Mattie Gordon

Breast cancer prognosis and treatment is generally dependent on a patient’s molecular subtype, those being luminal A, luminal B, HER2-enriched, or basal-like (triple-negative). Current subtyping tests rely on fluorescence-based reporting with barcoded probes, but have low sampling efficiency (>100 ng RNA) and as such, may not accommodate liquid biopsy samples. The goal of this project is to develop a single-molecule mRNA expression assay for breast cancer molecular subtyping using a solid-phase isolation and hybridization approach followed by resistive pulse sensing (RPS). Tumor-derived exosomes are first enriched from plasma samples using a specially designed microfluidic chip with the appropriate affinity markers followed by exosomal mRNA isolated using immobilized gene-specific capture probes. The enriched exosomal mRNA is then hybridized to gene-specific avidin-containing reporter probes. A photocleavable linker allows for release of labeled mRNA-probe complexes with subsequent RPS using a dual in-plane nanopore sensor to identify specific mRNA molecules with single-molecule sensitivity.