Mature B-cell Tumors Research Articles

Phase I study of the Syk inhibitor sovleplenib in relapsed or refractory mature B-cell tumors.

Sovleplenib (HMPL-523) is a selective spleen tyrosine kinase (Syk) inhibitor with anti-tumor activity in preclinical models of B-cell malignancy. We conducted a dose-escalation and dose-expansion phase I study of sovleplenib in patients with relapsed/ refractory mature B-cell tumors. Dose escalation followed a 3+3 design; patients received oral sovleplenib (200-800 mg once daily [q.d.] or 200 mg twice daily [b.i.d.], 28-day cycles). During dose expansion, patients were enrolled into four cohorts per lymphoma classification and treated at the recommended phase II dose (RP2D) (clinicaltrials gov. Identifier: NCT02857998). Overall, 134 Chinese patients were enrolled (dose escalation, N=27; dose expansion, N=107). Five patients experienced dose-limiting toxicities: one each of amylase increased (200 mg q.d.), febrile neutropenia (800 mg q.d.), renal failure (800 mg q.d.), hyperuricemia and blood creatine phosphokinase increased (200 mg b.i.d.) and blood bilirubin increased and pneumonia (200 mg b.i.d.). RP2D was determined as 600 mg (>65 kg) or 400 mg (≤65 kg) q.d.. The primary efficacy end point of independent review committee-assessed objective response rate in indolent B-cell lymphoma was 50.8% (95% confidence interval: 37.5- 64.1) in 59 evaluable patients at RP2D (follicular lymphoma: 60.5%, marginal zone lymphoma: 28.6%, lymphoplasmacytic lymphoma/Waldenström macroglobulinemia, 0%). The most common (≥10% patients) grade ≥3 treatment-related adverse events in the dose-expansion phase were decreased neutrophil count (29.9%), pneumonia (12.1%) and decreased white blood cell count (11.2%). Pharmacokinetic exposures increased dose-proportionally with ascending dose levels from 200-800 mg, without observed saturation. Sovleplenib showed anti-tumor activity in relapsed/refractory B-cell lymphoma with acceptable safety. Further studies are warranted.

IGLL5 controlled by super-enhancer affects cell survival and MYC expression in mature B-cell lymphoma

IGLL5 is shown to be located near super-enhancer (SE) in B-cell tumors, and this gene is frequently mutated and a target of translocation in B-cell tumors. These results suggest roles of the IGLL5 in tumorigenesis; however, its functional properties have been unclear. We found that two mature B-cell lymphoma cell lines expressed IGLL5 mRNA with Cλ1 segment. JQ1 treatment resulted in down-expression of IGLL5, indicating that IGLL5 is controlled by SE. IGLL5 knockdown induced cell death with down-expression of MYC. Our results suggested that IGLL5 might have a role in survival of mature B-cell tumors and involvement in MYC expression. (100 words)

Inferred Gene Expression By Cell-Free DNA Profiling Allows Noninvasive Lymphoma Classification

Background : Current diagnostic criteria for mature B-cell tumors require a combination of histopathological, immunophenotypic, cytogenetic, and genetic evaluations on tissue biopsy specimens (Campo, Blood 2022; Alaggio, Leuk 2022). Despite this battery of techniques, substantial heterogeneity remains in specific subgroups that can be further resolved using additional molecular diagnostic methods, including gene expression profiling (GEP). For example, among aggressive B-cell tumors, a subset recognized as high-grade B-cell lymphomas can be identified as harboring MYC+BCL2 lesions by FISH (HGBCL-DH-BCL2). However, a significant remaining high-risk subset also have a characteristic tumor gene expression “double-hit signature” or “dark zone signature” (DZsig) (Ennishi, JCO 2018; Alduaij, Blood 2023). Yet, inadequate tissue specimens can limit the application of these techniques for some patients. Separately, the invasive nature of tissue biopsies and their attendant risks can preclude adequate diagnostic evaluations in some patients, and logistical barriers for obtaining surgical tissue specimens can result in diagnostic delays. To address these unmet needs, we tested the performance of a novel noninvasive strategy to detect and classify mature B-cell tumors using plasma cfDNA, with special attention to HGBCL-DH-BCL2 and DZsig. Methods : We used EPIC-Seq to infer expression levels for genes of interest, using cfDNA fragmentomic signals at their transcription start sites (Esfahani, Nat Biotech 2022). We first curated and catalogued genes from prior GEP studies (n=56) of >10k diverse lymphoid tumors profiled by various RNA techniques. We systematically prioritized genes recurrently identified in multiple studies of tumor-specific expression profiles as compared with other tumor types and normal tissues. We included canonical markers used for immunodiagnosis by IHC and FACS, as well as key lineage and differentiation markers of normal B and T cells, and other leukocyte subsets. Finally, we also included recurrently mutated genomic regions and fusion hotspots for quantifying ctDNA levels using variant allelic fractions (VAF). To validate performance of DZsig in FFPE for HGBCL-DH-BCL2, we analyzed 95 FFPE biopsies by FISH (20% HGBCL-DH-BCL2), IHC, and RNA-seq. We then analyzed 36 corresponding pretreatment cfDNA samples (28% HGBCL-DH-BCL2) and used EPIC-Seq to infer gene expression. Results: Starting from our curated catalogue, we designed a targeted lymphoid EPIC-Seq panel (1676 genes; 2.6 MB) to resolve 11 major mature lymphoid malignancies and their clinically relevant molecular subtypes (cHL, DLBCL, HGBCL, FL, MCL, BL, MZL, PMBCL, SLL/CLL, PTCL, and MM). We next applied this EPIC-Seq panel to profile cfDNA samples from 207 lymphoma patients, including cHL (n=113), DLBCL (n=66), FL (n=15), and MCL (n=13) as well as healthy adults to assess specificity. We tested histology specific signatures derived from several existing RNA GEP datasets for cHL from sorted HRS cells (~85k by scRNA-Seq) and for DLBCL (n=959), FL (n=635), and MCL (n=100) from bulk RNA-Seq. Using this approach, we found high correlations between EPIC-Seq signature scores from cfDNA and corresponding circulating tumor VAFs in each histology [cHL (R p=0.83), DLBCL (R p=0.83), FL (R p=0.87), MCL (R p=0.81); Fig A]. In addition, when measuring these tumor derived signatures in cfDNA, each histology was significantly distinguishable from healthy controls (AUCs: cHL 0.94, DLBCL 0.91, FL 0.77, MCL 0.96). We next evaluated the DZsig when measured in LBCL patients and comparing paired tumor and cfDNA samples. We first confirmed the performance of the DZsig for detection of HGBCL-DH-BCL2 in 95 FFPE tumors by RNA-Seq (p<0.0001, AUC 0.85). We then noninvasively measured the DZsig in plasma cfDNA by EPIC-Seq (cfDZsig) and found significant discrimination of HGBCL-DH-BCL2 and DLBCL (p=0.0088, AUC 0.78, Fig B). Conclusions: These results confirm that inferred gene expression by cfDNA profiling allows noninvasive diagnosis of multiple lymphoma subtypes, including classification of challenging diagnostic entities such as HGBCL and DZsig+ tumors. Our ability to design and validate a pan-lymphoid gene panel for detection and classification of several lymphoma subtypes suggests the promise of this approach for other diverse tumors as well as the refinement of cfDZsig using a larger cohort.

