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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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Irreversible phenotypic perturbation and functional impairment of B cells during HIV-1 infection

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Frontiers of Medicine 2017年第4期11卷 536-547页

作者： Jingjing Yan Shuye Zhang Jun Sun Jianqing Xu Xiaoyang Zhang shanghai public health clinical center & institutes of biomedical sciences Fudan University Shanghai 201508 China

Human immunodeficiency virus type 1 （HIV-1） infection can damage humoral immunity. The knowledge of B cell perturbations during chronic HIV-1 infection and their recovery after combined antiretroviral therapy （cART） is not complete yet, and thus attempts to further improve humoral immunity are impeded. In this study, an HIV-1 chronically infected cohort with similar demographics, infection history, genetic background, and HIV-1 genotype was established to probe B cell perturbations. Results showed that the B cells from this cohort were highly activated and prone to cell death, and B cell compartments were altered significantly. Notably, although cART partially reversed the hyperactivation and reduced tissue-like memory B cells, other B cell perturbations, including impaired expression of survival factor Bcl-2, costimulatory molecules, and shrunken resting memory B cells, were irreversible. Further functional characterization revealed that the influenza HA- specific antibody-secreting cells were significantly lower during HIV-1 infection, whereas the recalled antibody response to HIV-l-specific antigens was decreased after cART. Finally, CpG plus R848 treatment increased the survival of B cells and memory B cells in vitro from HIV-l-infected patients. In conclusion, this study identified irreversible B cell immune perturbations in chronic HIV-1 infections regardless of cART and proposed the potential strategy to enhance B cell functions through the improvement of cell survival.

关键词： B cell HIV-1 phenotype functionality antiretroviral therapy

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The Establishment of Infectious Clone and Single Round Infectious Particles for Coxsackievirus A10

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Virologica Sinica 2020年第4期35卷 426-435页

作者： Min Wang Jingjing Yan Liuyao Zhu Meng Wang Lizhen Liu Rui Yu Ming Chen Jingna Xun Yuling Zhang Zhigang Yi Shuye Zhang shanghai public health clinical center and Institute of biomedical sciences Fudan UniversityShanghai 201508China

Coxsackievirus A10(CVA10)is one of the major etiological agents of hand,foot,and mouth *** are no vaccine and antiviral drugs for controlling CVA10 *** genetic tools for CVA10 will benefit its mechanistic study and development of vaccines and ***,two infectious clones for the prototype and a Myc-tagged CVA10 were *** CVA10 viruses were harvested by transfecting the viral m RNA into human rhabdomyosarcoma(RD)*** CVA10 was further confirmed by next generation sequencing and characterized *** also constructed the vectors for CVA10 subgenomic replicon with luciferase reporter and viral capsid with EGFP reporter,***-transfection of the viral replicon RNA and capsid expresser in human embryonic kidney 293 T(HEK293 T)cells led to the production of single round infectious particles(SRIPs).Based on CVA10 replicon RNA,SRIPs with either the enterovirus A71(EVA71)capsid or the CVA10 capsid were *** by EVA71 SRIPs required SCARB2,while CVA10 SRIPs did ***,we showed great improvement of the replicon activity and SRIPs production by insertion of a cis-active hammerhead ribozyme(HHRib)before the 50-untranslated region(UTR).In summary,reverse genetic tools for prototype strain of CVA10,including both the infectious clone and the SRIPs system,were successfully *** tools will facilitate the basic and translational study of CVA10.

关键词： Coxsackievirus A10(CVA10) Reverse genetics Enterovirus Single round infectious particles(SRIPs) Replicon

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Freeze-Drying Formulations Increased the Adenovirus and Poxvirus Vaccine Storage Times and Antigen Stabilities

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Virologica Sinica 2021年第3期36卷 365-372页

作者： Ye Chen Qibin Liao Tianyue Chen Yuchao Zhang Weien Yuan Jianqing Xu Xiaoyan Zhang shanghai public health clinical center and institutes of biomedical sciences Fudan UniversityShanghai 201508China Engineering Research center of Cell and Therapeutic Antibody Ministry of Educationand School of PharmacyShanghai Jiao Tong UniversityShanghai 200000China

