时空转录组研究进展

doi:10.11983/CBB22220

植物学报 ›› 2023, Vol. 58 ›› Issue (2): 214-232.DOI: 10.11983/CBB22220

时空转录组研究进展

肖宇彬¹^,², 张子旭¹, 王玉珠¹, 刘欢²^,³^,^*(), 陈乐天¹^,^*()

¹华南农业大学生命科学学院, 亚热带农业作物资源保护与利用国家重点实验室, 岭南现代农业科学与技术广东省实验室, 广州 510642
²深圳华大生命科学研究院, 农业基因组学国家重点实验室, 深圳 518083
³岭南现代农业科学与技术广东省实验室深圳分中心, 深圳 518083

收稿日期:2022-09-12 接受日期:2023-01-10 出版日期:2023-03-01 发布日期:2023-03-15
通讯作者: ^*E-mail: liuhuan@genomics.cn;lotichen@scau.edu.cn
基金资助:
国家自然科学基金创新研究群体(31921004);中国博士后基金(2022M711210)

Research Progress of Spatiotemporal Transcriptomes

Yubin Xiao¹^,², Zixu Zhang¹, Yuzhu Wang¹, Huan Liu²^,³^,^*(), Letian Chen¹^,^*()

¹Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
²State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
³Shenzhen Branch of Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518083, China

Received:2022-09-12 Accepted:2023-01-10 Online:2023-03-01 Published:2023-03-15
Contact: ^*E-mail: liuhuan@genomics.cn;lotichen@scau.edu.cn

摘要/Abstract

摘要： 时空异质性是造成不同组织功能差异的关键因素, 在细胞命运调控过程中发挥重要作用。时空转录组(stRNA-seq)是一项将定量转录组与高分辨率组织成像相结合的新兴组学技术。它将表达数据锚定到目标器官或组织的物理图上, 并以无偏见的生物信息学方式对组织切片和细胞层进行分子表征, 反映特定细胞内基因的时空异质性表达丰度。受益于高通量测序技术的快速发展, 时空转录组为探究各类细胞基因表达的时空异质性提供了新的实验思路和方法。该文介绍了时空转录组的原理和发展进程, 以及不同时空转录组的技术特点和优劣, 总结了时空转录组在动物、植物和微生物中的应用, 可为今后系统开展时空转录组研究提供理论参考。

关键词: 时空转录组学, 时空异质性, 单细胞

Abstract: Spatiotemporal heterogeneity is a key factor for functional differentiation in different tissues and plays an important role in regulating cell fate. Spatiotemporal transcriptomic sequencing (stRNA-seq) is an emerging omics technology that combines quantitative transcriptome with high-resolution tissue imaging. It anchors expression data to the physical map of a target organ or tissue and molecularly characterizes tissue sections and cell layers via unbiased bioinformatic analysis, which reflects the spatiotemporal heterogeneity of gene expression abundances within specific cells. Benefiting from the rapid development of high-throughput sequencing, the spatiotemporal heterogeneity of gene expression in various cells can be explored by new experimental approaches. In this review, we first briefly introduce the principle and development process of stRNA-seq, providing readers an overview on the characteristics, advantages and disadvantages of different stRNA-seq techniques. Then, we summarize the applications of stRNA-seq in animals, plants and microorganisms, which provide theoretical references for the systematic research of stRNA-seq in future.

Key words: spatiotemporal transcriptomics, spatial and temporal heterogeneity, single cell

肖宇彬, 张子旭, 王玉珠, 刘欢, 陈乐天. 时空转录组研究进展. 植物学报, 2023, 58(2): 214-232.

