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Organoid research on human early development and beyond

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Medical Review 2022年第5期2卷 512-523页

作者： Lu Wen fuchou tang Biomedical Pioneering Innovation Center Beijing Advanced Innovation Center for GenomicsSchool of Life SciencesPeking UniversityNO.5 Yiheyuan RoadBeijing 100871China

The organoid field has been developing rapidly during the last *** for human pre-,peri-and post-implantation development have opened an avenue to study these biological processes in vitro,which have been hampered by lack of accessible research models for long *** technologies of four fields,single cell omics sequencing,genome editing and lineage tracing,micro-fluidics and tissue engineering,have fueled the rapid development of the organoid *** this review,we will discuss the organoid research on human early development as well as future directions of the organoid field combining with other powerful technologies.

关键词： genome editing implantation microfluidics organoid single cell sequencing tissue engineering

Advanced Single-cell Omics Technologies and Informatics Toolsfor Genomics, Proteomics, and Bioinformatics Analysis

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Genomics, Proteomics & Bioinformatics 2021年第3期19卷 343-345页

作者： Luonan Chen Rong Fan fuchou tang State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai 200031China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China Key Laboratory of Systems Health Science of Zhejiang Province Hangzhou Institute for Advanced StudyChinese Academy of SciencesHangzhou 310024China Department of Biomedical Engineering Yale UniversityNew HavenCT 06520USA Beijing Advanced Innovation Center for Genomics Biomedical Pioneering Innovation CenterSchool of Life SciencesPeking UniversityBeijing 100871China

The newly developed technologies for profiling cellular heterogeneity have spurred a world-wide pursuit of singlecell analysis in the field of omics studies,investigating the genome,epigenome,transcriptome,proteome,metabolome,and their inherent *** obtained through such analysis facilitates a deeper understanding of how underlying molecular and architectural changes alter cell behaviors,development,and disease ***-scale amplification of genomic DNAs or cDNAs from mRNAs transcribed in single cells allows for the measurement of genetic alterations and cell types at an unprecedented *** emerging microchip-based tools for single-cell omics analysis further enable the evaluation of cellular omics with high throughput,improved sensitivity,and reduced *** the other hand,single-cell high-dimensional data obtained with high-throughput technologies also pose new challenges in bioinformatics to analyze,process,and make sense of the big data,in order to deliver new biological insights and knowledge.

关键词： Tools analysis architectural

Recent advances in single-cell sequencing technologies

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Precision Clinical Medicine 2022年第1期5卷 13-22页

作者： Lu Wen fuchou tang Beijing Advanced Innovation Center for Genomics(ICG) Biomedical Pioneering Innovation Center(BIOPIC)School of Life SciencesPeking UniversityBeijing 100871China

Single-cell omics sequencingwas first achieved for the transcriptome in 2009,whichwas followed by fast development of technologies for profiling the genome,DNA methylome,3D genome architecture,chromatin accessibility,histone modifications,etc.,in an individual *** this review we mainly focus on the recent progress in four topics in the single-cell omics field:single-cell epigenome sequencing,single-cell genome sequencing for lineage tracing,spatially resolved single-cell transcriptomics and third-generation sequencing platform-based single-cell omics *** also discuss the potential applications and future directions of these single-cell omics sequencing technologies for different biomedical systems,especially for the human stem cell field.

关键词： single-cell omics genome sequencing epigenome sequencing lineage tracing third-generation sequencing human stem cell

Integrative single-cell multiomics analyses dissect molecular signatures of intratumoral heterogeneities and differentiation states of human gastric cancer

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National Science Review 2023年第6期10卷 96-107页

作者： Shuhui Bian Yicheng Wang Yuan Zhou Wendong Wang Limei Guo Lu Wen Wei Fu Xin Zhou fuchou tang Biomedical Pioneering Innovation Center School of Life Sciences Department of General Surgery Third Hospital Peking University State Key Laboratory of Reproductive Medicine and Offspring Health Nanjing Medical University Collaborative Innovation Center for Cancer Personalized Medicine Nanjing Medical University Beijing Advanced Innovation Center for Genomics (ICG) Ministry of Education Key Laboratory of Cell Proliferation and Differentiation Department of Pathology Peking University Third Hospital School of Basic Medical Science Peking University Health Science Center Peking University Third Hospital Cancer Center Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies Peking University

