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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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Future of non-invasive graft evaluation:A systematic review of proteomics in kidney transplantation

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World Journal of Transplantation 2025年第1期15卷 135-149页

作者： Eleni Avramidou Konstantina Psatha Kallisti St John Georgios Tsoulfas Michalis Aivaliotis Department of Transplantation Surgery Center for Research and Innovation in Solid Organ TransplantationAristotle University of ThessalonikiSchool of MedicineThessaloniki 54642Greece Laboratory of Medical biology-Genetics School of MedicineAristotle University of ThessalonikiThessaloniki 54124Greece Functional Proteomics and Systems biology(FunPATh) Center for Interdisciplinary Research and Innovation(CIRI-AUTH)Thessaloniki GR-57001Greece Laboratory of Biological Chemistry School of MedicineAristotle University of ThessalonikiThessaloniki 54124Greece

BACKGROUND Despite the developments in the field of kidney transplantation,the already existing diagnostic techniques for patient monitoring are considered *** biomarkers that can be derived from modern approaches of proteomic analysis of liquid biopsies(serum,urine)represent a promising innovation in the monitoring of kidney transplant *** To investigate the diagnostic utility of protein biomarkers derived from proteomics approaches in renal allograft *** A systematic review was conducted in accordance with PRISMA guidelines,based on research results from the PubMed and Scopus *** primary focus was on evaluating the role of biomarkers in the non-invasive diagnosis of transplant-related *** criteria included protein biomarkers and urine and blood samples,while exclusion criteria were language other than English and the use of low resolution and sensitivity *** selected research articles,were categorized based on the biological sample,condition and methodology and the significantly and reproducibly differentiated proteins were manually selected and *** and network analysis of the selected proteins was *** In 17 included studies,58 proteins were studied,with the cytokine CXCL10 being the most *** pathways related to immune response and fibrosis have shown to be *** of biomarkers for the assessment of renal damage as well as the prediction of short-term and long-term function of the graft were ***,all studies have shown satisfactory diagnostic accuracy of proteins alone or in combination with conventional methods,as far as renal graft assessment is *** Our review suggests that protein biomarkers,evaluated in specific biological fluids,can make a significant contribution to the timely,valid and non-invasive assessment of kidney graft.

关键词： Proteomics Kidney transplantation Graft evaluation Non-invasive diagnosis Kidney graft function

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Long-range electron synergy over Pt_(1)-Co_(1)/CN bimetallic single-atom catalyst in enhancing charge separation for photocatalytic hydrogen production

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Journal of Energy Chemistry 2023年第6期81卷 502-509,I0011页

作者： Man Yang Jing Mei Yujing Ren Jie Cui Shuhua Liang Shaodong Sun Engineering research center of Conducting Materials and Composite Technology Ministry of EducationShaanxi Engineering Research Center of Metal-Based Heterogeneous Materials and Advanced Manufacturing TechnologyShaanxi Province Key Laboratory for Electrical Materials and Infiltration TechnologySchool of Materials Science and EngineeringXi’an University of TechnologyXi’an 710048ShaanxiChina interdisciplinary research center of biology&catalysis School of Life SciencesNorthwestern Polytechnical UniversityXi’an 710072ShaanxiChina

The development of novel single-atom catalysts with optimal electron configuration and economical noble-metal cocatalyst for efficient photocatalytic hydrogen production is of great importance,but still ***,we fabricate Pt and Co single-atom sites successively on polymeric carbon nitride(CN).In this Pt_(1)-Co_(1)/CN bimetallic single-atom catalyst,the noble-metal active sites are maximized,and the single-atomic Co_(1)N_4sites are tuned to Co_(1)N_3sites by photogenerated electrons arising from the introduced single-atomic Pt_(1)N_*** studies and density functional theory(DFT)calculations reveal that the 3d orbitals of Co_(1)N_3single sites are filled with unpaired d-electrons,which lead to the improved visible-light response,carrier separation and charge migration for CN ***,the protons adsorption and activation are *** this advantage of long-range electron synergy in bimetallic single atomic sites,the photocatalytic hydrogen evolution activity over Pt_(1)-Co_(1)/CN achieves 915.8 mmol g^(-1)Pt h^(-1),which is 19.8 times higher than Co_(1)/CN and 3.5 times higher to Pt_(1)/*** this electron-synergistic effect is not so efficient for Pt *** results demonstrate the synergistic effect at electron-level and provide electron-level guidance for the design of efficient photocatalysts.

