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Advances and applications in single-cell and spatial genomics

Science China Life Sciences 2025年

作者： Jingjing wang Fang Ye Haoxi Chai Yujia Jiang Teng wang Xia Ran Qimin Xia Ziye Xu Yuting Fu Guodong Zhang Hanyu Wu Guoji Guo Hongshan Guo Yijun Ruan yongcheng wang Dong Xing Xun Xu Zemin Zhang Beijing Advanced Innovation Center for Genomics (ICG) Peking University Guangdong Provincial Key Laboratory of Genome Read and Write BGI Research Bone Marrow Transplantation Center of the First Affiliated Hospital & Liangzhu Laboratory Zhejiang University School of Medicine Life Sciences Institute and The Second Affiliated Hospital Zhejiang University BGI Research Biomedical Pioneering Innovation Center (BIOPIC) and School of Life Sciences Peking University Academy for Advanced Interdisciplinary Studies Peking University Institute of Hematology Zhejiang University Department of Laboratory Medicine of The First Affiliated Hospital & Liangzhu Laboratory Zhejiang University School of Medicine Center for Stem Cell and Regenerative Medicine Zhejiang University School of Medicine Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine Dr.Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine

The applications of single-cell and spatial technologies in recent times have revolutionized the present understanding of cellular states and the cellular heterogeneity inherent in complex biological systems. These advancements offer unprecedented resolution in the examination of the functional genomics of individual cells and their spatial context within tissues. In this review, we have comprehensively discussed the historical development and recent progress in the field of single-cell and spatial genomics. We have reviewed the breakthroughs in single-cell multi-omics technologies, spatial genomics methods, and the computational strategies employed toward the analyses of singlecell atlas data. Furthermore, we have highlighted the advances made in constructing cellular atlases and their clinical applications,particularly in the context of disease. Finally, we have discussed the emerging trends, challenges, and opportunities in this rapidly evolving field.

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MicroRNA-214调控骨关节炎软骨和软骨下骨代谢的机制

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中国组织工程研究 2025年第12期29卷 2466-2474页

作者：天生王玺王永成刘亚宁阳鸿全内蒙古科技大学包头医学院研究生院内蒙古自治区包头市014000 广安市广安区人民医院四川省广安市638000 内蒙古医科大学内蒙古自治区呼和浩特市010000 内蒙古自治区人民医院骨科中心内蒙古自治区呼和浩特010000

背景:microRNA-214(miR-214)在骨质疏松中的作用国内外已有相关报道,而miR-214与骨关节炎关节软骨及软骨下骨退变之间的相互关系尚不清楚。目的:探讨miR-214与小鼠膝骨关节炎软骨及软骨下骨退变之间存在的关系。方法:取30只C57BL/6J小... 详细信息

背景:microRNA-214(miR-214)在骨质疏松中的作用国内外已有相关报道,而miR-214与骨关节炎关节软骨及软骨下骨退变之间的相互关系尚不清楚。目的:探讨miR-214与小鼠膝骨关节炎软骨及软骨下骨退变之间存在的关系。方法:取30只C57BL/6J小鼠随机分组:①实验一:分为假手术组和内侧半月板失稳组(n=3),分别进行苏木精-伊红染色和荧光定量PCR检测miR-214基因的表达变化;②实验二:分为假手术组、内侧半月板失稳组、内侧半月板失稳+空载腺病毒组(空载组)、内侧半月板失稳+miR-214拮抗剂过表达腺病毒组(拮抗剂组)(n=6),术后4周各组分别取软骨组织,进行苏木精-伊红、番红O固绿、甲苯胺蓝染色分析;荧光定量PCR、Western blot检测关节软骨中相关因子的表达情况。结果与结论:①实验一中,苏木精-伊红染色结果显示,与假手术组相比,内侧半月板失稳组可见软骨退变;荧光定量PCR检测结果显示,所有样本均有miR-214表达,而内侧半月板失稳组软骨样本中miR-214的表达水平明显高于假手术组(P<0.05);②实验二中,苏木精-伊红染色、番红O固绿染色、甲苯胺蓝染色结果显示,拮抗剂组软骨退变程度低于内侧半月板失稳组;腺病毒验证PCR检测结果显示,空载组软骨中miR-214表达水平高于拮抗剂组(P<0.05);③实验二中,X射线片显示,内侧半月板失稳组和空载组呈典型骨关节炎影像学变化,拮抗剂组关节退行性病变程度相对较轻;Mirco-CT检测结果显示,拮抗剂组在注入miR-214拮抗剂后,骨小梁结构模型指数变小,各项数据整体好于内侧半月板失稳组及空载组;④实验二Western blot检测结果显示,内侧半月板失稳组、空载组软骨标本中软骨相关因子Ⅱ型胶原α1、性别决定区Y框转录因子9、Runt相关转录因子2、骨桥蛋白的相对表达水平低于假手术组及拮抗剂组(P<0.05);而金属基质蛋白酶13的相对表达水平在内侧半月板失稳组、空载组高于假手术组及拮抗剂组(P<0.05);⑤实验二荧光定量PCR检测结果显示,与假手术组比较,肿瘤坏死因子α和白细胞介素6 mRNA的相对表达量在内侧半月板失稳组、空载组中表达相对较高,拮抗剂组中表达相对较低(P<0.05);内侧半月板失稳组、空载组高于拮抗剂组(P<0.05);⑥结果表明,骨关节炎小鼠模型的关节软骨中miR-214表达水平明显升高,提示miR-214表达水平的升高与骨关节炎有密切联系;而在骨关节炎小鼠模型膝关节腔内注入miR-214拮抗剂,可以延缓关节软骨退化、促进软骨下骨重塑,改善骨关节炎进展。

