Fig. 1

Clonal isolates from MMTV-PyMT breast cancer model exhibit distinct gene expression patterns. A Overview of cell isolation procedures and gene expression analyses. Tumors were harvested from mice and single cell suspensions were prepared. Cells were sorted based on CD44 and EpCAM expression. RNA was extracted for transcriptome profiling. Select samples were further analyzed via single-cell RNA-seq. B Heat map of DEGs from tissue-specific metastatic cell lines and primary tumor sample. Expression levels for 5509 unique genes are shown. Values were normalized by row, and hierarchical clustering was used to sort the transcripts. Columns were clustered based on the tissue origin and CD44 expression level for each sample. Eight distinct gene clusters were observed, with clusters of interest annotated A–E. C GO-term enrichment analysis of clusters A–E from (B). GO terms were used to identify ontologies and biological processes relevant to cancer metastasis. Terms were also analyzed for signatures specific to the tissue of origin. The heat maps indicate the relative enrichment of the pathways across each cluster (columns). D Bulk RNA analysis revealed distinct gene expression patterns relevant to organ tropism. A panel of markers associated with tissue-tropic breast cancer metastases was examined across all samples. Clusters were assigned based on the tissue origin and CD44 expression level for each sample