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Plant Communications 2023年第5期4卷 46-62页

作者： Renhui Li Zhifeng Wang Jia-Wei Wang Laigeng Li National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China University of the Chinese Academy of Sciences Beijing 100049China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China

Primary and secondary growth of the tree stem are responsible for corresponding increases in trunk height and ***,our molecular understanding of the biological processes that underlie these two types of growth is *** this study,we used single-cell RNA sequencing and spatial transcriptome sequencing to reveal the transcriptional landscapes of primary and secondary growth tissues in the Populus *** between the cell atlas and differentiation trajectory of primary and secondary growth revealed different regulatory networks involved in cell differentiation from cambium to xylem precursors and phloem *** regulatory networks may be controlled by auxin accumulation and *** of cell differentiation trajectories suggested that vessel and fiber development followed a sequential pattern of progressive transcriptional *** research provides new insights into the processes of cell identity and differentiation that occur throughout primary and secondary growth of tree stems,increasing our understanding of the cellular differentiation dynamics that occur during stemgrowth in trees.

关键词： scRNA-seq spatial transcriptome primary growth secondary growth secondary cell wall SCW Populus

High-resolution anatomical and spatial transcriptome analyses reveal two types of meristematic cell pools within the secondary vascular tissue of poplar stem

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Molecular Plant 2023年第5期16卷 809-828页

作者： Juan Du Yichen Wang Wenfan Chen Mingling Xu Ruhong Zhou Huixia Shou Jun Chen State Key Laboratory of Plant Physiology and Biochemistry College of Life SciencesZhejang University866Yu Hangtang RoadHangzhouZhejiang 310058China MOE Key Laboratory of Biosystems Homeostasis&Protection College of Life SciencesZhejang University866 Yu Hangtang RoadHangzhouZhejang 310058China Institute of Quantitative Biology College of Life SciencesZhejiang UniversityHangzhouZhejiang 310058China Hangzhou Botanical Garden Taoyuanling RoadHangzhouZhejiang 310013China

The secondary vascular tissue emanating from meristems is central to understanding how vascular plants such as forest trees evolve,grow,and regulate secondary radial ***,the overall molecular characterization of meristem origins and developmental trajectories from primary to secondary vascular tissues in woody tree stems is technically *** this study,we combined high-resolution anatomic analysis with a spatial transcriptome(ST)technique to define features of meristematic cells in a developmental gradient from primary to secondary vascular tissues in poplar *** tissue-specific gene expression of meristems and derived vascular tissue types were accordingly mapped to specific anatomical *** analyses were used to track the origins and changes of meristems throughout the development from primary to secondary vascular ***,two types of meristematic-like cell pools within secondary vascular tissues were inferred based on high-resolution microscopy combined with ST,and the results were confirmed by in situ hybridization of,transgenic trees,and single-cell *** rectangle shape procambium-like(PCL)cells develop from procambium meristematic cells and are located within the phloem domain to produce phloem cells,whereas fusiform shape cambium zone(CZ)meristematic cells develop from fusiform metacambium meristematic cells and are located inside the CZ to produce xylem *** gene expression atlas and transcriptional networks spanning the primary transition to secondary vascular tissues generated in this work provide new resources for studying the regulation of meristem activities and the evolution of vascular plants.A web server(https://***/stRNAPal/)was also established to facilitate the use of ST RNA-seq data.

关键词： poplar stem primary and secondary meristem primary and secondary vascular tissue spatial transcriptome single-cell sequencing

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

Aging hallmarks of the primate ovary revealed by spatiotemporal transcriptomics

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Protein & Cell 2024年第5期15卷 364-384页

作者： Huifen Lu Ying Jing Chen Zhang Shuai Ma Weiqi Zhang Daoyuan Huang Bin Zhang Yuesheng Zuo Yingying Qin Guang-Hui Liu Yang Yu Jing Qu Si Wang Advanced Innovation Center for Human Brain Protection National Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Aging Translational Medicine Center International Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuanwu HospitalCapital Medical UniversityBeijing 100053China State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China Institute for Stem cell and Regeneration CASBeijing 100101China China National Center for Bioinformation Beijing 100101China The Fifth People’s Hospital of Chongqing Chongqing 400062China Sino-Danish College University of Chinese Academy of SciencesBeijing 101408China Sino-Danish Center for Education and Research Beijing 101408China Department of Obstetrics and Gynecology Center for Reproductive MedicinePeking UniversityThird HospitalBeijing 100191China Clinical Stem Cell Research Center Peking UniversityThird HospitalBeijing 100191China Center for Reproductive Medicine Cheeloo College of MedicineShandong UniversityJinan 250012China Key Laboratory of Reproductive Endocrinology of Ministry of Education National Research Center for Assisted Reproductive Technology and Reproductive GeneticsShandong Key Laboratory of Reproductive MedicineShandong Provincial Clinical Research Center for Reproductive HealthJinan 250012China Key Laboratory of Organ Regeneration and Reconstruction Institute of ZoologyChinese Academy of SciencesBeijing 100101China Aging Biomarker Consortium Beijing 100101China

