Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq

Mihriban Karaayvaz,Anoop P Patel,Simona Cristea,Franziska Michor,Ravindra Mylvaganam,Christina C Luo,Michelle C Specht,Leif W Ellisen,Shawn M Gillespie,Bradley E Bernstein

doi:10.1038/s41467-018-06052-0

Abstract

Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by extensive intratumoral heterogeneity. To investigate the underlying biology, we conducted single-cell RNA-sequencing (scRNA-seq) of >1500 cells from six primary TNBC. Here, we show that intercellular heterogeneity of gene expression programs within each tumor is variable and largely correlates with clonality of inferred genomic copy number changes, suggesting that genotype drives the gene expression phenotype of individual subpopulations. Clustering of gene expression profiles identified distinct subgroups of malignant cells shared by multiple tumors, including a single subpopulation associated with multiple signatures of treatment resistance and metastasis, and characterized functionally by activation of glycosphingolipid metabolism and associated innate immunity pathways. A novel signature defining this subpopulation predicts long-term outcomes for TNBC patients in a large cohort. Collectively, this analysis reveals the functional heterogeneity and its association with genomic evolution in TNBC, and uncovers unanticipated biological principles dictating poor outcomes in this disease.

Highlights

Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by extensive intratumoral heterogeneity
Prior studies have documented that TNBCs exhibit ongoing mutational diversification, giving rise to genomic heterogeneity that can be inferred through deep sequencing and confers worse clinical outcomes[3,7]
A failure to achieve pathologic complete response following pre-operative chemotherapy is associated with high relapse rates, consistent with evidence we provide that a minor refractory subpopulation of cells determines patient outcomes

Summary

Introduction

Triple-negative breast cancer (TNBC) is an aggressive subtype characterized by extensive intratumoral heterogeneity. A novel signature defining this subpopulation predicts long-term outcomes for TNBC patients in a large cohort This analysis reveals the functional heterogeneity and its association with genomic evolution in TNBC, and uncovers unanticipated biological principles dictating poor outcomes in this disease. A small number of studies have characterized the genomic diversity of TNBC at the single-cell level, revealing a pattern that reflects punctuated evolution of copy number variations during TNBC progression, followed by expansion of a dominant subclone[7,12] While these findings imply that such subclones harbor properties driving their selective advantage, DNA-based analyses alone have been unable to elucidate the cell states and fates that underlie this process. Through detailed computational analyses of individual tumor cells and the subpopulations they encompass, we reveal the phenotypes and biology underlying the genetic evolution and clinical behavior of TNBC

Methods

Results

Conclusion