Background-Intra-tumor heterogeneity implies that sub-populations of cancer cells that differ in genetic, phenotypic, or behavioral characteristics coexist in a single tumor 1,2. Tumor heterogeneity drives progression, metastasis and treatment resistance, but its relationship with tumor infiltrating immune cells is a matter of debate where some argue that tumors with high heterogeneity may generate neo-antigens that attract immune cells, and the others claim that immune cells provide selection pressure that shapes tumor heterogeneity 3,4. Here we sought to study the association between tumor heterogeneity and immune cells in a real-world cohort utilizing The Cancer Genome Atlas (TCGA). Methods-Mutant Allele Tumor Heterogeneity (MATH) was calculated to estimate intra-tumoral heterogeneity, and immune cell compositions were estimated by CIBERSORT. Survival analyses were demonstrated by Kaplan Meir curves. Results-Tumors with high heterogeneity (High MATH) associated with worse overall survival (p=0.049) as well as ER+ (p=0.011) and non-triple negative tumors (p=0.01). High MATH tumors associated with less infiltration of anti-tumor CD8 (p<0.013) and CD4 T cells (p<0.00024), more tumor promoting regulatory T cells (p<4e-04), lower expression of T cell exhaustion markers; PDL-1 (p=0.0031), IDO2 (p=0.34), ADORA2A (p=0.018), VISTA (p=0.00013), and CCR4 (p<0.00001), lower expression of cytolytic enzymes granzyme-A (p=0.0056) and perforin 1 (p=0.053) as well as low cytolytic activity score (p=0.0028). Conclusions-High heterogeneity tumors are associated with less immune cell infiltration, less activation of the immune response, and worse survival in breast cancer. Our results support the notion that tumor heterogeneity is shaped by selection pressure of tumor infiltrating immune cells.

Breast cancer (BC) patients experience increased stress with elevated cortisol levels, increasing risk of cancer recurrence. Cortisol binds to a cytoplasmic receptor, glucocorticoid receptor (GR) encoded by GR gene (NR3C1). We hypothesized that not only cancer cells, but even immune cells in the tumor microenvironment (TME) may contribute to GR expression in bulk tumor and influence prognosis. To test this, mRNA expression data was accessed from METABRIC and TCGA. “High” and “low” expression was based on highest and lowest quartiles of NR3C1 gene expression, respectively. Single-cell sequencing data were obtained from GSE75688 and GSE114725 cohorts. Computer algorithms CIBERSORT, Gene Set Enrichment Analysis and TIMER were used. GR-high BC has better median disease-free and disease-specific survival. Single cell sequencing data showed higher GR expression on immune cells compared to cancer and stromal cells. Positive correlation between GR-high BC and CD8+ T-cells was noted. In GR-high tumors, higher cytolytic activity (CYT) with decreased T-regulatory and T-follicular helper cells was observed. High GR expression was associated with lower proliferation index Ki67, enriched in IL-2_STAT5, apoptosis, KRAS, TGF-β signaling, and epithelial-to-mesenchymal transition. Immune cells significantly contribute to GR expression of bulk BC. GR-high BC has a favorable TME with higher CYT with favorable outcomes.

DNA abnormalities are used in inclusion criteria of clinical trials for treatments with specific targeted molecules. MYC is one of the most powerful oncogenes and is known to be associated with triple-negative breast cancer (TNBC). Its DNA amplification is often part of the targeted DNA-sequencing panels under the assumption of reflecting upregulated signaling. However, it remains unclear if MYC DNA amplification is a surrogate of its upregulated signaling. Thus, we investigated the difference between MYC DNA amplification and mRNA high expression in TNBCs utilizing publicly available cohorts. MYC DNA amplified tumors were found to have various mRNA expression levels, suggesting that MYC DNA amplification does not always result in elevated MYC mRNA expression. Compared to other subtypes, both MYC DNA amplification and mRNA high expression were more frequent in the TNBCs. MYC mRNA high expression, but not DNA amplification, was significantly associated with worse overall survival in the TNBCs. The TNBCs with MYC mRNA high expression enriched MYC target genes, cell cycle related genes, and WNT/β-catenin gene sets, whereas none of them were enriched in MYC DNA amplified TNBCs. In conclusion, MYC mRNA high expression, but not DNA amplification, reflects not only its upregulated signaling pathway, but also clinical significance in TNBCs.

There is a limited clinical activity of palbociclib combinations after progression with everolimus combination therapy. Further studies are necessary to confirm these findings.