Abstract P4-08-09: DNA methylation markers predict recurrence-free interval in triple-negative breast cancer
Authors: Fackler MJ , Cho SS , Cope LM , Gabrielson E , Wilsbach K , Lynch C , Marks JR , Geradts J , Regan MM , Viale G , Wolff AC , Umbricht CB , Sukumar S 
Published: May 2019

Abstract
BACKGROUND. Chemotherapy remains the treatment mainstay for triple-negative breast cancer (TNBC). Nevertheless, randomized trials have shown that not all TNBC require it, nor does it benefit all patients that receive it. Molecular tools to risk-stratify TNBC are currently lacking. In light of the importance of epigenetic processes modulating gene expression, we performed an array-based genome-wide DNA methylation search in well-documented institutional and clinical trial cohorts of TNBC for markers that can distinguish breast cancers with a favorable natural history from those with a high risk of recurrence.
METHODS. We performed an array-based genome-wide DNA methylation survey of well-documented institutional and clinical trial cohorts of TNBC and conducted molecular marker discovery on institutional TNBCs (115 patient samples; 53 recurrences) treated by locoregional therapy (LRT) alone. The identified hypermethylated gene signatures were then tested in a TNBC cohort (50 patient samples; 16 recurrences) from the no chemotherapy arms of IBCSG trials VIII and IX, and in a separate combined cohort of TNBCs (131 patient samples; 33 recurrences) treated with chemotherapy from an institutional repository and from IBCSG trials VIII and IX. Cross platform validation was conducted using quantitative multiplexed methylation specific PCR (QM-MSP) on hypermethylated markers in samples from both the Discovery Set and IBCSG LRT Test Set.
RESULTS. We identified methylation signatures in the discovery cohort consisting of 100 or 30 CpG probes that discriminated patients who remained recurrence-free from those with recurrent disease. These signatures were then tested in the IBCSG no chemotherapy cohort, and we found that hypermethylation was associated with shorter recurrence-free interval (RFI). A significant association of both 100 CpG (P&lt;0.0001) and 30 CpG (P=0.0021) signatures with shorter RFI was found in the combined institutional and IBCSG chemotherapy cohort. We observed an enrichment of methylation probes residing on chromosome 19, particularly within 19q13.41-43, that significantly correlated with RFI following chemotherapy. QM-MSP results reflected that of the methylation array [Spearman correlation coefficient of r = 0.495 (P = 0.0009)] indicating that the relationship between high methylation and short RFI is detectable independent of analytical platform. We also observed enrichment for Chromosome 19-specific probes within the 100 and 30 probe sets. While only 5% of all CpG markers are located within Chr19, 15% of the 100 CpG set, 37% of the 30 CpG set, and 47% of the 17 CpGs that are statistically significantly correlated with RFI in the chemotherapy group reside on the Chr19, mostly within 19q13.41-43.
CONCLUSIONS. Methylation markers may be of prognostic importance in TNBC and our findings should be validated in additional clinical trial cohorts.
Citation Format: Fackler MJ, Cho SS, Cope LM, Gabrielson E, Wilsbach K, Lynch C, Marks JR, Geradts J, Regan MM, Viale G, Wolff AC, Umbricht CB, Sukumar S. DNA methylation markers predict recurrence-free interval in triple-negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-08-09.