[Show abstract][Hide abstract] ABSTRACT: New biomarkers are needed to improve the specificity of prostate cancer detection and characterisation of individual tumors. In a proteomics profiling approach using MALDI-MS tissue imaging on frozen tissue sections, we identified discriminating masses. Imaging analysis of cancer, non-malignant benign epithelium and stromal areas of 15 prostatectomy specimens in a test and 10 in a validation set identified characteristic m/z peaks for each tissue type, e.g. m/z 10775 for benign epithelial, m/z 6284 and m/z 6657.5 for cancer and m/z 4965 for stromal tissue. A 10-fold cross-validation analysis showed highest discriminatory ability to separate tissue types for m/z 6284 and m/z 6657.5, both overexpressed in cancer, and a multicomponent mass peak cluster at m/z 10775-10797.4 overexpressed in benign epithelial tissue. ROC AUC values for these three masses ranged from 0.85 to 0.95 in the discrimination of malignant and non-malignant tissue. To identify the underlying proteins, prostate whole tissue extract was separated by nano-HPLC and subjected to MALDI TOF/TOF analysis. Proteins in fractions containing discriminatory m/z masses were identified by MS/MS analysis and candidate marker proteins subsequently validated by immunohistochemistry (IHC). Biliverdin reductase B (BLVRB) turned out to be overexpressed in PCa tissue.
In this study on cryosections of radical prostatectomies of prostate cancer patients, we performed a MALDI-MS tissue imaging analysis and a consecutive protein identification of significant m/z masses by nano-HPLC, MALDI TOF/TOF and MS/MS analysis. We identified BLVRB as a potential biomarker in the discrimination of PCa and benign tissue, also suggesting BVR as a feasible therapeutic target.
Full-text · Article · Aug 2013 · Journal of proteomics
[Show abstract][Hide abstract] ABSTRACT: Loss of cell cycle control is a prerequisite for cancer onset and progression. In prostate cancer, increased activity of cell cycle genes has been associated with prognostic parameters such as biochemical relapse and survival. The identification of novel oncogenic and druggable targets in patient subgroups with poor prognosis may help to develop targeted therapy approaches. We analyzed prostate cancer and corresponding benign tissues (n = 98) using microarrays. The comparison of high- and low-grade tumors (Gleason score ≥ 4 + 3 vs. ≤ 3 + 4) revealed 144 differentially expressed genes (p < 0.05). Out of these, 15 genes were involved in the cell cycle process. The gene maternal embryonic leucine zipper kinase (MELK) was identified to be highly correlated with cell cycle genes like UBE2C, TOP2A, CCNB2, and AURKB. Increased MELK gene expression in high-risk prostate cancer was validated by qPCR in an independent patient cohort (p < 0.005, n = 79). Immunohistochemistry analysis using a tissue microarray (n = 94) revealed increased MELK protein expression in prostate cancer tissues of high Gleason scores. RNAi-based inhibition of MELK in PC3 and LNCaP cells suggested putative function in chromatin modification, embryonic development and cell migration. The concerted inhibition of MELK and other cell cycle targets by the antibiotic siomycin A strongly impaired cell viability of prostate cancer cells, and may point to a novel therapy approach for a subset of high-risk prostate cancer patients.
No preview · Article · Sep 2012 · Journal of Molecular Medicine
[Show abstract][Hide abstract] ABSTRACT: Vibrational spectroscopic imaging has become an essential tool for tissue analyses in life science and represents a modern analytical technique enabling the detection and characterization of molecular components of biological samples. It is based on the absorption of IR radiation by vibrational transitions in covalent bonds and enables global analysis of samples, with resolution close to the cellular level. Advantage of vibrational spectroscopic imaging is the acquisition of local molecular expression profiles, while maintaining the topographic integrity of the tissue by avoiding time-consuming extraction, purification and/or separation steps, respectively. With this nondestructive analytical method it is possible to get both qualitative and quantitative information of heterogeneous samples and unique chemimorphological information about the tissue status, which represents an important benefit for future analytical interpretation of pathological changes of a tissue.
