| 1. |
- Danielsson, Anna, 1973, et al.
(författare)
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Differential gene expression in human fibroblasts after alpha-particle emitter (211)At compared with (60)Co irradiation.
- 2013
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Ingår i: International journal of radiation biology. - : Informa UK Limited. - 1362-3095 .- 0955-3002. ; 89:4, s. 250-258
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: The aim of this study was to identify gene expression profiles distinguishing alpha-particle (211)At and (60)Co irradiation. Materials and methods: Gene expression microarray profiling was performed using total RNA from confluent human fibroblasts 5 hours after exposure to (211)At labeled trastuzumab monoclonal antibody (0.25, 0.5, and 1 Gy) and (60)Co (1, 2, and 3 Gy). Results: We report gene expression profiles that distinguish the effect different radiation qualities and absorbed doses have on cellular functions in human fibroblasts. In addition, we identified commonly expressed transcripts between (211)At and (60)Co irradiation. A greater number of transcripts were modulated by (211)At than (60)Co irradiation. In addition, down-regulation was more prevalent than up-regulation following (211)At irradiation. Several biological processes were enriched for both irradiation qualities such as transcription, cell cycle regulation, and cell cycle arrest, whereas mitosis, spindle assembly checkpoint, and apoptotic chromosome condensation were uniquely enriched for alpha particle irradiation. Conclusions: LET-dependent transcriptional modulations were observed in human fibroblasts 5 hours after irradiation exposure. These findings suggest that in comparison with (60)Co, (211)At has the clearest influence on both tumor protein p53-activated and repressed genes, which impose a greater overall burden to the cell following alpha particle irradiation.
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| 2. |
- Genell, Anna, et al.
(författare)
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Model selection in Medical Research: A simulation study comparing Bayesian Model Averaging and Stepwise Regression.
- 2010
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Ingår i: BMC medical research methodology. - : Springer Science and Business Media LLC. - 1471-2288. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Automatic variable selection methods are usually discouraged in medical research although we believe they might be valuable for studies where subject matter knowledge is limited. Bayesian model averaging may be useful for model selection but only limited attempts to compare it to stepwise regression have been published. We therefore performed a simulation study to compare stepwise regression with Bayesian model averaging. Methods We simulated data corresponding to five different data generating processes and thirty different values of the effect size (the parameter estimate divided by its standard error). Each data generating process contained twenty explanatory variables in total and had between zero and two true predictors. Three data generating processes were built of uncorrelated predictor variables while two had a mixture of correlated and uncorrelated variables. We fitted linear regression models to the simulated data. We used Bayesian model averaging and stepwise regression respectively as model selection procedures and compared the estimated selection probabilities. Results The estimated probability of not selecting a redundant variable was between 0.99 and 1 for Bayesian model averaging while approximately 0.95 for stepwise regression when the redundant variable was not correlated with a true predictor. These probabilities did not depend on the effect size of the true predictor. In the case of correlation between a redundant variable and a true predictor, the probability of not selecting a redundant variable was 0.95 to 1 for Bayesian model averaging while for stepwise regression it was between 0.7 and 0.9, depending on the effect size of the true predictor. The probability of selecting a true predictor increased as the effect size of the true predictor increased and leveled out at between 0.9 and 1 for stepwise regression, while it leveled out at 1 for Bayesian model averaging. Conclusions Our simulation study showed that under the given conditions, Bayesian model averaging had a higher probability of not selecting a redundant variable than stepwise regression and had a similar probability of selecting a true predictor. Medical researchers building regression models with limited subject matter knowledge could thus benefit from using Bayesian model averaging.
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| 3. |
- Greene, Meridith E, et al.
(författare)
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Education Attainment is Associated With Patient-reported Outcomes: Findings From the Swedish Hip Arthroplasty Register.
- 2014
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Ingår i: Clinical orthopaedics and related research. - : Ovid Technologies (Wolters Kluwer Health). - 1528-1132 .- 0009-921X. ; 472:6, s. 1868-76
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Tidskriftsartikel (refereegranskat)abstract
- Age, sex, and medical comorbidities may be associated with differences in patient-reported outcome scores after THA. Highest level of education may be a surrogate for socioeconomic status, but the degree to which this is associated with patient-reported outcomes after THA is not known.
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| 4. |
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| 5. |
- Hayes, Catherine A, et al.
(författare)
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Glycomic work-flow for analysis of mucin o-linked oligosaccharides.
