Endometrial transcriptomic and ciliation analysis after scratch shows no signature linked to live birth following IVF

Objective: To determine whether endometrial scratch induces differences in transcriptomic profiles or epithelial cell ciliation in the endometrium at the window of implantation that associate with live birth following IVF. Design: Secondary analysis of 50 matched endometrial biopsies collected within a randomised controlled trial evaluating the clinical effectiveness of endometrial scratch before first time IVF. Setting: Endometrial biopsy samples were obtained from women attending the Jessop Wing of Sheffield Teaching Hospitals. Population or Sample: Women undergoing first time IVF who received an endometrial scratch in the preceding cycle at the window of implantation (6-10 days after LH surge). Methods: Endometrial biopsies were molecularly dated using transcriptomic menstrual cycle staging algorithms. Bulk RNA sequencing was analysed using DESeq2 with FDR correction, and principal component analysis (PCA) assessed clustering patterns. Epithelial cell ciliation was quantified using immunohistochemistry and an automated Python based image analysis pipeline. Main Outcome Measures: Differential endometrial gene expression between women with and without live birth after IVF; percentage coverage of ciliated epithelial cells in luminal and glandular regions. Results: Transcriptomic dating confirmed no differences in menstrual cycle timing between live birth and no live birth groups. No significant differential gene expression was detected (log2FC >2, FDR <0.05), and PCA showed no clustering by pregnancy outcome. Ciliation coverage did not differ between outcome groups or between glandular and luminal surfaces. Conclusions: When implantation timing is precisely defined, endometrial scratch does not produce detectable transcriptomic changes or alterations in epithelial ciliation that distinguish women who achieve live birth after IVF. Funding: Wellbeing of Women RG2147; Wessex Medical Research; Rosetrees Trust. Keywords: Endometrial scratch, IVF, transcriptomics, epithelial ciliation, window of implantation, bulk RNA sequencing, endometrial receptivity.