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Understanding the biological and clinical impact of copy number aberrations (CNA) in cancer remains an unmet challenge. Genetic amplification of chromosome 1q (chr1q-amp) is a major CNA conferring adverse prognosis in several cancers, including the blood cancer, multiple myeloma (MM). Although several chr1q genes portend high-risk MM disease, the underpinning molecular aetiology remains elusive. Here we integrate patient multi-omics datasets with genetic variables to identify 103 adverse prognosis genes in chr1q-amp MM. Amongst these, the transcription factor PBX1 is ectopically expressed by genetic amplification and epigenetic activation of its own preserved 3D regulatory domain. By binding to reprogrammed super-enhancers, PBX1 directly regulates critical oncogenic pathways, whilst in co-operation with FOXM1, activates a proliferative gene signature which predicts adverse prognosis across multiple cancers. Notably, pharmacological disruption of the PBX1-FOXM1 axis, including with a novel PBX1 inhibitor is selectively toxic against chr1q-amp cancer cells. Overall, our systems medicine approach successfully identifies CNA-driven oncogenic circuitries, links them to clinical phenotypes and proposes novel CNA-targeted therapy strategies in cancer.SignificanceWe provide a comprehensive systems medicine strategy to unveil oncogenic circuitries and inform novel precision therapy decisions against CNA in cancer. This first clinical multi-omic analysis of chr1q-amp in MM identifies a central PBX1-FOXM1 regulatory axis driving high-risk prognosis, as a novel therapeutic target against chr1q-amp in cancer.

Ribosome dysfunction underlies the pathogenesis of many cancers and heritable ribosomopathies. Here, we investigate how mutations in either ribosomal protein large (RPL) or ribosomal protein small (RPS) subunit genes selectively affect erythroid progenitor development and clinical phenotypes in Diamond-Blackfan anemia (DBA), a rare ribosomopathy with limited therapeutic options. Using single-cell assays of patient-derived bone marrow, we delineated two distinct cellular trajectories segregating with ribosomal protein genotypes. Almost complete loss of erythroid specification was observed in RPS-DBA. In contrast, we observed relative preservation of qualitatively abnormal erythroid progenitors and precursors in RPL-DBA. Although both DBA genotypes exhibited a proinflammatory bone marrow milieu, RPS-DBA was characterized by erythroid differentiation arrest, whereas RPL-DBA was characterized by preserved GATA1 expression and activity. Compensatory stress erythropoiesis in RPL-DBA exhibited disordered differentiation underpinned by an altered glucocorticoid molecular signature, including reduced ZFP36L2 expression, leading to milder anemia and improved corticosteroid response. This integrative analysis approach identified distinct pathways of erythroid failure and defined genotype-phenotype correlations in DBA. These findings may help facilitate therapeutic target discovery.

Multiple myeloma is a genetically heterogeneous cancer of the bone marrow plasma cells (PC). Distinct myeloma transcriptome profiles are primarily driven by myeloma initiating events (MIE) and converge into a mutually exclusive overexpression of the CCND1 and CCND2 oncogenes. Here, with reference to their normal counterparts, we find that myeloma PC enhanced chromatin accessibility combined with paired transcriptome profiling can classify MIE-defined genetic subgroups. Across and within different MM genetic subgroups, we ascribe regulation of genes and pathways critical for myeloma biology to unique or shared, developmentally activated or de novo formed candidate enhancers. Such enhancers co-opt recruitment of existing transcription factors, which although not transcriptionally deregulated per se, organise aberrant gene regulatory networks that help identify myeloma cell dependencies with prognostic impact. Finally, we identify and validate the critical super-enhancer that regulates ectopic expression of CCND2 in a subset of patients with MM and in chronic lymphocytic leukemia., Despite extensive genetic heterogeneity, nearly half of all multiple myeloma (MM) cases are driven by cyclin D2 (CCND2) over-expression. Here the authors dissect the chromatin landscape of MM to provide insights into the transcriptional regulatory landscape driving MM and divergent transcriptomes corresponding to different MM genetic subtypes.

Summary Human hematopoiesis is a dynamic process that starts in utero 18–21 days post-conception. Understanding the site- and stage-specific variation in hematopoiesis is important if we are to understand the origin of hematological disorders, many of which occur at specific points in the human lifespan. To unravel how the hematopoietic stem/progenitor cell (HSPC) compartment changes during human ontogeny and the underlying gene regulatory mechanisms, we compare 57,489 HSPCs from 5 different tissues spanning 4 developmental stages through the human lifetime. Single-cell transcriptomic analysis identifies significant site- and developmental stage-specific transitions in cellular architecture and gene regulatory networks. Hematopoietic stem cells show progression from cycling to quiescence and increased inflammatory signaling during ontogeny. We demonstrate the utility of this dataset for understanding aberrant hematopoiesis through comparison to two cancers that present at distinct time points in postnatal life—juvenile myelomonocytic leukemia, a childhood cancer, and myelofibrosis, which classically presents in older adults., Graphical abstract, Highlights • Sampling of >57,000 hematopoietic cells over 4 stages of human development • Gene regulatory networks underpin changes in lineage specification through ontogeny • Stem cells show progressive changes in cell cycling and inflammatory signaling • Resource enables understanding of hematopoietic disorders presenting at specific age, Roy et al. use single-cell transcriptomics to compare lineage specification and gene regulatory networks of hematopoietic stem/progenitor cells (HSPCs) from multiple tissues over human ontogeny. Comparison to HSPCs from two blood cancers demonstrates the utility of the dataset for understanding disease processes and the emergence of age-specific blood malignancies.

BACKGROUND: Allogeneic haematopoietic cell transplantation (HCT) is often associated with poor oral intake due to painful mucositis and gastrointestinal sequalae that occur following a preparative regimen of intensive chemotherapy and/or total body radiation. Although attractive to assume that optimal nutrition improves HCT outcomes, there are limited data to support this. It is also unclear whether artificial nutrition support should be provided as enteral tube feeding or parenteral nutrition (PN). METHODS: We analysed day-100 non-relapse mortality (NRM), incidence of acute graft-versus-host disease (GvHD), acute gastrointestinal GvHD, 5-year survival and GvHD-free/relapse-free survival (GRFS) according to both route and adequacy of nutritional intake prior to neutrophil engraftment, together with other known prognostic factors, in a retrospective cohort of 484 patients who underwent allogeneic HCT for haematologic malignancy between 2000 and 2014. RESULTS: Multivariate analyses showed increased NRM with inadequate nutrition (hazard ratio (HR) 4.1; 95% confidence interval (CI) 2.2-7.2) and adequate PN (HR 2.9; 95% CI 1.6-5.4) compared to adequate enteral nutrition (EN) both P

BackgroundEndogenous retroviruses (ERVs) play a role in a variety of biological processes, including embryogenesis and cancer. DNA methyltransferase inhibitors (DNMTi)-induced ERV expression triggers interferon responses in ovarian cancer cells via the viral sensing machinery. Baseline expression of ERVs also occurs in cancer cells, though this process is poorly understood and previously unexplored in epithelial ovarian cancer (EOC). Here, the prognostic and immunomodulatory consequences of baseline ERV expression was assessed in EOC.MethodsERV expression was assessed using EOC transcriptional data from The Cancer Genome Atlas (TCGA) and from an independent cohort (Hammersmith Hospital, HH), as well as from untreated or DNMTi-treated EOC cell lines. Least absolute shrinkage and selection operator (LASSO) logistic regression defined an ERV expression score to predict patient prognosis. Immunohistochemistry (IHC) was conducted on the HH cohort. Combination of DNMTi treatment with γδ T cells was tested in vitro, using EOC cell lines and patient-derived tumor cells.ResultsERV expression was found to define clinically relevant subsets of EOC patients. An ERV prognostic score was successfully generated in TCGA and validated in the independent cohort. In EOC patients from this cohort, a high ERV score was associated with better survival (log-rank p=0.0009) and correlated with infiltration of CD8+PD1+T cells (r=0.46, p=0.0001). In the TCGA dataset, a higher ERV score was found in BRCA1/2 mutant tumors, compared to wild type (p=0.015), while a lower ERV score was found in CCNE1 amplified tumors, compared to wild type (p=0.019). In vitro, baseline ERV expression dictates the level of ERV induction in response to DNMTi. Manipulation of an ERV expression threshold by DNMTi resulted in improved EOC cell killing by cytotoxic immune cells.ConclusionsThese findings uncover the potential for baseline ERV expression to robustly inform EOC patient prognosis, influence tumor immune infiltration and affect antitumor immunity.

