Abstract A19: Epigenetic drug combination induces genome-wide demethylation and altered gene expression in neuro-ectodermal tumor-derived cell lines

Background: Epigenetic alterations are inherent to cancer cells, and epigenetic drugs are currently primarily used to treat hematological malignancies. Pediatric neuro-ectodermal tumors originate from neural crest cells and also exhibit epigenetic alterations involving e.g. apoptotic pathways, which suggests that also these tumors may be sensitive to epigenetic drugs. This notion prompted us to assess molecular and functional effects of low dosage epigenetic drugs in neuro-ectodermal tumor-derived cell lines of pediatric origin.

Results: In 17 neuroblastoma (NBL) and 5 peripheral primitive neuro-ectodermal tumor (PNET) cell lines a combination treatment of 5-aza-2′-deoxycytidine (DAC) and Trichostatin A (TSA) at nanomolar dosages was found to reduce proliferation and to induce wide-spread DNA demethylation, accompanied by major changes in gene expression profiles. Approximately half of the genes that were significantly up-regulated upon treatment exhibited a significant demethylation in their promoter regions. In the NBL cell lines, almost every cellular pathway (193/200) investigated showed expression alterations after treatment, especially a marked up-regulation of genes in the p53 pathway. The combination treatment also resulted in up-regulation of known epigenetically regulated genes such as X-chromosomal genes, tissue-specific genes and a limited number of imprinted genes, as well as known tumor suppressor genes and oncogenes.

Conclusions: Nanomolar dosages of epigenetic drugs have a dramatic impact on the genomes of neuro-ectodermal tumor derived cell lines, including alterations in DNA methylation and concomitant alterations in gene expression.

Citation Format: Max M. van Noesel, Floor A M Duijkers, Renee X. de Menezes, Dominique J. P. M. Stumpel, Pieter Admiraal, Rob Pieters, Jules P P Meijerink. Epigenetic drug combination induces genome-wide demethylation and altered gene expression in neuro-ectodermal tumor-derived cell lines. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A19.

A novel and fast normalization method for high-density arrays

BACKGROUND

Among the most commonly applied microarray normalization methods are intensity-dependent normalization methods such as lowess or loess algorithms. Their computational complexity makes them slow and thus less suitable for normalization of large datasets. Current implementations try to circumvent this problem by using a random subset of the data for normalization, but the impact of this modification has not been previously assessed. We developed a novel intensity-dependent normalization method for microarrays that is fast, simple and can include weighing of observations.

RESULTS

Our normalization method is based on the P-spline scatterplot smoother using all data points for normalization. We show that using a random subset of the data for normalization should be avoided as unstable results can be produced. However, in certain cases normalization based on an invariant subset is desirable, for example, when groups of samples before and after intervention are compared. We show in the context of DNA methylation arrays that a constant weighted P-spline normalization yields a more reliable normalization curve than the one obtained by normalization on the invariant subset only.

CONCLUSIONS

Our novel intensity-dependent normalization method is simpler and faster than current loess algorithms, and can be applied to one- and two-colour array data, similar to normalization based on loess.

AVAILABILITY

An implementation of the method is currently available as an R package called TurboNorm from www.bioconductor.org.

Abstract 4347: Anaplastic lymphoma kinase (ALK) expression is an independent prognostic factor in neuroblastoma patients and correlates well with ALK inhibitor response in vitro

Introduction: ALK mutations are one of the most common genetic aberrations occurring in 3-11% of the neuroblastoma (NBL) patients and are considered oncogenic. We determined the role of ALK protein levels on survival of NBL patients. Secondly, we tested in vitro responsiveness to ALK inhibitors in NBL cell lines with and without ALK mutation.

Results: Formalin-Fixed, Paraffin-Embedded material of 71 NBL, 12 ganglioneuroblastoma (GNBL) and 20 ganglioneuroma (GN) patients was stained for total ALK protein by immunohistochemistry (IHC). The percentage of ALK positive cells in IHC was stratified in 4 Ccategories; Category 1 (n=40): < 20% ALK-positive cells, category 2 (n=25): 20-50% ALK positive cells, category 3 (n=25): 50-75% ALK positive cells, and category 4 (n=13): 75-100% ALK positive cells. These categories correlate significantly with overall survival in the spectrum of NBL, GNBL and GN (p=0.002, Logrank test). ALK mutations were identified in 2/63 NBL (3.2%) and 2/11 GNBL (18.2%) patients by sequencing. Importantly, in NBL and GNBL patients, ALK protein expression remains a significant factor in a multivariate model (Cox Proportional Hazard model) including the COG risk stratification (p<0.000), which encompasses stage and NMYC status (see table).

