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He M, Li X, Xu B, Lu Y, Lai J, Ling Y, Liu H, An Z, Zhang W, Li F. Reprogramming of 3D genome structure underlying HSPC development in zebrafish. Stem Cell Res Ther 2024; 15:172. [PMID: 38886858 PMCID: PMC11184745 DOI: 10.1186/s13287-024-03798-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Development of hematopoietic stem and progenitor cells (HSPC) is a multi-staged complex process that conserved between zebrafish and mammals. Understanding the mechanism underlying HSPC development is a holy grail of hematopoietic biology, which is helpful for HSPC clinical application. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision; however, its dynamic and role in HSPC development is poorly investigated. METHODS We performed chromatin structure and multi-omics dissection across different stages of HSPC developmental trajectory in zebrafish for the first time, including Hi-C, RNA-seq, ATAC-seq, H3K4me3 and H3K27ac ChIP-seq. RESULTS The chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure. We revealed the multi-scale reorganization of chromatin structure and its influence on transcriptional regulation and transition of cell fate during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably, PU.1 was identified as a potential factor mediating formation of promoter-involved loops and regulating gene expression of HSPC. CONCLUSIONS Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factors involved in HSPC chromatin interactions, which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision.
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Affiliation(s)
- Min He
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Xiaoli Li
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China
- Laboratory of Developmental Biology, Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Bingxiang Xu
- Key Laboratory of Hebei Province for Molecular Biophysics, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300130, China
| | - Yinbo Lu
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Jingyi Lai
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Yiming Ling
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Huakai Liu
- Vehicle Engineering, School of Mechanical and Automotive Engineering, South China University of Technology, Guangzhou, 510000, China
| | - Ziyang An
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Wenqing Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China.
| | - Feifei Li
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, 510006, China.
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Li J, Wang Y, Raina MA, Xu C, Su L, Guo Q, Ma Q, Wang J, Xu D. scBSP: A fast and accurate tool for identifying spatially variable genes from spatial transcriptomic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592851. [PMID: 38765956 PMCID: PMC11100755 DOI: 10.1101/2024.05.06.592851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Spatially resolved transcriptomics have enabled the inference of gene expression patterns within two and three-dimensional space, while introducing computational challenges due to growing spatial resolutions and sparse expressions. Here, we introduce scBSP, an open-source, versatile, and user-friendly package designed for identifying spatially variable genes in large-scale spatial transcriptomics. scBSP implements sparse matrix operation to significantly increase the computational efficiency in both computational time and memory usage, processing the high-definition spatial transcriptomics data for 19,950 genes on 181,367 spots within 10 seconds. Applied to diverse sequencing data and simulations, scBSP efficiently identifies spatially variable genes, demonstrating fast computational speed and consistency across various sequencing techniques and spatial resolutions for both two and three-dimensional data with up to millions of cells. On a sample with hundreds of thousands of sports, scBSP identifies SVGs accurately in seconds to on a typical desktop computer.
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3
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Zhong X, Chen J, Zhang Z, Zhu Q, Ji D, Ke W, Niu C, Wang C, Zhao N, Chen W, Jia K, Liu Q, Song M, Liu C, Wei Y. Development of an Automated Morphometric Approach to Assess Vascular Outcomes following Exposure to Environmental Chemicals in Zebrafish. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:57001. [PMID: 38701112 PMCID: PMC11068156 DOI: 10.1289/ehp13214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 01/17/2024] [Accepted: 03/18/2024] [Indexed: 05/05/2024]
Abstract
BACKGROUND Disruptions in vascular formation attributable to chemical insults is a pivotal risk factor or potential etiology of developmental defects and various disease settings. Among the thousands of chemicals threatening human health, the highly concerning groups prevalent in the environment and detected in biological monitoring in the general population ought to be prioritized because of their high exposure risks. However, the impacts of a large number of environmental chemicals on vasculature are far from understood. The angioarchitecture complexity and technical limitations make it challenging to analyze the entire vasculature efficiently and identify subtle changes through a high-throughput in vivo assay. OBJECTIVES We aimed to develop an automated morphometric approach for the vascular profile and assess the vascular morphology of health-concerning environmental chemicals. METHODS High-resolution images of the entire vasculature in Tg(fli1a:eGFP) zebrafish were collected using a high-content imaging platform. We established a deep learning-based quantitative framework, ECA-ResXUnet, combined with MATLAB to segment the vascular networks and extract features. Vessel scores based on the rates of morphological changes were calculated to rank vascular toxicity. Potential biomarkers were identified by vessel-endothelium-gene-disease integrative analysis. RESULTS Whole-trunk blood vessels and the cerebral vasculature in larvae exposed to 150 representative chemicals were automatically segmented as comparable to human-level accuracy, with sensitivity and specificity of 95.56% and 95.81%, respectively. Chemical treatments led to heterogeneous vascular patterns manifested by 31 architecture indexes, and the common cardinal vein (CCV) was the most affected vessel. The antipsychotic medicine haloperidol, flame retardant 2,2-bis(chloromethyl)trimethylenebis[bis(2-chloroethyl) phosphate], and tert-butylphenyl diphenyl phosphate ranked as the top three in vessel scores. Pesticides accounted for the largest group, with a vessel score of ≥ 1 , characterized by a remarkable inhibition of subintestinal venous plexus and delayed development of CCV. Multiple-concentration evaluation of nine per- and polyfluoroalkyl substances (PFAS) indicated a low-concentration effect on vascular impairment and a positive association between carbon chain length and benchmark concentration. Target vessel-directed single-cell RNA sequencing of f l i 1 a + cells from larvae treated with λ -cyhalothrin , perfluorohexanesulfonic acid, or benzylbutyl phthalate, along with vessel-endothelium-gene-disease integrative analysis, uncovered potential associations with vascular disorders and identified biomarker candidates. DISCUSSION This study provides a novel paradigm for phenotype-driven screenings of vascular-disrupting chemicals by converging morphological and transcriptomic profiles at a high-resolution level, serving as a powerful tool for large-scale toxicity tests. Our approach and the high-quality morphometric data facilitate the precise evaluation of vascular effects caused by environmental chemicals. https://doi.org/10.1289/EHP13214.
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Affiliation(s)
- Xiali Zhong
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Junzhou Chen
- School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Zhuyi Zhang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Qicheng Zhu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Di Ji
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Weijian Ke
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Congying Niu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Can Wang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, California, USA
| | - Nan Zhao
- School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Wenquan Chen
- School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Kunkun Jia
- School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Qian Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Maoyong Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Chunqiao Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yanhong Wei
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
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Han Y, Sun K, Yu S, Qin Y, Zhang Z, Luo J, Hu H, Dai L, Cui M, Jiang C, Liu F, Huang Y, Gao P, Chen X, Xin T, Ren X, Wu X, Song J, Wang Q, Tang Z, Chen J, Zhang H, Zhang X, Liu M, Luo D. A Mettl16/m 6A/mybl2b/Igf2bp1 axis ensures cell cycle progression of embryonic hematopoietic stem and progenitor cells. EMBO J 2024; 43:1990-2014. [PMID: 38605226 PMCID: PMC11099167 DOI: 10.1038/s44318-024-00082-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/13/2024] Open
Abstract
Prenatal lethality associated with mouse knockout of Mettl16, a recently identified RNA N6-methyladenosine (m6A) methyltransferase, has hampered characterization of the essential role of METTL16-mediated RNA m6A modification in early embryonic development. Here, using cross-species single-cell RNA sequencing analysis, we found that during early embryonic development, METTL16 is more highly expressed in vertebrate hematopoietic stem and progenitor cells (HSPCs) than other methyltransferases. In Mettl16-deficient zebrafish, proliferation capacity of embryonic HSPCs is compromised due to G1/S cell cycle arrest, an effect whose rescue requires Mettl16 with intact methyltransferase activity. We further identify the cell-cycle transcription factor mybl2b as a directly regulated by Mettl16-mediated m6A modification. Mettl16 deficiency resulted in the destabilization of mybl2b mRNA, likely due to lost binding by the m6A reader Igf2bp1 in vivo. Moreover, we found that the METTL16-m6A-MYBL2-IGF2BP1 axis controlling G1/S progression is conserved in humans. Collectively, our findings elucidate the critical function of METTL16-mediated m6A modification in HSPC cell cycle progression during early embryonic development.
