33 research outputs found
Gene-expression analysis of gleason grade 3 tumor glands embedded in low- and high-risk prostate cancer
The Gleason score (GS) of prostate cancer on diagnostic biopsies is an important
parameter for therapeutic decision-making. Biopsy GS under-estimates the actual GS at
radical prostatectomy in a significant number of patients due to sampling artifact. The
aim of this study was to identify markers that are differentially expressed in Gleason
grade 3 (GG3) tumor glands embedded in GS 4 + 3 = 7 and GS 3 + 3 = 6 prostate
cancer using laser capture microdissection and RNA sequencing.
GG3 tumor glands embedded in nine GS 3 + 3 = 6 and nine GS 4 + 3 = 7 prostate
cancers were isolated by laser capture microdissection of frozen radical prostatectomy
specimens. After RNA amplification and RNA sequencing, differentially expressed genes
in both GG3 components were identified by a 2log fold change > 1.0 and p-value < 0.05.
We applied immunohistochemistry on a tissue micro-array representing 481 radical
prostatectomy samples for further validation on protein level.
A total of 501 genes were up-regulated and 421 down-regulated in GG3 glands
embedded in GS 4 + 3 = 7 as compared to GS 3 + 3 = 6 prostate cancer. We selected
HELLS, ZIC2 and ZIC5 genes for further validation. ZIC5 mRNA was up-regulated 17 fold
(p = 8.4Eâ07), ZIC2 8 fold (p = 1.3Eâ05) and HELLS 2 fold (p = 0.006) in GG3 glands
derived from GS 4 + 3 = 7. HELLS expression of â„ 1% occurred in 10% GS < 7, 17% GS 7
and 43% GS >7 prostate cancer (p < 0.001). Using a cut-off of â„ 1%, protein expression
of ZIC5 was present in 28% GS 7 cancer (p < 0.001).
ZIC2 was neither associated with GS nor outcome in our validation set. HELLS was
independently predictive for biochemical-recurrence after radical prostatectomy
(HR 2.3; CI 1.5â3.6; p < 0.01).
In conclusion, HELLS and ZIC5 might be promising candidate markers for selection
of biopsy GS 6 prostate cancer being at risk for up-grading at prostatectomy
IReport: A generalised Galaxy solution for integrated experimental reporting
Background: Galaxy offers a number of visualisation options with components, such as Trackster, Circster and Galaxy Charts, but currently lacks the ability to easily combine outputs from different tools into a single view or report. A number of tools produce HTML reports as output in order to combine the various output files from a single tool; however, this requires programming and knowledge of HTML, and the reports must be custom-made for each new tool.Findings: We have developed a generic and flexible reporting tool for Galaxy, iReport, that allows users to create interactive HTML reports directly from the Galaxy UI, with the ability to combine an arbitrary number of outputs from any number of different tools. Content can be organised into different tabs, and interactivity can be added to components. To demonstrate the capability of iReport we provide two publically available examples, the first is an iReport explaining about iReports, created for, and using content from the recent Galaxy Community Conference 2014. The second is a genetic report based on a trio analysis to determine candidate pathogenic variants which uses our previously developed Galaxy toolset for whole-genome NGS analysis, CGtag. These reports may be adapted for outputs from any sequencing platform and any results, such as omics data, non-high throughput results and clinical variables.Conclusions: iReport provides a secure, collaborative, and flexible web-based reporting system that is compatible with Galaxy (and non-Galaxy) generated content. We demonstrate its value with a real-life example of reporting genetic trio-analysis
Mining microarray datasets aided by knowledge stored in literature
DNA microarray technology produces large amounts of data. For data mining
of these datasets, background information on genes can be helpful.
Unfortunately most information is stored in free text. Here, we present an
approach to use this information for DNA microarray data mining
A mononucleotide repeat in PRRT2 is an important, frequent target of mismatch repair deficiency in cancer
The DNA mismatch repair (MMR) system corrects DNA replication mismatches thereby contributing to the maintenance of genomic stability. MMR deficiency has been observed in prostate cancer but its impact on the genomic landscape of these tumours is not known. In order to identify MMR associated mutations in prostate cancer we have performed whole genome sequencing of the MMR deficient PC346C prostate cancer cell line. We detected a total of 1196 mutations in PC346C which was 1.5-fold higher compared to a MMR proficient prostate cancer sample (G089). Of all different mutation classes, frameshifts in mononucleotide repeat (MNR) sequences were significantly enriched in the PC346C sample. As a result, a selection of genes with frameshift mutations in MNR was further assessed regarding its mutational status in a comprehensive panel of prostate, ovarian, endometrial and colorectal cancer cell lines. We identified PRRT2 and DAB2IP to be frequently mutated in MMR deficient cell lines, colorectal and endometrial cancer patient samples. Further characterization of PRRT2 revealed an important role of this gene in cancer biology. Both normal prostate cell lines and a colorectal cancer cell line showed increased proliferation, migration and invasion when expressing the mutated form of PRRT2 (ÎPRRT2). The wild-type PRRT2 (PRRT2wt) had an inhibitory effect in proliferation, consistent with the low expression level of PRRT2 in cancer versus normal prostate samples
CGtag: Complete genomics toolkit and annotation in a cloud-based Galaxy
