The Philadelphia chromosome is the single most significant adverse prognostic marker in adult ALL. Expression of BCR-ABL1 in haematopoietic stem cells can alone induce a CML-like myeloproliferative disease, but cooperating oncogenic lesions are required for the generation of a blastic leukemia. To identify, at submicroscopic level, oncogenic lesions that cooperate with BCR-ABL1 to induce ALL we profiled the genomes of 36 Ph+ adult ALL patients by 250K NspI single nucleotide polymorphism (SNP) array (Affymetrix Inc., USA). High level amplification and homozygous deletion were identified in all patients, with deletions outnumbering amplification almost 3:1. The most frequent somatic copy number alteration was deletion of IKZF1, which encodes the transcription factor Ikaros, in 25/36 cases (69%). Ikaros is required for the earliest stages of lymphoid lineage commitment and acts as tumor suppressor in mice. The IKZF1 deletions were predominantly mono-allelic and were limited to the gene in 22 cases, identifying IKZF1 as the genetic target. Real-time quantitative PCR and FISH analysis confirmed SNP results and gene expression analysis showed that the genomic alteration in IKZF1 leads to a significant down-modulation of the transcript level. The deletions of IKZF1 in 12/25 patients were limited to an internal subset of exons ( 4-7), with a complete concordance between the extent of this deletion and the expression of the dominant-negative isoform Ik6 with cytoplasmatic localization and oncogenic activity. The deletions were restricted to highly localized sequences in introns 3 and 7. Heptamer recombination signal sequences recognized by the RAG enzymes during V(D)J recombination were located immediately internal to the deletion breakpoints, and a variable number of additional nucleotides (patient specific) were present between the consensus intron 3 and 7 sequences, suggestive of the action of terminal deoxynucleotidyl transferase (TdT) and aberrant RAG-mediated recombination. Deletion of IKZF1 was not identified in chronic phase CML (n=40) patients. In BCR-ABL1 ALL we also frequently observed a deletion of PAX5, CDKN2A, CDKN2B and BTG1. In conclusion, deletion of IKZF1 resulting in either haploinsuffciency and in the expression of the dominant negative isoform Ik6 is an important event in the development of BCR-ABL1 B-progenitor ALL. European LeukemiaNet, AIL, AIRC, FIRB 2006, Fondazione del Monte di Bologna e Ravenna, Strategico di Ateneo.
IKZF1 (IKAROS) DELETIONS ARE A CENTRAL EVENT IN THE PATHOGENESIS OF BCR-ABL1 POSITIVE ACUTE LYMPHOBLASTIC LEUKEMIA
IACOBUCCI, ILARIA;OTTAVIANI, EMANUELA;LONETTI, ANNALISA;ASTOLFI, ANNALISA;TESTONI, NICOLETTA;BALDAZZI, CARMEN;SOVERINI, SIMONA;PAOLINI, STEFANIA;PAPAYANNIDIS, CRISTINA;MARTINELLI, GIOVANNI
2008
Abstract
The Philadelphia chromosome is the single most significant adverse prognostic marker in adult ALL. Expression of BCR-ABL1 in haematopoietic stem cells can alone induce a CML-like myeloproliferative disease, but cooperating oncogenic lesions are required for the generation of a blastic leukemia. To identify, at submicroscopic level, oncogenic lesions that cooperate with BCR-ABL1 to induce ALL we profiled the genomes of 36 Ph+ adult ALL patients by 250K NspI single nucleotide polymorphism (SNP) array (Affymetrix Inc., USA). High level amplification and homozygous deletion were identified in all patients, with deletions outnumbering amplification almost 3:1. The most frequent somatic copy number alteration was deletion of IKZF1, which encodes the transcription factor Ikaros, in 25/36 cases (69%). Ikaros is required for the earliest stages of lymphoid lineage commitment and acts as tumor suppressor in mice. The IKZF1 deletions were predominantly mono-allelic and were limited to the gene in 22 cases, identifying IKZF1 as the genetic target. Real-time quantitative PCR and FISH analysis confirmed SNP results and gene expression analysis showed that the genomic alteration in IKZF1 leads to a significant down-modulation of the transcript level. The deletions of IKZF1 in 12/25 patients were limited to an internal subset of exons ( 4-7), with a complete concordance between the extent of this deletion and the expression of the dominant-negative isoform Ik6 with cytoplasmatic localization and oncogenic activity. The deletions were restricted to highly localized sequences in introns 3 and 7. Heptamer recombination signal sequences recognized by the RAG enzymes during V(D)J recombination were located immediately internal to the deletion breakpoints, and a variable number of additional nucleotides (patient specific) were present between the consensus intron 3 and 7 sequences, suggestive of the action of terminal deoxynucleotidyl transferase (TdT) and aberrant RAG-mediated recombination. Deletion of IKZF1 was not identified in chronic phase CML (n=40) patients. In BCR-ABL1 ALL we also frequently observed a deletion of PAX5, CDKN2A, CDKN2B and BTG1. In conclusion, deletion of IKZF1 resulting in either haploinsuffciency and in the expression of the dominant negative isoform Ik6 is an important event in the development of BCR-ABL1 B-progenitor ALL. European LeukemiaNet, AIL, AIRC, FIRB 2006, Fondazione del Monte di Bologna e Ravenna, Strategico di Ateneo.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