Yubin Xiao, Zixu Zhang, Yuzhu Wang, Huan Liu, Letian Chen. Research Progress of Spatiotemporal Transcriptomes. Chinese Bulletin of Botany, 2023, 58(2): 214-232.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB22220

https://www.chinbullbotany.com/CN/Y2023/V58/I2/214

图/表 5

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	动物	植物
特有结构	?	细胞壁(初生壁和次生壁)、液泡和叶绿体
包埋方法	冷冻包埋和石蜡包埋	冷冻包埋
组织切片	相对简单	相对困难, 高度木质化组织容易开裂、液泡易产生结晶等
染色方法	苏木精-伊红染色和ssDNA染色	甲苯铵蓝染色、ssDNA染色和钙白染色
组织透化	透化细胞膜	透化细胞壁和细胞膜, 且不同植物细胞的细胞壁成分存在较大异质性
组织移除	相对简单	高度成熟组织的降解可能需要较长的时间和苛刻的组织移除操作, 可能会影响逆转录产物
参考基因组	参考基因组较为完善	参考基因组有待进一步完善
技术平台	大量时空组技术优先适配于动物组织	时空组技术在植物组织中的应用条件仍有待进一步优化
时空组学文献数量	~5000	<1000

	动物	植物
特有结构	?	细胞壁(初生壁和次生壁)、液泡和叶绿体
包埋方法	冷冻包埋和石蜡包埋	冷冻包埋
组织切片	相对简单	相对困难, 高度木质化组织容易开裂、液泡易产生结晶等
染色方法	苏木精-伊红染色和ssDNA染色	甲苯铵蓝染色、ssDNA染色和钙白染色
组织透化	透化细胞膜	透化细胞壁和细胞膜, 且不同植物细胞的细胞壁成分存在较大异质性
组织移除	相对简单	高度成熟组织的降解可能需要较长的时间和苛刻的组织移除操作, 可能会影响逆转录产物
参考基因组	参考基因组较为完善	参考基因组有待进一步完善
技术平台	大量时空组技术优先适配于动物组织	时空组技术在植物组织中的应用条件仍有待进一步优化
时空组学文献数量	~5000	<1000

