Abstract
The method Arc-well was developed for high-throughput single-cell DNA sequencing of archival FFPE material.
Major Finding: The method Arc-well was developed for high-throughput single-cell DNA sequencing of archival FFPE material.
Concept: Arc-well was used to show the genomic and evolutionary features of DCIS progression and recurrence.
Impact: These results suggest that Arc-well can be used to analyze large clinical FFPE blocks across cancer types.
A common precursor to invasive breast cancer is ductal carcinoma in situ (DCIS), and about 20% of patients with DCIS will experience recurrence or progression to invasive disease. Despite this prevalence, the clonal diversity of DCIS as well as its genomic evolution to recurrent disease are not well understood, which is due, in part, to difficulties in the single-cell profiling of formalin-fixed, paraffin-embedded (FFPE) materials. To address these technical issues, Wang, Kumar, and colleagues developed Arc-well, a method that can be used for high-throughput single-cell DNA sequencing of cells obtained from FFPE tissues. Arc-well was validated in 40,330 single cells that spanned cell lines, frozen tissue, and 27 FFPE tumor samples, which had been stored for 3 to 31 years, and was then applied to 10 patients with matched DCIS and cancers that recurred in 2 to 16 years to investigate the copy-number landscape of primary DCIS with matched recurrent DCIS or invasive ductal carcinoma. Results showed that individual patients with DCIS and matched recurrent disease had a common genetic lineage between the primary DCIS and recurrence, with evidence of genome doubling, extensive aneuploidy, and genomic rearrangements already being present in DCIS lesions prior to recurrence or disease progression. Moreover, the recurrent common ancestor (RCA) was demonstrated to consistently have an increased number of copy-number alteration (CNA) events as compared to the primary common ancestor (PCA), and comparison of the RCA with the PCA led to the identification of recurrent patient-specific CNA events associated with progression and recurrence, including PIK3CA, MYC, CCNE2, ZNF217, and AURKA. Additionally, most DCIS cases exhibited an evolutionary bottleneck, in which a common ancestor of a persistent subclone was selected to undergo expansion and form recurrent cancers. In summary, this study describes the development of Arc-well as well as its use in determining the genomic and evolutionary features of DCIS progression and recurrence and suggests that this method can be broadly applied across cancer types to further the analysis of large collections of clinical FFPE tissue.
Note:Research Watch is written by Cancer Discovery editorial staff. Readers are encouraged to consult the original articles for full details. For more Research Watch, visit Cancer Discovery online at http://cancerdiscovery.aacrjournals.org/CDNews.
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