Doǧan, Ahmet

Abstract Abstract 4160 We propose that the pathophysiology of marginal zone B-cell lymphomas (MZL) could allow for their classification into lymphoid organs located in MZL and extra-nodal MZL of MALT type; the former category encompassing splenic MZL (SMZL) and nodal MZL (NMZL). The rarity of these lymphomas and difficulty in distinguishing them from other low-grade B-cell lymphoma such as lymphoplasmacytic lymphomas hampers further understanding of disease biology. In an attempt to better characterize the genetic basis of these entities and compare acquired genetic changes based on this categorization we performed array-based comparative genomic hybridization (using the 244A array, Agilent) in a cohort of MZL cases. In total we analyzed 101 MZL, including 46 MALT (including 8 cases with t(11;18)(q21;q21)), 35 SMZL and 20 NMZL. Overall, 90.1% cases have copy-number abnormalities (CNA). Genomic complexity was greatest in MALT without t(11;18)(q21;q21)(4 CNA), followed NMZL (3.5 CNA), SMZL (3 CNA) and MALT with t(11;18)(q21;21)(1 CNA). Seventeen minimal deleted regions (MDRs) and 9 minimal amplified regions (MARs) were defined based on the presence in at least one entity with a frequency of 10% or higher. Gains of chromosomes 3, 12 and 18 were found in all entities. Deletion of 6q was the most common abnormality in MALT (21.1%) and, to less extent, SMZL and NMZL. Biallelic and focal monoallelic deletions on 6q23.3-q24.1 identified TNFAIP3 as the sole gene inside the common MDR between entities. Deletion of chromosome 13 was observed in all entities, but NMZL and MALT were characterized by whole chromosome deletions, whereas focal deletions on 13q14.3 (MIR16-1/MIR15A) were identified in SMZL. A subset of abnormalities was shared for more than one entity: deletions 9p21.3 (CDKN2A) and 11q21-q22 (ATM) were found in NMZL and SMZL but not in MALT; deletion 7q32.1-q33 was the most common CNA in of SMZL but was also found in MALT; gain of 6p was found in MALT and NMZL but not in SMZL. Other CNA were only found in one entity such as deletion of 17p13.3-p12 (TP53) in SMZL, deletion of 15q25.3-q26.2 in NMZL. In addition to 17% of cases with the t(11;18)(q21;q21), extra copies of MALT1, focal amplifications of REL and/or monoallelic/biallelic deletions of TNFAIP3 were identified in an additional 46% of MALT lymphomas. These CNA were identified alone or in combination, but all of them were mutually exclusive with the t(11;18)(q21;21), thus totalizing 63% of MALT lymphomas with abnormalities affecting regulator genes from the NF-kB signaling pathway. Moreover, depending on the anatomic site of the MALT lymphoma, the prevalence of CNA affecting the NF-kB pathways varies from 50% in lacrimal glands to 75% in salivary glands. Abnormalities affecting regulator genes of the NF-kB signaling pathways were identified in a significantly lower frequency in NMZL (30%) and SMZL (31%) entities, suggesting its differential role in the pathogenesis of different entities. Using this high-resolution approach we show that while many abnormalities are shared unique patterns of genomic gains and losses characterize subgroups of MZL. Extranodal MZL seems to have a higher propensity of constitutive genetic upregulation of NF-kB pathways. Furthermore, this study remarks the importance of this pathway also in the subgroup of MALT lymphomas without translocations affecting the pathway. Disclosures: Fonseca: Genzyme: Consultancy; Medtronic: Consultancy; BMS: Consultancy; AMGEN: Consultancy; Otsuka: Consultancy; Celgene: Consultancy, Research Funding; Intellikine: Consultancy; Cylene: Research Funding; Onyx: Research Funding; FISH probes prognostication in myeloma: Patents & Royalties.