- 2012
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Ingår i: Methods in molecular biology. - Totowa, NJ : Humana Press. - 1940-6029. ; 842, s. 141-63
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Tidskriftsartikel (refereegranskat)abstract
- The high-throughput analysis of the glycosylation of high molecular weight proteins, such as mucins, has been the aim of glycomics initiatives for the last decade. Here, we present a work-flow for the efficient and reproducible analysis of reduced oligosaccharides from a typical mucin sample. This work-flow can be applied to any similar samples of oligosaccharides. We include recently developed bioinformatic procedures for the statistical analysis of sample sets. These procedures can be applied in any laboratory environment, using free programs that are platform independent. The scripts are explained and can be adjusted to suit the individual experiment. Finally, a number of example results are given to highlight the use of the statistical analysis in a biological context.
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| 6. |
- Hayes, Catherine A, et al.
(författare)
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Statistical analysis of glycosylation profiles to compare tissue type and inflammatory disease state.
- 2012
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4811 .- 1367-4803. ; 28:13, s. 1669-76
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Glycosylation is one of the most important post-translational modifications of proteins and explains some aspects of the diversification of higher organisms not explained by template-driven synthesis. For glycomics to mature as much as genomics and proteomics, the necessary tools need to be developed and tested. Liquid chromatography-mass spectrometry is one of the gold standards for oligosaccharide analysis and leads to large amounts of data, not easily interpreted manually. We present a study on the testing and validation of statistical analysis tools to aid the structural elucidation of these analyses as well as using the results to answer biologically relevant questions. Results: We show the usefulness of data reduction and statistical analysis in the interpretation of complex glycosylation data. The reduction does not result in the loss of importance of the glycosylation information as shown by comparison of control and disease samples in two tissue types.
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| 7. |
- Horvath, György, 1942, et al.
(författare)
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Cancer odor in the blood of ovarian cancer patients: a retrospective study of detection by dogs during treatment, 3 and 6 months afterward.
- 2013
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Ingår i: BMC cancer. - : Springer Science and Business Media LLC. - 1471-2407. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- In recent decades it has been noted that trained dogs can detect specific odor molecules emitted by cancer cells. We have shown that the same odor can also be detected in the patient's blood with high sensitivity and specificity by trained dogs. In the present study, we examined how the ability of dogs to detect this smell was affected by treatment to reduce tumor burden, including surgery and five courses of chemotherapy.
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| 8. |
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| 9. |
- Möllerström, Elin, et al.
(författare)
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Up-regulation of cell cycle arrest protein BTG2 correlates with increased overall survival in breast cancer, as detected by immunohistochemistry using tissue microarray.
- 2010
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Ingår i: BMC cancer. - : Springer Science and Business Media LLC. - 1471-2407. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- ABSTRACT: BACKGROUND: Previous studies have shown that the ADIPOR1, ADORA1, BTG2 and CD46 genes differ significantly between long-term survivors of breast cancer and deceased patients, both in levels of gene expression and DNA copy numbers. The aim of this study was to characterize the expression of the corresponding proteins in breast carcinoma and to determine their correlation with clinical outcome. METHODS: Protein expression was evaluated using immunohistochemistry in an independent breast cancer cohort of 144 samples represented on tissue microarrays. Fisher's exact test was used to analyze the differences in protein expression between dead and alive patients. We used Cox-regression multivariate analysis to assess whether the new markers predict the survival status of the patients better than the currently used markers. RESULTS: BTG2 expression was demonstrated in a significantly lower proportion of samples from dead patients compared to alive patients, both in overall expression (P=0.026) and cell membrane specific expression (P=0.013), whereas neither ADIPOR1, ADORA1 nor CD46 showed differential expression in the two survival groups. Furthermore, a multivariate analysis showed that a model containing BTG2 expression in combination with HER2 and Ki67 expression along with patient age performed better than a model containing the currently used prognostic markers (tumour size, nodal status, HER2 expression, hormone receptor status, histological grade, and patient age). Interestingly, BTG2 has previously been described as a tumour suppressor gene involved in cell cycle arrest and p53 signalling. CONCLUSIONS: We conclude that high-level BTG2 protein expression correlates with prolonged survival in patients with breast carcinoma.
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| 10. |
- Nemes, Szilard, 1977, et al.
(författare)
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A diagnostic algorithm to identify paired tumors with clonal origin.