Genome-Wide Association Study for Waldenström Macroglobulinemia Identifies Novel Susceptibility Loci

Waldenström macroglobulinemia (WM) is a unique subset of lymphoplasmacytic lymphoma (LPL) that is defined by the presence of an LPL infiltrate in the bone marrow together with a monoclonal IgM protein in the serum. Family history is strongly associated with risk of WM, and the estimated heritability is high; however, the genetic basis for WM predisposition remains unknown. To identify susceptibility loci for WM, we conducted a two-stage genome-wide association study (GWAS) in over 500 WM/LPL cases and 4300 controls of European ancestry. In the discovery stage (stage 1), 217 unrelated WM cases (40% familial) and 3,798 controls were genotyped on the Illumina Omni Express or Illumina Omni2.5 platforms. After quality control filtering, the data were imputed using the Haplotype Reference Consortium panel and analyzed using logistic regression. Eleven promising loci (P <5.0 x 10-7) were selected for replication in 313 WM/LPL cases and 564 controls. Two novel loci were convincingly replicated in stage 2 (P<1.2 x 10-5) and reached genome-wide significance in the combined analysis of both stages: 6p25.3 (EXOC2, OR=21.14, P=1.36 x 10-54) and 14q32.13 (intergenic near TCL1, OR=4.90, P=8.74 x 10-19). A possible second independent signal was observed at 14q32.13 but did not reach genome-wide significance (P=4.66 x 10-7). When the analysis was limited to WM, results were slightly stronger but generally similar to those for WM/LPL combined. Dysregulated TCL1 expression in B cells enhances cell proliferation and survival, leading to cell transformation and mature B-cell tumors, and TCL1 has been shown to be aberrantly expressed in WM. EXOC2 interacts with Ral proteins to mediate oncogenic RAS signaling that is critical for cancer cell survival and proliferation. We found that cells transduced with the EXOC2 variant allele reporter pCS-EGFP-3'G showed significantly increased EGFP fluorescence compared to the wildtype, suggesting the variant is associated with increased EXOC2 protein levels. Cells harboring the EXOC2 variant allele were also observed to have significantly increased cell proliferation compared to wildtype cells. We further discovered that the E XOC2 variant abrogates a miRNA binding site, possibly contributing to gene expression changes for NF-κB pathway constituents. Together these newly discovered loci explain ~4% of the familial risk and suggest possible underlying biological mechanisms, significantly increasing our understanding of the genetic susceptibility of WM/LPL. DisclosuresCerhan:Janssen: Other: Scientific Advisory Board (REMICADELYM4001); Janssen: Other: Multiple Myeloma Registry Steering .

New responsibilities for aged kinases in B-lymphomas.

The knowledge accumulated over the last decade on B-cell-derived non-Hodgkin lymphoma (B-NHL) pathogenesis has led to the identification of several molecular abnormalities, opening new perspectives in the design of novel therapies. Indeed, drugs targeting specific biochemical pathways critical for B-NHL cell survival, proliferation, and fitness within the malignant microenvironment are now available to the clinician: the B-cell receptor signaling inhibitors of BTK, PI3Kδ, ζ, γ, and SYK or the pro-apoptotic BH3-mimetics are clear examples of it. Moreover, it is emerging that malignant B-cell growth is sustained not only by mutations in oncogenes/tumor suppressors but also by the "addiction" to nononcogene (ie, nonstructurally altered) molecules. In this regard, a consistent body of data has established that the Ser/Thr kinases CK1, CK2, and GSK3 are involved in malignant lymphocyte biology and act as pro-survival and signaling-boosting molecules, both in precursor and mature B-cell tumors. Currently, an experimental and clinical groundwork is available, upon which to design CK1-, CK2-, and GSK3-directed antilymphoma/leukemia therapies. In this review, we have examined the main features of CK1, CK2, and GSK3 kinases, summarized the data in B-NHL supporting them as suitable therapeutic targets, and proposed a perspective on potential future research development.