Multiple myeloma is a malignancy of plasma cells initiated and driven by primary and secondary genetic events. However, myeloma plasma cell survival and proliferation might be sustained by non-genetic drivers. Z-DNA-binding protein 1 (ZBP1; also known as DAI) is an interferon-inducible, Z-nucleic acid sensor that triggers RIPK3-MLKL-mediated necroptosis in mice. ZBP1 also interacts with TBK1 and the transcription factor IRF3 but the function of this interaction is unclear, and the role of the ZBP1-IRF3 axis in cancer is not known. Here we show that ZBP1 is selectively expressed in late B-cell development in both human and murine cells and it is required for optimal T-cell-dependent humoral immune responses. In myeloma plasma cells, the interaction of constitutively expressed ZBP1 with TBK1 and IRF3 results in IRF3 phosphorylation. IRF3 directly binds and activates cell cycle genes, in part through co-operation with the plasma cell lineage-defining transcription factor IRF4, thereby promoting myeloma cell proliferation. This generates a novel, potentially therapeutically targetable and relatively selective myeloma cell addiction to the ZBP1-IRF3 axis. Our data also show a noncanonical function of constitutive ZBP1 in human cells and expand our knowledge of the role of cellular immune sensors in cancer biology.

Multiple myeloma is a genetically heterogeneous cancer of the bone marrow plasma cells (PC). Myeloma initiating genetic events define subgroups (MIE) and drive distinct oncogenic transcriptomes that converge into a mutually exclusive overexpression of CCND1 and CCND2 oncogenes. Here, with reference to normal PC, we dissect how MIE impact the chromatin regulatory landscape of MM. We find that chromatin accessibility combined with transcriptome profiling classifies myeloma genetic subgroups, while in a topologically constrained manner, distal rather than proximal regulatory elements influence myeloma transcriptomes. Across and within MIE-defined subgroups, genes and pathways critical for myeloma biology can be linked to developmentally activated or de novo formed enhancers. We show that existing transcription factors, co-opted to organise highly ordered, aberrant regulatory networks, generate known and novel myeloma cell dependencies and help identify prognostic markers. Finally, we discover and functionally validate the critical enhancer that regulates ectopic expression of CCND2 in MM.

Chimeric antigen receptor T cell (CART) therapy has dramatically changed the therapeutic prospects for B cell malignancies. Over the last decade CD19-redirected CART have demonstrated the ability to induce deep, long-lasting remissions and possibly cure patients with relapsing B cell neoplasms. Such impressive results with CART19 fostered efforts to expand this technology to other incurable malignancies that naturally do not express CD19, such as acute myeloid leukemia (AML), Hodgkin lymphoma (HL) and multiple myeloma (MM). However, to reach this goal, several hurdles have to be overcome, in particular: (i) the apparent lack of suitable targets as effective as CD19; (ii) the immunosuppressive tumor microenvironment; (iii) intra-tumoral heterogeneity and antigen-negative relapses. Therefore, new strategies that allow safer and more potent CART platforms are under development and may provide grounds for new exciting breakthroughs in the field.

Background: Diamond- Blackfan Anemia (DBA) is a rare, heritable ribosomopathy caused by mutations in ribosomal protein large (RPL) and small (RPS) subunit genes. The diagnostic criteria of DBA include presentation in infancy with virtually no mature erythroblasts (EB) on bone marrow (BM) examination, however atypical presentations in later life with milder haematological manifestations are increasingly reported. The cellular and molecular mechanisms underpinning variable clinical phenotypes, and how they relate to genotype, are yet to be elucidated. Furthermore, as many DBA patients do not respond to corticosteroids, understanding the pathological processes contributing to erythroid failure is a prerequisite for developing novel, precision-medicine therapies. Aim: To elucidate phenotypic and functional differences in erythropoiesis in RPS- and RPL-DBA, using primary BM samples from patients. Methods: We performed single-cell transcriptome profiling (scRNAseq), using the 10X Genomics chromium platform, of 45,488 CD34+ Lineage negative (Lin-) BM hematopoietic stem and progenitor cells (HSPC), purified by fluorescence-activated cell sorting. We included six patients with red cell transfusion-dependent DBA (aged 2-19y) with mutations in RPS19 (n=3), RPL11 (n=1) and RPL5 (n=2) and three healthy donors (aged 3-17y). We validated our findings using bulk RNAseq, functional assays, and deep immunophenotyping-based dissection of the haematopoietic architecture of DBA BM ex vivo. Results: High quality sequencing data was obtained for all nine donors; after quality control, 41,415 single cells were carried forward for analysis. Unsupervised clustering analysis and lineage identification revealed two divergent cellular patterns in DBA compared with age-matched control BM that segregated with genotype: a selective loss of erythromegakaryocyte (E/MK) progenitors in RPS-DBA, but relative preservation of the erythroid developmental trajectory in RPL-DBA, at the expense of megakaryopoiesis (Fig 1a). Gene Set Enrichment Analysis (GSEA) of differentially expressed genes between control and DBA HSPC clusters revealed p53-mediated apoptosis, TNFa-, IFNa- and IFNg-mediated inflammatory pathways in DBA EP. Although these pathways were enriched across all HSPC populations irrespective of genotype, they were detected at an earlier stage of the stem cell hierarchy, and more potently, in RPS- versus RPL-EP. Expression of transcriptional targets of the master E/MK transcription factor, GATA1, was significantly upregulated in RPL- versus RPS-DBA EP (Fig 1b), supporting the maintained erythroid program in RPL-DBA HSPC. However, expression of genes denoting erythroid differentiation, including adult haemoglobin (Hb) genes, was significantly elevated in RPL-DBA, suggesting aberrant accelerated differentiation to EB. These findings were confirmed by immunophenotypic examination of patient BM and bulk RNAseq of RPL-EB. Additionally, single-cell clonogenic assays of RPL-DBA EP showed severe qualitative defects. Thus, although erythroid commitment occurs in RPL-DBA, it is coupled with accelerated maturation beyond EP to functionally impaired mature EB, enriched in inflammatory and p53 pathways. Finally, we analysed the clinical characteristics of the 161 patients comprising the U.K DBA registry. In line with the milder erythroid specification defect, patients with RPL-DBA (n=44) presented with anaemia later (P=0.004), and with a higher average Hb concentration (P=0.04), than those with RPS-DBA (n=63). Furthermore, we identified higher corticosteroid responses in RPL-DBA, assessed at 6 months post initiation (P=0.006), consistent with our findings in RPL-DBA of preservation of the cellular EP populations that are targeted by corticosteroids. Impact: In conclusion, a preserved but distinct erythroid developmental trajectory, characterised by accelerated differentiation, underpins a milder haematological phenotype in RPL-DBA. Furthermore, we reveal the first single-cell transcriptomic dataset from haematopoietic cells in a ribosomopathy, uncovering novel cell intrinsic and extrinsic pathogenetic insights into failing erythropoiesis in DBA. Integration of these data with clinical genomics and phenomics provides a paradigm by which single cell approaches can be used to decipher genotype-phenotype relationships in Mendelian genetic disorders. Disclosures Mead: Novartis: Consultancy, Honoraria, Other: travel, accommodations, expenses, Research Funding, Speakers Bureau; Celgene/BMS: Consultancy, Honoraria, Other: travel, accommodations, expenses, Research Funding; Abbvie: Consultancy; CTI: Consultancy; Gilead: Consultancy.

Chimeric antigen receptor (CAR)-T cell immunotherapy is highly effective against B lineage cancers but at the expense of potentially serious toxicity such as cytokine release syndrome (CRS) and neurotoxicity. Recent work provided clinical evidence that allogeneic, cord blood CAR-NK cells induce high rates of non-durable clinical responses without CRS or neurotoxicity.

Diamond-Blackfan anaemia (DBA) is a rare bone marrow failure syndrome characterised by anaemia, congenital anomalies and cancer predisposition. Although infections are the second leading cause of mortality in non-transplanted patients, immune function is largely unexplored. We identified quantitative deficits in serum immunoglobulins and/or circulating T, natural killer and B lymphocytes in 59 of 107 unselected patients (55·1%) attending our centre over a 7-year period. Immune abnormalities were independent of ribosomal protein genotype and arose in both steroid-treated and steroid-untreated patients. In summary, these data highlight the high prevalence and spectrum of infections and immune defects in DBA.

Human lymphopoiesis is a dynamic lifelong process that starts in utero 6 weeks post-conception. Although fetal B-lymphopoiesis remains poorly defined, it is key to understanding leukemia initiation in early life. Here, we provide a comprehensive analysis of the human fetal B-cell developmental hierarchy. We report the presence in fetal tissues of 2 distinct CD191 B-progenitors, an adult-type CD10+ve ProB-progenitor and a new CD10-ve PreProB-progenitor, and describe their molecular and functional characteristics. PreProB-progenitors and ProB-progenitors appear early in the first trimester in embryonic liver, followed by a sustained second wave of B-progenitor development in fetal bone marrow (BM), where together they form > 40% of the total hematopoietic stem cell/progenitor pool. Almost one-third of fetal B-progenitors are CD10-ve PreProB-progenitors, whereas, by contrast, PreProB-progenitors are almost undetectable (0.53% +/- 0.24%) in adult BM. Single-cell transcriptomics and functional assays place fetal PreProB-progenitors upstream of ProB-progenitors, identifying them as the first B-lymphoid-restricted progenitor in human fetal life. Although fetalBMPreProB-progenitors and ProB-progenitors both give rise solely to B-lineage cells, they are transcriptionally distinct. As with their fetal counterparts, adult BM PreProB-progenitors give rise only to B-lineage cells in vitro and express the expected B-lineage gene expression program. However, fetal PreProB-progenitors display a distinct, ontogeny-related gene expression pattern that is not seen in adult PreProB-progenitors, and they share transcriptomic signatures with CD10-ve B-progenitor infant acute lymphoblastic leukemia blast cells. These data identify PreProB-progenitors as the earliest B-lymphoid-restricted progenitor in human fetal life and suggest that this fetal-restricted committed B-progenitor might provide a permissive cellular context for prenatal B-progenitor leukemia initiation.

