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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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STOCHASTIC SYNCHRONIZATION OF CIRCADIAN RHYTHMS

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Journal of Systems Science & Complexity 2010年第5期23卷 978-988页

作者： RajKumar Brojen SINGH Vikram SINGH Ram RAMASWAMY centre for interdisciplinary Research in Basic Sciences Jamia Milia Islamia New Delhi 110025 India Center for Computational Biology and bioinformatics School of Information Technology Jawaharlal Nehru University New Delhi 110067 India Center for Computational Biology and bioinformatics School of Information Technology and School of Physical Sciences Jawaharlal Nehru University New Delhi 110067 India

Models of circadian genetic oscillators involving interlinked feedback processes in molecular level genetic networks in Drosophila melanogaster and Neurospora crassa are studied, and mechanisms whereby synchronization can arise in an assembly of cells are examined. The individual subcellular circadian oscillatory processes are stochastic in nature due to the small numbers of molecules that are involved, and are subject to large fluctuations. The authors investigate and present the simulations of the stochastic dynamics of ensembles of clock-regulating proteins in different nuclei that communicate via ancillary small molecules, environmental parameters, additive cellular noise, or through diffusive processes. The results show that the emergence of collective oscillations is a macroscopic observable which has its origins in the microscopic coupling between distinct cellular oscillators.

关键词： Coupling stochastic dynamics synchrony.

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Monascus pilosus-fermented black soybean inhibits lipid accumulation in adipocytes and in high-fat diet-induced obese mice

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Asian Pacific Journal of Tropical Medicine 2015年第4期8卷 276-282页

作者： Young-Sil Lee Bong-Keun Choi Hae Jin Lee Dong-Ryung Lee Jinhua Cheng Won-Keun Lee Seung Hwan Yang Joo-Won Suh Center for Nutraceutical and Pharmaceutical Materials Myongji University interdisciplinary Program of Biomodulation Myongji University Division of Bioscience and bioinformatics College of Natural ScienceMyongji University

Objective:To explore the anti-obesity effects and the mechanism of action of Monascus pilosus(***)-fermented black soybean(MFBS)extracts(MFBSE)and MFBS powders(MFBSP)in adipocytes and high-fat diet(HFD)-induced obese mice,***:Black soybean was fermented with ***,and the main constituents in MFBS were analyzed by HPLC *** vitro,MFBSE were examined for anti-adipogenic effects using Oil-Red O *** vivo,mice were fed a normal-fat diet(NFD)control,HFD control or HFD containing 1 g/kg MFBSP for 12 weeks,and then body weight gain and tissues weight ***-time PCR and western blot assay were used to determine the mechanism of anti-adipogenic ***:MFBSE inhibited lipid accumulation in 3T3-L1 adipocytes without exerting cell *** treatment in HFD-fed mice significantly decreased the body weight gain compared with the HFD control *** and MFBSP treatment resulted in significantly lower mRNA levels of adipogenesis-related genes,such as peroxisome proliferator-activated receptorγ(PPARγ),fatty acid-binding protein 4(FABP4),and fatty acid synthase(FAS),in adipocytes and in white adipose tissue(WAT)of HFD-induced obese ***:These results suggest that the anti-obesity effects of MFBS are elicited by regulating the expression of adipogenesis-related genes in adipocytes and WAT of HFDinduced obese mice.

关键词： Monascus pilosus Black soybean Adipocytes High-fat diet-induced obese mice Anti-obesity Adipogenesis-related genes

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Structural and Functional Analysis of NS1 and NS2 Proteins of H1N1 Subtype

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Genomics, Proteomics & bioinformatics 2010年第3期8卷 190-199页

作者： Parveen Salahuddin Asad U.Khan Distributed Information Sub-centre Interdisciplinary Biotechnology UnitAligarh Muslim University

Influenza A virus （H1N1）, a genetic reassortment of endemic strains of human, avian and swine flu, has crossed species barrier to human and apparently acquired the capability of human to human transmission. Some strains of H5N1 subtype are highly virulent because NS 1 protein inhibits antiviral interferon α/β production. Another protein NS2 mediates export of viral ribonucleoprotein from nucleus to the cytoplasm through export signal. In this paper, we have studied structure-function relationships of these proteins of H1N1 subtype and have determined the cause of their pathogenicity. Our results showed that non-conservative mutations slightly stabilized or destabilized structural domains of NS1 or NSI-dsRNA complex, hence slightly increased or decreased the function of NS 1 protein and consequently enhanced or reduced the pathogenicity of the H1N1 virus. NS2 protein of different strains carried non-conservative mutations in different domains, resulting in slight loss of function. These mutations slightly decreased the pathogenicity of the virus. Thus, the results confirm the structure-function relationships of these viral proteins.