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Affiliation(s)
- Yunqiao Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Kui Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Shanshan Yu
- Institute of Visual Neuroscience and Stem Cell Engineering, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, China
| | - Yayun Qin
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, 430070, China
| | - Zuxiao Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Jiong Luo
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Hualei Hu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Liyan Dai
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Manman Cui
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, Hubei, 430071, China
| | - Chaolin Jiang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fei Liu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Pan Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Xiang Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Tianqing Xin
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Xiang Ren
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Xiaoyan Wu
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China
| | - Jieping Song
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, 430070, China
| | - Qing Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Haojian Zhang
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, Hubei, 430071, China
| | - Xianqin Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
| | - Daji Luo
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, 430072, China.
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5
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Lv Y, Li J, Yu S, Zhang Y, Hu H, Sun K, Jia D, Han Y, Tu J, Huang Y, Liu X, Zhang X, Gao P, Chen X, Shaw Williams MT, Tang Z, Shu X, Liu M, Ren X. The splicing factor Prpf31 is required for hematopoietic stem and progenitor cell expansion during zebrafish embryogenesis. J Biol Chem 2024; 300:105772. [PMID: 38382674 PMCID: PMC10959673 DOI: 10.1016/j.jbc.2024.105772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 01/17/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Pre-mRNA splicing is a precise regulated process and is crucial for system development and homeostasis maintenance. Mutations in spliceosomal components have been found in various hematopoietic malignancies (HMs) and have been considered as oncogenic derivers of HMs. However, the role of spliceosomal components in normal and malignant hematopoiesis remains largely unknown. Pre-mRNA processing factor 31 (PRPF31) is a constitutive spliceosomal component, which mutations are associated with autosomal dominant retinitis pigmentosa. PRPF31 was found to be mutated in several HMs, but the function of PRPF31 in normal hematopoiesis has not been explored. In our previous study, we generated a prpf31 knockout (KO) zebrafish line and reported that Prpf31 regulates the survival and differentiation of retinal progenitor cells by modulating the alternative splicing of genes involved in mitosis and DNA repair. In this study, by using the prpf31 KO zebrafish line, we discovered that prpf31 KO zebrafish exhibited severe defects in hematopoietic stem and progenitor cell (HSPC) expansion and its sequentially differentiated lineages. Immunofluorescence results showed that Prpf31-deficient HSPCs underwent malformed mitosis and M phase arrest during HSPC expansion. Transcriptome analysis and experimental validations revealed that Prpf31 deficiency extensively perturbed the alternative splicing of mitosis-related genes. Collectively, our findings elucidate a previously undescribed role for Prpf31 in HSPC expansion, through regulating the alternative splicing of mitosis-related genes.
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Affiliation(s)
- Yuexia Lv
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Department of Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jingzhen Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Research Center for Biochemistry and Molecular Biology, Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, China
| | - Shanshan Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Institute of Visual Neuroscience and Stem Cell Engineering, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Yangjun Zhang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hualei Hu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kui Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Danna Jia
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jiayi Tu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiliang Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xianghan Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pan Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiang Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mark Thomas Shaw Williams
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xinhua Shu
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, United Kingdom
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiang Ren
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.
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6
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Zhang Y, Liu F. The evolving views of hematopoiesis: from embryo to adulthood and from in vivo to in vitro. J Genet Genomics 2024; 51:3-15. [PMID: 37734711 DOI: 10.1016/j.jgg.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
Abstract
The hematopoietic system composed of hematopoietic stem and progenitor cells (HSPCs) and their differentiated lineages serves as an ideal model to uncover generic principles of cell fate transitions. From gastrulation onwards, there successively emerge primitive hematopoiesis (that produces specialized hematopoietic cells), pro-definitive hematopoiesis (that produces lineage-restricted progenitor cells), and definitive hematopoiesis (that produces multipotent HSPCs). These nascent lineages develop in several transient hematopoietic sites and finally colonize into lifelong hematopoietic sites. The development and maintenance of hematopoietic lineages are orchestrated by cell-intrinsic gene regulatory networks and cell-extrinsic microenvironmental cues. Owing to the progressive methodology (e.g., high-throughput lineage tracing and single-cell functional and omics analyses), our understanding of the developmental origin of hematopoietic lineages and functional properties of certain hematopoietic organs has been updated; meanwhile, new paradigms to characterize rare cell types, cell heterogeneity and its causes, and comprehensive regulatory landscapes have been provided. Here, we review the evolving views of HSPC biology during developmental and postnatal hematopoiesis. Moreover, we discuss recent advances in the in vitro induction and expansion of HSPCs, with a focus on the implications for clinical applications.
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Affiliation(s)
- Yifan Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China
| | - Feng Liu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China; State Key Laboratory of Membrane Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China.
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7
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Bobrovskikh AV, Zubairova US, Doroshkov AV. Fishing Innate Immune System Properties through the Transcriptomic Single-Cell Data of Teleostei. BIOLOGY 2023; 12:1516. [PMID: 38132342 PMCID: PMC10740722 DOI: 10.3390/biology12121516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
The innate immune system is the first line of defense in multicellular organisms. Danio rerio is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among Teleostei. We summarized the scRNAseq and spatial transcriptomics experiments related to the IIS for zebrafish and other Teleostei from the GEO NCBI and the Single-Cell Expression Atlas. We found a considerable number of scRNAseq experiments at different stages of zebrafish development in organs such as the kidney, liver, stomach, heart, and brain. These datasets could be further used to conduct large-scale meta-analyses and to compare the IIS of zebrafish with the mammalian one. However, only a small number of scRNAseq datasets are available for other fish (turbot, salmon, cavefish, and dark sleeper). Since fish biology is very diverse, it would be a major mistake to use zebrafish alone in fish immunology studies. In particular, there is a special need for new scRNAseq experiments involving nonmodel Teleostei, e.g., long-lived species, cancer-resistant fish, and various fish ecotypes.
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Affiliation(s)
- Aleksandr V. Bobrovskikh
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
| | - Ulyana S. Zubairova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
- Department of Information Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexey V. Doroshkov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (U.S.Z.); (A.V.D.)
- Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia
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8
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Wang J, Li J, Kramer ST, Su L, Chang Y, Xu C, Eadon MT, Kiryluk K, Ma Q, Xu D. Dimension-agnostic and granularity-based spatially variable gene identification using BSP. Nat Commun 2023; 14:7367. [PMID: 37963892 PMCID: PMC10645821 DOI: 10.1038/s41467-023-43256-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/03/2023] [Indexed: 11/16/2023] Open
Abstract
Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression with corresponding spatial coordinates in two or three dimensions and can be used to infer SVGs effectively. However, current computational methods may not achieve reliable results and often cannot handle three-dimensional spatial transcriptomic data. Here we introduce BSP (big-small patch), a non-parametric model by comparing gene expression pattens at two spatial granularities to identify SVGs from two or three-dimensional spatial transcriptomics data in a fast and robust manner. This method has been extensively tested in simulations, demonstrating superior accuracy, robustness, and high efficiency. BSP is further validated by substantiated biological discoveries in cancer, neural science, rheumatoid arthritis, and kidney studies with various types of spatial transcriptomics technologies.
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Affiliation(s)
- Juexin Wang
- Department of BioHealth Informatics, Luddy School of Informatics, Computing, and Engineering, Indiana University Indianapolis, Indianapolis, IN, 46202, USA.
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, USA.
| | - Jinpu Li
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Skyler T Kramer
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Li Su
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Yuzhou Chang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Chunhui Xu
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Michael T Eadon
- Department of Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, NY, 10027, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, 65211, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
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9
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Gomes MC, Brokatzky D, Bielecka MK, Wardle FC, Mostowy S. Shigella induces epigenetic reprogramming of zebrafish neutrophils. SCIENCE ADVANCES 2023; 9:eadf9706. [PMID: 37672585 PMCID: PMC10482349 DOI: 10.1126/sciadv.adf9706] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
Trained immunity is a long-term memory of innate immune cells, generating an improved response upon reinfection. Shigella is an important human pathogen and inflammatory paradigm for which there is no effective vaccine. Using zebrafish larvae, we demonstrate that after Shigella training, neutrophils are more efficient at bacterial clearance. We observe that Shigella-induced protection is nonspecific and has differences with training by BCG and β-glucan. Analysis of histone ChIP-seq on trained neutrophils revealed that Shigella training deposits the active H3K4me3 mark on promoter regions of 1612 genes, dramatically changing the epigenetic landscape of neutrophils toward enhanced microbial recognition and mitochondrial ROS production. Last, we demonstrate that mitochondrial ROS plays a key role in enhanced antimicrobial activity of trained neutrophils. It is envisioned that signals and mechanisms we discover here can be used in other vertebrates, including humans, to suggest new therapeutic strategies involving neutrophils to control bacterial infection.
