title: Application of Affymetrix array and Massively Parallel Signature Sequencing for identification of genes involved in prostate cancer progression.
abstract: BACKGROUND
  Affymetrix GeneChip Array and Massively Parallel Signature Sequencing (MPSS) are two high throughput methodologies used to profile transcriptomes. Each method has certain strengths and weaknesses; however, no comparison has been made between the data derived from Affymetrix arrays and MPSS. In this study, two lineage-related prostate cancer cell lines, LNCaP and C4-2, were used for transcriptome analysis with the aim of identifying genes associated with prostate cancer progression.
  
  
  METHODS
  Affymetrix GeneChip array and MPSS analyses were performed. Data was analyzed with GeneSpring 6.2 and in-house perl scripts. Expression array results were verified with RT-PCR.
  
  
  RESULTS
  Comparison of the data revealed that both technologies detected genes the other did not. In LNCaP, 3,180 genes were only detected by Affymetrix and 1,169 genes were only detected by MPSS. Similarly, in C4-2, 4,121 genes were only detected by Affymetrix and 1,014 genes were only detected by MPSS. Analysis of the combined transcriptomes identified 66 genes unique to LNCaP cells and 33 genes unique to C4-2 cells. Expression analysis of these genes in prostate cancer specimens showed CA1 to be highly expressed in bone metastasis but not expressed in primary tumor and EPHA7 to be expressed in normal prostate and primary tumor but not bone metastasis.
  
  
  CONCLUSIONS
  Our data indicates that transcriptome profiling with a single methodology will not fully assess the expression of all genes in a cell line. A combination of transcription profiling technologies such as DNA array and MPSS provides a more robust means to assess the expression profile of an RNA sample. Finally, genes that were differentially expressed in cell lines were also differentially expressed in primary prostate cancer and its metastases.
authors.affiliation: Institute for Systems Biology, Seattle, USA. aoudes@systemsbiology.org
authors.forename: Asa J
authors.initials: AJ
authors.lastname: Oudes
authors.forename: Jared C
authors.initials: JC
authors.lastname: Roach
authors.forename: Laura S
authors.initials: LS
authors.lastname: Walashek
authors.forename: Lillian J
authors.initials: LJ
authors.lastname: Eichner
authors.forename: Lawrence D
authors.initials: LD
authors.lastname: True
authors.forename: Robert L
authors.initials: RL
authors.lastname: Vessella
authors.forename: Alvin Y
authors.initials: AY
authors.lastname: Liu
mesh_terms: D045744:Cell Line, Tumor; D019295:Computational Biology; D018450:Disease Progression; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011471:Prostatic Neoplasms / Q000175:diagnosis / Q000473:pathology*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012984:Software; D014158:Transcription, Genetic