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Single-cell omics: experimental workflow, data analyses and applications

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Science China Life Sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin wang Xin Dong Bin Duan Feiyang Xing jun wu Minmin Xiao Fangqing Zhao jing-Dong j.Han Qi Liu Xiaohui Fan Chen Li Chenfei wang Tieliu Shi Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

双能CT动脉增强分数对甲状腺乳头状癌颈部淋巴结转移术前诊断的附加价值：初步研究结果

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国际医学放射学杂志 2024年第2期 256页

作者： Y.Zhou Y.K.Xu D.Geng j.w.wang X.B.Chen Y.Si 王俊

摘要目的探讨双能CT(DECT)的动脉增强分数（AEF）在术前诊断甲状腺乳头状癌（PTC）颈部淋巴结转移中的附加价值，并与传统的CT影像特征进行比较。方法本研究从92

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Treating amyotrophic lateral sclerosis with allogeneic Schwann cell-derived exosomal vesicles: a case report

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Neural Regeneration Research 2025年第4期20卷 1207-1216页

作者： Pascal j.Goldschmidt-Clermont Aisha Khan George jimsheleishvili Patricia Graham Adriana Brooks Risset Silvera Alexander j.P.Goldschmidt Damien D.Pearse w.Dalton Dietrich Allan D.Levi james D.Guest Miller School of Medicine University of MiamiMiamiFLUSA Stem Cell Institute Miller School of MedicineUniversity of MiamiMiamiFLUSA The Miami Project to Cure Paralysis Miller School of MedicineUniversity of MiamiMiamiFLUSA Alzady International LLC MiamiFLUSA Neurological Surgery Miller School of MedicineUniversity of MiamiMiamiFLUSA

Schwann cells are essential for the maintenance and function of motor neurons,axonal networks,and the neuromuscular *** amyotrophic lateral sclerosis,where motor neuron function is progressively lost,Schwann cell function may also be ***,important signaling and potential trophic activities of Schwann cell-derived exosomal vesicles have been *** case report describes the treatment of a patient with advanced amyotrophic lateral sclerosis using serial intravenous infusions of allogeneic Schwann cell-derived exosomal vesicles,marking,to our knowledge,the first instance of such *** 81-year-old male patient presented with a 1.5-year history of rapidly progressive amyotrophic lateral *** initial diagnosis,the patient underwent a combination of generic riluzole,sodium phenylbutyrate for the treatment of amyotrophic lateral sclerosis,and *** patient volunteered to participate in an FDA-approved single-patient expanded access treatment and received weekly intravenous infusions of allogeneic Schwann cell-derived exosomal vesicles to potentially restore impaired Schwann cell and motor neuron *** confirmed that cultured Schwann cells obtained from the amyotrophic lateral sclerosis patient via sural nerve biopsy appeared impaired(senescent)and that exposure of the patient’s Schwann cells to allogeneic Schwann cell-derived exosomal vesicles,cultured expanded from a cadaver donor improved their growth capacity in *** a period of observation lasting 10 weeks,during which amyotrophic lateral sclerosis Functional Rating Scale-Revised and pulmonary function were regularly monitored,the patient received weekly consecutive infusions of 1.54×1012(×2),and then consecutive infusions of 7.5×1012(×6)allogeneic Schwann cell-derived exosomal vesicles diluted in 40 mL of Dulbecco’s phosphate-buffered *** of the infusions were associated with adverse events such as infusion reactions(allergic or otherwise)or

关键词： allogeneic amyotrophic lateral sclerosis exosomes infusion neuromuscular junction Schwann cell

Satellite remote sensing reveals overwhelming recovery of forest from disturbances in Asia

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Atmospheric and Oceanic Science Letters 2025年第1期18卷 46-51页

作者： Yiying Zhu Hesong wang Anzhi Zhang School of Ecology and Nature Conservation Beijing Forestry UniversityBeijingChina Key Laboratory of Regional Climate and Environment for Temperate East Asia Institute of Atmospheric PhysicsChinese Academy of SciencesBeijingChina College of Forestry and Landscape Architecture Xinjiang Agricultural UniversityUrumqiChina

Forest ecosystems play key roles in mitigating human-induced climate change through enhanced carbon uptake;however,frequently occurring climate extremes and human activities have considerably threatened the stability of *** the same time,detailed accounts of disturbances and forest responses are not yet well quantified in *** study employed the Breaks For Additive Seasonal and Trend method-an abrupt-change detection method-to analyze the Enhanced Vegetation Index time series in East Asia,South Asia,and Southeast *** approach allowed us to detect forest disturbance and quantify the resilience after *** showed that 20%of forests experienced disturbance with an increasing trend from 2000 to 2022,and Southeast Asian countries were more severely affected by ***,95%of forests had robust resilience and could recover from disturbance within a few *** resilience of forests suffering from greater magnitude of disturbance tended to be stronger than forests with lower disturbance *** summary,this study investigated the resilience of forests across the low and middle latitudes of Asia over the past two *** authors found that most forests exhibited good resilience after disturbance and about two-thirds had recovered to a better state in *** findings of this study underscore the complex relationship between disturbance and resilience,contributing to comprehension of forest resilience through satellite remote sensing.

