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Connecting past and present:single-cell lineage tracing

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Protein & Cell 2022年第11期13卷 790-807页

作者： Cheng Chen Yuanxin Liao guangdun peng Center for Cell Lineage and Development CAS Key Laboratory of Regenerative BiologyGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineGIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research CentreGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou 510530China Center for Cell Lineage and Atlas Bioland Laboratory(Guangzhou Regenerative Medicine and Health Guangdong Laboratory)Guangzhou 510005China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Central to the core principle of cell theory,depicting cells'history,state and fate is a fundamental goal in modern *** leveraging clonal analysis and sin-gle-cell RNA-seq technologies,single-cell lineage trac-ing provides new opportunities to interrogate both cell states and lineage *** the past few years,many strategies to achieve lineage tracing at single-cell resolution have been developed,and three of them(in-tegration barcodes,polylox barcodes,and CRISPR barcodes)are noteworthy as they are amenable in experimentally tractable *** the above strategies have been demonstrated in animal develop-ment and stem cell research,much care and effort are still required to implement these *** we review the development of single-cell lineage tracing,major characteristics of the cell barcoding strategies,applications,as well as technical considerations and limitations,providing a guide to choose or improve the single-cell barcoding lineage tracing.

关键词： single-cell lineage tracing integration barcodes polylox barcodes CRISPR barcodes

维普期刊数据库

Spatial transcriptomics: new dimension of understanding biological complexity

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Biophysics Reports 2022年第3期8卷 119-135页

作者： Zhuxia Li guangdun peng Ceter for Cell Lineage and Development CAS Key Laboratory of Regenerative Biology Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine Guangzhou Institutes of Biomedicine and Health Chinese Academy of Sciences University of Chinese Academy of Sciences Center for Cell Lineage and Atlas Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory) Institute for Stem Cell and Regeneration Chinese Academy of Sciences

Cells and tissues are exquisitely organized in a complex but ordered manner to form organs and bodies so that individuals can function properly. The spatial organization and tissue architecture represent a keynote property underneath all living organisms. Molecular architecture and cellular composition within intact tissues play a vital role in a variety of biological processes, such as forming the complicated tissue functionality, precise regulation of cell transition in all living activities, consolidation of central nervous system, cellular responses to immunological and pathological cues. To explore these biological events at a large scale and fine resolution, a genome-wide understanding of spatial cellular changes is essential. However, previous bulk RNA sequencing and single-cell RNA sequencing technologies could not obtain the important spatial information of tissues and cells, despite their ability to detect high content transcriptional changes. These limitations have prompted the development of numerous spatially resolved technologies which provide a new dimension to interrogate the regional gene expression, cellular microenvironment, anatomical heterogeneity and cell-cell interactions. Since the advent of spatial transcriptomics, related works that use these technologies have increased rapidly, and new methods with higher throughput and resolution have grown quickly, all of which hold great promise to accelerate new discoveries in understanding the biological complexity. In this review, we briefly discussed the historical evolution of spatially resolved transcriptome. We broadly surveyed the representative methods. Furthermore, we summarized the general computational analysis pipeline for the spatial gene expression data. Finally, we proposed perspectives for technological development of spatial multi-omics.

关键词： Spatial transcriptomics Spatial data analysis Spatial multi-omics Histology Single-cell sequencing

Comments on ‘Molecular architecture of lineage allocation and tissue organization in early mouse embryo’

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Journal of Molecular Cell Biology 2019年第11期11卷 1024-1025页

作者： Guizhong Cui Naihe jing guangdun peng Guangzhou Regenerative Medicine and Health Guangdong Laboratory(GRMH-GDL) GuangzhouChina State Key Laboratory of Cell Biology CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouChina Institute for Stem Cells and Regeneration Chinese Academy of SciencesBeijingChina

Single-cell RNA-seq,with its capability to align cells of continuously changed status by pseudo-time reconstruction,has greatly revolutionized the understanding of cell fate transition during embryo development(Shapir... 详细信息

关键词： al. continuously embryo

Lineage specification of early embryos and embryonic stem cells at the dawn of enabling technologies

