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Refined Picture of Breast Cancer Clone Evolution Emerges from Phylogenetic Study

NEW YORK — Driver mutations that ultimately lead to breast cancer can appear long before the time of diagnosis, often in puberty or adolescence, but additional mutations that separate cancer from non-cancer clones often happen a decade or more after that, according to a new phylogenetic study by researchers in Japan.

In a new paper published in Nature on Wednesday, a team led by researchers at Kyoto University traced the evolution of a type of breast cancer harboring der(1;16), a chromosomal fusion that is a common driver alteration found in roughly 20 percent of breast cancers, including one-third of Luminal A and two-thirds of invasive lobular breast cancers. They also established the rate at which normal breast epithelial cells acquire mutations during a woman's lifetime.

"Our findings may contribute to the understanding of breast carcinogenesis and the development of new strategies for prediction, early diagnosis, and even prevention of breast cancer," corresponding author Seishi Ogawa, a professor of molecular oncology at Kyoto University, wrote along with his colleagues.

Many previous studies on cancer evolution had only looked at cancer tissues, which could not determine the early driver events, the authors noted. Neither did those studies map the time at which cancer clones emerged or track the fate of related non-cancer clones, they added.

For their study, they first sought to determine the rate of mutation accumulation in normal mammary epithelial cells during different times of a woman's life. For this, the researchers established 71 single-cell-derived organoids from normal mammary tissues from patients with breast cancer and from breast milk provided by healthy volunteers. In total, they sequenced and evaluated somatic mutations in 64 organoids from six pre- and nine postmenopausal patients with breast cancer and in 12 organoids from six healthy women.

A central finding was a significantly reduced mutation rate after menopause, likely explained by the reduced cell turnover associated with the cessation of menstrual cycles and lower estrogen levels. Moreover, mutation rates agreed with the epidemiological finding that late menopause and low parity correlate with an elevated risk of breast cancer.

Next, the researchers analyzed the genomes of breast cancer samples and noncancerous benign breast lesions (BBLs), which are thought to have a common ancestor. For that, they selected five patients whose surgically removed samples contained cancer and three or more BBLs. Using whole-genome sequencing, they analyzed 69 laser-capture microdissected samples for somatic mutations and copy number alterations.

By combining the previously established mutation rates and the sequencing data from the cancer lesions, BBLs, and normal tissues, the researchers built a phylogenetic tree of the evolution of breast cancer. Their findings showed that cancer lesions and BBLs had a single ancestor in all five cases. The progenies from this common ancestor expanded over the years and occupied a large area in the affected breast by the time of cancer diagnosis.

The author noted that cancer clones often evolved from several clonally related non-cancer ancestors. "Being distinct from the classical linear model for the evolution of a single cancer founder, such a branching pattern of evolution of multiple cancer founders from within a non-cancer population might be more common than expected during cancer development," they wrote.

Compared to previous studies, their analysis also enabled them to determine the timing and order of early driver events more accurately. The first driver events occurred long before the cancer diagnosis, around puberty or late adolescence. However, the most recent common ancestors (MRCAs) of cancer and non-cancer clones appeared no earlier than the patient’s 20s to early 30s, suggesting that the MRCA mutations occurred over ten years after the initial driver alterations were acquired.

Whether or not this type of cancer evolution happens in other breast cancer subtypes is still open. The researchers noted similar patterns in cancers with AKT1 founder mutations but said that this needs to be confirmed by future studies.

According to Ogawa, these findings open the possibility of using cell-free DNA to understand a young individual's breast cell mutational profile, which could help in early diagnosis.