Abstract P1-05-27: Liquid Biopsy for HER2 Status Assessment in Breast Cancer Using Surrogate DNA Methylation Markers

Abstract Background: Emerging HER2-targeted drugs especially antibody–drug conjugates (ADCs) are promising and provide more options for breast cancer management. Current assessment of HER2 status and treatment decisions are mainly dependent on immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) on the primary tumor tissues. With the disease progression, the molecular status of the tumor may evolve and become discordant with the primary site. However, longitudinal monitoring of HER2 status is limited by infeasible repeated sampling of the tumor tissues. A non-invasive and accurate approach to obtaining real-time samples for measuring HER2 alterations is thus an unmet need for surveillance and guiding treatment selection in breast cancer. Detecting HER2 aberration in cell-free DNA (cfDNA) can allow repeated sampling and avoid effects from tumor heterogeneity of tissue biopsy. Previous approaches for HER2 status determination using liquid biopsy were mostly dependent on the detection of copy number changes in cfDNA, but the limited signal-to-noise ratio poses a great challenge to the accuracy and robustness of the tests. In this study, we identified a group of DNA methylation markers for determining HER2 status in cfDNA for breast cancer. Methods: Genome-wide DNA methylation sequencing was conducted in tissue (25 HER2-positive and 35 HER2-negative) and plasma (32 HER2-positive and 107 HER2-negative) samples to identify specific methylation markers for HER2 status. HER2-positive samples were defined by IHC 3+ and 2+ with FISH positive, while HER2-negative ones were IHC 0/1+ and 2+ with FISH negative. Candidate markers were verified in another two sets of plasma samples (1. 30 HER2-positive and 40 HER2-negative; 2. 33 HER2-positive and 53 HER2-negative) by using quantitative methylation-specific PCR (qMSP). The performance of the markers was estimated by the Wilcoxon test, receiver operating characteristic curve, and logistic regression modelling. Results: 36 HER2 status-specific markers were discovered from genome-wide DNA methylation sequencing. Based on the qMSP results, 11 markers were verified by the performance analyses. The individual area under the curve (AUC) of these markers was from 0.58 to 0.68. From logistic regression modelling and 2-fold cross-validation, a 7-marker diagnostic model was built and validated on plasma samples, with the highest AUC of 0.812. Conclusion: cfDNA methylation detection inferring HER2 overexpression is a novel and non-invasive option for monitoring HER2 status in breast cancer patients, with a potential application in response prediction of HER2-targeted treatments. Further validation of the test is undergoing in large multi-centre cohorts in China. Citation Format: Xianyu Zhang, Shiyao Lu, Hui Li, Xin Liu, Jun Wang, Liuhong Zeng, Zhipeng Lu, Siyu Liu, Yanling Yin, Marina Bibikova, Zhiwei Chen, Jian-Bing Fan, Da Pang. Liquid Biopsy for HER2 Status Assessment in Breast Cancer Using Surrogate DNA Methylation Markers [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-05-27.