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1.
Mol Oncol ; 10(2): 303-16, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26590090

ABSTRACT

Periampullary adenocarcinomas can be of two histological subtypes, intestinal or pancreatobiliary. The latter is more frequent and aggressive, and characterized by a prominent desmoplastic stroma, which is tightly related to the biology of the cancer, including its poor response to chemotherapy. Whereas miRNAs are known to regulate various cellular processes and interactions between cells, their exact role in periampullary carcinoma remains to be characterized, especially with respect to the prominent stromal component of pancreatobiliary type cancers. The present study aimed at elucidating this role by miRNA expression profiling of the carcinomatous and stromal component in twenty periampullary adenocarcinomas of pancreatobiliary type. miRNA expression profiles were compared between carcinoma cells, stromal cells and normal tissue samples. A total of 43 miRNAs were found to be differentially expressed between carcinoma and stroma of which 11 belong to three miRNA families (miR-17, miR-15 and miR-515). The levels of expression of miRNAs miR-17, miR-20a, miR-20b, miR-223, miR-10b, miR-2964a and miR-342 were observed to be higher and miR-519e to be lower in the stromal component compared to the carcinomatous and normal components. They follow a trend where expression in stroma is highest followed by carcinoma and then normal tissue. Pathway analysis revealed that pathways regulating tumor-stroma interactions such as ECM interaction remodeling, epithelial-mesenchymal transition, focal adhesion pathway, TGF-beta, MAPK signaling, axon guidance and endocytosis were differently regulated. The miRNA-mRNA mediated interactions between carcinoma and stromal cells add new knowledge regarding tumor-stroma interactions.


Subject(s)
Adenocarcinoma/genetics , Common Bile Duct Neoplasms/genetics , MicroRNAs/genetics , Pancreatic Neoplasms/genetics , RNA, Messenger/genetics , Stromal Cells/metabolism , Adenocarcinoma/metabolism , Adenocarcinoma/pathology , Adult , Aged , Common Bile Duct Neoplasms/metabolism , Common Bile Duct Neoplasms/pathology , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , MAP Kinase Signaling System , Male , MicroRNAs/metabolism , Middle Aged , Pancreatic Neoplasms/metabolism , Pancreatic Neoplasms/pathology , RNA, Messenger/metabolism , Transforming Growth Factor beta , Tumor Microenvironment
2.
Mol Oncol ; 9(4): 758-71, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25579086

ABSTRACT

Periampullary adenocarcinomas include four anatomical sites of origin (the pancreatic duct, bile duct, ampulla and duodenum) and most of them fall into two histological subgroups (pancreatobiliary and intestinal). Determining the exact origin of the tumor is sometimes difficult, due to overlapping histopathological characteristics. The prognosis depends on the histological subtype, as well as on the anatomical site of origin, the former being the more important. The molecular basis for these differences in prognosis is poorly understood. Whole-genome analyses were used to investigate the association between molecular tumor profiles, pathogenesis and prognosis. A total of 85 periampullary adenocarcinomas were characterized by mRNA and miRNA expressions profiling. Molecular profiles of the tumors from the different anatomical sites of origin as well as of the different histological subtypes were compared. Differentially expressed mRNAs and miRNAs between the two histopathological subtypes were linked to specific molecular pathways. Six miRNA families were downregulated and four were upregulated in the pancreatobiliary type as compared to the intestinal type (P < 0.05). miRNAs and mRNAs associated with improved overall and recurrence free survival for the two histopathological subtypes were identified. For the pancreatobiliary type the genes ATM, PTEN, RB1 and the miRNAs miR-592 and miR-497, and for the intestinal type the genes PDPK1, PIK3R2, G6PC and the miRNAs miR-127-3p, miR-377* were linked to enriched pathways and identified as prognostic markers. The molecular signatures identified may in the future guide the clinicians in the therapeutic decision making to an individualized treatment, if confirmed in other larger datasets.


