Biology subjects

Han, W.

Publications and source records attributed to Han, W..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Nitroxoline evidence Amoebicidal Activity against Acanthamoeba castellanii through DNA damage and the stress response pathways

Acanthamoeba castellanii is a widespread unicellular eukaryote found in diverse environments, including tap water, soil, and swimming pools. It is responsible for severe infections, such as Acanthamoeba keratitis and granulomatous amebic encephalitis, particularly in individuals with immunocompromisation. The ability of protozoans to form dormant cysts complicates treatment, as current therapies are ineffective against cyst stages and suffer from poor specificity and side effects. Nitroxoline, a quinoline derivative with well-established antibacterial, antifungal, and antiviral properties, is a promising therapeutic candidate. This study aimed to elucidate cellular signalling events that counteract the effects of nitroxoline. In this study, nitroxoline significantly reduced the viability of A. castellanii trophozoites in a dose- and time-dependent manner, inducing morphological changes and apoptosis. Transcriptomic analysis revealed substantial alterations in gene expression, including enrichment of metabolic pathways, DNA damage responses, and iron ion binding. Nitroxoline treatment upregulated genes involved in DNA repair and oxidative stress response while regulating genes in the methionine and cysteine cycles. It also decreased the mitochondrial membrane potential, H2S production, and total iron amount in A. castellanii. Bioinformatics analyses and molecular docking studies suggest direct interactions between nitroxoline and A. castellanii proteins. Our research provides a comprehensive molecular map of the response of A. castellanii to nitroxoline, revealing significant changes in gene expression related to the stress response and metabolic pathways. These findings underscore the potential of nitroxoline as a potent anti-Acanthamoeba agent, offering new insights into its mechanism of action and paving the way for effective therapeutic strategies.

microbiology↗

bioRxiv2024

Modeling the antigenic evolution of seasonal influenza viruses with PREDAC for vaccine strain selection in the season of 2025

IntroductionThe antigenic evolution of seasonal influenza viruses have been reported to be discontinuous as clusters. Timely identification of antigenic clusters could help for influenza virus vaccine strain selections. MethodsHere, we revealed the antigenic evolution of seasonal influenza viruses, including A(H3N2), A(H1N1pdm) and B-Victoria, using our previously developed PREDAC methods, and identified antigenic clusters of seasonal influenza viruses based on existing HA protein sequences in GISAID database. ResultsDuring the last six months (2024.2[~]2024.7), for the influenza A(H3N2) virus, the antigenic clusters DA21 (A/Darwin/6/2021-like and A/Massachusetts/18/2022-like) continuously dominated and nearly all viruses are antigenic similar to the current vaccine strain A/Massachusetts/18/2022; for the influenza A(H1N1pdm) virus, the antigenic cluster SY21 (A/Sydney/5/2021-like and A/Victoria/4897/2022-like) dominated and nearly all viruses are antigenic similar to the current vaccine strain A/Victoria/4897/2022; for the influenza B-Victoria, antigenic clusters AU21 (B/Austria/1359417/2021-like) dominated and nearly all viruses are antigenic similar to the current vaccine strain B/Austria/1359417/2021. ConclusionThe analysis suggests that there is no need to update the vaccine strains in the flu season of 2025 on the aspect of antigenicity.

microbiology↗

bioRxiv2024

PRISM: Multiplexed Profiling of RNA In-Situ through Single-round of Imaging in Three-Dimensional Tissue

Spatial RNA imaging has not been widely adopted because conventional fluorescence microscopy is limited to only a few channels, and the cyclic reactions needed to increase multiplexing in techniques such as sequential fluorescence in-situ hybridization (FISH) require sophisticated instrumentation. Here, we introduce Profiling of RNA In-situ through Single-round iMaging (PRISM), a method that expands coding capacity through color intensity grading. Using a radius vector filtering strategy to ensure the distinguishability of codewords in color space, PRISM achieves up to 64-plex color-barcoded RNA imaging in a single imaging round with conventional microscopes. We validate PRISMs versatility across various tissues by generating a 3D atlas of mouse embryonic development from E12.5 to E14.5, a quasi-3D tumor-normal transition landscape of human hepatocellular carcinoma (HCC), and a 3D cell atlas and subcellular RNA localization landscapes of mouse brain. Additionally, we show the critical role of cancer-associated fibroblasts (CAFs) in mediating immune infiltration and immune response heterogeneity within and between tumor microenvironments.

