Massaia Andrea, Chaves Patricia, Samari Sara, Miragaia Ricardo Júdice, Meyer Kerstin, Teichmann Sarah Amalia, Noseda Michela
British Heart Foundation Centre of Research Excellence and British Heart Foundation Centre for Regenerative Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom.
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom.
Front Cardiovasc Med. 2018 Nov 21;5:167. doi: 10.3389/fcvm.2018.00167. eCollection 2018.
The recent development of single cell gene expression technologies, and especially single cell transcriptomics, have revolutionized the way biologists and clinicians investigate organs and organisms, allowing an unprecedented level of resolution to the description of cell demographics in both healthy and diseased states. Single cell transcriptomics provide information on prevalence, heterogeneity, and gene co-expression at the individual cell level. This enables a cell-centric outlook to define intracellular gene regulatory networks and to bridge toward the definition of intercellular pathways otherwise masked in bulk analysis. The technologies have developed at a fast pace producing a multitude of different approaches, with several alternatives to choose from at any step, including single cell isolation and capturing, lysis, RNA reverse transcription and cDNA amplification, library preparation, sequencing, and computational analyses. Here, we provide guidelines for the experimental design of single cell RNA sequencing experiments, exploring the current options for the crucial steps. Furthermore, we provide a complete overview of the typical data analysis workflow, from handling the raw sequencing data to making biological inferences. Significantly, advancements in single cell transcriptomics have already contributed to outstanding exploratory and functional studies of cardiac development and disease models, as summarized in this review. In conclusion, we discuss achievable outcomes of single cell transcriptomics' applications in addressing unanswered questions and influencing future cardiac clinical applications.
单细胞基因表达技术，尤其是单细胞转录组学的最新发展，彻底改变了生物学家和临床医生研究器官和生物体的方式，使他们能够以前所未有的分辨率描述健康和患病状态下的细胞群体。单细胞转录组学在单个细胞水平上提供了有关细胞丰度、异质性和基因共表达的信息。这使得以细胞为中心的观点能够定义细胞内基因调控网络，并有助于定义在整体分析中被掩盖的细胞间通路。这些技术发展迅速，产生了多种不同的方法，在任何步骤都有几种选择，包括单细胞分离和捕获、裂解、RNA逆转录和cDNA扩增、文库制备、测序以及计算分析。在这里，我们提供单细胞RNA测序实验的实验设计指南，探讨关键步骤的当前选择。此外，我们提供了从处理原始测序数据到进行生物学推断的典型数据分析工作流程的完整概述。值得注意的是，单细胞转录组学的进展已经为心脏发育和疾病模型的杰出探索性和功能性研究做出了贡献，本综述对此进行了总结。总之，我们讨论了单细胞转录组学在解决未回答问题和影响未来心脏临床应用方面的可实现成果。