Full-text · Article · May 2012 · Current Proteomics
[Show abstract][Hide abstract] ABSTRACT: Copy number variants (CNVs) are a recently recognized class of human germ line polymorphisms and are associated with a variety of human diseases, including cancer. Because of the strong genetic influence on prostate cancer, we sought to identify functionally active CNVs associated with susceptibility of this cancer type. We queried low-frequency biallelic CNVs from 1,903 men of Caucasian origin enrolled in the Tyrol Prostate Specific Antigen Screening Cohort and discovered two CNVs strongly associated with prostate cancer risk. The first risk locus (P = 7.7 × 10(-4), odds ratio = 2.78) maps to 15q21.3 and overlaps a noncoding enhancer element that contains multiple activator protein 1 (AP-1) transcription factor binding sites. Chromosome conformation capture (Hi-C) data suggested direct cis-interactions with distant genes. The second risk locus (P = 2.6 × 10(-3), odds ratio = 4.8) maps to the α-1,3-mannosyl-glycoprotein 4-β-N-acetylglucosaminyltransferase C (MGAT4C) gene on 12q21.31. In vitro cell-line assays found this gene to significantly modulate cell proliferation and migration in both benign and cancer prostate cells. Furthermore, MGAT4C was significantly overexpressed in metastatic versus localized prostate cancer. These two risk associations were replicated in an independent PSA-screened cohort of 800 men (15q21.3, combined P = 0.006; 12q21.31, combined P = 0.026). These findings establish noncoding and coding germ line CNVs as significant risk factors for prostate cancer susceptibility and implicate their role in disease development and progression.
Full-text · Article · Apr 2012 · Proceedings of the National Academy of Sciences
[Show abstract][Hide abstract] ABSTRACT: PurposeIdentifiable causes of hypospadias, a midline fusion defect of the male ventral urethra, are still infrequently well-known. The aim of this study was to quantify the androgen receptor mRNA and androgen receptor protein in prepuces of boys with and without hypospadias.Material and Methods
Forty prepuce specimens of circumcised boys, aged between 12 and 14 months, with (n=20) and without hypospadias (n=20), were investigated. Immediately after surgery all probes were fixed in formaldehyde and small parts were deep frozen in liquid nitrogen at -80° C. The total RNA of the specimens was isolated and cDNA was written. With the aid of real time PCR the amount of present androgen receptor mRNA was measured. For quantification of present androgen receptor protein, Western Blot (Bradford method) and immunohistochemistry for androgen receptor using standardized automated procedures (Discovery XT, Ventana) were performed. Statistical analyses using the the Kolmogorov-Smirnov and Mann-Whitney U-test were done.ResultsOur observations show that the androgen receptor mRNA is significantly increased in the prepuce of hypospadiac boys compared to specimens of boys with phimosis.(p<0,01) similarly the amount of androgen receptor protein is increased compared to healthy boys. (p<0.01) Our results provide evidence that the rise of androgen receptor mRNA and protein seems to be an indirect expression of a decreased androgen receptor DNA binding capability possibly indicating further missing polypeptide encoding.Conclusions
Our results provide evidence that the different expression of androgen receptor mRNA indicates the extent of a defect androgen receptor signalling in boys with hypospadias.
No preview · Article · Apr 2012 · The Journal of Urology
[Show abstract][Hide abstract] ABSTRACT: The currently used prostate cancer serum marker has a low cancer specificity and improved diagnostics are needed. Here we evaluated whether autoantibodies are present in sera of prostate cancer patients and whether they are useful diagnostic markers for prostate cancer.
Sera from 20 prostate cancer patients and 20 healthy controls were incubated on expression clone arrays containing more than 37,000 recombinant human proteins. Functional annotation clustering of the identified autoantigens was performed using the DAVID database. Autoantigens identified in the prostate cancer group were validated on microarrays using sera of 40 prostate cancer patients, 40 patients with elevated PSA levels but prostate cancer negative biopsies (benign disease), and 40 healthy controls.
We detected autoantibodies against 408 different antigens in sera of prostate cancer patients. One hundred seventy-four of these were exclusively detected in the cancer group compared to the healthy control group. Functional annotation clustering revealed an enrichment of RNA-associated, cytoskeleton, and nuclear proteins. The autoantibody panel was validated in serum samples of independent prostate cancer patients. Autoantibody profiles discriminated between prostate cancer patients and benign disease patients with an ROC curve AUC of 0.71. TTLL12, a protein recently described to be over-expressed in prostate cancer, was the highest ranked discrimination autoantigen.
