DNA Hydrogel with Aptamer-Toehold-Based Recognition, Cloaking, and Decloaking of Circulating Tumor Cells for Live Cell Analysis

Abstract

Circulating tumor cells (CTCs) contain molecular information on the primary tumor and can be used for predictive cancer diagnostics. Capturing rare live CTCs and their quantification in whole blood remain technically challenging. Here we report an aptamer-trigger clamped hybridization chain reaction (atcHCR) method for in situ identification and subsequent cloaking/decloaking of CTCs by porous DNA hydrogels. These decloaked CTCs were then used for live cell analysis. In our design, a DNA staple strand with aptamer-toehold biblocks specifically recognizes epithelial cell adhesion molecule (EpCAM) on the CTC surface that triggers subsequent atcHCR via toehold-initiated branch migration. Porous DNA hydrogel based-cloaking of single/cluster of CTCs allows capturing of living CTCs directly with minimal cell damage. The ability to identify a low number of CTCs in whole blood by DNA hydrogel cloaking would allow high sensitivity and specificity for diagnosis in clinically relevant settings. More significantly, decloaking of CTCs using controlled and defined chemical stimuli can release living CTCs without damages for subsequent culture and live cell analysis. We expect this liquid biopsy tool to open new powerful and effective routes for cancer diagnostics and therapeutics.

Tumor microenvironment complexity and therapeutic implications at a glance

“…The hydrogel is ATP-responsive which allows further stimuli-responsive shifting of gel to sol state, to decloak and release CTC for live cell analysis ( Fig. 4) [156].…”

“…DNA hydrogel-based liquid biopsy provides a highly sensitive platform for isolating CTCs expressing EpCAM and enables further live analysis with minimal damage. Adapted with permission from [156]. Copyright (2017) American Chemical Society inhibition of the exosome production, secretion, cell-tocell communication as well as removal of exosomalspecific loads [179,180].…”

Bioinspired Engineering of a Multivalent Aptamer‐Functionalized Nanointerface to Enhance the Capture and Release of Circulating Tumor Cells

“…Fore xample,a ptamer SYL3C was successfully identified against transfer membrane cancer biomarker protein EpCAM, [11] which has been widely applied as binding ligand in diverse CTC analysis platforms. [12] While SYL3C works well in buffer, its binding performance was compromised when used in complex biological samples. [11] Additionally,a ptamers can be easily digested by nucleases in blood.…”

DNA hydrogel-empowered biosensing

“…The encapsulated AuNPs were exploited as the indicators of hydrogel formation via generating a red color at this state. Moreover, for real-time monitoring of DNA gelation, the rate of bacterial movement was considered as the criterion, which was decreased under gel formation [48].…”