L. Baumbusch - Academia.edu (original) (raw)

Papers by L. Baumbusch

Disease Markers, 2018

Background. After perinatal asphyxia, the cerebellum presents more damage than previously suggest... more Background. After perinatal asphyxia, the cerebellum presents more damage than previously suggested. Objectives. To explore if the antioxidant N-acetylcysteine amide (NACA) could reduce cerebellar injury after hypoxia-reoxygenation in a neonatal pig model. Methods. Twenty-four newborn pigs in two intervention groups were exposed to 8% oxygen and hypercapnia, until base excess fell to −20 mmol/l or the mean arterial blood pressure declined to <20 mmHg. After hypoxia, they received either NACA (NACA group, n=12) or saline (vehicle-treated group, n=12). One sham-operated group (n=5) served as a control and was not subjected to hypoxia. Observation time after the end of hypoxia was 9.5 hours. Results. The intranuclear proteolytic activity in Purkinje cells of asphyxiated vehicle-treated pigs was significantly higher than that in sham controls (p=0.03). Treatment with NACA was associated with a trend to decreased intranuclear proteolytic activity (p=0.08), There were significantly les...

Breast Cancer Research, 2005

There is compelling evidence from transgenic mouse studies and analysis of mutations in human car... more There is compelling evidence from transgenic mouse studies and analysis of mutations in human carcinomas indicating that the TGF-β signal transduction pathway is tumor suppressive. We have shown that overexpression of TGF-β1 in mammary epithelial cells suppresses the development of carcinomas and that expression of a dominant negative type II TGF-β receptor (DNIIR) in mammary epithelial cells under control of the MMTV promoter/enhancer increases the incidence of mammary carcinomas. Studies of human tumors have demonstrated inactivating mutations in human tumors of genes encoding proteins involved in TGF-β signal transduction, including DPC4/Smad4, Smad2, and the type II TGF-β receptor (TβRII). There is also evidence that TGF-β can enhance the progression of tumors. This hypothesis is being tested in genetically modified mice. To attain complete loss of TβRII, we have generated mice with loxP sites flanking exon 2 of Tgfbr2 and crossed them with mice expressing Cre recombinase under control of the MMTV promoter/enhancer to obtain Tgfbr2 mgKO mice. These mice show lobuloalveolar hyperplasia. Mice are being followed for mammary tumor development. Tgfbr2 mgKO mice that also express polyoma virus middle T antigen under control of the MMTV promoter (MMTV-PyVmT) develop mammary tumors with a significantly shorter latency than MMTV-PyVmT mice and show a marked increase in pulmonary metastases. Our data do not support the hypothesis that TGF-β signaling in mammary carcinoma cells is important for invasion and metastasis, at least in this model system. The importance of stromal-epithelial interactions in mammary gland development and tumorigenesis is well established. These interactions probably involve autocrine and paracrine action of multiple growth factors, including members of the TGF-β family, which are expressed in both stroma and epithelium. Again, to accomplish complete knockout of the type II TGF-β receptor gene in mammary stromal cells, FSP1-Cre and Tgfbr2 flox/flox mice were crossed to attain Tgfbr2 fspKO mice. The S.03 Genomic analysis of human breast cancer in families and populations

Nucleic Acids Research, 2001

Journal of Experimental Botany, 2003

Dormant Arabidopsis seeds require strati®cation and light for germination. To study gene expressi... more Dormant Arabidopsis seeds require strati®cation and light for germination. To study gene expression during establishment, maintenance and release of dormancy, various Arabidopsis ecotypes that are different in their degree of dormancy were investigated; three nsm mutants that lack the strati®cationdependency, and the precocious germination and reduced dormancy of the abi3-1 mutant (insensitive to ABA). Genes examined by mRNA abundance include LEC1, FUS3 and ABI3, transcription factors that are major regulators of embryo development and, at least indirectly, play some role in the control of dormancy. Moreover, the late embryogenesis marker genes, AtEm1 and AtEm6, were examined in relation to the state of dormancy. The expression of LEC1, FUS3 and ABI3 mRNA is only marginally different during seed development in various strong or moderate dormancy wild types, nsm mutants and abi3-1. Therefore, it is unlikely that these transcription factors directly control the establishment of dormancy in Arabidopsis. Sole and various combinations of light, temperature, and after-ripening regimes that alter germination behaviour were examined to determine if the expression of ABI3, AtEm1 and AtEm6 mRNAs were correlated with dormancy-breaking processes. ABI3 expression is in¯uenced by cold and light, in a similar way in both dormant and nondormant wild-type seeds. ABI3 transcript abundance in the nsm1 and nsm2 mutants is higher and in the nsm5-1 mutant is marginally lower than in wild-type seeds, but changes due to temperature and light factors are very similar to those that occur in wild-type seeds. The abundances of AtEm1 and AtEm6 mRNAs are equally affected by imbibition and cold temperature in mature and after-ripened seeds. The LEA transcript abundances for AtEm1 and AtEm6 are reduced in nsm mutants in a common, ABI3-independent pathway.

