Complex composition is one of the most important features of the immune system, involving many types of organs, tissues, cells, and molecules that perform immune functions. The normal function of each component of the immune system is the guarantee for maintaining the relatively stable immune function of the body. When the self-immune tolerance mechanism of the body is unregulated or destroyed, the immune system reacts to autoantigens, resulting in damage to self-tissues and organs or an immunopathological state with abnormal functions. Autoimmune diseases are diverse, and their pathogenesis is complicated. Various immune cells and their interactions play significant roles in the occurrence and development of diseases. The solution to heterogeneity of immune cells is the basic science and translational understanding of how genes and the environment interact to induce disease so that we can develop personalized medicine, a goal that has to this point eluded scientists. Single-cell RNA sequencing (scRNA-Seq) refers to a new technique allowing high-throughput sequencing analysis of the whole transcriptome to reveal the gene expression status of individual cells. It has emerged as an indispensable tool in the field of life science research, and can help identify the complex mechanism of cell heterogeneity, discover new cell subsets, and help uncover the molecular mechanisms of pathogenesis, the evolution of disorders, and drug resistance. This information can provide us with new strategies for diagnosis and prognostic evaluation, as well as monitoring treatment responses. In this review, we summarize the crucial experimental procedures used for single-cell RNA sequencing, and the current applications of this technique to study autoimmune diseases are described in detail. This technique will be widely used in more in-depth studies of autoimmune diseases and will contribute to the diagnosis and therapies of these disorders.

复杂的组成是免疫系统最重要的特征之一，涉及执行免疫功能的多种器官、组织、细胞和分子。免疫系统各组成部分的正常功能是维持机体免疫功能相对稳定的保证。当机体自身免疫耐受机制失控或被破坏时，免疫系统会对自身抗原产生反应，导致自身组织和器官受损或功能异常的免疫病理状态。自身免疫性疾病种类繁多，发病机制复杂。各种免疫细胞及其相互作用在疾病的发生和发展中起着重要作用。解决免疫细胞异质性的方法是对基因和环境如何相互作用以诱发疾病的基础科学和转化理解，以便我们可以开发个性化医疗，而这一目标迄今为止科学家们还没有达到。单细胞RNA测序（scRNA-Seq）是指一种新技术，可以对整个转录组进行高通量测序分析，以揭示单个细胞的基因表达状态。它已成为生命科学研究领域不可或缺的工具，有助于识别细胞异质性的复杂机制，发现新的细胞亚群，并有助于揭示发病机制、疾病演变和耐药性的分子机制。这些信息可以为我们提供诊断和预后评估的新策略，以及监测治疗反应。在这篇综述中，我们总结了用于单细胞 RNA 测序的关键实验程序，并详细描述了该技术目前在研究自身免疫性疾病中的应用。该技术将广泛用于更深入的自身免疫性疾病研究，并将有助于这些疾病的诊断和治疗。