Synergistic Targeting of the Regulatory and Catalytic Subunits of PI3Kδ in Mature B-cell Malignancies.

Purpose: Aberrant activation of the B-cell receptor (BCR) is implicated in the pathogenesis of mature B-cell tumors, a concept validated in part by the clinical success of inhibitors of the BCR-related kinases BTK (Bruton's tyrosine kinase) and PI3Kδ. These inhibitors have limitations, including the paucity of complete responses, acquired resistance, and toxicity. Here, we examined the mechanism by which the cyclic-AMP/PDE4 signaling axis suppresses PI3K, toward identifying a novel mechanism-based combinatorial strategy to attack BCR-dependency in mature B-cell malignancies.Experimental Design: We used in vitro and in vivo diffuse large B-cell lymphoma (DLBCL) cell lines and primary chronic lymphocytic leukemia (CLL) samples to preclinically evaluate the effects of the combination of the FDA-approved phosphodiesterase 4 (PDE4) inhibitor roflumilast and idelalisib on cell survival and tumor growth. Genetic models of gain- and loss-of-function were used to map multiple signaling intermediaries downstream of the BCR.Results: Roflumilast elevates the intracellular levels of cyclic-AMP and synergizes with idelalisib in suppressing tumor growth and PI3K activity. Mechanistically, we show that roflumilast suppresses PI3K by inhibiting BCR-mediated activation of the P85 regulatory subunit, distinguishing itself from idelalisib, an ATP-competitive inhibitor of the catalytic P110 subunit. Using genetic models, we linked the PDE4-regulated modulation of P85 activation to the oncogenic kinase SYK.Conclusions: These data demonstrate that roflumilast and idelalisib suppress PI3K by distinct mechanisms, explaining the basis for their synergism, and suggest that the repurposing of PDE4 inhibitors to treat BCR-dependent malignancies is warranted. Clin Cancer Res; 24(5); 1103-13. ©2017 AACR.

Synergism Between PDE4 and PI3Kδ Inhibitors in DLBCL: Improved Clinical Activity with the Potential for Lower Toxicity

Aberrant activation of the B cell receptor (BCR) is a hallmark of mature B-cell tumors. A better understanding of this process will spearhead effective clinical translation. The initiation and amplification of BCR signaling are well-defined events, and the successful deployment of BTK and PI3Kδ inhibitors in the clinic capitalizes on this knowledge. Conversely, the intricacies of the termination of BCR signals are less well-understood, and to date no rational therapeutic approach has been developed that exploit this aspect of the oncogenic BCR. Cyclic-AMP (cAMP) is a second messenger with marked growth suppression properties towards immune cells, including neoplastic mature B lymphocytes. In earlier work, we showed that inhibition of phosphodiesterase 4 (PDE4), the enzyme that hydrolyzes cAMP, downmodulates the activity of classical effectors of BCR signals, including SYK and PI3K. Herein, we attempted to gain further mechanistic understanding on how cAMP suppresses the proximal BCR activity, and built on this information to pre-clinically test therapeutic strategies that simultaneously attack the BCR at its amplification and termination points.Using diffuse large B cell lymphoma (DLBCL) as a model, we focused our attention on the interplay between cAMP and LCK, as we unexpectedly found that this cAMP-regulated canonical T-cell kinase is also widely expressed in DLBCL. Working with LCK-positive PDE4-low/null DLBCL cell lines, we found a marked increase in the phosphorylation of the inhibitory Y505 of LCK following elevation of intra-cellular cAMP. Next, we showed that ectopic expression of wild-type (WT) PDE4B, but not of a phosphodiesterase-inactive (PI) mutant, abrogated the cAMP-mediated, CSK-dependent, phosphorylation of LCK. Active LCK can phosphorylate PI3K's p85 regulatory subunit, thus freeing the catalytic domain from its structural constraints to promote lipid kinase activity. Thus, we tested whether the cAMP-mediated inhibition of LCK, by suppressing p85 phosphorylation, down-modulated PI3K activity. In LCK-positive PDE4B-null DLBCL, we showed that cAMP readily decreased the phosphorylation of p85 that followed BCR engagement; using the WT and PI PDE4B genetic models, we demonstrated that PDE4B expression abrogated cAMP effects and led to sustained PI3K activity following BCR engagement.These data suggested that inhibition of PDE4, by unleashing the negative effects of cAMP on LCK/p85, could accelerate the termination of PI3K activation that follows BCR engagement. If this hypothesis was correct, then the combination of PI3K and PDE4 inhibitors by attacking the BCR at its amplification and termination points, respectively, may synergistically suppress the growth of DLBCL. In in vitro studies with multiple DLBCL cell lines (WSU-NHL, OCI-Ly7, OCI-Ly18, OCI-Ly3, HBL-1, and OCI-Ly10) we showed that the combination of the FDA-approved PDE4 inhibitor roflumilast with idelalisib synergistically suppresses DLBCL growth (combination index < 1). This synergism was associated with a significant suppression of PI3K and AKT activities (p<0.05, cells treated with the drug combination vs. single agents). We expanded this observation to an in vivo xenograft model of human DLBCL, and showed that mice treated with roflumilast and idelalisib had a significantly smaller tumor burden than those receiving single agents (p< 0.01, two cohorts, n=47 mice). We also found a greater suppression of PI3K activity in the xenografts from mice treated with the combination of PDE4 and PI3Kδ inhibitors (p< 0.0001), as well as increased apoptosis.Together, these data further delineated how cAMP suppresses the BCR and showed that the rational combination PDE4 and PI3Kδ inhibitors synergistically suppresses DLBCL growth. These results are particularly important given the recent evidence of inflammatory/immune toxicity associated with the use of idelalisib, which we propose could be countered by the well-established anti-inflammatory properties of PDE4 inhibitors. Thus, we hypothesize that combining PDE4 and PI3Kδ inhibitors will enhance anti-lymphoma activity while decreasing clinical toxicity. This concept is ripe for clinical testing as we have recently completed a phase Ib trial showing that roflumilast is safe and active in patients with advanced B cell malignancies. DisclosuresNo relevant conflicts of interest to declare.

