Carl Sandén

Antibodies targeting human IL1RAP (IL1R3) show therapeutic effects in xenograft models of acute myeloid leukemia

Significance Acute myeloid leukemia (AML) is a hematologic malignancy with poor survival. Current treatment with chemotherapy does not target the leukemic cells specifically and is associated with severe side effects. Here we demonstrate that antibodies directed at the cell surface molecule IL-1 receptor accessory protein (IL1RAP), expressed on immature AML cells, show strong antileukemic effects in mice transplanted with human AML cells and that the mechanism behind the cell killing is through recruitment of effector cells. Using antibodies against IL1RAP also capable of blocking IL-1 signaling, we show that the proliferation of human AML cells can be inhibited, providing a second mode of action of IL1RAP antibodies. These results provide critical evidence in support of a rapid clinical development of an antibody-based anti-IL1RAP therapy in AML. Acute myeloid leukemia (AML) is associated with a poor survival rate, and there is an urgent need for novel and more efficient therapies, ideally targeting AML stem cells that are essential for maintaining the disease. The interleukin 1 receptor accessory protein (IL1RAP; IL1R3) is expressed on candidate leukemic stem cells in the majority of AML patients, but not on normal hematopoietic stem cells. We show here that monoclonal antibodies targeting IL1RAP have strong antileukemic effects in xenograft models of human AML. We demonstrate that effector-cell–mediated killing is essential for the observed therapeutic effects and that natural killer cells constitute a critical human effector cell type. Because IL-1 signaling is important for the growth of AML cells, we generated an IL1RAP-targeting antibody capable of blocking IL-1 signaling and show that this antibody suppresses the proliferation of primary human AML cells. Hence, IL1RAP can be efficiently targeted with an anti-IL1RAP antibody capable of both achieving antibody-dependent cellular cytotoxicity and blocking of IL-1 signaling as modes of action. Collectively, these results provide important evidence in support of IL1RAP as a target for antibody-based treatment of AML.

Forced expression of the DEK-NUP214 fusion protein promotes proliferation dependent on upregulation of mTOR

BackgroundThe t(6;9)(p23;q34) chromosomal translocation is found in 1% of acute myeloid leukemia and encodes the fusion protein DEK-NUP214 (formerly DEK-CAN) with largely uncharacterized functions.MethodsWe expressed DEK-NUP214 in the myeloid cell lines U937 and PL-21 and studied the effects on cellular functions.ResultsIn this study, we demonstrate that expression of DEK-NUP214 increases cellular proliferation. Western blot analysis revealed elevated levels of one of the key proteins regulating proliferation, the mechanistic target of rapamycin, mTOR. This conferred increased mTORC1 but not mTORC2 activity, as determined by the phosphorylation of their substrates, p70 S6 kinase and Akt. The functional importance of the mTOR upregulation was determined by assaying the downstream cellular processes; protein synthesis and glucose metabolism. A global translation assay revealed a substantial increase in the translation rate and a metabolic assay detected a shift from glycolysis to oxidative phosphorylation, as determined by a reduction in lactate production without a concomitant decrease in glucose consumption. Both these effects are in concordance with increased mTORC1 activity. Treatment with the mTORC1 inhibitor everolimus (RAD001) selectively reversed the DEK-NUP214-induced proliferation, demonstrating that the effect is mTOR-dependent.ConclusionsOur study shows that the DEK-NUP214 fusion gene increases proliferation by upregulation of mTOR, suggesting that patients with leukemias carrying DEK-NUP214 may benefit from treatment with mTOR inhibitors.

The DEK oncoprotein binds to highly and ubiquitously expressed genes with a dual role in their transcriptional regulation

BackgroundThe DEK gene is highly expressed in a wide range of cancer cells, and a recurrent translocation partner in acute myeloid leukemia. While DEK has been identified as one of the most abundant proteins in human chromatin, its function and binding properties are not fully understood.MethodsWe performed ChIP-seq analysis in the myeloid cell line U937 and coupled it with epigenetic and gene expression analysis to explore the genome-wide binding pattern of DEK and its role in gene regulation.ResultsWe show that DEK preferentially binds to open chromatin, with a low degree of DNA methylation and scarce in the heterochromatin marker H3K9me3 but rich in the euchromatin marks H3K4me2/3, H3K27ac and H3K9ac. More specifically, DEK binding is predominantly located at the transcription start sites of highly transcribed genes and a comparative analysis with previously established transcription factor binding patterns shows a similarity with that of RNA polymerase II. Further bioinformatic analysis demonstrates that DEK mainly binds to genes that are ubiquitously expressed across tissues. The functional significance of DEK binding was demonstrated by knockdown of DEK by shRNA, resulting in both significant upregulation and downregulation of DEK-bound genes.ConclusionsWe find that DEK binds to transcription start sites with a dual role in activation and repression of highly and ubiquitously expressed genes.