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Affiliation(s)
- Margarida C. Gomes
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Dominik Brokatzky
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Magdalena K. Bielecka
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Fiona C. Wardle
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, UK
| | - Serge Mostowy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
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10
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Hagedorn EJ, Perlin JR, Freeman RJ, Wattrus SJ, Han T, Mao C, Kim JW, Fernández-Maestre I, Daily ML, D'Amato C, Fairchild MJ, Riquelme R, Li B, Ragoonanan DAVE, Enkhbayar K, Henault EL, Wang HG, Redfield SE, Collins SH, Lichtig A, Yang S, Zhou Y, Kunar B, Gomez-Salinero JM, Dinh TT, Pan J, Holler K, Feldman HA, Butcher EC, van Oudenaarden A, Rafii S, Junker JP, Zon LI. Transcription factor induction of vascular blood stem cell niches in vivo. Dev Cell 2023; 58:1037-1051.e4. [PMID: 37119815 PMCID: PMC10330626 DOI: 10.1016/j.devcel.2023.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/08/2023] [Accepted: 04/07/2023] [Indexed: 05/01/2023]
Abstract
The hematopoietic niche is a supportive microenvironment composed of distinct cell types, including specialized vascular endothelial cells that directly interact with hematopoietic stem and progenitor cells (HSPCs). The molecular factors that specify niche endothelial cells and orchestrate HSPC homeostasis remain largely unknown. Using multi-dimensional gene expression and chromatin accessibility analyses in zebrafish, we define a conserved gene expression signature and cis-regulatory landscape that are unique to sinusoidal endothelial cells in the HSPC niche. Using enhancer mutagenesis and transcription factor overexpression, we elucidate a transcriptional code that involves members of the Ets, Sox, and nuclear hormone receptor families and is sufficient to induce ectopic niche endothelial cells that associate with mesenchymal stromal cells and support the recruitment, maintenance, and division of HSPCs in vivo. These studies set forth an approach for generating synthetic HSPC niches, in vitro or in vivo, and for effective therapies to modulate the endogenous niche.
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Affiliation(s)
- Elliott J Hagedorn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA; Section of Hematology and Medical Oncology and Center for Regenerative Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Julie R Perlin
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Rebecca J Freeman
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Samuel J Wattrus
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Tianxiao Han
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Clara Mao
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Ji Wook Kim
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Inés Fernández-Maestre
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Madeleine L Daily
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Christopher D'Amato
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Michael J Fairchild
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Raquel Riquelme
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Brian Li
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Dana A V E Ragoonanan
- Section of Hematology and Medical Oncology and Center for Regenerative Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Khaliun Enkhbayar
- Section of Hematology and Medical Oncology and Center for Regenerative Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Emily L Henault
- Section of Hematology and Medical Oncology and Center for Regenerative Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Helen G Wang
- Section of Hematology and Medical Oncology and Center for Regenerative Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Shelby E Redfield
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Samantha H Collins
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Asher Lichtig
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Song Yang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Yi Zhou
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA
| | - Balvir Kunar
- Ansary Stem Cell Institute, Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jesus Maria Gomez-Salinero
- Ansary Stem Cell Institute, Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thanh T Dinh
- Veterans Affairs Palo Alto Health Care System, The Palo Alto Veterans Institute for Research and the Department of Pathology, Stanford University, Stanford, CA, USA
| | - Junliang Pan
- Veterans Affairs Palo Alto Health Care System, The Palo Alto Veterans Institute for Research and the Department of Pathology, Stanford University, Stanford, CA, USA
| | - Karoline Holler
- Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Henry A Feldman
- Institutional Centers for Clinical and Translational Research, Boston Children's Hospital, Boston, MA, USA
| | - Eugene C Butcher
- Veterans Affairs Palo Alto Health Care System, The Palo Alto Veterans Institute for Research and the Department of Pathology, Stanford University, Stanford, CA, USA
| | - Alexander van Oudenaarden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Shahin Rafii
- Ansary Stem Cell Institute, Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - J Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA, USA.
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11
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Wang J, Li J, Kramer ST, Su L, Chang Y, Xu C, Ma Q, Xu D. Dimension-agnostic and granularity-based spatially variable gene identification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533713. [PMID: 36993544 PMCID: PMC10055351 DOI: 10.1101/2023.03.21.533713] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression with corresponding spatial coordinates in two or three dimensions and can be used to infer SVGs effectively. However, current computational methods may not achieve reliable results and often cannot handle three-dimensional spatial transcriptomic data. Here we introduce BSP (big-small patch), a spatial granularity-guided and non-parametric model to identify SVGs from two or three-dimensional spatial transcriptomics data in a fast and robust manner. This new method has been extensively tested in simulations, demonstrating superior accuracy, robustness, and high efficiency. BSP is further validated by substantiated biological discoveries in cancer, neural science, rheumatoid arthritis, and kidney studies with various types of spatial transcriptomics technologies.
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Affiliation(s)
- Juexin Wang
- Department of BioHealth Informatics, Luddy School of Informatics, Computing, and Engineering, Indiana University Purdue University Indianapolis, Indianapolis, IN 46202, USA
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Jinpu Li
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Skyler T Kramer
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Li Su
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Yuzhou Chang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Chunhui Xu
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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12
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Duan H, Cheng T, Cheng H. Spatially resolved transcriptomics: advances and applications. BLOOD SCIENCE 2023; 5:1-14. [PMID: 36742187 PMCID: PMC9891446 DOI: 10.1097/bs9.0000000000000141] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Spatial transcriptomics, which is capable of both measuring all gene activity in a tissue sample and mapping where this activity occurs, is vastly improving our understanding of biological processes and disease. The field has expanded rapidly in recent years, and the development of several new technologies has resulted in spatially resolved transcriptomics (SRT) becoming highly multiplexed, high-resolution, and high-throughput. Here, we summarize and compare the major methods of SRT, including imaging-based methods, sequencing-based methods, and in situ sequencing methods. We also highlight some typical applications of SRT in neuroscience, cancer biology, developmental biology, and hematology. Finally, we discuss future possibilities for improving spatially resolved transcriptomic methods and the expected applications of such methods, especially in the adult bone marrow, anticipating that new developments will unlock the full potential of spatially resolved multi-omics in both biological research and the clinic.
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Affiliation(s)
- Honglin Duan
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
- Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin, China
- Department of Stem Cell & Regenerative Medicine, Peking Union Medical College, Tianjin, China
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13
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Ya D, Zhang Y, Cui Q, Jiang Y, Yang J, Tian N, Xiang W, Lin X, Li Q, Liao R. Application of spatial transcriptome technologies to neurological diseases. Front Cell Dev Biol 2023; 11:1142923. [PMID: 36936681 PMCID: PMC10020196 DOI: 10.3389/fcell.2023.1142923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Spatial transcriptome technology acquires gene expression profiles while retaining spatial location information, it displays the gene expression properties of cells in situ. Through the investigation of cell heterogeneity, microenvironment, function, and cellular interactions, spatial transcriptome technology can deeply explore the pathogenic mechanisms of cell-type-specific responses and spatial localization in neurological diseases. The present article overviews spatial transcriptome technologies based on microdissection, in situ hybridization, in situ sequencing, in situ capture, and live cell labeling. Each technology is described along with its methods, detection throughput, spatial resolution, benefits, and drawbacks. Furthermore, their applications in neurodegenerative disease, neuropsychiatric illness, stroke and epilepsy are outlined. This information can be used to understand disease mechanisms, pick therapeutic targets, and establish biomarkers.