bioengineering↗

bioRxiv2024

Defining cellular determinants of resistance to PD-1 pathway blockade in non-small-cell lung cancer

Despite sustained clinical responses to immune-checkpoint blockade (ICB) therapies in non-small-cell lung cancer (NSCLC), the majority of patients derive no clinical benefits, and the cellular and molecular underpinnings of such resistance remain incompletely understood. To identify cell types that may influence immunotherapy responses, we first integrated newly generated and previously published single-cell RNA sequencing data from 110 treatment-naive patients with NSCLC. Among tumor-resident cell types, we identified MMP1+ cancer-associated fibroblasts (CAFs), which were inversely correlated with the level of tumor-reactive T cells--a key determinant of response to ICB. Further single-cell analysis for newly collected 21 tumor samples from NSCLC patients treated with anti-PD-1/PD-L1 agents revealed that MMP1+ fibroblasts were indeed enriched in treatment-refractory patients, and this observation was also validated in an independent dataset of bulk RNA sequencing from 344 NSCLC patients treated with PD-L1 agents. Examination of the spatial architecture showed that MMP1+ fibroblasts were located at the tumor-stroma boundary, forming a single-cell layer that encircled the cancer cell aggregates, and we hence defined MMP1+ fibroblasts as tumor-stroma boundary (tsb)CAFs. Such tsbCAFs likely promote resistance to ICB by functioning as a physical barrier that prevents tumor-reactive T cells from recognizing and killing cancer cells. Our study provides a new framework to identify cellular underpinnings of resistance to ICB and suggests new strategies to overcome ICB resistance. Highlights{lozenge} Identification and characterization of MMP1+ fibroblasts in lung cancer. {lozenge}Single-cell meta-analysis reveals cell populations impeding the accumulation of tumor-reactive T cells. {lozenge}MMP1+ fibroblasts correlate with the low infiltration of tumor-reactive T cells and the resistance to anti-PD-1/PD-L1 treatment. {lozenge}MMP1+ fibroblasts appear to form a space barrier between malignant and T cells.

immunology↗

bioRxiv2024

An Amygdalar-Vagal-Glandular Circuit Controls the Intestinal Microbiome

Psychological states can regulate intestinal mucosal immunity by altering the gut microbiome. However, the link between the brain and microbiome composition remains elusive. We show that Brunners glands in the duodenal submucosa couple brain activity to intestinal bacterial homeostasis. Brunners glands mediated the enrichment of gut probiotic species in response to stimulation of abdominal vagal fibers. Cell-specific ablation of the glands triggered transmissible dysbiosis associated with an immunodeficiency syndrome that led to mortality upon gut infection with pathogens. The syndrome could be largely prevented by oral or intra-intestinal administration of probiotics. In the forebrain, we identified a vagally-mediated, polysynaptic circuit connecting the glands of Brunner to the central nucleus of the amygdala. Intra-vital imaging revealed that excitation of central amygdala neurons activated Brunners glands and promoted the growth of probiotic populations. Our findings unveil a vagal-glandular neuroimmune circuitry that may be targeted for the modulation of the gut microbiome. The glands of Brunner may be the critical cells that regulate the levels of Lactobacilli species in the intestine.

neuroscience↗

bioRxiv2024

Spatiotemporal control of subcellular O-GlcNAc signaling using Opto-OGT

The posttranslational modification of intracellular proteins through O-linked {beta}-N-acetylglucosamine (O-GlcNAc) is a conserved regulatory mechanism in multicellular organisms. Catalyzed by O-GlcNAc transferase (OGT), this dynamic modification plays an essential role in signal transduction, gene expression, organelle function, and systemic physiology. Here we present Opto-OGT, an optogenetic probe that allows for precise spatiotemporal control of OGT activity through light stimulation. By fusing a photosensitive cryptochrome protein to OGT, Opto-OGT can be robustly and reversibly activated with high temporal resolution by blue light and exhibits minimal background activity without illumination. Transient activation of Opto-OGT results in mTORC activation and AMPK suppression which recapitulate nutrient-sensing signaling. Furthermore, Opto-OGT can be customized to be localized at specific subcellular sites. By targeting OGT to the plasma membrane, we demonstrate downregulation of site-specific AKT phosphorylation and signaling outputs in response to insulin stimulation. Thus, Opto-OGT is a powerful tool to define the role of O-GlcNAcylation in cell signaling and physiology.