PLoS ONE, 2014

Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disea... more Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disease, characterized by distinct genomic and transcriptomic profiles. Transcriptome analyses prevalently assessed protein-coding genes; however, the majority of the mammalian genome is expressed in numerous non-coding transcripts. Emerging evidence supports that many of these non-coding RNAs are specifically expressed during development, tumorigenesis, and metastasis. The focus of this study was to investigate the expression features and molecular characteristics of long non-coding RNAs (lncRNAs) in breast cancer. We investigated 26 breast tumor and 5 normal tissue samples utilizing a custom expression microarray enclosing probes for mRNAs as well as novel and previously identified lncRNAs. We identified more than 19,000 unique regions significantly differentially expressed between normal versus breast tumor tissue, half of these regions were noncoding without any evidence for functional open reading frames or sequence similarity to known proteins. The identified non-coding regions were primarily located in introns (53%) or in the intergenic space (33%), frequently orientated in antisense-direction of protein-coding genes (14%), and commonly distributed at promoter-, transcription factor binding-, or enhancer-sites. Analyzing the most diverse mRNA breast cancer subtypes Basal-like versus Luminal A and B resulted in 3,025 significantly differentially expressed unique loci, including 682 (23%) for non-coding transcripts. A notable number of differentially expressed protein-coding genes displayed non-synonymous expression changes compared to their nearest differentially expressed lncRNA, including an antisense lncRNA strongly anticorrelated to the mRNA coding for histone deacetylase 3 (HDAC3), which was investigated in more detail. Previously identified chromatin-associated lncRNAs (CARs) were predominantly downregulated in breast tumor samples, including CARs located in the protein-coding genes for CALD1, FTX, and HNRNPH1. In conclusion, a number of differentially expressed lncRNAs have been identified with relation to cancer-related protein-coding genes.

Physiologia Plantarum, 1998

European Journal of Cancer Supplements, 2010

Background: Thyroid nodules are clinically evident in about 5% of women and 1% of men therefore r... more Background: Thyroid nodules are clinically evident in about 5% of women and 1% of men therefore represent the most common endocrine pathology. Although more than 90% are benign a significant number undergo surgical excision. In 10% of all follicular patterned lesions diagnostic dilemma is presented in a subset of encapsulated lesions with partial nuclear features of papillary thyroid carcinoma and with histological features that fail to place them reliably in either the benign or the malignant category. Microarray gene profiling has shown a promise in the accurate discrimination of benign-malignant discrimination and molecular characterization of thyroid lesions. We focused on not particularly for significantly modulated candidate genes, but for sets of genes acting on similar antiapoptotic and signaling pathways. Materials and Methods: Tumour samples were obtained from 25 patients undergoing thyroid surgery and evaluated on histopathology prior to our experiments. Genomic RNA was isolated from the snap frozen tumour samples of follicular adenomas and sporadic type of papillary carcinomas. We used NimbleGen Human Expression 12X135K Arrays to analyze gene expression alterations between follicular thyroid adenoma and papillary thyroid carcinoma expression profiles. Quantitative RT-PCR and Western blot analysis were done in case of the 10 genes showing the highest expression changes on the array. Results: We found the consequent significant expression regulation of 378 genes 233 of them found to be significantly underexpressed in papillary carcinomas compared to the follicular adenoma tissues. Papillary thyroid carcinomas expressed modulated genes on the NFúB regulatory pathway. Nfúb itself was found to be up-regulated as well as its activator Med17 and the Eda1, the member of the TNF-related ligand family regulating epithelial development, wich has regulatory role in Nfúb-promoted transcription and Jnk signaling. additionally represented constitutive down-regulation Pparg and Mapk, 4, 8 and 10 partaking in NFúB inhibition, and Cyld1 over expression closely connected to NFúB signaling. Conclusions: Considering the fact that NFkB has already been found to be a promising diagnostic and therapeutic target, our investigation could provide new possibilities for diagnostic, therapeutic and preventative perspectives.

