Investigator: Saraswati Sukumar Johns Hopkins School of Medicine
The Sukumar laboratory has performed seminal studies to unravel the roles of members of the HOX gene family in breast cancer progression [1] and pioneered the application of intraductally administered therapeutic agents to treat preneoplastic ductal lesions [2]. Her lab's discovery of novel methylated genes through first ever SAGE analysis of breast cancer followed by the development of multiplexed quantitative PCR assays set the foundation for monitoring tumor burden based on aberrantly methylated genes [3].
In the clinical management of breast cancer patients, hypermethylation in circulating cell-free DNA is of great interest in various contexts: first, when primary tumor or metastatic tissue samples are not available; second, for surveillance of asymptomatic cancer survivors; third, for evaluating response to systemic therapies in the neoadjuvant, adjuvant and metastatic settings; and finally, as potential diagnostic surrogates. Hence, methods that can quantitate multiple methylated gene markers at exceedingly low concentrations from small volumes with easily achievable sample processing requirements are highly desirable.
Because the levels of DNA shed are so low, especially in patients with no symptoms of metastatic disease, this collaborative project proposes to develop an ultrasensitive and multiplexed platform featuring surface-enhanced Raman spectroscopy (SERS) and highly selective single base extension reaction [4]. Using DNA methylation analysis, the Sukumar lab has characterized a 10-gene panel composed of seven novel and three known breast cancer hypermethylated markers (Fig. 1). The panel displayed >90% sensitivity and 100% specificity when tested in sera of metastatic breast cancer patients. A decrease in median serum DNA methylation levels was observed in the selected genes in patients with stable disease or a therapeutic response but not in patients with progressive disease. Leveraging this panel, the LBRC proposes to develop a SERS assay by extending their recently established breast tumor antigen detection method. The benchmarks for the proposed assay development will be the sensitivity, specificity and reproducibility offered by the cMethDNA assay.
To enable ultrasensitive and multiplexed detection of methylated breast cancer markers, LBRC will develop a SERS assay by extending Sukamar's recently established breast tumor antigen detection method. Working with the Sukumar lab, we will use the sera already acquired at different time points from the metastatic breast cancer patients undergoing chemotherapy to demonstrate the feasibility of our new SERS assay in monitoring response to breast cancer therapy.
LBRC aims to develop rationally tailored plasmonic nanoprobes, and a new method for sensing of gene-specific (rather than genome-wide) methylation for breast cancer detection. The Sukumar lab is also embarking on analyzing the prognostic and predictive utility of cMethDNA, CA 27.29 antigen and CTC, using prospectively collected serum. To support this effort, LBRC will develop an integrated SERS-based platform for detecting circulating tumor antigens and methylated markers. Furthermore, the LBRC will also design and engineer SERS nanoprobe constructs to assist our investigator in their study of microRNAs (miRNA) to reveal tumor-specific alterations.