Enhancing Epigenetic Analysis Of Rare Cells With Multi-Phase Microfluidics

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PROJECT SUMMARY While the genomic revolution has identified several important mutations involved in cancer progression, only a minority of patients benefit from therapies that target these alterations. An emerging area of interest involves aberrant epigenetic modifications, which have been implicated in a broad range of solid tumor malignancies. Importantly, specific epigenetic biomarkers have been identified, often at much higher frequencies than genomic markers (e.g., hypermethylation of the GSTP1 promoter is found in more than 90% of prostate cancer primary tumors). Thus, there is a critical need to extend the concepts of precision medicine beyond genomic aberrations to include epigenomic alterations that drive cancer progression and treatment resistance. Unfortunately, assays to identify epigenetic biomarkers lack the sensitivity to measure many clinical samples, which often contain relatively low cell numbers. Much of this insensitivity stems from the extensive manipulation of DNA/protein complexes required to identify specific epigenetic markers and the associated inadvertent dissociation of these interactions (resulting in analyte loss). Therefore, we aim to improve the state-of-the-art of epigenetic analyses via the implementation of two technologies to preserve molecular interactions: 1) Exclusion-based Sample Preparation (ESP) and 2) Exclusive Liquid Repellency (ELR). With ESP, analytes are bound to functionalized paramagnetic particles (PMPs) and magnetically transferred across phase boundaries (e.g., air/aqueous, oil/aqueous) to isolate the PMP-bound analyte(s). The rapid and non-dilutive nature of ESP preserves molecular interactions, particularly those that are labile or short-lived. ELR utilizes aqueous droplets in oil that are “repelled” from a surface (i.e., they remain suspended and do not contact the surface) to minimize surface-derived analyte loss (e.g., adsorption) while also minimizing reaction volumes (mitigating inadvertent dissociation). Together, the combination of ESP-ELR platform will significantly improve the efficiency of epigenetic analyses, facilitating epigenetic measurements within small clinical samples (e.g., needle biopsies, circulating tumor cells). Specifically, we will develop, optimize, and benchmark ESP-ELR versions of methylation analysis (where a methylated DNA binding protein (MBD2) is employed to selectively capture methylated DNA sequences) and chromatin immunoprecipitation (ChIP; where histone/DNA complexes are isolated in order to interrogate chromatin status). Lastly, we will automate the platform and use it to perform a prospective biomarker validation study of GSTP1 paving the way for it’s use in clinical trials. Here we focus on prostate cancer as a model system, but we expect that an improved platform for epigenetic analysis will have broad impact across the biomedical sciences.