Revealing the Wonder of the Female Reproductive System

Mapping cells of the reproductive tract across the lifespan will help fill critical gaps in our knowledge about health

The formation of the reproductive system starts in the embryo, when cells that will eventually form the ovaries, fallopian tubes, and uterus divide and differentiate, ultimately developing into a system capable of perpetuating life. That system changes monthly and also over a lifetime, undergoing major transitions at puberty and menopause.

Researchers supported by the Chan Zuckerberg Initiative’s Seed Networks for the Human Cell Atlas (HCA) program are mapping that journey, cell by cell, across the female reproductive system — from the earliest stages of human development to old age. Their data will contribute to a draft of the Human Cell Atlas, an international effort to map all the cells in the human body fueled by new methods for isolating and analyzing individual cells.

The resulting series of atlases will help fill persistent, even grievous, gaps in our knowledge about reproduction and women’s health, and diseases such as ovarian cancer, endometriosis, and infertility. They also represent a step in the march toward sex and gender equality in reproductive health research and care.

A typical fallopian tube epithelium stained to highlight cell membranes (red), nuclei (blue), and PAX8 genes (green). Photo provided by Ernst Lengyel, University of Chicago.

“In terms of scientific questions, women’s health is always somewhere in the background,” said Ariella Shikanov, PhD, associate professor of biomedical engineering at the University of Michigan (UMich) and a Seed Networks investigator. “Through this research, we now have the perfect opportunity to go out and ask long-standing questions about women’s reproductive health — and, using technical advances in single-cell genomics, we can actually try to answer them.”

Shikanov is part of the UMich team mapping tissue of the ovary, fallopian tubes and uterus in healthy premenopausal women; a second team, based at the University of Chicago, is characterizing the array of cells in reproductive tissue from post-menopausal women; and a third CZI-funded researcher is contributing to efforts to map the cells of the uterus over a lifetime and the ovaries from the very beginning of life.

That is where this story begins.

The early years

Imagine. Ovarian development begins three weeks after conception, so a pregnant woman’s health, lifestyle and environmental exposures influence the reproductive potential of her granddaughter. That’s a point of fascination — and motivation — for Roser Vento-Tormo, a group leader at the Wellcome Sanger Institute in the United Kingdom, who has applied single-cell technologies to a variety of reproductive tissues.

Currently, she is part of two major European research collaborations focused on women’s reproductive health: The Human Uterus Cell Atlas and the Human Gonad Developmental Cell Atlas. Both initiatives launched in 2020 and are funded by the European Commission as part of its support for the Human Cell Atlas; plus, with additional support from funders in the United Kingdom, she is studying ovarian and endometrial tissue. Together, the results of these projects will complement CZI-funded research on the female reproductive tract.

Roser Vento-Tormo, a geneticist at the Wellcome Sanger Institute, is working on atlases of the ovaries, endometrium, uterus and gonads.

In 2018, Vento-Tormo generated a single-cell map of the maternal-fetal interface during pregnancy — a remarkable cellular environment in which a pregnant person’s local immune system adapts to allow the coexistence of maternal and fetal tissue. (Building on this research, Vento-Tormo is also helping to produce an integrated map of the human immune system across tissues and ages as part of CZI’s Seed Networks program).

The uterus is a highly dynamic organ in which the inner layer, or endometrium, is in constant flux as hormones wax and wane over the menstrual cycle. Despite its importance in reproduction, Vento-Tormo says very little is known about the fundamental biology of healthy endometrial tissue: “That has repercussions when you have pathology. For example, one out of 10 women of reproductive age suffer from endometriosis, but we don’t have a diagnostic tool and we don’t have a treatment for it.”

The Human Uterus Cell Atlas project will reveal the transcriptomic, genomic, and spatial changes in the uterus at the single-cell level throughout the menstrual cycle and over the course of a woman’s life. The results will illuminate the organ’s basic biology and, in the future, how that changes in diseases like endometriosis, infertility, or certain cancers. They could also lead to advances in regenerative medicine because the endometrium is remarkably plastic: It regenerates monthly and is remodeled during pregnancy. Understanding the biological mechanisms that drive these transformations could be applied to other cells or tissues.

In the second pilot project, Vento-Tormo is helping to identify the cellular makeup and organization of the developing ovaries and testes using a suite of single-cell and spatial transcriptomic technologies. This project could lead researchers to a better understanding of the mechanisms that influence sex determination and, eventually, differences of sex development.

Vento-Tormo welcomes the swell in support for research on the human reproductive system across the lifespan, and says it is enabling researchers to apply state-of-the art techniques to reproductive tissues for the first time.

“There is so much variability with these tissues that the more people working on them the better. At the end of the day, I would really like to integrate all the data. Combining our work with the results from other teams could be very powerful,” she says.