A variety of autoantibodies were identified in sera of prostate cancer patients and provide a first step towards autoantibody diagnostics. Serum autoantibodies reflect the disease and represent valuable tools not only for prostate cancer, but also for other diseases affecting the immune response.
[Show abstract][Hide abstract] ABSTRACT: Matrix-assisted laser desorption-ionization (MALDI) imaging mass spectrometry (IMS) is a powerful tool in histopathological characterization and represents a modern analytical technique, enabling two-dimensional detection of molecular components of biological samples. Using this method, it is possible to investigate the spatial distribution of proteins, lipids, carbohydrates, cholesterols, nucleic acids, phospholipids, and small molecules in biological systems by in-situ analysis of cell cultures and tissue sections. Recently, MALDI-IMS has become an essential tool for tissue analyses in life science applications, offering global analysis of tissue samples. An advantage of this imaging technique is the acquisition of local molecular expression profiles up to the microscopic level, while maintaining the topographic integrity of the tissue by avoiding time-consuming extraction, purification, or separation steps, respectively. With MALDI-IMS it is possible to determine the distribution of hundreds of unknown compounds in a single measurement, allowing rapid probing of the tissues' biochemistry. Moreover, MALDI-IMS results include qualitative and semiquantitative information, providing unique chemi-morphological information about the tissue status, which represents an important benefit for future analytical interpretation of pathological changes of a tissue. This article summarizes the most recent advances in sample preparation, instrumentation, and data-processing techniques for MALDI-IMS.
No preview · Article · Oct 2011 · Lc Gc North America
[Show abstract][Hide abstract] ABSTRACT: Massively parallel sequencing technologies have brought an enormous increase in sequencing throughput. However, these technologies need to be further improved with regard to reproducibility and applicability to clinical samples and settings.
Using identification of genetic variations in prostate cancer as an example we address three crucial challenges in the field of targeted re-sequencing: Small nucleotide variation (SNV) detection in samples of formalin-fixed paraffin embedded (FFPE) tissue material, minimal amount of input sample and sampling in view of tissue heterogeneity.
We show that FFPE tissue material can supplement for fresh frozen tissues for the detection of SNVs and that solution-based enrichment experiments can be accomplished with small amounts of DNA with only minimal effects on enrichment uniformity and data variance.Finally, we address the question whether the heterogeneity of a tumor is reflected by different genetic alterations, e.g. different foci of a tumor display different genomic patterns. We show that the tumor heterogeneity plays an important role for the detection of copy number variations.
The application of high throughput sequencing technologies in cancer genomics opens up a new dimension for the identification of disease mechanisms. In particular the ability to use small amounts of FFPE samples available from surgical tumor resections and histopathological examinations facilitates the collection of precious tissue materials. However, care needs to be taken in regard to the locations of the biopsies, which can have an influence on the prediction of copy number variations. Bearing these technological challenges in mind will significantly improve many large-scale sequencing studies and will - in the long term - result in a more reliable prediction of individual cancer therapies.
Full-text · Article · Sep 2011 · BMC Medical Genomics
[Show abstract][Hide abstract] ABSTRACT: To describe two predictive models that predict for prostate cancer on biopsy derived from a large screening population. There are no published predictive models that predict prostate cancer in a screened population.
The patients from the Tyrol screening study of known age, total prostate-specific antigen (PSA) level, digital rectal examination (DRE) findings, prostate volume, and percentage of free PSA, and who underwent an initial prostate biopsy from January 1992 to June 2004 were included (n = 2271). Multivariate logistic regression models were used to develop the biopsy positivity predictive models: nomogram 1, age, DRE, and total PSA; and nomogram 2, age, DRE, total PSA, and percentage of free PSA. The predictive accuracy of the models was assessed in terms of discrimination and calibration. External validation of the nomograms was performed using a urologically referred population of patients who underwent prostate biopsy (n = 599).
Both nomograms were well-calibrated internally and externally and discriminated well between patients with positive and negative biopsy findings for both the European and U.S. cohorts (model 2 better than model 1).
Our nomogram with age, total PSA, and DRE had good predictive ability to differentiate between screened patients with cancer on the initial prostate biopsy and those without. Adding the percentage of free PSA improves this predictive power further. These models might aid in clinical decision making regarding the need for biopsy in both European and U.S. populations.