Human gastric cancer is a highly lethal disease,but the underlying multiomic mole cular signatures remain largely uncle ***,we performed multi-regional sampling,parallel single-cell multiomics sequencing and integrated analyses of human gastric *** identified common transcrip tomic alterations of gastric cancer cells,such as aberrant down-regulation of genes associated with normal stomach function and up-regulation of KRT7,PI3,S100A4,***,aberrant and prevalent up-regulation of genes highly expressed in normal colorectal epithelial cells were also identified in cancer cells,which maybe partially regulated by promoter chromatin accessibility and DNA methylation *** reve aled the single-cell DNA methylome landscape of gastric cancer,and identified candidate DNA methylation biomarkers,such as hypermethylated promoters of TMEM240 and HAGLROS,and hypomethylated promoters of TRPM2-AS and ***,the relationships between genetic lineages,D NA methylation and transcriptomic clusters were systematically revealed at single-cell *** showed that DNA methylation heterogeneities were mainly among different genetic lineages of cancer ***,we found that D NA methylation levels of cancer cells with poorer differentiation states tend to be higher than those of cancer cells with better differentiation states in the primary tumor within the same patient,although still lower than in normal gastric epithelial *** cells with poorer differentiation states also prevalently down-regulated MUC1 expression and immune-related pathways,and had poor infiltration of CD 8+T *** study dissected the mole cular signatures of intratumoral heterogeneities and differentiation states of human gastric cancer using integrative single-cell multiomics analyses.

关键词： gastric cancer single-cell multiomics analysis intratumoral heterogeneity tumor differentiation

Blastoids generated purely from embryonic stem cells both in mice and humans

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Science China(Life Sciences) 2024年第2期67卷 418-420页

作者： Baojiang Wu Yanqiu Wang Jia Yan Mengya Liu Xihe Li fuchou tang Siqin Bao The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock Inner Mongolia UniversityHohhot 010020China Research Center for Animal Genetic Resources of Mongolia Plateau College of Life SciencesInner Mongolia UniversityHohhot 010020China Beijing Advanced Innovation Center for Genomics and Biomedical Pioneering Innovation Center College of Life SciencesPeking UniversityBeijing 100871China Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal Hohhot 011517China

Dear Editor,Embryonic stem cells(ESCs)and trophoblast stem cells(TSCs)are derived from blastocysts(Lu et al.,2001).Blastocyst-like structures(blastoids)are self-assembled structures formed by a combination of ESCs and TSCs(Rivron et al.,2018).To increase the success rate of blastoid formation and its similarity with the features of blastocysts,some reports showed that blastoid could also be derived from a combination of three cell lines,ESCs,TSCs,and extraembryonic endoderm cells(XENs),or novel type of stem cells(Sozen et al.,2018;Weatherbee et al.,2023:Wu et al.,2023;Zhang et al.,2023;Zhang et al.,2019).

关键词： purely similarity

Drug repurposing screening and mechanism analysis based on human colorectal cancer organoids

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Protein & Cell 2024年第4期15卷 285-304页

作者： Yunuo Mao Wei Wang Jingwei Yang Xin Zhou Yongqu Lu Junpeng Gao Xiao Wang Lu Wen Wei Fu fuchou tang School of Life Sciences Biomedical Pioneering Innovation CenterDepartment of General SurgeryThird HospitalPeking UniversityBeijing 100871China Beijing Advanced Innovation Center for Genomics(ICG) Ministry of Education Key Laboratory of Cell Proliferation and DifferentiationBeijing 100871China Peking-Tsinghua Center for Life Sciences Peking UniversityBeijing 100871China Peking University Third Hospital Cancer Center Beijing 100871China The Research Center of Stem Cell and Regenerative Medicine School of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinan 250012China

