title: Identification of a candidate prognostic gene signature by transcriptome analysis of matched pre- and post-treatment prostatic biopsies from patients with advanced prostate cancer.
abstract: BACKGROUND
  Although chemotherapy for prostate cancer (PCa) can improve patient survival, some tumours are chemo-resistant. Tumour molecular profiles may help identify the mechanisms of drug action and identify potential prognostic biomarkers. We performed in vivo transcriptome profiling of pre- and post-treatment prostatic biopsies from patients with advanced hormone-naive prostate cancer treated with docetaxel chemotherapy and androgen deprivation therapy (ADT) with an aim to identify the mechanisms of drug action and identify prognostic biomarkers.
  
  
  METHODS
  RNA sequencing (RNA-Seq) was performed on biopsies from four patients before and ~22 weeks after docetaxel and ADT initiation. Gene fusion products and differentially-regulated genes between treatment pairs were identified using TopHat and pathway enrichment analyses undertaken. Publically available datasets were interrogated to perform survival analyses on the gene signatures identified using cBioportal.
  
  
  RESULTS
  A number of genomic rearrangements were identified including the TMPRSS2/ERG fusion and 3 novel gene fusions involving the ETS family of transcription factors in patients, both pre and post chemotherapy. In total, gene expression analyses showed differential expression of at least 2 fold in 575 genes in post-chemotherapy biopsies. Of these, pathway analyses identified a panel of 7 genes (ADAM7, FAM72B, BUB1B, CCNB1, CCNB2, TTK, CDK1), including a cell cycle-related geneset, that were differentially-regulated following treatment with docetaxel and ADT. Using cBioportal to interrogate the MSKCC-Prostate Oncogenome Project dataset we observed a statistically-significant reduction in disease-free survival of patients with tumours exhibiting alterations in gene expression of the above panel of 7 genes (p = 0.015).
  
  
  CONCLUSIONS
  Here we report on the first "real-time" in vivo RNA-Seq-based transcriptome analysis of clinical PCa from pre- and post-treatment TRUSS-guided biopsies of patients treated with docetaxel chemotherapy plus ADT. We identify a chemotherapy-driven PCa transcriptome profile which includes the down-regulation of important positive regulators of cell cycle progression. A 7 gene signature biomarker panel has also been identified in high-risk prostate cancer patients to be of prognostic value. Future prospective study is warranted to evaluate the clinical value of this panel.
authors.affiliation: Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK. p.rajan@beatson.gla.ac.uk.
authors.forename: Prabhakar
authors.initials: P
authors.lastname: Rajan
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Stockley
authors.forename: Ian M
authors.initials: IM
authors.lastname: Sudbery
authors.forename: Janis T
authors.initials: JT
authors.lastname: Fleming
authors.forename: Ann
authors.initials: A
authors.lastname: Hedley
authors.forename: Gabriela
authors.initials: G
authors.lastname: Kalna
authors.forename: David
authors.initials: D
authors.lastname: Sims
authors.forename: Chris P
authors.initials: CP
authors.lastname: Ponting
authors.forename: Andreas
authors.initials: A
authors.lastname: Heger
authors.forename: Craig N
authors.initials: CN
authors.lastname: Robson
authors.forename: Rhona M
authors.initials: RM
authors.lastname: McMenemin
authors.forename: Ian D
authors.initials: ID
authors.lastname: Pedley
authors.forename: Hing Y
authors.initials: HY
authors.lastname: Leung
mesh_terms: D000971:Antineoplastic Combined Chemotherapy Protocols / Q000627:therapeutic use; D001706:Biopsy; D019295:Computational Biology; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D008297:Male; D060787:Neoplasm Grading; D009367:Neoplasm Staging; D011379:Prognosis; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000401:mortality* / Q000473:pathology / Q000628:therapy; D059467:Transcriptome