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Single-Cell Sequencing Reveals Breast, Ovarian Cancer-Related Mutational Processes

NEW YORK – New research is uncovering the genetic variants and mutational processes that contribute to genomic instability in human cells, including alterations and processes found in full-blown breast and ovarian cancer cases.

"Our study reveals three sources of cell-to-cell variation in cancer genomes, with implications for interpreting phenotypic diversity and evolutionary selection in cancers with genomic instability," co-senior and co-corresponding authors Samuel Aparicio, a researcher affiliated with the British Columbia Cancer Research Centre and the University of British Columbia, and Sohrab Shah, a scientist at Memorial Sloan Kettering Cancer Center, and their colleagues wrote in Nature on Wednesday.

For their study, the researchers performed single-cell genome sequencing of more than 13,800 individual mammary epithelial cells with or without mutations in TP53, BRCA1, or BRCA2 that result in homologous recombination deficiency (HRD). They then used single-cell structural variant and haplotype patterns to tease out the mutational processes at play in cells with or without HRD.

The team went on to relate those "foreground" mutational events to the patterns found in single-cell genome sequences for 22,057 individual triple-negative breast cancer (TNBC) or high-grade serous ovarian cancer (HGSC) cells; in new and previously published bulk tumor genome sequence data for tumor-normal samples from 139 TNBC patients and 170 HGSC patients; and in patient-derived xenograft samples generated from nearly two dozen of the TNBC or HGSC patients.

"Our findings show that cell-to-cell variation at the level of structural and copy number alteration is a pervasive 'foreground' feature of TNBC and HGSC cancers that is exhibited against distinct endogenous mutational processes of genomic instability," the authors wrote. "Because [copy number alterations] can influence the expression levels of hundreds of genes, each of the foreground mutational patterns provides extensive and distinct genomic diversity upon which selection may act."

Not surprisingly, the team noted that copy number alterations, whole-genome polyploidy, chromosomal missegregation, and loss of heterozygosity ticked up in the mammary epithelial cell models as TP53, BRCA1, or BRCA2 function declined, pointing to increased genomic instability.

Digging into these and other alterations, the researchers were able to get a closer look at the mutational processes that appear to influence the biological features and evolutionary trajectories of specific cells or clones in the HRD cell models and in individual breast or ovarian cancer cells.

In particular, the team saw a rise in typically rare high-level amplifications (HLAMPS) in the absence of TP53 and BRCA1/2 gene functions, including oncogene-impacting HLAMPS linked to "breakage-fusion-bridge cycle" mutational activity.

When it came to parallel haplotype-specific copy number (HSCN) alterations, meanwhile, the researchers again saw enhanced levels of the transcription-altering parallel maternal or paternal losses and gains at specific loci when TP53 activity was diminished — an effect that was amplified in the absence of BRCA1 or BRCA2.

The single-cell sequence profiles also pointed to diverse copy number segment length variants, also known as "serrate structural variations," from one cell to the next and over time as cell lines continued to grow. 

"[T]he induction of genomic instability in breast epithelium yielded progressively higher rates of genomic divergence between individual cells, measurable as rate distributions with scaled single-cell [whole-genome sequencing] and cell-specific [copy number alterations]," the authors reported, noting that results from the individual TNBC and HGSC cell sequences further refined the role of such foreground mutational events within clonal cancer populations.

The team documented particularly pronounced levels of HLAMPS in TNBC or HGSC clones containing so-called "fold-back inversion" mutations, for example, while the HLAMPS were less common in clonal populations or tumors with HRD.

Similarly, fold-back inversions appeared to coincide with the presence of serrate structural variants and enhanced genetic diversity, while parallel haplotype-specific changes corresponded to everything from mono-allelic expression within specific cancer clones to diversity within tumors.

"We observed each of the foreground mutational processes in all mutational processes, but [fold-back inversion]-type tumors showed a significant enrichment in all three foreground patterns," the authors noted, adding that the fold-back inversion-type tumors "may comprise a distinct phenotypic class in which foreground mutational patterns generated diversity that could underlie poor prognostic significance."