European Journal of Cancer Supplements, 2010

fluorescence quenching, ELISA, quartz crystal microbalance, fluorescence microscopy and enzyme in... more fluorescence quenching, ELISA, quartz crystal microbalance, fluorescence microscopy and enzyme inhibition assays, as well as immunohistochemistry. Results: Aptamers were selected for both enzymes, and showed high affinity binding, in the low nanomolar range, and selectivity for their respective targets, as characterised by fluorescence quenching and ELISA. Enzyme inhibition assays demonstrated the capability of the aptamers to successfully inhibit their cognate enzymes, both in direct assays against the enzyme in the presence of its substrate, and in functional assays in tissue where the enzymes are naturally expressed, demonstrating their therapeutic potential. Fluorescent labelled aptamers were shown to successfully stain the enzyme in immunohistochemistry experiments, and were able to bind to the enzyme in quartz crystal microbalance assays, demonstrating the diagnostic potential of the aptamers. Following small modifications, these aptamers also demonstrated stability in serum and urine, exhibiting potential for in vivo use as inhibitors, or for analysis of biological material in diagnostic assays, including immunohistochemistry and as recognition units in biosensors. Conclusions: Aptamers against tumour enzymes can prove a great alternative to antibodies and small molecule inhibitors, offering greater affinity, specificity and temperature stability, no immunogenicity, and great flexibility in a variety of modifications and uses.

European Journal of Cancer Supplements, 2010

Background: Each year breast cancer is diagnosed in an estimated 1 million women worldwide, and i... more Background: Each year breast cancer is diagnosed in an estimated 1 million women worldwide, and is the cause of death of over 400,000. Most breast cancers originate from previously normal breast epithelial cells. During their transformation into cancer cells, the epithelial cells often lose the expression of cell adhesion proteins, which may also confer a motile or migratory advantage to breast cancer cells. Among the cell adhesion proteins potentially affected by this transformation is Junctional Adhesion Molecule A (JAM-A) a membranous cell-cell adhesion protein involved in tight junction formation in epithelial cells. Previous data by McSherry et al. (2009) demonstrated a novel association between JAM-A gene and protein upregulation and aggressive tumours in breast cancer patients.

European Journal of Cancer Supplements, 2009

European Journal of Cancer Supplements, 2010

Background: DNA methylation plays an important part in development of breast cancer. The mechanis... more Background: DNA methylation plays an important part in development of breast cancer. The mechanisms by which DNA methylation can influence cancer development include hypermethylation of CpG islands in tumour suppressor genes resulting in gene inactivation, and global genomic hypomethylation causing chromosome instability, aneuploidy, and up-regulated gene expression. Breast cancer is a heterogeneous disease that can be divided in subtypes (luminal A, luminal B, normal-like, ErbB2 positive and basal-like) based on mRNA expression with significantly different prognosis and survival. Distinct global DNA methylation profiles have been reported in breast tumours, but the influence of the tumour methylome on the development of the mRNA expression subgroups of breast cancer has not yet been defined. Material: DNA material from 80 tumours with existing information from whole genome expression analysis was available for methylation analysis. The samples were collected at hospitals in Oslo/Akershus and all patients have given informed consent and the projects are approved by the local ethical committee. Results and Conclusions: Three major clusters were identified based on methylation profiling of the 80 breast tumours, and these 80 tumours were also classified as belonging to one of the five mRNA expression subgroups. Cluster 1 (N = 23) contained 65.3% luminal A, 21.7% luminal B and 13% normal-like tumours. Cluster 2 (N = 28) contained 39.3% ErbB2 positive, 25% basal-like, 17.9% luminal B, 10.7% normal-like and 7.1% luminal A tumours. Cluster 3 (N = 24) contained 66.7% luminal A, 16.7% basal-like, 8.3% ErbB2 positive, 4.2% luminal B and 4.2% normal-like tumours. A strong concordance between the methylation and expression based classification was observed. Interestingly, luminal A were split between cluster 1 and 3, basal-like tumours were split between cluster 2 and 3, and both luminal B and normal-like were split between cluster 1 and 2. This distribution suggests that despite the strong concordance to the mRNA expression clusters, additional information was provided by the clustering by methylation. The three major methylation clusters of patients were studied for differences in survival, and significant differences were found with Cluster 2 showing shortest survival times. We will also present analyses comparing survival between patients within the same mRNA expression subgroup but in different methylation clusters to determine the clinical implication of methylation profile combined with expression profile.

