Single-cell RNA-seq uncovers unanticipated biological principles dictating poor outcomes in breast cancer

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, researchers from Massachusetts General Hospital and Harvard Medical School 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.

Intercellular heterogeneity in TNBC quantified by scRNA-seq


a Workflow showing collection and processing of fresh TNBC primary tumors for generating scRNA-seq data. b Heatmap of the 1189 cells that passed quality control, with columns representing cells and rows representing established gene expression markers for the cell types indicated on the left, clustered separately for each of the six TNBC cases. The upper bar denotes inferred high cycling (pink) and low cycling (gray) cells, as identified by quantifying the expression of a set of relevant genes. Bottom bar denotes cells collected in the presence/absence of CD45 + cell depletion. c Bar plot depicting the distribution of the 1112 cells assigned to specific cell types, by patient. d Bar plot depicting the high cycling/low cycling distribution of the 1112 cells, by patient. e Proliferation characteristics for two representative TNBC patients, depicted as either the inferred cycling status of single cells (left) or immunohistochemistry staining for Ki67 (right). Scale bars represent 50 µm. A cell is considered high cycling if it has high G1/S or G2/M scores, as identified by quantifying the expression of a set of relevant genes. The two ways of quantifying proliferation show good concordance

Karaayvaz M, Cristea S, Gillespie SM, Patel AP, Mylvaganam R, Luo CC, Specht MC, Bernstein BE, Michor F, Ellisen LW. (2018) Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. Nat Commun 9(1):3588. [article]

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