Design and Application of a Novel PNA Probe for the Detection At a Single Cell Level of BCR-ABL T315I Mutation in Chronic Myeloid Leukemia Patients

The BCR-ABL T315I mutation at the gatekeeper residue is frequent in advanced phases of chronic myeloid leukemia (CML) and is one of the main cause of resistance to Tyrosine Kinase Inhibitors (TKI) by disrupting important contact points between the drugs and the enzyme. Although this mutation can be detected by different techniques and at different levels of the mutated clone, the prognostic significance of the absolute amount of the mutated allele is widely unknown.

The aim of the study was to develope a novel assay based on peptide nucleic acid (PNA) technology coupled to immuno-fluorescence microscopy (PNA-FISH) for the specific detection at a single cell level of T315I mutation thus improving both the diagnostic resolution and the knowledge on the behaviour of the mutated clone.

We designed a fluorescently-labelled PNA probe, coupled to FISH technology, which allows to distinguish with a high degree of specificity between CD34+ progenitor stem cells harbouring T315I mutation or the wild type form of BCR-ABL. CD34+ cells were enriched from CML patients who were positive for T315I mutation, or from patients who lost T315I mutation after ponatinib treatment. In addition we tested CML patients without T315I mutation as control and BM samples from healthy donors to establish the specificity of the method. CD34+ progenitors cells were enriched by MACS and then cytospun onto slides and hybridized with human species-specific fluorescinated 15 base pairs (bp)-long oligo-PNA, specifically recognizing the BCR-ABL T315I sequence. Slides were analyzed by fluorescence confocal microscopy.

We found, with a rather wide variability occurring among patients, a percentage of mutated CD34+ cells ranging from 3 to 90%. In addition these data indicate that fluorescinated BCR-ABL T315I/PNA probe displays a very high specificity towards a single base-pair mismatch. Interestingly, when evaluating the presence of T315I positive cells collected from a patient who lost the mutation (evaluated by sequencing) after ponatinib therapy and acquired T317 mutation a small amount of T315I positive CD34+ cells were still present. This percent did not exceeded 2% of the total CD34+ cell population. Importantly, the lack of positivity detected in CD34 positive cells from CML patient without mutations or in 20 healthy subjects demonstrates a high specificity of this method.

BCR/ABL T315I/PNA probe method displays high specificity and reliability in discriminating cell subpopulations harbouring the mutation. In addition, it allows to analyze the CD34+ population at the single cell level and to monitor the behaviour of the clone at the stem/progenitor cell level. This approach allows to monitor longitudinally the evolution of the mutated population over time, the response to specific drugs active against T315I mutants and to characterization the mutated stem/progenitor cell compartment in patients with CML.

Saglio:Novartis: Consultancy, Speakers Bureau; BMS: Consultancy, Speakers Bureau; Pfizer: Consultancy.