Despite encouraging therapeutic advances, multiple myeloma (MM) remains an incurable malignancy. The exciting results of chimaeric antigen receptor (CAR)-based immunotherapy in CD19(+) B-cell malignancies have spurred a great interest in extending the use of the CAR technology to other cancers, including MM. Availability of a specific, tumour-restricted antigen is crucial for the design of successful antibody-based CAR therapy. However, in MM, as in other malignancies, the relative dearth of such antigens-targets represents the main obstacle for the wider pre-clinical development and clinical application of the CAR technology. Here we provide an overview of the current progress and future promises of CAR technology in MM therapy. We highlight that, owing to its complexity, phenotypic and functional heterogeneity and the impact of the microenvironment, MM poses several challenges for CAR-based therapeutic approaches. Nevertheless, for the same reasons, MM can serve as a paradigm for better understanding, optimization and overall improvement of the CAR technology for the benefit of cancer and myeloma patients.

BACKGROUND: The biological basis for the adverse prognosis of chr1q gain/amplification (1q+) present in ~30% of patients with multiple myeloma (MM) remains ill-defined. The transcription factor (TF) Pre-B-cell leukaemia homeobox 1 (PBX1), encoded on chr1q, acts as master regulator of early hematopoiesis and as an oncogene in leukemia and other malignancies. Herein, we hypothesized that PBX1 orchestrates proliferative regulatory networks that underpin the poor prognosis associated with 1q+ in MM. METHODS: We employed qPCR for mRNA quantification, western blotting and immunohistochemistry for protein analysis, lentiviral shRNA-mediated knock-down, Hoechst/Annexin V staining and flow-cytometry for apoptosis and cell cycle analysis, ChIPseq for cistrome and RNAseq after knock-down for transcriptome analysis. Additional data were obtained from MMRF/CoMMpass, Blueprint Consortium and Arkansas datasets. Computational analysis of clinical and "-omics" data was performed using standard bioinformatic work-flows; pathway enrichment analysis using EnrichR and GSEA. RESULTS: Combined genomic (WGS/WES) and transcriptomic (RNAseq) analysis of the CoMMpass dataset identified a subgroup of 1q+ MM patients (60%) characterized by aberrant PBX1 overexpression and amplification (PBX1amp); survival analysis revealed significantly worse outcome of this subgroup compared to 1q+ non-PBX1amp (p Depletion of PBX1 using 2 validated shRNAs was toxic to the 1q+ MM1.S t(14;16) and U266 t(11;14) myeloma cell lines (MMCL) in vitro, revealing a novel myeloma cell addiction to PBX1. Transcriptome analysis of PBX1-depleted cells showed significant de-regulation of genes (MM1.S: 753down/320up; U266: 598 down/288up) highly enriched in cell cycle and proteasome/ER stress response pathways. Flow-cytometric analysis confirmed that PBX1-depleted myeloma cells undergo cell cycle arrest (G0/1 phase) and apoptosis (n=3; p Genome-wide binding profiling of PBX1 identified 7,354 significantly enriched peaks shared between MM1.S and U266 MMCL. These peaks were distributed at active promoters (~50%) and active enhancers (~30%), as defined by ChromHMM maps; the PBX1 consensus binding motif was identified as top hit upon motif enrichment analysis. Transcriptome-cistrome integration identified 728 and 282 genes directly activated or repressed, respectively, by PBX1 in MM1.S cells. Again, pathway enrichment analysis of PBX1 direct targets demonstrated significant over-representation of cell cycle and proliferation pathways, as well as positive regulation of various metabolic processes (oxidative phosphorylation, glycolysis, unfolded protein response). Strikingly, enrichment analysis against public ChIPseq datasets revealed significant overlap with gene targets of FOXM1 (200) and E2F (150) TF, suggesting the presence of a united PBX1-FOXM1-E2F regulatory circuitry. In fact, PBX1 binding was detected at an active FOXM1 enhancer and at the E2F1/2 promoters, while FOXM1 and E2F1/2 mRNA levels decreased significantly upon PBX1 depletion in two MMCL. To further explore the PBX1-FOXM1 interaction, we overlaid the FOXM1-depleted transcriptome with the PBX1 network in MM.1S cells. This identified 160 genes to be co-regulated by PBX1 and FOXM1, including genes previously linked to myeloma cell drug resistance (NEK2, TOP2A, AURKA); however, PBX1 expression was not altered in FOXM1-depleted cells, suggesting that PBX1 is functionally upstream of FOXM1. Additional analysis across 814 primary MM patient CoMMpass transcriptomes confirmed significant co-expression of PBX1 with FOXM1, E2F1/2 and another 67 PBX1-FOXM1 highly expressed, co-regulated gene targets, conferring poor OS (p CONCLUSIONS: We found that genetic amplification and overexpression of PBX1 defines an ultra high-risk subgroup of 1q+ MM with proliferative features. Myeloma cells are addicted to aberrant PBX1 expression. As well as essential metabolic pathways, PBX1 regulates cell cycle progression by direct transcriptional regulation of FOXM1 and of its target genes. These data reveal PBX1 as a critical biological link between chr1q gain/amplification and poor prognosis in a subset of MM patients. Disclosures Auner: Karyopharm: Consultancy; Amgen: Other: Consultancy and Research Funding; Takeda: Consultancy. Caputo:GSK: Research Funding. Karadimitris:GSK: Research Funding.

In multiple myeloma (MM), a malignancy of the bone marrow plasma cells (BMPC), hyperdiploidy (HY) and oncogene over-expression via chromosomal translocation [including CCND1- t(11;14), MAF- t(14;16), MMSET-t(4;14)] are the primary myeloma initiating events (MIE) that drive distinct transcriptional programs. These are further shaped by secondary SNV and CNV events. This genetic heterogeneity converges, in most cases, to a functionally dichotomous state of CCND1 or CCND2 overexpression. The molecular mechanisms underlying each of the distinct myelomagenic transcriptomes and the CCND1 vs CCND2 dichotomy have not been defined. To address these questions, we obtained highly purified BMPC from 3 healthy donors and 30 MM patients (HY: 15; CCND1: 4; MMSET: 5; MAF: 2; other: 4), either at diagnosis or relapse, and mapped their chromatin accessibility and transcriptome profiles by ATAC-seq and RNA-seq, respectively. In total, we obtained ~300K regions with accessible chromatin in either MM or normal PC. Overall chromatin accessibility increased in myeloma compared to normal PC, particularly in MAF- and MMSET-translocated subtypes. Analysis of combined ATAC-seq/RNA-seq by Multi-Omics Factor Analysis (MOFA) resulted in a clearer samples distinction than either ATAC-seq or RNA-seq alone, with altered chromatin accessibility accounting for more of the variance than expression. Of the top five identified factors, the top two (one transcriptome driven, one accessibility driven) distinguished normal from MM samples, whilst two more separated MMSET, MAF and CCND1 subgroups. Ninety seven, 157, 256 and 348 overexpressed genes in the CCND1, HY, MMSET and MAF subgroups, respectively, were predicted to be regulated by differentially accessible enhancers. Twenty percent (165/858) of these genes were overexpressed in >1 subgroup suggesting a process of chromatin accessibility-based convergence evolution. Enrichment analysis suggested direct or indirect involvement of Polycomb and chromatin remodellers; significant enrichment was also found for genes involved in neurogenesis. ATAC-seq footprinting predicted binding sites for 250 expressed transcription factors (TFs), 116 of which displayed higher binding frequency in myeloma than in normal PC and included both known (e.g., XBP1, RELA, IRF4, PRDM1) and potentially novel regulators of myeloma biology (e.g., CXXC1 and NFE2L1). The remaining 134 TF were predicted to be present in at least one MM subgroup, but absent in normal PC. Amongst them, as expected, MAF was active in the MMSET- and more so in the MAF-translocated subgroups. DepMap database analysis suggested myeloma cell dependency on 181/250 TF (CRISPR/Cas9 CERES score < -0.1 in >3/14 MMCL analysed). In dissecting the regulatory basis of CCND2 vs CCND1 dichotomy, one MOFA factor completely separated MAF from CCND1 samples, placing extreme opposite weights on the expression of CCND2 and CCND1 respectively. Interestingly, the same factor identified open-chromatin clusters upstream of CCND2 and linked them to its over-expression. These clusters were also open in the MMSET group and in CCND2-expressing HY samples. Conversely, no accessibility was detected in the CCND1 group, the CCND1-expressing HY samples or in normal PCs. Further, super-enhancer calling using the H3K27ac histone mark in MAF-translocated JJN3 cells identified the region of interest as a bona fide super-enhancer. Chromatin long range interactions, as assessed by Capture-HiC, demonstrated high frequency interactions of the CCND2 promoter with the constituent elements of the putative super-enhancer. Experimental validation using a CRISPR/Cas9i system confirmed the functional role of all 4 super-enhancer constituents tested in the regulation of CCND2 expression, while TF footprinting predicted MAF binding to the super-enhancer in MAF-translocated PC. In conclusion, we show that distinct oncogenic transcriptomes in MM are underpinned by extensive chromatin changes, accompanied by TF activity 're-wiring' that does not necessarily require transcriptional deregulation of the TF themselves. We identify novel, non-oncogene TF dependencies that suggest therapeutic opportunities in MM and we discover and characterise the critical super-enhancer that drives overexpression of the CCND2 oncogene in MM. Disclosures Auner: Amgen: Other: Consultancy and Research Funding; Takeda: Consultancy; Karyopharm: Consultancy. Hatjiharissi:Janssen: Honoraria. Caputo:GSK: Research Funding. Karadimitris:GSK: Research Funding.

