A novel assay may be effective at detecting a unique molecular marker in patients with acute myeloid leukemia (AML), according to a recent study published by Young et al in The Journal of Molecular Diagnostics. The new findings may revolutionize the way AML is detected and treated.
Background
AML is a rare and aggressive type of hematologic malignancy diagnosed in about 120,000 patients globally per year. Detecting measurable residual disease during treatment—with methods such as bone marrow morphology, multiparameter flow cytometry, and DNA sequencing—may be essential for determining prognoses and guiding treatment decisions. However, morphologic assessments can only detect leukemic cells at a 5% limit of detection. Multiparameter flow cytometry has a more sensitive limit of detection at 0.01% to 0.001%, but is often challenging to implement and interpret and is not standardized between laboratories. Further, DNA sequencing approaches can identify leukemic cells by their somatic mutation profile, but are expensive and can be confounded by clonal hematopoiesis in nonleukemic blood cells.
There are at least 80 known KMT2A fusion partners, but about 80% of the fusions involve just five partners: AF9, AF6, AF4, ELL, and ENL.
“Oncogenic fusions are often disease-defining and present a unique marker of leukemic cells that are not usually present in healthy cells. Other diseases such as chronic myeloid leukemia (CML) can already be tracked by the canonical BCR-ABL fusion and sensitively detecting these fusions has revolutionized how CML is treated,” explained senior study author Grant A. Challen, PhD, of the Division of Oncology in the Department of Medicine at the Washington University School of Medicine in St. Louis. “For [patients with] AML with oncogenic fusions driving their disease, the KMT2A fusion is a molecular marker that can be leveraged for sensitive [measurable residual disease] detection. We therefore wanted to develop a platform for sensitive KMT2A fusion detection to improve how we detect and treat this disease,” he added.
Study Methods and Results
In the new study, the researchers developed a novel droplet digital polymerase chain reaction assay to enable sensitive KMT2A fusion detection with the five most common fusion partners.
They then benchmarked the assay in human cell lines and patient samples to demonstrate sensitive and specific KMT2A fusion detection. The researchers noted that the assay is capable of detecting these fusions by partitioning cDNA molecules into microfluidic droplets that are assayed with primers and probes that only produce a positive signal when fusion transcripts are present. They were able to combine multiple primer and probe sets targeting different fusions into a pooled fusion detection reagent. The researchers also demonstrated detection of KMT2A fusions in patient samples known to harbor KMT2A fusions.
Conclusions
The researchers hope their novel assay can help improve treatment decision-making, therapy response assessment, and long-term surveillance.
“We show that the assay does not produce false-positive signals in samples from healthy individuals. The assay is easily expanded to include additional oncogenic fusions. Knowing whether a treatment is working or not is critically important for decisions regarding when to escalate therapy or pursue hematopoietic stem cell transplant,” Dr. Challen underscored. “This is a robust new tool for sensitive KMT2A fusion detection that is directly applicable for disease detection in patients with leukemia driven by these fusions. It fills a void for oncogenic fusion detection and provides some technical improvements. The assay is also scalable—additional fusions can be easily added to the assay—to expand coverage for other oncogenic fusions. We are improving [hematologic malignancy] detection one drop at a time,” he concluded.
Disclosure: For full disclosures of the study authors, visit jmdjournal.org.
