Background. Recently, using single nucleotide polymorphism (SNP) microarrays, a high frequency of genetic alterations of regulators of Blymphoid development (Mullighan et al., Nature 2008) was described in paediatric B- ALL, but a comprehensive analysis in adults is still lacking. Aim. To characterize, by high resolution SNP arrays, the rearrangements on 9p involving the PAX5 locus. Patients and Methods. Affymetrix Human Mapping 250K NspI and SNP6.0 arrays and FISH assay were used to profile the genome of 98 adult BCR-ABL1-positive ALL patients. Results. The most frequent somatic copy number alterations affecting B-lymphoid development were deletions on 7p12 involving the IKZF1 gene (76/98, 78%), which encodes the transcription factor Ikaros, and monoallelic copy number changes on 9p chromosome involving the PAX5 gene (31/98, 32%). Overall mono-allelic loss of PAX5 was identified in 28 patients (29%), whereas internal amplification in only 3 cases (3%). Four major PAX5 losses occurred: 1) focal deletions involving only the PAX5 gene (3%) with the minimal overlapping region of 101 kb; 2) deletions involving only a portion of PAX5 and flanking genes (8%) with a median size of 364 kb; 3) broader deletions involving PAX5 and a variable number of flanking genes (11%) with a median size of 947 kb; 4) deletion of all chromosome 9 or 9p (6%). In 23 patients (23%) we identified the deletions of both IKZF1 and PAX5; in 51 patients (52%) only the deletion of IKZF1 was found, while the presence of deletion or rearrangements of only PAX5 gene was found in 5 patients (5%). In two cases we identified the loss of IKZF1 and the gain of an internal region of PAX5. According to the type of deletion we could have PAX5 haploinsufficiency or PAX5 mutants with impaired DNA-binding or transactivating activity. FISH analysis with three overlapping BAC probes encompassing the whole PAX5 gene confirmed what obtained by SNParray analysis. To investigate the consequences of genomic PAX5 alteration, quantitative PCR (q-PCR) was used, demonstrating that genomic alterations on 9p13.2 lead to a significant down-modulation at the transcript level of the Pax5. Conclusions. PAX5 rearrangements occurred at an incidence of about 30% in adult BCR-ABL1 ALL and its impairment may be associated with the development of this poor prognosis subtype of leukemia. Supported by: European LeukemiaNet, AIL, AIRC, FIRB 2006, Strategico di Ateneo, GIMEMA Onlus.
PAX5 GENE IS FREQUENTLY THE TARGET OF GENETIC ALTERATIONS IN BCR-ABL1-POSITIVE ACUTE LYMPHOBLASTIC LEUKEMIA PATIENTS
IACOBUCCI, ILARIA;LONETTI, ANNALISA;PAPAYANNIDIS, CRISTINA;OTTAVIANI, EMANUELA;SOVERINI, SIMONA;PICCALUGA, PIER PAOLO;PAOLINI, STEFANIA;MARTINELLI, GIOVANNI
2009
Abstract
Background. Recently, using single nucleotide polymorphism (SNP) microarrays, a high frequency of genetic alterations of regulators of Blymphoid development (Mullighan et al., Nature 2008) was described in paediatric B- ALL, but a comprehensive analysis in adults is still lacking. Aim. To characterize, by high resolution SNP arrays, the rearrangements on 9p involving the PAX5 locus. Patients and Methods. Affymetrix Human Mapping 250K NspI and SNP6.0 arrays and FISH assay were used to profile the genome of 98 adult BCR-ABL1-positive ALL patients. Results. The most frequent somatic copy number alterations affecting B-lymphoid development were deletions on 7p12 involving the IKZF1 gene (76/98, 78%), which encodes the transcription factor Ikaros, and monoallelic copy number changes on 9p chromosome involving the PAX5 gene (31/98, 32%). Overall mono-allelic loss of PAX5 was identified in 28 patients (29%), whereas internal amplification in only 3 cases (3%). Four major PAX5 losses occurred: 1) focal deletions involving only the PAX5 gene (3%) with the minimal overlapping region of 101 kb; 2) deletions involving only a portion of PAX5 and flanking genes (8%) with a median size of 364 kb; 3) broader deletions involving PAX5 and a variable number of flanking genes (11%) with a median size of 947 kb; 4) deletion of all chromosome 9 or 9p (6%). In 23 patients (23%) we identified the deletions of both IKZF1 and PAX5; in 51 patients (52%) only the deletion of IKZF1 was found, while the presence of deletion or rearrangements of only PAX5 gene was found in 5 patients (5%). In two cases we identified the loss of IKZF1 and the gain of an internal region of PAX5. According to the type of deletion we could have PAX5 haploinsufficiency or PAX5 mutants with impaired DNA-binding or transactivating activity. FISH analysis with three overlapping BAC probes encompassing the whole PAX5 gene confirmed what obtained by SNParray analysis. To investigate the consequences of genomic PAX5 alteration, quantitative PCR (q-PCR) was used, demonstrating that genomic alterations on 9p13.2 lead to a significant down-modulation at the transcript level of the Pax5. Conclusions. PAX5 rearrangements occurred at an incidence of about 30% in adult BCR-ABL1 ALL and its impairment may be associated with the development of this poor prognosis subtype of leukemia. Supported by: European LeukemiaNet, AIL, AIRC, FIRB 2006, Strategico di Ateneo, GIMEMA Onlus.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