Abstract Introduction : Follicular lymphoma (FL) remains an incurable malignancy as patients eventually experience progressive disease. A subset of patients is at risk of early lymphoma-related mortality due to histological transformation (TFL) to aggressive lymphoma (2-3% of patients per year) or early progression after immuno-chemotherapy, each of which leads to shortened survival. Mutations associated with transformation and/or early progression have been reported in the literature (e.g. CDKN2A, TP53, B2M) and the m7-FLIPI clinico-genetic risk model defines a high-risk patient group with poor failure-free survival after first-line treatment. However, the current knowledge of genetic alterations underlying transformation and/or early progression is inadequate to explain the majority of transformed cases and accurately predict early progressive disease. Materials and Methods: We performed targeted capture-based sequencing of 94 genes in a large cohort of fresh-frozen and formalin-fixed and paraffin-embedded patient specimens (402 samples in total). This cohort comprised 277 samples from 159 patients that experienced transformation (including 128 samples at T1 (the time of FL) and 149 samples at T2 (the time of transformation) with 118 paired biopsies) and 125 samples from 125 patients (pre-treatment samples only) presenting with either early progression within 2.5 years after starting immunochemotherapy (n=41) or late or never progression for at least 5 years after starting immunochemotherapy or observation (n=84). Mutations were called using MutationSeq and putative single nucleotide polymorphisms were filtered out using either matching germline samples (n=84) or dbSNP (v147). Bayesian proportion tests were used to compare the prevalence of gene mutations between groups. Results : We first compared T1 (n=128) and T2 (n=149) samples from 159 patients experiencing transformation. Eleven genes were more commonly altered in transformed lymphoma. These included genes that had previously been associated with transformation, such as TP53, B2M, MYC and EBF1, as well as genes that have not yet been implicated as contributing to this process, for example EZH2, CCND3, PIM1 and ITPKB. Moreover, mutations in GNA13, S1PR2 and P2RY8, that have been implicated in dissemination of germinal centre B cells, were enriched in T2 samples. In addition, cell-of-origin classification was available for 108 of the TFL cases with DLBCL histology, 18 and 90 of which were of the ABC and GCB subtype, respectively. Although the number of ABC-TFL cases was small, we observed higher percentages of BCL10 (16% versus 1%, Fisher P=0.004), CD79B (22% versus 4%, Fisher P=0.005) and MYD88 mutations (28% versus 9%, P=0.006) in ABC-TFL than in GCB-TFL, suggesting that B-cell receptor signaling and NF-κB signaling are important contributors to the ABC phenotype in TFL. Next, we assessed the association of gene mutations with patient outcomes contrasting early progressers (n=41) and late or non-progressers (n=84). Eleven genes were mutated more commonly in early progressers than in late progressers, including KMT2C, TP53, BTG1, MKI67, XBP1 and SOCS1. Overall, 32 out of 41 early progressers (78%) had mutations in at least one of the 11 early progression-associated genes, but none of the individual early progression-associated genes were mutated at a frequency > 22%. Thus, early progression appears to be related to relatively infrequent genetic alterations. None of the early progression-associated gene mutations form part of the m7-FLIPI outcome predictor. Furthermore, in our cohort that was enriched for clinical extremes, the m7-FLIPI was similarly associated with early progression when compared to the FLIPI but it was not superior, having higher specificity (89% versus 76%), but lower sensitivity (36% versus 63%). Conclusions: We found novel associations of gene mutations with transformation and showed that TFL is molecularly heterogeneous, with the ABC subtype being characterized by differential gene mutation when compared to the GCB subtype. With regards to progressive disease after immuno-chemotherapy, our approach identified early progression as a distinct clinico-genetic disease category that is imperfectly captured by traditional prognostic tools. Disclosures Connors: Seattle Genetics: Research Funding; Bristol Myers Squib: Research Funding; F Hoffmann-La Roche: Research Funding; NanoString Technologies: Research Funding; Millennium Takeda: Research Funding. Scott:NanoString Technologies: Patents & Royalties: named inventor on a patent for molecular subtyping of DLBCL that has been licensed to NanoString Technologies.

Abstract Abstract 2702 Background: CXCR5 [chemokine (C-X-C motif) receptor 5; also known as Burkitt lymphoma receptor 1 (BCR1)] is expressed on mature B-cells, subsets of CD4+ and CD8+ T-cells, and skin-derived migratory dendritic cells. CXCL13 is the ligand for CXCR5, and together they are involved in guiding B-cells into the B-cell zones of secondary lymphoid organs as well as T-cell migration. CXCR5 is also expressed in malignant cells in NHL patients. Single nucleotide polymorphisms (SNPs) in CXCR5 have not been extensively studied, although two studies reported that SNPs from this chromosome 11 gene were associated with risk of primary biliary cirrhosis in a European population and with risk of NHL in an Asian population. This study evaluated the role of common germline genetic variation in the risk and prognosis of the common NHL subtypes of diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), mantle cell lymphoma (MCL), marginal