A Multigene Assay Determines Risk of Recurrence in Patients with Triple-Negative Breast Cancer

Abstract

Approximately 40% of patients with stage I-III triple-negative breast cancer (TNBC) recur after standard treatment, whereas the remaining 60% experience long-term disease-free survival (DFS). There are currently no clinical tests to assess the risk of recurrence in TNBC patients. We previously determined that TNBC patients with MHC class II (MHCII) pathway expression in their tumors experienced significantly longer DFS. To translate this discovery into a clinical test, we developed an MHCII Immune Activation assay, which measures expression of 36 genes using NanoString technology. Preanalytical testing confirmed that the assay is accurate and reproducible in formalin-fixed paraffin-embedded (FFPE) tumor specimens. The assay measurements were concordant with RNA-seq, MHCII protein expression, and tumor-infiltrating lymphocyte counts. In a training set of 44 primary TNBC tumors, the MHCII Immune Activation Score was significantly associated with longer DFS (HR ¼ 0.17; P ¼ 0.015). In an independent validation cohort of 56 primary FFPE TNBC tumors, the Immune Activation Score was significantly associated with longer DFS (HR ¼ 0.19; P ¼ 0.011) independent of clinical stage. An Immune Activation Score threshold for identifying patients with very low risk of relapse in the training set provided 100% specificity in the validation cohort. The assay format enables adoption as a standardized clinical prognostic test for identifying TNBC patients with a low risk of recurrence. Correlative data support future studies to determine if the assay can identify patients in whom chemotherapy can be safely deescalated and patients likely to respond to immunotherapy.Significance: The MHCII Immune Activation assay identifies TNBC patients with a low risk of recurrence, addressing a critical need for prognostic biomarker tests that enable precision medicine for TNBC patients.

Spatially-resolved quantification of proteins in triple negative breast cancers reveals differences in the immune microenvironment associated with prognosis

“…3E). These findings validate the DSP detection of HLA-DR expression in epithelial tumor ROIs www.nature.com/scientificreports www.nature.com/scientificreports/ and confirm that a subset of patient-derived breast cancer epithelial cells can express MHCII proteins such as HLA-DR, which is consistent with our previous observations 2, 3 , as well as with those of other investigators 4,[17][18][19][20][21] .…”

“…We have previously demonstrated that elevated expression of HLA-DRB1 mRNA in patient-derived TNBC tumors is significantly associated with long-term disease-free survival (DFS) 3 , though it has been unclear whether stromal or epithelial expression is more predictive of patient outcomes. Using DSP, we found that HLA-DR protein expression in both epithelial and stromal ROIs was significantly higher in patients with long-term DFS when compared to patients that relapsed (P < 0.001; Fig.…”

“…Using RNA-seq of patient-derived TNBCs, we have shown that elevated expression of genes in the major histocompatibility complex Class II antigen presentation pathway (MHCII) is a favorable prognostic factor that is associated with long-term DFS 2 . This genomics discovery led us to develop and validate a clinical prognostic assay that measures expression of MHCII and tumor-infiltrating lymphocyte (TIL) genes in formalin-fixed, paraffin embedded (FFPE) clinical samples using NanoString technology 3 . We recently confirmed the prognostic significance of this MHCII Immune Activation assay in two independent cohorts of patients with TNBC 3 .…”

“…This genomics discovery led us to develop and validate a clinical prognostic assay that measures expression of MHCII and tumor-infiltrating lymphocyte (TIL) genes in formalin-fixed, paraffin embedded (FFPE) clinical samples using NanoString technology 3 . We recently confirmed the prognostic significance of this MHCII Immune Activation assay in two independent cohorts of patients with TNBC 3 . Mechanistic studies support our clinical findings, as ectopic expression of MHCII has been shown to induce Th1-mediated anti-tumor immunity in mouse models of human cancer [4][5][6] .…”

The Use of a Humanized NSG-β2m−/− Model for Investigation of Immune and Anti-tumor Effects Mediated by the Bifunctional Immunotherapeutic Bintrafusp Alfa

“…Immune activation scoring was calculated as previously described (20). Briefly, the immune activation score was determined by taking the geometric mean of normalized counts for each of the following genes inserted into the following equation:…”