Thomas Mikeska

Publications

• 2.40

  Impact points

  No evidence for DNA methylation of the ATM promoter CpG island in chronic lymphocytic leukemia.

  Thomas Mikeska, Dennis A Carney, John F Seymour, Alexander Dobrovic

  Leukemia & lymphoma. 12/2011;
• 4.70

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  Aberrant DNA methylation but not mutation of CITED4 is associated with alteration of HIF-regulated genes in breast cancer.

  Katie T Huang, Elena A Takano, Thomas Mikeska, David J Byrne, Alexander Dobrovic, Stephen B Fox

  Breast cancer research and treatment. 07/2011; 130(1):319-29.

  CBP/p300-interacting transactivator with ED-rich carboxy-terminal domain 4 (CITED4) inhibits HIF-1α transactivation by binding to CBP/p300. We hypothesised that either somatic mutation or hypermethylation of the CITED4 gene underlies CITED4 down-regulation and thus enhanced HIF-1α expression in some... [more] CBP/p300-interacting transactivator with ED-rich carboxy-terminal domain 4 (CITED4) inhibits HIF-1α transactivation by binding to CBP/p300. We hypothesised that either somatic mutation or hypermethylation of the CITED4 gene underlies CITED4 down-regulation and thus enhanced HIF-1α expression in some breast tumours. DNA sequencing was used to screen for somatic mutations. Methylation-sensitive high resolution melting was performed to identify CITED4 methylation. RT-qPCR was carried out to measure the expression of CITED4 and selected HIF downstream targets. HIF-1α and downstream gene expression was assessed with immunohistochemistry. No somatic mutations of CITED4 were identified in 10 tumour cell lines and 100 breast carcinomas. However, CITED4 promoter methylation was identified in 5/168 breast carcinomas (four infiltrating ductal carcinomas and one infiltrating lobular carcinoma) and in 3/10 breast cancer cell lines (MDA-MB-453, MDA-MB-231 and Hs578T). CITED4 mRNA expression in cell lines was inversely correlated with DNA methylation. CITED4 mRNA expression was significantly increased in all three cell lines after 5-aza-2-deoxycytidine (DAC) treatment. Treatment of the MDA-MB-231 cell line with DAC followed by hypoxia (0.1% O²) resulted in down-regulation of expression of the HIF-1α downstream genes VEGFA and SLC2A1 (P = 0.0029). HIF-1α downstream SLC2A1 was decreased (P = 0.021) after CITED4 was re-expressed under hypoxia. Loss of expression of CITED4 in breast cancer may be due to DNA methylation but is unlikely to be due to mutation. Demethylation and histone modification can potentially reactivate CITED4 gene expression in some breast cancers and lead to changes in tumour behaviour. Strategies such as HDAC inhibitors may overcome this effect.
• 4.72

  Impact points

  p75(NTR) induces apoptosis in medulloblastoma cells.

  Jan Küchler, Wolfgang Hartmann, Anke Waha, Arend Koch, Elmar Endl, Peter Wurst, Dagmar Kindler, Thomas Mikeska, Andreas Waha, Cynthia G Goodyer, Reinhard Büttner, Karl Schilling, Torsten Pietsch

  International journal of cancer. Journal international du cancer. 04/2011; 128(8):1804-12.

  The classic medulloblastoma (CMB) and the desmoplastic medulloblastoma (DMB) subtypes represent the major medulloblastoma variants. In contrast to CMB, DMB display high levels of the low-affinity nerve growth factor receptor p75(NTR) . Given the reports of a better clinical course of DMB, we hypothe... [more] The classic medulloblastoma (CMB) and the desmoplastic medulloblastoma (DMB) subtypes represent the major medulloblastoma variants. In contrast to CMB, DMB display high levels of the low-affinity nerve growth factor receptor p75(NTR) . Given the reports of a better clinical course of DMB, we hypothesized that p75(NTR) might act as a tumor suppressor in medulloblastomas. In a large set of medulloblastomas, p75(NTR) was screened for mutations, and its mRNA expression and the DNA methylation status of its 5'-region were assessed. p75(NTR) immunostainings were performed in wild-type murine cerebella and medulloblastomas arising in patched heterozygous mice, and murine cerebellar granule cell precursors (GCP) were analyzed in vitro. Medulloblastoma cells engineered to express p75(NTR) were characterized flow cytometrically and morphologically. One CMB displayed a mutation of the p75(NTR) coding sequence. p75(NTR) mRNA levels clearly delineated DMB and CMB; however, CpG island hypermethylation was excluded as the cause of low p75(NTR) expression in CMB. Sonic Hedgehog-treated GCP showed elevated p75(NTR) expression, and strong expression of p75(NTR) was detected in the external granule cell layer of wild-type mice and in murine ptc(±) medulloblastomas. CMB cells overexpressing p75(NTR) displayed a significant increase in apoptosis. In summary, our data link activated Hedgehog signaling in DMB with p75(NTR) expression and characterize p75(NTR) as a biologically relevant inductor of apoptosis in MB.
• 4.58

