OBJECTIVE: 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.
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.
RESULTS: 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.
CONCLUSIONS: 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.
目的:我们旨在回顾从使用单细胞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,突出它们的异同。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中的贡献和潜在应用。
方法:我们进行了全面的系统文献综述,以确定不同的细胞类型及其在人类母胎界面的功能,重点关注2023年3月之前发表的关于胎盘的所有原始scRNAseq研究以及使用PubMed搜索发表的评论(共确定28项研究).我们的方法涉及管理先前使用scRNAseq定义的细胞类型和亚型,并比较用作标记或鉴定为潜在新标记的基因。接下来,我们重新分析了来自六个可用的带有细胞注释的scRNAseq原始数据集的表达矩阵(四个来自前三个月,两个在足月),使用Wilcoxon秩和检验比较研究中的基因表达,并注释孕早期和足月胎盘中的滋养层细胞标志物。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。我们进一步将通过对注释和原始数据集的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常见签名基因列表。
结果:采样地点的变化,胎龄,胎儿性别,以及随后的测序和分析方法在研究之间进行了观察。尽管它们的比例各不相同,在所有scRNAseq研究中,这三种滋养层类型都得到了一致的鉴定,不同于其他非滋养层细胞类型。值得注意的是,对于所研究的任何细胞类型,所有研究均未共享标记基因.此外,一项研究中大多数新定义的标志物在其他研究中未观察到.我们对滋养层细胞类型的分析证实了这些差异,在每项研究中都鉴定出数百个潜在的标记基因,但在研究中几乎没有重叠。从35.461和23.378细胞的高质量在前三个月和足月胎盘,分别,我们获得了主要的胎盘细胞类型,包括以前在妊娠早期未发现的血管周围细胞。重要的是,基于我们广泛的研究,我们的荟萃分析提供了主要胎盘细胞类型的标记基因.
结论:这篇综述和荟萃分析强调了从scRNAseq数据中注释胎盘细胞类型建立共识的必要性。这里鉴定的标记基因可以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。