Deciphering Somatic Evolution and Metastasis Through Single-Cell Copy Number Profiling

Junke Wang, MS (Advisor: Nicholas E. Navin, PhD)                                               

          This dissertation deciphers somatic evolution and metastatic dissemination through single-cell copy-number profiling by integrating experimental and computational advances. First, to define the baseline of copy number mosaicism in healthy tissues, I profiled 83,206 epithelial cells from normal breast tissues of 49 healthy women using single-cell DNA sequencing and analyzed matched single-cell DNA&ATAC co-assays from 19 women, showing that all women harbor rare aneuploid epithelial cells (median 3.19%) that increase with age and most aneuploid cells undergo clonal expansion (median 82.22%). The recurrent CNA events, including 1q gain and 10q/16q/22q losses, overlap with alterations seen in invasive breast cancers while belong mainly to luminal lineages in histologically normal ductal and lobular structures. Second, I developed CopyKit, a scalable end-to-end framework for single-cell DNA copy number analysis, with a method to infer absolute ploidy at single-cell resolution. Applying these methods to 11,845 cells from primary tumors and matched metastases resolved clonal substructure, reconstructed metastatic lineages, identified primary tumor subclones that seeded distant metastasis, and revealed both spatial intermixing and regional segregation of subclones in liver metastases. Together, these results show that high-throughput single-cell copy number profiling, coupled with scalable and robust computational modeling, can resolve phylogenetic evolution from normal tissue mosaicism to malignant evolution and provide a quantitative framework for studying tumor initiation, progression and metastasis.

Advisory Committee:

• Nicholas Navin, PhD
• Ken Chen, PhD
• E. Scott Kopetz, MD, PhD
• Ruoyan Li, PhD
• Gillermina Lozano, PhD