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Yao, Y.

Publications and source records attributed to Yao, Y..

At least 55 records · Page 3Linked to original sources

Protected areas show substantial and increasing risk of wildfire globally

Protected area coverage is set to expand in response to climate change and the biodiversity crisis, but we lack assessments of wildfire incidence in protected areas. Here we quantify bigeographical variation in global patterns of burned area in protected areas. During the twenty-first century, wildfires have burned 2 billion hectares of protected areas - an area the size of Russia and India combined - and, while protected areas only cover 19.2% of semi-natural ecosystems, they concentrate 28.5% of the area burned annually. Wildfire in protected areas increased significantly between 2001-2024 (+0.46% yr-1), even after taking into account increases in protected area (+0.27% yr-1), pointing to a disproportional impact of fire on protected areas under increasingly severe fire weather. This pattern showed marked variation across biomes, with the largest disproportionate increases occurring in fire-prone biomes (e.g. Mediterranean and dry tropical forests, tropical grasslands and xeric shrublands). There were important exceptions to this general trend, and protected area fire was lower than expected in biomes where fire activity is naturally limited by moisture (e.g. tropical rainforests or montane grasslands). Wildfires are important for the health of many ecosystems, and such values of burned area will not always mean a negative outcome. Amidst concerted efforts to expand protected area coverage such as the Global Biodiversity Framework, our results highlight the need for new management strategies that address the globally increasing impacts of burned area across protected areas under unabated climate change.

ecology↗

Extracellular Vesicle Gene Expression Enables Sensitive Detection of Colorectal Neoplasia

BACKGROUND & AIMSExtracellular vesicles (EVs), including exosomes, are emerging as promising carriers of disease-specific biomarkers due to their molecular cargo reflective of cellular origin. While cell-free DNA (cfDNA) methylation assays have recently been developed for colorectal cancer (CRC) screening and perform well for cancer detection, they show limited sensitivity for advanced adenomas (AA), a key precursor in the CRC pathway. To address this gap, we sought to determine whether other blood-based analytes, specifically EV-derived long and small RNA transcriptomes and EV proteomes, could improve detection of AA and early-stage CRC. In a prospective cohort, we performed a head-to-head comparison of EV transcriptomics, EV proteomics, and their combinations against cfDNA methylation, all measured from the same patient cohort, enabling a direct performance benchmark and identification of the most promising modality for larger-scale CRC screening studies. METHODSWe prospectively collected pre-colonoscopy plasma samples from 220 participants across three clinical sites. EVs were isolated and profiled using long RNA-seq, small RNA-seq, and Olink-based proteomics. cfDNA was analyzed for methylation patterns. Analyses were conducted according to a statistical analysis plan pre-specified before unblinding. Machine learning models were developed under nested cross-validation to evaluate sensitivity for detecting AA and CRC at a fixed specificity of 91%, consistent with clinical screening benchmarks. RESULTSEV-derived gene expression on long RNA demonstrated the highest sensitivity for detecting AA as well as CRC: 54.8% (95% CI, 26.4%-75.6%) for AA and 94.1% (95% CI, 79.2%-100%) for CRC. This outperformed cfDNA methylation (33.6% [95% CI, 9.7%-60.3%] for AA, 81.3% [95% CI, 64.6%- 93.9%] for CRC) and other EV-based modalities. In addition, for small RNA the sensitivities were 42.6% (95% CI, 35.9%-47.4%) for AA, and 78.9% (95% CI, 69.2%-83.0%) for CRC, while for proteomics the sensitivities were 30.0% (95% CI, 13.9%-40.0%) for AA, and 64.2% (95% CI, 43.6%-87.2%) for CRC. Transcriptomic profiles revealed progressive enrichment of hallmarks of cancer pathways, including apoptosis and epithelial-mesenchymal transition, across disease stages. Multiomic integration did not improve performance beyond EV transcriptomics alone. CONCLUSIONSBy directly comparing multiple EV-based and cfDNA analytes within the same patient cohort, we found that EV transcriptomics delivers the strongest diagnostic performance for both AA and CRC. This rigorous benchmarking approach allows clear prioritization of the most promising modality guiding the design of larger validation studies and accelerating development of next-generation, blood-based CRC screening tools.