The genetics of nodal marginal zone lymphoma

AbstractNodal marginal zone lymphoma (NMZL) is a rare, indolent B-cell tumor that is distinguished from splenic marginal zone lymphoma (SMZL) by the different pattern of dissemination. NMZL still lacks distinct markers and remains orphan of specific cancer gene lesions. By combining whole-exome sequencing, targeted sequencing of tumor-related genes, whole-transcriptome sequencing, and high-resolution single nucleotide polymorphism array analysis, we aimed at disclosing the pathways that are molecularly deregulated in NMZL and we compare the molecular profile of NMZL with that of SMZL. These analyses identified a distinctive pattern of nonsilent somatic lesions in NMZL. In 35 NMZL patients, 41 genes were found recurrently affected in ≥3 (9%) cases, including highly prevalent molecular lesions of MLL2 (also known as KMT2D; 34%), PTPRD (20%), NOTCH2 (20%), and KLF2 (17%). Mutations of PTPRD, a receptor-type protein tyrosine phosphatase regulating cell growth, were enriched in NMZL across mature B-cell tumors, functionally caused the loss of the phosphatase activity of PTPRD, and were associated with cell-cycle transcriptional program deregulation and increased proliferation index in NMZL. Although NMZL shared with SMZL a common mutation profile, NMZL harbored PTPRD lesions that were otherwise absent in SMZL. Collectively, these findings provide new insights into the genetics of NMZL, identify PTPRD lesions as a novel marker for this lymphoma across mature B-cell tumors, and support the distinction of NMZL as an independent clinicopathologic entity within the current lymphoma classification.

The Genetics of Nodal Marginal Zone Lymphoma

Nodal marginal zone lymphoma (NMZL) is a rare, indolent B-cell tumor that is distinguished from splenic marginal zone lymphoma (SMZL) by the different pattern of dissemination. NMZL still lacks distinct markers and remains orphan of specific cancer gene lesions. By combining whole-exome sequencing, targeted sequencing of tumor-related genes, whole-transcriptome sequencing, and high-resolution single nucleotide polymorphism array analysis, we aimed at disclosing the pathways that are molecularly deregulated in NMZL and we compare the molecular profile of NMZL with that of SMZL. These analyses identified a distinctive pattern of nonsilent somatic lesions in NMZL. In 35 NMZL patients, 41 genes were found recurrently affected in ≥3 (9%) cases, including highly prevalent molecular lesions of MLL2 (also known as KMT2D; 34%), PTPRD (20%), NOTCH2 (20%), and KLF2 (17%). Mutations of PTPRD, a receptor-type protein tyrosine phosphatase regulating cell growth, were enriched in NMZL across mature B-cell tumors, functionally caused the loss of the phosphatase activity of PTPRD, and were associated with cell-cycle transcriptional program deregulation and increased proliferation index in NMZL. Although NMZL shared with SMZL a common mutation profile, NMZL harbored PTPRD lesions that were otherwise absent in SMZL. Collectively, these findings provide new insights into the genetics of NMZL, identify PTPRD lesions as a novel marker for this lymphoma across mature B-cell tumors, and support the distinction of NMZL as an independent clinicopathologic entity within the current lymphoma classification.

Liquid Biopsy As a Tool for Monitoring the Genotype of Diffuse Large B-Cell Lymphoma

