Harnessing Proteomics for Earlier Diagnosis of Women’s Health Conditions
Proteomics revealed protein signatures linked to endometriosis and PMOS.
For many women, obtaining a diagnosis for a reproductive health condition can be a long and frustrating journey.
Conditions such as endometriosis and polyendocrine metabolic ovarian syndrome (PMOS), previously named PCOS, affect millions worldwide, yet both remain challenging to diagnose, classify, and treat.
Researchers are turning to omics technologies to tackle these challenges.
While genomics has advanced our understanding of disease risk, proteomics offers something different: a snapshot of the proteins actively driving biological processes. By looking at proteins involved in cellular functions, scientists can get a better idea of disease activity, helping them to identify potential biomarkers and therapeutic targets.
Two researchers actively working in this field are Dr. Stella Irungu, a senior research scientist at the Kenya Institute of Primate Research, and Dr. Felix Day, a senior research associate in the Institute of Metabolic Science (IMS) Epidemiology, University of Cambridge, whose work focuses on applying genetics and proteomics to complex reproductive disorders.
Irungu and Day spoke with Technology Networks about how proteomics is rewriting our understanding of women's health conditions.
Why proteomics matters in women's health
Women's health research has historically received less attention and investment than many other fields of medicine. As a result, conditions that affect millions of women are still not fully understood, and clinicians often lack the tools needed for early diagnosis or personalized treatment.
This challenge is particularly evident in reproductive disorders. Conditions such as endometriosis and PMOS are highly heterogeneous, meaning patients may experience very different symptoms despite sharing the same diagnosis. Therefore, traditional symptom-based approaches can struggle to capture what is happening biologically.
Proteomics offers an opportunity to examine disease at a functional level. Unlike DNA, which provides a blueprint for how cells function, proteins reflect what cells are doing in real time. Their levels and activity change in response to environmental cues, hormones, inflammation, and other factors that shape disease progression.
“Because proteins are the functional effectors of biological processes and are strongly influenced by environmental signals and cellular context, proteomic analyses have uncovered disease mechanisms and biomarkers that were not predictable from RNA or DNA data,” said Irungu.
This ability to capture biological activity has made proteins particularly attractive as biomarkers in clinical medicine more broadly. Many established diagnostic tests already measure proteins, because their levels can change in response to disease, making them useful indicators of pathology.
Proteomics is also becoming increasingly valuable for identifying therapeutic targets; researchers can use protein data to pinpoint the molecules and pathways driving disease.
“Proteomic studies can provide evidence of very direct associations with the molecular targets of a potential therapy. Combining this with the robust causal associations that genetic variants associated with these proteomic levels can provide adds up to very useful evidence to help to identify new therapeutic targets,” said Day.
Recent advances in mass spectrometry (MS), data analysis, and computational biology have accelerated this work. Scientists can identify and quantify thousands of proteins from small biological samples, creating opportunities to understand diseases that have been difficult to study.
Endometriosis as a proteomics success story
Few conditions illustrate the promise of proteomics better than endometriosis.
This chronic inflammatory disease occurs when tissue similar to the lining of the uterus grows elsewhere in the body. Although it is estimated to affect ~190 million women of reproductive age globally, diagnosis often takes years, as symptoms such as pelvic pain and infertility overlap with many other conditions, and standard diagnostic pathways typically rely on laparoscopic surgery.
“Endometriosis is not a single uniform disease but rather a condition with several clinical phenotypes,” said Irungu. “This heterogeneity makes it difficult to identify consistent molecular signatures that define the disease.”
Proteomics helps researchers tackle this complexity from multiple angles. Scientists are using advanced technologies to analyze biological fluids such as blood, urine, peritoneal fluid, and menstrual fluid.
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“Techniques such as liquid chromatography tandem MS, data-independent acquisition, targeted proteomics, and spatial proteomics are proving particularly informative for analyzing endometriosis lesions and associated biological fluids,” explained Irungu.
These studies have revealed alterations in proteins linked to inflammation, immune regulation, angiogenesis, and tissue remodeling, processes believed to support lesion growth and persistence.
“Proteomic studies have revealed increased expression of proteins involved in oxidative stress responses and iron metabolism, helping explain the chronic inflammatory and pro-oxidant environment characteristic of the disease,” said Irungu.
One particularly exciting area is menstrual fluid proteomics.
“Menstrual fluid can be collected non-invasively and repeatedly across menstrual cycles, contains proteins derived directly from the endometrium and therefore reflects the local uterine environment, making it a valuable and accessible source of biological material,” noted Irungu.
