NOTCH1 Mutations Are Associated With The 14q Deletion In Chronic Lymphocytic Leukemia (CLL) and Small Lymphocytic Lymphoma (SLL)

Deletions of the long arm of chromosome 14 are rare (<5%) but recurrently observed in mature B-cell neoplasms, particularly in CLL. The size of the deletions is variable, and the molecular consequences are unknown. The aim of our study is to characterize this abnormality in a large cohort of patients.

The Groupe Francophone de Cytogenetique Hematologique (GFCH) collected data from 89 patients with CLL or Small Lymphocytic Lymphoma (SLL), harboring a del14q. Morphological review was performed for 65 of them and immunological review for 48. All karyotypes were reviewed by members of the GFCH. Fluorescence in situ hybridization (FISH) analysis was performed with CEP12, 13q14, TP53, ATM, 6q21, and IGH probes, and BACs RP11-35D12 and RP11-226F19 covering the ZFP36L1 gene on 14q24.1. SNP-array analysis (illumina omni1, omin2.5) was performed for 37 patients. The IGHV status was analyzed locally, or in our laboratory. The mutation hotspots of NOTCH1 (exon 34), SF3B1 (exons 14-16), XPO1 (exons 14-15), MYD88 (exon 5) and TP53 (exons 4-10) were analyzed by direct sequencing.

Patients were classified as 49 CLL Matutes score 4-5, 5 atypical CLL score 3 (all CD5+, CD23+), and 27 SLL. Eight patients were excluded with a Matutes score<3 or not evaluable. The sex ratio M/F was 1.02, the median age at diagnosis was 64.5 years [29-87]. Regarding all CLL, there were 35 (66%) stages A, 10 (19%) stages B and 8 (15%) stages C. The median time between diagnosis and the first treatment (TTT) was 17 months [0-144], the overall survival (OS) at 5 years was 93.7%. For the 27 SLL patients, the median TTT was 1 month [0-85], and the OS at 5 years was 88.1%.

The karyotype showed chromosomal translocation in 26/79 (33%) (10 balanced, 16 unbalanced) and was complex (> 3 abnormalities) in 26/79 (33%) cases. Using karyotype and FISH, we observed 28/79 (35%) trisomy 12, 12/79 (15%) 13q14 deletions, 11/80 (14%) TP53 deletions, 5/79 (6%) ATM deletions, 3/76 (4%) 6q21 deletions. The whole CLL cohort showed 15/53 (28%) tri 12, 11/53 (21%) del13q, 8/54 (15%) delTP53, 4/53 (7%) delATM, 2/50 (4%) del6q.

IGHV status was not mutated in 41/53 (77%) patients, and the gene IGHV1-69 was rearranged in 21/52 (40%) cases. NOTCH1 gene was mutated in 14/45 (31%) patients, SF3B1 in 2/45 (4%), XPO1 in 2/45 (4%), MYD88 in 0/43, TP53 in 6/43 (14%) cases. A significant association was observed between TP53 disrupted and NOTCH1 mutations (p=.04). NOTCH1 mutation was not correlated with tri12.

Regarding all the cytogenetic and molecular data, there was no significant difference between CLL score 4-5 and CLL score 3, and between CLL and SLL.

Compared with common CLL in the literature, CLL with del14q dysplayed more tri12 (p<.03) and NOTCH1 mutations (p<.003), less del13q (p<.0006), more unmutated IGHV (p<.00001) and V1-69 repertoire (p<.00001). Compared with common SLL in the literature, SLL with del14q also exhibited more tri12, unmutated IGHV (p<.01) and V1-69 (p<.04).

The 14q deletions appeared distributed along chromosome 14 from bands q11 to q32. The centromeric and telomeric breakpoints of the 14q deletion were investigated by FISH or SNP-array when material was available, and allowed us to identify a main group (Group 1) among 4 groups: Group 1: 37/77 (48%) patients, with IGH and ZFP36L1 loci rearranged; Group 2: 17/77 (22%), with ZFP36L1 deleted and IGH not deleted; Group 3: 7/77 (9%), with ZFP36L1 and IGH not deleted; Group 4, 16/77 (21%), all the other combinations. Group 1 showed a deletion del14q24.1-14q32.3 of about 38 megabases, which broke in or near ZFP36L1, and in the IGH gene. It included 26 (70%) CLL score 4-5 and 11 (30%) SLL. When compared to the other groups, Group 1 showed significantly more tri12 (p=.004), and NOTCH1 mutations (p=.02). IGHV status was unmutated in 22/24 (92%) patients in Group 1, 12/24 (50%) harboring the gene V1-69.

In conclusion, the size of the 14q deletion is variable, with in about half of the cases a recurrent interstitial deletion 14q24.1-14q32.3. Both CLL and SLL with del14q, particularly with the 14q24.1-14q32.3 deletion, are associated with poor prognosis parameters, like short time to treatment, trisomy 12, NOTCH1 mutated, and unmutated IGHV status, with an overrepresentation of the V1-69 gene.