genomics↗

HomRank: Homogeneous RNA Ranking for 3D Structure Evaluation

Leveraging rigorously curated RNA sequences and a novel ranking-based evaluation paradigm, we propose an improved pipeline for RNA 3D structure assessment. To enhance generalization, we construct a dataset comprising non-redundant single-chain RNA sequences from the PDB and apply unsupervised clustering to minimize data leakage. Based on this, we retrain the previous state-of-the-art method, ARES, to develop ARES+, which improves the top-1 success rate by 21% on the RNA Puzzles benchmark. To further boost near-native identification, we introduce HomRank, a homogeneous RNA ranking method that directly optimizes the selection of near-native conformations from candidate sets, resembling expert evaluation strategies. HomRank achieves 95% and 100% top-1 and top-5 success rates, respectively, significantly outperforming ARES+. These results demonstrate that carefully designed datasets and the expert-like selection paradigm can substantially improve the accuracy and robustness of RNA 3D structure assessment, offering a promising direction for deep learning-based RNA evaluation and near-native conformation selection.

bioinformatics↗

Intracranial Insights into the Developing Neural Basis of Moral Punishment

Third-party punishment (TPP) is a critical component of social regulation and justice, in-tegrating moral reasoning and emotional salience. However, the neural developmental basis underpinning this complex process remains largely unknown. Using rare intracranial stereo-electroencephalography (SEEG) in 14 children and 17 adults, we investigated the developing neural circuits of TPP. We found that broad-band gamma activity in the amygdala and ventromedial prefrontal cortex (vmPFC) encodes inferred intentions, with different patterns across age groups. Furthermore, the vmPFC, insula, and inferior parietal lobule (IPL) integrate punishment efficacy, also showing significant developmental differences. Combining task and resting state functional connectivity analyses, we further found age-dependent interactions among the amygdala-insula and IPL-vmPFC neural couplings during decision-making. These findings provide valuable intracranial evidence that the maturation of moral decision-making stems from the developmental refinement of subcortical-cortical circuits that integrate emotional and cognitive evaluations, explaining the shift from intuitive decisions in children to context-sensitive judgments in adults.

neuroscience↗

Palmitoylation-dependent activation of NADK promotes NADP+ synthesis and tumorigenesis

NAD kinase (NADK) is the sole cytosolic enzyme that catalyzes the synthesis of nicotinamide adenine dinucleotide phosphate (NADP+) from NAD+. NADP+ is essential for anabolic reactions and redox balance. Here, we show that palmitate facilitates NADP+ synthesis by enhancing NADK palmitoylation and activity. NADK is post-translationally S-palmitoylated on three cysteine residues (Cys22, Cys23, and Cys26) within the amino-terminal domain by the protein-acyl transferase ZDHHC5, which stimulates NADK activity. Fatty acids activate NADK by enhancing its palmitoylation and relief of an autoinhibitory function inherent to its amino terminus. Furthermore, ZDHHC5-/- mice showed defect in NADK palmitoylation and NADP+ production. Clinically, elevated expression of ZDHHC5 in pancreatic cancer patients was associated with increased NADK palmitoylation and correlated with poor prognoses for patients. These data reveal that fatty-acid and ZDHHC5-mediated palmitoylation has a critical role in NADP+ synthesis and cancers.

cancer biology↗

FLEXTAG: A Small and Self-renewable Protein Labeling System for Anti-fading Multi-color Super-resolution Imaging

Super-resolution fluorescence imaging enables visualization of subcellular structures and molecular interactions at the nanoscale, but its broader application has been hindered by long-standing limitations in current protein tagging systems, including rapid photobleaching, tag-induced artifacts, poor post-fixation labeling efficiency, and restricted multiplexing capability. Here, we present FLEXTAG (Fluorescent Labeling for Exchangeable, X-resilient Tagging in Advanced Generic Nanoscopy), a comprehensive protein labeling system comprising three orthogonal, ultrasmall (12-18 kDa), and self-renewable protein tags that collectively overcome these major limitations of existing tagging systems, enabling optimized multi-color super-resolution imaging. Through continuous exchange of organic fluorophores, FLEXTAG supports unprecedented durations of high-resolution imaging in both live and fixed cells with minimal photobleaching. It is compatible with major super-resolution modalities, such as SIM, STED, STORM, and PAINT, and is applicable to a wide range of subcellular targets. To further address fixation-induced labeling inefficiency and background fluorescence, we developed a novel protection-based fixation method and chemical blocking strategies that significantly preserve tag accessibility and enhance signal-to-noise ratio, improvements that are broadly applicable to other protein tagging systems. Altogether, FLEXTAG enables long-term tracking of dynamic behaviors and interactions of subcellular targets, as well as mapping of nanoscale protein organizations and cellular architecture, advancing both basic research and translational applications in cell biology.

