Amplifying mutational profiling of extracellular vesicle mRNA with SCOPE.

Autor: Song J; Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA.; Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.; Department of Forensic Sciences, Sungkyunkwan University, Suwon, Republic of Korea.; School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea., Cho MH; Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA.; Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Cho H; Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA., Song Y; Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea., Lee SW; RevoSketch, Inc., Daejeon, Republic of Korea., Nam HC; RevoSketch, Inc., Daejeon, Republic of Korea., Yoon TH; RevoSketch, Inc., Daejeon, Republic of Korea., Shin JC; RevoSketch, Inc., Daejeon, Republic of Korea., Hong JS; Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA.; Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Kim Y; Research Institute of Aging and Metabolism, Kyungpook National University, Daegu, Republic of Korea., Ekanayake E; Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA., Jeon J; Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA.; Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., You DG; Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA.; Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA., Im SG; Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea., Choi GS; Colorectal Cancer Center, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Daegu, Republic of Korea., Park JS; Colorectal Cancer Center, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Daegu, Republic of Korea., Carter BC; Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA., Balaj L; Department of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA., Seo AN; Department of Pathology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu, Republic of Korea., Miller MA; Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA.; Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA., Park SY; Colorectal Cancer Center, Kyungpook National University Chilgok Hospital, School of Medicine, Kyungpook National University, Daegu, Republic of Korea., Kang T; School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea. kangtaejoon@kribb.re.kr.; Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea. kangtaejoon@kribb.re.kr., Castro CM; Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA. castro.cesar@mgh.harvard.edu.; Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. castro.cesar@mgh.harvard.edu., Lee H; Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA, USA. hlee@mgh.harvard.edu.; Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. hlee@mgh.harvard.edu.; Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea. hlee@mgh.harvard.edu.
Jazyk: angličtina
Zdroj: Nature biotechnology [Nat Biotechnol] 2024 Oct 07. Date of Electronic Publication: 2024 Oct 07.
DOI: 10.1038/s41587-024-02426-6
Abstrakt: Sequencing of messenger RNA (mRNA) found in extracellular vesicles (EVs) in liquid biopsies can provide clinical information such as somatic mutations, resistance profiles and tumor recurrence. Despite this, EV mRNA remains underused due to its low abundance in liquid biopsies, and large sample volumes or specialized techniques for analysis are required. Here we introduce Self-amplified and CRISPR-aided Operation to Profile EVs (SCOPE), a platform for EV mRNA detection. SCOPE leverages CRISPR-mediated recognition of target RNA using Cas13 to initiate replication and signal amplification, achieving a sub-attomolar detection limit while maintaining single-nucleotide resolution. As a proof of concept, we designed probes for key mutations in KRAS, BRAF, EGFR and IDH1 genes, optimized protocols for single-pot assays and implemented an automated device for multi-sample detection. We validated SCOPE's ability to detect early-stage lung cancer in animal models, monitored tumor mutational burden in patients with colorectal cancer and stratified patients with glioblastoma. SCOPE can expedite readouts, augmenting the clinical use of EVs in precision oncology.
(© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)
Databáze: MEDLINE
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