- 2013
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Ingår i: Genes, chromosomes & cancer. - : Wiley. - 1098-2264 .- 1045-2257. ; 52:11, s. 1007-16
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Tidskriftsartikel (refereegranskat)abstract
- Despite practical implications we still lack standardized methods for clonality testing of tumor pairs. Each tumor is characterized by a set of chromosomal abnormalities, nonrandom changes preferentially involving specific chromosomes and chromosomal regions. Although tumors accumulate chromosomal abnormalities during their development, the majority of these alterations is specific and characteristic for each individual tumor is not exhibited at the population level. Assumingly, secondary tumors that develop from disseminated cells from the primary tumor inherit not only chromosomal changes specific for the cancerous process but also random chromosomal changes that accumulate during tumor development. Based on this assumption, we adopted an intuitive index for genomic similarities of paired tumors, which ranges between zero (completely different genomic profiles) and one (identical genomic profiles). To test the assumption that two tumors have clonal origins if they share a higher degree of genomic similarity than two randomly paired tumors, we built a permutation-based null-hypothesis procedure. The procedure is demonstrated using two publicly available data sets. The article highlights the complexities of clonality testing and aims to offer an easy to follow blueprint that will allow researchers to test genomic similarities of paired tumors, with the proposed index or any other index that fits their need. © 2013 Wiley Periodicals, Inc.
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| 11. |
- Nemes, Szilard, 1977
(författare)
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Integrative genomic and survival analysis of breast tumors
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- With the continued accumulation of genomic data at ever increasing resolution the challenge ahead lies in reading out meaningful clinical/biological information form the data that can contribute to a better understanding of the cancerous process. The need for novel approaches, new statistical methods is therefore strong. The present thesis aims to contribute to the field with three problem specific applications that that expectantly will aid researchers in a better understanding of genomic data. The first paper exemplifies the adaptation of a piecewise-linear regression framework to integrative analysis of DNA copy number aberrations and gene expression (mRNA) data. The methods allows it helps identify the association between copy number and gene expression but it takes a further step and allows detection of changing patterns and changepoints could serve as a proxy for the degree of genomic instability that causes disruptions in feedback-mechanisms. The second paper advocates the adaptation of a mediation analysis for a concomitant analysis of DNA copy number aberrations, mRNA and survival data. The paper offers ways of statistical inference by the means of Delta-method applicable concomitantly on a large number of genes. If a mediation effect is observed for a specific gene, we hypothesize that the specific gene is a driver gene. If no mediation effect is observed then possible associations between DNA copy number aberrations and the outcome are likely to indicate passenger genes. The third paper is a more applied/clinical work and using applied statistics identified a novel panel of 12-genes that can serve prognostic toll for breast cancer specific survival. The thesis concludes with a methodological description in which we describe an easy permutation based approach for testing the clonal origins of multiple tumors. The main assumption of the proposed method is that if two tumors that share a common origin or if the alleged secondary tumor is clonally related to the primary tumor then they share a higher and tumor specific amount of matching chromosomal aberrations (gains or deletions) than recurrent chromosomal aberrations can explain.
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| 12. |
- Nemes, Szilard, 1977, et al.
(författare)
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Integrative genomics with mediation analysis in a survival context
- 2013
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Ingår i: Computational and mathematical methods in medicine. - : Hindawi Limited. - 1748-6718 .- 1748-670X. ; 2013, s. 413783-
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Tidskriftsartikel (refereegranskat)abstract
- DNA copy number aberrations (DCNA) and subsequent altered gene expression profiles may have a major impact on tumor initiation, on development, and eventually on recurrence and cancer-specific mortality. However, most methods employed in integrative genomic analysis of the two biological levels, DNA and RNA, do not consider survival time. In the present note, we propose the adoption of a survival analysis-based framework for the integrative analysis of DCNA and mRNA levels to reveal their implication on patient clinical outcome with the prerequisite that the effect of DCNA on survival is mediated by mRNA levels. The specific aim of the paper is to offer a feasible framework to test the DCNA-mRNA-survival pathway. We provide statistical inference algorithms for mediation based on asymptotic results. Furthermore, we illustrate the applicability of the method in an integrative genomic analysis setting by using a breast cancer data set consisting of 141 invasive breast tumors. In addition, we provide implementation in R.
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| 13. |
- Nemes, Szilard, 1977, et al.
(författare)
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Projections of total hip replacement in Sweden from 2013 to 2030.
