Single-Cell RNA Sequencing Analysis of the Angiogenesis Mechanism in Endometriosis

doi:10.12280/gjfckx.20240982

Abstract

Abstract:

Endometriosis (EMs), as a disease with an unclear etiology, urgent to clarify its pathogenesis with the help of emerging new technologies. The application of single-cell RNA sequencing (scRNA-seq) technology in the research of EMs can obtain complete information about the differentiation, development, evolution, and intercellular interactions from the perspective of individual cells, to help to form a more comprehensive understanding of the pathogenic mechanism of EMs. This article reviews the emerging scRNA-seq technology and the research progress related to angiogenesis in EMs obtained through scRNA-seq in recent years. From multiple perspectives that affect angiogenesis, such as cellular dysfunction and immune imbalance, this article details the relationship between the associated cells of EMs and disease biological mechanisms such as angiogenesis, immune microenvironment changes, hormone responsiveness, and fibrosis, provides new ideas for exploring the pathogenesis of angiogenesis in EMs and finds new therapeutic targets.

Key words: Sequence analysis, RNA, High-throughput nucleotide sequencing, Endometriosis, Heteroplasmy, Single-cell RNA sequencing, Angiogenesis

CAO Xiu-rong, ZHOU Wen-bai, FAN Xiang, WANG Yi-fei, ZHU Peng-feng. Single-Cell RNA Sequencing Analysis of the Angiogenesis Mechanism in Endometriosis[J]. Journal of International Obstetrics and Gynecology, 2025, 52(2): 199-205.

Figures/Tables 2

References 36

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方法	实验目的	实验流程	数据分析
bulk RNA-seq	检测单个标本中的基因表达情况；比较多个标本间差异表达基因	从整个组织或全部细胞中提取RNA，逆转录，建库测序	评估转录本，基因的表达；差异基因表达分析；可变剪切
scRNA-seq	检测单个细胞中的基因表达情况；比较不同状态，细胞间的表达差异	解离单个细胞加标签，核苷酸序列扩增，建库测序	降维聚类；鉴定细胞亚群；差异基因表达；受体配体互作；拟时序，分化轨迹

方法	实验目的	实验流程	数据分析
bulk RNA-seq	检测单个标本中的基因表达情况；比较多个标本间差异表达基因	从整个组织或全部细胞中提取RNA，逆转录，建库测序	评估转录本，基因的表达；差异基因表达分析；可变剪切
scRNA-seq	检测单个细胞中的基因表达情况；比较不同状态，细胞间的表达差异	解离单个细胞加标签，核苷酸序列扩增，建库测序	降维聚类；鉴定细胞亚群；差异基因表达；受体配体互作；拟时序，分化轨迹

单细胞测序方法	测序原理	区域	UMI	扩增方法	捕获法	优点	缺点
Smart-seq	用含有PCR识别序列的引物和M-MLV RT	全长	×	PCR	流式分选或显微操作	高转录本覆盖，可实现SNP和可变剪切分析	不能分析非poly(A)的RNA；reads不带有mRNA链特异性
Drop-seq	基于微液滴技术，每个cDNA都用一个细胞特异性barcode和UMI标记	3′端	√	PCR	液滴	建库流程快，成本低	需要微流控平台；细胞捕获率较低
CEL-seq	通过逆转录和体外转录整合条形码和UMI；线性扩增	3′端	√	IVT	微流控	错误率比较低	强烈的3′偏好；高丰度转录本被优先扩增；总RNA需求多
10x Genomics	类似于Drop-seq，利用微流体“双十字”交叉系统分选，通过barcode磁珠-单细胞-油滴形成GEM	3′端	√	PCR	液滴	建库流程快，成本低，细胞可适性、捕获效率、通量高	非全长序列；样本要求高（80%活细胞数）
SCRB-seq	使用类似于Smart-seq的PCR扩增，同时集成barcode和UMI	3′端	√	PCR	流式分选	成本低，转录本精确量化，针对体积小、处理步骤少而优化	操作要求高，不能产生全长cDNA，3′偏好类似于CEL-seq

单细胞测序方法	测序原理	区域	UMI	扩增方法	捕获法	优点	缺点
Smart-seq	用含有PCR识别序列的引物和M-MLV RT	全长	×	PCR	流式分选或显微操作	高转录本覆盖，可实现SNP和可变剪切分析	不能分析非poly(A)的RNA；reads不带有mRNA链特异性
Drop-seq	基于微液滴技术，每个cDNA都用一个细胞特异性barcode和UMI标记	3′端	√	PCR	液滴	建库流程快，成本低	需要微流控平台；细胞捕获率较低
CEL-seq	通过逆转录和体外转录整合条形码和UMI；线性扩增	3′端	√	IVT	微流控	错误率比较低	强烈的3′偏好；高丰度转录本被优先扩增；总RNA需求多
10x Genomics	类似于Drop-seq，利用微流体“双十字”交叉系统分选，通过barcode磁珠-单细胞-油滴形成GEM	3′端	√	PCR	液滴	建库流程快，成本低，细胞可适性、捕获效率、通量高	非全长序列；样本要求高（80%活细胞数）
SCRB-seq	使用类似于Smart-seq的PCR扩增，同时集成barcode和UMI	3′端	√	PCR	流式分选	成本低，转录本精确量化，针对体积小、处理步骤少而优化	操作要求高，不能产生全长cDNA，3′偏好类似于CEL-seq