| 1. |
- Davidsson, Josef, et al.
(author)
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The DNA methylome of pediatric acute lymphoblastic leukemia
- 2009
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In: HUMAN MOLECULAR GENETICS. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 18:21, s. 4054-4065
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Journal article (peer-reviewed)abstract
- Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy, with high hyperdiploidy [51-67 chromosomes] and the t(12;21)(p13;q22) [ETV6/RUNX1 fusion] representing the most frequent abnormalities. Although these arise in utero, there is long latency before overt ALL, showing that additional changes are needed. Gene dysregulation through hypermethylation may be such an event; however, this has not previously been investigated in a detailed fashion. We performed genome-wide methylation profiling using bacterial artificial chromosome arrays and promoter-specific analyses of high hyperdiploid and ETV6/RUNX1-positive ALLs. In addition, global gene expression analyses were performed to identify associated expression patterns. Unsupervised cluster and principal component analyses of the chromosome-wide methylome profiles could successfully subgroup the two genetic ALL types. Analysis of all currently known promoter-specific CpG islands demonstrated that several B-cell- and neoplasia-associated genes were hypermethylated and underexpressed, indicating that aberrant methylation plays a significant leukemogenic role. Interestingly, methylation hotspots were associated with chromosome bands predicted to harbor imprinted genes and the tri-/tetrasomic chromosomes in the high hyperdiploid ALLs were less methylated than their disomic counterparts. Decreased methylation of gained chromosomes is a previously unknown phenomenon that may have ramifications not only for the pathogenesis of high hyperdiploid ALL but also for other disorders with acquired or constitutional numerical chromosome anomalies.
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| 2. |
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| 3. |
- Frigyesi, Attila, et al.
(author)
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Independent component analysis reveals new and biologically significant structures in micro array data
- 2006
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In: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 7
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Journal article (peer-reviewed)abstract
- Background: An alternative to standard approaches to uncover biologically meaningful structures in micro array data is to treat the data as a blind source separation ( BSS) problem. BSS attempts to separate a mixture of signals into their different sources and refers to the problem of recovering signals from several observed linear mixtures. In the context of micro array data, "sources" may correspond to specific cellular responses or to co-regulated genes. Results: We applied independent component analysis (ICA) to three different microarray data sets; two tumor data sets and one time series experiment. To obtain reliable components we used iterated ICA to estimate component centrotypes. We found that many of the low ranking components indeed may show a strong biological coherence and hence be of biological significance. Generally ICA achieved a higher resolution when compared with results based on correlated expression and a larger number of gene clusters with significantly enriched for gene ontology ( GO) categories. In addition, components characteristic for molecular subtypes and for tumors with specific chromosomal translocations were identified. ICA also identified more than one gene clusters significant for the same GO categories and hence disclosed a higher level of biological heterogeneity, even within coherent groups of genes. Conclusion: Although the ICA approach primarily detects hidden variables, these surfaced as highly correlated genes in time series data and in one instance in the tumor data. This further strengthens the biological relevance of latent variables detected by ICA.
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| 4. |
- Hedenfalk, Ingrid, et al.
(author)
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Microarray-based Analyses of Hypoxia-induced Transcriptional Changes in Breast Cancer Cell Lines
- 2005
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In: Cancer Genomics & Proteomics. - 1790-6245. ; 2:2, s. 83-95
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Journal article (peer-reviewed)abstract
- Background: Tumour hypoxia is a common characteristic of many solid human tumours, and is associated with a poor prognosis in various types of cancer. Metabolic changes occur when cells are exposed to low oxygen pressure; however, little is known about the mechanisms underlying malignant transformation and/or progression caused by hypoxia. Materials and Methods: We monitored global gene expression changes caused by hypoxia in four breast cancer cell lines using 27K cDNA microarrays. Cells were grown under hypoxic and normoxic conditions, and were harvested at four different time points. All genes were assigned to patterns (up, down, or unchanged) across the time points, followed by ontological mapping to investigate significant associations between genes belonging to specific patterns and Gene Ontology categories. Furthermore, we investigated genomic regions upstream of regulated genes for the presence of known regulatory motifs. Results: Several common effects of hypoxia were seen in the breast cancer cell lines, such as an increase in glycolytic metabolism; however, the response to hypoxia varied greatly between the cell lines. Oestrogen receptor (ER)-positive breast cancer cells displayed a partially unique response to hypoxia compared to ER-negative cells. Similarly, unique changes in e.g. RNA metabolism and DNA repair were seen in a BRCA1-deficient cell line. Whereas an enrichment of genes containing the HIF-1 binding site sequence was found among genes regulated by hypoxia in two of the cell lines investigated, this sequence was also identified in a considerable fraction of non-regulated genes. Conclusion: Global gene expression profiling of the cellular response to hypoxia revealed a multitude of novel mechanisms and functions affected by hypoxia in breast cancer cell lines. The findings also suggest a high degree of diversity in this response depending on the genetic background of the tumour cells. Specifically, down-regulation of genes involved in DNA repair mechanisms in a BRCA1-deficient cell line may reflect the crucial role played by the BRCA1 protein in instances of DNA damage, e.g. during hypoxia.
