to reveal insights about the brains causal-functional organization from both a stimulation and recording perspective. We also computed structural and functional maps and the electric field of each TMS stimulation condition. Altogether, we hope the release of this densely sampled (n=1) dataset will be a uniquely valuable resource for both basic and clinical neuroscience research.

neuroscience↗

bioRxiv2024

Poxvirus A52 is a host range factor for modified vaccinia virus Ankara (MVA) and promotes viral replication by disturbing the formation of autolysosomes

Many members of the poxvirus family are important zoonotic pathogens that pose a significant threat to human and animal health worldwide. Autophagy is a multi-step degradation pathway within cells, and one of its primary biological functions includes the clearance of invading viruses. Nevertheless, the interplay between poxviruses and host cell autophagy has not been fully elucidated. Here, we demonstrate that vaccinia virus (VACV) and lumpy skin disease virus (LSDV) induce incomplete autophagy and inhibit the fusion of autophagosomes and lysosomes, while modified vaccinia virus Ankara (MVA), an attenuated strain of VACV unable to replicate in almost all human cells, does not. Additionally, we screened and identified the VACV protein A52 as a key factor that obstruct the formation of autolysosomes. Mechanistically, A52 interacts with SNAP29 and inhibits its interaction with STX17 and VAMP8, both of which are binding partners of SNAP29 and are essential for complete autophagy. Moreover, A52 promotes the proteasomal degradation of SNAP29, which facilitates viral replication. We further revealed that SNAP29 functions as a restriction factor for MVA, as the suppression of SNAP29 allowed the replication of MVA in human cells. In summary, our data present a molecular mechanism by which poxviruses manipulate the cellular autophagic machinery and provide additional explanation for the restriction of MVA in human cells.

microbiology↗

bioRxiv2024

Cerebrospinal Fluid Dynamics: Uncovering Alternative Blood Vessel Clearance Mechanisms

The pathways that run along the olfactory nerves crossing the cribriform plate and connecting to lymphatic vessels in the nasal cavity, have been identified as a crucial route for cerebrospinal fluid (CSF) outflow. However, the presence of a CSF efflux pathway through blood vessels in this region has yet to be clarified. This study aimed to elucidate the anatomical connections between the subarachnoid space and the bloodstream at the nasal epithelium and the venous drainage routes of the nasal epithelium in mice. Our findings demonstrated that CSF tracers could be drained not only through lymphatic vessels in the nasal cavity and cervical lymph nodes (CLNs), but also through the blood vessels in this area that extend to its venous drainage routes, including the facial and jugular veins. Additionally, we showed that ligation of CLNs neither impeded the influx and efflux of CSF tracers nor exacerbated Alzheimers disease (AD)-related pathology in AD mice. Our work reveals a previously unrecognized pathway for CSF drainage through blood vessels within the nasal mucosa. These findings provide insight into the efficient removal of waste products, facilitating optimal functioning of neural tissue within the susceptible tissue of our brains.

neuroscience↗

bioRxiv2024

Single-shot water-fat imaging with multi-echo blip-rewound EPI

PurposeTo develop a method for single-shot water-fat imaging. MethodsSingle-shot blip-rewound EPI (rEPI) is a fast imaging technique that can acquire multiple echo MRI images with a snapshot. Dixons method separates water and fat signals using signals acquired with different echo times. Combining multi-echo rEPI with properly chosen echo times and Dixon-based post-processing generates water and fat images with a single-shot scan. ResultsPhantom and in vivo experiments were performed to evaluate the proposed method. In phantom scans, water and fat signals are robustly separated using the proposed method, and the obtained water signal is much cleaner than that obtained by conventional EPI acquisition with fat suppression. In vivo experiments show that fat suppression can be obtained using the proposed method without fat saturation pulses, reducing SAR and shortening scan time. In addition, fat signal can also be reconstructed based on the proposed method. ConclusionA single-shot water-fat imaging technique has been successfully developed, a significant advancement that offers speed and robustness in separating water and fat signals for human MRI scans.

bioengineering↗

bioRxiv2024

MAST-Decon: Smooth Cell-type Deconvolution Method for Spatial Transcriptomics Data

