Barcoding Oncogene-Transformed Cells Reveals Clonal Tumor Landscape

The timing and order of genomic and biologic changes that lead to human tumor formation remain poorly understood. To investigate early events in human breast cancer development, Nguyen, Pellacani, and colleagues transplanted DNA-barcoded normal human mammary cells transduced with lentiviruses encoding the oncogenes TP53^R273C, PIK3CA^H1047R, and KRAS^G12D, alone or in combination, into immunodeficient mice. Oncogene-transformed basal cells (BC) and luminal progenitors (LP) from the majority of donors tested formed invasive ductal carcinomas within 8 weeks, and most of these tumors could produce new tumors in secondary mice. In contrast, nonclonogenic luminal cells and stromal cells did not form tumors. Tumors produced from cells exposed to all three oncogenic viruses coexpressed all three oncogenes, but only KRAS^G12D was required for tumor formation. RNA-sequencing of cells from 3 BC- and 3 LP-derived tumors revealed all 6 tumor populations to be more similar to each other than to the parental cells, with a signature resembling normal-like human breast cancers. However, BC and LP tumors did cluster into distinct groups, suggesting that the cell of origin has some influence on gene expression. Both primary and secondary tumors were highly polyclonal, regardless of the cell of origin, with more than 75% of the clones present in secondary tumors not having been detectable in the corresponding primary tumors. This finding suggests that the genesis of a permanently growing tumor may be a stepwise process even after malignant features are acquired, or that different cell types may generate self-limited and permanently growing malignant populations. Increases in the numbers and sizes of KRAS^G12D-transduced barcoded clones were already detected at two weeks, highlighting early changes in clonal evolution. These findings provide insights into the early events underlying human mammary tumor initiation and support further use of this approach to study the acquisition of resistance to treatment.

Nguyen LV, Pellacani D, Lefort S, Kannan N, Osado T, Makarem M, et al. Barcoding reveals complex clonal dynamics of de novo transformed human mammary cells. Nature 2015 Dec 2 [Epub ahead of print].