Single cell transcriptome analysis of decidua macrophages in normal and recurrent spontaneous abortion patients

Due to the heterogeneity and different polarization state of decidual macrophages (dMΦ), they play an important role during the pregnancy, but their definition and exact function remain elusive. We isolated CD14+CD45+ dMΦ from the normal or RSA decidua by flow cytometry, followed by single cell RNA sequencing (scRNA-seq). In total, 23,062 single-cell transcriptomes of macrophage were profiled (12,470 Normal and 10,592 RSA), which were divided into 13 major clusters via T-distributed stochastic neighbor embedding (t-SNE) visualization. We observed that there is higher percentage composition of M1 cells (70.6%) in the normal decidua, and higher percentage composition of M2 cells (68.3%) in the RSA decidua. We identified new markers (M1: S100A8, S100A9, M2: SELENOP, FOLR2, RNASE1) and secreted cytokines (M1: IL1β, TNFSF13B and MMP9; M2: CCL3, CCL4) of the dMΦ. We found that cluster 10 as the specific cluster of dMΦ highly expressing BAG3 in normal group and cluster 7 specific highly expressing CXCL9/10/11 chemokine. After pseudo-time trajectory analysis, we found that the dMΦ formed a continuous “V-shaped” trajectory, with M1 and M2 type cells mainly occupying the two heads. We found that NFκB1, MYC and TCF12 acted as the key transcription factors of dMΦ. Our study redefined the polarization state and physiological characteristic of dMΦ in early normal and RSA pregnancy, which suggests a novel view and therapeutic target for spontaneous abortion prevention.