AO_SCPLOWBSTRACTC_SCPLOWSpatial transcriptomics (ST) technologies have gained increasing popularity due to their ability to provide positional context of gene expressions in a tissue. One major limitation of current commercially available ST methods such as the 10X Genomics Visium platform is the lack of single cell resolution. Cell type deconvolution for ST data is critical in order to fully reveal underlying biological mechanisms. Existing ST data deconvolution methods share two common limitations: first, few of them utilize spatial neighborhood information. Existing methods such as RCTD and SPOTlight intrinsically treat each spatial spot as independent of neighboring spots, although we anticipate nearby spots to share similar cell type compositions based on clinical evidence of tissue structures. Such limitation could be amplified when sequencing depths at single spots are relatively low so that borrowing information from neighboring spots is necessary in order to obtain reliable deconvolution results. Second, although Visium data provide us with a histological image which could add additional information regarding spot heterogeneity, most existing methods do not utilize this H&E image. To solve these two limitations, we developed Multiscale Adaptive ST Deconvolution (MAST-Decon), a smooth deconvolution method for ST data. MAST-Decon uses a weighted likelihood approach and incorporates both gene expression data, spatial neighborhood information and H&E image features by constructing different kernel functions to obtain a smooth deconvolution result. We showcased the strength of MAST-Decon through simulations based on real data, including a single-cell dataset of mouse brain primary visual cortex, and real-world Visium datasets to demonstrate its robust and superior performance compared with other state-of-the-art methods.

genomics↗

bioRxiv2024

Measuring single-cell density with high throughput enables dynamic profiling of immune cell and drug response from patient samples

Cell density, the ratio of cell mass to volume, is an indicator of molecular crowding and therefore a fundamental determinant of cell state and function. However, existing density measurements lack the precision or throughput to quantify subtle differences in cell states, particularly in primary samples. Here we present an approach for measuring the density of 30,000 single cells per hour with a precision of 0.03% (0.0003 g/mL) by integrating fluorescence exclusion microscopy with a suspended microchannel resonator. Applying this approach to human lymphocytes, we discovered that cell density and its variation decrease as cells transition from quiescence to a proliferative state, suggesting that the level of molecular crowding decreases and becomes more regulated upon entry into the cell cycle. Using a pancreatic cancer patient-derived xenograft model, we found that the ex vivo density response of primary tumor cells to drug treatment can predict in vivo tumor growth response. Our method reveals unexpected behavior in molecular crowding during cell state transitions and suggests density as a new biomarker for functional precision medicine.

bioengineering↗

bioRxiv2024

Microglial-Mediated Prevention of Axonal Degeneration in the Injured Spinal Cord: Insights from an In Vivo Imaging Study

Microglia, the primary immune cells in the central nervous system, play a critical role in regulating neuronal function and fate through their interaction with neurons. Despite extensive research, the specific functions and mechanisms of microglia-neuron interactions remain incompletely understood. In this study, we demonstrate that microglia establish direct contact with myelinated axons at Nodes of Ranvier in the spinal cord of mice. Under normal physiological conditions, microglia-node contact occurs in a random scanning pattern and is associated with neuronal activity. However, in response to axonal injury, microglia rapidly transform their contact into a robust wrapping form, preventing acute axonal degeneration from extending beyond the nodes. This neuroprotective wrapping behavior of microglia is dependent on the function of their P2Y12 receptors, which may be activated by ATP released through axonal volume-activated anion channels at the nodes. Additionally, voltage-gated sodium channels (NaV) contribute to the interaction between nodes and glial cells following injury, and inhibition of NaV delays axonal degeneration. Through in vivo imaging, our findings reveal a neuroprotective role of microglia during the acute phase of spinal cord injury, achieved through a novel form of neuron-glia interaction.

neuroscience↗

bioRxiv2024

Verbal semantic expertise is associated with reduced functional connectivity between left and right anterior temporal lobes

The left and right anterior temporal lobes (ATLs) encode semantic representations. They show graded hemispheric specialisation in function, with the left ATL contributing preferentially to verbal semantic processing. We investigated the underlying causes of this organisation, using resting-state functional connectivity as a measure of functional segregation between ATLs. We analysed two independent resting-state fMRI datasets (N=86 and N=642) in which participants verbal semantic expertise was measured using vocabulary tests. In both datasets, people with more advanced verbal semantic knowledge showed weaker functional connectivity between left and right ventral ATLs. This effect was highly specific. It was not observed for within-hemisphere connections between semantic regions (ventral ATL and inferior frontal gyrus; IFG, though it was found for left-right IFG connectivity in one dataset). Effects were not found for tasks probing semantic control, non-semantic cognition or face recognition. Our results suggest that hemispheric specialisation in the ATLs is not an innate property but rather emerges as people develop highly detailed verbal semantic representations. We propose that this effect is a consequence of the left ATLs greater connectivity with left-lateralised written word recognition regions, which causes it to preferentially represent meaning for advanced vocabulary acquired primarily through reading.

