Comparison of tumor immune microenvironments (TIMEs) between primary and metastatic sites (Mets) in triple-negative breast cancer (TNBC).
Authors: Yuan Yuan , Kang Irene , Bitar Jin Sun , Davis Andrew A. , Hilton Christie , Huang Minxuan , Thompson Michael A. , Mercer Jacob , Shiao Stephen Lawrence , Vail Eric 
Published: June 2024

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Background: The TIME is critical in determining response to immune checkpoint inhibitors (ICIs), but TIME differences across primary and mets in TNBC are not well understood. Since ICIs are standard of care for patients with TNBC, we studied the TIMEs of primary TNBC and mets to investigate how immune composition may affect ICI efficacy. Secondary analysis stratified cohorts by race and disease sites to compare TIMEs in Black or African American (B/AA) with White patients, since TNBC has a high prevalence of B/AA women who are underrepresented in studies and have a worse prognosis. Methods: We retrospectively analyzed de-identified next-generation sequencing data from TNBC patients (n=1,044) in the Tempus Database. Tumors from primary breast (PB, n=553), liver (n=153), lymph node (LN, n=174), lung (n=111), and bone (n=53) sites were sequenced with the Tempus xT DNA (648-gene panel) and xR RNA assays. Histologies included invasive ductal carcinoma (82%), lobular carcinoma (2.2%), mixed ductal and lobular carcinoma (1.7%), and other (14%). Demographics, TMB, MSI, PD-L1, and proportions of B, T (CD4+, CD8+), NK cells, and macrophages were compared across sites. LN were used as a positive control. Chi-squared/Fisher’s exact or Kruskal-Wallis tests were used to assess statistical significance (two-sided, evaluated at the 0.05 alpha level). Results: The cohort (median age=57 years, IQR 46-66) comprised a diverse population (65% White, 23% B/AA, 2.8% Asian, and 9.3% other). Liver exhibited a lower percentage of B cells and higher percentage of macrophages compared to PB (p<0.0001 for both), lung (p<0.0001 for both), and bone (B cells p<0.0001, macrophages p<0.05). Liver also exhibited lower percentages of CD8+ T cells compared to PB (p<0.05) and CD4+ and NK cells compared to lung (CD4+ cells p<0.01, NK cells p<0.0001). Bone had lower percentages of CD8+ cells compared to PB (p<0.0001), lung (p<0.001), and liver (p<0.01). Compared to lung, bone had a lower percentage of CD4+ cells (p<0.0001) and higher percentage of macrophages (p<0.01). PD-L1 positivity, TMB, and MSI exhibited no differences across sites. Secondary analysis compared the TIME between B/AA and White cohorts in PB (B/AA n=85 vs White n=204: %B cells, 15 vs 11, p=0.017; %CD8 cells, 4.9 vs 7.3, p=0.025), liver (B/AA n=15 vs White n=48: %B cells, 8 vs 4, p=0.2; %CD4, 23 vs 14, p=0.2; %CD8, 7.2 vs 4.6, p=0.07), and lung (B/AA n=9 vs White n=33: %B cells, 22 vs 11, p=0.021; %CD8, 7.9 vs 5.2, p=0.5). Conclusions: Compared to PB and lung, liver and bone had immune cell infiltrates indicating a less immunogenic TIME in the overall TNBC population. Although limited by sample size, this is one of the first studies to assess the TIME across race and sites of disease. These findings are hypothesis generating and provide further rationale to better understand how the TIME across disease sites and race may alter the efficacy of ICIs in TNBC.