  Impact points

  Assessing combined methylation-sensitive high resolution melting and pyrosequencing for the analysis of heterogeneous DNA methylation.

  Ida L M Candiloro, Thomas Mikeska, Alexander Dobrovic

  Epigenetics : official journal of the DNA Methylation Society. 04/2011; 6(4):500-7.

  Heterogeneous DNA methylation leads to difficulties in accurate detection and quantification of methylation. Methylation-sensitive high resolution melting (MS-HRM) is unique among regularly used methods for DNA methylation analysis in that heterogeneous methylation can be readily identified, althoug... [more] Heterogeneous DNA methylation leads to difficulties in accurate detection and quantification of methylation. Methylation-sensitive high resolution melting (MS-HRM) is unique among regularly used methods for DNA methylation analysis in that heterogeneous methylation can be readily identified, although not quantified, by inspection of the melting curves. Bisulfite pyrosequencing has been used to estimate the level of heterogeneous methylation by quantifying methylation levels present at individual CpG dinucleotides. Sequentially combining the two methodologies using MS-HRM to screen the amplification products prior to bisulfite pyrosequencing would be advantageous. This would not only replace the quality control step using agarose gel analysis prior to the pyrosequencing step but would also provide important qualitative information in its own right. We chose to analyze DAPK1 as it is an important tumor suppressor gene frequently heterogeneously methylated in a number of malignancies, including chronic lymphocytic leukemia (CLL). A region of the DAPK1 promoter was analyzed in ten CLL samples by MS-HRM. By using a biotinylated primer, bisulfite pyrosequencing could be used to directly analyze the samples. MS-HRM revealed the presence of various extents of heterogeneous DAPK1 methylation in all CLL samples. Further analysis of the biotinylated MS-HRM products by bisulfite pyrosequencing provided quantitative information for each CpG dinucleotide analyzed, and confirmed the presence of heterogeneous DNA methylation. Whereas each method could be used individually, MS-HRM and bisulfite pyrosequencing provided complementary information for the assessment of heterogeneous methylation.

• Methylation-sensitive high resolution melting for the rapid analysis of DNA methylation

  Thomas Mikeska, Alexander Dobrovic

  01/2011: pages 325-335;

• Analysing DNA methylation using bisulphite pyrosequencing.

  Thomas Mikeska, Jörg Felsberg, Chelsee A Hewitt, Alexander Dobrovic

  Methods in molecular biology (Clifton, N.J.). 01/2011; 791:33-53.

  Bisulphite pyrosequencing is a quantitative methodology for the investigation of DNA methylation of sequences up to 100-bp in length. Biotin-labelled, single-stranded PCR products generated from bisulphite-treated DNA are used as a template with an internal primer to perform the pyrosequencing react... [more] Bisulphite pyrosequencing is a quantitative methodology for the investigation of DNA methylation of sequences up to 100-bp in length. Biotin-labelled, single-stranded PCR products generated from bisulphite-treated DNA are used as a template with an internal primer to perform the pyrosequencing reaction. Nucleotides are added in a predetermined order in each pyrosequencing cycle and the amount of incorporated nucleotide results in a proportional emission of light. DNA methylation ratios are calculated from the levels of light emitted from each nucleotide incorporated at individual CpG positions in a strand-dependent manner. The methylation detection limit at individual CpG sites is approximately 5% and the results are displayed as an average methylation level for each CpG position assayed across all amplification products generated during a PCR reaction. As a consequence, bisulphite pyrosequencing allows the identification of heterogeneous DNA methylation patterns but does not provide information at a single allele resolution. This methodology is suited to analyse short DNA sequences such as those typically extracted from formalin-fixed paraffin-embedded specimens. Nevertheless, longer PCR products can be sequenced by serial bisulphite pyrosequencing, which utilises tandem assays along the amplicon. The general information provided is applicable for all formats of current pyrosequencing instruments, however, a specific protocol for the PyroMark Q24 instrument is provided.