关键词： Bimetallic single-atom catalyst Long-range electron synergy Charge separation/transfer Carbon nitride Hydrogen production

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Understanding the intrinsic synergistic mechanism between Pt-O-Ti interface sites and TiO_(2) surface sites of Pt/TiO_(2) catalysts in Fenton-like reaction

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Science China Chemistry 2022年第12期65卷 2596-2603页

作者： Yawen Ma Huibin Ge Siwen Yi Man Yang Dan Feng Yujing Ren Jie Gao Yong Qin interdisciplinary research center of biology&catalysis School of Life SciencesNorthwestern Polytechnical UniversityXi’an710072China School of Materials Science and Engineering Xi’an University of TechnologyXi’an710048China Analytical&Testing center Northwestern Polytechnical UniversityXi’an710072China State Key Laboratory of Coal Conversion Institute of Coal ChemistryChinese Academy of SciencesTaiyuan030001China

Identifying the active site of oxide-supported metal catalysts and revealing the intrinsic synergistic mechanism between metal and oxide support remain a large ***,we report the identification and separation of the Pt-O-Ti interface and TiO_(2) surface in Pt-TiO_(2)-based catalysts by depositing different thickness of TiO_(2) shell with∼0.4-nm micropores onto the surface of Pt/TiO_(2) catalyst through atomic layer deposition(ALD).In the oxidation of 3,3′,5,5′-tetramethylbenzidine(TMB)by hydrogen peroxide(H_(2)O_(2))process,the TiO_(2) microporous shells can prevent the contact between TMB and embedded Pt clusters,but not delay the diffusion of H_(2)O_(2).The heterolysis of H_(2)O_(2) to ·OH occurs on the Pt-O-Ti interface,and the generated•OH migrates to the TiO_(2) surface to supplement the surface lattice oxygen,which sequentially oxidizes TMB to *** the synergistic effect between Pt-O-Ti interface active sties and TiO_(2) surface active sites can significantly improve the catalytic *** study provides a guide for the understanding of the intrinsic synergistic mechanism between the metal and oxide support in the metal-oxide catalysts.

关键词： Intrinsic synergistic mechanism Pt-O-Ti interface site TiO_(2)surface site Fenton-like reaction metal-oxide catalyst

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Insights into the effect of substrate adsorption behavior over hemelike Fe_(1)/AC single-atom catalyst

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Nano research 2022年第7期15卷 5970-5976页

作者： Jianglin Duan Yanan Zhou Yujing Ren Dan Feng Jinlong Shang Huibin Ge Jie Gao Jinlong Yang Yong Qin interdisciplinary research center of biology&catalysis School of Life SciencesNorthwestern Polytechnical UniversityXi’an 710072China Hefei National Laboratory for Physical Sciences at the Microscale University of Science and Technology of ChinaHefei 230026China Analytical&Testing center Northwestern Polytechnical UniversityXi’an 710072China State Key Laboratory of Coal Conversion Institute of Coal ChemistryChinese Academy of SciencesTaiyuan 030001China