The DEK oncoprotein and its emerging roles in gene regulation

The DEK oncogene is highly expressed in cells from most human tissues and overexpressed in a large and growing number of cancers. It also fuses with the NUP214 gene to form the DEK-NUP214 fusion gene in a subset of acute myeloid leukemia. Originally characterized as a member of this translocation, DEK has since been implicated in epigenetic and transcriptional regulation, but its role in these processes is still elusive and intriguingly complex. Similarly multifaceted is its contribution to cellular transformation, affecting multiple cellular processes such as self-renewal, proliferation, differentiation, senescence and apoptosis. Recently, the roles of the DEK and DEK-NUP214 proteins have been elucidated by global analysis of DNA binding and gene expression, as well as multiple functional studies. This review outlines recent advances in the understanding of the basic functions of the DEK protein and its role in leukemogenesis.

The p53 target gene TRIM22 directly or indirectly interacts with the translation initiation factor eIF4E and inhibits the binding of eIF4E to eIF4G

The interferon (IFN)‐inducible protein TRIM22 (Staf50) is a member of the tripartite motif protein family and has been suggested a role in the regulation of viral replication as well as of protein ubiquitylation. In addition, we have previously shown that TRIM22 is a direct target gene for the tumour suppressor p53. Consistently, over‐expression of TRIM22 inhibits the clonogenic growth of monoblastic U937 cells, suggesting anti‐proliferative or cell death‐inducing effects.

Distinct global binding patterns of the Wilms' tumor gene 1 (WT1) -KTS and +KTS isoforms in leukemic cells

The zinc finger transcription factor Wilms tumor gene 1 (WT1) acts as an oncogene in acute myeloid leukemia. A naturally occurring alternative splice event between zinc fingers three and four, removing or retaining three amino acids (±KTS), is believed to change the DNA binding affinity of WT1, although there are conflicting data regarding the binding affinity and motifs of the different isoforms. Increased expression of the WT1 −KTS isoform at the expense of the WT1 +KTS isoform is associated with poor prognosis in acute myeloid leukemia. We determined the genome-wide binding pattern of WT1 −KTS and WT1 +KTS in leukemic K562 cells by chromatin immunoprecipitation and deep sequencing. We discovered that the WT1 −KTS isoform predominantly binds close to transcription start sites and to enhancers, in a similar fashion to other transcription factors, whereas WT1 +KTS binding is enriched within gene bodies. We observed a significant overlap between WT1 −KTS and WT1 +KTS target genes, despite the binding sites being distinct. Motif discovery revealed distinct binding motifs for the isoforms, some of which have been previously reported as WT1 binding sites. Additional analyses showed that both WT1 −KTS and WT1 +KTS target genes are more likely to be transcribed than non-targets, and are involved in cell proliferation, cell death, and development. Our study provides evidence that WT1 −KTS and WT1 +KTS share target genes yet still bind distinct locations, indicating isoform-specific regulation in transcription of genes related to cell proliferation and differentiation, consistent with the involvement of WT1 in acute myeloid leukemia.

The DEK oncoprotein is upregulated by multiple leukemia-associated fusion genes.

