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Articles by Ying Cai
ERα–PADI4–CXCL8 Axis Drives MDSC-Mediated Immune Evasion in Anaplastic Thyroid Carcinoma
1 Introduction Thyroid cancer is the most prevalent endocrine malignancy, with its global incidence having risen substantially over the past four decades [1]. While the vast majority of differentiated thyroid cancers—particularly papillary thyroid carcinoma (PTC)—carry an excellent prognosis following standard treatment with surgery, radioactive iodine, and thyroid-stimulating hormone suppression, a small subset of patients develops highly aggressive, undifferentiated disease [2].
Targeting the γ-glutamylcysteine-ferroptosis axis protects diabetic podocytes by dual-regulation of SAT1 and SLC7A11/GPX4
Abstract Diabetic kidney disease (DKD) remains the leading cause of end-stage renal disease worldwide, yet the mechanisms driving its progression are poorly understood. Here, through integrated multi-omics analyses of clinical serum samples and db/db mice, we identified a marked depletion of the glutathione biosynthetic intermediate γ-glutamylcysteine (γ-GC), which demonstrated strong diagnostic potential (AUC = 0.986).
Distributed Adaptive Probabilistic Event-Triggered Filtering for Fuzzy Systems Under Data-Important-Aware DoS Attack
1 Introduction Sensor networks (SNs) consist of spatially distributed smart sensor nodes deployed across specific regions to collaboratively collect, monitor, and process data. Recognized for their flexibility, scalability, and broad applicability in fields like environmental monitoring, industrial automation, and smart infrastructure [1, 2], SNs have attracted significant research interest and demonstrated considerable practical potential.
Paclitaxel prodrug loaded high-density lipoprotein nanoparticles for chemoimmunotherapy of triple-negative breast cancer
Abstract Insufficient tumor-specific immunogenicity and cytotoxic T lymphocytes infiltration limit the therapeutic efficacy of combined chemotherapy and immune checkpoint blockade for triple-negative breast cancer (TNBC). To address this limitation, we developed a paclitaxel prodrug-loaded synthetic high-density lipoprotein nanoparticle (P-sHDL) that both targets tumors and induces immunogenic cell death (ICD) to potentiate immune checkpoint blockade.
Vitamin D status, supplementation, and multiple sclerosis: a systematic review and meta-analysis
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Abstract Background: Multiple sclerosis (MS) is a chronic immune-mediated neurodegenerative disorder of the central nervous system and a leading cause of disability among young adults. The disease exhibits considerable heterogeneity in clinical progression, with some patients experiencing more aggressive disease activity and a rapid decline in quality of life.
By Yanyan Li Verified, Ying Xu, Xiaorui Pei, Ziqi Liu, Dan Gao, Lili Ma, Yan Wang, Yanan Fang, Ying Cai
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Frontiers in Immunology
Atlas of predicted protein complex structures across kingdoms
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Abstract Protein complexes are fundamental to all biological processes. Public repositories have expanded to include millions of potential protein–protein interactions (PPIs) from human and diverse model organisms. Yet, large-scale structural characterization of these complexes—especially across different biological kingdoms—has lagged far behind, leaving most potential and unidentified interactions unresolved.
By Jianqiang Liang, Shimin Wen, Yuanyuan Li, Kai Ding, Junjie Fei, Weian Mao, Zhiyu Lin, Yichong Shen, Hongjie Zhu, Yayun Hu, Rui Zhang, Yafei Lu, Bonan Liu, Han Wang, Yuxuan Chen, Zhenguo Ma, Peiyuan Yang, Xinyu Xu, Junlong Wu, Youyuan Zhu, Wencheng Zhu, Shuya Li, Hongyi Xin, Daji Ergu, Jianyang Zeng, Zhi-Xiong Xiao, Chunhua Shen, Ying Cai, Yong Yi, Dacheng Ma, Xianzhi Qi, Yongfu Hao, Liupeng Li, Pengli Ji, Qiaosha Zou, Kelu Yao
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Nature
Verified
Gut microbiota‐mediated branched‐chain amino acid metabolism: A novel mechanism by which Bacteroides uniformis improves type 2 diabetes mellitus
Corresponding Author Zhiyong Xie PhD School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, China Correspondence Zhiyong Xie, School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, 66 Gongchang Road, Shenzhen, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, 135 Xingang West Road, Guangzhou, China.
Robotic conformal 4D printing of liquid crystal elastomers
Abstract Four-dimensional (4D) printing of liquid crystal elastomers (LCEs) serves as a promising approach to create reversibly shape-changing structures for diverse applications, including soft robotics, deployable systems, and adaptive surfaces. Central to programming these shape transformations is the spatial alignment of microscale liquid crystal mesogens.