The mechanism of bone marrow failure (BMF) in paroxysmal nocturnal hemoglobinuria (PNH) is not yet known. Because in PNH the biosynthesis of the glycolipid molecule glycosylphosphatidylinositol (GPI) is disrupted in hematopoietic stem and progenitor cells by a somatic mutation in the PIG-A gene, BMF might result from an autoimmune attack, whereby T cells target GPI in normal cells, whereas PIG-A mutant GPI-negative cells are spared. In a deliberate test of this hypothesis, we have demonstrated in PNH patients the presence of CD8(+) T cells reactive against antigen-presenting cells (APCs) loaded with GPI. These T cells were significantly more abundant in PNH patients than in healthy controls; their reactivity depended on CD1d expression and they increased upon coculture with CD1d-expressing, GPI-positive APCs. In GPI-specific T cells captured by CD1d dimer technology, we identified, through global T-cell receptor α (TCRα) analysis, an invariant TCRVα21 sequence, which was then found at frequencies higher than background in the TCR repertoire of 6 of 11 PNH patients. Thus, a novel, autoreactive, CD1d-restricted, GPI-specific T-cell population, enriched in an invariant TCRα chain, is expanded in PNH patients and may be responsible for BMF in PNH.

A young man presented with overt multiple myeloma at the age of 28, and received cyclophosphamide pulses every 3-4 weeks for more than 3 years. He has remained in continuous complete remission for the past 23 years without further treatment and without evidence of disease. Five cases of multiple myeloma cured by conventional chemotherapy reported in literature are reviewed here.

Alterations in glycosphingolipid production results in lysosomal storage disorders associated with neurodegenerative changes. In Gauchers disease, the patients also develop osteoporosis that is ameliorated upon treatment for the underlying defect in glycosphingolipid metabolism. The role of glycosphingolipids in osteoclast and osteoblast formation is discussed here as well as the potential therapeutic uses of already approved drugs that limit glycosphingolipid production in bone loss disorders such as multiple myeloma and periodontal disease.

Glycosphingolipids (GSLs) are essential constituents of cell membranes and lipid rafts and can modulate signal transduction events. The contribution of GSLs in osteoclast (OC) activation and osteolytic bone diseases in malignancies such as the plasma cell dyscrasia multiple myeloma (MM) is not known. Here, we tested the hypothesis that pathological activation of OCs in MM requires de novo GSL synthesis and is further enhanced by myeloma cell-derived GSLs. Glucosylceramide synthase (GCS) inhibitors, including the clinically approved agent N-butyl-deoxynojirimycin (NB-DNJ), prevented OC development and activation by disrupting RANKL-induced localization of TRAF6 and c-SRC into lipid rafts and preventing nuclear accumulation of transcriptional activator NFATc1. GM3 was the prevailing GSL produced by patient-derived myeloma cells and MM cell lines, and exogenous addition of GM3 synergistically enhanced the ability of the pro-osteoclastogenic factors RANKL and insulin-like growth factor 1 (IGF-1) to induce osteoclastogenesis in precursors. In WT mice, administration of GM3 increased OC numbers and activity, an effect that was reversed by treatment with NB-DNJ. In a murine MM model, treatment with NB-DNJ markedly improved osteolytic bone disease symptoms. Together, these data demonstrate that both tumor-derived and de novo synthesized GSLs influence osteoclastogenesis and suggest that NB-DNJ may reduce pathological OC activation and bone destruction associated with MM.

Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative procedure for a number of hematological malignancies including leukemia and lymphoma. However, the anti-leukemia (graft-versus-leukemia, GVL) effect mediated by T cells transferred to the host with the allograft is often negated by the graft-versus-host (GVH) reaction imparted by the same cells. Acute graft-versus-host disease (aGVHD), an allogeneic reaction triggered in response to minor and major histocompatibility antigen disparities between donor and recipient, remains the main source of morbidity and mortality in T-cell-replete allogeneic HSCT. Here we review the biological properties, the pre-clinical work, and the recent clinical observations suggesting that invariant natural killer (iNK) T cells, a CD1d-restricted subset of immunoregulatory T cells, are important regulators of GVH and GVL reactions. Further, we outline strategies for manipulating iNKT cells to translate their therapeutic promise into clinical benefit in the context of allogeneic HSCT.

Immunohistochemistry can sub-classify diffuse large B-cell lymphoma (DLBCL) into germinal centre B-cell like (GCB) and non-GCB subtypes. The latter consists predominately of the activated B-cell like subgroup in which nuclear factor kappa-B activation is its characteristic. Expression of cellular caspase 8 (FLICE)-like inhibitory protein (cFLIP), a caspase 8 homologue, is regulated by nuclear factor kappa-B signalling, and it is the main inhibitor of Fas ligand activated apoptosis. To determine if cFLIP expression was confined to non-GCB subtype, we studied 66 cases of DLBCL. cFLIP expression showed no significant correlation to DLBCL subtypes (GCB or non-GCB) but was associated with a worse clinical outcome. For cFLIP positive and negative patients, the five-year event free survival was 20 and 31%, respectively (p = 0.049), and the five-year overall survival was 20 and 57%, respectively (p = 0.041). Copyright © 2011 John Wiley & Sons, Ltd.

BACKGROUND: Patients with relapsed and/or refractory non-Hodgkin's lymphoma (NHL), especially those with aggressive lymphomas, have overall poor prognosis. Novel targets and therapies are under investigation. Molibresib (GSK525762) is a potent and specific inhibitor of the bromodomain and extraterminal domain (BET) family of proteins, the inhibition of which prevents transcriptional complex assembly and the subsequent expression of oncogenic drivers. Molibresib inhibits growth in NHL cell lines, both in vitro and in vivo. Study BET116183 was designed to evaluate the safety, tolerability, and preliminary efficacy of molibresib in relapsed and refractory hematologic malignancies. Here we report the results from the NHL dose escalation cohort. METHODS: Eligible subjects were adults with relapsed or refractory NHL. An accelerated dose titration was employed with one subject per dose level until the occurrence of a ≥Grade 2 drug-related toxicity; thereafter, subjects were enrolled in a standard 3+3 design. A Neuenschwander continual reassessment method (N-CRM) model was used to provide guidance for the next dose level. Dose escalation continued until the maximum tolerated dose (MTD) was identified. All data, including safety, tolerability, pharmacokinetics (PK), and efficacy, were used to identify the recommended part 2 dose (RP2D). RESULTS: From 14 May 2014 to the data cutoff date of 24 June 2018, 27 NHL subjects were enrolled and received at least one dose of study drug. Of these, 19 (70%) had B-cell lymphomas (diffuse large B-cell lymphoma [DLBCL], mantle cell lymphoma, marginal zone lymphoma, follicular lymphoma , and Burkitt's lymphoma); eight subjects (30%) had T-cell lymphomas (cutaneous T-cell lymphoma [CTCL], anaplastic T-cell lymphoma [ATCL], peripheral T-cell lymphoma, and adult T-cell leukemia/lymphoma). The median age was 64 years (range 24 to 76); 20 subjects (76%) were male and 7 subjects (24%) were female. The median number of prior treatments was 3 (range 1 to > 4). From the starting dose of 10 mg molibresib orally once daily (QD), the dose was escalated to 80 mg QD. The median time on study was 1.4 months (range 0.2 to 20 months). Two dose-limiting toxicities (DLTs) were identified in subjects treated at 60 mg QD, though one was subsequently determined not to be a DLT. One subject experienced Grade 4 thrombocytopenia related to study drug. A second subject experienced a Grade 2 mechanical fall; this event was later revised to unrelated to study drug. Across all dose levels, all subjects experienced an adverse event (AE); 25 subjects (93%) experienced at least one AE that was deemed to be related to molibresib treatment. The most common related AEs across all dose levels were thrombocytopenia (n = 21 [78%]), fatigue (n = 6 [22%]), nausea (n = 6 [22%]), diarrhea (n = 4 [15%]), and rash (n = 4 [15%]). Blood bilirubin was increased in 3 subjects (11%), and prothrombin time and activated partial thromboplastin time were prolonged in 2 subjects each (7%). Common Grade 3 and Grade 4 related events included thrombocytopenia (n = 19 [70%]), as well as anemia, asthenia, and increased blood bilirubin (n = 2 [7%] each). No Grade 5 related AEs were reported. Among all subjects, 11 (41%) required dose reduction for toxicity: 7 subjects at the 60 mg dose level (39% treated at that dose) and 4 at the 80 mg dose level (57% treated at that dose). PK analyses showed dose-proportionality after single and repeat dosing, with large variability between subjects. One subject with DLBCL achieved a complete remission that was durable through week 54 on study. Four additional subjects (one DLBCL and 3 CTCL) achieved partial remission, for an objective response rate (ORR) of 5/27 (18.5%). Five more subjects had stable disease as best response. Of six CTCL/ATCL subjects enrolled, three subjects had partial response for an ORR of 50% in this sub-population. CONCLUSIONS: This is the first study evaluating the safety and efficacy of the BET inhibitor molibresib in NHL subjects. Overall, thrombocytopenia and other AEs were monitorable, manageable and reversible. The RP2D was identified as 60 mg QD. Single-agent activity was observed across multiple NHL subtypes at both 60 mg and 80 mg doses; most notable was a 50% response rate in subjects with CTCL. Because of the promising data, Part 2 of the BET116183 study is currently open and enrolling subjects with CTCL to better define the clinical activity of BET bromodomain inhibition in this histology. Disclosures Dickinson: GSK: Consultancy. Kamdar:Genentech: Consultancy; Seattle Genetics: Speakers Bureau. Mateos:Janssen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; GSK: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; GSK: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Takeda: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees. Alegre:Janssen: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees. Kim:Roche: Research Funding; Mundipharma: Research Funding; J&J: Research Funding; Novartis: Research Funding; Kyowa-Kirin: Research Funding; Celltrion: Research Funding; Takeda: Research Funding. Martín:Janssen: Honoraria, Other: Travel expenses; Celgene: Consultancy, Honoraria, Other: Travel expenses; Roche: Consultancy, Honoraria, Other: Travel expenses; Servier: Honoraria, Other: Travel expenses. Horner:GSK: Employment. Winnberg:GSK: Employment. Mathew:GSK: Employment. Botbyl:GSK: Employment. Karpinich:GSK: Employment. Kremer:GSK: Employment. Dhar:GSK: Employment. Karadimitris:GSK: Research Funding; Gilead: Honoraria; Celgene: Research Funding.

