Single-Cell Sequencing Sheds Light on Breast Cancer Genetics

By Dr. Chinta SidharthanReviewed by Bethan DaviesNov 29 2024

In a recent study published in Nature Genetics, researchers explored genetic alterations in breast epithelial cells that may contribute to cancer development. The study focused on somatic copy number alterations (CNAs), which are changes in chromosome sections that may predispose cells to malignancy.

The researchers examined these alterations in individuals with and without mutations in the breast cancer genes BRCA1 and BRCA2, which are known for increasing breast cancer risk. By analyzing single cells from breast tissue, the study identified patterns of CNAs in luminal cells, offering insights into the early genetic changes that occur before visible signs of cancer and potentially linking these mutations to the development of invasive breast tumors.

Background

Genetic mutations frequently accumulate in normal tissues, with the majority posing no harm. However, certain mutations can trigger processes that lead to malignancy. Among these, somatic copy number alterations (CNAs)—characterized by the loss or gain of chromosomal segments—are particularly common in breast cancer. These alterations play a crucial role in tumor development by disrupting normal gene regulation and promoting uncontrolled growth.

Research has identified somatic CNAs in pre-cancerous breast tissues, such as ductal carcinoma in situ, indicating their potential role as early drivers of cancer development. While CNAs are well-documented in advanced tumors, little is known about their prevalence and patterns in morphologically normal breast tissues.

Research Overview

This study utilized single-cell whole-genome sequencing to analyze breast epithelial cells from 28 donors, including both carriers and non-carriers of BRCA1/BRCA2 mutations. Breast tissue samples were collected during surgeries and dissociated into individual cells, which were then sorted into basal and luminal cell populations using fluorescence-activated cell sorting.

The cells underwent genomic analysis with a high-resolution sequencing method called Direct Library Preparation+, capable of detecting CNAs ranging from 500 kilobases to megabases in scale. This approach allowed the identification of chromosomal alterations, including gains, losses, and complex rearrangements.

The sequencing effort produced data from over 49,000 single cells. Rigorous quality control measures filtered out low-quality genomes to ensure reliable analysis. Computational models detected allele-specific CNAs, revealing the independent emergence of mutations within the genome. Statistical analyses further characterized CNA distribution patterns between basal and luminal cell populations.

To contextualize these findings, the study compared CNA profiles from normal epithelial cells with datasets from breast cancer. This comparison highlighted potential links between early chromosomal alterations and advanced cancer stages.

Chromosome-specific analyses identified recurrent CNAs, such as gains in chromosomal arm 1q and losses in arms 16q, 10q, and 22q, which were predominantly observed in luminal cells. These recurrent CNAs were cross-referenced with known cancer-related genetic changes to evaluate their significance in cancer initiation.

Major Findings

The researchers found that somatic CNAs are present even in normal breast epithelial cells, with luminal cells having a higher prevalence of CNAs than basal cells. Furthermore, these alterations were more frequent in individuals with BRCA1 or BRCA2 mutations.

The major CNAs that were identified in these cells included the gain of chromosome 1q and losses of 16q, 10q, and 22q, which were alterations commonly seen in breast cancers.

Crucially, it was found that these CNAs occurred prior to the loss of heterozygosity at BRCA1 or BRCA2 loci, suggesting they may represent early genetic changes in the pathway to cancer. Rare cells with extreme aneuploidy, resembling cancer genomes, were also identified, including mutations affecting tumor protein p53 (TP53) and BRCA1/BRCA2. These aneuploid cells were more common in tissues from BRCA mutation carriers, indicating a genetic predisposition to their development.

The allele-specific analyses also showed that CNAs often arose independently, indicating convergent evolutionary processes. Co-occurring alterations, such as a gain in the 1q arm along with a loss in 16q or 10q, were observed in multiple samples, which reinforced the idea that these mutations are critical early steps in breast cancer development. The findings also revealed distinct CNA distributions between luminal and basal cells, with luminal cells more closely mirroring the genomic alterations of advanced cancers.

Interestingly, some CNAs, such as 7q loss—commonly found in normal luminal cells but rarely observed in breast tumors—suggest that certain genetic changes may inhibit tumor progression. These findings reinforce the idea that specific alterations are advantageous only under certain conditions, shaping the trajectory of cancer development.

Conclusions

Overall, the study revealed the role of somatic CNAs in initiating breast cancer, especially in BRCA1/BRCA2 mutation carriers. The findings suggested that early genetic alterations in luminal cells create a foundation for malignancy.

By identifying these patterns at the single-cell level, the study provided critical insights into tumor evolution and emphasized the importance of early detection and potential intervention to disrupt these pre-cancerous processes before the development of tumors.