Occurrence of major earthquakes is as stochastic as smaller ones
Abstract Seismic hazard estimates rely on interevent time distributions between earthquakes of a given magnitude. In the Himalaya, recurrence intervals are usually modeled as cyclic or quasiperiodic, whereas globally, they range from periodic and clustered to random.
Spatially anion-confined electrolyte enables high-rate and durable anode-free sodium batteries
Abstract Anode-free sodium batteries (AFSBs) with near-theoretical energy density hold great promise for next-generation sustainable energy storage systems. However, their practical implementation is impeded by the low operating rate threshold (<1 milliampere per square centimeter) and poor cycling stability, owing to dendritic sodium (Na) growth. Here, a high-rate and durable AFSB is successfully realized via a spatially anion-confined electrolyte strategy.
YORU: Animal behavior detection with object-based approach for real-time closed-loop feedback
Abstract The advent of deep learning methodologies for animal behavior analysis has revolutionized neuroethology studies. However, the analysis of social behaviors, characterized by dynamic interactions among multiple individuals, continues to represent a major challenge. In this study, we present “YORU” (your optimal recognition utility), a behavior detection approach leveraging an object detection deep learning algorithm.
Genetic legacy and recent cross of two ancient lineages underlie the rebound of the world’s rarest primate
Abstract Despite a recent mass extinction, a few species have bounced back from the brink, but little is known about their intrinsic mechanisms. Hainan gibbons (Nomascus hainanus) feature a mysterious rebound, from ~13 individuals in 2003 to 42 currently.
Unraveling design principles of protein landscapes in photosynthetic membranes in plant chloroplasts
Abstract The supramolecular organization of proteins within photosynthetic membranes is crucial for energy conversion in plants. Here, we introduce an analytical and computational pipeline that integrates high-resolution cryo–scanning electron microscopy, biochemical quantification, advanced Monte Carlo computer simulations, and statistical methods to elucidate the elusive protein landscapes of grana membranes in intact Arabidopsis leaves.
Primate dexterous hand movements are controlled by functionally distinct premotoneuronal systems
Abstract Dexterous hand movements are uniquely developed in primates and indispensable for their daily activities. Traditionally, they were thought to depend primarily on the evolutionarily “newer” direct corticomotoneuronal (CM) pathway. However, recent studies suggest that the “older” indirect corticospinal pathways, mediated by spinal premotor interneurons (PreM-INs), also contribute, highlighting the need to clarify their functional differences.
Membrane-associated periodic skeleton regulates major forms of endocytosis in neurons through a signaling-driven positive feedback loop
Abstract Endocytosis enables neurons to internalize molecules, maintaining homeostasis and responsiveness. The neuronal membrane–associated periodic skeleton (MPS), an actin spectrin–based cytoskeletal lattice, is known to restrict clathrin-mediated endocytosis (CME) in axons, but its broader role in other neuronal compartments and endocytic pathways remains unclear.
Experimental quantum state certification by actively sampling photonic entangled states
Abstract Entangled quantum states are essential ingredients for many quantum technologies, but they must be validated before they are used. As a full characterization is prohibitively resource intensive, recent work has focused on developing methods to efficiently extract a few parameters of interest, in a so-called verification framework.
Halting predicted vertebrate declines requires tackling multiple drivers of biodiversity loss
Abstract Conservation policies aiming to halt biodiversity loss often focus on globally prevalent threats like habitat loss and exploitation, yet direct and interactive effects of multiple threats remain poorly quantified. Here, we go beyond prior meta-analyses or species-level studies by providing a global, population-level empirical analysis of threat interactions by examining 3129 vertebrate population time series worldwide with documented exposure to single and multiple threats.
E711-19 placement and orientation dictate CD8+ T cell response in structurally defined spherical nucleic acid vaccines
Abstract To develop effective nanostructured immunotherapeutics, identifying structural parameters that maximize immune response is essential. Spherical nucleic acids (SNAs) provide a modular platform for coordinated antigen-adjuvant delivery, where subtle structural differences can markedly influence potency. Herein, three SNAs were designed with HLA-A2–restricted HPV16 E711-19 peptide and CpG adjuvant, nearly identical in composition but differing in antigen presentation.
The allosteric landscape of the Src kinase
Abstract Enzymes catalyze the reactions of life and are the targets of many drugs. Most inhibitors bind conserved active sites, frequently lacking specificity. Targeting allosteric sites can increase specificity, reduce toxicity, and allow fine-tuning of activity; however, most allosteric sites in enzymes are unmapped. Here, we present a comprehensive experimental allosteric map of the Src protein kinase.
