Targeted gene expression profiling for accurate endometrial receptivity testing

Abstract

STUDY QUESTION How accurately can a targeted gene expression sequencing assay estimate endometrial receptivity corresponding to the window of implantation? DESIGN Endometrial biopsies (n=175) from healthy fertile volunteers (n=66), polycystic ovarian syndrome (PCOS) patients (n=39), and recurrent implantation failure (RIF) patients (n=44) were collected and sequenced with TAC-seq (Targeted Allele Counting by sequencing) method targeting 68 biomarker genes for endometrial receptivity. The expressional profiles were clustered, and differential expression analysis was performed on the model development group, using 63 endometrial biopsies spanning over proliferative (PE, n=18), early-secretory (ESE, n=18), mid-secretory (MSE, n=17) and late-secretory (LSE, n=10) endometrial phases. A quantitative predictor model was trained on the development group and validated on sequenced samples from healthy women, consisting of 52 paired samples taken from ESE and MSE phases and five LSE phase samples from 31 individuals. Finally, the developed test was applied to 44 MSE phase samples gathered from a study group of patients diagnosed with RIF. RESULTS The developed assay successfully captures the unique receptivity profile of the endometrium using 68 biomarker genes. When compared to healthy women of the same cycle phase, we did not detect any significant gene expression bias caused by PCOS in PE, ESE, MSE, and LSE samples. In validation samples (n=57), we detected displaced WOI in 1.8% of the samples from fertile women. In the RIF study group, we detected a significantly higher proportion of the samples with shifted WOI than in the validation set of samples from fertile women, 15.9% and 1.8%, respectively. CONCLUSIONS The developed beREADY screening test enables highly sensitive and dynamic detection of selected transcriptome biomarkers, providing a quantitative and accurate prediction of endometrial receptivity status for personalised embryo transfer.

Pilot proof for RNA biomarker-based minimally invasive endometrial receptivity testing using uterine fluid extracellular vesicles

“…This pilot study shows that beREADY computational model can be used to assess endometrial receptivity in a minimally invasive manner from UF-EV transcriptomic data with sensitivity of 75% and specificity of 100%. The lower sensitivity is expected since the beREADY computational model was developed for tissue biopsies in conjunction with a targeted sequencing assay and not the whole transcriptomic data used in this study (1,4). Alternatively, it cannot be ruled out that the endometrial maturation in these three LH+7 women classified as pre-receptive was slower and corresponded to the pre-receptive status.…”

“…beREADY test has been originally developed to assess endometrial receptivity from a tissue biopsy using 68 transcript biomarkers and 4 housekeeping genes (1). However, the biopsy procedure excludes the possibility of embryo transfer (ET) in the same cycle and thereby prolongs IVF treatment.…”

AI-algorithm training and validation for endometrial CD138+ cells in infertility-associated conditions; polycystic ovary syndrome (PCOS) and recurrent implantation failure (RIF)

“…Gene expression profiling was conducted using the beREADY test at CCHT, involving 57 known endometrial receptivity genes along with four housekeeping genes ( SDHA , CYC1 , TBP , and HMBS ) 23,24 . Endometrial RNA from RIF patients (n=29) was extracted using the Qiagen miRNeasy Mini kit, and according to the test results, the RIF samples were divided into pre-receptive ( n =9), receptive ( n =10), and post-receptive ( n =10) ( Table 1 ).…”

“…All experiments were performed in accordance with relevant guidelines/regulations in line with the Declaration of Helsinki. Their anonymized data and endometrial biopsies were obtained prior to the subsequent IVF treatment 23 using a Pipelle during a hormone replacement treatment (HRT) cycle on day 5 after initiation of P4 administration (HRT: P+5). The first day of P4 administration was considered day zero (HRT: P+0).…”

“…RIF, often defined as three or more failed in vitro fertilization (IVF) attempts with good-quality embryos transferred, significantly impacts IVF success rates 22 . Factors from the maternal side, including age, body mass index (BMI), and immunological factors 22 , as well as unprepared endometrium for embryo implantation (e.g., shifted window of implantation, impaired decidualization in stroma) 23,24 , have an impact on the implantation rate and reproductive outcomes 22,25 . Moreover, CE is prevalent in RIF patients, affecting up to 14% of this population 9 .…”