Unraveling the substrate adsorption structure–performance relationship is pivotal for heterogeneous carbon supported metal single-atom catalysts(M_(1)/C SACs).However,due to the complexity of the functional groups on carbon material surface,it is still a great ***,inspired by structure of enzymes,we used activated carbon(AC),which has adjustable surface oxygen functional groups(OFGs),supported atomically dispersed Fe-N_(4) sites as heme-like *** based on a combination of scanning transmission electron microscopy(STEM),X-ray photoelectron spectroscopy(XPS),X-ray absorption spectroscopy(XAS),Mössbauer spectroscopy,Fourier transform infrared(FT-IR)characterizations,kinetics experiments and density functional theory(DFT)calculations,we revealed the effect of substrate adsorption behavior on AC support surface,that is,with the increase of carboxyl group in OFGs,the adsorbed 3,3',5,5'-tetramethylbenzidine(TMB)molecular increased,and consequently the substrate enriched on AC *** carboxyl group as well as Fe-N_(4) active sites synergistically realized high-efficiency peroxidase-like activity,just like the *** work suggests that simultaneously constructing metal single-atom active sites and specific functional groups on carbon support surface may open an avenue for engineering metal-support synergistic catalysis in M_(1)/C SACs,which can further improve catalytic performance.

关键词： single-atom catalysts heme-like carboxyl group substrate adsorption behavior peroxidase-like activity

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Hope on the (fruit) fly: the Drosophila wing paradigm of axon injury

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Neural Regeneration research 2015年第2期10卷 173-175页

作者： Yanshan Fang Nancy M. Bonini interdisciplinary research center on biology and Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Department of biology University of Pennsylvania

Axon degeneration and regeneration are processes that are central to neural insults including spinal cord iniury, brain trauma, ischemia, infection, inflammation, neuro- degenerative diseases, and aging （Conforti et al., 2014）. Injured axons undergo progressive self-destruction, termed ＂Wallerian degeneration＂, which is named after August Volney Waller who was the first to describe de- generation of severed nerves in 1850 - the injured nerve fibers become fragmented like threaded beads and are gradually cleared away.

关键词： gene fly the Drosophila wing paradigm of axon injury Hope on the

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Portable visual and electrochemical detection of hydrogen peroxide release from living cells based on dual-functional Pt-Ni hydrogels

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Microsystems & Nanoengineering 2023年第6期9卷 185-194页

作者： Guanglei Li Yao Chen Fei Liu Wenhua Bi Chenxin Wang Danfeng Lu Dan Wen State Key Laboratory of Solidification Processing School of Materials Science and EngineeringNorthwestern Polytechnical University(NPU)and Shaanxi Joint Laboratory of GrapheneXi'an 710072P.R.China interdisciplinary research center of biology&catalysis School of Life SciencesNPUXi'an 710072P.R.China Faculty of Printing Packaging Engineeringand Digital Media TechnologyXi'an University of TechnologyXi'an 710048P.R.China

It is important to monitor the intra-/extracellular concentration of hydrogen peroxide(H_(2)O_(2))in biological ***,miniaturized devices that enable portable and accurate H_(2)O_(2)measurement are still in their infancy because of the difficulty of developing facile sensing strategies and highly integrated sensing *** this work,portable H_(2)O_(2)sensors based on Pt-Ni hydrogels with excellent peroxidase-like and electrocatalytic activities are ***,simple and sensitive H_(2)O_(2)sensing is achieved through both colorimetric and electrochemical *** as-fabricated H_(2)O_(2)sensing chips exhibit favorable performance,with low detection limits(0.030μM&0.15μM),wide linearity ranges(0.10μM-10.0 mM&0.50μM-5.0 mM),outstanding long-term stability(up to 60 days),and excellent *** the aid of an M5stack development board,portable visual and electrochemical H_(2)O_(2)sensors are successfully constructed without complicated and expensive equipment or professional *** applied to the detection of H_(2)O_(2)released from HeLa cells,the results obtained by the developed sensors are in good agreement with those from an ultraviolet‒visible spectrophotometer(UV‒vis)(1.97μM vs.2.08μM)and electrochemical station(1.77μM vs.1.84μM).

