Nanofluidic Wet-Cell for Genomic Analysis of Single Circulating Tumor Cells via Electron Microscopy

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Intratumor genetic heterogeneity is a fundamental challenge in cancer treatment. Genomic variation can occur spatially within a given tumor and between metastatic sub-populations established in different regions of the body. In addition, cancer evolves in time in response to therapy. In order to choose the most effective therapy, there is need for technologies that can yield a comprehensive picture of the "genomic landscape" of a patient's cancer and a measure of how this landscape is evolving. While repeated tissue biopsies are impractical, and provide only local information, circulating tumor cells (CTCs, cancer cells that have entered the bloodstream) may provide a minimally invasive picture of a patient's cancer status. CTCs, however, are both rare and necessarily heterogeneous: CTC-based genomic analysis must thus necessarily be performed at the single cell level. In this proposal we develop a novel approach for direct analysis of single-genomes extracted from single-CTCs at the single-molecule level. Our approach is based on developing a nanofluidic wet-cell that can be operated inside an electron microscope. The wet-cell, which is completely sealed, will permit cycling of DNA through nanochannel arrays positioned below an electronically transparent membrane (formed from either thin silicon nitride or atomically thin graphene sheets). The DNA molecules (specifically labeled with conductive as opposed to fluorescent tags) will be extended in the channels and then mapped via electron microscopy. The approach will yield a comprehensive highresolution map of the genome of a single CTC.