Rapid Screening of Targetable Kinase Gene Fusions in Acute Lymphoblastic Leukemia

Background: Philadelphia-like (Ph-like) acute lymphoblastic leukemia (ALL) is a high-risk subtype characterized by a similar expression profiling to ALL with BCR-ABL rearrangement, but due to different genomic alterations that activate cytokine receptor and kinase signaling. Diagnose of this type of leukemia is challenging and current diagnostic algorithms include a combination of different techniques, most of them time-consuming and expensive.

Here we present a multi-probe Fluorescence In Situ Hybridation (FISH)- Panel based screening test that permit a rapid diagnosis of ALL (including Ph-like ALL).

Methods: We analysed 42 adolescent and adult patients (13 - 72 years old) diagnosed with ALL without BCR/ABL and KMT2A rearrangements. We performed a one-slide custom designed FISH panel in parallel with chromosome banding analysis. The panel included probes for ETV6/RUNX1, KMT2A, BCR/ABL1, E2A, CRLF2/P 2RY8, CSF1R, EPOR, PDGFRB, ABL2, JAK2, and IGH probes (Custom chromoprobe multiprobe ALL, Cytocell).

Results: There were no hybridation failures. We identified 30 patients with alterations (71%), 20 of them (67%) with normal karyotype or without metaphases. The most common alterations were E2A deletion (8/30, 27%) [3 patients in a context of E2A/PBX rearrangement], hiperdiplid karyotype (6/30, 20%), ABL2 gain (5/30, 17%), CRLF2/IGH rearrangement (4/30, 13%), ETV6 deletion (4/30, 13%), IGH rearrangement (3/30, 10%) and JAK2 rearrangement (2/30, 7%). All together, Ph-like defining abnormalities comprised 20% of cases.

Conclusions: We have validated a rapid and easy test to improve ALL subtype diagnosis, including Ph-like ALL. The panel allowed for 24h-diagnosis in cases without or not assessable metaphases. In conclusion, this panel can be a complementary technique for the immediate identification of most common rearrangements in ALL, particullary those with treatment implications.