Time-series single-cell transcriptomic profiling of luteal-phase endometrium uncovers dynamic characteristics and its dysregulation in recurrent implantation failures

Understanding human endometrial dynamics remains a challenge, limiting early diagnosis and treatment of reproductive disorders. Here, we decoded the normal endometrial dynamics across the window of implantation (WOI) and its deficiency in endometrium from women with recurrent implantation failure (RIF) by analyzing data from over 220,000 cells, together with developing a computational model StemVAE that is capable of both temporal prediction and pattern discovery. Our time-series atlas highlighted a two-stage stromal decidualization process whereas a gradual epithelial transitional process across the WOI allowing the identification of a time-varying gene set regulating epithelial receptivity. The epithelial receptivity genes were able to stratify the RIF endometrium into two classes of receptivity-deficiency involving early and late implantation. Further investigation uncovered epithelial cell dysfunction under hyperinflammatory microenvironment in RIF endometrium. The holistic characterization of physiological and pathophysiological WOI, and a computational tool trained on this temporal atlas provide a platform for future therapeutic developments. To generate a high-resolution cellular map of human endometrium across WOI and to characterize the endometrial cellular profiles affecting embryo implantation, endometrial aspirates from fertile women and women with RIF were collected and subjected to droplet-based scRNA-seq. In total, 28 endometrial biopsies spanning 5 time points designated as LH+3 (Day 3 post-luteinizing hormone surge), LH+5, LH+7, LH+9, LH+11 were included. The time-point LH+7 contains two types of donors including fertile women (n=6), and women with RIF (n=10). The remaining time-points post LH surge contain samples only from fertile women (n=3 for each timepoint). All the recruited women had regular menstrual cycle. Dates of menstrual cycle were relative to LH surge as determined by serial blood tests for LH. The collected endometrial biopsies were enzymatically dispersed and single cells were captured using a 10X Chromium system.