Design of a comprehensive fluorescence in situ hybridization assay for genetic classification of T-cell acute lymphoblastic leukemia

T-cell acute lymphoblastic leukemia (T-ALL) results from deregulation of a number of genes via multiple genomic mechanisms. We designed a comprehensive fluorescence in situ hybridization assay (CI-FISH) which consists of genomic probes to simultaneously investigate oncogenes and oncosuppressors recurrently involved in chromosome rearrangements in T-ALL which was applied to 338 T-ALL cases. CI-FISH provided genetic classification into one of the well-defined genetic subgroups, ie, TAL/LMO, HOXA, TLX3, TLX1, NKX2-1/2-2, or MEF2C, in 80% of cases. Two patients with translocations of the LMO3 transcription factor were identified, suggesting that LMO3 activation may serve as an alternative to LMO1/LMO2 activation in the pathogenesis of this disease. Moreover, intra-chromosomal rearrangements involving the 10q24 locus were found as a new mechanism of TLX1 activation. An unequal distribution of cooperating genetic defects was found among the six genetic subgroups. Interestingly, deletions targeting TCF7 or TP53 were exclusively found in HOXA T-ALL, LEF1 defects were prevalent in NKX2-1 rearranged patients, CASP8AP2 and PTEN alterations were significantly enriched in TAL/LMO leukemias whereas PTPN2 and NUP214-ABL1 abnormalities occurred in TLX1/TLX3. This work convincingly shows that CI-FISH is a powerful tool to define genetic heterogeneity of T-ALL which may be applied as a rapid and accurate diagnostic test.