Deep-sea fish reveal an alternative developmental trajectory for vertebrate vision
Abstract Vertebrate vision relies on two photoreceptor types: cones for bright light and rods for dim light. The current dogma is that vertebrates develop cone-dominated retinas first, adding rods later. Here we show that larval deep-sea fishes have “hybrid” photoreceptors, expressing cone-specific genes in rod-like cells.
Tunable 3D optohydrodynamic torques from optical phase gradient-driven colloidal assemblies
Abstract Optohydrodynamic manipulation offers a versatile, noninvasive, and reconfigurable approach for controlling microscopic objects. Here, we present a strategy for generating tunable three-dimensional optohydrodynamic torques through phase gradient–driven nanoparticle assemblies.
A dual role of Arabidopsis PAL nuclear localization in fine tuning flavonoid biosynthesis
Abstract The phenylpropanoid pathway is essential for plant development and environmental adaptation, producing metabolites such as flavonoids, lignin, and salicylic acid. Phenylalanine ammonia-lyase (PAL) catalyzes the first committed step in this pathway and has long been viewed as a cytoplasmic enzyme. Here, we reveal that PAL responds to elevated flavonoid levels in Arabidopsis by undergoing phosphorylation and relocating to the nucleus.
Magnetoelectric nanoparticles drive TAF9B+ TH2 cell expansion to alleviate inflammation
Abstract Stimuli-responsive nanomaterials represent a promising platform for immunomodulation. However, their application in orchestrating T cell responses remains limited. Here, we develop a biomimetic magnetoelectric nanoparticle (DC@CFO/BFO) by coating core-shell CoFe2O4@BiFeO3 particles with dendritic cell membranes to enable selective targeting of CD4+ T cells.
VapC36-mediated intrinsic stress adaption is required for copper tolerance and pathogenesis of Mycobacterium tuberculosis
Abstract Here, we have used a comprehensive, system-wide approach to delineate the function of the virulence-associated proteins B and C 36 (VapBC36) toxin-antitoxin (TA) system in Mycobacterium tuberculosis pathophysiology. We show that VapC36 interacts with cognate and noncognate antitoxins. We demonstrate that serX is degraded in vitro by VapC36. We show that VapC36 binds copper, which enhances its ribonuclease activity.
Structure-based design of an opioid receptor modulator for enhanced morphine analgesia
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Abstract The alarming rates of deaths due to opioid overdose present an urgent need for safer opioid analgesics. Positive allosteric modulators (PAMs) of opioid receptors (ORs) offer a promising approach to enhance opioid efficacy while reducing risks of overdose.
By Ying Cai, Hayato M YAMANOUCHI, Xian Bing Hou, YUE WANG, Ping Luo, Haiyan Xu, Li Zhan, Kensuke Sakamoto, Mingyu Li, Jing Hui Wang, Xi-Ping Huang, Jianhui Zhou, Tao Liu, Yanrui Suo, Wenjia Fan, Xinheng He, Youwei Xu, Yongjie Cai, Chao Wang, Yuxi Zhao, Antao Dai, Qingning Yuan, Wen Hu, Kai Wu, Yali Lai
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Science Magazine
Verified
Navigating high-dimensional processing parameters in organic photovoltaics via a multitier machine learning framework
Abstract Optimizing organic photovoltaic (OPV) performance requires navigating the high-dimensional, interdependent processing parameters governing bulk heterojunction morphology. To address this, we have constructed a standardized database integrating donor/acceptor pairs, nine key fabrication parameters, and device efficiencies, consolidating over a decade of experimental results.
VMAT2 dysfunction impairs vesicular dopamine uptake, driving its oxidation and α-synuclein pathology in DJ-1-linked Parkinson’s neurons
Abstract Parkinson’s disease (PD) is characterized by α-synuclein accumulation and dopaminergic neuron degeneration, with dopamine (DA) oxidation emerging as a key pathological driver. However, the mechanisms underlying this neurotoxic process remain unclear.
Matrix-bound nanovesicles as epigenetic modulators of myeloid cells
Abstract Extracellular vesicles (EV) represent a conserved and highly efficient mechanism for cell-to-cell communication. Matrix-bound nanovesicles (MBV) are a recently identified type of EV embedded within the extracellular matrix with potent local and systemic immunomodulatory effects on myeloid cells. These effects are durable and last beyond the predicted life span of differentiated myeloid cells such as macrophages.
