When we talk about studying the human body, we usually picture techniques that analyze entire tissues—like observing a city from space. But what if we could zoom in to see each individual inhabitant? That’s the power of single-cell technologies: they allow us to study organs not as homogeneous blocks, but as dynamic communities of cells, each with its own functions and behaviors.
In the case of the female reproductive tract, this approach is opening a new chapter in biomedical research. Thanks to these tools, scientists can now reconstruct the cellular “map” of these organs with unprecedented resolution, leading to deeper insights into both physiological and pathological processes.
What is single-cell sequencing, and what is it for?
The most widely used technique today is scRNA-seq (single-cell RNA sequencing), which identifies which genes are active in each individual cell of a sample. By grouping cells with similar profiles, researchers can discover new cell types, understand their functions, and observe how they change during processes like menstruation, pregnancy, or disease.
But the value of this technology goes beyond identifying what’s there—it also reveals how cells communicate, how they shift from one state to another (for example, from a progenitor cell to a mature epithelial cell), or how they respond to inflammation or hormone treatments.
A technological and computational challenge
Analyzing this kind of data is no easy task. Each experiment generates information from thousands of cells that must be preprocessed, corrected, interpreted, and visualized. This is where computational biology comes in—and specifically, teams like CompBio at the Carlos Simon Foundation, which design analytical pipelines to:
- Clean and normalize the data
- Identify cell types and functional states
- Detect differences between healthy and diseased samples
- Infer developmental or transformational trajectories
- Study communication networks between cells
What does this mean for women’s health?
This approach holds enormous clinical potential:
- It can detect subtle cellular alterations that would previously have gone unnoticed
- It helps identify molecular biomarkers for diagnosing conditions like endometriosis, Asherman’s syndrome, or fibroids
- It offers new clues for discovering therapeutic targets and advancing precision medicine
In short, seeing the female reproductive tract “through single-cell looking glasses” means gaining a deep understanding of its biology—with direct implications for fertility, early diagnosis, and the development of personalized treatments.
Our work at the Carlos Simon Foundation
At the Carlos Simon Foundation, we actively contribute to this transformation. Our team participates in international initiatives such as the Human Uterus Cell Atlas and applies these technologies to unravel the cellular complexity of the human uterus, both in healthy conditions and disease.
A sample of this work is featured in the April 2025 special issue of The American Journal of Obstetrics and Gynecology (AJOG), in an article authored by members of our team and collaborators, titled:
“How to view the female reproductive tract through single-cell looking glasses.”
You can access the full article here: https://doi.org/10.1016/j.ajog.2024.08.040