Further, we studied the role of ALK levels in the response to ALK inhibitors in vitro in NBL cell lines. ALK inhibitor response (TAE684) correlates well with ALK protein levels (r=−0.813, p=0.001). ALK point mutated cell lines show higher ALK levels and a better ALK inhibitor response (LC50 values 14.9 fold lower, p=0.004) than WT and amplified cell lines.

In conclusion: ALK protein expression is an independent predictor of overall survival in NBL patients and ALK inhibitor response in vitro. ICH staining with ALK antibody is reliable and correlates well with prognosis.

Abstract 148: Development of a DNA methylation array normalization method for analyzing demethylating treatment effects in paired samples

Introduction: Normalization of high throughput array data reduces the background noise between samples. However, most normalization techniques will correct differences between paired samples after treatment similarly as background noise and remove valuable information. We developed a new normalization technique for analyzing methylation arrays data after demethylating treatment effects in paired samples.

Materials and methods: neuro-ectodermal tumor cell lines (18 NBL and 5 PNETs) were treated with methylation inhibitors and HDAC inhibitors. We used 30 nM Decitabine (DAC) for 72 hours and 25 nM Trichostatin A (TSA) for the last 48 hours of treatment. Samples before and after treatment were subjected to 244 K CpG island arrays (Agilent).

Results:

Conventional normalization: Normal Loess normalization and VSN two channel normalization were initially used and showed that the demethylation treatment induced an increase of methylation in 8% and a decrease in 10% of the CpGs after treatment, and suggested a Gaussian distribution with equal medians after treatment

Novel normalization: The new normalization technique is based on the restriction enzyme based Differential Methylation Hybridization technique (Yan et al. 2002). Methylation data on the arrays are based on differences in methylation sensitive enzymatic DNA cuts. Our new normalization method is based on fragments without methylation sensitive restriction sites. These data points are not methylation and treatment independent and used as controls in a weighed Loess normalization. This resulted in a significant decrease of methylation in 69.1% of all CpGs and an increase in 1% of the CpGs after the combined epigenetic treatment. This well represents the expected effect of the treatment. To confirm this, we tested the effect of demethylation after treatment on known methylated genes (DcR1, DcR2, RASSF1A, DR3). The test used the array data by using the conventional normalization, the new normalization and compared these results to methylation specific PCR (MSP) changes for these genes. The new normalization showed significant demethylation and compared best to the MSP data. Additionally, we confirmed the 69% decrease in global CpG methylation in one cell line pair (62% less methylation) and is currently being validated in 5 more cell lines with the Methylated DNA Quantification kit (Sigma-Aldrich).

Conclusion: We developed a new normalization technique for high resolution methylation arrays, based on the equal distribution of uncut DNA fragments after methylation specific enzymatic digestion in all samples. We showed that this technique will preserve the differences of demethylating effects in paired samples.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 148.

Bovine herpesvirus 1 UL49.5 protein inhibits the transporter associated with antigen processing despite complex formation with glycoprotein M

Bovine herpesvirus 1 (BHV-1) interferes with peptide translocation by the transporter associated with antigen processing (TAP). Recently, the UL49.5 gene product of BHV-1 was identified as the protein responsible for the observed inhibition of TAP. In BHV-1-infected cells and virions, the UL49.5 protein forms a complex with glycoprotein M (gM). Hence, it was investigated whether UL49.5 can combine the interactions with gM and the TAP complex. In cell lines constitutively expressing both UL49.5 and gM, UL49.5 appears to be required for functional processing of gM. Immunofluorescence-confocal laser scanning microscopy demonstrated that both proteins are interdependent for their redistribution from the endoplasmic reticulum to the trans-Golgi network. Remarkably, expression of cloned gM results in the abrogation of the UL49.5-mediated inhibition of TAP and prevents the degradation of the transporter. However, in BHV-1-infected cells, differences in UL49.5 and gM expression kinetics were seen to create a window of opportunity at the early stages of infection, during which time the UL49.5 protein can act on TAP without gM interference. Moreover, in later periods, non-gM-associated UL49.5 can be detected in addition to the UL49.5/gM complex. Thus, it has been deduced that different functions of UL49.5, editing of gM processing and inhibition of TAP, can be combined during BHV-1 infection.

