Molecular cytogenetic study of 126 unselected T-ALL cases reveals high incidence of TCR beta locus rearrangements and putative new T-cell oncogenes

Chromosomal aberrations of T-cell receptor (TCR) gene loci often involve the TCR alpha delta (14q11) locus and affect various known T-cell oncogenes. A systematic fluorescent in situ hybridization (FISH) screening for the detection of chromosomal aberrations involving the TCR loci, TCRad (14q11), TCR beta (7q34) and TCR gamma (7p14), has not been conducted so far. Therefore, we initiated a screening of 126 T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma cases and 19 T-ALL cell lines using FISH break-apart assays for the different TCR loci. Genomic rearrangements of the TCR beta locus were detected in 24/ 126 cases (19%), most of which (58.3%) were not detected upon banding analysis. Breakpoints in the TCR alpha delta locus were detected in 22/ 126 cases (17.4%), whereas standard cytogenetics only detected 14 of these 22 cases. Cryptic TCR alpha delta/ TCR beta chromosome aberrations were thus observed in 22 of 126 cases (17.4%). Some of these chromosome aberrations target new putative T-cell oncogenes at chromosome 11q24, 20p12 and 6q22. Five patients and one cell line carried chromosomal rearrangements affecting both TCR beta and TCR alpha delta loci. In conclusion, this study presents the first inventory of chromosomal rearrangements of TCR loci in T-ALL, revealing an unexpected high number of cryptic chromosomal rearrangements of the TCR beta locus and further broadening the spectrum of genes putatively implicated in T-cell oncogenesis.