Targeted gene expression profiling for accurate endometrial receptivity testing

Abstract

Expressional profiling of the endometrium enables the personalised timing of the window of implantation (WOI). This study presents and evaluates a novel analytical pipeline based on a TAC-seq (Targeted Allele Counting by sequencing) method for endometrial dating. 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 of the natural cycle. 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 from a study group of patients diagnosed with recurrent implantation failure (RIF). 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% (p = 0.012), respectively. The developed model was evaluated with an average cross-validation accuracy of 98.8% and an accuracy of 98.2% in the validation group. The developed beREADY screening model enables sensitive and dynamic detection of selected transcriptome biomarkers, providing a quantitative and accurate prediction of endometrial receptivity status.

The endometrial transcriptome of infertile women with and without implantation failure

“…69 A previous study that also used the beREADY model to determine receptivity profiles of endometrium samples, detected a significantly higher proportion of displaced WOI in the RIF group than in the fertile group. 43 The results of our study, however, do not indicate a displacement of the WOI in the RIF group compared with the fertile group (ie our long-term analysis). A potential explanation for this difference could be that the endometrium samples in our study were taken prospectively.…”

“…Individual receptivity profiles of endometrial biopsies were analyzed with the beREADY receptivity dating model. 43 Simulating the original targeted RNA‐seq method, 68 biomarkers with four housekeeping genes were selected from the quantified whole‐genome sequencing data. 44 This filtered gene set was then further analyzed with the beREADY model.…”

Dynamic changes in AI-based analysis of endometrial cellular composition: Analysis of PCOS and RIF endometrium

“…1 ). The beREADY test, which assesses endometrial receptivity based on receptivity-related gene expression, 16 , 17 was performed on all 29 RIF patients. 14 The endometrial RNA was extracted with a Qiagen miRNeasy Mini kit and sequenced and analyzed in CCHT.…”

When the Embryo Meets the Endometrium: Identifying the Features Required for Successful Embryo Implantation

“…So far, no proof exists to support such an assumption, and hence analyses performed in one cycle might not guarantee the correct identification of the WOI in the next cycle. Alternatives to the ERA test have been suggested [ 211 , 212 , 213 , 214 ]. Indeed, high throughput RT-qPCR has been applied to compare the expression of 184 genes involved in endometrial receptivity and immunity in endometrial biopsies from fertile and sub-fertile patients.…”

“…Using a similar approach, He et al developed an RNA-Seq-based endometrial receptivity test (rsERT) to identify the WOI in RIF patients, and reported a significant increase in implanted embryos, intrauterine pregnancy, and live birth rate in patients undergoing rsERT-guided pET, compared to patients undergoing conventional ET [ 213 ]. More recently, a new test based on Targeted Allele Counting by sequencing (TAC-seq) and named beREADY has been proposed for endometrial dating [ 214 ]. The analysis of 68 endometrial receptivity genes in endometrial biopsies of healthy volunteers allowed the researchers to identify pre-receptive (proliferative and early secretory samples), receptive (mid-secretory samples), and post-receptive (late secretory samples) stages of the endometrium, thus contributing to the identification of WOI displacement in RIF patients and when to proceed to a personalized embryo transfer.…”