DNA-Microarrays as Tools for the Identification of Tumor Specific Gene Expression Profiles: Applications in Tumor Biology, Diagnosis and Therapy

Ms, Staege; Ue, Hattenhorst; Ue, Neumann; Hutter, Christoph; Foja, Sabine; Burdach, Stefan

doi:10.1055/s-2003-39371

Cited by 15 publications

(3 citation statements)

References 24 publications

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“…Importantly, transgenic Ewing sarcoma cells stably expressed the Ewing sarcoma-specific oncofusion protein EWS-FLI1 (Figure 3 ). Other genes typically expressed in Ewing sarcoma cells that remained stably expressed after transfection included the putative cancer/testis antigen LIPI ( 4 , 5 ), LIPH ( 46 ), the surface glycoprotein CD99 ( 47 ), cyclin D1 [CCND1 ( 4 , 48 )], janus kinase 1 [JAK1 ( 4 )], and the retinoic acid metabolizing cytochrome P450 member 26B1 [CYP26B1 ( 4 , 49 )] (Figure 3 ).…”

Section: Resultsmentioning

confidence: 99%

Immunostimulation by OX40 Ligand Transgenic Ewing Sarcoma Cells

et al. 2015

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Interleukin-2 (IL-2) transgenic Ewing sarcoma cells can induce tumor specific T and NK cell responses and reduce tumor growth in vivo and in vitro. Nevertheless, the efficiency of this stimulation is not high enough to inhibit tumor growth completely. In addition to recognition of the cognate antigen, optimal T-cell stimulation requires signals from so-called co-stimulatory molecules. Several members of the tumor necrosis factor superfamily have been identified as co-stimulatory molecules that can augment antitumor immune responses. OX40 (CD134) and OX40 ligand (OX40L = CD252; also known as tumor necrosis factor ligand family member 4) is one example of such receptor/ligand pair with co-stimulatory function. In the present investigation, we generated OX40L transgenic Ewing sarcoma cells and tested their immunostimulatory activity in vitro. OX40L transgenic Ewing sarcoma cells showed preserved expression of Ewing sarcoma-associated (anti)gens including lipase member I, cyclin D1 (CCND1), cytochrome P450 family member 26B1 (CYP26B1), and the Ewing sarcoma breakpoint region 1-friend leukemia virus integration 1 (EWSR1-FLI1) oncogene. OX40L-expressing tumor cells showed a trend for enhanced immune stimulation against Ewing sarcoma cells in combination with IL-2 and stimulation of CD137. Our data suggest that inclusion of the OX40/OX40L pathway of co-stimulation might improve immunotherapy strategies for the treatment of Ewing sarcoma.

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Section: Resultsmentioning

confidence: 99%

Immunostimulation by OX40 Ligand Transgenic Ewing Sarcoma Cells

et al. 2015

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“…Therefore, we used DNA microarray data for the analysis of multiple ERV loci in HL cells. DNA microarrays can be used for the characterization of complete gene-expression profiles from normal and malignant cells in a single experiment (28). Modern DNA exon microarrays contain several probe sets with specificity for ERV and, therefore, can be used for analysis of expression of multiple ERV loci at once.…”

Section: Introductionmentioning

confidence: 99%

Expression and Regulation of the Endogenous Retrovirus 3 in Hodgkin’s Lymphoma Cells

Kewitz¹,

Staege²

2013

Front. Oncol.

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Human endogenous retroviruses (ERV) are an integral part of our genome. Expression of ERV is usually switched off but reactivation of ERV has been observed in varying human diseases including cancer. Recently, reactivation of ERV associated promoters in Hodgkin’s lymphoma (HL) cells has been described. Despite relatively good prognosis, not all patients with HL can be cured with the established therapy and this therapy is associated with severe late side effects. Therefore, new targets are required for the development of future treatment strategies. Reactivated ERV might represent such target structures. Therefore, we asked which ERV loci are expressed in HL cells. Using DNA microarray analysis, we found no evidence for a general activation of ERV transcription in HL cells. In contrast, we observed down-regulation of ERV3, an ERV with potential tumor suppressor function, in HL cells in comparison to normal blood cells. Interestingly, ERV3 was also differentially expressed in published DNA microarray data from resting versus cycling B cells. Treatment of HL cells with the histone deacetylase inhibitor vorinostat strongly up-regulated ERV3 expression. In addition, we observed up-regulation in HL cells after treatment with hypoxia-mimetic cobalt(II) chloride. Like vorinostat, cobalt(II) chloride inhibited cell growth of HL cells. Our results suggest that cell cycle inhibition of HL cells is accompanied by up-regulation of ERV3.

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“…for the identification of tumour-specific transcripts, and (iii) for biological studies, e.g. for the identification of pathways that drive tumour cell proliferation or cell death 1 . Today, the genome wide analysis of the complete transcriptome of individual samples is possible, e.g.…”

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confidence: 99%

A short treatise concerning a musical approach for the interpretation of gene expression data

Staege

2015

Sci Rep

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Recent technical developments allow the genome-wide and near-complete analysis of gene expression in a given sample, e.g. by usage of high-density DNA microarrays or next generation sequencing. The generated data structure is usually multi-dimensional and requires extensive processing not only for analysis but also for presentation of the results. Today, such data are usually presented graphically, e.g. in the form of heat maps. In the present paper, we propose an alternative form of analysis and presentation which is based on the transformation of gene expression data into sounds that are characterized by their frequency (pitch) and tone duration. Using DNA microarray data from a panel of neuroblastoma and Ewing sarcoma cell lines as well as from Hodgkin’s lymphoma cell lines and normal B cells, we demonstrate that this Gene Expression Music Algorithm (GEMusicA) can be used for discrimination between samples with different biology and for the characterization of differentially expressed genes.

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DNA-Microarrays as Tools for the Identification of Tumor Specific Gene Expression Profiles: Applications in Tumor Biology, Diagnosis and Therapy

Cited by 15 publications

References 24 publications

Immunostimulation by OX40 Ligand Transgenic Ewing Sarcoma Cells

Immunostimulation by OX40 Ligand Transgenic Ewing Sarcoma Cells

Expression and Regulation of the Endogenous Retrovirus 3 in Hodgkin’s Lymphoma Cells

A short treatise concerning a musical approach for the interpretation of gene expression data

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