scholarly journals Differential Genome-Wide Mutational Patterns in Indolent B-Cell Lymphomas

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 4102-4102
Author(s):  
Julieta Haydee Sepulveda Yanez ◽  
Diego Alvarez ◽  
Jose Fernandez-Goycoolea ◽  
Cornelis A.M. van Bergen ◽  
Hendrik Veelken ◽  
...  
Keyword(s):  
B Cell ◽  
Cell Lymphoma ◽  
R Package ◽  
Cpg Methylation ◽  
Unknown Etiology ◽  
Sequencing Data ◽  
B Cell Lymphomas ◽  
B Cell Malignancies ◽  
Mutational Signatures ◽  
Mutational Landscape

Abstract Introduction: In recent years, strategies have been developed to identify specific mutation patterns within next-generation sequencing data. Distinct mutational patterns can be linked to underlying mutagenic processes in human cancer. One approach analyzes single base substitutions in the context of their neighboring bases as trinucleotides. The relative prevalence of all possible 96 altered trinucleotides defines distinctive mutational signatures. The activity of activation-induced cytidine deaminase (AID) initiates a specific mutational process in B cells. AID induces deamination of deoxycytidine into deoxyuridine. Subsequent mechanisms to repair the resulting mismatch lead to different genomic alterations that can be assigned to three mutational signatures: a canonical signature characterized by C>T/G transitions at WRCY motifs, a non-canonical signature defined by A>C transversions at WAN motifs, and a third AID signature characterized by C>T transitions at RCG motifs with preference for methylated CpG (W: A or T; R: purine; Y: pyrimidine, N: any nucleotide). The latter signature has specifically been designated as AID-mediated CpG-methylation-dependent mutagenesis. AID activity has been linked to the pathogenesis of several B-cell lymphomas, including follicular lymphoma (FL), chronic lymphocytic leukemia (CLL), and mantle cell lymphoma (MCL). Therefore, we searched for the contribution of different AID signatures in these B-cell malignancies. Methods: We analyzed the mutational landscape in whole exome (WES) and whole genome (WGS) sequencing data from 41 FL, 30 CLL, 2 MBL, and 43 MCL cases. Somatic variants were called by comparison of tumor and germline DNA with an in-house developed pipeline. Mutational signatures were defined according to the 96-base substitution model (Alexandrov et al. 2013) by an unsupervised machine learning with implementation of the SomaticSignatures R package (Gehring et al. 2015). In addition, MutationalPattern R package (Blokzijl et al. 2018) was executed for comparison to mutational signatures defined in COSMIC. Results: In unsupervised analyses of FL, CLL/MBL, and MCL cases, 77% of the mutation spectrum variance was attributable to four signatures (S1-4). In FL, the mutational landscape was dominated by S4 characterized by mutations in both canonical and non-canonical AID motifs (40%, 95% CI: 35-76%). The second most frequent signature (S2; 27%, 21-49%) was characterized by C>A transitions in the context of the non-canonical AID and the CpG hotspot motifs (RCG). The mutational landscape of CLL and MBL was strongly dominated by signature S3 (50%, 45-95%). S3 contains mutations in RCG motifs as well as mutations in non-canonical AID motifs (NTW), but with a lower contribution that in S4. In contrast, the mutational landscape of MCL was dominated by S1 (31%, 24-55%) characterized by C>T transitions in the RCG motif in addition to a striking prevalence of the TCT>TTT transition that is known to be associated with the activity of APOBEC enzymes. In comparison to the mutational signatures in COSMIC, the lymphomas analyzed here carry a strong similarity to the COSMIC signatures 1, 5, and 25. These signatures are observed across a wide spectrum of cancer types and are either of unknown etiology (S5 and S25) or associated with age (S1). Conclusions: The most common point mutations in CLL/MBL and FL are C>T transitions and indicate a strong influence of AID on their mutational landscape. In the indolent B-cell malignancies, all three known AID-related signatures, i.e. canonical, non-canonical, and CpG-methylation-dependent can be found. In contrast, the genomic landscape of MCL is dominated by variants in CpG-methylation-dependent mutagenesis sites and by an APOBEC-related motif. In addition to AID-related signatures, we also found consensus signatures described in COSMIC such as the age-related spontaneous deamination signature 1. Our work independently confirms the role of AID in B-cell lymphoma pathogenesis but points to disease-specific mechanisms that modulate AID in the respective lymphoma cell of origin. In addition, our data suggest that distinctive repair mechanisms operate in different entities. Disclosures No relevant conflicts of interest to declare.

