As a medical student at the University of Copenhagen more than a decade ago, Jonas Ghouse learned about the hormones that fluctuate throughout the menstrual cycle: the rhythmic variations of estrogen, progesterone, follicle-stimulating hormone, and luteinizing hormone through ovulation and the period. “But beyond that, not much is really known,” said Ghouse, now a clinical biochemistry researcher at Aarhus University.
Jonas Ghouse is a medical doctor and clinical biochemistry researcher at Aarhus University.
Aarhus University
About one and a half years ago, he sought to change that. He joined forces with Iben Riishede, a reproductive medicine researcher at Copenhagen University Hospital, hoping to merge her expertise in the field with his experience working in omics-based research. “We thought about, ‘What if we could find data that maps the menstrual cycle in a woman and then try to add another layer of data on top of that,’” Ghouse recalled.
In a recent study, Ghouse and Riishede investigated how the menstrual cycle shapes biology beyond hormones.1 They identified nearly 200 proteins—some of which are linked to conditions like uterine fibroids and endometriosis—that varied throughout the menstrual cycle in thousands of people. Their findings, published in Nature Medicine, highlight the biological changes that occur during the cycle and could pave the way for identifying biomarkers associated with reproductive disorders.
“This is [an] excellent [study],” said Elisabet Stener-Victorin, a reproductive physiology researcher at Karolinska Institute, who was not involved in the research. Given that previous such proteomic data included up to 100 participants, “The strength of this is really that they have such a large sample size; that's generally impressive,” said Stener-Victorin.
Analyzing Plasma Proteins Across Menstrual Cycle Phases
For their investigations, Ghouse, Riishede, and their colleagues turned to the UK Biobank, a repository that houses biological samples and health data of nearly half a million people. The biobank contained data of more than 50,000 participants whose plasma samples underwent proteomic profiling.
The researchers focused on plasma proteins to obtain insights about circulating proteins that carry signals from different tissues to understand both local and systemic physiology. In contrast, researchers have previously focused mostly on analyzing menstrual blood or the endometrium, which offers tissue-level information.2,3
Iben Riishede is a medical doctor and reproductive health researcher at Aarhus University.
Aarhus University
“Plasma proteomics that they study here is based on circulatory markers, and it may then reflect all tissues in the body, not just the endometrium,” said Stener-Victorin. She also noted the ease of sampling blood instead of carrying out endometrial biopsies to identify biomarkers for diagnosis, disease prediction, and treatment.
Of the plasma proteomic samples they accessed, Ghouse and his team narrowed down their search to female participants aged 43 to 48 years who had filled out a questionnaire about their reproductive health. They were left with nearly 2,800 participants with 2,900 proteins measured in their blood plasma. By coupling this proteomics information with that about the participants’ menstrual cycles, the researchers identified almost 200 proteins that changed throughout the cycle, offering a comprehensive picture of menstrual cycle-induced biological changes.
While they expected to see variations in the levels of some proteins, “We saw more than we expected for sure,” said Ghouse. “And the fact that they map so beautifully and have these typical phases was also a very big surprise.”
These proteins encompass reproductive hormones, cytokines, and growth factors, consistent with their biological roles in different stages of the menstrual cycle. For instance, cytokine and hormone activity-related proteins peaked during the follicular phase before ovulation, corresponding to immune and endocrine signals preparing the uterus and ovaries for ovulation. Similarly, proteins elevated during the second half of the cycle were associated with cytokines and signaling pathways that participate in immune surveillance and endometrial maturation after ovulation.
By integrating the proteomic data with previously published transcriptomics data, Ghouse and his team identified that many of these proteins were enriched in the endometrium and expressed in epithelial and their supporting stromal cells within the tissue.
Implications of Identifying Protein Signatures Across the Menstrual Cycle
Elisabet Stener-Victorin, a reproductive endocrinology and metabolism researcher at the Karolinska Institute, studies mechanisms and treatment of polycystic ovary syndrome among other topics.
Elisabet Stener-Victorin
Upon mapping these proteins to menstrual cycle phases in healthy individuals, Ghouse and his team investigated their association with female reproductive diseases. They identified more than 40 proteins linked with conditions such as uterine fibroids, endometriosis, and irregular bleeding, indicating that these could eventually help diagnose and understand some of these conditions.
“For instance, [there is] endometriosis, which we are really not that good at predicting. So many patients will have diagnostic delays,” said Ghouse. “There's many perspectives in these kinds of studies to find biomarkers, diagnose earlier, treat earlier.”
Stener-Victorin agreed. “This way of identifying circulating markers that can align with a tissue level is [the] way forward to identify potential biomarkers [for tissue-specific dysfunction],” she said. While the researchers studied these markers in healthy individuals, doing so in those with irregular or dysfunctional menstrual cycles linked to implantation failure and early pregnancy loss could offer crucial clues.
Despite this, she noted that the researchers used older transcriptomic datasets with a small sample size to contextualize their findings.4 Using newer data, such as that from the recent Human Endometrial Cell Atlas, would have offered deeper insight, she noted.5 She added that the blood samples that Ghouse and his team used had been drawn only once from each participant, preventing an understanding of how each individual’s proteins cycle.
“We [are] using a snapshot,” agreed Ghouse. “If you want to get more information out of this, longitudinal sampling is going to be key. Having measurements taken at different time points during the menstrual cycle will be absolutely gold in this.”
Another limitation that both Ghouse and Stener-Victorin noted was that the proteomic data from the present study comes from mostly older individuals over 40 years of age, so perimenopausal changes could have influenced some proteomic profiles. In addition, Ghouse and Stener-Victorin both said that the team depended on self-reported questionnaires to determine the menstrual cycle day instead of objectively analyzing the cycle phase using gold-standard hormonal markers. “You tend to remember more accurately if your menstruation occurred yesterday compared to maybe 27 days ago, so there's some bias,” said Ghouse, adding that more work must be done.
“We've just scraped the surface,” Ghouse said. “We're obliged…that we try to learn as much as we can in biological systems and biological occurrences like menstruation which happens for half of the population for many, many years.”
- Riishede I, et al. Plasma proteomic signature of the human menstrual cycle. Nat Med. 2026.
- Yang H, et al. Proteomic analysis of menstrual blood. Mol Cell Proteomics. 2012;11(10):1024-1035.
- Hood BL, et al. Proteomics of the human endometrial glandular epithelium and stroma from the proliferative and secretory phases of the menstrual cycle. Biol Reprod. 2015;92(4):106.
- Satija R, et al. Spatial reconstruction of single-cell gene expression data. Nat Biotechnol. 2015;33(5):495-502.
- Marečková M, et al. An integrated single-cell reference atlas of the human endometrium. Nat Genet. 2024;56(9):1925-1937.
