单细胞转录组学技术及其在寄生虫研究中的应用进展

doi:10.11843/j.issn.0366-6964.2024.10.005

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (10): 4290-4301.doi: 10.11843/j.issn.0366-6964.2024.10.005

单细胞转录组学技术及其在寄生虫研究中的应用进展

周蜓蜓¹(), 李立¹, 吴燕涛¹, 逯文颖¹, 付宝权¹^,², 殷宏¹^,², 贾万忠¹^,²^,*(), 闫鸿斌¹^,*()

1. 中国农业科学院兰州兽医研究所, 兰州大学动物医学与生物安全学院, 动物疫病防控全国重点实验室, 国家动物包虫病专业实验室, 甘肃省病原生物学基础学科研究中心, 甘肃省动物寄生虫病重点实验室, 农业农村部动物病原生物学重点实验室, 农业农村部反刍动物重大疫病防控重点实验室(西部), 兰州 730000
2. 江苏省动物重要疫病与人兽共患病防控协同创新中心, 扬州 225009

收稿日期:2023-12-25 出版日期:2024-10-23 发布日期:2024-11-04
通讯作者: 贾万忠,闫鸿斌 E-mail:1305403647@qq.com;jiawanzhong@caas.cn;yanhongbin@caas.cn
作者简介:周蜓蜓(1999-), 女, 重庆云阳人, 硕士生, 主要从事棘球蚴病发育与致病机制研究, E-mail: 1305403647@qq.com
基金资助:
国家重点研发计划(2022YFD1800200);甘肃省科技重大专项(23ZDNA007);甘肃省科技重大专项(22ZD6NA001);甘肃省在站博士后专项(23JRRA558);国家肉牛牦牛产业技术体系项目(CARS-37);兰州大学中央高校基本科研业务费专项资金(lzujbky-2024-ydyl02);动物疫病防控全国重点实验室重大成果培育项目(SKLADCP2023HP05);中国农业科学院创新工程(CAASTIP-2024-5);中国农业科学院创新工程(CAAS-ASTIP-2021-LVRI)

Progress on Single-cell Transcriptomics Technology and Its Applications in Research on Parasites

Tingting ZHOU¹(), Li LI¹, Yantao WU¹, Wenying LU¹, Baoquan FU¹^,², Hong YIN¹^,², Wanzhong JIA¹^,²^,*(), Hongbin YAN¹^,*()

1. State Key Laboratory for Animal Disease Control and Prevention/College of Veterinary Medicine, Lanzhou University/National Para-reference Laboratory for Animal Echinococcosis/Gansu Province Research Center for Basic Disciplines of Pathogen Biology/Key Laboratory of Veterinary Parasitology of Gansu Province/Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs/Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China
2. Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease, Yangzhou 225009, China

Received:2023-12-25 Online:2024-10-23 Published:2024-11-04
Contact: Wanzhong JIA, Hongbin YAN E-mail:1305403647@qq.com;jiawanzhong@caas.cn;yanhongbin@caas.cn

摘要/Abstract

摘要：

单细胞转录组代表了某一时刻单个细胞内所有mRNA总表达量，其表达量反映该细胞的总体特征。通过单细胞转录组测序(single cell RNA sequencing, scRNA-seq)技术对单个细胞的全部RNA进行逆转录、扩增和测序，测序结果中包含的大量信息有可能重塑对发育生物学、基因调控以及健康和疾病中细胞异质性的理解。随着科学技术的不断发展，测序技术也在不断进步，scRNA-seq全方位、高通量以及高分辨率的特点可构建更细致、全面和精准的单细胞图谱。本文综述了常用scRNA-seq方法及其数据分析主要流程和单细胞转录组学技术在寄生虫学与寄生虫病领域研究中的应用，以期为该领域相关研究提供参考资料。

关键词: 单细胞测序, 转录组, 数据分析, 寄生虫病

Abstract:

The single cell transcriptome represents the total expression of all mRNA in a single cell at a certain time, and its expression level reflects the overall characteristics of the cell. The entire RNA of a single cell is reversely transcribed, amplified and sequenced by single cell RNA sequencing (scRNA-seq). The extensive information contained in the sequencing results has the potential to reshape the understanding of developmental biology, gene regulation and cellular heterogeneity in health and disease. With the continuous development of science and technology, sequencing technologies are also constantly improving. The omni-directional, high-throughput and high-resolution characteristics of scRNA-seq can build a more detailed, comprehensive and accurate single cell map. This paper summarizes the commonly used scRNA-seq methods, the main processes of data analysis, and the application of single cell transcriptome technology in the field of parasitology and parasitic diseases, in order to provide reference materials for related research in this field.

Key words: scRNA-seq, transcriptome, data analysis, parasitic diseases

中图分类号:

周蜓蜓, 李立, 吴燕涛, 逯文颖, 付宝权, 殷宏, 贾万忠, 闫鸿斌. 单细胞转录组学技术及其在寄生虫研究中的应用进展[J]. 畜牧兽医学报, 2024, 55(10): 4290-4301.

Tingting ZHOU, Li LI, Yantao WU, Wenying LU, Baoquan FU, Hong YIN, Wanzhong JIA, Hongbin YAN. Progress on Single-cell Transcriptomics Technology and Its Applications in Research on Parasites[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(10): 4290-4301.

图/表 1

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测序技术	单细胞分离技术	转录本覆盖范围	优势	扩增	唯一分子标识符
Sequencing technology	Single cell separation	Transcript coverage	Advantage	Amplification	UMI
CEL-seq/CEL-seq2	手动稀释分离	3′端序列	线性扩增以高精度减少非特异性片段的积累	IVT	有
MARS-seq/MARS-seq2	荧光激活细胞分选	3′端序列	高通量，良好的稳定性	IVT	有
SMART-seq/SMART-seq2	手动稀释分离	全长	cDNA文库的平均长度和产量升高，序列覆盖率较高	PCR	无
SMART-seq3	荧光激活细胞分选	全长	高灵敏度，能够较好地识别细胞类型、状态及亚型特异性	PCR	有
SMART-seq3xpress	荧光激活细胞分选	全长	高通量，耗时短，低成本	PCR	有
SCRB-seq	荧光激活细胞分选	3′端序列	高通量，低成本	PCR	有
Drop-seq	微滴技术	3′端序列	高通量，低成本	PCR	有
inDrop	微流体技术	3′端序列	高通量，低成本	IVT	有
10×Genomics	微流体技术	3′端序列	高通量，低成本，高灵敏度	PCR	有
Microwell-seq	琼脂糖微孔阵列	全长	高通量，低成本	PCR	无
Seq-well	微孔阵列	3′端序列	高通量，交叉污染较小	PCR	有
Live-seq	流体力显微镜技术	全长	保留细胞生物活性	PCR	无

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单细胞转录组学技术及其在寄生虫研究中的应用进展

Progress on Single-cell Transcriptomics Technology and Its Applications in Research on Parasites

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