The reproductive years

In Ann Arbor, Michigan, Shikanov is working to preserve fertility in young women undergoing cancer treatment or restore it later on. She specializes in engineering biomaterials to promote the survival and development of ovarian follicles in the lab. For these artificial systems to succeed, a deeper understanding of the cell types in the human ovaries and nearby tissue is needed.

Ariella Shikanov, a biomedical engineer at the University of Michigan, is part of a team mapping the female reproductive system in healthy premenopausal women.

Shikanov says researchers can culture ovarian follicles — the structural and functional unit of the ovary containing the immature oocyte and hormone-producing somatic cells — from mice but are struggling to do the same for human follicles. A major barrier to success has been access to healthy tissue that will help scientists understand the cellular processes that drive activation of primordial follicles and promote folliculogenesis to generate a mature fertilizable egg.

“Anything we can learn from nature and recapitulate in vitro is definitely going to be deal-breaking for us,” she says. “If we can identify the signals or the secretory factors, we could try to reconstitute the microenvironment using biomimetic materials and soluble factors to drive folliculogenesis in the lab.”

Shikanov, with three collaborators at the University of Michigan — geneticists Sue Hammoud, PhD, and Jun Li, PhD, and obstetrician-gynecologist Erica Marsh, MD — have begun mapping the cell types in the ovaries, fallopian tubes, and uterus using single-cell RNA sequencing (scRNAseq) in tissue from a handful of healthy donors. Their goal is to generate a comprehensive transcriptional map of follicular cells, and nearby support cells, at different stages of development.

Hammoud is an expert on germ cell development. Using scRNAseq, she recently identified the transcriptional signatures of the major germ and somatic cell types in the testes of humans, non-human primates, and mice. In the CZI Seed Network’s project, she is applying this knowledge to females.

“Analyzing multiple organs from the same individual gives us an opportunity to begin to understand the coordinated process that needs to occur in the female reproductive tract in order to generate this miracle child at the end. It requires multiple systems working together to get this to function in the right place at the right time,” says Hammoud.

A large blood vessel labeled with VA cadherin in the medula part of the ovary. | Photo provided by the Shikanov Lab.

In any complex system, there is also the potential for breakdowns, and the female reproductive system is no exception. Some cells transform to become cancerous; others are shed from the lining of the uterus, migrate to nearby organs and trigger inflammation and debilitating pain. Yet, fundamental questions about female reproductive tissue and its pathology remain, says Hammoud.

“What kind of cells are in there? Which cells contribute to the lining of the uterus every single month? Which cells transform into cancerous ones? Why do some transform and others migrate to other tissues? There’s a lot of really open questions that these data sets can be leveraged to explore, beyond our own labs. I think it would be a big resource for the community in general.”

The elder years

Ernst Lengyel, MD, PhD, has spent two decades studying ovarian cancer, which is typically diagnosed in women over 60 and is the fifth leading cause of cancer death among women in the United States. But he says progress toward a cure has been slow, hampered by surprising gaps in knowledge about healthy ovarian tissue and the pathway normal cells take to disease. Researchers are still unsure, for example, what cell type actually drives the disease — and even whether it originates in the ovaries. Yet without knowing the cell of origin for ovarian cancer and its molecular identity, it is difficult to design new treatments for the disease, an aggressive cancer associated with high mortality rates.

Ernst Lengyel is leading a team of researchers from the University of Chicago to characterize all cell types in the healthy female human reproductive system.

Lengyel is an obstetrician-gynecologist and translational researcher leading the University of Chicago team, which is focused on characterizing healthy tissue at the single-cell level from post-menopausal women. But his downstream goal is to better understand — and ultimately treat — ovarian cancer. He is banking that researchers can glean insights into the disease by comparing cancerous tissue to healthy tissue.

“Unfortunately, one-third to one-half of all female diseases are treated symptomatically. We’re not getting to the roots of the diseases — the why. These efforts will help with the why,” he says.

In North America, the average age of menopause, a time when reproductive tissue is remodeled by dramatic hormonal changes, is 52. Lengyel, geneticist Anindita Basu, PhD; bioinformatician Megnjie Chen, PhD; and cell biologist Mark Eckert, PhD; all faculty members at UChicago, are analyzing donated tissue from healthy women in their mid-to-late 50s and older. They are using single-cell RNA and ATAC sequencing, along with epigenetic and gene-expression profiling.

Together with the UMich and European teams focused on premenopausal tissue, the UChicago atlas could paint the most detailed picture yet of the cellular composition of the ovaries, fallopian tubes, uterus, cervix, and vagina — and how it changes over a person’s lifetime.

Lengyel says the Human Cell Atlas’s focus on healthy tissue represents a paradigm shift in biomedical research — one he is glad to be a part of: “We don’t spend enough time in the research community talking about what is normal and we are paying a high price for it. First defining what is normal — and then comparing normal with diseased tissue — might advance progress more.”

Written by Lindsay Borthwick

Supporting the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of the century.