- 2014
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Ingår i: Acta orthopaedica. - : Medical Journals Sweden AB. - 1745-3682 .- 1745-3674. ; 85:3, s. 238-243
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Tidskriftsartikel (refereegranskat)abstract
- Background and purpose - The continuously increasing demand for joint replacement surgery in the past decades imposes higher constraints on the budgets of hospitals and healthcare providers. We undertook an analysis of historical trends in total hip replacement performed in Sweden between 1968 and 2012 in order to provide projections of future demand. Data and methods - We obtained data on total hip replacements registered every year and on the evolution of the Swedish population between 1968 and 2012. We assumed the existence of a maximum incidence. So we adopted a regression framework that assumes the existence of an upper limit of total hip replacement incidence. Results - We found that the incidence of total hip replacement will continue to increase until a projected upper incidence level of about 400 total hip replacements per 10(5) Swedish residents aged 40 years and older will be reached around the year 2107. In 2020, the estimated incidence of total hip replacement will be 341 (95% prediction interval (PI): 302-375) and in 2030 it will be 358 (PI: 317-396). Using official forecasted population growth data, about 18,000 operations would be expected to be performed in 2020 and 20,000 would be expected to be performed in 2030. Interpretation - Growing incidence, population growth, and increasing life expectancy will probably result in increased demand for hip replacement surgery. Our findings could serve as a basis for decision making.
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| 14. |
- Nemes, Szilard, 1977, et al.
(författare)
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Segmented regression, a versatile tool to analyze mRNA levels in relation to DNA copy number aberrations.
- 2012
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Ingår i: Genes, chromosomes & cancer. - : Wiley. - 1098-2264 .- 1045-2257. ; 51:1, s. 77-82
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Tidskriftsartikel (refereegranskat)abstract
- DNA copy number aberrations (CNA) and subsequent altered gene expression profiles (mRNA levels) are characteristic features of cancerous cells. Integrative genomic analysis aims to identify recurrent CNA that may have a potential role in cancer development, assuming that gene amplification is accompanied by overexpression, while deletions give rise to downregulation of gene expression. We propose a segmented regression-based approach to identify CNA-driven alteration of gene expression profiles. Segmented regression allows to fit piecewise linear models in different domains of CNA joined by a change-point, where the mRNA-CNA relationship undergoes structural changes. Here, we illustrate the implementation and applicability of the proposed model using 1,161 chromosome fragments detected as DNA CNA in primary tumors from 97 breast cancer patients. We identified significant CNA-driven changes in gene expression levels for 341 chromosome fragments, of which 72 showed a nonlinear relationship to CNA. For 59 of 72 chromosome fragments (82%), we observed an initial increase in mRNA levels due to changes in CNA. After the change-point was passed, the mRNA levels reached a plateau, and a further increase in DNA copy numbers did not induce further elevation in mRNA levels. In contrast, for 13 chromosome fragments, the change-point marked the point where mRNA production accelerated. We conclude that segmented regression modeling may provide valuable insights into the impact CNA have on gene expression in cancer cells. © 2011 Wiley Periodicals, Inc.
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| 15. |
- Parris, Toshima Z, 1978, et al.
(författare)
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Additive effect of the AZGP1, PIP, S100A8, and UBE2C molecular biomarkers improves outcome prediction in breast carcinoma
- 2014
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Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 134:7, s. 1617-1629
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Tidskriftsartikel (refereegranskat)abstract
- The deregulation of key cellular pathways is fundamental for the survival and expansion of neoplastic cells, which in turn can have a detrimental effect on patient outcome. To develop effective individualized cancer therapies, we need to have a better understanding of which cellular pathways are perturbed in a genetically defined subgroup of patients. Here, we validate the prognostic value of a 13-marker signature in independent gene expression microarray datasets (n = 1,141) and immunohistochemistry with full-faced FFPE samples (n = 71). The predictive performance of individual markers and panels containing multiple markers was assessed using Cox regression analysis. In the external gene expression dataset, six of the 13 genes (AZGP1, NME5, S100A8, SCUBE2, STC2, and UBE2C) retained their prognostic potential and were significantly associated with disease-free survival (P < 0.001). Protein analyses refined the signature to a four-marker panel (AZGP1, PIP, S100A8, and UBE2C) significantly correlated with cycling, high grade tumors and lower disease-specific survival rates. AZGP1 and PIP were found in significantly lower levels in invasive breast tissue compared with adjacent normal tissue, whereas elevated levels of S100A8 and UBE2C were observed. A predictive model containing the four-marker panel in conjunction with established clinical variables outperformed a model containing the clinical variables alone. Our findings suggest that deregulated AZGP1, PIP, S100A8, and UBE2C are critical for the aggressive breast cancer phenotype, which may be useful as novel therapeutic targets for drug development to complement established clinical variables. © 2013 Wiley Periodicals, Inc.
