Estrogen receptor variants in ER-positive basal-type breast cancers responding to therapy like ER-negative breast cancers

Abstract

Immunohistochemically ER-positive HER2-negative (ER+HER2-) breast cancers are classified clinically as Luminal-type. We showed previously that molecular subtyping using the 80-gene signature (80-GS) reclassified a subset of ER+HER2- tumors to molecular Basal-type. We report here that molecular reclassification is associated with expression of dominant-negative ER variants and evaluate response to neoadjuvant therapy and outcome in the prospective neoadjuvant NBRST study (NCT01479101). The 80-GS reclassified 91 of 694 (13.1%) immunohistochemically Luminal-type tumors to molecular Basal-type. Importantly, all 91 discordant tumors were classified as high-risk, whereas only 66.9% of ER+/Luminal-type tumors were classified at high-risk for disease recurrence (i.e., Luminal B) (P < 0.001). ER variant mRNA (ER∆3, ER∆7, and ERα-36) analysis performed on 84 ER+/Basal tumors and 48 ER+/Luminal B control tumors revealed that total ER mRNA was significantly lower in ER+/Basal tumors. The relative expression of ER∆7/total ER was significantly higher in ER+/Basal tumors compared to ER+/Luminal B tumors (P < 0.001). ER+/Basal patients had similar pathological complete response (pCR) rates following neoadjuvant chemotherapy as ER-/Basal patients (34.3 vs. 37.6%), and much higher than ER+/Luminal A or B patients (2.3 and 5.8%, respectively). Furthermore, 3-year distant metastasis-free interval (DMFI) for ER+/Basal patients was 65.8%, significantly lower than 96.3 and 88.9% for ER+/Luminal A and B patients, respectively, (log-rank P < 0.001). Significantly lower total ER mRNA and increased relative ER∆7 dominant-negative variant expression provides a rationale why ER+/Basal breast cancers are molecularly ER-negative. Identification of this substantial subset of patients is clinically relevant because of the higher pCR rate to neoadjuvant chemotherapy and correlation with clinical outcome.

Keywords: Breast cancer; Cancer genomics.

Fig. 1

Normalized total ERalpha mRNA expression. Box plots showing normalized total ERalpha mRNA expression for ER+/Basal tumors (N = 81, blue box), ER+/Luminal B tumors (N = 48, orange box) and normal breast tissues (N = 8, gray box). Central line in boxes represent median value, boundaries of boxes represent the interquartile range and ends of whiskers represent the minimum and maximum values. P-values are obtained using the Mann–Whitney test

Fig. 2

Correlation between percentage ER staining by immunohistochemistry and normalized total ERalpha mRNA expression. Distribution plot showing the correlation between percentage ER staining by immunohistochemistry and normalized total ERalpha mRNA expression for ER+/Basal tumors (N = 81, blue dots) and ER+/Luminal B tumors (N = 48, orange dots). FF fresh frozen samples; FFPE formalin-fixed paraffin embedded samples

Fig. 3

Ratio of ER∆7 mRNA expression and total ERalpha mRNA expression. Box plots showing ratio of ER∆7 mRNA expression and total ERalpha mRNA expression for ER+/Basal tumors (blue boxes), ER+/Luminal B tumors (orange boxes) and normal breast tissues (gray box). Ratio’s for fresh frozen (FF) samples and formalin-fixed paraffin embedded (FFPE) samples are depicted in separate boxplots. Central line in boxes represent the median value, boundaries of boxes represent the interquartile range and ends of whiskers represent the minimum and maximum values. P-values are obtained using the Mann-Whitney test. a Box plots for all ER+/Basal and ER+/Luminal B tumors. b Box plots for subgroup of ER+/Basal and ER+/Luminal B tumors with ER-positivity of ≥10% by immunohistochemistry

Fig. 4

Kaplan Meier curves showing distant metastasis free interval (DMFI). Kaplan Meier curves showing distant metastasis free interval (DMFI) for HER2-negative patients in NBRST study with follow-up (N = 538). P-values are obtained using the log-rank test. a DMFI for all patients stratified by ER status and molecular subtyping. b DMFI of Basal patients (N = 252) stratified by ER status and response to neoadjuvant therapy (pCR pathological complete response or RD residual disease)