• Closed-tube PCR methods for locus-specific DNA methylation analysis.

  Ida L M Candiloro, Thomas Mikeska, Alexander Dobrovic

  Methods in molecular biology (Clifton, N.J.). 01/2011; 791:55-71.

  Closed-tube PCR methods (sometimes referred to as in-tube PCR methods) for locus-specific DNA -methylation analysis are methodologies in which the amplification and analysis of bisulphite-modified DNA take place in one tube without the need to remove the PCR products for further analysis. Closed-tub... [more] Closed-tube PCR methods (sometimes referred to as in-tube PCR methods) for locus-specific DNA -methylation analysis are methodologies in which the amplification and analysis of bisulphite-modified DNA take place in one tube without the need to remove the PCR products for further analysis. Closed-tube methodologies lend themselves to high-throughput applications and molecular diagnostics but are also applicable as a research tool. We review three closed-tube methodologies, methylation-sensitive high-resolution melting (MS-HRM), MethyLight, and sensitive melting after real-time analysis - methylation-specific PCR (SMART-MSP). Closed-tube detection can be performed by simultaneously amplifying both methylated and unmethylated templates and subsequent melting curve analysis (MS-HRM). Alternatively, methylation-specific primers are used in real-time quantitative PCR and monitored either by a fluorescent hydrolysis probe (MethyLight) or using a double-stranded DNA binding fluorescent dye with a subsequent quality control step by melting curve analysis (SMART-MSP).
• 3.86

  Impact points

  DNA methylation analysis of the HIF-1α prolyl hydroxylase domain genes PHD1, PHD2, PHD3 and the factor inhibiting HIF gene FIH in invasive breast carcinomas.

  Katie T Huang, Thomas Mikeska, Alexander Dobrovic, Stephen B Fox

  Histopathology. 09/2010; 57(3):451-60.

  Hypoxia-inducible factor-1 (HIF-1) activity is regulated by prolyl hydroxylase (PHD1, PHD2, PHD3) and factor inhibiting HIF-1 (FIH) that target the α subunit of HIF-1 (HIF-1α) for proteosomal degradation. We hypothesised that the elevated HIF-1α level is due in some tumours to epigenetic silencing b... [more] Hypoxia-inducible factor-1 (HIF-1) activity is regulated by prolyl hydroxylase (PHD1, PHD2, PHD3) and factor inhibiting HIF-1 (FIH) that target the α subunit of HIF-1 (HIF-1α) for proteosomal degradation. We hypothesised that the elevated HIF-1α level is due in some tumours to epigenetic silencing by DNA hypermethylation of the promoter region of one or more of the PHDs and FIH genes. The aims were to define the presence or absence of promoter methylation of PHDs and FIH in cell lines of various sources and breast carcinomas and, if present, determine its effect on mRNA and protein expression. Tumour cell lines (n = 20) and primary invasive breast carcinomas (n = 168) were examined for promoter region DNA methylation using methylation-sensitive high-resolution melting. There was evidence of PHD3 but not of PHD1, PHD2 or FIH DNA methylation in breast cancer (SkBr3) and leukaemic (HL60 and CCRF-CEM) cell lines, but there was no evidence of methylation in any of 168 breast cancers. Only the high-level PHD3 methylation seen in leukaemic cell lines correlated with absent mRNA and protein expression. Methylation-induced epigenetic silencing of PHD1, PHD2, PHD3 and FIH is unlikely to underlie up-regulated HIF-1α expression in human breast cancer but may play a role in other tumour types.

• The implications of heterogeneous DNA methylation for the accurate quantification of methylation.

  Thomas Mikeska, Ida L M Candiloro, Alexander Dobrovic

  Epigenomics. 08/2010; 2(4):561-73.