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Affiliation(s)
- Dongshan Ya
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Yingmei Zhang
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Qi Cui
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Yanlin Jiang
- Department of Pharmacology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Jiaxin Yang
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Ning Tian
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Wenjing Xiang
- Department of Neurology ward 2, Guilin People’s Hospital, Guilin, China
| | - Xiaohui Lin
- Department of Geriatrics, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Qinghua Li
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Rujia Liao
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- *Correspondence: Rujia Liao,
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14
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Genetic duplication of tissue factor reveals subfunctionalization in venous and arterial hemostasis. PLoS Genet 2022; 18:e1010534. [PMID: 36449521 PMCID: PMC9744294 DOI: 10.1371/journal.pgen.1010534] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/12/2022] [Accepted: 11/15/2022] [Indexed: 12/05/2022] Open
Abstract
Tissue factor (TF) is an evolutionarily conserved protein necessary for initiation of hemostasis. Zebrafish have two copies of the tissue factor gene (f3a and f3b) as the result of an ancestral teleost fish duplication event (so called ohnologs). In vivo physiologic studies of TF function have been difficult given early lethality of TF knockout in the mouse. We used genome editing to produce knockouts of both f3a and f3b in zebrafish. Since ohnologs arose through sub- or neofunctionalization, they can unmask unknown functions of non-teleost genes and could reveal whether mammalian TF has developmental functions distinct from coagulation. Here we show that a single copy of either f3a or f3b is necessary and sufficient for normal lifespan. Complete loss of TF results in lethal hemorrhage by 2-4 months despite normal embryonic and vascular development. Larval vascular endothelial injury reveals predominant roles for TFa in venous circulation and TFb in arterial circulation. Finally, we demonstrate that loss of TF predisposes to a stress-induced cardiac tamponade independent of its role in fibrin formation. Overall, our data suggest partial subfunctionalization of TFa and TFb. This multigenic zebrafish model has the potential to facilitate study of the role of TF in different vascular beds.
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15
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Jin B, Xie L, Zhan D, Zhou L, Feng Z, He J, Qin J, Zhao C, Luo L, Li L. Nrf2 dictates the neuronal survival and differentiation of embryonic zebrafish harboring compromised alanyl-tRNA synthetase. Development 2022; 149:276217. [DOI: 10.1242/dev.200342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 07/28/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
tRNA synthetase deficiency leads to unfolded protein responses in neuronal disorders; however, its function in embryonic neurogenesis remains unclear. This study identified an aars1cq71/cq71 mutant zebrafish allele that showed increased neuronal apoptosis and compromised neurogenesis. aars1 transcripts were highly expressed in primary neural progenitor cells, and their aberration resulted in protein overloading and activated Perk. nfe2l2b, a paralog of mammalian Nfe2l2, which encodes Nrf2, is a pivotal executor of Perk signaling that regulates neuronal phenotypes in aars1cq71/cq71 mutants. Interference of nfe2l2b in nfe2l2bΔ1/Δ1 mutants did not affect global larval development. However, aars1cq71/cq71;nfe2l2bΔ1/Δ1 mutant embryos exhibited increased neuronal cell survival and neurogenesis compared with their aars1cq71/cq71 siblings. nfe2l2b was harnessed by Perk at two levels. Its transcript was regulated by Chop, an implementer of Perk. It was also phosphorylated by Perk. Both pathways synergistically assured the nuclear functions of nfe2l2b to control cell survival by targeting p53. Our study extends the understanding of tRNA synthetase in neurogenesis and implies that Nrf2 is a cue to mitigate neurodegenerative pathogenesis.
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Affiliation(s)
- Binbin Jin
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Liqin Xie
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Dan Zhan
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Luping Zhou
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Zhi Feng
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Jiangyong He
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Jie Qin
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Congjian Zhao
- Chongqing Engineering Research Center of Medical Electronics and Information Technology, School of Biomedical Engineering and informatics, Chongqing University of Posts and Telecommunications 2 , Chongqing 40065 , China
| | - Lingfei Luo
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Li Li
- Research Center of Stem Cells and Ageing, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences 3 , Chongqing 400714 , China
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16
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Epigenetic modifier SMCHD1 maintains a normal pool of long-term hematopoietic stem cells. iScience 2022; 25:104684. [PMID: 35856023 PMCID: PMC9287190 DOI: 10.1016/j.isci.2022.104684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/16/2022] [Accepted: 06/24/2022] [Indexed: 11/30/2022] Open
Abstract
SMCHD1 (structural maintenance of chromosomes hinge domain containing 1) is a noncanonical SMC protein that mediates long-range repressive chromatin structures. SMCHD1 is required for X chromosome inactivation in female cells and repression of imprinted and clustered autosomal genes, with SMCHD1 mutations linked to human diseases facioscapulohumeral muscular dystrophy (FSHD) and bosma arhinia and micropthalmia syndrome (BAMS). We used a conditional mouse model to investigate SMCHD1 in hematopoiesis. Smchd1-deleted mice maintained steady-state hematopoiesis despite showing an impaired reconstitution capacity in competitive bone marrow transplantations and age-related hematopoietic stem cell (HSC) loss. This phenotype was more pronounced in Smchd1-deleted females, which showed a loss of quiescent HSCs and fewer B cells. Gene expression profiling of Smchd1-deficient HSCs and B cells revealed known and cell-type-specific SMCHD1-sensitive genes and significant disruption to X-linked gene expression in female cells. These data show SMCHD1 is a regulator of HSCs whose effects are more profound in females. SMCHD1 is not required to maintain steady-state hematopoiesis Smchd1-deletion leads to loss of adult hematopoietic stem cells Smchd1-deleted female mice are more severely affected than males SMCHD1 maintains cellular quiescence in female hematopoietic stem cells
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17
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Wang R, Peng G, Tam PPL, Jing N. Integration of computational analysis and spatial transcriptomics in single-cell study. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022:S1672-0229(22)00084-5. [PMID: 35901961 PMCID: PMC10372908 DOI: 10.1016/j.gpb.2022.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 06/08/2022] [Accepted: 06/19/2022] [Indexed: 04/08/2023]
Abstract
Recent advances of single-cell transcriptomics technologies and allied computational methodologies have revolutionized molecular cell biology. Meanwhile, pioneering explorations in spatial transcriptomics have opened avenues to address fundamental biological questions in health and diseases. Here, we review the technical attributes of single-cell RNA sequencing and spatial transcriptomics, and the core concepts of computational data analysis. We further highlight the challenges in the application of data integration methodologies and the interpretation of the biological context of the findings.
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Affiliation(s)
- Ran Wang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Guangdun Peng
- 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, Guangzhou 510530, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Patrick P L Tam
- Embryology Research Unit, Children's Medical Research Institute, University of Sydney, Sydney, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2145, Australia
| | - 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 Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; Guangzhou Laboratory, Guangzhou 510005, China; 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, Guangzhou 510530, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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18
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Klaus A, Clapes T, Yvernogeau L, Basu S, Weijts B, Maas J, Smal I, Galjart N, Robin C. CLASP2 safeguards hematopoietic stem cell properties during mouse and fish development. Cell Rep 2022; 39:110957. [PMID: 35705037 DOI: 10.1016/j.celrep.2022.110957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/28/2022] [Accepted: 05/23/2022] [Indexed: 11/27/2022] Open
Abstract
Hematopoietic stem cells (HSCs) express a large variety of cell surface receptors that are associated with acquisition of self-renewal and multipotent properties. Correct expression of these receptors depends on a delicate balance between cell surface trafficking, recycling, and degradation and is controlled by the microtubule network and Golgi apparatus, whose roles have hardly been explored during embryonic/fetal hematopoiesis. Here we show that, in the absence of CLASP2, a microtubule-associated protein, the overall production of HSCs is reduced, and the produced HSCs fail to self-renew and maintain their stemness throughout mouse and zebrafish development. This phenotype can be attributed to decreased cell surface expression of the hematopoietic receptor c-Kit, which originates from increased lysosomal degradation in combination with a reduction in trafficking to the plasma membrane. A dysfunctional Golgi apparatus in CLASP2-deficient HSCs seems to be the underlying cause of the c-Kit expression and signaling imbalance.
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Affiliation(s)
- Anna Klaus
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Thomas Clapes
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Laurent Yvernogeau
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Sreya Basu
- Department of Cell Biology, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Bart Weijts
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Joris Maas
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Ihor Smal
- Theme Biomedical Sciences and Departments of Cell Biology and Molecular Genetics, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Niels Galjart
- Department of Cell Biology, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, the Netherlands
| | - Catherine Robin
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Regenerative Medicine Center, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands.
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19
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Clinical and translational values of spatial transcriptomics. Signal Transduct Target Ther 2022; 7:111. [PMID: 35365599 PMCID: PMC8972902 DOI: 10.1038/s41392-022-00960-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
The combination of spatial transcriptomics (ST) and single cell RNA sequencing (scRNA-seq) acts as a pivotal component to bridge the pathological phenomes of human tissues with molecular alterations, defining in situ intercellular molecular communications and knowledge on spatiotemporal molecular medicine. The present article overviews the development of ST and aims to evaluate clinical and translational values for understanding molecular pathogenesis and uncovering disease-specific biomarkers. We compare the advantages and disadvantages of sequencing- and imaging-based technologies and highlight opportunities and challenges of ST. We also describe the bioinformatics tools necessary on dissecting spatial patterns of gene expression and cellular interactions and the potential applications of ST in human diseases for clinical practice as one of important issues in clinical and translational medicine, including neurology, embryo development, oncology, and inflammation. Thus, clear clinical objectives, designs, optimizations of sampling procedure and protocol, repeatability of ST, as well as simplifications of analysis and interpretation are the key to translate ST from bench to clinic.