Introduction. Accessible and real-time genotyping for diagnostic, prognostic or treatment purposes is increasingly impelling in diffuse large B-cell lymphoma (DLBCL). Since DLBCL lacks a leukemic phase, tumor genotyping has so far relied on the analysis of the diagnostic tissue biopsy. Cell-free DNA (cfDNA) is shed into the blood by tumor cells undergoing apoptosis and can be used as source of tumor DNA for the identification of cancer-gene somatic mutations. Accessing the blood has obvious sampling advantages in the monitoring of mutations in real-time. Also, cfDNA is representative of the entire tumor heterogeneity, thus allowing to identify mutations from tumor cells residing in non-biopsied sites. Here we aimed at tracking the DLBCL genetic profile using plasma cfDNA.Methods. The study was based on 26 consecutive DLBCL patients (age >65=15, male:female ratio=11:15) presenting in different Ann Arbor stages (III-IV=13) and age-adjusted IPI risk scores (2-3=13), and provided with cfDNA from plasma collected at diagnosis, during R-CHOP course, at the end of treatment and at progression. Paired normal genomic DNA from granulocytes was also collected for comparative purposes to filter out polymorphisms. A targeted resequencing panel including the coding exons and splice sites of 59 genes (207 kb) that are recurrently mutated in mature B-cell tumors was specifically designed to allow the recovery of at least one mutation in >90% of DLBCL. Ultra-deep next-generation-sequencing (NGS) of the gene panel was performed on MiSeq (Illumina) (coverage >2000x in >80% of the target) using a SeqCap library preparation strategy (NimbleGen). The somatic function of VarScan2 was used to call non-synonymous somatic mutations, and a stringent bioinformatic pipeline was developed and applied to filter out sequencing errors. The study cohort was divided in a training set of 17 patients provided with paired tumor DNA from the diagnostic tissue biopsy that was used for the set up of the ultra-deep NGS strategy, and an extension set of 9 patients lacking the tissue biopsy.Results. A total of 76 cfDNA samples (26 pretreatment, 28 during treatment, 18 at the end of treatment, and 4 at time of progression) were evaluated. Pretreatment cfDNA genotyping disclosed somatic mutations of heterogeneous abundance (median mutated molecules/ml of plasma: 3168, range 1.73-6.5x104) in known DLBCL-associated genes, including MLL2 (33%), TP53 (25%), CREBBP and TNFAIP3 (21%), EZH2, TBL1XR1, PIM1 (17%), B2M, BCL2, CARD11, CCND3, FBXW7 and STAT6 (13%) (Fig. 1A). The results of genotyping on cfDNA from plasma and of genomic DNA from tumor cells of the diagnostic biopsy (gold standard) were compared to derive the diagnostic accuracy of cfDNA genotyping (Fig. 1B). Genotyping of the paired plasma cfDNA correctly identified 79% of the tumor biopsy mutations. Most of the tumor variants not discovered in the cfDNA had a low representation in the tumor biopsy (median allelic abundance=5.7%; range 0.8-54%). Consistently, ROC analysis showed that cfDNA genotyping had the highest sensitivity (92%) if mutations were represented in >15% of the alleles of the tumor biopsy. Plasma cfDNA genotyping also disclosed a number of additional somatic mutations (~2 per case, range 1-6) that were not detectable in the tissue biopsy, including mutations of clinically relevant genes. Longitudinal analysis of plasma samples under R-CHOP chemotherapy showed a rapid clearance of the DLBCL mutations in the cfDNA already after the first cycle among responding patients (Fig. 1C). Among patients that were resistant to R-CHOP, basal DLBCL mutations did not disappear from cfDNA. In addition, among treatment-resistant patients, new mutations appeared in cfDNA that conceivably marked resistant clones selected during the clonal evolution process taking place under the pressure of treatment (Fig 1D).Conclusions. Overall, these results provide the proof of principle that cfDNA genotyping of DLBCL: i) is as accurate as genotyping of the diagnostic biopsy to detect somatic mutations of allelic abundance >15% in DLBCL; ii) allows the identification of mutations that are otherwise absent in the tissue biopsy conceivably because restricted to clones that are anatomically distant from the biopsy site; and iii) is a real-time and non-invasive way to track clonal evolution and emergence of treatment resistant clones. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

The Coding Genome of Nodal Marginal Zone Lymphoma Reveals Recurrent Molecular Alterations of PTPRD and Other Jak/Stat Signaling Genes

