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single cell rna sequencing reveals mesenchymal heterogeneity and critical functions of Cd271 in tooth development

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World Journal of Stem cells 2023年第6期15卷 589-605页

作者： Yan-Yan Zhang Feng Li Xiao-Ke Zeng Yan-Hui Zou Bing-Bing Zhu Jia-Jia Ye Yun-Xiao Zhang Qiu Jin Xin Nie School&Hospital of Stomatology Wenzhou Medical UniversityWenzhou 325027Zhejiang ProvinceChina

BACKGROUND Accumulating evidence suggests that the maxillary process,to which cranial crest cells migrate,is essential to tooth development.Emerging studies indicate that Cd271 plays an essential role in odontogenesis.However,the underlying mechanisms have yet to be elucidated.AIM To establish the functionally heterogeneous population in the maxillary process,elucidate the effects of Cd271 deficiency on gene expression differences.METHODS p75NTR knockout(Cd271-/-)mice(from American Jackson laboratory)were used to collect the maxillofacial process tissue of p75NTR knockout mice,and the wildtype maxillofacial process of the same pregnant mouse wild was used as control.After single cell suspension,the cDNA was prepared by loading the single cell suspension into the 10x Genomics Chromium system to be sequenced by NovaSeq6000 sequencing system.Finally,the sequencing data in Fastq format were obtained.The FastQC software is used to evaluate the quality of data and cellRanger analyzed the data.The gene expression matrix is read by R software,and Seurat is used to control and standardize the data,reduce the dimension and cluster.We search for marker genes for subgroup annotation by consulting literature and database;explore the effect of p75NTR knockout on mesenchymal stem cells(MSCs)gene expression and cell proportion by cell subgrouping,differential gene analysis,enrichment analysis and protein-protein interaction network analysis;understand the interaction between MSCs cells and the differentiation trajectory and gene change characteristics of p75NTR knockout MSCs by cell communication analysis and pseudo-time analysis.Last we verified the findings single cell sequencing in vitro.RESULTS We identified 21 cell clusters,and we re-clustered these into three subclusters.Importantly,we revealed the cell–cell communication networks between clusters.We clarified that Cd271 was significantly associated with the regulation of mineralization.CONCLUSION This study provides comprehensive mechanistic insights into the maxillary-pr

关键词： Cd271 Mesenchymal stem cells single cell rna sequencing Osteogenesis Mineralization Tooth development

single-cell transcriptomic dissection of the cellular and molecular events underlying the triclosan-induced liver fibrosis in mice

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Military Medical Research 2023年第5期10卷 599-619页

作者： Yun-Meng Bai Fan Yang Piao Luo Lu-Lin Xie Jun-Hui Chen Yu-Dong Guan Hong-Chao Zhou Teng-Fei Xu Hui-Wen Hao Bing Chen Jia-Hui Zhao Cai-Ling Liang Ling-Yun Dai Qing-Shan Geng Ji-Gang Wang Department of Nephrology Shenzhen Key Laboratory of Kidney Diseasesand Shenzhen Clinical Research Centre for GeriatricsShenzhen People’s Hospitalthe First Affiliated HospitalSouthern University of Science and TechnologyShenzhen 518020China Department of Urology Shenzhen People’s Hospitalthe First Affiliated HospitalSouthern University Science and Technologythe Second Clinical Medical CollegeJinan UniversityShenzhen 518020China Integrated Chinese and Western Medicine Postdoctoral Research Station Jinan UniversityGuangzhou 510632China Artemisinin Research Center and Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijing 100700China Guangdong Provincial Key Laboratory of New Drug Screening School of Pharmaceutical SciencesSouthern Medical UniversityGuangzhou 510515China Center for Reproductive Medicine Dongguan Maternal and Child Health Care HospitalSouthern Medical UniversityDongguan 523125GuangdongChina

