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ALK-dependent transcription factor networks are associated with epigenomic alterations of DNA methylation in ALCL

ABSTRACT: Aberrant DNA methylation patterns of malignant cells allow for the study of the tumor phenotype and behavior, and can be used for tumor classification. Here, we describe the genome-wide DNA methylation signatures of a T cell lymphoma that is driven by the oncogenic fusion protein NPM-ALK. Differences in DNA methylation of tumor cells compared to normal T cells concern pathways that are implicated in T cell development and function and reveal a close relationship to thymic progenitor cells. We find DNA hypomethylation in regulatory regions that are enriched for conserved transcription factor binding motifs for NPM-ALK dependent transcription factors, such as AP1. Our results suggest a direct relationship of oncogenic signaling with epigenetic modifications via transcription factor induction and occupancy. Archived fresh frozen tissue from 5 female ALK+ patients and blood samples for CD3 T cell isolation from 5 healthy age matched female patients as controls were used

ORGANISM(S): Homo sapiens

SUBMITTER: Walter Pulverer

PROVIDER: E-GEOD-66881 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Insights into molecular characteristics of anaplastic large cell lymphoma by genome-wide DNA methylation profiling

Project description:Aberrant DNA methylation patterns of malignant cells allow for the study of the tumor phenotype and behavior, and can be used for tumor classification. Here, we describe the genome-wide DNA methylation signatures of NPM-ALK positive and negative anaplastic large cell lymphoma (ALCL). Differences in DNA methylation of tumor cells compared to normal T cells concern pathways that are implicated in T cell development and function and reveal a close relationship to distinct developmental stages of thymocytes. We find DNA hypomethylation in regulatory regions that are enriched for conserved transcription factor binding motifs, such as AP1. Our results suggest a direct relationship of oncogenic signaling with epigenetic modifications via transcription factor induction and occupancy.

2015-04-01 | GSE66881 | GEO

Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK driven lymphomagenesis [RRBS]

Project description:Malignant transformation depends on genetic and epigenetic events that result in a burst of deregulated gene expression and chromatin changes. To dissect the sequence of events in this process, we used a T cell-specific lymphoma model based on the human oncogenic NPM-ALK translocation. We find that transformation of T cells shifts thymic cell populations to an undifferentiated immunophenotype, which occurs only after a period of latency, accompanied by induction of the MYC-NOTCH1 axis and deregulation of key epigenetic enzymes. We discover aberrant DNA methylation patterns, overlapping with regulatory regions, plus a high degree of epigenetic heterogeneity between individual tumors. In addition, ALK positive tumors show a loss of associated methylation patterns of neighboring CpG sites. Notably, deletion of the maintenance DNA methyltransferase DNMT1 completely abrogates lymphomagenesis in this model, despite oncogenic signaling through NPM-ALK, suggesting that faithful maintenance of tumor-specific methylation through DNMT1 is essential for sustained proliferation and tumorigenesis

2020-12-08 | GSE162217 | GEO

Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK driven lymphomagenesis [RNA-Seq]

2020-12-08 | GSE162216 | GEO

ALK–transformed mature T lymphocytes restores early thymus progenitor features

Project description:Anaplastic large cell lymphoma (ALCL) is a mature T cell neoplasm that often expresses the CD4+ T cell surface marker. (It usually harbors the t(2;5) (p23;q35) translocation, leading to the ectopic expression of NPM-ALK, a chimeric tyrosine kinase. We demonstrated that in vitro transduction of normal human CD4+ T lymphocytes with NPM-ALK results in their immortalization and malignant transformation. The tumor cells displayed morphological and immunophenotypical characteristics of primary patient–derived anaplastic large cell lymphomas. Cell growth, proliferation, and survival were strictly dependent on NPM-ALK activity and include activation of the key factors STAT3 and DNMT1 and expression of CD30 (the hallmark of anaplastic large-cell lymphoma). Implantation of NPM-ALK–transformed CD4+ T lymphocytes into immunodeficient mice resulted in the formation of tumors indistinguishable from patients’ anaplastic large cell lymphomas. Integration of “Omic” data revealed that NPM-ALK–transformed CD4+ T lymphocytes and primary NPM-ALK+ ALCL biopsies share similarities with early T cell precursors. Of note, these NPM-ALK+ lymphoma cells overexpress stem cell regulators (OCT4, SOX2, and NANOG) and HIF2A, which is known to affect hematopoietic precursor differentiation and NPM-ALK+ cell growth. Altogether, for the first time our findings suggest that NPM-ALK could restore progenitor-like features in mature CD30+ peripheral CD4+ T cells, in keeping with a thymic progenitor-like pattern.