European Journal of Cancer Supplements, 2010

163 Materials and Methods: Retroviral mediated expression of wild type and mutant Trib proteins a... more 163 Materials and Methods: Retroviral mediated expression of wild type and mutant Trib proteins and in vivo bone marrow cell transduction and transplantation used to assay AML. Protein expression analysis of C/EBPalpha following knockdown of COP1 E3 ligase. Binding interaction assays performed using immunofluorescence, subcellular fractionation, GST pulldown and peptide array technology. Results: In a murine bone marrow transplant model, mice reconstituted with hematopoietic stem cells (HSC) retrovirally expressing Trib1 or Trib2 but not Trib3, uniformly developed fatal transplantable AML. Investigation of the structural domains of Trib2 showed that the C-terminal COP1 E3 ligase binding site and the kinase domain are required for its oncogenic activity. Trib2 contains variant catalytic loop sequences compared to conventional kinases that we show are necessary for Trib2 function. Trib2 (and Trib1) associated with and led to the proteasomal-dependent degradation of C/EBPalpha, a critical nuclear transcription factor frequently dysregulated in AML. Trib2 localizes to both the cytoplasm and the nucleus, but interaction with C/EBPalpha is exclusively nuclear. Trib2 binding to C/EBPalpha results in COP1 E3 ligase mediated degradation of C/EBPalpha and is essential for Trib2-induced AML. Conclusion: This works highlights Trib proteins as potent AML oncogenes, and identify the structural domains that are required for oncogenic function in AML. These data strengthen the correlation between Trib2 mediated C/EBPalpha degradation and leukaemia which may have prognostic and therapeutic implications.

Nucleic Acids Research, 2009

Clinical DNA is often available in limited quantities requiring whole-genome amplification for su... more Clinical DNA is often available in limited quantities requiring whole-genome amplification for subsequent genome-wide assessment of copy-number variation (CNV) by array-CGH. In pre-implantation diagnosis and analysis of micrometastases, even merely single cells are available for analysis. However, procedures allowing high-resolution analyses of CNVs from single cells well below resolution limits of conventional cytogenetics are lacking. Here, we applied amplification products of single cells and of cell pools (5 or 10 cells) from patients with developmental delay, cancer cell lines and polar bodies to various oligo tiling array platforms with a median probe spacing as high as 65 bp. Our high-resolution analyses reveal that the low amounts of template DNA do not result in a completely unbiased whole genome amplification but that stochastic amplification artifacts, which become more obvious on array platforms with tiling path resolution, cause significant noise. We implemented a new evaluation algorithm specifically for the identification of small gains and losses in such very noisy ratio profiles. Our data suggest that when assessed with sufficiently sensitive methods highresolution oligo-arrays allow a reliable identification of CNVs as small as 500 kb in cell pools (5 or 10 cells), and of 2.6-3.0 Mb in single cells.

Science translational medicine, Jan 30, 2010

Distinct molecular subtypes of breast carcinomas have been identified, but translation into clini... more Distinct molecular subtypes of breast carcinomas have been identified, but translation into clinical use has been limited. We have developed two platform-independent algorithms to explore genomic architectural distortion using array comparative genomic hybridization data to measure (i) whole-arm gains and losses [whole-arm aberration index (WAAI)] and (ii) complex rearrangements [complex arm aberration index (CAAI)]. By applying CAAI and WAAI to data from 595 breast cancer patients, we were able to separate the cases into eight subgroups with different distributions of genomic distortion. Within each subgroup data from expression analyses, sequencing and ploidy indicated that progression occurs along separate paths into more complex genotypes. Histological grade had prognostic impact only in the luminal-related groups, whereas the complexity identified by CAAI had an overall independent prognostic power. This study emphasizes the relation among structural genomic alterations, molecu...

BMC Genomics, 2008

Background: Microarray Comparative Genomic Hybridization (array CGH) provides a means to examine ... more Background: Microarray Comparative Genomic Hybridization (array CGH) provides a means to examine DNA copy number aberrations. Various platforms, brands and underlying technologies are available, facing the user with many choices regarding platform sensitivity and number, localization, and density distribution of probes.

Bioinformatics, 2005

CGH-Explorer is a program for visualization and statistical analysis of microarray-based comparat... more CGH-Explorer is a program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion.

Nucleic acids research, 2001

SET domains are conserved amino acid motifs present in chromosomal proteins that function in epig... more SET domains are conserved amino acid motifs present in chromosomal proteins that function in epigenetic control of gene expression. These proteins can be divided into four classes as typified by their Drosophila members E(Z), TRX, ASH1 and SU(VAR)3-9. Homologs of all four classes have been identified in yeast and mammals, but not in plants. A BLASTP screening of the Arabidopsis genome identified 37 genes: three E(z) homologs, five trx homologs, four ash1 homologs and 15 genes similar to Su(var)3-9. Seven genes were assigned as trx-related and three as ash1-related. Only four genes have been described previously. Our classification is based on the characteristics of the SET domains, cysteine-rich regions and additional conserved domains, including a novel YGD domain. RT-PCR analysis, cDNA cloning and matching ESTs show that at least 29 of the genes are active in diverse tissues. The high number of SET domain genes, possibly involved in epigenetic control of gene activity during plant...