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National Science Review 2017年第4期4卷 533-542页

作者： guangdun peng Patrick P.L.Tam Naihe Jing State Key Laboratory of Cell Biology CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of SciencesUniversity of Chinese Academy of Sciences Embryology Unit Children’s Medical Research Institute School of Medical SciencesSydney Medical School University of Sydney School of Life Science and Technology Shanghai Tech University

Establishment of progenitor cell populations and lineage diversity during embryogenesis and the differentiation of pluripotent stem cells is a fascinating and intricate biological process. Conceptually, an understanding of this developmental process provides a framework to integrate stem-cell pluripotency, cell competence and differentiating potential with the activity of extrinsic and intrinsic molecular *** recent advent of enabling technologies of high-resolution transcriptome analysis at the cellular,population and spatial levels proffers the capability of gaining deeper insights into the attributes of the gene regulatory network and molecular signaling in lineage specification and differentiation. In this review, we provide a snapshot of the emerging enabling genomic technologies that contribute to the study of development and stem-cell biology.

关键词： early development cell lineage cell identity scRNA-seq spatial transcriptome

Integration of Computational Analysis and Spatial Transcriptomics in Single-cell Studies

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 13-23页

作者： Ran Wang guangdun peng Patrick P.L.Tam Naihe Jing State Key Laboratory of Cell Biology CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai 200031China CAS Key Laboratory of Regenerative Biology Guangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou 510530China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China Embryology Research Unit Children’s Medical Research InstituteUniversity of SydneySydneyNSW 2145Australia School of Medical Sciences Faculty of Medicine and HealthUniversity of SydneySydneyNSW 2145Australia Guangzhou Laboratory Guangzhou 510005China

Recent advances of single-cell transcriptomics technologies and allied computational methodologies have revolutionized molecular cell ***,pioneering explorations in spatial transcriptomics have opened up avenues to address fundamental biological questions in health and ***,we review the technical attributes of single-cell RNA sequencing and spatial transcriptomics,and the core concepts of computational data *** further highlight the challenges in the application of data integration methodologies and the interpretation of the biological context of the findings.

关键词： scRNA-seq Computational methodology Spatial transcriptome Data integration Mathematical model

Lung development and regeneration:newly defined cell types and progenitor status

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Cell Regeneration 2023年第1期12卷 271-283页

作者： Xiaogao Meng Guizhong Cui guangdun peng Center for Cell Lineage and Development Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou 510530GuangdongChina Life Science and Medicine University of Science and Technology of ChinaHefei 230026AnhuiChina School of Basic Medical Sciences Guangzhou LaboratoryGuangzhou Medical UniversityGuangzhou 510005China

The lung is the most critical organ of the respiratory system supporting gas *** interaction with the external environment makes the lung vulnerable to ***,a deeper understanding of cellular and molecular processes underlying lung development programs and evaluation of progenitor status within the lung is an essential part of lung regenerative *** this review,we aim to discuss the current understanding of lung development process and regenerative *** highlight the advances brought by multi-omics approaches,single-cell transcriptome,in particular,that can help us further dissect the cellular player and molecular signaling underlying those processes.

关键词： Lung development Regeneration Stem cell Progenitor scRNA-seq Lineage tracing

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CREST:高通量单细胞谱系示踪新工具

科学通报 2023年第27期68卷 3559-3561页

作者：廖远鑫彭广敦中国科学院广州生物医药与健康研究院广州510530

细胞谱系是指发育过程中产生的细胞类型及其先后代关系.高等动物的细胞类型多样,在发育、再生、癌变等不同的生命过程中,细胞谱系有不同的组成和变化[1].研究发育谱系能帮助我们厘清各类细胞所处的发育阶段与功能,对理解相关的发育疾病... 详细信息

细胞谱系是指发育过程中产生的细胞类型及其先后代关系.高等动物的细胞类型多样,在发育、再生、癌变等不同的生命过程中,细胞谱系有不同的组成和变化[1].研究发育谱系能帮助我们厘清各类细胞所处的发育阶段与功能,对理解相关的发育疾病机制、再生修复机理有着重要的作用.