bioengineering↗

Spatiotemporal dynamics of questing activity by four tick species in the central Great Plains

In this study, we explore a suite of new ecological niche modeling approaches to illuminate the distributional potential and distributional dynamics of questing individuals of four tick species in the central Great Plains region. Specifically, we improve on typical approaches in distributional ecology by (1) assigning time-specific environmental values to sampling events so that repeated sampling at the same points yields additional information, (2) using both positive and negative records of the species as inputs in model development, and (3) constraining model response shapes in models to resemble the shapes of fundamental ecological niches. Model outcomes demonstrate both seasonal dynamics and differences between species in terms of the geographic potential of questing behavior by Great Plains tick species. These improved approaches in distributional ecology have considerable potential to enrich distributional understanding of vector species distributions.

ecology↗

Granulin+ macrophages promote lineage plasticity in prostate cancer through paracrine signaling loops

The role of tumor-infiltrating immune cells in driving phenotype switching remains unclear, despite the well-established association between lineage transition and drug resistance in prostate cancer. This study employed an integrated analysis of single-cell multiomics to investigate the dynamics of immune infiltration, transcriptional programs, and cell-cell communication in prostate cancer. Our results demonstrated that granulin (GRN) positive macrophages facilitated the transition from adenocarcinoma to a multilineage state with mesenchymal and stem-like traits by activating intra-tumoral NF-{kappa}B signaling. Subsequently, the multilineage clones induced macrophages to highly express granulin through the secretion of CSF1, forming a positive feedback cell communication loop. Next, we validated the biological function of granulin in mediating epithelial-mesenchymal transition in vitro. Additionally, organoids drug resistance assay demonstrated that granulin drove resistance to androgen receptor (AR)-targeted drug (enzalutamide). Moreover, pharmacologic blockade of the CSF-1/CSF-1R axis in TRAMP mouse models reduced the expression of GRN in macrophages and suppressed the formation of multilineage subclones in prostate malignant cells. Furthermore, multiplex immunofluorescence staining of tumor samples from TRAMP mouse models revealed the VIM lineages were spatially in close contact with macrophages. Meanwhile, Cytometry by Time-Of-Flight (CyTOF) analysis validated our findings at single-cell protein level in patients with castration-resistant prostate cancer. Besides, three distinct tumor-infiltrating subsets associated with disease relapse were identified, including DCN+ endothelial cells, CCL7+ fibroblasts, and IFIT1+ neutrophils. These results offer potential therapeutic targets to address lineage plasticity-driven resistance to AR-targeted therapy.

cancer biology↗

Lysosome-like structures in the nucleolus mediate H2Aub degradation under glucose starvation

Glucose starvation leads to the degradation of intracellular proteins to generate amino acids for energy production. However, it remains unclear which proteins undergo rapid degradation to supply amino acids as energy sources during glucose starvation. To investigate the molecular mechanism underlying the transition of carbon source from glucose to proteins under glucose starvation, we first employed quantitative proteomics to examine the impact of glucose deprivation on protein levels. We discovered that histone degradation produces the highest amount of glutamine during glucose starvation. Further investigation revealed that histone H2A undergo degradation in the nucleolus in the form of mono-ubiquitination (H2Aub). The nucleolus contains lysosome-like structures that degrade monoubiquitinated histones, potentially participating in the carbon source shift from glucose to amino acids for energy production. Through preliminary screening, we identified Midnolin as the receptor for H2Aub, mediating its degradation in nucleolar lysosome-like structures. Dysregulation of carbon source transition from glucose to proteins, through knockdown of Midnolin results in cell cycle arrest, affecting cellular growth and proliferation. In conclusion, our findings demonstrate that nucleolar lysosome-like structures degrading monoubiquitinated histones exist during glucose starvation, which may play crucial roles in the carbon source transition from glucose to proteins, providing new potential therapeutic targets for metabolic disorders.

cell biology↗

Epithelial state-transitions permit inflammation-induced tumorigenesis.

