Author ORCID Identifier

Date of Graduation


Document Type

Dissertation (PhD)

Program Affiliation

Genes and Development

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Nicholas Navin

Committee Member

Funda Meric-Bernstam

Committee Member

Debasish Tripathy

Committee Member

Russell Broaddus

Committee Member

Ken Chen


Triple-negative breast cancer (TNBC) is an aggressive subtype that displays extensive intratumor heterogeneity and frequently (46%) develops resistance to neoadjuvant chemotherapy (NAC). Currently, the genomic basis of chemoresistance remains poorly understood. An important question is whether resistance to chemotherapy is driven by the selection of rare pre-existing subclones with genomic mutations and transcriptional programs that confer resistance to chemotherapy (adaptive resistance) or by the spontaneous induction of new mutations and expression changes that confer a resistant phenotype (acquired resistance). To investigate this question we applied single cell DNA and RNA sequencing methods and deep-exome sequencing to longitudinal time-point samples collected from a cohort of 20 TNBC patients. Deep-exome sequencing of the cohort at three time points revealed patterns of both clonal extinction and clonal persistence, with a subset of patients displaying adaptive selection of pre-existing rare mutations. Single-cell copy number profiling of 900 cells from 8 patients also identified an adaptive resistance model, wherein minor subclones from the pre-treatment tumors were selected and expanded in response to NAC. In contrast, single cell RNA sequencing of 6,862 cells from 8 patients identified subclones with chemoresistant phenotypes that were reprogrammed in response to NAC. These data suggest that chemoresistance at the genotypic level evolves through the selection of pre-existing point mutations and copy number changes, while chemoresistance at the phenotypic level evolves through the reprogramming of expression changes in signaling pathways associated with chemoresistance. These characterizations of adaptive and acquired resistance shed light on the evolutionary trajectory of chemoresistance in TNBC patients.


genomics, breast cancer, single cell sequencing, chemoresistance, heterogeneity