T-cell acute lymphoblastic leukemia (T-ALL) is mostly characterized by specific chromosomal abnormalities, some occurring in a mutually exclusive manner that possibly delineate specific T-ALL subgroups. One subgroup, including MLLrearranged, CALM-AF10 or inv (7)(p15q34) patients, is characterized by elevated expression of HOXA genes. Using a gene expression-based clustering analysis of 67 T-ALL cases with recurrent molecular genetic abnormalities and 25 samples lacking apparent aberrations, we identified 5 new patients with elevated HOXA levels. Using microarray-based comparative genomic hybridization (array-CGH), a cryptic and recurrent deletion, del (9)(q34.11q34.13), was exclusively identified in 3 of these 5 patients. This deletion results in a conserved SET-NUP214 fusion product, which was also identified in the T-ALL cell line LOUCY. SET-NUP214 binds in the promoter regions of specific HOXA genes, where it interacts with CRM1 and DOT1L, which may transcriptionally activate specific members of the HOXA cluster. Targeted inhibition of SET-NUP214 by siRNA abolished expression of HOXA genes, inhibited proliferation, and induced differentiation in LOUCY but not in other T-ALL lines. We conclude that SET-NUP214 may contribute to the pathogenesis of T-ALL by enforcing T-cell differentiation arrest.
IntroductionT-cell acute lymphoblastic leukemia (T-ALL) is a thymocyte malignancy, and represents about 15% of pediatric patients with ALL. T-ALL often presents with a high tumor mass, accompanied by a rapid progression of disease. Still, about 30% of patients with T-ALL relapse during therapy or within the first 2 years following treatment and eventually die. 1 Over the last few years, great progress has been made in unravelling the genetics of T-ALL, including recurrent chromosomal translocations (TAL1, LYL1, LMO1, LMO2, HOX11/TLX1, HOX11L2/TLX3, MYB, and Cyclin D2), deletions (SIL-TAL1, del(6q), del(9)(p21), and del(11)(p12p13)), amplifications (NUP214-ABL1), duplications (MYB), and mutations (RAS and NOTCH1). [2][3][4][5][6][7][8][9][10][11][12][13] Some of these abnormalities are mutually exclusive and may delineate distinct T-ALL subgroups (ie, TAL1, LMO1, LMO2, HOX11, HOX11L2, MLL, and Inv(7)). Others are shared by some of these subgroups and may lead to the deregulation of cell cycle (ie, del(9)(p21) that includes the CDKN2A/p15 and CDKN2B/p16 loci). 3,4 Some may be acquired during leukemic growth, like the episomal NUP214-ABL1 amplification. 6 NOTCH1 activation mutations are present in more than half of all patients with T-ALL regardless of the presence of other rearrangements. 7 It has been hypothesized that activation of NOTCH1 represents one of the most advanced abnormalities in T-ALL that may enable for uncontrolled proliferation and/or inhibition of apoptosis, possibly through up-regulation of the target genes cMYC and DELTEX1. [14][15][16] In contrast to the wide variety of genetic abnormalities in T-ALL, initial microarray studies have revealed only 5 different expression clusters: immature/LYL1, TAL...