zone lymphoma (MZL) and peripheral T-cell lymphoma (PTCL). Methods: Ten SNPs in CXCR5 were genotyped using a clinic-based study of 2694 NHL cases (including 586 DLBCL, 588 FL, 137 MCL, 230 MZL, and 158 PTCL) and 1521 controls enrolled from 2002–2009 in the Molecular Epidemiology Resource of the University of Iowa/Mayo Clinic Lymphoma SPORE. Clinical data were abstracted for all NHL patients and all were prospectively followed for disease progression, retreatment, transformation and death. SNPs were selected from HapMap using a standard tagging approach (r2≥0.80 and minor allele frequency (MAF) ≥0.05) and included SNPs 5kb upstream and downstream from the gene. Genotyping was conducted using a custom Illumina iSelect panel. All SNPs were in Hardy-Weinberg equilibrium in the control group. The most prevalent homozygous genotype was used as the reference group, and each SNP was modeled as having a log-additive effect in the regression model. For risk of NHL, odds ratios (ORs) and 95% confidence intervals were calculated using unconditional logistic regression, adjusted for age and gender. For prognosis, hazard ratios (HR) were calculated for both event-free (EFS) and overall (OS) survival using Cox proportional hazards regression, adjusting for age, treatment type, and IPI (DLBCL, PTCL), FLIPI (FL), or MIPI (MCL). To determine risk of FL transformation to DLBCL, a competing risk Cox model was used. A p<0.05 was declared as statistically significant. Results: Of the 10 CXCR5 tag SNPs in our study, 5 were associated with risk of NHL, with rs1790192 (MAF=0.39 among controls) having the strongest association (OR=1.19, 95%CI 1.08–1.30; p=0.0003). This SNP was strongly associated with FL (OR=1.44, 95%CI 1.25–1.66; p=3.1×10−7), and was also associated with DLBCL (OR=1.16, 95%CI 1.01–1.33; p=0.038) and PTCL (OR=1.29, 95%CI 1.02–1.64; p=0.037) but not MCL or MZL. For FL, none of the SNPs were associated with EFS or OS, although rs1790192 was associated with better outcome among FL patients that were observed (HR=0.64; 95%CI 0.47–0.87; p=0.0039). For DLBCL, none of the SNPs were associated with EFS, while three SNPs were associated with OS: rs523604 (HR=0.79; 95%CI 0.64–0.97; p=0.028), rs12363277 (HR=0.57; 95%CI 0.33–0.99; p=0.046), and rs3922 (HR=0.79; 95%CI 0.65–0.97; p=0.027). The latter SNP was also associated with risk of transformation from FL to DLBCL (HR=0.61; 95%CI 0.40–0.91; p=0.016). For MCL, MZL and PTCL, none of the SNPs were associated with either EFS or OS. Conclusions: Several germline CXCR5 polymorphisms were associated with NHL risk, particularly rs1790192 with risk of FL as well as DLBCL and PTCL. CXCR5 SNPs did not appear to be important in prognosis for most NHL subtypes, although rs1790192 was associated with a better outcome in untreated FL and rs3922 was associated with OS in DLBCL patients and with risk of FL transformation. These results provide additional evidence for a role of host genetic variation in CXCR5 in lymphomagenesis, mainly in risk of disease development, although there may also be a role for CXCR5 in FL and DLBCL prognosis. Replications of these findings in additional studies are needed. Disclosures: Ansell: Seattle Genetics, Inc.: Research Funding.

Abstract Abstract 2699 Myeloid differentiation factor 88 (MYD88) is an adaptor protein that plays a key role in mediating innate immune response. Upon activation of toll-like (TLRs) or IL-1b receptors, MYD88 activates a signaling cascade that culminates in activation of NF-kB and expression of proinflammatory genes. Activating mutations in MYD88 have been reported in non-Hodgkin's lymphoma (NHL) tumors, including diffuse large B cell and marginal zones lymphoma. The most common MYD88 mutation described thus far is a single base pair mismatch resulting in an amino acid switch from lysine to proline at position 265 (MYD88L265P). MYD88L265P functions as a constitutively active MYD88 protein resulting in dysregulated NF-kB and STAT3 signaling. This mutation has recently been reported to be present in lymphomoplasmacytic lymphoma/Waldenstrom macroglobulinemia (LPL/WM) at a high frequency, ∼ 90% (Xu et al, ASH, #261, 2011). The discovery of MYD88L265P in a high percentage of LPL/WM tumors, and other subtypes of NHL, provides the basis for the identification and targeting of MYD88 dependent pathways. Additionally, the ability of this mutation to drive NF-kB-mediated cytokine expression combined with our finding that LPL/WM patients have elevated serum cytokines suggests that the MYD88 mutation may play a significant role in LPL/WM pathogenesis. We first wanted to confirm the incidence of the MYD88L265P mutation in LPL/WM and other subtypes of indolent lymphoma. Using Sanger sequencing we found that 57% (n=58) of LPL, 4% of MALT (n=23), 5% of nodal marginal zone (n=34), and 6% of splenic marginal zone (n=34) lymphomas harbor the MYD88L265P mutation, with all but 1 case being heterozygous. When we specifically looked at the LPL cases with WM, we found that 70% of WM tumors have the MYD88L265P mutation. In a validation cohort of WM (n=41), we found a similar mutation rate of 68%. Additionally, the WM cell line MWCL1 and the IgM secreting cell line BCWM.1 also harbor the MYD88L265P mutation. The prevalence of the MYD88L265P mutation in NHL, specifically WM and LPL, suggests that it may be a novel driver of lymphoma pathogenesis and a potential therapeutic target. However, it is not yet clear if this mutation correlates with activation of signaling pathways, or cell growth and survival in LPL/WM. To address these questions we first explored the possibility that