Successful vaccines induce specific immune responses and protect against various viral and bacterial infections. Noninactivated vaccines, especially viral vector vaccines such as adenovirus and poxvirus vaccines, dominate the vaccine market because their viral particles are able to replicate and proliferate in vivo and produce lasting immunity in a manner similar to natural infection. One challenge of human and livestock vaccination is vaccine stability related to the antigenicity and infectivity. Freeze-drying is the typical method to maintain virus vaccine stability, while cold chain transportation is required for temperatures about 2 °C–8 °C. The financial and technological resource requirements hinder vaccine distribution in underdeveloped areas. In this study, we developed a freeze-drying formula consisting of bovine serum albumin(BSA), L-glutamic acid(L-Glu), polyethylene glycol(PEG), and dextran(DEX) to improve the thermal stability and activity of viral vaccines, including vaccinia recombinant vaccine(rTTV-OVA) and adenovirus vaccine(Ad5-ENV). We compared a panel of five different formulations(PEG: DEX: BSA: L-GLU = 50:9:0:0(#1), 50:5:4:0(#2), 50:10:9:0(#3),50:0:0:9(#4), and 50:1:0:8(#5), respectively) and optimized the freeze-drying formula for rTTV-OVA and Ad5-ENV. We found that the freeze-drying formulations #2 and #3 could maintain rTTV-OVA infectivity at temperatures of 4 °C and25 °C and that r TTV-OVA immunogenicity was retained during lyophilization. However, formulations #4 and #5 maintained Ad5-ENV infectivity under the same conditions, and Ad5-ENV immunogenicity had maximum retention with freeze-drying formulation #4. In summary, we developed new freeze-drying formulations that increased virus vaccine storage times and retained immunogenicity at an ambient temperature.

关键词： Adenovirus vaccine Poxvirus vaccine Freeze-drying formulation Stability Immunogenicity

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From Monovalent to Multivalent Vaccines, the Exploration for Potential Preventive Strategies Against Hand, Foot, and Mouth Disease(HFMD)

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Virologica Sinica 2021年第2期36卷 167-175页

作者： Xiangchuan He Miaomiao Zhang Chen Zhao Peiyong Zheng Xiaoyan Zhang Jianqing Xu shanghai public health clinical center and institutes of biomedical Science Shanghai Medical CollegeFudan UniversityShanghai 201508China Longhua Hospital Shanghai University of Traditional Chinese MedicineShanghai 200032China

Hand,foot,and mouth disease(HFMD)recently emerged as a global public *** licensure of inactivated enterovirus A71(EV-A71)vaccine was the first step in using a vaccine to control *** challenges arise from changes in the pathogen spectrum while vaccines directed against other common serotypes are in the preclinical *** mission of a broad-spectrum prevention strategy clearly favors multivalent *** development of multivalent vaccines was attempted via the simple combination of potent monovalent vaccines or the construction of chimeric vaccines comprised of epitopes derived from different virus *** present review summarizes recent advances in HFMD vaccine development and discusses the next steps toward a safe and effective HFMD vaccine that is capable of establishing a crossprotective antibody response.

关键词： Hand,foot,and mouth disease(HFMD) Inactivated whole virus vaccine Virus-like particles Multivalent vaccines Chimeric vaccines

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Nonmuscle myosin IIA promotes the internalization of influenza A virus and regulates viral polymerase activity through interacting with nucleoprotein in human pulmonary cells

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Virologica Sinica 2023年第1期38卷 128-141页

作者： Jian Chen Jian Liu Zhilu Chen Daobin Feng Cuisong Zhu Jun Fan Shuye Zhang Xiaoyan Zhang Jianqing Xu clinical center for Bio-Therapy Zhongshan HospitalFudan University(Xiamen Branch)Shanghai200032China center for Infectious Disease Research Science of Life SciencesWestlake UniversityHangzhou310024China shanghai public health clinical center&institutes of biomedical sciences Shanghai Medical CollegeFudan UniversityShanghai201508China

Influenza A virus(IAV),responsible for seasonal epidemics and recurring pandemics,represents a global threat to public *** the risk of a potential IAV pandemic,it is increasingly important to better understand virushost interactions and develop new anti-viral ***,we reported nonmuscle myosin IIA(MYH9)-mediated regulation of IAV ***9 depletion caused a profound inhibition of IAV infection by reducing viral attachment and internalization in human lung epithelial ***,overexpression of MYH9 also led to a significant reduction in viral productive ***,overexpression of MYH9 retained viral attachment,internalization,or uncoating,but suppressed the viral ribonucleoprotein(vRNP)activity in a minigenome *** analyses found that excess MYH9 might interrupt the formation of vRNP by interacting with the viral nucleoprotein(NP)and result in the reduction of the completed vRNP in the nucleus,thereby inhibiting subsequent viral RNA transcription and ***,we discovered that MYH9 can interact with IAV NP protein and engage in the regulation of vRNP complexes,thereby involving viral *** findings enlighten new mechanistic insights into the complicated interface of host-IAV interactions,ultimately making it an attractive target for the generation of antiviral drugs.