Silencer variants are key drivers of gene up-regulation in Alzheimer’s disease
Abstract The genetic mechanisms of ~90% of Alzheimer’s disease (AD)–associated variants residing in noncoding DNA remain poorly understood. To address this, we developed a deep learning framework that integrates bulk histone modification data with single-cell open chromatin profiles to evaluate the regulatory potential of noncoding variants.
Chiral hinge-surface transport across dimensions in three-dimensional magneto-optical topological materials
Abstract Chiral boundary states with perfect conducting channels are essential characteristics of magnetic topological materials. Prominent examples include the one-dimensional (1D) chiral edge and 2D chiral surface states found in 2D and 3D quantum Hall materials under magnetic fields, respectively. However, these boundary states are restricted to specific fixed dimensions, so they hardly facilitate cross-dimensional energy and information transport.
Octopamine and tyramine dynamics predict learning rate phenotypes during associative conditioning in honey bees
Abstract Biogenic amines are fundamental for physiological homeostasis and behavioral control in both vertebrates and invertebrates. Monoamine neurotransmitters released in target brain regions conjointly regulate adaptive learning and plasticity. However, our understanding of these multianalyte mechanisms remains nascent, in part due to limitations in measurement technology.
Circular RNA circHomer1 mediates hippocampal functions via ribonucleoprotein granule transport and dendritic targeting of synaptic RNAs
Abstract Circular RNAs are backspliced, closed-loop RNAs previously believed to be noncoding by-products formed during transcription. Increasing evidence suggests that circular RNAs have crucial functions in the brain, such as regulating neuronal transmission and synaptic plasticity. However, the specific molecular mechanisms by which circular RNAs function remain largely unexplored.
Lunar chronology model with the Chang’e-6 farside samples and implications for the early impact history
Abstract The radiometric ages of the returned samples are the cornerstone of lunar cratering chronology models. However, all the previous samples were from the lunar nearside and the radiometric ages of those samples that can be associated with particular surfaces are <4.0 billion years. On 25 June 2024, Chang’e-6 successfully returned 1.935-kilogram samples from the lunar farside.
Supreme People’s Court sets fresh rules for protecting data IP rights in China
In August 2025, the Supreme People's Court released the 47th batch of guiding cases, setting precedent for the judicial protection of data rights in China. For the first time, the court dedicated six guiding cases exclusively to data-related disputes, offering point of reference in this rapidly evolving field. These cases address recurring controversies in practice, seeking to balance the interests of data owners, processors and users.
The metformin mediated MAPK signaling pathway influences D-Xylose regulation during diabetic kidney disease therapy - Communications Medicine
Abstract Diabetic kidney disease (DKD) is a major cause of end-stage renal disease. Although metformin is widely prescribed, the mechanisms underlying its renoprotective effects remain incompletely understood. We integrated multi-omics approaches—including network pharmacology, phosphoproteomics, and targeted metabolomics—in both db/db mice (male) and human patients.
Single-stranded DNA-binding proteins are essential components of the architectural LDB1 protein complex
Keywords LDB1 single-stranded DNA-binding protein SSBP3 SSBP2 SSBP4 chromatin looping enhancer-promoter interaction transcription Get full text access Log in, subscribe or purchase for full access. References 1. Furlong, E.E.M. ∙ Levine, M. Developmental enhancers and chromosome topology Science. 2018; 361:1341-1345 2. Zheng, H. ∙ Xie, W. The role of 3D genome organization in development and cell differentiation Nat. Rev. Mol. Cell Biol. 2019; 20:535-550 3. Dekker, J. ∙ Misteli, T.
Single-stranded DNA binding proteins are essential components of the architectural LDB1 protein complex
Abstract Transcriptional enhancers are brought into proximity with promoters via chromatin looping. The architectural transcription cofactor LDB1 facilitates spatial connectivity among enhancers and promoters but whether this occurs through simple dimerization or requires partner molecules is unknown. Here we investigated single-stranded DNA binding proteins (SSBPs), known LDB1 interactors, in regulating LDB1-mediated chromatin looping and transcription.
The effect of lidocaine against sepsis-induced acute lung injury in a mouse model through the JAK2/STAT3 pathway
Citation: Cai Y, Zhang H, Cui L-M, Chen Q, Xie F-J (2025) The effect of lidocaine against sepsis-induced acute lung injury in a mouse model through the JAK2/STAT3 pathway. PLoS One 20(5): e0322653. https://doi.org/10.1371/journal.pone.0322653 Editor: Yong Jiang, Southern Medical University, CHINA Received: July 16, 2024; Accepted: March 25, 2025; Published: May 8, 2025 Copyright: © 2025 Cai et al.