Subject(s)
Adenocarcinoma/genetics , Ampulla of Vater/pathology , Biomarkers, Tumor/genetics , Gene Expression Regulation, Neoplastic/genetics , Intestinal Neoplasms/genetics , MicroRNAs/genetics , Pancreatic Neoplasms/genetics , RNA, Messenger/genetics , Adenocarcinoma/pathology , Adult , Aged , Aged, 80 and over , Ampulla of Vater/metabolism , Biomarkers, Tumor/metabolism , Cluster Analysis , Female , Gene Expression Profiling , Humans , Intestinal Neoplasms/pathology , Kaplan-Meier Estimate , Male , MicroRNAs/metabolism , Middle Aged , Pancreatic Neoplasms/pathology , Prognosis , Proportional Hazards Models , RNA, Messenger/metabolism
3.
Br J Cancer ; 111(11): 2142-51, 2014 Nov 25.
Article in English | MEDLINE | ID: mdl-25268374

ABSTRACT

BACKGROUND: Optimal expression and proper function of key mitotic proteins facilitate control and repair processes that aim to prevent loss or gain of chromosomes, a hallmark of cancer. Altered expression of small regulatory microRNAs is associated with tumourigenesis and metastasis but the impact on mitotic signalling has remained unclear. METHODS: Cell-based high-throughput screen identified miR-378a-5p as a mitosis perturbing microRNA. Transient transfections, immunofluorescence, western blotting, time-lapse microscopy, FISH and reporter assays were used to characterise the mitotic anomalies by excess miR-378a-5p. Analysis of microRNA profiles in breast tumours was performed. RESULTS: Overexpression of miR-378a-5p induced numerical chromosome changes in cells and abrogated taxol-induced mitotic block via premature inactivation of the spindle assembly checkpoint. Moreover, excess miR-378a-5p triggered receptor tyrosine kinase-MAP kinase pathway signalling, and was associated with suppression of Aurora B kinase. In breast cancer in vivo, we found that high miR-378a-5p levels correlate with the most aggressive, poorly differentiated forms of cancer. INTERPRETATION: Downregulation of Aurora B by excess miR-378a-5p can explain the observed microtubule drug resistance and increased chromosomal imbalance in the microRNA-overexpressing cells. The results suggest that breast tumours may deploy high miR-378a-5p levels to gain growth advantage and antagonise taxane therapy.


Subject(s)
Breast Neoplasms/pathology , MicroRNAs/physiology , Mitosis , Aurora Kinase B/antagonists & inhibitors , Breast Neoplasms/chemistry , Breast Neoplasms/genetics , Carrier Proteins/physiology , Cell Proliferation , Chromosome Segregation , Extracellular Signal-Regulated MAP Kinases/antagonists & inhibitors , Female , HeLa Cells , Humans , MAP Kinase Signaling System/physiology , Neoplasm Grading , RNA-Binding Proteins , Receptors, Estrogen/analysis , Vascular Endothelial Growth Factor A/biosynthesis
4.
Br J Cancer ; 111(2): 326-38, 2014 Jul 15.
Article in English | MEDLINE | ID: mdl-24901235

ABSTRACT

BACKGROUND: The multi-exon CSPP1 gene, encoding for centrosome and microtubule-associated proteins involved in ciliogenesis and cell division, is a candidate oncogene in luminal breast cancer but expression of CSPP1 proteins remained unexplored. METHODS: CSPP1 gene and protein expression was examined in normal mammary tissue, human breast cancer cell lines, and primary breast cancer biopsies from two patient cohorts. Cell type and epitope-dependent subcellular-specific CSPP1 staining pattern in normal mammary gland epithelium and cancer biopsies were correlated to molecular and clinical parameters. RESULTS: A novel, nuclear localised CSPP1 isoform was exclusively detected in luminal epithelial cells, whereas cytoplasmic CSPP-L was generally expressed in normal mammary epithelium. Luminal cell-related nuclear CSPP1 expression was preserved in type-matched cell lines and carcinomas, and correlated to gene copy number and mRNA expression. In contrast, basal-like carcinomas displayed generally lower CSPP1 mRNA expression. Yet, a subgroup of basal-like breast carcinomas depicted nuclear CSPP1 expression, displayed luminal traits, and differed from nuclear CSPP1 devoid counterparts in expression of eight genes. Eight-gene signature defined groups of basal-like tumours from an independent cohort showed significant differences in survival. CONCLUSIONS: Differential expression of a nuclear CSPP1 isoform identified biologically and clinically distinct subgroups of basal-like breast carcinoma.