cell biology↗

bioRxiv2024

Quantitative effects of co-culture on T cell motility and cancer-T cell interactions

One of the primary challenges in current cancer immunotherapy is the insufficient infiltration of cytotoxic T cells into solid tumors. Despite ongoing investigations, the mechanisms restricting T cell infiltration in immune-cold tumors remains elusive, hindered by the intricate tumor microenvironment. Here, we co-cultured mouse cancer cell lines with cancer-specific cytotoxic T cells to study the influence of cancer-T cell interactions on T cell motility, a crucial factor for effective tumor infiltration. By quantifying T cell motility patterns, we found that cancer-specific T cells exhibited extended contact time with cancer-cell clusters and higher directional persistence than non-specific T cells. Computational modelling suggested that T cells with stronger persistence could facilitate efficient searching for cancer clusters. Transcriptomic profiling revealed T cells recognizing cancer cells orchestrate accumulation on cancer cell clusters by activating adhesion proteins on both cancer cells and T cells, thereby fostering prolonged interaction on cancer cells. Furthermore, we observed that there were two distinct subpopulations of cancer cells after co-culturing with cancer-specific T cells: one expressing elevated levels of T-cell attractants and antigen-presentation molecules, while the other expressing immunosuppressive molecules and undergoing epithelial-to-mesenchymal transition. These dynamic insights into the complex interplay of cancer-T cell interactions and their impact on T cell motility hold implications for refining more efficacious cancer immunotherapy strategies.

systems biology↗

bioRxiv2024

Unraveling the gut microbiota of Tibetan chickens: insights into highland adaptation and ecological advantages

Tibetan animals have several unique advantages owing to the harsh ecological conditions under which they live. Tibetan mammals have been studied extensively. However, understanding of the advantages and underlying mechanisms of the representative high-latitude bird, the Tibetan chicken (Gallus gallus, TC), remains limited. The gut microbiota of animals has been conclusively shown to be closely related to both host health and host environmental adaptation. This study aimed to explore the relationships between the cecal microbiome and the advantages of TCs based on comparisons among three populations: native TCs residing on the plateau, domestic TCs living in the plain, and one native plain species. Metatranscriptomic sequencing revealed a significant enrichment of active Bacteroidetes but a loss of active Firmicutes in native TCs. Additionally, the upregulated expression of genes in the cecal microbiome of native TCs showed enriched pathways related to energy metabolism, glycan metabolism, and the immune response. Furthermore, the expression of genes involved in the biosynthesis of short-chain fatty acids (SCFAs) and secondary bile acids (SBAs) was upregulated in the cecal microbiome of native TCs. Data from targeted metabolomics further confirmed elevated levels of certain SCFAs and SBAs in the cecum of native TCs. Based on the multi-omics association analysis, we proposed that the higher ratio of active Bacteroidetes/Firmicutes may be attributed to the efficient energy metabolism and stronger immunological activity of native TCs. Our findings provide a better understanding of the interactions between gut microbiota and highland adaptation, and novel insights into the mechanisms by which Tibetan chickens adapt to the plateau hypoxic environment. IMPORTANCEThe composition and function of the active cecal microbiome were significantly different between the plateau Tibetan chicken population and the plain chicken population. Higher expression genes related to energy metabolism and immune response were found in the cecal microbiome of the plateau Tibetan chicken population. The cecal microbiome in the plateau Tibetan chicken population exhibited higher biosynthesis of short-chain fatty and secondary bile acids, resulting in higher cecal content of these metabolites. The active Bacteroidetes/Firmicutes ratio in the cecal microbiome may contribute to the high-altitude adaptive advantage of the plateau Tibetan chicken population.

microbiology↗

bioRxiv2023

EPAS1 Attenuates Atherosclerosis Initiation at Disturbed Flow Sites through Endothelial Fatty Acid Uptake

