Assisted reproductive technologies like in vitro fertilization (IVF) have helped many people become pregnant. However, even with the ability to screen embryos for chromosomal abnormalities before transplanting them into the uterus, 30 to 40 percent of transferred embryos do not implant, with some individuals failing to become pregnant after multiple cycles of IVF.
Besides the health of the embryo, the uterine lining, or endometrium, also must be receptive for implantation to be successful. While endometrial thickness is associated with implantation, the cellular and molecular components that influence this process remain unknown.
The question of what a normal endometrium looks like and the factors that influence embryo receptivity are at the heart of reproductive endocrinologist and infertility treatment specialist Nataki Douglas’s research. “Within the field of [reproductive endocrinology and infertility], this endometrium is still considered kind of this black box, where we really don't understand what underlies success,” she said.
To study the transcriptomic changes of the fertile endometrium, Douglas and her team at Rutgers Health New Jersey Medical School collaborated with reproductive biologists and bioinformaticians at Michigan State University. Additionally, because previous studies largely focused on white populations, the group enrolled Black and Hispanic participants to provide important insights for fertility in these populations.
In a study published in the Journal of Clinical Investigation Insight, the researchers identified key gene expression changes in specific cell types during the implantation window and into early pregnancy.1 From these, they developed a gene score that predicted fertility in previously published datasets. The findings could help offer biomarkers to improve implantation and therapy targets for people experiencing infertility.
“Clinically, this study is very important,” said Sara Arian, a reproductive endocrinologist and fertility specialist at Boston IVF and Harvard Medical School. Arian was not involved in the study.
The team collected endometrium biopsy samples from 27 women and assigned them to one of four groups based on the menstrual cycle phase at the time of their sampling: proliferative, early-, mid-, and late-secretory phase. The mid-secretory phase represents the period where the tissue is most receptive to implantation. The researchers also collected the endometrial material from participants who underwent an elective abortion between six and eight weeks of gestation. All of the women who supplied samples had had at least one live pregnancy and had not reported any fertility complications.
First, the researchers performed bulk RNA sequencing to study transcriptional changes across the endometrium. They observed that the gene expression patterns of proliferative and early secretory phase samples clustered together while mid- and late secretory phase samples formed a second, distinct cluster.
To study the transcriptional changes in the endometrium at a deeper level, the team applied single-cell RNA sequencing to the three secretory phase sample groups and the first trimester endometrium samples. The majority of the cells in the early secretory phase endometria were proliferative stromal cells, whereas immune cells and lymphatic endothelial cells dominated the first trimester endometrial tissue. The findings pointed to significant shifts in cell populations and gene expression across the menstrual cycle and in early pregnancy.
One of the researchers’ goals was to create a gene signature that would characterize the receptive endometrium. Scientists previously came up with a diagnostic tool for this, the endometrial receptivity array, using transcriptome data from bulk RNA sequencing, but recent studies have raised questions about its efficacy.2,3
Douglas and her team observed a decent overlap in genes used to define the established array with those expressed in the team’s mid-secretory phase bulk RNA sequencing data. Then, they applied this array to their single-cell sequencing data and saw that glandular and secretory glandular epithelial cells had the highest number of genes expressed from this signature. However, within these cells, the researchers saw that these same genes were also highly expressed at times beyond the implantation window, suggesting that single-cell RNA sequencing can offer more detailed insights into gene expression changes over time.
Douglas said that the results showing an important role for glandular and secretory glandular epithelial cells were exciting. While animal studies previously showed that these cells secreted factors important for implantation, “This is the first really human evidence that this cell type is also important,” Douglas said.
To create a more precise gene signature, the team compared differentially expressed genes in the secretory glandular epithelial cells between early and mid-secretory phase samples and found 556 genes. They referred to this signature as the glandular epithelium receptivity module (GERM).
The team used this GERM signature to study publicly available endometrium transcriptomes from both fertile patients and individuals experiencing implantation failures and pregnancy loss, including data from 190 patients in total. They observed that gene expression patterns that were highly similar to the GERM score correlated with samples from fertile patients, whereas individuals with fertility complications had lower GERM scores. Douglas said that these results were exciting. “It wasn't just finding a unique finding in our hands, but this was widely applicable.”
While Arian said that the results are compelling and provide promising insights into the key molecules and pathways involved in implantation, she added that it will be important to study the influence of these genes and cell types in larger studies. She said that including patients with infertility and comparing these gene signatures directly would also lead to deeper insights.
Douglas said that her team is interested in exploring the gene expression profiles of their GERM signature further in the hopes of narrowing it down to be more clinically translatable. They also want to explore the role of these genes and cell types in animal and cell culture models. “It would be very naive to think that your implantation failure or recurrent pregnancy loss is due to one particular defect,” she said. “But this gives us a starting point to really further understand some of the aberrations in patients who have infertility.”
- Burns GW, et al. Single-cell mapping of human endometrium and decidua reveals epithelial and stromal contributions to fertility. J Clin Invest Insights. 2026;11(2):e195254.
- Díaz-Gimeno P, et al. A genomic diagnostic tool for human endometrial receptivity based on the transcriptomic signature. Fertil Steril. 2011;95(1):50-60e.15.
- Arian SE, et al. Endometrial receptivity array before frozen embryo transfer cycles: a systematic review and meta-analysis. Fertil Steril. 2023;119(2):229-238.