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| 5. |
- Heidenblad, Markus, et al.
(author)
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Tiling resolution array CGH and high density expression profiling of urothelial carcinomas delineate genomic amplicons and candidate target genes specific for advanced tumors.
- 2008
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In: BMC Medical Genomics. - : Springer Science and Business Media LLC. - 1755-8794. ; 1:Jan 31
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Journal article (peer-reviewed)abstract
- ABSTRACT: BACKGROUND: Urothelial carcinoma (UC) is characterized by nonrandom chromosomal aberrations, varying from one or a few changes in early-stage and low-grade tumors, to highly rearranged karyotypes in muscle-invasive lesions. Recent array-CGH analyses have shed further light on the genomic changes underlying the neoplastic development of UC, and have facilitated the molecular delineation amplified and deleted regions to the level of specific candidate genes. In the present investigation we combine detailed genomic information with expression information to identify putative target genes for genomic amplifications. METHODS: We analyzed 38 urothelial carcinomas by whole-genome tiling resolution array-CGH and high density expression profiling to identify putative target genes in common genomic amplifications. When necessary expression profiling was complemented with Q-PCR of individual genes. RESULTS: Three genomic segments were frequently and exclusively amplified in high grade tumors; 1q23, 6p22 and 8q22, respectively. Detailed mapping of the 1q23 segment showed a heterogeneous amplification pattern and no obvious commonly amplified region. The 6p22 amplicon was defined by a 1.8 Mb core region present in all amplifications, flanked both distally and proximally by segments amplified to a lesser extent. By combining genomic profiles with expression profiles we could show that amplification of E2F3, CDKAL1, SOX4, and MBOAT1 as well as NUP153, AOF1, FAM8A1 and DEK in 6p22 was associated with increased gene expression. Amplification of the 8q22 segment was primarily associated with YWHAZ (14-3-3-zeta) and POLR2K over expression. The possible importance of the YWHA genes in the development of urothelial carcinomas was supported by another recurrent amplicon paralogous to 8q22, in 2p25, where increased copy numbers lead to enhanced expression of YWHAQ (14-3-3-theta). Homozygous deletions were identified at 10 different genomic locations, most frequently affecting CDKN2A/CDKN2B in 9p21 (32%). Notably, the latter occurred mutually exclusive with 6p22 amplifications. CONCLUSION: The presented data indicates 6p22 as a composite amplicon with more than one possible target gene. The data also suggests that amplification of 6p22 and homozygous deletions of 9p21 may have complementary roles. Furthermore, the analysis of paralogous regions that showed genomic amplification indicated altered expression of YWHA (14-3-3) genes as important events in the development of UC.
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| 6. |
- Veerla, Srinivas, et al.
(author)
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Analysis of promoter regions of co-expressed genes identified by microarray analysis
- 2006
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In: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 7
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Journal article (peer-reviewed)abstract
- Background: The use of global gene expression profiling to identify sets of genes with similar expression patterns is rapidly becoming a widespread approach for understanding biological processes. A logical and systematic approach to study co-expressed genes is to analyze their promoter sequences to identify transcription factors that may be involved in establishing specific profiles and that may be experimentally investigated. Results: We introduce promoter clustering i.e. grouping of promoters with respect to their high scoring motif content, and show that this approach greatly enhances the identification of common and significant transcription factor binding sites (TFBS) in co-expressed genes. We apply this method to two different dataset, one consisting of micro array data from 108 leukemias (AMLs) and a second from a time series experiment, and show that biologically relevant promoter patterns may be obtained using phylogenetic foot-printing methodology. In addition, we also found that 15% of the analyzed promoter regions contained transcription factors start sites for additional genes transcribed in the opposite direction. Conclusion: Promoter clustering based on global promoter features greatly improve the identification of shared TFBS in co-expressed genes. We believe that the outlined approach may be a useful first step to identify transcription factors that contribute to specific features of gene expression profiles.