scholarly journals Comprehensive Genomic Analysis of Primary Mediastinal B-Cell Lymphoma

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 1564-1564 ◽  
Author(s):  
Bjoern Chapuy ◽  
Chip Stewart ◽  
Andrew Dunford ◽  
Jaegil Kim ◽  
Kirsty Wienand ◽  
...  
Keyword(s):  
B Cell ◽  
Research Funding ◽  
Cell Lymphoma ◽  
Protein Structures ◽  
Genomic Analysis ◽  
B Cell Lymphoma ◽  
Genetic Alterations ◽  
B Cell Lymphomas ◽  
Mutational Signatures ◽  
Large B Cell

Abstract Primary mediastinal large B-cell lymphomas (PMBL) typically occur in young women who present with localized, large mediastinal masses. These tumors share certain clinical, pathomorphological and transcriptional features with classical Hodgkin lymphoma (cHL). To date, PMBL genetic analyses focused on limited sets of genes and recurrent somatic copy number alterations (SCNAs). Previously, we identified frequent 9p24.1/PD-L1/PD-L2 copy gains and increased expression of the PD-1 ligands as a genetically-defined immune escape mechanism in PMBL. The demonstrated efficacy of PD-1 blockade in relapsed/refractory PMBL led to recent FDA approval and underscored the importance of characterizing targetable genetic vulnerabilities in this disease. For these reasons, we obtained diagnostic biopsy specimens from 37 patients with PMBL (median age 34; female 70%) and performed whole exome sequencing (WES) with an expanded bait set to capture structural variants (SVs). Somatic alterations (mutations, SCNAs and SVs) were determined using established analytical pipelines including our algorithm for evaluating tumors without paired normal samples. Genes more frequently mutated than by chance, Candidate Cancer Genes (CCGs), were identified with MutSig2CV and recurrent SCNAs were defined with GISTIC2.0. SVs were characterized with a recently described 4-algorithm pipeline (Nature Medicine, 2018;24(5):679-690). First, we identified 15 CCGs (q-value <0.1) including genes with known roles in PMBL, such as IL4R and TNFAIP3 and mutational drivers in additional B-cell lymphomas (B2M, GNA13, STAT6, IKZF3, XPO1, TP53, PAX5) and other cancers (TP53, ZNF217 and XPO1). Overlaying the predicted protein changes onto available 3D protein structures highlighted the likely biological functions of specific alterations, such as mutational clustering in the STAT6 DNA-binding domain. We next analyzed the PMBL mutational signatures and identified 3 cases as hypermutators with MSI signatures, including 2 with MLH1 frameshift mutations and 1 with a nonsense PMS2 mutation. Despite the young age of the PMBL patient cohort, the majority of remaining mutations were caused by spontaneous deamination at CpGs, a genetic signature usually associated with aging. The next most prevalent mutational signatures were APOBEC and, infrequently, AID. We observed a higher median mutational density in PMBL (7.56 mutations/MB), compared to diffuse large B-cell lymphoma (DLBCL) and most solid cancers, providing a potential basis for increased neoantigen production and responsiveness to PD-1 blockade. Next, we identified 18 recurrent SCNAs, including 10 copy gains (2 focal and 8 arm level) and 8 copy losses (7 focal and 1 arm level). Copy gains of 9p24.1/PD-L1/PD-L2 were detected in 70% of cases. SVs were defined at base-pair resolution and included infrequent (2/37) tandem duplications of both PD-1 ligands and inactivating CTIIA SVs (deletions and inversions) in 10% (4/37) of cases. Although PMBL had a higher mutational density than DLBCL, the PMBL alterations involved a smaller number of median genetic drivers (9 [PMBL] vs 17 [DLBCL], respectively). Combined analyses of recurrent CCGs, SCNAs and SVs revealed that certain candidate driver genes were perturbed by multiple mechanisms. Examples include: TNFAIP3 (59% overall, 41% mutations, 24% copy loss, 6% biallelic); and B2M (51% overall, 30% mutations, 27% copy loss, 6% biallelic). Concurrent analyses of the 3 types of genetic alterations also revealed multiple bases of perturbing specific signaling pathways. In this PMBL series, 73% (27/33) of tumors exhibited one or more alterations of JAK/STAT pathway components: IL4R mutations (32%), JAK2 (9p24.1 focal copy gain [70%]) and STAT6 mutations (43%). Additionally, 59% of PMBLs had alterations of antigen presentation pathway components including B2M copy loss or mutations, copy loss of 6q21.33 (which includes the HLA class I/II loci) and SVs of CTIIA. These findings provide a genetic framework for analyzing the precise mechanism of action of PD-1 blockade in PMBL. Taken together, these findings underscore the importance of a comprehensive genomic analysis in PMBL and define additional candidate treatment targets and pathogenetic mechanisms in this disease. ____ BC, CS and AD contributed equally. GG and MAS contributed equally. Disclosures Rodig: Merck: Research Funding; KITE: Research Funding; Affimed: Research Funding; Bristol Myers Squibb: Research Funding. Shipp:Merck: Research Funding; AstraZeneca: Honoraria; Bristol-Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Bayer: Research Funding.