The ovary is indispensable for female reproduction,and its age-dependent functional decline is the primary cause of ***,the molecular basis of ovarian aging in higher vertebrates remains poorly ***,we apply spatiotemporal transcriptomics to benchmark architecture organization as well as cellular and molecular determinants in young primate ovaries and compare these to aged primate *** a global view,somatic cells within the non-follicle region undergo more pronounced transcriptional fluctuation relative to those in the follicle region,likely constituting a hostile microenvironment that facilitates ovarian ***,we uncovered that inflammation,the senescent-associated secretory phenotype,senescence,and fibrosis are the likely primary contributors to ovarian aging(PCOA).Of note,we identified spatial co-localization between a PCOA-featured spot and an unappreciated MT2(Metallothionein 2)highly expressing spot(MT2^(high))characterized by high levels of inflammation,potentially serving as an aging hotspot in the primate ***,with advanced age,a subpopulation of MT2^(high)accumulates,likely disseminating and amplifying the senescent signal *** study establishes the first primate spatiotemporal transcriptomic atlas,advancing our understanding of mechanistic determinants underpinning primate ovarian aging and unraveling potential biomarkers and therapeutic targets for aging and age-associated human ovarian disorders.

关键词： spatial transcriptome primate ovary aging senescence inflammation

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Single-cell spatial transcriptomics in cardiovascular development,disease,and medicine

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Genes & Diseases 2024年第6期11卷 192-204页

作者： Songjie Han Qianqian Xu Yawen Du Chuwei Tang Herong Cui Xiaofeng Xia Rui Zheng Yang Sun Hongcai Shang Key Laboratory of Chinese Internal Medicine of Ministry of Education Dongzhimen HospitalBeijing University of Chinese MedicineBeijing 100700China School of Life Sciences Beiing University of Chinese MedicineBeijing 102488China

Cardiovascular diseases(CVDs)impose a significant burden *** the elucidation of the etiology and underlying molecular mechanisms of cvDs by numerous studies and recent discovery of effective drugs,their morbidity,disability,and mortality are still ***,precise risk stratification and effective targeted therapies for CvDs are *** improvements in single-cell RNA sequencing and spatial transcriptomics have improved our understanding of the mechanisms and cells involved in cardiovascular phylogeny and ***-cell RNA sequencing can facilitate the study of the human heart at remarkably high res-olution and cellular and molecular ***,this technique does not provide spatial information,which is essential for understanding homeostasis and *** tran-scriptomics can elucidate intracellular interactions,transcription factor distribution,cell spatial localization,and molecular profiles of mRNA and identify cell populations causing the disease and their underlying mechanisms,including cell ***,we introduce the main methods of RNA-seq and spatial transcriptomics analysis and highlight the latest ad-vances in cardiovascular *** conclude that single-cell RNA sequencing interprets dis-ease progression in multiple dimensions,levels,perspectives,and dynamics by combining spatial and temporal characterization of the clinical phenome with multidisciplinary tech-niques such as spatial *** aligns with the dynamic evolution of CVDs(e.g.,"angina-myocardial infarction-heart failure"in coronary artery disease).The study of pathways for disease onset and mechanisms(e.g.,age,sex,comorbidities)in different patient subgroups should improve disease diagnosis and risk *** can facilitate precise individualized treatment of CVDs.

