title: RNA-seq profiling of a radiation resistant and radiation sensitive prostate cancer cell line highlights opposing regulation of DNA repair and targets for radiosensitization.
abstract: BACKGROUND
  Radiotherapy is a chosen treatment option for prostate cancer patients and while some tumours respond well, up to 50% of patients may experience tumour recurrence. Identification of functionally relevant predictive biomarkers for radioresponse in prostate cancer would enable radioresistant patients to be directed to more appropriate treatment options, avoiding the side-effects of radiotherapy.
  
  
  METHODS
  Using an in vitro model to screen for novel biomarkers of radioresistance, transcriptome analysis of a radioresistant (PC-3) and radiosensitive (LNCaP) prostate cancer cell line was performed. Following pathway analysis candidate genes were validated using qRT-PCR. The DNA repair pathway in radioresistant PC-3 cells was then targeted for radiation sensitization using the PARP inhibitor, niacinimide.
  
  
  RESULTS
  Opposing regulation of a DNA repair and replication pathway was observed between PC-3 and LNCaP cells from RNA-seq analysis. Candidate genes BRCA1, RAD51, FANCG, MCM7, CDC6 and ORC1 were identified as being significantly differentially regulated post-irradiation. qRT-PCR validation confirmed BRCA1, RAD51 and FANCG as being significantly differentially regulated at 24 hours post radiotherapy (p-value =0.003, 0.045 and 0.003 respectively). While the radiosensitive LNCaP cells down-regulated BRCA1, FANCG and RAD51, the radioresistant PC-3 cell line up-regulated these candidates to promote cell survival post-radiotherapy and a similar trend was observed for MCM7, CDC6 and ORC1. Inhibition of DNA repair using niacinamide sensitised the radioresistant cells to irradiation, reducing cell survival at 2 Gy from 66% to 44.3% (p-value =0.02).
  
  
  CONCLUSIONS
  These findings suggest that the DNA repair candidates identified via RNA-seq hold potential as both targets for radiation sensitization and predictive biomarkers in prostate cancer.
authors.forename: Arabella
authors.initials: A
authors.lastname: Young
authors.forename: Rachael
authors.initials: R
authors.lastname: Berry
authors.forename: Adele F
authors.initials: AF
authors.lastname: Holloway
authors.forename: Nicholas B
authors.initials: NB
authors.lastname: Blackburn
authors.forename: Joanne L
authors.initials: JL
authors.lastname: Dickinson
authors.forename: Marketa
authors.initials: M
authors.lastname: Skala
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Phillips
authors.affiliation: School of Medicine, University of Tasmania, Private Bag 23, Hobart, TAS 7000, Australia. khmoore@utas.edu.au.
authors.forename: Kate H
authors.initials: KH
authors.lastname: Brettingham-Moore
mesh_terms: D019313:BRCA1 Protein / Q000235:genetics / Q000378:metabolism; D014408:Biomarkers, Tumor / Q000235:genetics*; D018797:Cell Cycle Proteins / Q000235:genetics; D045744:Cell Line, Tumor; D002470:Cell Survival / Q000187:drug effects / Q000528:radiation effects; D004260:DNA Repair / Q000187:drug effects / Q000528:radiation effects*; D015536:Down-Regulation / Q000528:radiation effects; D004791:Enzyme Inhibitors / Q000494:pharmacology; D052241:Fanconi Anemia Complementation Group G Protein / Q000235:genetics; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000528:radiation effects*; D006801:Humans; D008297:Male; D064168:Minichromosome Maintenance Complex Component 7 / Q000235:genetics; D009536:Niacinamide / Q000494:pharmacology; D009687:Nuclear Proteins / Q000235:genetics; D051738:Origin Recognition Complex / Q000235:genetics; D000067856:Poly(ADP-ribose) Polymerase Inhibitors; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000532:radiotherapy*; D012333:RNA, Messenger / Q000032:analysis; D051135:Rad51 Recombinase / Q000235:genetics / Q000378:metabolism; D011836:Radiation Tolerance / Q000235:genetics*; D011838:Radiation-Sensitizing Agents / Q000627:therapeutic use; D015854:Up-Regulation / Q000528:radiation effects
chemical_list: D019313:BRCA1 Protein; D014408:Biomarkers, Tumor; C103706:CDC6 protein, human; D018797:Cell Cycle Proteins; D004791:Enzyme Inhibitors; C499909:FANCG protein, human; D052241:Fanconi Anemia Complementation Group G Protein; D009687:Nuclear Proteins; C497223:ORC1 protein, human; D051738:Origin Recognition Complex; D000067856:Poly(ADP-ribose) Polymerase Inhibitors; D012333:RNA, Messenger; D011838:Radiation-Sensitizing Agents; D009536:Niacinamide; D051135:Rad51 Recombinase; C101624:MCM7 protein, human; D064168:Minichromosome Maintenance Complex Component 7