Background: Multiple myeloma (MM) is a remitting-relapsing malignancy with variable clinical outcome. Certain cytogenetic abnormalities, either present at diagnosis or emerged at later stages, predict for poor outcome and highlight the clinical importance of MM genetic heterogeneity. Whole genome and exome sequencing studies reveal a complex intraclonal genetic landscape, organised in linear and branching Darwinian patterns, which evolves in space and time. Clones with a more complex genetic architecture may be more fit to escape treatment and those patients are likely to have a worse clinical outcome. Clinical multicolour flow cytometry (MFC) is routinely used in MM diagnosis and detection of minimal residual disease. Previous studies have shown that MM cell subpopulations with discrete phenotypic features correspond to genetic subclones, therefore it is plausible that MFC data captures clonal heterogeneity. On that basis, we propose that clustering analysis of MM phenotypic subpopulations could be clinically relevant. Methods: We retrospectively analysed clinical MCF data at diagnosis from 44 patients eligible for autologous stem cell transplantation (AutoSCT) and 14 ineligible patients and data from 52 relapsed patients after first AutoSCT. All patients were treated between 2012 - 2018. The 8-colour MCF marker panel included CD138, CD38, CD56, CD45, CD20, CD19, cytoplasmic kappa and lambda light chains (cytLC). Data was analysed in FlowJo software and MM plasma cells were identified as CD38high, CD19-, cytLC+, within their FSC-A/SSC-A physical gate. The gated events were exported in a new fcs file. Clustering analysis was performed in Cytofkit, a R-based Bioconductor package, using the Rphenograph, Cluster-X and FlowSOM algorithms. All fcs files were subjected in the same clustering analysis, but CD56 positive and CD56 negative cases were analysed separately to offset bias from differential CD56 expression. Parameters inserted in the algorithms were FSC-A, CD138, CD38, CD45, CD20 and CD56. The number of clusters was produced by FlowSOM (k=4) and only clusters with size >1% of the total events were accepted. Results: At diagnosis, FlowSOM identified 1 (n=32, 56.1%) or 2 clusters (n=19, 33.3%) in most cases. Three clusters were found only in 5 patients (8.8%) and 4 clusters in 1 patient (1.8%). The number of clusters at diagnosis did not correlate with cytogenetic risk group or ISS. Also, the number of clusters did not predict for depth of response or relapse free survival post AutoSCT. On the contrary, phenotypic patterns at relapse post AutoSCT were more complex, with 1 cluster identified in 2 patients only (3.8%), 2 clusters in 23 (44.2%), 3 clusters in 24 (46.2%) and 4 clusters in 3 patients (5.8%). Patients with >2 clusters (n=27) had a shorter survival post relapse (median 17 months - 95% CI, 7-26.6) compared to those (n=25) with 1-2 phenotypic clusters (median not reached, Log rank p=0.06). A phenotypic cluster characterised by CD138low/- at relapse, was also associated with adverse outcome and higher risk cytogenetics. In 14 patients with available serial samples at diagnosis and relapse we observed 3 patterns of phenotypic evolution: a. sustained pattern, b. change of dominant cluster and c. emergence of completely new subpopulations. These evolving phenotypes resemble changes in clonal composition over time observed in genetic studies. Conclusion: Clinical MCF, in addition to routine diagnostics, can be informative of MM biological and clinical heterogeneity. Particularly in the relapsed setting, complex phenotypic patterns identified by clustering analysis may be of prognostic value. Validation of this preliminary study results in larger patient cohorts or clinical trials, could provide a useful and readily available tool for patient stratification and prognosis. Disclosures Apperley: Novartis: Honoraria, Research Funding, Speakers Bureau; Pfizer: Honoraria, Speakers Bureau; BMS: Honoraria, Speakers Bureau; Incyte: Honoraria, Speakers Bureau. Karadimitris:Celgene: Research Funding; GSK: Research Funding; Gilead: Honoraria.

Ovarian cancer (OC) is regarded as being an immunogenic cancer and strategies to enhance immune function in patients are thought to confer benefit and improve prognosis. Immunotherapy has been shown to be most promising when combined with other therapeutic approaches. Recent evidence in the field and preliminary data from our group suggest that treatment with epigenetic drugs, such as DNA methyltransferase inhibitors (DNMTi), can lead to improved immune activation in several cancers including ovarian. The purpose of this study is to test the hypothesis that treatment with next generation hypomethylating agent SGI-110 can induce the re-expression of immunomodulatory genes and endogenous retroviruses (ERVs), which shifts OC cells towards a more immunogenic expression profile. OC cell lines SKOV3, Kuramochi and OVSAHO were treated with low dose SGI-110 and assessed for increased immunogenicity. Expression of immune biomarkers and ERVs was assessed at different time points at mRNA levels by qPCR and protein levels by Flow Cytometry. Treated cell lines were functionally tested for increased immunogenicity by co-culture with γδ T cells, which were isolated from healthy donors and expanded by zoledronic acid selection. MTT assays were performed to assess cell viability and T cell killing following co-culture. IFNγ and Granzyme B release from T cells and chemokine release from tumor cells were assessed by ELISA. Our results show up-regulation of key immunogenicity biomarkers and ERVs in our panel of OC cell lines, following treatment with SGI-110. Co-culturing SGI-110-treated cell lines with γδ T cells resulted in increased tumor cell killing and T cell activity. We are now analysing RNA-sequencing data of SGI-110-treated OC cell lines in an effort to dissect the immunomodulatory mechanism of action of this novel hypomethylating agent. Moreover, we plan to test the in vivo feasibility of a SGI-110/γδ T cell combination therapy, which if successful might be further optimised for a clinical trial. Citation Format: Marina Natoli, Anastasios Karadimitris, Sadaf Ghaem-Maghami. Immunomodulatory action of SGI-110 and combination with γδ T cell immunotherapy in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4567.

Down-regulation of conventional human leukocyte antigen (HLA) class I and II molecules from the surface of tumor cells is an important mechanism for tumor immune evasion, survival, and progression. Whether CD1d, a nonconventional, glycolipid-presenting HLA class I–like molecule instructing the function of the immunoregulatory invariant NKT cells can affect tumor cell survival is not known. Here we show that CD1d is highly expressed in premalignant and early myeloma, but with disease progression its expression is reduced and eventually in advanced stages and myeloma cell lines is lost altogether, suggesting that CD1d impacts negatively on myeloma cell survival. Consistent with this, engagement of CD1d by anti-CD1d monoclonal antibodies (mAbs) induces cell death of myeloma cell lines with restored CD1d expression and primary myeloma cells. Cell death induced by monoclonal antibody engagement of CD1d is associated with overexpression of proapoptotic Bax and mitochondrial membrane potential loss but it is caspase-activation independent; in addition, it requires the cytoplasmic tail but not the Tyr residue critical for lysosomal sorting of CD1d. Finally, anti-CD1d cooperates with antimyeloma agents in the killing of myeloma cells. Thus, this work provides evidence linking a novel function of CD1d in the regulation of cell death with tumor survival and progression in humans.

