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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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The emerging role of mesenchymal stem cell-derived extracellular vesicles to ameliorate hippocampal NLRP3 inflammation induced by binge-like ethanol treatment in adolescence

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Neural Regeneration Research 2025年第4期20卷 1153-1163页

作者： Susana Mellado María JoséMorillo-Bargues Carla Perpiñá-Clérigues Francisco García-García Victoria Moreno-Manzano Consuelo Guerri María Pascual Department of Physiology School of Medicine and DentistryUniversity of ValenciaValenciaSpain bioinformatics and Biostatistics Unit Príncipe Felipe Research CenterValenciaSpain Neuronal and Tissue Regeneration Laboratory Príncipe Felipe Research CenterValenciaSpain

Our previous studies have reported that activation of the NLRP3(NOD-,LRR-and pyrin domain-containing protein 3)-inflammasome complex in ethanol-treated astrocytes and chronic alcohol-fed mice could be associated with neuroinflammation and brain *** stem cell-derived extracellular vesicles(MSC-EVs)have been shown to restore the neuroinflammatory response,along with myelin and synaptic structural alterations in the prefrontal cortex,and alleviate cognitive and memory dysfunctions induced by binge-like ethanol treatment in adolescent *** the therapeutic role of the molecules contained in mesenchymal stem cell-derived extracellular vesicles,the present study analyzed whether the administration of mesenchymal stem cell-derived extracellular vesicles isolated from adipose tissue,which inhibited the activation of the NLRP3 inflammasome,was capable of reducing hippocampal neuroinflammation in adolescent mice treated with binge *** demonstrated that the administration of mesenchymal stem cell-derived extracellular vesicles ameliorated the activation of the hippocampal NLRP3 inflammasome complex and other NLRs inflammasomes(e.g.,pyrin domain-containing 1,caspase recruitment domain-containing 4,and absent in melanoma 2,as well as the alterations in inflammatory genes(interleukin-1β,interleukin-18,inducible nitric oxide synthase,nuclear factor-kappa B,monocyte chemoattractant protein-1,and C–X3–C motif chemokine ligand 1)and miRNAs(miR-21a-5p,miR-146a-5p,and miR-141-5p)induced by binge-like ethanol treatment in adolescent *** analysis further revealed the involvement of miR-21a-5p and miR-146a-5p with inflammatory target genes and NOD-like receptor signaling *** together,these findings provide novel evidence of the therapeutic potential of MSC-derived EVs to ameliorate the hippocampal neuroinflammatory response associated with NLRP3 inflammasome activation induced by binge drinking in adolescence.

关键词： adolescence binge-like ethanol treatment extracellular vesicles hippocampus mesenchymal stem cells neuroinflammation NOD-,LRR-and pyrin domain-containing protein 3(NLRP3)

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A homing rescue gene drive with multiplexed gRNAs reaches high frequency in cage populations but generates functional resistance

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Journal of Genetics and Genomics 2024年第8期51卷 836-843页

作者： Shibo Hou Jingheng Chen Ruobing Feng Xuejiao Xu Nan Liang Jackson Champer center for bioinformatics Center for Life SciencesSchool of Life SciencesPeking UniversityBeijing 100871China

CRISPR homing gene drives have considerable potential for managing populations of medically and agriculturally significant *** operate by Cas9 cleavage followed by homology-directed repair,copying the drive allele to the wild-type chromosome and thus increasing in frequency and spreading throughout a ***,resistance alleles formed by end-joining repair pose a significant *** address this,we create a homing drive targeting the essential hairy gene in Drosophila *** resistance alleles are recessive lethal,while drive carriers have a recoded“rescue”version of *** drive inheritance rate is moderate,and multigenerational cage studies show drive spread to 96%–97%of the ***,the drive does not reach 100%due to the formation of functional resistance alleles despite using four *** alleles have a large deletion but likely utilize an alternate start ***,revised designs targeting more essential regions of a gene may be necessary to avoid such functional *** of the rescue element’s native 3'UTR with a homolog from another species increases drive inheritance by 13%–24%.This was possibly because of reduced homology between the rescue element and surrounding genomic DNA,which could also be an important design consideration for rescue gene drives.