Chronic inflammation across tissues is associated with an increased risk of developing cancer1-3. While potentially oncogenic somatic mutations have been demonstrated to persist and expand in healthy organs4-6, what triggers a subset of cells harbouring deleterious mutations to transition into a neoplasm or an aggressive adenoma with poor prognosis7,8 is not well-understood. Unlike normal, healthy cells, benign cells harbouring mutations perceive inflammation in chronic disease differently, potentiating the progression from physiological inflammation to tumorigenesis9. Here, we reveal that a subset of epithelial cells with mutations are poised to transition from pre-neoplastic state to early neoplasm, through rewiring of epithelial IL-1{beta} responses and inflammatory macrophage recruitment. We characterise this process by leveraging a mouse model of biliary tract cancer (cholangiocarcinoma), in which deleterious mutations are introduced to tumour suppressor genes in common cancer pathways (Trp53 and Pten), and by quantifying differences in cell states and corresponding gene expression dependencies in the absence or presence of liver inflammation. Critically, we find that targeting the epithelial-derived signals of tissue-wide inflammation (namely COX2) is insufficient to limit tumorigenesis; rather, targeting the reactivation of oncogene-induced developmental signals, such as NOTCH, prevents this pre-neoplastic to neoplastic transition, demonstrating that oncofoetal switching is a pharmacologically-tractable target in patients with a high risk of developing cancers on the background of inflammation.

cancer biology↗

Cryo-EM Structure of the Erlin1/2 Complex Reveals a Dynamic Scaffold for Membrane Protein Sequestration and Microdomain Assembly

The SPFH (Stomatin, Prohibitin, Flotillin, and HflK/C) family of proteins are key scaffolding components involved in the organization of functional membrane microdomains (FMMs) across various subcellular membranes, including those of the endoplasmic reticulum (ER) and mitochondria, which are characterized by a low content of saturated lipids. Among this protein family, the erlin1/2 complex is specifically located on the ER membrane. Previous studies have shown that the erlin1/2 complex plays an essential role in the ER-associated degradation (ERAD) pathway, mediating the ubiquitin-dependent degradation of various proteins such as inositol 1,4,5-trisphosphate receptors (InsP3Rs), which are important calcium ion transporters on the ER membrane. However, the molecular mechanisms underlying erlin-mediated FMMs organization and its role in ERAD remain poorly understood. In this study, we determined the single-particle cryo-electron microscopy (cryo-EM) structure of the erlin1/2 complex under different detergent conditions. Our findings reveal that the erlin1/2 complex forms a 26-mer cage-like structure, composed of alternating erlin1 and erlin2 subunits. The erlin1/2 complex defines a nanodomain on the ER membrane, which could recruit various types of proteins to both the interior and exterior membrane regions of the cage. By caging cargo proteins, the erlin1/2 complex physically secludes them from their binding partners, leading to a potential halt in their function. Moreover, individual cages can further interact with one another, facilitating the organization of FMMs of different sizes on the ER membrane. These dynamic properties may play a general and critical role in various processes occurring on the ER, including viral replication, positioning the erlin1/2 complex as a promising new target for antiviral drug development.

biophysics↗

Type-I interferon priming signal balances anti-bacterial and anti-tumor trained immunity in alveolar macrophages

Tissue-resident macrophages may be trained to confer enhanced response to heterologous re-stimulation, and thus foster versatile trained immunity (TI) against both infections and tumors. However, key priming signals that contribute to such functional versatility in trained macrophages remain not fully understood. Here we show that influenza A virus (IAV) infection in mice induces lasting transcriptional imprints of acute type-I interferon (IFN-I) signaling in lung-resident alveolar macrophages (AMs) that confer balanced anti-bacterial and anti-tumor TI responses. In both IAV-infected mice and an ex vivo cytokine-mediated training system, IFN-I signaling is found to be critical to developing anti-tumor TI functions, although it limits anti-bacterial TI functions in AMs. Moreover, human AMs carrying transcriptional imprints of IFN-I signaling are associated with anti-tumor immunity and immune activation in lung cancer tissues. Our findings highlight IFN-I as a key priming signal required to developing versatile TI functions in AMs with balanced anti-bacterial and anti-tumor potential.