关键词： Forest ecosystem Enhanced vegetation index Breaks for additive seasonal and trend method Disturbance Resilience

Pyroptosis,ferroptosis,and autophagy in spinal cord injury:regulatory mechanisms and therapeutic targets

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Neural Regeneration Research 2025年第10期20卷 2787-2806页

作者： Qingcong Zheng Du wang Rongjie Lin weihong Xu Department of Spinal Surgery the First Affiliated Hospital of Fujian Medical UniversityFuzhouFujian ProvinceChina Arthritis Clinical and Research Center Peking University People’s HospitalBeijingChina Department of Orthopedic Surgery Fujian Medical University Union HospitalFuzhouFujian ProvinceChina

Regulated cell death is a form of cell death that is actively controlled by *** studies have shown that regulated cell death plays a key role after spinal cord *** and ferroptosis are newly discovered types of regulated cell deaths that have been shown to exacerbate inflammation and lead to cell death in damaged spinal ***,a complex form of cell death that is interconnected with various regulated cell death mechanisms,has garnered significant attention in the study of spinal cord *** injury triggers not only cell death but also cellular survival *** signaling pathways play pivotal roles in influencing the processes of both deterioration and repair in spinal cord injury by regulating pyroptosis,ferroptosis,and ***,this review aims to comprehensively examine the mechanisms underlying regulated cell deaths,the signaling pathways that modulate these mechanisms,and the potential therapeutic targets for spinal cord *** analysis suggests that targeting the common regulatory signaling pathways of different regulated cell deaths could be a promising strategy to promote cell survival and enhance the repair of spinal cord ***,a holistic approach that incorporates multiple regulated cell deaths and their regulatory pathways presents a promising multi-target therapeutic strategy for the management of spinal cord injury.

关键词： autophagy cell death ferroptosis inflammation pathological mechanisms pyroptosis regulated cell death regulatory pathways spinal cord injury therapeutic targets

Anomaly Detection of Controllable Electric Vehicles through Node Equation against Aggregation Attack

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Computers, Materials & Continua 2025年第1期82卷 427-442页

作者： jing Guo Ziying wang Yajuan Guo Haitao jiang State Grid jiangsu Electric Power Co. Ltd.Research InstituteState Grid Corporation of ChinaNanjing211100China

The rapid proliferation of electric vehicle(EV)charging infrastructure introduces critical cybersecurity vulnerabilities to power grids *** study presents an innovative anomaly detection framework for EV charging stations,addressing the unique challenges posed by third-party aggregation *** approach integrates node equations-based on the parameter identification with a novel deep learning model,xDeepCIN,to detect abnormal data reporting indicative of aggregation *** employ a graph-theoretic approach to model EV charging networks and utilize Markov Chain Monte Carlo techniques for accurate parameter *** xDeepCIN model,incorporating a Compressed Interaction Network,has the ability to capture complex feature interactions in sparse,high-dimensional charging *** results on both proprietary and public datasets demonstrate significant improvements in anomaly detection performance,with F1-scores increasing by up to 32.3%for specific anomaly types compared to traditional methods,such as wide&deep and DeepFM(Factorization-Machine).Our framework exhibits robust scalability,effectively handling networks ranging from 8 to 85 charging ***,we achieve real-time monitoring capabilities,with parameter identification completing within seconds for networks up to 1000 *** research contributes to enhancing the security and reliability of renewable energy systems against evolving cyber threats,offering a comprehensive solution for safeguarding the rapidly expanding EV charging infrastructure.

关键词： Anomaly detection electric vehicle aggregation attack deep cross-network

Design of a cationic accelerator enabling ultrafast ion diffusion kinetics in aqueous zinc-ion batteries

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journal of Energy Chemistry 2025年第1期100卷 377-384页

作者： Yawei Xiao Qianqian Gu Haoyu Li Mengyao Li Yude wang National Center for International Research on Photoelectric and Energy Materials School of Materials and Energy Yunnan University Key Laboratory of Ministry of Education for Advanced Materials in Tropical Island Resources School of Chemistry and Chemical Engineering Hainan University College of Chemical Engineering Fuzhou University Yunnan Key Laboratory of Carbon Neutrality and Green Low-carbon Technologies Yunnan University

Aqueous zinc-ion batteries are highly favored for grid-level energy storage owing to their low cost and high safety,but their practical application is limited by slow ion *** address this,a strategy has been developed to create a cation-accelerating electric field on the surface of the cathode to achieve ultrafast Zn2+diffusion *** employing electrodeposition to coat MoS2on the surface of BaV6O16·3H2O nanowires,the directional built-in electric field generated at the heterointerface acts as a cation accelerator,continuously accelerating Zn2+diffusion into the active *** optimized Zn2+diffusion coefficient in CC@BaV-6O16·3H2O@MoS2(7.5×10～8cm2s-1) surpasses that of most reported V-based ***,MoS2serving as a cathodic armor extends the cycling life of the Zn-CC@BaV6O16·3H2O@MoS2full batteries to over 10000 *** work provides valuable insights into optimizing ion diffusion kinetics for high-performance energy storage devices.

