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  • 1
    In: Leukemia, Springer Science and Business Media LLC, Vol. 33, No. 12 ( 2019-12), p. 2884-2897
    Abstract: Although the over-expression of angiogenic factors is reported in diffuse large B-cell lymphoma (DLBCL), the poor response to anti-VEGF drugs observed in clinical trials suggests that angiogenesis in these tumours might be driven by VEGF-independent pathways. We show that sphingosine kinase-1 (SPHK1), which generates the potent bioactive sphingolipid sphingosine-1-phosphate (S1P), is over-expressed in DLBCL. A meta-analysis of over 2000 cases revealed that genes correlated with SPHK1 mRNA expression in DLBCL were significantly enriched for tumour angiogenesis meta-signature genes; an effect evident in both major cell of origin (COO) and stromal subtypes. Moreover, we found that S1P induces angiogenic signalling and a gene expression programme that is present within the tumour vasculature of SPHK1-expressing DLBCL. Importantly, S1PR1 functional antagonists, including Siponimod, and the S1P neutralising antibody, Sphingomab, inhibited S1P signalling in DLBCL cells in vitro. Furthermore, Siponimod, also reduced angiogenesis and tumour growth in an S1P-producing mouse model of angiogenic DLBCL. Our data define a potential role for S1P signalling in driving an angiogenic gene expression programme in the tumour vasculature of DLBCL and suggest novel opportunities to target S1P-mediated angiogenesis in patients with DLBCL.
    Type of Medium: Online Resource
    ISSN: 0887-6924 , 1476-5551
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2019
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  • 2
    In: Blood, American Society of Hematology, Vol. 126, No. 23 ( 2015-12-03), p. 812-812
    Abstract: Introduction: DLBCL subtypes may be classified by gene expression corresponding to germinal centre (GCB) or activated peripheral blood (ABC) B-cells. Treatment outcomes with R-CHOP therapy were inferior for ABCs in retrospective series, and this study investigated whether adding bortezomib could reverse the adverse prognosis. The trial used gene expression profiling (GEP) to stratify cases, with adaptive design to analyse the outcome by subtypes at predefined timepoints. Methods: Newly diagnosed patients with DLBCL underwent staging and commenced standard R-CHOP. During cycle 1, formalin-fixed paraffin-embedded (FFPE) tissue was used to extract messenger RNA for GEP using the Illumina DASL array platform. Cases were allocated to GCB, ABC or Unclassifiable (Unc) type before starting cycle 2, using an established algorithm based upon 20 genes. Patients with successful GEP were randomised 1:1 to receive R-CHOP +/- bortezomib 1.6 mg/m2 s/c on days 1+8 in cycles 2-6. The study was powered to detect a difference in progression-free survival (PFS) of 10% with bortezomib, with a 2-sided significance, 5% and 90% power. The adaptive design allowed for closure of randomization for GCB cases if 1-year PFS was 〈 70% after 55 received RB-CHOP (interim safety analysis) or if 1-year PFS was 〈 85% after 73 received RB-CHOP and followed for 1 year (futility analysis). Results: Between 6/2011 and 5/2015 1132 patients were enrolled from 109 sites, with 1078 samples analysed. Of these, 157 (15%) biopsies had inadequate material for GEP, but the remaining 921 were classified as 246 (27%) ABC, 476 (52%) GCB and 199 (22%) Unc. Successful classification was possible from both surgical and needle core biopsies. Median laboratory turnaround time was 12 working days and all results were available prior to the scheduled administration of cycle 2. Characteristics of the patients of different subtypes are shown in the table. Following both interim analyses the DMEC recommended continued recruitment of patients with a GCB phenotype. Table. ABC GCB Unc Age (years): median 67 63 63 Age (years) : range 23 to 86 20 to 82 20 to 85 % performance status 0-1 88 88 90 % at least one extranodal site 53 54 62 % bone marrow involved 15 14 23 % LDH 〉 ULN 69 76 79 % IPI score 0/1 29 27 26 % IPI score 2/3 57 55 55 % IPI score 4/5 15 19 19 % B symptoms 46 43 49 % Bulk 〉 10cm 17 26 21 Conclusions: This study has demonstrated the feasibility of GEP at diagnosis to subsequently guide therapy in a large multicentre trial. Although patients with ABC type lymphoma were in general slightly older, they did not appear to have other adverse prognostic features at diagnosis vs GCB. All patients will have completed therapy by the time of the meeting, allowing the initial response and toxicity data to be available for presentation. Disclosures Davies: GIlead: Consultancy, Honoraria, Research Funding; Mundipharma: Honoraria, Research Funding; CTI: Honoraria; Takeda: Honoraria, Research Funding; Bayer: Research Funding; GSK: Research Funding; Janssen: Honoraria, Research Funding; Roche: Honoraria, Research Funding; Pfizer: Honoraria; Celgene: Honoraria, Research Funding. Off Label Use: The addition of bortezomib to R-CHOP chemotherapy in diffuse large B-cell lymphoma. Pocock:Janssen: Honoraria. Jack:Jannsen: Research Funding. Johnson:Takeda: Honoraria; Pfizer: Honoraria; Janssen: Research Funding.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2015
