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

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

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Anomalous quality factor evolution of induced transparency in a virtualized coupled-oscillator system

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 148-155页

作者： Yunhan Yang Han Jia Tuo Liu Yuzhen Yang Jun Yang Key Laboratory of Noise and Vibration research Institute of Acoustics Chinese Academy of Sciences University of Chinese Academy of sciences State Key Laboratory of Acoustics Institute of Acoustics Chinese Academy of Sciences

The phenomenon of induced transparency, characterized by a high quality(Q) factor, holds significant importance in the fields of high-precision sensing, energy storage and wave manipulation. Conventional transparency systems are often constrained by the limited experimentally accessible parameter space and the lack of independent control over intrinsic parameters, thereby hindering advanced research on high-Q effects. Here we propose a virtualized coupled-oscillator system that enables reconfigurable induced transparency in the reflection spectrum. By virtually incorporating a pair of coupled oscillators into an individual acoustic meta-atom, we achieve the manipulation of induced transparency in a decoupled, wide-ranging, and elaborate manner. Exploiting the diverse evolutions across the intrinsic parameter space, we show experimentally a counter-intuitive increase in the Q-factor of the transparency window, which is attributed to the enhanced dissipation of the bright ***, a constant group delay at the center frequency is observed accompanying this evolution. Our work demonstrates an intriguing platform as well as a novel strategy to engineer high-Q induced transparency phenomenon, and paves the way towards applications in programmable acoustic sensors, filters and slow-wave devices.

关键词： induced transparency acoustic meta-atom high quality-factor scattering programmable intrinsic parameter

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ImSpiRE: image feature-aided spatial resolution enhancement method

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Science China Life sciences 2025年第1期 272-283页

作者： Yuwei Hua Yizhi Zhang Zhenming Guo Shan Bian Yong Zhang State Key Laboratory of Cardiovascular Diseases and Medical Innovation center Institute for Regenerative MedicineDepartment of NeurosurgeryShanghai East HospitalShanghai Key Laboratory of Signaling and Disease ResearchFrontier Science Center for Stem Cell ResearchSchool of Life Sciences and TechnologyTongji University

The resolution of most spatially resolved transcriptomic technologies usually cannot attain the single-cell level, limiting their applications in biological discoveries. Here, we introduce ImSpiRE, an image feature-aided spatial resolution enhancement method for in situ capturing spatial transcriptome. Taking the information stored in histological images, ImSpiRE solves an optimal transport problem to redistribute the expression profiles of spots to construct new transcriptional profiles with enhanced resolution, together with extending the gene expression profiles into unmeasured regions. Applications to multiple datasets confirm that ImSpiRE can enhance spatial resolution to the subspot level while contributing to the discovery of tissue domains, signaling communication patterns, and spatiotemporal characterization.

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Molecular rotors as a class of generally highly active ion transporters

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Science China Chemistry 2021年第12期64卷 2154-2160页

作者： Jie Shen Joan Jia Ying Han Ruijuan Ye Huaqiang Zeng frontier research center for multidisciplinary sciences School of Chemistry and Chemical EngineeringNorthwestern Polytechnical UniversityXi’an710072China Temasek Polytechnic 21 Tampines Avenue 1Singapore529757Singapore

We describe here a class of unconventional ion transporters,molecular rotors that transport ions through a rotating function rather than via traditional carrier or channel *** macroscopic rotors,these molecular rotors consist of three modularly tunable components,i.e.,a membrane-anchoring stator,a crown ether-containing rotator for ion binding and transport,and a triple bond-based axle that allows the rotator to freely rotate around the stator in the lipid *** bilayer experiments reveal the generally high ability of all molecular rotors in promoting the highly efficient transmembrane K^(+)flux(EC50 values=0.49-1.37 mol%relative to lipid).While molecular rotors differing only in the ion-binding unit exhibit similar ion transport activities,those differing in the rotator’s length display activity differences by up to 174%.

