A 3-gene biomarker signature to predict response to taxane-based neoadjuvant chemotherapy in breast cancer

PLoS One. 2020 Mar 20;15(3):e0230313. doi: 10.1371/journal.pone.0230313. eCollection 2020.

Abstract

Breast cancer is the most common cancer in women worldwide, affecting one in eight women in their lifetime. Taxane-based chemotherapy is routinely used in the treatment of breast cancer. The purpose of this study was to develop and validate a predictive biomarker to improve the benefit/risk ratio for that cytotoxic chemotherapy. We explicitly strived for a biomarker that enables secure translation into clinical practice. We used genome-wide gene expression data of the Hatzis et al. discovery cohort of 310 patients for biomarker development and three independent cohorts with a total of 567 breast cancer patients for validation. We were able to develop a biomarker signature that consists of just the three gene products ELF5, SCUBE2 and NFIB, measured on RNA level. Compared to Hatzis et al., we achieved a significant improvement in predicting responders and non-responders in the Hatzis et al. validation cohort with an area under the receiver operating characteristics curve of 0.73 [95% CI, 69%-77%]. Moreover, we could confirm the performance of our biomarker on two further independent validation cohorts. The overall performance on all three validation cohorts expressed as area under the receiver operating characteristics curve was 0.75 [95% CI, 70%-80%]. At the clinically relevant classifier's operation point to optimize the exclusion of non-responders, the biomarker correctly predicts three out of four patients not responding to neoadjuvant taxane-based chemotherapy, independent of the breast cancer subtype. At the same time, the response rate in the group of predicted responders increased to 42% compared to 23% response rate in all patients of the validation cohorts.

MeSH terms

  • Adaptor Proteins, Signal Transducing / genetics
  • Adaptor Proteins, Signal Transducing / metabolism
  • Antineoplastic Agents / therapeutic use*
  • Biomarkers, Tumor / genetics*
  • Biomarkers, Tumor / metabolism
  • Breast Neoplasms / drug therapy
  • Breast Neoplasms / genetics*
  • Calcium-Binding Proteins / genetics
  • Calcium-Binding Proteins / metabolism
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Female
  • Humans
  • NFI Transcription Factors / genetics
  • NFI Transcription Factors / metabolism
  • Neoadjuvant Therapy
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Survival Analysis
  • Taxoids / therapeutic use*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcriptome*

Substances

  • Adaptor Proteins, Signal Transducing
  • Antineoplastic Agents
  • Biomarkers, Tumor
  • Calcium-Binding Proteins
  • DNA-Binding Proteins
  • ELF5 protein, human
  • NFI Transcription Factors
  • NFIB protein, human
  • RNA, Messenger
  • SCUBE2 protein, human
  • Taxoids
  • Transcription Factors

Grants and funding

The authors received no specific funding for this work.