  DNA methylation based biomarkers have considerable potential for molecular diagnostics, both as tumor specific biomarkers for the early detection or post-therapeutic monitoring of cancer as well as prognostic and predictive biomarkers for therapeutic stratification. Particularly in the former, the a... [more] DNA methylation based biomarkers have considerable potential for molecular diagnostics, both as tumor specific biomarkers for the early detection or post-therapeutic monitoring of cancer as well as prognostic and predictive biomarkers for therapeutic stratification. Particularly in the former, the accurate estimation of DNA methylation is of compelling importance. However, quantification of DNA methylation has many traps for the unwary, especially when heterogeneous methylation comprising multiple alleles with varied DNA methylation patterns (epialleles) is present. The frequent occurrence of heterogeneous methylation as distinct from a simple mixture of fully methylated and unmethylated alleles is generally not taken into account when DNA methylation is considered as a cancer biomarker. When heterogeneous DNA methylation is present, the proportion of methylated molecules is difficult to quantify without a method that allows the measurement of individual epialleles. In this article, we critically assess the methodologies frequently used to investigate DNA methylation, with an emphasis on the detection and measurement of heterogeneous DNA methylation. The adoption of digital approaches will enable the effective use of heterogeneous DNA methylation as a cancer biomarker.
• 7.54

  Impact points

  Epigenetic downregulation of mitogen-activated protein kinase phosphatase MKP-2 relieves its growth suppressive activity in glioma cells.

  Anke Waha, Jörg Felsberg, Wolfgang Hartmann, Anna von dem Knesebeck, Thomas Mikeska, Stefan Joos, Marietta Wolter, Arend Koch, Pearlly S Yan, Elmar Endl, Otmar D Wiestler, Guido Reifenberger, Torsten Pietsch, Andreas Waha

  Cancer research. 02/2010; 70(4):1689-99.

  Critical tumor suppression pathways in brain tumors have yet to be fully defined. Along with mutational analyses, genome-wide epigenetic investigations may reveal novel suppressor elements. Using differential methylation hybridization, we identified a CpG-rich region of the promoter of the dual-spec... [more] Critical tumor suppression pathways in brain tumors have yet to be fully defined. Along with mutational analyses, genome-wide epigenetic investigations may reveal novel suppressor elements. Using differential methylation hybridization, we identified a CpG-rich region of the promoter of the dual-specificity mitogen-activated protein kinase phosphatase-2 gene (DUSP4/MKP-2) that is hypermethylated in gliomas. In 83 astrocytic gliomas and 5 glioma cell lines examined, hypermethylation of the MKP-2 promoter was found to occur relatively more frequently in diffuse or anaplastic astrocytomas and secondary glioblastomas relative to primary glioblastomas. MKP-2 hypermethylation was associated with mutations in TP53 and IDH1, exclusive of EGFR amplification, and with prolonged survival of patients with primary glioblastoma. Expression analysis established that promoter hypermethylation correlated with reduced expression of MKP-2 mRNA and protein. Consistent with a regulatory role, reversing promoter hypermethylation by treating cells with 5-aza-2'-deoxycytidine increased MKP-2 mRNA levels. Furthermore, we found that glioblastoma cell growth was inhibited by overexpression of exogenous MKP-2. Our findings reveal MKP-2 as a common epigenetically silenced gene in glioma, the inactivation of which may play a significant role in glioma development.
• 2.72

  Impact points

  A multiplex endpoint RT-PCR assay for quality assessment of RNA extracted from formalin-fixed paraffin-embedded tissues.

  Elena A Takano, Thomas Mikeska, Alexander Dobrovic, David J Byrne, Stephen B Fox

  BMC biotechnology. 01/2010; 10:89.

  RNA extracted from formalin-fixed paraffin-embedded (FFPE) samples is chemically modified and degraded, which compromises its use in gene expression studies. Most of the current approaches for RNA quality assessment are not suitable for FFPE derived RNA. We have developed a single-tube multiplex end... [more] RNA extracted from formalin-fixed paraffin-embedded (FFPE) samples is chemically modified and degraded, which compromises its use in gene expression studies. Most of the current approaches for RNA quality assessment are not suitable for FFPE derived RNA. We have developed a single-tube multiplex endpoint RT-PCR assay specifically designed to evaluate RNA extracted from FFPE tissues for mRNA integrity and performance in reverse transcription - quantitative real-time PCR (RT-qPCR) assays. This single-tube quality control (QC) assay minimises the amount of RNA used in quality control. mRNA integrity and the suitability of RNA for RT-PCR is evaluated by the multiplex endpoint RT-PCR assay using the TBP gene mRNA as the target sequence. The RT-PCR amplicon sizes, 92, 161, 252 and 300 bp, cover a range of amplicon sizes suitable for a wide range of RT-qPCR assays. The QC assay was used to evaluate RNA prepared by two different protocols for extracting total RNA from needle microdissected FFPE breast tumour samples. The amplification products were analysed by gel electrophoresis where the spectrum of amplicon sizes indicated the level of RNA degradation and thus the suitability of the RNA for PCR. The ability of the multiplex endpoint RT-PCR QC assay to identify FFPE samples with an adequate RNA quality was validated by examining the Cq values of an RT-qPCR assay with an 87 bp amplicon. The multiplex endpoint RT-PCR assay is well suited for the determination of the quality of FFPE derived RNAs, to identify which RT-PCR assays they are suitable for, and is also applicable to assess non-FFPE RNA for gene expression studies. Furthermore, the assay can also be used for the evaluation of RNA extraction protocols from FFPE samples.
• 6.63