BackgroundAtherosclerotic plaques form unevenly due to disturbed blood flow, causing localized endothelial cell (EC) dysfunction. Obesity exacerbates this process, but the underlying molecular mechanisms are unclear. The transcription factor EPAS1 (HIF2A) has regulatory roles in endothelium, but its involvement in atherosclerosis remains unexplored. This study investigates the potential interplay between EPAS1, obesity, and atherosclerosis. MethodsResponses to shear stress were analysed using cultured porcine aortic EC exposed to flow in vitro coupled with metabolic and molecular analyses, and by en face immunostaining of murine aortic EC exposed to disturbed flow in vivo. Obesity and dyslipidemia were induced in mice via exposure to high-fat diet or through Leptin gene deletion. The role of Epas1 in atherosclerosis was evaluated by inducible endothelial Epas1 deletion, followed by hypercholesterolemia induction (AAV-PCSK9; high-fat diet). ResultsEn face staining revealed EPAS1 enrichment at sites of disturbed blood flow that are prone to atherosclerosis initiation. Obese mice exhibited substantial reduction in endothelial EPAS1 expression, correlating with hyperlipidaemia. Sulforaphane, a compound with known atheroprotective effects, restored EPAS1 expression and concurrently reduced plasma triglyceride levels in obese mice. Consistently, triglyceride derivatives (free fatty acids) suppressed EPAS1 in cultured EC by upregulating the negative regulator PHD3. Clinical observations revealed that reduced plasma EPAS1 correlated with increased endothelial PHD3 in obese individuals. Functionally, endothelial EPAS1 deletion increased lesion formation in hypercholesterolemic mice, indicating an atheroprotective function. Mechanistic insights revealed that EPAS1 protects arteries by maintaining endothelial proliferation by positively regulating CD36 and LIPG expression to increase fatty acid beta-oxidation. ConclusionsEndothelial EPAS1 attenuates atherosclerosis at sites of disturbed flow by maintaining EC proliferative via fatty acid uptake and metabolism. This endothelial repair pathway is inhibited in obesity, suggesting a novel triglyceride-PHD3 modulation pathway suppressing EPAS1 expression. These findings have implications for therapeutic strategies addressing vascular dysfunction in obesity.

physiology↗

bioRxiv2023

SHIELD: Skull-shaped hemispheric implants enabling large-scale-electrophysiology datasets in the mouse brain

To understand the neural basis of behavior, it is essential to measure spiking dynamics across many interacting brain regions. While new technologies, such as Neuropixels probes, facilitate multi-regional recordings, significant surgical and procedural hurdles remain for these experiments to achieve their full potential. Here, we describe a novel 3D-printed cranial-replacement implant (SHIELD) enabling electrophysiological recordings from distributed areas of the mouse brain. This skull-shaped implant is designed with customizable insertion holes, allowing dozens of cortical and subcortical structures to be recorded in a single mouse using repeated multi-probe insertions over many days. We demonstrate the procedures high success rate, biocompatibility, lack of adverse effects on behavior, and compatibility with imaging and optogenetics. To showcase the scientific utility of the SHIELD implant, we use multi-probe recordings to reveal novel insights into how alpha rhythms organize spiking activity across visual and sensorimotor networks. Overall, this method enables powerful large-scale electrophysiological measurements for the study of distributed brain computation.

neuroscience↗

bioRxiv2023

Dynamic encoding of biological motion information in macaque medial superior temporal area

The ability to decipher biological motion information is an essential brain function that develops early in life and is evolutionarily conserved across many species. However, the neuronal encoding of biological motion information remains unclear due to the scarce electrophysiological evidence. In the current study, we tackled this issue by examining whether and how neurons in the monkey medial superior temporal cortex (MST) extract form from biological motion and encode spatial transformations in biological motion. Results revealed that MST neurons are capable of encoding form information and discriminating the horizontal and the vertical mirror transformations of biological motion. More importantly, BM information is dynamically encoded in the modulation strength of evoked spike trains rather than the average firing rate during stimulus presentation. Furthermore, the ability of MST neurons to detect various biological motion features is closely linked with the neuronal selectivity for optic flow patterns.

neuroscience↗

bioRxiv2023

The brain time estimation system is dynamically assembled by non-temporal perceptual states

