Archival single-cell genomics reveals persistent subclones during DCIS progression.

Area of Science:

• Genomics
• Cancer Biology
• Molecular Pathology

Background:

• Ductal carcinoma in situ (DCIS) is a precursor to invasive breast cancer, but its genomic progression to recurrence is poorly understood.
• Genomic profiling of formalin-fixed paraffin-embedded (FFPE) tissues, common in clinical settings, presents significant challenges.

Purpose of the Study:

• To develop and validate a high-throughput single-cell DNA sequencing method compatible with FFPE materials.
• To investigate the genomic landscape and evolutionary trajectory of DCIS and its progression to recurrent disease.

Main Methods:

• Development of Arc-well, a novel single-cell DNA sequencing technique for FFPE samples.
• Profiling of 40,330 single cells from cell lines, frozen tissue, and 27 FFPE tumor samples (breast, lung, prostate) stored for 3-31 years.
• Comparative genomic analysis of matched DCIS and recurrent cancer samples from 10 patients.

Main Results:

• Arc-well successfully profiled single cells from aged FFPE samples.
• Many primary DCIS samples exhibited whole-genome doubling and clonal diversification.
• Genomic lineages were shared between primary DCIS and persistent subclones in recurrent cancers.
• Evolutionary bottleneck observed in most DCIS cases, with specific chromosome aberrations linked to recurrence.

Conclusions:

• Arc-well is a viable method for single-cell genomic analysis of FFPE tissues.
• Early-stage DCIS possesses significant genomic heterogeneity and evolutionary potential.
• Understanding DCIS genomic evolution is crucial for predicting and preventing cancer recurrence.