the MYD88 signaling pathway is constitutively active in cells that express MYD88L265P. Upon activation of TLRs or IL-1b receptors, MYD88 forms a homodiamer and recruits IRAK1/4 and TRAF6 into a complex resulting in association and phosphorylation of TAK1 followed by activation of NF-kB. Using three cell lines that express MYD88L265P (BCWM, MWCL1, and OCI-Ly3), we looked for complex formation of MYD88, IRAK1/4, TRAF6, and TAK1. Immunoprecipitation of either endogenous IRAK1 or TAK1 revealed constitutive association with both TRAF6 and MYD88. We also detected phosphorylation of TAK1, and taken together, these data suggest that the MYD88 pathway is activated in cells that harbor the MYD88L265P mutation. We next wanted to confirm the significance of the MYD88 pathway on lymphoma cell growth. Using our cell lines we tested the effect of IRAK1/4, TAK1, and NF-kB inhibitors on cell proliferation. All MYD88L265P expressing cell lines were sensitive to the TAK1 and NF-kB inhibitors in a dose dependent manner (0–10 uM), however, we only saw inhibition of cell proliferation with the IRAK1/4 inhibitor at the highest dose (10 uM) in the BCWM cell line. These data suggest that cell proliferation is dependent on the MYD88 signaling pathway, with some variation being detected between cell line models and inhibitors. Because the MYD88 pathway has also been shown to drive cytokine secretion we next tested the impact of the IRAK1/4, TAK1, and NF-kB inhibitors on expression of IL-10. Using drug doses that were shown to inhibit cell proliferation, but not impact survival, we found that all three inhibitors reduced the level of IL-10 secreted by each of cell lines. In summary, our data confirm the high incidence on the MYD88L265P mutation in LPL/WM, we find that the MYD88 signaling pathway is constitutively activated in cells the harbor the mutation, and we show that cell proliferation and cytokine secretion are dependent on MYD88 signaling targets. These studies highlight the biologic significance of the MYD88L265P mutation in LPL/WM and suggest that the MYD88 signaling pathway may be a novel therapeutic target. Disclosures: No relevant conflicts of interest to declare.

Abstract Abstract 1909 AL amyloidosis is the most common type of systemic amyloidosis. It is caused by extracellular deposition of circulating immunoglobulin light chains (LC) thought to be secreted by a primarily bone marrow based clonal plasma cell proliferative disorder. Although, invariably, the type of LC secreted by the plasma cell clone is identical to the LC deposited in the amyloid plaque, a comprehensive analysis of the re-arranged clonal LC gene coding secreted LC protein, the protein sequence of the serum and urine monoclonal band and the LC protein deposited in the amyloid plaques have not been previously performed. In this study, we compared the protein sequence predicted by the clonal LC gene sequence with the protein sequence identified in the serum and urine monoclonal bands and protein plaques by mass spectrometry (MS) based proteomics. 10 cases with systemic AL amyloidosis were studied. Bone marrow samples containing the clonal plasma cells were obtained and clonal LC variable gene sequences were determined by PCR amplification, cloning and sequencing as described previously (Abraham et al, Blood 2003, 101: 3801). For protein analysis, monoclonal protein bands identified in serum and/or urine protein electrophoresis and immunofixation were isolated from archival gels. For amyloid plaque protein analysis, the plaques were microdissected from paraffin embedded tissue. To identify the protein amino acid sequence of serum and urine bands and amyloid plaques, the samples were digested into peptides by trypsin and analyzed by MS based proteomic analysis. (see Vrana et al. and Blood 2009; 114: 4957 for methods). The results for amino acid sequence predicted from the clonal LC gene sequence, determined directly by MS from the serum and/or urine monoclonal band and amyloid plaques were then aligned and compared. In all 10 cases, the LC amino acid sequences predicted by sequencing of the clonal LC gene from bone marrow plasma cells, the amino acid sequence obtained directly from the monoclonal serum and/or urine protein and the amino acid sequence obtained from the amyloid plaque were identical. In most cases, both the complete variable region and constant regions were deposited as amyloid plaques. Some amyloid plaques showed cleavage of first 16 amino acids of the variable region suggesting that this part was not required for amyloid deposition. All LC variable region gene sequences were affected by somatic hypermutation, and identical mutations were present in both the serum and urine bands and in the amyloid plaques. In conclusion, these results, for the first time, comprehensively show that the monoclonal protein secreted by the neoplastic plasma cells is the pathogenetic protein causing the amyloid deposits in AL amyloidosis. Amyloid deposits contain virtually all of the LC protein identified in the serum or urine including both variable and constant regions, suggesting that the presence of the constant region may also play a role in amyloidogenesis. The technological capability to determine the complete protein sequence of the amyloidogenic monoclonal serum and urine LC protein isolated from archived gels will create new opportunities to develop diagnostic, predictive and prognostic serum or urine based tests for amyloidosis. Disclosures: Theis: Mayo Clinic: Patents & Royalties. Vrana:Mayo Clinic: Patents & Royalties. Dogan:Mayo Clinic: Patents & Royalties.