neuroscience↗

bioRxiv2024

Blocking MIF secretion enhances CAR T-cell efficacy against neuroblastoma

While chimeric antigen receptor (CAR) T-cell therapies are showing highly promising first results in neuroblastoma, immunosuppressive tumor microenvironments (TME) limit T cell persistence and durable clinical efficacy. To improve CAR T-cell efficacy further, we applied a multi-omics approach including single-cell RNA sequencing and proteomics, which identified 13 targetable immunosuppressive factors in neuroblastoma. Of these, macrophage migration inhibitory factor (MIF) and midkine (MDK) were validated across multiple published RNA datasets. Moreover, they were secreted in high abundance by neuroblastoma tumoroids. Functional validation experiments revealed MIF as a potent inhibitor of CAR T-cells, in vitro and in vivo. Degradation of MIF by PROTAC technology significantly enhanced CAR T-cell activation targeting GPC2 and B7-H3, providing a potential intervention against MIF. By defining the immunosuppressive effects of neuroblastomas TME on CAR T-cell efficacy, particularly the pivotal role of MIF, we provide a therapeutic strategy for improving adoptive cell therapies for this pediatric malignancy.

cancer biology↗

bioRxiv2024

CDK4 and CDK6 upregulation promotes DNA replication stress, genomic instability and resistance to EGFR targeted therapy in lung cancer

Epidermal growth factor receptor (EGFR) mutant lung adenocarcinomas (LUAD) harbor a complex landscape of genetic co-alterations and potential oncogenic interactions. Among them are recurrent amplifications of the cell cycle regulatory genes CDK4 and CDK6, which have been clinically implicated in resistance to EGFR tyrosine kinase inhibitors (TKIs). However, the mechanisms by which CDK4/6 upregulation promotes therapy resistance remain poorly defined. Here, we demonstrate that CDK4 or CDK6 overexpression limits EGFR inhibitor-induced proliferative arrest, promoting continued cell cycle progression. This is accompanied by elevated replication stress, increased TPX2 expression, DNA damage leading to ATM activation, and ultimately genomic instability. Integrative transcriptomic and copy number analyses of EGFR-mutant LUAD tumors from both patients and preclinical models revealed that CDK4 or CDK6 amplification is associated with the upregulation of genes linked to tumor progression, including AGR2, ASNS, and STEAP1. CDK4 amplification was also highly correlated with gene expression changes associated with epithelial-to-mesenchymal transition (EMT) in a single-cell RNA sequencing dataset from patient biopsies. In preclinical models, co-treatment with CDK4/6 and EGFR inhibitors restored proliferative arrest, induced tumor cell apoptosis, and reduced replication stress, DNA damage, and genomic instability. Our findings uncover a mechanistic basis for EGFR inhibitor resistance of CDK4 and CDK6 amplified EGFR-mutant LUAD. They also provide a rationale for the biomarker-driven clinical development of combination EGFR and CDK4/6-targeted therapies for the treatment of a subset of EGFR-mutant LUAD patients.

cancer biology↗

bioRxiv2024

Multiomics Analysis Reveals Extensive Remodeling of the Extracellular Matrix and Cellular Metabolism Due to Plakophilin-2 Knockdown in Guinea Pigs

Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a leading cause of sudden cardiac death (SCD) in young individuals, yet the mechanisms underlying its pathogenesis, particularly the role of plakophilin-2 (PKP2), remain incompletely understood. This study aimed to elucidate the profile of molecular and metabolic consequences of PKP2 knockdown in a guinea pig model of ARVC. We employed adeno-associated virus serotype 9 (AAV9) to deliver PKP2 shRNA, establishing a model that recapitulates key features of human ARVC, including right ventricular (RV) enlargement, sudden death, and cardiac lipid accumulation. Proteomic analysis revealed significant dysregulation of extracellular matrix (ECM) proteins, PI3K-Akt signaling, and energy metabolism in PKP2-deficient RVs. Metabolomic profiling further highlighted alterations in lipid metabolism and inter-metabolites of TCA cycle, with a notable shift towards fatty acid oxidation. These findings suggest that PKP2 deficiency triggers a cascade of molecular events leading to ECM remodeling, metabolic reconfiguration, and potential mitochondrial dysfunction, which may contribute to the development of ARVC. Our study provides novel insights into the early molecular mechanisms of ARVC and identifies potential therapeutic targets for this underexplored disease.

genetics↗

bioRxiv2024

Mechanisms mediating arylidene-indolinones induced degradation: thoughts on "Discovery of a Drug-like, Natural Product-Inspired, DCAF11 Ligand Chemotype"