Background. Nodal marginal zone lymphoma (NMZL) is one of the few B-cell tumors still remaining orphan of cancer gene lesions. By combining whole exome sequencing (WES), deep sequencing of tumor-related genes, high resolution SNP array and RNAseq, here we aim at characterizing the coding genome of NMZL and at disclosing the pathways that are molecularly deregulated in this lymphoma.Methods. The study was based on 35 NMZL (tumor representation >70%) with a diagnosis confirmed by: i) pathological revision of lymph node histology; and ii) lack of clinico-radiological evidence of extranodal or splenic disease either at diagnosis or during follow-up. Consistent with NMZL, the cases investigated: i) lacked CD5, CD10 and cyclin D1 expression, 7q deletion, t(11;14), t(14;18), t(11;18) and t(1;14) translocations; and ii) recurrently harbored +3 (14%), +12 (14%) and preferential usage of the IGHV4-34 gene (17%). WES (HiSeq 2500, Illumina; mean coverage per sample: 38x-114x) and high density SNP array (Cytoscan HD, Affymetrix) of tumor/normal DNA pairs from 18 discovery NMZL identified 557 non-synonymous somatic mutations (average: 30.9/case) affecting 504 genes and 61 copy number abnormalities (CNA) (average 3.4/case). To further characterize mutation recurrence, the 504 discovered genes were investigated in an independent validation panel of 17 NMZL by targeted sequencing of tumor/normal DNA pairs (MiSeq; target region: 1.6 Mb; mean coverage per sample: 171x-386x). The 17 validation NMZL were also assessed for CNA by high density SNP arrays. RNAseq of 11 discovery NMZL did not identify any recurrent gene fusion. Results. By compiling the results of WES and high resolution SNP array, 39 genes were recurrently affected in >3/35 (9%) NMZL by mutations (n=30 genes) or focal CNA (n=9 genes). Among these, MLL2 (34%), PTPRD (20%) and NOTCH2 (20%) were most frequently mutated. Overall, recurrently mutated genes pointed to the molecular deregulation of specific programs in NMZL, namely JAK/STAT, NOTCH, NF-κB and toll-like receptor (TLR) signaling, cell cycle, chromatin remodeling/transcriptional regulation and immune escape (Fig. 1A). JAK/STAT signaling was targeted by mutually exclusive lesions in 43% of NMZL, and the protein tyrosine phosphatase receptor delta (PTPRD) tumor suppressor was the most frequently affected gene of this system in 20% of NMZL (Fig. 1B-E). PTPRD inhibits JAK/STAT signaling through the dephosphorylation of active p-STAT3. PTPRD lesions in NMZL were represented by somatic mutations that truncated or modified the tyrosine phosphatase domain, as well as deletions of the entire gene locus, including focal and biallelic losses (Fig. 1B-C). Interrogation of institutional and public genomic datasets revealed that PTPRD mutations are specific for NMZL, being rare or absent in other mature B-cell tumors, including splenic marginal zone lymphoma (Fig. 1D). Other JAK/STAT signaling genes affected in NMZL were JAK2, CXCR4 (6%), PTPN2, JAK3, STAT2, SH2B3 and CUL3 (3%) (Fig. 1E). NF-kB signaling was altered in 54% of NMZL by lesions of TNFAIP3 (14%), BCL10, REL (11%), CARD11 (9%), TRAF3 and BIRC3 (6%). NOTCH signaling was targeted in 40% of NMZL by mutations that alternatively involved NOTCH2 (20%), SPEN (11%), RBPJL (6%), FBXW7, DTX1, ITCH and MAML2 (3%). TLR signaling was targeted in 17% of NMZL, including mutations of MYD88 (9%), IRAK1BP1, PELI2 and SEMP6 (3%). Several cell cycle genes were molecularly deregulated in 43% of NMZL, including CDKN2A, PARK2, PARKG (9%), CDC16, CDCA2 (6%), CCNA1, CCNT2, CDK5, CDK13, CDK20, BTG2, HECA and PLK2 (3%). Most (71%) NMZL harbored genetic lesions affecting epigenetic modifiers (MLL2: 34%; CREBBP: 9%; EP300: 6%; TRRAP: 6%), histones (20%) or transcriptional co-repressors (TBL1XR1: 14%; ARID1A: 14%; RCOR1: 11%; NCOR2: 9%, ARID1B: 9%). Finally, the TNFRSF14 and FAS genes, involved in T cell-mediated tumor surveillance, were disrupted by mutations and/or deletions in 17% and 14% NMZL, respectively.Conclusions. A number of actionable cellular programs are molecularly deregulated in NMZL, including JAK/STAT, NOTCH, NF-κB and TLR signaling, cell cycle and chromatin remodeling. PTPRD lesions are among the most recurrent alterations in NMZL and appear to be specific for this lymphoma type across mature B-cell tumors. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Abstract 5528: The BET Bromodomain inhibitor OTX015 targets the NFKB, TLR and JAK/STAT pathways and shows pre-clinical activity as single agent and in combination in mature B-cell tumors

Abstract Background: Lymphomas are still incurable in many patients and novel active compounds are actively being sought. We previously reported single agent activity of the BET bromodomain OTX015 in lymphoma cell lines and in vivo (AACR 2012; ICML 2013). Here, we report a study of the mechanism of action of OTX015 and its activity in combination with other anti-cancer compounds. Methods: Cell lines: 22 diffuse large B-cell lymphoma (DLBCL), 4 mantle cell lymphomas, 3 multiple myelomas, 3 splenic marginal zone lymphoma and 1 prolymphocytic leukemia. Anti-proliferative of OTX015 (OncoEthix SA, Switzerland) was assessed by MTT and its cytotoxic activity by Annexin V staining and gene expression profiling (GEP) with Illumina HumanHT-12 Expression BeadChips. Data mining was done with LIMMA, GSEA, Metacore. Synergy was assessed in cells (2-5 cell lines) exposed for 72 h to increasing doses of OTX015 alone or in combination with increasing doses of other agents. MTT assays were performed and Chou-Talalay combination index (CI) calculated. Results: OTX015 (500 nM, 72h) showed cytostatic activity in 29/33 (88%) cell lines and apoptosis in 3/22 (14%). Mutations in genes coding for MYD88 and components of BCR (P=0.027), and ABC signaling phenotypes (P=0.008) were significantly associated with apoptosis induction. We performed GEP on 2 cell lines (SU-DHL-6, SU-DHL-2), treated with DMSO or OTX015 (500 nM) for 1, 2, 4, 8 or 12 hours. Most upregulated genes were histones. MYC target genes were highly significantly enriched among all OTX015 regulated transcripts and MYC was the most frequently downregulated gene. OTX015 also downregulated MYD88, IRAK1, TLR6, IL6, STAT3, and TNFRSF17, members of the NFKB, TLR and JAK/STAT pathways. NFKB target genes (IRF4, TNFAIP3 and BIRC3) were also downregulated (PCR). Immunoblotting and immunohistochemistry showed a reduction of transcriptionally active pSTAT3 in 2 ABC cell lines, and a reduction in nuclear localization of p50 (NFKB1), indicating an inhibitory effect of OTX015 on the canonical NFKB pathway. Finally, IL10 and IL4 production was reduced after 24 hours OTX015 treatment. Synergy was observed with everolimus (median CI=0.1; range 0.1-0.2), ibrutinib in ABC-DLBCL (CI=0.04; 0.02-0.1), idelalisib (CAL101) (CI=0.5; 0.04-2.4), vorinostat (CI=0.5; 0.3-0.6), rituximab (CI=0.5; 0.4-0.5), decitabine (CI=0.6; 0.6-0.7), lenalidomide (CI=0.7; 0.6-0.7), and all-trans retinoic acid (CI=0.4; .1-1.6). Additive effects were observed for combinations with romidepsin (CI=1.08; 1-1.22), bendamustine (CI=0.92; 0.83-1.1), and doxorubicin (CI=0.83; 0.71-0.96). Conclusions: OTX015 is a promising candidate for targeted combination therapies. A phase I study (NCT01713582) in patients with hematological neoplasias is underway and together with our preclinical data, may support further clinical investigations. Citation Format: Eugenio Gaudio, Elena Bernasconi, Ivo Kwee, Michela Boi, Paola Bonetti, Chiara Tarantelli, Andrea Rinaldi, Monica Testoni, Maurilio Ponzoni, Anastasios Stathis, Georg Stüssi, Eugenia Riveiro, Patrice Herait, Emanuele Zucca, Francesco Bertoni. The BET Bromodomain inhibitor OTX015 targets the NFKB, TLR and JAK/STAT pathways and shows pre-clinical activity as single agent and in combination in mature B-cell tumors. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5528. doi:10.1158/1538-7445.AM2014-5528