Multiple myeloma (MM) is an incurable tumor of the plasma cells, the terminally differentiated immunoglobulin secreting B lineage cells. The genetic make-up of MM has been extensively characterized but its impact on the biology of the disease is incomplete without more precise knowledge of the identity and functional role of cells with multiple myeloma propagating activity (MMPA). We review here recent data that link MMPA with myeloma clonotypic populations organized in a cellular hierarchy that mirrors normal B cell development and also with drug resistance and disease relapse. We further propose a conceptual framework which, with optimal use of recent technological advances in genomics and phenomics, could allow dissection of the cellular and molecular properties of cells with MMPA, drug resistance and in vivo relapse in an integrated and patient-specific manner. There is real hope that these approaches will significantly contribute to further improvements in disease control, overall survival, and possibly cure of patients with MM. Stem Cells 2015;33:3205–3211

Diamond-Blackfan anemia (DBA) is a disorder characterized by a selective defect in erythropoiesis. Delineation of the precise defect is hampered by a lack of markers that define cells giving rise to erythroid burst- and erythroid colony-forming unit (BFU-E and CFU-E) colonies, the clonogenic assays that quantify early and late erythroid progenitor (EEP and LEP) potential, respectively. By combining flow cytometry, cell-sorting, and single-cell clonogenic assays, we identified Lin(-)CD34(+)CD38(+)CD45RA(-)CD123(-)CD71(+)CD41a(-)CD105(-)CD36(-) bone marrow cells as EEP giving rise to BFU-E, and Lin(-)CD34(+/-)CD38(+)CD45RA(-)CD123(-)CD71(+)CD41a(-)CD105(+)CD36(+) cells as LEP giving rise to CFU-E, in a hierarchical fashion. We then applied these definitions to DBA and identified that, compared with controls, frequency, and clonogenicity of DBA, EEP and LEP are significantly decreased in transfusion-dependent but restored in corticosteroid-responsive patients. Thus, both quantitative and qualitative defects in erythroid progenitor (EP) contribute to defective erythropoiesis in DBA. Prospective isolation of defined EPs will facilitate more incisive study of normal and aberrant erythropoiesis.

Attachment to the plasma membrane by linkage to a glycosylphosphatidylinositol (GPI) anchor1 is a mode of protein expression highly conserved from protozoa to mammals2. As a clinical entity, deficiency of GPI has been recognized as paroxysmal nocturnal hemoglobinuria, an acquired clonal disorder associated with somatic mutations of the X-linked PIGA gene in hematopoietic cells3,4. We have identified a novel disease characterized by a propensity to venous thrombosis and seizures in which deficiency of GPI is inherited in an autosomal recessive manner. In two unrelated kindreds, a point mutation (c → g) at position −270 from the start codon of PIGM, a mannosyltransferase-encoding gene, disrupts binding of the transcription factor Sp1 to its cognate promoter motif. This mutation substantially reduces transcription of PIGM and blocks mannosylation of GPI, leading to partial but severe deficiency of GPI. These findings indicate that biosynthesis of GPI is essential to maintain homeostasis of blood coagulation and neurological function.

There is mounting evidence to suggest that T-cell-mediated suppression of haemopoiesis is a pathogenetic mechanism in three bone marrow failure syndromes: aplastic anaemia (AA), paroxysmal nocturnal haemoglobinuria (PNH) and myelodysplasia (MDS). T-cell microclones can be detected by sensitive polymerase chain reaction (PCR)-based methods in all three disorders. Recently, larger clonal populations of T-cell large granular lymphocytes (T-LGLs) have been observed in some patients with AA and MDS. Here, we report the development of a large clonal T-LGL population in a patient with bona fide PNH. In this patient, we defined part of the sequence of the T-cell receptor (TCR) beta-chain gene, and we have shown that the large T-LGL population emerged from a background of multiple smaller T-cell clones. Thus, T-LGL clones in AA, MDS and PNH probably expand as a result of antigenic stimulation. It is postulated that the antigen driving clonal T-cell proliferations in these disorders exists on haemopoietic stem cells.

Paroxysmal nocturnal haemoglobinuria (PNH) is characterized by the expansion of a haematopoietic stem cell clone with a PIG-A mutation (the PNH clone) in an environment in which normal stem cells are lost or failing: it has been hypothesized that this abnormal marrow environment provides a relative advantage to the PNH clone. In patients with PNH, generally, the karyotype of bone marrow cells has been reported to be normal, unlike in myelodysplastic syndrome (MDS), another clonal condition in which cytogenetic abnormalities are regarded as diagnostic. In a retrospective review of 46 patients with a PNH clone, we found a karyotypic abnormality in 11 (24%). Upon follow-up, the proportion of cells with abnormal karyotype decreased significantly in seven of these 11 patients. Abnormal morphological bone marrow features reminiscent of MDS were common in PNH, regardless of the karyotype. However, none of our patients developed excess blasts or leukaemia. We conclude that in patients with PNH cytogenetically abnormal clones are not necessarily malignant and may not be predictive of evolution to leukaemia.

Background: Bromodomains (BRDs) are domains found in a variety of proteins that recognize and bind to acetylated lysine residues in histone and other target proteins. The BRD and extra-terminal (BET) family of BRD-containing proteins bind to acetylated histone tails, alters chromatin structure and facilitates transcriptional complex localization to specific genes, thereby regulating gene transcription. The investigational agent GSK525762 is a potent small molecule inhibitor of the BET family of proteins that prevents assembly of macromolecular complexes and transcriptional response. GSK525762 inhibits growth in a broad spectrum of human hematological cancer cell lines, including cell lines derived from human patients with acute myeloid leukemia (AML), non-Hodgkin's lymphoma (NHL), and multiple myeloma (MM). GSK525762 is orally bio-available and can cause tumor reduction and improved animal survival in in vivo xenograft models of hematologic malignancies. Methods: This is a Phase I/II, open-label, 2-part study. Part 1 is a dose-escalation phase to determine the safety, tolerability, and recommended Phase 2 dose (RP2D) of GSK525762 in adult subjects with relapsed/refractory AML, NHL, and MM. Dose escalation is performed independently for each of these three cohorts. An accelerated dose titration was employed with one subject per dose level until the occurrence of a ≥Grade 2 drug-related toxicity or dose-limiting toxicity; thereafter, subjects have been enrolled in a standard 3+3 design. A Neuenschwander continual reassessment method (N-CRM) model is used at each dose escalation decision to provide guidance for the next dose escalation level. Starting dose is 5 mg GSK525762 orally once daily and dose escalation continues until the MTD is identified. All data, including safety, tolerability, pharmacokinetics (PK), and efficacy, are used to identify the RP2D. In Part 1, approximately 60-70 subjects will be enrolled (approximately 20 in each of three disease-specific cohorts); no hypothesis is being tested, and all analysis will be descriptive and exploratory. In Part 2, the clinical activity of GSK525762 (overall response rate) will be evaluated in expansion cohorts of subjects with AML, NHL, and MM. Up to 32 subjects may be enrolled into the AML and NHL cohorts, and up to 37 subjects may be enrolled in the MM cohort. Cohorts may be closed early if they do not exceed futility assessment. In addition, an exploratory cohort of subjects with double-hit lymphoma (DHL) and triple-hit lymphoma (THL) will be enrolled to evaluate clinical activity in this patient population. Additional study objectives include analysis of PK after single and repeat dosing, evaluation of pharmacodynamics (PD) and the relationship between GSK525762 exposure and safety/efficacy/PD parameters. Recruitment is ongoing across five centers (USA, UK, and Australia). Currently, 40 subjects have been enrolled (29 AML, 8 NHL, and 3 with MM). Study funded by GSK. Disclosures Stein: Seattle Genetics: Research Funding; Agios Pharmaceuticals: Other: Advisory Board, Research Funding; Celgene: Other: Advisory Board, Research Funding; Novartis: Consultancy. Huntly:Novartis: Speakers Bureau; BMS: Speakers Bureau; Ariad: Speakers Bureau; Pfizer: Speakers Bureau. Dickinson:GlaxoSmithKline: Consultancy, Research Funding. Horner:GlaxoSmithKline: Employment. Brennan:GlaxoSmithKline: Employment. Baron:GlaxoSmithKline: Employment. Kremer:GlaxoSmithKline: Employment, Equity Ownership. Dhar:GlaxoSmithKline: Employment.

