Human Breast Cell Atlas reveals all cells in human breast tissue, with some surprises

For the past seven years, researchers around the world have been carefully mapping all the types, genes and proteins of every cell in the human body. Called the Human Cell Atlas, the project aims to create a “Google Map” of tissues that will be used as a guide for everything from diagnosing disease to developing new treatments.

Now, a team led by scientists at the University of Texas MD Anderson Cancer Center, University of California Irvine and Baylor School of Medicine has unveiled its contribution to the effort: the largest atlas of cells in healthy human breasts. Called the Human Cell Breast Atlas, the open-source guide contains biological data on all the cells present in mammary tissue. A paper on the development was published June 28 in Nature. 

“It’s an effort to understand all the cell types that are present, and more importantly the cell states,” Navin said.

Navin likened the work to the Human Genome Project, but for breast tissue. Similar to the way scientists in that project collected blood samples from volunteers, the researchers working on the Human Breast Cell Atlas collected 220 breast tissue samples from 132 women who underwent breast reduction or prophylactic mastectomy at one of four hospitals. Forty-six percent were white, 41% were Black, 7% were Hispanic, and the rest were of unknown ethnicity. Thirty-eight of them had breast cancer; in those cases, the researchers took tissue from the unaffected breast.

Breasts are made up of lobules, ducts and fatty tissue. Most of the cells within them are epithelial cells, which make up organs and tissues throughout the body. Though the function of epithelial cells in the breast play a critical role in both health and disease—which is why they’ve previously been characterized with molecular studies—they’re far from the only type of cell in mammary tissue. One of the project’s goals was to shed light on the many less-studied cells there, Navin said. 

“There are roughly 10 cell types in the breast that you can identify with a microscope, but their molecular subtypes aren’t really well understood,” he explained. “So this project really aimed to map and look at all the different cell types present in an unbiased way.”

To do that, the team used spatial mapping and single-cell RNA sequencing, techniques that allow them to characterize the types of cells in different locations in the breast along with their gene and protein expression. They sequenced 714,331 cells in total, revealing 12 major cell types and 58 different biological states, or configurations of gene and protein expression, morphology and metabolic activity.

Among the most surprising findings was the number of immune cells present in the breasts, including many subtypes of B cells, T cells and myeloid cells. Together they made up around 17% of tissue, much more than the researchers had expected. They were mainly embedded within epithelial cells of the milk-producing lobules and the ducts, with few found in the fatty or connective tissue. While there are still open questions about their function, it’s likely that the cells are keeping bacteria and pathogens from harming the ductal network, which is exposed to the outside environment, Navin explained.

“It’s important to really define and understand these immune cells and the localization, because in breast cancer, we’re studying immune cell populations quite a lot, especially now with immunotherapy,” Navin said.

One of the study’s strengths was the amount of metadata collected on participants, which enabled the researchers to stratify how demographic and hormonal characteristics affect breast cell composition. The variables with the greatest impact on cell type variation between participants were ethnicity, menopause status and age—though not whether the women had previously been pregnant, Navin noted.

“This was quite surprising to us, because a lot of the data had been more focused on parity, pregnancy and lactation,” he said. “[For women who had previously been pregnant], we really only saw significant changes in the T cell populations, but not many of the other cell types.”

In terms of ethnicity, a strength of the study was the nearly one-to-one ratio of African American to white participants, Navin noted, which could help future researchers understand baseline differences between the two groups to explain their relative risk factors for cancer. While Black and African American women have an 8% lower likelihood of developing breast cancer than white women, they’re at greater risk of developing more aggressive forms of the disease—and 41% more likely to die.

“We know that African American women have a much higher rate of triple-negative breast cancer and inflammatory breast cancers, so to be able to understand how the normal breast tissue biology differs between African American and Caucasian women is really important,” Navin said.

Older participants, including those who had gone through menopause, had fewer epithelial cells and fibroblasts, a type of connective tissue cell, compared to younger women. In contrast, older women had more of some types of macrophages and natural killer cells. Whether these changes had any relationship to the age-related rise in breast cancer risk isn’t yet clear, Navin said.

“I think we’re going to have to study a lot of these populations in more detail,” he said.

The researchers will also work to add samples from Asian, Latin American and Native women, who were underrepresented in the study. Enrolling them may require better community outreach efforts, Navin said, as some populations are hesitant to participate in medical research due to its history of discrimination.

On top of that, the scientists also hope to eventually integrate their findings with those of international research teams to see if they can identify more demographic differences. This will allow them to capture the influence of other variables on breast cells.

“That will understand not just the role of different ethnic or ancestral backgrounds, but also things like culture, environment and diet,” Navin said.