Background: Complete Genomics provides an open-source suite of command-line tools for the analysis of their CG-formatted mapped sequencing files. Determination of; for example, the functional impact of detected variants, requires annotation with various databases that often require command-line and/or programming experience; thus, limiting their use to the average research scientist. We have therefore implemented this CG toolkit, together with a number of annotation, visualisation and file manipulation tools in Galaxy called CGtag (Complete Genomics Toolkit and Annotation in a Cloud-based Galaxy).Findings: In order to provide research scientists with web-based, simple and accurate analytical and visualisation applications for the selection of candidate mutations from Complete Genomics data, we have implemented the open-source Complete Genomics tool set, CGATools, in Galaxy. In addition we implemented some of the most popular command-line annotation and visualisation tools to allow research scientists to select candidate pathological mutations (SNV, and indels). Furthermore, we have developed a cloud-based public Galaxy instance to host the CGtag toolkit and other associated modules.Conclusions: CGtag provides a user-friendly interface to all research scientists wishing to select candidate variants from CG or other next-generation sequencing platforms' data. By using a cloud-based infrastructure, we can also assure sufficient and on-demand computation and storage resources to handle the analysis tasks. The tools are freely available for use from an NBIC/CTMM-TraIT (The Netherlands Bioinformatics Center/Center for Translational Molecular Medicine) cloud-based Galaxy instance, or can be installed to a local (production) Galaxy via the NBIC Galaxy tool shed
Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes
MOTIVATION: The advent of high-throughput experiments in molecular biology creates a need for methods to efficiently extract and use information for large numbers of genes. Recently, the associative concept space (ACS) has been developed for the representation of information extracted from biomedical literature. The ACS is a Euclidean space in which thesaurus concepts are positioned and the distances between concepts indicates their relatedness. The ACS uses co-occurrence of concepts as a source of information. In this paper we evaluate how well the system can retrieve functionally related genes and we compare its performance with a simple gene co-occurrence method. RESULTS: To assess the performance of the ACS we composed a test set of five groups of functionally related genes. With the ACS good scores were obtained for four of the five groups. When compared to the gene co-occurrence method, the ACS is capable of revealing more functional biological relations and can achieve results with less literature available per gene. Hierarchical clustering was performed on the ACS output, as a potential aid to users, and was found to provide useful clusters. Our results suggest that the algorithm can be of value for researchers studying large numbers of genes. AVAILABILITY: The ACS program is available upon request from the authors
Androgen receptor mutations
Male sexual differentiation and development proceed under direct control of androgens. Androgen action is mediated by the intracellular androgen receptor, which belongs to the superfamily of ligand-dependent transcription factors. At least three pathological situations are associated with abnormal androgen receptor structure and function: androgen insensitivity syndrome (AIS), spinal and bulbar muscular atrophy (SBMA) and prostate cancer. In the X-linked androgen insensitivity syndrome, defects in the androgen receptor gene have prevented the normal development of both internal and external male structures in 46,XY individuals. Complete or gross deletions of the androgen receptor gene have not been found frequently in persons with complete androgen insensitivity syndrome. Point mutations at several different sites in exons 2â8 encoding the DNA- and androgen-binding domain, have been reported for partial and complete forms of androgen insensitivity. A relatively high number of mutations were reported in two different clusters in exon 5 and in exon 7. The number of mutations in exon 1 is extremely low and no mutations have been reported in the hinge region, located between the DNA-binding domain and the ligand-binding domain and which is encoded by the first half of exon 4. Androgen receptor gene mutations in prostate cancer are very rare and are reported only in exons 4â8. The X-linked spinal and bulbar muscle atrophy (SBMA; Kennedy's disease) is associated with an expanded length (> 40 residues) of one of the polyglutamine stretches in the N-terminal domain of the androgen receptor
Differential tissue expression of extracellular vesicle-derived proteins in prostate cancer
Abstract
Background: Proteomic profiling of extracellular vesicles (EVs) from prostate cancer
(PCa) and normal prostate cell lines, led to the identification of new candidate PCa
markers. These proteins included the nuclear exportin proteins XPO1 (also known as
CRM1), the EVâassociated PDCD6IP (also known as ALIX), and the previously
published fatty acid synthase FASN. In this study, we investigated differences in
expression of XPO1 and PDCD6IP on wellâcharacterized prostate cancer cohorts
using mass spectrometry and tissue microarray (TMA) immunohistochemistry to
determine their diagnostic and prognostic value.
Methods: Protein fractions from 67 tissue samples (n = 33 normal adjacent prostate
[NAP] and n = 34 PCa) were analyzed by mass spectrometry (nanoâLCâMSâMS). Labelâfree
quantification of EVs was performed to identify differentially expressed proteins between
PCa and NAP. Prognostic evaluation of the candidate markers was performed with a TMA,
containing 481 radical prostatectomy samples. Samples were stained for the candidate
markers and correlated with patient information and clinicopathological outcome.
Results: XPO1 was higher expressed in PCa compared to NAP in the MS data analysis
(P > 0.0001). PDCD6IP was not significantly higher expressed (P = 0.0501). High
cytoplasmic XPO1 staining in the TMA immunohistochemistry, correlated in a multivariable model with high Gleason scores (P = 0.002) and PCaârelated death (P = 0.009).
Conclusion: High expression of cytoplasmic XPO1 shows correlation with prostate
cancer and has added clinical value in tissue samples. Furthermore, as an extracellular
vesiclesâassociated protein, it might be a novel relevant liquid biomarker