Identification of prognostic indicators to predict outcomes of hematopoietic cell transplantation (HCT) is important for selection of patients most likely to benefit from the procedure. Widely validated systems such as the HCT-Comorbidity Index (HCT-CI) and the modified EBMT risk score provide consistent prediction of outcomes, in particular non-relapse mortality (NRM) and survival. In this retrospective study we identified neutropenia prior to initiation of conditioning regimen as an additional prognostic factor in 117 adults with high risk acute myeloid leukemia (AML) who received HCT at a single institution from January 2005 to December 2015. The main endpoints of the study were day 100 non-relapse mortality and survival at 5 years. The median age at HCT was 50 years (range 21-68); 65% had an EBMT score of ≥4. In total 107 (91%) patients had poor risk disease, with classification for poor risk including; patients undergoing HCT due to failure to achieve complete remission (CR) after induction chemotherapy, patients in 2nd CR, patients in 1st CR with adverse karyotype, patients with standard karyotype but with a FLT-3 mutation, patients with measurable residual disease (MRD) by immunophenotyping or molecular monitoring and patients with secondary AML. Conditioning was myeloablative (Cy-TBI: N=41, Bu-Cy: N=3) for patents younger than 51 years with good performance status; the intensity of conditioning was reduced for the others (N=73). Standard methotrexate and cyclosporine was used as graft versus host disease prophylaxis in recipients of sibling cells, and unrelated graft recipients also received alemtuzumab. With a median follow-up of 3.1 years (range 0.3 - 10.0), day 100 NRM for the whole group was 17.3% (95% confidence interval (CI) 11 - 25) and the probability of survival at 5 years was 40.3% (95% CI 31 - 50). The effects of patient, disease and transplant factors were analysed in univariate analyses on both NRM and survival. Significant factors were then entered into multivariate analyses which yielded significant associations with improved NRM for preconditioning absolute neutrophil count (ANC) >= 1000/microL and HCT-CI < 3 (Figure) (hazard ratio (HR) 0.36; 95% CI 0.1 - 0.9 and HR 0.39; 95% CI 0.2 - 0.9 respectively). The factors associated with improved survival in multivariate analysis included preconditioning neutrophil count >= 1000/microL (HR 2.9; 95% CI 1.6 -5.4, P= 0.01), absence of any measurable disease prior to conditioning (HR 2.1; 95% CI 1.1 -4.2, P= 0.03), and less than 2 disease risk defining criteria (HR 15.8; 95% CI 2.0 -124.4, P= 0.01). In conclusion, patients with ANC of 1000/microL and above prior to initiation of conditioning and those with HCT-CI below 3 had significantly better day 100 NRM. ANC of 1000/microL or above was also associated with better survival at 5 years together with disease specific factors, absence of measurable residual disease prior to initiation of condition and less than two adverse prognostic factors. A simple measurement such as the neutrophil count helps to predict outcome: this might reflect the presence of on-going disease but it is also possible that delaying transplant until neutrophil count recovery might impact favourably on the results. Our findings therefore advocate integration of preconditioning neutrophil count into existing risk assessment tools when considering HCT. Figure Figure. Disclosures Milojkovic: Bristol Myers Squibb: Honoraria; Pfizer: Honoraria; Ariad: Honoraria; Novartis: Honoraria.

The bromodomain and extraterminal (BET) protein BRD2-4 inhibitors hold therapeutic promise in preclinical models of hematologic malignancies. However, translation of these data to molecules suitable for clinical development has yet to be accomplished. Herein we expand the mechanistic understanding of BET inhibitors in multiple myeloma by using the chemical probe molecule I-BET151. I-BET151 induces apoptosis and exerts strong antiproliferative effect in vitro and in vivo. This is associated with contrasting effects on oncogenic MYC and HEXIM1, an inhibitor of the transcriptional activator P-TEFb. I-BET151 causes transcriptional repression of MYC and MYC-dependent programs by abrogating recruitment to the chromatin of the P-TEFb component CDK9 in a BRD2-4-dependent manner. In contrast, transcriptional upregulation of HEXIM1 is BRD2-4 independent. Finally, preclinical studies show that I-BET762 has a favorable pharmacologic profile as an oral agent and that it inhibits myeloma cell proliferation, resulting in survival advantage in a systemic myeloma xenograft model. These data provide a strong rationale for extending the clinical testing of the novel antimyeloma agent I-BET762 and reveal insights into biologic pathways required for myeloma cell proliferation.

The mechanism responsible for the bone marrow failure that is almost invariable in paroxysmal nocturnal haemoglobinuria (PNH) is unknown. Based on the close association between PNH and idiopathic aplastic anaemia, a plausible pathogenetic model predicts that, in PNH, autoreactive T cells specific for haemopoietic stem cells (HSCs) cause depletion of normal HSCs, whereas PNH HSCs escape this T-cell-mediated attack. In this study, we addressed the hypothesis that PNH HSCs are resistant to the cytotoxic effect of T cells because they lack surface expression of one or more glycosylphosphatidylinositol (GPI)-linked molecules. We tested the sensitivity of normal and PNH Epstein-Barr virus (EBV)-transformed B-cell lymphoblastoid cell lines (BLCLs) to the cytotoxic effect of autologous EBV-specific T-cell lines and clones from a patient with PNH in an in vitro experimental system. We found that the PNH BLCLs were no less sensitive to T-cell-mediated cytotoxicity than non-PNH isogenic BLCLs, indicating that GPI-linked molecules on the surface of target cells are not required for killing by T cells. This suggests that the mechanism whereby PNH HSCs survive T-cell attack is not because of the lack of surface expression of one or more GPI-linked molecules. By implication, other mechanisms become more probable.

Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired clonal disorder of the hematopoietic stem cell (HSC). Somatic mutations in thePIG-A gene result in the deficiency of several glycosylphosphatidylinositol-linked proteins from the surface of blood cells. This explains intravascular hemolysis but does not explain the mechanism of bone marrow failure that is almost invariably seen in PNH. In view of the close relationship between PNH and idiopathic aplastic anemia (IAA), it has been suggested that the 2 disorders might have a similar cellular pathogenesis, namely, that autoreactive T-cell clones are targeting HSCs. In this paper, we searched for abnormally expanded T-cell clones by size analysis of the complementarity-determining region 3 (CDR3) in the beta variable chain (BV) messenger RNA (mRNA) of the T-cell receptor (TCR) in 19 patients with PNH, in 7 multitransfused patients with hemoglobinopathy. and in 11 age-matched healthy individuals. We found a significantly higher degree of skewness in the TCR BV repertoire of patients with PNH, compared with controls (R2 values 0.82 vs 0.91,P

A most distinctive feature of paroxysmal nocturnal hemoglobinuria (PNH) is that in each patient glycosylphosphatidylinositol-negative (GPI–) and GPI+ hematopoietic stem cells (HSCs) coexist, and both contribute to hematopoiesis. Telomere size correlates inversely with the cell division history of HSCs. In 10 patients with hemolytic PNH the telomeres in sorted GPI– granulocytes were shorter than in sorted GPI+ granulocytes in 4 cases, comparable in 2 cases, and longer in the remaining 4 cases. Furthermore, the telomeres of both GPI– and GPI+ hematopoietic cells were markedly shortened compared with age-matched controls. The short telomeres in the GPI– cells probably reflect the large number of cell divisions required for the progeny of a single cell to contribute a large proportion of hematopoiesis. The short telomeres of the GPI+ cells indicate that the residual hematopoiesis contributed by these cells is not normal. This epigenetic change is an additional feature shared by PNH and aplastic anemia.

Copyright @ 2013 Macmillan Publishers Limited. This is the author's accepted manuscript. The final published article is available from the link below. Regulation of cell survival is a key part of the pathogenesis of multiple myeloma (MM). Jun N-terminal kinase (JNK) signaling has been implicated in MM pathogenesis, but its function is unclear. To elucidate the role of JNK in MM, we evaluated the specific functions of the two major JNK proteins, JNK1 and JNK2. We show here that JNK2 is constitutively activated in a panel of MM cell lines and primary tumors. Using loss-of-function studies, we demonstrate that JNK2 is required for the survival of myeloma cells and constitutively suppresses JNK1-mediated apoptosis by affecting expression of poly(ADP-ribose) polymerase (PARP)14, a key regulator of B-cell survival. Strikingly, we found that PARP14 is highly expressed in myeloma plasma cells and associated with disease progression and poor survival. Overexpression of PARP14 completely rescued myeloma cells from apoptosis induced by JNK2 knockdown, indicating that PARP14 is critically involved in JNK2-dependent survival. Mechanistically, PARP14 was found to promote the survival of myeloma cells by binding and inhibiting JNK1. Moreover, inhibition of PARP14 enhances the sensitization of MM cells to anti-myeloma agents. Our findings reveal a novel regulatory pathway in myeloma cells through which JNK2 signals cell survival via PARP14, and identify PARP14 as a potential therapeutic target in myeloma. Kay Kendall Leukemia Fund, NIH, Cancer Research UK, Italian Association for Cancer Research and the Foundation for Liver Research.