Subject(s)
Breast Neoplasms/metabolism , Cell Cycle Proteins/biosynthesis , Microtubule-Associated Proteins/biosynthesis , Neoplasms, Basal Cell/metabolism , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Cell Culture Techniques , Cell Cycle Proteins/genetics , Cell Line, Tumor , Cell Nucleus/genetics , Cell Nucleus/metabolism , Epithelial Cells/metabolism , Epithelial Cells/pathology , Female , Gene Expression , Gene Expression Profiling , HEK293 Cells , Humans , Immunohistochemistry , MCF-7 Cells , Microtubule-Associated Proteins/genetics , Neoplasms, Basal Cell/genetics , Neoplasms, Basal Cell/pathology , Transfection
5.
Br J Cancer ; 110(8): 2072-80, 2014 Apr 15.
Article in English | MEDLINE | ID: mdl-24577056

ABSTRACT

BACKGROUND: B7-H3, an immunoregulatory protein, is overexpressed in several cancers and is often associated with metastasis and poor prognosis. Here, our aim was to identify microRNAs (miRNAs) regulating B7-H3 and assess their potential prognostic implications in breast cancer. METHODS: MicroRNAs targeting B7-H3 were identified by transfecting two breast cancer cell lines with a library of 810 miRNA mimics and quantifying changes of B7-H3 protein levels using protein lysate microarrays. For validations we used western immunoblotting and 3'-UTR luciferase assays. Clinical significance of the miRNAs was assayed by analysing whether their expression levels correlated with outcome in two cohorts of breast cancer patients (142 and 81 patients). RESULTS: We identified nearly 50 miRNAs that downregulated B7-H3 protein levels. Western immunoblotting validated the impact of the 20 most effective miRNAs. Thirteen miRNAs (miR-214, miR-363*, miR-326, miR-940, miR-29c, miR-665, miR-34b*, miR-708, miR-601, miR-124a, miR-380-5p, miR-885-3p, and miR-593) targeted B7-H3 directly by binding to its 3'-UTR region. Finally, high expression of miR-29c was associated with a significant reduced risk of dying from breast cancer in both cohorts. CONCLUSIONS: We identified miRNAs efficiently downregulating B7-H3 expression. The expression of miR-29c correlated with survival in breast cancer patients, suggesting a tumour suppressive role for this miRNA.


Subject(s)
B7 Antigens/genetics , Breast Neoplasms/genetics , MicroRNAs/genetics , B7 Antigens/biosynthesis , Breast Neoplasms/pathology , Cell Line, Tumor , Disease-Free Survival , Female , Gene Expression Regulation, Neoplastic , Humans , Kaplan-Meier Estimate , MicroRNAs/isolation & purification
6.
Br J Cancer ; 107(10): 1722-8, 2012 Nov 06.
Article in English | MEDLINE | ID: mdl-23079576

ABSTRACT

BACKGROUND: Targeting differentially activated or perturbed tumour pathways is the key idea in individualised cancer therapy, which is emerging as an important option in treating cancers with poor prognostic profiles. TP53 mutation status is known as a core determinant of survival in breast cancer. The pathways disrupted in association with TP53 mutation status in tumours are not well characterised. METHOD: In this study, we stratify breast cancers based on their TP53 mutation status and identify the set of dysregulated tumorigenic pathways and corresponding candidate driver genes using breast cancer gene expression profiles. Expressions of these genes were evaluated for their effect on patient survival first in univariate models, followed by multivariate models with TP53 status as a covariate. RESULTS: The most strongly differentially enriched pathways between breast cancers stratified by TP53 mutation status include in addition to TP53 signalling, several known cancer pathways involved in renal, prostate, pancreatic, colorectal, lung and other cancers, and signalling pathways such as calcium signalling, MAPK, ERBB and vascular endothelial growth factor (VEGF) signalling pathways. We found that mutant TP53 in conjunction with active estrogen receptor (ER) signalling significantly influence survival. We also found that upregulation of VEGFA mRNA levels in association with active ER signalling is a significant marker for poor survival, even in the presence of wild-type TP53. CONCLUSION: Mutation status of TP53 in breast cancer involves wide ranging derangement of several pathways. Among the candidate genes of the significantly deranged pathways, we identified VEGFA expression as an important marker of survival even when controlled by TP53 mutation status. Interestingly, independent of the TP53 mutation status, the survival effect of VEGFA was found significant in patients with active ER signalling (ER/PgR+), but not in those with ER/PgR- status. Therefore, we propose more studies to focus on the role of complex interplay between TP53, ER and VEGF signalling from therapeutic and prognostic context in breast cancer.