2020-12-07 | GSE160123 | GEO

Generation of NPM1-ALK translocation in human T lymphocytes faithfully recapitulates the diversity of ALK+ ALCL tumor phenotype

Project description:To recapitulate the t(2;5)(p23;q35) chromosomal translocation, activated T lymphocytes from healthy donors PBMC were transfected with the RNP complex composed of the protein Cas9 with gRNA NPM1 (targeting NPM1 gene) and gRNA ALK (targeting ALK gene). Control cells were wild-type CD4+ activated lymphocytes. Cells were grown for 10-15 days in vitro prior to engraftment in vivo. Mice engrafted with NPM1-ALK+ T-cells developed T-cell lymphoma after 2-5 months. To get insights into the molecular bases of NPM1-ALK transformation, we next established the transcriptomes at an early in vitro stage and in fully transformed in vivo models. For this, we performed RNAseq analysis from 3 groups: 1-in vitro wild-type CD4+ activated lymphocytes [n=3], 2-in vitro NA-engineered CD4+ lymphocytes [n=3] and 3-in vivo derived CD4+ lymphoma cells purified by flow cytometry to distinguish CD3+ [n=3] and CD3- populations [n=3].

2022-02-09 | E-MTAB-10924 | biostudies-arrayexpress

Expression data from NPM-ALK T cell lymphoma in WT or WASP-deficient background

Project description:Total RNA was extracted from primary T cell lymphoma that spontaneously developed in either NPM-ALK or NPM-ALK/WASP-deficent transgenic mice

2018-11-08 | GSE102889 | GEO

JAK dependent survival of ALK- ALCL

Project description:Activating JAK and STAT mutations were discovered in many T-cell malignancies including ALK- anaplastic large cell lymphomas (ALCL). However, such mutations often occur in a minority of patients. To investigate the clinical application of targeting Janus Kinase (JAK) for ALK- ALCL, we treated ALK- cell lines of different histologic origins with JAK inhibitors. Interestingly, most exogenous cytokine independent cell lines responded to JAK inhibition regardless of JAK mutation status. JAK inhibitor sensitivity correlated with STAT3 phosphorylation status of tumor cells. Employing retroviral shRNA knockdown, we demonstrated that these JAK inhibitor sensitive cells were dependent on both JAK1 and STAT3 for survival. JAK1 and STAT3 gain-of-function mutations were found in some but not all JAK inhibitor sensitive cells. Moreover, the mutations alone could not explain the JAK1/STAT3 dependency as wild-type JAK1 or STAT3 was sufficient to promote cell survival in the cells that had either JAK1or STAT3 mutations. To investigate whether other mechanisms were involved, we knocked down upstream receptors GP130 or IL-2Rγ. Knockdown of GP130 or IL-2Rγ induced cell death in select JAK inhibitor sensitive cells. High levels of cytokine expression including IL-6 were demonstrated in cell lines as well as in primary ALK- ALCL tumors. Finally, ruxolitinib, a JAK1/2 inhibitor, was effective in vivo in a xenograft ALK- ALCL model. Our data suggest cytokine receptor signaling was required for tumor cell survival in diverse forms of ALK- ALCL even in the presence of JAK1/STAT3 mutations. Therefore, JAK-inhibitor therapy might benefit patients with ALK- ALCL that are pSTAT3+.