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CD36 defines primitive chronic myeloid leukemia cells less responsive to imatinib but vulnerable to antibody-based therapeutic targeting

Tyrosine kinase inhibitors (TKIs) are highly effective for the treatment of chronic myeloid leukemia (CML), but very few patients are cured. The major drawbacks regarding TKIs are their low efficacy in eradicating the leukemic stem cells responsible for disease maintenance and relapse upon drug cessation. Herein, we performed ribonucleic acid sequencing of flow-sorted primitive (CD34+CD38low) and progenitor (CD34+ CD38+) chronic phase CML cells, and identified transcriptional upregulation of 32 cell surface molecules relative to corresponding normal bone marrow cells. Focusing on novel markers with increased expression on primitive CML cells, we confirmed upregulation of the scavenger receptor CD36 and the leptin receptor by flow cytometry. We also delineate a subpopulation of primitive CML cells expressing CD36 that is less sensitive to imatinib treatment. Using CD36 targeting antibodies, we show that the CD36 positive cells can be targeted and killed by antibody-dependent cellular cytotoxicity. In summary, CD36 defines a subpopulation of primitive CML cells with decreased imatinib sensitivity that can be effectively targeted and killed using an anti-CD36 antibody.

Abstract 762: Genome-wide mapping of binding sites for the DEK oncoprotein by ChIP-seq.

Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC The DEK oncogene is overexpressed in a wide range of cancers, including acute myeloid leukemia (AML). While DEK was initially described as a protein binding to certain topological chromatin structures, recent studies implicate DEK in the epigenetic and transcriptional regulation of specific genes. To assess the global gene binding of DEK, we performed chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). We demonstrate that DEK does not bind evenly throughout the genome, but rather accumulates around transcription start sites, with binding to promoters and initial parts of the coding sequences. Furthermore, gene set enrichment analysis revealed that DEK preferentially binds genes associated with epigenetic regulation of gene expression. Our results represent the first genome-wide characterization of DEK binding, and further establish DEK as a transcriptional regulator with a specific set of target genes. Citation Format: Carl Sanden, Linnea Jarvstrat, Tove Ullmark, Bjorn Nilsson, Urban Gullberg. Genome-wide mapping of binding sites for the DEK oncoprotein by ChIP-seq. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 762. doi:10.1158/1538-7445.AM2013-762

Abstract 4005: The leukemia-associated fusion protein DEK-NUP214 induces proliferation through an mTOR-dependent mechanism

Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL Acute myeloid leukemia (AML) is characterized by the dysregulated proliferation and impaired differentiation of myeloid precursor cells. The majority of these leukemias harbor genetic translocations, which determine both the molecular mechanistics and the prognosis of the disease. The t(6;9)(p22;q34) chromosomal translocation is found in 1% of AML, where it is associated with young age and poor prognosis. The translocation occurs between specific introns in the gene DEK on chromosome 6 and the gene NUP214 on chromosome 9, creating the fusion gene DEK-NUP214. The role of DEK-NUP214 in leukemogenesis is still largely uncharacterized. To obtain an experimental model of the disease, we expressed the fusion gene in the myeloid cell line U937 and studied the phenotype of the stable clones. We show that cells expressing DEK-NUP214 proliferate faster and also sustain their proliferative capacity longer in culture than their normal counterparts. Cellular proliferation is regulated by a wide range of signaling pathways, but many converge on the activating phosphorylation of the mechanistic target of rapamycin (mTOR) at Ser2448. Western blot analysis of the clones revealed that cells expressing DEK-NUP214 have higher levels of both phosphorylated and total mTOR protein. To determine the effect on downstream cellular functions, we proceeded to study mTOR-dependent translation and metabolism. We performed a global translation assay where the incorporation of radioactively labeled amino acids into newly synthesized proteins reflects the rate of translation. The results show that cells expressing DEK-NUP214 have a markedly increased translation rate. Cellular metabolism was studied by measuring the consumption of glucose and the production of lactate in cell supernatant. We demonstrate that cells expressing DEK-NUP214 produce less lactate, despite equal glucose consumption and increased proliferation. In concordance with increased mTOR activity, our results suggest that cells expressing DEK-NUP214 shift their metabolism from glycolysis to oxidative phosphorylation. The increased activity of mTOR thus leads to translational and metabolic changes that could play a role in the leukemogenic effect of DEK-NUP214. Interestingly, proliferation induced by DEK-NUP214 is highly dependent on mTOR. Treatment with the mTOR inhibitor everolimus (RAD001) reduces the proliferation of the DEK-NUP214 cells to the level of the control cells, without affecting the control cells. This pivotal role of mTOR suggests that leukemias harboring the t(6;9)(p22;q34) translocation may be susceptible to treatment with either rapamycin or the novel mTOR inhibitors that are approaching the clinic. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4005. doi:10.1158/1538-7445.AM2011-4005