Background: Triclosan [5-chloro-2-(2,4-dichlorophenoxy) phenol, TCS], a common antimicrobial additive in many personal care and health care products, is frequently detected in human blood and urine. Therefore, it has been considered an emerging and potentially toxic pollutant in recent years. Long-term exposure to TCS has been suggested to exert endocrine disruption effects, and promote liver fibrogenesis and tumorigenesis. This study was aimed at clarifying the underlying cellular and molecular mechanisms of hepatotoxicity effect of TCS at the initiation stage.Methods: C57BL/6 mice were exposed to different dosages of TCS for 2 weeks and the organ toxicity was evaluated by various measurements including complete blood count, histological analysis and TCS quantification. single cell rna sequencing(scrna-seq) was then carried out on TCS-or mock-treated mice livers to delineate the TCS-induced hepatotoxicity. The acquired single-cell transcriptomic data were analyzed from different aspects including differential gene expression, transcription factor(TF) regulatory network, pseudotime trajectory, and cellular communication, to systematically dissect the cellular and molecular events after TCS exposure. To verify the TCS-induced liver fibrosis,the expression levels of key fibrogenic proteins were examined by Western blotting, immunofluorescence, Masson’s trichrome and Sirius red stainings. In addition, normal hepatocyte cell MIHA and hepatic stellate cell LX-2 were used as in vitro cell models to experimentally validate the effects of TCS by immunological, proteomic and metabolomic technologies.Results: We established a relatively short term TCS exposure murine model and found the TCS mainly accumulated in the liver. The scrna-seq performed on the livers of the TCS-treated and control groups profiled the gene expressions of > 76,000 cells belonging to 13 major cell types. Among these types, hepatocytes and hepatic stellate cells(HSCs)were significantly increased in TCS-treated group. We found that TCS promoted fibros

关键词： Triclosan single cell rna sequencing Liver fibrogenesis Hepatic stellate cell

Advancement in research on genes associated with fetal congenital heart disease(CHD)and diagnostic testing methods

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Gynecology and Obstetrics Clinical Medicine 2023年第2期3卷 94-99页

作者： Junshu Xie Kexin Zhang Xiaohong Zhang Obstetrics and Gynecology Peking University People's HospitalBeijing100044China

Introduction:Congenital heart disease(CHD)is one of the most common congenital malformations,and is a polygenic disease related to some major genes and involved in environmental factors.With the progress of science and technology,the progress was both in the studies of genetic patterns and testing methods.Understanding how each gene participates in normal and pathological anatomy is an important goal of CHD research.We reviewed the development of testing methods and CHD-related genes,to provide some enlightenment for the CHD prenatal diagnosis and hope to realize the intervention and treatment on the gene level of CHD in the future.

关键词： Congenital heart disease single cell rna sequencing Genetic factors Gene network

Longitudinal single-cell rna-seq of hESCs-derived retinal organoids

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Science China(Life Sciences) 2021年第10期64卷 1661-1676页

作者： Shaojun Wang Sergio Poli Xiaoliang Liang Guang-Hua Peng Laboratory of Visual cell Differentiation and Regulation Basic Medical CollegeZhengzhou UniversityZhengzhou 450001China Department of Ophthalmology First medical center of Chinese PLA General HospitalBeijing 100853China Department of Ophthalmology Fifth medical center of Chinese PLA General HospitalBeijing 100071China Division of Pulmonary and Critical Care Medicine Brigham and Women’s HospitalHarvard Medical SchoolBoston 02115USA Department of Pathophysiology Basic Medical CollegeZhengzhou UniversityZhengzhou 450001China Division of Internal Medicine Mount Sinai Medical CenterMiamiFlorida 33140USA

Human retina development involves multiple well-studied signaling pathways that promote the genesis of a wide arrange of different cell types in a complex architectural structure.Human embryonic stem cells(hESCs)-derived retinal organoids could recapitulate the human retinal development.We performed single-cell rna-seq of retinal organoids from 5 time points(D36,D66,D96,D126,D186)and identified 9 distinct populations of cells.In addition,we analyzed the molecular characteristics of each main population and followed them from genesis to maturity by pseudotime analysis and characterized the cell-cell interactions between different cell types.Interestingly,we identified insulin receptor(INSR)as a specifically expressed receptor involved in the genesis of photoreceptors,and pleiothropin(PTN)-protein tyrosine phosphatase receptor type Z1(PTPRZ1)as a mediator of a previously unknown interaction between Müller and retinal progenitor cells.Taken together,these findings provide a rich transcriptome-based lineage map for studying human retinal development and modeling developmental disorders in retinal organoids.

关键词： human embryonic stem cell photoreceptor cell single cell rna sequencing retinal pigment epithelium retinal organoid

Illuminating Neural Circuits in Alzheimer’s Disease

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Neuroscience Bulletin 2021年第8期37卷 1203-1217页

作者： Yang Ying Jian-Zhi Wang Department of Pathophysiology School of Basic MedicineMinistry of Education Key Laboratory for Neurological DisordersHubei Key Laboratory for Neurological DisordersTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China

Alzheimer’s disease(AD)is the most common neurodegenerative disorder and there is currently no cure.Neural circuit dysfunction is the fundamental mechanism underlying the learning and memory deficits in patients with AD.Therefore,it is important to understand the structural features and mechanisms underlying the deregulated circuits during AD progression,by which new tools for intervention can be developed.Here,we briefly summarize the most recently established cutting-edge experimental approaches and key techniques that enable neural circuit tracing and manipulation of their activity.We also discuss the advantages and limitations of these approaches.Finally,we review the applications of these techniques in the discovery of circuit mechanisms underlyingβ-amyloid and tau pathologies during AD progression,and as well as the strategies for targeted AD treatments.

