Researchers in a 2025 study found that women with RPL show distinct immune-related gene activity in their endometrium, identifying a possible molecular signature that could help diagnose or personalize treatment for RPL in the future.
Recurrent pregnancy loss (RPL) is usually defined as three or more miscarriages. Some people with RPL have identifiable risk factors like uterine anomalies, autoimmune disease, thrombophilia or chromosomal issues, but for many with RPL there is no identifiable cause.
For these patients with RPL, immune dysfunction in the endometrium may play a role. A successful pregnancy requires proper functioning of the maternal immune system. NK cells, T cells and macrophages help create an environment that supports implantation and early pregnancy.
In a recent study published by Andersen et al. (2025), researchers explored whether the endometrium of women with RPL have a unique molecular signature that could help predict or diagnose RPL. Previous studies have focused on the secretory phase of the menstrual cycle (the time around implantation), but this phase can be very variable between individuals due to hormone level fluctuations. Instead, this study focused on the proliferative phase, when the endometrium is rebuilding after menstruation and may offer a more stable baseline for comparison.
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Study design
- This was a retrospective study that took place between 2016 and 2019 in Denmark.
- Exclusion criteria included known uterine abnormalities.
- Biopsies were timed to the proliferative phase (cycle day 3–10) and collected mostly during natural cycles.
- Women were between 18 and 42 years old.
Two groups were included:
- 108 women with RPL, defined as ≥3 first-trimester losses or ≥2 second-trimester losses or stillbirths.
- 27 IVF controls, presumed to have healthy endometrial function but undergoing IVF for reasons like male factor or tubal infertility.
RPL patients show differences in immune-regulated genes
The researchers used a technique called RNA-seq to analyze gene expression in the endometrial biopsies, finding a clear separation between RPL and control samples. They found that immune-regulated genes were consistently upregulated in RPL patients compared to controls.
Four subgroups emerged from the gene expression data:
- One group included only control women with no signs of abnormal immune activity.
- One group was mixed, with mostly controls but also a few RPL patients.
- Two groups included only RPL patients, and one of these stood out with very high levels of immune-related gene activity. This group had especially strong signals from immune cells like NK cells and macrophages, both in gene expression and by staining the tissue for immune markers.
These results suggest that some RPL patients may have a unique, immune-driven form of the condition, which could eventually help guide more personalized treatments.
Differences in RPL endometrial gene expression might lead to a diagnostic test
To see whether these gene differences could help classify patients, they trained a machine-learning model on gene expression data from the biopsies. The model achieved:
- 96.6% accuracy
- 95.7% sensitivity (correctly identifying RPL patients)
- 99.5% specificity (correctly identifying controls)
- AUC of 0.996 — nearly perfect classification performance!
They then repeated the analysis using only the top 20 most informative genes and found nearly the same results. In fact, even with just two genes, they achieved 99.9% accuracy. This suggests that a diagnostic test based on a small gene panel could be feasible.
Conclusions
This study suggests that immune dysfunction in the early (proliferative) endometrium may play a key role in RPL. By analyzing gene expression, the researchers identified clear differences between RPL patients and controls, including distinct subgroups, with one group showing signs of strong immune activation.
A machine-learning model trained on this data showed that the gene expression data could be used to classify RPL patients with high accuracy, suggesting that a diagnostic test may be possible.
This study supports the idea that RPL may sometimes be driven by an overactive or imbalanced immune response. This dysfunctional response might leave a lasting “immunological scar” in the endometrium that can be detected, which could possibly lead to the development of a diagnostic test for RPL.
While the results are promising, the study has limitations: it used IVF patients as controls (who may not be representative of women with fully normal fertility) and some of them had pregnancy losses, didn’t account for aneuploid embryo loss in all cases, and didn’t show that these differences in immune gene expression actually cause RPL.
The researchers note that more studies need to be done before this can be moved to an actual diagnostic test.
For more reading on the immune system and infertility, check out my post The role of the immune system in infertility and IVF.
Reference
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About Embryoman
Embryoman (Sean Lauber) is a former embryologist and the founder of Remembryo, an IVF research and fertility education website. After working in an IVF lab in the US, he returned to Canada and now focuses on making fertility research more accessible. He holds a Master’s in Immunology and launched Remembryo in 2018 to help patients and professionals make sense of IVF research. Sean shares weekly study updates on Facebook, Instagram, and Reddit regularly. He also answers questions on Reddit or in his private Facebook group.
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Complete guide to embryo implantation and implantation failure
Why do embryos in IVF fail to implant or miscarry?
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Study investigates the use of EMMA & ALICE in IVF patients with RIF, RPL