RNA Sequencing to Predict Response to Neoadjuvant Anti-HER2 Therapy

Abstract

IMPORTANCE In neoadjuvant trials, treatment of human epidermal growth factor receptor 2 (HER2)-positive breast cancers with dual HER2 blockade resulted in increased pathologic complete response (pCR) rates compared with each targeted agent alone. Amplification and/or overexpression of HER2 currently remains the only biomarker for therapeutic decisions, but it is insufficient to explain the heterogeneous response to anti-HER2 agents. OBJECTIVE To investigate the ability of clinically and biologically relevant genes and gene signatures (GSs) measured by RNA sequencing to predict the efficacy of anti-HER2 agents. DESIGN, SETTING, AND PARTICIPANTS The neoadjuvant NeoALTTO trial randomized 455 women with HER2-positive early-stage breast cancer to trastuzumab, lapatinib, or the combination for 6 weeks followed by the addition of weekly paclitaxel for 12 weeks, followed by 3 cycles of fluorouracil, epirubicin, and cyclophosphamide after surgery. The present substudy, which was planned in the NeoALTTO main protocol, evaluated the association of pretreatment gene expression levels defined using RNA sequencing with pCR and event-free survival (EFS). MAIN OUTCOMES AND MEASURES Gene expression–based biomarkers using RNA sequencing were examined for their association with response to anti-HER2 therapy and long-term outcome. RESULTS Sequencing data were available for 254 (56%) of the NeoALTTO participants (mean [SD] age of substudy participants, 48.8 [11.2] years). The expression of ERBB2/HER2 was the most significant predictor of pCR, followed by HER2-enriched subtype, ESR1, treatment arm, ER immunohistochemical analysis scores, Genomic Grade Index, immune, proliferation, and AKT/mTOR GSs. Adjusting for clinicopathological variables and treatment arms, ERBB2/HER2, HER2-enriched subtype, ESR1, and Genomic Grade Index remained significant. Immune GSs were associated with higher pCR only in the combination arm (odds ratio, 2.1; 95%CI, 1.2–4.0; interaction test P = .01), while the stroma GSs were significantly associated with higher pCR in the single arms and with lower pCR in the combination arm (odds ratio, 0.46; 95%CI, 0.25–0.84; P = .009). None of the evaluated variables was associated with EFS after correction for multiple testing, but this analysis was underpowered. CONCLUSIONS AND RELEVANCE High levels of ERBB2/HER2 and low levels of ESR1 were associated with pCR in all treatment arms. In the combination arm, high expression of immune and stroma GSs were significantly associated with higher and lower pCR rates, respectively, and should be further explored as candidate predictive markers. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00553358

Predicting the Efficacy of HER2-Targeted Therapies: A Look at the Host

“…The application of PAM50 predictor of tumors to the major neoadjuvant clinical trials of anti-HER2 agents (NOAH, CALGB 40601, NeoALTTO, and CHER-LOB) found that patients with HER2-E tumors benefited substantially from a trastuzumab-based treatment, achieving a significantly higher pCR rate than those with other tumors [ 84 , 94 – 96 ] ( Table 1 ). Notably, in the NeoALTTO trial, PAM50 had a significant effect on pCR across arms [ 95 ], similar to that observed in the CALGB 40601 trial [ 84 ], supporting its predictive value for both trastuzumab and lapatinib. In the adjuvant phase III NSABP B-31 trial, PAM50 failed to identify subgroups that benefited differentially from trastuzumab [ 97 ], whereas in the NCCTG-N9831 trial, patients with HER2-E or luminal tumors benefited from the addition of trastuzumab to chemotherapy, unlike those with basal-like tumors [ 98 ], suggesting the need to further evaluate this predictor in the adjuvant setting.…”

“…In the neoadjuvant setting, ESR1 and ERBB2 levels, as determined by mRNAseq, when considered as continuous variables, were individually linked to pCR, and their incorporation into an exploratory multivariate model removed intrinsic subtype, HER2 amplicon signature, and clinical assays for ER or HER2 from the model in the CALGB 40601 trial [ 84 ]. The levels of ERBB2 and ESR1 were confirmed in the NeoALTTO trial across arms [ 95 ] as the most important determinants of pCR compared with standard tests, in the GeparQuattro [ 101 ] and in the TRYPHAENA trials [ 77 ] ( Table 1 ). Additional evidence is needed before ESR1 and ERBB2 RNA can be implemented in the clinical setting, but their predictive ability in HER2-positive BC supports the superiority of evaluating their mRNA levels over standard IHC tests and suggests that they better mirror activity of HER2 and tumor-addiction to its downstream signals, as PAM50 did.…”

HER2 signaling regulates the tumor immune microenvironment and trastuzumab efficacy

“…C-E) Number of infiltrating macrophages ( C ), T cells ( D ), and NK cells ( E ) in FVB mice treated as in A. Shown are the numbers of each immune population calculated for 10 5 live cells, as determined by flow cytometry. p-values by unpaired t-test.…”

“…3 Recently, analyses of gene expression profiles of tumor blocks from patients enrolled in clinical trials support a relationship between tumor dependence on HER2 signaling (HER2-E by PAM50) and trastuzumab sensitivity. 4,5 Moreover, based on increasing evidence of the role of both innate and adaptive immunity in trastuzumab mechanism of action, 6,7 immune-related information such as tumor infiltrating lymphocyte count or immune-related signatures were explored and found to be predictive of trastuzumab benefit in several studies. 8 In this context, through transcriptome profiling of archival formalin-fixed paraffin embedded (FFPE) tumor blocks from HER2+ cases treated with adjuvant trastuzumab in our Institute during routine clinical practice, 9 we identified BCs exquisitely sensitive to treatment as those with both tumor dependence on HER2 signaling by PAM50 classification, as well as enriched in immune genes, 9 supporting the predictive power of both addiction to HER2 signaling and immune infiltration because of their ability to identify the same tumors.…”

Optimal treatment of early stage HER2‐positive breast cancer

“…11,44 Molecular intrinsic subtypes play a key role in determining response to anti-HER2 treatment, as reported in several neoadjuvant trials. 11,44,58,59 In those trials, the HER2-enriched subtype has consistently been associated with having the highest rate of pCR. Moreover, the PAMELA trial 44 was the first study to demonstrate prospectively that the HER2-enriched molecular subtype within HER2-positive breast cancer is associated with a pCR after neoadjuvant therapy with only dual HER2-blockade (with or without endocrine therapy) and no chemotherapy.…”