A variety of investigational HER2-inhibitor agents/combinations have been tested in I-SPY 2, including neratinib (N), TDM1 combined with pertuzumab (P) (TDM1/P), and trastuzumab (H) combined with pertuzumab (H/P; prior to this combination becoming standard of care), all with trastuzumab as control (Ctr). All three experimental arms graduated, showing improved efficacy over control in one or more receptor subsets (HR+HER2+, HR-HER2+, or/and HER2+). Here we assess 10 biomarkers in the HER2, ER/PR, and proliferation pathways on multiple levels of resolution (expression, protein, phospho-protein) as predictors of response in these four arms, hypothesizing that highly HER2-activated, proliferative tumors may be more sensitive to HER2-inhibition than those that are more luminal and quiescent.
192 HER2+ patients were considered in this analysis: (31 Ctr, 65 N, 52 TDM1/P, and 44 H/P). 10 biomarkers relating to HER2, ER, or proliferation were evaluated from pre-treatment biopsies: HER2 IHC (n=145), 3 expression signatures (n=192), BluePrint subtype (n=192), and 5 protein/phospho-protein analytes by RPPA (n=175) . Each biomarker was tested for association with pCR in the whole population and within each arm using a logistic model. This analysis was adjusted for HR status and treatment arm as covariates, and performed within receptor subtypes. This analysis does not adjust for multiplicities of other biomarkers.
In the population as a whole, HER2 and HER2-signaling biomarkers, evaluated at multiple levels of resolution: IHC, total-/phospho-protein by RPPA, and mRNA (HER2 amplicon module) - are highly correlated (rho=0.8 [0.65-0.92]). Higher HER2 levels and activity are associated with response: HER2 IHC 3+ status (LR p=0.00032), total quantitative ERBB2 protein by RPPA (LR p=5.4E-09), ERBB2 activation levels (LR p=6.58E-06 (pERBB2 (Y1248)) and 9.95E-06 (pEGFR Y1173)), and the ERBB2 amplicon expression signature (LR p=2.38E-08). In contrast, higher average ER/PR expression associates with non-response to HER2-targeted therapy (LR p=4.28E-08). Both HER2 and ER/PR signaling phenotypes are captured by BluePrint subtyping; and consistent with the individual pathway markers, tumors classified Luminal-type had a lower pCR rate relative to those classified as Her2-type (or Basal-type) (LR p=4.84E-11). These associations all retain significance in a model adjusting for HR status and treatment arm, and in the HR+HER2+ subset. In addition, we quantitatively assessed proliferation markers at the total protein (RPPA: Ki67), phospho-protein (pAURKA) and mRNA (proliferation signature Module11_Prolif) levels. All three proliferation biomarkers predict response overall; but this association is strongest within the HR+HER2+ subset (LR p=0.0012 (Module11_prolif), 0.0036 (pAURK), and 0.045 (Ki67)). None of the biomarkers tested were associated with response in the HR-HER2+ subset. Numbers are small within individual arms. Within the HR+HER2+ subtype, higher HER2 and lower ER/PR is observed in responders in all experimental arms; but the proliferation markers Module11_Prolif (LR p=0.0031) and Ki67 total protein (LR p=0.0029) are associated with response to TDM1/P but not H/P or N.
High HER2 signaling at the expression, protein, and phospho-protein levels, and low ER signaling, all predict response to HER2-inhibition across treatment arms. Proliferation markers may be useful for prioritizing therapies in the HR+HER2+ subset.