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Cheng M, Jiang Y, Xu J, Mentis AFA, Wang S, Zheng H, Sahu SK, Liu L, Xu X. Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges. J Genet Genomics 2023; 50:625-640. [PMID: 36990426 DOI: 10.1016/j.jgg.2023.03.011] [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: 10/05/2022] [Revised: 03/11/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology, from the invention of the microscope 350 years ago to the recent emergence of single-cell sequencing, by which the scientific community has been able to visualize life at an unprecedented resolution. Most recently, the Spatially Resolved Transcriptomics (SRT) technologies have filled the gap in probing the spatial or even three-dimensional organization of the molecular foundation behind the molecular mysteries of life, including the origin of different cellular populations developed from totipotent cells and human diseases. In this review, we introduce recent progresses and challenges on SRT from the perspectives of technologies and bioinformatic tools, as well as the representative SRT applications. With the currently fast-moving progress of the SRT technologies and promising results from early adopted research projects, we can foresee the bright future of such new tools in understanding life at the most profound analytical level.
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Affiliation(s)
| | - Yujia Jiang
- BGI-Hangzhou, Hangzhou, Zhejiang 310012, China
| | | | | | - Shuai Wang
- BGI-Hangzhou, Hangzhou, Zhejiang 310012, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Sunil Kumar Sahu
- BGI-Shenzhen, Shenzhen, Guangdong 518103, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Longqi Liu
- BGI-Hangzhou, Hangzhou, Zhejiang 310012, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xun Xu
- BGI-Hangzhou, Hangzhou, Zhejiang 310012, China; BGI-Shenzhen, Shenzhen, Guangdong 518103, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, Guangdong 518120, China.
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Patterning the cerebral cortex into distinct functional domains during development. Curr Opin Neurobiol 2023; 80:102698. [PMID: 36893490 DOI: 10.1016/j.conb.2023.102698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/05/2023] [Indexed: 03/11/2023]
Abstract
The cerebral cortex is compartmentalized into multiple regions, including the newly evolved neocortex and evolutionarily older paleocortex and archicortex. These broad cortical regions can be further subdivided into different functional domains, each with its own unique cytoarchitecture and distinct set of input and output projections to perform specific functions. While many excitatory projection neurons show region-specific gene expression profiles, the cells are derived from the seemingly uniform progenitors in the dorsal telencephalon. Much progress has been made in defining the genetic mechanisms involved in generating the morphological and functional diversity of the central nervous system. In this review, we summarize the current knowledge of mouse corticogenesis and discuss key events involved in cortical patterning during early developmental stages.
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Liu Z, Zhai M, Zhang Q, Yang T, Wan Z, Li J, Liu X, Xu B, Du L, Chan RWS, Zhang L, Yeung WSB, Cheung KW, Chiu PCN, Wang WJ, Lee CL, Gao Y. Resolving the gene expression maps of human first-trimester chorionic villi with spatial transcriptome. Front Cell Dev Biol 2022; 10:1060298. [PMID: 36561369 PMCID: PMC9763897 DOI: 10.3389/fcell.2022.1060298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
The placenta is important for fetal development in mammals, and spatial transcriptomic profiling of placenta helps to resolve its structure and function. In this study, we described the landscape of spatial transcriptome of human placental villi obtained from two pregnant women at the first trimester using the modified Stereo-seq method applied for paraformaldehyde (PFA) fixation samples. The PFA fixation of human placenta villi was better than fresh villi embedded in optimum cutting temperature (OCT) compound, since it greatly improved tissue morphology and the specificity of RNA signals. The main cell types in chorionic villi such as syncytiotrophoblasts (SCT), villous cytotrophoblasts (VCT), fibroblasts (FB), and extravillous trophoblasts (EVT) were identified with the spatial transcriptome data, whereas the minor cell types of Hofbauer cells (HB) and endothelial cells (Endo) were spatially located by deconvolution of scRNA-seq data. We demonstrated that the Stereo-seq data of human villi could be used for sophisticated analyses such as spatial cell-communication and regulatory activity. We found that the SCT and VCT exhibited the most ligand-receptor pairs that could increase differentiation of the SCT, and that the spatial localization of specific regulons in different cell types was associated with the pathways related to hormones transport and secretion, regulation of mitotic cell cycle, and nutrient transport pathway in SCT. In EVT, regulatory pathways such as the epithelial to mesenchyme transition, epithelial development and differentiation, and extracellular matrix organization were identified. Finally, viral receptors and drug transporters were identified in villi according to the pathway analysis, which could help to explain the vertical transmission of several infectious diseases and drug metabolism efficacy. Our study provides a valuable resource for further investigation of the placenta development, physiology and pathology in a spatial context.
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Affiliation(s)
| | | | - Qingqing Zhang
- Department of Obstetrics and Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China,Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Tingyu Yang
- BGI-Shenzhen, Shenzhen, China,Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Jianlin Li
- Department of Obstetrics and Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Xiaofeng Liu
- Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Bo Xu
- Department of Obstetrics and Gynaecology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Libei Du
- Department of Obstetrics and Gynaecology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Rachel W. S. Chan
- Department of Obstetrics and Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China,Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Li Zhang
- Department of Obstetrics and Gynaecology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - William S. B. Yeung
- Department of Obstetrics and Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China,Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Ka Wang Cheung
- Department of Obstetrics and Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Philip C. N. Chiu
- Department of Obstetrics and Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China,Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Wen-Jing Wang
- BGI-Shenzhen, Shenzhen, China,*Correspondence: Wen-Jing Wang, ; Cheuk-Lun Lee, ; Ya Gao,
| | - Cheuk-Lun Lee
- Department of Obstetrics and Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China,Shenzhen Key Laboratory of Fertility Regulation, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China,*Correspondence: Wen-Jing Wang, ; Cheuk-Lun Lee, ; Ya Gao,
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China,Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China,*Correspondence: Wen-Jing Wang, ; Cheuk-Lun Lee, ; Ya Gao,
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Faure L, Techameena P, Hadjab S. Emergence of neuron types. Curr Opin Cell Biol 2022; 79:102133. [PMID: 36347131 DOI: 10.1016/j.ceb.2022.102133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 01/31/2023]
Abstract
Neuron types are the building blocks of the nervous system, and therefore, of functional circuits. Understanding the origin of neuronal diversity has always been an essential question in neuroscience and developmental biology. While knowledge on the molecular control of their diversification has largely increased during the last decades, it is now possible to reveal the dynamic mechanisms and the actual stepwise molecular changes occurring at single-cell level with the advent of single-cell omics technologies and analysis with high temporal resolution. Here, we focus on recent advances in the field and in technical and analytical tools that enable detailed insights into the emergence of neuron types in the central and peripheral nervous systems.
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Affiliation(s)
- Louis Faure
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, 1090, Vienna, Austria
| | - Prach Techameena
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Saida Hadjab
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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