Gene Signature Predicts Anthracycline Benefit in HR+/HER2– Breast Cancer

A 70-gene expression assay can identify which patients with hormone receptor–positive, HER2-negative (HR+/HER2–) early-stage breast cancer are most likely to benefit from anthracycline-containing chemotherapy, according to results from the prospective FLEX registry study (NCT03053193) published in JCO Precision Oncology.^1,2

The findings, drawn from 1259 patients with stage I to III HR+/HER2– disease classified by the 70-gene signature (MammaPrint) as high risk 1 or high risk 2 and by the 80-gene molecular subtyping assay BluePrint as luminal B, showed that genomic risk category—not clinical risk features alone—predicted which patients gained additional benefit from anthracycline-based regimens.

Patients classified as high risk 2 who received doxorubicin and cyclophosphamide plus a taxane (AC-T) had a 3-year invasive disease-free survival (IDFS) rate of 100%, compared with 94.8% among those who received taxane plus cyclophosphamide (TC) without an anthracycline, an absolute difference of 5.2 percentage points (P =.023). Among patients classified as high risk 1, 3-year IDFS rates were identical between the regimens, at 95.9% for both AC-T and TC, despite these patients sharing overlapping clinical high-risk features with the high risk 2 group. A treatment-by-genomic-risk interaction test confirmed that anthracycline benefit increased with genomic risk classification (P =.036), supporting the high risk 2 signature as a predictive—not merely prognostic—biomarker.

Study Design

Patients were enrolled in FLEX, a prospective, real-world, whole-transcriptome registry of early-stage breast cancer, and had a median follow-up of 3.2 years. Investigators used inverse probability of treatment weighting to balance baseline clinical characteristics between treatment groups, approximating the design of a randomized trial using observational data.

“Patients with HR+/HER2– breast cancer who are candidates for adjuvant chemotherapy continue to face uncertainty around whether they will derive meaningful benefit from anthracycline-containing regimens,” said Joyce O’Shaughnessy, MD, principal investigator of the FLEX Study and a medical oncologist at Texas Oncology–Baylor Charles A. Sammons Cancer Center, in a news release.² “This long-standing clinical dilemma underscores the need for predictive biomarkers that can identify which patients are most likely to benefit from anthracyclines and who may safely avoid unnecessary toxicity.”

The question has persisted because anthracyclines, while effective antitumor agents, carry risks of cardiotoxicity and secondary leukemia. Several randomized controlled trials, including the ABC trials, the West German Study Group PlanB trial, a Chinese phase 3 noninferiority trial, and the Danish Breast Cancer Group DBCG 07-READ trial, tested whether anthracycline-free regimens were noninferior to anthracycline-containing regimens in clinically high-risk, HER2-negative early-stage breast cancer.^3-6 None demonstrated a significant difference in outcomes specifically among HR+/HER2– patients, leaving clinicians without a reliable way to identify who needs an anthracycline and who can avoid one.

Clinical Context

The new data led the National Comprehensive Cancer Network (NCCN) to update its Clinical Practice Guidelines in Oncology to recognize the 70-gene signature as a genomic test that can guide anthracycline use in this population, according to the study sponsor, Agendia, Inc., which markets the MammaPrint and BluePrint assays.

“This study answers a question that randomized clinical trials have been unable to resolve, illustrating the value of genomic profiling to predict benefit from a specific cancer therapy,” said William Audeh, MD, MS, chief medical officer of Agendia and a study co-author, in a news release.² “The FLEX study highlights the power of a multimodal real-world evidence database to produce robust, clinically relevant data which not only inform treatment decisions but also change clinical practice guidelines.”

For clinicians selecting adjuvant chemotherapy in HR+/HER2– early-stage breast cancer, the results suggest that genomic risk stratification rather than clinical risk features alone may help distinguish patients likely to gain incremental benefit from anthracycline-containing regimens from those for whom a taxane-and-cyclophosphamide regimen offers comparable disease-free survival with less treatment-related toxicity. The FLEX registry continues to enroll patients, and the authors noted that longer follow-up will help confirm whether the survival differences observed at 3 years persist over time.

REFERENCES

1. O’Shaughnessy J, Brufsky AM, Rahman RL, et al. Prediction of Anthracycline Benefit in Hormone Receptor–Positive, Human Epidermal Growth Factor Receptor 2–Negative Early-Stage Breast Cancer by the MammaPrint 70-Gene Signature for Patients Enrolled in the FLEX Study. JCO Precis Oncol. 10, e2501285(2026).doi:10.1200/PO-25-01285
2. Genomic Profiling with MammaPrint + BluePrint Predicts Anthracycline Chemotherapy Benefit and Guides Personalized Treatment Selection in HR+HER2- Early-Stage Breast Cancer. News release. Agendia Inc. June 25, 2026. Accessed June 26, 2026. https://tinyurl.com/mpd533r8

3. Flynn PJ, Yothers G, et al. Anthracyclines in early breast cancer: The ABC Trials—USOR 06-090, NSABP B-46-I/USOR 07132, and NSABP B-49 (NRG Oncology). J Clin Oncol. 2017;35(23):2647-55. doi:10.1200/JCO.2016.71.4147

4. Nitz U, Gluz O, Clemens M, et al. West German Study PlanB Trial: Adjuvant four cycles of epirubicin and cyclophosphamide plus docetaxel versus six cycles of docetaxel and cyclophosphamide in HER2-negative early breast cancer. J Clin Oncol. 2019;37(10):799-808. doi:10.1200/JCO.18.00028

5. Yu KD, Liu XY, Chen L, et al. Anthracycline-free or short-term regimen as adjuvant chemotherapy for operable breast cancer: A phase III randomized non-inferiority trial. Lancet Reg Health West Pac. 2021;11:100158. doi:10.1016/j.lanwpc.2021.100158

6. Ejlertsen B, Tuxen MK, Jakobsen EH, et al. Adjuvant cyclophosphamide and docetaxel with or without epirubicin for early TOP2A-normal breast cancer: DBCG 07-READ, an open-label, phase III, randomized trial. J Clin Oncol. 2017;35(23):2639-2646. doi:10.1200/JCO.2017.72.3494.