Structural Variations Involving Programmed Death Ligands in B-Cell and T-Cell Lymphomas

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4105-4105
Author(s):  
Keisuke Kataoka ◽  
Hiroaki Miyoshi ◽  
Yasunori Kogure ◽  
Yasuharu Sato ◽  
Kenji Nishida ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
Research Funding ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Sequencing Data ◽  
B Cell Lymphomas ◽  
Structural Variations ◽  
Chugai Pharmaceutical ◽  
T Cell Lymphomas

Abstract Immune checkpoint blockade using anti-PD-1 or anti-PD-L1 antibodies is a highly promising therapy that can induce a durable anti-tumor response and a long-term remission in many patients with multiple cancer types. In particular, the excellent efficacy of anti-PD-1 antibody has been reported in advanced cases with classical Hodgkin lymphoma (cHL), of which high frequency of genetic lesions involving PD-L1 and/or PD-L2 somatic alterations is a defining feature, suggesting a close link between the relevant genetic lesions and the efficacy of anti-PD-1/PD-L1 therapy. In addition to cHL, several subtypes of B-cell lymphomas are shown to have structural variations (SVs) involving PD-1 ligands, such as gene amplification and chromosomal translocation causing promoter replacement. Moreover, recently we reported unique SVs disrupting the 3′-untranslated region (UTR) of PD-L1 in a diversity of cancers, including adult T-cell leukemia/lymphoma (ATL) and diffuse large B-cell lymphoma (DLBCL). However, the comprehensive landscape of PD-L1 and PD-L2 alterations in non-Hodgkin lymphomas has not been fully elucidated. Therefore, in this study, we interrogated PD-L1 and PD-L2 genetic aberrations and characterized their features in a variety of non-Hodgkin lymphomas. To do this, lymphoma-derived DNA was captured for the entire region of PD-L1 and PD-L2 genes including their exons, introns, and 3′- and 5′-untranslated regions (UTRs) and subjected to high-throughput DNA sequencing. More than 300 samples from different lymphoma subtypes were analyzed, including DLBCL, follicular lymphoma, mantle cell lymphoma, MALT lymphoma, primary mediastinal B-cell lymphoma, peripheral T-cell lymphoma-not otherwise specified, and cutaneous T-cell lymphoma. We also analyzed publicly available sequencing data as well as our own data for lymphomas, which included Burkitt and angioimmunoblastic T-cell lymphomas as well. PD-L1/PD-L2-involving SVs were most frequently observed in PMBCL, accounting for 26.3% of the cases, but widely observed in various B- and T-cell lymphomas at varying but generally low frequencies. However, in contrast to PD-L1-involving SVs, which were found in both B- and T-cell lymphomas, PD-L2-involving SVs were exclusively seen in B-cell lymphomas. Depending on samples, different SV types were observed, including deletion, inversion, tandem duplication, and translocation, but