Abstract Background The lymphoma proteome is the phenotypic representation of the underlying genetic and epigenetic makeup of each individual patient's tumor. The proteome is rich in druggable targets and offers a unique opportunity for the hematologist to personalize therapy. We developed a deep proteomic profiling method using ion exchange fractionation and tandem mass spectrometry. In this pilot study, we applied this method to detect differentially expressed proteins in anaplastic large cell lymphoma (ALCL) cell lines with previously known (ALK-positive) and unknown (ALK-negative) therapeutic targets. We then asked whether integrative informatic analysis of these data could be used to predict drug sensitivity in each of the cell lines. Methods To examine reproducibility of our method, proteins were extracted independently from 4 pellets each of FE-PD (ALK-negative) and Karpas 299 (ALK-positive) ALCL cells, reduced with dithiothreitol, alkylated with iodoacetamide, and digested with trypsin. Resulting peptides were separated into 6 fractions using strong anion exchange (SAX) chromatography. Peptides in each fraction were analyzed via shotgun proteomics on a QExactive mass spectrometer. Peptide mass spectra (MS/MS) were matched against a RefSeq human protein sequence database using MyriMatch software. Reversed sequences were added to the database to measure identification false discovery rates (FDRs). IDPicker filtered the peptide identifications at 2% FDR. Proteins with at least two unique peptide identifications and five MS/MS matches were considered to be present in the sample. Filtered protein identifications and corresponding spectral counts were used as input to QuasiTel software, which was configured to use proteins with at least one spectrum per biological replicate. Proteins that were significantly differentially expressed (quasi p-value < 0.05) with an absolute log2 fold-change of at least 0.5 fold were loaded into the Ingenuity Pathway Analysis (IPA) software, and a master list of drugs and corresponding gene targets was assembled using PharmGKB database and the Drug-Gene Interaction Database (DGID). The resulting drug-gene target list was merged with the differentially expressed protein identifications. Candidate targets were validated by Western blot and candidate drugs were assessed in viability assays. Results The SAX-LC-MS/MS method identified 10,111 proteins from all replicate analyses of FE-PD and Karpas 299 samples, and 93% of the identified proteome was detected in all 4 replicate analyses. The detected proteome was well represented by key transcription factors, phophatases, kinases, translation regulators and transmembrane regulators. There were 1369 proteins differentially expressed between the 2 cell lines, 709 up regulated in Karpas 299 cell line and 673 up regulated in FE-PD. Differentially expressed proteins also showed consistent expression across the biological replicates (Figure 1). Our integrated approach to identify candidate targets and drugs “rediscovered” ALK in Karpas299 and unexpectedly identified relative overexpression of the IL2-IL2RA-STAT5A-STAT5B network in ALK-negative FE-PD cells. Western blot confirmed these findings. As expected, 50-100 nM crizotinib (ALK inhibitor) decreased Karpas 299 viability (p =0.016) but had no effect on FE-PD (Figure 2). In contrast, 50-100 nM of the experimental STAT5 inhibitor 573108 (EMD Millipore) decreased FE-PD viability (p=0.002) but had no effect on Karpas 299 (Figure 2). Conclusion The lymphoma proteome is complex with 10,000 proteins and contains druggable targets that can be reproducibly identified using SAX-LC-MS/MS. These targets vary across samples and integrated informatic analysis can predict target-drug combinations that have efficacy in an experimental model. These data suggest that SAX-LC-MS/MS could be used to personalize treatment regimens in lymphoma patients. Figure 1: Spectral counts of 1369 differentially expressed proteins between Karpas299 and FE-PD cell lines were normalized and plotted in a heat map. Red color indicates down regulation and yellow color indicates up regulation. Disclosures: No relevant conflicts of interest to declare.