Subject(s)
Breast Neoplasms/genetics , Cell Transformation, Neoplastic/genetics , Mutation , Tumor Suppressor Protein p53/genetics , Vascular Endothelial Growth Factor A/genetics , Breast Neoplasms/metabolism , Cell Transformation, Neoplastic/metabolism , Female , Humans , RNA, Messenger/genetics , Receptors, Estrogen/genetics , Receptors, Estrogen/metabolism , Signal Transduction/genetics , Transcriptome/genetics , Tumor Suppressor Protein p53/metabolism , Up-Regulation/genetics , Vascular Endothelial Growth Factor A/metabolism
7.
Vet Comp Oncol ; 9(4): 241-50, 2011 Dec.
Article in English | MEDLINE | ID: mdl-22077404

ABSTRACT

The incidence of canine mammary tumours (CMTs) differs significantly between breeds, strongly supporting an influence of genetic risk factors. We aimed at identifying germline genetic variations in mammary tumour-associated genes in dogs and survey whether these might alter the encoded proteins. We sequenced 11 genes (BRCA1, BRCA2, BRIP1, CDH1, CHEK2, EGFR, ESR1, HER2, PTEN, STK11 and TP53) and screened for genetic variations. Sixty-four single nucleotide polymorphisms (SNPs) were identified. Nine of the coding SNPs were non-synonymous, of which four were located in gene regions conserved across four species. Three of the non-synonymous SNPs might be damaging according to PolyPhen predictions. One of the indels identified has previously been associated with CMTs. Because of the founder effects, genetic drift and inbreeding in many dog breeds the allele frequencies of the genes studied are likely to vary significantly between breeds and contribute to the considerable difference in genetic risk associated with cancer.


Subject(s)
Dog Diseases/genetics , Mammary Neoplasms, Animal/genetics , Animals , Databases, Nucleic Acid , Dogs , Female , Genes, BRCA1 , Genes, BRCA2 , Genes, erbB-1/genetics , Genes, erbB-2/genetics , Genes, p53/genetics , Genetic Variation , Norway , PTEN Phosphohydrolase/genetics , Polymerase Chain Reaction/veterinary , Polymorphism, Single Nucleotide , Sequence Analysis/veterinary
8.
Br J Cancer ; 105(1): 9-12, 2011 Jun 28.
Article in English | MEDLINE | ID: mdl-21673677

ABSTRACT

BACKGROUND: Glomeruloid microvascular proliferation (GMP), a novel histology-based angiogenesis marker, has been associated with decreased survival in several human cancers. METHODS: In this study, we evaluated the ability of GMP to predict clinical response to neoadjuvant chemotherapy in a series of locally advanced breast cancers (n=112). RESULTS: Presence of GMP (21% of the cases) was significantly associated with high-grade tumours and TP53 mutations in addition to the basal-like and HER2 subtypes of breast cancer as defined by gene expression data. GMP was correlated to a gene expression signature for tumour hypoxia response. The GMP pattern was also significantly associated with lack of treatment response and progressive disease (P=0.004). INTERPRETATION: The findings suggest that GMP might be able to predict the lack of response to neoadjuvant chemotherapy in locally advanced breast cancer. Whether GMP may be an independent predictor compared with other factors including TP53 mutation status and tumour grade needs confirmation in larger studies.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Breast Neoplasms/blood supply , Breast Neoplasms/drug therapy , Carcinoma, Ductal, Breast/blood supply , Carcinoma, Ductal, Breast/drug therapy , Drug Resistance, Neoplasm , Neovascularization, Pathologic , Biomarkers, Tumor/analysis , Breast Neoplasms/pathology , Carcinoma, Ductal, Breast/pathology , Endothelium, Vascular/cytology , Endothelium, Vascular/drug effects , Endothelium, Vascular/metabolism , Female , Gene Expression Profiling , Humans , Middle Aged , Prospective Studies , Survival Rate , Treatment Outcome
9.
Pharmacogenomics J ; 10(6): 513-23, 2010 Dec.
Article in English | MEDLINE | ID: mdl-20157331