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  • 3
    In: Blood, American Society of Hematology, Vol. 116, No. 21 ( 2010-11-19), p. 2484-2484
    Abstract: Abstract 2484 Diffuse large B cell lymphoma (DLBCL) is a heterogenous disease, which has been subclassified into germinal centre (GCB) and activated B-cell (ABC) type using gene expression profiling. This has been shown to separate DLBCL into distinct prognostic sub-groups in patients treated with either CHOP or CHOP-R therapy. A number of published immunohistochemistry algorithms have attempted to replicate this subclassification using a limited number of markers, however, despite being widely adopted, the reproducibility of the algorithms has proven difficult, possibly due to the subjective nature of interpreting immunohistochemistry results. The aim of this study was therefore to evaluate the most widely accepted immunohistochemistry algorithms, and validate the results using RQ-PCR on RNA extracted from paraffin sections in a large series of well characterised formalin fixed paraffin embedded (FFPE) biopsies of R-CHOP treated DLBCLs. RNA was extracted using the Ambion Recoverall extraction kit. Applied Biosytems Taqman probes were used to evaluate gene expression of CD10, BCL6, GCET1, FOXP1 and IRF4. RQ-PCR was run on an Applied Biosystems 7500Fast cycler, and results were calculated using the deltadeltaCt method, using PGK1 as the reference housekeeper gene and either RAJI cell line or commercial RNA as the standard. Using the Hans criteria, 130/277 (47%) presentation DLBCL biopsies were classified as GCB and 147/277 (53%) were ABC. Further classification of a subset of cases using the Choi algorithm showed concordant results in 48/61 (78.7%) cases, with 1 (1.6%) case classified as GCB using Hans and ABC using Choi, and 12 (19.7%) cases classified as ABC using Hans and GCB using Choi. RQ-PCR data showed excellent correlation with immunohistochemistry for all genes incorporated into the algorithms (CD10, p 〈 0.0001; BCL6, p=0.0003; GCET1, p=0.009; FOXP1, p 〈 0.0001; and IRF4, p=0.008). RQ-PCR defined positivity was characterized by inspecting the distribution histograms of the range of values for each gene, and applying density smooths. Mixture distributions were identified and the minimum values of these plots were used to define the cut-points. Patients were then re-classified using RQ-PCR data to define GCB/ABC status. For the Hans classification, 50/79 (63%) patients were GCB and 29/79 (37%) were ABC. Of these 51/77 (66%) cases resulted in the same sub-classification using RQ-PCR compared to immunohistochemistry, with 26/77 (34%) cases classified differently. For the Choi algorithm, 49/79 (62%) patients were GCB and 30/79 (38%) were ABC, with 23/37 (62%) cases were classified the same using RQ-PCR and immunohistochemistry, and 14/37 (38%) classified differently. In univariate Kaplan-Meier survival analysis, there was no difference in outcome when comparing either Hans (n=170, p=0.7) or Choi (n=60, p=0.3) algorithms using immunohistochemistry, however using RQ-PCR data to define GCB and ABC subgroups, both algorithms showed a poorer survival in the ABC subgroup. For the Hans algorithm, 6 month overall survival (OS) was 76% in the GCB group compared to 55% in patients classified as ABC (p=0.06), and similarly for the Choi algorithm, 6 month OS was 77% in the GCB group and 53% for patients classified as ABC (p=0.03). This data supports the use of gene expression algorithms to classify DLBCL patients into clinically relevant prognostic groups, with patients classified as ABC exhibiting an inferior outcome compared to the GCB group. RQ-PCR provides a quantitative method to determine expression and eliminates the subjective element associated with interpreting immunohistochemistry. Using RQ-PCR to define prognostic subgroups in DLBCL provides a realistic alternative to gene expression profiling, which is currently not applicable to the majority of diagnostic laboratories. Patients classified as ABC type using this approach show early treatment failure with CHOP-R, and alternative therapies should be considered in this group. Disclosures: No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2010
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  • 4
    In: The Plant Journal, Wiley, Vol. 56, No. 5 ( 2008-12), p. 855-866
    Abstract: The moss Physcomitrella patens is a model for the study of plant cell biology and, by virtue of its basal position in land plant phylogeny, for comparative analysis of the evolution of plant gene function and development. It is ideally suited for ‘reverse genetic’ analysis by virtue of its outstanding ability to undertake targeted transgene integration by homologous recombination. However, gene identification through mutagenesis and map‐based cloning has hitherto not been possible, due to the lack of a genetic linkage map. Using molecular markers [amplified fragment length polymorphisms (AFLP) and simple sequence repeats (SSR)] we have generated genetic linkage maps for Physcomitrella. One hundred and seventy‐nine gene‐specific SSR markers were mapped in 46 linkage