PURPOSE: Gene expression profiling classifies breast cancer into intrinsic subtypes based on the biology of the underlying disease pathways. We have utilized material from a prospective randomized trial of tamoxifen versus placebo in pre-menopausal women with primary breast cancer (NCIC CTG MA.12) to evaluate the prognostic and predictive significance of intrinsic subtypes identified by both the PAM50 gene set and by immunohistochemistry (IHC).
EXPERIMENTAL DESIGN: Total RNA from 398/672 (59%) patients was available for intrinsic subtyping with a qRT-PCR 50 gene predictor (PAM50) for luminal A, luminal B, HER-2 enriched and basal like subtypes. A tissue microarray was also constructed from 492/672 (73%) of the study population to assess a panel of six IHC antibodies to define the same intrinsic subtypes.
RESULTS: Classification into intrinsic subtypes by the PAM50 assay was prognostic for both disease free survival (DFS) (p=0.0003) and overall survival (OS) (p=0.0002) whereas classification by the IHC panel was not. Luminal subtype by PAM50 was predictive of tamoxifen benefit (DFS: HR 0.52; 95% CI 0.32-0.86 vs HR 0.80; 95% CI 0.50-1.29 for non-luminal subtypes), though the interaction test was not significant (p=0.24), whereas neither subtyping by central IHC nor by local ER or PR status were predictive. Risk of relapse (ROR) modeling with the PAM50 assay produced a continuous risk score in both node negative and node positive disease.
CONCLUSIONS: In the MA.12 study, intrinsic subtype classification by qRT-PCR with the PAM50 assay was superior to IHC profiling for both prognosis and prediction of benefit from adjuvant tamoxifen.