ABSTRACT

The dose of docetaxel is currently calculated based on body surface area and does not reflect the pharmacokinetic, metabolic potential or genetic background of the patients. The influence of genetic variation on the clearance of docetaxel was analysed in a two-stage analysis. In step one, 583 single-nucleotide polymorphisms (SNPs) in 203 genes were genotyped on samples from 24 patients with locally advanced non-small cell lung cancer. We found that many of the genes harbour several SNPs associated with clearance of docetaxel. Most notably these were four SNPs in EGF, three SNPs in PRDX4 and XPC, and two SNPs in GSTA4, TGFBR2, TNFAIP2, BCL2, DPYD and EGFR. The multiple SNPs per gene suggested the existence of common haplotypes associated with clearance. These were confirmed with detailed haplotype analysis. On the basis of analysis of variance (ANOVA), quantitative mutual information score (QMIS) and Kruskal-Wallis (KW) analysis SNPs significantly associated with clearance of docetaxel were confirmed for GSTA4, PRDX4, TGFBR2 and XPC and additional putative markers were found in CYP2C8, EPHX1, IGF2, IL1R2, MAPK7, NDUFB4, TGFBR3, TPMT (2 SNPs), (P<0.05 or borderline significant for all three methods, 14 SNPs in total). In step two, these 14 SNPs were genotyped in additional 9 samples and the results combined with the genotyping results from the first step. For 7 of the 14 SNPs, the results are still significant/borderline significant by all three methods: ANOVA, QMIS and KW analysis strengthening our hypothesis that they are associated with the clearance of docetaxel.


Subject(s)
Carcinoma, Non-Small-Cell Lung/genetics , Reactive Oxygen Species/metabolism , Taxoids/pharmacokinetics , Carcinoma, Non-Small-Cell Lung/drug therapy , Docetaxel , Haplotypes , Humans , Linkage Disequilibrium , Polymorphism, Single Nucleotide , Taxoids/metabolism
10.
Oncogene ; 29(5): 774-9, 2010 Feb 04.
Article in English | MEDLINE | ID: mdl-19881546

ABSTRACT

DNA amplifications in breast cancer are frequent on chromosome 11q, in which multiple driver oncogenes likely reside in addition to cyclin D1 (CCND1). One such candidate, the scaffolding adapter protein, GRB2-associated binding protein 2 (GAB2), functions in ErbB signaling and was recently shown to enhance mammary epithelial cell proliferation, and metastasis of ERBB2 (HER2/neu)-driven murine breast cancer. However, the amplification status and function of GAB2 in the context of amplification remain undefined. In this study, by genomic profiling of 172 breast tumors, and fluorescence in situ hybridization validation in an independent set of 210 scorable cases, we observed focal amplification spanning GAB2 (11q14.1) independent of CCND1 (11q13.2) amplification, consistent with a driver role. Further, small interfering RNA (siRNA)-mediated knockdown of GAB2 in breast cancer lines (SUM52, SUM44PE and MDA468) with GAB2 amplification revealed a dependency on GAB2 for cell proliferation, cell-cycle progression, survival and invasion, likely mediated through altered phosphatidylinositol 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) signaling. GAB2 knockdown also reduced proliferation and survival in a cell line (BT474) with ERBB2 amplification, consistent with the possibility that GAB2 can function downstream of ERBB2. Our studies implicate focal amplification of GAB2 in breast carcinogenesis, and underscore an oncogenic role of scaffolding adapter proteins, and a potential new point of therapeutic intervention.


Subject(s)
Adaptor Proteins, Signal Transducing/genetics , Breast Neoplasms/genetics , Gene Amplification , Signal Transduction/physiology , Cell Proliferation , Cell Survival/physiology , Comparative Genomic Hybridization , Female , Gene Expression Profiling , Humans , In Situ Hybridization, Fluorescence , Oligonucleotide Array Sequence Analysis , Oncogenes
11.
Oncogene ; 28(44): 3926-36, 2009 Nov 05.
Article in English | MEDLINE | ID: mdl-19684618

ABSTRACT

Predicting the impact of microRNAs (miRNAs) on target proteins is challenging because of their different regulatory effects at the transcriptional and translational levels. In this study, we applied a novel protein lysate microarray (LMA) technology to systematically monitor for target protein levels after high-throughput transfections of 319 pre-miRs into breast cancer cells. We identified 21 miRNAs that downregulated the estrogen receptor-alpha (ERalpha), as validated by western blotting and quantitative real time-PCR, and by demonstrating the inhibition of estrogen-stimulated cell growth. Five potent ERalpha-regulating miRNAs, miR-18a, miR-18b, miR-193b, miR-206 and miR-302c, were confirmed to directly target ERalpha in 3'-untranslated region reporter assays. The gene expression signature that they repressed highly overlapped with that of a small interfering RNA against ERalpha, and across all the signatures tested, was most closely associated with the repression of known estrogen-induced genes. Furthermore, miR-18a and miR-18b showed higher levels of expression in ERalpha-negative as compared with ERalpha-positive clinical tumors. In summary, we present systematic and direct functional evidence of miRNAs inhibiting ERalpha signaling in breast cancer, and demonstrate the high-throughput LMA technology as a novel, powerful technique in determining the relative impact of various miRNAs on key target proteins and associated cellular processes and pathways.