Abstract Background Next Generation sequencing (NGS) is a powerful tool to identify somatic mutations associated with tumor onset and drug response. While it is well suited for high quality fresh/frozen samples, NGS is not proven for FFPE tissue which is the most common type of clinical specimen. Since the nucleic acids can be readily extracted from FFPE samples for a variety of genomic analyses, a comparative mutational analysis of paired frozen and FFPE tissues is urgently needed. Our long term goal is to establish a lab protocol to detect mutations in FFPE tumors using a targeted capture and sequencing approach for genes of interest. This pilot study focuses on the comparison of FFPE and frozen samples to test the validity of using FFPE tissues in such application. Methods Gene Selection: 128 genes associated with known pathogenic mutations in lymphoma Sample Selection: 9 diffuse large B-cell lymphoma (DLBCL) cases with FFPE, frozen and germline samples, as well as 10 frozen normal lymphatic tissues as references for CNV detections Capture Probe Design: We targeted coding exons and UTR, as well as the evolutionarily conserved intronic regions. The capture probes were designed using the Agilent eArray tool. The titling density of the probes was set to 3 probes overlapping with every base in the target region to improve the capture efficiency in FFPE samples. The least stringent masking of the repeat regions was allowed to include regions with small repeats that are shorter than the length of the sequencing reads (100-bp). In addition, boosting parameters were picked to set various levels of probe replication in different regions in order to minimize the local coverage differences (e.g. between regions of different GC contents) Sequencing and Bioinformatics: The target capture and sequencing were performed by the Mayo Clinic Medical Genome Facility. The reads were mapped to Human Reference Genome Build 37 using Novalign, and SNVs were called using GATK. The CNVs were identified using an in-house developed algorithm, patternCNV. Results The designed probes covered 99.65937% of the target regions. We generated 2.2-6.7 Gbp of reads per sample, 57.4-71.5% of which were on target. This equalled an average coverage of 2100-6700 folds which is 10-30 times higher than the minimal coverage recommended by Agilent. Due to this high coverage, we observed duplicate reads that accounted for 7.7-73.5% of the total reads. When we analysed the data with and without the duplicated reads, the concordance of the called SNVs was between 84-93% out of 207-249 mutated positions per trio-sample. There were 7.8-8.9% and 1.1-2.2% unique SNVs per sample by excluding or including duplicate reads, respectively. The dis-concordances were mostly missed calls, where a SNV was observed in only 1 or 2 of the trio samples. The missed calls from frozen samples ranged from 0-10.4% compared to 1.4-10.4% from the FFPE tissues, with 0.88-2.4% more SNVs missed in FFPE. Further analyses showed that all of the missing calls came from the lack of or low coverage of the corresponding positions. There were also differences of the called SNVs between the trio samples. However, this was extremely rare. Only 2 out of the 9 trio samples at a total of 3 positions had disagreements in called SNVs between FFPE and frozen tissues, all due to the allelic imbalance where the percentage of reads supporting the alternative alleles were below 20%. Therefore, this dis-concordance can be removed by back-filling of the read-level information for each position. Unfortunately only 11.9-47.4% of the CNVs called in frozen tissues were identified in FFPE samples, due to the widely various coverage in FFPE samples. The consequent large noises of the log ratio values between the FFPEs and normal references significantly reduced the sensitivity for CNV calling. Conclusions This pilot study compared the performance of SNV and CNV detection in FFPE and paired frozen tissues using a target capture and sequencing approach. With a capture probe design strategized to benefit FFPE samples, we observed SNV detection rates in FFPE that were only slightly lower (0.88-2.4%) than those of frozen tissues due to poor coverage of some positions in FFPE samples. With a proper back-filling step, there was no dis-concordance of the called SNVs between FFPE and frozen samples. However, CNV detections in FFPE were more problematic due to the un-predictable regional coverage in FFPE samples. Disclosures: No relevant conflicts of interest to declare.

