Quantitative Detection of Gene Rearrangements Using Circulating Tumor Cells Purified by a Covalent Chemistry-Enabled Platform
Yazhen Zhu,
Assistant Project Scientist,
David Geffen School of Medicine at UCLA
Recent research focus in the field of circulating tumor cells (CTCs) has moved beyond the simple capture or enumeration of CTCs and gravitated towards approaches that allow for in-depth molecular analysis. Unlike circulating tumor DNA or RNA which is highly fragmented and compounded by significant background, CTCs house intact genomic DNA and RNA,providing more reliable genetic information about tumors. Exploring the use of CTC-derived mRNA offers a non-invasive diagnostic solution for understanding underlying tumor biology, guiding treatment intervention, and monitoring disease progression. Recently, we demonstrated a new covalent chemistry-enabled CTC capture/release platform – “Click Chip”. This platform is designed by integrating bioorthogonal ligation-mediated CTC capture (sensitive and rapid) and disulfide cleavage-driven CTC release (mild, specific, and rapid) on nanostructured substrates to enable more efficient purification of pooled CTCs with high-quality intact CTC-derived mRNA. The CTC-derived mRNA was subjected to RT-droplet digital PCR (RT-ddPCR). ALK/ROS1 rearrangements were quantified using CTC-mRNA recovered by Click Chips and matched with those identified in biopsy specimen in late-stage ALK/ROS1 positive NSCLC patients. Moreover, copy numbers of ALK/ROS1 rearrangements in CTCs and CTC counts could be used together for evaluating ALK/ROS1-TKI treatment responses and disease progression. This streamlined diagnostic workflow is optimum for gene rearrangement detection and quantification based on high-quality intact CTC-derived mRNA.
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