[Show abstract][Hide abstract] ABSTRACT: The objective of this study was to update an in-depth analysis of the time trend for prostate cancer (PCA) mortality in the population of Tyrol by 5 years, namely to 2008. In Tyrol, prostate-specific antigen (PSA) tests were introduced in 1988/89; more than three-quarters of all men in the age group 45-74 had at least one PSA test in the past decade.
We applied the same model as in a previous publication, i.e., an age-period-cohort model using Poisson regression, to the mortality data covering more than three decades from 1970 to 2008.
For Tyrol from 2004 to 2008 in the age group 60+ period terms show a significant reduction in prostate cancer mortality with a risk ratio of 0.70 (95% confidence interval 0.57, 0.87) for Tyrol, and for Austria excluding Tyrol a moderate reduction with a risk ratio of 0.92 (95% confidence interval 0.87, 0.97), each compared to the mortality rate in the period 1989-1993.
This update strengthens our previously published results, namely that PSA testing offered to a population at no charge can reduce prostate cancer mortality. The extent of mortality reduction is in line with that reported in the other recent publications. However, our data do not permit us to fully assess the harms associated with PCA screening, and no recommendation for PSA screening can be made without a careful evaluation of overdiagnosis and overtreatment.
Full-text · Article · Jun 2011 · International Journal of Public Health
[Show abstract][Hide abstract] ABSTRACT: A core technology in proteomics is mass spectroscopy (MS) that permits the measurement of thousands of proteins/peptides simultanously. Sophisticated data mining methods are necessary to identify highly predictive proteomic biomarker candidates in generated MS spectra that are specific to a certain disease. However, before analysis can be started the preprocessing of raw mass spectra is an essential task, mainly due to the presence of back ground signals in the spectra such as electrical and chemical noise. In this work we present a new data mining workflow for the identification of proteomic biomarker candidates using mass spectrometry data. The workflow includes two major steps: 1) the preprocessing of raw spectra, and 2) the identification of highly discriminating candidate masses using a 3-step feature selection approach by combining the advantages of efficient filter and effective wrapper techniques. With the proposed workflow we were able to identify putative candidate biomarkers in a life-threatening human disease using matrix-assisted laser desorption/ionization imaging MS (MALDI-IMS).
[Show abstract][Hide abstract] ABSTRACT: • To evaluate the success of endoscopic dextranomer/hyaluronic acid copolymer (DHAC) application in the treatment of patients with recurrent urinary tract infections (UTIs) and vesico-ureteric reflux (VUR) into the transplanted graft after renal transplantation.
• Between January 2008 and April 2009, 19 patients with recurrent UTIs presented VUR proven by voiding cystourethrography. • To correct VUR of the transplanted ureter, DHAC was injected endoscopically using hydrodistention technique. • Pre- and postoperative serum creatinine levels, the number of pre- and postoperative UTIs, postoperative complications and reflux resolution rate were recorded. The mean follow-up was 6.5 months.
• The average number of UTIs was reduced significantly from 4.89 (range 2-14) to 1.31 (range 0-4) on pre- and postoperative follow-up, respectively, of 6 months (P < 0.001). The success rate increased from 57.9% after the first injection to 78.9% after the second injection. • The remaining four patients with residual VUR received long-term low dose antibiotic prophylaxis. In total, two (10.5%) patients developed increasing creatinine levels postoperatively as a result of distal ureteral obstruction, and temporary urinary drainage was necessary in both patients.
• DHAC appears to be an efficient and minimal invasive method for treating VUR after renal transplantation with respect to short-term success. • Further investigation with a larger group of patients and longer follow-up is needed to evaluate the prolonged effect, as well as any potential side effects.