The Brd-Inhibitor OTX015 Is Active in Pre-Clinical Models of Mature B-Cell Lymphoid Tumors

AbstractAbstract 1657 Background:Bromodomain-containing proteins play an important role in gene expression regulation, via chromatin structure remodelling. Antitumor activity has been reported in acute and chronic hematological malignancies using inhibitors of BRD2/3/4, members of the Bromodomain and Extraterminal (BET) family. Here, we report anti-proliferative activity of OTX015, a novel selective orally bioavailable BRD2/3/4 inhibitor, in a large panel of cell lines derived from mature B-cell lymphoid tumors. Material and Methods:Established human cell lines derived from 13 diffuse large B-cell lymphoma (DLBCL), 4 mantle cell lymphoma (MCL), three splenic marginal zone lymphoma (SMZL) and from three multiple myeloma (MM) were treated with increasing doses of OTX015 (OncoEthix SA) and MTT assays were performed after 72 hours exposure. For cell cycle analysis, cells were treated and stained with Click-iT Edu Flow Cytometry Assay Kits (Invitrogen) and 7-AAD and analyzed for DNA content using a FACScan flow cytometer. Results were analyzed with FlowJo 7.6.3 software. RNA extracted using the Qiagen RNAEasy kit and reverse-transcribed using the Superscript First-Strand Synthesis System for RT-PCR kit according to the manufacturer's instructions. RT-PCR was performed using Fast SYBR Green Master Mix on a StepOnePlus Real-Time PCR System. For senescence detection, cells were stained using a b-Galactosidase Staining Kit (Calbiochem). Results:OTX015 demonstrated anti-proliferative activity in DLBCL cell lines (median IC50 0.192μM; range 0.069–12.68μM). Similar results were obtained on SMZL (median IC50 0.165μM, range 0.105–0.24μM), and on MM cell lines (median IC50 0.449μM; range 0.06–0.7μM). Conversely, MCL cell lines appeared less sensitive to OTX015 (median IC50 2.01μM; range 1.22- >15μM). Among DLBCL cell lines, there was no significant difference based upon the cell of origin of the cell lines. OTX105 caused a cell cycle arrest in G1 in a dose-dependent manner in 5/5 DLBCL and 3/3 MM cell lines, without an increase in cell death. An increase in the percentage of senescent cells after treatment with the BRD-inhibitor was observed in 1/1 sensitive DLBCL cell line. In order to understand the mechanism of action of OTX015, we assessed MYC mRNA levels before and after 24h treatment with increasing doses. We observed a dose-dependent suppression of MYC mRNA by OTX015 in 4/5 DLBCL and in 2/2 MM cell lines. In DLBCL, down-regulation of MYC mRNA was observed within 1h after treatment with OTX015, suggesting a direct effect of the compound on the MYC gene. To determine whether the suppression of MYC gene by OTX015 was reversible, DLBCL cell lines were treated for 2h with OTX015 and then the inhibitor was removed from the media. MYC mRNA suppression appeared reversible, as shown in DLBCL cell lines, which, after 2h exposure to OTX015, showed a time-dependent restoration of MYC mRNA expression to untreated levels after 2–3h. In one of the most sensitive DLBCL cell lines no MYC mRNA down-regulation was observed after treatment, suggesting that alternative pathways can be affected by BRD-inhibition. Conclusion:OTX015 is a new potent BRD-inhibitor with evident anti-proliferative activity in several cell lines representative of mature B-cell tumors. An apparently reversible down-regulation of MYC mRNA was commonly observed, appearing as a possible mechanism of action of the compound. The compound appears worth of further investigation as a new promising therapeutic agent in mature B-cell origin malignancies. A phase I trial is scheduled to start in 2012. Disclosures:Bonetti:OncoEthix SA: Research Funding. Inghirami:OncoEthix SA: Research Funding. Noel:OncoEthix SA: Membership on an entity's Board of Directors or advisory committees. Bertoni:OncoEthix SA: Research Funding.

