BACKGROUND With increasing significance of developmental programming effects associated with placental dysfunction, more investigations are devoted to improving the characterization and understanding of placental signatures in health and disease. The placenta is a transitory but dynamic organ adapting to the shifting demands of fetal development and available resources of the maternal supply throughout pregnancy. Trophoblasts (cytotrophoblasts, syncytiotrophoblasts, and extravillous trophoblasts) are placental-specific cell types responsible for the main placental exchanges and adaptations. Transcriptomic studies with single-cell resolution have led to advances in understanding the placenta’s role in health and disease. These studies, however, often show discrepancies in characterization of the different placental cell types. OBJECTIVE AND RATIONALE We aim to review the knowledge regarding placental structure and function gained from the use of single-cell RNA sequencing (scRNAseq), followed by comparing cell-type-specific genes, highlighting their similarities and differences. Moreover, we intend to identify consensus marker genes for the various trophoblast cell types across studies. Finally, we will discuss the contributions and potential applications of scRNAseq in studying pregnancy-related diseases. SEARCH METHODS We conducted a comprehensive systematic literature review to identify different cell types and their functions at the human maternal–fetal interface, focusing on all original scRNAseq studies on placentas published before March 2023 and published reviews (total of 28 studies identified) using PubMed search. Our approach involved curating cell types and subtypes that had previously been defined using scRNAseq and comparing the genes used as markers or identified as potential new markers. Next, we reanalyzed expression matrices from the six available scRNAseq raw datasets with cell annotations (four from first trimester and two at term), using Wilcoxon rank-sum tests to compare gene expression among studies and annotate trophoblast cell markers in both first trimester and term placentas. Furthermore, we integrated scRNAseq raw data available from 18 healthy first trimester and nine term placentas, and performed clustering and differential gene expression analysis. We further compared markers obtained with the analysis of annotated and raw datasets with the literature to obtain a common signature gene list for major placental cell types. OUTCOMES Variations in the sampling site, gestational age, fetal sex, and subsequent sequencing and analysis methods were observed between the studies. Although their proportions varied, the three trophoblast types were consistently identified across all scRNAseq studies, unlike other non-trophoblast cell types. Notably, no marker genes were shared by all studies for any of the investigated cell types. Moreover, most of the newly defined markers in one study were not observed in other studies. These discrepancies were confirmed by our analysis on trophoblast cell types, where hundreds of potential marker genes were identified in each study but with little overlap across studies. From 35 461 and 23 378 cells of high quality in the first trimester and term placentas, respectively, we obtained major placental cell types, including perivascular cells that previously had not been identified in the first trimester. Importantly, our meta-analysis provides marker genes for major placental cell types based on our extensive curation. WIDER IMPLICATIONS This review and meta-analysis emphasizes the need for establishing a consensus for annotating placental cell types from scRNAseq data. The marker genes identified here can be deployed for defining human placental cell types, thereby facilitating and improving the reproducibility of trophoblast cell annotation.

中文翻译：

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揭示人类胎盘的分子景观：单细胞 RNA 测序研究的系统回顾和荟萃分析


背景技术随着与胎盘功能障碍相关的发育编程效应的重要性日益增加，更多的研究致力于改善健康和疾病中胎盘特征的表征和理解。胎盘是一个短暂但动态的器官，适应胎儿发育的变化需求和整个怀孕期间母体供应的可用资源。滋养层细胞（细胞滋养层细胞、合体滋养层细胞和绒毛外滋养层细胞）是负责胎盘主要交换和适应的胎盘特异性细胞类型。单细胞分辨率的转录组学研究使人们对胎盘在健康和疾病中的作用的理解取得了进展。然而，这些研究经常显示不同胎盘细胞类型的特征存在差异。目的和基本原理我们的目的是回顾通过使用单细胞 RNA 测序 (scRNAseq) 获得的有关胎盘结构和功能的知识，然后比较细胞类型特异性基因，突出它们的相似性和差异。此外，我们打算在研究中确定各种滋养层细胞类型的共有标记基因。最后，我们将讨论 scRNAseq 在研究妊娠相关疾病方面的贡献和潜在应用。搜索方法我们进行了全面的系统文献综述，以确定人类母胎界面的不同细胞类型及其功能，重点关注 2023 年 3 月之前发表的所有关于胎盘的原始 scRNAseq 研究，并使用 PubMed 搜索发表的评论（总共确定了 28 项研究） 。 我们的方法涉及整理先前使用 scRNAseq 定义的细胞类型和亚型，并比较用作标记或识别为潜在新标记的基因。接下来，我们重新分析了六个可用的带有细胞注释的 scRNAseq 原始数据集的表达矩阵（四个来自妊娠早期，两个足月），使用 Wilcoxon 秩和检验比较研究之间的基因表达，并注释妊娠早期和足月的滋养层细胞标记胎盘。此外，我们整合了来自 18 个健康孕早期和 9 个足月胎盘的 scRNAseq 原始数据，并进行了聚类和差异基因表达分析。我们进一步将通过注释和原始数据集分析获得的标记与文献进行比较，以获得主要胎盘细胞类型的共同特征基因列表。结果 研究之间观察到采样地点、胎龄、胎儿性别以及随后的测序和分析方法的差异。尽管它们的比例有所不同，但与其他非滋养层细胞类型不同，这三种滋养层类型在所有 scRNAseq 研究中均得到一致鉴定。值得注意的是，对于任何研究的细胞类型，所有研究都没有共享标记基因。此外，一项研究中大多数新定义的标记在其他研究中没有观察到。我们对滋养层细胞类型的分析证实了这些差异，每项研究中都鉴定了数百个潜在的标记基因，但研究之间几乎没有重叠。我们分别从妊娠早期和足月胎盘中的 35 461 个和 23 378 个高质量细胞中获得了主要胎盘细胞类型，包括以前在妊娠早期未发现的血管周围细胞。 重要的是，我们的荟萃分析根据我们的广泛管理提供了主要胎盘细胞类型的标记基因。更广泛的影响 本综述和荟萃分析强调需要就 scRNAseq 数据注释胎盘细胞类型建立共识。这里鉴定的标记基因可用于定义人类胎盘细胞类型，从而促进和提高滋养层细胞注释的可重复性。