Abstract Abstract 1999 Recurrent chromosomal translocations involving the IGH locus are characteristic of B-cell non-Hodgkin lymphoma (NHL) and MALT lymphoma in particular has been pathologically characterized by specific IGH translocations. However, these translocations are present in only a subset of cases, suggesting that additional uncharacterized translocations might exist. In previous studies we characterized the novel t(X;14)(p11.4;q32) translocation in a patient with MALT lymphoma and found that GPR34, an orphan G-protein coupled receptor (GPCR), was highly expressed due to its juxtaposition to the IGHSA2 switch region. Although the t(X;14)(p11;q32) translocation was only identified in one patient, we wanted to determine its expression across a spectrum or normal and malignant lymphoma tissue, as other mechanisms may contribute to overexpression of genes. We measured GPR34 mRNA expression by quantitative PCR in tissue biopsies from a panel of lymphomas. As controls, we also measured GPR34 mRNA expression in normal resting or activated CD19+ B cells, resting and activated CD3+ T cells, and CD14+ monocytes. Expression of GPR34 was significantly increased in MALT (37-fold, n=35), LPL (23-fold, n=23), nodal marginal zone B cell lymphoma (18-fold, n=21), and splenic marginal zone B cell lymphoma (21 fold, n=33) compared to resting CD19+ B cells (n=11). In a gastric MALT lymphoma specimen we detected GPR34 expression at levels similar to the t(X;14)(p11;q32) patient and interphase FISH studies showed an extra intact GPR34 signal, but no translocation involving IGH or GPR34, suggesting that other mechanisms, including gene dosage effect, can upregulate GPR34. The receptor encoded by GPR34 is most similar to the PY2 receptor subfamily of GPCRs and signaling studies suggest that overexpression of GPR34 results in an accumulation of inositol phosphates and MAP-kinase activation. To further characterize the impact of GPR34 overexpression on cell signaling, HeLa cells were transduced with WT GPR34, a signaling deficient GPR34 (GPR34 DRY), or a vector control. To determine if MAPK activity was upregulated, the phosphorylation status of ERK1/2 in GPR34 WT, GPR34 DRY, and vector control cells was analyzed and we found that ERK1/2 was constitutively phosphorylated at higher levels (1.6-fold) in GRP34 WT cells compared to GRR34 DRY or vector control cells. To further explore which signaling pathways were affected by GPR34 overexpression, GPR34 WT or vector control cells were transfected with an AP-1, CRE, NF-kB, E2F, SRE, NFAT, or ISRE- luciferase reporter plasmid. GPR34 expressing cells had increased luciferase activity driven by AP-1 (5.35-fold), CRE (4.7-fold), NF-kB (2.6-fold), and E2F (2.1) when compared to vector control cells. GPR34 DRY was unable to activate these pathways. AP-1 and CRE have been implicated in a large variety of cellular processes, including transformation, and both AP-1 and CRE activity is induced upon activation of MAP kinases. In untreated cells, both AP-1 and CRE activity were significantly higher in GPR34 WT cells compared to GPR34 DRY cells and both AP-1 and CRE luciferase activity was inhibited by the MEK1 inhibitor PD98059, suggesting that activation of these pathways is MAP-kinase dependent. To determine the biologic impact of GRP34 overexpression, the proliferation rates of vector control, GPR34 WT, and GPR34 DRY cells were compared and we found that proliferation of GPR34 WT cells was significantly higher (5.6-fold) than that seen in GPR34 DRY cells. We next tested the effect of the MEK inhibitor on proliferation and saw a dose dependent decrease in proliferation of GPR34 WT expressing cells. These results suggest that GPR34-mediated proliferation is dependent on MAPK. The presence of elevated GPR34 expression in tumors and the increased proliferation mediated by GPR34 suggests that it may have oncogenic potential. We therefore tested the ability of GPR34 WT cells to generate tumors in a tumor colony-forming assay. Only the GRP34 WT cells had the ability to form tumors in soft agar suggesting that overexpression of GPR34 can result in tumor formation. Taken together, our results identify a novel translocation in MALT lymphoma, emphasize a novel role for GPR34 in tumor cell growth, and suggest that MEK inhibitors may be useful in a subset of translocation-harboring or GRP34 high-expressing tumors. Disclosures: Fonseca: Genzyme: Consultancy; Medtronic: Consultancy; BMS: Consultancy; AMGEN: Consultancy; Otsuka: Consultancy; Celgene: Consultancy, Research Funding; Intellikine: Consultancy; Cylene: Research Funding; Onyx: Research Funding; FISH probes prognostication in myeloma: Patents & Royalties.

