Having extra or missing chromosomes or chromosome regions within a cell, a condition known as aneuploidy, is considered a hallmark of cancer (1). But a new single-cell DNA sequencing analysis revealed that even breast tissue in healthy women can contain a small percentage of cells with these abnormalities (2). The findings could influence current and future breast cancer diagnostic approaches.
Previous studies had hinted that healthy cells across various mammalian tissues could harbor aneuploid cells (3-5). However, technological limitations hindered progress, according to Zuzana Storchová, a molecular geneticist at the University of Kaiserslautern-Landau, who was not involved in the study. Many researchers have used fluorescence in situ hybridization (FISH) to explore the question, but it is not a very reliable method, she added. Errors such as probe misplacement, clustering, or failed hybridization can produce false signals, leading to underestimation or overestimation of aneuploidy (5). Some teams had also used single-cell sequencing methods, Storchová noted, but “that did not take off properly until maybe five years ago.” So, “it has not been so easy to do this analysis,” she said.
Motivated by the limited data on aneuploidy in normal tissues, a team led by Nicholas Navin, a genomic researcher at the University of Texas MD Anderson Cancer Center, used single-cell DNA sequencing to analyze 83,206 breast epithelial cells from 49 women aged 18 to 63 with no diagnosis of cancer. Histological analyses of the participants’ breast tissue samples further confirmed the absence of cancerous tissue.
Navin and his colleagues found that all 49 women had aneuploid cells, ranging from 0.2 to over 20 percent of the total cells analyzed in each participant, with a median of 3.19 percent. The researchers noticed that the proportion of aneuploid cells increased with age.
They also found that about 82 percent of aneuploid cells divided into cell clones with the same chromosomal abnormalities. “That’s presumably because [these cells] might have [gained] some type of selective advantage or fitness advantage that allows them to expand in the tissues,” said Navin.
The big question is: When do these additional events happen, or what additional mutations occur that really take you from this normal state to a breast cancer that will expand?
- Nicholas Navin, University of Texas MD Anderson Cancer Center
Storchová praised the large number of cells and patients analyzed, the histopathological validation confirming the tissues were non-cancerous, and the use of advanced single-cell sequencing technology.
The team characterized many of these abnormalities, finding that extra copies of the long arm of chromosome 1 and losses of the long arm of chromosomes 10, 16, and 22 were frequent. These chromosomal changes are commonly associated with invasive breast cancer. However, they also identified several aneuploidies likely unrelated to cancer, such as the loss of the X chromosome, and they also noted the absence of some aneuploid events that are common in cancer.
“The big question is: When do these additional events happen, or what additional mutations occur that really take you from this normal state to a breast cancer that will expand?” Navin said. “We really don’t know what’s causing that switch, but what these data show is that those events that were assumed to be caused later in tumorigenesis are actually there in normal tissues of many, many women in the population, if not all.”
Thus, the findings highlight that the types of aneuploidy reported in this study are not a reliable marker for cancer, said Navin. However, another important question is whether having more aneuploid cells increases the risk of developing cancer. Although it is challenging to answer, Navin said that his team is planning to investigate it further. “We would need to look at hundreds of patients, and we would need to collect samples from normal women that then 20 or 30 years later develop breast cancer,” he explained.
Consistent with Navin’s team’s findings, another recent study also reported that approximately 3.25 percent of normal breast epithelial cells were aneuploid (6). “These studies … show how we can use single-cell sequencing for really detailed analyses of the role of aneuploidy in cancer,” said Storchová.
References
- Sdeor, E. et al. Aneuploidy as a driver of human cancer. Nat Genet 56, 2014-2026 (2024).
- Lin, Y. et al. Normal breast tissues harbour rare populations of aneuploid epithelial cells. Nature 636, 663-670 (2024).
- Duncan, A.W. et al. Frequent Aneuploidy Among Normal Human Hepatocytes. Gastroenterology 142, 25-28 (2012).
- Wang, J. et al. Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm. Cell 150, 402-412 (2012).
- Knouse, K.A. et al. Single cell sequencing reveals low levels of aneuploidy across mammalian tissues. Proc Natl Acad Sci U S A 111, 13409-13414 (2014).
- Williams, M.J. et al. Luminal breast epithelial cells of BRCA1 or BRCA2 mutation carriers and noncarriers harbor common breast cancer copy number alterations. Nat Genet 56, 2753-2762 (2024).