Splenic marginal zone lymphoma (SMZL) is an indolent B-cell neoplasm involving the spleen, bone marrow, and, in a fraction of cases, the peripheral blood. With the exception of TP53 disruption in a minority of cases, the molecular pathogenesis of SMZL is poorly understood. Although activation of the NF-kB pathway occurs frequently in SMZL, knowledge of the genetic mechanism driving NF-kB deregulation in this lymphoma is lacking. This study aims at providing a comprehensive molecular characterization of the NF-kB pathway in SMZL. The study included 99 SMZL, and followed a discovery-validation approach. Mutation analysis of 33 NF-kB pathway genes (BIRC2, BIRC3, BCL10, CARD11, CD40, CD79A, CD79B, CHUK, CSNK1A1, CYLD, IKBKB, IKBKG, MALT1, MAP3K14, MAP3K7, MAP3K7IP2, MAP3K7IP3, NFKB1, NFKBIA, NFKBIB, PRKCB1, REL, RIPK1, TNFAIP3, TNFRSF11A, TNFRSF13C, TNFSF13B, TRAF1, TRAF2, TRAF3, TRAF4, TRAF5, TRAF6) was applied to a discovery panel of 16 SMZL. The discovery panel allowed the identification of at least 1 mutated case (probability >0.9) for mutations whose prevalence is ≥ 10% in the SMZL population. Genes found to be mutated in the discovery panel were further sequenced in a cohort of 83 SMZL in order to characterize the frequency and recurrency of the genetic lesion. Copy number changes of the 33 NF-kB genes investigated were obtained by SNP array (GeneChip Human Mapping 250K NspI, Affimetrix). SMZL was characterized by an array of lesions affecting genes at different levels of the NF-kB pathway. Overall, 15/99 SMZL (15.0%) carried somatic mutations in genes regulating the NF-kB pathway, including TNFAIP3, TRAF3, BIRC3 and CD79A. Mutations of TNFAIP3, TRAF3, BIRC3 and CD79A were mutually exclusive among SMZL cases. Mutations of TNFAIP3 were most frequent and occurred in 6/99 (6.0%) SMZL. All mutations were represented by small insertions/deletions leading to frameshift. By SNP array, deletions encompassing TNFAIP3 were observed in 9/99 (9.0%) SMZL. By combining SNP array and mutation analysis, 13/99 (13.0%) SMZL harbored TNFAIP3 disruption by mutation and/or deletion. Mutations of TRAF3 occurred in 4/99 (4.0%) SMZL. Mutations were small insertions/deletions leading to frameshift (n=2), non-sense mutations (n=1), and missense mutations (n=1). By SNP array, deletions encompassing TRAF3 were observed in 7/99 (7.7%) SMZL. By combining SNP array and mutation analysis, 10/99 (10.0%) SMZL harbored TRAF3 disruption by mutation and/or deletion. Mutations of BIRC3 occurred in 4/99 (4.0%) SMZL. Mutations were non-sense mutations (n=1) or insertions/deletions leading to frameshift (n=3). By SNP array, deletions encompassing BIRC3 were observed in 5/99 (5.0%) SMZL. By combining SNP array and mutation analysis, 9/99 (9.0%) SMZL harbored BIRC3 disruption by mutation and/or deletion. Mutations and deletion of BIRC3 were mutually exclusive, suggesting a haploinsufficiency effect of BIRC3 genetic lesions. One mutation of the CD79A gene was observed out of 99 SMZL, and was represented by a single bp insertion leading to frameshift of the entire ITAM domain. Overall, by combining mutation analysis with SNP array data of the TNFAIP3, TRAF3, BIRC3 and CD79A genes, 28/99 (28.2%) SMZL harbored at least one genetic lesion affecting the NF-kB pathway. The prevalence of genetic lesions affecting the NF-kB pathway did not differ between HCV- (20/77, 26.0%) and HCV+ (4/15, 26.7%) SMZL (p=1.000). Also, the prevalence of NF-kB pathway genetic lesions did not differ among SMZL subgroups defined by TP53 disruption, immunoglobulin gene mutation status, or stereotyped B cell receptor. These observations document that genetic lesions targeting the NF-kB pathway by mutation and/or deletion are frequently involved in the pathogenesis of SMZL and might provide novel therapeutic targets for this lymphoma. The novel finding of BIRC3 inactivating mutations in SMZL points to a more general role of BIRC3 (also known as cIAP2) in marginal zone lymphoma, since BIRC3/cIAP2 is also involved in the t(11;18) translocation of MALT lymphoma.
No relevant conflicts of interest to declare.
Asterisk with author names denotes non-ASH members.