Multiple myeloma shows no intra-disease clustering of immunoglobulin heavy chain genes

Characterization of the immunoglobulin gene repertoire has improved our understanding of the immunopathogenesis of lymphoid tumors. Early B-lymphocyte precursors of multiple myeloma are known to exist and might be susceptible to antigenic drive. To verify this hypothesis, we collected a database of 345 fully readable multiple myeloma immunoglobulin sequences. We characterized the immunoglobulin repertoire, analyzed the somatic hypermutation load, and investigated for stereotyped receptor clusters. Compared to the normal immunoglobulin repertoire, multiple myeloma displayed only modest differences involving only a few genes, showing that the myeloma immunoglobulin repertoire is the least skewed among mature B-cell tumors. Median somatic hypermutation load was 7.8%; median length of complementarity determining-region 3 was 15.5 amino acids. Clustering analysis showed the absence of myeloma specific clusters and no similarity with published chronic lymphocytic leukemia or lymphoma subsets. Analysis of multiple myeloma immunoglobulin repertoire does not support a pathogenetic role for antigen selection in this tumor.

Chromosomal Rearrangement of the PAX-5 Locus in Lymphoplasmacytic Lymphoma with t(9; 14) (p13; q32)

B-cell non-Hodgkin's lymphoma (NHL) consists of heterogeneous subtypes based on histologic, immunophenotypic, and clinical findings. Recent advances in molecular biology have provided us new insights into the pathogenesis of this neoplasm at the genetic level, such as the deregulation of the protooncogenes adjoining the immunoglobulin gene (Ig) loci, which is a specific event in mature B-cell tumors. Moreover, involvement of certain protooncogenes corresponds to certain subtypes of NHL. Recently, we found that t(9;14)(p13;q32) chromosomal translocation associated with lymphoplasmacytic lymphoma (LPL) juxtaposes PAX-5 gene encoding for an essential transcription factor (BSAP: B-cell specific activator protein) for B-cell proliferation and differentiation to the Ig heavy chain gene (IgH) locus. This results in deregulated expression of the PAX-5 mRNA. We also developed a diagnostic FISH (fluorescence in situ hybridization) procedure which is able to detect 80% of the widely scattering 9p13 breakpoints involved in this translocation. Thus, an understanding of the PAX-5 gene's physiological role in B-cell development and the pathological role in tumorigenesis may lead to the optimal clinical treatment strategy for LPL and LPL-derived diffuse large cell lymphoma (DLCL).

Novel functional activities of anti-DNA autoantibodies from sera of patients with lymphoproliferative and autoimmune diseases.

DNA-hydrolyzing activity of IgG autoantibodies from sera of patients with various types of lymphoproliferative diseases was investigated. The association of DNA-hydrolyzing activity with the antibody (Ab) fraction has been proved by newly developed affinity-capture assay. Study of abzyme incidence in blood tumors and systemic lupus erythematosis (SLE) revealed linkage of anti-DNA Ab catalysts to mature B-cell tumors, and increased probability of DNA-abzymes formation on the background of autoimmune manifestations. These data suggest possible similarity between mechanisms of abzyme formation in SLE and B-cell lymphomas. A new mechanism of formation of DNA-specific catalytic Abs has been proposed based on the increased crossreactivity of polyclonal DNA-abzymes to DNA-depleted nuclear matrix proteins. The possibility of the abzyme production as Ab to the energetically destabilized ground state of the antigen has been discussed. Preliminary results were obtained that indicate the complement-independent cytotoxicity of anti-DNA autoantibodies isolated from blood of patients with SLE and chronic lymphocytic leukemia.

Restrictions that influence avian leukosis virus-induced lymphoid leukosis.

Infection of one day old White leghorn chicks with avian leukosis virus (ALV) usually results in the development of a bursal- dependent B-cell lymphoma (Purchase and Burmester, 1978). This tumor requires the bursal environment to develop and is characterized by the presence of cell surface immunoglobulin M (IgM) (Cooper et al., 1974). Integration of the ALV provirus within the normal c-myc locus of the target cell disrupts the expression of this locus and appears to be important in the development of the primary tumor (Hayward et al., 1981; Payne et al., 1982). However, alterations that influence the expression of the c-myc locus have been implicated in the development of a variety of lymphoid tumors in several species (Dalla-Favera et al., 1982; Shen-Ong et al., 1982; Corcoran et al., 1984; Levy et al., 1984). These lymphoid tumors exhibit considerable variation in their phenotype and include not only B-cell tumors that express IgM but also mature B-cell tumors that secrete IgG and T-cell tumors. It is not known why ALV infection produces such a restricted type of lymphoid tumor in the chicken. A variety of factors including (i) access of the virus to a particular type of target tissue, (ii) the abundance and proliferative capacity of different target cells at the time of virus replication and (iii) specific and non-specific host defense mechanisms could influence tumor development following ALV infection.KeywordsInfectious VirusHaploid GenomeLymphoid TumorPreneoplastic LesionAvian Leukosis VirusThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.