关键词： influenza A virus H1N1 pathogenicity NS2 NS1

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Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data

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National Science Review 2016年第2期3卷 240-251页

作者： Yong Wang Rui Jiang Wing Hung Wong Department of Statistics Department of Biomedical Data ScienceBio-X ProgramStanford University Academy of Mathematics and Systems Science National Center for Mathematics and Interdisciplinary SciencesChinese Academy of Sciences MOE Key Laboratory of bioinformatics Bioinformatics Division and Center for Synthetic and Systems BiologyTNLISTDepartment of AutomationTsinghua University

Cell packs a lot of genetic and regulatory information through a structure known as chromatin,*** is wrapped around histone proteins and is tightly packed in a remarkable *** express a gene in a specific coding region,the chromatin would open up and DNA loop may be formed by interacting enhancers and ***,the mediator and cohesion complexes,sequence-specific transcription factors,and RNA polymerase Ⅱ are recruited and work together to elaborately regulate the expression *** is in pressing need to understand how the information,about when,where,and to what degree genes should be expressed,is embedded into chromatin structure and gene regulatory *** to large consortia such as Encyclopedia of DNA Elements(ENCODE) and Roadmap Epigenomic projects,extensive data on chromatin accessibility and transcript abundance are available across many tissues and cell *** rich data offer an exciting opportunity to model the causal regulatory ***,we will review the current experimental approaches,foundational data,computational problems,interpretive frameworks,and integrative models that will enable the accurate interpretation of regulatory ***,we will discuss the efforts to organize,analyze,model,and integrate the DNA accessibility data,transcriptional data,and functional genomic regions *** believe that these efforts will eventually help us understand the information flow within the cell and will influence research directions across many fields.

关键词： gene regulatory network open chromatin DNA accessibility transcription factor colocalization statistical model data integration

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Single-cell trajectories of melanoma cell resistance to targeted treatment

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Cancer Biology & Medicine 2022年第1期19卷 56-73页

作者： Maria Schmidt Lena Sünke Mortensen Henry Loeffler-Wirth Corinna Kosnopfel Knut Krohn Hans Binder Manfred Kunz interdisciplinary centre for bioinformatics University of LeipzigLeipzig 04107Germany Department of Dermatology Venereology and AllergologyUniversity of WürzburgWürzburg 97074Germany Core Unit DNA Technologies Medical FacultyUniversity of LeipzigLeipzig 04103Germany Department of Dermatology Venereology and AllergologyUniversity of Leipzig Medical CenterLeipzig 04103Germany

Objective:Cellular heterogeneity is regarded as a major factor affecting treatment response and resistance in malignant *** developments in single-cell sequencing technology have provided deeper insights into these ***:Here,we analyzed a BRAFV600 E-mutant melanoma cell line by single-cell RNA-seq under various conditions:cells sensitive to BRAF inhibition with BRAF inhibitor vemurafenib and cells resistant to BRAF inhibition with vemurafenib alone or vemurafenib in combination with the MEK1/2 inhibitors cobimetinib or *** reduction by t-distributed stochastic neighbor embedding and self-organizing maps identified distinct trajectories of resistance development clearly separating the 4 treatment conditions in cell and gene state ***:Trajectories associated with resistance to single-agent treatment involved cell cycle,extracellular matrix,and de-differentiation *** contrast,shifts detected in double-resistant cells primarily affected translation and mitogen-activated protein kinase pathway reactivation,with a small subpopulation showing markers of *** findings were validated in pseudotime analyses and RNA velocity ***:The single-cell transcriptomic analyses reported here employed a spectrum of bioinformatics methods to identify mechanisms of melanoma resistance to single-and double-agent *** study deepens our understanding of treatmentinduced cellular reprogramming and plasticity in melanoma cells and identifies targets of potential relevance to the management of treatment resistance.

关键词： Melanoma single-cell transcriptome sequencing treatment response

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Characterizing RNA Pseudouridylation by Convolutional Neural Networks

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Genomics, Proteomics & bioinformatics 2021年第5期19卷 815-833页

作者： Xuan He Sai Zhang Yanqing Zhang Zhixin Lei Tao Jiang Jianyang Zeng Institute for interdisciplinary Information Sciences Tsinghua UniversityBeijing 100084China Peking-Tsinghua Center for Life Sciences Peking UniversityBeijing 100871China Academy for Advanced interdisciplinary Studies Peking UniversityBeijing 100871China Department of Computer Science and Engineering University of CaliforniaRiversideCA 92521USA MOE Key Lab of bioinformatics and bioinformatics Division BNRIST/Department of Computer Science and TechnologyTsinghua UniversityBeijing 100084China Institute of Integrative Genome Biology University of CaliforniaRiversideCA 92521USA MOE Key Laboratory of bioinformatics Tsinghua UniversityBeijing 100084China

