Identification of New Recurrent Lesions and Clinical Subsets by Genome-Wide DNA Profiling in Chronic Lymphocytic Leukemia with 17p Deletion.

Abstract Chronic lymphocytic leukemia (CLL) with deletion of 17p(p53) locus (17p- CLL) identifies the most aggressive CLL subset, due to active disease course and resistance to current treatments. Intrinsic mechanisms of the poor prognosis of 17p- CLL are scarcely known. In order to identify additional lesions occurring in 17p- CLL which contribute to prognosis, we performed genome-wide DNA profiling in 18 cases of 17p- CLL (median follow-up 25 months, range 4–107), using high-resolution single-nucleotide polymorphism (SNP) arrays (Affymetrix Human Mapping Nsp 250 k arrays). Chromosomal 11q, 13q or 17p deletions and trisomy 12 were determined by FISH. Tumor IGHV usage and mutational status were determined by PCR/sequencing of the tumor gDNA/cDNA. Median interval from diagnosis to progression (11 months, p=0.000122) and treatment (16 months, p=0.000827) were representative of the bad behavior of our 17p- CLL cases if compared to 95 non17p- CLL patients from our internal cohort (68 and 69 months, respectively). Interestingly, 3/18 (16%) 17p- CLL expressed the IGHV3–74 segment which is rare in normal B-cells (1,4%, p=0.02) and in non17p- CLL (2.1%, p=0.02). Tumor IGHV genes were unmutated in 10/18 and mutated in 8/18 17p- CLL. All cases carried 17p13.1 deletion in more than 60% nuclei, as assessed by FISH. Genome-wide DNA profiling was 99% concordant with FISH (71/72 data-points; one 13q deletion detected by FISH in 20% of the nuclei was missed by the microarray) and confirmed 17p deletion in all cases. Deletions at the 13q14.3 locus recurred in 50% cases. Only one case had an extra-copy of chromosome 12. No cases carried ATM deletion. Other recurrent lesions identified by genome-wide DNA profiling were: gains of 2p16.1-pter (30%), 3q24-qter (20%), 8q23.3-qter (30%), 17q21.2-q22 (30%), 14q32 (30%); losses of 8p12-pter (30%), 9q21.33-q22.1 (20%), 14q32 (40%), 20p12.1-pter (20%). Approximately half of the cases had concomitant losses of 8p or 17p and gains of the 8q or 17q regions, respectively, suggesting the presence of isochromosomes 8 or 17. Indeed, isochromosome 17 was evident in one case analyzed by conventional cytogenetics. Six patients had one or more regions of loss of heterozygosity (LOH) longer than 5 Mb in the absence of copy number reduction, suggestive of uniparental disomy. Several lesions, such as those involving chromosomes 3, 8 and 9, associate with poor clinical behavior in other B-cell tumors. Thus, we investigated the prognostic significance of the lesions identified in our series. Despite the small number of cases, we found that 17p- CLLs with loss of 8p12-pter, which contains tumor necrosis factor and defensin family genes, associated with worse treatment free interval from diagnosis (12 vs 46 months in 8p- vs non 8p- CLL, p=0.04). Overall, our analysis identified new recurrent genomic abnormalities at high frequencies that may specifically contribute to a different biologic and clinical behavior within 17p- CLL. Among these, isochromosomes 8 and 17 were particularly common, and 8p loss might identify a new aggressive subentity within 17p- CLL.