关键词： Myosin IIA(MYH9) Influenza A virus(IAV) vRNP activity Virus-host interactions Virus entry

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Integration of HiBiT into enteroviruses:A universal tool for advancing enterovirus virology research

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Virologica Sinica 2024年第3期39卷 422-433页

作者： Rui Yu Xiaohong Li Peng Zhang Minghao Xu Jitong Zhao Jingjing Yan Chenli Qiu Jiayi Shu Shuo Zhang Miaomiao Kang Xiaoyan Zhang Jianqing Xu Shuye Zhang School of Medicine Shanghai UniversityShanghai200444China clinical center for Biotherapy Zhongshan HospitalFudan UniversityShanghai200433China Guangzhou institutes of Biomedicine and health The Chinese Academy of SciencesGuangzhou510530China institutes of biomedical sciences Fudan UniversityShanghai200032China shanghai Geriatric Medical center Shanghai201104China clinical center for Biotherapy Zhongshan Hospital/Zhongshan Hospital(Xiamen)Fudan University361015China shanghai public health clinical center Fudan UniversityShanghai201508China

The utilization of enteroviruses engineered with reporter genes serves as a valuable tool for advancing our understanding of enterovirus biology and its applications,enabling the development of effective therapeutic and preventive *** this study,our initial attempts to introduce a NanoLuc luciferase(NLuc)reporter gene into recombinant enteroviruses were unsuccessful in rescuing viable *** hypothesized that the size of the inserted tag might be a determining factor in the rescue of the ***,we inserted the 11-amino-acid HiBiT tag into the genomes of enterovirus A71(EV-A71),coxsackievirus A10(CVA10),coxsackievirus A7(CVA7),coxsackievirus A16(CVA16),namely EV-A71-HiBiT,CVA16-HiBiT,CVA10-HiBiT,CVA7-HiBiT,and observed that the HiBiT-tagged viruses exhibited remarkably high rescue ***,the HiBiT-tagged enteroviruses displayed comparable characteristics to the wild-type viruses.A direct comparison between CVA16-NLuc and CVA16-HiBiT recombinant viruses revealed that the tiny HiBiT insertion had minimal impact on virus infectivity and replication ***,these HiBiT-tagged enteroviruses demonstrated high genetic stability in different cell lines over multiple *** addition,the HiBiT-tagged viruses were successfully tested in antiviral drug assays,and the sensitivity of the viruses to drugs was not affected by the HiBiT ***,our findings provide definitive evidence that the integration of HiBiT into enteroviruses presents a universal,convenient,and invaluable method for advancing research in the realm of enterovirus ***,HiBiT-tagged enteroviruses exhibit great potential for diverse applications,including the development of antivirals and the elucidation of viral infection mechanisms.

关键词： Enterovirus Infectious clones Reporter genes Luciferase Drug screening

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Common genetic heterogeneity of human interleukin-37 leads to functional variance

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Cellular & Molecular Immunology 2017年第9期14卷 783-791页

作者： Jingjing Yan Yuling Zhang Shimeng Cheng Bin Kang Jinbiao Peng Xiaodan Zhang Meichun Yuan Wenqi Chu Wen Zhang Jiayin Shen Shuye Zhang shanghai public health clinical center and institutes of biomedical sciences Fudan UniversityShanghaiChina School of Life sciences Hebei Normal UniversityShi-JiazhuangHebei Key Laboratory of Medical Molecular Virology of Ministries of Education/health Institute of Medical MicrobiologyShanghai Medical College of Fudan UniversityShanghaiChina

Interleukin-37(IL-37)is an inhibitory member of the IL-1 family of *** previously found that balanced selection maintains common variations of the human IL37 ***,the functional consequences of this selection have yet to be ***,using cells expressing exogenous IL-37 variants,including IL-37 Ref and IL-37 Var1 and Var2,we found that the three variants of IL-37 exhibited different immunoregulatory potencies in response to immune *** protein level of IL-37 Var2 was found to be significantly less than that of IL-37 Ref or Var1,despite the comparable mRNA levels of all three *** study showed that IL-37 Var2 was rapidly degraded by a proteasome-dependent mechanism mediated by enhanced polyubiquitination,leading to a transient upregulation of IL-37 Var2 after immune ***,when ectopically expressed in cells,human IL-37 Var2 exerted less inhibition on proinflammatory cytokine production than did other IL-37 ***,purified extracellular IL-37 variant proteins demonstrated comparable inhibitory abilities in *** conclusion,our study reveals that common genetic variants of IL37 lead to different immune-inhibitory potencies,primarily as a result of differences in IL-37 protein stability,suggesting the possible involvement of these variants in various human diseases.

