Molecular Characterization and Prospective Evaluation of Pathologic Response and Outcomes with Neoadjuvant Therapy in Metaplastic Triple-Negative Breast Cancer

Abstract

Purpose: Metaplastic breast cancer (MpBC) is a rare subtype of breast cancer that is commonly triple-negative and poorly responsive to neoadjuvant therapy in retrospective studies.

Experimental design: To better define clinical outcomes and correlates of response, we analyzed the rate of pathologic complete response (pCR) to neoadjuvant therapy, survival outcomes, and genomic and transcriptomic profiles of the pretreatment tumors in a prospective clinical trial (NCT02276443). A total of 211 patients with triple-negative breast cancer (TNBC), including 39 with MpBC, received doxorubicin-cyclophosphamide-based neoadjuvant therapy.

Results: Although not meeting the threshold for statistical significance, patients with MpBCs were less likely to experience a pCR (23% vs. 40%; P = 0.07), had shorter event-free survival (29.4 vs. 32.2 months, P = 0.15), metastasis-free survival (30.3 vs. 32.4 months, P = 0.22); and overall survival (32.6 vs. 34.3 months, P = 0.21). This heterogeneity is mirrored in the molecular profiling. Mutations in PI3KCA (23% vs. 9%, P = 0.07) and its pathway (41% vs. 18%, P = 0.02) were frequently observed and enriched in MpBCs. The gene expression profiles of each histologically defined subtype were distinguishable and characterized by distinctive gene signatures. Among nonmetaplastic (non-Mp) TNBCs, 10% possessed a metaplastic-like gene expression signature and had pCR rates and survival outcomes similar to MpBC.

Conclusions: Further investigations will determine if metaplastic-like tumors should be treated more similarly to MpBC in the clinic. The 23% pCR rate in this study suggests that patients with MpBC should be considered for NAT. To improve this rate, a pathway analysis predicted enrichment of histone deacetylase (HDAC) and RTK/MAPK pathways in MpBC, which may serve as new targetable vulnerabilities.

FIGURE 1.. ARTEMIS (NCT02276443) Trial Schema.

Patients with stage I-III TNBC underwent a pre-treatment core needle biopsy prior to initiating standard of care NAT with doxorubicin and cyclophosphamide (AC). Clinical response by breast imaging (ultrasound and/or MRI) was performed after AC to determine if patients should receive standard taxane-based NAT or be offered enrollment on a clinical trial as part of therapeutic escalation.

FIGURE 2.. Survival outcomes in patients with metaplastic breast cancer (MpBC) and non-metaplastic (non-Mp) TNBC receiving neoadjuvant therapy (NAT).

(A) Kaplan-Meier plot of event-free survival for patients with MpBC (yellow) and non-Mp TNBC (blue); (B) Kaplan-Meier plot of event-free survival for patients with MpBC experiencing a pathological complete response (pCR) (solid yellow), patients with MpBC with residual disease (dashed yellow), patients with non-Mp TNBC experiencing a pCR (solid blue), and patients with non-Mp TNBC with residual disease (dashed blue); (C) Kaplan-Meier plot of metastasis-free survival for patients with MpBC (yellow) and non-Mp TNBC (blue); (D) Kaplan-Meier plot of metastasis-free survival for patients with MpBC experiencing a pCR (solid yellow), patients with MpBC with residual disease (dashed yellow), patients with non-Mp TNBC experiencing a pCR (solid blue), and patients with non-Mp TNBC with residual disease (dashed blue); (E) Kaplan-Meier plot of overall survival for patients with MpBC (yellow) and non-Mp TNBC (blue); (F) Kaplan-Meier plot of overall survival for patients with MpBC experiencing a pCR (solid yellow), patients with MpBC with residual disease (dashed yellow), patients with non-Mp TNBC experiencing a pCR (solid blue), and patients with non-Mp TNBC with residual disease (dashed blue).

FIGURE 3.. Metaplastic breast cancers (MpBCs) and non-metaplastic (non-Mp) TNBCs have distinct gene expression profiles.

(A) Bar plot showing the 10 Hallmarks pathways predicted to be most significantly activated in MpBC or non-MP TNBC. The x-axis shows the −log₁₀ of the false discovery rate (FDR), where the values for the pathways associated with non-Mp TNBCs are inversed so that the most significant ones go to the left. The pathways most significantly associated with MpBCs go to the right and are shown in red. The dotted lines indicate a 5% FDR. (B) Stacked bar graph showing the distribution of TNBC subtypes (legend) within MpBCs (left) and non-Mp TNBCs (right).

FIGURE 4.. Histologic subtypes of metaplastic breast cancer (MpBC) have heterogeneous gene expression profiles.

(A) Stacked bar graphs showing the distribution of TNBC subtypes within each histologic subtype of MpBC. The distribution of TNBC subtypes across the columns were compared, and the statistical significance is indicated according to: * p < 0.05, ** p < 0.01, *** p < 0.001, and **** p < 0.0001. (B) The Hallmarks pathways that are predicted to be up- or down- regulated (false discovery rate [FDR] < 5%) in each of the histologic subtypes of MpBC are shown. (C) The Canonical pathways that are enriched in the spindle (red bars, towards the left) and squamous (blue bars, towards the right) at a 5% FDR cutoff are shown. (D) Heatmap showing the expression levels of the significant genes (rows) from the Hallmarks Estrogen Response pathways across the MpBCs (columns). The colors indicate the normalized expression values of the genes, where warm and cold colors indicate higher and lower expression, respectively. The first row of boxes under the dendrogram show the subtype of the metaplastic tumors, and the second row indicates the data set. Beeswarm plots (right panel) show the expression level of FGFR3 and MAPK13 across each of the histologic subtypes of MpBCs (x-axis). The statistical significance is denoted using the same notation as in Fig 4A.

FIGURE 5.. Metaplastic-like TNBCs are a subset of non-metaplastic (non-Mp) TNBCs with gene expression profiles resembling metaplastic breast cancers (MpBC) and are associated with poor long-term outcomes.

(A) The distribution of TNBC subtypes for non-Mp TNBC, metaplastic-like TNBC, and bona-fide MpBCs are shown in the columns. The statistical significance is annotated as in Fig 4A. (B) Kaplan-Meier plots of event-free, metastasis-free, and overall survival for patients with MpBC (yellow line), non-Mp TNBC (blue line), and metaplastic-like TNBC (gray line).