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| 7. |
- Veerla, Srinivas
(author)
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CANCER-RELATED GENE REGULATION MECHANISMS
- 2008
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Doctoral thesis (other academic/artistic)abstract
- Cancer is a disease characterized by deregulation of cellular functions. The means by which these changes occur may differ among cancer types. However, common to all cancers are that they have changed the genetic programs that determine their characteristics. Genetic programs are mainly regulated by the action of transcription factors. Changes in transcription factor activity and modification of promoter functions are therefore important changes in the development of cancer. In the first paper a bioinformatical method is developed that identify transcription factors important for a given tumor type. The basic assumption is that genes that show co-expression are likely to be regulated by the same set of transcription factors. The method consists on several steps. First co-expressed genes are identified using an arbitrary clustering algorithm. Genes with similar promoters are then identified and enrichment for evolutionarily conserved binding sites is determined. We show by this method that transcription factors known to be important for the development of a subtype of leukemia (AML) may be identified and, by the analysis of a time series data, that biologically relevant time dependent interactions between transcriptions factors and genes may be identified. The second paper focus on the promoter sequences. It is well established that DNA modulation by methylation affects the accessibility of transcription factors and that this may inhibit gene activity. To identify genes potentially regulated by promoter methylation we treated bladder cancer cell lines with the drug 5-aza-2’-cytidine that specifically inhibits methylation and thereby reactivates methylated promoters. Our major finding is that many genes shows patchy promoter methylation patterns that frequently affect high scoring and evolutionarily conserved transcription factor binding sites. In addition we identified several genes that may be of importance for bladder cancer development. The third paper is entirely focused on microRNAs. MicroRNAs are small RNA molecules with an approximate size of 20bp that function in analogy to transcription factors. MicroRNAs do, however, not bind to the promoter but to the mRNA and thereby inhibit translation or induce mRNA degradation, in both cases resulting in down regulation of gene activity. We use micro array technology to study alterations in microRNA expression in bladder cancer. We show that microRNA expression is associated with tumor stage and that mir-10a is associated with Ta tumors, that mir-7 is associated with FGFR3 mutations, and that mirs 452 and 452* is associated with lymph node metastases and bad prognosis.
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| 8. |
- Veerla, Srinivas, et al.
(author)
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MiRNA expression in urothelial carcinomas: Important roles of miR-10a, miR-222, miR-125b, miR-7 and miR-452 for tumor stage and metastasis, and frequent homozygous losses of miR-31.
- 2009
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In: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 124, s. 2236-2242
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Journal article (peer-reviewed)abstract
- We analyzed 34 cases of urothelial carcinomas by miRNA, mRNA and genomic profiling. Unsupervised hierarchical clustering using expression information for 300 miRNAs produced 3 major clusters of tumors corresponding to Ta, T1 and T2-T3 tumors, respectively. A subsequent SAM analysis identified 51 miRNAs that discriminated the 3 pathological subtypes. A score based on the expression levels of the 51 miRNAs, identified muscle invasive tumors with high precision and sensitivity. MiRNAs showing high expression in muscle invasive tumors included miR-222 and miR-125b and in Ta tumors miR-10a. A miRNA signature for FGFR3 mutated cases was also identified with miR-7 as an important member. MiR-31, located in 9p21, was found to be homozygously deleted in 3 cases and miR-452 and miR-452* were shown to be over expressed in node positive tumors. In addition, these latter miRNAs were shown to be excellent prognostic markers for death by disease as outcome. The presented data shows that pathological subtypes of urothelial carcinoma show distinct miRNA gene expression signatures. (c) 2009 Wiley-Liss, Inc.
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| 9. |
- Veerla, Srinivas, et al.
(author)
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Promoter analysis of epigenetically controlled genes in bladder cancer.
- 2008
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In: Genes, Chromosomes and Cancer. - : Wiley. - 1045-2257 .- 1098-2264. ; 47, s. 368-378
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Journal article (peer-reviewed)abstract
- DNA methylation is an important epigenetic modification that regulates several genes crucial for tumor development. To identify epigenetically regulated genes in bladder cancer, we performed genome wide expression analyses of eight-bladder cancer cell lines treated with the demethylating agents 5-aza-2'-cytidine and zebularine. To identify methylated C-residues, we sequenced cloned DNA fragments from bisulfite-treated genomic DNA. We identified a total of 1092 genes that showed >/=2-fold altered expression in at least one cell line; 710 showed up-regulation and 382 down-regulation. Extensive sequencing of promoters from 25 genes in eight cell lines showed an association between methylation pattern and expression in 13 genes, including both CpG island and non-CpG island genes. Overall, the methylation patterns showed a patchy appearance with short segments showing high level of methylation separated by larger segments with no methylation. This pattern was not associated with MeCP2 binding sites or with evolutionarily conserved sequences. The genes UBXD2, AQP11, and TIMP1 showed particular patchy methylation patterns. We found several high-scoring and evolutionarily conserved transcription factor binding sites affected by methylated C residues. Two of the genes, FGF18 and MMP11, that were down-regulated as response to 5-aza-2'-cytidine and zebularine treatment showed methylation at specific sites in the untreated cells indicating an activating result of methylation. Apart from identifying epigenetically regulated genes, including TGFBR1, NUPR1, FGF18, TIMP1, and MMP11, that may be of importance for bladder cancer development the presented data also highlight the organization of the modified segments in methylated promoters. (c) 2008 Wiley-Liss, Inc.
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