most of SVs resulted in a truncation of the 3'-UTR of the PD-L1 or PD-L2 genes. Unlike previous reports, we rarely found those SVs that translocate PD-L1/PD-L2 to an ectopic regulatory element. Of particular interest were those cases in which multiple, independent SVs that converged to PD-L1 and PD-L2, were observed in a single tumor sample, underscoring the importance of PD-L1 and PD-L2 SVs in clonal selection and expansion of these tumors Given that PD-L1-involving SVs are detected not only in aggressive lymphomas but also in a variety of solid cancers, we hypothesized that PD-L2 genetic alterations are also present in other human cancers. However, no PD-L2-involving SVs were identified among > 10,000 cancer samples from 32 tumor panels, for which RNA sequencing data were available from the Cancer Genome Atlas (TCGA). These results suggest that PD-L1 is affected in a broad spectrum of human malignancies, whereas PD-L2 SVs are a characteristic alteration of B-cell lymphomas, which is consistent with their expression patterns. Based on these findings, we assessed whether disruption of PD-L2 3'-UTR also induces PD-L2 overexpression as seen for that of PD-L1 3'-UTR. When introduced in T2 human B and T lymphoblast hybrid cell line using the CRISPR/Cas9 system, SVs involving an almost entire PD-L2 3'-UTR sequence actually induced a significant elevation of PD-L2 expression, confirming the relevance of 3'-UTR in the regulation of PD-L2 expression. Taken together, our findings clarified the entire picture of PD-L1/PD-L2-involving SVs ligands in B- and T-cell lymphomas. Detection of these SVs might help the identification of patients with non-Hodgkin lymphomas who potentially benefit from PD-1/PD-L1 blockade therapy. Disclosures Kataoka: Kyowa Hakko Kirin: Honoraria; Boehringer Ingelheim: Honoraria; Yakult: Honoraria. Izutsu:Abbvie: Research Funding; Gilead: Research Funding; Celgene: Research Funding; Janssen Pharmaceutical K.K.: Honoraria; Eisai: Honoraria; Kyowa Hakko Kirin: Honoraria; Chugai Pharmaceutical: Honoraria, Research Funding; Takeda Pharmaceutical: Honoraria; Mundipharma KK: Research Funding. Ohshima:Kyowa Hakko Kirin Co., Ltd.: Research Funding, Speakers Bureau; CHUGAI PHARMACEUTICAL CO.,LTD.: Research Funding, Speakers Bureau. Ogawa:Kan research institute: Consultancy, Research Funding; Takeda Pharmaceuticals: Consultancy, Research Funding; Sumitomo Dainippon Pharma: Research Funding.

scholarly journals TCL1: a shared tumor-associated antigen for immunotherapy against B-cell lymphomas

Blood ◽  
2012 ◽  
Vol 120 (8) ◽  
pp. 1613-1623 ◽  
Author(s):  
Jinsheng Weng ◽  
Seema Rawal ◽  
Fuliang Chu ◽  
Hyun Jun Park ◽  
Rakesh Sharma ◽  
...  
Keyword(s):  
T Cells ◽  
B Cells ◽  
B Cell ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Lymphocytic Leukemia ◽  
Patient Specific ◽  
Autologous Tumor ◽  
B Cell Lymphomas ◽  
B Cell Malignancies

