Background. 9p21 is a major target in the pathogenesis of a number of human tumors. The locus harbors the CDKN2A/ARF tumor suppressor gene, which encodes two cell cycle regulatory proteins cyclin dependent kinase 2A (p16INK4a) and alternate reading frame (p14ARF). Patients and Methods. In order to assess whether and how it is inactivated in ALL, we studied 25 adult BCR-ABL1-positive ALL patients at the diagnosis and 5 only at the time of relapse following tyrosine kinase inhibitor treatments. Paired relapse samples were available for 4 patients. Affymetrix Single nucleotide polymorphism (SNP) Genome Wide SNP6.0 array was used to identify at the high resolution copy number changes on 9p21. FISH analysis was performed in order to confirm SNP results. PCR amplification and mutation screening of all exons by cloning and subsequent sequencing were performed. Results. SNP array analysis revealed CDKN2A genomic alterations in 28% of diagnosed patients and in 56% relapsed samples. Deletions were in the majority of cases biallelic and had a mean size of 101.5 kb (range, 27 kb-286 kb), ranging from 21823529 to 22122076. In two cases deletions of CDKN2A locus was due to losses of chromosome 9 involving the cytobands from 9p21.3 to 9p13.1 or to 9p13.2. FISH analysis confirmed these deletions but failed to detect focal alterations since most of them were below the resolution of the commercial FISH probes. In order to assess whether CDKN2A loss is responsible for progression, in four patients SNP analysis was performed both at diagnosis and at relapse. At diagnosis one patient showed a small monoallelic deletion (28.5 kb) that was maintained at the relapse. It is interesting to note that in another patient we found a focal heterozygous deletion (107.1 kb) at the diagnosis that became monoallelic at the relapse. In the two remaining patients, the alterations of CDKN2A were found only at the relapse, suggesting that loss of this locus is involved in disease progression. Mutation screening of all exons showed that CDKN2A locus is not affected by point mutations, since we only identified the SNP rs11515 (C/G) in 96%. Conclusions. Inactivation of the tumor suppressor gene CDKN2A by genomic deletions is a frequent event in Ph+ ALL and is involved in disease progression. Supported by: European LeukemiaNet, AIL, AIRC, FIRB 2006, Fondazione del Monte di Bologna e Ravenna, Strategico di Ateneo, GIMEMA Onlus.
GENOMIC DELETIONS OF THE CDKN2A LOCUS IN BCR-ABL1-POSITIVE ACUTE LYMPHOBLASTIC LEUKEMIA (ALL) DEREGULATE G1/S CONTROL AND CONTRIBUTE TO PROGRESSION OF DISEASE
Ferrari A.;IACOBUCCI, ILARIA;LONETTI, ANNALISA;PAPAYANNIDIS, CRISTINA;SOVERINI, SIMONA;PAOLINI, STEFANIA;MARTINELLI, GIOVANNI
2009
Abstract
Background. 9p21 is a major target in the pathogenesis of a number of human tumors. The locus harbors the CDKN2A/ARF tumor suppressor gene, which encodes two cell cycle regulatory proteins cyclin dependent kinase 2A (p16INK4a) and alternate reading frame (p14ARF). Patients and Methods. In order to assess whether and how it is inactivated in ALL, we studied 25 adult BCR-ABL1-positive ALL patients at the diagnosis and 5 only at the time of relapse following tyrosine kinase inhibitor treatments. Paired relapse samples were available for 4 patients. Affymetrix Single nucleotide polymorphism (SNP) Genome Wide SNP6.0 array was used to identify at the high resolution copy number changes on 9p21. FISH analysis was performed in order to confirm SNP results. PCR amplification and mutation screening of all exons by cloning and subsequent sequencing were performed. Results. SNP array analysis revealed CDKN2A genomic alterations in 28% of diagnosed patients and in 56% relapsed samples. Deletions were in the majority of cases biallelic and had a mean size of 101.5 kb (range, 27 kb-286 kb), ranging from 21823529 to 22122076. In two cases deletions of CDKN2A locus was due to losses of chromosome 9 involving the cytobands from 9p21.3 to 9p13.1 or to 9p13.2. FISH analysis confirmed these deletions but failed to detect focal alterations since most of them were below the resolution of the commercial FISH probes. In order to assess whether CDKN2A loss is responsible for progression, in four patients SNP analysis was performed both at diagnosis and at relapse. At diagnosis one patient showed a small monoallelic deletion (28.5 kb) that was maintained at the relapse. It is interesting to note that in another patient we found a focal heterozygous deletion (107.1 kb) at the diagnosis that became monoallelic at the relapse. In the two remaining patients, the alterations of CDKN2A were found only at the relapse, suggesting that loss of this locus is involved in disease progression. Mutation screening of all exons showed that CDKN2A locus is not affected by point mutations, since we only identified the SNP rs11515 (C/G) in 96%. Conclusions. Inactivation of the tumor suppressor gene CDKN2A by genomic deletions is a frequent event in Ph+ ALL and is involved in disease progression. Supported by: European LeukemiaNet, AIL, AIRC, FIRB 2006, Fondazione del Monte di Bologna e Ravenna, Strategico di Ateneo, GIMEMA Onlus.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