关键词： Cardiovascular disease Precision medicine Single-cellspatial transcriptomics Single-cell transcriptome spatial transcriptome Transcriptomics

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

Microbiota-mediated shaping of mouse spleen structure and immune function characterized by scRNA-seq and Stereo-seq

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Journal of Genetics and Genomics 2023年第9期50卷 688-701页

作者： Yin Zhang Juan Shen Wei Cheng Bhaskar Roy Ruizhen Zhao Tailiang Chai Yifei Sheng Zhao Zhang Xueting Chen Weiming Liang Weining Hu Qijun Liao Shanshan Pan Wen Zhuang Yangrui Zhang Rouxi Chen Junpu Mei Hong Wei Xiaodong Fang College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China BGI-Shenzhen ShenzhenGuangdong 518083China College of Animal Sciences and Technology Huazhong Agricultural UniversityWuhanHubei 430070China BGI-Qingdao BGI-ShenzhenQingdaoShandong 266555China BGI-Sanya BGI-ShenzhenSanyaHainan 572025China Precision Medicine Institute The First Affiliated HospitalSun Yat-sen UniversityGuangzhouGuangdong 510080China

Gut microbes exhibit complex interactions with their hosts and shape an organism's immune system throughout its *** the largest secondary lymphoid organ,the spleen has a wide range of immunological *** explore the role of microbiota in regulating and shaping the spleen,we employ scRNA-seq and Stereo-seq technologies based on germ-free(GF)mice to detect differences in tissue size,anatomical structure,cell types,functions,and spatial molecular *** identify 18 cell types,9 subtypes of T cells,and 7 subtypes of B *** differential expression analysis reveals that the absence of microorganisms results in alterations in erythropoiesis within the red pulp region and congenital immune deficiency in the white pulp ***-seq results demonstrate a clear hierarchy of immune cells in the spleen,including marginal zone(MZ)macrophages,MZ B cells,follicular B cells and T cells,distributed in a well-defined pattern from outside to ***,this hierarchical structure is disturbed in GF ***7 and Cxcl13 chemokines are specifically expressed in the spatial locations of T cells and B cells,*** speculate that the microbiota may mediate the structural composition or partitioning of spleen immune cells by modulating the expression levels of chemokines.

关键词： ScRNA-seq spatial transcriptome GF mouse Spleen structure Microbiota Immune function

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spatial transcriptomic analysis deciphers adipocyte-to-fibroblast transformation in bleomycin-induced murine skin fibrosis

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中华医学杂志(英文版) 2024年第22期137卷 2745页

作者： Zhang Yixiang He Jiahao Xie Fangzhou Shan Shengzhou Qin Jiaqi Wang Chuandong Li Qingfeng Xie Yun Fang Bin Department of Plastic & Reconstructive Surgery Shanghai Ninth People’s Hospital Shanghai Jiao Tong University School of Medicine Shanghai China Shanghai Institute for Plastic and Reconstructive Surgery Shanghai China. Department of Plastic &amp Department of Orthopedic Surgery Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM) Shanghai China

Background: Scleroderma is characterized by inflammation and fibrosis, predominantly occurring in the skin and extending to various parts of the body. The pathophysiology of scleroderma is multifaceted, with the current understanding including endothelial damage, inflammatory cell infiltration, and fibroblast activation in its progression. Nonetheless, the mechanism of cellular interactions and the precise spatial distribution of these cellular events within the fibrotic tissues remain elusive, highlighting a critical gap in our comprehensive understanding of scleroderma’s ***: In this study, we administered bleomycin intradermally to the dorsal skin of four individual murine models. Subsequently, skin tissues were harvested at predetermined intervals for comprehensive spatial transcriptomic analysis to determine the spatial dynamics influencing scleroderma pathogenesis. To validate the possible results from bioinformatic analysis, furtherin vitro andin vivo experiments were ***: Analysis of the spatial transcriptome revealed significant alterations in cell clusters during the progression of scleroderma. Gene Ontology analysis identified disruptions in lipid metabolism as the disease advanced. Pseudotime analysis provided evidence for a phenotypic transition from adipocytes to *** vitro studies demonstrated increased expression of Col1a1 and α-SMA as the disease progressed. These fibroblasts have been identified as key contributors to the increasing inflammation. Co-culturing TGF-β induced adipocytes with RAW264.7 cells resulted in overexpression of pro-inflammatory cytokines in the RAW264.7 cells. Bothin vitro andin vivo experiments confirmed adipocyte loss and fibroblast formation, with transformed fibroblasts showing pronounced pro-inflammatory characteristics, highlighting their crucial role in the disease ***: Our study showed the spatial distribution and dynamic alterations of various cell types durin

关键词： spatial transcriptome Scleroderma Adipocytes Fibroblasts