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| 2. |
- Brommesson, Sara, et al.
(författare)
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Tiling array-CGH for the assessment of genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs.
- 2008
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Ingår i: BMC Clinical Pathology. - : Springer Science and Business Media LLC. - 1472-6890. ; 8:July 10
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Tidskriftsartikel (refereegranskat)abstract
- ABSTRACT: BACKGROUND: Today, no objective criteria exist to differentiate between individual primary tumors and intra- or intermammary dissemination respectively, in patients diagnosed with two or more synchronous breast cancers. To elucidate whether these tumors most likely arise through clonal expansion, or whether they represent individual primary tumors is of tumor biological interest and may have clinical implications. In this respect, high resolution genomic profiling may provide a more reliable approach than conventional histopathological and tumor biological factors. METHODS: 32 K tiling microarray-based comparative genomic hybridization (aCGH) was used to explore the genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs, and was compared with histopathological and tumor biological parameters. RESULTS: Based on global copy number profiles and unsupervised hierarchical clustering, five of ten (p = 1.9 x 10-5) unilateral tumor pairs displayed similar genomic profiles within the pair, while only one of eight bilateral tumor pairs (p = 0.29) displayed pair-wise genomic similarities. DNA index, histological type and presence of vessel invasion correlated with the genomic analyses. CONCLUSION: Synchronous unilateral tumor pairs are often genomically similar, while synchronous bilateral tumors most often represent individual primary tumors. However, two independent unilateral primary tumors can develop synchronously and contralateral tumor spread can occur. The presence of an intraductal component is not informative when establishing the independence of two tumors, while vessel invasion, the presence of which was found in clustering tumor pairs but not in tumor pairs that did not cluster together, supports the clustering outcome. Our data suggest that genomically similar unilateral tumor pairs may represent a more aggressive disease that requires the addition of more severe treatment modalities, and underscores the importance of evaluating the clonality of multiple tumors for optimal patient management. In summary, our findings demonstrate the importance of evaluating the properties of both tumors in order to determine the most optimal patient management.
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| 3. |
- Brown, KM, et al.
(författare)
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cDNA Microarrays in Cancer Research.
- 2006
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Ingår i: Cancer: Principles and Practise of Oncology. - 0781774330 ; , s. 13-25
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 4. |
- Forsare, Carina, et al.
(författare)
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RNA quality in frozen breast cancer samples and the influence on gene expression analysis - a comparison of three evaluation methods using microcapillary electrophoresis traces
- 2007
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Ingår i: BMC Molecular Biology. - : Springer Science and Business Media LLC. - 1471-2199. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Background: Assessing RNA quality is essential for gene expression analysis, as the inclusion of degraded samples may influence the interpretation of expression levels in relation to biological and/ or clinical parameters. RNA quality can be analyzed by agarose gel electrophoresis, UV spectrophotometer, or microcapillary electrophoresis traces, and can furthermore be evaluated using different methods. No generally accepted recommendations exist for which technique or evaluation method is the best choice. The aim of the present study was to use microcapillary electrophoresis traces from the Bioanalyzer to compare three methods for evaluating RNA quality in 24 fresh frozen invasive breast cancer tissues: 1) Manual method = subjective evaluation of the electropherogram, 2) Ratio Method = the ratio between the 28S and 18S peaks, and 3) RNA integrity number (RIN) method = objective evaluation of the electropherogram. The results were also related to gene expression profiling analyses using 27K oligonucleotide microarrays, unsupervised hierarchical clustering analysis and ontological mapping. Results: Comparing the methods pair-wise, Manual vs. Ratio showed concordance (good vs. degraded RNA) in 20/ 24, Manual vs. RIN in 23/ 24, and Ratio vs. RIN in 21/ 24 samples. All three methods were concordant in 20/ 24 samples. The comparison between RNA quality and gene expression analysis showed that pieces from the same tumor and with good RNA quality clustered together in most cases, whereas those with poor quality often clustered apart. The number of samples clustering in an unexpected manner was lower for the Manual (n = 1) and RIN methods (n = 2) as compared to the Ratio method (n = 5). Assigning the data into two groups, RIN = 6 or RIN < 6, all but one of the top ten differentially expressed genes showed decreased expression in the latter group; i. e. when the RNA became degraded. Ontological mapping using GoMiner (p = 0.05; = 3 genes changed) revealed deoxyribonuclease activity, collagen, regulation of cell adhesion, cytosolic ribosome, and NADH dehydrogenase activity, to be the five categories most affected by RNA quality. Conclusion: The results indicate that the Manual and RIN methods are superior to the Ratio method for evaluating RNA quality in fresh frozen breast cancer tissues. The objective measurement when using the RIN method is an advantage. Furthermore, the inclusion of samples with degraded RNA may profoundly affect gene expression levels.
