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CRISPR-Based Rapid Molecular Diagnostic Tests for Fusion-Driven Leukemias

An assay enabling rapid and sensitive diagnosis for fusion-driven leukemias, suitable for remote and low-resource environments.

Diagnostics

Project Overview

Current diagnostic methods for fusion-driven leukemias, such as acute promyelocytic leukemia (APL), Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ ALL), and chronic myeloid leukemia (CML), rely on centralized tests that are often unavailable in many clinical settings, especially in low-resource environments, causing delays in diagnosis and treatment.
There is a critical need for rapid, accessible, and accurate point-of-care diagnostic tests to improve patient outcomes and expand access to life-saving therapies for these cancer types.
Dana-Farber scientists have developed a CRISPR-based assay that enables rapid and sensitive detection of fusion oncogenes suitable for use in low resource environments.
Dana-Farber is seeking commercialization partners with an interest in licensing this asset for further development.

Technology

The CRISPR-based SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) assay enables rapid and sensitive detection of fusion oncogenes in APL, Ph+ ALL, and CML. SHERLOCK combines isothermal reverse-transcription recombinase polymerase amplification (RT-RPA) with Cas13-mediated detection, which does not require the use of a thermocycler not often found in low-resource settings, to identify specific RNA fusion transcripts. Optimized guide RNAs (crRNAs) ensure high sensitivity and specificity.

SHERLOCK demonstrated 100% sensitivity and specificity for detecting PML::RARA (for APL) and BCR::ABL1 (for Ph+ ALL) fusion transcripts. A limit of detection (LOD) range from 100-500 picograms (pg) and 50-100 pg of RNA has been demonstrated for PML::RARA and BCR::ABL1, respectively.

Future optimizations include direct cell lysis for rapid RNA preparation and a “one-pot” reaction combining RT-RPA and Cas13 detection, which would reduce the need for specialized equipment, making the assay suitable for low-resource settings. Additionally, optimizing a lateral flow readout would provide a simple, portable method for visualizing results, enhancing usability in diverse settings.

Further details:

Vedula RS, et al. CRISPR-based rapid molecular diagnostic tests for fusion-driven leukemias. Blood (2024) 144 (12): 1290–1299.

Benefits:

High Sensitivity and Specificity Across Diverse Samples: Tested on dried blood spot samples from 11 countries, maintaining 100% sensitivity and specificity.
High Concordance: Validated with diagnostic samples, showing 100% concordance with clinical RT-PCR results.
Low Limit of Detection: As low as 100 pg and 50 pg target RNA detected in PML::RARA and BCR::ABL1, respectively.
Streamlined Workflow Potential: Direct cell lysis and “one-pot” reactions would further reduce the turnaround time, with a user-friendly lateral flow readout.

Team Members: R. Coleman Lindsley, MD, PhD, Omar Abudayyeh, PhD, Feng Zhang, PhD, Jeremy Koob, Rahul S. Vedula, MD, Jonathan Gootenberg, PhD

Applications

Academic Centers to Community Hospitals and Clinics: Rapid, on-site diagnostics for APL, Ph+ ALL, and CML.
Low-Resource Environments: Bridges the access gap to molecular diagnostics.
Remote Areas: Portable lateral flow readout development would support and widen access for field deployment.
Broader Applications: Adaptable for other oncologic indications, expanding global health impact.

Interested in learning more?

Rapid Blood Cancer Diagnostic Could Speed Decisions and Save Lives

Dana-Farber Newsroom

Opportunities

Dana-Farber Cancer Institute is seeking commercialization partners with an interest in licensing this asset for further development to serve the spectrum of healthcare settings, including low-resource environments, for fusion-driven leukemias to improve patient outcomes and expand access to life-saving therapies.

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