  Impact points

  MethMarker: User-friendly design and optimization of gene-specific DNA methylation assays.

  Peter Schuffler, Thomas Mikeska, Andreas Waha, Thomas Lengauer, Christoph Bock

  Genome biology. 10/2009; 10(10):R105.

  ABSTRACT: DNA methylation is a key mechanism of epigenetic regulation, and it is frequently altered in diseases such as cancer. To confirm the biological or clinical relevance of such changes, they need to be validated in multiple samples. We have developed the MethMarker (http://methmarker.mpi-inf.... [more] ABSTRACT: DNA methylation is a key mechanism of epigenetic regulation, and it is frequently altered in diseases such as cancer. To confirm the biological or clinical relevance of such changes, they need to be validated in multiple samples. We have developed the MethMarker (http://methmarker.mpi-inf.mpg.de/) software to help design robust and cost-efficient DNA methylation assays for six widely used methods. Furthermore, MethMarker implements a bioinformatic workflow for transforming disease-specific differentially methylated genomic regions into robust clinical biomarkers.

• Aberrant methylation and reduced expression of LHX9 in malignant gliomas of childhood.

  Valentina Vladimirova, Thomas Mikeska, Andreas Waha, Niels Soerensen, Jingying Xu, Patrick C Reynolds, Torsten Pietsch

  Neoplasia (New York, N.Y.). 08/2009; 11(7):700-11.

  High-grade gliomas (HGGs) of childhood represent approximately 7% of pediatric brain tumors. They are highly invasive tumors and respond poorly to conventional treatments in contrast to pilocytic astrocytomas, which usually are well demarcated and frequently can be cured by surgery. The molecular ev... [more] High-grade gliomas (HGGs) of childhood represent approximately 7% of pediatric brain tumors. They are highly invasive tumors and respond poorly to conventional treatments in contrast to pilocytic astrocytomas, which usually are well demarcated and frequently can be cured by surgery. The molecular events for this clinical relevant finding are only partially understood. In the current study, to identify aberrantly methylated genes that may be involved in the tumorigenesis of pediatric HGGs, we performed a microarray-based differential methylation hybridization approach and found frequent hypermethylation of the LHX9 (human Lim-homebox 9) gene encoding a transcription factor involved in brain development. Bisulfite genomic sequencing and combined bisulfite restriction analysis showed that HGGs were frequently methylated at two CpG-rich LHX9 regions in comparison to benign, nondiffuse pilocytic astrocytomas and normal brain tissues. The LHX9 hypermethylation was associated with reduced messenger RNA expression in pediatric HGG samples and corresponding cell lines. This epigenetic modification was reversible by pharmacological inhibition (5-aza-2'-deoxycytidine), and reexpression of LHX9 transcript was induced in pediatric glioma cell lines. Exogenous expression of LHX9 in glioma cell lines did not directly affect cell proliferation and apoptosis but specifically inhibited glioma cell migration and invasion in vitro, suggesting a possible implication of LHX9 in the migratory phenotype of HGGs. Our results demonstrate that the LHX9 gene is frequently silenced in pediatric malignant astrocytomas by hypermethylation and that this epigenetic alteration is involved in glioma cell migration and invasiveness.

• Validation of a primer optimisation matrix to improve the performance of reverse transcription - quantitative real-time PCR assays.

  Thomas Mikeska, Alexander Dobrovic

  BMC research notes. 07/2009; 2(1):112.