Abstract Background: Peripheral T-cell non-Hodgkin’s lymphomas (PTCL) account for approximately 10% of all non-Hodgkin’s lymphomas in the U.S. and Europe. PTCL, unspecified (PTCL-U), as classified by the WHO, is the most common subtype. The ability of high-dose therapy (HDT) and stem cell transplantation (SCT) to improve patient outcome was evaluated in the current study. Methods: All patients with PTCL-U evaluated at our institution who had tissue specimens available for review from January, 1994 to December, 2005 were identified and both clinical characteristics and treatment course obtained from the medical record. Results: 89 patients with PTCL-U were identified, with a median follow up of 13 months (range 1 month–12 years). The median age at diagnosis was 56 years (range 24–90). The IPI was low, intermediate or high in 34%, 44% and 22% of patients, respectively. On univariate analysis, age >60 (p<.0001), ECOG performance status >1 (p<.0001), LDH greater than normal (p=.004), Ann Arbor Stage III/IV (p=.01) and the presence of B symptoms (p=.0004) were associated with a poorer overall survival, as was an intermediate or high IPI (p<.0001). In contrast, on multivariate analysis only age >60 (p=.0006) and ECOG performance status >1 (p=.007) were independently associated with poorer overall survival. Fifty-seven percent of patients were treated initially with an anthracycline-based regimen, most commonly CHOP (53%). Patients with a low (0–1), intermediate (2–3) or high (4–5) IPI experienced a 61%, 29% and 18% 5-year overall survival, respectively. Fourteen patients (16%) received HDT and autologous (n=12) or allogeneic (n=2) SCT, either at the time of a first partial or complete response (n=11) or at the time of first relapse (n=3). The median survival in those patients treated initially with an anthracycline-based regimen alone was 11 months (95% CI 0.6–1.6 years). Improvement in both 5-year overall (75% vs 24%, HR=5.6, 95% CI 2.0–23.4, p=.0004) and disease-free (60% vs 26%, HR=3.2, 95% CI 1.3–9.3, p=.008) survival was observed in patients who received HDT/SCT, as compared to patients treated with anthracycline-based therapy alone. Furthermore, improvement in both 5-year overall (80% vs 26%, HR=5.8, 95% CI 1.7–35.7, p=.002) and disease free (72% vs 26%, HR=3.8, 95% CI 1.3–15.8, p=.009) survival was observed in patients who received HDT/SCT at the time of a first partial or complete response when compared to patients who received anthracycline-based therapy. When patients who failed to achieve a first partial or complete response were excluded from the analysis, improved 5-year overall (80% vs 57%, HR=0.5, 95% CI 0.1–2.1, p=.4) and disease-free (72% vs 53%, HR=0.7, 95% CI 0.1–2.3, p=.5) survival were observed in patients who received upfront HDT/SCT, although this failed to reach statistical significance. The improved overall and disease free survival observed in patients receiving HDT/SCT, either at the time of a first response or at the time of relapse, remained significant when accounting for differences in the IPI. In conclusion, selected patients with PTCL-U may benefit from treatment with HDT/SCT following a first response to conventional anthracycline-based chemotherapy.

Abstract Splenic marginal zone lymphoma (SMZL) is an indolent B cell malignancy whose diagnosis is based on lymphocyte morphology, immunophenotype and marrow and/or splenic histology. Unlike other lymphomas, there is not a common chromosomal translocation specific for SMZL, and genetic prognostic factors are poorly defined. To investigate the pattern of genomic aberrations in SMZL, we applied comparative genomic hybridization to BAC microarrays (array CGH) to a well characterized series of 75 SMZL specimens. We applied two different 1 Mb-resolution BAC arrays: UCSF HumArray 3.2 and a novel array CGH platform developed at Univ. of Salamanca. These arrays allowed us to detect DNA copy number changes across the genome with high accuracy in 67 of 75 patient samples. Data were compared with our previous array CGH studies of 170 samples from different B-cell lymphoma subgroups. FISH studies for IGH, IGK and IGL translocations and 7q deletion were performed on tissue microarrays in 24 cases. Of the 67 samples, 19 (28%) showed a normal genomic profile. The median number of genomic aberrations per tumor was 2.2 (1.3 gains and 0.9 losses), which was lower than the rates detected in other lymphoma subgroups (diffuse large cell lymphoma, 6.4; mantle cell lymphoma, 6; follicular lymphoma, 4.5) and comparable to MALT lymphomas (2 abnormalities per tumor). SMZL cells showed a genomic pattern characterized by gain of chromosomes 3q24-q29 (18%), 6p (9%), 12q (9%), and 18q (4%) and loss of 7q32 (34%), 8p21-p23 (13%), 17p13 (10%) at P53 locus and 6q21-q27 (9%). Notably, no alterations of the P16/ARF (9p21) or MYC loci (8q24) were detected. Correlation of array CGH data with conventional cytogenetics, FISH and LOH studies revealed a high concordance. Detailed mapping of 7q deletions delineated a consensus region of loss of 3 Mb in 7q32. This 7q deletion was almost exclusive to SMZL, being observed in only 5 of 170 non-SMZL B-cell lymphomas (p=0.0000001). Four cases presented IG-translocation. Mutation of IGH was observed in 62% and correlated with a complex karyotype (61 vs. 13%; p=0,0008) whereas unmutated IGH correlated with the deletion of 7q (56 vs. 23%; p=0,01). Among the various genomic abnormalities, only the deletion of 8p or the presence of a complex karyotype correlated with inferior overall survival (OS) (median OS, 58 vs. 110 months, p=0,004; and 60 vs. 105 months, p=0,01; respectively). In summary, array CGH has defined a pattern of genomic aberrations in SMZL that differs from other B-cell lymphoma subgroups and that may predict overall survival. Because the deletion of 7q32 is the most distinctive genetic marker in SMZL, the identification of a putative tumor suppressor gene inactivated within the region of deletion seems mandatory.