title: Differences in gene expression in prostate cancer, normal appearing prostate tissue adjacent to cancer and prostate tissue from cancer free organ donors.
abstract: BACKGROUND
  Typical high throughput microarrays experiments compare gene expression across two specimen classes - an experimental class and baseline (or comparison) class. The choice of specimen classes is a major factor in the differential gene expression patterns revealed by these experiments. In most studies of prostate cancer, histologically malignant tissue is chosen as the experimental class while normal appearing prostate tissue adjacent to the tumor (adjacent normal) is chosen as the baseline against which comparison is made. However, normal appearing prostate tissue from tumor free organ donors represents an alterative source of baseline tissue for differential expression studies.
  
  
  METHODS
  To examine the effect of using donor normal tissue as opposed to adjacent normal tissue as a baseline for prostate cancer expression studies, we compared, using oligonucleotide microarrays, the expression profiles of primary prostate cancer (tumor), adjacent normal tissue and normal tissue from tumor free donors.
  
  
  RESULTS
  Statistical analysis using Significance Analysis of Microarrays (SAM) demonstrates the presence of unique gene expression profiles for each of these specimen classes. The tumor v donor expression profile was more extensive that the tumor v adjacent normal profile. The differentially expressed gene lists from tumor v donor, tumor v adjacent normal and adjacent normal v donor comparisons were examined to identify regulated genes. When donors were used as the baseline, similar genes are highly regulated in both tumor and adjacent normal tissue. Significantly, both tumor and adjacent normal tissue exhibit significant up regulation of proliferation related genes including transcription factors, signal transducers and growth regulators compared to donor tissue. These genes were not picked up in a direct comparison of tumor and adjacent normal tissues.
  
  
  CONCLUSIONS
  The up-regulation of these gene types in both tissue types is an unexpected finding and suggests that normal appearing prostate tissue can undergo genetic changes in response to or in expectation of morphologic cancer. A possible field effect surrounding prostate cancers and the implications of these findings for characterizing gene expression changes in prostate tumors are discussed.
authors.affiliation: Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15232, USA. chandran@pitt.edu <chandran@pitt.edu>
authors.forename: Uma R
authors.initials: UR
authors.lastname: Chandran
authors.forename: Rajiv
authors.initials: R
authors.lastname: Dhir
authors.forename: Changqing
authors.initials: C
authors.lastname: Ma
authors.forename: George
authors.initials: G
authors.lastname: Michalopoulos
authors.forename: Michael
authors.initials: M
authors.lastname: Becich
authors.forename: John
authors.initials: J
authors.lastname: Gilbertson
mesh_terms: D000328:Adult; D000368:Aged; D018450:Disease Progression; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D008875:Middle Aged; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D011467:Prostate / Q000378:metabolism*; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000378:metabolism*; D018075:RNA, Complementary / Q000378:metabolism; D012044:Regression Analysis; D014019:Tissue Donors; D015854:Up-Regulation
chemical_list: D018075:RNA, Complementary