关键词： Zinc alloys

Human neural stem cell-derived extracellular vesicles protect against ischemic stroke by activating the PI3K/AKT/mTOR pathway

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Neural Regeneration Research 2025年第11期20卷 3245-3258页

作者： jiayi wang Mengke Zhao Dong Fu Meina wang Chao Han Zhongyue Lv Liang wang jing Liu Stem Cell Clinical Research Center The First Affiliated Hospital of Dalian Medical UniversityDalianLiaoning ProvinceChina Dalian Innovation Institute of Stem Cell and Precision Medicine DalianLiaoning ProvinceChina Institute(College)of Integrative Medicine Dalian Medical UniversityDalianLiaoning ProvinceChina

Human neural stem cell-derived extracellular vesicles exhibit analogous functions to their parental cells,and can thus be used as substitutes for stem cells in stem cell therapy,thereby mitigating the risks of stem cell therapy and advancing the frontiers of stem cell-derived *** lays a foundation for the development of potentially potent new treatment modalities for ischemic ***,the precise mechanisms underlying the efficacy and safety of human neural stem cell-derived extracellular vesicles remain unclear,presenting challenges for clinical *** promote the translation of therapy based on human neural stem cell-derived extracellular vesicles from the bench to the bedside,we conducted a comprehensive preclinical study to evaluate the efficacy and safety of human neural stem cell-derived extracellular vesicles in the treatment of ischemic *** found that administration of human neural stem cell-derived extracellular vesicles to an ischemic stroke rat model reduced the volume of cerebral infarction and promoted functional recovery by alleviating neuronal *** human neural stem cell-derived extracellular vesicles reduced neuronal apoptosis by enhancing phosphorylation of phosphoinositide 3-kinase,mammalian target of rapamycin,and protein kinase B,and these effects were reversed by treatment with a phosphoinositide 3-kinase *** findings suggest that human neural stem cell-derived extracellular vesicles play a neuroprotective role in ischemic stroke through activation of phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin signaling ***,we showed that human neural stem cell-derived extracellular vesicles have a good in vivo safety ***,human neural stem cell-derived extracellular vesicles are a promising potential agent for the treatment of ischemic stroke.

关键词： behavior exosome extracellular vesicles ischemic stroke mammalian target of rapamycin(mTOR) middle cerebral artery occlusion neural stem cells neuronal apoptosis phosphoinositide 3-kinase(PI3K) protein kinase B(AKT)

A surface engineering strategy for the stabilization of zinc metal anodes with montmorillonite layers toward long-life rechargeable aqueous zinc ion batteries

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journal of Energy Chemistry 2025年第1期100卷 94-105页

作者： wenbo wang Ruifeng Xu Xu Zhang Peiyu wang Bao Yang Bingjun Yang juan Yang Kailimai Su Pengjun Ma Yanan Deng Xianfeng Fan wanjun Chen Key Laboratory for Electronic Materials College of Electrical Engineering Northwest Minzu University Resource Chemistry and Energy Materials Research Center State Key Laboratory of Solid Lubrication Lanzhou Institute of Chemical Physics Chinese Academy of Sciences University of Chinese Academy of Sciences Institute for Materials and Processes School of Engineering University of Edinburgh

Rechargeable aqueous zinc-ion batteries （AZIBs） exhibit appreciable potential in the domain of electrochemical energy ***,there are serious challenges for AZIBs,for instance zinc dendrite growth,hydrogen evolution reaction （HER）,and corrosion side ***,we propose a surface engineering modification strategy for coating the montmorillonite （MMT） layer onto the surface of the Zn anode to tackle these issues,thereby achieving high cycling stability for rechargeable *** results reveal that the MMT layer on the surface of the Zn anode is able to provide ordered zincophilic channels for zinc ions migration,facilitating the reaction kinetics of zinc *** functional theory（DFT） calculations and water contact angle （CA） tests prove that MMT@Zn anode exhibits superior adsorption capacity for Zn2+and better hydrophobicity than the bare Zn anode,thereby achieving excellent cycling ***,the MMT@Zn||MMT@Zn symmetric cell holds the stable cycling over 5600 h at 0.5 mA cm-2and 0.125 m A h cm-2,even exceeding 1800 h long cycling under harsh conditions of 5 m A cm-2and 1.25 m A h *** MMT@Zn||V2O5full cell reaches over 3000 cycles at 2 A g-1with excellent rate ***,this surface engineering modification strategy for enhancing the electrochemical performance of AZIBs represents a promising application.

关键词： Hydrogen evolution reaction