Early-onset spontaneous murine mammary tumors show increased lymphocyte representation and reduced MHC antigen presentation

Simple Summary Not all breast tumors behave the same way, and part of the reason may be inherited rather than caused by the tumor itself. Using mice that carry the same cancer-causing HER2/neu gene but differ in genetic background, we found that introduction of the PWK/PhJ genetic background was associated with tumors that appeared about a month earlier. These early tumors contained a larger proportion of immune cells, including T and B cells, but the T-cell population showed reduced expression of genes associated with cytotoxic activity. At the same time, the tumors had lower levels of proteins and genes that let the immune system recognize tumor cells, alongside higher levels of structural proteins that can make tissue stiffer and easier for cancer to invade. These findings suggest that genetic background shapes not only how quickly breast tumors arise but also how well the immune system can recognize them, a distinction that may matter for future immune-based treatments. Background/Objectives: Genetic background modifies cancer risk and phenotype in humans, but its influence on the tumor immune microenvironment and antigen-presentation machinery in ErbB2 (HER2/neu)-driven breast cancer is not well defined. We used a genetically diverse mouse cross to test whether the wild-derived PWK/PhJ background alters immune representation and antigen presentation in a NeuT model of HER2/neu-positive breast cancer. Methods: Previously, quantitative trait locus (QTL) mapping using Diversity Outbred mice and r/qtl2 identified candidate loci driving tumor onset and growth. The wild-derived PWK/PhJ genetic background was predicted to harbor genes that regulated early onset of HER2/neu-driven tumors. BALB NeuT and (BALBxPWK) F1 NeuT female mice were monitored twice weekly for spontaneous mammary tumor onset and growth. Tumor immune composition was profiled by single-cell RNA sequencing. Protein abundance was measured by data-independent acquisition proteomics in formalin-fixed, paraffin-embedded tumor tissue (n=5 per genotype). Single-nucleus multiome (RNA + ATAC), bulk RNA-seq, and H3K27ac datasets from the same strain comparison were analyzed for focused MHC II cross-layer analyses. Results: As predicted, (BALBxPWK) F1 NeuT mice developed tumors significantly earlier than the parental BALB NeuT mice (10 vs. 15 weeks of age; p < 0.0001). In the scRNA-seq dataset, F1 tumors showed greater representation of Cd3e-expressing T cells and a Cd79a-expressing B-cell population not detected in BALB NeuT tumors, and a distinct neutrophil cluster; F1 T cells also showed lower expression of the cytotoxicity-associated genes Tox, Ltk, Nkg7, and Gzmb relative to BALB NeuT tumor-infiltrating T cells. Proteomics identified 46 differentially abundant proteins (25 higher, 21 lower in F1), with coordinate down-regulation of Stat1, Tapbp, Parp9, and Dtx3l alongside MHC class I and II proteins and up-regulation of extracellular-matrix and elastic-fiber proteins. Focused cross-layer analysis showed lower whole-tumor expression of a Stat1/MHC II-associated gene set together with reduced epithelial chromatin accessibility at selected regions near Cd74 and H2-Aa. Conclusions: The PWK/PhJ genetic background is associated with earlier HER2-driven tumor onset, greater lymphocyte proportion, and reduced activity of a STAT1-associated antigen-presentation program despite similar post-onset tumor growth kinetics.