DNA Methylation Markers for Breast Cancer Detection in the Developing World

• Authors: Bradley M. Downs, Johns Hopkins University; Claudia Mercado-Rodriguez, Johns Hopkins University; Ashley Cimino-Mathews, Johns Hopkins University; Chuang Chen, Wuhan University; Jing-Ping Yuan, Wuhan University; Eunice Van Den Berg, University of Witwatersrand; Leslie M. Cope, Johns Hopkins University; Fernando Schmitt, Porto University; Gary M. Tse, Chinese University of Hong Kong; Syed Z. Ali, Johns Hopkins University; Danielle Meir-Levi, Johns Hopkins University; Rupali Sood, Johns Hopkins University; Juanjuan Li, Johns Hopkins University; Andrea L. Richardson, Johns Hopkins University; Marina Mosunjac, Emory University; Monica Rizzo, Emory University; Suzana Tulac, Cepheid; Kriszten J. Kocmond, Cepheid; Timothy de Guzman, Cepheid; Edwin W. Lai, Cepheid; Brian Rhees, Cepheid; Michael Bates, Cepheid; Antonio C. Wolff, Johns Hopkins University; Edward Gabrielson, Johns Hopkins University; Susan C. Harvey, Cepheid; Christopher B. Umbricht, Johns Hopkins University; Kala Visvanathan, Johns Hopkins University; Mary Jo Fackler, Johns Hopkins University; Saraswati Sukumar, Johns Hopkins University
• Journal Title: Clinical Cancer Research
• Volume: Volume 25, Number 21
• Publisher: American Association for Cancer Research | 2019-11-01, Pages 6357-6367
• Type of Work: Article | Post-print: After Peer Review
• Publisher DOI: http://doi.org/10.1158/1078-0432.CCR-18-3277
• Subjects: Biology, Genetics; Health Sciences, Oncology; Health Sciences, Pathology; Health Sciences, Medicine and Surgery
• Keywords: Science & Technology; Life Sciences & Biomedicine; Oncology; Promoter hypermethylation; Serum DNA; Care; Countries; Genes; Biomarkers; Epithelium; Reveals; Income; Assay

Abstract

Purpose: An unmet need in low-resource countries is an automated breast cancer detection assay to prioritize women who should undergo core breast biopsy and pathologic review. Therefore, we sought to identify and validate a panel of methylated DNA markers to discriminate between cancer and benign breast lesions using cells obtained by fine-needle aspiration (FNA). Experimental Design: Two case-control studies were conducted comparing cancer and benign breast tissue identified from clinical repositories in the United States, China, and South Africa for marker selection/training (N = 226) and testing (N = 246). Twenty-five methylated markers were assayed by Quantitative Multiplex-Methylation-Specific PCR (QM-MSP) to select and test a cancer-specific panel. Next, a pilot study was conducted on archival FNAs (49 benign, 24 invasive) from women with mammographically suspicious lesions using a newly developed, 5-hour, quantitative, automated cartridge system. We calculated sensitivity, specificity, and area under the receiver-operating characteristic curve (AUC) compared with histopathology for the marker panel. Results: In the discovery cohort, 10 of 25 markers were selected that were highly methylated in breast cancer compared with benign tissues by QM-MSP. In the independent test cohort, this panel yielded an AUC of 0.937 (95% CI = 0.900- 0.970). In the FNA pilot, we achieved an AUC of 0.960 (95% CI = 0.883-1.0) using the automated cartridge system. Conclusions: We developed and piloted a fast and accurate methylation marker-based automated cartridge system to detect breast cancer in FNA samples. This quick ancillary test has the potential to prioritize cancer over benign tissues for expedited pathologic evaluation in poorly resourced countries.