groups, and 1574 polymorphic AFLP markers were identified. Integrating the SSR‐ and AFLP‐based maps generated 31 linkage groups comprising 1420 markers. Anchorage of the integrated linkage map with gene‐specific SSR markers coupled with computational prediction of AFLP loci has enabled its correspondence with the newly sequenced Physcomitrella genome. The generation of a linkage map densely populated with molecular markers and anchored to the genome sequence now provides a resource for forward genetic interrogation of the organism and for the development of a pipeline for the map‐based cloning of Physcomitrella genes. This will radically enhance the potential of Physcomitrella for determining how gene function has evolved for the acquisition of complex developmental strategies within the plant kingdom.
    Type of Medium: Online Resource
    ISSN: 0960-7412 , 1365-313X
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2008
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  • 5
    In: Neuro-Oncology, Oxford University Press (OUP), Vol. 21, No. Supplement_4 ( 2019-10-12), p. iv7-iv7
    Abstract: Recent findings from our group, and the wider community, show that standard treatment does not impose an apparent bottleneck on the clonal evolution of adult glioblastoma (GBM), implying a lack of direct therapeutic opportunity. This does not negate the possibility that multiple treatment-resistance mechanisms co-exist in tumours, repeated across patients, making a combination of targeted therapies a potentially effective approach. We investigated whether treatment resistance may be driven by selection of cellular properties conferred above the level of the genome. Differential expression analysis was performed on 23 pairs of primary and recurrent tumours from patients who received standard treatment and had a local recurrence treated by surgery and second line chemotherapy. This revealed a treatment-induced shift in cell states linked to normal neurodevelopment. The latter is orchestrated by cascades of transcription factors. We, therefore, applied a bespoke gene set enrichment analysis to our paired expression data to investigate whether any factors were implicated in co-regulation of the genes that were altered through therapy. This identified a specific chromatin remodelling machinery, instrumental in normal neurogenesis. We validated our results in an independent cohort of 22 paired GBM samples. Our results suggest that the chromatin remodelling machinery is responsible for determining transcriptional hierarchies in GBM, shown elsewhere to have different treatment sensitivities such that their relative abundances are altered through treatment.
    Type of Medium: Online Resource
    ISSN: 1522-8517 , 1523-5866
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
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  • 6
    In: The Journal of Pathology, Wiley, Vol. 248, No. 2 ( 2019-06), p. 142-154
    Abstract: The Epstein–Barr virus (EBV) is found almost exclusively in the activated B‐cell (ABC) subtype of diffuse large B‐cell lymphoma (DLBCL), yet its contribution to this tumour remains poorly understood. We have focused on the EBV‐encoded latent membrane protein‐1 (LMP1), a constitutively activated CD40 homologue expressed in almost all EBV‐positive DLBCLs and which can disrupt germinal centre (GC) formation and drive lymphomagenesis in mice. Comparison of the transcriptional changes that follow LMP1 expression with those that follow transient CD40 signalling in human GC B cells enabled us to define pathogenic targets of LMP1 aberrantly expressed in ABC‐DLBCL. These included the down‐regulation of S1PR2, a sphingosine‐1‐phosphate (S1P) receptor that is transcriptionally down‐regulated in ABC‐DLBCL, and when genetically ablated leads to DLBCL in mice. Consistent with this, we found that LMP1‐expressing primary ABC‐DLBCLs were significantly more likely to lack S1PR2 expression than were LMP1‐negative tumours. Furthermore, we showed that the down‐regulation of S1PR2 by LMP1 drives a signalling loop leading to constitutive activation of the phosphatidylinositol‐3‐kinase (PI3‐K) pathway. Finally, core LMP1‐PI3‐K targets were enriched for lymphoma‐related transcription factors and genes associated with shorter overall survival in patients with ABC‐DLBCL. Our data identify a novel function for LMP1 in aggressive DLBCL. Copyright © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
    Type of Medium: Online Resource
    ISSN: 0022-3417 , 1096-9896
    URL: Issue
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    Language: English
    Publisher: Wiley
    Publication Date: 2019
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  • 7
    In: Blood, American Society of Hematology, Vol. 128, No. 22 ( 2016-12-02), p. 3052-3052