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| 5. |
- Gruvberger, Sofia, et al.
(författare)
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Microarrays in breast cancer research and clinical practice - the future lies ahead
- 2006
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Ingår i: Endocrine-Related Cancer. - : Bioscientifica. - 1479-6821 .- 1351-0088. ; 13:4, s. 1017-1031
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Forskningsöversikt (refereegranskat)abstract
- Molecular profiling for classification and prognostic purposes has demonstrated that the genetic signatures of tumors contain information regarding biological properties as well as clinical behavior. This review highlights the progress that has been made in the field of gene expression profiling of human breast cancer. Breast cancer has become one of the most intensely studied human malignancies in the genomic era; several hundred papers over the last few years have investigated various clinical and biological aspects of human breast cancer using high-throughput molecular profiling techniques. Given the grossly heterogeneous nature of the disease and the lack of robust conventional markers for disease prediction, prognosis, and response to treatment, the notion that a transcriptional profile comprising multiple genes, rather than any single gene or other parameter, will be more predictive of tumor behavior is both appealing and reasonable. Promising results have emerged from these studies, correlating gene expression profiles with prognosis, recurrence, metastatic potential, therapeutic response, as well as biological and functional aspects of the disease. Clearly, the integration of genomic approaches into the clinic lies in the near future, but prospective studies based on larger patient cohorts representing the whole spectrum of breast cancer, oncogenic pathway-based studies, attendant care in bioinformatic analyses and validation studies are needed before the full promise of gene expression profiling can be realized in the clinical setting.
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| 7. |
- Hedenfalk, Ingrid, et al.
(författare)
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Microarray-based Analyses of Hypoxia-induced Transcriptional Changes in Breast Cancer Cell Lines
- 2005
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Ingår i: Cancer Genomics & Proteomics. - 1790-6245. ; 2:2, s. 83-95
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Tidskriftsartikel (refereegranskat)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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| 8. |
- Kronblad, Åsa, et al.
(författare)
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ERK1/2 inhibition increases antiestrogen treatment efficacy by interfering with hypoxia-induced downregulation of ERalpha: a combination therapy potentially targeting hypoxic and dormant tumor cells.
- 2005
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Ingår i: Oncogene. - : Springer Science and Business Media LLC. - 1476-5594 .- 0950-9232. ; 24:45, s. 6835-6841
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Tidskriftsartikel (refereegranskat)abstract
- Tumor hypoxia is associated with cancer invasiveness, metastasis and treatment failure. Recent data suggest that the major target for endocrine treatment in breast cancer, ER alpha, is downregulated during hypoxia, but the mechanism behind this remains unknown. MAPK signaling as well as ER alpha regulation has earlier been independently linked to hypoxia and we now demonstrate HIF-1 alpha and ERK1/2-activation in vivo towards the necrotic zone in DCIS of the breast, parallel with ER alpha downregulation. Hypoxia further caused transcriptional downregulation of ER alpha via activation of ERK1/2 in cell lines and, importantly, MEK1/2 inhibitors (U0126 or PD184352) or ERK1/2 suppression by siRNA partially restored the ERa expression. U0126 combined with tamoxifen accordingly produced an increased efficacy of the anti-estrogens during hypoxia. Base don these findings, we suggest a promising novel therapy for ER alpha-positive breast cancer where a combination of endocrine treatment and ERK1/2 inhibitors may increase treatment response by improved targeting of dormant hypoxic tumor cells.
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| 9. |
- Rennstam, Karin, et al.
(författare)
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High-throughput genomic technology in research and clinical management of breast cancer. Molecular signatures of progression from benign epithelium to metastatic breast cancer.
- 2006
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Ingår i: Breast Cancer Research. - : Springer Science and Business Media LLC. - 1465-5411 .- 1465-542X. ; 8:213:4
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Forskningsöversikt (refereegranskat)abstract
- It is generally accepted that early detection of breast cancer has great impact on patient survival, emphasizing the importance of early diagnosis. In a widely recognized model of breast cancer development, tumor cells progress through chronological and well defined stages. However, the molecular basis of disease progression in breast cancer remains poorly understood. High-throughput molecular profiling techniques are excellent tools for the study of complex molecular alterations. By accurately mapping changes in the genome and subsequent biological/molecular pathways, the chances of finding potential novel treatment targets as well as intervention strategies are enhanced, and ultimately lives can be saved. This review provides a brief summary of recent progress in identifying molecular markers for invasiveness in early breast lesions.
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