  ABSTRACT: BACKGROUND: The development of reverse transcription - quantitative real-time PCR (RT-qPCR) platforms that can simultaneously measure the expression of multiple genes is dependent on robust assays that function under identical thermal cycling conditions. The use of a primer optimisation ma... [more] ABSTRACT: BACKGROUND: The development of reverse transcription - quantitative real-time PCR (RT-qPCR) platforms that can simultaneously measure the expression of multiple genes is dependent on robust assays that function under identical thermal cycling conditions. The use of a primer optimisation matrix to improve the performance of RT-qPCR assays is often recommended in technical bulletins and manuals. Despite this recommendation, a comprehensive introduction to and evaluation of this approach has been absent from the literature. Therefore, we investigated the impact of varying the primer concentration, leaving all the other reaction conditions unchanged, on a large number of RT-qPCR assays which in this case were designed to be monitored using hydrolysis probes from the Universal Probe Library (UPL) library. FINDINGS: Optimal RT-qPCR conditions were determined for 60 newly designed assays. The calculated Cq (Quantification Cycle) difference, non-specific amplification, and primer dimer formation for a given assay was often dependent on primer concentration. The chosen conditions were further optimised by testing two different probe concentrations. Varying the primer concentrations had a greater effect on the performance of a RT-qPCR assay than varying the probe concentrations. CONCLUSION: Primer optimisation is important for improving the performance of RT-qPCR assays monitored by UPL probes. This approach would also be beneficial to the performance of other RT-qPCR assays such as those using other types of probes or fluorescent intercalating dyes.
• 7.39

  Impact points

  A systematic search for DNA methyltransferase polymorphisms reveals a rare DNMT3L variant associated with subtelomeric hypomethylation.

  Osman El-Maarri, Michael S Kareta, Thomas Mikeska, Tim Becker, Amalia Diaz-Lacava, Judith Junen, Nicole Nüsgen, Frank Behne, Thomas Wienker, Andreas Waha, Johannes Oldenburg, Frédéric Chédin

  Human molecular genetics. 02/2009;

  Causes underlying inter-individual variations in DNA methylation profiles among normal healthy populations are not thoroughly understood. To investigate the contribution of genetic variation in DNA methyltransferase (DNMT) genes to such epigenetic variation, we performed a systematic search for poly... [more] Causes underlying inter-individual variations in DNA methylation profiles among normal healthy populations are not thoroughly understood. To investigate the contribution of genetic variation in DNA methyltransferase (DNMT) genes to such epigenetic variation, we performed a systematic search for polymorphisms in all known human DNMT genes (DNMT1, DNMT3A, DNMT3B, DNMT3L, and DNMT2 (TRDMT1)) in 192 healthy males and females. One hundred and eleven different polymorphisms were detected. Of these, twenty four were located in coding regions and ten resulted in an amino acid change that may affect the corresponding DNMT protein structure or function. Association analysis between all major polymorphisms (frequency >1%) and quantitative DNA methylation profiles did not return significant results after correction for multiple testing. Polymorphisms leading to an amino acid change were further investigated for changes in global DNA methylation by Differential Methylation Hybridization (DMH). This analysis revealed that a rare change at DNMT3L (R271Q) was associated with significant DNA hypomethylation. Biochemical characterization confirmed that DNMT3L(R271Q) is impaired in its ability to stimulate de novo DNA methylation by DNMT3A. Methylated DNA Immunoprecipitation (MeDIP) based analysis using CpG island microarrays revealed that the hypomethylation in this sample preferentially clustered to subtelomeric genomic regions with affected loci corresponding to a subset of repetitive CpG islands with low predicted promoter potential located outside of genes.
• 4.72

  Impact points

  Selective inhibition of proliferation in colorectal carcinoma cell lines expressing mutant APC or activated B-Raf.

  Hui-Hua Zhang, Francesca Walker, Sara Kiflemariam, Robert H. Whitehead, David Williams, Wayne A Phillips, Thomas Mikeska, Alexander Dobrovic, Antony W Burgess

  International journal of cancer. Journal international du cancer. 02/2009;