    Abstract: Aggressive B-cell non-Hodgkin lymphomas are haematological malignancies that account for significant morbidity and mortality worldwide. They encompass a wide range of histological and clinical features: Diffuse large B-cell lymphoma (DLBCL) represents the most frequent subtype and Burkitt lymphoma (BL) occurs less frequently. Recent advances in molecular profiling have demonstrated considerable heterogeneity at the molecular level, and further classified DLBCL into germinal centre B-cell-like (GCB), activated B-cell-like (ABC), primary mediastinal B-cell lymphoma (PMBL) and type III subgroups, where ABC associates with the most unfavourable prognosis. Gene-expression profiling (GEP) also confirmed a subgroup with features intermediate between BL and DLBCL, and these cases particularly that have concurrent chromosomal rearrangements of MYC and BCL2are often associated with poor prognosis. Despite the progress made from GEP, the classification still has limited influence on clinical treatment decision-making. In fact, as more heterogeneity beyond the subtypes above has been discovered by recent next-generation sequencing studies the approach of dividing cases into limited subgroups makes less sense in clinical practice. It is clear that the subtypes overlap to an extent in the affected signalling and regulatory pathways, and that small groupings within subtypes exhibit clear mechanistic differences and treatment responses. We describe an alternative approach, where a large database of aggressive B-cell lymphomas is used in a similarity search to identify those cases most similar at a molecular level to a query case. The hypothesis is that the most similar cases provide the best guide to prognosis and treatment outcome in the query case, independent of any need to place the query case into a particular subtype. We used both large public datasets and data from our Haematological Malignancy Research Network (www.HMRN.org) to explore genes associated with pathogenic pathways and an unfavourable prognosis. We also defined similarity between cases according to their molecular features and treatment responses. We then trained the similarity search method, by employing a distance metric learning approach that has been successfully used in similar machine learning applications, to test our HMRN dataset which contains detailed clinical data with treatment and outcome information. The cross-validation result on the public dataset achieved nearly 90% accuracy in recognizing cases with similar overall survival, and initial test results on HMRN data also shows that over 80% cases can be correctly represented by similar cases. In summary, we present a similarity learning method as an alternative to the current sub-type classification method. This mathematical method is able to accurately recognise cases with similar molecular features and provides important information on predicted treatment response for any given query case. Disclosures Smith: Novartis: Research Funding; Celgene: Research Funding; Jansen Cilag: Research Funding; Amgen: Research Funding.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2016
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  • 8
    In: Blood, American Society of Hematology, Vol. 116, No. 21 ( 2010-11-19), p. 2485-2485
    Abstract: Abstract 2485 Diffuse large B cell lymphoma (DLBCL) is a heterogenous disease, which has been subclassified into germinal centre (GCB) and activated B-cell (ABC) type using gene expression profiling. This has been shown to separate DLBCL into distinct prognostic sub-groups in patients treated with either CHOP or CHOP-R therapy. Previous studies have required the use of fresh or frozen samples for the extraction of RNA of sufficient quality to permit whole genome expression analysis. The Illumina ‘DASL' platform allows for highly reproducible gene expression data to be generated from FFPE material, which opens up large series' of retrospective data for detailed expression studies. The aim of this study was therefore to determine whether the Illumina DASL platform could yield reproducible results on formalin fixed paraffin embedded (FFPE) biopsies from a large series of archival CHOP-R treated DLBCL samples. RNA was extracted from paraffin sections using the Ambion Recoverall extraction kit, with 179/206 (87%) of cases yielding 〉 200ng of RNA sufficient for DASL analysis. The DASL assay was performed according to Illumina protocols. Using stringent exclusion criteria, 157/179 (88%) cases yielding results that were considered to be of sufficiently high quality to be included in the analysis. To fully assess the reproducibility of the assay, 35 cases were analysed on 2–8 occasions across multiple experimental days. Using Pearson's correlation, with full-linkage clustering, four discrete clusters were identified (n=28, 40, 46 and 43). Of important note, 95% of the samples were seen to cluster more tightly with their repeats than with any other sample, with all duplicated samples being called in the same cluster with 100% accuracy, suggesting that the technique is highly reproducible. Univariate Kaplan-Meier survival analysis showed that the clusters identified patients with very different outcomes. Two of the clusters showed identical survival curves and therefore these clusters were merged to give 3 clusters with 2-year overall survivals (OS) of 51% (n=71), 65% (n=46) and 77% (n=40), log rank p=0.03, with a 3.7 year follow-up. This data supports the use of gene expression profiling to classify DLBCL patients into clinically relevant prognostic groups. The Illumina DASL assay allows for highly reproducible gene expression data to be produced in valuable, archival data series, and also in the context of clinical trials, where the majority of the tissue available for study is FFPE. The patients identified in this study as having a sub-optimal response to CHOP-R should be considered for alternative therapies, which should be validated in the context of a clinical trial. Disclosures: No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2010
