Comprehensive analysis of breast cell types helps better understand how the cancers start, grow and spread microbiologystudy

October is Breast Cancer Awareness Month, and fittingly, University of New Mexico Comprehensive Cancer Center biologist Curt Hines, Ph.D., has published a pair of papers that comprehensively describe the 12 major types of cells in the human breast.

“We are trying to understand all the different cell types that are collaborating and coordinating to make a tissue function,” he says, “and how these processes can go awry in a tumor.”

Over the past several decades, breast cancer has become a leading cause of cancer deaths among women, second only to lung cancer. Of all cancer types diagnosed in women each year, a third will be breast cancer—and there is a one in eight chance that a woman will develop breast cancer over her lifetime.

According to the National Cancer Institute, between 75% and 80% of breast cancer cases have features of luminal epithelial cells, which are a special cell type that forms the milk ducts of the breast. Cancers of this type are called ductal adenocarcinomas.

Organs and tissues comprise different types of cells that work together to form a functional unit. This normal balance of cell types is disrupted in tumors. These other non-cancerous cells influence how tumors behave.

“You need to know all the cell types in a tissue,” Hines says. “Tumors are diseases of the tissue. You really need to understand all the players.”

For the past 10 years, Hines’ laboratory has been compiling information about the types of cells in human breast tissue. Recently, he and his team published a pair of papers about their work.

The first paper, “Comprehensive identification, isolation, and culture of human breast cell types” published in Journal of Biological Chemistry, describes the process they used to identify, purify, and grow every major cell type in the human breast. The second paper, “Transcriptomic analysis of the twelve major human breast cell types reveals mechanisms of cell and tissue function” in press at PLOS Biology, describes in great detail each of the 12 major types of cells in a human breast.

Hines used non-diseased breast tissue that was discarded in breast reduction surgeries. He then used two different technologies—flow cytometry and RNA sequencing—to find, select and describe the cell types in those tissue samples.

Hines began his work using tissue staining and flow cytometry, which can analyze hundreds of thousands of cells by their specific traits, utilizing the UNM Comprehensive Cancer Center’s Flow Cytometry Shared Resource.

After unlocking the combination of specific antibodies required to detect all cell types, he and his team used flow sorting to isolate the different breast cell types. They then used RNA-sequencing to analyze the RNA transcripts made by each cell type.

RNA sequencing determines the sequences of all the different ribonucleic acid (RNA) transcripts in a cell. RNA transcripts are molecules that are copied from the DNA genome. These transcripts carry the code for the proteins that accomplish the cell’s processes; they define the nature and properties of that cell type.

“Every cell in an individual has the same DNA,” Hines says, “but they don’t have the same RNA. And it’s the RNA that tells the cell what to do, what their function is.”

Flow cytometry enabled Hines to identify the 12 different cell types composing the breast. He and his team purified each cell type to study them in greater detail. Guided by the differences in the RNA transcripts, they closely examined the biological nature of each cell type.

The resulting information was immense, as each cell type was found to express more than 20,000 individual genes. Among their findings, Hines and his team discovered a rare epithelial cell type which appeared to have stem cell properties. Stem cells have the ability to mature into an array of different cell types and serve as part of the body’s repair systems.

To further explore how the cells function, it was necessary to keep the cells alive in the laboratory—by growing them in plastic tissue dishes with cell medium—a mixture of sugars, amino acids, vitamins, and serum.

Hines and his team created cell models from nearly every cell type, expanding on the two to three that are commonly used in breast research. Their cell models are grown in the laboratory, and these cells retain the defining characteristics that they exhibit in the body.

These cell models will enable scientists to study the behavior of the different cell types and explore how each cell type may contribute to the malignant process of tumor formation.

The cell types and their descriptions are summarized in the published papers, and full data about each type is available online.

“We were really trying to get to the essence of each cell type,” Hines says. “There’s so much information.”

Hines says that the reference can help biologists who want to understand what all the different types of cells in a human breast do and how a disturbance in the balance of these cells can lead to cancer.

Hines and his team are now studying pericytes and how these cells may influence the growth of breast tumors. They are also using the breast cell reference to study how breast cells influence their microenvironment and how their microenvironment influences them.

The single-cell RNA sequencing capabilities at UNM Cancer Center’s Analytical and Translational Genomics shared resource have permitted Dr. Hines to explore the heterogeneity within the breast’s pericyte population. Their next grant proposal aims to elucidate the pericyte’s contributions to breast malignancies.

“We know that disturbing the microenvironment can propel tumor growth,” Hines says, but he also marvels that many cancer cells do not turn into tumors. “It is amazing that our tissues work in the way that they do.”