Varicelloviruses avoid T cell recognition by UL49.5-mediated inactivation of the transporter associated with antigen processing

Detection and elimination of virus-infected cells by cytotoxic T lymphocytes depends on recognition of virus-derived peptides presented by MHC class I molecules. A critical step in this process is the translocation of peptides from the cytoplasm into the endoplasmic reticulum by the transporter associated with antigen processing (TAP). Here, we identified the bovine herpesvirus 1-encoded UL49.5 protein as a potent inhibitor of TAP. The expression of UL49.5 results in down-regulation of MHC class I molecules at the cell surface and inhibits detection and lysis of the cells by cytotoxic T lymphocytes. UL49.5 homologs encoded by two other varicelloviruses, pseudorabies-virus and equine herpesvirus 1, also block TAP. Homologs of UL49.5 are widely present in herpesviruses, acting as interaction partners for glycoprotein M, but in several varicelloviruses UL49.5 has uniquely evolved additional functions that mediate its participation in TAP inhibition. Inactivation of TAP by UL49.5 involves two events: inhibition of peptide transport through a conformational arrest of the transporter and degradation of TAP by proteasomes. UL49.5 is degraded along with TAP via a reaction that requires the cytoplasmic tail of UL49.5. Thus, UL49.5 represents a unique immune evasion protein that inactivates TAP through a unique two-tiered process.

Auxin distribution in Lotus japonicus during root nodule development

For this work, Lotus japonicus transgenic plants were constructed expressing a fusion reporter gene consisting of the genes beta-glucuronidase (gus) and green fluorescent protein (gfp) under control of the soybean auxin-responsive promoter GH3. These plants expressed GUS and GFP in the vascular bundle of shoots, roots and leafs. Root sections showed that in mature parts of the roots GUS is mainly expressed in phloem and vascular parenchyma of the vascular cylinder. By detecting GUS activity, we describe the auxin distribution pattern in the root of the determinate nodulating legume L. japonicus during the development of nodulation and also after inoculation with purified Nod factors, N-naphthylphthalamic acid (NPA) and indoleacetic acid (IAA). Differently than white clover, which forms indeterminate nodules, L. japonicus presented a strong GUS activity at the dividing outer cortical cells during the first nodule cell divisions. This suggests different auxin distribution pattern between the determinate and indeterminate nodulating legumes that may be responsible of the differences in nodule development between these groups. By measuring of the GFP fluorescence expressed 21 days after treatment with Nod factors or bacteria we were able to quantify the differences in GH3 expression levels in single living roots. In order to correlate these data with auxin transport capacity we measured the auxin transport levels by a previously described radioactive method. At 48 h after inoculation with Nod factors, auxin transport showed to be increased in the middle root segment. The results obtained indicate that L. japonicus transformed lines expressing the GFP and GUS reporters under the control of the GH3 promoter are suitable for the study of auxin distribution in this legume.

Spinal subarachnoid hemorrhage due to a filum terminale ependymoma

We present a case of spinal subarachnoid hemorrhage due to an ependymoma of the filum terminale in a 23-year-old male. Clinical signs indicating a spinal origin of the subarachnoid hemorrhage are discussed. Subarachnoid hemorrhages are only rarely caused by an intraspinal tumor, most of which are located in the cauda equina. Our findings in this case proved the value of MRI examination in tumors of the cauda equina.

Characterization of five monoclonal antibodies obtained after immunization in vitro with a synthetic 19-amino acid peptide of thyroglobulin

A 19-amino acid synthetic peptide representing the highly conserved amino terminus of thyroglobulin was used for the production of monoclonal antibodies after immunization of splenocytes in vitro. The properties of five of the antibodies were studied. One reacted only with the synthetic peptide. The others reacted with both the synthetic peptide and with thyroglobulin from all species tested so far, confirming that the amino terminus of thyroglobulin is highly conserved. Two of the five antibodies showed a positive reaction when tested on frozen sections of thyroid tissue, but with different reaction patterns. Monoclonal antibody F4 gave a positive reaction in the colloid, which contains mainly 19S thyroglobulin. In contrast, monoclonal antibody G4 gave a positive reaction only in the follicular cells. Monoclonal antibody G4 binds primarily to low molecular weight compounds in thyroglobulin preparations, possibly representing breakdown products of the protein.