Disease Markers, 2018

Background. After perinatal asphyxia, the cerebellum presents more damage than previously suggest... more Background. After perinatal asphyxia, the cerebellum presents more damage than previously suggested. Objectives. To explore if the antioxidant N-acetylcysteine amide (NACA) could reduce cerebellar injury after hypoxia-reoxygenation in a neonatal pig model. Methods. Twenty-four newborn pigs in two intervention groups were exposed to 8% oxygen and hypercapnia, until base excess fell to −20 mmol/l or the mean arterial blood pressure declined to <20 mmHg. After hypoxia, they received either NACA (NACA group, n=12) or saline (vehicle-treated group, n=12). One sham-operated group (n=5) served as a control and was not subjected to hypoxia. Observation time after the end of hypoxia was 9.5 hours. Results. The intranuclear proteolytic activity in Purkinje cells of asphyxiated vehicle-treated pigs was significantly higher than that in sham controls (p=0.03). Treatment with NACA was associated with a trend to decreased intranuclear proteolytic activity (p=0.08), There were significantly les...

Breast Cancer Research, 2005

There is compelling evidence from transgenic mouse studies and analysis of mutations in human car... more There is compelling evidence from transgenic mouse studies and analysis of mutations in human carcinomas indicating that the TGF-β signal transduction pathway is tumor suppressive. We have shown that overexpression of TGF-β1 in mammary epithelial cells suppresses the development of carcinomas and that expression of a dominant negative type II TGF-β receptor (DNIIR) in mammary epithelial cells under control of the MMTV promoter/enhancer increases the incidence of mammary carcinomas. Studies of human tumors have demonstrated inactivating mutations in human tumors of genes encoding proteins involved in TGF-β signal transduction, including DPC4/Smad4, Smad2, and the type II TGF-β receptor (TβRII). There is also evidence that TGF-β can enhance the progression of tumors. This hypothesis is being tested in genetically modified mice. To attain complete loss of TβRII, we have generated mice with loxP sites flanking exon 2 of Tgfbr2 and crossed them with mice expressing Cre recombinase under control of the MMTV promoter/enhancer to obtain Tgfbr2 mgKO mice. These mice show lobuloalveolar hyperplasia. Mice are being followed for mammary tumor development. Tgfbr2 mgKO mice that also express polyoma virus middle T antigen under control of the MMTV promoter (MMTV-PyVmT) develop mammary tumors with a significantly shorter latency than MMTV-PyVmT mice and show a marked increase in pulmonary metastases. Our data do not support the hypothesis that TGF-β signaling in mammary carcinoma cells is important for invasion and metastasis, at least in this model system. The importance of stromal-epithelial interactions in mammary gland development and tumorigenesis is well established. These interactions probably involve autocrine and paracrine action of multiple growth factors, including members of the TGF-β family, which are expressed in both stroma and epithelium. Again, to accomplish complete knockout of the type II TGF-β receptor gene in mammary stromal cells, FSP1-Cre and Tgfbr2 flox/flox mice were crossed to attain Tgfbr2 fspKO mice. The S.03 Genomic analysis of human breast cancer in families and populations

Nucleic Acids Research, 2001

Journal of Experimental Botany, 2003

Dormant Arabidopsis seeds require strati®cation and light for germination. To study gene expressi... more Dormant Arabidopsis seeds require strati®cation and light for germination. To study gene expression during establishment, maintenance and release of dormancy, various Arabidopsis ecotypes that are different in their degree of dormancy were investigated; three nsm mutants that lack the strati®cationdependency, and the precocious germination and reduced dormancy of the abi3-1 mutant (insensitive to ABA). Genes examined by mRNA abundance include LEC1, FUS3 and ABI3, transcription factors that are major regulators of embryo development and, at least indirectly, play some role in the control of dormancy. Moreover, the late embryogenesis marker genes, AtEm1 and AtEm6, were examined in relation to the state of dormancy. The expression of LEC1, FUS3 and ABI3 mRNA is only marginally different during seed development in various strong or moderate dormancy wild types, nsm mutants and abi3-1. Therefore, it is unlikely that these transcription factors directly control the establishment of dormancy in Arabidopsis. Sole and various combinations of light, temperature, and after-ripening regimes that alter germination behaviour were examined to determine if the expression of ABI3, AtEm1 and AtEm6 mRNAs were correlated with dormancy-breaking processes. ABI3 expression is in¯uenced by cold and light, in a similar way in both dormant and nondormant wild-type seeds. ABI3 transcript abundance in the nsm1 and nsm2 mutants is higher and in the nsm5-1 mutant is marginally lower than in wild-type seeds, but changes due to temperature and light factors are very similar to those that occur in wild-type seeds. The abundances of AtEm1 and AtEm6 mRNAs are equally affected by imbibition and cold temperature in mature and after-ripened seeds. The LEA transcript abundances for AtEm1 and AtEm6 are reduced in nsm mutants in a common, ABI3-independent pathway.