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20
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Weijts B, Yvernogeau L, Robin C. Recent Advances in Developmental Hematopoiesis: Diving Deeper With New Technologies. Front Immunol 2021; 12:790379. [PMID: 34899758 PMCID: PMC8652083 DOI: 10.3389/fimmu.2021.790379] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
The journey of a hematopoietic stem cell (HSC) involves the passage through successive anatomical sites where HSCs are in direct contact with their surrounding microenvironment, also known as niche. These spatial and temporal cellular interactions throughout development are required for the acquisition of stem cell properties, and for maintaining the HSC pool through balancing self-renewal, quiescence and lineage commitment. Understanding the context and consequences of these interactions will be imperative for our understanding of HSC biology and will lead to the improvement of in vitro production of HSCs for clinical purposes. The aorta-gonad-mesonephros (AGM) region is in this light of particular interest since this is the cradle of HSC emergence during the embryonic development of all vertebrate species. In this review, we will focus on the developmental origin of HSCs and will discuss the novel technological approaches and recent progress made to identify the cellular composition of the HSC supportive niche and the underlying molecular events occurring in the AGM region.
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Affiliation(s)
- Bart Weijts
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) & University Medical Center Utrecht, Utrecht, Netherlands
| | - Laurent Yvernogeau
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) & University Medical Center Utrecht, Utrecht, Netherlands
| | - Catherine Robin
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) & University Medical Center Utrecht, Utrecht, Netherlands
- Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands
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21
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The spliceosome factor sart3 regulates hematopoietic stem/progenitor cell development in zebrafish through the p53 pathway. Cell Death Dis 2021; 12:906. [PMID: 34611130 PMCID: PMC8492694 DOI: 10.1038/s41419-021-04215-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/09/2021] [Accepted: 09/23/2021] [Indexed: 12/27/2022]
Abstract
Hematopoietic stem cells (HSCs) possess the potential for self-renew and the capacity, throughout life, to differentiate into all blood cell lineages. Yet, the mechanistic basis for HSC development remains largely unknown. In this study, we characterized a zebrafish smu471 mutant with hematopoietic stem/progenitor cell (HSPC) defects and found that sart3 was the causative gene. RNA expression profiling of the sart3smu471 mutant revealed spliceosome and p53 signaling pathway to be the most significantly enriched pathways in the sart3smu471 mutant. Knock down of p53 rescued HSPC development in the sart3smu471 mutant. Interestingly, the p53 inhibitor, mdm4, had undergone an alternative splicing event in the mutant. Restoration of mdm4 partially rescued HSPC deficiency. Thus, our data suggest that HSPC proliferation and maintenance require sart3 to ensure the correct splicing and expression of mdm4, so that the p53 pathway is properly inhibited to prevent definitive hematopoiesis failure. This study expands our knowledge of the regulatory mechanisms that impact HSPC development and sheds light on the mechanistic basis and potential therapeutic use of sart3 in spliceosome-mdm4-p53 related disorders.
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22
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Sugden WW, North TE. Making Blood from the Vessel: Extrinsic and Environmental Cues Guiding the Endothelial-to-Hematopoietic Transition. Life (Basel) 2021; 11:life11101027. [PMID: 34685398 PMCID: PMC8539454 DOI: 10.3390/life11101027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 01/10/2023] Open
Abstract
It is increasingly recognized that specialized subsets of endothelial cells carry out unique functions in specific organs and regions of the vascular tree. Perhaps the most striking example of this specialization is the ability to contribute to the generation of the blood system, in which a distinct population of “hemogenic” endothelial cells in the embryo transforms irreversibly into hematopoietic stem and progenitor cells that produce circulating erythroid, myeloid and lymphoid cells for the lifetime of an animal. This review will focus on recent advances made in the zebrafish model organism uncovering the extrinsic and environmental factors that facilitate hemogenic commitment and the process of endothelial-to-hematopoietic transition that produces blood stem cells. We highlight in particular biomechanical influences of hemodynamic forces and the extracellular matrix, metabolic and sterile inflammatory cues present during this developmental stage, and outline new avenues opened by transcriptomic-based approaches to decipher cell–cell communication mechanisms as examples of key signals in the embryonic niche that regulate hematopoiesis.
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Affiliation(s)
- Wade W. Sugden
- Stem Cell Program, Department of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
| | - Trista E. North
- Stem Cell Program, Department of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
- Correspondence:
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23
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Bader A, Gao J, Rivière T, Schmid B, Walzog B, Maier-Begandt D. Molecular Insights Into Neutrophil Biology From the Zebrafish Perspective: Lessons From CD18 Deficiency. Front Immunol 2021; 12:677994. [PMID: 34557186 PMCID: PMC8453019 DOI: 10.3389/fimmu.2021.677994] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 08/16/2021] [Indexed: 12/26/2022] Open
Abstract
Neutrophils are key players in innate immunity and originate from the bone marrow of the adult mammalian organism. In mammals, mature neutrophils are released from the bone marrow into the peripheral blood where they circulate until their recruitment to sites of inflammation in a multistep adhesion cascade. Here, adhesion molecules of the β2 integrin family (CD11/CD18) are critically required for the initial neutrophil adhesion to the inflamed endothelium and several post-adhesion steps allowing their extravasation into the inflamed tissue. Within the mammalian tissue, interstitial neutrophil migration can occur widely independent of β2 integrins. This is in sharp contrast to neutrophil recruitment in zebrafish larvae (Danio rerio) where neutrophils originate from the caudal hematopoietic tissue and mainly migrate interstitially to sites of lesion upon the early onset of inflammation. However, neutrophils extravasate from the circulation to the inflamed tissue in zebrafish larvae at later-time points. Although zebrafish larvae are a widely accepted model system to analyze neutrophil trafficking in vivo, the functional impact of β2 integrins for neutrophil trafficking during acute inflammation is completely unknown in this model. In this study, we generated zebrafish with a genetic deletion of CD18, the β subunit of β2 integrins, using CRISPR/Cas9 technology. Sequence alignments demonstrated a high similarity of the amino acid sequences between zebrafish and human CD18 especially in the functionally relevant I-like domain. In addition, the cytoplasmic domain of CD18 harbors two highly conserved NXXF motifs suggesting that zebrafish CD18 may share functional properties of human CD18. Accordingly, CD18 knock-out (KO) zebrafish larvae displayed the key symptoms of patients suffering from leukocyte adhesion deficiency (LAD) type I due to defects in ITGB2, the gene for CD18. Importantly, CD18 KO zebrafish larvae showed reduced neutrophil trafficking to sites of sterile inflammation despite the fact that an increased number of neutrophils was detectable in the circulation. By demonstrating the functional importance of CD18 for neutrophil trafficking in zebrafish larvae, our findings shed new light on neutrophil biology in vertebrates and introduce a new model organism for studying LAD type I.
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Affiliation(s)
- Almke Bader
- Institute of Cardiovascular Physiology and Pathophysiology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.,Walter Brendel Center of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jincheng Gao
- Institute of Cardiovascular Physiology and Pathophysiology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.,Walter Brendel Center of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thibaud Rivière
- Institute of Cardiovascular Physiology and Pathophysiology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.,Walter Brendel Center of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Bettina Schmid
- Fish Core Unit, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Barbara Walzog
- Institute of Cardiovascular Physiology and Pathophysiology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.,Walter Brendel Center of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Daniela Maier-Begandt
- Institute of Cardiovascular Physiology and Pathophysiology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.,Walter Brendel Center of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
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24
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Ulloa BA, Habbsa SS, Potts KS, Lewis A, McKinstry M, Payne SG, Flores JC, Nizhnik A, Feliz Norberto M, Mosimann C, Bowman TV. Definitive hematopoietic stem cells minimally contribute to embryonic hematopoiesis. Cell Rep 2021; 36:109703. [PMID: 34525360 PMCID: PMC8928453 DOI: 10.1016/j.celrep.2021.109703] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/29/2021] [Accepted: 08/20/2021] [Indexed: 01/23/2023] Open
Abstract
Hematopoietic stem cells (HSCs) are rare cells that arise in the embryo
and sustain adult hematopoiesis. Although the functional potential of nascent
HSCs is detectable by transplantation, their native contribution during
development is unknown, in part due to the overlapping genesis and marker gene
expression with other embryonic blood progenitors. Using single-cell
transcriptomics, we define gene signatures that distinguish nascent HSCs from
embryonic blood progenitors. Applying a lineage-tracing approach to selectively
track HSC output in situ, we find significantly delayed
lymphomyeloid contribution. An inducible HSC injury model demonstrates a
negligible impact on larval lymphomyelopoiesis following HSC depletion. HSCs are
not merely dormant at this developmental stage, as they showed robust
regeneration after injury. Combined, our findings illuminate that nascent HSCs
self-renew but display differentiation latency, while HSC-independent embryonic
progenitors sustain developmental hematopoiesis. Understanding these differences
could improve de novo generation and expansion of functional
HSCs. Ulloa et al. demonstrate that nascent HSCs robustly regenerate but
display differentiation latency, while HSC-independent embryonic progenitors
sustain developmental hematopoiesis. Their findings have implications for
dissecting the programs underlying the genesis of bona fide HSCs.