Subject(s)
Down-Regulation , Estrogen Receptor alpha/biosynthesis , Gene Expression Regulation, Neoplastic , MicroRNAs/metabolism , RNA, Neoplasm/metabolism , Signal Transduction , 3' Untranslated Regions , Breast Neoplasms , Cell Line, Tumor , Cell-Free System/metabolism , Female , Humans , Oligonucleotide Array Sequence Analysis
12.
Pharmacogenomics J ; 9(5): 333-40, 2009 Oct.
Article in English | MEDLINE | ID: mdl-19546881

ABSTRACT

Fatigue is one of the most frequent complaints among breast cancer survivors. However, mechanisms underlying persisting fatigue after end of treatment are poorly understood. To explore whether biological processes underlying persistent fatigue can affect gene expression of blood cells, genome-wide expression analyses were performed on whole blood samples from breast cancer survivors classified as chronic fatigued 2-6 years after diagnosis. Non-fatigued survivors served as controls. Several gene sets involved in plasma- and B-cell pathways differed between the chronic fatigued and the non-fatigued, suggesting that a dysregulation in these pathways is associated with chronic fatigue and that a B-cell-mediated inflammatory process might underlie fatigue. The chronic fatigued also had a higher level of leucocytes, lymphocytes and neutrophiles compared with the non-fatigued, thus further indicating that an activation of the immune system plays a role in the biology of chronic fatigue in breast cancer survivors.


Subject(s)
Breast Neoplasms/genetics , Fatigue/genetics , Survivors , Breast Neoplasms/blood , Breast Neoplasms/immunology , Breast Neoplasms/therapy , Case-Control Studies , Chemotherapy, Adjuvant/adverse effects , Chronic Disease , Fatigue/blood , Fatigue/diagnosis , Fatigue/immunology , Female , Gene Expression Profiling/methods , Gene Expression Regulation , Gene Regulatory Networks , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Mastectomy/adverse effects , Oligonucleotide Array Sequence Analysis , Radiotherapy, Adjuvant/adverse effects , Surveys and Questionnaires , Time Factors , Treatment Outcome
13.
BMC Genomics ; 9: 379, 2008 Aug 08.
Article in English | MEDLINE | ID: mdl-18691401

ABSTRACT

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. RESULTS: We evaluate three different platforms presenting different nature and arrangement of the probes: The Agilent Human Genome CGH Microarray 44 k, the ROMA/NimbleGen Representational Oligonucleotide Microarray 82 k, and the Illumina Human-1 Genotyping 109 k BeadChip, with Agilent being gene oriented, ROMA/NimbleGen being genome oriented, and Illumina being genotyping oriented. We investigated copy number changes in 20 human breast tumor samples representing different gene expression subclasses, using a suite of graphical and statistical methods designed to work across platforms. Despite substantial differences in the composition and spatial distribution of probes, the comparison revealed high overall concordance. Notably however, some short amplifications and deletions of potential biological importance were not detected by all platforms. Both correlation and cluster analysis indicate a somewhat higher similarity between ROMA/NimbleGen and Illumina than between Agilent and the other two platforms. The programs developed for the analysis are available from http://www.ifi.uio.no/bioinf/Projects/. CONCLUSION: We conclude that platforms based on different technology principles reveal similar aberration patterns, although we observed some unique amplification or deletion peaks at various locations, only detected by one of the platforms. The correct platform choice for a particular study is dependent on whether the appointed research intention is gene, genome, or genotype oriented.


Subject(s)
Breast Neoplasms/genetics , Gene Dosage , Oligonucleotide Array Sequence Analysis/methods , Algorithms , Chromosome Aberrations , Cluster Analysis , Databases, Genetic , Female , Gene Expression Profiling , Genome, Human , Humans , Male , Oligonucleotide Probes , ROC Curve , Sensitivity and Specificity
14.
Br J Cancer ; 98(4): 728-33, 2008 Feb 26.
Article in English | MEDLINE | ID: mdl-18253122