  Tumor-derived cell lines are indispensable tools for understanding the contribution of activated signaling pathways to the cancer phenotype and for the design and testing of targeted signal therapies. In our study, we characterize 10 colorectal carcinoma cell lines for the presence of mutations in t... [more] Tumor-derived cell lines are indispensable tools for understanding the contribution of activated signaling pathways to the cancer phenotype and for the design and testing of targeted signal therapies. In our study, we characterize 10 colorectal carcinoma cell lines for the presence of mutations in the wnt, Ras/MAPK, PI3K and p53 pathways. The mutational spectrum found in this panel of cell lines is similar to that detected in primary CRC, albeit with higher frequency of mutation in the beta-catenin and B-Raf genes. We have monitored activation of the wnt and Ras/MAPK pathways in these cells and analyzed their sensitivity to selective signaling inhibitors. Using beta-catenin subcellular distribution as a marker, we show that cells harboring APC mutations have low-level activated wnt signaling, which can be blocked by the extracellular wnt inhibitor DKK-1, suggesting autocrine activation of this pathway; proliferation of these cells is also blocked by DKK-1. In contrast, cells with beta-catenin mutations are unresponsive to extracellular wnt inhibition. Constitutive phosphorylation of MAPK is present in the majority of the cell lines and correlates with B-Raf but not K-Ras mutations; correspondingly, the proliferation of cells harboring mutations in B-Raf, but not K-Ras, is exquisitely sensitive inhibition of the MAPK pathway. We find no correlation between PI3K mutation or loss of PTEN expression and increased sensitivity to PI3K inhibitors. Our study discloses clear-cut differences in responsiveness to signaling inhibitors between individual mutations within an activated signaling pathway and suggests likely targets for signal-directed therapy of colorectal carcinomas. (c) 2009 UICC.
• 4.67

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  Rapid analysis of heterogeneously methylated DNA using digital methylation-sensitive high resolution melting: application to the CDKN2B (p15) gene.

  Ida Candiloro, Thomas Mikeska, Peter Hokland, Alexander Dobrovic

  Epigenetics & chromatin. 12/2008; 1(1):7.

  ABSTRACT: Background The p15 cell cycle progression inhibitor gene (CDKN2B) is inactivated by DNA methylation in a variety of malignancies, especially haematological malignancies of the myeloid lineage. Its promoter region usually shows heterogeneous methylation and is only rarely fully methylated. ... [more] ABSTRACT: Background The p15 cell cycle progression inhibitor gene (CDKN2B) is inactivated by DNA methylation in a variety of malignancies, especially haematological malignancies of the myeloid lineage. Its promoter region usually shows heterogeneous methylation and is only rarely fully methylated. The methylation status of CDKN2B is often used as a biomarker of response to treatment. Therefore the accurate and sensitive determination of its methylation level is desirable. However, most DNA methylation analysis methodologies are unable to recognise heterogeneous methylation. This presents major problems for quantification. We show that Methylation Sensitive High Resolution Melting (MS-HRM) methodology is able to readily recognise heterogeneously methylated sequences by their characteristic melting profiles. To quantify heterogeneously methylated sequences, we adopted a digital approach to MS-HRM (dMS-HRM) which involved the amplification of single templates as a method to quantify and to determine the degree of methylation of heterogeneously methylated sequences such as CDKN2B. Methods MS-HRM was used to assess CDKN2B methylation in acute myeloid leukaemia (AML) samples. dMS-HRM was then used to analyse CDKN2B methylation in AML samples by limiting dilution of the bisulphite modified template. Direct sequencing of representative digitally generated products was used to reveal the exact DNA methylation pattern. Results All the AML samples that were methylated at the CDKN2B promoter (40/93) showed varying degrees of heterogeneous methylation. Six representative samples were selected for further study. dMS-HRM was used to simultaneously count the methylated alleles and assess the degree of methylation. Direct sequencing of selected dMS-HRM products confirmed the degree of methylation estimated by dMS-HRM. Conclusions dMS-HRM is a powerful technique for the analysis of methylation in CDKN2B and other heterogeneously methylated genes. It eliminates both PCR and cloning bias towards either methylated or unmethylated DNA. Potentially complex information is simplified into a digital output, allowing counting of methylated and unmethylated alleles and an overall picture of methylation at the given locus. Downstream sequencing is minimised as dMS-HRM acts as a screen to select only methylated clones for further analysis.
• 4.93

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  Quality control of astrocyte-directed Cre transgenic mice: The benefits of a direct link between loss of gene expression and reporter activation.

