Alternative splicing and differential gene expression during changes in endometrial receptivity in patients with recurrent implantation failure

Recurrent implantation failure (RIF) remains a major challenge in assisted reproductive technology, and the molecular mechanisms underlying endometrial receptivity are incompletely understood. This study aimed to comprehensively characterize transcriptomic alterations, including alternative splicing events (ASEs), differential gene expression (DEGs), and immune cell dynamics across different phases of endometrial receptivity in women with RIF. Endometrial biopsies were collected from 90 healthy fertile controls and 73 RIF patients during pre-receptive, receptive, and post-receptive phases. High-throughput RNA sequencing was performed, and bioinformatic analyses were conducted to identify ASEs, DEGs, immune cell composition, and RNA-binding protein (RBP) networks. Skipped exons and mutually exclusive exons were the predominant splicing events observed. Both ASEs and DEGs were significantly enriched in pathways regulating cell adhesion, cytoskeletal organization, and immune modulation. KHDRBS3 emerged as a potential key RBP involved in splicing regulation during the window of implantation. Immune profiling revealed dynamic alterations in CD8 + T cells, NK cells, and monocytes between non-receptive and receptive phases, suggesting immune dysregulation associated with implantation failure. Drug repurposing analysis identified several small molecules targeting ASE-related genes, offering promising therapeutic options for RIF. These findings highlight the coordinated changes in alternative splicing, gene expression, and immune cell composition that characterize endometrial receptivity and provide insights that may guide the development of novel diagnostic biomarkers and targeted interventions to improve reproductive outcomes.