关键词： supramolecular chemistry molecular machines artificial membrane transporters molecular rotors K+transporters

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X-ray absorption near the edge structure and x-ray photoelectron spectroscopy studies on pyrite prepared by thermally sulfurizing iron films

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Chinese Physics B 2009年第7期18卷 2734-2738页

作者：张辉刘应书王宝义魏龙奎热西钱海杰 School of Mechanical Engineering University of Science and Technology Beijing multidisciplinary research center Chinese Academy of Sciences

This paper reports how pyrite films were prepared by thermal sulfurization of magnetron sputtered iron films and characterized by X-ray absorption near edge structure spectra and X-ray photoelectron spectroscopy on a 4B9B beam line at the Beijing Synchrotron Radiation Facility. The band gap of the pyrite agrees well with the optical band gap obtained by a spectrophotometer. The octahedral symmetry of pyrite leads to the splitting of the d orbit into t2g and eg levels. The high spin and low spin states were analysed through the difference of electron exchange interaction and the orbital crystal field. Only when the crystal field splitting is higher than 1.5 eV, the two weak peaks above the white lines can appear, and this was approved by experiments in the present work.

关键词： X-ray absorption near the edge structure spectra X-ray photoelectron spectroscopy iron pyrite films solar cells

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Detection of Adhesion Molecules on Inflamed Macrophages at Early-Stage Using SERS Probe Gold Nanorods

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Nano-Micro Letters 2017年第1期9卷 113-121页

作者： Dakrong Pissuwan Yusuke Hattori World Premier International Immunology frontier research center Osaka UniversityOsaka 5650871Japan Materials Science and Engineering Program Multidisciplinary UnitFaculty of ScienceMahidol UniversityBangkok 10400Thailand research Institute of Pharmaceutical sciences Musashino UniversityTokyo 2028585Japan

In recent years, it has been shown that inflammatory biomarkers can be used as an effective signal for disease diagnoses. The early detection of these signals provides useful information that could prevent the occurrence of severe diseases. Here, we employed surface-enhanced Raman scattering(SERS) probe gold nanorods(GNRs) as a tool for the early detection of inflammatory molecules in inflamed cells. A murine macrophage cell line(Raw264.7) stimulated with lipopolysaccharide(LPS) was used as a model in this study. The prepared SERS probe GNRs containing 4-mercaptobenzoic acid as a Raman reporter to generate SERS signals were used for detection of intracellular adhesion molecule-1(ICAM-1) in macrophages after treatment with LPS for varying lengths of time. Our results show that SERS probe GNRs could detect significant differences in the expression of ICAM-1 molecules in LPS-treated macrophages compared to those in untreated macrophages after only 1 h of LPS treatment. In contrast, when using fluorescent labeling or enzyme-linked immunosorbent assays(ELISA) to detect ICAM-1, significant differences between inflamed and un-inflamed macrophages were not seen until the cells had been treated with LPS for 5 h. These results indicate that our SERS probe GNRs provide a higher sensitivity for detecting biomarker molecules in inflamed macrophages than the conventional fluorescence and ELISA techniques, and could therefore be useful as a potential diagnostic tool for managing disease risk.

关键词： Gold nanorod SERS Inflamed cell Macrophage ICAM-1

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How variable progenitor clones construct a largely invariant neocortex

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National Science Review 2024年第1期11卷 129-144页

作者： Zhongfu Shen Jiajun Yang Qiangqiang Zhang Kuiyu Wang Xiaohui Lv Xiaolin Hu Jian Ma Song-Hai Shi New Cornerstone Science Laboratory IDG/McG overn Institute for Brain Research Tsinghua-Peking Center for Life Sciences Beijing Frontier Research Center for Biological Structure School of Life Sciences Tsinghua University Department of Computer sciences Tsinghua University College of Life sciences Nankai University Chinese Institute for Brain research