关键词： electrochemical peroxide ultraviolet

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Small extrachromosomal circular DNA in amyotrophic lateral sclerosis matter

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Neural Regeneration research 2025年第5期20卷 1411-1413页

作者： Marcos J.Arauzo-Bravo Daniela Gerovska Matthias Schwab Alexandra Kretz Computational biology and Systems Biomedicine Biodonostia Health Research InstituteSan SebastianSpain Basque Foundation for Science IKERBASQUEBilbaoSpainMax Planck Institute for Molecular BiomedicineComputational Biology and Bioinformatics GroupMünsterNorth Rhine-WestphaliaGermany Department of Cell biology and Histology Faculty of Medicine and NursingUniversity of Basque Country(UPV/EHU)LeioaSpain Department of Neurology Jena University HospitalJenaThuringiaGermany

Comprehensive studies identify motor neuron spectrum disorders including amyotrophic lateral sclerosis(ALS)as globally rising fatal disorders with the highest prevalence in aging populations,influenced by ethnicity and ancestry(GBD 2016 Motor Neuron Disease Colla borators,2018).While~10% of diagnoses involve a family history(fALS),most cases are considered sporadic(sALS).However,population-based studies suggest that even cases without a common index mutation impart heritability(Ryan et al.,2019),indicating a crucial role of rare and as yet unknown genetic denominators.

关键词： amyotrophic sclerosis

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PINK1 mediates neuronal survival in monkey

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Protein & Cell 2022年第1期13卷 4-5页

作者： Zhiyu Sun Jiangyu Ye Junying Yuan interdisciplinary research center on biology and Chemistry Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghai 201210China

Parkinson's disease(PD)is one of the most common neu-rodegenerative diseases with progressive motor dysfunction and pathologically characterized by the degeneration of dopaminergic neurons in the substantia nigra of the midbrain and the development of neuronal Lewy *** recessive mutations in the gene PINK1 leads to inherited idiopathic ***1 is known to regulate PARKIN translocation upon mitochondrial damage which drives their removal via selective autophagy,a process known as mito-phagy(Pickrell and Youle 2015;Cummins and Gotz 2018).While mitochondrial defects had been noted in postmortem studies of patient brain samples with PD,there is a continuing debate as how mutations in PINK1 may lead to selective neuronal death in the substantia nigra.

关键词： PINK1 PARK degeneration

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无溶剂合成以Co-N物种为活性位点的Co@NC催化剂用于芳香硝基化合物选择加氢

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Science China Materials 2023年第1期66卷 169-178页

作者：魏海生宋华兴任煜京颜晓瑞方葛钱王文华任万忠朱明远林坚 College of Chemistry and Chemical Engineering Yantai UniversityYantai 264005China CAS Key Laboratory of Science and Technology on Applied catalysis Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023China interdisciplinary research center of biology&catalysis School of Life SciencesNorthwestern Polytechnical UniversityXi’an 710072China

金属有机骨架(MOFs)衍生的Co基催化剂用于芳香硝基化合物选择加氢引起了广泛的关注,但催化剂合成过程中使用大量溶剂,且对催化剂中活性中心的认识存在争议.本文开发了一种固相合成策略,在不使用任何溶剂的情况下获得MOF前体材料,经发泡... 详细信息

金属有机骨架(MOFs)衍生的Co基催化剂用于芳香硝基化合物选择加氢引起了广泛的关注,但催化剂合成过程中使用大量溶剂,且对催化剂中活性中心的认识存在争议.本文开发了一种固相合成策略,在不使用任何溶剂的情况下获得MOF前体材料,经发泡和热解处理获得Co@NC催化剂.研究发现,800℃热解所得的催化剂中Co纳米颗粒被氮掺杂石墨烯壳层包裹,在3-硝基苯乙烯的加氢过程中表现出~100%的转化率,3-乙烯基苯胺的选择性大于99%,同时,该催化剂具有良好的循环稳定性和底物普适性.表征和实验结果证明该催化剂中Co–N物种为活性中心,其含量可通过热解温度进行调变,且催化性能与Co–N物种的含量存在正相关关系.本工作为设计用于选择加氢反应的高效Co基催化剂提供了一种新的绿色合成策略.

关键词：芳香硝基化合物金属有机骨架氮掺杂石墨烯活性中心合成策略选择加氢加氢过程固相合成

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