Abstract Immunotherapy with therapeutic idiotype vaccines offers promise for treatment of B-cell malignancies. However, identification of novel immunogenic lymphoma-associated antigens that are universally expressed is necessary to overcome the barriers of patient-specific idiotype vaccines. Here, we determined whether T-cell leukemia/lymphoma 1 (TCL1) oncoprotein encoded by the TCL1 gene could be a target for immunotherapy of B-cell malignancies. We show that TCL1 mRNA and protein are selectively expressed in normal B cells but markedly hyperexpressed in multiple human B-cell lymphomas, including follicular lymphoma, chronic lymphocytic leukemia, mantle cell lymphoma, diffuse large B-cell lymphoma, and splenic marginal zone B-cell lymphoma. We demonstrated that TCL1-specific CD8+ T cells can be generated from HLA-A*0201 (HLA-A2)+ normal donors and identified TCL171-78 (LLPIMWQL) as the minimal epitope recognized by these T cells. More importantly, TCL171-78 peptide-specific T cells were present in the peripheral blood and tumor-infiltrating lymphocytes of lymphoma patients, could be expanded in vitro, and lysed autologous tumor cells but not normal B cells in an HLA-A2–restricted manner. Our results suggest that TCL1 is naturally processed and presented on the surface of lymphoma cells for recognition by cytotoxic T cells and can serve as a novel target for development of immunotherapeutic strategies against common B-cell lymphomas.

scholarly journals Advances and Perspectives in the Treatment of B-Cell Malignancies

Cancers ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 2266
Author(s):  
Marta Cuenca ◽  
Victor Peperzak
Keyword(s):  
Cell Differentiation ◽  
B Cell ◽  
Plasma Cell ◽  
Heterogeneous Group ◽  
B Cell Differentiation ◽  
B Cell Lymphomas ◽  
B Cell Malignancies ◽  
Plasma Cell Dyscrasias

B-cell malignancies arise from different stages of B-cell differentiation and constitute a heterogeneous group of cancers including B-cell lymphomas, B-cell leukemias, and plasma cell dyscrasias [...]

scholarly journals Correlations between baseline 18F-FDG PET tumour parameters and circulating DNA in diffuse large B cell lymphoma and Hodgkin lymphoma

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Pierre Decazes ◽  
Vincent Camus ◽  
Elodie Bohers ◽  
Pierre-Julien Viailly ◽  
Hervé Tilly ◽  
...  
Keyword(s):  
B Cell ◽  
Hodgkin Lymphoma ◽  
Fdg Pet ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Circulating Dna ◽  
Tumour Burden ◽  
B Cell Malignancies ◽  
Large B Cell Lymphoma ◽  
Large B Cell

Abstract Background 18F-FDG PET/CT is a standard for many B cell malignancies, while blood DNA measurements are emerging tools. Our objective was to evaluate the correlations between baseline PET parameters and circulating DNA in diffuse large B cell lymphoma (DLBCL) and classical Hodgkin lymphoma (cHL). Methods Twenty-seven DLBCL and forty-eight cHL were prospectively included. Twelve PET parameters were analysed. Spearman’s correlations were used to compare PET parameters each other and to circulating cell-free DNA ([cfDNA]) and circulating tumour DNA ([ctDNA]). p values were controlled by Benjamini–Hochberg correction. Results Among the PET parameters, three different clusters for tumour burden, fragmentation/massiveness and dispersion parameters were observed. Some PET parameters were significantly correlated with blood DNA parameters, including the total metabolic tumour surface (TMTS) describing the tumour–host interface (e.g. ρ = 0.81 p < 0.001 for [ctDNA] of DLBLC), the tumour median distance between the periphery and the centroid (medPCD) describing the tumour’s massiveness (e.g. ρ = 0.81 p < 0.001 for [ctDNA] of DLBLC) and the volume of the bounding box including tumours (TumBB) describing the disease’s dispersion (e.g. ρ = 0.83 p < 0.001 for [ctDNA] of DLBLC). Conclusions Some PET parameters describing tumour burden, fragmentation/massiveness and dispersion are significantly correlated with circulating DNA parameters of DLBCL and cHL patients. These results could help to understand the pathophysiology of B cell malignancies.