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Affiliation(s)
- Bianca A Ulloa
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Samima S Habbsa
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Kathryn S Potts
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Alana Lewis
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Mia McKinstry
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Sara G Payne
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Julio C Flores
- Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Anastasia Nizhnik
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Maria Feliz Norberto
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Christian Mosimann
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine and Children's Hospital Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Teresa V Bowman
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA; Albert Einstein College of Medicine and Montefiore Medical Center, Department of Medicine (Oncology), Bronx, NY, USA.
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25
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Feng Z, Lin C, Tu L, Su M, Song C, Liu S, Suryanto ME, Hsiao CD, Li L. FDA-Approved Drug Screening for Compounds That Facilitate Hematopoietic Stem and Progenitor Cells (HSPCs) Expansion in Zebrafish. Cells 2021; 10:cells10082149. [PMID: 34440919 PMCID: PMC8393331 DOI: 10.3390/cells10082149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are a specialized subset of cells with self-renewal and multilineage differentiation potency, which are essential for their function in bone marrow or umbilical cord blood transplantation to treat blood disorders. Expanding the hematopoietic stem and progenitor cells (HSPCs) ex vivo is essential to understand the HSPCs-based therapies potency. Here, we established a screening system in zebrafish by adopting an FDA-approved drug library to identify candidates that could facilitate HSPC expansion. To date, we have screened 171 drugs of 7 categories, including antibacterial, antineoplastic, glucocorticoid, NSAIDS, vitamins, antidepressant, and antipsychotic drugs. We found 21 drugs that contributed to HSPCs expansion, 32 drugs’ administration caused HSPCs diminishment and 118 drugs’ treatment elicited no effect on HSPCs amplification. Among these drugs, we further investigated the vitamin drugs ergocalciferol and panthenol, taking advantage of their acceptability, limited side-effects, and easy delivery. These two drugs, in particular, efficiently expanded the HSPCs pool in a dose-dependent manner. Their application even mitigated the compromised hematopoiesis in an ikzf1−/− mutant. Taken together, our study implied that the larval zebrafish is a suitable model for drug repurposing of effective molecules (especially those already approved for clinical use) that can facilitate HSPCs expansion.
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Affiliation(s)
- Zhi Feng
- Key Laboratory of Freshwater Fish Reproduction and Development, Institute of Developmental Biology and Regenerative Medicine, Ministry of Education, Southwest University, Chongqing 400715, China; (Z.F.); (C.L.); (L.T.); (M.S.); (C.S.); (S.L.)
| | - Chenyu Lin
- Key Laboratory of Freshwater Fish Reproduction and Development, Institute of Developmental Biology and Regenerative Medicine, Ministry of Education, Southwest University, Chongqing 400715, China; (Z.F.); (C.L.); (L.T.); (M.S.); (C.S.); (S.L.)
| | - Limei Tu
- Key Laboratory of Freshwater Fish Reproduction and Development, Institute of Developmental Biology and Regenerative Medicine, Ministry of Education, Southwest University, Chongqing 400715, China; (Z.F.); (C.L.); (L.T.); (M.S.); (C.S.); (S.L.)
| | - Ming Su
- Key Laboratory of Freshwater Fish Reproduction and Development, Institute of Developmental Biology and Regenerative Medicine, Ministry of Education, Southwest University, Chongqing 400715, China; (Z.F.); (C.L.); (L.T.); (M.S.); (C.S.); (S.L.)
- Research Center of Stem Cells and Ageing, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Chunyu Song
- Key Laboratory of Freshwater Fish Reproduction and Development, Institute of Developmental Biology and Regenerative Medicine, Ministry of Education, Southwest University, Chongqing 400715, China; (Z.F.); (C.L.); (L.T.); (M.S.); (C.S.); (S.L.)
| | - Shengnan Liu
- Key Laboratory of Freshwater Fish Reproduction and Development, Institute of Developmental Biology and Regenerative Medicine, Ministry of Education, Southwest University, Chongqing 400715, China; (Z.F.); (C.L.); (L.T.); (M.S.); (C.S.); (S.L.)
| | - Michael Edbert Suryanto
- Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan 320314, Taiwan;
| | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan 320314, Taiwan;
- Center for Nanotechnology, Chung Yuan Christian University, Taoyuan 320314, Taiwan
- Research Center for Aquatic Toxicology and Pharmacology, Chung Yuan Christian University, Taoyuan 320314, Taiwan
- Correspondence: (C.-D.H.); (L.L.)
| | - Li Li
- Research Center of Stem Cells and Ageing, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Correspondence: (C.-D.H.); (L.L.)
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26
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Smarca5-mediated epigenetic programming facilitates fetal HSPC development in vertebrates. Blood 2021; 137:190-202. [PMID: 32756943 DOI: 10.1182/blood.2020005219] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
Nascent hematopoietic stem and progenitor cells (HSPCs) acquire definitive hematopoietic characteristics only when they develop into fetal HSPCs; however, the mechanisms underlying fetal HSPC development are poorly understood. Here, we profiled the chromatin accessibility and transcriptional features of zebrafish nascent and fetal HSPCs using ATAC-seq and RNA-seq and revealed dynamic changes during HSPC transition. Functional assays demonstrated that chromatin remodeler-mediated epigenetic programming facilitates fetal HSPC development in vertebrates. Systematical screening of chromatin remodeler-related genes identified that smarca5 is responsible for the maintenance of chromatin accessibility at promoters of hematopoiesis-related genes in fetal HSPCs. Mechanistically, Smarca5 interacts with nucleolin to promote chromatin remodeling, thereby facilitating genomic binding of transcription factors to regulate expression of hematopoietic regulators such as bcl11ab. Our results unravel a new role of epigenetic regulation and reveal that Smarca5-mediated epigenetic programming is responsible for fetal HSPC development, which will provide new insights into the generation of functional HSPCs both in vivo and in vitro.
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27
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A single-cell resolution developmental atlas of hematopoietic stem and progenitor cell expansion in zebrafish. Proc Natl Acad Sci U S A 2021; 118:2015748118. [PMID: 33785593 PMCID: PMC8040670 DOI: 10.1073/pnas.2015748118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The caudal hematopoietic tissue (CHT) is characterized as a hematopoietic organ for fetal hematopoietic stem and progenitor cell (HSPC) expansion in zebrafish. In this study, we used scRNA-seq combined with functional assays to decode the developing CHT. First, we resolved fetal HSPC heterogeneity, manifested as lineage priming and metabolic gene signatures. We further analyzed the cellular interactions among nonhematopoietic niche components and HSPCs and identified an endothelial cell-specific factor, Gpr182, followed by experimental validation of its role in promoting HSPC expansion. Finally, we uncovered the conservation and divergence of developmental hematopoiesis between human fetal liver and zebrafish CHT. Our study provides a valuable resource for fetal HSPC development and clues to establish a supportive niche for HSPC expansion in vitro. During vertebrate embryogenesis, fetal hematopoietic stem and progenitor cells (HSPCs) exhibit expansion and differentiation properties in a supportive hematopoietic niche. To profile the developmental landscape of fetal HSPCs and their local niche, here, using single-cell RNA-sequencing, we deciphered a dynamic atlas covering 28,777 cells and 9 major cell types (23 clusters) of zebrafish caudal hematopoietic tissue (CHT). We characterized four heterogeneous HSPCs with distinct lineage priming and metabolic gene signatures. Furthermore, we investigated the regulatory mechanism of CHT niche components for HSPC development, with a focus on the transcription factors and ligand–receptor networks involved in HSPC expansion. Importantly, we identified an endothelial cell-specific G protein–coupled receptor 182, followed by in vivo and in vitro functional validation of its evolutionally conserved role in supporting HSPC expansion in zebrafish and mice. Finally, comparison between zebrafish CHT and human fetal liver highlighted the conservation and divergence across evolution. These findings enhance our understanding of the regulatory mechanism underlying hematopoietic niche for HSPC expansion in vivo and provide insights into improving protocols for HSPC expansion in vitro.
