Deletion 7q Is Associated with KLF2 and NOTCH2 Mutations and Is Strongly Correlated with Splenic Marginal Zone Lymphoma but Also Found in Lymphoplasmacytic Lymphoma and Hairy Cell Leukemia Variant

Introduction: Deletion 7q (del(7q)) isa common cytogenetic aberration in lymphoma and has been associated with splenic marginal zone lymphoma (SMZL). Del(7q) has been proposed to distinguish SMZL from other forms of MZL, i.e. MALT lymphoma and nodal MZL. However, the value of del(7q) in the differential diagnosis of other lymphoid malignancies has not been elucidated. Furthermore, the overall increasing diagnostic and prognostic importance of somatic mutations in hematologic malignancies prompted us to analyze the mutational landscape in lymphomas with del(7q).

Aims: To understand the role of del(7q) in lymphoma diagnosis, to define the minimal deleted region in del(7q) bearing lymphomas and to analyze co-occurring cytogenetic aberrations and co-mutations.

Patients and Methods: From 2005 to 2017 a total of 5251 patients were diagnosed with lymphoma at our institution by flow cytometry, chromosome banding analysis (CBA) and FISH (2547 (48%) in bone marrow, 2704 (52%) in peripheral blood). Subject of the present study were 3917 patients who were selected based on an aberrant karyotype by (CBA) in order to exclude inclusion of false negative CBA due to limited lymphoma infiltration. To evaluate del(7q) as biological relevant primary hit, del(7q) had to be part of the major clone without a complex karyotype (≥3 abnormalities). 109/3917 patients met this criterion. CD5 negative lymphomas were diagnosed by flow cytometry according to the respective suggestive phenotype as SMZL or lymphoplasmacytic lymphoma (LPL). For 37/109 patients (34%) that had ≥ 20% of lymphoma infiltration by flow cytometry the diagnostic sample was available for array comparative genomic hybridization (aCGH). For 44/109 patients (40%) that had ≥10% infiltration by flow cytometry the diagnostic sample was available for sequencing of 63 genes frequently mutated in hematologic malignancies.

Results: We found 109/3917 patients with a del(7q) by CBA (3%). Lymphoma diagnosis with del(7q) included the following eight entities as defined by flow cytometry at decreasing frequency: SMZL (59%), LPL (21%), B-cell prolymphocytic leukemia (6%), hairy cell leukemia variant (HCLv, 6%), chronic lymphocytic leukemia (CLL, 4%), mantle cell lymphoma (2%), aggressive lymphoma (2%), and follicular lymphoma (0.9%). The presence of del(7q) was significantly associated with SMZL, LPL and HCLv (each p<0.0001). Del(7q) was negatively correlated with CLL (p<0.0001). Recurrent cytogenetic aberrations that co-occurred with del(7q) include del(11q), trisomy 3 and dup(1q) in 9%, 3% and 2%, respectively.

We analyzed 37/109 patients with aCGH and defined a minimal deleted region of 1.9 MB (Chr7; 128.973.948-130.908.181). Deleted genes in this region include KLF14 (kruppel-like factor 14) and a microRNA (MIR) cluster associated with tumor suppression (MIR182-96-183, MIR 29A, MIR96). The deletion was not entity specific, but 2/5 CLL samples showed a deletion outside the common region of the other lymphomas (7q35-q36.3 and 7q11.21-q21.2).

In 44/109 patients the diagnostic sample was analyzed by gene panel sequencing (63 genes) to identify the mutational landscape of del(7q) lymphoma. We identified a total of 53 mutations in 19 different genes in 29/44 patients (66%). The top 10 mutated genes were: KLF2 (27%), NOTCH2 (23%), CXCR4 (9%), MYD88 (9%), NOTCH1 (7%), BIRC3 (7%), MAP2K1 (5%), NRAS (5%), TET2 (5%) and TP53 (5%). Co-occurring mutations in KLF2 and NOTCH2 were observed in 4/44 patients (9%).

Somatic mutations in NOTCH2 (10/10) and/or KLF2 (12/12) were exclusively observed in SMZL, and MYD88 (4/4) mutations exclusively in LPL as described in the literature (Fig.). The presence of del(7q) and a mutation in KLF2 and/or NOTCH2 was highly predictive for the diagnosis of SMZL (p<0.0001). Moreover in the presence of del(7q) 18/44 analyzed patients (41%) had NOTCH2 or KLF2 mutations compared to 8% in the control cohort (p<0.0001).

Conclusion: Our analysis shows that del(7q) is not restricted to SMZL and is in fact associated also with LPL and HCLv. There is a small common deleted region spanning 1.9 MB at 7q31.32q32.3 which is not entity specific and includes a MIR cluster associated with tumor suppression. Mutations in KLF2 and NOTCH2 were found to be associated with del(7q), which raises the possibility of a common mechanism that remains to be elucidated. Taken together del(7q) combined with somatic mutations in KLF2 and/or NOTCH2 is highly specific for SMZL.

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