Colorectal cancer(CRC)is a highly heterogeneous cancer and exploring novel therapeutic options is a pressing issue that needs to be ***,we established human CRC tumor-derived organoids that well represent both morphological and molecular heterogeneities of original *** efficiently identify repurposed drugs for CRC,we developed a robust organoid-based drug screening *** combining the repurposed drug library and computation-based drug prediction,335 drugs were tested and 34 drugs with anti-CRC effects were *** importantly,we conducted a detailed transcriptome analysis of drug responses and divided the drug response signatures into five representative patterns:differentiation induction,growth inhibition,metabolism inhibition,immune response promotion,and cell cycle *** anticancer activities of drug candidates were further validated in the established patient-derived organoids-based xenograft(PDOX)system in *** found that fedratinib,trametinib,and bortezomib exhibited effective anticancer ***,the concordance and discordance of drug response signatures between organoids in vitro and pairwise PDOX in vivo were *** study offers an innovative approach for drug discovery,and the representative transcriptome features of drug responses provide valuable resources for developing novel clinical treatments for CRC.

关键词： colorectal cancer organoids drug repurposing patient-derived organoids-based xenograft mechanism of action

Dissecting Human Gonadal Cell Lineage Specification and Sex Determination Using A Single-cell RNA-seq Approach

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Genomics, Proteomics & Bioinformatics 2022年第2期20卷 223-245页

作者： Rui Wang Xixi Liu Li Li Ming Yang Jun Yong Fan Zhai Lu Wen Liying Yan Jie Qiao fuchou tang Biomedical Pioneering Innovation Center Department of Obstetrics and GynecologyThird HospitalSchool of Life SciencesPeking UniversityBeijing 100871China Beijing Advanced Innovation Center for Genomics and Center for Reproductive Medicine Third HospitalPeking UniversityBeijing 100191China Academy for Advanced Interdisciplinary Studies Peking UniversityBeijing 100871China Key Laboratory of Assisted Reproduction and Key Laboratory of Cell Proliferation and Differentiation Ministry of EducationBeijing 100191China Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology Beijing 100191China Peking-Tsinghua Center for Life Sciences Peking UniversityBeijing 100871China

Gonadal somatic cells are the main players in gonad development and are important for sex determination and germ cell ***,using a time-series single-cell RNA sequencing(scRNA-seq)strategy,we analyzed fetal germ cells(FGCs)and gonadal somatic cells in human embryos and *** analysis of testes and ovaries revealed several novel cell subsets,including POU5F1^(+)SPARC^(+)FGCs and KRT19^(+) somatic ***,our data indicated that the bone morphogenetic protein(BMP)signaling pathway plays cell type-specific and developmental stage-specific roles in testis development and promotes the gonocyte-to-spermatogonium transition(GST)in late-stage testicular mitotic arrest ***,testosterone synthesis function transitioned from fetal Sertoli cells to adult Leydig cells in a stepwise *** our study,potential interactions between gonadal somatic cells were systematically explored and we identified cell type-specific developmental defects in both FGCs and gonadal somatic cells in a Turner syndrome embryo(45,XO).Our work provides a blueprint of the complex yet highly ordered development of and the interactions among human FGCs and gonadal somatic cells.

关键词： Human gonad scRNA-seq Turner syndrome Leydig-Sertoli cell-cell interaction Gonocyte-tospermatogonium transition

MR-seq:measuring a single cell's transcriptome repeatedly by RNA-seq

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Science Bulletin 2017年第6期62卷 391-398页

