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 (dM{Phi}), they play an important role during the pregnancy, but their definition and exact function remain elusive. We isolated CD14+CD45+ dM{Phi} 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: IL1{beta}, TNFSF13B and MMP9; M2: CCL3, CCL4) of the dM{Phi}. We found that cluster 10 as the specific cluster of dM{Phi} 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 dM{Phi} formed a continuous "V-shaped" trajectory, with M1 and M2 type cells mainly occupying the two heads. We found that NF{kappa}B1, MYC and TCF12 acted as the key transcription factors of dM{Phi}. Our study redefined the polarization state and physiological characteristic of dM{Phi} in early normal and RSA pregnancy, which suggests a novel view and therapeutic target for spontaneous abortion prevention.