关键词：细胞类型细胞谱系发育阶段修复机理高通量单细胞谱系示踪疾病机制

维普期刊数据库

Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells

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Cell Regeneration 2023年第1期12卷 317-337页

作者： He Jax Xu Yao Yao Fenyong Yao Jiehui Chen Meishi Li Xianfa Yang Sheng Li Fangru Lu Ping Hu Shuijin He guangdun peng Naihe Jing State Key Laboratory of Cell Biology CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesShanghai 200031China University of Chinese Academy of Sciences BeijingChina School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China Center for Cell Lineage and Development CAS Key Laboratory of Regenerative BiologyGuangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineGIBH‑HKU Guangdong‑Hong Kong Stem Cell and Regenerative Medicine Research CentreGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhou 510530China Guangzhou Laboratory/Bioland Laboratory Guangzhou 510005China Xinhua Hospital affiliated to Shanghai Jiao Tong University School of Medicine Shanghai 20023China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China Center for Cell Lineage and Atlas Bioland LaboratoryGuangzhou 510005China

Spinal motor neurons deficiency results in a series of devastating disorders such as amyotrophic lateral sclerosis(ALS),spinal muscular atrophy(SMA)and spinal cord injury(SCI).These disorders are currently incurable,while human pluripotent stem cells(hPSCs)-derived spinal motor neurons are promising but suffered from inappropriate regional identity and functional immaturity for the study and treatment of posterior spinal cord related *** this study,we have established human spinal cord neural progenitor cells(hSCNPCs)via hPSCs differentiated neuromesodermal progenitors(NMPs)and demonstrated the hSCNPCs can be continuously expanded up to 40 *** can be rapidly differentiated into posterior spinal motor neurons with high *** functional maturity has been examined in ***,a co-culture scheme which is compatible for both neural and muscular differentiation is developed to mimic the neuromuscular junction(NMJ)formation in ***,these studies highlight the potential avenues for generating clinically relevant spinal motor neurons and modeling neuromuscular diseases through our defined hSCNPCs.

关键词： Motor neuron Motor neuron differentiation Neuromesodermal progenitors Neuromuscular junction

Mouse knockout models reveal largely dispensable but context-dependent functions of IncRNAs during development

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Journal of Molecular Cell Biology 2018年第2期10卷 175-178页

作者： Xue Han Sai Luo guangdun peng Yuyang Lu Guizhong Cui Lichao Liu Pixi Yan Yafei Yin Wei Liu Ran Wang Jiejie Zhang Shanshan Ai Zai Chang Jie Na Aibin He Naihe Jing Xiaohua Shen Tsinghua-Peking Center for Life Sciences School of Medicine Tsinghua University Beijing 100084 China State Key Laboratory of Cell Biology CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy ofSciences University of Chinese Academy ofSciences Shanghai 200031 China Peking Center for Life Sciences Institute of Molecular Medicine Beijing Key Laboratory ofCardiometabolic Molecular Medicine PekingUniversity Beijing 100871 China School of Life Sciences Tsinghua UniversityBeijing 100084 China Program in Cellular and Molecular Medicine Boston Children's Hospital Department of Genetics Harvard Medical School Boston MA 02115 USA

Dear Editor, In mammalian genomes, pervasive transcription produces thousands of long non-coding RNA （IncRNA） transcripts （Olebali et al., 2012; Hon et al., 2017）. Compared to protein-coding mRNAs, IncRNAs are less conserved, and often exhibit low-level, developmental stage-and tissue-specific expression （Pauli et al., 2011; Hu et al., 2012; Lee, 2012; Ulitsky and Bartel, 2013; Cech and Steitz, 2014; Hon et al., 2017）. Many IncRNAs are strongly correlated with their neighboring mRNA genes in terms of expression and function, and tend to regulate nearby transcription （Orom et al., 2010; Engreitz et al., 2016; Luo etal., 2016）. It has been implicated that IncRNAs play versatile roles in regulating diverse aspects of cell biology through mechanisms at multiple levels （Pauli et al., 2011; Lee.

关键词：泡利不相容原理上下文编码蛋白质开发模型鼠标 mRNA 哺乳动物