KP Ramirez Week 11

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Top 10 Definitions

Carcinoma: A malignant new growth that arises from epithelium, found in skin or, more commonly, the lining of body organs. Carcinomas tend to infiltrate into adjacent tissue and spread to distant organs.

Metastatic: The spread of a disease from the organ or tissue of origin to another part of the body.

Disseminate: To scatter or distribute over a considerable area.

Neoplastic: Pertaining to or like a neoplasm with new and abnormal growth.

Cryostat: A vessel, similar in construction to a vacuum flask or dewar used to maintain cold cryogenic temperatures.

Oligonucleotide: A linear sequence of up to 20 nucleotides joined by phosphodiester bonds.

Immunohistochemistry: Histochemistry localization of immunoreactive substances using labeled antibodies as reagents

Transcriptional Control: Control of gene expression by controlling the number of rNA transcripts of a region of dNA. A major regulatory mechanism for differential control of protein synthesis in both pro and eukaryotic cells

Nucleoside: A nitrogenous base bound to a pentose sugar ribose or deoxyribose.

Cryogenic: The study of the production of a very low temperature and the behavior of materials in those temperatures.



  • Carcinoma of the prostate is the most common caner in the United states and has increased dramatically in the proportion of patients diagnosed with tumors that are significantly confined to the prostate gland. The majority of patients actually die from their tumors as opposed to treatment or other causes. This has led to the study of looking at the state of how the tumors have metastatsized as a framework to assess the clinical and biological factors associated with specific phenotypes and outcomes.
  • Identifying the genes, gene expression profiles, and biological pathways that contribute to metastasis will be a significant benefit to improve tumor classification and therapy. This can be explored by preforming a genome wide expression analysis and identifying genes differentially expressed in primary and metastatic prostate cancers.

Materials and Methods

  • Tissues were taken as followed
3 non cancerous patients
23 Primary prostate cancer patients
9 Metastatic prostate cancer patients
  • Collected as biopsies from 1993-1999
  • Because this was preformed with Affymetrix there is no Cy3 or Cy5
  • Gene expression analysis was carried out using Affymetrix U95 human gene arrays
  • Five distint microarrays (A-E)
  • Expression values on each array were multiplicatively scaled to have an average expression of 2500 across the central 96% of all genes on the array
  • The expression data set was first filtered to include only those probe sets detecting genes with mean expression values that differed by at least 3 fold between the two groups. Absolute base 10 Log of the ratio of the means
  • Probes were then ranked based on the relative magnitude of the difference preformed by T test.
  • Nonneoplastic tissues were removed from the ranking. Datasets were normalized by standardizing each gene and array to Mean 0 and Variance 1


  • Expression of genes corresponding to 5992 probe sets were reliably detected in all 23 primary prostate carcinomas.
  • 22665 did not detect expression in any of the samples
  • Gene expression corresponding to 7713 probe sets were detected in all 9 metastatic prostate cancers whereas 29784 genes were variably expressed and 25678 genes were not detected in any.
  • An unsupervised analysis of gene expression in all 32 prostate cancers based on the hybridization results for the U95A array revealed a strong tendency for primary and metastatic tumors to have distinct expression profiles.
  • 9 of 23 primary sample patients experienced a recurrence. We compared the subset of 14 primary tumors from patients that did not recur with the 9 metastatic prostate cancers to identify differentially expressed genes in these clinically distinct groups.
  • 132 were overexpressed in primary tumors and 360 in metastasis. 100 were the most highly ranked tumor intrinsic.
  • 26 of the 100 most highly ranked genes are believed to play a role in some aspects of cell cycle regulation. This included DNA replication and repair, or mitosis including many genes such as RFC5, TOP2A, RFC4 and MAD2L1 that were up-regulated in highly proliferative cells.
  • These findings suggest that the development and progression of prostate cancer metastases are associated with many gene expression changes related to cell proliferation, interactions with the microenvironment, properties that might contribute to cell motility, activated signal transduction pathways, and regulation of gene product synthesis and function.


  • Few prior studies had used high-throughput gene expression analysis to study prostate cancer metastases.
  • One of these reasons is that well preserved surgical tissue samples of metastatic prostate cancers are rare, which limits the availability.
  • Identifying these

genes in specific tumor samples may, therefore, provide diagnostic information and serve as a therapeutic target.



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