No preview · Article · Nov 2010 · BJU International
[Show abstract][Hide abstract] ABSTRACT: Prostate cancer has become one of the most common malignancies worldwide. Morphological and histomorphological evaluation of this disease is a well established technique for the cancer classification and has remained relatively unchanged since several decades, although it remains a time consuming and subjective technique, with unsatisfactory levels of inter- and intra-observer discrepancy. Novel approaches for histological recognition are necessary to identify and to investigate cancer in detail. Fourier transform infrared (FTIR) spectroscopic imaging has become an essential tool for the detection, identification and characterization of the molecular components of biological processes, such as those responsible for the dynamic properties of cancer progression. Major advantage of this new technique is the acquisition of local molecular expression profiles while maintaining the topographic integrity of the tissue and avoiding time-consuming extraction, purification and separation steps. By using this method it is possible to investigate the spatial distribution of proteins, lipids, carbohydrates, cholesterols, nucleic acids, phospholipids and small molecules within biological systems by in situ analysis of tissue sections. We applied this technique on prostate cancer patients radical prostatectomy specimens in order to develop new tools for histomorphological analysis and the characterization of snap frozen prostate cancer tissues. As a first step, an optimization of sample preparation, tissue section thickness and IR slide material was performed. Special preparation methods for FTIR imaging are the essential requirements to maintain the spatial arrangement of compounds and avoid delocalization and degradation of the analytes. Subsequently, selected cancer samples were characterized with the prior optimized parameters and analyzed by univariate and cluster analysis. For the interpretation and calibration of the system we correlated the FTIR-images with the histopathological information. With this method it is possible to distinguish between cancer and noncancer areas within a prostate cancer tissue with a resolution of 6.25 μm × 6.25 μm on frozen sections.
Full-text · Article · Nov 2010 · Molecular BioSystems
[Show abstract][Hide abstract] ABSTRACT: Proteomics screening methods for the identification of diagnostic and prognostic biomarkers in cancer are still lagging behind DNA- or RNA-based analysis. We used two-dimensional differential gel electrophoresis (2D-DIGE) in combination with laser capture microdissection (LCM) and MALDI-TOF/TOF mass spectrometry to determine differentially abundant proteins and candidate biomarkers in prostate cancer. Paired (benign and tumor) samples were isolated from 23 Gleason Score 6 (GS 6) and 23 Gleason Score 8 and higher (GS 8+) radical prostatectomy specimens and subjected to 2D-DIGE analysis. Minimal fluorescent dye labeling was applied and electrophoresis performed with triple samples (paired benign and tumor; internal control) for each case of tumor. Nineteen differently abundant proteins were identified by mass spectrometry and further validated. One half of them were associated with glycolysis and the Warburg effect; these were upregulated in tumors. The upregulation correlated with tumor dedifferentiation and might be relevant for selection of therapeutic strategies. Among the other proteins, heat shock protein 60 (HSP60) was significantly upregulated in tumor tissue compared to its benign counterpart. Furthermore, lamin A was statistically highly discriminatory between low and high Gleason score tumors and might serve as a new biomarker of tumor differentiation and prognosis.
No preview · Article · Oct 2010 · Journal of Proteome Research
[Show abstract][Hide abstract] ABSTRACT: Introduction: We retrospectively analysed the predictive value of numerous clinical and radiological parameters to identify a predictor for either necrosis or residual tumors found by retroperitoneal lymph node dissection (RPLND) histology in a collection of nonseminomatous germ cell tumor (NSGCT) patients. Materials and Methods: A database was created containing detailed clinical, radiological and histological information of all consecutive NSGCT patients, who underwent post chemotherapy RPLND between 1984 and 2007. According to the histology of the RPLND specimen, patients were assigned to the “necrosis-only” group or the “residual tumor” group. Associations between clinical and radiological parameters and histology of RPLND were analyzed. Results: Histology of dissected masses showed complete necrosis in 57.4% of patients and residual tumors in 42.6% (3.1% viable cancer and 39.5% teratoma). Univariate analysis showed significant correlation of RPLND histology and the following parameters: teratoma-positive primary tumors, pre-chemotherapy α-fetoprotein (AFP) and – less pronounced – human chorionic gonadotropin levels, size of metastatic mass, total volume of metastatic retroperitoneal lymph nodes, and percentage of volume reduction. The best prediction for necrosis in RPLND histology was in patients with no evidence of teratomatous elements in primary tumors and with normal pre-chemotherapy AFP levels and small lymph nodes. Stepwise multivariate logistic regression analysis confirmed AFP < 10 ng/ml as the best independent predictor for only necrosis in RPLND histology. Conclusions: At the present time we still consider all patients with metastatic NSGCT as candidates for a post-chemotherapy RPLND, arguing that in experienced hands mortality is negligible and morbidity is low and therefore not relevant compared to the risk of missing a residual tumor.