PLoS ONE, 2014

Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disea... more Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disease, characterized by distinct genomic and transcriptomic profiles. Transcriptome analyses prevalently assessed protein-coding genes; however, the majority of the mammalian genome is expressed in numerous non-coding transcripts. Emerging evidence supports that many of these non-coding RNAs are specifically expressed during development, tumorigenesis, and metastasis. The focus of this study was to investigate the expression features and molecular characteristics of long non-coding RNAs (lncRNAs) in breast cancer. We investigated 26 breast tumor and 5 normal tissue samples utilizing a custom expression microarray enclosing probes for mRNAs as well as novel and previously identified lncRNAs. We identified more than 19,000 unique regions significantly differentially expressed between normal versus breast tumor tissue, half of these regions were noncoding without any evidence for functional open reading frames or sequence similarity to known proteins. The identified non-coding regions were primarily located in introns (53%) or in the intergenic space (33%), frequently orientated in antisense-direction of protein-coding genes (14%), and commonly distributed at promoter-, transcription factor binding-, or enhancer-sites. Analyzing the most diverse mRNA breast cancer subtypes Basal-like versus Luminal A and B resulted in 3,025 significantly differentially expressed unique loci, including 682 (23%) for non-coding transcripts. A notable number of differentially expressed protein-coding genes displayed non-synonymous expression changes compared to their nearest differentially expressed lncRNA, including an antisense lncRNA strongly anticorrelated to the mRNA coding for histone deacetylase 3 (HDAC3), which was investigated in more detail. Previously identified chromatin-associated lncRNAs (CARs) were predominantly downregulated in breast tumor samples, including CARs located in the protein-coding genes for CALD1, FTX, and HNRNPH1. In conclusion, a number of differentially expressed lncRNAs have been identified with relation to cancer-related protein-coding genes.

Physiologia Plantarum, 1998

European Journal of Cancer Supplements, 2010

Background: Thyroid nodules are clinically evident in about 5% of women and 1% of men therefore r... more Background: Thyroid nodules are clinically evident in about 5% of women and 1% of men therefore represent the most common endocrine pathology. Although more than 90% are benign a significant number undergo surgical excision. In 10% of all follicular patterned lesions diagnostic dilemma is presented in a subset of encapsulated lesions with partial nuclear features of papillary thyroid carcinoma and with histological features that fail to place them reliably in either the benign or the malignant category. Microarray gene profiling has shown a promise in the accurate discrimination of benign-malignant discrimination and molecular characterization of thyroid lesions. We focused on not particularly for significantly modulated candidate genes, but for sets of genes acting on similar antiapoptotic and signaling pathways. Materials and Methods: Tumour samples were obtained from 25 patients undergoing thyroid surgery and evaluated on histopathology prior to our experiments. Genomic RNA was isolated from the snap frozen tumour samples of follicular adenomas and sporadic type of papillary carcinomas. We used NimbleGen Human Expression 12X135K Arrays to analyze gene expression alterations between follicular thyroid adenoma and papillary thyroid carcinoma expression profiles. Quantitative RT-PCR and Western blot analysis were done in case of the 10 genes showing the highest expression changes on the array. Results: We found the consequent significant expression regulation of 378 genes 233 of them found to be significantly underexpressed in papillary carcinomas compared to the follicular adenoma tissues. Papillary thyroid carcinomas expressed modulated genes on the NFúB regulatory pathway. Nfúb itself was found to be up-regulated as well as its activator Med17 and the Eda1, the member of the TNF-related ligand family regulating epithelial development, wich has regulatory role in Nfúb-promoted transcription and Jnk signaling. additionally represented constitutive down-regulation Pparg and Mapk, 4, 8 and 10 partaking in NFúB inhibition, and Cyld1 over expression closely connected to NFúB signaling. Conclusions: Considering the fact that NFkB has already been found to be a promising diagnostic and therapeutic target, our investigation could provide new possibilities for diagnostic, therapeutic and preventative perspectives.