关键词： Cytokine gene variation inflammation protein stability

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New insights into hepatitis B virus biology and implications for novel antiviral strategies

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National Science Review 2015年第3期2卷 296-313页

作者： Jieliang Chen Min Wu Kuancheng Liu Wen Zhang Yaming Li Xiaohui Zhou Lu Bai Zhenghong Yuan Key Laboratory of Medical Molecular Virology Ministry of Education and Healthand Department of Medical MicrobiologySchool of Basic Medical SciencesShanghai Medical CollegeFudan University Research Unit Shanghai Public Health Clinical CenterFudan University institutes of Medical Microbiology and biomedical sciences Fudan University

Hepatitis B virus(HBV), a small DNA virus with a unique replication mode, can cause chronic hepatitis(CHB), which is characterized by the persistence of the viral covalently closed circular DNA that serves as the template for HBV replication and the production of large amounts of secreted HBV surface antigen(HBs Ag) that is present in excess of the levels of infectious virus. Despite the success of currently approved antiviral treatments for CHB patients, including interferon and nucleotide analogs, which suppress HBV replication and reduce the risk of CHB-related liver diseases, these therapies fail to eradicate the virus in most of the patients. With the development of the cell and animal models for HBV study, a beter understanding of the HBV life cycle has been achieved and a series of novel antiviral strategies that target diferent stages of HBV replication have been designed to overcome the viral factors that contribute to HBV persistence. Such basic HBV research advancements and therapeutic developments are the subject of this review.

关键词： HBV ccc DNA HBs Ag persistence antiviral targets

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Hymecromone:a clinical prescription hyaluronan inhibitor for efficiently blocking COVID-19 progression

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Signal Transduction and Targeted Therapy 2022年第4期7卷 1287-1296页

作者： Shuai Yang Yun Ling Fang Zhao Wei Li Zhigang Song Lu Wang Qiuting Li Mengxing Liu Ying Tong Lu Chen Daoping Ru Tongsheng Zhang Kaicheng Zhou Baolong Zhang Peng Xu Zhicong Yang Wenxuan Li Yuanlin Song Jianqing Xu Tongyu Zhu Fei Shan Wenqiang Yu Hongzhou Lu Laboratory of RNA Epigenetics Institutes of Biomedical Sciences&Shanghai Public Health Clinical Center&Department of General SurgeryHuashan HospitalCancer Metastasis Institute Shanghai Medical CollegeFudan UniversityShanghaiP.R.China shanghai public health clinical center Fudan UniversityShanghaiP.R.China Department of Radiology Shanghai Public Health Clinical CenterFudan UniversityShanghaiP.R.China Zhongshan Hospital Fudan UniversityShanghaiP.R.China The Third People’s Hospital of Shenzhen ShenzhenP.R.China

Currently,there is no effective drugs for treating clinically COVID-19 except *** previously revealed that human identical sequences of SARS-CoV-2 promote the COVID-19 progression by upregulating hyaluronic acid(HA).As the inhibitor of HA synthesis,hymecromone is an approved prescription drug used for treating biliary ***,we aimed to investigate the relation between HA and COVID-19,and evaluate the therapeutic effects of hymecromone on ***,HA was closely relevant to clinical parameters,including lymphocytes(n=158;r=−0.50;P<0.0001),C-reactive protein(n=156;r=0.55;P<0.0001),D-dimer(n=154;r=0.38;P<0.0001),and fibrinogen(n=152;r=0.37;P<0.0001),as well as the mass(n=78;r=0.43;P<0.0001)and volume(n=78;r=0.41;P=0.0002)of ground-glass opacity,the mass(n=78;r=0.48;P<0.0001)and volume(n=78;r=0.47;P<0.0001)of consolidation in patient with low level of hyaluronan(HA<48.43 ng/mL).Furthermore,hyaluronan could directly cause mouse pulmonary ***,hymecromone remarkably reduced HA via downregulating HAS2/HAS3 ***,89%patients with hymecromone treatment had pulmonary lesion absorption while only 42%patients in control group had pulmonary lesion absorption(P<0.0001).In addition,lymphocytes recovered more quickly in hymecromone-treated patients(n=8)than control group(n=5)(P<0.05).These findings suggest that hymecromone is a promising drug for COVID-19 and deserves our further efforts to determine its effect in a larger cohort.

关键词： prescription clinical identical

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