Research Spotlight: Researchers Develop SCOPE to Improve Early-Stage Cancer Detection

Cesar M. Castro, MD, MSc, of the Department of Medicine and Center for Systems Biology at Massachusetts General Hospital, and Hakho Lee, PhD, of the Department of Radiology and Center for Systems Biology at Massachusetts General Hospital and the Hostetter MGH Research Scholar, are co-corresponding authors of a paper published in Nature Biotechnology, “Amplifying mutational profiling of extracellular vesicle mRNA with SCOPE.”

 

How would you summarize your work? 

Our team is working to develop a better blood test for detecting cancers earlier, whether new diagnoses or recurrence. In our paper, we present SCOPE (self-amplified and CRISPR-aided operation to profile EVs), a new approach that provides several advantages over existing blood tests that analyze tumor DNA. Currently available tests focus on circulating tumor DNA (ctDNA), which breaks down quickly, but SCOPE uses extracellular vesicles (EVs). These tiny particles encapsulate and protect messenger RNA (mRNA), making them a better source for detecting cancer’s signatures.

EV mRNA also provides a richer molecular snapshot of actionable and relevant tumor mutations and information on how tumors may resist treatment. SCOPE employs a novel CRISPR-based assay we developed that allows us to detect mutations with high precision and sensitivity, unlike conventional PCR approaches. SCOPE is poised to advance precision oncology by better detecting early tumors and monitoring treatment response through liquid biopsies

What knowledge gap does your study help to fill?

The use of liquid biopsy for detecting actionable cancer mutations and minimal residual disease is gaining momentum. However, its widespread adoption and clinical impact are limited by the reliance on ctDNA, which exists in low concentrations and primarily reflects dying cells. In contrast, analyzing mRNA offers promising advantages, as it is more abundant than ctDNA and can provide deeper insights into the functional state of tumors, which could enhance both preclinical and clinical research.

EVs have emerged as valuable targets for mRNA analysis. These nanoscale particles shield mRNA from degradation. However, detecting mRNA within EVs presents significant technical challenges. The mRNA content in individual EVs is typically low, and only a small fraction of circulating EVs originate from tumors. As a result, current EV-mRNA analyses require large sample volumes and access to advanced analytical tools, hindering their routine clinical use. Overcoming these challenges required more sensitive and efficient methods to fully integrate EV-based mRNA detection into standard liquid biopsy workflows, until now.

What approach did you use?

We drew inspiration from CRISPR technology for biosensing. CRISPR has become a powerful tool in molecular diagnostics because it can target and cut DNA or RNA at precise locations. Cas proteins, which are used together with CRISPR, can recognize and target specific nucleic acids. While most assays first rely on making copies of nucleic acids to help Cas proteins recognize the target, any errors during the copying process would be amplified, resulting in false positives.

In our approach, we re-engineered Cas13a activity to amplify both the target mRNA and the detection signal simultaneously. Our unique method allows us to precisely identify single-nucleotide polymorphisms in EVs, a distinction made possible by the high specificity of Cas13a. Furthermore, the dual amplification allows us to detect mRNA at extremely low concentrations, down to the sub-attomolar range.

What did you find?

We named this new method SCOPE and validated its performance through comprehensive preclinical and clinical studies. Notably, SCOPE successfully distinguished KRAS wild-type mRNA in EVs from key mutations such as G12C, G12D, G12S, and G12V, even outperforming a powerful commercial assay designed for these variants. We validated the work using preclinical and clinical samples.

What are the implications?

SCOPE offers new insights into the characteristics of EVs, allowing us to detect highly sensitive and specific tumor mutations in both preclinical and clinical research. Our findings show that SCOPE identifies circulating EVs carrying genetic mutations that match those detected in corresponding tumor tissues, confirming that EVs are reliable biomarkers for liquid biopsy. This platform holds great potential for cancer research and could help us unravel the mechanisms behind cancer progression and resistance, assess treatment responses, and identify cancer cells that remain after treatment (a concept known as minimal residual disease). SCOPE offers many advantages over currently available methods and could accelerate clinical decision-making and expand the role of EVs in liquid biopsy applications.

What are the next steps?

We are exploring whether SCOPE could extend beyond oncology into fields like infectious diseases and agriculture, where rapid, sensitive, and precise diagnostics are essential. This expansion would broaden its applicability and enhance its impact across multiple scientific and clinical domains.

Authorship: In addition to Castro and Lee, Massachusetts General Hospital authors include Jayeon Song, Mi Hyeon Cho, Hayoung Cho, Jae-Sang Hong, Emil Ekanayake, Jueun Jeon, Dong Gil You, Bob C. Carter, Leonora Balaj, Miles A. Miller.

Paper cited: Song J et al. “Amplifying mutational profiling of extracellular vesicle mRNA with SCOPE” Nature Biotechnology DOI: 10.1038/s41587-024-02426-6

Funding: This work was supported by National Institutes of Health grants and the MGH Scholar Fund.

Disclosures: Castro, Lee, Song and Taejoon Kang declare the filing of a provisional patent that was assigned to and handled by Massachusetts General Hospital and the Korea Research Institute of Bioscience and Biotechnology. Miller declares research support from Ionis Pharmaceuticals, Genentech and Pfizer, all of which are unrelated to the present manuscript.