MYC Deregulation and PTEN Loss Model Tumor and Stromal Heterogeneity of Aggressive Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) patients have a poor prognosis and few treatment options. Mouse models of TNBC are important for development of new therapies, however, few mouse models represent the complexity of TNBC. Here, we develop a female TNBC murine model by mimicking two common TNBC mutations with high co-occurrence: amplification of the oncogene MYC and deletion of the tumor suppressor PTEN. This Myc;Ptenfl model develops heterogeneous triple-negative mammary tumors that display histological and molecular features commonly found in human TNBC. Our research involves deep molecular and spatial analyses on Myc;Ptenfl tumors including bulk and single-cell RNA-sequencing, and multiplex tissue-imaging. Through comparison with human TNBC, we demonstrate that this genetic mouse model develops mammary tumors with differential survival and therapeutic responses that closely resemble the inter- and intra-tumoral and microenvironmental heterogeneity of human TNBC, providing a pre-clinical tool for assessing the spectrum of patient TNBC biology and drug response. - RNA was extracted from Myc;Ptenfl tumor tissue (n = 13) or normal mammary gland as control (n=3) using Trizol (Invitrogen). Normalized count data was generated using the standard DESeq2 (v1.36.0) workflow with Variance Stabilizing Transformation. - Single-cell suspensions of 11 Myc;Ptenfl tumors were obtained by enzymatic digestion. Library prepared with the Chromium Single Cell 3’ V3 (10X Genomics) following the manufacturer’s protocol with a targeted recovery of 20,000 cells per library. Libraries were sequenced on an Illumina NovaSeq. BCL files were converted to fastq format with bcl2fastq2 (Illumina), and then aligned to mouse genome build mm10-2020-A (10X Genomics) using Cellranger (10X Genomics, version 6.0.2).