ABSTRACT

The protein encoded by the CHEK2 gene is involved in cellular repair of DNA damage. The truncating mutation, CHEK2*1100delC, seems to increase the risk for breast cancer. We investigated whether the CHEK2*1100delC mutation carrier status increases the risk for asynchronous contralateral breast cancer (CBC) and whether it interacts with radiation therapy (RT) or chemotherapy in regard to CBC risk. The germline mutation frequency was assessed in 708 women with CBC and 1395 women with unilateral breast cancer (UBC) in the Women's Environment, Cancer and Radiation Epidemiology (WECARE) Study whose first primary breast cancer was diagnosed before age 55 years and during 1985--1999. Seven women with CBC (1.0%) and 10 women with UBC (0.7%) were CHEK2*1100delC variant carriers (rate ratio (RR)=1.8, 95% confidence interval (CI)=0.6-5.4 for CBC vs UBC). Carriers who received RT for their first breast cancer, compared with non-carriers not treated with RT, had an RR of developing CBC of 2.6 (95% CI=0.8-8.7). We found no significant associations between the CHEK2*1100delC mutation and CBC overall or among those treated with RT. However, the sampling variability was such that modest increases in risk could not be excluded. Nonetheless, because this is a rare mutation, it is unlikely to explain a major fraction of CBC in the population.


Subject(s)
Breast Neoplasms/genetics , Germ-Line Mutation/genetics , Protein Serine-Threonine Kinases/genetics , Breast Neoplasms/epidemiology , Breast Neoplasms/radiotherapy , Case-Control Studies , Checkpoint Kinase 2 , Female , Genotype , Humans , Middle Aged , Protein Serine-Threonine Kinases/metabolism , Risk Factors , SEER Program
15.
J Pathol ; 214(3): 357-67, 2008 Feb.
Article in English | MEDLINE | ID: mdl-18044827

ABSTRACT

Prediction of the clinical outcome of breast cancer is multi-faceted and challenging. There is growing evidence that the complexity of the tumour micro-environment, consisting of several cell types and a complex mixture of proteins, plays an important role in development, progression, and response to therapy. In the current study, we investigated whether invasive breast tumours can be classified on the basis of the expression of extracellular matrix (ECM) components and whether such classification is representative of different clinical outcomes. We first examined the matrix composition of 28 primary breast carcinomas by morphology and gene expression profiling using 22K oligonucleotide Agilent microarrays. Hierarchical clustering of the gene expression profile of 278 ECM-related genes derived from the literature divided the tumours into four main groups (ECM1-4). A set of selected differentially expressed genes was validated by immunohistochemistry. The robustness of the ECM classification was confirmed by studying the four ECM groups in a previously published gene expression data set of 114 early-stage primary breast carcinomas profiled using cDNA arrays. Univariate survival analysis showed significant differences in clinical outcome among the various ECM subclasses. One set of tumours, designated ECM4, had a favourable outcome and was defined by the overexpression of a set of protease inhibitors belonging to the serpin family, while tumours with an ECM1 signature had a poorer prognosis and showed high expression of integrins and metallopeptidases, and low expression of several laminin chains. Furthermore, we identified three surrogate markers of ECM1 tumours: MARCO, PUNC, and SPARC, whose expression levels were associated with breast cancer survival and risk of recurrence. Our findings suggest that primary breast tumours can be classified based upon ECM composition and that this classification provides relevant information on the biology of breast carcinomas, further supporting the hypothesis that clinical outcome is strongly related to stromal characteristics.


Subject(s)
Breast Neoplasms/classification , Extracellular Matrix Proteins/genetics , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Oligonucleotide Array Sequence Analysis , Biomarkers, Tumor , Breast Neoplasms/genetics , Cell Adhesion Molecules, Neuronal/genetics , Female , Humans , Immunoglobulins/genetics , Immunohistochemistry , Osteonectin/genetics , Prognosis , Receptors, Immunologic/genetics , Survival Analysis
16.
Eur J Paediatr Neurol ; 11(6): 375-80, 2007 Nov.
Article in English | MEDLINE | ID: mdl-17540590

ABSTRACT

The elevated serum alpha fetoprotein (AFP) concentration in ataxia-telangiectasia (A-T) patients has been known for decades, but the individual variation of AFP levels over time has not been studied. We have followed 12 patients (five girls and seven boys) for 1-12 years (mean 5.5 years) measuring in each patient AFP 2-8 (mean 4) times. Serum AFP levels were increased in all patients, mean 168.7 (range 40-373) kU/L, and without significant differences between the patients. There was a significant age related difference in the serum AFP level. A positive linear relationship (r=0.61, p=0.04) could be found between AFP level and age. Albumin levels were within normal range and did not change with age. Four patients had slightly increased aspartate aminotransferase (AST) levels. None of the patients had serological evidence of infectious hepatitis, and none had increased levels of carcinoembryonic antigen. Repeated standardized observations of gait function revealed no major difference in neurological deterioration between our patients. All had classical A-T disease and mainly truncating mutations; 21 out of 24 possible mutations were either frameshift or nonsense. Four were homozygous for the Norwegian ATM founder mutation. No correlation between serum AFP levels and the different ATM genotypes could be found. We conclude that serum AFP is not only elevated, but also is continuously increasing with age in patients with classical A-T disease.