immunology↗

BioLogical: a universal analysis framework for biosystem logical dynamic

Complex biosystems exhibit ordered, functional, self-organized features. How-ever, a universal framework for exploring their logical paradigms and dynamic characteristics remains lacking. Here we describe BioLogical, a user-friendly R package, designed for analyzing properties of biosystems. We demonstrate its versatile capacities of deciphering multi-valued logical paradigms, calculating order parameters, and simulating system dynamic, even multi-valued Quine-McCluskey and logical satisfiability analysis. The open-source software is available at https://github.com/YuxiangYao/BioLogical.

systems biology↗

CSFeatures improves identification of cell type-specific differential features in single-cell and spatial omics data

Recent advancements in single-cell and spatial omics have enabled the analysis of gene expression patterns in cells and tissues with unprecedented precision. Genes that exhibit significant variation across different cell types or states are typically closely linked to cellular functional states and disease processes. However, current differential analysis methods often fail to adequately account for cell type specificity when identifying differentially expressed genes. CSFeatures effectively addresses this issue by comprehensively considering the expression level, the smoothness of expression distribution, and the proportion of gene expression in the target cell population as well as in each of the other cell populations. Through comprehensive experiments on eight single-cell RNA-seq datasets, it was demonstrated that CSFeatures can effectively identify cell type-specific genes that are highly expressed in the target cell population while being lowly expressed in all other populations. Moreover, it was validated that the underlying principle of CSFeatures can be generalized to other omics data, including single-cell ATAC-seq, spatial transcriptomics, and spatial ATAC-seq data. Furthermore, the differential features identified by CSFeatures are enriched in pathways, functional categories, and regulatory regions that are highly relevant to the specific functional states of the target cell population, providing insights into its gene regulation.

bioinformatics↗

Fat-rich diet reprograms intrapulmonary neutrophils to boost tissue-specific antitumor immunity

Neutrophils adapt to tissue-specific signals and exert innate defense functions against infections and malignancies. Fat-rich diet (FRD), such as high-fat diet (HFD) and ketogenic diet (KD), has complex impacts on immunity. However, whether and how FRD shapes tissue-specific functions of neutrophils remain unclear. Here we show that both isocaloric HFD- and KD-fed mice demonstrate enhanced neutrophil-mediated pulmonary tumor resistance than chow diet-fed mice. Intrapulmonary but not systemic neutrophils in FRD-fed mice bear enhanced potential of reactive oxygen species (ROS) production and ROS-dependent tumor cytotoxicity. Mechanistically, FRD-induced increased serum saturated fatty acids and cholesterol stimulate lung vascular endothelial cells (LVECs), which reprogram intrapulmonary neutrophils via contact- and intercellular adhesion molecule-1 (ICAM-1)-dependent mechanisms. Analysis on human lung single-cell RNA sequencing data showed that intensified cell adhesion and priming signals from human LVECs are associated with enhanced antitumor functions in intrapulmonary neutrophils. Our findings highlight the roles of dietary fats in shaping neutrophil functions in a tissue-specific manner. Dietary intervention targeting tissue-specific reprogramming of neutrophils therefore represents a potential strategy against malignancies in the lungs.

immunology↗

HUWE1 stimulates mTORC1 activity by enhancing Rheb interaction with mTORC1 and supports de novo pyrimidine synthesis

