Journal Article

CRISPR-Cas-amplified urinary biomarkers for multiplexed and portable cancer diagnostics

Ko, Henry, Ngambenjawong, Chayanon, Bhatia, Sangeeta N., Fleming, Heather E., Hao, Liangliang, Tan, Edward Kah Wei, Sabeti, Pardis C., Zhong, Qian, Welch, Nicole L., Harzallah, Nour Saida, Zhao, Renee T.

2023

Overview

Synthetic biomarkers, bioengineered sensors that generate molecular reporters in diseased microenvironments, represent an emerging paradigm in precision diagnostics. Despite the utility of DNA barcodes as a multiplexing tool, their susceptibility to nucleases in vivo has limited their utility. Here we exploit chemically stabilized nucleic acids to multiplex synthetic biomarkers and produce diagnostic signals in biofluids that can be ‘read out’ via CRISPR nucleases. The strategy relies on microenvironmental endopeptidase to trigger the release of nucleic acid barcodes and polymerase-amplification-free, CRISPR-Cas-mediated barcode detection in unprocessed urine. Our data suggest that DNA-encoded nanosensors can non-invasively detect and differentiate disease states in transplanted and autochthonous murine cancer models. We also demonstrate that CRISPR-Cas amplification can be harnessed to convert the readout to a point-of-care paper diagnostic tool. Finally, we employ a microfluidic platform for densely multiplexed, CRISPR-mediated DNA barcode readout that can potentially evaluate complex human diseases rapidly and guide therapeutic decisions. Protease profiling of the tumour microenvironment using DNA-barcoded nanosensors and CRISPR amplification enables portable cancer diagnosis in preclinical models.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/61/350/59 / 639/166/985 / Amplification / Animal models / Animals / Bioengineering / Biomarkers / Cancer / Chemistry and Materials Science / CRISPR / CRISPR-Cas Systems - genetics / Deoxyribonucleic acid / DNA / DNA barcoding / Humans / Materials Science / Mice / Microenvironments / Microfluidics / Multiplexing / Nanosensors / Nanotechnology / Nanotechnology and Microengineering / Neoplasms - diagnosis / Neoplasms - genetics / Nuclease / Nucleic Acids / Portability / Tumor Microenvironment