2017-08-22 | GSE96048 | GEO

NPM-ALK metabolic regulation

Project description:The mechanisms underlying the pathogenesis of the constitutively active tyrosine kinase nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) expressing anaplastic large cell lymphoma are not completely understood. Here we show using an integrated phosphoproteomic and metabolomic strategy that NPM-ALK induces a metabolic shift toward aerobic glycolysis, increased lactate production, and biomass production. The metabolic shift is mediated through the anaplastic lymphoma kinase (ALK) phosphorylation of the tumor-specific isoform of pyruvate kinase (PKM2) at Y105, resulting in decreased enzymatic activity. Small molecule activation of PKM2 or expression of Y105F PKM2 mutant leads to reversal of the metabolic switch with increased oxidative phosphorylation and reduced lactate production coincident with increased cell death, decreased colony formation, and reduced tumor growth in an in vivo xenograft model. This study provides comprehensive profiling of the phosphoproteomic and metabolomic consequences of NPM-ALK expression and reveals a novel role of ALK in the regulation of multiple components of cellular metabolism. Our studies show that PKM2 is a novel substrate of ALK and plays a critical role in mediating the metabolic shift toward biomass production and tumorigenesis. Research is published: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3739039/

2013-09-24 | ST000016 | MetabolomicsWorkbench

NPM-ALK expression levels identify two distinct signatures in Anaplastic Large Cell Lymphoma of Childhood

Project description:Anaplastic large-cell lymphoma (ALCL) makes up approximately 15% of paediatric non-Hodgkin's lymphomas of childhood. The vast majority of them is associated with the t(2;5)(p23;q35) translocation that results in the expression of a hybrid oncogenic tyrosine kinase, NPM-ALK. In order to investigate ALCL biological characteristics we used transcriptional profiling approach. Genome-wide gene expression profiling, performed on 23 paediatric ALCL and 12 reactive lymph nodes specimens, showed two novel ALCL subgroups based on their NPM-ALK expression levels (named (ALK low and ALK high). Gene set enrichment analysis revealed, in ALK low samples, a positive enrichment of genes involved in the Interleukin signaling pathway, whereas we found increased expression of genes related to cell cycle progression and division in ALK high tumour samples, such as Aurora Kinase A (AURKA) and B (AURKB). Growth inhibition was observed upon administration of AURKA and AURKB inhibitors Alisertib and Barasertib and it was associated with perturbation of the cell cycle and induction of apoptosis. In conclusion we identified two novel ALCL subgroups, which display unique biological characteristics suggesting sensitivity to distinct targeted therapies.

2016-11-04 | GSE78513 | GEO

A genome-scale CRISPR-Cas9 loss-of-function screen in ALCL cells treated with crizotinib

Project description:We used a CRISPR-Cas9-based genome-wide guide RNA (sgRNA) library to identify genes responsible for driving drug resistance in ALK+ ALCL cells under crizotinib treatment.We screened 4 diffrerent ALK+ ALCL cell lines, TS, SU-DHL1, COST and KARPAS299. Every cell line was transduced with GeCKO A and GeCKO B sgRNA libraries separately. After puromycin selection, cells were splitted into 3 groups: Day 0 (baseline time point), crizotinib treated group (treated for 14 days) and DMSO treated group (treated for 14 days). TS and SU-DHL1 cells were treated with 40nM criztonib for 14 days and at the end of this period crizotinib concentration was increased to 80nM. COST cells received 50nM crizotinib for 14 days. KARPAS299 cells first received 50nM crizotinib for 14 days and at the end of this period crizotinib concentration was increased to 100nM. Crizotinib concentrations were determined based on their sensitivity for crizotinib for each cell line. The screening was repeated twice for TS and SU-DHL1 ALK+ ALCL cells. DNA isolotation was performed from all groups and each sgRNA sequence served as a barcode for Next Generation Illumina-based DNA sequencing. We compared enriched sgRNA sequences between Day 0 and DMSO conditions. We found that while PTPN2 was a top hit for all 4 ALK+ ALCL cells, PTPN1 was a top hit for TS and SU-DHL1 cells. We subsequently validated roles of PTPN1 and PTPN2 in crizotinib resistance separately. We demonstrated that both PTPN1 and PTPN2 can drive crizotinib resistance in ALK+ ALCL cells. In this study, we found two phosphatases, PTPN1 and PTPN2, involved in drug resitance in ALK+ ALCL using a CRSIPR Cas9-based screening approach. These two phosphatases regulate ALK phospharylation and therefore affect downstream signalling pathways involved in tumor growth and proliferation.

2023-03-15 | GSE152926 | GEO

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