Amplifying Mutational Profiling of Extracellular Vesicle MRNA with SCOPE

Overview

Journal Nat Biotechnol

Specialty Biotechnology

Date 2024 Oct 7

PMID 39375445

Authors

Jayeon Song

Mi Hyeon Cho

Hayoung Cho

Younseong Song

Sung Woon Lee

Ho Chul Nam

Tae Ho Yoon

Jong Cheol Shin

Jae-Sang Hong

Yejin Kim

Emil Ekanayake

Jueun Jeon

Dong Gil You

Sung Gap Im

Gyu-Seog Choi

Jun Seok Park

Bob C Carter

Leonora Balaj

An Na Seo

Miles A Miller

Soo Yeun Park

Taejoon Kang

Cesar M Castro

Hakho Lee

Affiliations

Soon will be listed here.

Abstract

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.

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