Proteomic analyses of menstrual blood have identified differences in proteins involved in inflammation and the extracellular matrixin women with endometriosis compared with healthy controls.
The search for non-invasive biomarkers has become a focus of endometriosis research, driven in part by the lengthy diagnostic delays, on average over 9 years in the UK, experienced by many patients. A recent study from researchers at the University of Melbourne and the Royal Women's Hospital, in collaboration with Proteomics International Laboratories, analyzed plasma samples from more than 800 participants. They identified a panel of 10 protein biomarkers capable of distinguishing women with endometriosis from symptomatic controls, including patients with earlier-stage disease.
“Current diagnosis often requires laparoscopic surgery because non-invasive biomarkers have lacked sufficient sensitivity and specificity. Future plasma, serum, peritoneal fluid, or menstrual-fluid proteomic panels may detect subtle but reproducible combinations of different biomarkers associated with disease presence and subtype,” said Irungu.
However, challenges still remain—small patient cohorts, disease heterogeneity, and differences between studies continue to complicate biomarker validation.
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Even so, endometriosis is emerging as an example of how proteomics can illuminate disease biology while simultaneously driving diagnostic innovation.
“Improvements in quantitative MS and targeted proteomic assays will enable these biomarker panels to be translated into clinically practical diagnostic tests, potentially allowing earlier detection and reducing diagnostic delays that currently affect many patients,” Irungu added.
Using proteomics to understand PMOS disease heterogeneity
If endometriosis highlights the diagnostic potential of proteomics, PMOS may demonstrate its power to understand biological complexity.
PMOS is among the most common reproductive disorders, but, similar to endometriosis, the condition is difficult to define as a single disease entity. Patients can present with very different combinations of symptoms, including irregular menstrual cycles, infertility, metabolic dysfunction, insulin resistance, and elevated androgen levels.
“The problems of studying PMOS in many cases stem from issues of under-diagnosis. This is not unique to PMOS and often impacts studies of reproductive conditions,” said Day.
The condition's diversity creates significant challenges for researchers attempting to determine its underlying causes.
“Some researchers have suggested that PMOS might be a constellation of related conditions. If that is the case, and those conditions have specific proteomic or genetic signatures, that might help our understanding of the etiology of PMOS,” Day explained.
This idea is influencing how PMOS is studied; rather than viewing all patients as having the same disease, researchers are investigating whether distinct biological subtypes exist beneath the umbrella diagnosis. Proteomics offers a powerful way to explore these key differences.
By comparing protein profiles across different patient groups, scientists can identify signatures associated with clinical features.
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Emerging studies have linked proteomic changes to inflammation, insulin signaling, lipid metabolism, and broader metabolic dysfunction. In one study, researchers identified 80 proteins that were differentially expressed in women with PMOS, highlighting disruptions in inflammatory and metabolic pathways.
Proteomics is also helping researchers understand why some women with PMOS experience more severe metabolic complications than others. One study identified protein signatures associated with insulin resistance, including changes in apolipoprotein C3, a protein involved in lipid metabolism that correlates with measures of insulin resistance in women with PMOS.
If distinct protein signatures consistently identify different PMOS subgroups, clinicians may eventually be able to stratify patients more precisely, which could help explain why certain treatments work well for some individuals but not others.
“We are still in the early stages of our understanding of the etiology of PMOS. But given the diversity of the ways that women with the condition present, there is certainly the possibility that some potential therapies will only be effective in some people,” Day added.
What’s next for proteomics in women’s health?
Although significant progress has been made, both researchers emphasize that the field remains in its early stages.
“PMOS has been comparatively understudied, compared to other complex conditions. But hopefully it will be the focus of more studies in the future,” said Day.
For endometriosis, the outlook is similarly encouraging. Advances in proteomics, spatial biology, and computational analysis are providing detailed views of disease mechanisms, while also accelerating the search for non-invasive diagnostics and novel therapeutic targets.
“Despite these advances, several challenges remain before proteomic discoveries can be translated into clinical practice,” said Irungu. “Nevertheless, proteomics is beginning to close the knowledge gap by providing deeper insight into the molecular mechanisms underlying endometriosis.”
The research emerging from endometriosis and PMOS illustrates a change in women's health. Moving beyond symptoms and examining the proteins that drive disease processes is allowing scientists to build a more nuanced understanding of conditions that have been under-studied for far too long.
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