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  • microarrays  (4)
  • 1
    Keywords: CANCER ; tumor ; Germany ; PROSTATE ; LUNG-CANCER ; AMPLIFICATION ; microarrays ; prostate cancer ; PROSTATE-CANCER ; EFFICIENT ; MUTATIONS ; OVEREXPRESSION ; molecular ; HER2 ; GEFITINIB
    Type of Publication: Journal article published
    PubMed ID: 17628772
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  • 2
    Keywords: CANCER ; EXPRESSION ; IN-VITRO ; tumor ; carcinoma ; COMBINATION ; Germany ; PROSTATE ; VITRO ; POPULATION ; CDNA ; GENE ; GENE-EXPRESSION ; GENES ; GENOME ; microarray ; PROTEIN ; RNA ; transcription ; TISSUE ; MECHANISM ; BIOMARKERS ; mechanisms ; DOWN-REGULATION ; PROGRESSION ; gene expression ; microarrays ; prostate cancer ; PROSTATE-CANCER ; LOCALIZATION ; CARCINOMAS ; CDNA MICROARRAYS ; microdissection ; prostate carcinoma ; QUANTITIES ; MANAGEMENT ; CDNA MICROARRAY ; HETEROGENEITY ; molecular ; RADICAL PROSTATECTOMY ; EXTRACTION ; PROTOCOL ; MOLECULAR-MECHANISMS ; biomarker ; RECOVERY ; RNAS ; PRESERVATION ; HIGH-GRADE ; NEEDLE BIOPSIES ; ALTERNATE READING FRAME ; COA RACEMASE P504S ; ISCHEMIA TIME ; laser microdissection ; tissue banking
    Abstract: Molecular analyses of early-stage prostate cancers are necessary to assess their potential clinical significance based on established and/or novel biomarkers for tailored clinical management. A prerequisite for the application of RNA-based analyses of such, mostly macroscopically-undetectable, small prostate carcinomas is the recovery and preservation of sufficient RNA quantities and quality. Furthermore, in prostate cancer, heterogeneity is a common phenomenon that includes a juxtaposition of different tissue compositions and variable histological grades within the same tumor focus. To better understand the molecular mechanisms of prostate cancer, it is essential to correlate molecular data with a specific cell type. Here, we present a tissue collecting protocol which is aligned with the preoperative evaluation of tumor localization. In combination with the technique of laser microdissection and pressure catapulting, we are able to preserve RNA of high quality from homogeneous cell populations of macroscopically-undetectable small prostate carcinomas. To obtain the necessary RNA quantities for whole genome cDNA microarrays, the isolated total RNAs were amplified by T7-based RNA-polymerase in vitro transcription. The microarray analyses (Human Unigene Set RZPD3.1) resulted in 216 differentially expressed genes (191 down-regulated, 25 Up-regulated). Among these were several known prostate cancer relevant genes, such as AMACR, TARP, LIM, GPR160 (all up-regulated), CAVI, NTNI, MTIX; CLU, TRIM29, SPARCLI and HSPB8 (,all down-regulated)
    Type of Publication: Journal article published
    PubMed ID: 16077921
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  • 3
    Keywords: CANCER ; EXPRESSION ; tumor ; Germany ; PROSTATE ; DISEASE ; GENE ; GENE-EXPRESSION ; GENES ; RNA ; TISSUE ; SURGERY ; TIME ; PATIENT ; REPERFUSION ; TISSUES ; BIOLOGY ; ASSOCIATION ; PATTERNS ; gene expression ; EXPRESSION ANALYSIS ; microarrays ; prostate cancer ; PROSTATE-CANCER ; DEGRADATION ; NETHERLANDS ; ISCHEMIA ; BIOPSY ; HYPOXIA ; molecular ; CHAIN ; PATTERN ; TUMOR TISSUE ; LEVEL ; methods ; ISCHEMIA TIME ; quantitative
    Abstract: Objectives: Gene expression analyses have become an important approach to understand the biology of cancer. However, transcript level patterns and RNA quality could rapidly change in response to ischemic and mechanical stress. Studies have shown that this occurs both perioperatively and after surgical removal of organs. Methods: To better understand the relative importance of perioperative and postoperative gene expression changes, we performed quantitative reverse transcription-polymerase chain reactions on the transcripts of 91 cancer-related genes from normal and cancerous prostate tissues from 10 patients at eight different time points during surgical manipulation and after removal of the prostate. Results: The mRNA levels of 8 (EGR1, p21, KRT17, PIM1, S100P, TNFRSF, WFDC2, and TRIM29) of 91 genes changed significantly with time of surgery in normal and tumor tissue. Remarkably, all eight genes were up-regulated, a reaction that was most prominent during the early intraoperative period. Additional changes occurred but were much less prominent during the first postoperative hour. Conclusions: Our results substantially challenge the utility of immediate postoperative tissue sampling. At least for prostate cancer, the data suggest that preoperative tissue collection by core biopsies is optimal for studying molecular changes in normal and neoplastic prostate tissues. (c) 2007 European Association of Urology. Published by Elsevier BY. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 17448597
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  • 4
    Keywords: CANCER ; CELL ; Germany ; QUANTIFICATION ; GENOME ; PROTEIN ; PROTEINS ; validation ; LINES ; BIOMARKERS ; CELL-LINES ; PHOSPHORYLATION ; antibodies ; antibody ; TARGET ; PERFORMANCE ; AMPLIFICATION ; microarrays ; ARRAYS ; CELL-LINE ; LINE ; Jun ; STRATEGIES ; sensitivity ; cell lines ; IMMUNOASSAYS ; signaling ; HUMAN CANCER ; proteome ; methods ; high throughput ; HIGH-THROUGHPUT ; PHASE ; SPECIMENS ; STRATEGY ; RANGE ; CATALYZED REPORTER DEPOSITION ; STROMAL-TUMORS GISTS
    Abstract: Background: Reverse phase protein arrays (RPPA) emerged as a useful experimental platform to analyze biological samples in a high-throughput format. Different signal detection methods have been described to generate a quantitative readout on RPPA including the use of fluorescently labeled antibodies. Increasing the sensitivity of RPPA approaches is important since many signaling proteins or posttranslational modifications are present at a low level. Results: A new antibody-mediated signal amplification ( AMSA) strategy relying on sequential incubation steps with fluorescently-labeled secondary antibodies reactive against each other is introduced here. The signal quantification is performed in the near-infrared range. The RPPA-based analysis of 14 endogenous proteins in seven different cell lines demonstrated a strong correlation (r = 0.89) between AMSA and standard NIR detection. Probing serial dilutions of human cancer cell lines with different primary antibodies demonstrated that the new amplification approach improved the limit of detection especially for low abundant target proteins. Conclusions: Antibody-mediated signal amplification is a convenient and cost-effective approach for the robust and specific quantification of low abundant proteins on RPPAs. Contrasting other amplification approaches it allows target protein detection over a large linear range
    Type of Publication: Journal article published
    PubMed ID: 20569466
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