Subject(s)
Aging/blood , Ataxia Telangiectasia/blood , alpha-Fetoproteins/metabolism , Analysis of Variance , Aspartate Aminotransferases/blood , Aspartate Aminotransferases/genetics , Ataxia Telangiectasia/physiopathology , Child , Child, Preschool , Female , Frameshift Mutation/genetics , Humans , Immunoradiometric Assay/methods , Infant , Male , Walking/physiology
17.
Radiother Oncol ; 83(3): 256-60, 2007 Jun.
Article in English | MEDLINE | ID: mdl-17512073

ABSTRACT

BACKGROUND AND PURPOSE: Radiation is a common treatment of cancer, but some patients show severe side effects when exposed to small doses of radiation. The aim of this study was to explore the underlying cause of radiation sensitivity in a group of radiation sensitive patients. MATERIALS AND METHODS: Lymphoblastoid cell lines from 5 normal individuals, 4 Ataxia Telangiectasia (AT), and 12 non-AT radiation sensitive (RS) patients were irradiated. RNA was isolated before and after radiation and hybridized to 15k cDNA microarrays and gene expression was recorded. RESULTS AND CONCLUSION: The RS cell lines showed an expression phenotype different from both the AT and normal cell lines. Six of the RS cell lines had a distinct expression profile before radiation. This implies that the RS patients are a heterogeneous group, but that six of the patients may have a common cause of radiation sensitivity.


Subject(s)
Cell Cycle Proteins/metabolism , DNA-Binding Proteins/metabolism , Protein Serine-Threonine Kinases/metabolism , Radiation Tolerance , Transcription, Genetic/radiation effects , Tumor Suppressor Proteins/metabolism , Ataxia Telangiectasia/pathology , Ataxia Telangiectasia Mutated Proteins , Cell Cycle Proteins/genetics , Cell Line , Cell Line, Tumor , DNA-Binding Proteins/genetics , Humans , Protein Serine-Threonine Kinases/genetics , RNA/biosynthesis , Radiation, Ionizing , Reference Values , Tumor Suppressor Proteins/genetics
19.
Oncogene ; 26(15): 2157-65, 2007 Apr 02.
Article in English | MEDLINE | ID: mdl-17401424

ABSTRACT

A large amount of data is available on the functional impact of missense mutations in TP53 and on mutation patterns in many different cancers. New data on mutant p53 protein function, cancer phenotype and prognosis have recently been integrated in the International Agency for Research on Cancer TP53 database (http://www-p53.iarc.fr/). Based on these data, we summarize here current knowledge on the respective roles of mutagenesis and biological selection of mutations with specific functional characteristic in shaping the patterns and phenotypes of mutations observed in human cancers. The main conclusion is that intrinsic mutagenicity rates, loss of transactivation activities, and to a lesser extent, dominant-negative activities are the main driving forces that determine TP53 mutation patterns and influence tumor phenotype. In contrast, current experimental data on the acquisition of oncogenic activities (gain of function) by p53 mutants are too scarce and heterogenous to assess whether this property has an impact on tumor development and outcome. In the case of inherited TP53 mutations causing Li-Fraumeni and related syndromes, the age at onset of some tumor types is in direct relation with the degree of loss of transactivation capacity of missense mutations. Finally, studies on large case series demonstrate that TP53 mutations are independent markers of bad prognosis in breast and several other cancers, and that the exact type and position of the mutation influences disease outcome. Further studies are needed to determine how TP53 haplotypes or loss of alleles interact with mutations to modulate their impact on cancer development and prognosis.


Subject(s)
Biomarkers, Tumor/genetics , Neoplasms/genetics , Neoplasms/pathology , Tumor Suppressor Protein p53/genetics , Genetic Markers , Humans , Li-Fraumeni Syndrome/genetics , Mutagenesis , Mutation , Polymorphism, Genetic , Prognosis
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