转录组技术				空间分辨率	细胞通量	优缺点	应用范围		参考文献
传统转录组学				组织水平	高	+ 成本低, 检测速度快 ? 掩盖了细胞的时空异质性	动植物微生物		Costa et al., 2010
单细胞转录组学				单细胞水平	高	+ 通量高, 检测深度较深 ? 忽略了细胞的空间信息	动植物微生物		Kolodziejczyk et al., 2015
时空转录组学		基于微解剖基因表达的技术	LCM	单细胞水平	低	+ 可人工挑选感兴趣的细胞 ? 通量低, 操作难度大	动植物微生物		Emmert-buck et al., 1996
			TIVA	单细胞水平	低	+ 能应用于活细胞 ? 通量低, 分析结果有限	动物		Lovatt et al., 2014
			Tomo-seq	单个切片	低	+ 可构建3D轮廓表达谱 ? 需多个相同的生物样本, 不能应用于人体样本	动物		Junker et al., 2014
			Geo-seq	单细胞水平	低	+ 比LCM更灵敏 ? 通量低	动物		Chen et al., 2017
			NICHE-seq	单细胞水平	高	+ 通量高 ? 只能确定特定生态位的空间位置, 不能应用于人体样本	动物		Medaglia et al., 2017
			proximID	单细胞水平	低	+ 保留部分细胞相互作用的互作结构 ? 需基于LCM进行细胞分离, 通量低	动物		Boisset et al., 2018
		原位杂交技术	smFISH	亚细胞水平	低	+ 灵敏度高, 检测效率相对较高 ? 检测的RNA数量有限	动植物微生物		Femino et al., 1998
			RNA-scope	亚细胞水平	低	+ 特异性高, 信噪比极高, 灵敏度高 ? 通量低	动植物微生物		Wang et al., 2013
			seqFISH	亚细胞水平	低	+ 高度多重化 ? 需要专门的设备, 视野受限	动物		Lubeck et al., 2014
			MERFISH	单细胞水平	较高	+ 高度多重化 ? 需要专门的设备, 视野受限	动物		Chen et al., 2015
			osmFISH	亚细胞水平	较高	+ 可检测更大的组织区域, 半自动化 ? 通量相对较低	动物		Codeluppi et al., 2018
			seqFISH+	单细胞水平	较高	+ 极度多重化 ? 需要专门的设备, 视野受限	动物		Eng et al., 2019
			DNA microscpy	单细胞水平	较高	+ 不依赖光或任何类型的光学器件进行组织的基因表达成像 ? 仅在乳腺癌细胞中应用过	动物		Weinstein et al., 2019
		原位测序技术	ISS using padlock probes	亚细胞水平	较低	+ 亚细胞分辨率检测SNV的能力 ? 转录本检测灵敏度低	动植物微生物		Ke et al., 2013
			FISSEQ	亚细胞水平	较低	+ 可捕获所有类型的RNA ? 转录本检测灵敏度相对较低	动物		Lee et al., 2014
			Barista Seq	亚细胞水平	较低	+ 探针缺口内读取长度可达15个碱基 ? 仅在培养细胞上应用过	动物		Chen et al., 2018
			STARmap	亚细胞水平	较高	+ 不需要反转录步骤, 灵敏度高 ? 转录本检测灵敏度低, 视野有限	动物		Mano et al., 2019
			INSTA-seq	亚细胞水平	较高	+ 一种非靶标的方法, 原位测序区域条形码, 异位测序转录本 ? 检测灵敏度相对较低	动物		Fürth et al., 2019
	原位捕获技术		ST/10× Visium	100 μm/ 55 μm	高	+ 可检测完整组织切片中总mRNA ? 条形码区域可能覆盖多个细胞, 未达到单细胞水平	动植物微生物		St?hl et al., 2016
			Nanostring GeoMx	10 μm	高	+ 在蛋白质/RNA分析之间选择高度自动化 ? 使用较小ROI时灵敏度低, 需要手动选择区域	动物微生物		Merritt et al., 2020
			Slide-seq	10 μm	高	+ 高分辨率 ? 检测灵敏度相对较低	动物		Rodriques et al., 2019
时空转录组学	原位捕获技术		APEX-seq	亚细胞水平	高	+ 可以在活细胞中进行 ? 需要让特定APEX2酶在特定的亚细胞区域重组表达, 并不适用于正常组织		动物		Fazal et al., 2019
			HDST	2 μm	高	+ 高分辨率 ? 稀疏数据需要分箱, 检测灵敏度相对较低		动物		Vickovic et al., 2019
			DBiT-seq	10 μm	高	+ 可同时构建mRNA和蛋白质的空间多组学图谱 ? 检测灵敏度相对较低		动物		Liu et al., 2020
			Stereo-seq	0.5 μm	高	+ 亚细胞分辨率和厘米级视野 ? 检测灵敏度相对较低		动植物微生物		Chen et al., 2022
			Seq-scope	0.5 μm	高	+ 亚细胞分辨率 ? 检测灵敏度相对较低		动物		Cho et al., 2021
			PIXEL-seq	1 μm	高	+ 亚细胞分辨率, 成本低 ? 检测灵敏度相对较低		动物		Fu et al., 2021, 2022
			sci-Space	单细胞水平	高	+ 利用sci-RNA-seq进行测序, 检测灵敏度相对较高 ? 依赖于sci-Plex进行空间信息记录, 分辨率相对较低, 只进行核基因测序		动物		Srivatsan et al., 2020, 2021