关键词： microRNA-214 骨关节炎关节软骨肿瘤坏死因子α 白细胞介素6 软骨下骨

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Coordinate registration algorithms for over-the-horizon radar

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Journal of Systems Engineering and Electronics 2006年第4期17卷 725-730页

作者： Kong Min wang Cruohong wang yongcheng Research Inst. of Information Fusion Naval Aeronautical Engineering Inst. Yantai 264001 P. R. China The 14th Inst. of China Electronics & Technology Cooperation Nanjing 210013 P. R. China

Different from the other conventional radars, the over the horizon radar （OTHR） faces complicated nonlinear coordinate transform due to electromagnetic wave propagation and reflection in ionospheres. A significant problem is the phenomenon of multi-path propagation. Considering it, the coordinate registration algorithms of planar measurement model and spherical measurement model are respectively derived in detail. Noticeably, a new transforming expression of apparent azimuth and an integrated form of transforming expressions from measurement vector to ground state vector in coordinate registration algorithm of spherical measurement model are proposed. And then simulations are made to verify the correctness of the proposed algorithms and expression. Besides this, the transforming error rate of slant range, Doppler and apparent azimuth of the two kinds of models are given respectively. Then the quantitative analysis of error rate is also given. It can be drawn a conclusion that the coordinate registration algorithms of planar measurement model and spherical measurement model are both correct.

关键词： over-the-horizon radar coordinate registration error rate

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New paleomagnetic and magnetic fabric results for Early Cretaceous rocks from the Turpan intramontane basin,east Tianshan,northwest China

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Science China Earth Sciences 2004年第6期47卷 540-550页

作者： HUANG Baochun wang yongcheng ZHU Rixiang Institute of Geology and Geophysics Chinese Academy of Sciences Beijing 100029 China Institute of Geology and Geophysics Chinese Academy of Sciences Beijing 100029 China Institute of Geology and Geophysics Chinese Academy of Sciences Beijing 100029 China

In order to further constrain the tectonic configuration of the Tianshan fold belt and the blocks of its northern and southern sides prior to the Eocene India/Eurasia collision and to reveal their general kinematic characteristics after the collision,we carried out pa- leomagnetic study for Early Cretaceous rocks collected from the Turpan intramontane basin of east Tianshan,northwest China.A high-temperature component (HTC)with dual polarities can be isolated from most samples after progressive thermal *** demagnetization behavior and some rock magnetic features of the samples indicate that this HTC resides mainly in *** positive fold and reversal tests suggest that the HTC may be a primary mag- netization acquired at or close to the time of formation of the *** to previous results obtained from Cretaceous rocks in western China,paleomagnetic results from the Turpan in- tramontane basin retain also the inclination shallowing relative to stable ***, the anisotropy of magnetic susceptibility (AMS)measurements showed weak anisotropy degrees for Early Cretaceous Shengjinkou sandstones from the Turpan *** weak anisotropy degrees are independent of inclinations of the HTC,confirming that the effect of sedimentary compaction in most of these rocks can generally be neglected. Comparison of the Early Cretaceous results from Turpan with the coeval ones from Tarim, Junggar and stable Eurasia suggests that the Turpan intramontane basin displaced with no or slightly relative tectonic movement compared with Tarim but with a distinguishable latitudinal conver-gence relative to both Junggar and stable Eurasia since the India/Eurasia collision.

关键词： Turpan Basin, Early Cretaceous, paleomagnetism, kinematics.