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28
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Transcriptional and epigenetic control of hematopoietic stem cell fate decisions in vertebrates. Dev Biol 2021; 475:156-164. [PMID: 33689804 DOI: 10.1016/j.ydbio.2021.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/24/2021] [Accepted: 03/04/2021] [Indexed: 12/20/2022]
Abstract
Hematopoietic stem cells (HSCs) are the foundation of adult hematopoiesis that produce all types of mature blood lineages. In vertebrates, HSC development is a stepwise process, coordinately regulated by chromatin architectures and a group of transcriptional and epigenetic regulators. A deeper understanding of the molecular mechanisms governing the generation, expansion, and function of HSCs holds great promise in the generation and expansion of engraftable HSCs in vitro for clinical applications. This study reviewed recent advances in transcriptional and epigenetic control of hematopoietic stem cell fate decisions in vertebrates.
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29
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Hu Y, Fang K, Wang Y, Lu N, Sun H, Zhang C. Single-cell analysis reveals the origins and intrahepatic development of liver-resident IFN-γ-producing γδ T cells. Cell Mol Immunol 2021; 18:954-968. [PMID: 33692482 PMCID: PMC8115257 DOI: 10.1038/s41423-021-00656-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/13/2021] [Indexed: 11/09/2022] Open
Abstract
γδ T cells are heterogeneous lymphocytes located in various tissues. However, a systematic and comprehensive understanding of the origins of γδ T cell heterogeneity and the extrathymic developmental pathway associated with liver γδ T cells remain largely unsolved. In this study, we performed single-cell RNA sequencing (scRNA-seq) to comprehensively catalog the heterogeneity of γδ T cells derived from murine liver and thymus samples. We revealed the developmental trajectory of γδ T cells and found that the liver contains γδ T cell precursors (pre-γδ T cells). The developmental potential of hepatic γδ T precursor cells was confirmed through in vitro coculture experiments and in vivo adoptive transfer experiments. The adoptive transfer of hematopoietic progenitor Lin-Sca-1+Mac-1+ (LSM) cells from fetal or adult liver samples to sublethally irradiated recipients resulted in the differentiation of liver LSM cells into pre-γδ T cells and interferon-gamma+ (IFN-γ+) but not interleukin-17a+ (IL-17a+) γδ T cells in the liver. Importantly, thymectomized mouse models showed that IFN-γ-producing γδ T cells could originate from liver LSM cells in a thymus-independent manner. These results suggested that liver hematopoietic progenitor LSM cells were able to differentiate into pre-γδ T cells and functionally mature γδ T cells, which implied that these cells are involved in a distinct developmental pathway independent of thymus-derived γδ T cells.
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Affiliation(s)
- Yuan Hu
- Institute of Immunopharmaceutical Sciences, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Keke Fang
- Institute of Immunopharmaceutical Sciences, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yanan Wang
- Institute of Immunopharmaceutical Sciences, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Nan Lu
- Institute of Diagnostics, School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Haoyu Sun
- Institute of Immunology, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Cai Zhang
- Institute of Immunopharmaceutical Sciences, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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Bergo V, Trompouki E. New tools for 'ZEBRA-FISHING'. Brief Funct Genomics 2021:elab001. [PMID: 33605988 DOI: 10.1093/bfgp/elab001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/14/2020] [Accepted: 01/04/2021] [Indexed: 11/14/2022] Open
Abstract
Zebrafish has been established as a classical model for developmental studies, yet in the past years, with the explosion of novel technological methods, the use of zebrafish as a model has expanded. One of the prominent fields that took advantage of zebrafish as a model organism early on is hematopoiesis, the process of blood cell generation from hematopoietic stem and progenitor cells (HSPCs). In zebrafish, HSPCs are born early during development in the aorta-gonad-mesonephros region and then translocate to the caudal hematopoietic tissue, where they expand and finally take residence in the kidney marrow. This journey is tightly regulated at multiple levels from extracellular signals to chromatin. In order to delineate the mechanistic underpinnings of this process, next-generation sequencing techniques could be an important ally. Here, we describe genome-wide approaches that have been undertaken to delineate zebrafish hematopoiesis.
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Armingol E, Officer A, Harismendy O, Lewis NE. Deciphering cell-cell interactions and communication from gene expression. Nat Rev Genet 2021; 22:71-88. [PMID: 33168968 PMCID: PMC7649713 DOI: 10.1038/s41576-020-00292-x] [Citation(s) in RCA: 472] [Impact Index Per Article: 157.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 12/13/2022]
Abstract
Cell-cell interactions orchestrate organismal development, homeostasis and single-cell functions. When cells do not properly interact or improperly decode molecular messages, disease ensues. Thus, the identification and quantification of intercellular signalling pathways has become a common analysis performed across diverse disciplines. The expansion of protein-protein interaction databases and recent advances in RNA sequencing technologies have enabled routine analyses of intercellular signalling from gene expression measurements of bulk and single-cell data sets. In particular, ligand-receptor pairs can be used to infer intercellular communication from the coordinated expression of their cognate genes. In this Review, we highlight discoveries enabled by analyses of cell-cell interactions from transcriptomic data and review the methods and tools used in this context.
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Affiliation(s)
- Erick Armingol
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Adam Officer
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA
| | - Olivier Harismendy
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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Phosphatidylinositol-3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells. Oncogene 2021; 40:2741-2755. [PMID: 33714985 PMCID: PMC8049872 DOI: 10.1038/s41388-021-01733-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 02/17/2021] [Accepted: 02/24/2021] [Indexed: 01/31/2023]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are multipotent cells giving rise to all blood lineages during life. HSPCs emerge from the ventral wall of the dorsal aorta (VDA) during a specific timespan in embryonic development through endothelial hematopoietic transition (EHT). We investigated the ontogeny of HSPCs in mutant zebrafish embryos lacking functional pten, an important tumor suppressor with a central role in cell signaling. Through in vivo live imaging, we discovered that in pten mutant embryos a proportion of the HSPCs died upon emergence from the VDA, an effect rescued by inhibition of phosphatidylinositol-3 kinase (PI3K). Surprisingly, inhibition of PI3K in wild-type embryos also induced HSPC death. Surviving HSPCs colonized the caudal hematopoietic tissue (CHT) normally and committed to all blood lineages. Single-cell RNA sequencing indicated that inhibition of PI3K enhanced survival of multipotent progenitors, whereas the number of HSPCs with more stem-like properties was reduced. At the end of the definitive wave, loss of Pten caused a shift to more restricted progenitors at the expense of HSPCs. We conclude that PI3K signaling tightly controls HSPCs survival and both up- and downregulation of PI3K signaling reduces stemness of HSPCs.
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33
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Molecular Modulation of Fetal Liver Hematopoietic Stem Cell Mobilization into Fetal Bone Marrow in Mice. Stem Cells Int 2020; 2020:8885154. [PMID: 33381191 PMCID: PMC7755487 DOI: 10.1155/2020/8885154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 11/03/2020] [Accepted: 12/04/2020] [Indexed: 11/24/2022] Open
Abstract
Development of hematopoietic stem cells is a complex process, which has been extensively investigated. Hematopoietic stem cells (HSCs) in mouse fetal liver are highly expanded to prepare for mobilization of HSCs into the fetal bone marrow. It is not completely known how the fetal liver niche regulates HSC expansion without loss of self-renewal ability. We reviewed current progress about the effects of fetal liver niche, chemokine, cytokine, and signaling pathways on HSC self-renewal, proliferation, and expansion. We discussed the molecular regulations of fetal HSC expansion in mouse and zebrafish. It is also unknown how HSCs from the fetal liver mobilize, circulate, and reside into the fetal bone marrow niche. We reviewed how extrinsic and intrinsic factors regulate mobilization of fetal liver HSCs into the fetal bone marrow, which provides tools to improve HSC engraftment efficiency during HSC transplantation. Understanding the regulation of fetal liver HSC mobilization into the fetal bone marrow will help us to design proper clinical therapeutic protocol for disease treatment like leukemia during pregnancy. We prospect that fetal cells, including hepatocytes and endothelial and hematopoietic cells, might regulate fetal liver HSC expansion. Components from vascular endothelial cells and bones might also modulate the lodging of fetal liver HSCs into the bone marrow. The current review holds great potential to deeply understand the molecular regulations of HSCs in the fetal liver and bone marrow in mammals, which will be helpful to efficiently expand HSCs in vitro.
