Single cell transcriptomes of brain metastases and micrometastases derived from triple negative human breast cancer cell line in mouse model.

In order to gainan understanding of potential mechanisms by which dystroglycan could effect DTC quiescence signaling in brain, we took an unbiased approach. We inoculated a series of mice with a tdTomato-positive, brain metastatic variant of T4-2 cells, and examined mice after 6-weeks in order to identify those with distinct brain metastases. Metastatic lesions were surgically dissected, digested and flow sorted to purify tdTomato+ cells (“Metastases”). In parallel, the remaining uninvolved brain was digested, and residual tdTomato+tumour cells were purified from this digest via flow sorting (“Micromets”). These two populations were indexed, and the libraries were prepared following standard 10X Genomics protocols. In total, 1,779 micromet-derived DTCs (including both mVenus-p27+ and p27- cells from uninvolved brain) were subjected to single cell RNAseq. 4,032 mVenus-p27- and 251 mVenus-p27+ (quiescent) cells from metastatic lesions were profiled.