Distinct roles for PARP-1 and PARP-2 in c-Myc-driven B-cell lymphoma in mice

Blood ◽  
2021 ◽  
Author(s):  
Miguel A Galindo-Campos ◽  
Nura Lutfi ◽  
Sarah Bonnin ◽  
Carlos Martínez ◽  
Talia Velasco-Hernandez ◽  
...  
Keyword(s):  
Dna Damage ◽  
B Cells ◽  
B Cell ◽  
Immune Escape ◽  
Cell Lymphoma ◽  
Tumour Progression ◽  
Cancer Therapeutics ◽  
B Cell Lymphoma ◽  
B Cell Lymphomas ◽  
Parp 1

Dysregulation of the c-Myc oncogene occurs in a wide variety of haematologic malignancies and its overexpression has been linked with aggressive tumour progression. Here, we show that Poly (ADP-ribose) polymerase (PARP)-1 and PARP-2 exert opposing influences on progression of c-Myc-driven B-cell lymphomas. PARP-1 and PARP-2 catalyse the synthesis and transfer of ADP-ribose units onto amino acid residues of acceptor proteins in response to DNA-strand breaks, playing a central role in the response to DNA damage. Accordingly, PARP inhibitors have emerged as promising new cancer therapeutics. However, the inhibitors currently available for clinical use are not able to discriminate between individual PARP proteins. We found that genetic deletion of PARP-2 prevents c-Myc-driven B-cell lymphomas, while PARP-1-deficiency accelerates lymphomagenesis in the Em-Myc mouse model of aggressive B-cell lymphoma. Loss of PARP-2 aggravates replication stress in pre-leukemic Em-Myc B cells resulting in accumulation of DNA damage and concomitant cell death that restricts the c-Myc-driven expansion of B cells, thereby providing protection against B-cell lymphoma. In contrast, PARP-1-deficiency induces a proinflammatory response, and an increase in regulatory T cells likely contributing to immune escape of B-cell lymphomas, resulting in an acceleration of lymphomagenesis. These findings pinpoint specific functions for PARP-1 and PARP-2 in c-Myc-driven lymphomagenesis with antagonistic consequences that may help inform the design of new PARP-centred therapeutic strategies with selective PARP-2 inhibition potentially representing a new therapeutic approach for the treatment of c-Myc-driven tumours.

Diagnostic utility of SOX11 immunohistochemistry in differentiating cutaneous spread of mantle cell lymphoma from primary cutaneous B-cell lymphomas

2016 ◽  
Vol 43 (4) ◽  
pp. 354-361 ◽  
Author(s):  
Andy C. Hsi ◽  
M. Yadira Hurley ◽  
Sena J. Lee ◽  
Ilana S. Rosman ◽  
Xiaofan Pang ◽  
...  
Keyword(s):  
B Cell ◽  
Mantle Cell Lymphoma ◽  
Cell Lymphoma ◽  
Diagnostic Utility ◽  
B Cell Lymphomas ◽  
Mantle Cell

scholarly journals Recurrent Mutations within the Nfkbie gene: A Novel Mechanism for NF-κB Deregulation in Aggressive Chronic Lymphocytic Leukemia

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 297-297
Author(s):  
Larry Mansouri ◽  
Lesley-Ann Sutton ◽  
Viktor Ljungstrom ◽  
Sina Bondza ◽  
Linda Arngarden ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
B Cell ◽  
Mutant Allele ◽  
B Cell Lymphoma ◽  
Lymphocytic Leukemia ◽  
B Cell Lymphomas ◽  
Tlr Signaling ◽  
B Cell Malignancies ◽  
Recurrent Mutations ◽  
Genomic Aberrations