To investigate how neural integration of visual signals distorts human time perception, we developed a novel apparent motion paradigm. We found that the higher the frequency of visual events defined by spatial location, the longer the perception duration. At the same visual event frequency, perceptual duration was shorter when motion perception was evoked. We propose that the non-temporal perceptual states dynamically determine which core brain region (read-out system) and which group of activated neurons (timing units) assemble into a time estimation system. Timing units have activation delays in integrating input signals, which results in shorter perceptual time since perceptual duration depends only on the outputs of timing units. The read-out system consumes operating time to accumulate each timing unit, this results in a longer perception time the more timing units are accumulated in the same physical duration. Subsequently, experiments further validated two predictions of our perceptual assembly model.

neuroscience↗

bioRxiv2023

GLP-1 Receptor Agonist Improves Metabolic Disease in a Pre-clinical Model of Lipodystrophy

Individuals with lipodystrophies typically suffer from significant metabolic disease linked to adipose tissue dysfunction including severe insulin resistance and lipoatrophic diabetes, hepatic steatosis and hyperphagia. Current treatment options are limited and beter therapies for affected individuals are urgently needed. No systematic, detailed analyses exist of the effects of glucagon like peptide-1 receptor (GLP-1R) agonists in the treatment of lipoatrophic diabetes. Here we examined the effects of the GLP-1R agonist liraglutide in seipin knockout mice, a pre-clinical model of generalised lipodystrophy. Acute liraglutide treatment of seipin knockout mice significantly improved insulin, glucose and pyruvate tolerance. Once-daily injection of seipin knockout mice with liraglutide for 14 days led to a modest reduction in food intake but significant improvements in hepatomegaly associated with steatosis and significantly reduced markers of liver fibrosis. Detailed examination of the pancreas revealed that liraglutide enhanced insulin secretion in response to glucose challenge with concomitantly improved glucose control. Thus, GLP-1R agonist liraglutide significantly improved multiple aspects of lipoatrophic diabetes and hepatic steatosis in mice with congenital generalised lipodystrophy. This provides important insights regarding the benefits of GLP-1R agonists for treating lipodystrophy, informing more widespread use to improve the health of individuals with this condition.

pharmacology and toxicology↗

bioRxiv2023

Epithelial Yap/Taz are required for functional alveolar regeneration following acute lung injury

A hallmark of idiopathic pulmonary fibrosis (IPF) and other interstitial lung diseases is dysregulated repair of the alveolar epithelium. The Hippo pathway effector transcription factors YAP and TAZ have been implicated as essential for type 1 and type 2 alveolar epithelial cell (AT1 and AT2) differentiation in the developing lung, yet aberrant activation of YAP/TAZ is a prominent feature of the dysregulated alveolar epithelium in IPF. In these studies, we sought to define the functional role of YAP/TAZ activity during alveolar regeneration. We demonstrate that Yap and Taz are normally activated in AT2 cells shortly after injury, and deletion of Yap/Taz in AT2 cells led to pathologic alveolar remodeling, failure of AT2 to AT1 cell differentiation, increased collagen deposition, exaggerated neutrophilic inflammation, and increased mortality following injury induced by a single dose of bleomycin. Loss of Yap/Taz activity prior to a LPS injury prevented AT1 cell regeneration, led to intra-alveolar collagen deposition, and resulted in persistent innate inflammation. Together these findings establish that AT2 cell Yap/Taz activity is essential for functional alveolar epithelial repair and prevention of fibrotic remodeling.

cell biology↗

bioRxiv2023

Recurrent pattern completion drives the neocortical representation of sensory inference

When sensory information is incomplete or ambiguous, the brain relies on prior expectations to infer perceptual objects. Despite the centrality of this process to perception, the neural mechanism of sensory inference is not known. Illusory contours (ICs) are key tools to study sensory inference because they contain edges or objects that are implied only by their spatial context. Using cellular resolution, mesoscale two-photon calcium imaging and multi-Neuropixels recordings in the mouse visual cortex, we identified a sparse subset of neurons in the primary visual cortex (V1) and higher visual areas that respond emergently to ICs. We found that these highly selective IC-encoders mediate the neural representation of IC inference. Strikingly, selective activation of these neurons using two-photon holographic optogenetics was sufficient to recreate IC representation in the rest of the V1 network, in the absence of any visual stimulus. This outlines a model in which primary sensory cortex facilitates sensory inference by selectively strengthening input patterns that match prior expectations through local, recurrent circuitry. Our data thus suggest a clear computational purpose for recurrence in the generation of holistic percepts under sensory ambiguity. More generally, selective reinforcement of top-down predictions by pattern-completing recurrent circuits in lower sensory cortices may constitute a key step in sensory inference.