In the recent issue of Nature Communications (2023 Nov 30;14(1):7908), Xue et. al. reported a very interesting and significant discovery of a possible DCAF11 ligand chemotype that could be used as the "warhead" to design bifunctional compounds for targeted degradation via engaging the E3 ligase DCAF11 1 (annotated as ref 1 hereafter). The discovery is of importance to the targeted protein degradation field and was inspired by previous reports suggesting that similar compounds may also engage the autophagosome protein LC3 for degradation and function as autophagy-tethering compounds (ATTECs) 2, 3, 4, 5, 6, 7, which seem to be inconsistent with ref 1. We think that the conclusions based on these data are not necessarily mutually exclusive. After performing additional experiments and analyses, we would like to discuss some possibilities explaining such discrepancies and make a few points of clarification.

biochemistry↗

bioRxiv2024

Profound synthetic lethality between SMARCAL1 and FANCM

DNA replication stress is a threat to genome integrity. The large SNF2-family of ATPases participates in preventing and mitigating DNA replication stress by employing their ATP-driven motor to remodel DNA or DNA-bound proteins. To understand the contribution of these ATPases in genome maintenance, we undertook CRISPR-based synthetic lethality screens with three SNF2-type ATPases: SMARCAL1, ZRANB3 and HLTF. Here we show that SMARCAL1 displays a profound synthetic lethal interaction with FANCM, another ATP-dependent translocase involved in DNA replication and genome stability. Their combined loss causes severe genome instability that we link to chromosome breakage at loci enriched in simple repeats, which are known to challenge replication fork progression. Our findings illuminate a critical genetic buffering mechanism that provides an essential function for maintaining genome integrity.

molecular biology↗

bioRxiv2024

Neurons enhance blood-brain barrier function via upregulating claudin-5 and VE-cadherin expression due to GDNF secretion

Blood-brain barrier (BBB) prevents neurotoxins from entering central nervous system. We aimed to establish and characterize an in vitro triple co-culture BBB model consisting of brain endothelial cells hCMEC/D3, astrocytoma U251 cells, and neuroblastoma SH-SY5Y cells. Co-culture of SH-SY5Y and U251 cells markedly enhanced claudin-5 and VE-cadherin expression in hCMEC/D3 cells, accompanied by increased transendothelial electrical resistance and decreased permeability. Conditioned medium (CM) from SH-SY5Y cells (S-CM), U251 cells (U-CM), and co-culture of SH-SY5Y and U251 cells (US-CM) also promoted claudin-5 and VE-cadherin expression. Glial cell line-derived neurotrophic factor (GDNF) levels in S-CM and US-CM were significantly higher than CMs from hCMEC/D3 and U-CM. Both GDNF and US-CM upregulated claudin-5 and VE-cadherin expression, which were attenuated by anti-GDNF antibody and GDNF signaling inhibitors. GDNF increased claudin-5 expression via the PI3K/AKT/FOXO1 and MAPK/ERK pathways. Meanwhile, GDNF promoted VE-cadherin expression by activating PI3K/AKT/ETS1 and MAPK/ERK/ETS1 signaling. The roles of GDNF in BBB integrity were validated using brain-specific Gdnf silencing mice. The developed triple co-culture BBB model was successfully applied to predict BBB permeability. In conclusion, neurons enhance BBB integrity by upregulating claudin-5 and VE-cadherin expression through GDNF secretion and established triple co-culture BBB model may be used to predict drugs BBB permeability. Impact StatementNeurons and astrocytes enhance the integrity of BBB by releasing GDNF. The released GDNF upregulated claudin-5 and VE-cadherin expression by the activation of PI3K/AKT and MAPK/ERK pathways.

cell biology↗

bioRxiv2024

Discovering and overcoming the bias in neoantigen identification by unified machine learning models

Neoantigens play a crucial role in tumor immune process and precisely identifying them can greatly contribute to tumor immunotherapy design. There are three main steps in the neoantigen immune process, i.e., binding with MHCs, extracellular presentation, and immunogenicity induction. Various computational methods have been developed, but the overall accuracy of neoantigen identification remains relatively low. Here, we established a unified transformer-based framework ImmuBPI that comprised three tasks. Cross-task model interpretation discovered a counterfactual pattern learned by the immunogenicity prediction model overlooked in previous studies. We demonstrated that this model bias arose from training data imbalance and the neglect of bias control would not only mislead the models but also hinder existing benchmarks from fair evaluation. We further designed a mutual information-based debiasing strategy that showed preliminary potential in alleviating the bias. We believe these observations will provide insightful perspectives for future neoantigen prediction by high-lighting the necessity of bias control.

bioinformatics↗