The 40-fold increase in childhood megakaryocyte-erythroid and B-cell leukemia in Down syndrome implicates trisomy 21 (T21) in perturbing fetal hematopoiesis. Here, we show that compared with primary disomic controls, primary T21 fetal liver (FL) hematopoietic stem cells (HSC) and megakaryocyte-erythroid progenitors are markedly increased, whereas granulocyte-macrophage progenitors are reduced. Commensurately, HSC and megakaryocyte-erythroid progenitors show higher clonogenicity, with increased megakaryocyte, megakaryocyte-erythroid, and replatable blast colonies. Biased megakaryocyte-erythroid–primed gene expression was detected as early as the HSC compartment. In lymphopoiesis, T21 FL lymphoid-primed multipotential progenitors and early lymphoid progenitor numbers are maintained, but there was a 10-fold reduction in committed PreproB-lymphoid progenitors and the functional B-cell potential of HSC and early lymphoid progenitor is severely impaired, in tandem with reduced early lymphoid gene expression. The same pattern was seen in all T21 FL samples and no samples had GATA1 mutations. Therefore, T21 itself causes multiple distinct defects in FL myelo- and lymphopoiesis.

Immunophenotyping is indispensable in the differential diagnosis of B-cell chronic lymphoproliferative disorders (B-CLPDs). However, B-CLPDs often show overlapping immunophenotypic profiles and may be diagnostically challenging. CD1d is an HLA class I-like molecule that presents glycolipids to invariant natural killer T cells. Normal mature B cells constitutively express CD1d, but with the exception of some conflicting data, its expression in B-CLPDs is unknown. We demonstrate that in 222 B-CLPD cases, CD1d expression of less than 45% is strongly predictive of CLL (likelihood ratio, 32.3; specificity, 97.4%; sensitivity, 84.1%). In addition, CD1d showed significantly higher staining intensity in splenic marginal zone lymphoma compared with atypical hairy cell leukemia, lymphoplasmacytic lymphoma, and mantle cell lymphoma, thus allowing the discrimination of the former from the latter immunophenotypically overlapping B-CLPDs. It is important to note that in a given patient, CD1d expression on malignant B cells was similar between tissues and remained unaffected by disease stage and treatment status. Our findings strongly argue for the incorporation of CD1d into routine lymphoma panels.

Abstract 876 Children with Down syndrome (DS), under the age of 4 years, have a 150-fold excess risk of myeloid leukaemia (DS-ML), which arises in utero and is of erythro-megakaryocyte phenotype. Two known factors required for leukemic transformation- are: (i) presence of trisomy 21 (T21) in fetal liver (FL) hematopoietic cells and (ii) acquired N terminal-truncating mutation(s) of the transcription factor gene GATA1. Together, they lead to the preleukemic condition, Transient Abnormal Myelopoiesis (TAM). In humans, T21 provides the crucial initiating perturbation of hematopoiesis by inducing a marked expansion of FL megakaryocyte-erythroid progenitors (MEP) during the second trimester[1]. Mouse models have suggested that effects of T21 are confined to FL and are lost post-natally[2]. However, retrospective studies have reported blood counts abnormalities in some neonates with DS suggesting abnormal fetal hematopoiesis may persist beyond the second trimester into post-natal life. To investigate this, blood counts and smears in the first week of life from the first 100 babies with DS enrolled in a prospective, longitudinal study have been compared with blood counts and smears from normal term cords (n=100) and normal term and preterm neonates in the first week of life (n=200). 11/100 neonates with DS had a diagnosis of Transient Abnormal Myelopoiesis (TAM) by WHO criteria and confirmed by GATA1 mutation; 22 (2 with TAM) were preterm- gestational age (GA)< 37 weeks). In neonates with DS, with or without TAM, Hb concentrations, hematocrits and RBC counts were higher than GA matched neonates without DS; 51 (57.3%) of babies with DS had a Hb concentration of >20 g/dl (vs 2% of non DS neonates); only 2 (2.2%) of DS neonates had a Hb Although total white cell, neutrophil, lymphocyte and eosinophil counts in DS neonates without TAM were not significantly different from normal term cord or GA-matched peripheral blood samples, monocyte (median 0.97 vs 0.7 × 109/L) and basophil counts (median 0.2 vs 0 × 109/L) were increased. Dysplastic features, (abnormal granulation and nuclear morphology) were seen in neutrophils, monocytes and basophils in ∼80% of DS neonates without TAM and in 11/11 with TAM; these findings were rare in term and preterm neonates without DS. Circulating blasts were seen on blood smears from all neonates with DS both with TAM (median 34%; range 15–54%) and without TAM (median 3%; range 0.5– 11%) but rarely in normal controls (median 0, range 0–8%). Many, but not all, blasts in neonates with DS without TAM were morphologically megakaryoblasts and indistinguishable from those in TAM. Thus, abnormalities of hematopoiesis affecting all myeloid lineages are present in most, if not all, neonates with DS, regardless of whether or not they have TAM and GATA1 mutation(s). Consistent with this, we found that although cord blood from DS neonates without TAM had normal overall numbers of MEP, CMP and GMP compared to normal term cord, clonogenicity of megakaryocyte and erythroid progenitors cultured from flow sorted DS cord blood MEP and CMP was markedly increased compared to normal term cord blood (MEP 55 vs 18%; CMP 67 vs 10%; DS vs normal) whilst DS cord blood HSC and MPP populations gave rise to increased numbers of GM and myeloid blast colonies. These data show that in humans with DS, trilineage perturbation of fetal hematopoiesis persists into post-natal life, in contrast to mouse models. 1. Tunstall-Pedoe, O., et al., Abnormalities in the myeloid compartment in Down Syndrome fetal liver precede acquisition of GATA1 mutations. Blood, 2008. 112: 4507–11 2. Alford, K.A., et al., Perturbed hematopoiesis in the Tc1 mouse model of Down syndrome. Blood, 2010. 115: 2928-37 Disclosures: No relevant conflicts of interest to declare.

1. Abstract Cell surface expression through attachment to glycosylphosphatidylinositol (GPI) is a mode of protein expression highly conserved in eukaryotes. GPI‐anchored proteins (GPI‐AP) serve a variety of functions that include adhesion, receptors, signal transduction, and complement activation. Paroxysmal nocturnal hemoglobinuria, a rare acquired disorder of hematopoiesis caused by somatic mutations in the X‐linked PIG‐A gene, was until recently the only genetic disorder affecting GPI biosynthesis. The strict requirement for intact GPI biosynthesis during embryonic and fetal development accounted for the paucity of reported cases of inherited forms of GPI deficiency. Here, we review the clinical spectrum, biochemical defect, and genetic pathogenesis of the first cases of inherited GPI deficiency (IGD), an autosomal recessive disorder caused by a hypomorphic mutation in the promoter of PIG‐M, a gene which like PIG‐A, is indispensable for GPI biosynthesis. Further, we discuss the evidence suggesting that IGD is a disorder of gene‐specific histone hypoacetylation and that pharmacological manipulation targeted to histone acetylation is of therapeutic benefit in IGD.

Paroxysmal Noctumal Hemoglobinuria (PNH) is an acquired clonal disorder of the hematopoietic stem cell (HSC), characterized by blood cells deficient in the glycosylphosphatidylinositol (GPI)-anchored proteins. The GPI-deficient blood cells result from a somatic mutation of the X-linked PIG-A gene in one or more HSC of the PNH patients, in whom the HSC carrying the mutated PIG-A gene expand; to the extent that in many cases GPI-deficient cells eventually comprise most of hematopoiesis. In PNH patients the expansion of the GPI-deficient hematopoiesis is almost invariably associated with features of bone marrow failure. This fact, together with other clinical and experimental evidence, suggests that the expansion of PIG-A mutant clones is due to a concomitant selective process against the normal HSC carrying the wild type PIG-A, rather than to an intrinsic growth advantage of the mutated HSC.

PNH is characterized by expansion of one or more stem cell clones with a PIG-A mutation, which causes a severe deficiency in the expression of glycosylphosphatidylinositol (GPI)-anchored proteins. There is evidence that the expansion of PIG-A mutant clones is concomitant with negative selection against PIG-A wild-type stem cells by an aplastic marrow environment. We studied 36 patients longitudinally by serial flow cytometry, and we determined the proportion of PNH red cells and granulocytes over a period of 1-6 years. We observed expansion of the PNH blood cell population(s) (at a rate of over 5% per year) in 12 out of 36 patients; in all other patients the PNH cell population either regressed or remained stable. The dynamics of the PNH cell population could not be predicted by clinical or hematologic parameters at presentation. These data indicate that in most cases the PNH cell expansion has already run its course by the time of diagnosis. In addition, since in most cases no further expansion takes place, we can infer that the tendency to overgrow normal cells is not an intrinsic property of the PNH clone.

Paroxysmal nocturnal haemoglobinuria (PNH) is a unique disorder characterised by the triad of intravascular haemolysis, thrombosis and bone marrow failure. In the early seventies it was shown that PNH is a clonal disease; and in the nineties the molecular basis of the PNH abnormality was elucidated. However, what makes a PNH clone expand is still not known. Here, we suggest that this is due to somatic cell selection, resulting from the presence in the patient of autoreactive T cells that target glycosylphosphatidylinositol (GPI) in the context of an MHC-like molecule on the surface of haemopoietic stem cells. PNH cells would escape damage precisely because they have lost most or all of their ability to produce GPI.