作者： Lu Yang Zhaochun Ma Chen Cao Yuhao Zhang Xinglong Wu Raymond Lee Boqiang Hu Lu Wen Hao Ge Yanyi Huang Kaiqin Lao fuchou tang Biodynamic Optical Imaging Center School of Life Sciences Peking University Beijing 100871 China Thermo Fisher Scientific.South San Francisco CA 94080 USA Peking-Tsinghua Center for Life Sdences Beijing 100084 China Beijing International Center for Mathematical Research (BICMR) Peking University Beijing 100871 China College of Engineering Peking University Beijing 100871 China China Center for Molecular and Translationai Medicine (CMTM) Beijing 100101 China Beijing Advanced Innovation Center for Cenomics (ICG) Peking University Beijing 100871 China

We described a novel single-cell RNA-seq technique called MR-seq （measure a single-cell transcriptome repeatedly）, which permits statistically assessing the technical variation and identifying the differentially expressed genes between just two single ceils by measuring each single cell twice. We demonstrated that MR-seq gave sensitivity and reproducibility similar to the standard single-cell RNA-seq and increased the positive predicate value, Application of MR-seq to early mouse embryos identified hundreds of candidate intra-embryonic heterogeneous genes among mouse 2-, 4- and 8-cell stage embryos. MR-seq should be useful for detecting differentially exnre^ed ~enes ~rnnn~ ~ ~m^ll nHmhpr nf c^ll~

关键词： Single-cell RNA-seqDifferentially expressed geneslntra-embryonic heterogeneity Mouse early preimplantation embryos

Characterization of mesenchymal stem cells in human fetal bone marrow by single-cell transcriptomic and functional analysis

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Signal Transduction and Targeted Therapy 2023年第4期8卷 2022-2034页

作者： Ping Zhang Ji Dong Xiaoying Fan Jun Yong Ming Yang Yunsong Liu Xiao Zhang Longwei Lv Lu Wen Jie Qiao fuchou tang Yongsheng Zhou Department of Prosthodontics Peking University School and Hospital of Stomatology100081 BeijingChina National Center for Stomatology&National Clinical Research Center for Oral Diseases&National Engineering Reasearch Center of Oral Biomaterials and Digital Medical Devices&Beijing Key Laboratory of Digital Stomatology&National Health Commission Key Laboratory of Digital Technology of Stomatology 100081 BeijingChina Guangzhou Laboratory 510005 GuangzhouChina Biomedical Pioneering Innovation Center and Center for Reproductive Medicine Ministry of Education Key Laboratory of Cell Proliferation and Differentiation100871 BeijingChina Beijing Advanced Innovation Center for Genomics School of Life SciencesDepartment of Obstetrics and GynecologyThird HospitalPeking University100871 BeijingChina Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology 100191 BeijingChina Peking-Tsinghua Center for Life Sciences Peking University100871 BeijingChina

Bone marrow mesenchymal stromal/stem cells (MSCs) are a heterogeneous population that can self-renew and generate stroma,cartilage, fat, and bone. Although a significant progress has been made toward recognizing about the phenotypic characteristics ofMSCs, the true identity and properties of MSCs in bone marrow remain unclear. Here, we report the expression landscape of humanfetal BM nucleated cells (BMNCs) based on the single-cell transcriptomic analysis. Unexpectedly, while the common cell surfacemarkers such as CD146, CD271, and PDGFRa used for isolating MSCs were not detected, LIFR+PDGFRB+ were identified to bespecific markers of MSCs as the early progenitors. In vivo transplantation demonstrated that LIFR+PDGFRB+CD45-CD31-CD235a-MSCs could form bone tissues and reconstitute the hematopoietic microenvironment (HME) effectively in vivo. Interestingly, wealso identified a subpopulation of bone unipotent progenitor expressing TM4SF1+CD44+CD73+CD45-CD31-CD235a-, which hadosteogenic potentials, but could not reconstitute HME. MSCs expressed a set of different transcription factors at the different stagesof human fetal bone marrow, indicating that the stemness properties of MSCs might change during development. Moreover,transcriptional characteristics of cultured MSCs were significantly changed compared with freshly isolated primary MSCs. Ourcellular profiling provides a general landscape of heterogeneity, development, hierarchy, microenvironment of the human fetal BMderivedstem cells at single-cell resolution.

关键词： CD146 fetal CD45