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Dambroise E, Ktorza I, Brombin A, Abdessalem G, Edouard J, Luka M, Fiedler I, Binder O, Pelle O, Patton EE, Busse B, Menager M, Sohm F, Legeai-Mallet L. Fgfr3 Is a Positive Regulator of Osteoblast Expansion and Differentiation During Zebrafish Skull Vault Development. J Bone Miner Res 2020; 35:1782-1797. [PMID: 32379366 DOI: 10.1002/jbmr.4042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/09/2020] [Accepted: 04/27/2020] [Indexed: 12/20/2022]
Abstract
Gain or loss-of-function mutations in fibroblast growth factor receptor 3 (FGFR3) result in cranial vault defects highlighting the protein's role in membranous ossification. Zebrafish express high levels of fgfr3 during skull development; in order to study FGFR3's role in cranial vault development, we generated the first fgfr3 loss-of-function zebrafish (fgfr3lof/lof ). The mutant fish exhibited major changes in the craniofacial skeleton, with a lack of sutures, abnormal frontal and parietal bones, and the presence of ectopic bones. Integrated analyses (in vivo imaging and single-cell RNA sequencing of the osteoblast lineage) of zebrafish fgfr3lof/lof revealed a delay in osteoblast expansion and differentiation, together with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis. We conclude that changes in the extracellular matrix within growing bone might impair cell-cell communication, mineralization, and new osteoblast recruitment. © 2020 American Society for Bone and Mineral Research.
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Affiliation(s)
- Emilie Dambroise
- Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Ivan Ktorza
- Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Alessandro Brombin
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ghaith Abdessalem
- Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Joanne Edouard
- UMS AMAGEN, CNRS, INRA, Université Paris-Saclay, Gif-sur-Yvette, France.,Institute for Integrative Biology of the Cell (I2BC)-CNRS, Gif-sur-Yvette, France
| | - Marine Luka
- Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Imke Fiedler
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Olivia Binder
- Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Olivier Pelle
- Flow Cytometry Core Facility, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - E Elizabeth Patton
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Björn Busse
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mickaël Menager
- Laboratory of Inflammatory Responses and Transcriptomic Networks in Diseases, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Frederic Sohm
- UMS AMAGEN, CNRS, INRA, Université Paris-Saclay, Gif-sur-Yvette, France.,Institute for Integrative Biology of the Cell (I2BC)-CNRS, Gif-sur-Yvette, France.,Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Flow Cytometry Core Facility, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France.,Functional Genomics Institute of Lyon, University of Lyon, CNRS, INRA, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Laurence Legeai-Mallet
- Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
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35
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Lv P, Ma D, Gao S, Zhang Y, Bae YK, Liang G, Gao S, Choi JH, Kim CH, Wang L, Liu F. Generation of foxn1/Casper Mutant Zebrafish for Allograft and Xenograft of Normal and Malignant Cells. Stem Cell Reports 2020; 15:749-760. [PMID: 32822590 PMCID: PMC7486299 DOI: 10.1016/j.stemcr.2020.07.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
Cell transplantation into immunodeficient recipients is a widely used approach to study stem cell and cancer biology; however, studying cell states post transplantation in vivo is inconvenient in mammals. Here, we generated a foxn1/Casper mutant zebrafish that is transparent and exhibits T cell deficiency. By employing the line for hematopoietic stem cell (HSC) transplantation (HSCT), we could achieve nonconditioned transplantation. Meanwhile, we found that fetal HSCs from 3 days post fertilization zebrafish embryos produce a better transplant outcome in foxn1/Casper mutants, compared with adult HSCs. In addition to HSCT, the foxn1/Casper mutant is feasible for allografts of myelodysplastic syndrome-like and muscle cells, as well as xenografts of medaka muscle cells. In summary, foxn1/Casper mutants permit the nonconditioned engraftment of multiple cell types and visualized characterization of transplanted cells in vivo. foxn1/Casper mutant zebrafish permit unconditioned and visualized cell transplantation Zebrafish fetal HSCs possess more robust engraftment ability than adult HSCs foxn1/Casper mutant zebrafish permit allogeneic MDS-like cell transplantation Allograft and xenograft of muscle cells can be monitored in foxn1/Casper mutant zebrafish
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Affiliation(s)
- Peng Lv
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Dongyuan Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Shuai Gao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Yifan Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Young-Ki Bae
- Comparative Biomedical Research Branch, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea
| | - Guixian Liang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Suwei Gao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Jung-Hwa Choi
- Department of Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Lu Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Science, Beijing 100049, China.
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36
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Teves JM, Won KJ. Mapping Cellular Coordinates through Advances in Spatial Transcriptomics Technology. Mol Cells 2020; 43:591-599. [PMID: 32507771 PMCID: PMC7398793 DOI: 10.14348/molcells.2020.0020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/22/2020] [Accepted: 05/10/2020] [Indexed: 12/13/2022] Open
Abstract
Complex cell-to-cell communication underlies the basic processes essential for homeostasis in the given tissue architecture. Obtaining quantitative gene-expression of cells in their native context has significantly advanced through single-cell RNA sequencing technologies along with mechanical and enzymatic tissue manipulation. This approach, however, is largely reliant on the physical dissociation of individual cells from the tissue, thus, resulting in a library with unaccounted positional information. To overcome this, positional information can be obtained by integrating imaging and positional barcoding. Collectively, spatial transcriptomics strategies provide tissue architecture-dependent as well as position-dependent cellular functions. This review discusses the current technologies for spatial transcriptomics ranging from the methods combining mechanical dissociation and single-cell RNA sequencing to computational spatial re-mapping.
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Affiliation(s)
- Joji Marie Teves
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-00 Copenhagen, Denmark
| | - Kyoung Jae Won
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-00 Copenhagen, Denmark
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37
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Pijuan-Sala B, Wilson NK, Xia J, Hou X, Hannah RL, Kinston S, Calero-Nieto FJ, Poirion O, Preissl S, Liu F, Göttgens B. Single-cell chromatin accessibility maps reveal regulatory programs driving early mouse organogenesis. Nat Cell Biol 2020; 22:487-497. [PMID: 32231307 PMCID: PMC7145456 DOI: 10.1038/s41556-020-0489-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/20/2020] [Indexed: 11/29/2022]
Abstract
During mouse embryonic development, pluripotent cells rapidly divide and diversify, yet the regulatory programs that define the cell repertoire for each organ remain ill-defined. To delineate comprehensive chromatin landscapes during early organogenesis, we mapped chromatin accessibility in 19,453 single nuclei from mouse embryos at 8.25 days post-fertilization. Identification of cell-type-specific regions of open chromatin pinpointed two TAL1-bound endothelial enhancers, which we validated using transgenic mouse assays. Integrated gene expression and transcription factor motif enrichment analyses highlighted cell-type-specific transcriptional regulators. Subsequent in vivo experiments in zebrafish revealed a role for the ETS factor FEV in endothelial identity downstream of ETV2 (Etsrp in zebrafish). Concerted in vivo validation experiments in mouse and zebrafish thus illustrate how single-cell open chromatin maps, representative of a mammalian embryo, provide access to the regulatory blueprint for mammalian organogenesis.
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Affiliation(s)
- Blanca Pijuan-Sala
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nicola K Wilson
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jun Xia
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaomeng Hou
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Rebecca L Hannah
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Sarah Kinston
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Fernando J Calero-Nieto
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Olivier Poirion
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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38
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Sidhaye VK, Wu M, Tesfaigzi Y. Jumping on the Single-Cell RNA-Sequencing Bandwagon: Take Care Not to Put the Cart before the Horse. Am J Respir Cell Mol Biol 2020; 62:267. [PMID: 32003599 DOI: 10.1165/rcmb.2019-0389le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
| | - Min Wu
- University of North DakotaGrand Forks, North Dakotaand
| | - Yohannes Tesfaigzi
- Brigham and Women's Hospital-Harvard Medical SchoolBoston, Massachusetts
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