mTORC1 is a central regulator of cell growth that is directly activated by the small GTPase Rheb on the lysosomal membrane in response to growth factors. We recently reported that polyubiquitinated Rheb facilitates its interaction with mTORC1, leading to mTORC1 activation. However, the molecular mechanisms underlying the ubiquitination of Rheb and its interaction with mTORC1 for activation are not fully understood. In this study, we demonstrate that HUWE1, an E3 ubiquitin ligase, preferentially interacts with ubiquitinated Rheb and is essential for the interaction between Rheb and mTOR, as well as for mTORC1 activation. Additionally, HUWE1 is necessary for Rheb to interact with CAD, a crucial enzyme involved in de novo pyrimidine biosynthesis, and for its activation through the mTORC1-S6K1 pathway. Knocking down HUWE1 in cultured cells or in the liver tissues of mice inhibits mTORC1 activity without affecting the phosphorylation of Akt or TSC2, nor does it affect the lysosomal localization of TSC2 or mTORC1. Furthermore, HUWE1 specifically enhances the expression of CAD without influencing other enzymes involved in de novo pyrimidine synthesis and maintains UMP levels in the hepatocytes of liver tissues. These findings indicate that HUWE1 serves as a key organizer of the Rheb ubiquitin complex, amplifying mTORC1 activity and playing a vital role in stimulating de novo pyrimidine synthesis by enhancing CAD expression and activity. HighlightsO_LIHUWE1 and CAD preferentially interact with ubiquitinated Rheb. C_LIO_LIHUWE1 further ubiquitinates Rheb and supports Rheb interaction with mTORC1 and CAD. C_LIO_LIHUWE1 stimulates mTORC1 activity through its E3 ligase activity. C_LIO_LIHUWE1 also supports pyrimidine synthesis by enhancing CAD expression. C_LI

biochemistry↗

Tissue scarring provides a biomechanical framework to promote mammalian bile duct regeneration through the activation of integrin-SRC/FAK signalling.

Following chronic injury, the adult mammalian bile duct regenerates by forming new branches, essentially replumbing the ductular system to overcome blockages and breaks. To regenerate effectively, biliary epithelial cells (BECs) receive a range of pro-mitogenic signals from myofibroblasts, which concurrently deposit a collagen-rich scar around the duct as it regrows. Despite epithelial regeneration and scarring occurring side-by-side, whether the deposition of scar tissue regulates ductular regeneration per se remains unclear. By inducing ductular fibrosis and regeneration in vivo, we show that the formation of collagen-I-rich scars around regenerating ducts changes the local biomechanical properties of these tissues, promoting the growth of ducts. Critically, this changing structural landscape is perceived by a spatially restricted population of biliary epithelial cells which forms a "leading-tip" of integrin-2-high cells. This leading-tip undergoes partial-EMT-type reprogramming, allowing it to become migratory and coordinate ductular regeneration. We show that this process is directly driven through an integrin-2-SRC/FAK signalling axis; thereby connecting epithelial regeneration directly to the changing fibrotic environment in chronic ductular disease. HighlightsO_LIChronic liver disease results in the formation of stiff, collagen scars around ducts. C_LIO_LINew ducts acquire high levels of integrin-2 which is spatially localised to a "leading-tip", which loses epithelial features. C_LIO_LIIntegrin-2{beta}1-SRC/FAK signalling regulates ductular migration by linking changes in the bio-structural composition of the liver with ductular cells. C_LI

cell biology↗

Effect Of Perinatal Perfluorinated Compounds (PFASs) Exposure On Behavior Of SD Rats

Perfluorinated compounds (PFASs) are persistent environmental pollutants recognized for their bioaccumulation and potential neurotoxic effects, particularly in relation to attention deficit hyperactivity disorder (ADHD). This study investigated the effects of perinatal PFAS exposure on Sprague-Dawley (SD) rats, with a focus on behavioral outcomes and dopamine metabolism in the prefrontal cortex (PFC). Pregnant rats were administered PFASs at concentrations of 1 mg/L, 3 mg/L, and 10 mg/L through drinking water during gestation and lactation, with a control group included for comparison. The offspring were subjected to behavioral assessments, including open field, marble burying, and jump tests, to evaluate locomotor activity, attention, and impulsivity. Neurochemical analyses were conducted to measure the expression of tyrosine hydroxylase (TH), aromatic L-amino acid decarboxylase (DDC), and dopamine receptor D1 (Drd1) in the PFC using Western blotting and quantitative PCR (qPCR). The results indicated that high-dose PFAS exposure (10 mg/L) resulted in hyperactivity, attention deficits, and impulsive behavior (p < 0.05), along with decreased TH and DDC expression and altered Drd1 levels, suggesting disrupted dopamine metabolism. These findings imply that perinatal PFAS exposure leads to behavioral abnormalities and disruptions in dopamine-related processes.

animal behavior and cognition↗