The neocortex contains a vast collection of diverse neurons organized into distinct layers. While nearly all neocortical neurons are generated by radial glial progenitors(RGPs), it remains largely unclear how a complex yet organized neocortex is constructed reliably and robustly. Here, we show that the division behavior and neuronal output of RGPs are highly constrained with patterned variabilities to support the reliable and robust construction of the mouse neocortex. The neurogenic process of RGPs can be well-approximated by a consistent Poisson-like process unfolding over time, producing deep to superficial layer neurons progressively. The exact neuronal outputs regarding layer occupation are variable; yet, this variability is constrained systematically to support all layer formation, largely reflecting the variable intermediate progenitor generation and RGP neurogenic entry and exit timing differences. Together, these results define the fundamental features of neocortical neurogenesis with a balanced reliability and variability for the construction of the complex neocortex.

关键词： neocortex radial glial progenitor intermediate progenitor neurogenesis clonal variability layer formation

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Metabolomics in drug research and development: The recent advances in technologies and applications

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Acta Pharmaceutica Sinica B 2023年第8期13卷 3238-3251页

作者： Huanhuan Pang Zeping Hu School of Pharmaceutical sciences Tsinghua-Peking Center for Life SciencesBeijing Frontier Research Center for Biological StructureTsinghua UniversityBeijing 100084China Artemisinin research center Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijing 100700china

Emerging evidence has demonstrated the vital role of metabolism in various diseases or *** provides a comprehensive understanding of metabolism in biological *** advanced analytical techniques,metabolomics exhibits unprecedented significant value in basic drug research,including understanding disease mechanisms,identifying drug targets,and elucidating the mode of action of *** importantly,metabolomics greatly accelerates the drug development process by predicting pharmacokinetics,pharmacodynamics,and drug *** addition,metabolomics facilitates the exploration of drug repurposing and drug-drug interactions,as well as the development of personalized treatment ***,we briefly review the recent advances in technologies in metabolomics and update our knowledge of the applications of metabolomics in drug research and development.

关键词： Metabolomics Technology Drug researchand development Drug target Modeof action of drug Drug response Personalizedtreatment

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Tuning oxygen redox via transition-metal cation species

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Science China Chemistry 2024年第7期67卷 2130-2131页

作者： Sichen Jiao Xuelong Wang Xiqian Yu Beijing frontier research center on Clean Energy Institute of PhysicsChinese Academy of SciencesBeijing 100190China center of Materials Science and Optoelectronics Engineering University of Chinese Academy of SciencesBeijing 100049China

Lithium-rich layered oxides with a general formula of Li[Li_(x)Ni_(y)MnzCo_(1–x–y–z)]O_(2)(Li-rich NMCs,elements in bracket reside in the same layer)are recognized as promising candidates for the next generation hi... 详细信息

关键词： lithium oxides transition

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Cost effective approach to identify multiple influential spreaders based on the cycle structure in networks

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Science China(Information sciences) 2023年第9期66卷 184-193页

作者： Wenfeng SHI Shuqi XU Tianlong FAN Linyuan Lü Institute of Fundamental and frontier sciences University of Electronic Science and Technology of China Institute of Dataspace Hefei Comprehensive National Science Center Department of Physics University of Fribourg Alibaba research center for Complexity sciences Hangzhou Normal University

Identifying influential spreaders has theoretical and practical significance in complex *** centrality methods can efficiently find a single spreader, but it could lead to influence redundancy and high initializing costs when used to identify a set of multiple spreaders. A cycle structure is one of the most crucial reasons for the complexity of a network and the cornerstone of the feedback effect. From this novel perspective, we propose a new method based on basic cycles in networks to identify multiple influential spreaders with superior spreading performance and low initializing costs. Experiments on six empirical networks show that the spreaders selected by the proposed method are more scattered in the network and yield the best spreading performance compared with those on seven well-known methods. Importantly, the proposed method is the most cost effective under the same spreading performance. The cycle-based method has the advantage of generating multiple solutions. Our work provides new insights into identifying multiple spreaders and hence can benefit wide applications in practical scenarios.

关键词： multiple spreaders basic cycle complex network cycle structure spreading dynamics

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