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  • 9
    In: Journal of Clinical Immunology, Springer Science and Business Media LLC, Vol. 43, No. 7 ( 2023-10), p. 1543-1556
    Abstract: The human CD19 antigen is expressed throughout B cell ontogeny with the exception of neoplastic plasma cells and a subset of normal plasma cells. CD19 plays a role in propagating signals from the B cell receptor and other receptors such as CXCR4 in mature B cells. Studies of CD19-deficient patients have confirmed its function during the initial stages of B cell activation and the production of memory B cells; however, its role in the later stages of B cell differentiation is unclear. Objective Using B cells from a newly identified CD19-deficient individual, we investigated the role of CD19 in the generation and function of plasma cells using an in vitro differentiation model. Methods Flow cytometry and long-read nanopore sequencing using locus-specific long-range amplification products were used to screen a patient with suspected primary immunodeficiency. Purified B cells from the patient and healthy controls were activated with CD40L, IL-21, IL-2, and anti-Ig, then transferred to different cytokine conditions to induce plasma cell differentiation. Subsequently, the cells were stimulated with CXCL12 to induce signalling through CXCR4. Phosphorylation of key downstream proteins including ERK and AKT was assessed by Western blotting. RNA-seq was also performed on in vitro differentiating cells. Results Long-read nanopore sequencing identified the homozygous pathogenic mutation c.622del (p.Ser208Profs*19) which was corroborated by the lack of CD19 cell surface staining. CD19-deficient B cells that are predominantly naïve generate phenotypically normal plasma cells with expected patterns of differentiation-associated genes and normal levels of CXCR4. Differentiated CD19-deficient cells were capable of responding to CXCL12; however, plasma cells derived from naïve B cells, both CD19-deficient and sufficient, had relatively diminished signaling compared to those generated from total B cells. Additionally, CD19 ligation on normal plasma cells results in AKT phosphorylation. Conclusion CD19 is not required for generation of antibody-secreting cells or the responses of these populations to CXCL12, but may alter the response other ligands that require CD19 potentially affecting localization, proliferation, or survival. The observed hypogammaglobulinemia in CD19-deficient individuals is therefore likely attributable to the lack of memory B cells.
    Type of Medium: Online Resource
    ISSN: 0271-9142 , 1573-2592
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
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  • 10
    Online Resource
    Online Resource
    American Society of Hematology ; 2011
    In:  Blood Vol. 118, No. 21 ( 2011-11-18), p. 3682-3682
    In: Blood, American Society of Hematology, Vol. 118, No. 21 ( 2011-11-18), p. 3682-3682
    Abstract: Abstract 3682 Cell of origin classification of diffuse large B-cell lymphoma (DLBCL) identifies biologically and clinically meaningful subsets. In future these classes may inform distinct treatment. However a meta-analysis to assess consistency of class and gene signature associations across multiple DLBCL gene expression datasets is lacking. Furthermore diagnostic material is routinely available in formalin-fixed paraffin embedded (FFPE) form, and there is limited evidence that for DLBCL FFPE derived RNA can produce gene expression datasets comparable to freshly extracted RNA. Using an FFPE derived data-set we develop a platform robust implementation of the cell of origin classifier. With this classifier we observe comparable separation of survival in distinct data-sets derived from fresh and FFPE material. Classification of six data-sets encompassing a total of 〉 900 DLBCL samples with this implementation establishes very similar patterns of gene expression for each DLBCL class. When tested against 12,000 signatures derived from LLMPP, MSigDB, GeneSigDB and genome wide transcription factor motif analysis of all TRANSFAC and JASPAR matrices, this communality translates into reproducible association of ABC and GCB-DLBCL with distinct molecular pathways, chromosomal regions and transcription factor motifs. This meta-analysis thus confirms the validity of FFPE derived data, identifies the most robust DLBCL class and signature associations and provides evidence for specific transcription factor signatures in both ABC and GCB-DLBCL. Disclosures: No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2011
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