title: Characterization of 1577 primary prostate cancers reveals novel biological and clinicopathologic insights into molecular subtypes.
abstract: BACKGROUND
  Prostate cancer (PCa) molecular subtypes have been defined by essentially mutually exclusive events, including ETS gene fusions (most commonly involving ERG) and SPINK1 overexpression. Clinical assessment may aid in disease stratification, complementing available prognostic tests.
  
  
  OBJECTIVE
  To determine the analytical validity and clinicopatholgic associations of microarray-based molecular subtyping.
  
  
  METHODS
  We analyzed Affymetrix GeneChip expression profiles for 1577 patients from eight radical prostatectomy cohorts, including 1351 cases assessed using the Decipher prognostic assay (GenomeDx Biosciences, San Diego, CA, USA) performed in a laboratory with Clinical Laboratory Improvements Amendment certification. A microarray-based (m-) random forest ERG classification model was trained and validated. Outlier expression analysis was used to predict other mutually exclusive non-ERG ETS gene rearrangements (ETS(+)) or SPINK1 overexpression (SPINK1(+)).
  
  
  METHODS
  Associations with clinical features and outcomes by multivariate logistic regression analysis and receiver operating curves.
  
  
  CONCLUSIONS
  The m-ERG classifier showed 95% accuracy in an independent validation subset (155 samples). Across cohorts, 45% of PCas were classified as m-ERG(+), 9% as m-ETS(+), 8% as m-SPINK1(+), and 38% as triple negative (m-ERG(-)/m-ETS(-)/m-SPINK1(-)). Gene expression profiling supports three underlying molecularly defined groups: m-ERG(+), m-ETS(+), and m-SPINK1(+)/triple negative. On multivariate analysis, m-ERG(+) tumors were associated with lower preoperative serum prostate-specific antigen and Gleason scores, but greater extraprostatic extension (p<0.001). m-ETS(+) tumors were associated with seminal vesicle invasion (p=0.01), while m-SPINK1(+)/triple negative tumors had higher Gleason scores and were more frequent in Black/African American patients (p<0.001). Clinical outcomes were not significantly different among subtypes.
  
  
  CONCLUSIONS
  A clinically available prognostic test (Decipher) can also assess PCa molecular subtypes, obviating the need for additional testing. Clinicopathologic differences were found among subtypes based on global expression patterns.
  
  
  RESULTS
  Molecular subtyping of prostate cancer can be achieved using extra data generated from a clinical-grade, genome-wide expression-profiling prognostic assay (Decipher). Transcriptomic and clinical analysis support three distinct molecular subtypes: (1) m-ERG(+), (2) m-ETS(+), and (3) m-SPINK1(+)/triple negative (m-ERG(-)/m-ETS(-)/m-SPINK1(-)). Incorporation of subtyping into a clinically available assay may facilitate additional applications beyond routine prognosis.
authors.affiliation: Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA. Electronic address: tomlinss@umich.edu.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Tomlins
authors.affiliation: GenomeDx Bioscience Inc., Vancouver, British Columbia, Canada.
authors.forename: Mohammed
authors.initials: M
authors.lastname: Alshalalfa
authors.affiliation: GenomeDx Bioscience Inc., Vancouver, British Columbia, Canada.
authors.forename: Elai
authors.initials: E
authors.lastname: Davicioni
authors.affiliation: GenomeDx Bioscience Inc., Vancouver, British Columbia, Canada.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Erho
authors.affiliation: GenomeDx Bioscience Inc., Vancouver, British Columbia, Canada.
authors.forename: Kasra
authors.initials: K
authors.lastname: Yousefi
authors.affiliation: Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI, USA.
authors.forename: Shuang
authors.initials: S
authors.lastname: Zhao
authors.affiliation: GenomeDx Bioscience Inc., Vancouver, British Columbia, Canada.
authors.forename: Zaid
authors.initials: Z
authors.lastname: Haddad
authors.affiliation: Kimmel Cancer Center, Jefferson Medical College of Thomas Jefferson University, Philadelphia, PA, USA.
authors.forename: Robert B
authors.initials: RB
authors.lastname: Den
authors.affiliation: Kimmel Cancer Center, Jefferson Medical College of Thomas Jefferson University, Philadelphia, PA, USA.
authors.forename: Adam P
authors.initials: AP
authors.lastname: Dicker
authors.affiliation: James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA.
authors.forename: Bruce J
authors.initials: BJ
authors.lastname: Trock
authors.affiliation: James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA.
authors.forename: Angelo M
authors.initials: AM
authors.lastname: DeMarzo
authors.affiliation: James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA.
authors.forename: Ashley E
authors.initials: AE
authors.lastname: Ross
authors.affiliation: James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA.
authors.forename: Edward M
authors.initials: EM
authors.lastname: Schaeffer
authors.affiliation: Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Eric A
authors.initials: EA
authors.lastname: Klein
authors.affiliation: Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH, USA.
authors.forename: Cristina
authors.initials: C
authors.lastname: Magi-Galluzzi
authors.affiliation: Department of Urology, Mayo Clinic, Rochester, MN, USA.
authors.forename: R Jeffrey
authors.initials: RJ
authors.lastname: Karnes
authors.affiliation: Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, USA.
authors.forename: Robert B
authors.initials: RB
authors.lastname: Jenkins
authors.affiliation: Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI, USA. Electronic address: ffeng@med.umich.edu.
authors.forename: Felix Y
authors.initials: FY
authors.lastname: Feng
mesh_terms: D019540:Area Under Curve; D014408:Biomarkers, Tumor / Q000235:genetics*; D002352:Carrier Proteins / Q000235:genetics; D016000:Cluster Analysis; D005060:Europe; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D050939:Gene Fusion; D015321:Gene Rearrangement; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D006801:Humans; D016015:Logistic Models; D008297:Male; D015999:Multivariate Analysis; D060787:Neoplasm Grading; D016017:Odds Ratio; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D011237:Predictive Value of Tests; D011468:Prostatectomy; D011471:Prostatic Neoplasms / Q000145:classification / Q000235:genetics* / Q000473:pathology* / Q000601:surgery; D050783:Proto-Oncogene Proteins c-ets / Q000235:genetics; D012372:ROC Curve; D015203:Reproducibility of Results; D015534:Trans-Activators / Q000235:genetics; D000071230:Transcriptional Regulator ERG; D014359:Trypsin Inhibitor, Kazal Pancreatic; D014481:United States; D015854:Up-Regulation
chemical_list: D014408:Biomarkers, Tumor; D002352:Carrier Proteins; C072312:ERG protein, human; D050783:Proto-Oncogene Proteins c-ets; C486642:SPINK1 protein, human; D015534:Trans-Activators; D000071230:Transcriptional Regulator ERG; D014359:Trypsin Inhibitor, Kazal Pancreatic
keywords: ERG; ETS; Microarray; Prognosis; Prostate cancer; SPINK1