Development of Spatial Transcriptomics and Its Applications

doi:10.13304/j.nykjdb.2024.0609

Journal of Agricultural Science and Technology ›› 2024, Vol. 26 ›› Issue (11): 23-31.DOI: 10.13304/j.nykjdb.2024.0609

• BIOTECHNOLOGY & LIFE SCIENCE • Previous Articles Next Articles

Development of Spatial Transcriptomics and Its Applications

Yongzi CHEN¹^,²(), Hua WANG¹^,³^,⁴, Weixuan WANG⁵^,⁶()

^1.National Clinical Research Center for Cancer，Tianjin’s Clinical Research Center for Cancer，Key Laboratory of Cancer Prevention and Therapy，Tianjin Medical University Cancer Institute and Hospital，Tianjin 300060，China
^2.Laboratory of Tumor Cell Biology，Tianjin Medical University Cancer Institute and Hospital，Tianjin 300060，China
^3.Department of Radiology，Tianjin Cancer Hospital Airport Hospital，Tianjin 300038，China
^4.Department of Radiology，Tianjin Medical University Cancer Institute and Hospital，Tianjin 300060，China
^5.Biotechnology Research Institute，Chinese Academy of Agricultural Sciences，Beijing 100081，China
^6.National Nanfan Research Institute （Sanya），Chinese Academy of Agricultural Sciences，Hainan Sanya 572024，China

Received:2024-07-30 Accepted:2024-08-28 Online:2024-11-15 Published:2024-11-19
Contact: Weixuan WANG

空间转录组学的发展及其应用进展

陈永孜¹^,²(), 王化¹^,³^,⁴, 王维轩⁵^,⁶()

^1.天津医科大学肿瘤医院，天津市恶性肿瘤临床医学研究中心，国家恶性肿瘤临床医学研究中心，天津市肿瘤防治重点实验室，天津 300060
^2.天津医科大学肿瘤医院肿瘤细胞生物学实验室，天津 300060
^3.天津市肿瘤医院空港医院放射诊断科，天津 300038
^4.天津医科大学肿瘤医院放射科，天津 300060
^5.中国农业科学院生物技术研究所，北京 100081
^6.三亚中国农业科学院国家南繁研究院，海南三亚 572024

通讯作者: 王维轩
作者简介:陈永孜 E-mail： yzchen@tmu.edu.cn；
基金资助:
三亚中国农业科学院国家南繁研究院南繁专项(YYLH2305);中国农业科学院科技创新工程项目(WLSZD2020-001);天津市医学重点学科（专科）建设项目(TJYXZDXK-009A);天津市卫生健康科技项目(TJWJ2022MS052)

Abstract

Abstract:

Spatial transcriptomics is a disruptive biological technique that integrates molecular biology and spatial imaging technologies to reveal the spatial distribution of gene expression within tissues or cells. Through the analysis of transcriptomics data， the spatial expression patterns of genes at tissue or cellular level could be understanded comprehensively， and then the spatiotemporal characteristics of gene regulation in biological systems and their functional significance in biological processes could be deeply uncovered. This technology provided unprecedented assistance for the research in developmental biology， immunology， tumor research and agriculture fields etc， and provided support for understanding of key processes such as cell differentiation and crop development etc. This article detaily overviewed the development of spatial transcriptomics technology， data analysis， and its major applications in the fields of medicine and agriculture. It also identified the challenges existed in the field and offered insights into future development trends.

Key words: spatial transcriptomics, data analysis, research progress, applications

摘要：

空间转录组学是一项颠覆性的生物学技术，融合了分子生物学和空间成像技术，旨在揭示组织或细胞中基因表达的空间分布。其通过对转录组数据进行分析，可以全面理解基因在组织或细胞水平上的空间表达规律，从而深入揭示生物系统中基因调控的时空特征及其在生物学过程中的功能和意义。该技术为发育生物学、免疫学、医学以及农业等领域的研究提供了前所未有的帮助，为理解细胞分化、农作物发育等关键过程提供了支撑。详细介绍了空间转录组技术的发展进程、数据分析及其在医学以及农业领域中的主要应用，提出了该领域所存在的问题并对未来发展趋势进行展望。

关键词: 空间转录组学, 数据分析, 研究进展, 应用

CLC Number:

Yongzi CHEN, Hua WANG, Weixuan WANG. Development of Spatial Transcriptomics and Its Applications[J]. Journal of Agricultural Science and Technology, 2024, 26(11): 23-31.

陈永孜, 王化, 王维轩. 空间转录组学的发展及其应用进展[J]. 中国农业科技导报, 2024, 26(11): 23-31.

Figures/Tables 3

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工具 Tool	开发语言 Development language	步骤 Procedure	链接 Link
Seurat^［9］	R	批量效应校正；降维与聚类；空间细胞类型注释；空间可变基因 Batch effect correction； dimensionality reduction and clustering； spatial cell type annotation； and spatially variable genes	https：//github.com/satijalab/seurat
Harmony^［10］	R	批量效应校正 Batch effect correction	https：//github.com/immunogenomics/harmony
stLearn	Python	降维与聚类；空间可变基因；空间轨迹 Dimensionality reduction and clustering； spatially variable genes； spatial trajectory	https：//github.com/BiomedicalMachineLearning/stLearn
cell2location^［11］	Python	空间细胞类型注释；空间区域定位 Spatial cell type annotation； spatial region localization	https：//github.com/BayraktarLab/cell2location/
Scanorama^［12］	Python	批量效应校正 Batch effect correction	https：//github.com/brianhie/scanorama
scHOT^［13］	R	基因-基因相互作用 Gene-gene interaction	https：//bioconductor.org/packages/release/bioc/html/scHOT.html
STUtility^［14］	R	降维与聚类；空间可变基因；三维模型构建 Dimensionality reduction and clustering； spatially variable genes； 3D model construction	https：//github.com/jbergenstrahle/STUtility

工具 Tool	开发语言 Development language	步骤 Procedure	链接 Link
Seurat^［9］	R	批量效应校正；降维与聚类；空间细胞类型注释；空间可变基因 Batch effect correction； dimensionality reduction and clustering； spatial cell type annotation； and spatially variable genes	https：//github.com/satijalab/seurat
Harmony^［10］	R	批量效应校正 Batch effect correction	https：//github.com/immunogenomics/harmony
stLearn	Python	降维与聚类；空间可变基因；空间轨迹 Dimensionality reduction and clustering； spatially variable genes； spatial trajectory	https：//github.com/BiomedicalMachineLearning/stLearn
cell2location^［11］	Python	空间细胞类型注释；空间区域定位 Spatial cell type annotation； spatial region localization	https：//github.com/BayraktarLab/cell2location/
Scanorama^［12］	Python	批量效应校正 Batch effect correction	https：//github.com/brianhie/scanorama
scHOT^［13］	R	基因-基因相互作用 Gene-gene interaction	https：//bioconductor.org/packages/release/bioc/html/scHOT.html
STUtility^［14］	R	降维与聚类；空间可变基因；三维模型构建 Dimensionality reduction and clustering； spatially variable genes； 3D model construction	https：//github.com/jbergenstrahle/STUtility

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Development of Spatial Transcriptomics and Its Applications

空间转录组学的发展及其应用进展

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