  Robert Pascal Requardt, Lech Kaczmarczyk, Pavel Dublin, Anke Wallraff-Beck, Thomas Mikeska, Joachim Degen, Andreas Waha, Christian Steinhäuser, Klaus Willecke, Martin Theis

  Glia. 11/2008;

  Cre recombinase activity for cell-type restricted deletion of floxed target genes (i.e., flanked by Cre recognition loxP-sites) is often measured by separate matings with recombination-activated reporter gene mice. Using a floxed Gja1 (Cx43) allele, we demonstrate the benefits of a direct link betwe... [more] Cre recombinase activity for cell-type restricted deletion of floxed target genes (i.e., flanked by Cre recognition loxP-sites) is often measured by separate matings with recombination-activated reporter gene mice. Using a floxed Gja1 (Cx43) allele, we demonstrate the benefits of a direct link between reporter gene expression and target gene deletion to overcome critical limitations of the Cre/loxP system. The widely used human glial fibrillary acidic protein (hGFAP)-Cre transgene exhibits variable recombination activity and requires postexperimental validation. Such quality control is essential to correlate the extent of Cre-mediated Gja1 ablation with phenotypical alterations and to maintain the activity status of hGFAP-Cre in transgenic mouse colonies. We present several strategies to control for the fidelity of hGFAP-Cre mediated recombination. (c) 2008 Wiley-Liss, Inc.
• 4.35

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  In vitro sensitivity testing of minimally passaged and uncultured gliomas with TRAIL and/or chemotherapy drugs.

  D M Ashley, C D Riffkin, M M Lovric, T Mikeska, A Dobrovic, J A Maxwell, H S Friedman, K J Drummond, A H Kaye, H K Gan, T G Johns, C J Hawkins

  British journal of cancer. 08/2008; 99(2):294-304.

  TRAIL/Apo-2L has shown promise as an anti-glioma drug, based on investigations of TRAIL sensitivity in established glioma cell lines, but it is not known how accurately TRAIL signalling pathways of glioma cells in vivo are reproduced in these cell lines in vitro. To replicate as closely as possible ... [more] TRAIL/Apo-2L has shown promise as an anti-glioma drug, based on investigations of TRAIL sensitivity in established glioma cell lines, but it is not known how accurately TRAIL signalling pathways of glioma cells in vivo are reproduced in these cell lines in vitro. To replicate as closely as possible the in vivo behaviour of malignant glioma cells, 17 early passage glioma cell lines and 5 freshly resected gliomas were exposed to TRAIL-based agents and/or chemotherapeutic drugs. Normal human hepatocytes and astrocytes and established glioma cell lines were also tested. Cross-linked TRAIL, but not soluble TRAIL, killed both normal cell types and cells from three tumours. Cells from only one glioma were killed by soluble TRAIL, although only inefficiently. High concentrations of cisplatin were lethal to glioma cells, hepatocytes and astrocytes. Isolated combinations of TRAIL and chemotherapy drugs were more toxic to particular gliomas than normal cells, but no combination was generally selective for glioma cells. This study highlights the widespread resistance of glioma cells to TRAIL-based agents, but suggests that a minority of high-grade glioma patients may benefit from particular combinations of TRAIL and chemotherapy drugs. In vitro sensitivity assays may help identify effective drug combinations for individual glioma patients.
• 7.48

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  Sensitive Melting Analysis after Real Time- Methylation Specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection.

  Lasse S Kristensen, Thomas Mikeska, Michael Krypuy, Alexander Dobrovic

  Nucleic acids research. 05/2008; 36(7):e42.

  DNA methylation changes that are recurrent in cancer have generated great interest as potential biomarkers for the early detection and monitoring of cancer. In such situations, essential information is missed if the methylation detection is purely qualitative. We describe a new probe-free quantitati... [more] DNA methylation changes that are recurrent in cancer have generated great interest as potential biomarkers for the early detection and monitoring of cancer. In such situations, essential information is missed if the methylation detection is purely qualitative. We describe a new probe-free quantitative methylation-specific PCR (MSP) assay that incorporates evaluation of the amplicon by high-resolution melting (HRM) analysis. Depending on amplicon design, different types of information can be obtained from the HRM analysis. Much of this information cannot be obtained by electrophoretic analysis. In particular, identification of false positives due to incomplete bisulphite conversion or false priming is possible. Heterogeneous methylation can also be distinguished from homogeneous methylation. As proof of principle, we have developed assays for the promoter regions of the CDH1, DAPK1, CDKN2A (p16(INK4a)) and RARB genes. We show that highly accurate quantification is possible in the range from 100% to 0.1% methylated template when 25 ng of bisulphite-modified DNA is used as a template for PCR. We have named this new approach to quantitative methylation detection, Sensitive Melting Analysis after Real Time (SMART)-MSP.