关键词： Genedrive Homing drive Rescueelement Population modification Multiplexed gRNAs Resistance alleles Cage study

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Single-cell technologies: current and near future

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Science China life Sciences 2025年第1期 1-4页

作者： Chenfei Wang Qi Liu Xiaohui Fan Tieliu Shi Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration Ministry of EducationOrthopedics 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 Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University 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 Key Laboratory of Advanced Theory and Application in Statistics and Data Science (MOE) School of StatisticsEast China Normal University

Single-cell technologies enable the indepth exploration of multiple biological hierarchies at the scale of individual cells,which have deepened our knowledge of cellular diversity, tissue organization, and overall organism function(Sun et al.,2024). In 2009, single-cell RNA sequencing(sc RNA-seq) was first developed as a powerful tool to dissect gene expression and uncover transcriptional *** the rapid advancement of technology, single-cell approaches have expanded to encompass other omics, such as genomics, epigenomics, proteomics,and metabolomics.

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Comparative genetic analysis of Arabidopsis purple acid phosphatases AtPAP10, AtPAP12, and AtPAP26 provides new insights into their roles in plant adaptation to phosphate deprivation

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Journal of Integrative Plant Biology 2014年第3期56卷 299-314页

作者： Liangsheng Wang Shan Lu Ye Zhang Zheng Li Xiaoqiu Du Dong Liu MOE Key Laboratory of bioinformatics Center for Plant Biology School of Life Sciences Tsinghua University

Induction and secretion of acid phosphatases （APases） is thought to be an adaptive mechanism that helps plants survive and grow under phosphate （Pi） deprivation, in Arabidopsis, there are 29 purple acid phosphatase （AtPAP） genes. To systematically investigate the roles of different AtPAPs, we first identified knockout or knock-down T-DNA lines for all 29 AtPAP genes. Using these atpap mutants combined with in-gel and quantitative APase enzyme assays, we demonstrated that AtPAP12 and AtPAP26 are two major intracellular and secreted APases in Arabidopsis while AtPAPlo is mainly a secreted APase. On Pi-deficient （P-） medium or P- medium supplemented with the organophosphates ADP and fructose-6-phosphate （Fru-6-P）, growth of atpaplo was significantly reduced whereas growth of atpap12 was only moderately reduced, and growth of atpap26 was nearly equal to that of the wild type （WT）. Overexpression of the AtPAP12 or AtPAP26 gene, however, caused plants to grow better on P- or P- medium supplemented with ADP or Fru-6-P. Interest-ingly, Pi levels are essentially the same for the WT and overexpressing lines, although these two types of plants have significantly different growth phenotypes. These results suggest that the APases may have other roles besides enhancing internal Pi recycling or releasing Pi from external organophosphates for plant uptake.

关键词： Phosphate starvation responses acid phosphatase activity atpap mutants~ AtPAP overexpression~ tolerance to phosphatedeprivation

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Comparative Study of Apoptosis-related Gene Loci in Human,Mouse and Rat Genomes

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Acta Biochimica et Biophysica Sinica 2005年第5期37卷 341-348页

作者： Yan-Bin YIN Yong ZHANG Peng YU Jing-Chu LUO Ying JIANG Song-Gang LI center of bioinformatics, National Laboratory. of Genetic Engineering and Protein Engineering, College of life Sciences Peking University,Beijing 100871, China center of bioinformatics National Laboratory of Genetic Engineering and Protein Engineering College of Life Sciences Peking UniversityBeijing 100871 China

Many genes are involved in mammalian cell apoptosis *** apoptosis genes oftencontain characteristic functional domains,and can be classified into at least 15 functional groups,accordingto previous *** an integrated bioinformatics platform for motif or domain search from threepublic mammalian proteomes(International Protein Index database for human,mouse,and rat),we system-atically cataloged all of the proteins involved in mammalian apoptosis *** localizing those proteinsonto the genomes,we obtained a gene locus centric apoptosis gene catalog for human,mouse and *** phylogenetic analysis showed that most of the apoptosis related gene loci are conserved amongthese three ***,about one-third of apoptosis gene loci form gene clusters on mammalchromosomes,and exist in the three species,which indicated that mammalian apoptosis gene orders arealso *** addition,some tandem duplicated gene loci were revealed by comparing gene loci clustersin the three *** data produced in this work were stored in a relational database and may be viewedat http://***/database/***.

关键词： apoptosis gene cluster comparative genomics bioinformatics

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mTORC1 signaling in hepatic lipid metabolism

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Protein & Cell 2018年第2期9卷 145-151页

作者： Jinbo Han Yiguo Wang MOE Key Laboratory of bioinformatics Tsinghua-Peking Center for Life Sciences School of Life Sciences Tsinghua University Beijing 100084 China

The mechanistic target of rapamycin （mTOR） signaling pathway regulates many metabolic and physiological processes in different organs or tissues. DysregulaUon of mTOR signaling has been implicated in many human diseases including obesity, diabetes, cancer, fatty liver diseases, and neuronal disorders. Here we review recent progress in understanding how mTORC1 （mTOR complex 1） signaling regulates lipid metabolism in the liver.