转录组技术				空间分辨率	细胞通量	优缺点	应用范围		参考文献
传统转录组学				组织水平	高	+ 成本低, 检测速度快 ? 掩盖了细胞的时空异质性	动植物微生物		Costa et al., 2010
单细胞转录组学				单细胞水平	高	+ 通量高, 检测深度较深 ? 忽略了细胞的空间信息	动植物微生物		Kolodziejczyk et al., 2015
时空转录组学		基于微解剖基因表达的技术	LCM	单细胞水平	低	+ 可人工挑选感兴趣的细胞 ? 通量低, 操作难度大	动植物微生物		Emmert-buck et al., 1996
			TIVA	单细胞水平	低	+ 能应用于活细胞 ? 通量低, 分析结果有限	动物		Lovatt et al., 2014
			Tomo-seq	单个切片	低	+ 可构建3D轮廓表达谱 ? 需多个相同的生物样本, 不能应用于人体样本	动物		Junker et al., 2014
			Geo-seq	单细胞水平	低	+ 比LCM更灵敏 ? 通量低	动物		Chen et al., 2017
			NICHE-seq	单细胞水平	高	+ 通量高 ? 只能确定特定生态位的空间位置, 不能应用于人体样本	动物		Medaglia et al., 2017
			proximID	单细胞水平	低	+ 保留部分细胞相互作用的互作结构 ? 需基于LCM进行细胞分离, 通量低	动物		Boisset et al., 2018
		原位杂交技术	smFISH	亚细胞水平	低	+ 灵敏度高, 检测效率相对较高 ? 检测的RNA数量有限	动植物微生物		Femino et al., 1998
			RNA-scope	亚细胞水平	低	+ 特异性高, 信噪比极高, 灵敏度高 ? 通量低	动植物微生物		Wang et al., 2013
			seqFISH	亚细胞水平	低	+ 高度多重化 ? 需要专门的设备, 视野受限	动物		Lubeck et al., 2014
			MERFISH	单细胞水平	较高	+ 高度多重化 ? 需要专门的设备, 视野受限	动物		Chen et al., 2015
			osmFISH	亚细胞水平	较高	+ 可检测更大的组织区域, 半自动化 ? 通量相对较低	动物		Codeluppi et al., 2018
			seqFISH+	单细胞水平	较高	+ 极度多重化 ? 需要专门的设备, 视野受限	动物		Eng et al., 2019
			DNA microscpy	单细胞水平	较高	+ 不依赖光或任何类型的光学器件进行组织的基因表达成像 ? 仅在乳腺癌细胞中应用过	动物		Weinstein et al., 2019
		原位测序技术	ISS using padlock probes	亚细胞水平	较低	+ 亚细胞分辨率检测SNV的能力 ? 转录本检测灵敏度低	动植物微生物		Ke et al., 2013
			FISSEQ	亚细胞水平	较低	+ 可捕获所有类型的RNA ? 转录本检测灵敏度相对较低	动物		Lee et al., 2014
			Barista Seq	亚细胞水平	较低	+ 探针缺口内读取长度可达15个碱基 ? 仅在培养细胞上应用过	动物		Chen et al., 2018
			STARmap	亚细胞水平	较高	+ 不需要反转录步骤, 灵敏度高 ? 转录本检测灵敏度低, 视野有限	动物		Mano et al., 2019
			INSTA-seq	亚细胞水平	较高	+ 一种非靶标的方法, 原位测序区域条形码, 异位测序转录本 ? 检测灵敏度相对较低	动物		Fürth et al., 2019
	原位捕获技术		ST/10× Visium	100 μm/ 55 μm	高	+ 可检测完整组织切片中总mRNA ? 条形码区域可能覆盖多个细胞, 未达到单细胞水平	动植物微生物		St?hl et al., 2016
			Nanostring GeoMx	10 μm	高	+ 在蛋白质/RNA分析之间选择高度自动化 ? 使用较小ROI时灵敏度低, 需要手动选择区域	动物微生物		Merritt et al., 2020
			Slide-seq	10 μm	高	+ 高分辨率 ? 检测灵敏度相对较低	动物		Rodriques et al., 2019
时空转录组学	原位捕获技术		APEX-seq	亚细胞水平	高	+ 可以在活细胞中进行 ? 需要让特定APEX2酶在特定的亚细胞区域重组表达, 并不适用于正常组织		动物		Fazal et al., 2019
			HDST	2 μm	高	+ 高分辨率 ? 稀疏数据需要分箱, 检测灵敏度相对较低		动物		Vickovic et al., 2019
			DBiT-seq	10 μm	高	+ 可同时构建mRNA和蛋白质的空间多组学图谱 ? 检测灵敏度相对较低		动物		Liu et al., 2020
			Stereo-seq	0.5 μm	高	+ 亚细胞分辨率和厘米级视野 ? 检测灵敏度相对较低		动植物微生物		Chen et al., 2022
			Seq-scope	0.5 μm	高	+ 亚细胞分辨率 ? 检测灵敏度相对较低		动物		Cho et al., 2021
			PIXEL-seq	1 μm	高	+ 亚细胞分辨率, 成本低 ? 检测灵敏度相对较低		动物		Fu et al., 2021, 2022
			sci-Space	单细胞水平	高	+ 利用sci-RNA-seq进行测序, 检测灵敏度相对较高 ? 依赖于sci-Plex进行空间信息记录, 分辨率相对较低, 只进行核基因测序		动物		Srivatsan et al., 2020, 2021

时空转录组研究进展

Research Progress of Spatiotemporal Transcriptomes

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