关键词： Neural circuit Alzheimer’s disease single cell rna sequencing Neural circuit tracing Optogenetics Chemogenetics

VASC: Dimension Reduction and Visualization of single-cell rna-seq Data by Deep Variational Autoencoder

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Genomics, Proteomics & Bioinformatics 2018年第5期16卷 320-331页

作者： Dongfang Wang Jin Gu MOE Key Laboratory of Bioinformatics BNRIST Bioinformatics Division & Center for Synthetic and Systems BiologyDepartment of Automation Tsinghua University

single-cell rna sequencing(scrna-seq) is a powerful technique to analyze the transcriptomic heterogeneities at the single cell level. It is an important step for studying cell subpopulations and lineages, with an effective low-dimensional representation and visualization of the original scrna-Seq data. At the single cell level, the transcriptional fluctuations are much larger than the average of a cell population, and the low amount of rna transcripts will increase the rate of technical dropout events. Therefore, scrna-seq data are much noisier than traditional bulk rna-seq data. In this study, we proposed the deep variational autoencoder for scrna-seq data(VASC), a deep multi-layer generative model, for the unsupervised dimension reduction and visualization of scrna-seq data. VASC can explicitly model the dropout events and find the nonlinear hierarchical feature representations of the original data. Tested on over 20 datasets, VASC shows superior performances in most cases and exhibits broader dataset compatibility compared to four state-of-the-art dimension reduction and visualization methods. In addition, VASC provides better representations for very rare cell populations in the 2D visualization. As a case study, VASC successfully re-establishes the cell dynamics in pre-implantation embryos and identifies several candidate marker genes associated with early embryo development. Moreover, VASC also performs well on a 10× Genomics dataset with more cells and higher dropout rate.

关键词： single cell rna sequencing Deep variational autoencoder Dimension reduction Visualization Dropout

FSPAM:A Feature Construction Method to Identifying cell Populations in Scrna-seq Data

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Computer Modeling in Engineering & Sciences 2020年第1期122卷 377-397页

作者： Amin Einipour Mohammad Mosleh Karim Ansari-Asl Department of Computer Engineering Dezful BranchIslamic Azad UniversityDezfulIran Department of Electrical Engineering Faculty of EngineeringShahid Chamran University of AhvazAhvazIran

The emergence of single-cell rna-sequencing(scrna-seq)technology has introduced new information about the structure of cells,diseases,and their associated biological factors.One of the main uses of scrna-seq is identifying cell populations,which sometimes leads to the detection of rare cell populations.However,the new method is still in its infancy and with its advantages comes computational challenges that are just beginning to address.An important tool in the analysis is dimensionality reduction,which transforms high dimensional data into a meaningful reduced subspace.The technique allows noise removal,visualization and compression of high-dimensional data.This paper presents a new dimensionality reduction approach where,during an unsupervised multistage process,a feature set including high valuable markers is created which can facilitate the isolation of cell populations.Our proposed method,called fusion of the Spearman and Pearson affinity matrices(FSPAM),is based on a graph-based Gaussian kernel.Use of the graph theory can be effective to overcome the challenge of the nonlinear relations between cellular markers in scrna-seq data.Furthermore,with a proper fusion of the Pearson and Spearman correlation coefficient criteria,it extracts a set of the most important features in a new space.In fact,the FSPAM aggregates the various aspects of cell-to-cell similarity derived from the Pearson and Spearman metrics,and reveals new aspects of cell-to-cell similarity,which can be used to extract new features.The results of the identification of cell populations via k-means++clustering method based on the features extracted from the FSPAM and different datasets of scrna-seq suggested that the proposed method,regardless of the characteristics that govern each dataset,enjoys greater accuracy and better quality compared to previous methods.

关键词： single cell rna sequencing cell population feature extraction fusion

TotalSeqTM, Standardized oligonucleotide barcode antibody conjugates for multiplex immunophenotyping by single cell sequencing

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TotalSeqTM, Standardized oligonucleotide barcode antibody co...