European Journal of Cancer Supplements, 2010

fluorescence quenching, ELISA, quartz crystal microbalance, fluorescence microscopy and enzyme in... more fluorescence quenching, ELISA, quartz crystal microbalance, fluorescence microscopy and enzyme inhibition assays, as well as immunohistochemistry. Results: Aptamers were selected for both enzymes, and showed high affinity binding, in the low nanomolar range, and selectivity for their respective targets, as characterised by fluorescence quenching and ELISA. Enzyme inhibition assays demonstrated the capability of the aptamers to successfully inhibit their cognate enzymes, both in direct assays against the enzyme in the presence of its substrate, and in functional assays in tissue where the enzymes are naturally expressed, demonstrating their therapeutic potential. Fluorescent labelled aptamers were shown to successfully stain the enzyme in immunohistochemistry experiments, and were able to bind to the enzyme in quartz crystal microbalance assays, demonstrating the diagnostic potential of the aptamers. Following small modifications, these aptamers also demonstrated stability in serum and urine, exhibiting potential for in vivo use as inhibitors, or for analysis of biological material in diagnostic assays, including immunohistochemistry and as recognition units in biosensors. Conclusions: Aptamers against tumour enzymes can prove a great alternative to antibodies and small molecule inhibitors, offering greater affinity, specificity and temperature stability, no immunogenicity, and great flexibility in a variety of modifications and uses.

European Journal of Cancer Supplements, 2010

Background: Each year breast cancer is diagnosed in an estimated 1 million women worldwide, and i... more Background: Each year breast cancer is diagnosed in an estimated 1 million women worldwide, and is the cause of death of over 400,000. Most breast cancers originate from previously normal breast epithelial cells. During their transformation into cancer cells, the epithelial cells often lose the expression of cell adhesion proteins, which may also confer a motile or migratory advantage to breast cancer cells. Among the cell adhesion proteins potentially affected by this transformation is Junctional Adhesion Molecule A (JAM-A) a membranous cell-cell adhesion protein involved in tight junction formation in epithelial cells. Previous data by McSherry et al. (2009) demonstrated a novel association between JAM-A gene and protein upregulation and aggressive tumours in breast cancer patients.

European Journal of Cancer Supplements, 2009

European Journal of Cancer Supplements, 2010

Background: DNA methylation plays an important part in development of breast cancer. The mechanis... more Background: DNA methylation plays an important part in development of breast cancer. The mechanisms by which DNA methylation can influence cancer development include hypermethylation of CpG islands in tumour suppressor genes resulting in gene inactivation, and global genomic hypomethylation causing chromosome instability, aneuploidy, and up-regulated gene expression. Breast cancer is a heterogeneous disease that can be divided in subtypes (luminal A, luminal B, normal-like, ErbB2 positive and basal-like) based on mRNA expression with significantly different prognosis and survival. Distinct global DNA methylation profiles have been reported in breast tumours, but the influence of the tumour methylome on the development of the mRNA expression subgroups of breast cancer has not yet been defined. Material: DNA material from 80 tumours with existing information from whole genome expression analysis was available for methylation analysis. The samples were collected at hospitals in Oslo/Akershus and all patients have given informed consent and the projects are approved by the local ethical committee. Results and Conclusions: Three major clusters were identified based on methylation profiling of the 80 breast tumours, and these 80 tumours were also classified as belonging to one of the five mRNA expression subgroups. Cluster 1 (N = 23) contained 65.3% luminal A, 21.7% luminal B and 13% normal-like tumours. Cluster 2 (N = 28) contained 39.3% ErbB2 positive, 25% basal-like, 17.9% luminal B, 10.7% normal-like and 7.1% luminal A tumours. Cluster 3 (N = 24) contained 66.7% luminal A, 16.7% basal-like, 8.3% ErbB2 positive, 4.2% luminal B and 4.2% normal-like tumours. A strong concordance between the methylation and expression based classification was observed. Interestingly, luminal A were split between cluster 1 and 3, basal-like tumours were split between cluster 2 and 3, and both luminal B and normal-like were split between cluster 1 and 2. This distribution suggests that despite the strong concordance to the mRNA expression clusters, additional information was provided by the clustering by methylation. The three major methylation clusters of patients were studied for differences in survival, and significant differences were found with Cluster 2 showing shortest survival times. We will also present analyses comparing survival between patients within the same mRNA expression subgroup but in different methylation clusters to determine the clinical implication of methylation profile combined with expression profile.