neuroscience↗

bioRxiv2023

Repetitive Sulfur Dioxide Exposure in Mice Models Post-Deployment Respiratory Syndrome

Soldiers deployed to Iraq and Afghanistan have a higher prevalence of respiratory symptoms than non-deployed military personnel and some have been shown to have a constellation of findings on lung biopsy termed post-deployment respiratory syndrome (PDRS). Since many of the deployers in this cohort reported exposure to sulfur dioxide (SO2), we developed a model of repetitive exposure to SO2 in mice that phenocopies many aspects of PDRS, including adaptive immune activation, airway wall remodeling, and pulmonary vascular disease (PVD). Although abnormalities in small airways were not sufficient to alter lung mechanics, PVD was associated with the development of pulmonary hypertension and reduced exercise tolerance in SO2 exposed mice. Further, we used pharmacologic and genetic approaches to demonstrate a critical role for oxidative stress and isolevuglandins in mediating PVD in this model. In summary, our results indicate that repetitive SO2 exposure recapitulates many aspects of PDRS and that oxidative stress may mediate PVD in this model, which may be helpful for future mechanistic studies examining the relationship between inhaled irritants, PVD, and PDRS.

pathology↗

bioRxiv2023

ScRNA-seq of Diverse Pheochromocytoma Patients Reveals Distinct Microenvironment Characteristics and Supports an Informative Molecular Classification System

Pheochromocytomas (PCCs) are rare neuroendocrine tumors that originate from chromaffin cells in the adrenal gland. However, the cellular molecular characteristics and immune microenvironment of PCCs are incompletely understood. Here, we performed single-cell RNA sequencing (scRNA-seq) on 16 tissues from 4 sporadic unclassified PCC patients and 1 hereditary PCC patient with Von Hippel-Lindau (VHL) syndrome. We found that intra-tumoral heterogeneity was less extensive than the inter-individual heterogeneity of PCCs. Further, the unclassified PCC patients were divided into two types, metabolism-type (marked by NDUFA4L2 and COX4I2) and kinase-type (marked by RET and PNMT), validated by immunohistochemical staining. Trajectory analysis of tumor evolution revealed that metabolism-type PCC cells display phenotype of consistently active metabolism and increased metastasis potential, while kinase-type PCC cells showed decreased epinephrine synthesis and neuron-like phenotypes. Cell-cell communication analysis showed activation of the annexin pathway and a strong inflammation reaction in metabolism-type PCCs and activation of FGF signaling in the kinase-type PCC. Although multispectral immunofluorescence staining showed a lack of CD8+ T cell infiltration in both metabolism-type and kinase-type PCCs, only the kinase-type PCC exhibited downregulation of HLA-I molecules that possibly regulated by RET, suggesting the potential of combined therapy with kinase inhibitors and immunotherapy for kinase-type PCCs; in contrast, the application of immunotherapy to metabolism-type PCCs (with antigen presentation ability) is likely unsuitable. Our study presents a single-cell transcriptomics-based molecular classification and microenvironment characterization of PCCs, providing clues for potential therapeutic strategies to treat PCCs.

cancer biology↗

bioRxiv2023

Long-B prokaryotic Argonaute systems employ various effectors to confer immunity via abortive infection

Argonaute proteins (Agos) bind short nucleic acids as guides and are directed by them to recognize target complementary nucleic acids. Prokaryotic Agos (pAgos) are extremely diverse, with potential functions in microbial defense. The functions and mechanisms of a group of full-length yet inactive pAgos, long-B pAgos, remain enigmatic. Here, we show that most long-B pAgos constitute cell suicide systems together with their various associated proteins, including nucleases, Sir2-domain-containing proteins and trans-membrane proteins, respectively. Among them, the long-B pAgo-nuclease system utilizes an RNA-programmed and target-recognition-activated collateral DNA cleavage activity to sense invaders and kill the infected cells. This results in depletion of the invading plasmid from the cell population. Together, our data indicate that the long-B pAgo systems induce cell death with various effector proteins after recognition of invading nucleic acids, corresponding to an immune response via abortive infection.

microbiology↗