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Density functional theory study of the mechanism of the acid-catalyzed decarboxylation of pyrrole-2-carboxylic acid and mesitoic acid

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Science China Chemistry 2011年第5期54卷 762-768页

作者： ZHANG XingHui GENG ZhiYuan wang yongcheng Gansu Key Laboratory of Polymer Materials College of Chemistry and Chemical EngineeringNorthwest Normal UniversityLanzhou 730070China College of Chemical Engineering Gansu Lianhe UniversityLanzhou 730010China

The mechanisms of the acid-catalyzed decarboxylation of pyrrole-2-carboxylic acid and mesitoic acid have been investigated based on density functional theory calculations at the B3LYP/6-311G (d,p) level. A polarizable continuum model (PCM) has been established in order to evaluate the effects of solvents on these reactions. The results of the calculations indicate that the first step of the acid-catalyzed decarboxylation of the pyrrole-2-carboxylic acid has two possible pathways,that is,the proton of H3O+ attacks either the-carbon atom or the carboxyl oxygen atom. The subsequent process of forming a four-membered ring transition state is the rate-determining step. The activation energies of acid-catalyzed decarboxylation of pyrrole-2-carboxylic acid proceeding via attack at the-carbon atom and the carboxyl oxygen atom are determined to be 194.21 and 210.41 kJ/mol,respectively. The computational results show that both pathways are favored. However,for the reaction of mesitoic acid with H3O+,the reaction barrier for the former pathway is calculated to be 212.15 kJ/mol,whilst the latter pathway has a reaction barrier of 200.45 kJ/mol. Our computational results are consistent with the experimental observations of Mundle and Kluger.

关键词： decarboxylation pyrrole-2-carboxylic acid acid-catalyzed density functional theory

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Branched Co3O4/Fe2O3 nanowires as high capacity lithium-ion battery anodes

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Nano Research 2013年第3期6卷 167-173页

作者： Hao Wu Ming Xu yongcheng wang Gengfeng Zheng Laboratory of Advanced Materials Department of Chemistry Fudan University Shanghai200433 China

We report a facile, two-step hydrothermal synthesis of a novel Co304/a-Fe2O3 branched nanowire heterostructure, which can serve as a good candidate for lithium-ion battery anodes with high Li＋ storage capacity and stability. The single-crystalline, primary C0304 nanowire trunk arrays directly grown on Ti substrates allow for efficient electrical and ionic transport. The secondary a-Fe2O3 branches provide enhanced surface area and high theoretical Li＋ storage capacity, and can also serve as volume spacers between neighboring Co3O4 NW arrays to maintain electrolyte penetration as well as reduce the aggregation during Li＋ intercalation, thus leading to improved electrochemical energy storage performance.

关键词： Co3O4 a-Fe2O3 nanowire branched lithium-ion battery Nyquist plot

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A theoretical study of the proton transfer process in the spin-forbidden reaction 1~HNO(1~A')+OH^-→3~NO^-(3~Σ^-)+H_2O

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Chinese Science Bulletin 2008年第10期53卷 1489-1496页

作者： LU LingLing wang XiaoFang wang yongcheng DAI GuoLiang College of Life science and Chemistry Tianshui Normal University Tianshui 741001 China College of Chemistry and Chemical Engineering Northwest Normal University Lanzhou 730070.China Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Department of Chemistry Fudan University Shanghai 200433 China

The spin-forbidden reaction 1HNO(1A')+OH-→3NO-(3Σ-)+H2O has been extensively explored using various CASSCF active spaces with MP2 corrections in several basis sets. Natural bond orbital (NBO) analysis, together with the NBO energetic (deletion) analysis, indicates that the two isomers have nearly equal total energy and could compete with each other in the title reaction. More significantly, the singlet/triplet surface crossing regions have been examined and the spinorbit coupling (SOC) and energetics have been computed. The computational results indicate that the SOC is very large at the crossing point T1/S0 trans (ca.40.9 cm-1). Moreover, the T1/S0 trans has a low energy of 10.67 kcal/mol relative to that of trans-S0. Therefore, the surface crossing to the triplet state seems much more efficient at the T1/S0 trans region along the minimum energy path (MEP), However, The values of single (P1ISC) and double (P2ISC) passes estimated at T1/S0 trans show that the ISC occurs with a little probability.

