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Tumor and serum DNA methylation in women receiving preoperative chemotherapy with or without vorinostat in TBCRC008



Methylated gene markers have shown promise in predicting breast cancer outcomes and treatment response. We evaluated whether baseline and changes in tissue and serum methylation levels would predict pathological complete response (pCR) in patients with HER2-negative early breast cancer undergoing preoperative chemotherapy.


The TBCRC008 trial investigated pCR following 12 weeks of preoperative carboplatin and albumin-bound paclitaxel + vorinostat/placebo (n = 62). We measured methylation of a 10-gene panel by quantitative multiplex methylation-specific polymerase chain reaction and expressed results as cumulative methylation index (CMI). We evaluated association between CMI level [baseline, day 15 (D15), and change] and pCR using univariate and multivariable logistic regression models controlling for treatment and hormone receptor (HR) status, and performed exploratory subgroup analyses.


In univariate analysis, one log unit increase in tissue CMI levels at D15 was associated with 40% lower chance of obtaining pCR (odds ratio, OR 0.60, 95% CI 0.37–0.97; p = 0.037). Subgroup analyses suggested a significant association between tissue D15 CMI levels and pCR in vorinostat-treated [OR 0.44 (0.20, 0.93), p = 0.03], but not placebo-treated patients.


In this study investigating the predictive roles of tissue and serum CMI levels in patients with early breast cancer for the first time, we demonstrate that high D15 tissue CMI levels may predict poor response. Larger studies and improved analytical procedures to detect methylated gene markers in early stage breast cancer are needed. TBCRC008 is registered on (NCT00616967).

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The authors thank the patients who participated in this study: NIH grant P30 CA006973, SPORE in breast cancer (P50 CA88843), TBCRC and its founding partners (The AVON Foundation, The Breast Cancer Research Foundation and Susan G. Komen for the Cure); Abraxis Bioscience: Merck Oncology: and the Cindy Rosencrans Fund for Triple Negative Breast Cancer Research for generous funding. The authors also thank the TBCRC participating site investigators, research nurses, study coordinators, and the staff of the Breast and Ovarian Cancer Program and Avon Breast Center at Johns Hopkins.

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Correspondence to Vered Stearns or Saraswati Sukumar.

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Women enrolling in the study signed an informed consent approved by the Institutional Review Boards of participating institutions.

Conflicts of interest

VS has received research Grants from Merck, Celgene Corporation, Abbvie, Pfizer, Novartis, Medimmune, and Puma Biotechnology. RC has received research Grants from Novartis, Puma Biotechnology, Genentech, Merrimack, Clovis, Merck. AMS has received consulting fees from Eli Lilly and Co., and Pfizer. SS has received research Grants from AVON Foundation, Grants, licensing/royalty fees and consulting fees from Cepheid for QM-MSP and cMethDNA assays. MJF has received licensing/royalty fees and consulting fees from Cepheid. The remaining authors have no conflicts of interest to disclose.

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Supplementary material 1 (PPTX 156 kb)

Supplementary Fig. 1: Quantitative Gene Methylation by Treatment Arm. Scatter plots indicate methylation levels in tissues from individuals treated either with vorinostat (V) or placebo (P) in addition to standard therapy. Cumulative methylation index (CMI) was calculated for tissue samples in which PCR-amplification was successful for all 10 genes in the panel. CMI = the sum of individual gene methylation within the 10 gene-panel (possible 1000 CMI units, 100% × 10 genes). Gene methylation is defined as % methylation = (# copies methylated DNA/# total copies unmethylated DNA + methylated DNA) (100). The median is shown by bar and significance was calculated using the Mann–Whitney U test

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Connolly, R.M., Fackler, M.J., Zhang, Z. et al. Tumor and serum DNA methylation in women receiving preoperative chemotherapy with or without vorinostat in TBCRC008. Breast Cancer Res Treat 167, 107–116 (2018).

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  • Preoperative chemotherapy
  • Breast cancer
  • Methylation
  • cMethDNA
  • Biomarkers