Comparative Analysis of the Tumor Immune Microenvironment (TIME) and Primary and Metastatic Tissue in HR+/HER2- and Triple-Negative Breast Cancer (TNBC)

Background: Immune checkpoint inhibitor (ICI) based regimens are standard of care for patients with TNBC and clinical trials are investigating ICI in HR+/HER2- breast cancer, with encouraging results in a subset of patients. The tumor immune microenvironment (TIME) plays a critical role in ICI response and can differ significantly by metastatic site. Given the expanding integration of ICIs in HR+/HER2- breast cancer trials, we examined the TIME across sites of disease and subtypes to illustrate how these anatomical sites are molecularly different and may impact ICI benefit.

Methods: We used Tempus Lens (Tempus AI, Inc., Chicago, IL) to retrospectively analyze de-identified next-generation sequencing data from patients with HR+/HER2- breast cancer (n=6,818) and TNBC (n=2,715) in the Tempus Database. Metaplastic histology was excluded. Among HR+/HER2- breast cancer and TNBC, tumors from primary breast (PB, n=4451), liver (n=1117), bone (n=845), lymph node (LN, n=425), lung (n=388), and brain/CNS (n=234) metastatic sites were sequenced with Tempus xT DNA (648-gene panel) and xR RNA assays. TMB, MSI, PD-L1 (CPS, clone 22c3), and proportions of B, T (CD4+, CD8+), NK cells, and macrophages of immune cells via quanTIseq deconvolution were compared across metastatic sites in HR+/HER2- breast cancer and compared to TNBC. Chi-squared/Fisher’s exact or Kruskal-Wallis tests were used to assess statistical significance.

Results: In this study, the median age at diagnosis in the HR+/HER2- and TNBC cohort was 58 and 57, respectively and both cohorts were diverse: White (50%/44%), African American (8%/14%), Hispanic (6.7%/7%), Asian (3.1%/2.3%), other race (5.5%/5.5%) and unknown (33%/34%). Overall, 67% of patients were stage IV. Among patients with HR+/HER2- breast cancer, brain/CNS (14%) was most commonly TMB high (≥10 mut/mB) followed by bone (9.4%) and liver (8.9%) (p<0.001). PD-L1 >=10% (positive) proportions were highest in PB (4.1%), lung (3.6%) and LN (4.9%) (p<0.001). LN had the highest proportions of B cells and T cells (CD4+ and CD8+) and the lowest proportion of macrophages (M1 and M2) and NK cells (p<0.001). Besides LN, CD8+ T cells were in higher proportions in lung and PB compared to liver, bone, and brain/CNS metastases (p<0.001). In TNBC, PB, lung, and LN metastases had the highest proportions of PD-L1 positive status as well as CD8+ T cell proportions compared to liver, bone, and brain/CNS (both, p<0.001). Compared to TNBC, HR+/HER2- breast cancer had different proportions for all immune cell populations in PB and all non-breast sites (exception NK cells, all else p<0.05). Notably, HR+/HER2- breast cancer had lower proportions of CD8+ T cells and M1 macrophages and higher proportions of M2 macrophages across PB and all non-breast sites compared to TNBC (all, p<0.001). Liver metastases had the highest proportions of M1 macrophages, NK cells, and neutrophils compared to all other sites in HR+/HER2- breast cancer, with a similar pattern seen in TNBC (all, p<0.001).

Conclusions: In HR+/HER2- and TNBC, the TIME significantly differed according to site of disease. Although more commonly TMB high, liver, bone, and brain/CNS metastases were composed of lower proportions of CD8+ T cells in HR+/HER2- breast cancer. HR+/HER2- breast cancer was less immunogenic across all disease sites compared to TNBC. However, patients with breast, lung, and LN metastases had the highest proportions of CD8+ T cells in both subtypes, indicating a subset of patients with HR+/HER2- breast cancer that could be enriched for ICI response. These analyses may support TIME biomarkers for patient selection in ICI focused clinical trials for patients with breast cancer.