关键词：硝酰质子迁移反应内部系统交叉理论自旋轨迹耦合

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Mechanism of Ethylene Migratory Insertion and Dimerization Catalyzed by σ-Alkyl Platinum Complexes--A DFT Study

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Chinese Journal of Chemistry 2011年第6期29卷 1084-1094页

作者： Sheng, Yu Geng, Zhiyuan wang, yongcheng wang, Yuzhi Sun, Xiaojian Gansu Key Laboratory of Polymer Materials College of Chemistry and Chemical Engineering Key Laboratory of Eco-environment-related Polymer Materials Ministry of Education Northwest Normal University Lanzhou Gansu 730070 China

The mechanism of ethylene insertion reactions catalyzed by cationic a-alkyl platinum complexes has been studied at the B3LYP level of density functional theory. The initial steps of the reactions proceed via the coordination of ethylene to the reactants L2Pt（II）R＋, where L2=none, （NH3）2, （CHNH）2; R=H, CH3, C2H5 in which ethylene coordinates strongly to the complexes PtCH＋ and PtC2H＋（coordination energies （CE） are 296.52 and 229.28 kJ/mol, respectively）, while nitrogen-containing ligands decrease the energies： Pt（NH3）2CH＋（CE： 180.04 kJ/mol）, Pt（NH3）2C2H＋（CE： 97.86 kJ/mol）, Pt（CHNH）2 CH＋（CE ： 176.31 kJ/mol） and Pt（CHNH）2 C2H＋（CE： 91.00 kJ/mol）. Moreover, ethylene insertion into the Pt-alkyl bond, which is the rate-determining step, is endothermic with barrier heights for LzPtCH3（CzH4）＋ decreasing in the order： PtCH＋（164.18 kJ/mol）〉（NH3）2 PtCH＋（129.95 kJ/mol）〉（CHNH）2 PtCH＋（115.27 kJ/mol）, which has the same tendency for the ethyl case. The insertion product will continually undergo t-hydride elimination, which is exothermic. On the other hand, the effects of solvent （dichloromethane, THF and benzene） are investigated with PCM method, but the inclusion of the effects in the computations only slightly affects the results. Beside that, a complete catalytic cycle for ethylene dimerization is studied in detail and the calculations agree well with known energetic and recognized tendencies.

关键词： platinum ethylene insertion reaction DFT (B3LYP)

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Single-cell and spatially resolved omics:Advances and limitations

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Journal of Pharmaceutical Analysis 2023年第8期13卷 833-835页

作者： Jiaye Chen yongcheng wang Jina Ko Liangzhu Laboratory Zhejiang UniversityHangzhou310058China Department of Bioengineering University of PennsylvaniaPhiladelphiaUSA

Recent advances in experimental and computational single-cell and spatially resolved omics have opened new avenues for research in biology and *** technologies allow for the study of individual cells in unprecedented detail,providing insights into the heterogeneity within tissues and organs,and how different cells interact with each *** and other eukaryotes are composed of billions of cells,each with vastly heterogeneous cell types and functional cell states determined by intrinsic and extrinsic factors.

关键词： organs spatially resolved

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Theoretical study of spin-orbit coupling and intersystem crossing in the two-state reaction between Nb(NH_2)_3 and N_2O

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Science China Chemistry 2012年第1期55卷 158-166页

作者： LV LingLing wang XiaoFang ZHU YuanCheng LIU XinWen wang-yongcheng College of Life Science and Chemistry Tianshui Normal UniversityTianshui 741001China College of Chemistry and Chemical Engineering Northwest Normal UniversityLanzhou 730070China

The two-state mechanism of the reaction of Nb(NH2)3 with N2O on the singlet and triplet potential energy surfaces has been investigated at the B3LYP *** points between the potential energy surfaces have been located using different *** of the strain model shows that the singlet state of the four-coordinate(N2O)Nb(NH2)3 complex with N2O bonded via terminal N atom coordination(12) is more stable in the initial stage of reaction,since the bending of the N2O fragment [Edef(N2O) = 86.1 kcal mol-1] results in an energy splitting of the doubly degenerate LUMO;the low-energy LUMO can now strongly couple with the occupied Nb-localized d orbitals,forming a back-bond and transferring charge(q = 0.82 e) from Nb(NH2)3 to the N2O *** from 32 to 12,the reacting system changes spin multiplicity near the MECP(minimal energy crossing point) region,which takes place with a spin crossing barrier of 9.6-10.0 kcal *** of spin-orbit coupling(SOC) indicates that MECP will produce a significant SOC matrix *** value of SOC is 111.52 cm-1,due to the electron shift between two perpendicular φ orbitals with the same rotation direction,and the magnitude of the spin-multi-plicity mixing increases in the small energy gap between high-and low-spin states,greatly enhancing the probability of intersystem *** probabilities of single(P1 ISC) and double(P2 ISC) passes estimated at MECP(SOC = 111.52 cm-1) are approximately 1.17×10-2 and 2.32×10-2,respectively.

关键词： two-state reaction mechanism spin-orbit coupling(SOC) transition probability

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