Comprehensive Profiling of Poor-Risk Paired Primary and Recurrent Triple-Negative Breast Cancers Reveals Immune Phenotype Shifts

Abstract

Purpose: Emerging data suggest immune checkpoint inhibitors have reduced efficacy in heavily pretreated triple-negative breast cancers (TNBC), but underlying mechanisms are poorly understood. To better understand the phenotypic evolution of TNBCs, we studied the genomic and transcriptomic profiles of paired tumors from patients with TNBC.Experimental Design: We collected paired primary and metastatic TNBC specimens from 43 patients and performed targeted exome sequencing and whole-transcriptome sequencing. From these efforts, we ascertained somatic mutation profiles, tumor mutational burden (TMB), TNBC molecular subtypes, and immune-related gene expression patterns. Stromal tumor-infiltrating lymphocytes (stromal TIL), recurrence-free survival, and overall survival were also analyzed.Results: We observed a typical TNBC mutational landscape with minimal shifts in copy number or TMB over time. However, there were notable TNBC molecular subtype shifts, including increases in the Lehmann/Pietenpol-defined basal-like 1 (BL1, 11.4%-22.6%) and mesenchymal (M, 11.4%-22.6%) phenotypes, and a decrease in the immunomodulatory phenotype (IM, 31.4%-3.2%). The Bursteindefined basal-like immune-activated phenotype was also decreased (BLIA, 42.2%-17.2%). Among downregulated genes from metastases, we saw enrichment of immune-related Kyoto Encyclopedia of Genes and Genomes pathways and gene ontology (GO) terms, and decreased expression of immunomodulatory gene signatures (P < 0.03) and percent stromal TILs (P ¼ 0.03). There was no clear association between stromal TILs and survival.Conclusions: We observed few mutational shifts, but largely consistent transcriptomic shifts in longitudinally paired TNBCs. Transcriptomic and IHC analyses revealed significantly reduced immune-activating gene expression signatures and TILs in recurrent TNBCs. These data may explain the observed lack of efficacy of immunotherapeutic agents in heavily pretreated TNBCs. Further studies are ongoing to better understand these initial observations.See related commentary by Savas and Loi, p. 526

Neoadjuvant Treatment for Triple Negative Breast Cancer: Recent Progresses and Challenges

“…Mean sTILs was 23% and increased sTILs were significantly associated with improved survival: HR for a 10% increase in sTILs was 0.83 (95% CI, 0.78-0.87) for distant DFS and 0.83 (95% CI, 0.79-0.88) for OS. sTILs significantly decreased in metastatic TNBCs as compared with matched primary [100,101]. Higher TIL PD1 expression was associated with better prognosis in early stage TNBCs [102].…”

Comprehensive Genomic Profile of Heterogeneous Long Follow-Up Triple-Negative Breast Cancer and Its Clinical Characteristics Shows DNA Repair Deficiency Has Better Prognostic

“…An active immune response involving high levels of TILs has been associated with a better prognosis and a better response to treatment [86]. Here we identified samples with high and low TILs from the pathology report and identified six genes associated with immunological responses according to Hutchinson [87]: STAT4 and TLR6 with Th1 response, CIITA, TAGAP, PDCD1, and TLR6 with an interferon-γ response and CD247 with a T cell-inflamed response. Despite the observed trend, neither TILs nor the alteration of immunological genes was associated with the clinical outcome.…”

Comparison of PD-L1 protein expression between primary tumors and metastatic lesions in triple negative breast cancers

“…Multiple lines of evidence suggest that certain metastatic sites are more immune attenuated than others 11 12 and primary breast cancers on average have greater immune cell infiltration and higher expression of immune activation markers than metastatic lesions. [3][4][5][6] Preclinical data also suggests that metastatic lesions have a different proportion of monocytes and macrophages that mediate prometastatic functions, including altering antigen presentation, dendritic cell maturation and cytokine signaling. 13 The clinical implications of the substantial heterogeneity in PD-L1 expression that we observed across metastatic sites are not yet understood.…”

“…1 2 Several recent studies that compared small cohorts of metastatic and primary lesions, as well as paired metastatic and primary breast tumors from the same patient, suggested substantial heterogeneity in tumor infiltrating lymphocyte count, immune gene expression and PD-L1 protein expression across different metastatic sites and between primary breast cancers and metastases. [3][4][5][6] Understanding the frequency of PD-L1 positivity rates across different tissue sites can indicate differences in the immune microenvironment and may also guide biopsy site selection. Using the Foundation Medicine PD-L1 immunohistochemistry (IHC) database, we present PD-L1 positivity data by metastatic tissue site of origin.…”