关键词： mTOR mTORC1 lipogenesis lipophagy

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Regulation of Stamen Development by Coordinated Actions of Jasmonate, Auxin, and Gibberellin in Arabidopsis

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Molecular Plant 2013年第4期6卷 1065-1073页

作者： Susheng Song Tiancong Qi Huang Huang Daoxin Xie Tsinghua-Peking center for life Sciences MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China

Proper stamen development is essential for plants to achieve their life cycles. Defects in stamen development will cause male sterility. A vast array of research efforts have been made to understand stamen developmental processes and reg- ulatory mechanisms over the past decades. It is so far reported that phytohormones, including jasmonate, auxin, gibberellin, brassinosteroid, and cytokinin, play essential roles in regulation of stamen development. This review will briefly summarize the molecular basis for coordinated regulation of stamen development by jasmonate, auxin, and gibberellin in Arabidopsis.

关键词： stamen jasmonate gibberellin auxin.

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PKM2 coordinates glycolysis with mitochondrial fusion and oxidative phosphorylation

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Protein & Cell 2019年第8期10卷 583-594页

作者： Tong Li Jinbo Han Liangjie Jia Xiao Hu Liqun Chen Yiguo Wang MOE Key Laboratory of bioinformatics Tsinghua-Peking Joint Center for Life Sciences School of Life Sciences Tsinghua University Beijing 100084 China

A change in the metabolic flux of glucose from mitochondrial oxidative phosphorylation (OXPHOS) to aerobic glycolysis is regarded as one hallmark of cancer. However, the mechanisms underlying the metabolic switch between aerobic glycolysis and OXPHOS are unclear. Here we show that the M2 isoform of pyruvate kinase (PKM2), one of the rate-limiting enzymes in glycolysis, interacts with mitofusin 2 (MFN2), a key regulator of mitochondrial fusion, to promote mitochondrial fusion and OXPHOS, and attenuate glycolysis. mTOR increases the PKM2:MFN2 interaction by phosphorylating MFN2 and thereby modulates the effect of PKM2: MFN2 on glycolysis, mitochondrial fusion and OXPHOS. Thus, an mTOR-MFN2-PKM2 signaling axis couples glycolysis and OXPHOS to modulate cancer cell growth.

关键词： PKM2 MFN2 mTOR glycolysis oxidative phosphorylation

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A novel solution treatment and aging for powder bed fusion-laser beam Ti-6Al-2Sn-4Zr-6Mo alloy:Microstructural and mechanical characterization

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International Journal of Minerals,Metallurgy and Materials 2025年第2期32卷 414-424页

作者： Gianluca Pirro Alessandra Martucci Alessandro Morri Mariangela Lombardi Lorella Ceschini Department of Industrial Engineering(DIN) Alma Mater Studiorum-University of BolognaBologna 40136Italy Department of applied Science and Technology(DISAT) Politecnico di TorinoTorino TO 10129Italy

Ti-6Al-4Zr-2Sn-6Mo alloy is one of the most recent titanium alloys processed using powder bed fusion-laser beam(PBF-LB)*** alloy has the potential to replace Ti-6Al-4V in automotive and aerospace applications,given its superior mechanical properties,which are approximately 10%higher in terms of ultimate tensile strength(UTS)and yield strength after appropriate heat *** as-built conditions,the alloy is characterized by the presence of soft orthorhombicα″martensite,necessitating a postprocessing heat treatment to decompose this phase and enhance the mechanical properties of the ***,PBFed Ti6246 components undergo an annealing process that transforms theα″martensite into anα-βlamellar *** primary objective of this research was to develop a solution treatment and aging(STA)heat treatment tailored to the unique microstructure produced by the additive manufacturing process to achieve an ultrafine bilamellar microstructure reinforced by precipitation *** study investigated the effects of various solution temperatures in theα-βfield(ranging from 800 to 875℃),cooling media(air and water),and aging time to determine the optimal heat treatment parameters for achieving the desired bilamellar *** each heat treatment condition,differentα-βmicrostructures were found,varying in terms of theα/βratio and the size of the primaryα-phase *** attention was given to how these factors were influenced by increases in solution temperature and how microhardness correlated with the percentage of the metastableβphase present after *** tests were performed on samples subjected to the most promising heat treatment parameters.A comparison with literature data revealed that the optimized STA treatment enhanced hardness and UTS by13%and 23%,respectively,compared with those of the annealed *** surface analyses were conducted to investigate fracture mechanisms.

关键词： powder bed fusion-laser beam titanium alloys heat treatments mechanical properties fractographic analysis

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