New Assay Could Revolutionize Acute Myeloid Leukemia Treatment

Researchers report that enhancing the accuracyHow close the measured value conforms to the correct value.” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]” tabindex=”0″ role=”link”>accuracy of detecting a particular molecular marker in leukemic cells can significantly improve the assessment of measurable residual disease. This advancement can lead to better-informed treatment decisions, ultimately enhancing patient outcomes.

A novel assay that detects a unique molecular marker in patients with acute myeloid leukemia (AML) may revolutionize the way this disease is detected and treated according to a new report recently published in The Journal of Molecular Diagnostics published by Elsevier. This assay may improve the detection of AML driven by KMT2A gene fusions and may impact treatment decision-making, assessing response to therapy, and long-term surveillance.

AML is a rare, aggressive blood cancer diagnosed in around 120,000 individuals worldwide each year. Detecting residual disease during treatment is essential for determining prognosis and guiding treatment decisions. Currently, the methods for detecting measurable residual disease (MRD) during treatment for AML include bone marrow morphology, multiparameter flow cytometry (MPFC), and DNADNA, or deoxyribonucleic acid, is a molecule composed of two long strands of nucleotides that coil around each other to form a double helix. It is the hereditary material in humans and almost all other organisms that carries genetic instructions for development, functioning, growth, and reproduction. Nearly every cell in a person’s body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA).” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]” tabindex=”0″ role=”link”>DNA sequencing.

Morphologic assessment only detects leukemic cells at a 5% limit of detection. MPFC has a more sensitive limit of detection at 0.01% to 0.001%, but is challenging to implement and interpret, and is not standardized between laboratories. DNA sequencing approaches can identify leukemic cells by their somatic mutation profile but are expensive and can be confounded by clonal hematopoiesis in non-leukemic blood cells.

A Leap Forward in Leukemia Research

Lead investigator Grant A. Challen, Ph.D., Division of Oncology, Department of Medicine, Washington University School of Medicine in St. Louis, explains, “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. For AML patients with oncogenic fusions driving their disease, the KMT2A fusion is a molecular marker that can be leveraged for sensitive MRD detection. We therefore wanted to develop a platform for sensitive KMT2A fusion-detection to improve how we detect and treat this disease.”

Investigators developed a novel droplet digital PCR assay enabling sensitive KMT2A fusion detection with the five most common fusion partners. There are at least 80 known KMT2A fusion partners, but about 80% of fusions involve just five partners — AF9, AF6, AF4, ELL, and ENL. They benchmarked the assay in human cell lines and patient samples to demonstrate sensitive and specific KMT2A fusion detection.

The assay detects 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. Investigators were able to combine multiple primer/probe sets targeting different fusions into a pooled fusion detection reagent. They also showed the detection of KMT2A fusions in patient samples known to harbor KMT2A fusions.

Implications for AML Treatment and Future Research

Dr. Challen notes, “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. This has a potential impact on treatment decision-making and assessing response to therapy. Knowing whether a treatment is working or not is critically important for decisions regarding when to escalate therapy or pursue hematopoietic stem cell transplant.”

He concludes, “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 blood cancer detection one drop at a time!”

Reference: “Droplet Digital PCR for Oncogenic KMT2A Fusion Detection” by Andrew L. Young, Hannah C. Davis and Grant A. Challen, 7 October 2023, The Journal of Molecular Diagnostics.
DOI: 10.1016/j.jmoldx.2023.09.006

The study was funded by the National Institutes of HealthThe National Institutes of Health (NIH) is the primary agency of the United States government responsible for biomedical and public health research. Founded in 1887, it is a part of the U.S. Department of Health and Human Services. The NIH conducts its own scientific research through its Intramural Research Program (IRP) and provides major biomedical research funding to non-NIH research facilities through its Extramural Research Program. With 27 different institutes and centers under its umbrella, the NIH covers a broad spectrum of health-related research, including specific diseases, population health, clinical research, and fundamental biological processes. Its mission is to seek fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to enhance health, lengthen life, and reduce illness and disability.” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]” tabindex=”0″ role=”link”>National Institutes of Health and the Leukemia and Lymphoma Society.