Cryo‐Shocked Tumor‐Reprogrammed Sonosensitive Antigen‐Presenting Cells Improving Sonoimmunotherapy via T Cells and NK Cells Immunity
Conflict of Interest The authors declare no conflict of interest. Supporting Information Filename Description adma202413289-sup-0001-SuppMat.docx15 MB Supporting Information References 1a) , , , , , , , J. Hematol. Oncol. 2022, 15, 121; b) , , , , CA Cancer J. Clin. 2023, 73, 17. 2, , , , Nat. Rev. Clin. Oncol. 2022, 19, 91. 3, , Rep. Pract. Oncol. Radiother. 2022, 27, 3. 4, , , , , , , J. Hematol. Oncol. 2023, 16, 100. 5a) , , , , , , J. Hematol. Oncol. 2022, 15, 28; b) , , , , , Sci. Immunol. 2023, 8, eabq3016.
The noncoding circular RNA circHomer1 regulates synaptic development and experience-dependent plasticity in mouse visual cortex
Abstract Circular RNAs (circRNAs) are a class of closed-loop, single stranded RNAs whose expression is particularly enriched in the brain. Despite this enrichment and evidence that the expression of circRNAs are altered by synaptic development and in response to synaptic plasticity in vitro, the regulation by and function of the majority of circRNAs in experience-dependent plasticity in vivo remain unexplored.
Advancing AAV manufacturing: strategic insights and cost-effective solutions for the future of gene therapies
Thursday 08:00 PST / 11:00 EST / 16:00 GMT / 17:00 CET AAV manufacturing experts are continually seeking innovative technologies and solutions to address the significant hurdles faced in ensuring efficient and cost-effective production of the vectors.
Chemo‐/Regioselective [5+1] Annulation with gem‐Difluoromethylene Allenes for the Assembly of Fluorinated 2H‐Chromenes and Dihydroquinolines
Supporting Information As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Filename Description adsc202401110-s1-SI_1.pdf8.4 MB Supplementary
Conformation Influences Biological Fates of Peptide‐Based Nanofilaments by Modulating Protein Adsorption and Interfilament Entanglement
Conflict of Interest The authors declare no conflict of interest. Supporting Information Filename Description adma202409130-sup-0001-SuppMat.pdf5.8 MB Supporting Information References 1, , Science 2002, 295, 2418. 2a) , , , Nat. Rev. Mol. Cell Biol. 2014, 15, 771; b) , , , , Nat. Rev. Mol. Cell Biol. 2021, 22, 625. 3a) , , Cell 2019, 176, 281; b) , , , Nat. Rev. Microbiol. 2021, 19, 272; c) , , , , , , , Nat. Microbiol. 2021, 6, 617. 4, , Biochem. Biophys. Res. Commun. 1984, 120, 885. 5a) , , , , , , , Nat.
Berberine Mediates Exosomes Regulating the Lipid Metabolism Pathways to Promote Apoptosis of RA-FLS Cells
All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of the article may be reused without permission provided that the original article is clearly cited. For more information, please refer to https://www.mdpi.com/openaccess.
Copper-Catalyzed Benzothiazolyldifluoroalkylation of Arylidenemalonitriles or para-Quinone Methides
1. Introduction The selective introduction of a fluoroalkyl group into biologically active molecules has emerged as a reliable strategy to modulate pharmacological properties in drug discovery and development [1,2,3,4,5,6]. Therefore, establishing new efficient methods for the synthesis of fluoroalkyl-containing compounds is currently a hot topic in the field of synthetic chemistry.
Endo‐Lysosomal Network Disorder Reprograms Energy Metabolism in SorL1‐Null Rat Hippocampus
1 Introduction In 2007, haplotype insufficiency of Sortilin-related receptor 1 (SorL1) was found to increase the risk of Alzheimer's disease (AD).[1] Exome sequencing revealed that SorL1 coding variants are closely associated with early-onset familial AD.[2] Mutations with coding sequence truncation occurred exclusively in AD patients,[2, 3] confirming the role of SorL1 as a critical protector against AD.
Dose-Response Relationship Between Alcohol Consumption and Gout Risk: Do Subtypes of Alcoholic Beverages Make a Difference?
Key indexing terms: alcohol cohort study gout UK Biobank Gout is one of the most common inflammatory arthritides, characterized by hyperuricemia and with the main clinical manifestation being rapidly evolving extreme pain mostly in 1 joint.1 It was estimated that there were 41 million gout cases worldwide in 2017, and both the prevalence and incidence of gout seem to be rising across the globe.2-4 Further, the age-standardized disability-adjusted life-year rate increased by 2.7% from 2007 to...
SegStitch: Multidimensional Transformer for Robust and Efficient Medical Imaging Segmentation
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