Pseudouridine(Ψ)is the most prevalent post-transcriptional RNA modification and is widespread in small cellular RNAs and m ***,the functions,mechanisms,and precise distribution ofΨs(especially in m RNAs)still remain largely *** landscape ofΨs across the transcriptome has not yet been fully ***,we present a highly effective model based on a convolutional neural network(CNN),called Pseudo Uridy Lation Site Estimator(PULSE),to analyze large-scale profiling data ofΨsites and characterize the contextual sequence features of ***,consisting of two alternatively-stacked convolution and pooling layers followed by a fully-connected neural network,can automatically learn the hidden patterns of pseudouridylation from the local sequence *** validation tests demonstrated that PULSE can outperform other state-of-the-art prediction methods and achieve high prediction accuracy,thus enabling us to further characterize the transcriptome-wide landscape ofΨ*** further showed that the prediction results derived from PULSE can provide novel insights into understanding the functional roles of pseudouridylation,such as the regulations of RNA secondary structure,codon usage,translation,and RNA stability,and the connection to single nucleotide *** source code and final model for PULSE are available at https://***/mlcb-thu/PULSE.

关键词： Pseudouridylation Convolution neural network Sequence motif Translation RNA stability

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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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Discovering peptides and computational investigations of a multiepitope vaccine target Mycobacterium tuberculosis

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Synthetic and Systems Biotechnology 2024年第3期9卷 391-405页

作者： Truc Ly Nguyen Heebal Kim Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National UniversitySeoul08826Republic of Korea interdisciplinary Program in bioinformatics Seoul National UniversitySeoul08826Republic of Korea eGnome Inc.Seoul05836Republic of Korea

Mycobacterium tuberculosis(MTB)is the causative agent of tuberculosis(TB),a prevalent airborne infectious *** the availability of the Bacille Calmette-Guerin vaccine,its global efficacy remains modest,and tuberculosis persists as a significant global public health *** this challenge and advancing towards the End MTB Strategy,we developed a multiepitope vaccine(MEV)based on immunoinformatics and compu-tational *** screening of MBT protein identified immune-dominant epitopes based on Major Histocompatibility Complex(MHC)allele binding,immunogenicity,antigenicity,allergenicity,toxicity,and cytokine *** epitopes were integrated into an MEV construct with adjuvant and linkers,forming a fully immunogenic vaccine *** analyses encompassed the evaluation of immunological and physicochemical properties,determination of tertiary structure,molecular docking with Toll-Like Receptors(TLR),molecular dynamics(MD)simulations for all atoms,and immune *** MEV comprises 534 amino acids,featuring 6 cytotoxic T lymphocyte,8 helper T lymphocyte,and 7 linear B lymphocyte epitopes,demonstrating high antigenicity and ***,molecular docking studies and triplicate MD simulations revealed enhanced interactions and stability of MEV with the TLR4 complex compared to *** addition,the immune simulation indicated the capacity to effectively induce elevated levels of an-tibodies and cytokines,emphasizing the vaccine’s robust immunogenic *** study presents a promising MEV against TB,exhibiting favorable immunological and physicochemical *** findings provide theoretical support for TB vaccine *** study aligns with the global initiative of the End MTB Strategy,emphasizing its potential impact on addressing persistent challenges in TB control.

关键词： Mycobacterium tuberculosis Tuberculosis Multiepitope vaccine Docking molecular Molecular dynamics simulation Immune simulation

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dbSCI:A manually curated database of SARS-CoV-2 inhibitors for COVID-19

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BIOCELL 2023年第2期47卷 367-371页

作者： QIANG WANG GUO ZHAO LONGXIANG XIE XUAN LI XIXI YU QIONGSHAN LI BAOPING ZHENG ZULIPINUER WUSIMAN XIANGQIAN GUO Institute of Biomedical Informatics School of SoftwareBioinformatics CenterHenan Provincial Engineering Center for Tumor Molecular MedicineSchool of Basic Medical SciencesAcademy for Advanced Interdisciplinary StudiesHenan UniversityKaifeng475004China

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)is the pathogen of the ongoing coronavirus disease 2019(COVID-19)global ***,by centralizing published cell-based experiments,clinical trials,and virtual drug screening data from the NCBI PubMed database,we developed a database of SARS-CoV-2 inhibitors for COVID-19,dbSCI,which includes 234 SARS-CoV-2 inhibitors collected from publications based on cell-based experiments,81 drugs of COVID-19 in clinical trials and 1305 potential SARS-CoV-2 inhibitors from bioinformatics *** provides four major functions:(1)search the drug target or its inhibitor for SARS-CoV-2,(2)browse target/inhibitor information collected from cell experiments,clinical trials,and virtual drug screenings,(3)download,and(4)submit *** entry in dbSCI contains 18 types of information,including inhibitor/drug name,targeting protein,mechanism of inhibition,experimental technique,experimental sample type,and reference *** summary,dbSCI provides a relatively comprehensive,credible repository for inhibitors/drugs against SARS-CoV-2 and their potential targeting mechanisms and it will be valuable for further studies to control COVID-19.

关键词： SARS-CoV-2 COVID-19 Inhibitors Drugs Database

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