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| 16. |
- Parris, Toshima Z, 1978, et al.
(författare)
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Clinical implications of gene dosage and gene expression patterns in diploid breast carcinoma.
- 2010
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Ingår i: Clinical cancer research : an official journal of the American Association for Cancer Research. - 1078-0432. ; 16:15, s. 3860-74
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Tidskriftsartikel (refereegranskat)abstract
- Deregulation of key cellular pathways is fundamental for the survival and expansion of neoplastic cells. In cancer, regulation of gene transcription can be mediated in a variety of ways. The purpose of this study was to assess the impact of gene dosage on gene expression patterns and the effect of other mechanisms on transcriptional levels, and to associate these genomic changes with clinicopathologic parameters.
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| 17. |
- Parris, Toshima Z, 1978, et al.
(författare)
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Clinical relevance of breast cancer-related genes as potential biomarkers for oral squamous cell carcinoma
- 2014
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Ingår i: BMC Cancer. - : Springer Science and Business Media LLC. - 1471-2407. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Background: Squamous cell carcinoma of the oral cavity (OSCC) is a common cancer form with relatively low 5-year survival rates, due partially to late detection and lack of complementary molecular markers as targets for treatment. Molecular profiling of head and neck cancer has revealed biological similarities with basal-like breast and lung carcinoma. Recently, we showed that 16 genes were consistently altered in invasive breast tumors displaying varying degrees of aggressiveness. Methods: To extend our findings from breast cancer to another cancer type with similar characteristics, we performed an integrative analysis of transcriptomic and proteomic data to evaluate the prognostic significance of the 16 putative breast cancer-related biomarkers in OSCC using independent microarray datasets and immunohistochemistry. Predictive models for disease-specific (DSS) and/or overall survival (OS) were calculated for each marker using Cox proportional hazards models. Results: We found that CBX2, SCUBE2, and STK32B protein expression were associated with important clinicopathological features for OSCC (peritumoral inflammatory infiltration, metastatic spread to the cervical lymph nodes, and tumor size). Consequently, SCUBE2 and STK32B are involved in the hedgehog signaling pathway which plays a pivotal role in metastasis and angiogenesis in cancer. In addition, CNTNAP2 and S100A8 protein expression were correlated with DSS and OS, respectively. Conclusions: Taken together, these candidates and the hedgehog signaling pathway may be putative targets for drug development and clinical management of OSCC patients.
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| 18. |
- Parris, Toshima Z, 1978, et al.
(författare)
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Frequent MYC coamplification and DNA hypomethylation of multiple genes on 8q in 8p11-p12-amplified breast carcinomas
- 2014
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Ingår i: Oncogenesis. - : Springer Science and Business Media LLC. - 2157-9024. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Genetic and epigenetic (DNA methylation, histone modifications, microRNA expression) crosstalk promotes inactivation of tumor suppressor genes or activation of oncogenes by gene loss/hypermethylation or duplications/hypomethylation, respectively. The 8p11-p12 chromosomal region is a hotspot for genomic aberrations (chromosomal rearrangements, amplifications and deletions) in several cancer forms, including breast carcinoma where amplification has been associated with increased proliferation rates and reduced patient survival. Here, an integrative genomics screen (DNA copy number, transcriptional and DNA methylation profiling) performed in 229 primary invasive breast carcinomas identified substantial coamplification of the 8p11-p12 genomic region and the MYC oncogene (8q24.21), as well as aberrant methylation and transcriptional patterns for several genes spanning the 8q12.1-q24.22 genomic region (ENPP2, FABP5, IMPAD1, NDRG1, PLEKHF2, RRM2B, SQLE, TAF2, TATDN1, TRPS1, VPS13B). Taken together, our findings suggest that MYC activity and aberrant DNA methylation may also have a pivotal role in the aggressive tumor phenotype frequently observed in breast carcinomas harboring 8p11-p12 regional amplification.
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| 26. |
- Shubbar, Emman, 1974, et al.
(författare)
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Elevated cyclin B2 expression in invasive breast carcinoma is associated with unfavorable clinical outcome.