Abstract Dysregulated NF-κB signaling appears to be particularly important in B-cell malignancies, with recurrent mutations identified within both the canonical and non-canonical NF-κB pathways, as well as in components of the B-cell receptor (BcR) and Toll-like receptor (TLR) signaling pathways. In chronic lymphocytic leukemia (CLL), although recurrent mutations have been identified in MYD88 (TLR signaling) and BIRC3 (non-canonical NF-κB pathway), their frequency is low (<3%) and hence the extent to which genetic aberrations may contribute to constitutional NF-κB activation remains largely unknown. To gain further insight into this issue, we designed a HaloPlex gene panel (Agilent Technologies) and performed targeted next-generation sequencing (NGS) (HiSeq 2000/Illumina) of 18 NF-κB genes in a discovery cohort of 124 CLL patients, intentionally biased towards poor-prognostic patients with either unmutated IGHV genes or high-risk genomic aberrations. Using a conservative cutoff of >10% for the mutant allele, we identified mutations (n=35) within 30/124 (24%) patients in 14/18 NF-κB genes analyzed. IκB genes, which encode for cytoplasmic inhibitor proteins, accounted for 20/35 (57%) mutations, with IκBε (encoded by NFKBIE) mutated in 8 patients; notably, 3/8 cases carried an identical 4bp deletion within exon 1 of NFKBIE. Prompted by these findings, we proceeded to validate our findings in an independent CLL cohort (n=168) using the same methodology as above and primarily focusing on cases with poor-prognostic features. We identified 30 mutations within 28 CLL patients in 11/18 NF-κB genes analyzed. Strikingly, 13/30 mutations were found within IκBε, with 10/13 patients carrying the same 4bp NFKBIE deletion. Notably, investigations into whether additional cases (within both the discovery and validation cohort) may harbor mutations of low clonal abundance (<10% mutant allele), led to the detection of the NFKBIE deletion in another 18 cases. Owing to the prevalence of this 4bp deletion within the NFKBIE gene, we developed a GeneScan assay and screened an additional 312 CLL cases. Collectively, 40/604 (6.6%) CLL patients were found to carry this frame-shift deletion within the NFKBIE gene, which is in line with a recent publication reporting that 10% of Binet stage B/C patients carried this mutation (Damm et al. Cancer Discovery 2014). Remarkably, the majority of these NFKBIE mutations (16/40) were found in a subgroup of patients that expressed highly similar or stereotyped BcRs and are known to have a particularly poor outcome, denoted as subset #1. This finding thus alludes to a subset-biased acquisition and/or selection of genomic aberrations, similar to what has been reported for subset #2 and SF3B1, perhaps as a result of particular modes of BcR/antigen interaction. We utilized proximity-ligation assays to test the functional impact of the NFKBIE deletion by investigating protein-protein interactions. This analysis revealed reduced interaction between the inhibitor IκBε and the transcription factor p65 in NFKBIE-deleted CLL cells; IκBε-knock-down shRNA experiments confirmed dysregulated apoptosis/NF-κB signaling. Finally, to assess whether the NFKBIE deletion could also be present in other B-cell malignancies, we screened 372 mature B-cell lymphoma cases using NGS or the GeneScan assay and found the deletion in 7/136 (5.1%) mantle cell lymphomas, 3/66 (4.5%) diffuse large B-cell lymphomas and 3/170 (1.8%) splenic marginal zone lymphomas. Taken together, our analysis revealed that inactivating mutations within the NFKBIE gene lead to NF-κB activation in CLL and potentially several other B-cell-derived malignancies. Considering the central role of BcR stimulation in the natural history of CLL, the functional loss of IκBε may significantly contribute to sustained CLL cell survival and shape the disease evolution. This novel data strongly indicates that components of the NF-κB signaling pathway may be prime targets for future targeted therapies not only in CLL but also other mature B-cell lymphomas. Disclosures No relevant conflicts of interest to declare.

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