European Journal of Cancer Supplements, 2010

163 Materials and Methods: Retroviral mediated expression of wild type and mutant Trib proteins a... more 163 Materials and Methods: Retroviral mediated expression of wild type and mutant Trib proteins and in vivo bone marrow cell transduction and transplantation used to assay AML. Protein expression analysis of C/EBPalpha following knockdown of COP1 E3 ligase. Binding interaction assays performed using immunofluorescence, subcellular fractionation, GST pulldown and peptide array technology. Results: In a murine bone marrow transplant model, mice reconstituted with hematopoietic stem cells (HSC) retrovirally expressing Trib1 or Trib2 but not Trib3, uniformly developed fatal transplantable AML. Investigation of the structural domains of Trib2 showed that the C-terminal COP1 E3 ligase binding site and the kinase domain are required for its oncogenic activity. Trib2 contains variant catalytic loop sequences compared to conventional kinases that we show are necessary for Trib2 function. Trib2 (and Trib1) associated with and led to the proteasomal-dependent degradation of C/EBPalpha, a critical nuclear transcription factor frequently dysregulated in AML. Trib2 localizes to both the cytoplasm and the nucleus, but interaction with C/EBPalpha is exclusively nuclear. Trib2 binding to C/EBPalpha results in COP1 E3 ligase mediated degradation of C/EBPalpha and is essential for Trib2-induced AML. Conclusion: This works highlights Trib proteins as potent AML oncogenes, and identify the structural domains that are required for oncogenic function in AML. These data strengthen the correlation between Trib2 mediated C/EBPalpha degradation and leukaemia which may have prognostic and therapeutic implications.

Nucleic Acids Research, 2009

Clinical DNA is often available in limited quantities requiring whole-genome amplification for su... more Clinical DNA is often available in limited quantities requiring whole-genome amplification for subsequent genome-wide assessment of copy-number variation (CNV) by array-CGH. In pre-implantation diagnosis and analysis of micrometastases, even merely single cells are available for analysis. However, procedures allowing high-resolution analyses of CNVs from single cells well below resolution limits of conventional cytogenetics are lacking. Here, we applied amplification products of single cells and of cell pools (5 or 10 cells) from patients with developmental delay, cancer cell lines and polar bodies to various oligo tiling array platforms with a median probe spacing as high as 65 bp. Our high-resolution analyses reveal that the low amounts of template DNA do not result in a completely unbiased whole genome amplification but that stochastic amplification artifacts, which become more obvious on array platforms with tiling path resolution, cause significant noise. We implemented a new evaluation algorithm specifically for the identification of small gains and losses in such very noisy ratio profiles. Our data suggest that when assessed with sufficiently sensitive methods highresolution oligo-arrays allow a reliable identification of CNVs as small as 500 kb in cell pools (5 or 10 cells), and of 2.6-3.0 Mb in single cells.

Science translational medicine, Jan 30, 2010

Distinct molecular subtypes of breast carcinomas have been identified, but translation into clini... more Distinct molecular subtypes of breast carcinomas have been identified, but translation into clinical use has been limited. We have developed two platform-independent algorithms to explore genomic architectural distortion using array comparative genomic hybridization data to measure (i) whole-arm gains and losses [whole-arm aberration index (WAAI)] and (ii) complex rearrangements [complex arm aberration index (CAAI)]. By applying CAAI and WAAI to data from 595 breast cancer patients, we were able to separate the cases into eight subgroups with different distributions of genomic distortion. Within each subgroup data from expression analyses, sequencing and ploidy indicated that progression occurs along separate paths into more complex genotypes. Histological grade had prognostic impact only in the luminal-related groups, whereas the complexity identified by CAAI had an overall independent prognostic power. This study emphasizes the relation among structural genomic alterations, molecu...

BMC Genomics, 2008

Background: Microarray Comparative Genomic Hybridization (array CGH) provides a means to examine ... more Background: Microarray Comparative Genomic Hybridization (array CGH) provides a means to examine DNA copy number aberrations. Various platforms, brands and underlying technologies are available, facing the user with many choices regarding platform sensitivity and number, localization, and density distribution of probes.

Bioinformatics, 2005

CGH-Explorer is a program for visualization and statistical analysis of microarray-based comparat... more CGH-Explorer is a program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion.

Nucleic acids research, 2001

SET domains are conserved amino acid motifs present in chromosomal proteins that function in epig... more SET domains are conserved amino acid motifs present in chromosomal proteins that function in epigenetic control of gene expression. These proteins can be divided into four classes as typified by their Drosophila members E(Z), TRX, ASH1 and SU(VAR)3-9. Homologs of all four classes have been identified in yeast and mammals, but not in plants. A BLASTP screening of the Arabidopsis genome identified 37 genes: three E(z) homologs, five trx homologs, four ash1 homologs and 15 genes similar to Su(var)3-9. Seven genes were assigned as trx-related and three as ash1-related. Only four genes have been described previously. Our classification is based on the characteristics of the SET domains, cysteine-rich regions and additional conserved domains, including a novel YGD domain. RT-PCR analysis, cDNA cloning and matching ESTs show that at least 29 of the genes are active in diverse tissues. The high number of SET domain genes, possibly involved in epigenetic control of gene activity during plant...