- 2013
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Ingår i: BMC cancer. - : Springer Science and Business Media LLC. - 1471-2407. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- ABSTRACT: BACKGROUND: Breast cancer is a potentially fatal malignancy in females despite the improvement in therapeutic techniques. The identification of novel molecular signatures is needed for earlier detection, monitoring effects of treatment, and predicting prognosis. We have previously used microarray analysis to identify differentially expressed genes in aggressive breast tumors. The purpose of the present study was to investigate the prognostic value of the candidate biomarkers CCNB2, ASPM, CDCA7, KIAA0101, and SLC27A2 in breast cancer. METHODS: The expression levels and subcellular localization of the CCNB2, ASPM, CDCA7, KIAA0101, and SLC27A2 proteins were measured using immunohistochemistry (IHC) on a panel of 80 primary invasive breast tumors. Furthermore, the mRNA levels of CCNB2, KIAA0101, and SLC27A2 were subsequently examined by qRT-PCR to validate IHC results. Patient disease-specific survival (DSS) was evaluated in correlation to protein levels using the Kaplan-Meier method. Multivariate Cox regression analysis was used to determine the impact of aberrant protein expression of the candidate biomarkers on patient DSS and to estimate the hazard ratio at 8-year follow-up. RESULTS: Elevated cytoplasmic CCNB2 protein levels were strongly associated with short-term disease-specific survival of breast cancer patients (<= 8 years; P<0.001) and with histological tumor type (P= 0.04). However, no association with other clinicopathological parameters was observed. Multivariate Cox regression analysis specified that CCNB2 protein expression is an independent prognostic marker of DSS in breast cancer. The predictive ability of several classical clinicopathological parameters was improved when used in conjunction with CCNB2 protein expression (C-index = 0.795) in comparison with a model without CCNB2 expression (C-index = 0.698). The protein levels of ASPM, CDCA7, KIAA0101, and SLC27A2 did not correlate with any clinicopathological parameter and had no influence on DSS. However, a significant correlation between the expression of the CCNB2 and ASPM proteins was detected (P = 0.03). CONCLUSION: These findings suggest that cytoplasmic CCNB2 may function as an oncogene and could serve as a potential biomarker of unfavorable prognosis over short-term follow-up in breast cancer.
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| 27. |
- Shubbar, Emman, 1974, et al.
(författare)
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High levels of γ-glutamyl hydrolase (GGH) are associated with poor prognosis and unfavorable clinical outcomes in invasive breast cancer.
- 2013
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Ingår i: BMC Cancer. - : Springer Science and Business Media LLC. - 1471-2407. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Background: Previously, we performed analysis of gene expression in 46 axillary lymph node negative tumors and identified molecular gene signatures that resulted in different clinical outcomes. The aim of this study was to determine the correlation of γ-glutamyl hydrolase (GGH), fatty acid amide hydrolase (FAAH), Pirin (PIR) and TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kDa (TAF5L), selected from identified gene signatures, with clinical outcomes as well as classical clinicopathological characteristics in primary invasive breast cancer patients. Methods: The protein levels of GGH, FAAH, PIR and TAF5L were assessed by immunohistochemistry (IHC) on a panel of 80 primary invasive breast tumors. Quantitative real-time PCR (qRT-PCR) and western blot analysis were performed to verify the expression levels of the candidate biomarkers. Patient disease-specific survival (DSS) and recurrence-free survival (RFS) were evaluated using the Kaplan-Meier method. The prognostic biomarkers were identified by univariate analysis with a log-rank test and by multivariate analysis with Cox proportional hazards regression models. Results: The GGH and FAAH protein levels were significantly up-regulated in invasive breast cancer tumors compared with adjacent non-cancerous tissues. Furthermore, the protein levels of GGH and FAAH were significantly correlated in tumor tissues. Tumoral GGH protein expression was significantly correlated with shorter DSS and RFS. Furthermore, the protein expression of GGH was positively correlated with undifferentiated tumors (BRE grade III) and ER/PR expressing tumors. Multivariate regression analysis showed that only GGH protein expression independently predicts DSS. No such correlations were found for FAAH, PIR and TAF5L protein expression. However, elevated protein levels of FAAH were positively associated with high number of lymph node involvement and upregulated levels of PIR were positively related with lymph node metastasis. The TAF5L was pronouncedly down-regulated in primary invasive breast cancer tissues compared to matched adjacent non-cancerous tissues. Conclusion: These data show for the first time that cytoplasmic GGH might play a relevant role in the development and progression of invasive breast cancer, warranting further investigations. Our findings suggest that GGH serve as a potential biomarker of unfavorable clinical outcomes over short-term follow-up in breast cancer. The GGH may be a very attractive targeted therapy for selected patients.
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