Background
Gene expression tests are new tools to clinically determine the risk of relapse in early-stage breast cancer (BC) [
1,
2]. The 21-gene recurrence score (Oncotype DX) and Mammaprint (NKI-70) [
3‐
10] have been shown to impact treatment decisions [
11‐
13]. Novel prognostic tests, such as EndoPredict and PAM50, are also able to predict early, as well as late metastases [
14,
15].
EndoPredict is a standardized test for the molecular pathology laboratory and was the first multigene test used in a decentralized setting [
16,
17]. It was established and validated in two independent clinical validation studies (ABCSG6 and ABCSG8) involving patients with ER+/HER2− BC treated with adjuvant endocrine therapy (ET) only [
18]. EndoPredict provides prognostic information beyond all common clinicopathological parameters [
18] and clinical guidelines [
19]. The molecular information (EP score) is further combined with tumor size and nodal status resulting in the EPclin score.
The PAM50 assay is an optimized gene set used to identify intrinsic subtypes and predict the Risk Of Recurrence (ROR) at 10 years [
20,
21]. The ROR score was developed in a microarray-based cohort of node-negative, untreated BC patients [
6,
20]. Four versions of ROR exist in the research setting: ROR based on subtype information (ROR-S), ROR-S with proliferation (ROR-P), ROR-S with tumor size (ROR-T), and ROR-P with tumor size (ROR-PT) [
20,
21]. The minimum ROR score of all Luminal B scores was assigned as the low-risk threshold for each model and the maximum ROR score of all Luminal A scores as the high-risk threshold [
21].
The inclusion of established clinicopathological risk factors in ROR and EP scores, such as tumor size (ROR-T, ROR-PT, and EPclin) and nodal status (EPclin), increases their predictive performance [
18‐
21]. EndoPredict and research-based PAM50 were evaluated independently in the GEICAM/9906 trial [
22‐
25]. We compared the prognostic performance of the EP test with the research-based, non-standardized PAM50 assay in node-positive, ER+/HER2− BC patients treated with adjuvant chemotherapy followed by ET.
Discussion
We compared the prognostic performance of research-based and non-standardized versions of PAM50-ROR scores and EndoPredict in ER+/HER2−, node-positive chemotherapy-treated BC patients from the GEICAM/9906 trial.
ROR-S and ROR-P were significantly correlated with EP score, and gene signatures showed agreement in risk classification, indicating that PAM50-ROR and EP scores identify tumors with similar properties. Despite the significant correlation, the discordance rate of 20–21 % can be explained by the tests’ inherent characteristics. Our c-index analysis indicated that only EP added significant information to ROR-P. None of the other molecular signatures added information to each other, suggesting that additional predictors would not improve prognostic performance. These findings are concordant with our previous combined analysis of hundreds of signatures and clinical-pathological data for prognostic prediction in ER-positive breast cancer where we observed that not much more prognostic power was obtained by including hundreds of signatures into a single model beyond the power contained within a well-developed individual signature when combined with clinical variables [
28].
The PAM50-based ROR-T and ROR-PT scores include tumor size, whereas the EPclin score considers nodal status and tumor size, as part of the risk prediction algorithm. Similar to the research-based version, a ROR-PT score weighted for tumor size and proliferation was used to validate the standardized version of PAM50 assay in the ATAC and ABCSG8 trials. In our analysis, all hybrid scores contributed to identifying low-risk groups for distant metastasis, although number of patients and events differed across score categories. The EPclin low-risk group was smaller than the ROR-T and ROR-PT ones and showed no distant-metastatic events. EPclin had been established in a node-positive/node-negative cohort and the predefined cut-off level consequently classified more patients as high-risk in the node-positive GEICAM/9906 trial. In contrast, the research-based versions of ROR-T and ROR-PT scores were derived in a systemically untreated node-negative BC cohort, and thresholds were based on subtype distribution and not actual survival outcomes; therefore, the number of low-risk cases with distant-metastatic events was higher, as reflected by an MFS of 87–92 % in low-risk groups.
Kaplan–Meier analysis of discordant cases, c-index analysis, and log-likelihood tests showed that the EPclin-based risk classification provided independent prognostic information to the ROR-T and ROR-PT scores. The improved performance of the EPclin score over pure molecular scores may be partially explained by the inclusion of nodal status, one of the strongest single prognostic factors, in the EPclin score, but which is not included in any of the other models tested. EndoPredict validation studies demonstrated that molecular EP score, tumor size, and nodal status were the only independent prognostic parameters [
18]. Hybrid scores’ superior performance compared to their molecular counterparts supports the recommendation of the Evaluation of Genomic Application in Practice and Prevention working group to integrate clinicopathological factors into gene expression tests [
29] rather than relying on pure RNA-based molecular scores.
To the best of our knowledge, our study reports the first direct comparison of EndoPredict and a research-based version of the PAM50 assay. Earlier comparisons of multigene signatures suggested similar prognostic performances [
30,
31]. Recently, the transATAC study, the first large phase III study comparing different standardized gene expression-based biomarkers in the same patient cohort [
32], compared the standardized and clinically validated version of PAM50 assay, developed under the nCounter system (Nanostring Technologies), with the 21-gene recurrence score. PAM50-ROR provided more prognostic information than the recurrence score [
32]. Although our study did not evaluate the standardized and clinically validated PAM50-ROR score, the GEICAM/9906 trial is an additional valuable source for biomarker comparisons. In the context of this trial, we could identify high-risk patients who need additional treatment to the standard anthracycline-based chemotherapy (±taxane) and could be eligible for further treatment with novel drugs, such as CDK4/6 or mTOR inhibitors.
Our results should be interpreted in the context of its limitations. First, ROR scores were generated using research-based and non-standardized versions from qRT-PCR platform. Although research-based PAM50 classification has been evaluated in several clinical trials using qRT-PCR [
22,
33,
34], different methods may influence prognostic ability. Of note, large validation studies (ATAC and ABCSG8) for the PAM50 assay were performed using the standardized version with pre-specified cutoffs based on actual survival outcomes (<10, 10–20, and >20 % risk of distant relapse at 10 years) and not subtype distribution [
32]. Second, the PAM50 vs. EP comparison was not conducted according to their intended use. Whereas our patients were treated with chemotherapy, these predictors were clinically validated using patients cohorts receiving endocrine therapy alone. Therefore, next steps should compare PAM50 and EP in clinical trials with ER+/HER2− BC patients treated with ET alone. EndoPredict and the standardized PAM50 were recently evaluated in the ABCSG8 trial, which would allow a direct comparison of both clinical predictors [
35].
Conclusions
Despite the differences in establishment and the limited overlap in genes, all molecular predictors evaluated showed similar prognostic performance. The addition of clinical parameters, such as tumor size and nodal status, into risk-score determination improves the prognostic ability of these assays.
Compliance with ethical standards
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